pygamess is a GAMESS wrapper for Python
- Python 3.7 or later (pygamess <0.5 supports only Python2)
- RDKit >= 2020.03.5
- GAMESS > Jun2020R1
- ruamel.YAML
$ pip install pygamess
set GAMESS_HOME environment in your .bashrc or .zshrc:
$ export GAMESS_HOME=/usr/local/gamess
Windows/Mac users can obtain the pre-compiled binary executables from GAMESS download site. But Linux users need to compile the souce code.
$ pytest
>>> from pygamess import Gamess
>>> from pygamess.utils import rdkit_optimize
>>> m = rdkit_optimize("CCO")
>>> g = Gamess()
>>> r = g.run(m)
>>> r.total_energy
-152.127991054
Or use rdkit directly:
>>> from pygamess import Gamess
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> m = Chem.MolFromSmiles("CCO")
>>> m = Chem.AddHs(m)
>>> AllChem.EmbedMolecule(m)
0
>>> AllChem.UFFOptimizeMolecule(m,maxIters=200)
0
>>> g = Gamess()
>>> r = g.run(m)
>>> r.total_energy
-152.1279910526
The GamessOut object(r) contains the results of the GAMESS calculation and the RDKit Chem object with the calculation results:
>>> r.total_energy
-152.1279910526
>>> r.HOMO
-0.3453
>>> r.nHOMO
-0.3978
>>> r.LUMO
0.5594
>>> r.nLUMO
0.6127
>>> r.dipole_moment
[0.681619, -0.605188, 1.146253, 1.464497]
>>> r.orbital_energies
[-20.2521, -11.0932, -11.0402, -1.286, -0.9614, -0.7909, -0.6269, -0.5716, -0.5347, -0.4976, -0.4705, -0.3978, -0.3453, 0.5594, 0.6127, 0.6639, 0.69, 0.7002, 0.7388, 0.7549, 0.7852]
>>> r.mulliken_charges
[-0.171226, 0.024351, -0.298162, 0.049615, 0.055831, 0.061924, 0.042714, 0.061112, 0.173842]
>>> r.lowdin_charges
[-0.089262, 0.062464, -0.212689, 0.022024, 0.02752, 0.031644, 0.010235, 0.026611, 0.121453]
The RDKit Chem object has the same information to store these data into SDF:
>>> r.mol
<rdkit.Chem.rdchem.Mol object at 0x7ffd48217f30>
>>> r.mol.GetProp("total_energy")
'-152.12799105260001'
>>> r.mol.GetProp("HOMO")
'-0.3453'
>>> r.mol.GetProp("nHOMO")
'-0.39779999999999999'
>>> r.mol.GetProp("LUMO")
'0.55940000000000001'
>>> r.mol.GetProp("nLUMO")
'0.61270000000000002'
>>> r.mol.GetProp("dipole_moment")
'1.4644969999999999'
>>> r.mol.GetProp("dx")
'0.68161899999999997'
>>> r.mol.GetProp("dy")
'-0.60518799999999995'
>>> r.mol.GetProp("dz")
'1.146253'
>>> r.mol.GetProp("orbital_energies")
'-20.2521 -11.0932 -11.0402 -1.286 -0.9614 -0.7909 -0.6269 -0.5716 -0.5347 -0.4976 -0.4705 -0.3978 -0.3453 0.5594 0.6127 0.6639 0.69 0.7002 0.7388 0.7549 0.7852'
>>> for a in r.mol.GetAtoms():
... print("{}:\t{:.4f}\t{:.4f}".format(a.GetSymbol(), float(a.GetProp("mulliken_charge")), float(a.GetProp("lowdin_charge"))))
...
C: -0.1712 -0.0893
C: 0.0244 0.0625
O: -0.2982 -0.2127
H: 0.0496 0.0220
H: 0.0558 0.0275
H: 0.0619 0.0316
H: 0.0427 0.0102
H: 0.0611 0.0266
H: 0.1738 0.1215
Set the run_type as 'optimize'. This optimization process updates the coordinates of the molecule:
>>> from pygamess import Gamess
>>> from pygamess.utils import rdkit_optimize
>>> m = rdkit_optimize("CCO")
>>> g = Gamess()
>>> g.run_type('optimize')
>>> r = g.run(m)
>>> r.total_energy
-152.1330661028
>>> original_conf = m.GetConformer(0)
>>> optimized_conf = r.mol.GetConformer(0)
>>> for c in original_conf.GetPositions():
... print(c)
...
[ 0.91206647 -0.11944851 -0.1294722 ]
[-0.47153193 0.42043351 0.21118521]
[-1.44831334 -0.21539324 -0.56715297]
[ 0.9650486 -1.2050043 0.09903891]
[1.67955732 0.41189183 0.47186063]
[ 1.12654515 0.0378618 -1.20780162]
[-0.67995345 0.27545635 1.29552482]
[-0.49851483 1.50993204 -0.00177488]
[-1.58490399 -1.11572948 -0.17140791]
>>> for c in optimized_conf.GetPositions():
... print(c)
...
[ 0.91442972 -0.13086468 -0.12174822]
[-0.48373921 0.42850882 0.23169745]
[-1.54145595 -0.17763397 -0.52424945]
[ 0.97874385 -1.18768306 0.12185969]
[1.67944907 0.39674369 0.43935649]
[ 1.11452802 -0.00923776 -1.18177409]
[-0.65534535 0.31918718 1.31002371]
[-0.51450285 1.49751073 0.00304491]
[-1.4921073 -1.13653094 -0.2782105 ]
Or pass the options to a constractor::
>>> from pygamess import Gamess
>>> from pygamess.utils import rdkit_optimize
>>> m = rdkit_optimize("CCO")
>>> g = Gamess(options={"contrl":{"runtyp":"optimize"}})
>>> r = g.run(m)
>>> r.total_energy
-152.1330661279
>>> from pygamess import Gamess
>>> from pygamess.utils import rdkit_optimize
>>> m = rdkit_optimize("CCC(=O)O")
>>> g = Gamess()
>>> g.run_type('optimize', hessend=True)
>>> r = g.run(m)
>>> r.ir_spectra
[('1.078', '0.058962'), ('0.361', '0.000420'), ('0.119', '0.000239'), ('0.703', '0.027425'), ('1.694', '0.025676'), ('3.212', '0.064166'), ('80.809', '0.030877'), ('220.540', '0.023447'), ('255.386', '0.510706'), ('362.039', '1.450661'), ('461.248', '0.076788'), ('590.483', '0.244231'), ('743.957', '0.128188'), ('915.147', '0.079289'), ('941.690', '0.122604'), ('1163.260', '0.213250'), ('1262.233', '0.180680'), ('1283.531', '0.070173'), ('1451.777', '0.939433'), ('1514.198', '0.042036'), ('1564.520', '3.659319'), ('1627.441', '0.509608'), ('1736.037', '0.011788'), ('1799.935', '0.021852'), ('1830.887', '0.076255'), ('1834.826', '0.085977'), ('2153.439', '1.875334'), ('3572.386', '0.028347'), ('3609.011', '0.023501'), ('3730.553', '0.009088'), ('3752.383', '0.015918'), ('3758.396', '0.003956'), ('4272.454', '0.229192')]
### GAMESS ###
# DFT ANALYTIC HESSIAN PRESENTLY HAS 5 RESTRICTIONS:
# $CONTRL: SCFTYP MUST BE EITHER RHF OR UHF
# $CONTRL: POINT GROUP SYMMETRY NOT ALLOWED, SET NOSYM=1
# $SCF: AO INTEGRAL DIRECT: SET DIRSCF=.TRUE.
# $CPHF: AO INTEGRAL DRIVEN: SET CPHF=AO
# AND THE FUNCTIONAL MUST NOT BE OF META-GGA TYPE.
Use basis_sets method:
>>> from pygamess import Gamess
>>> from pygamess.utils import rdkit_optimize
>>> m = rdkit_optimize("CCO")
>>> g = Gamess()
>>> g.run_type = "optimize"
>>> g.run(m).total_energy
-152.127991054
>>> g.basis_sets("3-21G")
>>> g.run(m).total_energy
-153.2170653562
>>> g.basis_sets("6-31G")
>>> g.run(m).total_energy
-154.0054866151
>>> g.basis_sets("6-31G*")
>>> g.run(m).total_energy
-154.0702703669
>>> g.basis_sets("6-31G**")
>>> g.run(m).total_energy
-154.0843823698
Or edit the basis attribute directly:
>>> g.options({'basis':{'gbasis': 'sto', 'ngauss': '3'}})
>>> g.run(m).total_energy
-152.127991054
The ground state (default):
>>> from pygamess.utils import rdkit_optimize
>>> from pygamess import Gamess
>>> g = Gamess()
>>> g.basis_sets("6-31G*")
>>> m = rdkit_optimize("CCO")
>>> g.run_type("optimize")
>>> r = g.run(m)
>>> r.total_energy
-154.0755757352
The cationic state:
>>> g.scf_type("uhf")
>>> g.charge(1)
>>> g.multiplicity(2)
>>> r = g.run(m)
>>> r.total_energy
-153.7367666449
Or:
>>> g.options({"contrl":{"icharg": 1, "mult": 2, "scftyp": "uhf"}})
>>> r = g.run(m)
>>> r.total_energy
-153.7367666449
The anionic state:
>>> g.options({"contrl":{"icharg": -1, "mult": 2, "scftyp": "uhf"}})
>>> r = g.run(m)
>>> r.total_energy
-153.9302151707
The triplet state:
>>> g.options({"contrl":{"icharg": 0, "mult": 3, "scftyp": "uhf"}})
>>> r = g.run(m)
>>> r.total_energy
-153.9581403463
B3LYP/6-31G*:
>>> from pygamess import Gamess
>>> from pygamess.utils import rdkit_optimize
>>> m = rdkit_optimize("CCO")
>>> g = Gamess()
>>> g.run_type("optimize")
>>> g.basis_sets("6-31G*")
>>> g.dft_type("B3LYP")
>>> g.run(m).total_energy
-154.9387962055
M062X/6-31G**:
>>> from pygamess import Gamess
>>> from pygamess.utils import rdkit_optimize
>>> m = rdkit_optimize("CCO")
>>> g = Gamess()
>>> g.run_type("optimize")
>>> g.dft_type("M06-2X")
>>> g.basis_sets("6-31G**")
>>> g.run(m).total_energy
-154.9636095207
Pygamess currently only supports CPCM, but will support IEFPCM in the future:
>>> from pygamess import Gamess
>>> from pygamess.utils import rdkit_optimize
>>> m = rdkit_optimize("CCO")
>>> g = Gamess()
>>> g.basis_sets("6-31G*")
>>> g.pcm_type("water")
>>> g.run_type("optimize")
>>> r = g.run(m)
>>> r.total_energy
-154.0824604616
>>> r.internal_energy
-154.0748367584
>>> r.delta_internal_energy
0.0
>>> r.electrostatic_interaction
-0.0076237032
>>> r.pierotti_cavitation_energy
0.0
>>> r.dispersion_free_energy
0.0
>>> r.repulsion_free_energy
0.0
>>> r.total_interacion
-0.0076237032
The example compound(Methyl yellow) was downloaded from PubchemQC project.
>>> from pygamess import Gamess
>>> from rdkit import Chem
>>> m = Chem.MolFromMolFile("examples/methyl_yellow.mol", removeHs=False)
>>> g = Gamess()
>>> g.dft_type("b3lyp", tddft=True)
>>> g.basis_sets("6-31G*")
>>> r = g.run(m)
>>> r.uv_spectra # (exitation ev, oscillator strength)
[('2.629', '0.0000'), ('3.217', '0.9349'), ('4.209', '0.0066'), ('4.263', '0.0020'), ('4.424', '0.1041'), ('4.779', '0.1068'), ('4.913', '0.0563'), ('4.940', '0.0001'), ('5.051', '0.0000'), ('5.430', '0.0006')]
Optimizing the compound:
>>> from pygamess import Gamess
>>> from rdkit import Chem
>>> g = Gamess()
>>> from pygamess.utils import rdkit_optimize
>>> m = rdkit_optimize("C=CCBr")
>>> g.run_type("optimize")
>>> g.dft_type("b3lyp")
>>> g.basis_sets("6-31G*")
>>> r = g.run(m)
>>> with open("examples/C=CCBr.mol", "w") as f:
... f.write(Chem.MolToMolBlock(r.mol))
...
NMR spectra calculation (It takes a long time):
>>> from pygamess import Gamess
>>> from rdkit import Chem
>>> m = Chem.MolFromMolFile("examples/C=CCBr.mol", removeHs=False)
>>> g = Gamess(num_cores=1) # PARALLEL EXECUTION IS NOT ENABLED.
>>> g.basis_sets("6-31G*")
>>> g.run_type("nmr")
>>> r = g.run(m)
>>> r.isotropic_shielding
[79.8218, 68.6661, 157.7233, 2476.7501, 27.0851, 27.2072, 26.4652, 28.7654, 28.7932]
# NMR MAY BE COMPUTED ONLY FOR SCFTYP=RHF,
# NO CORRELATION OPTION (DFTTYP, CITYP, CCTYP, MPLEVL) MAY BE CHOSEN
# NO SEMI-EMPIRICAL OPTION (GBASIS=AM1/PM3/MNDO) MAY BE CHOSEN
# DIRECT AO INTEGRAL CALCULATION (DIRSCF) IS NOT ENABLED,
# AND/OR PARALLEL EXECUTION IS NOT ENABLED.
use input method:
>>> from pygamess import Gamess
>>> from pygamess.utils import rdkit_optimize
>>> m = rdkit_optimize("CO")
>>> g = Gamess()
>>> print(g.input(m))
$contrl scftyp=rhf runtyp=energy $end
$basis gbasis=sto ngauss=3 $end
$system mwords=100 $end
$DATA
6324
C1
C 6.0 -0.3577002260 0.0075902163 -0.0214817423
O 8.0 0.9087355734 -0.5349924519 -0.2611189822
H 1.0 -0.5468334701 0.0717914414 1.0721087268
H 1.0 -0.4337681128 1.0193437527 -0.4757947304
H 1.0 -1.1269974200 -0.6479305528 -0.4789564639
H 1.0 1.5565636556 0.0841975943 0.1652431920
$END
use gparse:
>>> from pygamess.gamout_parser import gparse
>>> r = gparse("/somewhere/gamess.out")
save sdf file:
>>> from pygamess import Gamess
>>> from pygamess.utils import rdkit_optimize
>>> from rdkit import Chem
>>> m = rdkit_optimize("CCO")
>>> g = Gamess()
>>> r = g.run(m)
>>> w = Chem.SDWriter("CCO.sdf")
>>> w.write(r.mol)
>>> w.close()
load from sdf file:
>>> from pygamess.utils import sdf2gamout
>>> r = sdf2gamout("CCO.sdf")
>>> r = rs[0]
>>> r.HOMO
-0.3453
>>> r.mulliken_charges
['-0.17122599999999999', '0.024351000000000001', '-0.29816199999999998', '0.049614999999999999', '0.055830999999999999', '0.061924', '0.042714000000000002', '0.061112', '0.173842']
set PYGAMESS_DEBUG environment:
$ export PYGAMESS_DEBUG=1
This won't remove the all files generated by the GAMESS executable, including the output files.
set logger level:
>>> from pygamess import Gamess, logger
>>> import logging
>>> logger.setLevel(logging.DEBUG)
>>> g = Gamess()
DEBUG:pygamess.gamess:tmpdir: /var/folders/gm/4tcnnyqd09d2jt7p0dtvr28m0000gn/T/tmp889j9c7e
- Fix Mulliken/Lowdin population bug
- Add Mulliken/Lowdin population
- Bug fix (options)
- Support Windows pre-compiled GAMESS (#11)
- OS-dependent termination detection (#12)
- Bug fix (SDF -> GamessOut)
- Add SDF -> GamessOut object parser for persistence of calculation results
- Store UV-spectra NMR-spectra and IR-spectra into Chem object
- Support hessend (#8)
- Support TD-DFT (#2)
- Store the energy of each step during structural optimization (#7)
- Add the calculation condition into Chem object (#6)
- Support NMR calculation
- Support options
- Add parser description
- Fix bug (ModuleNotFoundError: No module named 'pygamess_utils')
- Change README format (rst -> md)
- Support DFT calculation
- Support PCM calculation (C-PCM only)
- Improve the parser
- Support logger levels
- Change method name from "basis_set" to "basis_sets"
- Support Python3
- Update Readme
- Bug fix (coordinates problem)
- Change the backend library from openbabel to RDKit
- Use internal rungms (default)
- Add basis_set method(STO-3G,3-21G,6-31G,6-311G,6-31G*,6-31G**,AM1,PM3,MNDO)
- Constructor can accept options
- Bug fixed (spin multiplicity)
- Add charge settings
- Change Method name (gamess_input -> input)
- Bug fix (multiplicity setting for pybel)
- Bug fix (print error when rungms exec failed)
- Add document
- Run method accepts OBMol and Pybel-Molecule object
- Add CIS method (and optimization)
- Update document
- Semiempical method (AM1, PM3, MNDO)
- Add statpt option
- Change default error print message (10 lines)
- First release