pygamess 0.4.0

single point calculation with RDKit

>>> from pygamess import Gamess
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> m = Chem.MolFromSmiles("CC")
>>> m = Chem.AddHs(m)
>>> AllChem.EmbedMolecule(m)
0
>>> AllChem.UFFOptimizeMolecule(m,maxIters=200)
0
>>> g = Gamess()
>>> nm = g.run(m)
>>> nm.GetProp("total_energy")
'-78.302511990200003'

optimize calculation with RDKit

Change run_type:

>>> from pygamess import Gamess
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> m = Chem.MolFromSmiles("CC")
>>> m = Chem.AddHs(m)
>>> AllChem.EmbedMolecule(m)
0
>>> AllChem.UFFOptimizeMolecule(m,maxIters=200)
0
>>> g = Gamess()
>>> g.run_type('optimize')
>>> optimized_mol = g.run(mol)
>>> optimized_mol.GetProp("total_energy")
'-78.306179626599999'

change basis-sets

Change basis set:

>>> from pygamess import Gamess
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> m = Chem.MolFromSmiles("CC")
>>> m = Chem.AddHs(m)
>>> AllChem.EmbedMolecule(m)
0
>>> AllChem.UFFOptimizeMolecule(m,maxIters=200)
0
>>> g = Gamess()
>>> g.run_type = "optimize"
>>> g.run(m).GetProp("total_energy")
'-78.302511907400003'
>>> g.basis_set("3-21G")
{'gbasis': 'N21', 'ngauss': '3'}
>>> g.run(m).GetProp("total_energy")
'-78.790442552000002'
>>> g.basis_set("6-31G")
{'gbasis': 'N31', 'ngauss': '6'}
>>> g.run(m).GetProp("total_energy")
'-79.194024566899998'
>>> g.basis_set("6-31G*")
{'gbasis': 'N31', 'ndfunc': '1', 'ngauss': '6'}
>>> g.run(m).GetProp("total_energy")
'-79.225521673399996'
>>> g.basis_set("6-31G**")
{'gbasis': 'N31', 'ndfunc': '1', 'npfunc': '1', 'ngauss': '6'}
>>> g.run(m).GetProp("total_energy")
'-79.235082450899995'

or edit property of Gamess instance:

>>> g.basis = {'gbasis': 'sto', 'ngauss': '3'}
>>> mol_sto3g = g.run(m)
>>> mol_sto3g.GetProp("total_energy")
'-78.302511907400003'

print GAMESS INPUT

use input method:

>>> g.input(mol)

0.4.0 (2017-09-13)

• Changed the backend library from openbabel to RDKit

0.3.0 (2012-03-31)

• no more required rungms script and use internal rungms (default)

• added 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)

0.2.2 (2012-03-30)

• added charge settings

• method name changed (gamess_input -> input)

0.2.1 (2012-03-23)

• bug fixed (multiplicity setting for pybel)

• bug fixed (print error when rungms exec failed)

• added document

0.2.0 (2012-03-06)

• run method can accept OBMol and Pybel-Molecule object

0.1.2 (2011-09-23)

• added CIS method (and optimization)

0.1.1 (2011-08-06)

• updated document

• semiempical method (AM1, PM3, MNDO)

• added statpt option

• changed default error print (10 lines)

0.1 (2011-6-25)

• first release