pygamess 0.3.0

single point calculation with pybel

>>> from pygamess import Gamess
>>> import pybel
>>> g = Gamess()
>>> mol = pybel.readstring('smi','C=C')
>>> mol.make3D()
>>> optimized_mol = g.run(mol)
>>> optimized_mol.energy
-77.0722784993

single point calculation with openbabel

>>> import pygamess
>>> g = pygamess.Gamess()
>>> import openbabel as ob
>>> obc = ob.OBConversion()
>>> obc.SetInFormat("mol")
True
>>> mol = ob.OBMol()
>>> obc.ReadFile(mol, "examples/ethane.mol")
True
>>> try:
...     newmol = g.run(mol)
... except GamessError, gerr:
...     print gerr.value
...
>>> newmol.GetEnergy()
-78.305307479999996

optimize calculation with pybel

set run_type:

>>> from pygamess import Gamess
>>> import pybel
>>> g = Gamess()
>>> g.run_type('optimize')
>>> mol = pybel.readstring('smi','C')
>>> mol.make3D()
>>> optimized_mol = g.run(mol)
>>> optimized_mol.energy
-37.0895866208

changing basis-sets

basis_type method:

>>> import pybel
>>> from pygamess import Gamess
>>> g = Gamess()
>>> mol = pybel.readstring('smi', 'O')
>>> mol.make3D()
>>> g.run(mol).energy
-74.96450135
>>> g.run_type('optimize')
>>> g.run(mol).energy
-74.9659012146
>>> g.basis_set('3-21G')
{'gbasis': 'N21', 'ngauss': '3'}
>>> g.run(mol).energy
-75.585959758
>>> g.basis_set('6-31G')
{'gbasis': 'N31', 'ngauss': '6'}
>>> g.run(mol).energy
-75.9853591564
>>> g.basis_set('6-311G')
{'gbasis': 'N311', 'ngauss': '6'}
>>> g.run(mol).energy
-76.0109546389
>>> g.basis_set('6-31G*')
{'gbasis': 'N31', 'ndfunc': '1', 'ngauss': '6'}
>>> g.run(mol).energy
-76.0107465155
>>> g.basis_set('6-31G**')
{'gbasis': 'N31', 'ndfunc': '1', 'npfunc': '1', 'ngauss': '6'}
>>> g.run(mol).energy
-76.0236150193

or edit property of Gamess instance:

>>> g.basis = {'gbasis': 'sto', 'ngauss': '3'}
>>> mol_sto3g = g.run(mol)
>>> mol_sto3g.GetEnergy()
-78.305307479999996

print GAMESS INPUT

use input method:

>>> g.input(mol)

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