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Big update #422

Merged
merged 308 commits into from
Sep 16, 2024
Merged

Big update #422

merged 308 commits into from
Sep 16, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jun 29, 2024

  1. fix

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    RagnarB83 committed Jun 29, 2024
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  2. cleanup

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    RagnarB83 committed Jun 29, 2024
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  3. coulombcharge: cupy version in MM_module. Default for TerachemTheory

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    RagnarB83 committed Jun 29, 2024
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Commits on Jun 30, 2024

  1. test: coulombcharge_cupy version with batching

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  2. module_MM: coulombcharge, julia option

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  3. julia-interface: allow pythoncall to install julia

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  4. fix

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  5. module_MM julia: fix

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Commits on Jul 1, 2024

  1. fix

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    RagnarB83 committed Jul 1, 2024
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Commits on Jul 3, 2024

  1. - ASH_Results object: write_to_disk method, more freq properties 

    - Module_freq: internal cleanup
- CP2KTheory: print settings
- ORCATheory: print_dipole_moment
- PySCFTHeory: bugfix, prepare_run was only run once, has to be run always to update  coordinates properly
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  2. - pyscftheory: bugfix, basis_functions logic, mol.build 

    - masses option to AnFreq, Numfreq.
- use_full_geo_in_rotational_analysis option to thermochemcalc
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  3. - ASH Results.write_to_disk: bugfix for list handling 

    - read_results_from_file standalone function. Reads JSON file back into a Dataclass
- NuMFreq: hessatoms, recognition of hessatoms list same length as system
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  4. - ASH_Results: writing to disk by default for all major jobtypes

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Commits on Jul 9, 2024

  1. - ASH-packages.sh: julia-interface recommendation 

    - Preliminary ONIOM (not ready)
- MLatom: minor tweaks
- xtb interface: additional charges-grab function
- check_charge_mult: added ONIOM theory check
- QMTheory class (unused so far)
- New module machine_learning: function create_ML_training_data
- ASH_Results.write_to_disk: fix for empty list
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    RagnarB83 committed Jul 9, 2024
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  2. fixes

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    RagnarB83 committed Jul 9, 2024
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  3. - write_pdbfile_openmm: fix with file extension 

    - create_adaptive_minimal_basis_set
- grab_basis_from_ORCAinputfile
- ORCATHeory: support for atombasisdict and ecpdict
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  4. OpenMMTheory: pdb_pbc_vectors in set_periodics_before_system_creation

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  5. fix

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    RagnarB83 committed Jul 9, 2024
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  6. fixes to create_adaptive_minimal_basis_set

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  7. fix

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    RagnarB83 committed Jul 9, 2024
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  8. Fragment.method get_subset_coords_with_linkatoms

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  9. fix

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    RagnarB83 committed Jul 9, 2024
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  10. fix

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    RagnarB83 committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. Optimizer: not including geometry in ASH_Results for now

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  2. fix: ecpbasisblock and basis_blocks in ORCATheory

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  3. fix

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    RagnarB83 committed Jul 10, 2024
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  4. wrap_box_coords: remove debugging print statements

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Commits on Jul 14, 2024

  1. - Changes to add_centerforce option to MolecularDynamics function: no… 

    …w adding a flatbottom force
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Commits on Jul 16, 2024

  1. OpenMM_MD: timestep is now 0.001 by default

    @RagnarB83
    RagnarB83 committed Jul 16, 2024
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Commits on Jul 17, 2024

  1. minor work on polembed

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    RagnarB83 committed Jul 17, 2024
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  2. pyscf: minor embedding fix

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    RagnarB83 committed Jul 17, 2024
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  3. fix

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    RagnarB83 committed Jul 17, 2024
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Commits on Jul 20, 2024

  1. - General check_program_location function 

    - modifcations to DaltonTheory (incomplete)
- insert_solute_into_solvent, option to delete solute connectivity
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    RagnarB83 committed Jul 20, 2024
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Commits on Jul 22, 2024

  1. - skip_connectivity option to write_pdbfile_openmm 

    - ASH Results: skip printing of large arrays and None values
- insert_solute_into_solvent: write_solute_connectivity True/False option. Also PBC info written to PDB-file
- QMPC_fragexpand function
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    RagnarB83 committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. - minor ONIOMTheory modifications (incomplete) 

    - Block2 gradient (untested)
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Commits on Jul 25, 2024

  1. - ONIOMTheory moved to file. Changes to ONIOM, incomplete 

    - pygrep/pygrep2 functions: option to ignore errors
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  2. - ORCA file grab: errors=ignore

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  3. fix

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    RagnarB83 committed Jul 25, 2024
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Commits on Jul 27, 2024

  1. PES: deltaSCF option

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Commits on Jul 28, 2024

  1. - changes to create_ORCA_json_file (ORCA6) 

    - PES updates
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  2. pes: fixes

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  3. fixes

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  4. fixes

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  5. debugging

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    RagnarB83 committed Jul 28, 2024
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  6. fixes

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  7. fixes

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  8. debugging

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    RagnarB83 committed Jul 28, 2024
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  9. fixes

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    RagnarB83 committed Jul 28, 2024
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  10. cleanup

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    RagnarB83 committed Jul 28, 2024
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  11. PES: tddft fixes

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  12. fix

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  13. fix

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  14. fixes

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  15. fixes

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  16. fix

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  17. fixes

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  18. fixes

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  19. fixes

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  20. fix

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    RagnarB83 committed Jul 28, 2024
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Commits on Jul 29, 2024

  1. - ccpy: updates 

    - orca: dipole integrals
- pyscf: default symmetry is C1
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  2. ccpy update

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  3. fix

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  4. fix

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    RagnarB83 committed Jul 29, 2024
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Commits on Jul 30, 2024

  1. ccpy interface: work

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  2. fixes

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  3. fix

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  4. fix

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  5. fix

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  6. fix

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  7. fixes

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  8. fix

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  9. fix

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  10. fix

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    RagnarB83 committed Jul 30, 2024
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  11. ccpy: tests

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  12. fix

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  13. fix

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    RagnarB83 committed Jul 30, 2024
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  14. ccpy: adaptive fix 

    pyscf: create_fcidump_file
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Commits on Jul 31, 2024

  1. ccpy: eom printout, cipsi-driven cc, fixes

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  2. fix

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  3. fix

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  4. fix

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  5. fix

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  6. fix

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  7. fix

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  8. fix

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  9. fix

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  10. fixes

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  11. fix

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  12. fix

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  13. EOM_guess_symmetry

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  14. ccpy: multiplicity for EOM and IPEOM

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  15. fix

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Commits on Aug 1, 2024

  1. - ORCATheory: deal with error-ignore option 

    - vpot: incomplete, wait for bugfix
- jsonfile: changes, incomplete
- basic read/write trexio_files, not ready
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  2. fix

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  3. fix

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  4. debug

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  5. debug

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  6. fix

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    RagnarB83 committed Aug 1, 2024
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  7. trexio read/write fixes

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    RagnarB83 committed Aug 1, 2024
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  8. fix

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  9. - Created and moved ASH_write_integralfile (previously MRCC_write_int… 

    …egralfile) to functions.elstructure, now supports MRCC and FCIDUMP headers

- create_ORCA_json_file: support for integrals option
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  10. fix to ASH_write_integralfile

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Commits on Aug 2, 2024

  1. - pyscftheory: option to read in FCIDUMP-file (needs more testing) 

    - pyscftheory run_SCF: tweaks
- get_dipole_moment inside try
- ASH_write_integralfile: cleanup
- new function:  create_ORCA_FCIDUMP
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  2. create_ORCA_FCIDUMP fix

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  3. debugging

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  4. fix for create_ORCA_json_file

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  5. fix for read_ORCA_json_file

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  6. fix

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  7. fix

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  8. create_ORCA_FCIDUMP and create_ORCA_json_file: full_int_transform option

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  9. fix

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  10. fix

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  11. fix

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  12. fixes

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  13. fix

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  14. hacky attempt of UHF->ROHF for FCIDUMP

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Commits on Aug 4, 2024

  1. - functions elstructure: General check_occupations function (detect R… 

    …HF, UHF, ROHF, fract etc.)

- ccpy: work on ORCA interface, incomplete
- create_ORCA_json_file: allow bson
- create_ORCA_FCIDUMP : tweaks
- work on ONIOM: incomplete
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  2. ccpy: fix

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  3. fix

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  4. fix

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  5. fix

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  6. fix

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  7. debug

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  8. debug

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  9. - pyscftheory: improved logic in read_chkfile 

    - Better error message for databasefile not found
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  10. debug

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  11. debug

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  12. debug

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  13. debug

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  14. fix

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  15. fix

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  16. debug

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  17. fixes

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  18. debug

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  19. debug

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  20. debug

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Commits on Aug 5, 2024

  1. debugging

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  2. debug

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  3. bug

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  4. fixes

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  5. ccpy: some timings

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  6. more timings

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  7. fixes

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  8. support for bson

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  9. fix

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  10. fix

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  11. read_ORCA_json_file: ujson option

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  12. json changes

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  13. fix

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  14. read_ORCA_msgpack_file: support for msgspec or msgpack

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  15. fix

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  16. read_ORCA_json_file: support for orjson, ujson and json libraries

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  17. load_orca_integrals: convert_UHF_to_ROHF

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  18. fix

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  19. fix

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  20. fix

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  21. fix

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  22. fix

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  23. fix

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  24. fix

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  25. fix

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  26. fixes

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  27. ccpy: minor cleanup

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  28. Added ROHF-UHF swap feature in ORCATheory, added gbwfile attribute to… 

    … ORCATheory in general, added to ccpytheory
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  29. create_ORCA_json_file: file-size printed

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Commits on Aug 6, 2024

  1. - ccpytheory: orca_gbwfile option

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  2. fix

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  3. minor fix

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  4. oops

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  5. WrapTheory subclass of Theory

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  6. fix

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  7. MLatomTheory: path handling for modelfile

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  8. minor create_ML_training_data cleanup

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  9. minor printing

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  10. mlatom: fixes

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  11. mlatom fix

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  12. fix

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  13. parallelization option for create_ML_training_data: untested

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  14. debugging

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  15. fix

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  16. ORCA_orbital_setup: FIC_DDCI3

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Commits on Aug 7, 2024

  1. Some fixes to grab_ORCA_wfn and make_molden_file

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  2. - grab_ORCA_wfn: C now transposed 

    - make_molden_file: C transposed again (due to particular logic inside function)
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Commits on Aug 8, 2024

  1. ONIOM: linkatom projection work, not ready.

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  2. oniom testing

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  3. test

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  4. - oniom attempts 

    - ccpy: attempt at molden natorb write
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  5. test

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  6. fix

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Commits on Aug 9, 2024

  1. - Basic trexio support in Fragment, read and write. Molecular info on… 

    …ly for now

- nucchargestoelems function
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  2. pyscf: analytic Hessian support, IR for anHessian 

    - Anfreq: grabs IR intensities from ORCA, pyscf. CFour TODO
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  3. updates to interface

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  4. fix

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  5. fix

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  6. fix

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  7. fix

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  8. fix

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  9. fix

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  10. fix

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Commits on Aug 11, 2024

  1. - create_GBW_from_json_file: bugfix 

    - calculate_ORCA_natorbs_from_density function
- work on DLPNO-CCSD as natorbs option in ORCA_orbital_setup: not yet ready
- QMMMTheory: reading in new charges to QMMMTheory now works for OpenMMTheory (was broken). not sure how useful feature is
- QMMMTheory: mechanical embedding enabled. Needs more testing
- Updates on tests: MeOH-H2O system for both NonBondedTheory and OpenMMTheory
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Commits on Aug 12, 2024

  1. fix

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  2. fix

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  3. QM/MM: embedding choice logic cleanup, test fixed

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  4. xmlfile fix

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  5. scipy.linalg submodule import bugfix

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  6. write_ORCA_json_file

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  7. create_GBW_from_json_file

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  8. new_ORCA_natorbsfile_from_density

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  9. fix

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  10. test

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  11. ORCA_orbital_setup: support for DLPNO-CCSD and CCSD(T) natural orbitals

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  12. fix

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  13. fix

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  14. fix

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  15. test

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  16. fix

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  17. fix

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  18. fix

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  19. fix

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  20. fix

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  21. fix

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  22. fix

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  23. fix

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  24. fix

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  25. debug

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  26. fix

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  27. debug

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  28. test

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  29. fix

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  30. fix

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  31. fix

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  32. fix

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  33. fix

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  34. - update_LJ_epsilons: confirmed to work, cleanup 

    - Singlepoint using QM/MM now writes QM, MM and QM/MM energies to ASH_Results object.
- Singlepoint: some cleanup
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Commits on Aug 13, 2024

  1. - Moved trexio functions to interface_Trexio 

    -pyscf: frozencore minor fix
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  2. fix

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  3. ccpy: changes to run_density and make_natural_orbitals: Now doing ful… 

    …l rdm with frozen core and diagonalizing
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  4. fix

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  5. cleanup

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Commits on Aug 14, 2024

  1. - debugging 

    - small_molecule_parameterizer: import error message
- work on ONIOM: incomplete
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  2. fix

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    RagnarB83 committed Aug 14, 2024
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  3. cleanup

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    RagnarB83 committed Aug 14, 2024
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  4. tweaks to mlatom kreg interface

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  5. tweaks

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  6. fix

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  7. fix

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Commits on Sep 12, 2024

  1. - ONIOMTheory: linkatom changes, RCD option, ONIOM-2 gradient complet… 

    …e, ONIOM-3 gradient not ready

- QMMMTheory: linkatom changes, RCD shifting,
- calculate_RMSD function for 2 fragments, allows subset match and heavyatoms option
- get_linkatom_positions function extension: simple and ratio method
- grabatomcharges_ORCA: bugfix for BS job,
- write freqs and normal mode comps to file by default
- various cleanup
    @RagnarB83
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  2. fix

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    RagnarB83 committed Sep 12, 2024
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  3. QM/MM fix

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    RagnarB83 committed Sep 12, 2024
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Commits on Sep 13, 2024

  1. cleanup: QM/MM linkatom printing

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