QE tutorial (#33)

* added new FAQs * Added Quantum Espresso tutorial * Improving collect_bandstr_data_only_in_energy_window() functionality * Upgraded return of band_ceneter_determination() function * Added effective mass error estimation from fitting error --------- Co-authored-by: Badal Mondal <[email protected]>
band-unfolding · Oct 14, 2024 · fdaebb7 · fdaebb7
1 parent b88180a
commit fdaebb7
Show file tree

Hide file tree

Showing 19 changed files with 3,086 additions and 18 deletions.
diff --git a/README.md b/README.md
@@ -143,7 +143,7 @@ If you use `BandUPpy` in your work, please:
 
   * **State EXPLICITLY that you have used the BandUP code** (or a modified version of it, if this is the case), for instance, adding a sentence like: 
 
-         "The unfolding has been performed using the BandUP(py) code"
+         "The unfolding is performed using the BandUP(py) code"
 
   * **Read and cite the following papers** (and the appropriate references therein):
 

diff --git a/banduppy/BasicFunctions/general_functions.py b/banduppy/BasicFunctions/general_functions.py
@@ -94,7 +94,7 @@ def _save_2_file(data=None, save_dir='.', file_name:str='', file_name_suffix:str
             Directory to save the file. The default is current directory.
         file_name : str, optional
             Name of the file. The default is ''.
-            If file_format is vasp, file_name=KPOINTS_<file_name_suffix>
+            If file_format is vasp/qe, file_name=KPOINTS_<file_name_suffix>
         file_name_suffix : str, optional
             Suffix to add after the file_name. The default is ''.
         header_txt : str, optional
@@ -144,16 +144,16 @@ def _save_sc_kpts_2_file(data=None, save_dir='.', file_name:str='',
             Directory to save the file. The default is current directory.
         file_name : str, optional
             Name of the file. The default is ''.
-            If file_format is vasp, file_name=KPOINTS_<file_name_suffix>
+            If file_format is vasp/qe, file_name=KPOINTS_<file_name_suffix>
         file_name_suffix : str, optional
             Suffix to add after the file_name. The default is ''.
-        file_format : ['vasp'], optional
+        file_format : ['vasp', 'qe'], optional
             Format of the file. The default is 'vasp'. 
-            If file_format is vasp, file_name=KPOINTS_<file_name_suffix>
+            If file_format is vasp/qe, file_name=KPOINTS_<file_name_suffix>
         header_txt : str, optional
             String that will be written at the beginning of the file. The default is None.
         footer_txt : str, optional
-            String that will be written at the end of the file.. The default is None.
+            String that will be written at the end of the file. The default is None.
         comments_symbol : str, optional
             String that will be prepended to the header and footer strings, 
             to mark them as comments. The default is ‘!‘. 
@@ -171,6 +171,12 @@ def _save_sc_kpts_2_file(data=None, save_dir='.', file_name:str='',
         if file_format == 'vasp':
             file_name = 'KPOINTS'
             comments_symbol = ''
+        elif file_format in ['qe', 'espresso', 'quantum_espresso']:
+            file_name = 'KPOINTS'
+            comments_symbol = ''
+            tmp_header = header_txt.split('\n')
+            if tmp_header[-1] == 'reciprocal':
+                header_txt = f'!{tmp_header[0]}\nK_POINTS crystal\n{tmp_header[1]}'          
 
         if print_log: print(f"{'='*_draw_line_length}\n- {print_msg}.")
 

diff --git a/banduppy/src/folding.py b/banduppy/src/folding.py
@@ -374,7 +374,7 @@ def _generate_header_text(self, save_all_kpts:bool=False):
         header_msg['SC'] += f"\n{len(self.SBZ_kpts_list)}\nreciprocal"
 
         header_msg['SpecialKpoints']   = f"Special SC kpoints indices generated using banduppy-{__version__} package"
-        header_msg['SpecialKpoints']  += "Kpoints index: Kpoints lebel"
+        header_msg['SpecialKpoints']  += "\nKpoints index: Kpoints label"
 
         # Generate header text for PC kpoints, SC-PC kpoints mapping, and special kpoints  
         if save_all_kpts:
@@ -383,7 +383,7 @@ def _generate_header_text(self, save_all_kpts:bool=False):
             header_msg['PC'] += f"\n{len(self.PBZ_kpts_list_org)}\nreciprocal"
 
             header_msg['SCPC_map']  = f"Mapping for SC Kpoints to PC kpoints indices generated using banduppy-{__version__} package"
-            header_msg['SCPC_map'] += "K-k relation: (K index: K -> k index unique: k unique -> k index: k)"
+            header_msg['SCPC_map'] += "\nK-k relation: (K index: K -> k index unique: k unique -> k index: k)"
 
         return header_msg
 
@@ -652,12 +652,12 @@ def _generate_K_from_k(self, kpointsPBZ=None, kpts_weights=None,
             Directory to save the file. The default is current directory.
         file_name : str, optional
             Name of the file. The default is ''.
-            If file_format is vasp, file_name=KPOINTS_<file_name_suffix>
+            If file_format is vasp/qe, file_name=KPOINTS_<file_name_suffix>
         file_name_suffix : str, optional
             Suffix to add after the file_name. The default is ''.
-        file_format : ['vasp'], optional
+        file_format : ['vasp','qe'], optional
             Format of the file. The default is 'vasp'. 
-            If file_format is vasp, file_name=KPOINTS_<file_name_suffix>
+            If file_format is vasp/qe, file_name=KPOINTS_<file_name_suffix>
         footer_msg : str, optional
             String that will be written at the end of the file. The default is PC kpoints list.
         special_kpoints_pos_labels : dictionary, optional

diff --git a/banduppy/unfolding.py b/banduppy/unfolding.py
@@ -131,12 +131,12 @@ def generate_SC_Kpts_from_pc_k_path(self, pathPBZ=None, nk=11, labels=None, kpts
             Directory to save the file. The default is current directory.
         file_name : str, optional
             Name of the file. The default is ''.
-            If file_format is vasp, file_name=KPOINTS_<file_name_suffix>
+            If file_format is vasp/qe, file_name=KPOINTS_<file_name_suffix>
         file_name_suffix : str, optional
             Suffix to add after the file_name. The default is ''.
-        file_format : ['vasp'], optional
+        file_format : ['vasp', 'qe'], optional
             Format of the file. The default is 'vasp'. 
-            If file_format is vasp, file_name=KPOINTS_<file_name_suffix>
+            If file_format is vasp/qe, file_name=KPOINTS_<file_name_suffix>
 
         Returns
         -------
@@ -182,12 +182,12 @@ def generate_SC_Kpts_from_pc_kpts(self, kpointsPBZ=None, kpts_weights=None,
             Directory to save the file. The default is current directory.
         file_name : str, optional
             Name of the file. The default is ''.
-            If file_format is vasp, file_name=KPOINTS_<file_name_suffix>
+            If file_format is vasp/qe, file_name=KPOINTS_<file_name_suffix>
         file_name_suffix : str, optional
             Suffix to add after the file_name. The default is ''.
-        file_format : ['vasp'], optional
+        file_format : ['vasp', 'qe'], optional
             Format of the file. The default is 'vasp'. 
-            If file_format is vasp, file_name=KPOINTS_<file_name_suffix>
+            If file_format is vasp/qe, file_name=KPOINTS_<file_name_suffix>
         footer_msg : str, optional
             String that will be written at the end of the file. The default is PC kpoints list.
         special_kpoints_pos_labels : dictionary, optional

diff --git a/docs/FAQs.md b/docs/FAQs.md
@@ -19,6 +19,20 @@ The information required is essentially the same for BandUP and BandUPpy, only a
 
 Regarding the necessary modifications for different reference primitive unit cell calculations: you need to adjust the `super_cell_size` parameter in for example the `run_banduppy_vasp.py`, which is the primitive-to-supercell transformation matrix.
 
+__Question:__ How can I write the label Gamma (Greek letter) instead of G in the plots?
+
+__Answer:__ You have to use the list.
+
+`special_k_points = ["L","G","X","U","K",r'$\Gamma$'] #instead of "LGXUKG"`
+
+__Question:__ How one can remove the text with 'supercell and unfolded' that is displayed over the bands in the figure?
+
+__Answer:__ To turn off the legends, you can use 'show_legend=False' in banduppy.Plotting.plot_ebs() function.
+
+__Question:__ How can change the color of the gray supercell points to a different color or lighter shade?
+
+ __Answer:__ Unfortunately, at the moment, the supercell points color can not be changed from banduppy.Plotting.plot_ebs().
+
 
 ##
 __If you are not satisfied with the answers, cannot find an answer to your question, or have new suggestions, please feel free to reach out to us. We are committed to providing the best experience for our users and greatly value your feedback.__

diff --git a/docs/RELEASE.md b/docs/RELEASE.md
@@ -2,8 +2,9 @@ __Latest release: v0.3.4__
 
 __v0.3.4__
 
+* Added Quantum Espresso tutorial
 * Improving collect_bandstr_data_only_in_energy_window() functionality 
-* Upgraded return of band_ceneter_determination function
+* Upgraded return of band_ceneter_determination() function
 * Added effective mass error estimation from fitting error
 
 __v0.3.3__

diff --git a/tutorials/QuantumEspresso/input/KPOINTS_PC b/tutorials/QuantumEspresso/input/KPOINTS_PC
@@ -0,0 +1,105 @@
+!k-points for PC bandstructure generated using banduppy-0.3.4 package
+K_POINTS crystal
+88
+  0.50000000   0.50000000   0.50000000
+  0.47727273   0.47727273   0.47727273
+  0.45454545   0.45454545   0.45454545
+  0.43181818   0.43181818   0.43181818
+  0.40909091   0.40909091   0.40909091
+  0.38636364   0.38636364   0.38636364
+  0.36363636   0.36363636   0.36363636
+  0.34090909   0.34090909   0.34090909
+  0.31818182   0.31818182   0.31818182
+  0.29545455   0.29545455   0.29545455
+  0.27272727   0.27272727   0.27272727
+  0.25000000   0.25000000   0.25000000
+  0.22727273   0.22727273   0.22727273
+  0.20454545   0.20454545   0.20454545
+  0.18181818   0.18181818   0.18181818
+  0.15909091   0.15909091   0.15909091
+  0.13636364   0.13636364   0.13636364
+  0.11363636   0.11363636   0.11363636
+  0.09090909   0.09090909   0.09090909
+  0.06818182   0.06818182   0.06818182
+  0.04545455   0.04545455   0.04545455
+  0.02272727   0.02272727   0.02272727
+  0.00000000   0.00000000   0.00000000
+  0.00000000   0.00000000   0.00000000
+  0.01923077   0.00000000   0.01923077
+  0.03846154   0.00000000   0.03846154
+  0.05769231   0.00000000   0.05769231
+  0.07692308   0.00000000   0.07692308
+  0.09615385   0.00000000   0.09615385
+  0.11538462   0.00000000   0.11538462
+  0.13461538   0.00000000   0.13461538
+  0.15384615   0.00000000   0.15384615
+  0.17307692   0.00000000   0.17307692
+  0.19230769   0.00000000   0.19230769
+  0.21153846   0.00000000   0.21153846
+  0.23076923   0.00000000   0.23076923
+  0.25000000   0.00000000   0.25000000
+  0.26923077   0.00000000   0.26923077
+  0.28846154   0.00000000   0.28846154
+  0.30769231   0.00000000   0.30769231
+  0.32692308   0.00000000   0.32692308
+  0.34615385   0.00000000   0.34615385
+  0.36538462   0.00000000   0.36538462
+  0.38461538   0.00000000   0.38461538
+  0.40384615   0.00000000   0.40384615
+  0.42307692   0.00000000   0.42307692
+  0.44230769   0.00000000   0.44230769
+  0.46153846   0.00000000   0.46153846
+  0.48076923   0.00000000   0.48076923
+  0.50000000   0.00000000   0.50000000
+  0.50000000   0.00000000   0.50000000
+  0.51562500   0.03125000   0.51562500
+  0.53125000   0.06250000   0.53125000
+  0.54687500   0.09375000   0.54687500
+  0.56250000   0.12500000   0.56250000
+  0.57812500   0.15625000   0.57812500
+  0.59375000   0.18750000   0.59375000
+  0.60937500   0.21875000   0.60937500
+  0.62500000   0.25000000   0.62500000
+  0.37500000   0.37500000   0.75000000
+  0.36160714   0.36160714   0.72321429
+  0.34821429   0.34821429   0.69642857
+  0.33482143   0.33482143   0.66964286
+  0.32142857   0.32142857   0.64285714
+  0.30803571   0.30803571   0.61607143
+  0.29464286   0.29464286   0.58928571
+  0.28125000   0.28125000   0.56250000
+  0.26785714   0.26785714   0.53571429
+  0.25446429   0.25446429   0.50892857
+  0.24107143   0.24107143   0.48214286
+  0.22767857   0.22767857   0.45535714
+  0.21428571   0.21428571   0.42857143
+  0.20089286   0.20089286   0.40178571
+  0.18750000   0.18750000   0.37500000
+  0.17410714   0.17410714   0.34821429
+  0.16071429   0.16071429   0.32142857
+  0.14732143   0.14732143   0.29464286
+  0.13392857   0.13392857   0.26785714
+  0.12053571   0.12053571   0.24107143
+  0.10714286   0.10714286   0.21428571
+  0.09375000   0.09375000   0.18750000
+  0.08035714   0.08035714   0.16071429
+  0.06696429   0.06696429   0.13392857
+  0.05357143   0.05357143   0.10714286
+  0.04017857   0.04017857   0.08035714
+  0.02678571   0.02678571   0.05357143
+  0.01339286   0.01339286   0.02678571
+  0.00000000   0.00000000   0.00000000
+
+
+! The above SCKPTS (and/or some other SCKPTS related to them by symm. ops. of the SCBZ)
+! unfold onto the pckpts listed below (selected by you):
+! k-points for PC bandstructure L-G-X-U,K-G
+! 23 27 9 29
+! reciprocal
+!  0.50000000   0.50000000   0.50000000   L
+!  0.00000000   0.00000000   0.00000000   G
+!  0.50000000   0.00000000   0.50000000   X
+!  0.62500000   0.25000000   0.62500000   U
+! 
+!  0.37500000   0.37500000   0.75000000   K
+!  0.00000000   0.00000000   0.00000000   G
diff --git a/tutorials/QuantumEspresso/input/KPOINTS_SC b/tutorials/QuantumEspresso/input/KPOINTS_SC
@@ -0,0 +1,101 @@
+!K-points for SC bandstructure generated using banduppy-0.3.4 package
+K_POINTS crystal
+84
+  0.00000000   0.00000000   0.00000000   1.00000000
+  0.00000000   0.03846154   0.00000000   1.00000000
+  0.00000000   0.07692308   0.00000000   1.00000000
+  0.00000000   0.11538462   0.00000000   1.00000000
+  0.00000000   0.15384615   0.00000000   1.00000000
+  0.00000000   0.19230769   0.00000000   1.00000000
+  0.00000000   0.23076923   0.00000000   1.00000000
+  0.00000000   0.26923077   0.00000000   1.00000000
+  0.00000000   0.30769231   0.00000000   1.00000000
+  0.00000000   0.34615385   0.00000000   1.00000000
+  0.00000000   0.38461538   0.00000000   1.00000000
+  0.00000000   0.42307692   0.00000000   1.00000000
+  0.00000000   0.46153846   0.00000000   1.00000000
+  0.00000000   0.50000000   0.00000000   1.00000000
+  0.00000000   0.53846154   0.00000000   1.00000000
+  0.00000000   0.57692308   0.00000000   1.00000000
+  0.00000000   0.61538462   0.00000000   1.00000000
+  0.00000000   0.65384615   0.00000000   1.00000000
+  0.00000000   0.69230769   0.00000000   1.00000000
+  0.00000000   0.73076923   0.00000000   1.00000000
+  0.00000000   0.76923077   0.00000000   1.00000000
+  0.00000000   0.80769231   0.00000000   1.00000000
+  0.00000000   0.84615385   0.00000000   1.00000000
+  0.00000000   0.88461538   0.00000000   1.00000000
+  0.00000000   0.92307692   0.00000000   1.00000000
+  0.00000000   0.96153846   0.00000000   1.00000000
+  0.02272727   0.02272727   0.02272727   1.00000000
+  0.02678571   0.02678571   1.00000000   1.00000000
+  0.03125000   0.00000000   0.03125000   1.00000000
+  0.04545455   0.04545455   0.04545455   1.00000000
+  0.05357143   0.05357143   0.00000000   1.00000000
+  0.06250000   0.00000000   0.06250000   1.00000000
+  0.06818182   0.06818182   0.06818182   1.00000000
+  0.08035714   0.08035714   1.00000000   1.00000000
+  0.09090909   0.09090909   0.09090909   1.00000000
+  0.09375000   0.00000000   0.09375000   1.00000000
+  0.10714286   0.10714286   0.00000000   1.00000000
+  0.11363636   0.11363636   0.11363636   1.00000000
+  0.12500000   0.00000000   0.12500000   1.00000000
+  0.13392857   0.13392857   0.00000000   1.00000000
+  0.13636364   0.13636364   0.13636364   1.00000000
+  0.15625000   0.00000000   0.15625000   1.00000000
+  0.15909091   0.15909091   0.15909091   1.00000000
+  0.16071429   0.16071429   0.00000000   1.00000000
+  0.18181818   0.18181818   0.18181818   1.00000000
+  0.18750000   0.00000000   0.18750000   1.00000000
+  0.18750000   0.18750000   0.00000000   1.00000000
+  0.20454545   0.20454545   0.20454545   1.00000000
+  0.21428571   0.21428571   1.00000000   1.00000000
+  0.21875000   0.00000000   0.21875000   1.00000000
+  0.22727273   0.22727273   0.22727273   1.00000000
+  0.24107143   0.24107143   0.00000000   1.00000000
+  0.25000000   0.00000000   0.25000000   1.00000000
+  0.25000000   0.25000000   0.25000000   1.00000000
+  0.26785714   0.26785714   1.00000000   1.00000000
+  0.27272727   0.27272727   0.27272727   1.00000000
+  0.29464286   0.29464286   0.00000000   1.00000000
+  0.29545455   0.29545455   0.29545455   1.00000000
+  0.31818182   0.31818182   0.31818182   1.00000000
+  0.32142857   0.32142857   0.00000000   1.00000000
+  0.34090909   0.34090909   0.34090909   1.00000000
+  0.34821429   0.34821429   0.00000000   1.00000000
+  0.36363636   0.36363636   0.36363636   1.00000000
+  0.37500000   0.37500000   0.00000000   1.00000000
+  0.38636364   0.38636364   0.38636364   1.00000000
+  0.40178571   0.40178571   1.00000000   1.00000000
+  0.40909091   0.40909091   0.40909091   1.00000000
+  0.42857143   0.42857143   0.00000000   1.00000000
+  0.43181818   0.43181818   0.43181818   1.00000000
+  0.45454545   0.45454545   0.45454545   1.00000000
+  0.45535714   0.45535714   1.00000000   1.00000000
+  0.47727273   0.47727273   0.47727273   1.00000000
+  0.48214286   0.48214286   0.00000000   1.00000000
+  0.50000000   0.50000000   0.50000000   1.00000000
+  0.50892857   0.50892857   0.00000000   1.00000000
+  0.53571429   0.53571429   0.00000000   1.00000000
+  0.56250000   0.56250000   0.00000000   1.00000000
+  0.58928571   0.58928571   1.00000000   1.00000000
+  0.61607143   0.61607143   0.00000000   1.00000000
+  0.64285714   0.64285714   1.00000000   1.00000000
+  0.66964286   0.66964286   0.00000000   1.00000000
+  0.69642857   0.69642857   0.00000000   1.00000000
+  0.72321429   0.72321429   0.00000000   1.00000000
+  0.75000000   0.75000000   0.00000000   1.00000000
+
+
+! The above SCKPTS (and/or some other SCKPTS related to them by symm. ops. of the SCBZ)
+! unfold onto the pckpts listed below (selected by you):
+! k-points for PC bandstructure L-G-X-U,K-G
+! 23 27 9 29
+! reciprocal
+!  0.50000000   0.50000000   0.50000000   L
+!  0.00000000   0.00000000   0.00000000   G
+!  0.50000000   0.00000000   0.50000000   X
+!  0.62500000   0.25000000   0.62500000   U
+! 
+!  0.37500000   0.37500000   0.75000000   K
+!  0.00000000   0.00000000   0.00000000   G
diff --git a/tutorials/QuantumEspresso/input/KPOINTS_SCPC_map.pkl b/tutorials/QuantumEspresso/input/KPOINTS_SCPC_map.pkl
diff --git a/tutorials/QuantumEspresso/input/KPOINTS_SpecialKpoints.pkl b/tutorials/QuantumEspresso/input/KPOINTS_SpecialKpoints.pkl
diff --git a/tutorials/QuantumEspresso/input/bulk_Si_nscf.in b/tutorials/QuantumEspresso/input/bulk_Si_nscf.in
@@ -0,0 +1,41 @@
+! SYSTEM = Bulk Silicon - Self Consistent calculation
+! Non-SCF calculation to generate supercell wave function file
+
+&control
+    title = 'Silicon Supercell SCF',
+    calculation = 'bands',
+    restart_mode = 'restart',
+    prefix = 'bulk_Si',       ! Output files will have this prefix
+    pseudo_dir = './',   ! Directory where pseudopotentials are stored
+    disk_io = 'default'
+    wf_collect = .TRUE.,
+/
+&system
+    smearing = 'gaussian',
+    occupations = 'smearing',
+    lspinorb = .false.,
+    noncolin = .false.,
+    degauss = 0.005,
+    ibrav = 1,
+    A = 5.43,
+    nat = 8,
+    ntyp = 1,
+    ecutwfc = 35,
+    ecutrho = 350,
+    nbnd = 48
+/
+&electrons
+    conv_thr = 1.0D-6,   ! Convergence threshold
+    mixing_beta = 0.7,   ! Mixing factor for electron density
+/
+ATOMIC_SPECIES
+  Si  28.0855  Si.pbe-rrkj.UPF ! Silicon pseudopotential
+ATOMIC_POSITIONS alat
+  Si  0.000000000   0.000000000   0.000000000
+  Si  0.000000000   0.500000000   0.500000000
+  Si  0.500000000   0.500000000   0.000000000
+  Si  0.500000000   0.000000000   0.500000000
+  Si  0.750000000   0.250000000   0.750000000
+  Si  0.250000000   0.250000000   0.250000000
+  Si  0.250000000   0.750000000   0.750000000
+  Si  0.750000000   0.750000000   0.250000000