Merge branch 'main' of https://github.com/lrgresearch/gpaw-tools

CONTRIBUTING.md

@@ -5,14 +5,14 @@ We welcome contributions and hope this guide will make the `gpaw-tools` code rep
 
 Being Respectful
 ----------------
-Please show empathy and kindness towards other people, other software, and communities that work diligently to develop other tools.
+Please show empathy and kindness towards other people, software, and communities working diligently to develop other tools.
 
-In pull requests and issues, please do not speak in a way that negatively portrays other people or their work.
+Please do not speak negatively about other people or their work in pull requests and issues.
 
 Cloning the Source Repository
 -----------------------------
 
-Before cloning the source repository to your computer, please visit the [installation page](https://www.lrgresearch.org/gpaw-tools/installation/) of `gpaw-tools` to install ASE, GPAW and other all needed packages to your computer. Then, you can clone the source of the `gpaw-tools` from related repository:
+Before cloning the source repository to your computer, please visit the [installation page](https://www.lrgresearch.org/gpaw-tools/installation/) of `gpaw-tools` to install ASE, GPAW, and all other needed packages to your computer. Then, you can clone the source of the `gpaw-tools` from the related repository:
 [Main Github repository](https://github.com/lrgresearch/gpaw-tools) by:
 
     git clone https://github.com/lrgresearch/gpaw-tools.git
@@ -21,35 +21,35 @@ Before cloning the source repository to your computer, please visit the [install
 Questions
 ---------
 
-We do not have any email-list, IRC channel, Slack room, etc. 
-* For general questions about the project, and all other things, we will use [Discussions](https://github.com/lrgresearch/gpaw-tools/discussions) page of Github repository. 
-* For more technical problems, you are welcome to create an issue on the [Issues](https://github.com/lrgresearch/gpaw-tools/issues) page of Github repository. Posting to the issues page allows community members with the required expertise to answer your question, and the information obtained remains available to other users on the issues page for future usage.
+We do not have any email list, IRC channel, Slack room, etc. 
+* For general questions about the project and all other things, we will use the [Discussions](https://github.com/lrgresearch/gpaw-tools/discussions) page of the GitHub repository. 
+* For more technical problems, you can create an issue on the [Issues](https://github.com/lrgresearch/gpaw-tools/issues) page of the GitHub repository. Posting to the issues page allows community members with the required expertise to answer your question, and the information obtained remains available to other users on the issues page for future usage.
 
 Reporting Bugs and Feature Requests
 -----------------------------------
 
-If you encounter any bugs, crashes or quirks while using the code, please report it on the [Issues](https://github.com/lrgresearch/gpaw-tools/issues) page with an appropriate tag so that the developers can take care of it immediately. When reporting an issue, please be overly descriptive so we can reproduce it. If possible, provide trackbacks, screenshots and sample files to help us resolve the issue. For reporting a bug, please create an issue with the "Bug report" template.
+If you encounter any bugs, crashes, or quirks while using the code, please report it on the [Issues](https://github.com/lrgresearch/gpaw-tools/issues) page with an appropriate tag so that the developers can take care of it immediately. When reporting an issue, please be overly descriptive so we can reproduce it. Provide trackbacks, screenshots, and sample files to help us resolve the issue. Please create an issue with the "Bug report" template for reporting a bug.
 
-Please do not hesitate to submit ideas for improvements to the `gpaw-tools` software. To suggest an improvement, please create an [Issue](https://github.com/lrgresearch/gpaw-tools/issues) with the "Feature Request" template. Please use a descriptive and extensive information (links, videos, possible screenshots etc.) to help the developers to implement this functionality.
+Please do not hesitate to submit ideas for improvements to the `gpaw-tools` software. To suggest an improvement, please create an [Issue](https://github.com/lrgresearch/gpaw-tools/issues) with the "Feature Request" template. Please use descriptive and extensive information (links, videos, possible screenshots, etc.) to help the developers implement this functionality.
 
 Contributing New Code
 ---------------------
-If you have an idea to solve a bug or implementing a new feature, please first create an issue as a bug report/feature request and we can use that issue as a discussion thread to resolve the implementation of the contribution.
+If you have an idea to solve a bug or implement a new feature, please first create an issue as a bug report/feature request. We can then use that issue as a discussion thread to resolve the contribution implementation.
 
 Licensing
 ---------
 
-All code is licensed under the MIT License. If you didn't write the code yourself, it's your responsibility to make sure the existing license is compatible and included with the contributed files.
+All code is licensed under the MIT License. If you didn't write the code yourself, it's your responsibility to ensure that the existing license is compatible with and included with the contributed files.
 
 New Release
 -----------
 
 In each new release, the following steps must be completed.
-- Update __version__ variable in `gpawsolve.py` (Approximate place is line 168) as vYY.m.x. Here YY is year and m (or mm) is month, and x is the step number of release for that month. There is no minor or major release.
-- Update __version__ variable in `asapsolve.py` (Approximate place is line 77) as vYY.m.x. Here YY is year and m (or mm) is month, and x is the step number of release for that month. There is no minor or major release.
-- Click `Draft a new release`on releases page and create a new tag with the version number.
+- Update __version__ variable in `gpawsolve.py` (Approximate place is line 1783) as vYY.m.x. Here, YY is the year, m (or mm) is the month, and x is the step number of releases for that month. There is no minor or major release.
+- Update __version__ variable in `asapsolve.py` (Approximate place is line 77) as vYY.m.x. Here, YY is the year, m (or mm) is the month, and x is the step number of releases for that month. There is no minor or major release.
+- On the releases page, Click `Draft a new release` and create a new tag with the version number.
 - Give a general title, give some highlights information, write Release Notes (copy/paste from gh-pages/releasenotes.md webpage).
-- Select `Create a discussion for this release` and then finish release.
+- Select `Create a discussion for this release` and then finish the release.
 - Update __version__ variable in `gpawsolve.py` and `asapsolve.py` as vYY.m.y. Here y= (x+1)b1. For example for x=0 -> y=1b1 for x=1 -> y=2b1 ...etc...
 - Update `gh-pages/releasenotes.md`
 - Update `gh-pages/index.md`

gpawsolve.py

@@ -25,9 +25,9 @@
 import textwrap
 import requests
 import pickle
-import spglib as spg
 from argparse import ArgumentParser, HelpFormatter
 from ase import *
+from ase.spacegroup import get_spacegroup
 from ase.dft.kpoints import get_special_points
 from ase.parallel import paropen, world, parprint, broadcast
 from gpaw import GPAW, PW, Davidson, FermiDirac, MixerSum, MixerDif, Mixer
@@ -78,7 +78,7 @@ def struct_from_file(inputfile, geometryfile):
         struct = Path(geometryfile).stem
         bulk_configuration = read(geometryfile, index='-1')
         parprint("Number of atoms imported from CIF file:"+str(bulk_configuration.get_global_number_of_atoms()))
-        parprint("Spacegroup of CIF file (from SPGlib):",spg.get_spacegroup(bulk_configuration))
+        parprint("Spacegroup of CIF file:",get_spacegroup(bulk_configuration, symprec=1e-2))
         parprint("Special Points usable for this spacegroup:",get_special_points(bulk_configuration.get_cell()))
 
     # Output directory
@@ -226,7 +226,7 @@ def structurecalc(self):
 
         with paropen(struct+'-0-Result-Spacegroup-and-SpecialPoints.txt', "w") as fd:
             print("Number of atoms imported from CIF file:"+str(bulk_configuration.get_global_number_of_atoms()), file=fd)
-            print("Spacegroup of CIF file (from SPGlib):",spg.get_spacegroup(bulk_configuration), file=fd)
+            print("Spacegroup of CIF file:",get_spacegroup(bulk_configuration, symprec=1e-2), file=fd)
             print("Special Points usable for this spacegroup:",get_special_points(bulk_configuration.get_cell()), file=fd)
 
     def groundcalc(self):
@@ -376,7 +376,7 @@ def groundcalc(self):
                 # Writes final configuration as CIF file
                 write_cif(struct+'-Final.cif', bulk_configuration)
                 # Print final spacegroup information
-                parprint("Final Spacegroup (SPGlib):",spg.get_spacegroup(bulk_configuration))
+                parprint("Final Spacegroup:",get_spacegroup(bulk_configuration, symprec=1e-2))
             else:
                 parprint("Passing ground state calculation for GW calculation...")
                 # Control the ground state GPW file
@@ -465,7 +465,7 @@ def groundcalc(self):
                 # Writes final configuration as CIF file
                 write_cif(struct+'-Final.cif', bulk_configuration)
                 # Print final spacegroup information
-                parprint("Final Spacegroup (SPGlib):",spg.get_spacegroup(bulk_configuration))
+                parprint("Final Spacegroup:",get_spacegroup(bulk_configuration, symprec=1e-2))
             else:
                 parprint("Passing LCAO ground state calculation...")
                 # Control the ground state GPW file
@@ -502,8 +502,8 @@ def elasticcalc(self, drawfigs = False):
         time151 = time.time()
         parprint('Starting elastic tensor calculations (\033[93mWARNING:\033[0mNOT TESTED FEATURE, PLEASE CONTROL THE RESULTS)...')
         calc = GPAW(struct+'-1-Result-Ground.gpw').fixed_density(txt=struct+'-1.5-Log-Elastic.txt')
-        # Getting space group from SPGlib
-        parprint('Spacegroup:',spg.get_spacegroup(bulk_configuration))
+        # Getting space group
+        parprint("Spacegroup:",get_spacegroup(bulk_configuration, symprec=1e-2))
         # Calculating equation of state
         parprint('Calculating equation of state...')
         eos = calculate_eos(bulk_configuration, trajectory=struct+'-1.5-Result-Elastic.traj')
@@ -518,7 +518,7 @@ def elasticcalc(self, drawfigs = False):
             print("Elastic constants: Standart elasticity theory calculated by -Elastic- library", file=fd)
             print("Ref: European Physical Journal B; 15, 2 (2000) 265-268", file=fd)
             print("-----------------------------------------------------------------------------", file=fd)
-            print("Spacegroup: "+str(spg.get_spacegroup(bulk_configuration)), file=fd)
+            print("Spacegroup: "+str(get_spacegroup(bulk_configuration, symprec=1e-2)), file=fd)
             print("B (GPa): "+str(B / kJ * 1.0e24), file=fd)
             print("e (eV): "+str(e), file=fd)
             print("v (Ang^3): "+str(v), file=fd)