V2.4.0 - (1) Spinor wavefunctions are now supported. (2) New: GUI for…

… the plotting tool. (3) BandUP now accepts some optional command-line arguments and flags. (4) Added some new command-line options to the plotting tool. (5) Pythonification of the plotting tool script. All changes are backwards compatible.

README

@@ -45,9 +45,29 @@ System requirements:
             * argparse
             * heapq
         * Please let me know if I've forgotten to list any other package!
+    * Optional: If you want to use the graphical user interface (GUI) version
+                of the plotting tool, you will need to have the PyQt4 package
+                available in your python install.
+                If you cannot use the GUI, you can keep using the plotting tool 
+                in the command line, just as usual.
 
 
 
+===================================================================================
+Tips:
+===================================================================================
+    * It might be handy to include the BandUP_bin folder in your PATH. By doing so,
+      you'll be able to use BandUP in whataver folder you're working at.
+    * BandUP accepts some optional command line options. Run the code with the flag
+      '-help' to see a list of allowed arguments/flags.
+    * Since the plotting tol has a lot of different options, I've given it a GUI:
+          utils/post_unfolding/plot/plotting_tool_GUI/BandUP_plot_GUI.pyw
+      You'll find a symlink to it (bandup_plot) in the BandUP_bin folder.
+      * The GUI requires that you have PyQt4 in you python install.
+      * If you move the BandUP_plot_GUI.pyw file, move the BandUP_plot_GUI.ui too.
+
+
+
 ===================================================================================
 Please mind that:
 ===================================================================================

build.sh

@@ -4,14 +4,57 @@ working_dir=`pwd`
 bin_folder="${working_dir}/BandUP_bin"
 mkdir -p ${bin_folder}
 rm -f ${bin_folder}/BandUP.x
+rm -f ${bin_folder}/bandup
 
 cd ${working_dir}/src/external
     ./BandUP_configure_spglib.sh
+    ./BandUP_configure_cla.sh
 cd ${working_dir}/utils/pre_unfolding/get_SCKPTS_pre_BandUP
     make
     make clean
+    rm -f ${bin_folder}/get_SCKPTS_pre_BandUP.x
+    ln -s `pwd`/get_SCKPTS_pre_BandUP.x ${bin_folder}/get_SCKPTS_pre_BandUP.x
 cd ${working_dir}/src
     make
     make clean
-    mv -f BandUP.x  ${bin_folder} 
+    mv -f BandUP.x  ${bin_folder}
+    ln -s ${bin_folder}/BandUP.x  ${bin_folder}/bandup
 cd ${working_dir}
+
+BANDUP="${bin_folder}/BandUP.x"
+BANDUPBINPATH="${bin_folder}"
+BANDUPPLOTPATH="${working_dir}/utils/post_unfolding/plot/"
+bandup_folder="${working_dir}"
+
+rm -f ${BANDUPBINPATH}/'bandup_plot'
+rm -f ${BANDUPBINPATH}/'BandUP_plot_GUI.ui'
+rm -f ${BANDUPBINPATH}/'plot_unfolded_EBS_BandUP.py'
+ln -s ${BANDUPPLOTPATH}/plotting_tool_GUI/BandUP_plot_GUI.pyw ${BANDUPBINPATH}/'bandup_plot'
+ln -s ${BANDUPPLOTPATH}/plotting_tool_GUI/BandUP_plot_GUI.ui ${BANDUPBINPATH}/'BandUP_plot_GUI.ui'
+ln -s ${BANDUPPLOTPATH}/plot_unfolded_EBS_BandUP.py ${BANDUPBINPATH}/'plot_unfolded_EBS_BandUP.py'
+
+now="$(date +'%Y_%m_%d-%T')"
+for var_name in 'BANDUP' 'BANDUPBINPATH' 'BANDUPPLOTPATH' 'bandup_folder'
+do
+    export_statement="export $var_name=${!var_name}"
+    for filename in ".bashrc" ".bash_profile" ".profile" 
+    do
+        file="${HOME}/${filename}"
+        if [ -e "${file}" ] && [ ! -L "${file}" ]
+        then
+            if ! grep -Fq "$export_statement" $file # if environment variable has not been exported before
+            then
+                # Making a backup of the file in case it needs to be changed
+                backup_file="${file}.backup.before_installing_BandUP_${now}"
+                if [ ! -e "${backup_file}" ]
+                then
+                    cp "${file}" "${backup_file}"
+                    echo "" >> ${file}
+                fi
+                echo "${export_statement} # Set by BandUP in ${now}" >> ${file}
+            fi
+        fi
+    done
+done
+
+# End of script

src/Makefile

@@ -23,13 +23,15 @@ FCFLAGS += -diag-disable remark
 # Aliases
 current_dir = $(shell pwd)
 BandUP_src_folder = $(current_dir)
+cla_folder = $(BandUP_src_folder)/external/claf90
 spglib_folder = $(BandUP_src_folder)/external/spglib-1.5.2
 vasp_related_modules_folder = $(BandUP_src_folder)/vasp_related_modules
 
 # libraries needed for linking
 LIBS = $(spglib_folder)/src/.libs/libsymspg.a
 
 # Folders containing needed sources
+vpath %.f90 $(cla_folder)
 vpath %.f90 $(spglib_folder)/example
 vpath %.f90 $(BandUP_src_folder)
 vpath %.f90 $(vasp_related_modules_folder)
@@ -42,14 +44,16 @@ EXE = BandUP.x
 # "make" builds all
 all: $(EXE)
 
+cla.o: kinds.o
+options_setup_mod.o: cla.o kinds.o
 math_mod.o: spglib_f08.o
 band_unfolding_routines_mod.o: math_mod.o
 read_wavecar_mod.o: math_mod.o general_io_mod.o
 read_vasp_files_mod.o: math_mod.o general_io_mod.o strings_mod.o
 write_vasp_files_mod.o: math_mod.o general_io_mod.o strings_mod.o
 io_routines_mod.o: math_mod.o strings_mod.o general_io_mod.o read_vasp_files_mod.o write_vasp_files_mod.o read_wavecar_mod.o
-$(OBJ): spglib_f08.o math_mod.o io_routines_mod.o read_wavecar_mod.o read_vasp_files_mod.o write_vasp_files_mod.o band_unfolding_routines_mod.o
-$(EXE): spglib_f08.o math_mod.o band_unfolding_routines_mod.o general_io_mod.o read_wavecar_mod.o read_vasp_files_mod.o write_vasp_files_mod.o strings_mod.o io_routines_mod.o $(OBJ)
+$(OBJ): cla.o kinds.o options_setup_mod.o spglib_f08.o math_mod.o io_routines_mod.o read_wavecar_mod.o read_vasp_files_mod.o write_vasp_files_mod.o band_unfolding_routines_mod.o
+$(EXE): cla.o kinds.o options_setup_mod.o spglib_f08.o math_mod.o band_unfolding_routines_mod.o general_io_mod.o read_wavecar_mod.o read_vasp_files_mod.o write_vasp_files_mod.o strings_mod.o io_routines_mod.o $(OBJ)
 
 # ======================================================================
 # General rules

src/band_unfolding_routines_mod.f90

@@ -192,22 +192,22 @@ end subroutine define_pckpts_to_be_checked
 
 
 subroutine select_coeffs_to_calc_spectral_weights(selected_coeff_indices, &
-                                                  iall_G,b_matrix_pc,B_matrix_SC,nplane, & 
+                                                  iall_G,b_matrix_pc,B_matrix_SC, & 
                                                   folding_G, &
                                                   tol_for_vec_equality)
 !! Copyright (C) 2013, 2014 Paulo V. C. Medeiros
 implicit none
 integer, dimension(:), allocatable, intent(out) :: selected_coeff_indices
 integer, dimension(:,:), intent(in) :: iall_G !Coordinates of the G points in the [b1, b2, b3] basis.
 real(kind=dp), dimension(1:3,1:3), intent(in) :: b_matrix_pc,B_matrix_SC
-integer, intent(in) :: nplane
 real(kind=dp), dimension(1:3), intent(in) :: folding_G
 real(kind=dp), intent(in) :: tol_for_vec_equality
-integer :: alloc_stat, ig
+integer :: alloc_stat, ig, nplane
 real(kind=dp), dimension(1:3) :: SC_G, trial_pc_g,g
 real(kind=dp) :: tol
 
     tol = 0.1_dp * tol_for_vec_equality
+    nplane = size(iall_G, dim=2)
     deallocate(selected_coeff_indices, stat=alloc_stat)
     do while((.not. allocated(selected_coeff_indices)) .and. &
               (tol <= max_tol_for_vec_equality))
@@ -375,29 +375,35 @@ subroutine get_delta_Ns_for_output(delta_N_only_selected_dirs,delta_N_symm_avrgd
                                    delta_N,dirs_req_for_symmavgd_EBS_along_pcbz_dir,pckpts_to_be_checked)
 !! Copyright (C) 2013, 2014 Paulo V. C. Medeiros
 implicit none
-type(delta_Ns_for_output), intent(out) :: delta_N_only_selected_dirs, delta_N_symm_avrgd_for_EBS
-type(delta_Ns), intent(in) :: delta_N
+type(delta_Ns_for_output), dimension(:), allocatable, intent(out) :: delta_N_only_selected_dirs, delta_N_symm_avrgd_for_EBS
+type(delta_Ns), dimension(:), intent(in) :: delta_N
 type(selected_pcbz_directions), intent(in) :: pckpts_to_be_checked
 type(irr_bz_directions), dimension(:), intent(in) :: dirs_req_for_symmavgd_EBS_along_pcbz_dir
-integer :: nener,i_selec_pcbz_dir,ipc_kpt,i_needed_dirs
+integer :: nener, i_selec_pcbz_dir, ipc_kpt, i_needed_dirs, n_spinor_components, i_spinor
 real(kind=dp), dimension(:), allocatable :: avrgd_dNs
 real(kind=dp) :: weight
 
-    call allocate_delta_Ns_for_output_type(delta_N_only_selected_dirs,pckpts_to_be_checked)
-    call allocate_delta_Ns_for_output_type(delta_N_symm_avrgd_for_EBS,pckpts_to_be_checked)
-    nener = size(delta_N%selec_pcbz_dir(1)%needed_dir(1)%pckpt(1)%dN(:))
+    n_spinor_components = size(delta_N, dim=1)
+    allocate(delta_N_only_selected_dirs(1:n_spinor_components))
+    allocate(delta_N_symm_avrgd_for_EBS(1:n_spinor_components))
+
+    nener = size(delta_N(1)%selec_pcbz_dir(1)%needed_dir(1)%pckpt(1)%dN(:))
     allocate(avrgd_dNs(1:nener))
-    do i_selec_pcbz_dir=1,size(delta_N%selec_pcbz_dir(:))
-        delta_N_only_selected_dirs%pcbz_dir(i_selec_pcbz_dir) = delta_N%selec_pcbz_dir(i_selec_pcbz_dir)%needed_dir(1)
-        do ipc_kpt=1, size(delta_N%selec_pcbz_dir(i_selec_pcbz_dir)%needed_dir(1)%pckpt(:))
-            avrgd_dNs(:) = 0.0_dp
-            allocate(delta_N_symm_avrgd_for_EBS%pcbz_dir(i_selec_pcbz_dir)%pckpt(ipc_kpt)%dN(1:nener))
-            do i_needed_dirs=1,size(delta_N%selec_pcbz_dir(i_selec_pcbz_dir)%needed_dir(:))
-                weight = dirs_req_for_symmavgd_EBS_along_pcbz_dir(i_selec_pcbz_dir)%irr_dir(i_needed_dirs)%weight
-                avrgd_dNs = avrgd_dNs + weight*delta_N%selec_pcbz_dir(i_selec_pcbz_dir)%needed_dir(i_needed_dirs)%pckpt(ipc_kpt)%dN(:)
-            enddo
-            delta_N_symm_avrgd_for_EBS%pcbz_dir(i_selec_pcbz_dir)%pckpt(ipc_kpt)%dN(:) = avrgd_dNs(:)
-       enddo     
+    do i_spinor=1,n_spinor_components
+        call allocate_delta_Ns_for_output_type(delta_N_only_selected_dirs(i_spinor), pckpts_to_be_checked)
+        call allocate_delta_Ns_for_output_type(delta_N_symm_avrgd_for_EBS(i_spinor), pckpts_to_be_checked)
+        do i_selec_pcbz_dir=1,size(delta_N(i_spinor)%selec_pcbz_dir(:))
+            delta_N_only_selected_dirs(i_spinor)%pcbz_dir(i_selec_pcbz_dir) = delta_N(i_spinor)%selec_pcbz_dir(i_selec_pcbz_dir)%needed_dir(1)
+            do ipc_kpt=1, size(delta_N(i_spinor)%selec_pcbz_dir(i_selec_pcbz_dir)%needed_dir(1)%pckpt(:))
+                avrgd_dNs(:) = 0.0_dp
+                allocate(delta_N_symm_avrgd_for_EBS(i_spinor)%pcbz_dir(i_selec_pcbz_dir)%pckpt(ipc_kpt)%dN(1:nener))
+                do i_needed_dirs=1,size(delta_N(i_spinor)%selec_pcbz_dir(i_selec_pcbz_dir)%needed_dir(:))
+                    weight = dirs_req_for_symmavgd_EBS_along_pcbz_dir(i_selec_pcbz_dir)%irr_dir(i_needed_dirs)%weight
+                    avrgd_dNs = avrgd_dNs + weight*delta_N(i_spinor)%selec_pcbz_dir(i_selec_pcbz_dir)%needed_dir(i_needed_dirs)%pckpt(ipc_kpt)%dN(:)
+                enddo
+                delta_N_symm_avrgd_for_EBS(i_spinor)%pcbz_dir(i_selec_pcbz_dir)%pckpt(ipc_kpt)%dN(:) = avrgd_dNs(:)
+           enddo     
+        enddo
     enddo
 
 end subroutine get_delta_Ns_for_output

src/external/BandUP_configure_cla.sh

@@ -0,0 +1,4 @@
+#! /bin/sh
+
+rm -rf claf90
+tar -xvzf claf90.tgz

src/general_io_mod.f90

@@ -1,4 +1,4 @@
-!! Copyright (C) 2013 Paulo V. C. Medeiros
+!! Copyright (C) 2013, 2014 Paulo V. C. Medeiros
 !!
 !! This file is part of BandUP: Band Unfolding code for Plane-wave based calculations.
 !!
@@ -17,16 +17,25 @@
 
 module general_io
 implicit none
+SAVE
 PRIVATE
-PUBLIC :: available_io_unit, package_version, file_header_BandUP, file_header_BandUP_short, &
-          file_for_pc_reduced_to_prim_cell, file_for_SC_reduced_to_prim_cell
-
-character(len=30), parameter :: package_version="2.3.0, 2014-06-11"
-character(len=127), parameter :: file_header_BandUP="# File created by BandUP - Band Unfolding code for Plane-wave based calculations, &
-                                                     V"//trim(adjustl(package_version)), &
-                                 file_header_BandUP_short="# File created by BandUP, V"//trim(adjustl(package_version)), &
-                                 file_for_pc_reduced_to_prim_cell="BandUP_suggestion_of_pc_for_your_reference_unit_cell.POSCAR", &
-                                 file_for_SC_reduced_to_prim_cell="BandUP_suggestion_of_smaller_SC_based_on_your_input_SC.POSCAR"
+PUBLIC :: available_io_unit, file_extension, filename_without_extension, & 
+          str_len, package_version, file_header_BandUP, file_header_BandUP_short, &
+          file_for_pc_reduced_to_prim_cell, file_for_SC_reduced_to_prim_cell, &
+          input_file_prim_cell, input_file_supercell, input_file_pc_kpts, input_file_energies, &
+          output_file_only_user_selec_direcs, output_file_symm_averaged_EBS, WF_file
+
+integer, parameter :: str_len=256
+character(len=30), parameter :: package_version="2.4.0 (BETA), 2014-07-19"
+character(len=str_len), parameter :: file_header_BandUP="# File created by BandUP - Band Unfolding code for Plane-wave based calculations, &
+                                                        V"//trim(adjustl(package_version)), &
+                                     file_header_BandUP_short="# File created by BandUP, V"//trim(adjustl(package_version)), &
+                                     file_for_pc_reduced_to_prim_cell="BandUP_suggestion_of_pc_for_your_reference_unit_cell.POSCAR", &
+                                     file_for_SC_reduced_to_prim_cell="BandUP_suggestion_of_smaller_SC_based_on_your_input_SC.POSCAR"
+
+character(len=str_len) :: input_file_prim_cell, input_file_supercell, &
+                          input_file_pc_kpts, input_file_energies, WF_file, &
+                          output_file_only_user_selec_direcs, output_file_symm_averaged_EBS
 !! Functions and subroutines
 CONTAINS 
 
@@ -66,5 +75,49 @@ function available_io_unit(min_unit,max_unit) result(unit_num)
 
 end function available_io_unit
 
+function file_extension(filename, extention_length) result(ext)
+implicit none
+character(len=:), allocatable :: ext
+character(len=*), intent(in) :: filename
+integer, intent(in), optional :: extention_length
+integer :: ext_length, dot_position
+
+    ext_length = 3
+    if(present(extention_length))then
+        ext_length = extention_length
+    endif
+    allocate(character(ext_length) :: ext)
+
+    ext = ''
+    if(len(filename) >= ext_length + 1)then
+        dot_position = scan(filename, '.', back=.TRUE.)
+        if(dot_position > 0)then
+            ext = trim(adjustl(filename(dot_position + 1:len(filename))))
+        endif
+    endif
+
+end function file_extension
+
+
+function filename_without_extension(filename) result(rtn)
+implicit none
+character(len=*), intent(in) :: filename
+character(len=len(filename)) :: rtn
+integer :: dot_position
+
+    if(trim(adjustl(filename))=='')then
+        rtn = ''
+        return
+    endif
+
+    dot_position = scan(filename, '.', back=.TRUE.)
+    if(dot_position > 0)then
+       rtn = filename(1:dot_position-1)
+    else
+        rtn = trim(adjustl(filename))
+    endif
+
+end function filename_without_extension
+
 
 end module general_io