chemsmart 0.1.0__tar.gz

chemsmart-0.1.0/CHANGELOG.md

@@ -0,0 +1,904 @@
+Changelog
+=========
+
+
+(unreleased)
+------------
+- Clean up make fmt and make lint in Makefile. [xinglong-zhang]
+- Added comments to the codes. [xinglong-zhang]
+- Further fix. [xinglong-zhang]
+- Fix basis. [xinglong-zhang]
+- Modify route string in writer, if project setting uses heavy elements
+  but molecule has no heavy elements. [xinglong-zhang]
+- Merge pull request #92 from xinglong-zhang/readme. [Xinglong Zhang]
+
+  use conda
+- Merge branch 'main' into readme. [Xinglong Zhang]
+- Merge pull request #91 from xinglong-zhang/mf. [Xinglong Zhang]
+
+  update Makefile to use path to chemsmart exe
+- Update Makefile to use path to chemsmart exe. [xinglong-zhang]
+- Merge pull request #90 from xinglong-zhang/xinglong-zhang-patch-5.
+  [Xinglong Zhang]
+
+  Update README.md
+- Update README.md. [Xinglong Zhang]
+- Merge pull request #88 from xinglong-zhang/mf. [Xinglong Zhang]
+
+  Fix makefile
+- Merge branch 'main' into mf. [Xinglong Zhang]
+- Merge pull request #89 from xinglong-zhang/xinglong-zhang-patch-4.
+  [Xinglong Zhang]
+
+  Update Makefile
+- Update Makefile. [Xinglong Zhang]
+- Merge pull request #87 from xinglong-zhang/xinglong-zhang-patch-3.
+  [Xinglong Zhang]
+
+  Update README.md
+- Update README.md. [Xinglong Zhang]
+- Merge pull request #86 from xinglong-zhang/readme. [Xinglong Zhang]
+
+  Readme
+- Update make file. [xinglong-zhang]
+- Fix Makefile. [xinglong-zhang]
+- Clean Makefile. [xinglong-zhang]
+- Use conda. [Zhang Xinglong]
+- Merge branch 'main' into readme. [Zhang Xinglong]
+- Merge pull request #84 from xinglong-zhang/readme. [Xinglong Zhang]
+
+  updated Makefile to remove poetry
+- Merge pull request #85 from xinglong-zhang/xinglong-zhang-patch-2.
+  [Xinglong Zhang]
+
+  Update README.md
+- Update README.md. [Xinglong Zhang]
+- Merge pull request #82 from xinglong-zhang/xinglong-zhang-patch-1.
+  [Xinglong Zhang]
+
+  Update README.md
+- Update README.md. [Xinglong Zhang]
+- Merge pull request #83 from xinglong-zhang/readme. [Xinglong Zhang]
+
+  fix Makefile to use conda
+- Merge pull request #81 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  renamed program_type to program
+- Logger defults to no-stream. [xinglong-zhang]
+- Renamed program_type to program. [xinglong-zhang]
+- Merge pull request #80 from xinglong-zhang/readme. [Xinglong Zhang]
+
+  Updated Makefile
+- Merge pull request #79 from xinglong-zhang/xinglong-zhang-patch-1.
+  [Xinglong Zhang]
+
+  Update README.md
+- Update README.md. [Xinglong Zhang]
+- Merge pull request #78 from xinglong-zhang/readme. [Xinglong Zhang]
+- Merge pull request #77 from xinglong-zhang/readme. [Xinglong Zhang]
+
+  updated readme
+- Merge pull request #75 from xinglong-zhang/readme. [Xinglong Zhang]
+
+  added LGPL license
+- Merge pull request #74 from xinglong-zhang/xinglong-zhang-patch-1.
+  [Xinglong Zhang]
+
+  Update LICENSE
+- Update LICENSE. [Xinglong Zhang]
+- Merge pull request #73 from xinglong-zhang/readme. [Xinglong Zhang]
+- Relax setuptools version. [Zhang Xinglong]
+- Updated Makefile to remove poetry. [Zhang Xinglong]
+- Fix Makefile to use conda. [Zhang Xinglong]
+- Chemsmart config. [Xinglong Zhang]
+- Fix config ctx. [Xinglong Zhang]
+- Config as a class. [Xinglong Zhang]
+- Updated readme for installation instructions. [Xinglong Zhang]
+- Added a simple configuration script for configuring chemsmart.
+  [Xinglong Zhang]
+- Added .chemsmart to chemsmart/settings/templates/.chemsmart. [Xinglong
+  Zhang]
+- Updated readme. [Xinglong Zhang]
+- Added LGPL license. [Xinglong Zhang]
+- Updated readme. [Xinglong Zhang]
+- Merge pull request #72 from xinglong-zhang/conda. [Xinglong Zhang]
+
+  remove poetry.lock
+- Remove poetry.lock. [Xinglong Zhang]
+- Merge pull request #71 from xinglong-zhang/conda. [Xinglong Zhang]
+- Updated Makefile, which works for installing the package via make +
+  updated dependencies versions in pyproject.tmol file. [Xinglong Zhang]
+- Merge pull request #41 from xinglong-zhang/gaussian. [Xinglong Zhang]
+- Merge pull request #70 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  fix Make file to generate coverage report
+- Fix Make file to generate coverage report. [Xinglong Zhang]
+- Merge pull request #69 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  Use --cov= to not do any source filtering and record everything
+- Use --cov= to not do any source filtering and record everything.
+  [Xinglong Zhang]
+- Merge pull request #68 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  added cmp_with_ignore() function to utils + test for this function
+- Added cmp_with_ignore() function to utils + test for this function.
+  [Xinglong Zhang]
+- Merge pull request #67 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  added  cmp_with_ignore() function to utils.utils.py
+- Added         # compare the written input file with the expected input
+  file, except. [Xinglong Zhang]
+- Merge pull request #66 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  added filecmp.clear_cache()
+- Added filecmp.clear_cache() [Xinglong Zhang]
+- Merge pull request #65 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  fix indexing + tests
+- Fix indices + tests + black formatting. [Xinglong Zhang]
+- Help strings. [Xinglong Zhang]
+- Merge pull request #64 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  indices fix
+- Fix indices to use 1-based string2index_1based and
+  get_list_from_string_range. [Xinglong Zhang]
+- Fix GaussianCrestJob. [Xinglong Zhang]
+- Cmp to take shallow=False to compare file contents. [Xinglong Zhang]
+- Remove print statements. [Xinglong Zhang]
+- Merge pull request #63 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  remove print statements
+- Remove print statements. [Xinglong Zhang]
+- Merge pull request #62 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  added log files
+- Readme. [Xinglong Zhang]
+- Added log files; remove *.log from .gitignore. [Xinglong Zhang]
+- Merge pull request #61 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  added .log files to orca branch
+- Update Makefile remove cov= from it. [Xinglong Zhang]
+- Merge pull request #60 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  modified .github/workflows/main.yml and Makefile
+- Modified .github/workflows/main.yml and Makefile. [Xinglong Zhang]
+- Merge pull request #59 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  comment out token generation in .github/workflows/main.yml
+- Comment out token generation in .github/workflows/main.yml. [Xinglong
+  Zhang]
+- Merge pull request #58 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  modified .github/workflows/main.yml and Makefile
+- Modified .github/workflows/main.yml and Makefile. [Xinglong Zhang]
+- Merge pull request #57 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  change chemsmart/tests back to tests
+- Change chemsmart/tests back to tests. [Xinglong Zhang]
+- Merge pull request #56 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  change tests to chemsmart/tests for pytest
+- Change tests to chemsmart/tests for pytest. [Xinglong Zhang]
+- Merge pull request #55 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  modified Makefile + .github/workflows/main.yml
+- Modified .github/workflows/main.yml and Makefile. [Xinglong Zhang]
+- Added () to pytest.fixture for consistency. [Xinglong Zhang]
+- Test. [Xinglong Zhang]
+- Merge pull request #54 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  added --cov= to not do any source filteritering and record everything
+- Add test_base.py. [Xinglong Zhang]
+- Modified .github/workflows/main.yml. [Xinglong Zhang]
+- Added --cov= to not do any source filteritering and record everything.
+  [Xinglong Zhang]
+- Merge pull request #53 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  remove --cov=chemsmart in Makefile
+- Remove --cov=[SOURCE]        Path or package name to measure during
+  execution (multi-allowed). Use --cov= to not do any source filtering
+  and record. [Xinglong Zhang]
+- Merge pull request #52 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  install ruff black in workflows/main.yml + get correct path of test data
+- Install ruff black in workflows/main.yml + get correct path of test
+  data. [Xinglong Zhang]
+- Merge pull request #51 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  renamed AllTest.py files to test_All.py
+- Renamed AllTest.py files to test_All.py to follow pytest automatic
+  discovery naming convention. [Xinglong Zhang]
+- Merge pull request #50 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  updated workflow
+- Modified .github/workflows/main.yml. [Xinglong Zhang]
+- Remove _USE_CP_SENDFILE for BlockingIOError: [Errno 11] [Xinglong
+  Zhang]
+- Remove commented out to remove script when job is completed in
+  GaussianJobrunner and ORCAJobrunner. [Xinglong Zhang]
+- Merge pull request #49 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  update .github/workflows/main.yml to install dependencies from pyproj…
+- Update .github/workflows/main.yml to install dependencies from
+  pyproject.toml. [Xinglong Zhang]
+- Merge pull request #48 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  merge orca into gaussian
+- Updated ase version in pyproject.toml. [Xinglong Zhang]
+- Comment out job run in writer test, WIP: to write in JobTest.
+  [Xinglong Zhang]
+- Merge pull request #47 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  updated ase version in pyproject.toml
+- Updated ase version in pyproject.toml. [Xinglong Zhang]
+- Merge pull request #46 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  black formatting
+- Black formatting. [Xinglong Zhang]
+- Merge pull request #45 from xinglong-zhang/orca. [Xinglong Zhang]
+
+  lint + fmt
+- Lint + fmt. [Xinglong Zhang]
+- Merge pull request #44 from xinglong-zhang/orca. [Xinglong Zhang]
+- Added orca sp job. [Xinglong Zhang]
+- Linting fix. [Xinglong Zhang]
+- Added ts job. [Xinglong Zhang]
+- Added orca scan job, which works. [Xinglong Zhang]
+- Rename get_setting_from_jobtype to
+  get_setting_from_jobtype_for_gaussian. [Xinglong Zhang]
+- Change back get_setting_from_jobtype for gaussian. [Xinglong Zhang]
+- Change back get_setting_from_jobtype for gaussian. [Xinglong Zhang]
+- Tried to write get_setting_from_jobtype() as one function for both
+  gaussian and orca but seems more complicated than for individual one.
+  [Xinglong Zhang]
+- Remove ORCAConstrainedOptJobSettings. [Xinglong Zhang]
+- Clean up ORCAInpJob. [Xinglong Zhang]
+- Clean up orca irc job. [Xinglong Zhang]
+- Orca irc job works; WIP: to add tests. [Xinglong Zhang]
+- Orca IRC job works. [Xinglong Zhang]
+- Added orca modred job. [Xinglong Zhang]
+- Remove jobs/orca/execution.py; no jobs/programs/execution.py required
+  for chemsmart. [Xinglong Zhang]
+- Clean up FakeOrcaJobrunner. [Xinglong Zhang]
+- Orca opt jobs done with frozen atoms, orca writer done, WIP: tests.
+  [Xinglong Zhang]
+- Refactor GaussianRef() and ORCARef() [Xinglong Zhang]
+- Orca runs opt job correctly. [Xinglong Zhang]
+- Read_molecular_job_yaml() function to take in program argument; no
+  defaults.yaml present, will use ProgramJobSettings.defaults()
+  [Xinglong Zhang]
+- Add title attribute to base MolecularJobSettings class. [Xinglong
+  Zhang]
+- Isort then black. [Xinglong Zhang]
+- Xml. [Xinglong Zhang]
+- Refactor test folders in tests/data/ORCATests. [Xinglong Zhang]
+- Implemented orca input writer. [Xinglong Zhang]
+- Orca inp file runs correctly as supplied. [Xinglong Zhang]
+- Refactor input_string attribute to base JobSettings class. [Xinglong
+  Zhang]
+- Backup files. [Xinglong Zhang]
+- Refactor intermediate points and job.is_complete to parent class Job.
+  [Xinglong Zhang]
+- Fix conflicts. [Xinglong Zhang]
+- Black formatting. [Xinglong Zhang]
+- Changed to 1-index for accessing structures. [Xinglong Zhang]
+- ORCAOutput fix + passed all tests. [Xinglong Zhang]
+- Black formatting. [Xinglong Zhang]
+- Added orca cb object + refactor forces_in_eV_per_angstrom and
+  input_translation_vectors, symbols, list_of_pbc_conditions (derived
+  from self.input_coordinates_block) to FileMixin. [Xinglong Zhang]
+- Implement forces in orca output. [Xinglong Zhang]
+- Clean up package files. [Xinglong Zhang]
+- If usersettings.yaml not found in ~/.chemsmart set data = {} [Xinglong
+  Zhang]
+- Fix conftest to user server inside the package instead of from
+  ~/.chemsmart. [Xinglong Zhang]
+- Remove mypy linter. [Xinglong Zhang]
+- # noqa F811 for chemsmart/jobs/gaussian/runner.py. [Xinglong Zhang]
+- Exclude rdkit-stubs due to an error in rdkit python3.10/site-
+  packages/rdkit-stubs/Chem/rdMolDescriptors.pyi:185: error: Duplicate
+  argument "self" in function definition. [Xinglong Zhang]
+- Add quotations. [Xinglong Zhang]
+- Ruff and black for py310. [Xinglong Zhang]
+- Use python 3.10. [Xinglong Zhang]
+- Gaussian black formatting. [Xinglong Zhang]
+- Fix ruff. [Xinglong Zhang]
+- Requires python 3.9. [Xinglong Zhang]
+- Remove yaml. [Xinglong Zhang]
+- Fix yaml version. [Xinglong Zhang]
+- Add yaml 1.2.2 to pyproject.toml. [Xinglong Zhang]
+- Clean up project metadata. [Xinglong Zhang]
+- Requirements fix in pyproject.toml. [Xinglong Zhang]
+- Remove crest version from pyproject.toml. [Xinglong Zhang]
+- Pyproject.toml fix. [Xinglong Zhang]
+- Pyproject.toml fix. [Xinglong Zhang]
+- Pyproject.toml fix. [Xinglong Zhang]
+- Migrate configurations to pyproject.toml. [Xinglong Zhang]
+- Further fixes. [Xinglong Zhang]
+- Initial fixes. [Xinglong Zhang]
+- Rolled back to using python 3.9. [Xinglong Zhang]
+- Use python 3.10 in .github/workflows/release.yml. [Xinglong Zhang]
+- Added clear cache in .github/workflows/main.yml. [Xinglong Zhang]
+- Explicit python-version: 3.10 for ubuntu. [Xinglong Zhang]
+- Explicit imports in __init__.py using __all__ [Xinglong Zhang]
+- [flake8] [Xinglong Zhang]
+- Use python 3.10 instead of 3.9 in ./.github/workflows/main.yml.
+  [Xinglong Zhang]
+- .flake8 ignore F401. [Xinglong Zhang]
+- Ruff fix. [Xinglong Zhang]
+- Assemble molecules from GaussianOutput with pbc + tests. [Xinglong
+  Zhang]
+- Removed tests/data/GaussianTests/text/genecp_txt_from_api.txt in test.
+  [Xinglong Zhang]
+- Black formatting. [Xinglong Zhang]
+- Removed tests/data/GaussianTests/text/genecp_txt_from_api.txt.
+  [Xinglong Zhang]
+- Writer test. [Xinglong Zhang]
+- Add empty line to custom_solvent if not there. [Xinglong Zhang]
+- Turn off freq for certain jobs. [Xinglong Zhang]
+- Added tests for writer. [Xinglong Zhang]
+- Fix gaussian settings test; WIP: test gaussian writter. [Xinglong
+  Zhang]
+- Fix settings + tests. [Xinglong Zhang]
+- Added project settings from tests. [Xinglong Zhang]
+- Fix writer. [Xinglong Zhang]
+- Command not in run. [Xinglong Zhang]
+- Write extra commands. [Xinglong Zhang]
+- Rm logging for default settings. [Xinglong Zhang]
+- Rm logging for default settings. [Xinglong Zhang]
+- Logger filter once. [Xinglong Zhang]
+- Logger filter once. [Xinglong Zhang]
+- Logger filter once. [Xinglong Zhang]
+- Logger. [Xinglong Zhang]
+- Write envs. [Xinglong Zhang]
+- Write envs. [Xinglong Zhang]
+- Scheduling info. [Xinglong Zhang]
+- Scheduling slurm mail type. [Xinglong Zhang]
+- Scheduling info fix. [Xinglong Zhang]
+- Fix submitter. [Xinglong Zhang]
+- Fix _write_submission_script. [Xinglong Zhang]
+- Fix _write_submission_script. [Xinglong Zhang]
+- Rm unused imports. [Xinglong Zhang]
+- Pass Server object to Submitter. [Xinglong Zhang]
+- Get submitter type from scheduler with Submitter.NAME attribute.
+  [Xinglong Zhang]
+- Fix jobrunner. [Xinglong Zhang]
+- Black formatting. [Xinglong Zhang]
+- Added cli_args to runscript writing. [Xinglong Zhang]
+- Orca settings todo. [Xinglong Zhang]
+- Test gaussian job setting from orca input. [Xinglong Zhang]
+- Added back changes in commit e5d0419c1c9415 less removal of orca.
+  [Xinglong Zhang]
+- Revert "branched from cli; gaussian only; removed orca" [Xinglong
+  Zhang]
+
+  This reverts commit e5d0419c1c9415700d65bde02c37b1b7d41884f4.
+- Merge branch 'main0' into gaussian0 main0 has cli0 merged into main,
+  where cli0 was everything before removal of orca, based on commit
+  5c55d8d. [Xinglong Zhang]
+- Merge pull request #40 from xinglong-zhang/cli0. [Xinglong Zhang]
+
+  Cli0 to merge into main0, which will be merged into main once orca jobs have been fixed
+- Orca todo. [Xinglong Zhang]
+- Added more gaussian tests. [Xinglong Zhang]
+- Added gaussian job settings test. [Xinglong Zhang]
+- Black formatting. [Xinglong Zhang]
+- Added write_coordinates method for Molecule class + tests; molecular
+  coordinates can be written in different formats. [Xinglong Zhang]
+- Branched from cli; gaussian only; removed orca. [Xinglong Zhang]
+- Recover orca from 5c55d8d70de27366ba. [Xinglong Zhang]
+- Simplified sub.py. [Xinglong Zhang]
+- Added submit_command and Server.submit. [Xinglong Zhang]
+- Write program specifics in submission script and remove specifications
+  from ~/.chemsmart/{self.job.PROGRAM}/{self.job.PROGRAM}.modules |
+  .scripts | .envars. [Xinglong Zhang]
+- Make executable property of Submitter. [Xinglong Zhang]
+- Write conda specific envs. [Xinglong Zhang]
+- Added program specific envs + tests. [Xinglong Zhang]
+- Renamed scratch to scratch_dir in Server, + add default values +
+  change server.execution_type to server.submit_command. [Xinglong
+  Zhang]
+- ENH: improvement to GaussianFakeRunner so that fake flag is added to
+  filename automatically. [Xinglong Zhang]
+- Added wbi job. [Xinglong Zhang]
+- WIP: UVVis job to be added. [Xinglong Zhang]
+- Added TS job, with options to freeze atoms. [Xinglong Zhang]
+- Added tddft job. [Xinglong Zhang]
+- Added sp job. [Xinglong Zhang]
+- Scan job added. [Xinglong Zhang]
+- WIP: Grouper for molecular systems matching, saopt job to be fixed.
+  [Xinglong Zhang]
+- WIP: Grouper for molecular systems matching. [Xinglong Zhang]
+- Added resp job. [Xinglong Zhang]
+- Added nci job, to check writer and refactor it into settings.
+  [Xinglong Zhang]
+- Added modred job. [Xinglong Zhang]
+- Added link jobs. [Xinglong Zhang]
+- Added irc. [Xinglong Zhang]
+- Remove unused imports. [Xinglong Zhang]
+- Added dias job, use 1-indexed. [Xinglong Zhang]
+- Clean crest job to remove skip_completed kwarg. [Xinglong Zhang]
+- Added userjob + make everything (indices of list of structures and
+  atoms in molecule) 1-indexed. [Xinglong Zhang]
+- Master crest job to run modred, scan, opt, ts etc. [Xinglong Zhang]
+- Rename modredundant to modred. [Xinglong Zhang]
+- Chemsmart run -s SLURM --debug gaussian -p dee -f crest_conformers.xyz
+  -l cc -c 0 -m 1 crest -j modred -c [1,2] -n 5 -R. [Xinglong Zhang]
+- Add crest job to run all jobs from crest. [Xinglong Zhang]
+- Added crest command to run crest jobs. [Xinglong Zhang]
+- Added imports in chemsmart/jobs/gaussian/__init__.py. [Xinglong Zhang]
+- Broken. [Xinglong Zhang]
+- Remove imports in chemsmart/jobs/gaussian/__init__.py. [Xinglong
+  Zhang]
+- Added crestopt job. [Xinglong Zhang]
+- Rm comments. [Xinglong Zhang]
+- Cleanup. [Xinglong Zhang]
+- Added g16com job. [Xinglong Zhang]
+- GaussianGeneralJob fix. [Xinglong Zhang]
+- GaussianComJob for direct run. [Xinglong Zhang]
+- Num cores to cli base jobrunner. [Xinglong Zhang]
+- Add num cores to cli base jobrunner. [Xinglong Zhang]
+- Add num cores to cli. [Xinglong Zhang]
+- Get server from_servername. [Xinglong Zhang]
+- Distinguish servername from Server object. [Xinglong Zhang]
+- Added debug messages. [Xinglong Zhang]
+- Rm kwargs. [Xinglong Zhang]
+- Added kwargs. [Xinglong Zhang]
+- Added debug messages. [Xinglong Zhang]
+- Add update os environ. [Xinglong Zhang]
+- Servers from yaml. [Xinglong Zhang]
+- Servers from yaml. [Xinglong Zhang]
+- Servers from yaml. [Xinglong Zhang]
+- Servers from yaml. [Xinglong Zhang]
+- Create subclass. [Xinglong Zhang]
+- Scheduler type name. [Xinglong Zhang]
+- Remove comments and prints. [Xinglong Zhang]
+- Added obtain structure from pubchem, runs correctly locally with and
+  without fake. [Xinglong Zhang]
+- Black formatting. [Xinglong Zhang]
+- Improved logger so that it logs only once if it occurs in lru_cache
+  functions + remove self.executable.env. [Xinglong Zhang]
+- Get_list_from_string_range() function to return 1-indexed list.
+  [Xinglong Zhang]
+- Remove unused import in chemsmart.cli.__init__.py. [Xinglong Zhang]
+- Refactor utils.logger.py. [Xinglong Zhang]
+- Refine run options. [Xinglong Zhang]
+- Delete write methods from JobSettings and relegate to InputWriter
+  class. [Xinglong Zhang]
+- Remove commented out codes that remove duplicate last structures in
+  io.gaussian.output.py. [Xinglong Zhang]
+- Remove prints. [Xinglong Zhang]
+- Runs in scratch if set correctly. Eg in
+  ~/.chemsmart/server/local.yaml. [Xinglong Zhang]
+- WIP: to fix scratch directory. [Xinglong Zhang]
+- Added executables. [Xinglong Zhang]
+- WIP: cli no outputs. [Xinglong Zhang]
+- Fix class Server. [Xinglong Zhang]
+- WIP: run.py and jobrunners. [Xinglong Zhang]
+- Added servers. [Xinglong Zhang]
+- Read project settings from user yaml files only. [Xinglong Zhang]
+- Fix. [Xinglong Zhang]
+- WIP: introduce InputWriter class. [Xinglong Zhang]
+- WIP: gaussian subcommands work with MyCommand cls. [Xinglong Zhang]
+- WIP: add job and jobrunner base class. [Xinglong Zhang]
+- WIP: servers. [Xinglong Zhang]
+- Added ibm submitter. [Xinglong Zhang]
+- Added slurm submitter. [Xinglong Zhang]
+- Added pbs submitter. [Xinglong Zhang]
+- Added server from yaml + tests. [Xinglong Zhang]
+- Read yaml file. [Xinglong Zhang]
+- Merge branch 'main' into cli. [Xinglong Zhang]
+- Merge pull request #39 from xinglong-zhang/wbi. [Xinglong Zhang]
+- Ruff check . --fix : remove unused imports. [Xinglong Zhang]
+- Black formatting. [Xinglong Zhang]
+- Added test for SDFFile for .sdf structure. [Xinglong Zhang]
+- Clean up. [Xinglong Zhang]
+- Ruff check . --fix : remove unused imports. [Xinglong Zhang]
+- Bug fix for using CM5 charges. [Xinglong Zhang]
+- Black formatting. [Xinglong Zhang]
+- ENH: added script for computing Fukui reactivity indices. [Xinglong
+  Zhang]
+- Merge pull request #37 from xinglong-zhang/wbi. [Xinglong Zhang]
+- Black formatting. [Xinglong Zhang]
+- Added in mulliken charges and spin densities for gaussian output file.
+  [Xinglong Zhang]
+- Merge pull request #36 from xinglong-zhang/wbi. [Xinglong Zhang]
+- Black formatting. [Xinglong Zhang]
+- Remove unused import statements. [Xinglong Zhang]
+- ENH: added Hirshfeld analysis for Gaussian output files. [Xinglong
+  Zhang]
+- Merge pull request #35 from xinglong-zhang/wbi. [Xinglong Zhang]
+- Remove unused imports + black formatting. [Xinglong Zhang]
+- Added script to obtain natural charges from NBO calcs. [Xinglong
+  Zhang]
+- Black length fix. [Xinglong Zhang]
+- Chemsmart as executable. [Xinglong Zhang]
+- Initial cli files. [Xinglong Zhang]
+- Merge pull request #34 from xinglong-zhang/gaussian_io. [Xinglong
+  Zhang]
+- Fix filenames errors in GaussianGenECPTest due to renaming. [Xinglong
+  Zhang]
+- TODO: improve ORCA output parser. [Xinglong Zhang]
+- Update orca input molecule. [Xinglong Zhang]
+- Comment out method _read_xyz_file_structures_and_comments() in
+  Molecule class since this is refactored into XYZFile class. [Xinglong
+  Zhang]
+- Improved parser for gaussian input file + additional tests. [Xinglong
+  Zhang]
+- Improved molecule for coordination block. [Xinglong Zhang]
+- Create molecules from .xyz files. [Xinglong Zhang]
+- Read structure from xyz files. [Xinglong Zhang]
+- Rm commented out codes - alternative for getting all_structures from
+  Gaussian output file. [Xinglong Zhang]
+- Include get_molecule() method for Gaussian16Output class. [Xinglong
+  Zhang]
+- Remove unused imports. [Xinglong Zhang]
+- Added parser for gaussian pbc log files + tests. [Xinglong Zhang]
+- Added molecules with energy and forces. [Xinglong Zhang]
+- Added optimized structures to gaussian output. [Xinglong Zhang]
+- Added num energies. [Xinglong Zhang]
+- Added energies for QM, MP2 and ONIOM. [Xinglong Zhang]
+- Rm .swp file. [Xinglong Zhang]
+- Include vibrational modes for both normal and frozen atoms frequency
+  calcs + tests. [Xinglong Zhang]
+- Black formatting. [Xinglong Zhang]
+- Added frozen coordinates and free coordinates and tests. [Xinglong
+  Zhang]
+- TODO: vibrational freq normal modes. [Xinglong Zhang]
+- Merge pull request #33 from xinglong-zhang/gaussian_io. [Xinglong
+  Zhang]
+- Requires basis-set-exchange and not bse. [Xinglong Zhang]
+- Remove .swp. [Xinglong Zhang]
+- Merge pull request #27 from xinglong-zhang/wbi. [Xinglong Zhang]
+- Merge pull request #31 from xinglong-zhang/main. [Xinglong Zhang]
+
+  merge main to wbi
+- Black formatting to 79 char lengths. [Xinglong Zhang]
+- ENH: added in gen and genecp. [Xinglong Zhang]
+- Remove comparison functions in GaussianGenECPTest.py. [Xinglong Zhang]
+- Added genecp and tests. [Xinglong Zhang]
+- Test. [Xinglong Zhang]
+- Test. [Xinglong Zhang]
+- Bump actions/setup-python from 3 to 5. [dependabot[bot]]
+
+  Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3 to 5.
+  - [Release notes](https://github.com/actions/setup-python/releases)
+  - [Commits](https://github.com/actions/setup-python/compare/v3...v5)
+
+  ---
+  updated-dependencies:
+  - dependency-name: actions/setup-python
+    dependency-type: direct:production
+    update-type: version-update:semver-major
+  ...
+- Bump actions/checkout from 3 to 4. [dependabot[bot]]
+
+  Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
+  - [Release notes](https://github.com/actions/checkout/releases)
+  - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
+  - [Commits](https://github.com/actions/checkout/compare/v3...v4)
+
+  ---
+  updated-dependencies:
+  - dependency-name: actions/checkout
+    dependency-type: direct:production
+    update-type: version-update:semver-major
+  ...
+- Merge pull request #26 from xinglong-zhang/main. [Xinglong Zhang]
+- Merge pull request #32 from xinglong-zhang/gaussian_io. [Xinglong
+  Zhang]
+- ORCAFileMixin. [Xinglong Zhang]
+- Make ORCAFileMixin as a subclass of FileMixin. [Xinglong Zhang]
+- Make ORCAFileMixin as a subclass of FileMixin. [Xinglong Zhang]
+- Black formating and removed unused imports. [Xinglong Zhang]
+- Refactored route_object and dervied properties into GaussianFileMixin.
+  [Xinglong Zhang]
+- Refactored _get_chk(), _get_mem() and _get_nproc() to
+  GaussianFileMixin. [Xinglong Zhang]
+- Merge pull request #30 from xinglong-zhang/gassian_io. [Xinglong
+  Zhang]
+- Black formatting to 79 char lengths. [Xinglong Zhang]
+- ENH: added in gen and genecp. [Xinglong Zhang]
+- Remove comparison functions in GaussianGenECPTest.py. [Xinglong Zhang]
+- Added genecp and tests. [Xinglong Zhang]
+- Test. [Xinglong Zhang]
+- Test. [Xinglong Zhang]
+- Merge pull request #29 from xinglong-
+  zhang/dependabot/github_actions/actions/setup-python-5. [Xinglong
+  Zhang]
+
+  Bump actions/setup-python from 3 to 5
+- Bump actions/setup-python from 3 to 5. [dependabot[bot]]
+
+  Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3 to 5.
+  - [Release notes](https://github.com/actions/setup-python/releases)
+  - [Commits](https://github.com/actions/setup-python/compare/v3...v5)
+
+  ---
+  updated-dependencies:
+  - dependency-name: actions/setup-python
+    dependency-type: direct:production
+    update-type: version-update:semver-major
+  ...
+- Merge pull request #28 from xinglong-
+  zhang/dependabot/github_actions/actions/checkout-4. [Xinglong Zhang]
+
+  Bump actions/checkout from 3 to 4
+- Bump actions/checkout from 3 to 4. [dependabot[bot]]
+
+  Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
+  - [Release notes](https://github.com/actions/checkout/releases)
+  - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
+  - [Commits](https://github.com/actions/checkout/compare/v3...v4)
+
+  ---
+  updated-dependencies:
+  - dependency-name: actions/checkout
+    dependency-type: direct:production
+    update-type: version-update:semver-major
+  ...
+- Merge pull request #22 from xinglong-
+  zhang/dependabot/github_actions/codecov/codecov-action-5. [Xinglong
+  Zhang]
+
+  Bump codecov/codecov-action from 4 to 5
+- Bump codecov/codecov-action from 4 to 5. [dependabot[bot]]
+
+  Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5.
+  - [Release notes](https://github.com/codecov/codecov-action/releases)
+  - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
+  - [Commits](https://github.com/codecov/codecov-action/compare/v4...v5)
+
+  ---
+  updated-dependencies:
+  - dependency-name: codecov/codecov-action
+    dependency-type: direct:production
+    update-type: version-update:semver-major
+  ...
+- Merge pull request #25 from xinglong-zhang/jobs_io. [Xinglong Zhang]
+- Remove token generation in .github/workflows/main.yml. [Xinglong
+  Zhang]
+- Remove toxyz.py. [Xinglong Zhang]
+- Dataset method to be added. [Xinglong Zhang]
+- Removed xtb io, which is not included yet. [Xinglong Zhang]
+- Keep line lengths to 79 characters. [Xinglong Zhang]
+- Removed dataset.py. [Xinglong Zhang]
+- Keep only io. [Xinglong Zhang]
+- Black formatting. [Xinglong Zhang]
+- Black fix to length 79. [Xinglong Zhang]
+- Xtb parser. [Xinglong Zhang]
+- Update gaussian output parser. [Xinglong Zhang]
+- Remove cli. [Xinglong Zhang]
+- Fix tests. [Xinglong Zhang]
+- Merge newio to wbi. [Xinglong Zhang]
+- Added ruff as requirement-test.txt. [Xinglong Zhang]
+- Black fix length 79. [Xinglong Zhang]
+- .flake8 length to 121. [Xinglong Zhang]
+- Added io.gaussian.__init__.py. [Xinglong Zhang]
+- Merge remote-tracking branch 'origin' into newio. [Xinglong Zhang]
+- Merge local io to newio. [Xinglong Zhang]
+- Merge pull request #16 from xinglong-zhang/main. [Xinglong Zhang]
+
+  Merge pull request #14 from xinglong-zhang/logfiles
+- Fix conflict. [Xinglong Zhang]
+- Merge pull request #12 from xinglong-zhang/main. [Xinglong Zhang]
+
+  main to io
+- Black reformat. [Xinglong Zhang]
+- Black reformat. [Xinglong Zhang]
+- Add file. [Xinglong Zhang]
+- Merge pull request #9 from xinglong-zhang/revert-8-uvvis. [Xinglong
+  Zhang]
+
+  Revert "EHN: Uvvis read transitions and MO contributions without pymatgen "
+- Revert "EHN: Uvvis read transitions and MO contributions without
+  pymatgen " [Xinglong Zhang]
+- Merge pull request #8 from xinglong-zhang/uvvis. [Xinglong Zhang]
+- Merge pull request #7 from xinglong-zhang/uvvis. [Xinglong Zhang]
+
+  Able to parse and operate on .cube files
+- Initial cli for gaussian and orca. [Xinglong Zhang]
+- Streamlined coordinate block. [Xinglong Zhang]
+- Updates. [Xinglong Zhang]
+- Fix hirshfeld when values of dict are the same + toxyz.py todo.
+  [Xinglong Zhang]
+- Script to read hirshfeld analysis. [Xinglong Zhang]
+- Add hirshfeld analysis orca. [Xinglong Zhang]
+- Refactor so that orca SP output files can also read up till rotational
+  constants. [Xinglong Zhang]
+- Refactor energies so that optimized and sp output files can use the
+  same code to get. [Xinglong Zhang]
+- Use repattern in orca outputs.py. [Xinglong Zhang]
+- Use standard_coord_pattern. [Xinglong Zhang]
+- Add hirshefeld. [Xinglong Zhang]
+- Cleaned with black. [Xinglong Zhang]
+- Fix homo-lumo gap in gaussian output. [Xinglong Zhang]
+- Fix orca fmo energies. [Xinglong Zhang]
+- Run black. [Xinglong Zhang]
+- Linting. [Xinglong Zhang]
+- Safe delete chemsmart/io/orca/utils.py. [Xinglong Zhang]
+- Added FMO energies for gaussian and orca. [Xinglong Zhang]
+- Orca outputs.py + tests. [Xinglong Zhang]
+- Orca outputs.py + tests. [Xinglong Zhang]
+- Added ORCA IO inputs.py + fix tests. [Xinglong Zhang]
+- Refactor gaussian io. [Xinglong Zhang]
+- Remove rename_project.yml in github workflow. [Xinglong Zhang]
+- Add github workflow auto tests. [Xinglong Zhang]
+- Add github workflow auto tests. [Xinglong Zhang]
+- Add github workflow auto tests. [Xinglong Zhang]
+- Collect all patterns together. [Xinglong Zhang]
+- Added num atoms of the molecule. [Xinglong Zhang]
+- Fix orca route. [Xinglong Zhang]
+- Add orca. [Xinglong Zhang]
+- Fmo energies. [Xinglong Zhang]
+- Added fmo gap. [Xinglong Zhang]
+- Add in orbital energies. [Xinglong Zhang]
+- Add utils test. [Xinglong Zhang]
+- Black max length 79. [Xinglong Zhang]
+- Changed max line lengths to 79. [Xinglong Zhang]
+- Black fix. [Xinglong Zhang]
+- Added tests for gaussian input files. [Xinglong Zhang]
+- Add gaussian output parser. [Xinglong Zhang]
+- Make length to 79. [Xinglong Zhang]
+- Run black -l 121. [Xinglong Zhang]
+- Remove unused imports. [Xinglong Zhang]
+- Black linting. [Xinglong Zhang]
+- Get electronic configurations. [Xinglong Zhang]
+- Merge remote-tracking branch 'origin' into wbi. [Xinglong Zhang]
+- Merge pull request #19 from xinglong-zhang/winfix. [Xinglong Zhang]
+
+  fix win workflow error
+- Fix win workflow error. [Xinglong Zhang]
+- Fix win workflow error. [Xinglong Zhang]
+- Merge pull request #18 from xinglong-zhang/winfix. [Xinglong Zhang]
+- Fix win workflow error. [Xinglong Zhang]
+- Merge pull request #17 from xinglong-zhang/clean. [Xinglong Zhang]
+- Clean up main. [Xinglong Zhang]
+- Test push to main. [Xinglong Zhang]
+- Test push to main. [Xinglong Zhang]
+- Test push to main. [Xinglong Zhang]
+- Parser for NAO. [Xinglong Zhang]
+- Working parser for nao. [Xinglong Zhang]
+- Merge pull request #14 from xinglong-zhang/logfiles. [Xinglong Zhang]
+
+  add log files tddft
+- Add log files tddft. [Xinglong Zhang]
+- Merge pull request #13 from xinglong-zhang/test. [Xinglong Zhang]
+
+  io fix genecp
+- Black reformat tests. [Xinglong Zhang]
+- Black reformat. [Xinglong Zhang]
+- Io fix genecp. [Xinglong Zhang]
+- Added tddft. [Xinglong Zhang]
+- Gaussian16Input. [Xinglong Zhang]
+- Refactor. [Xinglong Zhang]
+- Remove sponsor. [Xinglong Zhang]
+- 88 to 121 fix. [Xinglong Zhang]
+- In Makefile change line characters from 88 to 121. [Xinglong Zhang]
+- In Makefile change line characters from 79 to 88. [Xinglong Zhang]
+- Black fix. [Xinglong Zhang]
+- Black fix E206 see .flake8 comments. [Xinglong Zhang]
+- Extend-ignore flake8. [Xinglong Zhang]
+- Extend-ignore flake8. [Xinglong Zhang]
+- Black fix tests. [Xinglong Zhang]
+- Flake ignore E203. [Xinglong Zhang]
+- Flake fix. [Xinglong Zhang]
+- Black fix. [Xinglong Zhang]
+- Black fix. [Xinglong Zhang]
+- Black fix line lengths. [Xinglong Zhang]
+- Flake8. [Xinglong Zhang]
+- Fix flake8 errors. [Xinglong Zhang]
+- Linting fix. [Xinglong Zhang]
+- Add error messages. [Xinglong Zhang]
+- Cube operator fix. [Xinglong Zhang]
+- Write cube diff. [Xinglong Zhang]
+- Cube operation. [Xinglong Zhang]
+- Cube operator done. [Xinglong Zhang]
+- Ruff fix. [Xinglong Zhang]
+- Cube file operator. [Xinglong Zhang]
+- Add gridpoints data. [Xinglong Zhang]
+- Add structure. [Xinglong Zhang]
+- Molecule structure class. [Xinglong Zhang]
+- Periodic table. [Xinglong Zhang]
+- Added FileMixin. [Xinglong Zhang]
+- Uvvis init. [Xinglong Zhang]
+- Merge pull request #3 from xinglong-
+  zhang/dependabot/github_actions/actions/setup-python-5. [Xinglong
+  Zhang]
+
+  Bump actions/setup-python from 4 to 5
+- Bump actions/setup-python from 4 to 5. [dependabot[bot]]
+
+  Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
+  - [Release notes](https://github.com/actions/setup-python/releases)
+  - [Commits](https://github.com/actions/setup-python/compare/v4...v5)
+
+  ---
+  updated-dependencies:
+  - dependency-name: actions/setup-python
+    dependency-type: direct:production
+    update-type: version-update:semver-major
+  ...
+- Merge pull request #4 from xinglong-
+  zhang/dependabot/github_actions/stefanzweifel/git-auto-commit-
+  action-5. [Xinglong Zhang]
+
+  Bump stefanzweifel/git-auto-commit-action from 4 to 5
+- Bump stefanzweifel/git-auto-commit-action from 4 to 5.
+  [dependabot[bot]]
+
+  Bumps [stefanzweifel/git-auto-commit-action](https://github.com/stefanzweifel/git-auto-commit-action) from 4 to 5.
+  - [Release notes](https://github.com/stefanzweifel/git-auto-commit-action/releases)
+  - [Changelog](https://github.com/stefanzweifel/git-auto-commit-action/blob/master/CHANGELOG.md)
+  - [Commits](https://github.com/stefanzweifel/git-auto-commit-action/compare/v4...v5)
+
+  ---
+  updated-dependencies:
+  - dependency-name: stefanzweifel/git-auto-commit-action
+    dependency-type: direct:production
+    update-type: version-update:semver-major
+  ...
+- Merge pull request #5 from xinglong-
+  zhang/dependabot/github_actions/codecov/codecov-action-4. [Xinglong
+  Zhang]
+
+  Bump codecov/codecov-action from 3 to 4
+- Bump codecov/codecov-action from 3 to 4. [dependabot[bot]]
+
+  Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
+  - [Release notes](https://github.com/codecov/codecov-action/releases)
+  - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
+  - [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)
+
+  ---
+  updated-dependencies:
+  - dependency-name: codecov/codecov-action
+    dependency-type: direct:production
+    update-type: version-update:semver-major
+  ...
+- Merge pull request #2 from xinglong-
+  zhang/dependabot/github_actions/softprops/action-gh-release-2.
+  [Xinglong Zhang]
+
+  Bump softprops/action-gh-release from 1 to 2
+- Bump softprops/action-gh-release from 1 to 2. [dependabot[bot]]
+
+  Bumps [softprops/action-gh-release](https://github.com/softprops/action-gh-release) from 1 to 2.
+  - [Release notes](https://github.com/softprops/action-gh-release/releases)
+  - [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md)
+  - [Commits](https://github.com/softprops/action-gh-release/compare/v1...v2)
+
+  ---
+  updated-dependencies:
+  - dependency-name: softprops/action-gh-release
+    dependency-type: direct:production
+    update-type: version-update:semver-major
+  ...
+- Merge pull request #1 from xinglong-
+  zhang/dependabot/github_actions/actions/checkout-4. [Xinglong Zhang]
+
+  Bump actions/checkout from 3 to 4
+- Bump actions/checkout from 3 to 4. [dependabot[bot]]
+
+  Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
+  - [Release notes](https://github.com/actions/checkout/releases)
+  - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
+  - [Commits](https://github.com/actions/checkout/compare/v3...v4)
+
+  ---
+  updated-dependencies:
+  - dependency-name: actions/checkout
+    dependency-type: direct:production
+    update-type: version-update:semver-major
+  ...
+- Update readme. [Xinglong Zhang]
+- Merge pull request #6 from xinglong-zhang/ct. [Xinglong Zhang]
+
+  Ct
+- Readme chemsmart to pychemsmart. [Xinglong Zhang]
+- Readme chemsmart to pychemsmart. [Xinglong Zhang]
+- Initial commit. [Xinglong Zhang]
+- ✅ Ready to clone and code. [xinglong-zhang]
+- Initial commit. [Xinglong Zhang]
+
+