Adding phono3py input/output modules. Note: need to fix pydocstyle formatting

.gitignore

@@ -103,4 +103,15 @@ ENV/
 # mypy
 .mypy_cache/
 
-.pytest_cache/
+.pytest_cache/
+
+#Test files for io modules
+jarvis/io/phono3py/Si-testing/
+jarvis/io/phonopy/Si-testing/
+jarvis/io/phono3py/almaBTE_files/
+
+#MacOS Finder files
+.DS_Store
+
+#Downloaded zip files
+*.zip

jarvis/analysis/elastic/tensor.py

@@ -94,6 +94,24 @@ def average_modulus(self):
             np.array(self.voigt_modulus) + np.array(self.reuss_modulus)
         ) / 2
 
+
+    # def debye_temperature(self, atoms=None):
+    #     """Debye temperature."""
+    #     const = 1.05457e-34 / 1.38065e-23  # (h/kb)
+    #     amu_gm = 1.66054e-24 * 1e-3#convert to kilograms 
+    #     factor = ((3 * atoms.num_atoms * atoms.density) / (
+    #         4 * np.pi * atoms.composition.weight * amu_gm
+    #     )) ** (1/3)
+    #     theta = const * factor * self.velocity_average(atoms=atoms)
+    #     return theta
+
+    # def debye_temperature_toberer(self, atoms=None):
+    #     const = 1.05457e-34 / 1.38065e-23  # (h/kb)
+    #     vs =self.velocity_average(atoms)
+    #     V0 = atoms.volume / sum([v for v in atoms.composition.to_dict().values()])
+    #     return (6 * np.pi**2 / (V0 * 1e-30)) ** (1/3) * vs * const
+
+
     @property
     def pugh_ratio_voigt(self):
         """Get Voigt Pugh ratio."""
@@ -132,6 +150,8 @@ def cauchy_pressure(self):
         c = self.et_tensor
         return c[0][1] - c[3][3]
 
+
+
     @property
     def poisson_ratio(self):
         """Get poisson's ratio."""

jarvis/core/kpoints.py

@@ -999,7 +999,7 @@ def trib(self):
         return HighSymmetryKpoint3DFactory(kpoints=kpoints, path=path)
 
 
-"""
+
 if __name__ == "__main__":
     from jarvis.core.atoms import Atoms
     box = [[2.715, 2.715, 0], [0, 2.715, 2.715], [2.715, 0, 2.715]]
@@ -1009,15 +1009,16 @@ def trib(self):
     lattice_mat = Si.lattice_mat
     kp = Kpoints3D().automatic_length_mesh(lattice_mat=lattice_mat)
     # print(kp.__repr__(0))
-    kp.write_file("KPOINTS")
+    #kp.write_file("KPOINTS")
     sym = kp.high_symm_path(Si)._path
     # print (sym)
     x, y = kp.interpolated_points(Si)
+'''
     # for i,j in zip(x,y):
     #   print (i,j)
     Si = Poscar.from_file(
         "/rk2/knc6/JARVIS-DFT/TE-bulk/mp-541837_bulk_PBEBO/MAIN-RELAX-bulk@mp_541837/CONTCAR"
     ).atoms
     kp = Kpoints3D().kpath(atoms=Si)
     kp.write_file("KPOINTS")
-"""
+'''

jarvis/io/phono3py/Si-testing/FORCE_CONSTANTS

@@ -0,0 +1,129 @@
+   2   16
+1 1
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jarvis/io/phono3py/Si-testing/POSCAR-minus

@@ -0,0 +1,10 @@
+Si
+5.371306124482983
+     0.0000000000000000    0.5071343999939496    0.5071343999939496
+     0.5071343999939496    0.0000000000000000    0.5071343999939496
+     0.5071343999939496    0.5071343999939496    0.0000000000000000
+   Si
+   2
+Direct
+  0.8750000000000000  0.8750000000000000  0.8750000000000000
+  0.1250000000000000  0.1250000000000000  0.1250000000000000

jarvis/io/phono3py/Si-testing/POSCAR-plus

@@ -0,0 +1,10 @@
+Si
+5.407354155
+     0.0000000000000000    0.5071343999939496    0.5071343999939496
+     0.5071343999939496    0.0000000000000000    0.5071343999939496
+     0.5071343999939496    0.5071343999939496    0.0000000000000000
+   Si
+   2
+Direct
+  0.8750000000000000  0.8750000000000000  0.8750000000000000
+  0.1250000000000000  0.1250000000000000  0.1250000000000000

jarvis/io/phono3py/Si-testing/POSCAR-unitcell

@@ -0,0 +1,10 @@
+Si
+   5.38930000000000     
+     0.0000000000000000    0.5071343999939496    0.5071343999939496
+     0.5071343999939496    0.0000000000000000    0.5071343999939496
+     0.5071343999939496    0.5071343999939496    0.0000000000000000
+   Si
+   2
+Direct
+  0.8750000000000000  0.8750000000000000  0.8750000000000000
+  0.1250000000000000  0.1250000000000000  0.1250000000000000