├── docs ├── source │ ├── api.rst │ ├── index.rst │ └── conf.py └── Makefile ├── src ├── __init__.py ├── extras.py ├── stage2_helper.py └── vdw_surface.py ├── tests ├── acetic_acid.xyz ├── phosphate.xyz ├── ethanol_1.xyz ├── ethanol_2.xyz ├── phosphate.py ├── resp_unconstrained_a.ini ├── phosphate.ini ├── resp_two_confs_a.ini ├── resp_unconstrained_b.ini.old ├── resp_unconstrained_b.ini ├── resp_two_confs_b.ini ├── resp_constrained_a.ini ├── resp_unconstrained_b.out ├── resp_unconstrained_a.out ├── resp_two_confs_a.out ├── resp_constrained_a.out ├── resp_two_confs_b.out ├── test_resp.py ├── acetic_acid.log ├── ethanol_2_esp.dat ├── ethanol_1_esp.dat ├── ethanol_1-psi.log ├── ethanol_2-psi.log ├── acetic_acid_esp.dat └── acetic_acid-psi.log ├── examples ├── README.md └── 2-methylpropanol │ ├── 2_methylpropanal_1.xyz │ ├── 2_methylpropanal_2.xyz │ ├── 2_methylpropanal_3.xyz │ ├── 2_methylpropanal_4.xyz │ ├── 2_methylpropanal_5.xyz │ ├── 2_methylpropanal_6.xyz │ ├── 2_methylpropanal_stage_1.ini │ ├── 2_methylpropanal_stage_2.ini │ ├── 2_methylpropanal_stage_1.out │ ├── 2_methylpropanal_stage_2.out │ ├── 2_methylpropanal_4_esp.dat │ ├── 2_methylpropanal_1_esp.dat │ ├── 2_methylpropanal_3_esp.dat │ ├── 2_methylpropanal_6_esp.dat │ ├── 2_methylpropanal_2_esp.dat │ └── 2_methylpropanal_5_esp.dat ├── .gitignore ├── LICENSE └── README.md /docs/source/api.rst: -------------------------------------------------------------------------------- 1 | ======== 2 | RESP API 3 | ======== 4 | 5 | .. automodapi:: resp 6 | 7 | .. automodapi:: resp.espfit 8 | 9 | -------------------------------------------------------------------------------- /src/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | """Top-level package for RESP.""" 4 | 5 | __authors__ = "Asem Alenaizan" 6 | __version__ = '0.8' 7 | __license__ = "BSD-3-Clause" 8 | __date__ = "2019-08-07" 9 | 10 | from .driver import resp 11 | from . import espfit 12 | from .extras import test 13 | from .stage2_helper import set_stage2_constraint 14 | from .vdw_surface import vdw_surface 15 | -------------------------------------------------------------------------------- /tests/acetic_acid.xyz: -------------------------------------------------------------------------------- 1 | 8 2 | acetic_acid 3 | C 1.45051389 -0.06628932 0.00000000 4 | H 1.75521613 -0.62865986 -0.87500146 5 | H 1.75521613 -0.62865986 0.87500146 6 | H 1.92173244 0.90485897 0.00000000 7 | C -0.04233122 0.09849378 0.00000000 8 | O -0.67064817 -1.07620915 0.00000000 9 | H -1.60837259 -0.91016601 0.00000000 10 | O -0.62675864 1.13160510 0.00000000 11 | -------------------------------------------------------------------------------- /examples/README.md: -------------------------------------------------------------------------------- 1 | ## Examples 2 | - `example1.py`: Two-stage fitting for one ethanol conformer 3 | - `example2.py`: Two-stage fitting for two ethanol conformers 4 | - `example3.py`: Two-stage fitting for three ethanol conformers 5 | - `example4.py`: Two-stage fitting for four ethane-1,2-diol conformers with complex constraints 6 | - `constraints.py`: Additional examples on how to specify intramolecular constraints 7 | -------------------------------------------------------------------------------- /tests/phosphate.xyz: -------------------------------------------------------------------------------- 1 | 11 2 | obj01 3 | P 0.421971 0.102832 0.135690 4 | O 0.710282 0.929406 -1.093764 5 | C 0.507647 2.313485 -0.796841 6 | H 0.206144 2.817489 -1.667230 7 | H 1.404131 2.730276 -0.443143 8 | H -0.236200 2.409513 -0.062014 9 | O -0.863359 -0.782297 -0.306176 10 | O -0.058027 0.808221 1.380723 11 | H 1.581135 -1.399071 -0.459463 12 | O 1.359696 -0.977171 0.373942 13 | H -1.544731 -0.110743 -0.483852 14 | -------------------------------------------------------------------------------- /tests/ethanol_1.xyz: -------------------------------------------------------------------------------- 1 | 9 2 | ethanol_conf1 3 | C 0.00000000 0.00000000 0.00000000 4 | C 1.48805540 -0.00728176 0.39653260 5 | O 2.04971655 1.37648153 0.25604810 6 | H 3.06429978 1.37151670 0.52641124 7 | H 1.58679428 -0.33618761 1.43102358 8 | H 2.03441010 -0.68906454 -0.25521028 9 | H -0.40814044 -1.00553466 0.10208540 10 | H -0.54635470 0.68178278 0.65174288 11 | H -0.09873888 0.32890585 -1.03449097 -------------------------------------------------------------------------------- /tests/ethanol_2.xyz: -------------------------------------------------------------------------------- 1 | 9 2 | ethanol_conf2 3 | C 0.00000000 0.00000000 0.00000000 4 | C 1.48013500 -0.00724300 0.39442200 5 | O 2.00696300 1.29224100 0.26232800 6 | H 2.91547900 1.25572900 0.50972300 7 | H 1.61500700 -0.32678000 1.45587700 8 | H 2.07197500 -0.68695100 -0.26493400 9 | H -0.32500012 1.02293415 -0.30034094 10 | H -0.18892141 -0.68463906 -0.85893815 11 | H -0.64257065 -0.32709111 0.84987482 -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- 1 | .. resp documentation master file, created by 2 | sphinx-quickstart on Wed May 30 19:16:00 2018. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to resp's documentation! 7 | ================================ 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | :caption: Contents: 12 | 13 | api 14 | 15 | 16 | Indices and tables 17 | ================== 18 | 19 | * :ref:`genindex` 20 | * :ref:`modindex` 21 | * :ref:`search` 22 | -------------------------------------------------------------------------------- /tests/phosphate.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, absolute_import, print_function 2 | 3 | import pytest 4 | import sys 5 | 6 | import numpy as np 7 | import psi4 8 | 9 | #sys.path.insert(1, '/home/kkirsc3m/git/resp_w_psi4/src') 10 | sys.path.insert(1, '/home/karl/git/resp_w_psi4/src') 11 | 12 | import driver as resp 13 | 14 | charges = resp.resp('phosphate.ini') 15 | 16 | print('Unrestrained Electrostatic Potential Charges') 17 | print(f'{charges[0]}\n') 18 | 19 | print('Restrained Electrostatic Potential (RESP) Charges') 20 | print(f'{charges[1]}\n') 21 | 22 | -------------------------------------------------------------------------------- /examples/2-methylpropanol/2_methylpropanal_1.xyz: -------------------------------------------------------------------------------- 1 | 13 2 | conformer_1 3 | C 1.18807296 0.00000000 -0.00000000 4 | H 1.73769890 -0.94942350 0.00040129 5 | C 2.05994583 1.23628674 -0.00376657 6 | H 2.64872469 1.18261093 0.91290488 7 | C 1.23262322 2.51828219 0.00000000 8 | H 0.63081383 2.59153195 -0.89895304 9 | H 0.55974355 2.54752416 0.84822128 10 | H 1.88167197 3.38672974 0.04717944 11 | O 0.00000000 0.00000000 0.00000000 12 | C 3.03702733 1.16659508 -1.18689891 13 | H 2.50542875 1.21333731 -2.13258966 14 | H 3.61923181 0.24993306 -1.17312032 15 | H 3.73109559 1.99885781 -1.15280577 -------------------------------------------------------------------------------- /examples/2-methylpropanol/2_methylpropanal_2.xyz: -------------------------------------------------------------------------------- 1 | 13 2 | conformer_2 3 | C 1.18810366 0.00000000 0.00000000 4 | H 1.74084512 -0.67040815 -0.67139455 5 | C 2.05185834 0.87597578 0.87726389 6 | H 1.37794052 1.47614882 1.47832541 7 | C 2.91484888 1.79218260 0.00000000 8 | H 3.57048696 1.21501802 -0.64662795 9 | H 2.30183738 2.43175261 -0.62661254 10 | H 3.53886750 2.42858624 0.61823622 11 | O 0.00000000 0.00000000 0.00000000 12 | C 2.91485829 -0.00263271 1.79217231 13 | H 3.57049853 -0.64840414 1.21405200 14 | H 2.30185362 -0.63019217 2.43081985 15 | H 3.53887521 0.61466838 2.42948470 -------------------------------------------------------------------------------- /examples/2-methylpropanol/2_methylpropanal_3.xyz: -------------------------------------------------------------------------------- 1 | 13 2 | conformer_3 3 | C 1.18807296 0.00000000 0.00000000 4 | H 1.73769890 -0.66581347 -0.67682906 5 | C 2.05994583 0.86929903 0.87905533 6 | H 2.64872469 0.17792112 1.48334353 7 | C 1.23262322 1.76526649 1.79598981 8 | H 0.63081383 2.45772894 1.21808163 9 | H 0.55974355 1.18082965 2.41143112 10 | H 1.88167197 2.34038376 2.44842155 11 | O 0.00000000 0.00000000 0.00000000 12 | C 3.03702733 1.66423349 0.00000000 13 | H 2.50542875 2.37144710 -0.62957505 14 | H 3.61923181 1.01184474 -0.64408698 15 | H 3.73109559 2.22331879 0.61745219 -------------------------------------------------------------------------------- /examples/2-methylpropanol/2_methylpropanal_4.xyz: -------------------------------------------------------------------------------- 1 | 13 2 | conformer_4 3 | C 0.00000000 0.00000000 0.00000000 4 | H -0.93955321 0.47477680 -0.30874032 5 | C 1.25151499 0.71485368 -0.45964751 6 | H 1.20826188 0.71020891 -1.54957218 7 | C 2.51867622 0.00000000 0.00000000 8 | H 2.58126974 -0.01622165 1.08234724 9 | H 2.53601175 -1.02661274 -0.34477131 10 | H 3.39846826 0.50570949 -0.38459746 11 | O -0.02101459 -0.99630517 0.64687847 12 | C 1.19911681 2.17954679 -0.00000000 13 | H 1.23644884 2.24804801 1.08306361 14 | H 0.29289621 2.67387281 -0.33738283 15 | H 2.04352600 2.73067227 -0.39848234 -------------------------------------------------------------------------------- /examples/2-methylpropanol/2_methylpropanal_5.xyz: -------------------------------------------------------------------------------- 1 | 13 2 | conformer_5 3 | C 1.18810366 0.00000000 -0.00000000 4 | H 1.74084512 -0.67040899 0.67139371 5 | C 2.05185834 0.87597613 -0.87726354 6 | H 1.37794052 1.47615534 -1.47831889 7 | C 2.91484888 -0.00263273 -1.79218067 8 | H 3.57048696 -0.64841212 -1.21406681 9 | H 2.30183738 -0.63018412 -2.43082949 10 | H 3.53886750 0.61466794 -2.42949181 11 | O 0.00000000 0.00000000 0.00000000 12 | C 2.91485829 1.79217424 0.00000000 13 | H 3.57049853 1.21500320 0.64661999 14 | H 2.30185362 2.43174299 0.62662061 15 | H 3.53887521 2.42857912 -0.61823665 -------------------------------------------------------------------------------- /examples/2-methylpropanol/2_methylpropanal_6.xyz: -------------------------------------------------------------------------------- 1 | 13 2 | conformer_6 3 | C 0.00000000 0.00000000 0.00000000 4 | H -0.09926923 -0.05878765 1.09198465 5 | C 1.23012323 0.72853758 -0.48890436 6 | H 1.19473724 0.70758019 -1.57239708 7 | C 2.48868792 0.00000000 -0.00000000 8 | H 2.52795986 -0.03308339 1.08557411 9 | H 2.52393202 -1.01970359 -0.36937598 10 | H 3.37994981 0.51216000 -0.34636574 11 | O -0.82435098 -0.48822460 -0.70261832 12 | C 1.19619137 2.18236026 0.00000000 13 | H 1.18605886 2.23269987 1.08557414 14 | H 0.31894035 2.70338793 -0.36937391 15 | H 2.07369574 2.71774821 -0.34636781 -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | SPHINXPROJ = resp 8 | SOURCEDIR = source 9 | BUILDDIR = build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # Distribution / packaging 7 | .Python 8 | build/ 9 | develop-eggs/ 10 | dist/ 11 | downloads/ 12 | eggs/ 13 | .eggs/ 14 | lib/ 15 | lib64/ 16 | parts/ 17 | sdist/ 18 | var/ 19 | wheels/ 20 | *.egg-info/ 21 | .installed.cfg 22 | *.egg 23 | MANIFEST 24 | 25 | # Installer logs 26 | pip-log.txt 27 | pip-delete-this-directory.txt 28 | 29 | # Unit test 30 | .cache 31 | 32 | # Sphinx documentation 33 | docs/_build/ 34 | docs/source/api/ 35 | 36 | # specifics 37 | # Jupyter Notebook 38 | .ipynb_checkpoints 39 | 40 | # Environments 41 | .env 42 | .venv 43 | env/ 44 | venv/ 45 | ENV/ 46 | env.bak/ 47 | venv.bak/ -------------------------------------------------------------------------------- /tests/resp_unconstrained_a.ini: -------------------------------------------------------------------------------- 1 | [molecules] 2 | input_files: acetic_acid.xyz 3 | 4 | [vdw.surface.options] 5 | vdw_scale_factors : 1.4, 1.6, 1.8, 2.0 6 | vdw_point_density : 1.0 7 | esp : None 8 | grid : None 9 | vdw_radii : None 10 | 11 | [hyperbolic.restraint.options] 12 | weight : 1.0 13 | restraint : True 14 | resp_a : 0.0005 15 | resp_b : 0.1 16 | ihfree : True 17 | toler : 1e-5 18 | max_it : 25 19 | 20 | [constraints] 21 | constraint_charge : None 22 | equivalent_groups : None 23 | 24 | [qm.options] 25 | method_esp : scf 26 | basis_esp : assign H 6-31g*, 27 | assign C 6-31g*, 28 | assign O 6-31g* 29 | 30 | formal_charge : 0 31 | multiplicity : 1 -------------------------------------------------------------------------------- /tests/phosphate.ini: -------------------------------------------------------------------------------- 1 | [molecules] 2 | input_files: phosphate.xyz 3 | 4 | [vdw.surface.options] 5 | vdw_scale_factors : 1.4, 1.6, 1.8, 2.0 6 | vdw_point_density : 1.0 7 | esp : None 8 | grid : None 9 | vdw_radii : None 10 | 11 | [hyperbolic.restraint.options] 12 | weight : 1.0 13 | restraint : True 14 | resp_a : 0.001 15 | resp_b : 0.1 16 | ihfree : True 17 | toler : 1e-5 18 | max_it : 25 19 | 20 | [constraints] 21 | # fixed charges: atom_number (in xyz file) = partial_charge, 22 | constraint_charge : None 23 | 24 | #groups of equivalent atoms -> group_n = atom_number list, 25 | equivalent_groups : None 26 | 27 | [qm.options] 28 | method_esp : scf 29 | basis_esp : assign 6-31g* 30 | formal_charge : 0 31 | multiplicity : 1 -------------------------------------------------------------------------------- /tests/resp_two_confs_a.ini: -------------------------------------------------------------------------------- 1 | [molecules] 2 | input_files: ethanol_1.xyz, ethanol_2.xyz 3 | 4 | [vdw.surface.options] 5 | vdw_scale_factors : 1.4, 1.6, 1.8, 2.0 6 | vdw_point_density : 1.0 7 | esp : None 8 | grid : None 9 | vdw_radii : None 10 | 11 | [hyperbolic.restraint.options] 12 | weight : 1.0, 1.0 13 | restraint : True 14 | resp_a : 0.0005 15 | resp_b : 0.1 16 | ihfree : False 17 | toler : 1e-5 18 | max_it : 25 19 | 20 | [constraints] 21 | # fixed charges: atom_number (in xyz file) = partial_charge, 22 | constraint_charge : None 23 | 24 | #groups of equivalent atoms -> group_n = atom_number list, 25 | equivalent_groups : None 26 | 27 | [qm.options] 28 | method_esp : scf 29 | basis_esp : assign 6-31g* 30 | formal_charge : 0 31 | multiplicity : 1 -------------------------------------------------------------------------------- /tests/resp_unconstrained_b.ini.old: -------------------------------------------------------------------------------- 1 | # read in saved esp and grid files 2 | # If you know how these files were created, you should fill in: 3 | # - vdw_scale_factors 4 | # - vdw_radii, 5 | # - method_esp 6 | # - basis_esp 7 | 8 | [molecules] 9 | input_files: acetic_acid.xyz 10 | 11 | [vdw.surface.options] 12 | vdw_scale_factors : 1.4, 1.6, 1.8, 2.0 13 | vdw_point_density : 1.0 14 | esp : acetic_acid_esp.dat 15 | grid : acetic_acid_grid.dat 16 | vdw_radii : H=1.20, 17 | C=1.50, 18 | O=1.40 19 | 20 | [hyperbolic.restraint.options] 21 | weight : 1.0 22 | restraint : True 23 | resp_a : 0.0005 24 | resp_b : 0.1 25 | ihfree : True 26 | toler : 1e-5 27 | max_it : 25 28 | 29 | [constraints] 30 | constraint_charge : None 31 | equivalent_groups : None 32 | 33 | [qm.options] 34 | method_esp : scf 35 | basis_esp : 6-31g* -------------------------------------------------------------------------------- /tests/resp_unconstrained_b.ini: -------------------------------------------------------------------------------- 1 | # read in saved esp and grid files 2 | # If you know how these files were created, you should fill in: 3 | # - vdw_scale_factors 4 | # - vdw_radii, 5 | # - method_esp 6 | # - basis_esp 7 | 8 | [molecules] 9 | input_files: acetic_acid.xyz 10 | 11 | [vdw.surface.options] 12 | vdw_scale_factors : 1.4, 1.6, 1.8, 2.0 13 | vdw_point_density : 1.0 14 | esp : acetic_acid_esp.dat 15 | grid : acetic_acid_grid.dat 16 | vdw_radii : H=1.20, 17 | C=1.50, 18 | O=1.40 19 | 20 | [hyperbolic.restraint.options] 21 | weight : 1.0 22 | restraint : True 23 | resp_a : 0.0005 24 | resp_b : 0.1 25 | ihfree : True 26 | toler : 1e-5 27 | max_it : 25 28 | 29 | [constraints] 30 | constraint_charge : None 31 | equivalent_groups : None 32 | 33 | [qm.options] 34 | method_esp : None 35 | basis_esp : None 36 | formal_charge : 0 37 | multiplicity : 1 -------------------------------------------------------------------------------- /tests/resp_two_confs_b.ini: -------------------------------------------------------------------------------- 1 | [molecules] 2 | input_files: ethanol_1.xyz, ethanol_2.xyz 3 | 4 | [vdw.surface.options] 5 | vdw_scale_factors : 1.4, 1.6, 1.8, 2.0 6 | vdw_point_density : 1.0 7 | esp : ethanol_1_esp.dat, ethanol_2_esp.dat 8 | grid : ethanol_1_grid.dat, ethanol_2_grid.dat 9 | vdw_radii : None 10 | 11 | [hyperbolic.restraint.options] 12 | weight : 1.0, 1.0 13 | restraint : True 14 | resp_a : 0.001 15 | resp_b : 0.1 16 | ihfree : False 17 | toler : 1e-5 18 | max_it : 25 19 | 20 | [constraints] 21 | # fixed charges: atom_number (in xyz file) = partial_charge, 22 | constraint_charge : 3 = -0.63087078, 23 | 4 = 0.377965 24 | 25 | #groups of equivalent atoms -> group_n = atom_number list, 26 | equivalent_groups : group_1 = 7 8 9, 27 | group_2 = 5 6 28 | 29 | [qm.options] 30 | method_esp : None 31 | basis_esp : None 32 | formal_charge : 0 33 | multiplicity : 1 -------------------------------------------------------------------------------- /tests/resp_constrained_a.ini: -------------------------------------------------------------------------------- 1 | [molecules] 2 | input_files: acetic_acid.xyz 3 | 4 | [vdw.surface.options] 5 | vdw_scale_factors : 1.4, 1.6, 1.8, 2.0 6 | vdw_point_density : 1.0 7 | esp : None 8 | grid : None 9 | vdw_radii : None 10 | 11 | [hyperbolic.restraint.options] 12 | weight : 1.0 13 | restraint : True 14 | resp_a : 0.001 15 | resp_b : 0.1 16 | ihfree : True 17 | toler : 1e-5 18 | max_it : 25 19 | 20 | [constraints] 21 | # fixed charges: atom_number (in xyz file) = partial_charge, 22 | constraint_charge : 5 = 0.8043282118269929, 23 | 6 = -0.6614656885808026, 24 | 7 = 0.45334412484467956, 25 | 8 = -0.6002604772446537 26 | 27 | #groups of equivalent atoms -> group_n = atom_number list, 28 | equivalent_groups : group_1 = 2 3 4 29 | 30 | [qm.options] 31 | method_esp : scf 32 | basis_esp : assign 6-31g* 33 | formal_charge : 0 34 | multiplicity : 1 -------------------------------------------------------------------------------- /examples/2-methylpropanol/2_methylpropanal_stage_1.ini: -------------------------------------------------------------------------------- 1 | [molecules] 2 | input_files: 2_methylpropanal_1.xyz, 3 | 2_methylpropanal_2.xyz, 4 | 2_methylpropanal_3.xyz, 5 | 2_methylpropanal_4.xyz, 6 | 2_methylpropanal_5.xyz, 7 | 2_methylpropanal_6.xyz 8 | 9 | [vdw.surface.options] 10 | vdw_scale_factors : 1.4, 1.6, 1.8, 2.0 11 | vdw_point_density : 1.0 12 | esp : None 13 | grid : None 14 | vdw_radii : None 15 | 16 | [hyperbolic.restraint.options] 17 | weight : 1.0, 1.0, 1.0, 1.0, 1.0, 1.0 18 | restraint : True 19 | resp_a : 0.0005 20 | resp_b : 0.1 21 | toler : 1e-5 22 | max_it : 25 23 | ihfree : False 24 | 25 | [constraints] 26 | # fixed charges: atom_number (in xyz file) = partial_charge, 27 | constraint_charge : None 28 | 29 | #groups of equivalent atoms -> group_n = atom_number list, 30 | equivalent_groups : None 31 | 32 | [qm.options] 33 | method_esp : scf 34 | basis_esp : 6-31g* 35 | -------------------------------------------------------------------------------- /src/extras.py: -------------------------------------------------------------------------------- 1 | import os 2 | 3 | 4 | def test(extent='full', extras=None): 5 | """Runs a test suite through pytest. 6 | 7 | Parameters 8 | ---------- 9 | extent : {'smoke', 'quick', 'full', 'long'} 10 | All choices are defined, but choices may be redundant in some projects. 11 | _smoke_ will be minimal "is-working?" test(s). 12 | _quick_ will be as much coverage as can be got quickly, approx. 1/3 tests. 13 | _full_ will be the whole test suite, less some exceedingly long outliers. 14 | _long_ will be the whole test suite. 15 | extras : list 16 | Additional arguments to pass to `pytest`. 17 | 18 | Returns 19 | ------- 20 | int 21 | Return code from `pytest.main()`. 0 for pass, 1 for fail. 22 | 23 | """ 24 | try: 25 | import pytest 26 | except ImportError: 27 | raise RuntimeError('Testing module `pytest` is not installed. Run `conda install pytest`.') 28 | abs_test_dir = os.path.sep.join([os.path.abspath(os.path.dirname(__file__)), "tests"]) 29 | 30 | command = ['-rws', '-v'] 31 | if extent.lower() in ['smoke', 'quick', 'full', 'long']: 32 | pass 33 | if extras is not None: 34 | command.extend(extras) 35 | command.extend(['--capture=sys', abs_test_dir]) 36 | 37 | retcode = pytest.main(command) 38 | return retcode 39 | -------------------------------------------------------------------------------- /tests/resp_unconstrained_b.out: -------------------------------------------------------------------------------- 1 | Electrostatic potential parameters 2 | van der Waals radii (Angstrom): 3 | C = 1.500 4 | H = 1.200 5 | O = 1.400 6 | VDW scale factors: 1.4 1.6 1.8 2.0 7 | VDW point density: 1.0 8 | ESP method: None 9 | ESP basis set: None 10 | 11 | Grid information 12 | Quantum ESP File(s): 13 | acetic_acid_esp.dat 14 | 15 | Grid Points File(s) (# of points): 16 | acetic_acid_grid.dat (534) 17 | 18 | Constraints 19 | Charge constraints: None 20 | 21 | Equivalent charges on atoms: None 22 | 23 | Restraint 24 | ihfree: True 25 | resp_a: 0.0005 26 | resp_b: 0.1000 27 | 28 | Fit 29 | Electrostatic Potential Charges: 30 | Center Symbol esp resp 31 | 1 C -0.47448293 -0.29504701 32 | 2 H 0.15053456 0.10713424 33 | 3 H 0.15053456 0.10713424 34 | 4 H 0.13074761 0.08483234 35 | 5 C 0.88861006 0.80432822 36 | 6 O -0.67611997 -0.66146571 37 | 7 H 0.45167236 0.45334414 38 | 8 O -0.62149626 -0.60026044 39 | 40 | Total Charge: -0.00000000 -0.00000000 41 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | BSD 3-Clause License 2 | 3 | Copyright (c) 2017-2018, A. Alenaizan 4 | All rights reserved. 5 | 6 | Redistribution and use in source and binary forms, with or without 7 | modification, are permitted provided that the following conditions are met: 8 | 9 | * Redistributions of source code must retain the above copyright notice, this 10 | list of conditions and the following disclaimer. 11 | 12 | * Redistributions in binary form must reproduce the above copyright notice, 13 | this list of conditions and the following disclaimer in the documentation 14 | and/or other materials provided with the distribution. 15 | 16 | * Neither the name of the copyright holder nor the names of its 17 | contributors may be used to endorse or promote products derived from 18 | this software without specific prior written permission. 19 | 20 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 21 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 22 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 23 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 24 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 25 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 26 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 27 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 28 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 29 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 30 | -------------------------------------------------------------------------------- /tests/resp_unconstrained_a.out: -------------------------------------------------------------------------------- 1 | Electrostatic potential parameters 2 | van der Waals radii (Angstrom): 3 | C = 1.500 4 | H = 1.200 5 | O = 1.400 6 | VDW scale factors: 1.4 1.6 1.8 2.0 7 | VDW point density: 1.0 8 | ESP method: scf 9 | ESP basis set: 10 | assign H 6-31g* 11 | assign C 6-31g* 12 | assign O 6-31g* 13 | 14 | Grid information 15 | Quantum ESP File(s): 16 | acetic_acid_grid_esp.dat 17 | 18 | Grid Points File(s) (# of points): 19 | acetic_acid_grid.dat (534) 20 | 21 | Constraints 22 | Charge constraints: None 23 | 24 | Equivalent charges on atoms: None 25 | 26 | Restraint 27 | ihfree: True 28 | resp_a: 0.0005 29 | resp_b: 0.1000 30 | 31 | Fit 32 | Electrostatic Potential Charges: 33 | Center Symbol esp resp 34 | 1 C -0.47448293 -0.29504701 35 | 2 H 0.15053456 0.10713424 36 | 3 H 0.15053456 0.10713424 37 | 4 H 0.13074761 0.08483234 38 | 5 C 0.88861006 0.80432822 39 | 6 O -0.67611997 -0.66146571 40 | 7 H 0.45167236 0.45334414 41 | 8 O -0.62149626 -0.60026044 42 | 43 | Total Charge: -0.00000000 0.00000000 44 | -------------------------------------------------------------------------------- /tests/resp_two_confs_a.out: -------------------------------------------------------------------------------- 1 | Electrostatic potential parameters 2 | van der Waals radii (Angstrom): 3 | C = 1.500 4 | O = 1.400 5 | H = 1.200 6 | VDW scale factors: 1.4 1.6 1.8 2.0 7 | VDW point density: 1.0 8 | ESP method: scf 9 | ESP basis set: 10 | assign 6-31g* 11 | 12 | Grid information 13 | Quantum ESP File(s): 14 | ethanol_1_grid_esp.dat 15 | ethanol_2_grid_esp.dat 16 | 17 | Grid Points File(s) (# of points): 18 | ethanol_1_grid.dat (520) 19 | ethanol_2_grid.dat (517) 20 | 21 | Constraints 22 | Charge constraints: None 23 | 24 | Equivalent charges on atoms: None 25 | 26 | Restraint 27 | ihfree: False 28 | resp_a: 0.0005 29 | resp_b: 0.1000 30 | 31 | Fit 32 | Electrostatic Potential Charges: 33 | Center Symbol esp resp 34 | 1 C -0.34439874 -0.14913242 35 | 2 C 0.44968713 0.27429926 36 | 3 O -0.66234715 -0.63087080 37 | 4 H 0.37783974 0.37796664 38 | 5 H -0.05136520 -0.01101877 39 | 6 H -0.05027645 -0.00944599 40 | 7 H 0.10301264 0.05857539 41 | 8 H 0.08913477 0.04479657 42 | 9 H 0.08871326 0.04483012 43 | 44 | Total Charge: 0.00000000 0.00000000 45 | -------------------------------------------------------------------------------- /examples/2-methylpropanol/2_methylpropanal_stage_2.ini: -------------------------------------------------------------------------------- 1 | [molecules] 2 | input_files: 2_methylpropanal_1.xyz, 3 | 2_methylpropanal_2.xyz, 4 | 2_methylpropanal_3.xyz, 5 | 2_methylpropanal_4.xyz, 6 | 2_methylpropanal_5.xyz, 7 | 2_methylpropanal_6.xyz 8 | 9 | [vdw.surface.options] 10 | vdw_radii : None 11 | vdw_scale_factors : None 12 | vdw_point_density : None 13 | esp : 2_methylpropanal_1_esp.dat, 14 | 2_methylpropanal_2_esp.dat, 15 | 2_methylpropanal_3_esp.dat, 16 | 2_methylpropanal_4_esp.dat, 17 | 2_methylpropanal_5_esp.dat, 18 | 2_methylpropanal_6_esp.dat 19 | 20 | grid : 2_methylpropanal_1_grid.dat, 21 | 2_methylpropanal_2_grid.dat, 22 | 2_methylpropanal_3_grid.dat, 23 | 2_methylpropanal_4_grid.dat, 24 | 2_methylpropanal_5_grid.dat, 25 | 2_methylpropanal_6_grid.dat 26 | 27 | [hyperbolic.restraint.options] 28 | weight : 1.0, 1.0, 1.0, 1.0, 1.0, 1.0 29 | restraint : True 30 | resp_a : 0.001 31 | resp_b : 0.1 32 | ihfree : False 33 | max_it : 25 34 | toler : 1e-5 35 | 36 | [constraints] 37 | # fixed charges: atom_number (in xyz file) = partial_charge, 38 | constraint_charge : 1 = 0.41874585, 39 | 2 = -0.01842201, 40 | 3 = 0.23432552, 41 | 9 = -0.48568103 42 | 43 | #groups of equivalent atoms -> group_n = atom_number list, 44 | equivalent_groups : group_1 = 6 7 8 11 12 13, 45 | group_3 = 5 10 46 | 47 | [qm.options] 48 | method_esp : None 49 | basis_esp : None 50 | -------------------------------------------------------------------------------- /tests/resp_constrained_a.out: -------------------------------------------------------------------------------- 1 | Electrostatic potential parameters 2 | van der Waals radii (Angstrom): 3 | C = 1.500 4 | H = 1.200 5 | O = 1.400 6 | VDW scale factors: 1.4 1.6 1.8 2.0 7 | VDW point density: 1.0 8 | ESP method: scf 9 | ESP basis set: 10 | assign 6-31g* 11 | 12 | Grid information 13 | Quantum ESP File(s): 14 | acetic_acid_grid_esp.dat 15 | 16 | Grid Points File(s) (# of points): 17 | acetic_acid_grid.dat (534) 18 | 19 | Constraints 20 | Charge constraints: 21 | Atom 5 = 0.8043282118269929 22 | Atom 6 = -0.6614656885808026 23 | Atom 7 = 0.45334412484467956 24 | Atom 8 = -0.6002604772446537 25 | 26 | Equivalent charges on atoms (group = atom numbers): 27 | group_1 = 2 3 4 28 | 29 | Restraint 30 | ihfree: True 31 | resp_a: 0.0010 32 | resp_b: 0.1000 33 | 34 | Fit 35 | Electrostatic Potential Charges: 36 | Center Symbol esp resp 37 | 1 C -0.30721261 -0.29096151 38 | 2 H 0.10375548 0.09833845 39 | 3 H 0.10375548 0.09833845 40 | 4 H 0.10375548 0.09833845 41 | 5 C 0.80432821 0.80432821 42 | 6 O -0.66146569 -0.66146569 43 | 7 H 0.45334412 0.45334412 44 | 8 O -0.60026048 -0.60026048 45 | 46 | Total Charge: -0.00000000 -0.00000000 47 | -------------------------------------------------------------------------------- /tests/resp_two_confs_b.out: -------------------------------------------------------------------------------- 1 | Electrostatic potential parameters 2 | van der Waals radii (Angstrom): 3 | C = 1.500 4 | O = 1.400 5 | H = 1.200 6 | VDW scale factors: 1.4 1.6 1.8 2.0 7 | VDW point density: 1.0 8 | ESP method: None 9 | ESP basis set: None 10 | 11 | Grid information 12 | Quantum ESP File(s): 13 | ethanol_1_esp.dat 14 | ethanol_2_esp.dat 15 | 16 | Grid Points File(s) (# of points): 17 | ethanol_1_grid.dat (520) 18 | ethanol_2_grid.dat (517) 19 | 20 | Constraints 21 | Charge constraints: 22 | Atom 3 = -0.63087078 23 | Atom 4 = 0.377965 24 | 25 | Equivalent charges on atoms (group = atom numbers): 26 | group_1 = 7 8 9 27 | group_2 = 5 6 28 | 29 | Restraint 30 | ihfree: False 31 | resp_a: 0.0010 32 | resp_b: 0.1000 33 | 34 | Fit 35 | Electrostatic Potential Charges: 36 | Center Symbol esp resp 37 | 1 C -0.26320349 -0.07985543 38 | 2 C 0.30502817 0.25393230 39 | 3 O -0.63087078 -0.63087078 40 | 4 H 0.37796500 0.37796500 41 | 5 H -0.01339645 -0.00771573 42 | 6 H -0.01339645 -0.00771573 43 | 7 H 0.07929133 0.03142012 44 | 8 H 0.07929133 0.03142012 45 | 9 H 0.07929133 0.03142012 46 | 47 | Total Charge: 0.00000000 -0.00000000 48 | -------------------------------------------------------------------------------- /examples/2-methylpropanol/2_methylpropanal_stage_1.out: -------------------------------------------------------------------------------- 1 | Electrostatic potential parameters 2 | van der Waals radii (Angstrom): 3 | C = 1.500 4 | H = 1.200 5 | O = 1.400 6 | VDW scale factors: [1.4, 1.6, 1.8, 2.0] 7 | VDW point density: 1.0 8 | ESP method: scf 9 | ESP basis set: 6-31g* 10 | 11 | Grid information 12 | Quantum ESP File(s): 13 | 2_methylpropanal_1_grid_esp.dat 14 | 2_methylpropanal_2_grid_esp.dat 15 | 2_methylpropanal_3_grid_esp.dat 16 | 2_methylpropanal_4_grid_esp.dat 17 | 2_methylpropanal_5_grid_esp.dat 18 | 2_methylpropanal_6_grid_esp.dat 19 | 20 | Grid Points File(s) (# of points): 21 | 2_methylpropanal_1_grid.dat (656) 22 | 2_methylpropanal_2_grid.dat (684) 23 | 2_methylpropanal_3_grid.dat (673) 24 | 2_methylpropanal_4_grid.dat (655) 25 | 2_methylpropanal_5_grid.dat (684) 26 | 2_methylpropanal_6_grid.dat (673) 27 | 28 | Constraints 29 | Charge constraints: None 30 | 31 | Equivalent charges on atoms: None 32 | 33 | Restraint 34 | ihfree: False 35 | resp_a: 0.0005 36 | resp_b: 0.1000 37 | 38 | Fit 39 | Electrostatic Potential Charges: 40 | Center Symbol esp resp 41 | 1 C 0.41891069 0.41874585 42 | 2 H -0.02293850 -0.01842201 43 | 3 C 0.38662443 0.23432552 44 | 4 H -0.05230765 -0.03191152 45 | 5 C -0.43059623 -0.20593247 46 | 6 H 0.10297957 0.04745197 47 | 7 H 0.10037548 0.04943501 48 | 8 H 0.10635493 0.04942897 49 | 9 O -0.49270981 -0.48568103 50 | 10 C -0.40715765 -0.19390885 51 | 11 H 0.09836720 0.04619511 52 | 12 H 0.08711065 0.03902606 53 | 13 H 0.10498688 0.05124738 54 | 55 | Total Charge: -0.00000000 0.00000000 56 | -------------------------------------------------------------------------------- /examples/2-methylpropanol/2_methylpropanal_stage_2.out: -------------------------------------------------------------------------------- 1 | Electrostatic potential parameters 2 | van der Waals radii (Angstrom): 3 | C = 1.500 4 | H = 1.200 5 | O = 1.400 6 | VDW scale factors: None 7 | VDW point density: None 8 | 9 | Grid information 10 | Quantum ESP File(s): 11 | 2_methylpropanal_1_grid_esp.dat 12 | 2_methylpropanal_2_grid_esp.dat 13 | 2_methylpropanal_3_grid_esp.dat 14 | 2_methylpropanal_4_grid_esp.dat 15 | 2_methylpropanal_5_grid_esp.dat 16 | 2_methylpropanal_6_grid_esp.dat 17 | 18 | Grid Points File(s) (# of points): 19 | 2_methylpropanal_1_grid.dat (656) 20 | 2_methylpropanal_2_grid.dat (684) 21 | 2_methylpropanal_3_grid.dat (673) 22 | 2_methylpropanal_4_grid.dat (655) 23 | 2_methylpropanal_5_grid.dat (684) 24 | 2_methylpropanal_6_grid.dat (673) 25 | 26 | Constraints 27 | Charge constraints: 28 | Atom 1 = 0.41874585 29 | Atom 2 = -0.01842201 30 | Atom 3 = 0.23432552 31 | Atom 9 = -0.48568103 32 | 33 | Equivalent charges on atoms (group = atom numbers): 34 | group_1 = 6 7 8 11 12 13 35 | group_2 = 5 10 36 | 37 | Restraint 38 | ihfree: False 39 | resp_a: 0.0010 40 | resp_b: 0.1000 41 | 42 | Fit 43 | Electrostatic Potential Charges: 44 | Center Symbol esp resp 45 | 1 C 0.41874585 0.41874585 46 | 2 H -0.01842201 -0.01842201 47 | 3 C 0.23432552 0.23432552 48 | 4 H -0.01979723 -0.03851195 49 | 5 C -0.26767099 -0.17059482 50 | 6 H 0.06769515 0.03845554 51 | 7 H 0.06769515 0.03845554 52 | 8 H 0.06769515 0.03845554 53 | 9 O -0.48568103 -0.48568103 54 | 10 C -0.26767099 -0.17059482 55 | 11 H 0.06769515 0.03845554 56 | 12 H 0.06769515 0.03845554 57 | 13 H 0.06769515 0.03845554 58 | 59 | Total Charge: 0.00000000 0.00000000 60 | -------------------------------------------------------------------------------- /src/stage2_helper.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, absolute_import, print_function 2 | 3 | import numpy as np 4 | 5 | import psi4 6 | 7 | """ 8 | A helper script to facilitate the use of constraints for two-stage fitting. 9 | """ 10 | 11 | def _get_stage2_atoms(molecule): 12 | """Determines atoms for second stage fit. The atoms 13 | are identified as sp3 carbons that have one or more hydrogens. 14 | 15 | Parameters 16 | ---------- 17 | molecule : psi4.Molecule instance 18 | 19 | Returns 20 | ------- 21 | groups : dict 22 | a dictionary whose keys are the indecies+1 of carbon 23 | atoms and whose elements are the indecies+1 of the 24 | connected hydrogen atoms. 25 | 26 | """ 27 | 28 | symbols = [] 29 | for i in range(molecule.natom()): 30 | symbols.append(molecule.symbol(i)) 31 | 32 | groups = {} 33 | bond_profile = psi4.qcdb.parker._bond_profile(molecule) 34 | for i in range(molecule.natom()): 35 | # Find carbon atoms 36 | if symbols[i] != 'C': 37 | continue 38 | # Check that it has 4 bonds 39 | bonds_for_atom = [j for j in bond_profile if i in j[:2]] 40 | if len(bonds_for_atom) == 4: 41 | group = [] 42 | for atoms in bonds_for_atom: 43 | j = atoms[0] if atoms[0] != i else atoms[1] 44 | if symbols[j] == 'H': 45 | group.append(j + 1) 46 | if group: 47 | groups[i + 1] = group 48 | 49 | return groups 50 | 51 | 52 | def set_stage2_constraint(molecule, charges, options): 53 | """Sets default constraints for the second stage fit. 54 | 55 | The default constraints are the following: 56 | Atoms that are excluded from the second stage fit are constrained 57 | to their charges from the first stage fit. C-H groups determined 58 | by _get_stage2_atoms are refitted and the hydrogen atoms connected 59 | to the same carbon are constrained to have identical charges. 60 | 61 | Parameters 62 | ---------- 63 | molecule : psi4.core.Molecule 64 | 65 | charges : :py:class:`numpy.ndarray` 66 | array containing the charges from the first stage fit 67 | options : dict 68 | dictionary of the fitting options. To be modified in place. 69 | cutoff : float, optional 70 | cutoff distance in Angstroms, exclusive 71 | 72 | Return 73 | ------ 74 | None 75 | 76 | """ 77 | second_stage = _get_stage2_atoms(molecule) 78 | atoms = list(range(1, molecule.natom()+1)) 79 | constraint_group = [] 80 | for i in second_stage.keys(): 81 | atoms.remove(i) 82 | group = [] 83 | for j in second_stage[i]: 84 | atoms.remove(j) 85 | group.append(j) 86 | constraint_group.append(group) 87 | constraint_charge = [] 88 | for i in atoms: 89 | constraint_charge.append([charges[i-1], [i]]) 90 | options['constraint_charge'] = constraint_charge 91 | options['constraint_group'] = constraint_group 92 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 |

2 |
3 | 4 | 5 | 6 |
7 | 8 | 9 | 10 | 11 |
12 |

13 | 14 | Restrained Electrostatic Potential 15 | ================================== 16 | 17 | ## Installation 18 | This RESP code is a plug-in to the Psi4 quantum chemistry package. 19 | To install Psi4, go to the this website: https://admiring-tesla-08529a.netlify.com/installs/latest/ and 20 | choose your preferred option (conda package recommended). If the RESP program was not installed by 21 | default, execute `conda install resp -c psi4`. To test that the RESP plug-in works, 22 | execute `python -c "import resp, sys; sys.exit(resp.test('long'))"`. 23 | Two examples on how to use the plug-in are available in the directory `examples`. 24 | 25 | ## Code 26 | The following codes are available: 27 | - `resp/espfit.py`: The restrained electrostatic potential (RESP) fitting procedure. 28 | - `resp/driver.py`: Driver of the code. 29 | - `resp/tests/test_resp.py` contains: 30 | - `test_resp_1`: Example for two-stage charge fitting for one conformer. 31 | - `test_resp_2`: Example for two-stage charge fitting for two conformers. 32 | 33 | Helper programs: 34 | - `resp/vdw_surface.py` 35 | - `resp/stage2_helper.py` 36 | 37 | ## Examples 38 | There are several examples in `examples` on how to use the code for computing 39 | RESP charges and for enforcing charge constraints 40 | 41 | ## RESP Method Summary 42 | RESP charges result from fitting the classical electrostatic potential (ESP) 43 | generated by atom-centered point charges to the quantum ESP computed outside 44 | the van der Waals surface of the molecule. The fitted charges are restrained 45 | by a hyperbolic term, which requires an iterative fitting procedure to compute 46 | the charges. 47 | 48 | The charges (**q**) are computed by solving the following equation: 49 | 50 | **A** **q** = **B**. 51 | 52 | The left-hand side contains the information about the classical ESP while the 53 | right-hand side contains information about the quantum ESP. 54 | A hyperbolic restraint term that depends on the charges is added to the diagonal 55 | elements of matrix **A**. The charges and the diagonal elements of **A** are 56 | changed iteratively until the charges converge. 57 | 58 | ## References: 59 | - [[Bayly:93:10269-10280](https://pubs.acs.org/doi/abs/10.1021/j100142a004)] C. I. Bayly *et. al.* *J. Phys. Chem.* **97**, 10269 (1993) 60 | 61 | Please cite this article if you use this program: 62 | - [[Alenaizan:19](https://doi.org/10.1002/qua.26035)] A. Alenaizan, L. A. Burns, C. D. Sherrill, Python implementation of the restrained electrostatic potential charge model. *Int. J. Quantum Chem.*. (2019) 63 | -------------------------------------------------------------------------------- /tests/test_resp.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, absolute_import, print_function 2 | 3 | import pytest 4 | import sys 5 | 6 | import numpy as np 7 | import psi4 8 | 9 | sys.path.insert(1, '../src/') 10 | 11 | import driver as resp 12 | 13 | 14 | def test_resp_unconstrained_a(): 15 | ''' One-stage fitting of charges. 16 | 17 | - ESP is compute using Psi4 18 | - resp_a = 0.001 19 | 20 | Reference charges were generated by R.E.D.-III.5 and GAMESS. 21 | ''' 22 | 23 | reference_charges = np.array([-0.294974, 0.107114, 0.107114, 0.084795, 24 | 0.803999, -0.661279, 0.453270, -0.600039]) 25 | 26 | charges = resp.resp('resp_unconstrained_a.ini') 27 | 28 | print('Unrestrained Electrostatic Potential Charges') 29 | print(f'{charges[0]}\n') 30 | 31 | print('Restrained Electrostatic Potential (RESP) Charges') 32 | print(f'{charges[1]}\n') 33 | 34 | print('Reference RESP Charges (via RED-III 5)') 35 | print(f'{reference_charges}\n') 36 | 37 | print('Difference') 38 | print(f'{charges[1]-reference_charges}\n') 39 | 40 | assert np.allclose(charges[1], reference_charges, atol=5e-4) 41 | 42 | 43 | def test_resp_unconstrained_b(): 44 | ''' One-stage fitting of charges. 45 | 46 | - ESP is read in (i.e., output from previous test) 47 | - resp_a = 0.001 48 | 49 | Reference charges were generated by R.E.D.-III.5 and GAMESS. 50 | ''' 51 | 52 | reference_charges = np.array([-0.294974, 0.107114, 0.107114, 0.084795, 53 | 0.803999, -0.661279, 0.453270, -0.600039]) 54 | 55 | charges = resp.resp('resp_unconstrained_b.ini') 56 | 57 | print('Unrestrained Electrostatic Potential Charges') 58 | print(f'{charges[0]}\n') 59 | 60 | print('Restrained Electrostatic Potential (RESP) Charges') 61 | print(f'{charges[1]}\n') 62 | 63 | print('Reference RESP Charges (via RED-III 5)') 64 | print(f'{reference_charges}\n') 65 | 66 | print('Difference') 67 | print(f'{charges[1]-reference_charges}\n') 68 | 69 | assert np.allclose(charges[1], reference_charges, atol=5e-4) 70 | 71 | 72 | def test_resp_constrained_a(): 73 | ''' Two-stage fitting of charges. 74 | 75 | - ESP is compute using Psi4 76 | - resp_a = 0.001 77 | - last four atoms constrained to certain values 78 | - methyl hydrogens force to be equivalent 79 | ''' 80 | 81 | reference_charges = np.array([-0.290893, 0.098314, 0.098314, 0.098314, 82 | 0.803999, -0.661279, 0.453270, -0.600039]) 83 | 84 | charges = resp.resp('resp_constrained_a.ini') 85 | 86 | print('Unrestrained Electrostatic Potential Charges') 87 | print(f'{charges[0]}\n') 88 | 89 | print('Restrained Electrostatic Potential (RESP) Charges') 90 | print(f'{charges[1]}\n') 91 | 92 | print('Reference RESP Charges (via RED-III 5)') 93 | print(f'{reference_charges}\n') 94 | 95 | print('Difference') 96 | print(f'{charges[1]-reference_charges}\n') 97 | 98 | assert np.allclose(charges[1], reference_charges, atol=5e-4) 99 | # 100 | # 101 | def test_resp_two_conformers_a(): 102 | ''' One-stage fitting of charges using two conformations. 103 | 104 | - ESP is compute using Psi4 105 | - resp_a = 0.0005 106 | ''' 107 | 108 | reference_charges = np.array([-0.149134, 0.274292, -0.630868, 0.377965, -0.011016, 109 | -0.009444, 0.058576, 0.044797, 0.044831]) 110 | 111 | charges = resp.resp('resp_two_confs_a.ini') 112 | 113 | print('Unrestrained Electrostatic Potential Charges') 114 | print(f'{charges[0]}\n') 115 | 116 | print('Restrained Electrostatic Potential (RESP) Charges') 117 | print(f'{charges[1]}\n') 118 | 119 | print('Reference RESP Charges (via RED-III 5)') 120 | print(f'{reference_charges}\n') 121 | 122 | print('Difference') 123 | print(f'{charges[1]-reference_charges}\n') 124 | 125 | assert np.allclose(charges[1], reference_charges, atol=1e-5) 126 | 127 | 128 | def test_resp_two_conformers_b(): 129 | ''' Note: the comparison tolerance had to be slightly adjusted here 130 | to 1.5e-5 for the assert to be passed. 131 | ''' 132 | reference_charges = np.array([-0.079853, 0.253918, -0.630868, 0.377965, -0.007711, 133 | -0.007711, 0.031420, 0.031420, 0.031420]) 134 | 135 | charges = resp.resp('resp_two_confs_b.ini') 136 | 137 | print('Unrestrained Electrostatic Potential Charges') 138 | print(f'{charges[0]}\n') 139 | 140 | print('Restrained Electrostatic Potential (RESP) Charges') 141 | print(f'{charges[1]}\n') 142 | 143 | print('Reference RESP Charges (via RED-III 5)') 144 | print(f'{reference_charges}\n') 145 | 146 | print('Difference') 147 | print(f'{charges[1]-reference_charges}\n') 148 | 149 | assert np.allclose(charges[1], reference_charges, atol=1.5e-5) 150 | -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # 3 | # Configuration file for the Sphinx documentation builder. 4 | # 5 | # This file does only contain a selection of the most common options. For a 6 | # full list see the documentation: 7 | # http://www.sphinx-doc.org/en/master/config 8 | 9 | # -- Path setup -------------------------------------------------------------- 10 | 11 | # If extensions (or modules to document with autodoc) are in another directory, 12 | # add these directories to sys.path here. If the directory is relative to the 13 | # documentation root, use os.path.abspath to make it absolute, like shown here. 14 | # 15 | import os 16 | import sys 17 | sys.path.insert(0, os.path.abspath('../../')) 18 | 19 | 20 | # -- Project information ----------------------------------------------------- 21 | 22 | project = 'resp' 23 | copyright = '2018, Asem Alenaizan' 24 | author = 'Asem Alenaizan' 25 | 26 | # The short X.Y version 27 | version = '' 28 | # The full version, including alpha/beta/rc tags 29 | release = '0.8' 30 | 31 | 32 | # -- General configuration --------------------------------------------------- 33 | 34 | # If your documentation needs a minimal Sphinx version, state it here. 35 | # 36 | # needs_sphinx = '1.0' 37 | 38 | # Add any Sphinx extension module names here, as strings. They can be 39 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 40 | # ones. 41 | extensions = [ 42 | # from Sphinx 43 | 'sphinx.ext.autodoc', 44 | 'sphinx.ext.intersphinx', 45 | 'sphinx.ext.todo', 46 | 'sphinx.ext.coverage', 47 | 'sphinx.ext.mathjax', 48 | 'sphinx.ext.viewcode', 49 | 'sphinx.ext.extlinks', 50 | 'sphinx.ext.graphviz', 51 | 'sphinx.ext.autosummary', 52 | 'sphinx.ext.napoleon', 53 | # from Astropy 54 | 'sphinx_automodapi.automodapi', 55 | 'sphinx_automodapi.automodsumm', 56 | 'sphinx_automodapi.smart_resolver', 57 | ] 58 | 59 | autosummary_generate = True 60 | automodapi_toctreedirnm = 'api' 61 | 62 | 63 | # Add any paths that contain templates here, relative to this directory. 64 | templates_path = ['ytemplates'] 65 | 66 | # The suffix(es) of source filenames. 67 | # You can specify multiple suffix as a list of string: 68 | # 69 | # source_suffix = ['.rst', '.md'] 70 | source_suffix = '.rst' 71 | 72 | # The master toctree document. 73 | master_doc = 'index' 74 | 75 | # The language for content autogenerated by Sphinx. Refer to documentation 76 | # for a list of supported languages. 77 | # 78 | # This is also used if you do content translation via gettext catalogs. 79 | # Usually you set "language" from the command line for these cases. 80 | language = None 81 | 82 | # List of patterns, relative to source directory, that match files and 83 | # directories to ignore when looking for source files. 84 | # This pattern also affects html_static_path and html_extra_path . 85 | exclude_patterns = [] 86 | 87 | # The name of the Pygments (syntax highlighting) style to use. 88 | pygments_style = 'sphinx' 89 | 90 | 91 | # -- Options for HTML output ------------------------------------------------- 92 | 93 | # The theme to use for HTML and HTML Help pages. See the documentation for 94 | # a list of builtin themes. 95 | # 96 | html_theme = 'alabaster' 97 | 98 | # Theme options are theme-specific and customize the look and feel of a theme 99 | # further. For a list of options available for each theme, see the 100 | # documentation. 101 | # 102 | # html_theme_options = {} 103 | 104 | # Add any paths that contain custom static files (such as style sheets) here, 105 | # relative to this directory. They are copied after the builtin static files, 106 | # so a file named "default.css" will overwrite the builtin "default.css". 107 | html_static_path = ['_static'] 108 | 109 | # Custom sidebar templates, must be a dictionary that maps document names 110 | # to template names. 111 | # 112 | # The default sidebars (for documents that don't match any pattern) are 113 | # defined by theme itself. Builtin themes are using these templates by 114 | # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', 115 | # 'searchbox.html']``. 116 | # 117 | # html_sidebars = {} 118 | 119 | 120 | # -- Options for HTMLHelp output --------------------------------------------- 121 | 122 | # Output file base name for HTML help builder. 123 | htmlhelp_basename = 'respdoc' 124 | 125 | 126 | # -- Options for LaTeX output ------------------------------------------------ 127 | 128 | latex_elements = { 129 | # The paper size ('letterpaper' or 'a4paper'). 130 | # 131 | # 'papersize': 'letterpaper', 132 | 133 | # The font size ('10pt', '11pt' or '12pt'). 134 | # 135 | # 'pointsize': '10pt', 136 | 137 | # Additional stuff for the LaTeX preamble. 138 | # 139 | # 'preamble': '', 140 | 141 | # Latex figure (float) alignment 142 | # 143 | # 'figure_align': 'htbp', 144 | } 145 | 146 | # Grouping the document tree into LaTeX files. List of tuples 147 | # (source start file, target name, title, 148 | # author, documentclass [howto, manual, or own class]). 149 | latex_documents = [ 150 | (master_doc, 'resp.tex', 'resp Documentation', 151 | 'Asem Alenaizan', 'manual'), 152 | ] 153 | 154 | 155 | # -- Options for manual page output ------------------------------------------ 156 | 157 | # One entry per manual page. List of tuples 158 | # (source start file, name, description, authors, manual section). 159 | man_pages = [ 160 | (master_doc, 'resp', 'resp Documentation', 161 | [author], 1) 162 | ] 163 | 164 | 165 | # -- Options for Texinfo output ---------------------------------------------- 166 | 167 | # Grouping the document tree into Texinfo files. List of tuples 168 | # (source start file, target name, title, author, 169 | # dir menu entry, description, category) 170 | texinfo_documents = [ 171 | (master_doc, 'resp', 'resp Documentation', 172 | author, 'resp', 'One line description of project.', 173 | 'Miscellaneous'), 174 | ] 175 | 176 | 177 | # -- Extension configuration ------------------------------------------------- 178 | 179 | # -- Options for intersphinx extension --------------------------------------- 180 | 181 | # Example configuration for intersphinx: refer to the Python standard library. 182 | intersphinx_mapping = {'python': ('http://docs.python.org/3.6', None), 183 | 'numpy': ('http://docs.scipy.org/doc/numpy/', None), 184 | 'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None), 185 | 'matplotlib': ('http://matplotlib.sourceforge.net/', None), 186 | 'psi4.core': ('http://psicode.org/psi4manual/master/', None), 187 | } 188 | 189 | # -- Options for todo extension ---------------------------------------------- 190 | 191 | # If true, `todo` and `todoList` produce output, else they produce nothing. 192 | todo_include_todos = True 193 | -------------------------------------------------------------------------------- /src/vdw_surface.py: -------------------------------------------------------------------------------- 1 | """ 2 | A srcipt to generate van der Waals surface of molecules. 3 | """ 4 | 5 | from __future__ import division, absolute_import, print_function 6 | 7 | import numpy as np 8 | 9 | 10 | def vdw_radii(element: str) -> float: 11 | """ Assign the van der Waals radius to an element. 12 | The values were taken from GAMESS. 13 | Args 14 | element : one or two letter element identifier 15 | Returns 16 | van der Waals radius (Angstrom) 17 | """ 18 | 19 | if not isinstance(element, str): 20 | raise TypeError(f'The element was not given as a string (i.e., {element} variable).') 21 | else: 22 | radii = {'H': 1.20, 'HE': 1.20, 23 | 'LI': 1.37, 'BE': 1.45, 'B': 1.45, 'C': 1.50, 24 | 'N': 1.50, 'O': 1.40, 'F': 1.35, 'NE': 1.30, 25 | 'NA': 1.57, 'MG': 1.36, 'AL': 1.24, 'SI': 1.17, 26 | 'P': 1.80, 'S': 1.75, 'CL': 1.70} 27 | 28 | if element in radii.keys(): 29 | return radii[element] 30 | else: 31 | raise KeyError(f'{element} is not internally supported; use the "vdw_radii" option to add its vdw radius.') 32 | 33 | 34 | def surface(n_points: int) -> np.ndarray: 35 | """ Computes approximately n points on a unit sphere. 36 | 37 | Code was adapted from GAMESS. 38 | 39 | Args 40 | n_points : number of surface points 41 | 42 | Returns 43 | xyz coordinates of surface points 44 | 45 | Library dependencies 46 | numpy 47 | """ 48 | 49 | if not isinstance(n_points, int): 50 | raise TypeError(f'The number of points was not given as an integer (i.e., {n_points} variable).') 51 | else: 52 | surface_points = [] 53 | eps = 1e-10 54 | 55 | nequat = int(np.sqrt(np.pi * n_points)) 56 | nvert = int(nequat / 2) 57 | nu = 0 58 | 59 | for i in range(nvert + 1): 60 | fi = np.pi * i / nvert 61 | z = np.cos(fi) 62 | xy = np.sin(fi) 63 | nhor = int(nequat * xy + eps) 64 | 65 | if nhor < 1: 66 | nhor = 1 67 | 68 | for j in range(nhor): 69 | fj = 2 * np.pi * j / nhor 70 | x = np.cos(fj) * xy 71 | y = np.sin(fj) * xy 72 | 73 | if nu >= n_points: 74 | return np.array(surface_points) 75 | 76 | nu += 1 77 | surface_points.append([x, y, z]) 78 | 79 | return np.array(surface_points) 80 | 81 | 82 | def vdw_surface(coordinates: np.ndarray, element_list: list, scale_factor: float, 83 | density: float, radii: dict) -> np.ndarray: 84 | """ Computes a molecular surface at points extended from the atoms' van der 85 | Waals radii. 86 | 87 | This is done using the Connolly [1] approach. As stated by Besler et al. [2], 88 | "Such a method is the surface generation algorithm of Connolly. It 89 | computes a spherical surface of points around each atom at a specified 90 | multiple of the atoms' van der Waals radius and density. The molecular 91 | surface is then constructed by taking the union of all of the atom 92 | surfaces and eliminating those points that are within the specified 93 | multiple of the van derWaals radius of any of the atoms." 94 | 95 | Args 96 | coordinates : cartesian coordinates of the nuclei (Angstroms) 97 | element_list : element symbols (e.g., C, H) 98 | scale_factor : scaling factor - the points on the molecular surface are 99 | set at a distance of scale_factor * vdw_radius away from 100 | each of the atoms. Recommended scaling factors are 101 | 1.4, 1.6, 1.8, 2.0 [3] 102 | density : The (approximate) number of points to generate per Angstrom^2 103 | of surface area. 1.0 is recommended [2]. 104 | radii : VDW radii 105 | 106 | Returns 107 | surface_points (ndarray) : coordinates of the points on the extended surface 108 | 109 | Library dependencies 110 | numpy 111 | 112 | References: 113 | 1. Connolly, M. L. Analytical Molecular-surface Calculation Journal of Applied 114 | Crystallography, 1983, 16, 548-558 115 | 2. Besler, B. H.; Merz Jr., K. M. & Kollman, P. A. Atomic charges derived from 116 | semiempirical methods J. Comput. Chem., 1990, 11, 431-439 117 | 3. Singh, U. C. & Kollman, P. A. An approach to computing electrostatic charges 118 | or molecules J. Comput. Chem., John Wiley & Sons, Ltd, 1984, 5, 129-145 119 | 120 | Also related: 121 | 4. Bayly, C. I.; Cieplak, P.; Cornell, W. & Kollman, P. A. A well-behaved 122 | electrostatic potential based method using charge restraints for deriving 123 | atomic charges: the RESP model J. Phys. Chem., 1993, 97, 10269-10280 124 | """ 125 | 126 | if not isinstance(coordinates, np.ndarray): 127 | raise TypeError(f'The coordinate were not given as an ndarray (i.e., {coordinates} variable).') 128 | elif not isinstance(element_list, list): 129 | raise TypeError(f'The elements were not given as a list (i.e., {element_list} variable).') 130 | elif not isinstance(scale_factor, float): 131 | raise TypeError(f'The scale_factor was not given as a float (i.e., {scale_factor} variable).') 132 | elif not isinstance(density, float): 133 | raise TypeError(f'The density was not given as a float (i.e., {density} variable).') 134 | elif not isinstance(radii, dict): 135 | raise TypeError(f'The radii were not given as a dictionary (i.e., {radii} variable).') 136 | else: 137 | radii_scaled = {} 138 | surface_points = [] 139 | 140 | # scale radii 141 | for element in element_list: 142 | radii_scaled[element] = radii[element] * scale_factor 143 | 144 | # loop over atomic coordinates 145 | # for element, coordinate in zip(element_list, coordinates): # TODO, alternative approach - test later. 146 | for i in range(len(coordinates)): 147 | 148 | # calculate approximate number of ESP grid points 149 | n_points = int(density * 4.0 * np.pi * np.power(radii_scaled[element_list[i]], 2)) # why 4.0? 150 | 151 | # generate an array of n_points in a unit sphere around the atom 152 | dots = surface(n_points=n_points) 153 | 154 | # scale the unit sphere by the VDW radius and translate 155 | dots = coordinates[i] + radii_scaled[element_list[i]] * dots 156 | 157 | # determine which points should be included or removed due to overlaps 158 | for j in range(len(dots)): 159 | save = True 160 | for k in range(len(coordinates)): 161 | if i == k: 162 | continue 163 | 164 | # exclude points within the scaled VDW radius of other atoms 165 | d = np.linalg.norm(dots[j] - coordinates[k]) 166 | 167 | if d < radii_scaled[element_list[k]]: 168 | save = False 169 | break 170 | if save: 171 | surface_points.append(dots[j]) 172 | 173 | # could also return radii_scaled if desired 174 | return np.array(surface_points) 175 | -------------------------------------------------------------------------------- /tests/acetic_acid.log: -------------------------------------------------------------------------------- 1 | 2 | *** tstart() called on earth 3 | *** at Fri Oct 27 13:55:45 2023 4 | 5 | => Loading Basis Set <= 6 | 7 | Name: ANONYMOUS9A87E3BC 8 | Role: ORBITAL 9 | Keyword: BASIS 10 | atoms 1, 5 entry C line 111 file /media/storage-1/miniconda3/envs/psi4/share/psi4/basis/6-31gs.gbs 11 | atoms 2-4, 7 entry H line 44 file /media/storage-1/miniconda3/envs/psi4/share/psi4/basis/6-31gs.gbs 12 | atoms 6, 8 entry O line 145 file /media/storage-1/miniconda3/envs/psi4/share/psi4/basis/6-31gs.gbs 13 | 14 | 15 | --------------------------------------------------------- 16 | SCF 17 | by Justin Turney, Rob Parrish, Andy Simmonett 18 | and Daniel G. A. Smith 19 | RHF Reference 20 | 1 Threads, 500 MiB Core 21 | --------------------------------------------------------- 22 | 23 | ==> Geometry <== 24 | 25 | Molecular point group: cs 26 | Full point group: Cs 27 | 28 | Geometry (in Angstrom), charge = 0, multiplicity = 1: 29 | 30 | Center X Y Z Mass 31 | ------------ ----------------- ----------------- ----------------- ----------------- 32 | C 1.450513985071 -0.066289322590 0.000000000000 12.000000000000 33 | H 1.755216225071 -0.628659862590 -0.875001460000 1.007825032230 34 | H 1.755216225071 -0.628659862590 0.875001460000 1.007825032230 35 | H 1.921732535071 0.904858967410 0.000000000000 1.007825032230 36 | C -0.042331124929 0.098493777410 0.000000000000 12.000000000000 37 | O -0.670648074929 -1.076209152590 0.000000000000 15.994914619570 38 | H -1.608372494929 -0.910166012590 0.000000000000 1.007825032230 39 | O -0.626758544929 1.131605097410 0.000000000000 15.994914619570 40 | 41 | Running in cs symmetry. 42 | 43 | Rotational constants: A = 0.39043 B = 0.31910 C = 0.18142 [cm^-1] 44 | Rotational constants: A = 11704.88734 B = 9566.37076 C = 5438.92090 [MHz] 45 | Nuclear repulsion = 122.456331812614820 46 | 47 | Charge = 0 48 | Multiplicity = 1 49 | Electrons = 32 50 | Nalpha = 16 51 | Nbeta = 16 52 | 53 | ==> Algorithm <== 54 | 55 | SCF Algorithm Type is DF. 56 | DIIS enabled. 57 | MOM disabled. 58 | Fractional occupation disabled. 59 | Guess Type is SAD. 60 | Energy threshold = 1.00e-06 61 | Density threshold = 1.00e-06 62 | Integral threshold = 1.00e-12 63 | 64 | ==> Primary Basis <== 65 | 66 | Basis Set: ANONYMOUS9A87E3BC 67 | Blend: 6-31G* 68 | Number of shells: 32 69 | Number of basis functions: 68 70 | Number of Cartesian functions: 68 71 | Spherical Harmonics?: false 72 | Max angular momentum: 2 73 | 74 | => Loading Basis Set <= 75 | 76 | Name: (ANONYMOUS9A87E3BC AUX) 77 | Role: JKFIT 78 | Keyword: DF_BASIS_SCF 79 | atoms 1, 5 entry C line 121 file /media/storage-1/miniconda3/envs/psi4/share/psi4/basis/cc-pvdz-jkfit.gbs 80 | atoms 2-4, 7 entry H line 51 file /media/storage-1/miniconda3/envs/psi4/share/psi4/basis/cc-pvdz-jkfit.gbs 81 | atoms 6, 8 entry O line 221 file /media/storage-1/miniconda3/envs/psi4/share/psi4/basis/cc-pvdz-jkfit.gbs 82 | 83 | ==> Integral Setup <== 84 | 85 | DFHelper Memory: AOs need 0.017 GiB; user supplied 0.366 GiB. Using in-core AOs. 86 | 87 | ==> MemDFJK: Density-Fitted J/K Matrices <== 88 | 89 | J tasked: Yes 90 | K tasked: Yes 91 | wK tasked: No 92 | OpenMP threads: 1 93 | Memory [MiB]: 375 94 | Algorithm: Core 95 | Schwarz Cutoff: 1E-12 96 | Mask sparsity (%): 0.1298 97 | Fitting Condition: 1E-10 98 | 99 | => Auxiliary Basis Set <= 100 | 101 | Basis Set: (ANONYMOUS9A87E3BC AUX) 102 | Blend: CC-PVDZ-JKFIT 103 | Number of shells: 132 104 | Number of basis functions: 424 105 | Number of Cartesian functions: 424 106 | Spherical Harmonics?: false 107 | Max angular momentum: 3 108 | 109 | Minimum eigenvalue in the overlap matrix is 4.2608135153E-03. 110 | Reciprocal condition number of the overlap matrix is 6.4577348776E-04. 111 | Using symmetric orthogonalization. 112 | 113 | ==> Pre-Iterations <== 114 | 115 | SCF Guess: Superposition of Atomic Densities via on-the-fly atomic UHF (no occupation information). 116 | 117 | ------------------------- 118 | Irrep Nso Nmo 119 | ------------------------- 120 | A' 50 50 121 | A" 18 18 122 | ------------------------- 123 | Total 68 68 124 | ------------------------- 125 | 126 | ==> Iterations <== 127 | 128 | Total Energy Delta E RMS |[F,P]| 129 | 130 | @DF-RHF iter SAD: -227.05485235117851 -2.27055e+02 0.00000e+00 131 | @DF-RHF iter 1: -227.67394837556134 -6.19096e-01 1.03326e-02 DIIS 132 | @DF-RHF iter 2: -227.76968356227019 -9.57352e-02 6.38494e-03 DIIS 133 | @DF-RHF iter 3: -227.80826866722481 -3.85851e-02 9.45470e-04 DIIS 134 | @DF-RHF iter 4: -227.80992914060249 -1.66047e-03 4.20674e-04 DIIS 135 | @DF-RHF iter 5: -227.81024835672997 -3.19216e-04 1.03767e-04 DIIS 136 | @DF-RHF iter 6: -227.81028116218630 -3.28055e-05 5.01904e-05 DIIS 137 | @DF-RHF iter 7: -227.81028924913824 -8.08695e-06 1.67466e-05 DIIS 138 | @DF-RHF iter 8: -227.81029035029403 -1.10116e-06 4.58755e-06 DIIS 139 | @DF-RHF iter 9: -227.81029043548853 -8.51945e-08 8.70199e-07 DIIS 140 | Energy and wave function converged. 141 | 142 | 143 | ==> Post-Iterations <== 144 | 145 | Orbital Energies [Eh] 146 | --------------------- 147 | 148 | Doubly Occupied: 149 | 150 | 1Ap -20.615370 2Ap -20.553269 3Ap -11.386018 151 | 4Ap -11.240483 5Ap -1.477175 6Ap -1.368197 152 | 7Ap -1.027199 8Ap -0.831485 9Ap -0.702647 153 | 10Ap -0.683124 1App -0.653675 11Ap -0.581735 154 | 12Ap -0.572252 2App -0.562216 3App -0.480404 155 | 13Ap -0.449171 156 | 157 | Virtual: 158 | 159 | 4App 0.193128 14Ap 0.226895 15Ap 0.259331 160 | 16Ap 0.309105 5App 0.328774 17Ap 0.398399 161 | 18Ap 0.479557 19Ap 0.523182 6App 0.730786 162 | 20Ap 0.763438 21Ap 0.808767 22Ap 0.820802 163 | 7App 0.824643 23Ap 0.953120 24Ap 1.004773 164 | 25Ap 1.071232 26Ap 1.106893 8App 1.125663 165 | 27Ap 1.163208 28Ap 1.209854 9App 1.213181 166 | 29Ap 1.250408 30Ap 1.325811 10App 1.328902 167 | 31Ap 1.350886 32Ap 1.598115 11App 1.636077 168 | 12App 1.676098 33Ap 1.764096 34Ap 1.858989 169 | 13App 2.001155 35Ap 2.027555 14App 2.096641 170 | 36Ap 2.101068 37Ap 2.145710 38Ap 2.243935 171 | 15App 2.302197 39Ap 2.384862 16App 2.535440 172 | 40Ap 2.555539 41Ap 2.652676 17App 2.795933 173 | 42Ap 2.823082 18App 3.010754 43Ap 3.084202 174 | 44Ap 3.228901 45Ap 3.359022 46Ap 3.468113 175 | 47Ap 4.228754 48Ap 4.461892 49Ap 4.587300 176 | 50Ap 4.856778 177 | 178 | Final Occupation by Irrep: 179 | Ap App 180 | DOCC [ 13, 3 ] 181 | 182 | @DF-RHF Final Energy: -227.81029043548853 183 | 184 | => Energetics <= 185 | 186 | Nuclear Repulsion Energy = 122.4563318126148204 187 | One-Electron Energy = -554.1643895929145174 188 | Two-Electron Energy = 203.8977673448111432 189 | Total Energy = -227.8102904354885254 190 | 191 | Computation Completed 192 | 193 | 194 | Properties will be evaluated at 0.000000, 0.000000, 0.000000 [a0] 195 | 196 | Properties computed using the SCF density matrix 197 | 198 | Nuclear Dipole Moment: [e a0] 199 | X: 3.5785 Y: -1.1834 Z: 0.0000 200 | 201 | Electronic Dipole Moment: [e a0] 202 | X: -3.2706 Y: 0.5485 Z: 0.0000 203 | 204 | Dipole Moment: [e a0] 205 | X: 0.3079 Y: -0.6349 Z: 0.0000 Total: 0.7056 206 | 207 | Dipole Moment: [D] 208 | X: 0.7826 Y: -1.6138 Z: 0.0000 Total: 1.7936 209 | 210 | 211 | Electrostatic potential computed on the grid and written to grid_esp.dat 212 | 213 | *** tstop() called on earth at Fri Oct 27 13:55:47 2023 214 | Module time: 215 | user time = 1.97 seconds = 0.03 minutes 216 | system time = 0.02 seconds = 0.00 minutes 217 | total time = 2 seconds = 0.03 minutes 218 | Total time: 219 | user time = 1.97 seconds = 0.03 minutes 220 | system time = 0.02 seconds = 0.00 minutes 221 | total time = 2 seconds = 0.03 minutes 222 | -------------------------------------------------------------------------------- /tests/ethanol_2_esp.dat: -------------------------------------------------------------------------------- 1 | -0.0040322146 2 | 0.0063682439 3 | -0.0038178211 4 | -0.0037337303 5 | -0.0141300197 6 | 0.0114027026 7 | -0.0039446400 8 | -0.0107808165 9 | -0.0129527014 10 | -0.0352106962 11 | -0.0227184179 12 | -0.0456926223 13 | 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-------------------------------------------------------------------------------- /tests/ethanol_1-psi.log: -------------------------------------------------------------------------------- 1 | 2025-04-15:15:17:44,706 INFO [psi4.driver.task_planner:285] PLANNING Atomic: keywords={'SCF__INTS_TOLERANCE': 1e-12, 'function_kwargs': {}} 2 | 2025-04-15:15:17:44,707 INFO [psi4.driver.driver:788] Compute properties(): method=scf, basis=anonymousf32d2b4a, molecule=ethanol_1, nre=79.48506899653815 3 | 2025-04-15:15:17:44,972 INFO [psi4.driver.driver:791] Return properties(): -154.06011082233073 4 | 2025-04-15:15:17:45,9 INFO [psi4.driver.task_planner:285] PLANNING Atomic: keywords={'SCF__INTS_TOLERANCE': 1e-12, 'function_kwargs': {}} 5 | 2025-04-15:15:17:45,10 INFO [psi4.driver.driver:788] Compute properties(): method=scf, basis=anonymous742eaaa7, molecule=ethanol_2, nre=81.45479184863332 6 | 2025-04-15:15:17:45,274 INFO [psi4.driver.driver:791] Return properties(): -154.06621251818407 7 | 152(18) 184108 (2020). https://doi.org/10.1063/5.0006002 8 | 9 | Additional Code Authors 10 | E. T. Seidl, C. L. Janssen, E. F. Valeev, M. L. Leininger, 11 | J. F. Gonthier, R. M. Richard, H. R. McAlexander, M. Saitow, X. Wang, 12 | P. Verma, M. H. Lechner, A. Jiang, S. Behnle, A. G. Heide, 13 | M. F. Herbst, and D. L. Poole 14 | 15 | Previous Authors, Complete List of Code Contributors, 16 | and Citations for Specific Modules 17 | https://github.com/psi4/psi4/blob/master/codemeta.json 18 | https://github.com/psi4/psi4/graphs/contributors 19 | http://psicode.org/psi4manual/master/introduction.html#citing-psifour 20 | 21 | ----------------------------------------------------------------------- 22 | 23 | 24 | Psi4 started on: Tuesday, 15 April 2025 03:17PM 25 | 26 | Process ID: 14790 27 | Host: eifel 28 | PSIDATADIR: /home/karl/miniconda3/envs/psi4/share/psi4 29 | Memory: 500.0 MiB 30 | Threads: 1 31 | 32 | *** tstart() called on eifel 33 | *** at Tue Apr 15 15:17:44 2025 34 | 35 | => Libint2 <= 36 | 37 | Primary basis highest AM E, G, H: 6, 6, 3 38 | Auxiliary basis highest AM E, G, H: 7, 7, 4 39 | Onebody basis highest AM E, G, H: -, -, - 40 | Solid Harmonics ordering: Gaussian 41 | => Loading Basis Set <= 42 | 43 | Name: ANONYMOUSF32D2B4A 44 | Role: ORBITAL 45 | Keyword: BASIS 46 | atoms 1-2 entry C line 111 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/6-31gs.gbs 47 | atoms 3 entry O line 145 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/6-31gs.gbs 48 | atoms 4-9 entry H line 44 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/6-31gs.gbs 49 | 50 | 51 | --------------------------------------------------------- 52 | SCF 53 | by Justin Turney, Rob Parrish, Andy Simmonett 54 | and Daniel G. A. Smith 55 | RHF Reference 56 | 1 Threads, 500 MiB Core 57 | --------------------------------------------------------- 58 | 59 | ==> Geometry <== 60 | 61 | Molecular point group: c1 62 | Full point group: C1 63 | 64 | Geometry (in Angstrom), charge = 0, multiplicity = 1: 65 | 66 | Center X Y Z Mass 67 | ------------ ----------------- ----------------- ----------------- ----------------- 68 | C 0.000000000000 0.000000000000 0.000000000000 12.000000000000 69 | C 1.488055400000 -0.007281760000 0.396532600000 12.000000000000 70 | O 2.049716550000 1.376481530000 0.256048100000 15.994914619570 71 | H 3.064299780000 1.371516700000 0.526411240000 1.007825032230 72 | H 1.586794280000 -0.336187610000 1.431023580000 1.007825032230 73 | H 2.034410100000 -0.689064540000 -0.255210280000 1.007825032230 74 | H -0.408140440000 -1.005534660000 0.102085400000 1.007825032230 75 | H -0.546354700000 0.681782780000 0.651742880000 1.007825032230 76 | H -0.098738880000 0.328905850000 -1.034490970000 1.007825032230 77 | 78 | Running in c1 symmetry. 79 | 80 | Rotational constants: A = 1.07422 B = 0.12113 C = 0.11353 [cm^-1] 81 | Rotational constants: A = 32204.19926 B = 3631.24897 C = 3403.64238 [MHz] 82 | Nuclear repulsion = 79.485068996538146 83 | 84 | Charge = 0 85 | Multiplicity = 1 86 | Electrons = 26 87 | Nalpha = 13 88 | Nbeta = 13 89 | 90 | ==> Algorithm <== 91 | 92 | SCF Algorithm Type is DF. 93 | DIIS enabled. 94 | MOM disabled. 95 | Fractional occupation disabled. 96 | Guess Type is SAD. 97 | Energy threshold = 1.00e-06 98 | Density threshold = 1.00e-06 99 | Integral threshold = 1.00e-12 100 | 101 | ==> Primary Basis <== 102 | 103 | Basis Set: ANONYMOUSF32D2B4A 104 | Blend: 6-31G* 105 | Number of shells: 30 106 | Number of basis functions: 57 107 | Number of Cartesian functions: 57 108 | Spherical Harmonics?: false 109 | Max angular momentum: 2 110 | 111 | => Loading Basis Set <= 112 | 113 | Name: (ANONYMOUSF32D2B4A AUX) 114 | Role: JKFIT 115 | Keyword: DF_BASIS_SCF 116 | atoms 1-2 entry C line 121 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/cc-pvdz-jkfit.gbs 117 | atoms 3 entry O line 221 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/cc-pvdz-jkfit.gbs 118 | atoms 4-9 entry H line 51 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/cc-pvdz-jkfit.gbs 119 | 120 | ==> Integral Setup <== 121 | 122 | DFHelper Memory: AOs need 0.011 GiB; user supplied 0.366 GiB. 123 | Using in-core AOs. 124 | 125 | ==> MemDFJK: Density-Fitted J/K Matrices <== 126 | 127 | J tasked: Yes 128 | K tasked: Yes 129 | wK tasked: No 130 | OpenMP threads: 1 131 | Memory [MiB]: 375 132 | Algorithm: Core 133 | Schwarz Cutoff: 1E-12 134 | Mask sparsity (%): 0.0616 135 | Fitting Condition: 1E-10 136 | 137 | => Auxiliary Basis Set <= 138 | 139 | Basis Set: (ANONYMOUSF32D2B4A AUX) 140 | Blend: CC-PVDZ-JKFIT 141 | Number of shells: 126 142 | Number of basis functions: 393 143 | Number of Cartesian functions: 393 144 | Spherical Harmonics?: false 145 | Max angular momentum: 3 146 | 147 | Minimum eigenvalue in the overlap matrix is 6.4657671192E-03. 148 | Reciprocal condition number of the overlap matrix is 9.9216712214E-04. 149 | Using symmetric orthogonalization. 150 | 151 | ==> Pre-Iterations <== 152 | 153 | SCF Guess: Superposition of Atomic Densities via on-the-fly atomic UHF (no occupation information). 154 | 155 | ------------------------- 156 | Irrep Nso Nmo 157 | ------------------------- 158 | A 57 57 159 | ------------------------- 160 | Total 57 57 161 | ------------------------- 162 | 163 | ==> Iterations <== 164 | 165 | Total Energy Delta E RMS |[F,P]| 166 | 167 | @DF-RHF iter SAD: -153.07739014059152 -1.53077e+02 0.00000e+00 168 | @DF-RHF iter 1: -153.96434001751871 -8.86950e-01 7.33753e-03 DIIS/ADIIS 169 | @DF-RHF iter 2: -154.03873491080984 -7.43949e-02 4.11703e-03 DIIS/ADIIS 170 | @DF-RHF iter 3: -154.05885941532333 -2.01245e-02 7.09177e-04 DIIS/ADIIS 171 | @DF-RHF iter 4: -154.06000108018918 -1.14166e-03 2.30742e-04 DIIS/ADIIS 172 | @DF-RHF iter 5: -154.06010459420486 -1.03514e-04 4.48411e-05 DIIS 173 | @DF-RHF iter 6: -154.06011046269472 -5.86849e-06 9.43002e-06 DIIS 174 | @DF-RHF iter 7: -154.06011080013576 -3.37441e-07 2.34944e-06 DIIS 175 | @DF-RHF iter 8: -154.06011082233073 -2.21950e-08 7.42141e-07 DIIS 176 | Energy and wave function converged. 177 | 178 | 179 | ==> Post-Iterations <== 180 | 181 | Orbital Energies [Eh] 182 | --------------------- 183 | 184 | Doubly Occupied: 185 | 186 | 1A -20.560809 2A -11.280548 3A -11.217879 187 | 4A -1.303714 5A -1.007053 6A -0.831776 188 | 7A -0.655791 8A -0.636510 9A -0.553886 189 | 10A -0.526659 11A -0.523600 12A -0.477769 190 | 13A -0.440781 191 | 192 | Virtual: 193 | 194 | 14A 0.210847 15A 0.256072 16A 0.305976 195 | 17A 0.310515 18A 0.323898 19A 0.345113 196 | 20A 0.369236 21A 0.399420 22A 0.725704 197 | 23A 0.753606 24A 0.781646 25A 0.794435 198 | 26A 0.897721 27A 0.920891 28A 1.050710 199 | 29A 1.126822 30A 1.132331 31A 1.178051 200 | 32A 1.186966 33A 1.193073 34A 1.241030 201 | 35A 1.269962 36A 1.296230 37A 1.437714 202 | 38A 1.625411 39A 1.719002 40A 1.747870 203 | 41A 1.909744 42A 2.065641 43A 2.070073 204 | 44A 2.241715 45A 2.244961 46A 2.303367 205 | 47A 2.484271 48A 2.518535 49A 2.639352 206 | 50A 2.647005 51A 2.690102 52A 2.769785 207 | 53A 2.933508 54A 3.157637 55A 4.087288 208 | 56A 4.595129 57A 4.821187 209 | 210 | Final Occupation by Irrep: 211 | A 212 | DOCC [ 13 ] 213 | NA [ 13 ] 214 | NB [ 13 ] 215 | 216 | @DF-RHF Final Energy: -154.06011082233073 217 | 218 | => Energetics <= 219 | 220 | Nuclear Repulsion Energy = 79.4850689965381463 221 | One-Electron Energy = -367.0569004182393087 222 | Two-Electron Energy = 133.5117205993704488 223 | Total Energy = -154.0601108223307278 224 | 225 | Computation Completed 226 | 227 | 228 | Properties will be evaluated at 0.000000, 0.000000, 0.000000 [a0] 229 | 230 | Properties computed using the SCF density matrix 231 | 232 | 233 | Multipole Moments: 234 | 235 | ------------------------------------------------------------------------------------ 236 | Multipole Electronic (a.u.) Nuclear (a.u.) Total (a.u.) 237 | ------------------------------------------------------------------------------------ 238 | 239 | L = 1. Multiply by 2.5417464519 to convert [e a0] to [Debye] 240 | Dipole X : -58.1850753 58.5027743 0.3176991 241 | Dipole Y : -22.0597867 21.3909064 -0.6688803 242 | Dipole Z : -10.8289667 11.0532769 0.2243102 243 | Magnitude : 0.7737238 244 | 245 | ------------------------------------------------------------------------------------ 246 | 247 | Electrostatic potential to be computed on the grid and written to grid_esp.dat 248 | 249 | *** tstop() called on eifel at Tue Apr 15 15:17:44 2025 250 | Module time: 251 | user time = 0.26 seconds = 0.00 minutes 252 | system time = 0.01 seconds = 0.00 minutes 253 | total time = 0 seconds = 0.00 minutes 254 | Total time: 255 | user time = 1.05 seconds = 0.02 minutes 256 | system time = 0.07 seconds = 0.00 minutes 257 | total time = 1 seconds = 0.02 minutes 258 | -------------------------------------------------------------------------------- /tests/ethanol_2-psi.log: -------------------------------------------------------------------------------- 1 | 2025-04-15:15:17:45,9 INFO [psi4.driver.task_planner:285] PLANNING Atomic: keywords={'SCF__INTS_TOLERANCE': 1e-12, 'function_kwargs': {}} 2 | 2025-04-15:15:17:45,10 INFO [psi4.driver.driver:788] Compute properties(): method=scf, basis=anonymous742eaaa7, molecule=ethanol_2, nre=81.45479184863332 3 | 2025-04-15:15:17:45,274 INFO [psi4.driver.driver:791] Return properties(): -154.06621251818407 4 | M. James, S. Lehtola, J. P. Misiewicz, M. Scheurer, 5 | R. A. Shaw, J. B. Schriber, Y. Xie, Z. L. Glick, D. A. Sirianni, 6 | J. S. O'Brien, J. M. Waldrop, A. Kumar, E. G. Hohenstein, 7 | B. P. Pritchard, B. R. Brooks, H. F. Schaefer III, A. Yu. Sokolov, 8 | K. Patkowski, A. E. DePrince III, U. Bozkaya, R. A. King, 9 | F. A. Evangelista, J. M. Turney, T. D. Crawford, C. D. Sherrill, 10 | J. Chem. Phys. 152(18) 184108 (2020). https://doi.org/10.1063/5.0006002 11 | 12 | Additional Code Authors 13 | E. T. Seidl, C. L. Janssen, E. F. Valeev, M. L. Leininger, 14 | J. F. Gonthier, R. M. Richard, H. R. McAlexander, M. Saitow, X. Wang, 15 | P. Verma, M. H. Lechner, A. Jiang, S. Behnle, A. G. Heide, 16 | M. F. Herbst, and D. L. Poole 17 | 18 | Previous Authors, Complete List of Code Contributors, 19 | and Citations for Specific Modules 20 | https://github.com/psi4/psi4/blob/master/codemeta.json 21 | https://github.com/psi4/psi4/graphs/contributors 22 | http://psicode.org/psi4manual/master/introduction.html#citing-psifour 23 | 24 | ----------------------------------------------------------------------- 25 | 26 | 27 | Psi4 started on: Tuesday, 15 April 2025 03:17PM 28 | 29 | Process ID: 14790 30 | Host: eifel 31 | PSIDATADIR: /home/karl/miniconda3/envs/psi4/share/psi4 32 | Memory: 500.0 MiB 33 | Threads: 1 34 | 35 | *** tstart() called on eifel 36 | *** at Tue Apr 15 15:17:45 2025 37 | 38 | => Libint2 <= 39 | 40 | Primary basis highest AM E, G, H: 6, 6, 3 41 | Auxiliary basis highest AM E, G, H: 7, 7, 4 42 | Onebody basis highest AM E, G, H: -, -, - 43 | Solid Harmonics ordering: Gaussian 44 | => Loading Basis Set <= 45 | 46 | Name: ANONYMOUS742EAAA7 47 | Role: ORBITAL 48 | Keyword: BASIS 49 | atoms 1-2 entry C line 111 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/6-31gs.gbs 50 | atoms 3 entry O line 145 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/6-31gs.gbs 51 | atoms 4-9 entry H line 44 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/6-31gs.gbs 52 | 53 | 54 | --------------------------------------------------------- 55 | SCF 56 | by Justin Turney, Rob Parrish, Andy Simmonett 57 | and Daniel G. A. Smith 58 | RHF Reference 59 | 1 Threads, 500 MiB Core 60 | --------------------------------------------------------- 61 | 62 | ==> Geometry <== 63 | 64 | Molecular point group: c1 65 | Full point group: C1 66 | 67 | Geometry (in Angstrom), charge = 0, multiplicity = 1: 68 | 69 | Center X Y Z Mass 70 | ------------ ----------------- ----------------- ----------------- ----------------- 71 | C 0.000000000000 0.000000000000 0.000000000000 12.000000000000 72 | C 1.480135000000 -0.007243000000 0.394422000000 12.000000000000 73 | O 2.006963000000 1.292241000000 0.262328000000 15.994914619570 74 | H 2.915479000000 1.255729000000 0.509723000000 1.007825032230 75 | H 1.615007000000 -0.326780000000 1.455877000000 1.007825032230 76 | H 2.071975000000 -0.686951000000 -0.264934000000 1.007825032230 77 | H -0.325000120000 1.022934150000 -0.300340940000 1.007825032230 78 | H -0.188921410000 -0.684639060000 -0.858938150000 1.007825032230 79 | H -0.642570650000 -0.327091110000 0.849874820000 1.007825032230 80 | 81 | Running in c1 symmetry. 82 | 83 | Rotational constants: A = 1.11614 B = 0.12722 C = 0.11955 [cm^-1] 84 | Rotational constants: A = 33461.06137 B = 3813.86435 C = 3583.99902 [MHz] 85 | Nuclear repulsion = 81.454791848633320 86 | 87 | Charge = 0 88 | Multiplicity = 1 89 | Electrons = 26 90 | Nalpha = 13 91 | Nbeta = 13 92 | 93 | ==> Algorithm <== 94 | 95 | SCF Algorithm Type is DF. 96 | DIIS enabled. 97 | MOM disabled. 98 | Fractional occupation disabled. 99 | Guess Type is SAD. 100 | Energy threshold = 1.00e-06 101 | Density threshold = 1.00e-06 102 | Integral threshold = 1.00e-12 103 | 104 | ==> Primary Basis <== 105 | 106 | Basis Set: ANONYMOUS742EAAA7 107 | Blend: 6-31G* 108 | Number of shells: 30 109 | Number of basis functions: 57 110 | Number of Cartesian functions: 57 111 | Spherical Harmonics?: false 112 | Max angular momentum: 2 113 | 114 | => Loading Basis Set <= 115 | 116 | Name: (ANONYMOUS742EAAA7 AUX) 117 | Role: JKFIT 118 | Keyword: DF_BASIS_SCF 119 | atoms 1-2 entry C line 121 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/cc-pvdz-jkfit.gbs 120 | atoms 3 entry O line 221 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/cc-pvdz-jkfit.gbs 121 | atoms 4-9 entry H line 51 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/cc-pvdz-jkfit.gbs 122 | 123 | ==> Integral Setup <== 124 | 125 | DFHelper Memory: AOs need 0.011 GiB; user supplied 0.366 GiB. 126 | Using in-core AOs. 127 | 128 | ==> MemDFJK: Density-Fitted J/K Matrices <== 129 | 130 | J tasked: Yes 131 | K tasked: Yes 132 | wK tasked: No 133 | OpenMP threads: 1 134 | Memory [MiB]: 375 135 | Algorithm: Core 136 | Schwarz Cutoff: 1E-12 137 | Mask sparsity (%): 0.0616 138 | Fitting Condition: 1E-10 139 | 140 | => Auxiliary Basis Set <= 141 | 142 | Basis Set: (ANONYMOUS742EAAA7 AUX) 143 | Blend: CC-PVDZ-JKFIT 144 | Number of shells: 126 145 | Number of basis functions: 393 146 | Number of Cartesian functions: 393 147 | Spherical Harmonics?: false 148 | Max angular momentum: 3 149 | 150 | Minimum eigenvalue in the overlap matrix is 5.6683463339E-03. 151 | Reciprocal condition number of the overlap matrix is 8.6166426980E-04. 152 | Using symmetric orthogonalization. 153 | 154 | ==> Pre-Iterations <== 155 | 156 | SCF Guess: Superposition of Atomic Densities via on-the-fly atomic UHF (no occupation information). 157 | 158 | ------------------------- 159 | Irrep Nso Nmo 160 | ------------------------- 161 | A 57 57 162 | ------------------------- 163 | Total 57 57 164 | ------------------------- 165 | 166 | ==> Iterations <== 167 | 168 | Total Energy Delta E RMS |[F,P]| 169 | 170 | @DF-RHF iter SAD: -153.28118562967401 -1.53281e+02 0.00000e+00 171 | @DF-RHF iter 1: -153.97437992702010 -6.93194e-01 7.30360e-03 DIIS/ADIIS 172 | @DF-RHF iter 2: -154.04802041471351 -7.36405e-02 3.79348e-03 DIIS/ADIIS 173 | @DF-RHF iter 3: -154.06520027758222 -1.71799e-02 6.37169e-04 DIIS/ADIIS 174 | @DF-RHF iter 4: -154.06614707062369 -9.46793e-04 1.79649e-04 DIIS/ADIIS 175 | @DF-RHF iter 5: -154.06620856990730 -6.14993e-05 3.91374e-05 DIIS 176 | @DF-RHF iter 6: -154.06621236056469 -3.79066e-06 6.64353e-06 DIIS 177 | @DF-RHF iter 7: -154.06621251117014 -1.50605e-07 1.51801e-06 DIIS 178 | @DF-RHF iter 8: -154.06621251818407 -7.01394e-09 5.04636e-07 DIIS 179 | Energy and wave function converged. 180 | 181 | 182 | ==> Post-Iterations <== 183 | 184 | Orbital Energies [Eh] 185 | --------------------- 186 | 187 | Doubly Occupied: 188 | 189 | 1A -20.551403 2A -11.279499 3A -11.221195 190 | 4A -1.360229 5A -1.000956 6A -0.828327 191 | 7A -0.697654 8A -0.638872 9A -0.565301 192 | 10A -0.525075 11A -0.523172 12A -0.483095 193 | 13A -0.428248 194 | 195 | Virtual: 196 | 197 | 14A 0.220302 15A 0.265678 16A 0.274138 198 | 17A 0.298505 18A 0.324150 19A 0.383785 199 | 20A 0.407886 21A 0.436566 22A 0.741917 200 | 23A 0.756776 24A 0.794127 25A 0.846091 201 | 26A 0.918382 27A 0.987471 28A 1.074722 202 | 29A 1.093005 30A 1.119519 31A 1.146603 203 | 32A 1.155404 33A 1.189544 34A 1.217430 204 | 35A 1.276740 36A 1.288866 37A 1.402068 205 | 38A 1.581896 39A 1.685872 40A 1.773453 206 | 41A 1.943133 42A 2.037010 43A 2.112219 207 | 44A 2.258785 45A 2.268150 46A 2.366548 208 | 47A 2.423603 48A 2.537561 49A 2.667229 209 | 50A 2.742848 51A 2.763269 52A 2.861486 210 | 53A 2.970749 54A 3.210936 55A 4.162519 211 | 56A 4.567955 57A 4.842019 212 | 213 | Final Occupation by Irrep: 214 | A 215 | DOCC [ 13 ] 216 | NA [ 13 ] 217 | NB [ 13 ] 218 | 219 | @DF-RHF Final Energy: -154.06621251818407 220 | 221 | => Energetics <= 222 | 223 | Nuclear Repulsion Energy = 81.4547918486333202 224 | One-Electron Energy = -370.8360333341902333 225 | Two-Electron Energy = 135.3150289673728537 226 | Total Energy = -154.0662125181840736 227 | 228 | Computation Completed 229 | 230 | 231 | Properties will be evaluated at 0.000000, 0.000000, 0.000000 [a0] 232 | 233 | Properties computed using the SCF density matrix 234 | 235 | 236 | Multipole Moments: 237 | 238 | ------------------------------------------------------------------------------------ 239 | Multipole Electronic (a.u.) Nuclear (a.u.) Total (a.u.) 240 | ------------------------------------------------------------------------------------ 241 | 242 | L = 1. Multiply by 2.5417464519 to convert [e a0] to [Debye] 243 | Dipole X : -57.0775820 57.4145715 0.3369896 244 | Dipole Y : -20.4824535 19.9322113 -0.5502422 245 | Dipole Z : -10.8634429 11.0670256 0.2035827 246 | Magnitude : 0.6765902 247 | 248 | ------------------------------------------------------------------------------------ 249 | 250 | Electrostatic potential to be computed on the grid and written to grid_esp.dat 251 | 252 | *** tstop() called on eifel at Tue Apr 15 15:17:45 2025 253 | Module time: 254 | user time = 0.26 seconds = 0.00 minutes 255 | system time = 0.00 seconds = 0.00 minutes 256 | total time = 0 seconds = 0.00 minutes 257 | Total time: 258 | user time = 1.35 seconds = 0.02 minutes 259 | system time = 0.07 seconds = 0.00 minutes 260 | total time = 2 seconds = 0.03 minutes 261 | -------------------------------------------------------------------------------- /tests/acetic_acid_esp.dat: -------------------------------------------------------------------------------- 1 | 0.0110092461 2 | 0.0113200583 3 | 0.0142017180 4 | 0.0084545848 5 | 0.0148106354 6 | 0.0152890751 7 | 0.0110092461 8 | 0.0113200583 9 | 0.0108424069 10 | 0.0150301408 11 | 0.0161122125 12 | 0.0140091845 13 | 0.0055503936 14 | 0.0142562725 15 | 0.0170830712 16 | 0.0174095756 17 | 0.0138869438 18 | 0.0181343894 19 | 0.0155867351 20 | 0.0178307493 21 | 0.0173646272 22 | 0.0173646272 23 | 0.0174095756 24 | 0.0138869438 25 | 0.0181343894 26 | 0.0155867351 27 | 0.0178307493 28 | 0.0161122125 29 | 0.0140091845 30 | 0.0055503936 31 | 0.0142562725 32 | 0.0170830712 33 | 0.0108424069 34 | 0.0150301408 35 | 0.0123689290 36 | 0.0077088681 37 | 0.0138396643 38 | 0.0130176682 39 | 0.0060758252 40 | -0.0157635333 41 | 0.0138396643 42 | 0.0130176682 43 | 0.0060758252 44 | -0.0157635333 45 | 0.0123689290 46 | 0.0077088681 47 | 0.0149090208 48 | 0.0030157645 49 | 0.0052745068 50 | 0.0030157645 51 | 0.0052745068 52 | 0.0149090208 53 | -0.0006680189 54 | 0.0130010336 55 | -0.0065807067 56 | 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469 | -0.0064223360 470 | -0.0015928418 471 | 0.0093857165 472 | 0.0013409897 473 | -0.0037925376 474 | -0.0026307296 475 | 0.0050152273 476 | 0.0009130456 477 | 0.0002870623 478 | 0.0029760200 479 | 0.0037788372 480 | 0.0108711733 481 | 0.0125397797 482 | 0.0160751997 483 | 0.0129014202 484 | 0.0104714127 485 | 0.0175658743 486 | 0.0184204622 487 | 0.0144613004 488 | 0.0104714127 489 | 0.0175658743 490 | 0.0184204622 491 | 0.0144613004 492 | 0.0125397797 493 | 0.0160751997 494 | 0.0129014202 495 | 0.0037788372 496 | 0.0108711733 497 | -0.0071141825 498 | -0.0129408282 499 | -0.0163599986 500 | -0.0101747937 501 | -0.0171556167 502 | -0.0218874260 503 | -0.0223089219 504 | -0.0188486346 505 | -0.0103294340 506 | -0.0147305486 507 | -0.0227268198 508 | -0.0257329571 509 | -0.0255951857 510 | -0.0226634931 511 | -0.0153473496 512 | 0.0004879191 513 | -0.0214384224 514 | -0.0259104815 515 | -0.0270934653 516 | -0.0260732493 517 | -0.0226168123 518 | -0.0148243820 519 | -0.0147305486 520 | -0.0227268198 521 | -0.0257329571 522 | -0.0255951857 523 | -0.0226634931 524 | -0.0153473496 525 | 0.0004879191 526 | -0.0171556167 527 | -0.0218874260 528 | -0.0223089219 529 | -0.0188486346 530 | -0.0103294340 531 | -0.0129408282 532 | -0.0163599986 533 | -0.0101747937 534 | -0.0071141825 535 | -------------------------------------------------------------------------------- /tests/acetic_acid-psi.log: -------------------------------------------------------------------------------- 1 | 2 | ----------------------------------------------------------------------- 3 | Psi4: An Open-Source Ab Initio Electronic Structure Package 4 | Psi4 1.9.1 release 5 | 6 | Git: Rev {} zzzzzzz 7 | 8 | 9 | D. G. A. Smith, L. A. Burns, A. C. Simmonett, R. M. Parrish, 10 | M. C. Schieber, R. Galvelis, P. Kraus, H. Kruse, R. Di Remigi2025-04-15:15:17:44,347 INFO [psi4.driver.task_planner:285] PLANNING Atomic: keywords={'SCF__INTS_TOLERANCE': 1e-12, 'function_kwargs': {}} 11 | 2025-04-15:15:17:44,348 INFO [psi4.driver.driver:788] Compute properties(): method=scf, basis=anonymous8183206b, molecule=acetic_acid, nre=122.45633181261483 12 | 2025-04-15:15:17:44,669 INFO [psi4.driver.driver:791] Return properties(): -227.81029043552195 13 | 2025-04-15:15:17:44,706 INFO [psi4.driver.task_planner:285] PLANNING Atomic: keywords={'SCF__INTS_TOLERANCE': 1e-12, 'function_kwargs': {}} 14 | 2025-04-15:15:17:44,707 INFO [psi4.driver.driver:788] Compute properties(): method=scf, basis=anonymousf32d2b4a, molecule=ethanol_1, nre=79.48506899653815 15 | 2025-04-15:15:17:44,972 INFO [psi4.driver.driver:791] Return properties(): -154.06011082233073 16 | 2025-04-15:15:17:45,9 INFO [psi4.driver.task_planner:285] PLANNING Atomic: keywords={'SCF__INTS_TOLERANCE': 1e-12, 'function_kwargs': {}} 17 | 2025-04-15:15:17:45,10 INFO [psi4.driver.driver:788] Compute properties(): method=scf, basis=anonymous742eaaa7, molecule=ethanol_2, nre=81.45479184863332 18 | 2025-04-15:15:17:45,274 INFO [psi4.driver.driver:791] Return properties(): -154.06621251818407 19 | :17PM 20 | 21 | Process ID: 14790 22 | Host: eifel 23 | PSIDATADIR: /home/karl/miniconda3/envs/psi4/share/psi4 24 | Memory: 500.0 MiB 25 | Threads: 1 26 | 27 | *** tstart() called on eifel 28 | *** at Tue Apr 15 15:17:44 2025 29 | 30 | => Libint2 <= 31 | 32 | Primary basis highest AM E, G, H: 6, 6, 3 33 | Auxiliary basis highest AM E, G, H: 7, 7, 4 34 | Onebody basis highest AM E, G, H: -, -, - 35 | Solid Harmonics ordering: Gaussian 36 | => Loading Basis Set <= 37 | 38 | Name: ANONYMOUS8183206B 39 | Role: ORBITAL 40 | Keyword: BASIS 41 | atoms 1, 5 entry C line 111 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/6-31gs.gbs 42 | atoms 2-4, 7 entry H line 44 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/6-31gs.gbs 43 | atoms 6, 8 entry O line 145 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/6-31gs.gbs 44 | 45 | 46 | --------------------------------------------------------- 47 | SCF 48 | by Justin Turney, Rob Parrish, Andy Simmonett 49 | and Daniel G. A. Smith 50 | RHF Reference 51 | 1 Threads, 500 MiB Core 52 | --------------------------------------------------------- 53 | 54 | ==> Geometry <== 55 | 56 | Molecular point group: cs 57 | Full point group: Cs 58 | 59 | Geometry (in Angstrom), charge = 0, multiplicity = 1: 60 | 61 | Center X Y Z Mass 62 | ------------ ----------------- ----------------- ----------------- ----------------- 63 | C 1.450513890000 -0.066289320000 0.000000000000 12.000000000000 64 | H 1.755216130000 -0.628659860000 -0.875001460000 1.007825032230 65 | H 1.755216130000 -0.628659860000 0.875001460000 1.007825032230 66 | H 1.921732440000 0.904858970000 0.000000000000 1.007825032230 67 | C -0.042331220000 0.098493780000 0.000000000000 12.000000000000 68 | O -0.670648170000 -1.076209150000 0.000000000000 15.994914619570 69 | H -1.608372590000 -0.910166010000 0.000000000000 1.007825032230 70 | O -0.626758640000 1.131605100000 0.000000000000 15.994914619570 71 | 72 | Running in cs symmetry. 73 | 74 | Rotational constants: A = 0.39043 B = 0.31910 C = 0.18142 [cm^-1] 75 | Rotational constants: A = 11704.88734 B = 9566.37076 C = 5438.92090 [MHz] 76 | Nuclear repulsion = 122.456331812614835 77 | 78 | Charge = 0 79 | Multiplicity = 1 80 | Electrons = 32 81 | Nalpha = 16 82 | Nbeta = 16 83 | 84 | ==> Algorithm <== 85 | 86 | SCF Algorithm Type is DF. 87 | DIIS enabled. 88 | MOM disabled. 89 | Fractional occupation disabled. 90 | Guess Type is SAD. 91 | Energy threshold = 1.00e-06 92 | Density threshold = 1.00e-06 93 | Integral threshold = 1.00e-12 94 | 95 | ==> Primary Basis <== 96 | 97 | Basis Set: ANONYMOUS8183206B 98 | Blend: 6-31G* 99 | Number of shells: 32 100 | Number of basis functions: 68 101 | Number of Cartesian functions: 68 102 | Spherical Harmonics?: false 103 | Max angular momentum: 2 104 | 105 | => Loading Basis Set <= 106 | 107 | Name: (ANONYMOUS8183206B AUX) 108 | Role: JKFIT 109 | Keyword: DF_BASIS_SCF 110 | atoms 1, 5 entry C line 121 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/cc-pvdz-jkfit.gbs 111 | atoms 2-4, 7 entry H line 51 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/cc-pvdz-jkfit.gbs 112 | atoms 6, 8 entry O line 221 file /home/karl/miniconda3/envs/psi4/share/psi4/basis/cc-pvdz-jkfit.gbs 113 | 114 | ==> Integral Setup <== 115 | 116 | DFHelper Memory: AOs need 0.017 GiB; user supplied 0.366 GiB. 117 | Using in-core AOs. 118 | 119 | ==> MemDFJK: Density-Fitted J/K Matrices <== 120 | 121 | J tasked: Yes 122 | K tasked: Yes 123 | wK tasked: No 124 | OpenMP threads: 1 125 | Memory [MiB]: 375 126 | Algorithm: Core 127 | Schwarz Cutoff: 1E-12 128 | Mask sparsity (%): 0.1298 129 | Fitting Condition: 1E-10 130 | 131 | => Auxiliary Basis Set <= 132 | 133 | Basis Set: (ANONYMOUS8183206B AUX) 134 | Blend: CC-PVDZ-JKFIT 135 | Number of shells: 132 136 | Number of basis functions: 424 137 | Number of Cartesian functions: 424 138 | Spherical Harmonics?: false 139 | Max angular momentum: 3 140 | 141 | Minimum eigenvalue in the overlap matrix is 4.2608135153E-03. 142 | Reciprocal condition number of the overlap matrix is 6.4577348776E-04. 143 | Using symmetric orthogonalization. 144 | 145 | ==> Pre-Iterations <== 146 | 147 | SCF Guess: Superposition of Atomic Densities via on-the-fly atomic UHF (no occupation information). 148 | 149 | ------------------------- 150 | Irrep Nso Nmo 151 | ------------------------- 152 | A' 50 50 153 | A" 18 18 154 | ------------------------- 155 | Total 68 68 156 | ------------------------- 157 | 158 | ==> Iterations <== 159 | 160 | Total Energy Delta E RMS |[F,P]| 161 | 162 | @DF-RHF iter SAD: -227.05485235121759 -2.27055e+02 0.00000e+00 163 | @DF-RHF iter 1: -227.67394837560067 -6.19096e-01 1.03326e-02 DIIS/ADIIS 164 | @DF-RHF iter 2: -227.76968356231106 -9.57352e-02 6.38494e-03 DIIS/ADIIS 165 | @DF-RHF iter 3: -227.80805859849920 -3.83750e-02 1.06878e-03 DIIS/ADIIS 166 | @DF-RHF iter 4: -227.80993048482142 -1.87189e-03 4.20050e-04 DIIS/ADIIS 167 | @DF-RHF iter 5: -227.81024848736291 -3.18003e-04 1.03509e-04 DIIS/ADIIS 168 | @DF-RHF iter 6: -227.81028124572725 -3.27584e-05 5.00232e-05 DIIS 169 | @DF-RHF iter 7: -227.81028925488650 -8.00916e-06 1.67378e-05 DIIS 170 | @DF-RHF iter 8: -227.81029035080905 -1.09592e-06 4.57017e-06 DIIS 171 | @DF-RHF iter 9: -227.81029043552195 -8.47129e-08 8.71373e-07 DIIS 172 | Energy and wave function converged. 173 | 174 | 175 | ==> Post-Iterations <== 176 | 177 | Orbital Energies [Eh] 178 | --------------------- 179 | 180 | Doubly Occupied: 181 | 182 | 1Ap -20.615370 2Ap -20.553268 3Ap -11.386018 183 | 4Ap -11.240483 5Ap -1.477175 6Ap -1.368197 184 | 7Ap -1.027199 8Ap -0.831485 9Ap -0.702647 185 | 10Ap -0.683124 1App -0.653675 11Ap -0.581735 186 | 12Ap -0.572252 2App -0.562216 3App -0.480404 187 | 13Ap -0.449171 188 | 189 | Virtual: 190 | 191 | 4App 0.193128 14Ap 0.226895 15Ap 0.259331 192 | 16Ap 0.309105 5App 0.328774 17Ap 0.398399 193 | 18Ap 0.479557 19Ap 0.523182 6App 0.730786 194 | 20Ap 0.763438 21Ap 0.808767 22Ap 0.820802 195 | 7App 0.824643 23Ap 0.953120 24Ap 1.004773 196 | 25Ap 1.071232 26Ap 1.106893 8App 1.125663 197 | 27Ap 1.163208 28Ap 1.209854 9App 1.213181 198 | 29Ap 1.250408 30Ap 1.325811 10App 1.328902 199 | 31Ap 1.350886 32Ap 1.598115 11App 1.636077 200 | 12App 1.676098 33Ap 1.764096 34Ap 1.858989 201 | 13App 2.001155 35Ap 2.027555 14App 2.096641 202 | 36Ap 2.101068 37Ap 2.145710 38Ap 2.243935 203 | 15App 2.302197 39Ap 2.384862 16App 2.535440 204 | 40Ap 2.555539 41Ap 2.652676 17App 2.795933 205 | 42Ap 2.823082 18App 3.010754 43Ap 3.084202 206 | 44Ap 3.228901 45Ap 3.359023 46Ap 3.468113 207 | 47Ap 4.228754 48Ap 4.461892 49Ap 4.587300 208 | 50Ap 4.856778 209 | 210 | Final Occupation by Irrep: 211 | Ap App 212 | DOCC [ 13, 3 ] 213 | NA [ 13, 3 ] 214 | NB [ 13, 3 ] 215 | 216 | @DF-RHF Final Energy: -227.81029043552195 217 | 218 | => Energetics <= 219 | 220 | Nuclear Repulsion Energy = 122.4563318126148346 221 | One-Electron Energy = -554.1643877598309018 222 | Two-Electron Energy = 203.8977655116941037 223 | Total Energy = -227.8102904355219493 224 | 225 | Computation Completed 226 | 227 | 228 | Properties will be evaluated at 0.000000, 0.000000, 0.000000 [a0] 229 | 230 | Properties computed using the SCF density matrix 231 | 232 | 233 | Multipole Moments: 234 | 235 | ------------------------------------------------------------------------------------ 236 | Multipole Electronic (a.u.) Nuclear (a.u.) Total (a.u.) 237 | ------------------------------------------------------------------------------------ 238 | 239 | L = 1. Multiply by 2.5417464519 to convert [e a0] to [Debye] 240 | Dipole X : -3.2705647 3.5784490 0.3078843 241 | Dipole Y : 0.5484743 -1.1834077 -0.6349334 242 | Dipole Z : 0.0000000 0.0000000 0.0000000 243 | Magnitude : 0.7056438 244 | 245 | ------------------------------------------------------------------------------------ 246 | 247 | Electrostatic potential to be computed on the grid and written to grid_esp.dat 248 | 249 | *** tstop() called on eifel at Tue Apr 15 15:17:44 2025 250 | Module time: 251 | user time = 0.31 seconds = 0.01 minutes 252 | system time = 0.01 seconds = 0.00 minutes 253 | total time = 0 seconds = 0.00 minutes 254 | Total time: 255 | user time = 0.76 seconds = 0.01 minutes 256 | system time = 0.06 seconds = 0.00 minutes 257 | total time = 1 seconds = 0.02 minutes 258 | -------------------------------------------------------------------------------- /examples/2-methylpropanol/2_methylpropanal_4_esp.dat: 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