diff --git a/docs/.buildinfo b/docs/.buildinfo index 4dc57091..79ad74b9 100644 --- a/docs/.buildinfo +++ b/docs/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 61e2986449091a7be4f25a8af15fb3b5 +config: 96a29a2f0251ba919add6b6d29b22740 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_downloads/064c0d2777aed39cc8bf9734f26c68a0/plot_noncolinear_qe.py b/docs/_downloads/064c0d2777aed39cc8bf9734f26c68a0/plot_noncolinear_qe.py index c6dd77c7..953fa4c9 100644 --- a/docs/_downloads/064c0d2777aed39cc8bf9734f26c68a0/plot_noncolinear_qe.py +++ b/docs/_downloads/064c0d2777aed39cc8bf9734f26c68a0/plot_noncolinear_qe.py @@ -38,6 +38,7 @@ pyprocar.bandsplot( code='qe', mode='plain', + fermi=18.0536, dirname=data_dir) ############################################################################### @@ -55,6 +56,7 @@ pyprocar.bandsplot( code='qe', mode='parametric', + fermi=18.0536, atoms=atoms, orbitals=orbitals, spins=spins, diff --git a/docs/_downloads/0ae4717a2ffa80a361725a23ff73d2e0/plot_spin_polarized_dos.py b/docs/_downloads/0ae4717a2ffa80a361725a23ff73d2e0/plot_spin_polarized_dos.py index 2eeb8696..c2d4c309 100644 --- a/docs/_downloads/0ae4717a2ffa80a361725a23ff73d2e0/plot_spin_polarized_dos.py +++ b/docs/_downloads/0ae4717a2ffa80a361725a23ff73d2e0/plot_spin_polarized_dos.py @@ -36,6 +36,7 @@ pyprocar.dosplot( code='vasp', mode='plain', + fermi=5.590136, dirname=data_dir) ############################################################################### @@ -46,6 +47,7 @@ pyprocar.dosplot( code='vasp', mode='plain', + fermi=5.590136, spins=spins, dirname=data_dir) @@ -64,6 +66,7 @@ pyprocar.dosplot( code='vasp', mode='parametric', + fermi=5.590136, atoms=atoms, orbitals=orbitals, spins=spins, @@ -84,6 +87,7 @@ pyprocar.dosplot( code='vasp', mode='parametric_line', + fermi=5.590136, atoms=atoms, orbitals=orbitals, spins=spins, @@ -103,6 +107,7 @@ pyprocar.dosplot( code='vasp', mode='stack_species', + fermi=5.590136, orbitals=orbitals, spins=spins, dirname=data_dir) @@ -118,6 +123,7 @@ pyprocar.dosplot( code='vasp', mode='stack_orbitals', + fermi=5.590136, atoms=atoms, spins=spins, dirname=data_dir) @@ -136,6 +142,60 @@ pyprocar.dosplot( code='vasp', mode='stack', + fermi=5.590136, + items=items, + spins=spins, + dirname=data_dir) + + +############################################################################### +# overlay_species mode +# +++++++++++++++++++++++++++++++++++++++ +# +# +# +orbitals=[4,5,6,7,8] +spins=[0,1] + +pyprocar.dosplot( + code='vasp', + mode='overlay_species', + fermi=5.590136, + orbitals=orbitals, + spins=spins, + dirname=data_dir) + +############################################################################### +# overlay_orbtials mode +# +++++++++++++++++++++++++++++++++++++++ +# +# +# +atoms=[0] +spins=[0,1] +pyprocar.dosplot( + code='vasp', + mode='overlay_orbitals', + fermi=5.590136, + atoms=atoms, + spins=spins, + dirname=data_dir) + + + +############################################################################### +# overlay mode +# +++++++++++++++++++++++++++++++++++++++ +# +# +# + +items={'Fe':[4,5,6,7,8]} +spins=[0,1] +pyprocar.dosplot( + code='vasp', + mode='overlay', + fermi=5.590136, items=items, spins=spins, dirname=data_dir) diff --git a/docs/_downloads/0b72843559a0e5323f24e00c93009819/plot_fermi3d_plain.ipynb b/docs/_downloads/0b72843559a0e5323f24e00c93009819/plot_fermi3d_plain.ipynb index 57856e24..ccbc274b 100644 --- a/docs/_downloads/0b72843559a0e5323f24e00c93009819/plot_fermi3d_plain.ipynb +++ b/docs/_downloads/0b72843559a0e5323f24e00c93009819/plot_fermi3d_plain.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting fermi3d plain {#ref_plotting_fermi3d_plain}\r\n\r\nSymmetry does not currently work! Make sure for fermi surface\r\ncalculations turn off symmetry\r\n\r\nPlotting fermi3d plain example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='fermi')\r\n```\r\n" + "\n\n# Plotting fermi3d plain\n\nSymmetry does not currently work! Make sure for fermi surface calculations turn off symmetry\n\nPlotting fermi3d plain example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='fermi')\n" ] }, { @@ -33,7 +33,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -51,7 +51,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n" + "## Plain mode\n\n\n\n" ] }, { @@ -69,7 +69,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Parametric mode\r\n" + "## Parametric mode\n\n\n\n" ] }, { diff --git a/docs/_downloads/108db922454e1f15c7e1561bfc36c9de/plot_colinear.ipynb b/docs/_downloads/108db922454e1f15c7e1561bfc36c9de/plot_colinear.ipynb index a6126437..8a0b490a 100644 --- a/docs/_downloads/108db922454e1f15c7e1561bfc36c9de/plot_colinear.ipynb +++ b/docs/_downloads/108db922454e1f15c7e1561bfc36c9de/plot_colinear.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting band structure {#ref_plotting_colinear_bands}\r\n\r\nPlotting band structure example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='bands')\r\n```\r\n" + "\n\n# Plotting band structure\n\nPlotting band structure example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='bands')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n" + "## Plain mode\n\n" ] }, { @@ -40,14 +40,14 @@ }, "outputs": [], "source": [ - "pyprocar.bandsplot(\n code='vasp', \n mode='plain',\n dirname=data_dir)" + "pyprocar.bandsplot(\n code='vasp', \n mode='plain',\n fermi=5.599480,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Parametric mode\r\n\r\nFor details on the meaning of the indices of the atomic projection\r\nplease refer to the user guide :ref:\\'atomic_projections\\'\r\n" + "## Parametric mode\n\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n\n\n" ] }, { @@ -58,14 +58,14 @@ }, "outputs": [], "source": [ - "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='parametric',\n fermi=5.599480,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# parametric_linemode\r\n\r\nFor details on the meaning of the indices of the atomic projection\r\nplease refer to the user guide :ref:\\'atomic_projections\\'\r\n" + "## parametric_linemode\n\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n\n\n" ] }, { @@ -76,14 +76,14 @@ }, "outputs": [], "source": [ - "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='parametric',\n fermi=5.599480,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Scatter mode\r\n" + "## Scatter mode\n\n\n\n\n" ] }, { @@ -94,14 +94,14 @@ }, "outputs": [], "source": [ - "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='scatter',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='scatter',\n fermi=5.599480,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# overlay_species mode\r\n" + "## overlay_species mode\n\n\n\n\n" ] }, { @@ -112,14 +112,14 @@ }, "outputs": [], "source": [ - "orbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='overlay_species',\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "orbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='overlay_species',\n fermi=5.599480,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# overlay_orbtials mode\r\n" + "## overlay_orbtials mode\n\n\n\n\n" ] }, { @@ -130,14 +130,14 @@ }, "outputs": [], "source": [ - "atoms=[0]\nspins=[0]\npyprocar.bandsplot(\n code='vasp', \n mode='overlay_orbitals',\n atoms=atoms,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\nspins=[0]\npyprocar.bandsplot(\n code='vasp', \n mode='overlay_orbitals',\n fermi=5.599480,\n atoms=atoms,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# overlay mode\r\n" + "## overlay mode\n\n\n\n\n" ] }, { @@ -148,14 +148,14 @@ }, "outputs": [], "source": [ - "items={'Fe':[4,5,6,7,8]}\npyprocar.bandsplot(\n code='vasp', \n mode='overlay',\n items=items,\n dirname=data_dir)" + "items={'Fe':[4,5,6,7,8]}\npyprocar.bandsplot(\n code='vasp', \n mode='overlay',\n fermi=5.599480,\n items=items,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# overlay mode by orbital names\r\n" + "### overlay mode by orbital names\n\n\n\n\n" ] }, { @@ -166,7 +166,7 @@ }, "outputs": [], "source": [ - "items={'Fe':['p','d']}\npyprocar.bandsplot(\n code='vasp', \n mode='overlay',\n items=items,\n dirname=data_dir)" + "items={'Fe':['p','d']}\npyprocar.bandsplot(\n code='vasp', \n mode='overlay',\n fermi=5.599480,\n items=items,\n dirname=data_dir)" ] } ], diff --git a/docs/_downloads/118695b22cb342905260e71e7c4f819c/plot_noncolinear_dos_qe.ipynb b/docs/_downloads/118695b22cb342905260e71e7c4f819c/plot_noncolinear_dos_qe.ipynb index 4644e668..54b5e8dd 100644 --- a/docs/_downloads/118695b22cb342905260e71e7c4f819c/plot_noncolinear_dos_qe.ipynb +++ b/docs/_downloads/118695b22cb342905260e71e7c4f819c/plot_noncolinear_dos_qe.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting non colinear dos in Quantum Espresso {#ref_plotting_noncolinear_dos_qe}\r\n\r\nPlotting non colinear dos in Quantum Espresso.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='qe', \r\n spin_calc_type='non-colinear',\r\n calc_type='dos')\r\n```\r\n" + "\n\n# Plotting non colinear dos in Quantum Espresso\n\nPlotting non colinear dos in Quantum Espresso.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='qe', \n spin_calc_type='non-colinear',\n calc_type='dos')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Parametric mode\r\n\r\nQuantum Espresso expresses the projections in the coupled basis,\r\ntherefore orbitals takes different meanings. For details on the meaning\r\nof the indices of the atomic projection please refer to the user guide\r\n:ref:\\'atomic_projections\\'\r\n" + "## Parametric mode\nQuantum Espresso expresses the projections in the coupled basis, \ntherefore orbitals takes different meanings.\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n\n\n" ] }, { @@ -40,7 +40,7 @@ }, "outputs": [], "source": [ - "atoms=[0]\nspins=[0]\norbitals=[8,9,10,11,12,13,14,15,16,17]\n\npyprocar.dosplot(\n code='qe', \n mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\nspins=[0]\norbitals=[8,9,10,11,12,13,14,15,16,17]\n\npyprocar.dosplot(\n code='qe', \n mode='parametric',\n fermi=18.0536,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] } ], diff --git a/docs/_downloads/1d7bddaa2f20c6f6d31ec8edb52ba8e9/plot_kpath_generation.ipynb b/docs/_downloads/1d7bddaa2f20c6f6d31ec8edb52ba8e9/plot_kpath_generation.ipynb index cde22daf..60e116fb 100644 --- a/docs/_downloads/1d7bddaa2f20c6f6d31ec8edb52ba8e9/plot_kpath_generation.ipynb +++ b/docs/_downloads/1d7bddaa2f20c6f6d31ec8edb52ba8e9/plot_kpath_generation.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Example of kpath_generator {#ref_example_kpath_generator}\r\n\r\nIn order to plot a band structure, one must define a set of $k$-points\r\nfollowing a desired $k$-path in momentum space. PyProcar\\'s $k$-path\r\ngeneration utility enables a the user to automatically generate a\r\nsuitable and sufficient $k$-path given the crystal structure, typically\r\nread from the POSCAR file (VASP).\r\n\r\n``` {caption=\"General Format\"}\r\npyprocar.kpath(infile, outfile, grid-size, with-time-reversal, recipe, threshold, symprec, angle-tolerance,supercell_matrix)\r\n```\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='bands')\r\n```\r\n\r\nThis information is automatically written to a KPOINTS file. The\r\nretrieved $k$-path can be used for other DFT codes with slight\r\nmodifications.\r\n\r\nMore details regarding these parameters can be found in the [SeeK-path\r\nmanual](https://seekpath.readthedocs.io/en/latest/module_guide/index.html).\r\nThe $k$-path generation utility within PyProcar is based on the Python\r\nlibrary **seekpath** developed by Hinuma et al:\r\n\r\n Y. Hinuma, G. Pizzi, Y. Kumagai, F. Oba, I. Tanaka, Band structure diagram paths based on crystallography, Computational Materials Science 128 (2017) 140\u2013184.doi:10.1016/j.commatsci.2016.10.015.\r\n" + "\n\n# Example of kpath_generator \n\nIn order to plot a band structure, one must define a set of $k$-points following a desired $k$-path in momentum space. \nPyProcar's $k$-path generation utility enables a the user to automatically generate \na suitable and sufficient $k$-path given the crystal structure, typically read from the POSCAR file (VASP). \n\n\n.. code-block::\n :caption: General Format\n\n pyprocar.kpath(infile, outfile, grid-size, with-time-reversal, recipe, threshold, symprec, angle-tolerance,supercell_matrix)\n\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='bands')\n\nThis information is automatically written to a KPOINTS file. The retrieved $k$-path can be used for other DFT codes with slight modifications.\n\nMore details regarding these parameters can be found in the [SeeK-path manual](https://seekpath.readthedocs.io/en/latest/module_guide/index.html).\nThe $k$-path generation utility within PyProcar is based on the Python library **seekpath** developed by Hinuma et al::\n\n Y. Hinuma, G. Pizzi, Y. Kumagai, F. Oba, I. Tanaka, Band structure diagram paths based on crystallography, Computational Materials Science 128 (2017) 140\u2013184.doi:10.1016/j.commatsci.2016.10.015.\n" ] }, { @@ -22,7 +22,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting K Path\r\n" + "## Plotting K Path\n\n" ] }, { @@ -40,7 +40,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { diff --git a/docs/_downloads/1dee1a739fe9f2d431f3a2a69b9efbea/plot_fermi3d_configurations.ipynb b/docs/_downloads/1dee1a739fe9f2d431f3a2a69b9efbea/plot_fermi3d_configurations.ipynb index 182da8cc..8baf2e80 100644 --- a/docs/_downloads/1dee1a739fe9f2d431f3a2a69b9efbea/plot_fermi3d_configurations.ipynb +++ b/docs/_downloads/1dee1a739fe9f2d431f3a2a69b9efbea/plot_fermi3d_configurations.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting with Configurations in [pyprocar]{.title-ref} {#ref_plot_fermi3d_configurations}\r\n\r\nThis example illustrates how to utilize various configurations for\r\nplotting the 3D Fermi surface using the [pyprocar]{.title-ref} package.\r\nIt provides a structured way to explore and demonstrate different\r\nconfigurations for the [plot_fermi_surface]{.title-ref} function.\r\n\r\nSymmetry does not currently work! Make sure for Fermi surface\r\ncalculations to turn off symmetry.\r\n\r\n## Preparation\r\n\r\nBefore diving into plotting, we need to download the example files. Use\r\nthe following code to do this. Once downloaded, specify the\r\n[data_dir]{.title-ref} to point to the location of the downloaded data.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='fermi')\r\n```\r\n" + "\n\n# Plotting with Configurations in `pyprocar`\n\nThis example illustrates how to utilize various configurations for plotting the 3D Fermi surface using the `pyprocar` package. It provides a structured way to explore and demonstrate different configurations for the `plot_fermi_surface` function. \n\nSymmetry does not currently work! Make sure for Fermi surface calculations to turn off symmetry.\n\n## Preparation\nBefore diving into plotting, we need to download the example files. Use the following code to do this. Once downloaded, specify the `data_dir` to point to the location of the downloaded data.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='fermi')\n" ] }, { diff --git a/docs/_downloads/1eece99f8b23cdc98ef72380a2df4e50/plot_colinear_dos.ipynb b/docs/_downloads/1eece99f8b23cdc98ef72380a2df4e50/plot_colinear_dos.ipynb index 89f64d02..042e6877 100644 --- a/docs/_downloads/1eece99f8b23cdc98ef72380a2df4e50/plot_colinear_dos.ipynb +++ b/docs/_downloads/1eece99f8b23cdc98ef72380a2df4e50/plot_colinear_dos.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting density of states {#ref_plotting_colinear_dos}\r\n\r\nPlotting density example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='qe', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='dos')\r\n```\r\n" + "\n\n# Plotting density of states\n\nPlotting density example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='qe', \n spin_calc_type='non-spin-polarized',\n calc_type='dos')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n" + "## Plain mode\n\n" ] }, { @@ -40,14 +40,14 @@ }, "outputs": [], "source": [ - "pyprocar.dosplot(\n code='qe', \n mode='plain',\n dirname=data_dir)" + "pyprocar.dosplot(\n code='qe', \n mode='plain',\n fermi=5.599480,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Parametric mode\r\n\r\nFor details on the meaning of the indices of the atomic projection\r\nplease refer to the user guide :ref:\\'atomic_projections\\'\r\n" + "## Parametric mode\n\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n\n\n" ] }, { @@ -58,14 +58,14 @@ }, "outputs": [], "source": [ - "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.dosplot(\n code='qe', \n mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.dosplot(\n code='qe', \n mode='parametric',\n fermi=5.599480,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# parametric_line mode\r\n\r\nFor details on the meaning of the indices of the atomic projection\r\nplease refer to the user guide :ref:\\'atomic_projections\\'\r\n" + "## parametric_line mode\n\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n\n\n" ] }, { @@ -76,14 +76,14 @@ }, "outputs": [], "source": [ - "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.dosplot(\n code='qe', \n mode='parametric_line',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.dosplot(\n code='qe', \n mode='parametric_line',\n fermi=5.599480,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# stack_species mode\r\n" + "## stack_species mode\n\n\n\n\n" ] }, { @@ -94,14 +94,14 @@ }, "outputs": [], "source": [ - "orbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.dosplot(\n code='qe', \n mode='stack_species',\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "orbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.dosplot(\n code='qe', \n mode='stack_species',\n fermi=5.599480,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# stack_orbtials mode\r\n" + "## stack_orbtials mode\n\n\n\n\n" ] }, { @@ -112,14 +112,14 @@ }, "outputs": [], "source": [ - "atoms=[0]\nspins=[0]\npyprocar.dosplot(\n code='qe', \n mode='stack_orbitals',\n atoms=atoms,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\nspins=[0]\npyprocar.dosplot(\n code='qe', \n mode='stack_orbitals',\n fermi=5.599480,\n atoms=atoms,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# overlay mode\r\n" + "## stack mode\n\n\n\n\n" ] }, { @@ -130,7 +130,61 @@ }, "outputs": [], "source": [ - "items={'Fe':[4,5,6,7,8]}\npyprocar.dosplot(\n code='qe', \n mode='stack',\n items=items,\n dirname=data_dir)" + "items={'Fe':[4,5,6,7,8]}\npyprocar.dosplot(\n code='qe', \n mode='stack',\n fermi=5.599480,\n items=items,\n dirname=data_dir)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## overlay_species mode\n\n\n\n\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "orbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.dosplot(\n code='qe', \n mode='overlay_species',\n fermi=5.599480,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## overlay_orbtials mode\n\n\n\n\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "atoms=[0]\nspins=[0]\npyprocar.dosplot(\n code='qe', \n mode='overlay_orbitals',\n fermi=5.599480,\n atoms=atoms,\n spins=spins,\n dirname=data_dir)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## overlay mode\n\n\n\n\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "items={'Fe':[4,5,6,7,8]}\npyprocar.dosplot(\n code='qe', \n mode='overlay',\n fermi=5.599480,\n items=items,\n dirname=data_dir)" ] } ], diff --git a/docs/_downloads/1efe8c4aa8431c5249fe9e1cacb09796/plot_bandsplot_configurations.ipynb b/docs/_downloads/1efe8c4aa8431c5249fe9e1cacb09796/plot_bandsplot_configurations.ipynb index 80d5f48b..0bf5e66b 100644 --- a/docs/_downloads/1efe8c4aa8431c5249fe9e1cacb09796/plot_bandsplot_configurations.ipynb +++ b/docs/_downloads/1efe8c4aa8431c5249fe9e1cacb09796/plot_bandsplot_configurations.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting with Configurations in [pyprocar]{.title-ref} {#ref_plot_bandsplot_configuration}\r\n\r\nThis example illustrates how to utilize various configurations for\r\nplotting band structures using the [pyprocar]{.title-ref} package. It\r\nprovides a structured way to explore and demonstrate different\r\nconfigurations for the [bandsplot]{.title-ref} function.\r\n\r\n## Preparation\r\n\r\nBefore diving into plotting, we need to download the example files. Use\r\nthe following code to do this. Once downloaded, specify the\r\n[data_dir]{.title-ref} to point to the location of the downloaded data.\r\n\r\n``` {caption=\"Downloading example\"}\r\nimport pyprocar\r\n\r\ndata_dir = pyprocar.download_example(\r\n save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='spin-polarized-colinear',\r\n calc_type='bands'\r\n )\r\n```\r\n" + "\n\n# Plotting with Configurations in `pyprocar`\n\nThis example illustrates how to utilize various configurations for plotting band structures using the `pyprocar` package. It provides a structured way to explore and demonstrate different configurations for the `bandsplot` function.\n\n## Preparation\nBefore diving into plotting, we need to download the example files. Use the following code to do this. Once downloaded, specify the `data_dir` to point to the location of the downloaded data.\n\n.. code-block::\n :caption: Downloading example\n\n import pyprocar\n\n data_dir = pyprocar.download_example(\n save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='spin-polarized-colinear',\n calc_type='bands'\n )\n" ] }, { @@ -26,7 +26,7 @@ }, "outputs": [], "source": [ - "# Section 1: Locating and Printing Configuration Files\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates where the configuration files are located in the package.\n# It also shows how to print the configurations by setting print_plot_ops=True.\n#\n\n# Path to the configuration files in the package\nconfig_path = os.path.join(pyprocar.__path__[0], 'cfg')\nprint(f\"Configuration files are located at: {config_path}\")\n\n# Print the configurations\npyprocar.bandsplot(code=code,dirname=data_dir,print_plot_opts=True)" + "# Section 1: Locating and Printing Configuration Files\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates where the configuration files are located in the package.\n# It also shows how to print the configurations by setting print_plot_ops=True.\n#\n\n# Path to the configuration files in the package\nconfig_path = os.path.join(pyprocar.__path__[0], 'cfg')\nprint(f\"Configuration files are located at: {config_path}\")\n\n# Print the configurations\npyprocar.bandsplot(code=code,dirname=data_dir,fermi=5.590136,print_plot_opts=True)" ] }, { @@ -37,7 +37,7 @@ }, "outputs": [], "source": [ - "# Section 2: Changing cmap, clim, and Fermi line properties in Parametric Mode\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to change the colormap (cmap), color limits (clim),\n# and Fermi line properties (color, linestyle, and linewidth) in parametric mode.\n#\n\npyprocar.bandsplot(\n code=code,\n dirname=data_dir,\n mode='parametric',\n atoms=[0],\n orbitals=[4,5,6,7,8],\n cmap='viridis', # Colormap\n clim=[0, 1], # Color limits\n fermi_color='red', # Fermi line color\n fermi_linestyle='--', # Fermi line linestyle\n fermi_linewidth=2.0 # Fermi line linewidth\n)" + "# Section 2: Changing cmap, clim, and Fermi line properties in Parametric Mode\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to change the colormap (cmap), color limits (clim),\n# and Fermi line properties (color, linestyle, and linewidth) in parametric mode.\n#\n\npyprocar.bandsplot(\n code=code,\n dirname=data_dir,\n mode='parametric',\n fermi=5.590136,\n atoms=[0],\n orbitals=[4,5,6,7,8],\n cmap='viridis', # Colormap\n clim=[0, 1], # Color limits\n fermi_color='red', # Fermi line color\n fermi_linestyle='--', # Fermi line linestyle\n fermi_linewidth=2.0 # Fermi line linewidth\n)" ] }, { @@ -48,7 +48,7 @@ }, "outputs": [], "source": [ - "# Section 3: Setting Marker and Marker Size in Scatter Mode\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to set the marker style and marker size in scatter mode.\n#\n\npyprocar.bandsplot(\n code=code,\n dirname=data_dir,\n mode='scatter',\n atoms=[0],\n orbitals=[4,5,6,7,8],\n marker=['v','o'], # Marker style\n markersize=[10,5] # Marker size list for the 2 spin plots\n)" + "# Section 3: Setting Marker and Marker Size in Scatter Mode\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to set the marker style and marker size in scatter mode.\n#\n\npyprocar.bandsplot(\n code=code,\n dirname=data_dir,\n mode='scatter',\n fermi=5.590136,\n atoms=[0],\n orbitals=[4,5,6,7,8],\n marker=['v','o'], # Marker style\n markersize=[10,5] # Marker size list for the 2 spin plots\n)" ] }, { @@ -59,7 +59,7 @@ }, "outputs": [], "source": [ - "# Section 4: Setting the Figure Size and DPI\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to set the figure size and dots per inch (DPI) for the plot.\n#\n\npyprocar.bandsplot(\n code=code,\n dirname=data_dir,\n mode='scatter',\n atoms=[0],\n orbitals=[4,5,6,7,8],\n figure_size=(10, 6), # Figure size (width, height)\n dpi=300 # Dots per inch\n)" + "# Section 4: Setting the Figure Size and DPI\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to set the figure size and dots per inch (DPI) for the plot.\n#\n\npyprocar.bandsplot(\n code=code,\n dirname=data_dir,\n mode='scatter',\n fermi=5.590136,\n atoms=[0],\n orbitals=[4,5,6,7,8],\n figure_size=(10, 6), # Figure size (width, height)\n dpi=300 # Dots per inch\n)" ] } ], diff --git a/docs/_downloads/2ccce647e0ac59b9f555853f69095794/plot_unfolding.ipynb b/docs/_downloads/2ccce647e0ac59b9f555853f69095794/plot_unfolding.ipynb index a4f8be2b..d03f214d 100644 --- a/docs/_downloads/2ccce647e0ac59b9f555853f69095794/plot_unfolding.ipynb +++ b/docs/_downloads/2ccce647e0ac59b9f555853f69095794/plot_unfolding.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Unfolding Band Structure {#ref_plot_unfolding}\r\n\r\nUnfolding Band Structure example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\nsupercell_dir = pyprocar.download_example(save_dir='', \r\n material='MgB2',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='supercell_bands')\r\n\r\nprimitive_dir = pyprocar.download_example(save_dir='', \r\n material='MgB2',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='primitive_bands')\r\n```\r\n" + "\n\n# Unfolding Band Structure\n\nUnfolding Band Structure example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n supercell_dir = pyprocar.download_example(save_dir='', \n material='MgB2',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='supercell_bands')\n\n primitive_dir = pyprocar.download_example(save_dir='', \n material='MgB2',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='primitive_bands')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting primitive bands\r\n" + "## Plotting primitive bands\n\n" ] }, { @@ -40,14 +40,14 @@ }, "outputs": [], "source": [ - "pyprocar.bandsplot(\n code='vasp', \n mode='plain',\n elimit=[-15,5],\n dirname=primitive_dir)" + "pyprocar.bandsplot(\n code='vasp', \n mode='plain',\n fermi=4.993523,\n elimit=[-15,5],\n dirname=primitive_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Unfolding of the supercell bands\r\n\r\nHere we do unfolding of the supercell bands. In this calculation, the\r\nPOSCAR and KPOINTS will be different from the primitive cell For the\r\nPOSCAR, we create a 2 2 2 supercell from the primitive. For the KPOINTS,\r\nthe paths need to be changed to reflect the change in the unitcell\r\n" + "## Unfolding of the supercell bands\n\nHere we do unfolding of the supercell bands. In this calculation, \nthe POSCAR and KPOINTS will be different from the primitive cell\nFor the POSCAR, we create a 2 2 2 supercell from the primitive.\nFor the KPOINTS, the paths need to be changed to reflect the change in the unitcell\n\n" ] }, { @@ -58,7 +58,7 @@ }, "outputs": [], "source": [ - "pyprocar.unfold(\n code='vasp',\n mode='plain',\n unfold_mode='both',\n dirname= supercell_dir,\n elimit=[-15,5],\n supercell_matrix=np.diag([2, 2, 2]))" + "pyprocar.unfold(\n code='vasp',\n mode='plain',\n unfold_mode='both',\n fermi=5.033090,\n dirname= supercell_dir,\n elimit=[-15,5],\n supercell_matrix=np.diag([2, 2, 2]))" ] } ], diff --git a/docs/_downloads/2d70e171141e0fb73b229e20e47d4698/plot_fermi2d.py b/docs/_downloads/2d70e171141e0fb73b229e20e47d4698/plot_fermi2d.py index e88d5446..f8f9c8c6 100644 --- a/docs/_downloads/2d70e171141e0fb73b229e20e47d4698/plot_fermi2d.py +++ b/docs/_downloads/2d70e171141e0fb73b229e20e47d4698/plot_fermi2d.py @@ -36,6 +36,7 @@ pyprocar.fermi2D(code = 'vasp', mode='plain', + fermi=5.590136, dirname=data_dir) @@ -48,6 +49,7 @@ pyprocar.fermi2D(code = 'vasp', mode='plain_bands', add_legend=True, + fermi=5.590136, dirname=data_dir) @@ -69,7 +71,8 @@ atoms=atoms, orbitals=orbitals, spins=spins, - dirname=data_dir, + dirname=data_dir, + fermi=5.590136, spin_texture=False) @@ -88,4 +91,5 @@ band_indices = band_indices, band_colors=band_colors, add_legend=True, + fermi=5.590136, dirname=data_dir) \ No newline at end of file diff --git a/docs/_downloads/3199d9cf1b4a404903cfdfdd5d748571/plot_atomic_levels.ipynb b/docs/_downloads/3199d9cf1b4a404903cfdfdd5d748571/plot_atomic_levels.ipynb index 429567fc..fdf99cbf 100644 --- a/docs/_downloads/3199d9cf1b4a404903cfdfdd5d748571/plot_atomic_levels.ipynb +++ b/docs/_downloads/3199d9cf1b4a404903cfdfdd5d748571/plot_atomic_levels.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting Atomic Levels {#ref_plotting_atomic_levels}\r\n\r\nThis example illustrates how to plot atomic energy levels for the\r\ncompound hBN-CNCN at the GAMMA point using the [pyprocar]{.title-ref}\r\npackage.\r\n\r\n## Preparation\r\n\r\nBefore diving into plotting, we need to download the example files. Use\r\nthe following code to do this. Once downloaded, specify the\r\n[data_dir]{.title-ref} to point to the location of the downloaded data.\r\n\r\n``` {caption=\"Downloading example\"}\r\nimport pyprocar\r\n\r\ndata_dir = pyprocar.download_example(\r\n save_dir='', \r\n material='hBN-CNN',\r\n code='vasp', \r\n spin_calc_type='spin-polarized-colinear',\r\n calc_type='gamma'\r\n )\r\n```\r\n" + "\n\n# Plotting Atomic Levels\n\nThis example illustrates how to plot atomic energy levels for the compound hBN-CNCN at the GAMMA point using the `pyprocar` package.\n\n## Preparation\nBefore diving into plotting, we need to download the example files. Use the following code to do this. Once downloaded, specify the `data_dir` to point to the location of the downloaded data.\n\n.. code-block::\n :caption: Downloading example\n\n import pyprocar\n\n data_dir = pyprocar.download_example(\n save_dir='', \n material='hBN-CNN',\n code='vasp', \n spin_calc_type='spin-polarized-colinear',\n calc_type='gamma'\n )\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Setting up the environment\r\n\r\nFirst, we will import the necessary libraries and set up our data\r\ndirectory path.\r\n" + "## Setting up the environment\nFirst, we will import the necessary libraries and set up our data directory path.\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting in Atomic Mode\r\n\r\nThe atomic mode is used to plot the energy levels at a specific k-point.\r\nIn this example, we focus on the GAMMA point. The plot will display\r\nenergy levels for specific atoms in the range of -6 to 6 eV.\r\n" + "## Plotting in Atomic Mode\nThe atomic mode is used to plot the energy levels at a specific k-point. In this example, we focus on the GAMMA point. \nThe plot will display energy levels for specific atoms in the range of -6 to 6 eV. \n\n" ] }, { diff --git a/docs/_downloads/36ac06b70334644e00a88e872a435e53/plot_fermi3d_spin-polarized.ipynb b/docs/_downloads/36ac06b70334644e00a88e872a435e53/plot_fermi3d_spin-polarized.ipynb index ba9b8af6..b785556f 100644 --- a/docs/_downloads/36ac06b70334644e00a88e872a435e53/plot_fermi3d_spin-polarized.ipynb +++ b/docs/_downloads/36ac06b70334644e00a88e872a435e53/plot_fermi3d_spin-polarized.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting fermi3d spin-polarized {#ref_plotting_fermi3d_spin-polarized}\r\n\r\nSymmetry does not currently work! Make sure for fermi surface\r\ncalculations turn off symmetry\r\n\r\nPlotting fermi3d spin-polarized example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='spin-polarized-colinear',\r\n calc_type='fermi')\r\n```\r\n" + "\n\n# Plotting fermi3d spin-polarized\n\nSymmetry does not currently work! Make sure for fermi surface calculations turn off symmetry\n\nPlotting fermi3d spin-polarized example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='spin-polarized-colinear',\n calc_type='fermi')\n" ] }, { @@ -33,7 +33,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -51,7 +51,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n" + "## Plain mode\n\n\n\n" ] }, { @@ -69,7 +69,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Parametric mode\r\n" + "## Parametric mode\n\n\n\n" ] }, { diff --git a/docs/_downloads/3739bb205ce0e303e427132a106bf011/plot_noncolinear_dos_vasp.py b/docs/_downloads/3739bb205ce0e303e427132a106bf011/plot_noncolinear_dos_vasp.py index 2ce3135c..397ad7aa 100644 --- a/docs/_downloads/3739bb205ce0e303e427132a106bf011/plot_noncolinear_dos_vasp.py +++ b/docs/_downloads/3739bb205ce0e303e427132a106bf011/plot_noncolinear_dos_vasp.py @@ -42,6 +42,7 @@ pyprocar.dosplot( code='vasp', mode='parametric', + fermi=5.5962, atoms=atoms, orbitals=orbitals, spins=spins, diff --git a/docs/_downloads/377e353d48622178b3f91c5361149c6a/plot_noncolinear_dos_qe.py b/docs/_downloads/377e353d48622178b3f91c5361149c6a/plot_noncolinear_dos_qe.py index 5ba54988..2f208799 100644 --- a/docs/_downloads/377e353d48622178b3f91c5361149c6a/plot_noncolinear_dos_qe.py +++ b/docs/_downloads/377e353d48622178b3f91c5361149c6a/plot_noncolinear_dos_qe.py @@ -43,6 +43,7 @@ pyprocar.dosplot( code='qe', mode='parametric', + fermi=18.0536, atoms=atoms, orbitals=orbitals, spins=spins, diff --git a/docs/_downloads/3a34777fc720c39085494138831a04fa/plot_spin_polarized_dos.ipynb b/docs/_downloads/3a34777fc720c39085494138831a04fa/plot_spin_polarized_dos.ipynb index 4aaa13a6..4d8549be 100644 --- a/docs/_downloads/3a34777fc720c39085494138831a04fa/plot_spin_polarized_dos.ipynb +++ b/docs/_downloads/3a34777fc720c39085494138831a04fa/plot_spin_polarized_dos.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting spin-polarized density of states {#ref_plotting_spin_polarized_dos}\r\n\r\nPlotting spin-polarized density of states example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='spin-polarized-colinear',\r\n calc_type='dos')\r\n```\r\n" + "\n\n# Plotting spin-polarized density of states\n\nPlotting spin-polarized density of states example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='spin-polarized-colinear',\n calc_type='dos')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n\r\nWhen the calculation is a spin-polarized calculation. There are few more\r\nfeatures features bandsplot can do. The default settings bandsplot will\r\nplot the spin-up and spin-down bands on the same plot.\r\n" + "## Plain mode\n\nWhen the calculation is a spin-polarized calculation. There are few more features features bandsplot can do. \nThe default settings bandsplot will plot the spin-up and spin-down bands on the same plot.\n\n" ] }, { @@ -40,14 +40,14 @@ }, "outputs": [], "source": [ - "pyprocar.dosplot(\n code='vasp', \n mode='plain',\n dirname=data_dir)" + "pyprocar.dosplot(\n code='vasp', \n mode='plain',\n fermi=5.590136,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "The line-styles or line-colors, these may be changed in the ebs section\r\nin the :doc:\\'pyprocar/utils/default_settings.ini\\' file.\r\n\r\nThe keyword spins can also be used to select which spin bands to plot\r\n" + "The line-styles or line-colors, these may be changed in the ebs section in the :doc:'pyprocar/utils/default_settings.ini' file.\n\nThe keyword spins can also be used to select which spin bands to plot\n\n" ] }, { @@ -58,14 +58,14 @@ }, "outputs": [], "source": [ - "spins = [1]\npyprocar.dosplot(\n code='vasp', \n mode='plain',\n spins=spins,\n dirname=data_dir)" + "spins = [1]\npyprocar.dosplot(\n code='vasp', \n mode='plain',\n fermi=5.590136,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Parametric mode\r\n\r\nFor details on the meaning of the indices of the atomic projection\r\nplease refer to the user guide :ref:\\'atomic_projections\\'\r\n" + "## Parametric mode\n\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n\n\n" ] }, { @@ -76,14 +76,14 @@ }, "outputs": [], "source": [ - "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0,1]\n\npyprocar.dosplot(\n code='vasp', \n mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0,1]\n\npyprocar.dosplot(\n code='vasp', \n mode='parametric',\n fermi=5.590136,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# parametric_line mode\r\n\r\nFor details on the meaning of the indices of the atomic projection\r\nplease refer to the user guide :ref:\\'atomic_projections\\'\r\n" + "## parametric_line mode\n\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n\n\n" ] }, { @@ -94,14 +94,14 @@ }, "outputs": [], "source": [ - "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0,1]\n\npyprocar.dosplot(\n code='vasp', \n mode='parametric_line',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0,1]\n\npyprocar.dosplot(\n code='vasp', \n mode='parametric_line',\n fermi=5.590136,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# stack_species mode\r\n" + "## stack_species mode\n\n\n\n\n" ] }, { @@ -112,14 +112,14 @@ }, "outputs": [], "source": [ - "orbitals=[4,5,6,7,8]\nspins=[0,1]\n\npyprocar.dosplot(\n code='vasp', \n mode='stack_species',\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "orbitals=[4,5,6,7,8]\nspins=[0,1]\n\npyprocar.dosplot(\n code='vasp', \n mode='stack_species',\n fermi=5.590136,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# stack_orbtials mode\r\n" + "## stack_orbtials mode\n\n\n\n\n" ] }, { @@ -130,14 +130,14 @@ }, "outputs": [], "source": [ - "atoms=[0]\nspins=[0,1]\npyprocar.dosplot(\n code='vasp', \n mode='stack_orbitals',\n atoms=atoms,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\nspins=[0,1]\npyprocar.dosplot(\n code='vasp', \n mode='stack_orbitals',\n fermi=5.590136,\n atoms=atoms,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# stack mode\r\n" + "## stack mode\n\n\n\n\n" ] }, { @@ -148,7 +148,61 @@ }, "outputs": [], "source": [ - "items={'Fe':[4,5,6,7,8]}\nspins=[0,1]\npyprocar.dosplot(\n code='vasp', \n mode='stack',\n items=items,\n spins=spins,\n dirname=data_dir)" + "items={'Fe':[4,5,6,7,8]}\nspins=[0,1]\npyprocar.dosplot(\n code='vasp', \n mode='stack',\n fermi=5.590136,\n items=items,\n spins=spins,\n dirname=data_dir)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## overlay_species mode\n\n\n\n\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "orbitals=[4,5,6,7,8]\nspins=[0,1]\n\npyprocar.dosplot(\n code='vasp', \n mode='overlay_species',\n fermi=5.590136,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## overlay_orbtials mode\n\n\n\n\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "atoms=[0]\nspins=[0,1]\npyprocar.dosplot(\n code='vasp', \n mode='overlay_orbitals',\n fermi=5.590136,\n atoms=atoms,\n spins=spins,\n dirname=data_dir)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## overlay mode\n\n\n\n\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "items={'Fe':[4,5,6,7,8]}\nspins=[0,1]\npyprocar.dosplot(\n code='vasp', \n mode='overlay',\n fermi=5.590136,\n items=items,\n spins=spins,\n dirname=data_dir)" ] } ], diff --git a/docs/_downloads/3b7521f82ed503140f6ba66d69ec9d0a/plot_autobands.ipynb b/docs/_downloads/3b7521f82ed503140f6ba66d69ec9d0a/plot_autobands.ipynb index c4cf780e..f981e09f 100644 --- a/docs/_downloads/3b7521f82ed503140f6ba66d69ec9d0a/plot_autobands.ipynb +++ b/docs/_downloads/3b7521f82ed503140f6ba66d69ec9d0a/plot_autobands.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Autobands plotting {#ref_plot_autbands}\r\n\r\nOne of the most powerful capabilities of PyProcar is allowing to\r\ncorrelate real space with electronic structure, for instance finding\r\nsurface states or defect levels. Traditionally this task is done by the\r\nuser, providing a list of atoms representing the surface or the defect\r\n(parameter `atom` in `bandsplot`). Also the user needs to choose a\r\nrelevant energy window for the plot and setting the boundaries of the\r\ncolor scale to highlight the relevant states. That process is both\r\ntedious and error prone: for instance the user need to find the special\r\natoms (*e.g.* defect, surface, etc.) and take care of whether the\r\nindexes are 0- or 1-based.\r\n\r\nSpecifically, the function aims to: - Determine an optimal energy window\r\nfor the plot, which includes bulk-like bands both above and below the\r\n*fundamental* band gap for insulators, as well as any localized states\r\nwithin that gap. - Identify important real-space features such as\r\ndefects, surfaces, and van der Waals layers. - Locate localized\r\nelectronic states within the selected energy window. - Calculate\r\nsuitable values for the color map to emphasize these localized states.\r\n\r\nAll these tasks are executed without requiring user intervention. The\r\nidentification of real-space features is carried out using PyPoscar.\r\nLocalized states are identified through the Inverse Participation Ratio\r\n(IPR). The function correlates the geometry and electronic structure by\r\nevaluating the participation of relevant atoms in the IPR calculations.\r\n\r\nThis automated identification of key features is most effective when the\r\natoms of interest are statistically distinct from the rest of the\r\nsystem, both in real space and electronic structure. In scenarios where\r\nsuch distinctions are not readily apparent, the function will default to\r\ngenerating a standard band structure plot. It\\'s important to note that\r\nwhile our current implementation is robust, there may be some\r\ngeometrical features it does not yet capture. However, we anticipate\r\nthat the function will continue to improve based on user feedback.\r\n\r\n## Preparation\r\n\r\nBefore diving into plotting, we need to download the example files. Use\r\nthe following code to do this. Once downloaded, specify the\r\n[data_dir]{.title-ref} to point to the location of the downloaded data.\r\n\r\n``` {caption=\"Downloading example\"}\r\nimport pyprocar\r\n\r\nbi2se3_data_dir = pyprocar.download_example(\r\n save_dir='', \r\n material='auto',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='bands'\r\n )\r\n```\r\n" + "\n\n# Autobands plotting\n\nOne of the most powerful capabilities of PyProcar is allowing to correlate real space with electronic structure, \nfor instance finding surface states or defect levels. Traditionally this task is done by the user, \nproviding a list of atoms representing the surface or the defect (parameter ``atom`` in ``bandsplot``). \nAlso the user needs to choose a relevant energy window for the plot and setting the boundaries of the color scale to highlight the relevant states. \nThat process is both tedious and error prone: for instance the user need to find the special atoms (*e.g.* defect, surface, etc.) \nand take care of whether the indexes are 0- or 1-based.\n\nSpecifically, the function aims to:\n- Determine an optimal energy window for the plot, which includes bulk-like bands both above and below the *fundamental* band gap for insulators, as well as any localized states within that gap.\n- Identify important real-space features such as defects, surfaces, and van der Waals layers.\n- Locate localized electronic states within the selected energy window.\n- Calculate suitable values for the color map to emphasize these localized states.\n\nAll these tasks are executed without requiring user intervention. The identification of real-space features is carried out using PyPoscar. \nLocalized states are identified through the Inverse Participation Ratio (IPR). \nThe function correlates the geometry and electronic structure by evaluating the participation of relevant atoms in the IPR calculations.\n\nThis automated identification of key features is most effective when the atoms of interest are statistically distinct from the rest of the system, \nboth in real space and electronic structure. In scenarios where such distinctions are not readily apparent, the function will default to generating \na standard band structure plot. It's important to note that while our current implementation is robust, there may be some geometrical features it does not yet capture. \nHowever, we anticipate that the function will continue to improve based on user feedback.\n\n## Preparation\nBefore diving into plotting, we need to download the example files. \nUse the following code to do this. Once downloaded, specify the `data_dir` to point to the location of the downloaded data.\n\n.. code-block::\n :caption: Downloading example\n\n import pyprocar\n\n bi2se3_data_dir = pyprocar.download_example(\n save_dir='', \n material='auto',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='bands'\n )\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Setting up the environment\r\n\r\nFirst, we will import the necessary libraries and set up our data\r\ndirectory path.\r\n" + "## Setting up the environment\nFirst, we will import the necessary libraries and set up our data directory path.\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Autobands Example\r\n\r\nAs an example of this functionality, we calculate a slab of a\r\ntopologically non-trivial phase of Bi. It features surface states with\r\nDirac cones at high-symmetry points. The code used to plot the band\r\nstructure is below. The title of the figure is `Defect 0`, which\r\ncorresponds to the upper surface of the slab, the other surface\r\ngenerates a second figure, with title `Defect 1`. When running the code\r\nabove, a file `report.txt` is generated with info about the atoms\r\ncomprising each defect, and the associated localized states.\r\n" + "## Autobands Example\n\nAs an example of this functionality, we calculate a slab of a topologically non-trivial phase of Bi. \nIt features surface states with Dirac cones at high-symmetry points. The code used to plot the band structure is below.\nThe title of the figure is ``Defect 0``, which corresponds to the upper surface of the slab, the other surface generates a second figure, \nwith title ``Defect 1``. When running the code above, a file ``report.txt`` is generated with info about the atoms comprising each defect, \nand the associated localized states.\n\n" ] }, { diff --git a/docs/_downloads/42a7aa17c794954244d9b4ffa5a2ac60/plot_bandsplot_configurations.py b/docs/_downloads/42a7aa17c794954244d9b4ffa5a2ac60/plot_bandsplot_configurations.py index e82239ec..871b1a9c 100644 --- a/docs/_downloads/42a7aa17c794954244d9b4ffa5a2ac60/plot_bandsplot_configurations.py +++ b/docs/_downloads/42a7aa17c794954244d9b4ffa5a2ac60/plot_bandsplot_configurations.py @@ -47,7 +47,7 @@ print(f"Configuration files are located at: {config_path}") # Print the configurations -pyprocar.bandsplot(code=code,dirname=data_dir,print_plot_opts=True) +pyprocar.bandsplot(code=code,dirname=data_dir,fermi=5.590136,print_plot_opts=True) ############################################################################### @@ -62,6 +62,7 @@ code=code, dirname=data_dir, mode='parametric', + fermi=5.590136, atoms=[0], orbitals=[4,5,6,7,8], cmap='viridis', # Colormap @@ -84,6 +85,7 @@ code=code, dirname=data_dir, mode='scatter', + fermi=5.590136, atoms=[0], orbitals=[4,5,6,7,8], marker=['v','o'], # Marker style @@ -102,6 +104,7 @@ code=code, dirname=data_dir, mode='scatter', + fermi=5.590136, atoms=[0], orbitals=[4,5,6,7,8], figure_size=(10, 6), # Figure size (width, height) diff --git a/docs/_downloads/44002a32a2c12b63ac956f30ab9fbeca/plot_dosplot_configurations.py b/docs/_downloads/44002a32a2c12b63ac956f30ab9fbeca/plot_dosplot_configurations.py index ed8efd22..06c98bc4 100644 --- a/docs/_downloads/44002a32a2c12b63ac956f30ab9fbeca/plot_dosplot_configurations.py +++ b/docs/_downloads/44002a32a2c12b63ac956f30ab9fbeca/plot_dosplot_configurations.py @@ -47,7 +47,7 @@ print(f"Configuration files are located at: {config_path}") # Print the configurations -pyprocar.dosplot(code=code, dirname=data_dir, print_plot_opts=True) +pyprocar.dosplot(code=code, dirname=data_dir,fermi=5.599480, print_plot_opts=True) ############################################################################### @@ -61,6 +61,7 @@ pyprocar.dosplot( code=code, dirname=data_dir, + fermi=5.599480, atoms=[0], orbitals=[4,5,6,7,8], mode='parametric', @@ -82,6 +83,7 @@ pyprocar.dosplot( code=code, dirname=data_dir, + fermi=5.599480, atoms=[0], orbitals=[4,5,6,7,8], mode='parametric_line', diff --git a/docs/_downloads/458d1f0647d99fcac120ceb3cbf2dacc/plot_bandgap.ipynb b/docs/_downloads/458d1f0647d99fcac120ceb3cbf2dacc/plot_bandgap.ipynb index eea0cff2..425dcf02 100644 --- a/docs/_downloads/458d1f0647d99fcac120ceb3cbf2dacc/plot_bandgap.ipynb +++ b/docs/_downloads/458d1f0647d99fcac120ceb3cbf2dacc/plot_bandgap.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Example of finding the bandgap {#ref_example_bandgap}\r\n\r\nThe bandgap of a calculation can be found by:\r\n\r\n``` {caption=\"General Format\"}\r\npyprocar.bandgap(procar=\"PROCAR\", outcar=\"OUTCAR\", code=\"vasp\")\r\n```\r\n\r\nNOTE: The bandgap calculation should be done for non-self consistent\r\n(band structure) calculations.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='bands')\r\n```\r\n" + "\n\n# Example of finding the bandgap\n\nThe bandgap of a calculation can be found by:\n\n.. code-block::\n :caption: General Format\n\n pyprocar.bandgap(procar=\"PROCAR\", outcar=\"OUTCAR\", code=\"vasp\")\n\n\nNOTE:\nThe bandgap calculation should be done for non-self consistent (band structure) calculations. \n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='bands')\n" ] }, { @@ -22,7 +22,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { diff --git a/docs/_downloads/498b7e12b5246f70935a30cb0236fa20/plot_rashba_spin_spliting.ipynb b/docs/_downloads/498b7e12b5246f70935a30cb0236fa20/plot_rashba_spin_spliting.ipynb index 9456ad02..9cdfd084 100644 --- a/docs/_downloads/498b7e12b5246f70935a30cb0236fa20/plot_rashba_spin_spliting.ipynb +++ b/docs/_downloads/498b7e12b5246f70935a30cb0236fa20/plot_rashba_spin_spliting.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting rashba spin splitting {#ref_plotting_plotting_rashba_spin_spliting}\r\n\r\nPlotting rashba spin splitting example. From our first paper we had an\r\nexample to plot the different spin texture projections of BiSb at a\r\nconstant energy surface 0.60eV above the fermei level and -0.90ev below\r\nthe fermi level.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='BiSb_monolayer',\r\n code='vasp', \r\n spin_calc_type='non-colinear',\r\n calc_type='fermi')\r\n```\r\n" + "\n\n# Plotting rashba spin splitting\n\nPlotting rashba spin splitting example. \nFrom our first paper we had an example to plot the different spin texture projections of BiSb at a constant energy surface 0.60eV above the fermei level and -0.90ev below the fermi level. \n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='BiSb_monolayer',\n code='vasp', \n spin_calc_type='non-colinear',\n calc_type='fermi')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# energy = 0.60 sx projection no arrows\r\n" + "## energy = 0.60 sx projection no arrows \n\n\n" ] }, { @@ -40,14 +40,14 @@ }, "outputs": [], "source": [ - "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=0.60,\n spin_texture=True,\n no_arrow=True,\n spin_projection='x',\n plot_color_bar=True)" + "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=0.60,\n fermi=-1.1904,\n spin_texture=True,\n no_arrow=True,\n spin_projection='x',\n plot_color_bar=True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# energy = 0.60 sy projection no arrows\r\n" + "## energy = 0.60 sy projection no arrows \n\n\n" ] }, { @@ -58,14 +58,14 @@ }, "outputs": [], "source": [ - "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=0.60,\n spin_texture=True,\n no_arrow=True,\n spin_projection='y',\n plot_color_bar=True)" + "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=0.60,\n fermi=-1.1904,\n spin_texture=True,\n no_arrow=True,\n spin_projection='y',\n plot_color_bar=True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# energy = 0.60 sz projection no arrows\r\n" + "## energy = 0.60 sz projection no arrows \n\n\n" ] }, { @@ -76,14 +76,14 @@ }, "outputs": [], "source": [ - "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=0.60,\n spin_texture=True,\n no_arrow=True,\n spin_projection='z',\n plot_color_bar=True)" + "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=0.60,\n fermi=-1.1904,\n spin_texture=True,\n no_arrow=True,\n spin_projection='z',\n plot_color_bar=True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# energy = -0.90 sx projection no arrows\r\n" + "## energy = -0.90 sx projection no arrows \n\n\n" ] }, { @@ -94,14 +94,14 @@ }, "outputs": [], "source": [ - "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=-0.90,\n spin_texture=True,\n no_arrow=True,\n spin_projection='x',\n plot_color_bar=True)" + "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=-0.90,\n fermi=-1.1904,\n spin_texture=True,\n no_arrow=True,\n spin_projection='x',\n plot_color_bar=True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# energy = -0.90 sy projection no arrows\r\n" + "## energy = -0.90 sy projection no arrows \n\n\n" ] }, { @@ -112,14 +112,14 @@ }, "outputs": [], "source": [ - "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=-0.90,\n spin_texture=True,\n no_arrow=True,\n spin_projection='y',\n plot_color_bar=True)" + "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=-0.90,\n fermi=-1.1904,\n spin_texture=True,\n no_arrow=True,\n spin_projection='y',\n plot_color_bar=True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# energy = -0.90 sz projection no arrows\r\n" + "## energy = -0.90 sz projection no arrows \n\n\n" ] }, { @@ -130,14 +130,14 @@ }, "outputs": [], "source": [ - "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=-0.90,\n spin_texture=True,\n no_arrow=True,\n spin_projection='z',\n plot_color_bar=True)" + "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=-0.90,\n fermi=-1.1904,\n spin_texture=True,\n no_arrow=True,\n spin_projection='z',\n plot_color_bar=True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# energy = 0.60 sx projection with arrows\r\n" + "## energy = 0.60 sx projection with arrows \n\n\n" ] }, { @@ -148,14 +148,14 @@ }, "outputs": [], "source": [ - "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=0.60,\n spin_texture=True,\n spin_projection='x',\n arrow_size=3,\n arrow_density=6,\n plot_color_bar=True)" + "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=0.60,\n fermi=-1.1904,\n spin_texture=True,\n spin_projection='x',\n arrow_size=3,\n arrow_density=6,\n plot_color_bar=True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# energy = -0.90 sx projection with arrows\r\n" + "## energy = -0.90 sx projection with arrows \n\n\n" ] }, { @@ -166,7 +166,7 @@ }, "outputs": [], "source": [ - "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=-0.90,\n spin_texture=True,\n spin_projection='x',\n arrow_size=3,\n arrow_density=6,\n plot_color_bar=True)" + "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n energy=-0.90,\n fermi=-1.1904,\n spin_texture=True,\n spin_projection='x',\n arrow_size=3,\n arrow_density=6,\n plot_color_bar=True)" ] } ], diff --git a/docs/_downloads/4c96c34eae3806b1f0b68a4b273c321f/plot_compare_bands.py b/docs/_downloads/4c96c34eae3806b1f0b68a4b273c321f/plot_compare_bands.py index 3b439f90..412deec5 100644 --- a/docs/_downloads/4c96c34eae3806b1f0b68a4b273c321f/plot_compare_bands.py +++ b/docs/_downloads/4c96c34eae3806b1f0b68a4b273c321f/plot_compare_bands.py @@ -41,5 +41,5 @@ # When show is equal to False, bandsplot will return a maplotlib.Figure and maplotlib.axes.Axes object # -fig, ax = pyprocar.bandsplot(code='vasp', dirname = vasp_data_dir, mode='parametric', elimit=[-5,5], orbitals=[4,5,6,7,8], show=False) -pyprocar.bandsplot(code='qe', dirname = qe_data_dir, mode='plain', elimit=[-5,5], color='k',ax=ax, show =True) \ No newline at end of file +fig, ax = pyprocar.bandsplot(code='vasp', dirname = vasp_data_dir, mode='parametric',fermi=5.599480, elimit=[-5,5], orbitals=[4,5,6,7,8], show=False) +pyprocar.bandsplot(code='qe', dirname = qe_data_dir, mode='plain',fermi=18.2398, elimit=[-5,5], color='k',ax=ax, show =True) \ No newline at end of file diff --git a/docs/_downloads/4df4aea1a6f82010ff5f16d9d88e8610/plot_compare_bands.ipynb b/docs/_downloads/4df4aea1a6f82010ff5f16d9d88e8610/plot_compare_bands.ipynb index 160296de..1787ed81 100644 --- a/docs/_downloads/4df4aea1a6f82010ff5f16d9d88e8610/plot_compare_bands.ipynb +++ b/docs/_downloads/4df4aea1a6f82010ff5f16d9d88e8610/plot_compare_bands.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Comparing band structures {#ref_plotting_compare_bands}\r\n\r\nComparing band structures example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\nvasp_data_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='bands')\r\n\r\nqe_data_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='qe', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='bands')\r\n```\r\n" + "\n\n# Comparing band structures\n\nComparing band structures example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n vasp_data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='bands')\n\n qe_data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='qe', \n spin_calc_type='non-spin-polarized',\n calc_type='bands')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "When show is equal to False, bandsplot will return a maplotlib.Figure\r\nand maplotlib.axes.Axes object\r\n" + "When show is equal to False, bandsplot will return a maplotlib.Figure and maplotlib.axes.Axes object\n\n\n" ] }, { @@ -40,7 +40,7 @@ }, "outputs": [], "source": [ - "fig, ax = pyprocar.bandsplot(code='vasp', dirname = vasp_data_dir, mode='parametric', elimit=[-5,5], orbitals=[4,5,6,7,8], show=False)\npyprocar.bandsplot(code='qe', dirname = qe_data_dir, mode='plain', elimit=[-5,5], color='k',ax=ax, show =True)" + "fig, ax = pyprocar.bandsplot(code='vasp', dirname = vasp_data_dir, mode='parametric',fermi=5.599480, elimit=[-5,5], orbitals=[4,5,6,7,8], show=False)\npyprocar.bandsplot(code='qe', dirname = qe_data_dir, mode='plain',fermi=18.2398, elimit=[-5,5], color='k',ax=ax, show =True)" ] } ], diff --git a/docs/_downloads/596210a8656d0349621199ea5ab59d0e/plot_dosplot_configurations.ipynb b/docs/_downloads/596210a8656d0349621199ea5ab59d0e/plot_dosplot_configurations.ipynb index ba63da53..e799977a 100644 --- a/docs/_downloads/596210a8656d0349621199ea5ab59d0e/plot_dosplot_configurations.ipynb +++ b/docs/_downloads/596210a8656d0349621199ea5ab59d0e/plot_dosplot_configurations.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting with Configurations in [pyprocar]{.title-ref} {#ref_plot_dos_configuration}\r\n\r\nThis example illustrates how to utilize various configurations for\r\nplotting the density of states (DOS) using the [pyprocar]{.title-ref}\r\npackage. It provides a structured way to explore and demonstrate\r\ndifferent configurations for the [dosplot]{.title-ref} function.\r\n\r\n## Preparation\r\n\r\nBefore diving into plotting, we need to download the example files. Use\r\nthe following code to do this. Once downloaded, specify the\r\n[data_dir]{.title-ref} to point to the location of the downloaded data.\r\n\r\n``` {caption=\"Downloading example\"}\r\nimport pyprocar\r\n\r\ndata_dir = pyprocar.download_example(\r\n save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='spin-polarized-colinear',\r\n calc_type='dos'\r\n )\r\n```\r\n" + "\n\n# Plotting with Configurations in `pyprocar`\n\nThis example illustrates how to utilize various configurations for plotting the density of states (DOS) using the `pyprocar` package. It provides a structured way to explore and demonstrate different configurations for the `dosplot` function.\n\n## Preparation\nBefore diving into plotting, we need to download the example files. Use the following code to do this. Once downloaded, specify the `data_dir` to point to the location of the downloaded data.\n\n.. code-block::\n :caption: Downloading example\n\n import pyprocar\n\n data_dir = pyprocar.download_example(\n save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='spin-polarized-colinear',\n calc_type='dos'\n )\n" ] }, { @@ -26,7 +26,7 @@ }, "outputs": [], "source": [ - "# Section 1: Locating and Printing Configuration Files\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates where the configuration files are located in the package.\n# It also shows how to print the configurations by setting print_plot_opts=True.\n#\n\n# Path to the configuration files in the package\nconfig_path = os.path.join(pyprocar.__path__[0], 'cfg')\nprint(f\"Configuration files are located at: {config_path}\")\n\n# Print the configurations\npyprocar.dosplot(code=code, dirname=data_dir, print_plot_opts=True)" + "# Section 1: Locating and Printing Configuration Files\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates where the configuration files are located in the package.\n# It also shows how to print the configurations by setting print_plot_opts=True.\n#\n\n# Path to the configuration files in the package\nconfig_path = os.path.join(pyprocar.__path__[0], 'cfg')\nprint(f\"Configuration files are located at: {config_path}\")\n\n# Print the configurations\npyprocar.dosplot(code=code, dirname=data_dir,fermi=5.599480, print_plot_opts=True)" ] }, { @@ -37,7 +37,7 @@ }, "outputs": [], "source": [ - "# Section 2: Changing cmap, clim, and Fermi line properties\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to change the colormap (cmap), color limits (clim),\n# and Fermi line properties (color, linestyle, and linewidth).\n#\n\npyprocar.dosplot(\n code=code,\n dirname=data_dir,\n atoms=[0],\n orbitals=[4,5,6,7,8],\n mode='parametric',\n cmap='viridis', # Colormap\n clim=[0, 1], # Color limits\n fermi_color='red', # Fermi line color\n fermi_linestyle='--', # Fermi line linestyle\n fermi_linewidth=2.0 # Fermi line linewidth\n)" + "# Section 2: Changing cmap, clim, and Fermi line properties\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to change the colormap (cmap), color limits (clim),\n# and Fermi line properties (color, linestyle, and linewidth).\n#\n\npyprocar.dosplot(\n code=code,\n dirname=data_dir,\n fermi=5.599480,\n atoms=[0],\n orbitals=[4,5,6,7,8],\n mode='parametric',\n cmap='viridis', # Colormap\n clim=[0, 1], # Color limits\n fermi_color='red', # Fermi line color\n fermi_linestyle='--', # Fermi line linestyle\n fermi_linewidth=2.0 # Fermi line linewidth\n)" ] }, { @@ -48,7 +48,7 @@ }, "outputs": [], "source": [ - "# Section 4: Setting the Figure Size and DPI\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to set the figure size and dots per inch (DPI) for the plot.\n#\n\npyprocar.dosplot(\n code=code,\n dirname=data_dir,\n atoms=[0],\n orbitals=[4,5,6,7,8],\n mode='parametric_line',\n figure_size=(10, 6), # Figure size (width, height)\n dpi=300, # Dots per inch\n grid=True, # Boolean for grid\n)" + "# Section 4: Setting the Figure Size and DPI\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to set the figure size and dots per inch (DPI) for the plot.\n#\n\npyprocar.dosplot(\n code=code,\n dirname=data_dir,\n fermi=5.599480,\n atoms=[0],\n orbitals=[4,5,6,7,8],\n mode='parametric_line',\n figure_size=(10, 6), # Figure size (width, height)\n dpi=300, # Dots per inch\n grid=True, # Boolean for grid\n)" ] } ], diff --git a/docs/_downloads/5fb746fda43862186a77b594e97d94d7/plot_rashba_spin_spliting.py b/docs/_downloads/5fb746fda43862186a77b594e97d94d7/plot_rashba_spin_spliting.py index 8965f2a2..ec23e35d 100644 --- a/docs/_downloads/5fb746fda43862186a77b594e97d94d7/plot_rashba_spin_spliting.py +++ b/docs/_downloads/5fb746fda43862186a77b594e97d94d7/plot_rashba_spin_spliting.py @@ -37,6 +37,7 @@ pyprocar.fermi2D(code = 'vasp', dirname=data_dir, energy=0.60, + fermi=-1.1904, spin_texture=True, no_arrow=True, spin_projection='x', @@ -50,6 +51,7 @@ pyprocar.fermi2D(code = 'vasp', dirname=data_dir, energy=0.60, + fermi=-1.1904, spin_texture=True, no_arrow=True, spin_projection='y', @@ -64,6 +66,7 @@ pyprocar.fermi2D(code = 'vasp', dirname=data_dir, energy=0.60, + fermi=-1.1904, spin_texture=True, no_arrow=True, spin_projection='z', @@ -77,6 +80,7 @@ pyprocar.fermi2D(code = 'vasp', dirname=data_dir, energy=-0.90, + fermi=-1.1904, spin_texture=True, no_arrow=True, spin_projection='x', @@ -90,6 +94,7 @@ pyprocar.fermi2D(code = 'vasp', dirname=data_dir, energy=-0.90, + fermi=-1.1904, spin_texture=True, no_arrow=True, spin_projection='y', @@ -104,6 +109,7 @@ pyprocar.fermi2D(code = 'vasp', dirname=data_dir, energy=-0.90, + fermi=-1.1904, spin_texture=True, no_arrow=True, spin_projection='z', @@ -118,6 +124,7 @@ pyprocar.fermi2D(code = 'vasp', dirname=data_dir, energy=0.60, + fermi=-1.1904, spin_texture=True, spin_projection='x', arrow_size=3, @@ -132,6 +139,7 @@ pyprocar.fermi2D(code = 'vasp', dirname=data_dir, energy=-0.90, + fermi=-1.1904, spin_texture=True, spin_projection='x', arrow_size=3, diff --git a/docs/_downloads/632225c37dff473638cb222867ee9a93/plot_finding_defects_pyposcar.ipynb b/docs/_downloads/632225c37dff473638cb222867ee9a93/plot_finding_defects_pyposcar.ipynb index ffa61f7f..1272d9b4 100644 --- a/docs/_downloads/632225c37dff473638cb222867ee9a93/plot_finding_defects_pyposcar.ipynb +++ b/docs/_downloads/632225c37dff473638cb222867ee9a93/plot_finding_defects_pyposcar.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Finding defects in a POSCAR file {#ref_example_finding_defect}\r\n\r\nIn this example, we\\'ll demonstrate how to automatically find defects in\r\na POSCAR file\r\n\r\nLet\\'s get started!\r\n" + "\n\n# Finding defects in a POSCAR file\n\nIn this example, we'll demonstrate how to automatically find defects in a POSCAR file\n\nLet's get started!\n" ] }, { @@ -22,7 +22,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Utility function for creating GIF visualizations\r\n" + "## Utility function for creating GIF visualizations\n\n" ] }, { @@ -40,7 +40,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Finding defects\r\n" + "## Finding defects\n\n" ] }, { diff --git a/docs/_downloads/6f007bae86be3db34e6881409cd42249/plot_fermi3d_spin_texture.ipynb b/docs/_downloads/6f007bae86be3db34e6881409cd42249/plot_fermi3d_spin_texture.ipynb index 33df5568..c48b54b0 100644 --- a/docs/_downloads/6f007bae86be3db34e6881409cd42249/plot_fermi3d_spin_texture.ipynb +++ b/docs/_downloads/6f007bae86be3db34e6881409cd42249/plot_fermi3d_spin_texture.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting fermi3d spin_texture {#ref_plotting_fermi3d_spin_texture}\r\n\r\nSymmetry does not currently work! Make sure for fermi surface\r\ncalculations turn off symmetry\r\n\r\nPlotting fermi3d spin_texture example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-colinear',\r\n calc_type='fermi')\r\n```\r\n" + "\n\n# Plotting fermi3d spin_texture\n\nSymmetry does not currently work! Make sure for fermi surface calculations turn off symmetry\n\nPlotting fermi3d spin_texture example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-colinear',\n calc_type='fermi')\n" ] }, { @@ -33,7 +33,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -51,7 +51,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Spin Texture mode\r\n" + "## Spin Texture mode\n\n\n\n" ] }, { diff --git a/docs/_downloads/72b1997c4cbf791739731e36013071ec/plot_colinear.py b/docs/_downloads/72b1997c4cbf791739731e36013071ec/plot_colinear.py index 8c23f4b3..8160cbc5 100644 --- a/docs/_downloads/72b1997c4cbf791739731e36013071ec/plot_colinear.py +++ b/docs/_downloads/72b1997c4cbf791739731e36013071ec/plot_colinear.py @@ -35,6 +35,7 @@ pyprocar.bandsplot( code='vasp', mode='plain', + fermi=5.599480, dirname=data_dir) ############################################################################### @@ -52,6 +53,7 @@ pyprocar.bandsplot( code='vasp', mode='parametric', + fermi=5.599480, atoms=atoms, orbitals=orbitals, spins=spins, @@ -72,6 +74,7 @@ pyprocar.bandsplot( code='vasp', mode='parametric', + fermi=5.599480, atoms=atoms, orbitals=orbitals, spins=spins, @@ -92,6 +95,7 @@ pyprocar.bandsplot( code='vasp', mode='scatter', + fermi=5.599480, atoms=atoms, orbitals=orbitals, spins=spins, @@ -110,6 +114,7 @@ pyprocar.bandsplot( code='vasp', mode='overlay_species', + fermi=5.599480, orbitals=orbitals, spins=spins, dirname=data_dir) @@ -125,6 +130,7 @@ pyprocar.bandsplot( code='vasp', mode='overlay_orbitals', + fermi=5.599480, atoms=atoms, spins=spins, dirname=data_dir) @@ -141,6 +147,7 @@ pyprocar.bandsplot( code='vasp', mode='overlay', + fermi=5.599480, items=items, dirname=data_dir) @@ -155,5 +162,6 @@ pyprocar.bandsplot( code='vasp', mode='overlay', + fermi=5.599480, items=items, dirname=data_dir) \ No newline at end of file diff --git a/docs/_downloads/739a73b2e22bcdfe7b8d83bdc731942f/plot_bandsdosplot.py b/docs/_downloads/739a73b2e22bcdfe7b8d83bdc731942f/plot_bandsdosplot.py index 025e79ca..8b8b08b7 100644 --- a/docs/_downloads/739a73b2e22bcdfe7b8d83bdc731942f/plot_bandsdosplot.py +++ b/docs/_downloads/739a73b2e22bcdfe7b8d83bdc731942f/plot_bandsdosplot.py @@ -40,11 +40,17 @@ # These keyword arguments can be set in bands_settings and dos_settings as done below. # -bands_settings = {'mode':'plain', - 'dirname': bands_dir} - -dos_settings = {'mode':'plain', - 'dirname': dos_dir} +bands_settings = { + 'mode':'plain', + 'fermi':5.599480, # This will overide the default fermi value found in bands directory + 'dirname': bands_dir + } + +dos_settings = { + 'mode':'plain', + 'fermi':5.599480, # This will overide the default fermi value found in dos directory + 'dirname': dos_dir + } pyprocar.bandsdosplot(code='vasp', bands_settings=bands_settings, diff --git a/docs/_downloads/74de0d0d5c3ecce985974c96c391ad6a/plot_noncolinear_qe.ipynb b/docs/_downloads/74de0d0d5c3ecce985974c96c391ad6a/plot_noncolinear_qe.ipynb index ce64eb74..9142f00f 100644 --- a/docs/_downloads/74de0d0d5c3ecce985974c96c391ad6a/plot_noncolinear_qe.ipynb +++ b/docs/_downloads/74de0d0d5c3ecce985974c96c391ad6a/plot_noncolinear_qe.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting non colinear band structures in Quantum Espresso {#ref_plotting_noncolinear_qe}\r\n\r\nPlotting non colinear band structures in Quantum Espresso.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='qe', \r\n spin_calc_type='non-colinear',\r\n calc_type='bands')\r\n```\r\n" + "\n\n# Plotting non colinear band structures in Quantum Espresso\n\nPlotting non colinear band structures in Quantum Espresso.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='qe', \n spin_calc_type='non-colinear',\n calc_type='bands')\n" ] }, { @@ -22,7 +22,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -40,7 +40,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n" + "## Plain mode\n\n" ] }, { @@ -51,14 +51,14 @@ }, "outputs": [], "source": [ - "pyprocar.bandsplot(\n code='qe', \n mode='plain',\n dirname=data_dir)" + "pyprocar.bandsplot(\n code='qe', \n mode='plain',\n fermi=18.0536,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Parametric mode\r\n\r\nQuantum Espresso expresses the projections in the coupled basis,\r\ntherefore orbitals takes different meanings. For details on the meaning\r\nof the indices of the atomic projection please refer to the user guide\r\n:ref:\\'atomic_projections\\'\r\n" + "## Parametric mode\nQuantum Espresso expresses the projections in the coupled basis, \ntherefore orbitals takes different meanings.\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n" ] }, { @@ -69,7 +69,7 @@ }, "outputs": [], "source": [ - "atoms=[0]\nspins=[0]\norbitals=[8,9,10,11,12,13,14,15,16,17]\n\npyprocar.bandsplot(\n code='qe', \n mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\nspins=[0]\norbitals=[8,9,10,11,12,13,14,15,16,17]\n\npyprocar.bandsplot(\n code='qe', \n mode='parametric',\n fermi=18.0536,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] } ], diff --git a/docs/_downloads/8495fda3a3e9038d76ed721a29deae61/plot_utils_pyposcar.ipynb b/docs/_downloads/8495fda3a3e9038d76ed721a29deae61/plot_utils_pyposcar.ipynb index b2912bfe..a2157d59 100644 --- a/docs/_downloads/8495fda3a3e9038d76ed721a29deae61/plot_utils_pyposcar.ipynb +++ b/docs/_downloads/8495fda3a3e9038d76ed721a29deae61/plot_utils_pyposcar.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Modifying a POSCAR File: Scaling, Supercells, and Defects {#ref_example_poscar_modifications}\r\n\r\nIn this example, we\\'ll demonstrate several modifications on a POSCAR\r\nfile using the [pyprocar]{.title-ref} package:\r\n\r\n1. Scaling the lattice vectors to reduce vacuum space.\r\n2. Generating a supercell.\r\n3. Introducing defects by changing atom types.\r\n\r\nLet\\'s get started!\r\n" + "\n\n# Modifying a POSCAR File: Scaling, Supercells, and Defects\n\nIn this example, we'll demonstrate several modifications on a POSCAR file using the `pyprocar` package:\n\n1. Scaling the lattice vectors to reduce vacuum space.\n2. Generating a supercell.\n3. Introducing defects by changing atom types.\n\nLet's get started!\n" ] }, { @@ -22,7 +22,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Utility function for creating GIF visualizations\r\n" + "## Utility function for creating GIF visualizations\n\n" ] }, { @@ -40,7 +40,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Scaling Vacuum Space in the Lattice\r\n" + "## Scaling Vacuum Space in the Lattice\n\n" ] }, { @@ -58,7 +58,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Creating a Supercell\r\n" + "## Creating a Supercell\n\n" ] }, { @@ -76,7 +76,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Introducing Defects\r\n" + "## Introducing Defects\n\n" ] }, { diff --git a/docs/_downloads/9158268fd95e17740417379b77c121fa/plot_de_hass_van_alphen.ipynb b/docs/_downloads/9158268fd95e17740417379b77c121fa/plot_de_hass_van_alphen.ipynb index 03c56349..c2ee3614 100644 --- a/docs/_downloads/9158268fd95e17740417379b77c121fa/plot_de_hass_van_alphen.ipynb +++ b/docs/_downloads/9158268fd95e17740417379b77c121fa/plot_de_hass_van_alphen.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Showing how to get van alphen fequencies from the fermi surface {#ref_plotting_de_hass_van_alphen}\r\n\r\nSymmetry does not currently work! Make sure for fermi surface\r\ncalculations turn off symmetry\r\n\r\nVan alphen fequencies example. De has van alphen frequencies (F) in\r\nterms of extremal fermi surface areas (A) is given below. To compare the\r\ntheoretical freuqencies we will compare with the results taken from the\r\nexperimental paper \\\"The Fermi surfaces of copper, silver and gold. I.\r\nThe de Haas-Van alphen\r\neffect\\\"().\r\n\r\n$$F = \\frac{ c \\hbar A }{ 2 \\pi e } !(cgs)$$$$e = 4.768e^{-10} !statcoulombs$$$$c = 3.0e^{10} !cm/s$$$$\\hbar = 1.0546e^{-27} !erg*s$$\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Au',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='fermi')\r\n```\r\n" + "\n\n# Showing how to get van alphen fequencies from the fermi surface\n\nSymmetry does not currently work! Make sure for fermi surface calculations turn off symmetry\n\nVan alphen fequencies example. De has van alphen frequencies (F) in terms of extremal fermi surface areas (A) is given below.\nTo compare the theoretical freuqencies we will compare with the results taken from the experimental paper\n\"The Fermi surfaces of copper, silver and gold. I. The de Haas-Van alphen effect\"(https://doi.org/10.1098/rsta.1962.0011).\n\n\n\\begin{align}F = \\frac{ c \\hbar A }{ 2 \\pi e } !(cgs)\n\n e = 4.768e^{-10} !statcoulombs\n\n c = 3.0e^{10} !cm/s\n\n \\hbar = 1.0546e^{-27} !erg*s\\end{align}\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Au',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='fermi')\n" ] }, { @@ -33,7 +33,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -51,7 +51,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Maximal cross sectional area along the (0,0,1)\r\n" + "## Maximal cross sectional area along the (0,0,1)\n\n\n" ] }, { @@ -69,14 +69,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "In the above figure we can see the cross section area is\r\n$A = 4.1586 Ang^{-2} = 4.1586e^{16} cm^{-2} (cgs)$.\r\n\r\n$F = \\frac{ c \\hbar A }{ 2 \\pi e } = 4.365e^8 G$\r\n\r\n$F_{exp} = 4.50e^7 G$\r\n" + "In the above figure we can see the cross section area is $A = 4.1586 Ang^{-2} = 4.1586e^{16} cm^{-2} (cgs)$.\n\n$F = \\frac{ c \\hbar A }{ 2 \\pi e } = 4.365e^8 G$\n\n$F_{exp} = 4.50e^7 G$\n\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Minimal cross sectional area along the (0,0,1)\r\n" + "## Minimal cross sectional area along the (0,0,1)\n\n\n\n" ] }, { @@ -94,14 +94,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "In the above figure we can see the cross section area is\r\n$A = 0.1596 Ang^{-2} = 0.1596e^{16} cm^{-2} (cgs)$.\r\n\r\n$F = \\frac{ c \\hbar A }{ 2 \\pi e } = 1.68e^7 G$\r\n\r\n$F_{exp} = 1.50e^7 G$\r\n" + "In the above figure we can see the cross section area is $A = 0.1596 Ang^{-2} = 0.1596e^{16} cm^{-2} (cgs)$.\n\n$F = \\frac{ c \\hbar A }{ 2 \\pi e } = 1.68e^7 G$\n\n$F_{exp} = 1.50e^7 G$\n\n\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Extremal cross sectional area along the (0,1,1)\r\n" + "## Extremal cross sectional area along the (0,1,1)\n\n\n\n" ] }, { @@ -119,7 +119,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "In the above figure we can see the cross section area is\r\n$A = 4.3956 Ang^{-2} = 4.3956e^{16} cm^{-2} (cgs)$.\r\n\r\n$F = \\frac{ c \\hbar A }{ 2 \\pi e } = 4.61e^8 G$\r\n\r\n$F_{exp} = 4.85e^8 G$\r\n" + "In the above figure we can see the cross section area is $A = 4.3956 Ang^{-2} = 4.3956e^{16} cm^{-2} (cgs)$.\n\n$F = \\frac{ c \\hbar A }{ 2 \\pi e } = 4.61e^8 G$\n\n$F_{exp} = 4.85e^8 G$\n\n" ] } ], diff --git a/docs/_downloads/944a0173409f4bb08246c2e0702fcaa4/plot_bandsdosplot.ipynb b/docs/_downloads/944a0173409f4bb08246c2e0702fcaa4/plot_bandsdosplot.ipynb index 138c7206..a9833fc4 100644 --- a/docs/_downloads/944a0173409f4bb08246c2e0702fcaa4/plot_bandsdosplot.ipynb +++ b/docs/_downloads/944a0173409f4bb08246c2e0702fcaa4/plot_bandsdosplot.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting bandsdosplot {#ref_plot_bandsdosplot}\r\n\r\nPlotting bandsdosplot example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\nbands_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='bands')\r\n\r\ndos_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='dos')\r\n```\r\n" + "\n\n# Plotting bandsdosplot\n\nPlotting bandsdosplot example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n bands_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='bands')\n\n dos_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='dos')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n\r\nThe keywords that works for bandsplot and dosplot will work in\r\nbandsdosplot. These keyword arguments can be set in bands_settings and\r\ndos_settings as done below.\r\n" + "## Plain mode\nThe keywords that works for bandsplot and dosplot will work in bandsdosplot. \nThese keyword arguments can be set in bands_settings and dos_settings as done below.\n\n\n" ] }, { @@ -40,7 +40,7 @@ }, "outputs": [], "source": [ - "bands_settings = {'mode':'plain',\n 'dirname': bands_dir}\n\ndos_settings = {'mode':'plain',\n 'dirname': dos_dir}\n\npyprocar.bandsdosplot(code='vasp',\n bands_settings=bands_settings,\n dos_settings=dos_settings,\n )" + "bands_settings = {\n 'mode':'plain',\n 'fermi':5.599480, # This will overide the default fermi value found in bands directory\n 'dirname': bands_dir\n }\n\ndos_settings = {\n 'mode':'plain',\n 'fermi':5.599480, # This will overide the default fermi value found in dos directory\n 'dirname': dos_dir\n }\n\npyprocar.bandsdosplot(code='vasp',\n bands_settings=bands_settings,\n dos_settings=dos_settings,\n )" ] } ], diff --git a/docs/_downloads/971f2bf2a71abdaf54ca964572abba65/plot_spin_polarized.py b/docs/_downloads/971f2bf2a71abdaf54ca964572abba65/plot_spin_polarized.py index 8f8a59e4..dd7a7a89 100644 --- a/docs/_downloads/971f2bf2a71abdaf54ca964572abba65/plot_spin_polarized.py +++ b/docs/_downloads/971f2bf2a71abdaf54ca964572abba65/plot_spin_polarized.py @@ -39,6 +39,7 @@ pyprocar.bandsplot( code='vasp', mode='plain', + fermi=5.590136, dirname=data_dir) ############################################################################### @@ -49,6 +50,7 @@ pyprocar.bandsplot( code='vasp', mode='plain', + fermi=5.590136, spins=spins, dirname=data_dir) @@ -66,6 +68,7 @@ pyprocar.bandsplot( code='vasp', mode='parametric', + fermi=5.590136, atoms=atoms, orbitals=orbitals, spins=spins, @@ -84,6 +87,7 @@ pyprocar.bandsplot( code='vasp', mode='scatter', + fermi=5.590136, atoms=atoms, orbitals=orbitals, spins=spins, diff --git a/docs/_downloads/a5890fb88d040bf16c474641f98c10b9/plot_ipr.ipynb b/docs/_downloads/a5890fb88d040bf16c474641f98c10b9/plot_ipr.ipynb index 6beeac55..4b2c1a63 100644 --- a/docs/_downloads/a5890fb88d040bf16c474641f98c10b9/plot_ipr.ipynb +++ b/docs/_downloads/a5890fb88d040bf16c474641f98c10b9/plot_ipr.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting Inverse participation ratio {#ref_plot_ipr}\r\n\r\nOften it is needed to search for **localized** modes within the band\r\nstructure, typical examples are surface/interface states and defect\r\nlevels. The usual procedure for detecting them is looking for bands with\r\na large projection around the atoms at the surface or defect. This\r\nprocedure is both cumbersome for the user and error-prone. For instance,\r\nthe lowest unoccupied levels of the neutral $C_N$ defect in h-BN has\r\npractically no projection on the defect atom and its nearest neighbors.\r\nThis delayed its identification as a single-photon\r\nemitter.\\[jara2021,auburger2021\\] A much simpler way to detect these\r\nlocalized levels is by means of the **Inverse Participation Ratio**,\r\ndefined as\r\n\r\n$$IPR_{nk} = \\frac{\\sum_{a} |c_{nki}|^4}{\\left(\\sum_a c_{nka}\\right)^2}$$\r\n\r\nwhere the indexes $n,k,a$ are the band, k-point and atom, respectively.\r\nThis function has been extensively applied in the context of Anderson\r\nlocalization.\\[Evers2000\\] However, can capture any kind of\r\nlocalization. A perfectly localized state -**i.e.** localized in a\r\nsingle atom- would have $IPR=1$, but a fully extended state has\r\n$IPR=\\frac{1}{N}$, with $N$ the total number of atoms.\r\n\r\n## Preparation\r\n\r\nBefore diving into plotting, we need to download the example files. Use\r\nthe following code to do this. Once downloaded, specify the\r\n[data_dir]{.title-ref} to point to the location of the downloaded data.\r\n\r\n``` {caption=\"Downloading example\"}\r\nimport pyprocar\r\n\r\nbi2se3_data_dir = pyprocar.download_example(\r\n save_dir='', \r\n material='Bi2Se3-spinorbit-surface',\r\n code='vasp', \r\n spin_calc_type='spin-polarized-colinear',\r\n calc_type='bands'\r\n )\r\n\r\nC_data_dir = pyprocar.download_example(\r\n save_dir='', \r\n material='NV-center',\r\n code='vasp', \r\n spin_calc_type='spin-polarized-colinear',\r\n calc_type='bands'\r\n )\r\n```\r\n" + "\n\n# Plotting Inverse participation ratio\n\nOften it is needed to search for **localized** modes within the band structure, typical examples are surface/interface states and defect levels. \nThe usual procedure for detecting them is looking for bands with a large projection around the atoms at the surface or defect. \nThis procedure is both cumbersome for the user and error-prone. For instance, the lowest unoccupied levels\nof the neutral $C_N$ defect in h-BN has practically no projection on the defect atom and its nearest neighbors. \nThis delayed its identification as a single-photon emitter.[jara2021,auburger2021] \nA much simpler way to detect these localized levels is by means of the **Inverse Participation Ratio**, defined as\n\n\\begin{align}IPR_{nk} = \\frac{\\sum_{a} |c_{nki}|^4}{\\left(\\sum_a c_{nka}\\right)^2}\\end{align}\n\nwhere the indexes $n,k,a$ are the band, k-point and atom, respectively. \nThis function has been extensively applied in the context of Anderson localization.[Evers2000] \nHowever, can capture any kind of localization. A perfectly localized state -**i.e.** \nlocalized in a single atom- would have $IPR=1$, but a fully extended state has $IPR=\\frac{1}{N}$, with $N$ the total number of atoms.\n\n## Preparation\nBefore diving into plotting, we need to download the example files. \nUse the following code to do this. Once downloaded, specify the `data_dir` to point to the location of the downloaded data.\n\n.. code-block::\n :caption: Downloading example\n\n import pyprocar\n\n bi2se3_data_dir = pyprocar.download_example(\n save_dir='', \n material='Bi2Se3-spinorbit-surface',\n code='vasp', \n spin_calc_type='spin-polarized-colinear',\n calc_type='bands'\n )\n\n C_data_dir = pyprocar.download_example(\n save_dir='', \n material='NV-center',\n code='vasp', \n spin_calc_type='spin-polarized-colinear',\n calc_type='bands'\n )\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Setting up the environment\r\n\r\nFirst, we will import the necessary libraries and set up our data\r\ndirectory path.\r\n" + "## Setting up the environment\nFirst, we will import the necessary libraries and set up our data directory path.\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Topologically-protected surface states in $Bi_2Se_3$\r\n\r\nThe first example is the detection of topologically-protected surface\r\nstates in $Bi_2Se_3$, \\[zhang2009\\]. The whole slab has six van der\r\nWaals layers (quintuple layers), each is five atom thick. The surface\r\nstates localize on the outer quintuple layers, in contrast a extended\r\nstate cover the six quintuple layers. The ratio between the localization\r\nof both types of states is 1 to 3, and the \\$IPR\\$ has enough resolution\r\nto provide a clear visual identification. The PyProcar code is:\r\n" + "## Topologically-protected surface states in $Bi_2Se_3$\n\nThe first example is the detection of topologically-protected surface states in $Bi_2Se_3$, [zhang2009]. \nThe whole slab has six van der Waals layers (quintuple layers), each is five atom thick. The surface states localize on the outer quintuple layers, \nin contrast a extended state cover the six quintuple layers. \nThe ratio between the localization of both types of states is 1 to 3, and the $IPR$ has enough resolution to provide a clear visual identification. \nThe PyProcar code is:\n\n" ] }, { @@ -47,7 +47,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# $NV^-$ defect in diamond\r\n\r\nThe second example is the $NV^-$ defect in diamond, it is a negatively\r\ncharged N substitution plus an adjacent vacancy. This defect if of\r\ninterest as a source of single photons. Its ground state is a triplet,\r\nallowing the control of the spin by microwave radiation.\\[DOHERTY2013\\]\r\nThe supercell has 215 atoms, hence $IPR\\to0$ for bulk states (blue\r\nlines). Several defect levels lie within the fundamental band gap of\r\ndiamond (dark red lines). The closest levels to the Fermi energy are\r\ndouble degenerate (**i.e.** triplet), but only occupied for the spin\r\nmajority. Hence, according to the optical transition takes place between\r\nthe bands with index $430\\to431$ or $430\\to432$ of the spin channel\r\nlabelled [spin-1]{.title-ref}. The calculation of the main emission line\r\ninvolves a calculation of the excited state, which can be simulated by\r\nfixing the occupations of the mentioned levels, **i.e.** the $\\Delta$\r\nSCFmethod.\\[Jin2021\\] The pyprocar code is:\r\n" + "## $NV^-$ defect in diamond\n\nThe second example is the $NV^-$ defect in diamond, it is a negatively charged N substitution plus an adjacent vacancy. \nThis defect if of interest as a source of single photons. Its ground state is a triplet, allowing the control of the spin by microwave radiation.[DOHERTY2013] \nThe supercell has 215 atoms, hence $IPR\\to0$ for bulk states (blue lines). \nSeveral defect levels lie within the fundamental band gap of diamond (dark red lines). The closest levels to the Fermi energy are double degenerate (**i.e.** triplet), \nbut only occupied for the spin majority. Hence, according to the optical transition takes place between the bands with index $430\\to431$ or $430\\to432$\nof the spin channel labelled `spin-1`. The calculation of the main emission line involves a calculation of the excited state, \nwhich can be simulated by fixing the occupations of the mentioned levels, **i.e.** the $\\Delta$ SCFmethod.[Jin2021]\nThe pyprocar code is:\n\n" ] }, { diff --git a/docs/_downloads/a6114776ebbf436fd6358daa96928b97/plot_fermi2d_configurations.ipynb b/docs/_downloads/a6114776ebbf436fd6358daa96928b97/plot_fermi2d_configurations.ipynb index a8d68e31..e592c847 100644 --- a/docs/_downloads/a6114776ebbf436fd6358daa96928b97/plot_fermi2d_configurations.ipynb +++ b/docs/_downloads/a6114776ebbf436fd6358daa96928b97/plot_fermi2d_configurations.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting with Configurations in [pyprocar]{.title-ref} {#ref_plotting_fermi2d_configurations}\r\n\r\nThis example illustrates how to utilize various configurations for\r\nplotting the 2D Fermi surface with non-colinear spin textures using the\r\n[pyprocar]{.title-ref} package. It provides a structured way to explore\r\nand demonstrate different configurations for the [fermi2D]{.title-ref}\r\nfunction. For more information about [fermi2D]{.title-ref}, refer to\r\n`fermi2d`{.interpreted-text role=\"ref\"}.\r\n\r\n## Preparation\r\n\r\nBefore diving into plotting, we need to download the example files. Use\r\nthe following code to do this. Once downloaded, specify the\r\n[data_dir]{.title-ref} to point to the location of the downloaded data.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-colinear',\r\n calc_type='fermi')\r\n```\r\n" + "\n\n# Plotting with Configurations in `pyprocar`\n\nThis example illustrates how to utilize various configurations for plotting the 2D Fermi surface with non-colinear spin textures using the `pyprocar` package. It provides a structured way to explore and demonstrate different configurations for the `fermi2D` function. For more information about `fermi2D`, refer to `fermi2d`.\n\n## Preparation\nBefore diving into plotting, we need to download the example files. Use the following code to do this. Once downloaded, specify the `data_dir` to point to the location of the downloaded data.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-colinear',\n calc_type='fermi')\n" ] }, { @@ -26,7 +26,7 @@ }, "outputs": [], "source": [ - "# Section 1: Locating and Printing Configuration Files\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates where the configuration files are located in the package.\n# It also shows how to print the configurations by setting print_plot_opts=True.\n#\n\n# Path to the configuration files in the package\nconfig_path = os.path.join(pyprocar.__path__[0], 'cfg')\nprint(f\"Configuration files are located at: {config_path}\")\n\n# Print the configurations\npyprocar.fermi2D(code='vasp', dirname=data_dir, print_plot_opts=True)" + "# Section 1: Locating and Printing Configuration Files\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates where the configuration files are located in the package.\n# It also shows how to print the configurations by setting print_plot_opts=True.\n#\n\n# Path to the configuration files in the package\nconfig_path = os.path.join(pyprocar.__path__[0], 'cfg')\nprint(f\"Configuration files are located at: {config_path}\")\n\n# Print the configurations\npyprocar.fermi2D(code='vasp', dirname=data_dir,fermi=5.599480, print_plot_opts=True)" ] }, { @@ -37,7 +37,7 @@ }, "outputs": [], "source": [ - "# Section 2: Spin Texture Projection with Custom Settings\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to customize the appearance of the spin texture arrows.\n# We'll adjust the colormap, color limits.\n#\n\npyprocar.fermi2D(code='vasp',\n dirname=data_dir,\n spin_texture=True,\n spin_projection='x',\n arrow_size=3,\n arrow_density=10,\n plot_color_bar=True,\n cmap='jet',\n clim=[0, 1])" + "# Section 2: Spin Texture Projection with Custom Settings\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to customize the appearance of the spin texture arrows.\n# We'll adjust the colormap, color limits.\n#\n\npyprocar.fermi2D(code='vasp',\n fermi=5.599480,\n dirname=data_dir,\n spin_texture=True,\n spin_projection='x',\n arrow_size=3,\n arrow_density=10,\n plot_color_bar=True,\n cmap='jet',\n clim=[0, 1])" ] }, { @@ -48,7 +48,7 @@ }, "outputs": [], "source": [ - "# Section 3: Adjusting DPI\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to adjust the dots per inch (DPI) for the combined plot.\n#\n\n\npyprocar.fermi2D(code='vasp',\n dirname=data_dir,\n spin_texture=True,\n spin_projection='z',\n arrow_size=3,\n arrow_density=10,\n plot_color_bar=True,\n cmap='jet',\n clim=[0, 1],\n dpi=300)" + "# Section 3: Adjusting DPI\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to adjust the dots per inch (DPI) for the combined plot.\n#\n\n\npyprocar.fermi2D(code='vasp',\n dirname=data_dir,\n fermi=5.599480,\n spin_texture=True,\n spin_projection='z',\n arrow_size=3,\n arrow_density=10,\n plot_color_bar=True,\n cmap='jet',\n clim=[0, 1],\n dpi=300)" ] } ], diff --git a/docs/_downloads/a61da4c0af389a0a799c3e2847eb8039/plot_bandsdosplot_configurations.py b/docs/_downloads/a61da4c0af389a0a799c3e2847eb8039/plot_bandsdosplot_configurations.py index 7c1893b4..7dc1be82 100644 --- a/docs/_downloads/a61da4c0af389a0a799c3e2847eb8039/plot_bandsdosplot_configurations.py +++ b/docs/_downloads/a61da4c0af389a0a799c3e2847eb8039/plot_bandsdosplot_configurations.py @@ -42,11 +42,18 @@ # These keyword arguments can be set in `bands_settings` and `dos_settings` as demonstrated below. # -bands_settings = {'mode':'plain', - 'dirname': bands_dir} -dos_settings = {'mode':'plain', - 'dirname': dos_dir} +bands_settings = { + 'mode':'plain', + 'fermi':5.599480, # This will overide the default fermi value found in bands directory + 'dirname': bands_dir + } + +dos_settings = { + 'mode':'plain', + 'fermi':5.599480, # This will overide the default fermi value found in dos directory + 'dirname': dos_dir + } pyprocar.bandsdosplot(code='vasp', bands_settings=bands_settings, @@ -65,6 +72,7 @@ bands_settings = { 'mode': 'scatter', 'dirname': bands_dir, + 'fermi':5.599480, # This will overide the default fermi value found in bands directory 'atoms':[0], 'orbitals':[4,5,6,7,8], 'cmap': 'viridis', @@ -77,6 +85,7 @@ dos_settings = { 'mode': 'parametric', 'dirname': dos_dir, + 'fermi':5.599480, # This will overide the default fermi value found in dos directory 'atoms':[0], 'orbitals':[4,5,6,7,8], 'cmap': 'viridis', diff --git a/docs/_downloads/acd59b108b19e5a25cade83b65959b58/plot_noncolinear_dos_vasp.ipynb b/docs/_downloads/acd59b108b19e5a25cade83b65959b58/plot_noncolinear_dos_vasp.ipynb index 93fac26f..ef0394bc 100644 --- a/docs/_downloads/acd59b108b19e5a25cade83b65959b58/plot_noncolinear_dos_vasp.ipynb +++ b/docs/_downloads/acd59b108b19e5a25cade83b65959b58/plot_noncolinear_dos_vasp.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting non colinear dos in VASP {#ref_plotting_noncolinear_dos_vasp}\r\n\r\nPlotting non colinear dos in VASP.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-colinear',\r\n calc_type='dos')\r\n```\r\n" + "\n\n# Plotting non colinear dos in VASP\n\nPlotting non colinear dos in VASP.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-colinear',\n calc_type='dos')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Parametric mode\r\n\r\nFor details on the meaning of the indices of the atomic projection\r\nplease refer to the user guide :ref:\\'atomic_projections\\'\r\n" + "## Parametric mode\n\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n\n\n" ] }, { @@ -40,7 +40,7 @@ }, "outputs": [], "source": [ - "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.dosplot(\n code='vasp', \n mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.dosplot(\n code='vasp', \n mode='parametric',\n fermi=5.5962,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] } ], diff --git a/docs/_downloads/b110f643ba1910417f890e1aace81279/plot_noncolinear_vasp.ipynb b/docs/_downloads/b110f643ba1910417f890e1aace81279/plot_noncolinear_vasp.ipynb index 53f7202f..8895243e 100644 --- a/docs/_downloads/b110f643ba1910417f890e1aace81279/plot_noncolinear_vasp.ipynb +++ b/docs/_downloads/b110f643ba1910417f890e1aace81279/plot_noncolinear_vasp.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting non colinear band structures in VASP {#ref_plotting_noncolinear_vasp}\r\n\r\nPlotting non colinear band structures in VASP.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-colinear',\r\n calc_type='bands')\r\n```\r\n" + "\n\n# Plotting non colinear band structures in VASP\n\nPlotting non colinear band structures in VASP.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-colinear',\n calc_type='bands')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n" + "## Plain mode\n\n\n\n" ] }, { @@ -40,14 +40,14 @@ }, "outputs": [], "source": [ - "pyprocar.bandsplot(\n code='vasp', \n mode='plain',\n dirname=data_dir)" + "pyprocar.bandsplot(\n code='vasp', \n mode='plain',\n fermi=5.596151,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Parametric mode\r\n\r\nFor details on the meaning of the indices of the atomic projection\r\nplease refer to the user guide :ref:\\'atomic_projections\\'\r\n" + "## Parametric mode\n\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n" ] }, { @@ -58,7 +58,7 @@ }, "outputs": [], "source": [ - "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='parametric',\n fermi=5.596151,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] } ], diff --git a/docs/_downloads/b21e89a2c703b6147c8f0a51fa78788c/plot_fermi2d.ipynb b/docs/_downloads/b21e89a2c703b6147c8f0a51fa78788c/plot_fermi2d.ipynb index 42b407ce..906744f4 100644 --- a/docs/_downloads/b21e89a2c703b6147c8f0a51fa78788c/plot_fermi2d.ipynb +++ b/docs/_downloads/b21e89a2c703b6147c8f0a51fa78788c/plot_fermi2d.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting fermi2d {#ref_plotting_fermi2d}\r\n\r\nPlotting fermi2d example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='spin-polarized-colinear',\r\n calc_type='fermi')\r\n```\r\n" + "\n\n# Plotting fermi2d\n\nPlotting fermi2d example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='spin-polarized-colinear',\n calc_type='fermi')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n" + "## Plain mode\n\n\n\n" ] }, { @@ -40,14 +40,14 @@ }, "outputs": [], "source": [ - "pyprocar.fermi2D(code = 'vasp', \n mode='plain',\n dirname=data_dir)" + "pyprocar.fermi2D(code = 'vasp', \n mode='plain',\n fermi=5.590136,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# plain_bands mode\r\n" + "## plain_bands mode\n\n\n\n" ] }, { @@ -58,14 +58,14 @@ }, "outputs": [], "source": [ - "pyprocar.fermi2D(code = 'vasp', \n mode='plain_bands',\n add_legend=True,\n dirname=data_dir)" + "pyprocar.fermi2D(code = 'vasp', \n mode='plain_bands',\n add_legend=True,\n fermi=5.590136,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# parametric mode\r\n\r\nDoes not work. Contact developers\r\n" + "## parametric mode\n\nDoes not work. Contact developers\n\n\n" ] }, { @@ -76,14 +76,14 @@ }, "outputs": [], "source": [ - "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0,1]\npyprocar.fermi2D(code = 'vasp',\n mode='parametric', \n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir, \n spin_texture=False)" + "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0,1]\npyprocar.fermi2D(code = 'vasp',\n mode='parametric', \n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir,\n fermi=5.590136,\n spin_texture=False)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Selecting band indices\r\n\r\nYou can specify specfic bands with the band indices keyword.\r\nband_indices will be a list of list that contain band indices to plot\r\nfor a given spin. Below I only plot bands 6 and 7 for spin 0 Also you\r\ncan specify the colors of the bands as well with band_colors\r\n" + "## Selecting band indices\n\nYou can specify specfic bands with the band indices keyword. \nband_indices will be a list of list that contain band indices to plot for a given spin. Below I only plot bands 6 and 7 for spin 0\nAlso you can specify the colors of the bands as well with band_colors\n\n" ] }, { @@ -94,7 +94,7 @@ }, "outputs": [], "source": [ - "band_indices = [[4,5],[]]\nband_colors = [['blue','navy'], []]\npyprocar.fermi2D(code = 'vasp', \n mode='plain_bands',\n band_indices = band_indices,\n band_colors=band_colors,\n add_legend=True,\n dirname=data_dir)" + "band_indices = [[4,5],[]]\nband_colors = [['blue','navy'], []]\npyprocar.fermi2D(code = 'vasp', \n mode='plain_bands',\n band_indices = band_indices,\n band_colors=band_colors,\n add_legend=True,\n fermi=5.590136,\n dirname=data_dir)" ] } ], diff --git a/docs/_downloads/b6c323afaddfad8e95934cc3242fdf06/plot_bandsdosplot_configurations.ipynb b/docs/_downloads/b6c323afaddfad8e95934cc3242fdf06/plot_bandsdosplot_configurations.ipynb index b7e6f1c2..bd33d9aa 100644 --- a/docs/_downloads/b6c323afaddfad8e95934cc3242fdf06/plot_bandsdosplot_configurations.ipynb +++ b/docs/_downloads/b6c323afaddfad8e95934cc3242fdf06/plot_bandsdosplot_configurations.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting bandsdosplot {#ref_plot_bandsdosplot_configurations}\r\n\r\nThis example illustrates how to utilize various configurations for\r\nplotting both band structures and density of states (DOS) side by side\r\nusing the [pyprocar]{.title-ref} package. It provides a structured way\r\nto explore and demonstrate different configurations for the\r\n[bandsdosplot]{.title-ref} function.\r\n\r\n## Preparation\r\n\r\nBefore diving into plotting, we need to download the example files. Use\r\nthe following code to do this. Once downloaded, specify the\r\n[bands_dir]{.title-ref} and [dos_dir]{.title-ref} to point to the\r\nlocation of the downloaded data.\r\n\r\n``` {caption=\"Downloading example\"}\r\nbands_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='bands')\r\n\r\ndos_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='dos')\r\n```\r\n" + "\n\n# Plotting bandsdosplot\n\nThis example illustrates how to utilize various configurations for plotting both band structures and density of states (DOS) side by side using the `pyprocar` package. It provides a structured way to explore and demonstrate different configurations for the `bandsdosplot` function.\n\n## Preparation\nBefore diving into plotting, we need to download the example files. Use the following code to do this. Once downloaded, specify the `bands_dir` and `dos_dir` to point to the location of the downloaded data.\n\n.. code-block::\n :caption: Downloading example\n\n bands_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='bands')\n\n dos_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='dos')\n" ] }, { @@ -26,7 +26,7 @@ }, "outputs": [], "source": [ - "# Section 1: Plain Mode with Default Settings\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to plot both band structures and DOS side by side using default settings.\n# The keywords that work for `bandsplot` and `dosplot` will also work in `bandsdosplot`. \n# These keyword arguments can be set in `bands_settings` and `dos_settings` as demonstrated below.\n#\n\nbands_settings = {'mode':'plain',\n 'dirname': bands_dir}\n\ndos_settings = {'mode':'plain',\n 'dirname': dos_dir}\n\npyprocar.bandsdosplot(code='vasp',\n bands_settings=bands_settings,\n dos_settings=dos_settings,\n )" + "# Section 1: Plain Mode with Default Settings\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to plot both band structures and DOS side by side using default settings.\n# The keywords that work for `bandsplot` and `dosplot` will also work in `bandsdosplot`. \n# These keyword arguments can be set in `bands_settings` and `dos_settings` as demonstrated below.\n#\n\n\nbands_settings = {\n 'mode':'plain',\n 'fermi':5.599480, # This will overide the default fermi value found in bands directory\n 'dirname': bands_dir\n }\n\ndos_settings = {\n 'mode':'plain',\n 'fermi':5.599480, # This will overide the default fermi value found in dos directory\n 'dirname': dos_dir\n }\n\npyprocar.bandsdosplot(code='vasp',\n bands_settings=bands_settings,\n dos_settings=dos_settings,\n )" ] }, { @@ -37,7 +37,7 @@ }, "outputs": [], "source": [ - "# Section 2: Customizing Bands and DOS Plots\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to customize the appearance of both the band structures and DOS plots.\n# We'll adjust the colormap, color limits, Fermi line properties, and other settings.\n#\n\nbands_settings = {\n 'mode': 'scatter',\n 'dirname': bands_dir,\n 'atoms':[0],\n 'orbitals':[4,5,6,7,8],\n 'cmap': 'viridis',\n 'clim': [0, 1],\n 'fermi_color': 'red',\n 'fermi_linestyle': '--',\n 'fermi_linewidth': 2.0\n}\n\ndos_settings = {\n 'mode': 'parametric',\n 'dirname': dos_dir,\n 'atoms':[0],\n 'orbitals':[4,5,6,7,8],\n 'cmap': 'viridis',\n 'clim': [0, 1],\n 'marker': ['v', 'o'],\n 'markersize': [10, 5]\n}\n\npyprocar.bandsdosplot(code='vasp',\n bands_settings=bands_settings,\n dos_settings=dos_settings,\n )" + "# Section 2: Customizing Bands and DOS Plots\n# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n#\n# This section demonstrates how to customize the appearance of both the band structures and DOS plots.\n# We'll adjust the colormap, color limits, Fermi line properties, and other settings.\n#\n\nbands_settings = {\n 'mode': 'scatter',\n 'dirname': bands_dir,\n 'fermi':5.599480, # This will overide the default fermi value found in bands directory\n 'atoms':[0],\n 'orbitals':[4,5,6,7,8],\n 'cmap': 'viridis',\n 'clim': [0, 1],\n 'fermi_color': 'red',\n 'fermi_linestyle': '--',\n 'fermi_linewidth': 2.0\n}\n\ndos_settings = {\n 'mode': 'parametric',\n 'dirname': dos_dir,\n 'fermi':5.599480, # This will overide the default fermi value found in dos directory\n 'atoms':[0],\n 'orbitals':[4,5,6,7,8],\n 'cmap': 'viridis',\n 'clim': [0, 1],\n 'marker': ['v', 'o'],\n 'markersize': [10, 5]\n}\n\npyprocar.bandsdosplot(code='vasp',\n bands_settings=bands_settings,\n dos_settings=dos_settings,\n )" ] }, { diff --git a/docs/_downloads/ba402954cf541dbfbd448e582cc302fd/plot_fermi2d_spin_texture.ipynb b/docs/_downloads/ba402954cf541dbfbd448e582cc302fd/plot_fermi2d_spin_texture.ipynb index 84fbaa33..1528a216 100644 --- a/docs/_downloads/ba402954cf541dbfbd448e582cc302fd/plot_fermi2d_spin_texture.ipynb +++ b/docs/_downloads/ba402954cf541dbfbd448e582cc302fd/plot_fermi2d_spin_texture.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting fermi2d noncolinear {#ref_plotting_fermi2d_noncolinear}\r\n\r\nPlotting fermi2d noncolinear example. For more information about fermi2d\r\nrefer to `fermi2d`{.interpreted-text role=\"ref\"}\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-colinear',\r\n calc_type='fermi')\r\n```\r\n" + "\n\n# Plotting fermi2d noncolinear\n\nPlotting fermi2d noncolinear example. For more information about fermi2d refer to `fermi2d`\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-colinear',\n calc_type='fermi')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Spin Texture Projection\r\n\r\nBy setting spin_texture to be true, You can plot the arrows for the spin\r\ntextures. By default the projected values of the arrows will be s_z. But\r\nyou can change this by setting arrow_projection to one of the following\r\n\\'x\\',\\'y\\',\\'z\\',\\'x\\^2\\',\\'y\\^2\\',\\'z\\^2\\'\r\n" + "## Spin Texture Projection\n\nBy setting spin_texture to be true, You can plot the arrows for the spin textures.\nBy default the projected values of the arrows will be s_z. \nBut you can change this by setting arrow_projection to one of the following\n'x','y','z','x^2','y^2','z^2'\n\n" ] }, { @@ -40,14 +40,14 @@ }, "outputs": [], "source": [ - "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n spin_texture=True,\n spin_projection='x',\n arrow_size=3,\n arrow_density=10,\n plot_color_bar=True)" + "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n fermi=5.5962,\n spin_texture=True,\n spin_projection='x',\n arrow_size=3,\n arrow_density=10,\n plot_color_bar=True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Spin Texture single color\r\n" + "## Spin Texture single color\n\n\n" ] }, { @@ -58,14 +58,14 @@ }, "outputs": [], "source": [ - "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n spin_texture=True,\n arrow_color = 'blue',\n arrow_size=3,\n arrow_density=10)" + "pyprocar.fermi2D(code = 'vasp',\n dirname=data_dir,\n fermi=5.5962,\n spin_texture=True,\n arrow_color = 'blue',\n arrow_size=3,\n arrow_density=10)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Selecting band indices\r\n\r\nYou can specify specfic bands with the band indices keyword.\r\nband_indices will be a list of list that contain band indices. Below I\r\nonly plot bands 14,15 Also you can specify the colors of the bands as\r\nwell with band_colors\r\n" + "## Selecting band indices\n\nYou can specify specfic bands with the band indices keyword. \nband_indices will be a list of list that contain band indices. Below I only plot bands 14,15\nAlso you can specify the colors of the bands as well with band_colors\n\n" ] }, { @@ -76,7 +76,7 @@ }, "outputs": [], "source": [ - "band_indices = [[6,7]]\nband_colors = [['blue','red']]\npyprocar.fermi2D(code = 'vasp', \n mode='plain_bands',\n band_indices = band_indices,\n band_colors=band_colors,\n spin_texture=True,\n arrow_size=3,\n arrow_density=10,\n dirname=data_dir)" + "band_indices = [[6,7]]\nband_colors = [['blue','red']]\npyprocar.fermi2D(code = 'vasp', \n mode='plain_bands',\n fermi=5.5962,\n band_indices = band_indices,\n band_colors=band_colors,\n spin_texture=True,\n arrow_size=3,\n arrow_density=10,\n dirname=data_dir)" ] } ], diff --git a/docs/_downloads/bb10880f5309d56f60b53105f5432b3d/plot_fermi3d_isovalue_gif.ipynb b/docs/_downloads/bb10880f5309d56f60b53105f5432b3d/plot_fermi3d_isovalue_gif.ipynb index e0a59115..ef9d7661 100644 --- a/docs/_downloads/bb10880f5309d56f60b53105f5432b3d/plot_fermi3d_isovalue_gif.ipynb +++ b/docs/_downloads/bb10880f5309d56f60b53105f5432b3d/plot_fermi3d_isovalue_gif.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting fermi3d isovalue_gif {#ref_plotting_fermi3d_isovalue_gif}\r\n\r\nSymmetry does not currently work! Make sure for fermi surface\r\ncalculations turn off symmetry\r\n\r\nPlotting fermi3d isovalue_gif example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='qe', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='fermi')\r\n```\r\n" + "\n\n# Plotting fermi3d isovalue_gif\n\nSymmetry does not currently work! Make sure for fermi surface calculations turn off symmetry\n\nPlotting fermi3d isovalue_gif example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='qe', \n spin_calc_type='non-spin-polarized',\n calc_type='fermi')\n" ] }, { @@ -33,7 +33,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -51,7 +51,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n" + "## Plain mode\n\n\n\n" ] }, { diff --git a/docs/_downloads/bc82bea3a5dd7bdba60b65220891d9e5/examples_python.zip b/docs/_downloads/bc82bea3a5dd7bdba60b65220891d9e5/examples_python.zip index 4fdc2b9f..c26ec6fc 100644 Binary files a/docs/_downloads/bc82bea3a5dd7bdba60b65220891d9e5/examples_python.zip and b/docs/_downloads/bc82bea3a5dd7bdba60b65220891d9e5/examples_python.zip differ diff --git a/docs/_downloads/c36ddad0d6a8eda5e730849b832d4505/plot_subsitution_pyposcar.ipynb b/docs/_downloads/c36ddad0d6a8eda5e730849b832d4505/plot_subsitution_pyposcar.ipynb index a715ff84..a8c357ca 100644 --- a/docs/_downloads/c36ddad0d6a8eda5e730849b832d4505/plot_subsitution_pyposcar.ipynb +++ b/docs/_downloads/c36ddad0d6a8eda5e730849b832d4505/plot_subsitution_pyposcar.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Substituting Atoms in a POSCAR File {#ref_subsitution_poscar}\r\n\r\nIn this example, we\\'ll demonstrate how to substitute atoms in a POSCAR\r\nfile using the [pyprocar]{.title-ref} package. Specifically, we will:\r\n\r\n1. Read a POSCAR file containing atomic positions and lattice vectors.\r\n2. Visualize the initial atomic positions.\r\n3. Substitute a boron (B) atom with a nitrogen (N) atom.\r\n4. Visualize the atomic positions after the substitution.\r\n5. Create GIFs to visualize the atomic structures from different\r\n angles.\r\n\r\nBefore diving in, make sure to have [pyvista]{.title-ref},\r\n[numpy]{.title-ref}, and [pyprocar]{.title-ref} installed.\r\n" + "\n\n# Substituting Atoms in a POSCAR File\n\nIn this example, we'll demonstrate how to substitute atoms in a POSCAR file using the `pyprocar` package. \nSpecifically, we will:\n\n1. Read a POSCAR file containing atomic positions and lattice vectors.\n2. Visualize the initial atomic positions.\n3. Substitute a boron (B) atom with a nitrogen (N) atom.\n4. Visualize the atomic positions after the substitution.\n5. Create GIFs to visualize the atomic structures from different angles.\n\nBefore diving in, make sure to have `pyvista`, `numpy`, and `pyprocar` installed.\n" ] }, { @@ -22,7 +22,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Reading and Parsing the POSCAR File\r\n" + "## Reading and Parsing the POSCAR File\n\n" ] }, { @@ -40,7 +40,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Atom Substitution\r\n" + "## Atom Substitution\n\n" ] }, { @@ -58,7 +58,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Visualization of Atomic Structures\r\n" + "## Visualization of Atomic Structures\n\n" ] }, { @@ -76,7 +76,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Creating GIFs for Visualization\r\n" + "## Creating GIFs for Visualization\n\n" ] }, { diff --git a/docs/_downloads/c3caa44ef3b6c685adf075dede68f1ff/plot_rdf_cutoff_pyposcar.ipynb b/docs/_downloads/c3caa44ef3b6c685adf075dede68f1ff/plot_rdf_cutoff_pyposcar.ipynb index 85bb27a8..534a7ec2 100644 --- a/docs/_downloads/c3caa44ef3b6c685adf075dede68f1ff/plot_rdf_cutoff_pyposcar.ipynb +++ b/docs/_downloads/c3caa44ef3b6c685adf075dede68f1ff/plot_rdf_cutoff_pyposcar.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Analyzing Radial Distribution Functions (RDF) {#ref_example_rdf}\r\n\r\nIn this example, we\\'ll explore the radial distribution functions (RDF)\r\nof an atomic structure. The RDF provides insights into the probability\r\nof finding an atom at a certain distance from another. This can be\r\nuseful for understanding the local environment of atoms.\r\n\r\nWe\\'ll use the [pyprocar]{.title-ref} package to:\r\n\r\n1. Parse the POSCAR file and obtain atomic positions.\r\n2. Compute the general KDE curve for all distances.\r\n3. Compute KDE curves for specific atomic species interactions.\r\n4. Visualize the results using [matplotlib]{.title-ref}.\r\n\r\nLet\\'s dive in!\r\n" + "\n\n# Analyzing Radial Distribution Functions (RDF)\n\nIn this example, we'll explore the radial distribution functions (RDF) of an atomic structure. The RDF provides insights into the probability of finding an atom at a certain distance from another. This can be useful for understanding the local environment of atoms.\n\nWe'll use the `pyprocar` package to:\n\n1. Parse the POSCAR file and obtain atomic positions.\n2. Compute the general KDE curve for all distances.\n3. Compute KDE curves for specific atomic species interactions.\n4. Visualize the results using `matplotlib`.\n\nLet's dive in!\n" ] }, { @@ -22,7 +22,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Parsing the POSCAR file\r\n" + "## Parsing the POSCAR file\n\n" ] }, { @@ -40,7 +40,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Computing RDF and KDE Curves\r\n" + "## Computing RDF and KDE Curves\n\n" ] }, { @@ -58,7 +58,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Visualizing the Results\r\n" + "## Visualizing the Results\n\n" ] }, { diff --git a/docs/_downloads/cc4da0ee3820da1d1048c855e1a3d8c1/plot_2d_bands.ipynb b/docs/_downloads/cc4da0ee3820da1d1048c855e1a3d8c1/plot_2d_bands.ipynb index 134bf9be..0965bce4 100644 --- a/docs/_downloads/cc4da0ee3820da1d1048c855e1a3d8c1/plot_2d_bands.ipynb +++ b/docs/_downloads/cc4da0ee3820da1d1048c855e1a3d8c1/plot_2d_bands.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting 2D band structure {#ref_plotting_2d_bands}\r\n\r\nPlotting 2D band structure example.\r\n\r\nFirst, specify the data directory where the band structure data is\r\nlocated.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='graphene',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='2d_bands')\r\n```\r\n" + "\n\n# Plotting 2D band structure\n\nPlotting 2D band structure example.\n\nFirst, specify the data directory where the band structure data is located.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='graphene',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='2d_bands')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n" + "## Plain mode\n\n" ] }, { @@ -40,14 +40,14 @@ }, "outputs": [], "source": [ - "spins=[0]\nhandler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,apply_symmetry=False)\nhandler.plot_band_structure(mode='plain',\n add_fermi_plane=True,\n bands=[3,4],\n fermi_plane_size=4,\n energy_lim=[-2.5,0.8],\n extended_zone_directions=[[1,0,0],[0,1,0],[-1,0,0],[0,-1,0],[1,-1,0],[-1,1,0],[-1,-1,0],[[1,1,0]]],\n spins=spins)" + "spins=[0]\nhandler = pyprocar.BandStructure2DHandler(code='vasp',\n dirname=data_dir,\n fermi=-0.795606,\n apply_symmetry=False,\n )\nhandler.plot_band_structure(mode='plain',\n add_fermi_plane=True,\n bands=[3,4],\n fermi_plane_size=4,\n energy_lim=[-2.5,0.8],\n extended_zone_directions=[[1,0,0],[0,1,0],[-1,0,0],[0,-1,0],[1,-1,0],[-1,1,0],[-1,-1,0],[[1,1,0]]],\n spins=spins)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Parametric mode\r\n" + "## Parametric mode\n\n" ] }, { @@ -58,14 +58,14 @@ }, "outputs": [], "source": [ - "atoms=[0,1]\norbitals=[1,2,3]\nspins=[0]\nhandler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,apply_symmetry=False)\nhandler.plot_band_structure(mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins)" + "atoms=[0,1]\norbitals=[1,2,3]\nspins=[0]\nhandler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,fermi=-0.795606,apply_symmetry=False)\nhandler.plot_band_structure(mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Property Projection mode\r\n" + "## Property Projection mode\n\n" ] }, { @@ -76,14 +76,14 @@ }, "outputs": [], "source": [ - "handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,apply_symmetry=False)\nhandler.plot_band_structure(mode='property_projection',\n property_name='band_velocity',\n bands=[3,4],\n fermi_plane_size=4,\n scalar_bar_position_x=0.3,\n energy_lim=[-2.5,0.8],\n scalar_bar_title=r'Band Velocity ($\\frac{m}{s}$)',\n add_fermi_plane=True,)" + "handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,fermi=-0.795606,apply_symmetry=False)\nhandler.plot_band_structure(mode='property_projection',\n property_name='band_velocity',\n bands=[3,4],\n fermi_plane_size=4,\n scalar_bar_position_x=0.3,\n energy_lim=[-2.5,0.8],\n scalar_bar_title=r'Band Velocity ($\\frac{m}{s}$)',\n add_fermi_plane=True,)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Spin Texture mode\r\n" + "## Spin Texture mode\n\n" ] }, { @@ -94,7 +94,7 @@ }, "outputs": [], "source": [ - "data_dir = os.path.join(pyprocar.utils.ROOT,'data','examples','BiSb_monolayer','vasp','non-colinear','fermi')\n\n\natoms=[0]\norbitals=[4,5,6,7,8]\nhandler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,apply_symmetry=False)\nhandler.plot_band_structure(mode='spin_texture',\n spin_texture=True,\n atoms=atoms,\n orbitals=orbitals,\n add_fermi_plane=True,\n fermi_plane_size=2,\n energy_lim=[-2,2],\n fermi_text_position=[0,0.5,0],\n scalar_bar_position_x=0.3,\n\n clip_brillouin_zone_factor=1,\n surface_clim=[-0.5,0.5])" + "data_dir = os.path.join(pyprocar.utils.ROOT,'data','examples','BiSb_monolayer','vasp','non-colinear','fermi')\n\n\natoms=[0]\norbitals=[4,5,6,7,8]\nhandler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,fermi=-1.1904,apply_symmetry=False)\nhandler.plot_band_structure(mode='spin_texture',\n spin_texture=True,\n atoms=atoms,\n orbitals=orbitals,\n add_fermi_plane=True,\n fermi_plane_size=2,\n energy_lim=[-2,2],\n fermi_text_position=[0,0.5,0],\n scalar_bar_position_x=0.3,\n\n clip_brillouin_zone_factor=1,\n surface_clim=[-0.5,0.5])" ] } ], diff --git a/docs/_downloads/cc74c3bdb45c45890fbe02c5da28aa4c/plot_unfolding.py b/docs/_downloads/cc74c3bdb45c45890fbe02c5da28aa4c/plot_unfolding.py index ee361760..798761a7 100644 --- a/docs/_downloads/cc74c3bdb45c45890fbe02c5da28aa4c/plot_unfolding.py +++ b/docs/_downloads/cc74c3bdb45c45890fbe02c5da28aa4c/plot_unfolding.py @@ -43,6 +43,7 @@ pyprocar.bandsplot( code='vasp', mode='plain', + fermi=4.993523, elimit=[-15,5], dirname=primitive_dir) @@ -60,6 +61,7 @@ code='vasp', mode='plain', unfold_mode='both', + fermi=5.033090, dirname= supercell_dir, elimit=[-15,5], supercell_matrix=np.diag([2, 2, 2])) diff --git a/docs/_downloads/ccab95f5bf6250cc0b98863e24c5392a/plot_fermi2d_spin_texture.py b/docs/_downloads/ccab95f5bf6250cc0b98863e24c5392a/plot_fermi2d_spin_texture.py index a974777a..7c57dae3 100644 --- a/docs/_downloads/ccab95f5bf6250cc0b98863e24c5392a/plot_fermi2d_spin_texture.py +++ b/docs/_downloads/ccab95f5bf6250cc0b98863e24c5392a/plot_fermi2d_spin_texture.py @@ -39,6 +39,7 @@ pyprocar.fermi2D(code = 'vasp', dirname=data_dir, + fermi=5.5962, spin_texture=True, spin_projection='x', arrow_size=3, @@ -54,6 +55,7 @@ pyprocar.fermi2D(code = 'vasp', dirname=data_dir, + fermi=5.5962, spin_texture=True, arrow_color = 'blue', arrow_size=3, @@ -73,6 +75,7 @@ band_colors = [['blue','red']] pyprocar.fermi2D(code = 'vasp', mode='plain_bands', + fermi=5.5962, band_indices = band_indices, band_colors=band_colors, spin_texture=True, diff --git a/docs/_downloads/d03c2f73b27d3251268e6bdebc82ddd5/plot_fermi3d_cross_section.ipynb b/docs/_downloads/d03c2f73b27d3251268e6bdebc82ddd5/plot_fermi3d_cross_section.ipynb index 59eb3313..c1b4826b 100644 --- a/docs/_downloads/d03c2f73b27d3251268e6bdebc82ddd5/plot_fermi3d_cross_section.ipynb +++ b/docs/_downloads/d03c2f73b27d3251268e6bdebc82ddd5/plot_fermi3d_cross_section.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting fermi3d cross_section {#ref_plotting_fermi3d_cross_section}\r\n\r\nSymmetry does not currently work! Make sure for fermi surface\r\ncalculations turn off symmetry\r\n\r\nPlotting fermi3d cross_section example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-colinear',\r\n calc_type='fermi')\r\n```\r\n" + "\n\n# Plotting fermi3d cross_section\n\nSymmetry does not currently work! Make sure for fermi surface calculations turn off symmetry\n\nPlotting fermi3d cross_section example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-colinear',\n calc_type='fermi')\n" ] }, { @@ -33,7 +33,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -51,7 +51,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Cross section\r\n" + "## Cross section\n\n\n\n" ] }, { @@ -69,7 +69,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Cross section. Save slice\r\n" + "## Cross section. Save slice\n\n\n\n" ] }, { diff --git a/docs/_downloads/d279bef957765a4d1e6ca116fee628b6/plot_2dkmesh_generation.ipynb b/docs/_downloads/d279bef957765a4d1e6ca116fee628b6/plot_2dkmesh_generation.ipynb index b082e023..49bdfd8e 100644 --- a/docs/_downloads/d279bef957765a4d1e6ca116fee628b6/plot_2dkmesh_generation.ipynb +++ b/docs/_downloads/d279bef957765a4d1e6ca116fee628b6/plot_2dkmesh_generation.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Example of kmesh_generator {#example_kmesh_generator}\r\n\r\nThis utility can be used to generate a 2D $k$-mesh centered at a given\r\n$k$-point and in a given $k$-plane. This is particularly useful in\r\ncomputing 2D spin-textures and plotting 2D Fermi-surfaces. For example,\r\nthe following command creates a 2D $k_{x}$-$k_{y}$ -mesh centered at the\r\n$\\Gamma$ point ($k_{z}= 0$) ranging from coordinates (-0.5, -0.5, 0.0)\r\nto (0.5, 0.5, 0.0) with 5 grids in the x direction and 7 grids in the y\r\ndirection\r\n\r\n``` {caption=\"General Format\"}\r\npyprocar.generate2dkmesh(x1,y1,x2,y2,z,num_grids_x,num_grids_y)\r\n```\r\n\r\nThis information is automatically written to a KPOINTS file.\r\n" + "\n\n# Example of kmesh_generator \n\nThis utility can be used to generate a 2D $k$-mesh centered at a given $k$-point and in a given $k$-plane. \nThis is particularly useful in computing 2D spin-textures and plotting 2D Fermi-surfaces. \nFor example, the following command creates a 2D $k_{x}$-$k_{y}$ -mesh centered at the $\\Gamma$ point ($k_{z}= 0$) \nranging from coordinates (-0.5, -0.5, 0.0) to (0.5, 0.5, 0.0) with 5 grids in the x direction and 7 grids in the y direction\n\n.. code-block::\n :caption: General Format\n\n pyprocar.generate2dkmesh(x1,y1,x2,y2,z,num_grids_x,num_grids_y)\n\nThis information is automatically written to a KPOINTS file.\n" ] }, { @@ -22,7 +22,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting Kmesh\r\n" + "## Plotting Kmesh\n\n" ] }, { @@ -40,7 +40,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { diff --git a/docs/_downloads/d532a8b4521662fcf3da475ac4bf8821/plot_ebs.ipynb b/docs/_downloads/d532a8b4521662fcf3da475ac4bf8821/plot_ebs.ipynb index 9ee93ea0..f8c71511 100644 --- a/docs/_downloads/d532a8b4521662fcf3da475ac4bf8821/plot_ebs.ipynb +++ b/docs/_downloads/d532a8b4521662fcf3da475ac4bf8821/plot_ebs.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Example of finding the bandgap {#ref_example_ebs}\r\n\r\nThe ElectronicBandStructure is used to handle the information related to\r\nthe electronic band structure.\r\n\r\n``` {caption=\"General Format\"}\r\nimport pyprocar\r\npyprocar.io.Parser(code=\"vasp\", dir=data_dir)\r\n```\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='bands')\r\n```\r\n" + "\n\n# Example of finding the bandgap\n\nThe ElectronicBandStructure is used to handle the information \nrelated to the electronic band structure.\n\n.. code-block::\n :caption: General Format\n\n import pyprocar\n pyprocar.io.Parser(code=\"vasp\", dir=data_dir)\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='bands')\n" ] }, { @@ -22,7 +22,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specify the local data_dir\r\n" + "importing pyprocar and specify the local data_dir\n\n" ] }, { @@ -40,7 +40,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Initialize the parser object and get the ElectronicBandStructure\r\n" + "Initialize the parser object and get the ElectronicBandStructure \n\n" ] }, { @@ -58,7 +58,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "You can print the object to see some information about the Band\r\nStructure\r\n" + "You can print the object to see some information about the Band Structure\n\n" ] }, { @@ -76,7 +76,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Let\\'s plot the kpoints\r\n" + "Let's plot the kpoints\n\n" ] }, { @@ -94,7 +94,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Other properties\r\n\r\n# Bands\r\n" + "## Other properties\n\n## Bands\n\n" ] }, { @@ -112,7 +112,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Projections\r\n" + "## Projections\n\n" ] }, { @@ -130,7 +130,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Gradients\r\n" + "## Gradients\n\n" ] }, { @@ -148,7 +148,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Band/Fermi velocities\r\n" + "## Band/Fermi velocities\n\n" ] }, { @@ -166,7 +166,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Effective mass\r\n" + "## Effective mass\n\n" ] }, { diff --git a/docs/_downloads/d71df43ce9ea3d07c48301fa4fb2d1df/plot_noncolinear_vasp.py b/docs/_downloads/d71df43ce9ea3d07c48301fa4fb2d1df/plot_noncolinear_vasp.py index 7c3471c8..6cbf927a 100644 --- a/docs/_downloads/d71df43ce9ea3d07c48301fa4fb2d1df/plot_noncolinear_vasp.py +++ b/docs/_downloads/d71df43ce9ea3d07c48301fa4fb2d1df/plot_noncolinear_vasp.py @@ -37,6 +37,7 @@ pyprocar.bandsplot( code='vasp', mode='plain', + fermi=5.596151, dirname=data_dir) ############################################################################### @@ -53,6 +54,7 @@ pyprocar.bandsplot( code='vasp', mode='parametric', + fermi=5.596151, atoms=atoms, orbitals=orbitals, spins=spins, diff --git a/docs/_downloads/d8d4fa5958c7469cbc4e4510d197e15e/plot_fermi3d_isoslider.ipynb b/docs/_downloads/d8d4fa5958c7469cbc4e4510d197e15e/plot_fermi3d_isoslider.ipynb index b1e3bb94..b1b44e3d 100644 --- a/docs/_downloads/d8d4fa5958c7469cbc4e4510d197e15e/plot_fermi3d_isoslider.ipynb +++ b/docs/_downloads/d8d4fa5958c7469cbc4e4510d197e15e/plot_fermi3d_isoslider.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting fermi3d isoslider {#ref_plotting_fermi3d_isoslider}\r\n\r\nSymmetry does not currently work! Make sure for fermi surface\r\ncalculations turn off symmetry\r\n\r\nPlotting fermi3d isoslider example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='qe', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='fermi')\r\n```\r\n" + "\n\n# Plotting fermi3d isoslider\n\nSymmetry does not currently work! Make sure for fermi surface calculations turn off symmetry\n\nPlotting fermi3d isoslider example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='qe', \n spin_calc_type='non-spin-polarized',\n calc_type='fermi')\n" ] }, { @@ -33,7 +33,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -51,7 +51,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n" + "## Plain mode\n\n\n\n" ] }, { diff --git a/docs/_downloads/ddce4f8cfa4d56c4c6cd0bbd3fee3ab6/plot_clusters_pyposcar.ipynb b/docs/_downloads/ddce4f8cfa4d56c4c6cd0bbd3fee3ab6/plot_clusters_pyposcar.ipynb index 2e46cadc..e31cac7a 100644 --- a/docs/_downloads/ddce4f8cfa4d56c4c6cd0bbd3fee3ab6/plot_clusters_pyposcar.ipynb +++ b/docs/_downloads/ddce4f8cfa4d56c4c6cd0bbd3fee3ab6/plot_clusters_pyposcar.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Visualizing Clusters in Bi2Se3 Slab {#ref_example_cluster_visualization}\r\n\r\nIn this example, we\\'ll explore the atomic clusters within a slab of\r\nBi2Se3. The slab structure is formed by quintuple layers (QL) where each\r\nQL can be regarded as a cluster. We\\'ll:\r\n\r\n1. Parse the POSCAR file to obtain atomic positions.\r\n2. Identify and label the atomic clusters within the slab.\r\n3. Visualize the atomic clusters using [pyvista]{.title-ref}.\r\n\r\nLet\\'s get started!\r\n" + "\n\n# Visualizing Clusters in Bi2Se3 Slab\n\nIn this example, we'll explore the atomic clusters within a slab of Bi2Se3. The slab structure is formed by quintuple layers (QL) where each QL can be regarded as a cluster. We'll:\n\n1. Parse the POSCAR file to obtain atomic positions.\n2. Identify and label the atomic clusters within the slab.\n3. Visualize the atomic clusters using `pyvista`.\n\nLet's get started!\n" ] }, { @@ -22,7 +22,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Utility function for creating GIF visualizations\r\n" + "## Utility function for creating GIF visualizations\n\n" ] }, { @@ -40,7 +40,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Parsing the POSCAR and Identifying Clusters\r\n" + "## Parsing the POSCAR and Identifying Clusters\n\n" ] }, { @@ -58,7 +58,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Visualizing the Clusters\r\n" + "## Visualizing the Clusters\n\n" ] }, { diff --git a/docs/_downloads/f513a0ae8a9d887aa2261eba0fd3d52b/plot_spin_polarized.ipynb b/docs/_downloads/f513a0ae8a9d887aa2261eba0fd3d52b/plot_spin_polarized.ipynb index 27ffc459..a384f3df 100644 --- a/docs/_downloads/f513a0ae8a9d887aa2261eba0fd3d52b/plot_spin_polarized.ipynb +++ b/docs/_downloads/f513a0ae8a9d887aa2261eba0fd3d52b/plot_spin_polarized.ipynb @@ -4,14 +4,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plotting spin polarized band structures {#ref_plotting_spin_polarized}\r\n\r\nPlotting spin polarized band structures.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='spin-polarized-colinear',\r\n calc_type='bands')\r\n```\r\n" + "\n\n# Plotting spin polarized band structures\n\nPlotting spin polarized band structures.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='spin-polarized-colinear',\n calc_type='bands')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "importing pyprocar and specifying local data_dir\r\n" + "importing pyprocar and specifying local data_dir\n\n" ] }, { @@ -29,7 +29,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Plain mode\r\n\r\nWhen the calculation is a spin-polarized calculation. There are few more\r\nfeatures features bandsplot can do. The default settings bandsplot will\r\nplot the spin-up and spin-down bands on the same plot.\r\n" + "## Plain mode\n\nWhen the calculation is a spin-polarized calculation. There are few more features features bandsplot can do. \nThe default settings bandsplot will plot the spin-up and spin-down bands on the same plot.\n\n" ] }, { @@ -40,14 +40,14 @@ }, "outputs": [], "source": [ - "pyprocar.bandsplot(\n code='vasp', \n mode='plain',\n dirname=data_dir)" + "pyprocar.bandsplot(\n code='vasp', \n mode='plain',\n fermi=5.590136,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "The line-styles or line-colors, these may be changed in the ebs section\r\nin the :doc:\\'pyprocar/utils/default_settings.ini\\' file.\r\n\r\nThe keyword spins can also be used to select which spin bands to plot\r\n" + "The line-styles or line-colors, these may be changed in the ebs section in the :doc:'pyprocar/utils/default_settings.ini' file.\n\nThe keyword spins can also be used to select which spin bands to plot\n\n" ] }, { @@ -58,14 +58,14 @@ }, "outputs": [], "source": [ - "spins = [1]\npyprocar.bandsplot(\n code='vasp', \n mode='plain',\n spins=spins,\n dirname=data_dir)" + "spins = [1]\npyprocar.bandsplot(\n code='vasp', \n mode='plain',\n fermi=5.590136,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Parametric mode\r\n\r\nFor details on the meaning of the indices of the atomic projection\r\nplease refer to the user guide :ref:\\'atomic_projections\\'\r\n" + "## Parametric mode\n\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n" ] }, { @@ -76,14 +76,14 @@ }, "outputs": [], "source": [ - "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0,1]\n\npyprocar.bandsplot(\n code='vasp', \n mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0,1]\n\npyprocar.bandsplot(\n code='vasp', \n mode='parametric',\n fermi=5.590136,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Scatter mode\r\n" + "## Scatter mode\n\n\n\n\n" ] }, { @@ -94,7 +94,7 @@ }, "outputs": [], "source": [ - "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0,1]\n\npyprocar.bandsplot(\n code='vasp', \n mode='scatter',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" + "atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0,1]\n\npyprocar.bandsplot(\n code='vasp', \n mode='scatter',\n fermi=5.590136,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)" ] } ], diff --git a/docs/_downloads/f543fc33d0c7e1250dd18eb4d5567496/plot_colinear_dos.py b/docs/_downloads/f543fc33d0c7e1250dd18eb4d5567496/plot_colinear_dos.py index 575bce50..e2b1bb3d 100644 --- a/docs/_downloads/f543fc33d0c7e1250dd18eb4d5567496/plot_colinear_dos.py +++ b/docs/_downloads/f543fc33d0c7e1250dd18eb4d5567496/plot_colinear_dos.py @@ -35,6 +35,7 @@ pyprocar.dosplot( code='qe', mode='plain', + fermi=5.599480, dirname=data_dir) ############################################################################### @@ -52,6 +53,7 @@ pyprocar.dosplot( code='qe', mode='parametric', + fermi=5.599480, atoms=atoms, orbitals=orbitals, spins=spins, @@ -72,6 +74,7 @@ pyprocar.dosplot( code='qe', mode='parametric_line', + fermi=5.599480, atoms=atoms, orbitals=orbitals, spins=spins, @@ -91,6 +94,7 @@ pyprocar.dosplot( code='qe', mode='stack_species', + fermi=5.599480, orbitals=orbitals, spins=spins, dirname=data_dir) @@ -106,13 +110,14 @@ pyprocar.dosplot( code='qe', mode='stack_orbitals', + fermi=5.599480, atoms=atoms, spins=spins, dirname=data_dir) ############################################################################### -# overlay mode +# stack mode # +++++++++++++++++++++++++++++++++++++++ # # @@ -122,6 +127,56 @@ pyprocar.dosplot( code='qe', mode='stack', + fermi=5.599480, items=items, dirname=data_dir) + +############################################################################### +# overlay_species mode +# +++++++++++++++++++++++++++++++++++++++ +# +# +# +orbitals=[4,5,6,7,8] +spins=[0] + +pyprocar.dosplot( + code='qe', + mode='overlay_species', + fermi=5.599480, + orbitals=orbitals, + spins=spins, + dirname=data_dir) + +############################################################################### +# overlay_orbtials mode +# +++++++++++++++++++++++++++++++++++++++ +# +# +# +atoms=[0] +spins=[0] +pyprocar.dosplot( + code='qe', + mode='overlay_orbitals', + fermi=5.599480, + atoms=atoms, + spins=spins, + dirname=data_dir) + + +############################################################################### +# overlay mode +# +++++++++++++++++++++++++++++++++++++++ +# +# +# + +items={'Fe':[4,5,6,7,8]} +pyprocar.dosplot( + code='qe', + mode='overlay', + fermi=5.599480, + items=items, + dirname=data_dir) diff --git a/docs/_downloads/fb15cc3f1cf9cfdc4c42fd1b26bacdef/plot_2d_bands.py b/docs/_downloads/fb15cc3f1cf9cfdc4c42fd1b26bacdef/plot_2d_bands.py index 6ce45d85..0f2cec04 100644 --- a/docs/_downloads/fb15cc3f1cf9cfdc4c42fd1b26bacdef/plot_2d_bands.py +++ b/docs/_downloads/fb15cc3f1cf9cfdc4c42fd1b26bacdef/plot_2d_bands.py @@ -34,7 +34,11 @@ # Plain mode # +++++++++++++++++++++++++++++++++++++++ spins=[0] -handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,apply_symmetry=False) +handler = pyprocar.BandStructure2DHandler(code='vasp', + dirname=data_dir, + fermi=-0.795606, + apply_symmetry=False, + ) handler.plot_band_structure(mode='plain', add_fermi_plane=True, bands=[3,4], @@ -50,7 +54,7 @@ atoms=[0,1] orbitals=[1,2,3] spins=[0] -handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,apply_symmetry=False) +handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,fermi=-0.795606,apply_symmetry=False) handler.plot_band_structure(mode='parametric', atoms=atoms, orbitals=orbitals, @@ -59,7 +63,7 @@ ############################################################################### # Property Projection mode # +++++++++++++++++++++++++++++++++++++++ -handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,apply_symmetry=False) +handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,fermi=-0.795606,apply_symmetry=False) handler.plot_band_structure(mode='property_projection', property_name='band_velocity', bands=[3,4], @@ -78,7 +82,7 @@ atoms=[0] orbitals=[4,5,6,7,8] -handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,apply_symmetry=False) +handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,fermi=-1.1904,apply_symmetry=False) handler.plot_band_structure(mode='spin_texture', spin_texture=True, atoms=atoms, diff --git a/docs/_downloads/fb625db3c50d423b1b7881136ffdeec8/examples_jupyter.zip b/docs/_downloads/fb625db3c50d423b1b7881136ffdeec8/examples_jupyter.zip index b0ecdb9e..b9880f42 100644 Binary files a/docs/_downloads/fb625db3c50d423b1b7881136ffdeec8/examples_jupyter.zip and b/docs/_downloads/fb625db3c50d423b1b7881136ffdeec8/examples_jupyter.zip differ diff --git a/docs/_downloads/fdb826763925695b13fb39139d369c9e/plot_fermi2d_configurations.py b/docs/_downloads/fdb826763925695b13fb39139d369c9e/plot_fermi2d_configurations.py index 69a2a678..3ca36e86 100644 --- a/docs/_downloads/fdb826763925695b13fb39139d369c9e/plot_fermi2d_configurations.py +++ b/docs/_downloads/fdb826763925695b13fb39139d369c9e/plot_fermi2d_configurations.py @@ -39,7 +39,7 @@ print(f"Configuration files are located at: {config_path}") # Print the configurations -pyprocar.fermi2D(code='vasp', dirname=data_dir, print_plot_opts=True) +pyprocar.fermi2D(code='vasp', dirname=data_dir,fermi=5.599480, print_plot_opts=True) ############################################################################### @@ -51,6 +51,7 @@ # pyprocar.fermi2D(code='vasp', + fermi=5.599480, dirname=data_dir, spin_texture=True, spin_projection='x', @@ -72,6 +73,7 @@ pyprocar.fermi2D(code='vasp', dirname=data_dir, + 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Overview: module code — PyProcar 6.1.8 documentation + Overview: module code — PyProcar 6.1.9 documentation @@ -39,7 +39,7 @@ - + @@ -109,7 +109,7 @@ -

PyProcar 6.1.8 documentation

+

PyProcar 6.1.9 documentation

@@ -447,11 +447,9 @@

All modules for which code is available

  • pyprocar.scripts.scriptBandGap
  • pyprocar.scripts.scriptBandsDosplot
  • pyprocar.scripts.scriptBandsplot
    • -
  • pyprocar.scripts.scriptBandsplot_2d
  • pyprocar.scripts.scriptCat
  • pyprocar.scripts.scriptDosplot
  • pyprocar.scripts.scriptFermi2D
    • -
  • pyprocar.scripts.scriptFermi3D
  • pyprocar.scripts.scriptFermiHandler
  • pyprocar.scripts.scriptFilter
  • pyprocar.scripts.scriptKmesh2D
    • diff --git a/docs/_modules/pyprocar/core/brillouin_zone.html b/docs/_modules/pyprocar/core/brillouin_zone.html index be16b298..4d5043d1 100644 --- a/docs/_modules/pyprocar/core/brillouin_zone.html +++ b/docs/_modules/pyprocar/core/brillouin_zone.html @@ -7,7 +7,7 @@ - pyprocar.core.brillouin_zone — PyProcar 6.1.7 documentation + pyprocar.core.brillouin_zone — PyProcar 6.1.9 documentation @@ -39,7 +39,7 @@ - + @@ -109,7 +109,7 @@ -

    PyProcar 6.1.7 documentation

    +

    PyProcar 6.1.9 documentation

    diff --git a/docs/_modules/pyprocar/core/dos.html b/docs/_modules/pyprocar/core/dos.html index 180c95c6..a1f10ff3 100644 --- a/docs/_modules/pyprocar/core/dos.html +++ b/docs/_modules/pyprocar/core/dos.html @@ -7,7 +7,7 @@ - pyprocar.core.dos — PyProcar 6.1.7 documentation + pyprocar.core.dos — PyProcar 6.1.9 documentation @@ -39,7 +39,7 @@ - + @@ -109,7 +109,7 @@ -

    PyProcar 6.1.7 documentation

    +

    PyProcar 6.1.9 documentation

    @@ -459,6 +459,8 @@

    Source code for pyprocar.core.dos

                 Points on energy spectrum. shape = (n_dos, )
         total : np.ndarray
             Densities at each point. shape = (n_dos, )
+        efermi : float
+            Fermi energy of the system.
         projected : np.ndarray, optional
             Projection of elements, orbitals, spin, etc. shape = (n_atoms, n_principals, n_orbitals, n_spins, n_dos)
             ``i_principal`` works like the principal quantum number n. The last
@@ -478,15 +480,17 @@ 
    Source code for pyprocar.core.dos
             self, 
         energies: npt.NDArray[np.float64],
         total: npt.NDArray[np.float64], 
+        efermi: float,
         projected: npt.NDArray[np.float64] = None, 
         interpolation_factor: int = 1,
         # interpolation_kind: str = 'cubic',
         ):
                 
 
-
+        
         self.energies = energies
         self.total = total
+        self.efermi = efermi
         self.projected = projected
         if interpolation_factor not in [1, 0]:
             interpolated = []
diff --git a/docs/_modules/pyprocar/core/ebs.html b/docs/_modules/pyprocar/core/ebs.html
index 3bbf145b..fa30003c 100644
--- a/docs/_modules/pyprocar/core/ebs.html
+++ b/docs/_modules/pyprocar/core/ebs.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.core.ebs — PyProcar 6.1.7 documentation
+    pyprocar.core.ebs — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
@@ -431,6 +431,7 @@ 
    Source code for pyprocar.core.ebs
     """
 Created on Sat Jan 16 2021
 
+@author: Logan Lang
 @author: Pedram Tavadze
 @author: Freddy Farah
 
@@ -1485,13 +1486,17 @@ 
    Source code for pyprocar.core.ebs
             if self.n_kx:
             if nk != self.n_kx*self.n_ky*self.n_kz:
 
-                err_text="""
+                err_text=f"""
                         nkpoints != n_kx*n_ky*n_kz
                         Error trying to symmetrize the irreducible kmesh. 
                         This is issue is most likely related to 
                         how the DFT code using symmetry operations to reduce the kmesh.
                         Check the recommendations for k-mesh type for the crystal system.
                         If all else fails turn off symmetry.
+                        n_kx={self.n_kx}
+                        n_ky={self.n_ky}
+                        n_kz={self.n_kz}
+                        nk={nk}
                         """
                 raise ValueError(err_text)
    
 
diff --git a/docs/_modules/pyprocar/core/fermisurface.html b/docs/_modules/pyprocar/core/fermisurface.html
index 57a746ad..8335913d 100644
--- a/docs/_modules/pyprocar/core/fermisurface.html
+++ b/docs/_modules/pyprocar/core/fermisurface.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.core.fermisurface — PyProcar 6.1.7 documentation
+    pyprocar.core.fermisurface — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
diff --git a/docs/_modules/pyprocar/core/fermisurface3D.html b/docs/_modules/pyprocar/core/fermisurface3D.html
index cd15d806..d45b2b2a 100644
--- a/docs/_modules/pyprocar/core/fermisurface3D.html
+++ b/docs/_modules/pyprocar/core/fermisurface3D.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.core.fermisurface3D — PyProcar 6.1.7 documentation
+    pyprocar.core.fermisurface3D — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    diff --git a/docs/_modules/pyprocar/core/isosurface.html b/docs/_modules/pyprocar/core/isosurface.html index 785241a7..5a344896 100644 --- a/docs/_modules/pyprocar/core/isosurface.html +++ b/docs/_modules/pyprocar/core/isosurface.html @@ -7,7 +7,7 @@ - pyprocar.core.isosurface — PyProcar 6.1.7 documentation + pyprocar.core.isosurface — PyProcar 6.1.9 documentation @@ -39,7 +39,7 @@ - + @@ -109,7 +109,7 @@ -

    PyProcar 6.1.7 documentation

    +

    PyProcar 6.1.9 documentation

    diff --git a/docs/_modules/pyprocar/core/kpath.html b/docs/_modules/pyprocar/core/kpath.html index 3a854ed9..a2287629 100644 --- a/docs/_modules/pyprocar/core/kpath.html +++ b/docs/_modules/pyprocar/core/kpath.html @@ -7,7 +7,7 @@ - pyprocar.core.kpath — PyProcar 6.1.7 documentation + pyprocar.core.kpath — PyProcar 6.1.9 documentation @@ -39,7 +39,7 @@ - + @@ -109,7 +109,7 @@ -

    PyProcar 6.1.7 documentation

    +

    PyProcar 6.1.9 documentation

    diff --git a/docs/_modules/pyprocar/core/structure.html b/docs/_modules/pyprocar/core/structure.html index 047a42e5..3c66fc36 100644 --- a/docs/_modules/pyprocar/core/structure.html +++ b/docs/_modules/pyprocar/core/structure.html @@ -7,7 +7,7 @@ - pyprocar.core.structure — PyProcar 6.1.7 documentation + pyprocar.core.structure — PyProcar 6.1.9 documentation @@ -39,7 +39,7 @@ - + @@ -109,7 +109,7 @@ -

    PyProcar 6.1.7 documentation

    +

    PyProcar 6.1.9 documentation

    diff --git a/docs/_modules/pyprocar/core/surface.html b/docs/_modules/pyprocar/core/surface.html index 4253f765..e0025c88 100644 --- a/docs/_modules/pyprocar/core/surface.html +++ b/docs/_modules/pyprocar/core/surface.html @@ -7,7 +7,7 @@ - pyprocar.core.surface — PyProcar 6.1.7 documentation + pyprocar.core.surface — PyProcar 6.1.9 documentation @@ -39,7 +39,7 @@ - + @@ -109,7 +109,7 @@ -

    PyProcar 6.1.7 documentation

    +

    PyProcar 6.1.9 documentation

    diff --git a/docs/_modules/pyprocar/io/abinit.html b/docs/_modules/pyprocar/io/abinit.html index 54bf4ad1..7d0f2696 100644 --- a/docs/_modules/pyprocar/io/abinit.html +++ b/docs/_modules/pyprocar/io/abinit.html @@ -7,7 +7,7 @@ - pyprocar.io.abinit — PyProcar 6.1.7 documentation + pyprocar.io.abinit — PyProcar 6.1.9 documentation @@ -39,7 +39,7 @@ - + @@ -109,7 +109,7 @@ -

    PyProcar 6.1.7 documentation

    +

    PyProcar 6.1.9 documentation

    @@ -893,6 +893,7 @@

    Source code for pyprocar.io.abinit

             self.dos = DensityOfStates(
             energies=self.energies,
             total=self.dos_total,
+            efermi=self.fermi,
             projected=self.projected,
             interpolation_factor=1,
         )
diff --git a/docs/_modules/pyprocar/io/bxsf.html b/docs/_modules/pyprocar/io/bxsf.html
index f3d46539..51963832 100644
--- a/docs/_modules/pyprocar/io/bxsf.html
+++ b/docs/_modules/pyprocar/io/bxsf.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.io.bxsf — PyProcar 6.1.7 documentation
+    pyprocar.io.bxsf — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    diff --git a/docs/_modules/pyprocar/io/lobster.html b/docs/_modules/pyprocar/io/lobster.html index 5919eb2c..1cffd510 100644 --- a/docs/_modules/pyprocar/io/lobster.html +++ b/docs/_modules/pyprocar/io/lobster.html @@ -7,7 +7,7 @@ - pyprocar.io.lobster — PyProcar 6.1.7 documentation + pyprocar.io.lobster — PyProcar 6.1.9 documentation @@ -39,7 +39,7 @@ - + @@ -109,7 +109,7 @@ -

    PyProcar 6.1.7 documentation

    +

    PyProcar 6.1.9 documentation

    diff --git a/docs/_modules/pyprocar/io/qe.html b/docs/_modules/pyprocar/io/qe.html index b86a1bfa..b2877ac7 100644 --- a/docs/_modules/pyprocar/io/qe.html +++ b/docs/_modules/pyprocar/io/qe.html @@ -7,7 +7,7 @@ - pyprocar.io.qe — PyProcar 6.1.7 documentation + pyprocar.io.qe — PyProcar 6.1.9 documentation @@ -39,7 +39,7 @@ - + @@ -109,7 +109,7 @@ -

    PyProcar 6.1.7 documentation

    +

    PyProcar 6.1.9 documentation

    @@ -637,6 +637,7 @@

    Source code for pyprocar.io.qe

             # print(projected_labels)
         dos = DensityOfStates(energies=energies,
                             total=total_dos,
+                            efermi=self.efermi,
                             projected=projected_dos, 
                             interpolation_factor = 1)
         return dos    
diff --git a/docs/_modules/pyprocar/io/siesta.html b/docs/_modules/pyprocar/io/siesta.html
index ff2b6ad6..e6110b61 100644
--- a/docs/_modules/pyprocar/io/siesta.html
+++ b/docs/_modules/pyprocar/io/siesta.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.io.siesta — PyProcar 6.1.7 documentation
+    pyprocar.io.siesta — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    diff --git a/docs/_modules/pyprocar/io/vasp.html b/docs/_modules/pyprocar/io/vasp.html index 647bf4dc..c5d7637e 100644 --- a/docs/_modules/pyprocar/io/vasp.html +++ b/docs/_modules/pyprocar/io/vasp.html @@ -7,7 +7,7 @@ - pyprocar.io.vasp — PyProcar 6.1.7 documentation + pyprocar.io.vasp — PyProcar 6.1.9 documentation @@ -39,7 +39,7 @@ - + @@ -109,7 +109,7 @@ -

    PyProcar 6.1.7 documentation

    +

    PyProcar 6.1.9 documentation

    @@ -1048,7 +1048,6 @@

    Source code for pyprocar.io.vasp

             if self.has_phase:
             self.carray = self.spd_phase[:, :, :, :-1, 1:-1]
 
-        # self.bands -= efermi
         self.ebs = ElectronicBandStructure(
             kpoints=self.kpoints,
             bands=self.bands,
@@ -2031,6 +2030,7 @@ 
    Source code for pyprocar.io.vasp
             return DensityOfStates(
             energies=energies,
             total=total,
+            efermi=self.fermi,
             projected=self.dos_projected,
             interpolation_factor=self.dos_interpolation_factor,
         )
diff --git a/docs/_modules/pyprocar/plotter/dos_plot.html b/docs/_modules/pyprocar/plotter/dos_plot.html
index 000e2d20..d61cc510 100644
--- a/docs/_modules/pyprocar/plotter/dos_plot.html
+++ b/docs/_modules/pyprocar/plotter/dos_plot.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.plotter.dos_plot — PyProcar 6.1.8 documentation
+    pyprocar.plotter.dos_plot — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.8 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
@@ -829,6 +829,7 @@ 
    Source code for pyprocar.plotter.dos_plot
                 principal_q_numbers:List[int]=[-1],
             orbitals:List[int]=None,
             spins:List[int]=None,
+            overlay_mode:bool=False,
             orientation:str="horizontal",
         ):
         """A method to plot the dos with the species contribution stacked on eachother
@@ -927,27 +928,37 @@ 
    Source code for pyprocar.plotter.dos_plot
     
                     x = self.dos.energies
                     y = (dos_projected[ispin]  / dos_projected_total[ispin] ) * dos_total[ispin]
-
-                    if ispin > 0 and len(spins) > 1:
-                        y *= -1
-                        handle = self.ax.fill_between(x,
-                                        bottom + y,
-                                        bottom,
-                                        color=self.config['colors']['value'][specie],
-                                        )
+                    # replace very large values above a threshold with 0. 
+                    # These are artifacts from the division of samll total values.
+                    y = np.nan_to_num(y, 0)
+                    threshold=50
+                    y[np.abs(y) > threshold] = 0
+                    if overlay_mode:
+                        if ispin > 0 and len(spins) > 1:
+                            y *= -1
+                            handle, = self.ax.plot(x,y,color=self.config['colors']['value'][specie])
+                        else:
+                            handle, = self.ax.plot(x,y,color=self.config['colors']['value'][specie])
                     else:
-                        handle = self.ax.fill_between(
-                            x,
-                            bottom + y,
-                            bottom,
-                            color=self.config['colors']['value'][specie],
-                        )
+                        if ispin > 0 and len(spins) > 1:
+                            y *= -1
+                            handle = self.ax.fill_between(x,
+                                            bottom + y,
+                                            bottom,
+                                            color=self.config['colors']['value'][specie],
+                                            )
+                        else:
+                            handle = self.ax.fill_between(
+                                x,
+                                bottom + y,
+                                bottom,
+                                color=self.config['colors']['value'][specie],
+                            )
                     self.handles.append(handle)
-                    label=self.structure.species[specie] + label + self.config['spin_labels']['value'][ispin]
-                    self.labels.append(label)
+                    self.labels.append(self.structure.species[specie] + label + self.config['spin_labels']['value'][ispin])
                     bottom += y
 
-                    if spins_index == 0:
+                    if ispin == 0:
                         self.ax.plot(
                                 self.dos.energies, self.dos.total[ispin, :], color= 'black', 
                                 alpha=self.config['opacity']['value'][ispin], 
@@ -991,26 +1002,37 @@ 
    Source code for pyprocar.plotter.dos_plot
                         x = self.dos.energies
                     y = (dos[ispin] * dos_total[ispin]) / dos_projected_total[ispin]
 
-                    if ispin > 0 and len(spins) > 1:
-                        y *= -1
-                        handle = self.ax.fill_betweenx(x,
-                                        bottom + y,
-                                        bottom,
-                                        color=self.config['colors']['value'][specie],
-                                        )
+                    # replace very large values above a threshold with 0. 
+                    # These are artifacts from the division of samll total values.
+                    y = np.nan_to_num(y, 0)
+                    threshold=50
+                    y[np.abs(y) > threshold] = 0
+                    if overlay_mode:
+                        if ispin > 0 and len(spins) > 1:
+                            y *= -1
+                            handle, = self.ax.plot(y,x,color=self.config['colors']['value'][specie])
+                        else:
+                            handle, = self.ax.plot(y,x,color=self.config['colors']['value'][specie])
                     else:
-                         handle = self.ax.fill_betweenx(x,
-                                        bottom + y,
-                                        bottom,
-                                        color=self.config['colors']['value'][specie],
-                                        )
+                        if ispin > 0 and len(spins) > 1:
+                            y *= -1
+                            handle = self.ax.fill_betweenx(x,
+                                            bottom + y,
+                                            bottom,
+                                            color=self.config['colors']['value'][specie],
+                                            )
+                        else:
+                            handle = self.ax.fill_betweenx(x,
+                                            bottom + y,
+                                            bottom,
+                                            color=self.config['colors']['value'][specie],
+                                            )
                     self.handles.append(handle)
-                    label=self.structure.species[specie] + label + self.config['spin_labels']['value'][ispin]
-                    self.labels.append(label)     
+                    self.labels.append(self.structure.species[specie] + label + self.config['spin_labels']['value'][ispin])     
                     bottom += y 
 
                 if self.config['plot_total']['value'] == True:
-                    if spins_index == 0:
+                    if ispin == 0:
                         self.ax.plot(
                                 self.dos.total[ispin, :], self.dos.energies, color= 'black', 
                                 alpha=self.config['opacity']['value'][ispin], 
@@ -1031,6 +1053,7 @@ 
    Source code for pyprocar.plotter.dos_plot
                 atoms:List[int]=None,
             spins:List[int]=None,
             principal_q_numbers:List[int]=[-1],
+            overlay_mode:bool=False,
             orientation:str="horizontal",
         ):
         """A method to plot dos orbitals contribution stacked.
@@ -1107,45 +1130,57 @@ 
    Source code for pyprocar.plotter.dos_plot
     
                     x = self.dos.energies
                     y = (dos[ispin] * dos_total[ispin]) / dos_projected_total[ispin]
+                    # replace very large values above a threshold with 0. 
+                    # These are artifacts from the division of samll total values.
                     y = np.nan_to_num(y, 0)
+                    threshold=50
+                    y[np.abs(y) > threshold] = 0
+
+                    if overlay_mode:
+                        if ispin > 0 and len(spins) > 1:
+                            y *= -1
+                            handle, =  self.ax.plot(x,y,color=self.config['colors']['value'][iorb])
+                        else:
+                            handle, = self.ax.plot(x,y,color=self.config['colors']['value'][iorb],)
 
-                    if ispin > 0 and len(spins) > 1:
-                        y *= -1
-                        handle =  self.ax.fill_between(x,
-                                        bottom + y,
-                                        bottom,
-                                        color=self.config['colors']['value'][iorb])
-                        
                     else:
-                        handle = self.ax.fill_between(
-                            x,
-                            bottom + y,
-                            bottom,
-                            color=self.config['colors']['value'][iorb],
-                        )
+                        if ispin > 0 and len(spins) > 1:
+                            y *= -1
+                            handle =  self.ax.fill_between(x,
+                                            bottom + y,
+                                            bottom,
+                                            color=self.config['colors']['value'][iorb])
+                            
+                        else:
+                            handle = self.ax.fill_between(
+                                x,
+                                bottom + y,
+                                bottom,
+                                color=self.config['colors']['value'][iorb],
+                            )
                         
 
                     self.labels.append(atom_names + orb_names[iorb] + self.config['spin_labels']['value'][ispin])
                     self.handles.append(handle)
                     bottom += y
 
-            if self.config['plot_total']['value'] == True:
-                if ispin == 0:
-                    self.ax.plot(
-                            self.dos.energies, self.dos.total[ispin, :], color= 'black', 
-                            alpha=self.config['opacity']['value'][ispin], 
-                            linestyle=self.config['linestyle']['value'][ispin], 
-                            label=self.config['spin_labels']['value'][ispin],
-                            linewidth=self.config['linewidth']['value'][ispin],
-                        )
-                else:
-                    self.ax.plot(
-                            self.dos.energies, -self.dos.total[ispin, :], color= 'black', 
-                            alpha=self.config['opacity']['value'][ispin], 
-                            linestyle=self.config['linestyle']['value'][ispin], 
-                            label=self.config['spin_labels']['value'][ispin],
-                            linewidth=self.config['linewidth']['value'][ispin],
-                        )
+                if self.config['plot_total']['value'] == True:
+                    if ispin == 0:
+                        self.ax.plot(
+                                self.dos.energies, self.dos.total[ispin, :], color= 'black', 
+                                alpha=self.config['opacity']['value'][ispin], 
+                                linestyle=self.config['linestyle']['value'][ispin], 
+                                label=self.config['spin_labels']['value'][ispin],
+                                linewidth=self.config['linewidth']['value'][ispin],
+                            )
+                    else:
+                        self.ax.plot(
+                                self.dos.energies, -self.dos.total[ispin, :], color= 'black', 
+                                alpha=self.config['opacity']['value'][ispin], 
+                                linestyle=self.config['linestyle']['value'][ispin], 
+                                label=self.config['spin_labels']['value'][ispin],
+                                linewidth=self.config['linewidth']['value'][ispin],
+                            )
 
         elif orientation == 'vertical':
             self.set_xlabel('DOS Cumlative')
@@ -1168,8 +1203,18 @@ 
    Source code for pyprocar.plotter.dos_plot
     
                     x = self.dos.energies
                     y = (dos[ispin] * dos_total[ispin]) / dos_projected_total[ispin]
+                    # replace very large values above a threshold with 0. 
+                    # These are artifacts from the division of samll total values.
                     y = np.nan_to_num(y, 0)
-
+                    threshold=50
+                    y[np.abs(y) > threshold] = 0
+
+                    if overlay_mode:
+                        if ispin > 0 and len(spins) > 1:
+                            y *= -1
+                            handle, =  self.ax.plot(y,x,color=self.config['colors']['value'][iorb])
+                        else:
+                            handle, = self.ax.plot(y,x,color=self.config['colors']['value'][iorb])
                     if ispin > 0 and len(spins) > 1:
                         y *= -1
                         handle =  self.ax.fill_betweenx(x,
@@ -1189,28 +1234,29 @@ 
    Source code for pyprocar.plotter.dos_plot
                         self.labels.append(atom_names + orb_names[iorb] + self.config['spin_labels']['value'][ispin])
                     self.handles.append(handle)
                     bottom += y
-            if self.config['plot_total']['value'] == True:
-                if ispin == 0:
-                    self.ax.plot(
-                            self.dos.total[ispin, :], self.dos.energies, color= 'black', 
-                            alpha=self.config['opacity']['value'][ispin], 
-                            linestyle=self.config['linestyle']['value'][ispin], 
-                            label=self.config['spin_labels']['value'][ispin],
-                            linewidth=self.config['linewidth']['value'][ispin],
-                        )
-                else:
-                    self.ax.plot(
-                            -self.dos.total[ispin, :], self.dos.energies, color= 'black', 
-                            alpha=self.config['opacity']['value'][ispin], 
-                            linestyle=self.config['linestyle']['value'][ispin], 
-                            label=self.config['spin_labels']['value'][ispin],
-                            linewidth=self.config['linewidth']['value'][ispin],
-                        )
    
+                if self.config['plot_total']['value'] == True:
+                    if ispin == 0:
+                        self.ax.plot(
+                                self.dos.total[ispin, :], self.dos.energies, color= 'black', 
+                                alpha=self.config['opacity']['value'][ispin], 
+                                linestyle=self.config['linestyle']['value'][ispin], 
+                                label=self.config['spin_labels']['value'][ispin],
+                                linewidth=self.config['linewidth']['value'][ispin],
+                            )
+                    else:
+                        self.ax.plot(
+                                -self.dos.total[ispin, :], self.dos.energies, color= 'black', 
+                                alpha=self.config['opacity']['value'][ispin], 
+                                linestyle=self.config['linestyle']['value'][ispin], 
+                                label=self.config['spin_labels']['value'][ispin],
+                                linewidth=self.config['linewidth']['value'][ispin],
+                            )
    
             
 
    [docs]    def plot_stack(self,
                 items:dict=None,
                 spins:List[int]=None,
                 plot_total:bool= True,
+                overlay_mode=False,
                 orientation:str='horizontal',
         ):
         """A method to plot dos contributions stacked.
@@ -1317,23 +1363,40 @@ 
    Source code for pyprocar.plotter.dos_plot
                                 label = ""
                 
                     x = self.dos.energies
+
+                    
                     y = (dos[ispin] * dos_total[ispin]) / dos_projected_total[ispin]
 
-                    if ispin > 0 and len(spins) > 1:
-                        y *= -1
-                        handle = self.ax.fill_between(x,
-                                        bottom + y,
-                                        bottom,
-                                        color=colors_dict[specie])
-                    else:
-                        handle = self.ax.fill_between(
-                                x,
-                                bottom + y,
-                                bottom,
-                                color=colors_dict[specie],
-                            )
-                    self.handles.append(handle)
+                    # replace very large values above a threshold with 0. 
+                    # These are artifacts from the division of samll total values.
+                    y = np.nan_to_num(y, 0)
+                    threshold=50
+                    y[np.abs(y) > threshold] = 0
+                    
+                    if overlay_mode:
+                        if ispin > 0 and len(spins) > 1:
+                            y *= -1
+                            handle, = self.ax.plot(x,y,color=colors_dict[specie])
+                        else:
+                            handle, = self.ax.plot(x,y,color=colors_dict[specie])
+                    else: 
+                        if ispin > 0 and len(spins) > 1:
+                            y *= -1
+                            handle = self.ax.fill_between(x,
+                                            bottom + y,
+                                            bottom,
+                                            color=colors_dict[specie])
+                        else:
+                            handle = self.ax.fill_between(
+                                    x,
+                                    bottom + y,
+                                    bottom,
+                                    color=colors_dict[specie],
+                                )
+                    
                     self.labels.append(specie + label + self.config['spin_labels']['value'][ispin])
+                    self.handles.append(handle)
+                        
                     bottom += y
                 if plot_total == True:
                     if ispin == 0:
@@ -1407,20 +1470,31 @@ 
    Source code for pyprocar.plotter.dos_plot
                     
                     x = self.dos.energies
                     y = (dos[ispin] * dos_total[ispin]) / dos_projected_total[ispin]
-
-                    if ispin > 0 and len(spins) > 1:
-                        y *= -1
-                        handle = self.ax.fill_betweenx(x,
-                                        bottom + y,
-                                        bottom,
-                                        color=colors_dict[specie])
+                    # replace very large values above a threshold with 0. 
+                    # These are artifacts from the division of samll total values.
+                    y = np.nan_to_num(y, 0)
+                    threshold=50
+                    y[np.abs(y) > threshold] = 0
+                    if overlay_mode:
+                        if ispin > 0 and len(spins) > 1:
+                            y *= -1
+                            handle, = self.ax.plot(y,x,color=colors_dict[specie])
+                        else:
+                            handle, = self.ax.plot(y,x,color=colors_dict[specie])
                     else:
-                        handle = self.ax.fill_betweenx(
-                                x,
-                                bottom + y,
-                                bottom,
-                                color=self.config['colors']['value'][specie],
-                            )
+                        if ispin > 0 and len(spins) > 1:
+                            y *= -1
+                            handle = self.ax.fill_betweenx(x,
+                                            bottom + y,
+                                            bottom,
+                                            color=colors_dict[specie])
+                        else:
+                            handle = self.ax.fill_betweenx(
+                                    x,
+                                    bottom + y,
+                                    bottom,
+                                    color=self.config['colors']['value'][specie],
+                                )
                     self.handles.append(handle)
                     self.labels.append(specie + label + self.config['spin_labels']['value'][ispin])
                     bottom += y
@@ -1522,7 +1596,10 @@ 
    Source code for pyprocar.plotter.dos_plot
             None
             None
         """
-        self.ax.set_xlabel(label)
+        if self.config['x_label']['value']:
+            self.ax.set_xlabel(self.config['x_label']['value'])
+        else:
+            self.ax.set_xlabel(label)
         return None
    
 
 
    [docs]    def set_ylabel(self, label:str):
@@ -1538,7 +1615,10 @@ 
    Source code for pyprocar.plotter.dos_plot
             None
             None
         """
-        self.ax.set_ylabel(label)
    
+        if self.config['y_label']['value']:
+            self.ax.set_ylabel(self.config['y_label']['value'])
+        else:
+            self.ax.set_ylabel(label)
    
     
 
    [docs]    def legend(self, 
                 labels:List[str]=None):
@@ -1557,11 +1637,12 @@ 
    Source code for pyprocar.plotter.dos_plot
             if labels == None:
             labels = self.labels
         if self.config['legend']['value'] and len(labels) != 0:
+            if len(self.handles) != len(labels):
+                raise ValueError(f"The number of labels and handles should be the same, currently there are {len(self.handles)} handles and {len(labels)} labels")
             self.ax.legend(self.handles, labels)
         return None
    
 
-
    [docs]    def draw_fermi(self, 
-                orientation:str='horizontal'):
+
    [docs]    def draw_fermi(self,value, orientation:str='horizontal'):
         """A method to draw the fermi surface
 
         Parameters
@@ -1581,11 +1662,11 @@ 
    Source code for pyprocar.plotter.dos_plot
                 None
         """
         if orientation == 'horizontal':
-            self.ax.axvline(x=0, color=self.config['fermi_color']['value'], 
+            self.ax.axvline(x=value, color=self.config['fermi_color']['value'], 
                                 linestyle=self.config['fermi_linestyle']['value'], 
                                 linewidth=self.config['fermi_linewidth']['value'])
         elif orientation == 'vertical':
-            self.ax.axhline(y=0, color=self.config['fermi_color']['value'], 
+            self.ax.axhline(y=value, color=self.config['fermi_color']['value'], 
                         linestyle=self.config['fermi_linestyle']['value'], 
                         linewidth=self.config['fermi_linewidth']['value'])
         return None
    
diff --git a/docs/_modules/pyprocar/plotter/ebs_plot.html b/docs/_modules/pyprocar/plotter/ebs_plot.html
index f94e5db0..224317b4 100644
--- a/docs/_modules/pyprocar/plotter/ebs_plot.html
+++ b/docs/_modules/pyprocar/plotter/ebs_plot.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.plotter.ebs_plot — PyProcar 6.1.8 documentation
+    pyprocar.plotter.ebs_plot — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.8 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
diff --git a/docs/_modules/pyprocar/plotter/procarplot.html b/docs/_modules/pyprocar/plotter/procarplot.html
index 3c554195..e3b9c26a 100644
--- a/docs/_modules/pyprocar/plotter/procarplot.html
+++ b/docs/_modules/pyprocar/plotter/procarplot.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.plotter.procarplot — PyProcar 6.1.7 documentation
+    pyprocar.plotter.procarplot — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
diff --git a/docs/_modules/pyprocar/pyposcar/poscar.html b/docs/_modules/pyprocar/pyposcar/poscar.html
index 6e30c046..58a23712 100644
--- a/docs/_modules/pyprocar/pyposcar/poscar.html
+++ b/docs/_modules/pyprocar/pyposcar/poscar.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.pyposcar.poscar — PyProcar 6.1.7 documentation
+    pyprocar.pyposcar.poscar — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
diff --git a/docs/_modules/pyprocar/pyposcar/poscarUtils.html b/docs/_modules/pyprocar/pyposcar/poscarUtils.html
index bcff0014..f1bd5716 100644
--- a/docs/_modules/pyprocar/pyposcar/poscarUtils.html
+++ b/docs/_modules/pyprocar/pyposcar/poscarUtils.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.pyposcar.poscarUtils — PyProcar 6.1.7 documentation
+    pyprocar.pyposcar.poscarUtils — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
diff --git a/docs/_modules/pyprocar/scripts/scriptBandGap.html b/docs/_modules/pyprocar/scripts/scriptBandGap.html
index 7f001877..d78c04b2 100644
--- a/docs/_modules/pyprocar/scripts/scriptBandGap.html
+++ b/docs/_modules/pyprocar/scripts/scriptBandGap.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.scripts.scriptBandGap — PyProcar 6.1.7 documentation
+    pyprocar.scripts.scriptBandGap — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
diff --git a/docs/_modules/pyprocar/scripts/scriptBandsDosplot.html b/docs/_modules/pyprocar/scripts/scriptBandsDosplot.html
index 0a7b6bb0..83e54120 100644
--- a/docs/_modules/pyprocar/scripts/scriptBandsDosplot.html
+++ b/docs/_modules/pyprocar/scripts/scriptBandsDosplot.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.scripts.scriptBandsDosplot — PyProcar 6.1.7 documentation
+    pyprocar.scripts.scriptBandsDosplot — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
diff --git a/docs/_modules/pyprocar/scripts/scriptBandsplot.html b/docs/_modules/pyprocar/scripts/scriptBandsplot.html
index 1fb15d12..a47e2aa8 100644
--- a/docs/_modules/pyprocar/scripts/scriptBandsplot.html
+++ b/docs/_modules/pyprocar/scripts/scriptBandsplot.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.scripts.scriptBandsplot — PyProcar 6.1.7 documentation
+    pyprocar.scripts.scriptBandsplot — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
@@ -457,6 +457,7 @@ 
    Source code for pyprocar.scripts.scriptBandsplot
    
     orbitals:List[int]=None,
     items:dict={},
     fermi:float=None,
+    fermi_shift:float=0,
     interpolation_factor:int=1,
     interpolation_type:str="cubic",
     projection_mask:np.ndarray=None,
@@ -489,7 +490,10 @@ 
    Source code for pyprocar.scripts.scriptBandsplot
    
     items : dict, optional
         A dictionary where the keys are the atoms and the values a list of orbitals, by default {}
     fermi : float, optional
-        Float for the fermi energy, by default None
+        Float for the fermi energy, by default None. By default the fermi energy will be shifted by the fermi value that is found in the directory. 
+        For band structure calculations, due to convergence issues, this fermi energy might not be accurate. If so add the fermi energy from the self-consistent calculation. 
+    fermi_shift : float, optional
+        Float to shift the fermi energy, by default 0.
     interpolation_factor : int, optional
         The interpolation_factor, by default 1
     interpolation_type : str, optional
@@ -516,13 +520,13 @@ 
    Source code for pyprocar.scripts.scriptBandsplot
    
            "overlay", "overlay_species", "overlay_orbitals", "ipr"]
     modes_txt=' , '.join(modes)
     message=f"""
-            --------------------------------------------------------
-            There are additional plot options that are defined in a configuration file. 
-            You can change these configurations by passing the keyword argument to the function
-            To print a list of plot options set print_plot_opts=True
+            ----------------------------------------------------------------------------------------------------------
+            There are additional plot options that are defined in the configuration file. 
+            You can change these configurations by passing the keyword argument to the function.
+            To print a list of all plot options set `print_plot_opts=True`
 
             Here is a list modes : {modes_txt}
-            --------------------------------------------------------
+            ----------------------------------------------------------------------------------------------------------
             """
     print(message)
     if print_plot_opts:
@@ -534,14 +538,20 @@ 
    Source code for pyprocar.scripts.scriptBandsplot
    
     structure = parser.structure
     kpath = parser.kpath
 
-    # shifting fermi to 0
-    ebs.bands -= ebs.efermi
-    if fermi:
-        ebs.bands += fermi
-        fermi_level = fermi
+    if fermi is not None:
+        ebs.bands -= fermi
+        ebs.bands += fermi_shift
+        fermi_level = fermi_shift
+        y_label=r"E - E$_F$ (eV)"
     else:
-        fermi_level = 0
+        y_label=r"E (eV)"
+        print("""
+            WARNING : `fermi` is not set! Set `fermi={value}`. The plot did not shift the bands by the Fermi energy.
+            ----------------------------------------------------------------------------------------------------------
+            """)
+    
 
+    
 
     # fixing the spin, to plot two channels into one (down is negative)
     if np.array_equal(spins, [-1,1]) or np.array_equal(spins, [1,-1]):
@@ -700,8 +710,11 @@ 
    Source code for pyprocar.scripts.scriptBandsplot
    
     ebs_plot.set_yticks(interval=elimit)
     ebs_plot.set_xlim()
     ebs_plot.set_ylim(elimit)
-    ebs_plot.draw_fermi(fermi_level=fermi_level)
-    ebs_plot.set_ylabel()
+    ebs_plot.set_ylabel(label=y_label)
+
+    if fermi is not None:
+        ebs_plot.draw_fermi(fermi_level=fermi_level)
+    
 
 
     ebs_plot.set_title()
diff --git a/docs/_modules/pyprocar/scripts/scriptCat.html b/docs/_modules/pyprocar/scripts/scriptCat.html
index ee77821a..2a890ff3 100644
--- a/docs/_modules/pyprocar/scripts/scriptCat.html
+++ b/docs/_modules/pyprocar/scripts/scriptCat.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.scripts.scriptCat — PyProcar 6.1.7 documentation
+    pyprocar.scripts.scriptCat — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
diff --git a/docs/_modules/pyprocar/scripts/scriptDosplot.html b/docs/_modules/pyprocar/scripts/scriptDosplot.html
index 50357a47..48a7e5c7 100644
--- a/docs/_modules/pyprocar/scripts/scriptDosplot.html
+++ b/docs/_modules/pyprocar/scripts/scriptDosplot.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.scripts.scriptDosplot — PyProcar 6.1.7 documentation
+    pyprocar.scripts.scriptDosplot — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
@@ -458,9 +458,11 @@ 
    Source code for pyprocar.scripts.scriptDosplot
    orbitals:List[int]=None,
         items:dict={},
         fermi:float=None,
+        fermi_shift:float=0,
         elimit:List[float]=None,
         dos_limit:List[float]=None,
         savefig:str=None,
+        labels:List[str]=None,
         projection_mask=None,
         ax:plt.Axes=None,
         show:bool=True,
@@ -586,6 +588,12 @@ 
    Source code for pyprocar.scripts.scriptDosplot
           e.g. ``dos_limit=[0, 30]``
 
+    labels : list str, optional
+        ``labels`` is a list of strings that will be used as the
+        legend of the plot. The length of the list should be equal to
+        the number of curves being plotted. If not provided the
+        default labels will be used.
+
     savefig : str , optional (default None)
         ``savefig`` defines the file that the plot is going to be
         saved in. ``savefig`` accepts all the formats accepted by
@@ -625,6 +633,11 @@ 
    Source code for pyprocar.scripts.scriptDosplot
            d orbitals in V.
         The default is set to take every atom and every orbital. Which
         will be equivalent to ``mode='stack_species'``
+    
+    fermi : float, optional
+        ``fermi`` defines the fermi energy. If not provided the
+        fermi energy will be read from the calculation directory
+
 
     ax : matplotlib ax object, optional
         ``ax`` is a matplotlib axes. In case one wants to put plot
@@ -678,8 +691,7 @@ 
    Source code for pyprocar.scripts.scriptDosplot
                To print a list of plot options set print_plot_opts=True
 
             Here is a list modes : {modes_txt}
-            --------------------------------------------------------
-            """
+            --------------------------------------------------------"""
     print(message)
     if print_plot_opts:
         for key,value in plot_opts.items():
@@ -696,6 +708,19 @@ 
    Source code for pyprocar.scripts.scriptDosplot
    dos = parser.dos
     structure = parser.structure
 
+    if fermi is not None:
+        dos.energies -= fermi
+        dos.energies += fermi_shift
+        fermi_level = fermi_shift
+        energy_label=r"Energy - E$_F$ (eV)"
+    else:
+        energy_label=r"Energy (eV)"
+        print("""
+            WARNING : `fermi` is not set! Set `fermi={value}`. The plot did not shift the energy by the Fermi energy.
+            ----------------------------------------------------------------------------------------------------------
+            """)
+
+
     if elimit is None:
         elimit = [dos.energies.min(), dos.energies.max()]
     
@@ -740,38 +765,70 @@ 
    Source code for pyprocar.scripts.scriptDosplot
    orbitals=orbitals,
             orientation=orientation,
         )
-
     elif mode == "stack_orbitals":
         edos_plot.plot_stack_orbitals(
             spins=spins,
             atoms=atoms,
             orientation=orientation,
         )
-
     elif mode == "stack":
         edos_plot.plot_stack(
             spins=spins,
             items=items,
             orientation=orientation,
         )
+    elif mode == "overlay_species":
+        edos_plot.plot_stack_species(
+            spins=spins,
+            orbitals=orbitals,
+            orientation=orientation,
+            overlay_mode=True
+        )
+    elif mode == "overlay_orbitals":
+        edos_plot.plot_stack_orbitals(
+            spins=spins,
+            atoms=atoms,
+            orientation=orientation,
+            overlay_mode=True
+        )
+    elif mode == "overlay":
+        edos_plot.plot_stack(
+            spins=spins,
+            items=items,
+            orientation=orientation,
+            overlay_mode=True
+        )
     else:
         raise ValueError("The mode needs to be in the List [plain,parametric,parametric_line,stack_species,stack_orbitals,stack]")
 
-    edos_plot.draw_fermi(orientation = orientation)
+    if fermi is not None:
+        edos_plot.draw_fermi(fermi_level, orientation = orientation)
 
+    
     if orientation == 'horizontal':
+        edos_plot.set_xlabel(label=energy_label)
+        edos_plot.set_ylabel(label="DOS")
         if elimit is not None:
             edos_plot.set_xlim(elimit)
         if dos_limit is not None:
             edos_plot.set_ylim(dos_limit)
-    elif orientation == 'vertical' :
+
+    elif orientation == 'vertical':
+        edos_plot.set_xlabel(label="DOS")
+        edos_plot.set_ylabel(label=energy_label)
         if elimit is not None:
             edos_plot.set_ylim(elimit)
         if dos_limit is not None:
             edos_plot.set_xlim(dos_limit)
 
     edos_plot.grid()
-    edos_plot.legend(edos_plot.labels)
+
+    if labels:
+        labels=labels
+    else:
+        labels=edos_plot.labels
+    edos_plot.legend(labels)
+
     if savefig is not None:
         edos_plot.save(savefig)
     if show:
diff --git a/docs/_modules/pyprocar/scripts/scriptFermi2D.html b/docs/_modules/pyprocar/scripts/scriptFermi2D.html
index afa95597..cf016036 100644
--- a/docs/_modules/pyprocar/scripts/scriptFermi2D.html
+++ b/docs/_modules/pyprocar/scripts/scriptFermi2D.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.scripts.scriptFermi2D — PyProcar 6.1.7 documentation
+    pyprocar.scripts.scriptFermi2D — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
@@ -448,10 +448,12 @@ 
    Source code for pyprocar.scripts.scriptFermi2D
    with open(os.path.join(ROOT,'pyprocar','cfg','fermi_surface_2d.yml'), 'r') as file:
     plot_opt = yaml.safe_load(file)
 
-
    [docs]def fermi2D(
+
    [docs]def fermi2D(
     code:str,
     dirname:str,
     mode:str='plain',
+    fermi:float=None,
+    fermi_shift:float=0.0,
     band_indices:List[List]=None,
     band_colors:List[List]=None,
     spins:List[int]=None,
@@ -477,6 +479,10 @@ 
    Source code for pyprocar.scripts.scriptFermi2D
            This parameter sets the code to parse, by default "vasp"
     dirname : str, optional
         This parameter is the directory of the calculation, by default ''
+    fermi : float, optional
+        The fermi energy. If none is given, the fermi energy in the directory will be used, by default None
+    fermi_shift : float, optional
+        The fermi energy shift, by default 0.0
     lobster : bool, optional
         A boolean value to determine to use lobster, by default False
     band_indices : List[List]
@@ -562,7 +568,24 @@ 
    Source code for pyprocar.scripts.scriptFermi2D
    parser = io.Parser(code = code, dir = dirname)
     ebs = parser.ebs
     structure = parser.structure
-    ebs.bands -= ebs.efermi
+
+    if fermi is not None:
+        ebs.bands -= fermi
+        ebs.bands += fermi_shift
+        fermi_level = fermi_shift
+    else:
+        print("""
+            WARNING : `fermi` is not set! Set `fermi={value}`. The plot did not shift the bands by the Fermi energy.
+            ----------------------------------------------------------------------------------------------------------
+            """)
+    print(
+        f"""
+            WARNING : Make sure the kmesh has kz points with kz={k_z_plane} +- {k_z_plane_tol}
+            ----------------------------------------------------------------------------------------------------------
+            """
+    )
+
+
 
     if structure.rotations is not None:
         ebs.ibz2fbz(structure.rotations)
diff --git a/docs/_modules/pyprocar/scripts/scriptFermiHandler.html b/docs/_modules/pyprocar/scripts/scriptFermiHandler.html
index a85b61ec..b06e5515 100644
--- a/docs/_modules/pyprocar/scripts/scriptFermiHandler.html
+++ b/docs/_modules/pyprocar/scripts/scriptFermiHandler.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.scripts.scriptFermiHandler — PyProcar 6.1.7 documentation
+    pyprocar.scripts.scriptFermiHandler — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
@@ -454,6 +454,7 @@ 
    Source code for pyprocar.scripts.scriptFermiHandler
    [docs]    def __init__(self, 
             code:str,
             dirname:str="",
+            fermi:float=None,
             repair:bool=False,
             apply_symmetry:bool=True,
             ):
@@ -467,6 +468,8 @@ 
    Source code for pyprocar.scripts.scriptFermiHandler
                The code name
         dirname : str, optional
             the directory name where the calculation is, by default ""
+        fermi : float, optional
+            The fermi energy. This will overide the default fermi value used found in the given directory, by default None
         repair : bool, optional
             Boolean to repair the PROCAR file, by default False
         apply_symmetry : bool, optional
@@ -479,7 +482,20 @@ 
    Source code for pyprocar.scripts.scriptFermiHandler
    self.apply_symmetry = apply_symmetry
         parser = io.Parser(code = code, dir = dirname)
         self.ebs = parser.ebs
-        self.e_fermi = parser.ebs.efermi
+
+
+        if fermi is None:
+            self.e_fermi=self.ebs.efermi
+            print("""
+                WARNING : Fermi Energy not set! Set `fermi={value}`. By default, using fermi energy found in given directory.
+                ---------------------------------------------------------------------------------------------------------------
+                """
+            )
+        else:
+            self.e_fermi=fermi
+
+
+
         self.structure = parser.structure
         if self.structure.rotations is not None:
             self.ebs.ibz2fbz(self.structure.rotations)
diff --git a/docs/_modules/pyprocar/scripts/scriptFilter.html b/docs/_modules/pyprocar/scripts/scriptFilter.html
index dcaf717e..3273b390 100644
--- a/docs/_modules/pyprocar/scripts/scriptFilter.html
+++ b/docs/_modules/pyprocar/scripts/scriptFilter.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.scripts.scriptFilter — PyProcar 6.1.7 documentation
+    pyprocar.scripts.scriptFilter — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
diff --git a/docs/_modules/pyprocar/scripts/scriptKmesh2D.html b/docs/_modules/pyprocar/scripts/scriptKmesh2D.html
index 7536dc2f..a4b0c745 100644
--- a/docs/_modules/pyprocar/scripts/scriptKmesh2D.html
+++ b/docs/_modules/pyprocar/scripts/scriptKmesh2D.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.scripts.scriptKmesh2D — PyProcar 6.1.7 documentation
+    pyprocar.scripts.scriptKmesh2D — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
diff --git a/docs/_modules/pyprocar/scripts/scriptKpath.html b/docs/_modules/pyprocar/scripts/scriptKpath.html
index 04de68bf..70ee95a2 100644
--- a/docs/_modules/pyprocar/scripts/scriptKpath.html
+++ b/docs/_modules/pyprocar/scripts/scriptKpath.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.scripts.scriptKpath — PyProcar 6.1.7 documentation
+    pyprocar.scripts.scriptKpath — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
diff --git a/docs/_modules/pyprocar/scripts/scriptRepair.html b/docs/_modules/pyprocar/scripts/scriptRepair.html
index 745f0cd3..44cd6dca 100644
--- a/docs/_modules/pyprocar/scripts/scriptRepair.html
+++ b/docs/_modules/pyprocar/scripts/scriptRepair.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.scripts.scriptRepair — PyProcar 6.1.7 documentation
+    pyprocar.scripts.scriptRepair — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
diff --git a/docs/_modules/pyprocar/scripts/scriptUnfold.html b/docs/_modules/pyprocar/scripts/scriptUnfold.html
index ae9c49b2..c5de2f95 100644
--- a/docs/_modules/pyprocar/scripts/scriptUnfold.html
+++ b/docs/_modules/pyprocar/scripts/scriptUnfold.html
@@ -7,7 +7,7 @@
   
     
     
-    pyprocar.scripts.scriptUnfold — PyProcar 6.1.7 documentation
+    pyprocar.scripts.scriptUnfold — PyProcar 6.1.9 documentation
   
   
   
@@ -39,7 +39,7 @@
   
 
 
-    
+    
     
     
     
@@ -109,7 +109,7 @@
   
   
   
-    
    PyProcar 6.1.7 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
@@ -456,6 +456,7 @@ 
    Source code for pyprocar.scripts.scriptUnfold
    unfold_mask=None,
 
         fermi=None,
+        fermi_shift=0,
         interpolation_factor=1,
         interpolation_type="cubic",
         vmax=None,
@@ -482,7 +483,8 @@ 
    Source code for pyprocar.scripts.scriptUnfold
            supercell_matrix: supercell matrix from primitive cell to supercell
         ispin: For non-spin polarized system, ispin=None.
            For spin polarized system: ispin=1 is spin up, ispin=2 is spin down.
-        efermi: Fermi energy
+        fermi: Fermi energy
+        fermi_shift: Shift the bands by the Fermi energy.
         elimit: range of energy to be plotted.
         kticks: the indices of K points which has labels given in knames.
         knames: see kticks
@@ -518,13 +520,17 @@ 
    Source code for pyprocar.scripts.scriptUnfold
    structure = parser.structure
     kpath = parser.kpath
 
-    # shifting fermi to 0
-    ebs.bands -= ebs.efermi
-    if fermi:
-        ebs.bands += fermi
-        fermi_level = fermi
+    if fermi is not None:
+        ebs.bands -= fermi
+        ebs.bands += fermi_shift
+        fermi_level = fermi_shift
+        y_label=r"E - E$_F$ (eV)"
     else:
-        fermi_level = 0
+        y_label=r"E (eV)"
+        print("""
+            WARNING : `fermi` is not set! Set `fermi={value}`. The plot did not shift the bands by the Fermi energy.
+            ----------------------------------------------------------------------------------------------------------
+            """)
 
     ebs_plot = EBSPlot(ebs, kpath, ax, spins)
     
@@ -675,8 +681,10 @@ 
    Source code for pyprocar.scripts.scriptUnfold
    ebs_plot.set_yticks(interval=elimit)
     ebs_plot.set_xlim()
     ebs_plot.set_ylim(elimit)
-    ebs_plot.draw_fermi(fermi_level=fermi_level)
-    ebs_plot.set_ylabel()
+    if fermi is not None:
+        ebs_plot.draw_fermi(fermi_level=fermi_level)
+    ebs_plot.set_ylabel(label=y_label)
+
     ebs_plot.grid()
     ebs_plot.legend(labels)
     if savefig is not None:
diff --git a/docs/_sources/api/cfg/band_structure_2d.rst.txt b/docs/_sources/api/cfg/band_structure_2d.rst.txt
index 045aa379..888cbde1 100644
--- a/docs/_sources/api/cfg/band_structure_2d.rst.txt
+++ b/docs/_sources/api/cfg/band_structure_2d.rst.txt
@@ -187,7 +187,7 @@ y_axes_label
 z_axes_label
 ------------
 
-:value: Kz
+:value: E
 
 :description: Controls kz axis label
 
@@ -376,6 +376,14 @@ grid_ztitle
 :description: Controls x axis of the grid
 
 
+grid_font_size
+--------------
+
+:value: 10
+
+:description: Controls the font size of the grid
+
+
 add_fermi_plane
 ---------------
 
diff --git a/docs/_sources/api/cfg/dos.rst.txt b/docs/_sources/api/cfg/dos.rst.txt
index 97b33b9a..ff6ae50e 100644
--- a/docs/_sources/api/cfg/dos.rst.txt
+++ b/docs/_sources/api/cfg/dos.rst.txt
@@ -293,7 +293,7 @@ x_label
 
 :description: The label for the x-axis.
 
-:value: Energy (eV)
+:value: None
 
 
 y_label
@@ -301,7 +301,7 @@ y_label
 
 :description: The label for the y-axis.
 
-:value: DOS
+:value: None
 
 
 dpi
diff --git a/docs/_sources/api/core/_autosummary/pyprocar.core.BrillouinZone.rst.txt b/docs/_sources/api/core/_autosummary/pyprocar.core.BrillouinZone.rst.txt
index fd46e097..1ecdf0b1 100644
--- a/docs/_sources/api/core/_autosummary/pyprocar.core.BrillouinZone.rst.txt
+++ b/docs/_sources/api/core/_autosummary/pyprocar.core.BrillouinZone.rst.txt
@@ -502,18 +502,6 @@
         
       
       
-        
-      
-      
-        
-      
-      
-        
-      
-      
-        
-      
-      
         
       
       
@@ -824,6 +812,9 @@
       
       
       
+      
+      
+      
       
       
       
diff --git a/docs/_sources/api/core/_autosummary/pyprocar.core.FermiSurface3D.rst.txt b/docs/_sources/api/core/_autosummary/pyprocar.core.FermiSurface3D.rst.txt
index f5f280e4..206810a0 100644
--- a/docs/_sources/api/core/_autosummary/pyprocar.core.FermiSurface3D.rst.txt
+++ b/docs/_sources/api/core/_autosummary/pyprocar.core.FermiSurface3D.rst.txt
@@ -173,11 +173,7 @@
       
       
         
-      
-      
-        
-      
-      
+          FermiSurface3D.extend_surface
         
       
       
@@ -194,8 +190,6 @@
       
       
         
-          FermiSurface3D.extend_surface
-        
       
       
         
@@ -352,34 +346,30 @@
       
       
         
-      
-      
+          FermiSurface3D.project_atomic_projections
         
       
       
         
-      
-      
+          FermiSurface3D.project_fermi_speed
         
       
       
         
-          FermiSurface3D.project_atomic_projections
+          FermiSurface3D.project_fermi_velocity
         
       
       
         
-          FermiSurface3D.project_fermi_speed
+          FermiSurface3D.project_harmonic_effective_mass
         
       
       
         
-          FermiSurface3D.project_fermi_velocity
-        
       
       
         
-          FermiSurface3D.project_harmonic_effective_mass
+          FermiSurface3D.project_spin_texture_atomic_projections
         
       
       
@@ -387,8 +377,6 @@
       
       
         
-          FermiSurface3D.project_spin_texture_atomic_projections
-        
       
       
         
@@ -849,6 +837,9 @@
       
       
       
+      
+      
+      
       
       
       
diff --git a/docs/_sources/api/core/_autosummary/pyprocar.core.Isosurface.rst.txt b/docs/_sources/api/core/_autosummary/pyprocar.core.Isosurface.rst.txt
index 9b9402da..60dddc2b 100644
--- a/docs/_sources/api/core/_autosummary/pyprocar.core.Isosurface.rst.txt
+++ b/docs/_sources/api/core/_autosummary/pyprocar.core.Isosurface.rst.txt
@@ -500,18 +500,6 @@
       
       
         
-      
-      
-        
-      
-      
-        
-      
-      
-        
-      
-      
-        
       
       
         
@@ -805,6 +793,7 @@
       
       
       
+      
       
       
         
@@ -851,6 +840,8 @@
       
       
       
+      
+      
         
           Isosurface.surface_boundaries
         
diff --git a/docs/_sources/api/core/_autosummary/pyprocar.core.Surface.rst.txt b/docs/_sources/api/core/_autosummary/pyprocar.core.Surface.rst.txt
index 7e8b6537..2269f964 100644
--- a/docs/_sources/api/core/_autosummary/pyprocar.core.Surface.rst.txt
+++ b/docs/_sources/api/core/_autosummary/pyprocar.core.Surface.rst.txt
@@ -170,11 +170,7 @@
       
       
         
-      
-      
-        
-      
-      
+          Surface.export
         
       
       
@@ -191,8 +187,6 @@
       
       
         
-          Surface.export
-        
       
       
         
@@ -424,30 +418,24 @@
       
       
         
-      
-      
+          Surface.set_color_with_cmap
         
       
       
         
-      
-      
+          Surface.set_scalars
         
       
       
         
-          Surface.set_color_with_cmap
+          Surface.set_vectors
         
       
       
         
-          Surface.set_scalars
-        
       
       
         
-          Surface.set_vectors
-        
       
       
         
@@ -803,6 +791,7 @@
       
       
       
+      
       
       
         
@@ -836,6 +825,8 @@
       
       
       
+      
+      
       
       
       
diff --git a/docs/_sources/api/scripts/index.rst.txt b/docs/_sources/api/scripts/index.rst.txt
index a8c4abf1..ece240ac 100644
--- a/docs/_sources/api/scripts/index.rst.txt
+++ b/docs/_sources/api/scripts/index.rst.txt
@@ -14,11 +14,6 @@ PyProcar has the following data types:
     Depending on the mode, the user may have to provide more information. 
     For instance is mode='parametric', the user must provide the atoms, orbitald, and spins to include
 
-- :func:`pyprocar.bandsplot_2d` plots the 2d band structure.
-    The user must provide the directory where the calculation takes place and some case specific files used. 
-    Depending on the mode, the user may have to provide more information. 
-    For instance is mode='parametric', the user must provide the atoms, orbitald, and spins to include
-
 - :func:`pyprocar.dosplot` plots the density of states.
     The user must provide the directory where the calculation takes place and some case specific files used. 
     Depending on the mode, the user may have to provide more information. 
@@ -30,8 +25,6 @@ PyProcar has the following data types:
 
 - :func:`pyprocar.fermi2d` plots the 2d fermi surface.
 
-- :func:`pyprocar.fermi3d` plots the 3d fermi surface.
-
 - :class:`pyprocar.FermiHandler` plots 3d fermi surface
 
 - :func:`pyprocar.generate2dkmesh` generates a 2d kmesh
@@ -45,12 +38,10 @@ PyProcar has the following data types:
 
     bandgap
     bandsplot
-    bandsplot_2d
     bandsdosplot
     cat
     dosplot
     fermi2d
-    fermi3d
     fermihandler
     generate2dkmesh
     kpath
diff --git a/docs/_sources/examples/00-band_structure/index.rst.txt b/docs/_sources/examples/00-band_structure/index.rst.txt
index 45d477a1..3a688a18 100644
--- a/docs/_sources/examples/00-band_structure/index.rst.txt
+++ b/docs/_sources/examples/00-band_structure/index.rst.txt
@@ -32,69 +32,69 @@ These examples demonstrate the band structure plotting capabilities.
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_noncolinear_vasp_thumb.png
+  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_compare_bands_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_00-band_structure_plot_noncolinear_vasp.py`
+  :ref:`sphx_glr_examples_00-band_structure_plot_compare_bands.py`
 
 .. raw:: html
 
-      
    Plotting non colinear band structures in VASP
    
+      
    Comparing band structures
    
     
    
 
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_compare_bands_thumb.png
+  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_atomic_levels_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_00-band_structure_plot_compare_bands.py`
+  :ref:`sphx_glr_examples_00-band_structure_plot_atomic_levels.py`
 
 .. raw:: html
 
-      
    Comparing band structures
    
+      
    Plotting Atomic Levels
    
     
    
 
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_noncolinear_qe_thumb.png
+  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_noncolinear_vasp_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_00-band_structure_plot_noncolinear_qe.py`
+  :ref:`sphx_glr_examples_00-band_structure_plot_noncolinear_vasp.py`
 
 .. raw:: html
 
-      
    Plotting non colinear band structures in Quantum Espresso
    
+      
    Plotting non colinear band structures in VASP
    
     
    
 
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_atomic_levels_thumb.png
+  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_noncolinear_qe_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_00-band_structure_plot_atomic_levels.py`
+  :ref:`sphx_glr_examples_00-band_structure_plot_noncolinear_qe.py`
 
 .. raw:: html
 
-      
    Plotting Atomic Levels
    
+      
    Plotting non colinear band structures in Quantum Espresso
    
     
    
 
 
@@ -168,35 +168,35 @@ These examples demonstrate the band structure plotting capabilities.
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_2d_bands_thumb.png
+  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_bandsplot_configurations_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_00-band_structure_plot_2d_bands.py`
+  :ref:`sphx_glr_examples_00-band_structure_plot_bandsplot_configurations.py`
 
 .. raw:: html
 
-      
    Plotting 2D band structure
    
+      
    Plotting with Configurations in pyprocar
    
     
    
 
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_bandsplot_configurations_thumb.png
+  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_2d_bands_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_00-band_structure_plot_bandsplot_configurations.py`
+  :ref:`sphx_glr_examples_00-band_structure_plot_2d_bands.py`
 
 .. raw:: html
 
-      
    Plotting with Configurations in pyprocar
    
+      
    Plotting 2D band structure
    
     
    
 
 
@@ -209,14 +209,14 @@ These examples demonstrate the band structure plotting capabilities.
    :hidden:
 
    /examples/00-band_structure/plot_autobands
-   /examples/00-band_structure/plot_noncolinear_vasp
    /examples/00-band_structure/plot_compare_bands
-   /examples/00-band_structure/plot_noncolinear_qe
    /examples/00-band_structure/plot_atomic_levels
+   /examples/00-band_structure/plot_noncolinear_vasp
+   /examples/00-band_structure/plot_noncolinear_qe
    /examples/00-band_structure/plot_ipr
    /examples/00-band_structure/plot_unfolding
    /examples/00-band_structure/plot_spin_polarized
    /examples/00-band_structure/plot_colinear
-   /examples/00-band_structure/plot_2d_bands
    /examples/00-band_structure/plot_bandsplot_configurations
+   /examples/00-band_structure/plot_2d_bands
 
diff --git a/docs/_sources/examples/00-band_structure/plot_2d_bands.rst.txt b/docs/_sources/examples/00-band_structure/plot_2d_bands.rst.txt
index de11f316..409656d9 100644
--- a/docs/_sources/examples/00-band_structure/plot_2d_bands.rst.txt
+++ b/docs/_sources/examples/00-band_structure/plot_2d_bands.rst.txt
@@ -63,12 +63,16 @@ importing pyprocar and specifying local data_dir
 Plain mode
 +++++++++++++++++++++++++++++++++++++++
 
-.. GENERATED FROM PYTHON SOURCE LINES 36-46
+.. GENERATED FROM PYTHON SOURCE LINES 36-50
 
 .. code-block:: default
 
     spins=[0]
-    handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,apply_symmetry=False)
+    handler = pyprocar.BandStructure2DHandler(code='vasp',
+                                              dirname=data_dir,
+                                              fermi=-0.795606,
+                                              apply_symmetry=False,
+                                              )
     handler.plot_band_structure(mode='plain',
                                 add_fermi_plane=True,
                                 bands=[3,4],
@@ -91,14 +95,14 @@ Plain mode
  .. code-block:: none
 
 
-                    --------------------------------------------------------
+                    ----------------------------------------------------------------------------------------------------------
                     There are additional plot options that are defined in a configuration file. 
                     You can change these configurations by passing the keyword argument to the function
                     To print a list of plot options set print_plot_opts=True
 
                     Here is a list modes : plain , parametric , spin_texture , overlay
                     Here is a list of properties: fermi_speed , fermi_velocity , harmonic_effective_mass
-                    --------------------------------------------------------
+                    ----------------------------------------------------------------------------------------------------------
                 
     Bands used in the plotting:  [3, 4]
     Z:\Research Projects\pyprocar\venv_docs\lib\site-packages\pyvista\core\utilities\points.py:52: UserWarning: Points is not a float type. This can cause issues when transforming or applying filters. Casting to ``np.float32``. Disable this by passing ``force_float=False``.
@@ -107,12 +111,12 @@ Plain mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 47-49
+.. GENERATED FROM PYTHON SOURCE LINES 51-53
 
 Parametric mode
 +++++++++++++++++++++++++++++++++++++++
 
-.. GENERATED FROM PYTHON SOURCE LINES 49-59
+.. GENERATED FROM PYTHON SOURCE LINES 53-63
 
 .. code-block:: default
 
@@ -120,7 +124,7 @@ Parametric mode
     atoms=[0,1]
     orbitals=[1,2,3]
     spins=[0]
-    handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,apply_symmetry=False)
+    handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,fermi=-0.795606,apply_symmetry=False)
     handler.plot_band_structure(mode='parametric',
                                atoms=atoms,
                                orbitals=orbitals,
@@ -140,30 +144,30 @@ Parametric mode
  .. code-block:: none
 
 
-                    --------------------------------------------------------
+                    ----------------------------------------------------------------------------------------------------------
                     There are additional plot options that are defined in a configuration file. 
                     You can change these configurations by passing the keyword argument to the function
                     To print a list of plot options set print_plot_opts=True
 
                     Here is a list modes : plain , parametric , spin_texture , overlay
                     Here is a list of properties: fermi_speed , fermi_velocity , harmonic_effective_mass
-                    --------------------------------------------------------
+                    ----------------------------------------------------------------------------------------------------------
                 
     Bands used in the plotting:  [3, 4]
 
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 60-62
+.. GENERATED FROM PYTHON SOURCE LINES 64-66
 
 Property Projection mode
 +++++++++++++++++++++++++++++++++++++++
 
-.. GENERATED FROM PYTHON SOURCE LINES 62-72
+.. GENERATED FROM PYTHON SOURCE LINES 66-76
 
 .. code-block:: default
 
-    handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,apply_symmetry=False)
+    handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,fermi=-0.795606,apply_symmetry=False)
     handler.plot_band_structure(mode='property_projection',
                                property_name='band_velocity',
                                bands=[3,4],
@@ -187,14 +191,14 @@ Property Projection mode
  .. code-block:: none
 
 
-                    --------------------------------------------------------
+                    ----------------------------------------------------------------------------------------------------------
                     There are additional plot options that are defined in a configuration file. 
                     You can change these configurations by passing the keyword argument to the function
                     To print a list of plot options set print_plot_opts=True
 
                     Here is a list modes : plain , parametric , spin_texture , overlay
                     Here is a list of properties: fermi_speed , fermi_velocity , harmonic_effective_mass
-                    --------------------------------------------------------
+                    ----------------------------------------------------------------------------------------------------------
                 
     Bands used in the plotting:  [3, 4]
     Z:\Research Projects\pyprocar\venv_docs\lib\site-packages\pyvista\core\utilities\points.py:52: UserWarning: Points is not a float type. This can cause issues when transforming or applying filters. Casting to ``np.float32``. Disable this by passing ``force_float=False``.
@@ -203,12 +207,12 @@ Property Projection mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 73-75
+.. GENERATED FROM PYTHON SOURCE LINES 77-79
 
 Spin Texture mode
 +++++++++++++++++++++++++++++++++++++++
 
-.. GENERATED FROM PYTHON SOURCE LINES 75-95
+.. GENERATED FROM PYTHON SOURCE LINES 79-99
 
 .. code-block:: default
 
@@ -218,7 +222,7 @@ Spin Texture mode
 
     atoms=[0]
     orbitals=[4,5,6,7,8]
-    handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,apply_symmetry=False)
+    handler = pyprocar.BandStructure2DHandler(code='vasp',dirname=data_dir,fermi=-1.1904,apply_symmetry=False)
     handler.plot_band_structure(mode='spin_texture',
                                spin_texture=True,
                                atoms=atoms,
@@ -246,14 +250,14 @@ Spin Texture mode
  .. code-block:: none
 
 
-                    --------------------------------------------------------
+                    ----------------------------------------------------------------------------------------------------------
                     There are additional plot options that are defined in a configuration file. 
                     You can change these configurations by passing the keyword argument to the function
                     To print a list of plot options set print_plot_opts=True
 
                     Here is a list modes : plain , parametric , spin_texture , overlay
                     Here is a list of properties: fermi_speed , fermi_velocity , harmonic_effective_mass
-                    --------------------------------------------------------
+                    ----------------------------------------------------------------------------------------------------------
                 
     Bands used in the plotting:  [16, 17, 18, 19, 20, 21]
 
@@ -263,7 +267,7 @@ Spin Texture mode
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 3 minutes  31.780 seconds)
+   **Total running time of the script:** ( 3 minutes  13.652 seconds)
 
 
 .. _sphx_glr_download_examples_00-band_structure_plot_2d_bands.py:
diff --git a/docs/_sources/examples/00-band_structure/plot_atomic_levels.rst.txt b/docs/_sources/examples/00-band_structure/plot_atomic_levels.rst.txt
index 8911b23f..11a242e5 100644
--- a/docs/_sources/examples/00-band_structure/plot_atomic_levels.rst.txt
+++ b/docs/_sources/examples/00-band_structure/plot_atomic_levels.rst.txt
@@ -105,13 +105,17 @@ The plot will display energy levels for specific atoms in the range of -6 to 6 e
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
+            
+
+                WARNING : `fermi` is not set! Set `fermi={value}`. The plot did not shift the bands by the Fermi energy.
+                ----------------------------------------------------------------------------------------------------------
             
     z:\research projects\pyprocar\pyprocar\plotter\ebs_plot.py:607: UserWarning: Attempting to set identical low and high xlims makes transformation singular; automatically expanding.
       self.ax.set_xlim(interval)
@@ -119,14 +123,14 @@ The plot will display energy levels for specific atoms in the range of -6 to 6 e
     Atomic plot: spd.shape    : (2, 246, 98, 1, 9, 2)
     Atomic plot: kpoints.shape: (2, 3)
 
-    (
    , )
+    (
    , )
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  1.468 seconds)
+   **Total running time of the script:** ( 0 minutes  1.275 seconds)
 
 
 .. _sphx_glr_download_examples_00-band_structure_plot_atomic_levels.py:
diff --git a/docs/_sources/examples/00-band_structure/plot_autobands.rst.txt b/docs/_sources/examples/00-band_structure/plot_autobands.rst.txt
index 894929d3..ff8d5ff6 100644
--- a/docs/_sources/examples/00-band_structure/plot_autobands.rst.txt
+++ b/docs/_sources/examples/00-band_structure/plot_autobands.rst.txt
@@ -135,33 +135,41 @@ and the associated localized states.
     [[0, 0.953], [0, 0.956]]
     []
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
     2 orbitals. (Some of) They are unknow (if you did 'filter' them it is OK).
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                WARNING : `fermi` is not set! Set `fermi={value}`. The plot did not shift the bands by the Fermi energy.
+                ----------------------------------------------------------------------------------------------------------
+            
+
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
     2 orbitals. (Some of) They are unknow (if you did 'filter' them it is OK).
 
+                WARNING : `fermi` is not set! Set `fermi={value}`. The plot did not shift the bands by the Fermi energy.
+                ----------------------------------------------------------------------------------------------------------
+            
+
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  26.997 seconds)
+   **Total running time of the script:** ( 0 minutes  25.670 seconds)
 
 
 .. _sphx_glr_download_examples_00-band_structure_plot_autobands.py:
diff --git a/docs/_sources/examples/00-band_structure/plot_bandsplot_configurations.rst.txt b/docs/_sources/examples/00-band_structure/plot_bandsplot_configurations.rst.txt
index ca131f27..e4134f9e 100644
--- a/docs/_sources/examples/00-band_structure/plot_bandsplot_configurations.rst.txt
+++ b/docs/_sources/examples/00-band_structure/plot_bandsplot_configurations.rst.txt
@@ -80,7 +80,7 @@ Before diving into plotting, we need to download the example files. Use the foll
     print(f"Configuration files are located at: {config_path}")
 
     # Print the configurations
-    pyprocar.bandsplot(code=code,dirname=data_dir,print_plot_opts=True)
+    pyprocar.bandsplot(code=code,dirname=data_dir,fermi=5.590136,print_plot_opts=True)
 
 
 
@@ -97,13 +97,13 @@ Before diving into plotting, we need to download the example files. Use the foll
 
     Configuration files are located at: z:\research projects\pyprocar\pyprocar\cfg
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
     spin_colors : {'description': 'The colors for the plot lines.', 'value': ['blue', 'red']}
     color : {'description': 'The colors for the plot lines.', 'value': 'black'}
@@ -141,7 +141,7 @@ Before diving into plotting, we need to download the example files. Use the foll
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 53-75
+.. GENERATED FROM PYTHON SOURCE LINES 53-76
 
 .. code-block:: default
 
@@ -157,6 +157,7 @@ Before diving into plotting, we need to download the example files. Use the foll
         code=code,
         dirname=data_dir,
         mode='parametric',
+        fermi=5.590136,
         atoms=[0],
         orbitals=[4,5,6,7,8],
         cmap='viridis',  # Colormap
@@ -181,20 +182,20 @@ Before diving into plotting, we need to download the example files. Use the foll
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 76-93
+.. GENERATED FROM PYTHON SOURCE LINES 77-95
 
 .. code-block:: default
 
@@ -209,6 +210,7 @@ Before diving into plotting, we need to download the example files. Use the foll
         code=code,
         dirname=data_dir,
         mode='scatter',
+        fermi=5.590136,
         atoms=[0],
         orbitals=[4,5,6,7,8],
         marker=['v','o'],  # Marker style
@@ -229,20 +231,20 @@ Before diving into plotting, we need to download the example files. Use the foll
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 94-111
+.. GENERATED FROM PYTHON SOURCE LINES 96-114
 
 .. code-block:: default
 
@@ -257,6 +259,7 @@ Before diving into plotting, we need to download the example files. Use the foll
         code=code,
         dirname=data_dir,
         mode='scatter',
+        fermi=5.590136,
         atoms=[0],
         orbitals=[4,5,6,7,8],
         figure_size=(10, 6),  # Figure size (width, height)
@@ -277,13 +280,13 @@ Before diving into plotting, we need to download the example files. Use the foll
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
@@ -293,7 +296,7 @@ Before diving into plotting, we need to download the example files. Use the foll
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  2.839 seconds)
+   **Total running time of the script:** ( 0 minutes  2.716 seconds)
 
 
 .. _sphx_glr_download_examples_00-band_structure_plot_bandsplot_configurations.py:
diff --git a/docs/_sources/examples/00-band_structure/plot_colinear.rst.txt b/docs/_sources/examples/00-band_structure/plot_colinear.rst.txt
index 99ab26db..93f31101 100644
--- a/docs/_sources/examples/00-band_structure/plot_colinear.rst.txt
+++ b/docs/_sources/examples/00-band_structure/plot_colinear.rst.txt
@@ -62,7 +62,7 @@ importing pyprocar and specifying local data_dir
 Plain mode
 +++++++++++++++++++++++++++++++++++++++
 
-.. GENERATED FROM PYTHON SOURCE LINES 34-40
+.. GENERATED FROM PYTHON SOURCE LINES 34-41
 
 .. code-block:: default
 
@@ -70,6 +70,7 @@ Plain mode
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='plain',
+                    fermi=5.599480,
                     dirname=data_dir)
 
 
@@ -86,20 +87,20 @@ Plain mode
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 41-48
+.. GENERATED FROM PYTHON SOURCE LINES 42-49
 
 Parametric mode
 +++++++++++++++++++++++++++++++++++++++
@@ -109,7 +110,7 @@ For details on the meaning of the indices of the atomic projection please refer
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 48-60
+.. GENERATED FROM PYTHON SOURCE LINES 49-62
 
 .. code-block:: default
 
@@ -120,6 +121,7 @@ For details on the meaning of the indices of the atomic projection please refer
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='parametric',
+                    fermi=5.599480,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -139,20 +141,20 @@ For details on the meaning of the indices of the atomic projection please refer
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 61-68
+.. GENERATED FROM PYTHON SOURCE LINES 63-70
 
 parametric_linemode
 +++++++++++++++++++++++++++++++++++++++
@@ -162,7 +164,7 @@ For details on the meaning of the indices of the atomic projection please refer
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 68-82
+.. GENERATED FROM PYTHON SOURCE LINES 70-85
 
 .. code-block:: default
 
@@ -173,6 +175,7 @@ For details on the meaning of the indices of the atomic projection please refer
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='parametric',
+                    fermi=5.599480,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -194,20 +197,20 @@ For details on the meaning of the indices of the atomic projection please refer
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 83-88
+.. GENERATED FROM PYTHON SOURCE LINES 86-91
 
 Scatter mode
 +++++++++++++++++++++++++++++++++++++++
@@ -215,7 +218,7 @@ Scatter mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 88-101
+.. GENERATED FROM PYTHON SOURCE LINES 91-105
 
 .. code-block:: default
 
@@ -226,6 +229,7 @@ Scatter mode
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='scatter',
+                    fermi=5.599480,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -246,20 +250,20 @@ Scatter mode
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 102-107
+.. GENERATED FROM PYTHON SOURCE LINES 106-111
 
 overlay_species mode
 +++++++++++++++++++++++++++++++++++++++
@@ -267,7 +271,7 @@ overlay_species mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 107-117
+.. GENERATED FROM PYTHON SOURCE LINES 111-122
 
 .. code-block:: default
 
@@ -277,6 +281,7 @@ overlay_species mode
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='overlay_species',
+                    fermi=5.599480,
                     orbitals=orbitals,
                     spins=spins,
                     dirname=data_dir)
@@ -295,20 +300,20 @@ overlay_species mode
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 118-123
+.. GENERATED FROM PYTHON SOURCE LINES 123-128
 
 overlay_orbtials mode
 +++++++++++++++++++++++++++++++++++++++
@@ -316,7 +321,7 @@ overlay_orbtials mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 123-133
+.. GENERATED FROM PYTHON SOURCE LINES 128-139
 
 .. code-block:: default
 
@@ -325,6 +330,7 @@ overlay_orbtials mode
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='overlay_orbitals',
+                    fermi=5.599480,
                     atoms=atoms,
                     spins=spins,
                     dirname=data_dir)
@@ -344,20 +350,20 @@ overlay_orbtials mode
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 134-139
+.. GENERATED FROM PYTHON SOURCE LINES 140-145
 
 overlay mode
 +++++++++++++++++++++++++++++++++++++++
@@ -365,7 +371,7 @@ overlay mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 139-147
+.. GENERATED FROM PYTHON SOURCE LINES 145-154
 
 .. code-block:: default
 
@@ -374,6 +380,7 @@ overlay mode
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='overlay',
+                    fermi=5.599480,
                     items=items,
                     dirname=data_dir)
 
@@ -391,20 +398,20 @@ overlay mode
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 148-153
+.. GENERATED FROM PYTHON SOURCE LINES 155-160
 
 overlay mode by orbital names
 =============================
@@ -412,7 +419,7 @@ overlay mode by orbital names
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 153-159
+.. GENERATED FROM PYTHON SOURCE LINES 160-167
 
 .. code-block:: default
 
@@ -421,6 +428,7 @@ overlay mode by orbital names
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='overlay',
+                    fermi=5.599480,
                     items=items,
                     dirname=data_dir)
 
@@ -436,13 +444,13 @@ overlay mode by orbital names
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
@@ -452,7 +460,7 @@ overlay mode by orbital names
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  3.591 seconds)
+   **Total running time of the script:** ( 0 minutes  3.212 seconds)
 
 
 .. _sphx_glr_download_examples_00-band_structure_plot_colinear.py:
diff --git a/docs/_sources/examples/00-band_structure/plot_compare_bands.rst.txt b/docs/_sources/examples/00-band_structure/plot_compare_bands.rst.txt
index 88a20474..1f51f684 100644
--- a/docs/_sources/examples/00-band_structure/plot_compare_bands.rst.txt
+++ b/docs/_sources/examples/00-band_structure/plot_compare_bands.rst.txt
@@ -76,8 +76,8 @@ When show is equal to False, bandsplot will return a maplotlib.Figure and maplot
 .. code-block:: default
 
 
-    fig, ax = pyprocar.bandsplot(code='vasp', dirname = vasp_data_dir, mode='parametric', elimit=[-5,5], orbitals=[4,5,6,7,8], show=False)
-    pyprocar.bandsplot(code='qe', dirname = qe_data_dir, mode='plain', elimit=[-5,5], color='k',ax=ax, show =True)
+    fig, ax = pyprocar.bandsplot(code='vasp', dirname = vasp_data_dir, mode='parametric',fermi=5.599480, elimit=[-5,5], orbitals=[4,5,6,7,8], show=False)
+    pyprocar.bandsplot(code='qe', dirname = qe_data_dir, mode='plain',fermi=18.2398, elimit=[-5,5], color='k',ax=ax, show =True)
 
 
 .. image-sg:: /examples/00-band_structure/images/sphx_glr_plot_compare_bands_001.png
@@ -91,22 +91,22 @@ When show is equal to False, bandsplot will return a maplotlib.Figure and maplot
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
@@ -116,7 +116,7 @@ When show is equal to False, bandsplot will return a maplotlib.Figure and maplot
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  1.747 seconds)
+   **Total running time of the script:** ( 0 minutes  1.631 seconds)
 
 
 .. _sphx_glr_download_examples_00-band_structure_plot_compare_bands.py:
diff --git a/docs/_sources/examples/00-band_structure/plot_ipr.rst.txt b/docs/_sources/examples/00-band_structure/plot_ipr.rst.txt
index 3f5b5495..5027a8cd 100644
--- a/docs/_sources/examples/00-band_structure/plot_ipr.rst.txt
+++ b/docs/_sources/examples/00-band_structure/plot_ipr.rst.txt
@@ -131,16 +131,20 @@ The PyProcar code is:
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
-    (
    , )
+                WARNING : `fermi` is not set! Set `fermi={value}`. The plot did not shift the bands by the Fermi energy.
+                ----------------------------------------------------------------------------------------------------------
+            
+
+    (
    , )
 
 
 
@@ -183,13 +187,17 @@ The pyprocar code is:
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
+            
+
+                WARNING : `fermi` is not set! Set `fermi={value}`. The plot did not shift the bands by the Fermi energy.
+                ----------------------------------------------------------------------------------------------------------
             
     z:\research projects\pyprocar\pyprocar\plotter\ebs_plot.py:607: UserWarning: Attempting to set identical low and high xlims makes transformation singular; automatically expanding.
       self.ax.set_xlim(interval)
@@ -197,14 +205,14 @@ The pyprocar code is:
     Atomic plot: spd.shape    : (2, 540, 215, 1, 9, 2)
     Atomic plot: kpoints.shape: (2, 3)
 
-    (
    , )
+    (
    , )
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  24.965 seconds)
+   **Total running time of the script:** ( 0 minutes  23.280 seconds)
 
 
 .. _sphx_glr_download_examples_00-band_structure_plot_ipr.py:
diff --git a/docs/_sources/examples/00-band_structure/plot_noncolinear_qe.rst.txt b/docs/_sources/examples/00-band_structure/plot_noncolinear_qe.rst.txt
index f0d4d9f8..fa7df18f 100644
--- a/docs/_sources/examples/00-band_structure/plot_noncolinear_qe.rst.txt
+++ b/docs/_sources/examples/00-band_structure/plot_noncolinear_qe.rst.txt
@@ -75,7 +75,7 @@ importing pyprocar and specifying local data_dir
 Plain mode
 +++++++++++++++++++++++++++++++++++++++
 
-.. GENERATED FROM PYTHON SOURCE LINES 36-43
+.. GENERATED FROM PYTHON SOURCE LINES 36-44
 
 .. code-block:: default
 
@@ -84,6 +84,7 @@ Plain mode
     pyprocar.bandsplot(
                     code='qe', 
                     mode='plain',
+                    fermi=18.0536,
                     dirname=data_dir)
 
 
@@ -100,20 +101,20 @@ Plain mode
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 44-50
+.. GENERATED FROM PYTHON SOURCE LINES 45-51
 
 Parametric mode
 +++++++++++++++++++++++++++++++++++++++
@@ -122,7 +123,7 @@ therefore orbitals takes different meanings.
 For details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 50-64
+.. GENERATED FROM PYTHON SOURCE LINES 51-66
 
 .. code-block:: default
 
@@ -134,6 +135,7 @@ For details on the meaning of the indices of the atomic projection please refer
     pyprocar.bandsplot(
                     code='qe', 
                     mode='parametric',
+                    fermi=18.0536,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -154,13 +156,13 @@ For details on the meaning of the indices of the atomic projection please refer
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
@@ -170,7 +172,7 @@ For details on the meaning of the indices of the atomic projection please refer
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  1.651 seconds)
+   **Total running time of the script:** ( 0 minutes  1.562 seconds)
 
 
 .. _sphx_glr_download_examples_00-band_structure_plot_noncolinear_qe.py:
diff --git a/docs/_sources/examples/00-band_structure/plot_noncolinear_vasp.rst.txt b/docs/_sources/examples/00-band_structure/plot_noncolinear_vasp.rst.txt
index 6b1c670d..4471622d 100644
--- a/docs/_sources/examples/00-band_structure/plot_noncolinear_vasp.rst.txt
+++ b/docs/_sources/examples/00-band_structure/plot_noncolinear_vasp.rst.txt
@@ -64,13 +64,14 @@ Plain mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 37-42
+.. GENERATED FROM PYTHON SOURCE LINES 37-43
 
 .. code-block:: default
 
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='plain',
+                    fermi=5.596151,
                     dirname=data_dir)
 
 
@@ -87,20 +88,20 @@ Plain mode
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 43-48
+.. GENERATED FROM PYTHON SOURCE LINES 44-49
 
 Parametric mode
 +++++++++++++++++++++++++++++++++++++++
@@ -108,7 +109,7 @@ Parametric mode
 For details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 48-62
+.. GENERATED FROM PYTHON SOURCE LINES 49-64
 
 .. code-block:: default
 
@@ -120,6 +121,7 @@ For details on the meaning of the indices of the atomic projection please refer
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='parametric',
+                    fermi=5.596151,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -140,13 +142,13 @@ For details on the meaning of the indices of the atomic projection please refer
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
@@ -156,7 +158,7 @@ For details on the meaning of the indices of the atomic projection please refer
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  2.116 seconds)
+   **Total running time of the script:** ( 0 minutes  1.975 seconds)
 
 
 .. _sphx_glr_download_examples_00-band_structure_plot_noncolinear_vasp.py:
diff --git a/docs/_sources/examples/00-band_structure/plot_spin_polarized.rst.txt b/docs/_sources/examples/00-band_structure/plot_spin_polarized.rst.txt
index 50741d35..0ea10de0 100644
--- a/docs/_sources/examples/00-band_structure/plot_spin_polarized.rst.txt
+++ b/docs/_sources/examples/00-band_structure/plot_spin_polarized.rst.txt
@@ -66,13 +66,14 @@ Plain mode
 When the calculation is a spin-polarized calculation. There are few more features features bandsplot can do. 
 The default settings bandsplot will plot the spin-up and spin-down bands on the same plot.
 
-.. GENERATED FROM PYTHON SOURCE LINES 39-44
+.. GENERATED FROM PYTHON SOURCE LINES 39-45
 
 .. code-block:: default
 
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='plain',
+                    fermi=5.590136,
                     dirname=data_dir)
 
 
@@ -89,26 +90,26 @@ The default settings bandsplot will plot the spin-up and spin-down bands on the
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 45-48
+.. GENERATED FROM PYTHON SOURCE LINES 46-49
 
 The line-styles or line-colors, these may be changed in the ebs section in the :doc:'pyprocar/utils/default_settings.ini' file.
 
 The keyword spins can also be used to select which spin bands to plot
 
-.. GENERATED FROM PYTHON SOURCE LINES 48-55
+.. GENERATED FROM PYTHON SOURCE LINES 49-57
 
 .. code-block:: default
 
@@ -116,6 +117,7 @@ The keyword spins can also be used to select which spin bands to plot
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='plain',
+                    fermi=5.590136,
                     spins=spins,
                     dirname=data_dir)
 
@@ -133,20 +135,20 @@ The keyword spins can also be used to select which spin bands to plot
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 56-61
+.. GENERATED FROM PYTHON SOURCE LINES 58-63
 
 Parametric mode
 +++++++++++++++++++++++++++++++++++++++
@@ -154,7 +156,7 @@ Parametric mode
 For details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 61-74
+.. GENERATED FROM PYTHON SOURCE LINES 63-77
 
 .. code-block:: default
 
@@ -166,6 +168,7 @@ For details on the meaning of the indices of the atomic projection please refer
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='parametric',
+                    fermi=5.590136,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -185,20 +188,20 @@ For details on the meaning of the indices of the atomic projection please refer
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 75-80
+.. GENERATED FROM PYTHON SOURCE LINES 78-83
 
 Scatter mode
 +++++++++++++++++++++++++++++++++++++++
@@ -206,7 +209,7 @@ Scatter mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 80-92
+.. GENERATED FROM PYTHON SOURCE LINES 83-96
 
 .. code-block:: default
 
@@ -217,6 +220,7 @@ Scatter mode
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='scatter',
+                    fermi=5.590136,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -236,13 +240,13 @@ Scatter mode
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
@@ -252,7 +256,7 @@ Scatter mode
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  3.518 seconds)
+   **Total running time of the script:** ( 0 minutes  2.439 seconds)
 
 
 .. _sphx_glr_download_examples_00-band_structure_plot_spin_polarized.py:
diff --git a/docs/_sources/examples/00-band_structure/plot_unfolding.rst.txt b/docs/_sources/examples/00-band_structure/plot_unfolding.rst.txt
index 5c93de76..404a0bc4 100644
--- a/docs/_sources/examples/00-band_structure/plot_unfolding.rst.txt
+++ b/docs/_sources/examples/00-band_structure/plot_unfolding.rst.txt
@@ -71,7 +71,7 @@ importing pyprocar and specifying local data_dir
 Plotting primitive bands
 +++++++++++++++++++++++++++++++++++++++
 
-.. GENERATED FROM PYTHON SOURCE LINES 42-50
+.. GENERATED FROM PYTHON SOURCE LINES 42-51
 
 .. code-block:: default
 
@@ -79,6 +79,7 @@ Plotting primitive bands
     pyprocar.bandsplot(
                     code='vasp', 
                     mode='plain',
+                    fermi=4.993523,
                     elimit=[-15,5],
                     dirname=primitive_dir)
 
@@ -97,20 +98,20 @@ Plotting primitive bands
  .. code-block:: none
 
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
     (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 51-58
+.. GENERATED FROM PYTHON SOURCE LINES 52-59
 
 Unfolding of the supercell bands
 +++++++++++++++++++++++++++++++++++++++
@@ -120,7 +121,7 @@ the POSCAR and KPOINTS will be different from the primitive cell
 For the POSCAR, we create a 2 2 2 supercell from the primitive.
 For the KPOINTS, the paths need to be changed to reflect the change in the unitcell
 
-.. GENERATED FROM PYTHON SOURCE LINES 58-67
+.. GENERATED FROM PYTHON SOURCE LINES 59-69
 
 .. code-block:: default
 
@@ -129,6 +130,7 @@ For the KPOINTS, the paths need to be changed to reflect the change in the unitc
             code='vasp',
             mode='plain',
             unfold_mode='both',
+            fermi=5.033090,
             dirname= supercell_dir,
             elimit=[-15,5],
             supercell_matrix=np.diag([2, 2, 2]))
@@ -154,7 +156,7 @@ For the KPOINTS, the paths need to be changed to reflect the change in the unitc
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -195,7 +197,7 @@ For the KPOINTS, the paths need to be changed to reflect the change in the unitc
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  23.457 seconds)
+   **Total running time of the script:** ( 0 minutes  21.979 seconds)
 
 
 .. _sphx_glr_download_examples_00-band_structure_plot_unfolding.py:
diff --git a/docs/_sources/examples/00-band_structure/sg_execution_times.rst.txt b/docs/_sources/examples/00-band_structure/sg_execution_times.rst.txt
index c49fcad6..5ea52cfb 100644
--- a/docs/_sources/examples/00-band_structure/sg_execution_times.rst.txt
+++ b/docs/_sources/examples/00-band_structure/sg_execution_times.rst.txt
@@ -6,28 +6,28 @@
 
 Computation times
 =================
-**05:04.130** total execution time for **examples_00-band_structure** files:
+**04:39.390** total execution time for **examples_00-band_structure** files:
 
 +--------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_00-band_structure_plot_2d_bands.py` (``plot_2d_bands.py``)                                 | 03:31.780 | 0.0 MB |
+| :ref:`sphx_glr_examples_00-band_structure_plot_2d_bands.py` (``plot_2d_bands.py``)                                 | 03:13.652 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_00-band_structure_plot_autobands.py` (``plot_autobands.py``)                               | 00:26.997 | 0.0 MB |
+| :ref:`sphx_glr_examples_00-band_structure_plot_autobands.py` (``plot_autobands.py``)                               | 00:25.670 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_00-band_structure_plot_ipr.py` (``plot_ipr.py``)                                           | 00:24.965 | 0.0 MB |
+| :ref:`sphx_glr_examples_00-band_structure_plot_ipr.py` (``plot_ipr.py``)                                           | 00:23.280 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_00-band_structure_plot_unfolding.py` (``plot_unfolding.py``)                               | 00:23.457 | 0.0 MB |
+| :ref:`sphx_glr_examples_00-band_structure_plot_unfolding.py` (``plot_unfolding.py``)                               | 00:21.979 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_00-band_structure_plot_colinear.py` (``plot_colinear.py``)                                 | 00:03.591 | 0.0 MB |
+| :ref:`sphx_glr_examples_00-band_structure_plot_colinear.py` (``plot_colinear.py``)                                 | 00:03.212 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_00-band_structure_plot_spin_polarized.py` (``plot_spin_polarized.py``)                     | 00:03.518 | 0.0 MB |
+| :ref:`sphx_glr_examples_00-band_structure_plot_bandsplot_configurations.py` (``plot_bandsplot_configurations.py``) | 00:02.716 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_00-band_structure_plot_bandsplot_configurations.py` (``plot_bandsplot_configurations.py``) | 00:02.839 | 0.0 MB |
+| :ref:`sphx_glr_examples_00-band_structure_plot_spin_polarized.py` (``plot_spin_polarized.py``)                     | 00:02.439 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_00-band_structure_plot_noncolinear_vasp.py` (``plot_noncolinear_vasp.py``)                 | 00:02.116 | 0.0 MB |
+| :ref:`sphx_glr_examples_00-band_structure_plot_noncolinear_vasp.py` (``plot_noncolinear_vasp.py``)                 | 00:01.975 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_00-band_structure_plot_compare_bands.py` (``plot_compare_bands.py``)                       | 00:01.747 | 0.0 MB |
+| :ref:`sphx_glr_examples_00-band_structure_plot_compare_bands.py` (``plot_compare_bands.py``)                       | 00:01.631 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_00-band_structure_plot_noncolinear_qe.py` (``plot_noncolinear_qe.py``)                     | 00:01.651 | 0.0 MB |
+| :ref:`sphx_glr_examples_00-band_structure_plot_noncolinear_qe.py` (``plot_noncolinear_qe.py``)                     | 00:01.562 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_00-band_structure_plot_atomic_levels.py` (``plot_atomic_levels.py``)                       | 00:01.468 | 0.0 MB |
+| :ref:`sphx_glr_examples_00-band_structure_plot_atomic_levels.py` (``plot_atomic_levels.py``)                       | 00:01.275 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------------+-----------+--------+
diff --git a/docs/_sources/examples/01-dos/index.rst.txt b/docs/_sources/examples/01-dos/index.rst.txt
index c6768a82..f9c01991 100644
--- a/docs/_sources/examples/01-dos/index.rst.txt
+++ b/docs/_sources/examples/01-dos/index.rst.txt
@@ -49,52 +49,52 @@ These examples demonstrate the density of states plotting capabilities.
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/01-dos/images/thumb/sphx_glr_plot_colinear_dos_thumb.png
+  .. image:: /examples/01-dos/images/thumb/sphx_glr_plot_dosplot_configurations_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_01-dos_plot_colinear_dos.py`
+  :ref:`sphx_glr_examples_01-dos_plot_dosplot_configurations.py`
 
 .. raw:: html
 
-      
    Plotting density of states
    
+      
    Plotting with Configurations in pyprocar
    
     
    
 
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/01-dos/images/thumb/sphx_glr_plot_spin_polarized_dos_thumb.png
+  .. image:: /examples/01-dos/images/thumb/sphx_glr_plot_colinear_dos_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_01-dos_plot_spin_polarized_dos.py`
+  :ref:`sphx_glr_examples_01-dos_plot_colinear_dos.py`
 
 .. raw:: html
 
-      
    Plotting spin-polarized density of states
    
+      
    Plotting density of states
    
     
    
 
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/01-dos/images/thumb/sphx_glr_plot_dosplot_configurations_thumb.png
+  .. image:: /examples/01-dos/images/thumb/sphx_glr_plot_spin_polarized_dos_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_01-dos_plot_dosplot_configurations.py`
+  :ref:`sphx_glr_examples_01-dos_plot_spin_polarized_dos.py`
 
 .. raw:: html
 
-      
    Plotting with Configurations in pyprocar
    
+      
    Plotting spin-polarized density of states
    
     
    
 
 
@@ -108,7 +108,7 @@ These examples demonstrate the density of states plotting capabilities.
 
    /examples/01-dos/plot_noncolinear_dos_vasp
    /examples/01-dos/plot_noncolinear_dos_qe
+   /examples/01-dos/plot_dosplot_configurations
    /examples/01-dos/plot_colinear_dos
    /examples/01-dos/plot_spin_polarized_dos
-   /examples/01-dos/plot_dosplot_configurations
 
diff --git a/docs/_sources/examples/01-dos/plot_colinear_dos.rst.txt b/docs/_sources/examples/01-dos/plot_colinear_dos.rst.txt
index 5ad9ab03..94cbc93e 100644
--- a/docs/_sources/examples/01-dos/plot_colinear_dos.rst.txt
+++ b/docs/_sources/examples/01-dos/plot_colinear_dos.rst.txt
@@ -62,7 +62,7 @@ importing pyprocar and specifying local data_dir
 Plain mode
 +++++++++++++++++++++++++++++++++++++++
 
-.. GENERATED FROM PYTHON SOURCE LINES 34-40
+.. GENERATED FROM PYTHON SOURCE LINES 34-41
 
 .. code-block:: default
 
@@ -70,6 +70,7 @@ Plain mode
     pyprocar.dosplot(
                     code='qe', 
                     mode='plain',
+                    fermi=5.599480,
                     dirname=data_dir)
 
 
@@ -93,13 +94,12 @@ Plain mode
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 41-48
+.. GENERATED FROM PYTHON SOURCE LINES 42-49
 
 Parametric mode
 +++++++++++++++++++++++++++++++++++++++
@@ -109,7 +109,7 @@ For details on the meaning of the indices of the atomic projection please refer
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 48-60
+.. GENERATED FROM PYTHON SOURCE LINES 49-62
 
 .. code-block:: default
 
@@ -120,6 +120,7 @@ For details on the meaning of the indices of the atomic projection please refer
     pyprocar.dosplot(
                     code='qe', 
                     mode='parametric',
+                    fermi=5.599480,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -146,13 +147,12 @@ For details on the meaning of the indices of the atomic projection please refer
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 61-68
+.. GENERATED FROM PYTHON SOURCE LINES 63-70
 
 parametric_line mode
 +++++++++++++++++++++++++++++++++++++++
@@ -162,7 +162,7 @@ For details on the meaning of the indices of the atomic projection please refer
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 68-82
+.. GENERATED FROM PYTHON SOURCE LINES 70-85
 
 .. code-block:: default
 
@@ -173,6 +173,7 @@ For details on the meaning of the indices of the atomic projection please refer
     pyprocar.dosplot(
                     code='qe', 
                     mode='parametric_line',
+                    fermi=5.599480,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -201,13 +202,12 @@ For details on the meaning of the indices of the atomic projection please refer
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 83-88
+.. GENERATED FROM PYTHON SOURCE LINES 86-91
 
 stack_species mode
 +++++++++++++++++++++++++++++++++++++++
@@ -215,7 +215,7 @@ stack_species mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 88-98
+.. GENERATED FROM PYTHON SOURCE LINES 91-102
 
 .. code-block:: default
 
@@ -225,6 +225,7 @@ stack_species mode
     pyprocar.dosplot(
                     code='qe', 
                     mode='stack_species',
+                    fermi=5.599480,
                     orbitals=orbitals,
                     spins=spins,
                     dirname=data_dir)
@@ -250,14 +251,13 @@ stack_species mode
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
     The plot only considers orbitals [4, 5, 6, 7, 8]
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 99-104
+.. GENERATED FROM PYTHON SOURCE LINES 103-108
 
 stack_orbtials mode
 +++++++++++++++++++++++++++++++++++++++
@@ -265,7 +265,7 @@ stack_orbtials mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 104-114
+.. GENERATED FROM PYTHON SOURCE LINES 108-119
 
 .. code-block:: default
 
@@ -274,6 +274,7 @@ stack_orbtials mode
     pyprocar.dosplot(
                     code='qe', 
                     mode='stack_orbitals',
+                    fermi=5.599480,
                     atoms=atoms,
                     spins=spins,
                     dirname=data_dir)
@@ -300,22 +301,21 @@ stack_orbtials mode
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
     The plot only considers atoms ['Fe']
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 115-120
+.. GENERATED FROM PYTHON SOURCE LINES 120-125
 
-overlay mode
+stack mode
 +++++++++++++++++++++++++++++++++++++++
 
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 120-128
+.. GENERATED FROM PYTHON SOURCE LINES 125-135
 
 .. code-block:: default
 
@@ -324,12 +324,14 @@ overlay mode
     pyprocar.dosplot(
                     code='qe', 
                     mode='stack',
+                    fermi=5.599480,
                     items=items,
                     dirname=data_dir)
 
 
 
 
+
 .. image-sg:: /examples/01-dos/images/sphx_glr_plot_colinear_dos_006.png
    :alt: plot colinear dos
    :srcset: /examples/01-dos/images/sphx_glr_plot_colinear_dos_006.png
@@ -348,16 +350,161 @@ overlay mode
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 136-141
+
+overlay_species mode
++++++++++++++++++++++++++++++++++++++++
+
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 141-152
+
+.. code-block:: default
+
+    orbitals=[4,5,6,7,8]
+    spins=[0]
+
+    pyprocar.dosplot(
+                    code='qe', 
+                    mode='overlay_species',
+                    fermi=5.599480,
+                    orbitals=orbitals,
+                    spins=spins,
+                    dirname=data_dir)
+
+
+
+
+.. image-sg:: /examples/01-dos/images/sphx_glr_plot_colinear_dos_007.png
+   :alt: plot colinear dos
+   :srcset: /examples/01-dos/images/sphx_glr_plot_colinear_dos_007.png
+   :class: sphx-glr-single-img
+
+
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                --------------------------------------------------------
+                There are additional plot options that are defined in a configuration file. 
+                You can change these configurations by passing the keyword argument to the function
+                To print a list of plot options set print_plot_opts=True
+
+                Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
+                --------------------------------------------------------
+    The plot only considers orbitals [4, 5, 6, 7, 8]
+
+    (
    , )
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 153-158
+
+overlay_orbtials mode
++++++++++++++++++++++++++++++++++++++++
+
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 158-169
+
+.. code-block:: default
+
+    atoms=[0]
+    spins=[0]
+    pyprocar.dosplot(
+                    code='qe', 
+                    mode='overlay_orbitals',
+                    fermi=5.599480,
+                    atoms=atoms,
+                    spins=spins,
+                    dirname=data_dir)
+
+
+
+
+
+.. image-sg:: /examples/01-dos/images/sphx_glr_plot_colinear_dos_008.png
+   :alt: plot colinear dos
+   :srcset: /examples/01-dos/images/sphx_glr_plot_colinear_dos_008.png
+   :class: sphx-glr-single-img
+
+
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                --------------------------------------------------------
+                There are additional plot options that are defined in a configuration file. 
+                You can change these configurations by passing the keyword argument to the function
+                To print a list of plot options set print_plot_opts=True
+
+                Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
+                --------------------------------------------------------
+    The plot only considers atoms ['Fe']
+
+    (
    , )
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 170-175
+
+overlay mode
++++++++++++++++++++++++++++++++++++++++
+
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 175-183
+
+.. code-block:: default
+
+
+    items={'Fe':[4,5,6,7,8]}
+    pyprocar.dosplot(
+                    code='qe', 
+                    mode='overlay',
+                    fermi=5.599480,
+                    items=items,
+                    dirname=data_dir)
+
+
+
+.. image-sg:: /examples/01-dos/images/sphx_glr_plot_colinear_dos_009.png
+   :alt: plot colinear dos
+   :srcset: /examples/01-dos/images/sphx_glr_plot_colinear_dos_009.png
+   :class: sphx-glr-single-img
+
+
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                --------------------------------------------------------
+                There are additional plot options that are defined in a configuration file. 
+                You can change these configurations by passing the keyword argument to the function
+                To print a list of plot options set print_plot_opts=True
+
+                Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
+                --------------------------------------------------------
+
+    (
    , )
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  29.245 seconds)
+   **Total running time of the script:** ( 0 minutes  28.883 seconds)
 
 
 .. _sphx_glr_download_examples_01-dos_plot_colinear_dos.py:
diff --git a/docs/_sources/examples/01-dos/plot_dosplot_configurations.rst.txt b/docs/_sources/examples/01-dos/plot_dosplot_configurations.rst.txt
index 5c59886b..dabdb502 100644
--- a/docs/_sources/examples/01-dos/plot_dosplot_configurations.rst.txt
+++ b/docs/_sources/examples/01-dos/plot_dosplot_configurations.rst.txt
@@ -80,7 +80,7 @@ Before diving into plotting, we need to download the example files. Use the foll
     print(f"Configuration files are located at: {config_path}")
 
     # Print the configurations
-    pyprocar.dosplot(code=code, dirname=data_dir, print_plot_opts=True)
+    pyprocar.dosplot(code=code, dirname=data_dir,fermi=5.599480, print_plot_opts=True)
 
 
 
@@ -104,7 +104,6 @@ Before diving into plotting, we need to download the example files. Use the foll
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
     cmap : {'description': 'The colormap used for the plot.', 'value': 'jet'}
     colors : {'description': 'List of colors for the plot lines.', 'value': ['red', 'green', 'blue', 'cyan', 'magenta', 'yellow', 'orange', 'purple', 'brown', 'navy', 'maroon', 'olive']}
     colorbar_title : {'description': 'Title of the colorbar.', 'value': 'Atomic Orbital Projections'}
@@ -141,15 +140,15 @@ Before diving into plotting, we need to download the example files. Use the foll
     weighted_width : {'description': 'If true, the width of the lines will be weighted.', 'value': False}
     clim : {'description': 'Value range to scale the colorbar', 'value': None}
     stack_y_label : {'description': 'The label for the y-axis for stack mode', 'value': 'DOS'}
-    x_label : {'description': 'The label for the x-axis.', 'value': 'Energy (eV)'}
-    y_label : {'description': 'The label for the y-axis.', 'value': 'DOS'}
+    x_label : {'description': 'The label for the x-axis.', 'value': None}
+    y_label : {'description': 'The label for the y-axis.', 'value': None}
     dpi : {'description': "The resolution in dots per inch. If 'figure', use the figure's dpi value.", 'value': 'figure'}
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 53-74
+.. GENERATED FROM PYTHON SOURCE LINES 53-75
 
 .. code-block:: default
 
@@ -164,6 +163,7 @@ Before diving into plotting, we need to download the example files. Use the foll
     pyprocar.dosplot(
         code=code,
         dirname=data_dir,
+        fermi=5.599480,
         atoms=[0],
         orbitals=[4,5,6,7,8],
         mode='parametric',
@@ -195,13 +195,12 @@ Before diving into plotting, we need to download the example files. Use the foll
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 75-92
+.. GENERATED FROM PYTHON SOURCE LINES 76-94
 
 .. code-block:: default
 
@@ -215,6 +214,7 @@ Before diving into plotting, we need to download the example files. Use the foll
     pyprocar.dosplot(
         code=code,
         dirname=data_dir,
+        fermi=5.599480,
         atoms=[0],
         orbitals=[4,5,6,7,8],
         mode='parametric_line',
@@ -243,16 +243,15 @@ Before diving into plotting, we need to download the example files. Use the foll
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  1.965 seconds)
+   **Total running time of the script:** ( 0 minutes  1.736 seconds)
 
 
 .. _sphx_glr_download_examples_01-dos_plot_dosplot_configurations.py:
diff --git a/docs/_sources/examples/01-dos/plot_noncolinear_dos_qe.rst.txt b/docs/_sources/examples/01-dos/plot_noncolinear_dos_qe.rst.txt
index 1f662cbb..cef64c81 100644
--- a/docs/_sources/examples/01-dos/plot_noncolinear_dos_qe.rst.txt
+++ b/docs/_sources/examples/01-dos/plot_noncolinear_dos_qe.rst.txt
@@ -68,7 +68,7 @@ For details on the meaning of the indices of the atomic projection please refer
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 39-49
+.. GENERATED FROM PYTHON SOURCE LINES 39-50
 
 .. code-block:: default
 
@@ -79,6 +79,7 @@ For details on the meaning of the indices of the atomic projection please refer
     pyprocar.dosplot(
                     code='qe', 
                     mode='parametric',
+                    fermi=18.0536,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -103,16 +104,15 @@ For details on the meaning of the indices of the atomic projection please refer
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  24.813 seconds)
+   **Total running time of the script:** ( 0 minutes  21.637 seconds)
 
 
 .. _sphx_glr_download_examples_01-dos_plot_noncolinear_dos_qe.py:
diff --git a/docs/_sources/examples/01-dos/plot_noncolinear_dos_vasp.rst.txt b/docs/_sources/examples/01-dos/plot_noncolinear_dos_vasp.rst.txt
index 57f56cdb..e34dba48 100644
--- a/docs/_sources/examples/01-dos/plot_noncolinear_dos_vasp.rst.txt
+++ b/docs/_sources/examples/01-dos/plot_noncolinear_dos_vasp.rst.txt
@@ -67,7 +67,7 @@ For details on the meaning of the indices of the atomic projection please refer
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 38-48
+.. GENERATED FROM PYTHON SOURCE LINES 38-49
 
 .. code-block:: default
 
@@ -78,6 +78,7 @@ For details on the meaning of the indices of the atomic projection please refer
     pyprocar.dosplot(
                     code='vasp', 
                     mode='parametric',
+                    fermi=5.5962,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -102,16 +103,15 @@ For details on the meaning of the indices of the atomic projection please refer
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  5.803 seconds)
+   **Total running time of the script:** ( 0 minutes  5.196 seconds)
 
 
 .. _sphx_glr_download_examples_01-dos_plot_noncolinear_dos_vasp.py:
diff --git a/docs/_sources/examples/01-dos/plot_spin_polarized_dos.rst.txt b/docs/_sources/examples/01-dos/plot_spin_polarized_dos.rst.txt
index 46986e6e..ef69f472 100644
--- a/docs/_sources/examples/01-dos/plot_spin_polarized_dos.rst.txt
+++ b/docs/_sources/examples/01-dos/plot_spin_polarized_dos.rst.txt
@@ -64,13 +64,14 @@ Plain mode
 When the calculation is a spin-polarized calculation. There are few more features features bandsplot can do. 
 The default settings bandsplot will plot the spin-up and spin-down bands on the same plot.
 
-.. GENERATED FROM PYTHON SOURCE LINES 36-41
+.. GENERATED FROM PYTHON SOURCE LINES 36-42
 
 .. code-block:: default
 
     pyprocar.dosplot(
                     code='vasp', 
                     mode='plain',
+                    fermi=5.590136,
                     dirname=data_dir)
 
 
@@ -94,19 +95,18 @@ The default settings bandsplot will plot the spin-up and spin-down bands on the
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 42-45
+.. GENERATED FROM PYTHON SOURCE LINES 43-46
 
 The line-styles or line-colors, these may be changed in the ebs section in the :doc:'pyprocar/utils/default_settings.ini' file.
 
 The keyword spins can also be used to select which spin bands to plot
 
-.. GENERATED FROM PYTHON SOURCE LINES 45-52
+.. GENERATED FROM PYTHON SOURCE LINES 46-54
 
 .. code-block:: default
 
@@ -114,6 +114,7 @@ The keyword spins can also be used to select which spin bands to plot
     pyprocar.dosplot(
                     code='vasp', 
                     mode='plain',
+                    fermi=5.590136,
                     spins=spins,
                     dirname=data_dir)
 
@@ -138,13 +139,12 @@ The keyword spins can also be used to select which spin bands to plot
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 53-60
+.. GENERATED FROM PYTHON SOURCE LINES 55-62
 
 Parametric mode
 +++++++++++++++++++++++++++++++++++++++
@@ -154,7 +154,7 @@ For details on the meaning of the indices of the atomic projection please refer
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 60-72
+.. GENERATED FROM PYTHON SOURCE LINES 62-75
 
 .. code-block:: default
 
@@ -165,6 +165,7 @@ For details on the meaning of the indices of the atomic projection please refer
     pyprocar.dosplot(
                     code='vasp', 
                     mode='parametric',
+                    fermi=5.590136,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -191,13 +192,12 @@ For details on the meaning of the indices of the atomic projection please refer
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 73-80
+.. GENERATED FROM PYTHON SOURCE LINES 76-83
 
 parametric_line mode
 +++++++++++++++++++++++++++++++++++++++
@@ -207,7 +207,7 @@ For details on the meaning of the indices of the atomic projection please refer
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 80-94
+.. GENERATED FROM PYTHON SOURCE LINES 83-98
 
 .. code-block:: default
 
@@ -218,6 +218,7 @@ For details on the meaning of the indices of the atomic projection please refer
     pyprocar.dosplot(
                     code='vasp', 
                     mode='parametric_line',
+                    fermi=5.590136,
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
@@ -246,13 +247,12 @@ For details on the meaning of the indices of the atomic projection please refer
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 95-100
+.. GENERATED FROM PYTHON SOURCE LINES 99-104
 
 stack_species mode
 +++++++++++++++++++++++++++++++++++++++
@@ -260,7 +260,7 @@ stack_species mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 100-110
+.. GENERATED FROM PYTHON SOURCE LINES 104-115
 
 .. code-block:: default
 
@@ -270,6 +270,7 @@ stack_species mode
     pyprocar.dosplot(
                     code='vasp', 
                     mode='stack_species',
+                    fermi=5.590136,
                     orbitals=orbitals,
                     spins=spins,
                     dirname=data_dir)
@@ -295,14 +296,13 @@ stack_species mode
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
     The plot only considers orbitals [4, 5, 6, 7, 8]
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 111-116
+.. GENERATED FROM PYTHON SOURCE LINES 116-121
 
 stack_orbtials mode
 +++++++++++++++++++++++++++++++++++++++
@@ -310,7 +310,7 @@ stack_orbtials mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 116-127
+.. GENERATED FROM PYTHON SOURCE LINES 121-133
 
 .. code-block:: default
 
@@ -319,6 +319,7 @@ stack_orbtials mode
     pyprocar.dosplot(
                     code='vasp', 
                     mode='stack_orbitals',
+                    fermi=5.590136,
                     atoms=atoms,
                     spins=spins,
                     dirname=data_dir)
@@ -346,14 +347,13 @@ stack_orbtials mode
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
     The plot only considers atoms ['Fe']
 
-    (
    , )
+    (
    , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 128-133
+.. GENERATED FROM PYTHON SOURCE LINES 134-139
 
 stack mode
 +++++++++++++++++++++++++++++++++++++++
@@ -361,7 +361,7 @@ stack mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 133-142
+.. GENERATED FROM PYTHON SOURCE LINES 139-151
 
 .. code-block:: default
 
@@ -371,12 +371,15 @@ stack mode
     pyprocar.dosplot(
                     code='vasp', 
                     mode='stack',
+                    fermi=5.590136,
                     items=items,
                     spins=spins,
                     dirname=data_dir)
 
 
 
+
+
 .. image-sg:: /examples/01-dos/images/sphx_glr_plot_spin_polarized_dos_007.png
    :alt: plot spin polarized dos
    :srcset: /examples/01-dos/images/sphx_glr_plot_spin_polarized_dos_007.png
@@ -395,16 +398,164 @@ stack mode
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
-    (
    , )
+    (
    , )
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 152-157
+
+overlay_species mode
++++++++++++++++++++++++++++++++++++++++
+
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 157-168
+
+.. code-block:: default
+
+    orbitals=[4,5,6,7,8]
+    spins=[0,1]
+
+    pyprocar.dosplot(
+                    code='vasp', 
+                    mode='overlay_species',
+                    fermi=5.590136,
+                    orbitals=orbitals,
+                    spins=spins,
+                    dirname=data_dir)
+
+
+
+
+.. image-sg:: /examples/01-dos/images/sphx_glr_plot_spin_polarized_dos_008.png
+   :alt: plot spin polarized dos
+   :srcset: /examples/01-dos/images/sphx_glr_plot_spin_polarized_dos_008.png
+   :class: sphx-glr-single-img
+
+
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                --------------------------------------------------------
+                There are additional plot options that are defined in a configuration file. 
+                You can change these configurations by passing the keyword argument to the function
+                To print a list of plot options set print_plot_opts=True
+
+                Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
+                --------------------------------------------------------
+    The plot only considers orbitals [4, 5, 6, 7, 8]
+
+    (
    , )
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 169-174
+
+overlay_orbtials mode
++++++++++++++++++++++++++++++++++++++++
+
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 174-186
+
+.. code-block:: default
+
+    atoms=[0]
+    spins=[0,1]
+    pyprocar.dosplot(
+                    code='vasp', 
+                    mode='overlay_orbitals',
+                    fermi=5.590136,
+                    atoms=atoms,
+                    spins=spins,
+                    dirname=data_dir)
+
+
+
+
+
+
+.. image-sg:: /examples/01-dos/images/sphx_glr_plot_spin_polarized_dos_009.png
+   :alt: plot spin polarized dos
+   :srcset: /examples/01-dos/images/sphx_glr_plot_spin_polarized_dos_009.png
+   :class: sphx-glr-single-img
+
+
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                --------------------------------------------------------
+                There are additional plot options that are defined in a configuration file. 
+                You can change these configurations by passing the keyword argument to the function
+                To print a list of plot options set print_plot_opts=True
+
+                Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
+                --------------------------------------------------------
+    The plot only considers atoms ['Fe']
+
+    (
    , )
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 187-192
+
+overlay mode
++++++++++++++++++++++++++++++++++++++++
+
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 192-202
+
+.. code-block:: default
+
+
+    items={'Fe':[4,5,6,7,8]}
+    spins=[0,1]
+    pyprocar.dosplot(
+                    code='vasp', 
+                    mode='overlay',
+                    fermi=5.590136,
+                    items=items,
+                    spins=spins,
+                    dirname=data_dir)
+
+
+
+.. image-sg:: /examples/01-dos/images/sphx_glr_plot_spin_polarized_dos_010.png
+   :alt: plot spin polarized dos
+   :srcset: /examples/01-dos/images/sphx_glr_plot_spin_polarized_dos_010.png
+   :class: sphx-glr-single-img
+
+
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                --------------------------------------------------------
+                There are additional plot options that are defined in a configuration file. 
+                You can change these configurations by passing the keyword argument to the function
+                To print a list of plot options set print_plot_opts=True
+
+                Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
+                --------------------------------------------------------
+
+    (
    , )
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  4.501 seconds)
+   **Total running time of the script:** ( 0 minutes  3.899 seconds)
 
 
 .. _sphx_glr_download_examples_01-dos_plot_spin_polarized_dos.py:
diff --git a/docs/_sources/examples/01-dos/sg_execution_times.rst.txt b/docs/_sources/examples/01-dos/sg_execution_times.rst.txt
index 06fc8113..42dd8be5 100644
--- a/docs/_sources/examples/01-dos/sg_execution_times.rst.txt
+++ b/docs/_sources/examples/01-dos/sg_execution_times.rst.txt
@@ -6,16 +6,16 @@
 
 Computation times
 =================
-**01:06.328** total execution time for **examples_01-dos** files:
+**01:01.351** total execution time for **examples_01-dos** files:
 
 +-----------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_01-dos_plot_colinear_dos.py` (``plot_colinear_dos.py``)                     | 00:29.245 | 0.0 MB |
+| :ref:`sphx_glr_examples_01-dos_plot_colinear_dos.py` (``plot_colinear_dos.py``)                     | 00:28.883 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_01-dos_plot_noncolinear_dos_qe.py` (``plot_noncolinear_dos_qe.py``)         | 00:24.813 | 0.0 MB |
+| :ref:`sphx_glr_examples_01-dos_plot_noncolinear_dos_qe.py` (``plot_noncolinear_dos_qe.py``)         | 00:21.637 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_01-dos_plot_noncolinear_dos_vasp.py` (``plot_noncolinear_dos_vasp.py``)     | 00:05.803 | 0.0 MB |
+| :ref:`sphx_glr_examples_01-dos_plot_noncolinear_dos_vasp.py` (``plot_noncolinear_dos_vasp.py``)     | 00:05.196 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_01-dos_plot_spin_polarized_dos.py` (``plot_spin_polarized_dos.py``)         | 00:04.501 | 0.0 MB |
+| :ref:`sphx_glr_examples_01-dos_plot_spin_polarized_dos.py` (``plot_spin_polarized_dos.py``)         | 00:03.899 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_01-dos_plot_dosplot_configurations.py` (``plot_dosplot_configurations.py``) | 00:01.965 | 0.0 MB |
+| :ref:`sphx_glr_examples_01-dos_plot_dosplot_configurations.py` (``plot_dosplot_configurations.py``) | 00:01.736 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------------+-----------+--------+
diff --git a/docs/_sources/examples/02-bands_dos/plot_bandsdosplot.rst.txt b/docs/_sources/examples/02-bands_dos/plot_bandsdosplot.rst.txt
index ffa5cca0..0c6a051b 100644
--- a/docs/_sources/examples/02-bands_dos/plot_bandsdosplot.rst.txt
+++ b/docs/_sources/examples/02-bands_dos/plot_bandsdosplot.rst.txt
@@ -70,16 +70,22 @@ The keywords that works for bandsplot and dosplot will work in bandsdosplot.
 These keyword arguments can be set in bands_settings and dos_settings as done below.
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 42-55
+.. GENERATED FROM PYTHON SOURCE LINES 42-61
 
 .. code-block:: default
 
 
-    bands_settings = {'mode':'plain',
-                    'dirname': bands_dir}
+    bands_settings = {
+                      'mode':'plain',
+                      'fermi':5.599480, # This will overide the default fermi value found in bands directory
+                      'dirname': bands_dir
+                      }
 
-    dos_settings = {'mode':'plain',
-                    'dirname': dos_dir}
+    dos_settings = {
+                   'mode':'plain',
+                   'fermi':5.599480,   # This will overide the default fermi value found in dos directory
+                   'dirname': dos_dir
+                    }
 
     pyprocar.bandsdosplot(code='vasp',
                     bands_settings=bands_settings,
@@ -108,7 +114,7 @@ These keyword arguments can be set in bands_settings and dos_settings as done be
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -129,13 +135,13 @@ These keyword arguments can be set in bands_settings and dos_settings as done be
     - Freddy Farah
     
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
                 --------------------------------------------------------
@@ -145,7 +151,6 @@ These keyword arguments can be set in bands_settings and dos_settings as done be
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
     (
    , , )
 
@@ -154,7 +159,7 @@ These keyword arguments can be set in bands_settings and dos_settings as done be
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.509 seconds)
+   **Total running time of the script:** ( 0 minutes  0.385 seconds)
 
 
 .. _sphx_glr_download_examples_02-bands_dos_plot_bandsdosplot.py:
diff --git a/docs/_sources/examples/02-bands_dos/plot_bandsdosplot_configurations.rst.txt b/docs/_sources/examples/02-bands_dos/plot_bandsdosplot_configurations.rst.txt
index 4d41208a..51bf4f12 100644
--- a/docs/_sources/examples/02-bands_dos/plot_bandsdosplot_configurations.rst.txt
+++ b/docs/_sources/examples/02-bands_dos/plot_bandsdosplot_configurations.rst.txt
@@ -62,7 +62,7 @@ Before diving into plotting, we need to download the example files. Use the foll
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 36-56
+.. GENERATED FROM PYTHON SOURCE LINES 36-63
 
 .. code-block:: default
 
@@ -75,11 +75,18 @@ Before diving into plotting, we need to download the example files. Use the foll
     # These keyword arguments can be set in `bands_settings` and `dos_settings` as demonstrated below.
     #
 
-    bands_settings = {'mode':'plain',
-                    'dirname': bands_dir}
 
-    dos_settings = {'mode':'plain',
-                    'dirname': dos_dir}
+    bands_settings = {
+                      'mode':'plain',
+                      'fermi':5.599480, # This will overide the default fermi value found in bands directory
+                      'dirname': bands_dir
+                      }
+
+    dos_settings = {
+                   'mode':'plain',
+                   'fermi':5.599480,   # This will overide the default fermi value found in dos directory
+                   'dirname': dos_dir
+                    }
 
     pyprocar.bandsdosplot(code='vasp',
                     bands_settings=bands_settings,
@@ -107,7 +114,7 @@ Before diving into plotting, we need to download the example files. Use the foll
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -128,13 +135,13 @@ Before diving into plotting, we need to download the example files. Use the foll
     - Freddy Farah
     
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
                 --------------------------------------------------------
@@ -144,13 +151,12 @@ Before diving into plotting, we need to download the example files. Use the foll
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
     (
    , , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 57-93
+.. GENERATED FROM PYTHON SOURCE LINES 64-102
 
 .. code-block:: default
 
@@ -165,6 +171,7 @@ Before diving into plotting, we need to download the example files. Use the foll
     bands_settings = {
         'mode': 'scatter',
         'dirname': bands_dir,
+        'fermi':5.599480, # This will overide the default fermi value found in bands directory
         'atoms':[0],
         'orbitals':[4,5,6,7,8],
         'cmap': 'viridis',
@@ -177,6 +184,7 @@ Before diving into plotting, we need to download the example files. Use the foll
     dos_settings = {
         'mode': 'parametric',
         'dirname': dos_dir,
+        'fermi':5.599480,   # This will overide the default fermi value found in dos directory
         'atoms':[0],
         'orbitals':[4,5,6,7,8],
         'cmap': 'viridis',
@@ -211,7 +219,7 @@ Before diving into plotting, we need to download the example files. Use the foll
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -232,13 +240,13 @@ Before diving into plotting, we need to download the example files. Use the foll
     - Freddy Farah
     
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
             
 
                 --------------------------------------------------------
@@ -248,13 +256,12 @@ Before diving into plotting, we need to download the example files. Use the foll
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
-            
 
     (
    , , )
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 94-118
+.. GENERATED FROM PYTHON SOURCE LINES 103-127
 
 .. code-block:: default
 
@@ -303,7 +310,7 @@ Before diving into plotting, we need to download the example files. Use the foll
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -324,13 +331,17 @@ Before diving into plotting, we need to download the example files. Use the foll
     - Freddy Farah
     
 
-                --------------------------------------------------------
-                There are additional plot options that are defined in a configuration file. 
-                You can change these configurations by passing the keyword argument to the function
-                To print a list of plot options set print_plot_opts=True
+                ----------------------------------------------------------------------------------------------------------
+                There are additional plot options that are defined in the configuration file. 
+                You can change these configurations by passing the keyword argument to the function.
+                To print a list of all plot options set `print_plot_opts=True`
 
                 Here is a list modes : plain , parametric , scatter , atomic , overlay , overlay_species , overlay_orbitals , ipr
-                --------------------------------------------------------
+                ----------------------------------------------------------------------------------------------------------
+            
+
+                WARNING : `fermi` is not set! Set `fermi={value}`. The plot did not shift the bands by the Fermi energy.
+                ----------------------------------------------------------------------------------------------------------
             
 
                 --------------------------------------------------------
@@ -340,16 +351,19 @@ Before diving into plotting, we need to download the example files. Use the foll
 
                 Here is a list modes : plain , parametric , parametric_line , stack , stack_orbitals , stack_species
                 --------------------------------------------------------
+
+                WARNING : `fermi` is not set! Set `fermi={value}`. The plot did not shift the energy by the Fermi energy.
+                ----------------------------------------------------------------------------------------------------------
             
 
-    (
    , , )
+    (
    , , )
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  2.862 seconds)
+   **Total running time of the script:** ( 0 minutes  2.275 seconds)
 
 
 .. _sphx_glr_download_examples_02-bands_dos_plot_bandsdosplot_configurations.py:
diff --git a/docs/_sources/examples/02-bands_dos/sg_execution_times.rst.txt b/docs/_sources/examples/02-bands_dos/sg_execution_times.rst.txt
index fa2c2bae..03b05bdc 100644
--- a/docs/_sources/examples/02-bands_dos/sg_execution_times.rst.txt
+++ b/docs/_sources/examples/02-bands_dos/sg_execution_times.rst.txt
@@ -6,10 +6,10 @@
 
 Computation times
 =================
-**00:03.371** total execution time for **examples_02-bands_dos** files:
+**00:02.660** total execution time for **examples_02-bands_dos** files:
 
 +---------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_02-bands_dos_plot_bandsdosplot_configurations.py` (``plot_bandsdosplot_configurations.py``) | 00:02.862 | 0.0 MB |
+| :ref:`sphx_glr_examples_02-bands_dos_plot_bandsdosplot_configurations.py` (``plot_bandsdosplot_configurations.py``) | 00:02.275 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_02-bands_dos_plot_bandsdosplot.py` (``plot_bandsdosplot.py``)                               | 00:00.509 | 0.0 MB |
+| :ref:`sphx_glr_examples_02-bands_dos_plot_bandsdosplot.py` (``plot_bandsdosplot.py``)                               | 00:00.385 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------------------+-----------+--------+
diff --git a/docs/_sources/examples/03-fermi2d/plot_fermi2d.rst.txt b/docs/_sources/examples/03-fermi2d/plot_fermi2d.rst.txt
index c8ee21a6..173476cc 100644
--- a/docs/_sources/examples/03-fermi2d/plot_fermi2d.rst.txt
+++ b/docs/_sources/examples/03-fermi2d/plot_fermi2d.rst.txt
@@ -64,13 +64,14 @@ Plain mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 36-42
+.. GENERATED FROM PYTHON SOURCE LINES 36-43
 
 .. code-block:: default
 
 
     pyprocar.fermi2D(code = 'vasp', 
                    mode='plain',
+                   fermi=5.590136,
                    dirname=data_dir)
 
 
@@ -95,7 +96,7 @@ Plain mode
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -142,14 +143,14 @@ Plain mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 43-47
+.. GENERATED FROM PYTHON SOURCE LINES 44-48
 
 plain_bands mode
 +++++++++++++++++++++++++++++++++++++++
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 47-57
+.. GENERATED FROM PYTHON SOURCE LINES 48-59
 
 .. code-block:: default
 
@@ -157,6 +158,7 @@ plain_bands mode
     pyprocar.fermi2D(code = 'vasp', 
                    mode='plain_bands',
                    add_legend=True,
+                   fermi=5.590136,
                    dirname=data_dir)
 
 
@@ -184,7 +186,7 @@ plain_bands mode
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -231,7 +233,7 @@ plain_bands mode
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 58-63
+.. GENERATED FROM PYTHON SOURCE LINES 60-65
 
 parametric mode
 +++++++++++++++++++++++++++++++++++++++
@@ -239,7 +241,7 @@ parametric mode
 Does not work. Contact developers
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 63-77
+.. GENERATED FROM PYTHON SOURCE LINES 65-80
 
 .. code-block:: default
 
@@ -252,7 +254,8 @@ Does not work. Contact developers
                     atoms=atoms,
                     orbitals=orbitals,
                     spins=spins,
-                    dirname=data_dir, 
+                    dirname=data_dir,
+                    fermi=5.590136,
                     spin_texture=False)
 
 
@@ -278,7 +281,7 @@ Does not work. Contact developers
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -325,7 +328,7 @@ Does not work. Contact developers
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 78-84
+.. GENERATED FROM PYTHON SOURCE LINES 81-87
 
 Selecting band indices
 +++++++++++++++++++++++++++++++++++++++
@@ -334,7 +337,7 @@ You can specify specfic bands with the band indices keyword.
 band_indices will be a list of list that contain band indices to plot for a given spin. Below I only plot bands 6 and 7 for spin 0
 Also you can specify the colors of the bands as well with band_colors
 
-.. GENERATED FROM PYTHON SOURCE LINES 84-91
+.. GENERATED FROM PYTHON SOURCE LINES 87-95
 
 .. code-block:: default
 
@@ -345,6 +348,7 @@ Also you can specify the colors of the bands as well with band_colors
                    band_indices = band_indices,
                    band_colors=band_colors,
                    add_legend=True,
+                   fermi=5.590136,
                    dirname=data_dir)
 
 
@@ -366,7 +370,7 @@ Also you can specify the colors of the bands as well with band_colors
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -416,7 +420,7 @@ Also you can specify the colors of the bands as well with band_colors
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  7.541 seconds)
+   **Total running time of the script:** ( 0 minutes  6.615 seconds)
 
 
 .. _sphx_glr_download_examples_03-fermi2d_plot_fermi2d.py:
diff --git a/docs/_sources/examples/03-fermi2d/plot_fermi2d_configurations.rst.txt b/docs/_sources/examples/03-fermi2d/plot_fermi2d_configurations.rst.txt
index 39332afa..599d90e3 100644
--- a/docs/_sources/examples/03-fermi2d/plot_fermi2d_configurations.rst.txt
+++ b/docs/_sources/examples/03-fermi2d/plot_fermi2d_configurations.rst.txt
@@ -72,7 +72,7 @@ Before diving into plotting, we need to download the example files. Use the foll
     print(f"Configuration files are located at: {config_path}")
 
     # Print the configurations
-    pyprocar.fermi2D(code='vasp', dirname=data_dir, print_plot_opts=True)
+    pyprocar.fermi2D(code='vasp', dirname=data_dir,fermi=5.599480, print_plot_opts=True)
 
 
 
@@ -96,7 +96,7 @@ Before diving into plotting, we need to download the example files. Use the foll
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -159,7 +159,7 @@ Before diving into plotting, we need to download the example files. Use the foll
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 45-64
+.. GENERATED FROM PYTHON SOURCE LINES 45-65
 
 .. code-block:: default
 
@@ -172,6 +172,7 @@ Before diving into plotting, we need to download the example files. Use the foll
     #
 
     pyprocar.fermi2D(code='vasp',
+                   fermi=5.599480,
                    dirname=data_dir,
                    spin_texture=True,
                    spin_projection='x',
@@ -203,7 +204,7 @@ Before diving into plotting, we need to download the example files. Use the foll
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -249,7 +250,7 @@ Before diving into plotting, we need to download the example files. Use the foll
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 65-84
+.. GENERATED FROM PYTHON SOURCE LINES 66-86
 
 .. code-block:: default
 
@@ -263,6 +264,7 @@ Before diving into plotting, we need to download the example files. Use the foll
 
     pyprocar.fermi2D(code='vasp',
                     dirname=data_dir,
+                    fermi=5.599480,
                     spin_texture=True,
                     spin_projection='z',
                     arrow_size=3,
@@ -293,7 +295,7 @@ Before diving into plotting, we need to download the example files. Use the foll
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -342,7 +344,7 @@ Before diving into plotting, we need to download the example files. Use the foll
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  20.442 seconds)
+   **Total running time of the script:** ( 0 minutes  17.872 seconds)
 
 
 .. _sphx_glr_download_examples_03-fermi2d_plot_fermi2d_configurations.py:
diff --git a/docs/_sources/examples/03-fermi2d/plot_fermi2d_spin_texture.rst.txt b/docs/_sources/examples/03-fermi2d/plot_fermi2d_spin_texture.rst.txt
index 3653f811..07cb8467 100644
--- a/docs/_sources/examples/03-fermi2d/plot_fermi2d_spin_texture.rst.txt
+++ b/docs/_sources/examples/03-fermi2d/plot_fermi2d_spin_texture.rst.txt
@@ -66,7 +66,7 @@ By default the projected values of the arrows will be s_z.
 But you can change this by setting arrow_projection to one of the following
 'x','y','z','x^2','y^2','z^2'
 
-.. GENERATED FROM PYTHON SOURCE LINES 38-49
+.. GENERATED FROM PYTHON SOURCE LINES 38-50
 
 .. code-block:: default
 
@@ -74,6 +74,7 @@ But you can change this by setting arrow_projection to one of the following
 
     pyprocar.fermi2D(code = 'vasp',
                    dirname=data_dir,
+                   fermi=5.5962,
                    spin_texture=True,
                    spin_projection='x',
                    arrow_size=3,
@@ -102,7 +103,7 @@ But you can change this by setting arrow_projection to one of the following
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -148,13 +149,13 @@ But you can change this by setting arrow_projection to one of the following
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 50-53
+.. GENERATED FROM PYTHON SOURCE LINES 51-54
 
 Spin Texture single color
 +++++++++++++++++++++++++++++++++++++++
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 53-64
+.. GENERATED FROM PYTHON SOURCE LINES 54-66
 
 .. code-block:: default
 
@@ -162,6 +163,7 @@ Spin Texture single color
 
     pyprocar.fermi2D(code = 'vasp',
                    dirname=data_dir,
+                   fermi=5.5962,
                    spin_texture=True,
                    arrow_color = 'blue',
                    arrow_size=3,
@@ -190,7 +192,7 @@ Spin Texture single color
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -236,7 +238,7 @@ Spin Texture single color
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 65-71
+.. GENERATED FROM PYTHON SOURCE LINES 67-73
 
 Selecting band indices
 +++++++++++++++++++++++++++++++++++++++
@@ -245,7 +247,7 @@ You can specify specfic bands with the band indices keyword.
 band_indices will be a list of list that contain band indices. Below I only plot bands 14,15
 Also you can specify the colors of the bands as well with band_colors
 
-.. GENERATED FROM PYTHON SOURCE LINES 71-81
+.. GENERATED FROM PYTHON SOURCE LINES 73-84
 
 .. code-block:: default
 
@@ -254,6 +256,7 @@ Also you can specify the colors of the bands as well with band_colors
     band_colors = [['blue','red']]
     pyprocar.fermi2D(code = 'vasp', 
                    mode='plain_bands',
+                   fermi=5.5962,
                    band_indices = band_indices,
                    band_colors=band_colors,
                    spin_texture=True,
@@ -280,7 +283,7 @@ Also you can specify the colors of the bands as well with band_colors
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -329,7 +332,7 @@ Also you can specify the colors of the bands as well with band_colors
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  20.464 seconds)
+   **Total running time of the script:** ( 0 minutes  17.939 seconds)
 
 
 .. _sphx_glr_download_examples_03-fermi2d_plot_fermi2d_spin_texture.py:
diff --git a/docs/_sources/examples/03-fermi2d/plot_rashba_spin_spliting.rst.txt b/docs/_sources/examples/03-fermi2d/plot_rashba_spin_spliting.rst.txt
index fa07e83c..2a44b34f 100644
--- a/docs/_sources/examples/03-fermi2d/plot_rashba_spin_spliting.rst.txt
+++ b/docs/_sources/examples/03-fermi2d/plot_rashba_spin_spliting.rst.txt
@@ -64,7 +64,7 @@ energy = 0.60 sx projection no arrows
 +++++++++++++++++++++++++++++++++++++++++++++
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 36-45
+.. GENERATED FROM PYTHON SOURCE LINES 36-46
 
 .. code-block:: default
 
@@ -72,6 +72,7 @@ energy = 0.60 sx projection no arrows
     pyprocar.fermi2D(code = 'vasp',
                    dirname=data_dir,
                    energy=0.60,
+                   fermi=-1.1904,
                    spin_texture=True,
                    no_arrow=True,
                    spin_projection='x',
@@ -98,7 +99,7 @@ energy = 0.60 sx projection no arrows
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -144,13 +145,13 @@ energy = 0.60 sx projection no arrows
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 46-49
+.. GENERATED FROM PYTHON SOURCE LINES 47-50
 
 energy = 0.60 sy projection no arrows 
 +++++++++++++++++++++++++++++++++++++++++++++
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 49-59
+.. GENERATED FROM PYTHON SOURCE LINES 50-61
 
 .. code-block:: default
 
@@ -158,6 +159,7 @@ energy = 0.60 sy projection no arrows
     pyprocar.fermi2D(code = 'vasp',
                    dirname=data_dir,
                    energy=0.60,
+                   fermi=-1.1904,
                    spin_texture=True,
                    no_arrow=True,
                    spin_projection='y',
@@ -185,7 +187,7 @@ energy = 0.60 sy projection no arrows
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -231,13 +233,13 @@ energy = 0.60 sy projection no arrows
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 60-63
+.. GENERATED FROM PYTHON SOURCE LINES 62-65
 
 energy = 0.60 sz projection no arrows 
 +++++++++++++++++++++++++++++++++++++++++++++
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 63-72
+.. GENERATED FROM PYTHON SOURCE LINES 65-75
 
 .. code-block:: default
 
@@ -245,6 +247,7 @@ energy = 0.60 sz projection no arrows
     pyprocar.fermi2D(code = 'vasp',
                    dirname=data_dir,
                    energy=0.60,
+                   fermi=-1.1904,
                    spin_texture=True,
                    no_arrow=True,
                    spin_projection='z',
@@ -271,7 +274,7 @@ energy = 0.60 sz projection no arrows
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -317,13 +320,13 @@ energy = 0.60 sz projection no arrows
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 73-76
+.. GENERATED FROM PYTHON SOURCE LINES 76-79
 
 energy = -0.90 sx projection no arrows 
 +++++++++++++++++++++++++++++++++++++++++++++
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 76-85
+.. GENERATED FROM PYTHON SOURCE LINES 79-89
 
 .. code-block:: default
 
@@ -331,6 +334,7 @@ energy = -0.90 sx projection no arrows
     pyprocar.fermi2D(code = 'vasp',
                    dirname=data_dir,
                    energy=-0.90,
+                   fermi=-1.1904,
                    spin_texture=True,
                    no_arrow=True,
                    spin_projection='x',
@@ -357,7 +361,7 @@ energy = -0.90 sx projection no arrows
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -403,13 +407,13 @@ energy = -0.90 sx projection no arrows
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 86-89
+.. GENERATED FROM PYTHON SOURCE LINES 90-93
 
 energy = -0.90 sy projection no arrows 
 +++++++++++++++++++++++++++++++++++++++++++++
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 89-99
+.. GENERATED FROM PYTHON SOURCE LINES 93-104
 
 .. code-block:: default
 
@@ -417,6 +421,7 @@ energy = -0.90 sy projection no arrows
     pyprocar.fermi2D(code = 'vasp',
                    dirname=data_dir,
                    energy=-0.90,
+                   fermi=-1.1904,
                    spin_texture=True,
                    no_arrow=True,
                    spin_projection='y',
@@ -444,7 +449,7 @@ energy = -0.90 sy projection no arrows
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -490,13 +495,13 @@ energy = -0.90 sy projection no arrows
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 100-103
+.. GENERATED FROM PYTHON SOURCE LINES 105-108
 
 energy = -0.90 sz projection no arrows 
 +++++++++++++++++++++++++++++++++++++++++++++
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 103-113
+.. GENERATED FROM PYTHON SOURCE LINES 108-119
 
 .. code-block:: default
 
@@ -504,6 +509,7 @@ energy = -0.90 sz projection no arrows
     pyprocar.fermi2D(code = 'vasp',
                    dirname=data_dir,
                    energy=-0.90,
+                   fermi=-1.1904,
                    spin_texture=True,
                    no_arrow=True,
                    spin_projection='z',
@@ -531,7 +537,7 @@ energy = -0.90 sz projection no arrows
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -577,13 +583,13 @@ energy = -0.90 sz projection no arrows
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 114-117
+.. GENERATED FROM PYTHON SOURCE LINES 120-123
 
 energy = 0.60 sx projection with arrows 
 +++++++++++++++++++++++++++++++++++++++++++++
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 117-127
+.. GENERATED FROM PYTHON SOURCE LINES 123-134
 
 .. code-block:: default
 
@@ -591,6 +597,7 @@ energy = 0.60 sx projection with arrows
     pyprocar.fermi2D(code = 'vasp',
                    dirname=data_dir,
                    energy=0.60,
+                   fermi=-1.1904,
                    spin_texture=True,
                    spin_projection='x',
                    arrow_size=3,
@@ -618,7 +625,7 @@ energy = 0.60 sx projection with arrows
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -664,13 +671,13 @@ energy = 0.60 sx projection with arrows
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 128-131
+.. GENERATED FROM PYTHON SOURCE LINES 135-138
 
 energy = -0.90 sx projection with arrows 
 +++++++++++++++++++++++++++++++++++++++++++++
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 131-140
+.. GENERATED FROM PYTHON SOURCE LINES 138-148
 
 .. code-block:: default
 
@@ -678,6 +685,7 @@ energy = -0.90 sx projection with arrows
     pyprocar.fermi2D(code = 'vasp',
                    dirname=data_dir,
                    energy=-0.90,
+                   fermi=-1.1904,
                    spin_texture=True,
                    spin_projection='x',
                    arrow_size=3,
@@ -704,7 +712,7 @@ energy = -0.90 sx projection with arrows
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -753,7 +761,7 @@ energy = -0.90 sx projection with arrows
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  51.878 seconds)
+   **Total running time of the script:** ( 0 minutes  47.411 seconds)
 
 
 .. _sphx_glr_download_examples_03-fermi2d_plot_rashba_spin_spliting.py:
diff --git a/docs/_sources/examples/03-fermi2d/sg_execution_times.rst.txt b/docs/_sources/examples/03-fermi2d/sg_execution_times.rst.txt
index 2295e6c6..c49f7591 100644
--- a/docs/_sources/examples/03-fermi2d/sg_execution_times.rst.txt
+++ b/docs/_sources/examples/03-fermi2d/sg_execution_times.rst.txt
@@ -6,14 +6,14 @@
 
 Computation times
 =================
-**01:40.326** total execution time for **examples_03-fermi2d** files:
+**01:29.837** total execution time for **examples_03-fermi2d** files:
 
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_03-fermi2d_plot_rashba_spin_spliting.py` (``plot_rashba_spin_spliting.py``)     | 00:51.878 | 0.0 MB |
+| :ref:`sphx_glr_examples_03-fermi2d_plot_rashba_spin_spliting.py` (``plot_rashba_spin_spliting.py``)     | 00:47.411 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_03-fermi2d_plot_fermi2d_spin_texture.py` (``plot_fermi2d_spin_texture.py``)     | 00:20.464 | 0.0 MB |
+| :ref:`sphx_glr_examples_03-fermi2d_plot_fermi2d_spin_texture.py` (``plot_fermi2d_spin_texture.py``)     | 00:17.939 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_03-fermi2d_plot_fermi2d_configurations.py` (``plot_fermi2d_configurations.py``) | 00:20.442 | 0.0 MB |
+| :ref:`sphx_glr_examples_03-fermi2d_plot_fermi2d_configurations.py` (``plot_fermi2d_configurations.py``) | 00:17.872 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_03-fermi2d_plot_fermi2d.py` (``plot_fermi2d.py``)                               | 00:07.541 | 0.0 MB |
+| :ref:`sphx_glr_examples_03-fermi2d_plot_fermi2d.py` (``plot_fermi2d.py``)                               | 00:06.615 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
diff --git a/docs/_sources/examples/04-fermi3d/plot_de_hass_van_alphen.rst.txt b/docs/_sources/examples/04-fermi3d/plot_de_hass_van_alphen.rst.txt
index 0984a1f0..adb918b9 100644
--- a/docs/_sources/examples/04-fermi3d/plot_de_hass_van_alphen.rst.txt
+++ b/docs/_sources/examples/04-fermi3d/plot_de_hass_van_alphen.rst.txt
@@ -110,6 +110,15 @@ importing pyprocar and specifying local data_dir
 
 
 
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                    WARNING : Fermi Energy not set! Set `fermi={value}`. By default, using fermi energy found in given directory.
+                    ---------------------------------------------------------------------------------------------------------------
+                
+
 
 
 
@@ -291,7 +300,7 @@ In the above figure we can see the cross section area is :math:`A = 4.3956 Ang^{
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  13.452 seconds)
+   **Total running time of the script:** ( 0 minutes  11.543 seconds)
 
 
 .. _sphx_glr_download_examples_04-fermi3d_plot_de_hass_van_alphen.py:
diff --git a/docs/_sources/examples/04-fermi3d/plot_fermi3d_configurations.rst.txt b/docs/_sources/examples/04-fermi3d/plot_fermi3d_configurations.rst.txt
index 26b7e555..40def4df 100644
--- a/docs/_sources/examples/04-fermi3d/plot_fermi3d_configurations.rst.txt
+++ b/docs/_sources/examples/04-fermi3d/plot_fermi3d_configurations.rst.txt
@@ -66,6 +66,15 @@ Before diving into plotting, we need to download the example files. Use the foll
 
 
 
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                    WARNING : Fermi Energy not set! Set `fermi={value}`. By default, using fermi energy found in given directory.
+                    ---------------------------------------------------------------------------------------------------------------
+                
+
 
 
 
@@ -223,7 +232,7 @@ Before diving into plotting, we need to download the example files. Use the foll
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  17.454 seconds)
+   **Total running time of the script:** ( 0 minutes  15.118 seconds)
 
 
 .. _sphx_glr_download_examples_04-fermi3d_plot_fermi3d_configurations.py:
diff --git a/docs/_sources/examples/04-fermi3d/plot_fermi3d_cross_section.rst.txt b/docs/_sources/examples/04-fermi3d/plot_fermi3d_cross_section.rst.txt
index 62b7cc90..2548c5d3 100644
--- a/docs/_sources/examples/04-fermi3d/plot_fermi3d_cross_section.rst.txt
+++ b/docs/_sources/examples/04-fermi3d/plot_fermi3d_cross_section.rst.txt
@@ -97,6 +97,15 @@ importing pyprocar and specifying local data_dir
 
 
 
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                    WARNING : Fermi Energy not set! Set `fermi={value}`. By default, using fermi energy found in given directory.
+                    ---------------------------------------------------------------------------------------------------------------
+                
+
 
 
 
@@ -238,7 +247,7 @@ Cross section. Save slice
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 2 minutes  14.053 seconds)
+   **Total running time of the script:** ( 2 minutes  2.077 seconds)
 
 
 .. _sphx_glr_download_examples_04-fermi3d_plot_fermi3d_cross_section.py:
diff --git a/docs/_sources/examples/04-fermi3d/plot_fermi3d_isoslider.rst.txt b/docs/_sources/examples/04-fermi3d/plot_fermi3d_isoslider.rst.txt
index 3f13676a..57f1d7e5 100644
--- a/docs/_sources/examples/04-fermi3d/plot_fermi3d_isoslider.rst.txt
+++ b/docs/_sources/examples/04-fermi3d/plot_fermi3d_isoslider.rst.txt
@@ -95,6 +95,15 @@ importing pyprocar and specifying local data_dir
 
 
 
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                    WARNING : Fermi Energy not set! Set `fermi={value}`. By default, using fermi energy found in given directory.
+                    ---------------------------------------------------------------------------------------------------------------
+                
+
 
 
 
@@ -158,7 +167,7 @@ Plain mode
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  33.821 seconds)
+   **Total running time of the script:** ( 0 minutes  30.350 seconds)
 
 
 .. _sphx_glr_download_examples_04-fermi3d_plot_fermi3d_isoslider.py:
diff --git a/docs/_sources/examples/04-fermi3d/plot_fermi3d_isovalue_gif.rst.txt b/docs/_sources/examples/04-fermi3d/plot_fermi3d_isovalue_gif.rst.txt
index e20734e0..16a504eb 100644
--- a/docs/_sources/examples/04-fermi3d/plot_fermi3d_isovalue_gif.rst.txt
+++ b/docs/_sources/examples/04-fermi3d/plot_fermi3d_isovalue_gif.rst.txt
@@ -94,6 +94,15 @@ importing pyprocar and specifying local data_dir
 
 
 
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                    WARNING : Fermi Energy not set! Set `fermi={value}`. By default, using fermi energy found in given directory.
+                    ---------------------------------------------------------------------------------------------------------------
+                
+
 
 
 
@@ -159,7 +168,7 @@ Plain mode
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  34.508 seconds)
+   **Total running time of the script:** ( 0 minutes  31.163 seconds)
 
 
 .. _sphx_glr_download_examples_04-fermi3d_plot_fermi3d_isovalue_gif.py:
diff --git a/docs/_sources/examples/04-fermi3d/plot_fermi3d_plain.rst.txt b/docs/_sources/examples/04-fermi3d/plot_fermi3d_plain.rst.txt
index 36f7f9d8..5c07e2e6 100644
--- a/docs/_sources/examples/04-fermi3d/plot_fermi3d_plain.rst.txt
+++ b/docs/_sources/examples/04-fermi3d/plot_fermi3d_plain.rst.txt
@@ -94,6 +94,15 @@ importing pyprocar and specifying local data_dir
 
 
 
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                    WARNING : Fermi Energy not set! Set `fermi={value}`. By default, using fermi energy found in given directory.
+                    ---------------------------------------------------------------------------------------------------------------
+                
+
 
 
 
@@ -195,7 +204,7 @@ Parametric mode
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  16.667 seconds)
+   **Total running time of the script:** ( 0 minutes  15.851 seconds)
 
 
 .. _sphx_glr_download_examples_04-fermi3d_plot_fermi3d_plain.py:
diff --git a/docs/_sources/examples/04-fermi3d/plot_fermi3d_spin-polarized.rst.txt b/docs/_sources/examples/04-fermi3d/plot_fermi3d_spin-polarized.rst.txt
index ac4d752b..b3336f5d 100644
--- a/docs/_sources/examples/04-fermi3d/plot_fermi3d_spin-polarized.rst.txt
+++ b/docs/_sources/examples/04-fermi3d/plot_fermi3d_spin-polarized.rst.txt
@@ -95,6 +95,15 @@ importing pyprocar and specifying local data_dir
 
 
 
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                    WARNING : Fermi Energy not set! Set `fermi={value}`. By default, using fermi energy found in given directory.
+                    ---------------------------------------------------------------------------------------------------------------
+                
+
 
 
 
@@ -235,7 +244,7 @@ Parametric mode
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  27.690 seconds)
+   **Total running time of the script:** ( 0 minutes  24.356 seconds)
 
 
 .. _sphx_glr_download_examples_04-fermi3d_plot_fermi3d_spin-polarized.py:
diff --git a/docs/_sources/examples/04-fermi3d/plot_fermi3d_spin_texture.rst.txt b/docs/_sources/examples/04-fermi3d/plot_fermi3d_spin_texture.rst.txt
index 0a725c98..3281b7d8 100644
--- a/docs/_sources/examples/04-fermi3d/plot_fermi3d_spin_texture.rst.txt
+++ b/docs/_sources/examples/04-fermi3d/plot_fermi3d_spin_texture.rst.txt
@@ -97,6 +97,15 @@ importing pyprocar and specifying local data_dir
 
 
 
+.. rst-class:: sphx-glr-script-out
+
+ .. code-block:: none
+
+
+                    WARNING : Fermi Energy not set! Set `fermi={value}`. By default, using fermi energy found in given directory.
+                    ---------------------------------------------------------------------------------------------------------------
+                
+
 
 
 
@@ -148,7 +157,7 @@ Spin Texture mode
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 1 minutes  10.996 seconds)
+   **Total running time of the script:** ( 1 minutes  2.304 seconds)
 
 
 .. _sphx_glr_download_examples_04-fermi3d_plot_fermi3d_spin_texture.py:
diff --git a/docs/_sources/examples/04-fermi3d/sg_execution_times.rst.txt b/docs/_sources/examples/04-fermi3d/sg_execution_times.rst.txt
index 0dd8545a..12d7d006 100644
--- a/docs/_sources/examples/04-fermi3d/sg_execution_times.rst.txt
+++ b/docs/_sources/examples/04-fermi3d/sg_execution_times.rst.txt
@@ -6,22 +6,22 @@
 
 Computation times
 =================
-**05:48.641** total execution time for **examples_04-fermi3d** files:
+**05:12.762** total execution time for **examples_04-fermi3d** files:
 
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_cross_section.py` (``plot_fermi3d_cross_section.py``)   | 02:14.053 | 0.0 MB |
+| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_cross_section.py` (``plot_fermi3d_cross_section.py``)   | 02:02.077 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_spin_texture.py` (``plot_fermi3d_spin_texture.py``)     | 01:10.996 | 0.0 MB |
+| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_spin_texture.py` (``plot_fermi3d_spin_texture.py``)     | 01:02.304 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_isovalue_gif.py` (``plot_fermi3d_isovalue_gif.py``)     | 00:34.508 | 0.0 MB |
+| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_isovalue_gif.py` (``plot_fermi3d_isovalue_gif.py``)     | 00:31.163 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_isoslider.py` (``plot_fermi3d_isoslider.py``)           | 00:33.821 | 0.0 MB |
+| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_isoslider.py` (``plot_fermi3d_isoslider.py``)           | 00:30.350 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_spin-polarized.py` (``plot_fermi3d_spin-polarized.py``) | 00:27.690 | 0.0 MB |
+| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_spin-polarized.py` (``plot_fermi3d_spin-polarized.py``) | 00:24.356 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_configurations.py` (``plot_fermi3d_configurations.py``) | 00:17.454 | 0.0 MB |
+| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_plain.py` (``plot_fermi3d_plain.py``)                   | 00:15.851 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_plain.py` (``plot_fermi3d_plain.py``)                   | 00:16.667 | 0.0 MB |
+| :ref:`sphx_glr_examples_04-fermi3d_plot_fermi3d_configurations.py` (``plot_fermi3d_configurations.py``) | 00:15.118 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_04-fermi3d_plot_de_hass_van_alphen.py` (``plot_de_hass_van_alphen.py``)         | 00:13.452 | 0.0 MB |
+| :ref:`sphx_glr_examples_04-fermi3d_plot_de_hass_van_alphen.py` (``plot_de_hass_van_alphen.py``)         | 00:11.543 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------+-----------+--------+
diff --git a/docs/_sources/examples/05-other/plot_2dkmesh_generation.rst.txt b/docs/_sources/examples/05-other/plot_2dkmesh_generation.rst.txt
index 0274ad3f..7d99bb6d 100644
--- a/docs/_sources/examples/05-other/plot_2dkmesh_generation.rst.txt
+++ b/docs/_sources/examples/05-other/plot_2dkmesh_generation.rst.txt
@@ -108,7 +108,7 @@ importing pyprocar and specifying local data_dir
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -135,7 +135,7 @@ importing pyprocar and specifying local data_dir
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.466 seconds)
+   **Total running time of the script:** ( 0 minutes  0.521 seconds)
 
 
 .. _sphx_glr_download_examples_05-other_plot_2dkmesh_generation.py:
diff --git a/docs/_sources/examples/05-other/plot_bandgap.rst.txt b/docs/_sources/examples/05-other/plot_bandgap.rst.txt
index 7d3571a9..70652bab 100644
--- a/docs/_sources/examples/05-other/plot_bandgap.rst.txt
+++ b/docs/_sources/examples/05-other/plot_bandgap.rst.txt
@@ -89,7 +89,7 @@ importing pyprocar and specifying local data_dir
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.138 seconds)
+   **Total running time of the script:** ( 0 minutes  0.129 seconds)
 
 
 .. _sphx_glr_download_examples_05-other_plot_bandgap.py:
diff --git a/docs/_sources/examples/05-other/plot_ebs.rst.txt b/docs/_sources/examples/05-other/plot_ebs.rst.txt
index 83b99c78..648b76d3 100644
--- a/docs/_sources/examples/05-other/plot_ebs.rst.txt
+++ b/docs/_sources/examples/05-other/plot_ebs.rst.txt
@@ -341,7 +341,7 @@ Effective mass
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  4.765 seconds)
+   **Total running time of the script:** ( 0 minutes  4.394 seconds)
 
 
 .. _sphx_glr_download_examples_05-other_plot_ebs.py:
diff --git a/docs/_sources/examples/05-other/plot_kpath_generation.rst.txt b/docs/_sources/examples/05-other/plot_kpath_generation.rst.txt
index aaab0ec8..e7006a2a 100644
--- a/docs/_sources/examples/05-other/plot_kpath_generation.rst.txt
+++ b/docs/_sources/examples/05-other/plot_kpath_generation.rst.txt
@@ -151,7 +151,7 @@ importing pyprocar and specifying local data_dir
            |___/
     A Python library for electronic structure pre/post-processing.
 
-    Version 6.1.6 created on Jun 10th, 2021
+    Version 6.1.9 created on Jun 10th, 2021
 
     Please cite:
      Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero.,
@@ -178,7 +178,7 @@ importing pyprocar and specifying local data_dir
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.599 seconds)
+   **Total running time of the script:** ( 0 minutes  0.573 seconds)
 
 
 .. _sphx_glr_download_examples_05-other_plot_kpath_generation.py:
diff --git a/docs/_sources/examples/05-other/sg_execution_times.rst.txt b/docs/_sources/examples/05-other/sg_execution_times.rst.txt
index e30e49cc..0ddc5918 100644
--- a/docs/_sources/examples/05-other/sg_execution_times.rst.txt
+++ b/docs/_sources/examples/05-other/sg_execution_times.rst.txt
@@ -6,14 +6,14 @@
 
 Computation times
 =================
-**00:05.968** total execution time for **examples_05-other** files:
+**00:05.617** total execution time for **examples_05-other** files:
 
 +-----------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_05-other_plot_ebs.py` (``plot_ebs.py``)                               | 00:04.765 | 0.0 MB |
+| :ref:`sphx_glr_examples_05-other_plot_ebs.py` (``plot_ebs.py``)                               | 00:04.394 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_05-other_plot_kpath_generation.py` (``plot_kpath_generation.py``)     | 00:00.599 | 0.0 MB |
+| :ref:`sphx_glr_examples_05-other_plot_kpath_generation.py` (``plot_kpath_generation.py``)     | 00:00.573 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_05-other_plot_2dkmesh_generation.py` (``plot_2dkmesh_generation.py``) | 00:00.466 | 0.0 MB |
+| :ref:`sphx_glr_examples_05-other_plot_2dkmesh_generation.py` (``plot_2dkmesh_generation.py``) | 00:00.521 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_05-other_plot_bandgap.py` (``plot_bandgap.py``)                       | 00:00.138 | 0.0 MB |
+| :ref:`sphx_glr_examples_05-other_plot_bandgap.py` (``plot_bandgap.py``)                       | 00:00.129 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------+-----------+--------+
diff --git a/docs/_sources/examples/06-PyPoscar/plot_clusters_pyposcar.rst.txt b/docs/_sources/examples/06-PyPoscar/plot_clusters_pyposcar.rst.txt
index c1e57209..767d5e98 100644
--- a/docs/_sources/examples/06-PyPoscar/plot_clusters_pyposcar.rst.txt
+++ b/docs/_sources/examples/06-PyPoscar/plot_clusters_pyposcar.rst.txt
@@ -176,7 +176,7 @@ Visualizing the Clusters
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  6.360 seconds)
+   **Total running time of the script:** ( 0 minutes  6.081 seconds)
 
 
 .. _sphx_glr_download_examples_06-PyPoscar_plot_clusters_pyposcar.py:
diff --git a/docs/_sources/examples/06-PyPoscar/plot_finding_defects_pyposcar.rst.txt b/docs/_sources/examples/06-PyPoscar/plot_finding_defects_pyposcar.rst.txt
index 808179e2..45292112 100644
--- a/docs/_sources/examples/06-PyPoscar/plot_finding_defects_pyposcar.rst.txt
+++ b/docs/_sources/examples/06-PyPoscar/plot_finding_defects_pyposcar.rst.txt
@@ -177,7 +177,7 @@ Finding defects
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  7.200 seconds)
+   **Total running time of the script:** ( 0 minutes  7.393 seconds)
 
 
 .. _sphx_glr_download_examples_06-PyPoscar_plot_finding_defects_pyposcar.py:
diff --git a/docs/_sources/examples/06-PyPoscar/plot_rdf_cutoff_pyposcar.rst.txt b/docs/_sources/examples/06-PyPoscar/plot_rdf_cutoff_pyposcar.rst.txt
index 56000718..9ec75402 100644
--- a/docs/_sources/examples/06-PyPoscar/plot_rdf_cutoff_pyposcar.rst.txt
+++ b/docs/_sources/examples/06-PyPoscar/plot_rdf_cutoff_pyposcar.rst.txt
@@ -237,7 +237,7 @@ Visualizing the Results
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.719 seconds)
+   **Total running time of the script:** ( 0 minutes  0.630 seconds)
 
 
 .. _sphx_glr_download_examples_06-PyPoscar_plot_rdf_cutoff_pyposcar.py:
diff --git a/docs/_sources/examples/06-PyPoscar/plot_subsitution_pyposcar.rst.txt b/docs/_sources/examples/06-PyPoscar/plot_subsitution_pyposcar.rst.txt
index 3cc78cac..f9d803e3 100644
--- a/docs/_sources/examples/06-PyPoscar/plot_subsitution_pyposcar.rst.txt
+++ b/docs/_sources/examples/06-PyPoscar/plot_subsitution_pyposcar.rst.txt
@@ -262,7 +262,7 @@ Creating GIFs for Visualization
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  6.106 seconds)
+   **Total running time of the script:** ( 0 minutes  6.288 seconds)
 
 
 .. _sphx_glr_download_examples_06-PyPoscar_plot_subsitution_pyposcar.py:
diff --git a/docs/_sources/examples/06-PyPoscar/plot_utils_pyposcar.rst.txt b/docs/_sources/examples/06-PyPoscar/plot_utils_pyposcar.rst.txt
index d250eb51..c3ce57f5 100644
--- a/docs/_sources/examples/06-PyPoscar/plot_utils_pyposcar.rst.txt
+++ b/docs/_sources/examples/06-PyPoscar/plot_utils_pyposcar.rst.txt
@@ -343,7 +343,7 @@ Introducing Defects
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  18.327 seconds)
+   **Total running time of the script:** ( 0 minutes  17.455 seconds)
 
 
 .. _sphx_glr_download_examples_06-PyPoscar_plot_utils_pyposcar.py:
diff --git a/docs/_sources/examples/06-PyPoscar/sg_execution_times.rst.txt b/docs/_sources/examples/06-PyPoscar/sg_execution_times.rst.txt
index 8f2d0f20..43bf247d 100644
--- a/docs/_sources/examples/06-PyPoscar/sg_execution_times.rst.txt
+++ b/docs/_sources/examples/06-PyPoscar/sg_execution_times.rst.txt
@@ -6,16 +6,16 @@
 
 Computation times
 =================
-**00:38.711** total execution time for **examples_06-PyPoscar** files:
+**00:37.848** total execution time for **examples_06-PyPoscar** files:
 
 +--------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_06-PyPoscar_plot_utils_pyposcar.py` (``plot_utils_pyposcar.py``)                     | 00:18.327 | 0.0 MB |
+| :ref:`sphx_glr_examples_06-PyPoscar_plot_utils_pyposcar.py` (``plot_utils_pyposcar.py``)                     | 00:17.455 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_06-PyPoscar_plot_finding_defects_pyposcar.py` (``plot_finding_defects_pyposcar.py``) | 00:07.200 | 0.0 MB |
+| :ref:`sphx_glr_examples_06-PyPoscar_plot_finding_defects_pyposcar.py` (``plot_finding_defects_pyposcar.py``) | 00:07.393 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_06-PyPoscar_plot_clusters_pyposcar.py` (``plot_clusters_pyposcar.py``)               | 00:06.360 | 0.0 MB |
+| :ref:`sphx_glr_examples_06-PyPoscar_plot_subsitution_pyposcar.py` (``plot_subsitution_pyposcar.py``)         | 00:06.288 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_06-PyPoscar_plot_subsitution_pyposcar.py` (``plot_subsitution_pyposcar.py``)         | 00:06.106 | 0.0 MB |
+| :ref:`sphx_glr_examples_06-PyPoscar_plot_clusters_pyposcar.py` (``plot_clusters_pyposcar.py``)               | 00:06.081 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_06-PyPoscar_plot_rdf_cutoff_pyposcar.py` (``plot_rdf_cutoff_pyposcar.py``)           | 00:00.719 | 0.0 MB |
+| :ref:`sphx_glr_examples_06-PyPoscar_plot_rdf_cutoff_pyposcar.py` (``plot_rdf_cutoff_pyposcar.py``)           | 00:00.630 | 0.0 MB |
 +--------------------------------------------------------------------------------------------------------------+-----------+--------+
diff --git a/docs/_sources/examples/index.rst.txt b/docs/_sources/examples/index.rst.txt
index 544f4138..993d0c05 100644
--- a/docs/_sources/examples/index.rst.txt
+++ b/docs/_sources/examples/index.rst.txt
@@ -50,69 +50,69 @@ These examples demonstrate the band structure plotting capabilities.
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_noncolinear_vasp_thumb.png
+  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_compare_bands_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_00-band_structure_plot_noncolinear_vasp.py`
+  :ref:`sphx_glr_examples_00-band_structure_plot_compare_bands.py`
 
 .. raw:: html
 
-      
    Plotting non colinear band structures in VASP
    
+      
    Comparing band structures
    
     
    
 
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_compare_bands_thumb.png
+  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_atomic_levels_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_00-band_structure_plot_compare_bands.py`
+  :ref:`sphx_glr_examples_00-band_structure_plot_atomic_levels.py`
 
 .. raw:: html
 
-      
    Comparing band structures
    
+      
    Plotting Atomic Levels
    
     
    
 
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_noncolinear_qe_thumb.png
+  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_noncolinear_vasp_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_00-band_structure_plot_noncolinear_qe.py`
+  :ref:`sphx_glr_examples_00-band_structure_plot_noncolinear_vasp.py`
 
 .. raw:: html
 
-      
    Plotting non colinear band structures in Quantum Espresso
    
+      
    Plotting non colinear band structures in VASP
    
     
    
 
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_atomic_levels_thumb.png
+  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_noncolinear_qe_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_00-band_structure_plot_atomic_levels.py`
+  :ref:`sphx_glr_examples_00-band_structure_plot_noncolinear_qe.py`
 
 .. raw:: html
 
-      
    Plotting Atomic Levels
    
+      
    Plotting non colinear band structures in Quantum Espresso
    
     
    
 
 
@@ -186,35 +186,35 @@ These examples demonstrate the band structure plotting capabilities.
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_2d_bands_thumb.png
+  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_bandsplot_configurations_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_00-band_structure_plot_2d_bands.py`
+  :ref:`sphx_glr_examples_00-band_structure_plot_bandsplot_configurations.py`
 
 .. raw:: html
 
-      
    Plotting 2D band structure
    
+      
    Plotting with Configurations in pyprocar
    
     
    
 
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_bandsplot_configurations_thumb.png
+  .. image:: /examples/00-band_structure/images/thumb/sphx_glr_plot_2d_bands_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_00-band_structure_plot_bandsplot_configurations.py`
+  :ref:`sphx_glr_examples_00-band_structure_plot_2d_bands.py`
 
 .. raw:: html
 
-      
    Plotting with Configurations in pyprocar
    
+      
    Plotting 2D band structure
    
     
    
 
 
@@ -269,52 +269,52 @@ These examples demonstrate the density of states plotting capabilities.
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/01-dos/images/thumb/sphx_glr_plot_colinear_dos_thumb.png
+  .. image:: /examples/01-dos/images/thumb/sphx_glr_plot_dosplot_configurations_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_01-dos_plot_colinear_dos.py`
+  :ref:`sphx_glr_examples_01-dos_plot_dosplot_configurations.py`
 
 .. raw:: html
 
-      
    Plotting density of states
    
+      
    Plotting with Configurations in pyprocar
    
     
    
 
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/01-dos/images/thumb/sphx_glr_plot_spin_polarized_dos_thumb.png
+  .. image:: /examples/01-dos/images/thumb/sphx_glr_plot_colinear_dos_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_01-dos_plot_spin_polarized_dos.py`
+  :ref:`sphx_glr_examples_01-dos_plot_colinear_dos.py`
 
 .. raw:: html
 
-      
    Plotting spin-polarized density of states
    
+      
    Plotting density of states
    
     
    
 
 
 .. raw:: html
 
-    
    
+    
    
 
 .. only:: html
 
-  .. image:: /examples/01-dos/images/thumb/sphx_glr_plot_dosplot_configurations_thumb.png
+  .. image:: /examples/01-dos/images/thumb/sphx_glr_plot_spin_polarized_dos_thumb.png
     :alt:
 
-  :ref:`sphx_glr_examples_01-dos_plot_dosplot_configurations.py`
+  :ref:`sphx_glr_examples_01-dos_plot_spin_polarized_dos.py`
 
 .. raw:: html
 
-      
    Plotting with Configurations in pyprocar
    
+      
    Plotting spin-polarized density of states
    
     
    
 
 
diff --git a/docs/_sources/user-guide/dos.rst.txt b/docs/_sources/user-guide/dos.rst.txt
index 80664ec7..b7290b12 100644
--- a/docs/_sources/user-guide/dos.rst.txt
+++ b/docs/_sources/user-guide/dos.rst.txt
@@ -73,20 +73,20 @@ This mode will use color coding to illustrate the projection of atoms and orbita
 3. ``mode='parametric_line'``
 =============================
 
-This mode might be the most familiar mode to the users. This mode will use curves to plot the projected density of states. The following will plot shows the projection of p orbitals(``orbitals=[1,2,3]``) of O(``atoms=[2,3,4]``) in SrVO\ :sub:`3`\
+This mode will use curves to plot the projected density of states. The following will plot shows the projection of d orbitals(``orbitals=[4,5,6,7,8]``) of Fe(``atoms=[0]``) in Fe.
 
 
->>>  pyprocar.bandsdosplot(code='vasp',
-...                        dirname='vasp_dir',
-...                        mode='parametric_line',
-...                        orbitals=[1, 2, 3],
-...                        atoms=[2, 3, 4],
-...                        elimit=[-4, 4],
-...                        labels=['O-up', 'O-down'],
-...                        plot_total=True)
+>>>  pyprocar.dosplot(
+...                  code='qe', 
+...                  mode='parametric_line',
+...                  fermi=5.599480,
+...                  atoms=[0],
+...                  orbitals=[4,5,6,7,8],
+...                  spins=[0],
+...                  dirname=data_dir)
 
 
-.. image:: ../images/dos_parameteric_line.png
+.. image:: ../images/dos_parametric_line.png
 
 
 4. ``mode='stack'``
@@ -137,7 +137,48 @@ This mode is another variation of ``mode=='stack'``, This mode will plot the sel
 ...                   elimit=[-4, 4],
 ...                   plot_total=True)
 
-.. image:: ../images/dos_stack_orbitals.png
+
+7. ``mode='overlay'``
+============================
+
+This mode is another variation of ``mode=='overlay'``. This mode will plot the selected atoms and orbitals. The following will plot shows the projection of d orbitals(``orbitals=[4,5,6,7,8]``) of Fe(``atoms=[0]``) in Fe.
+
+>>>  pyprocar.dosplot(
+...                  code='qe',
+...                  mode='overlay',
+...                  fermi=5.599480,
+...                  items=items,
+...                  dirname=data_dir)
+
+.. image:: ../images/dos_overlay.png
+
+8. ``mode='overlay_species'``
+===============================
+
+This mode is another variation of ``mode=='overlay_species'``. This mode will plot the selected orbitals for all the species. The plot will be stached curves with filled areas under the curve. This mode will plot the selected orbitals for all the species. For example if ``orbitals=[4,5,6,7,8]``, PyProcar will plot all the d orbitals of all the species. If no orbital is specifies, it will plot the projection over all the species. The following example is representing the stacked curves for all species, without orbitals defined(i.e. sum over all the orbitals)
+
+>>>  pyprocar.dosplot(
+...                  code='qe',
+...                  mode='overlay_species',
+...                  fermi=5.599480,
+...                  orbitals=[4,5,6,7,8],
+...                  dirname=data_dir)
+
+.. image:: ../images/dos_overlay_species.png
+
+9. ``mode='overlay_orbitals'``
+===============================
+
+This mode is another variation of ``mode=='overlay_orbitals'``. This mode will plot the selected atoms for all the orbitals. The list of atoms do not need to be from the same species. The following will plot shows all the orbitals for Fe(``atoms=[0]``).
+
+>>>  pyprocar.dosplot(
+...                  code='qe',
+...                  mode='overlay',
+...                  fermi=5.599480,
+...                  atoms=[0],
+...                  dirname=data_dir)
+
+.. image:: ../images/dos_overlay_orbitals.png
 
 .. automodule:: pyprocar.scriptDosplot
 	:members:
diff --git a/docs/_sources/user-guide/fermi3d.rst.txt b/docs/_sources/user-guide/fermi3d.rst.txt
index 12877f12..250c7e48 100644
--- a/docs/_sources/user-guide/fermi3d.rst.txt
+++ b/docs/_sources/user-guide/fermi3d.rst.txt
@@ -82,9 +82,7 @@ an isosurfcace which is handled by the class
 This function requires a list of kpoints and the eigen-values of the
 energy for a specific band. However one does not have to be concerned
 about the specifics of different layers and just use the
-pyprocar.fermi3D function to generate the fermi surface. The
-different arguments required by this function are explained in details
-at `the bottom of this page `_.
+pyprocar.fermi3D function to generate the fermi surface.
 This work would not have been possible without the amazing packages, `pyvista_doc
 `_ and `trimesh_doc
 `_.
@@ -208,6 +206,6 @@ shortcuts are available:
 | ``+``/``-``                                           | Increase/decrease the point size and line widths    |
 +-------------------------------------+-----------------+-----------------------------------------------------+
 
-.. automodule:: pyprocar.scripts.scriptFermi3D
+.. automodule:: pyprocar.scripts.scriptFermiHandler
 	:members:
 
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index c6a49541..d28d388c 100644
--- a/docs/_static/documentation_options.js
+++ b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '6.1.8',
+    VERSION: '6.1.9',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/api/cfg/band_structure.html b/docs/api/cfg/band_structure.html
index 6112f66e..f186d88d 100644
--- a/docs/api/cfg/band_structure.html
+++ b/docs/api/cfg/band_structure.html
@@ -8,7 +8,7 @@
     
     
 
-    band structure plotting Options — PyProcar 6.1.8 documentation
+    band structure plotting Options — PyProcar 6.1.9 documentation
   
   
   
@@ -40,7 +40,7 @@
   
 
 
-    
+    
     
     
     
@@ -112,7 +112,7 @@
   
   
   
-    
    PyProcar 6.1.8 documentation
    
+    
    PyProcar 6.1.9 documentation
    
   
 
    
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot
    • 
     
@@ -776,32 +776,24 @@
 
  • bandsplot
    • 
 
 
-
  • bandsplot_2d
-
    • 
-
  • bandsdosplot