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pygamess 0.4.1.1

GAMESS wrapper for Python

==========
pygamess
==========

`pygamess` is a GAMESS wrapper for Python

Requirements
------------
* Python 2.6 or later (not support 3.x)
* RDKit
* GAMESS

Features
--------
* nothing

Setup
-----
::

$ pip install pygamess

set GAMESS_HOME environment in your .bashrc::

$ export GAMESS_HOME=/usr/local/gamess

Basic Usage
-----------

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)


History
-------

0.4.1.1 (2017-09-16)
~~~~~~~~~~~~~~~~~~

* Update Readme

0.4.1 (2017-09-16)
~~~~~~~~~~~~~~~~~~

* Bug fixed (coordinates problem)

0.4.0 (2017-09-13)
~~~~~~~~~~~~~~~~~~

* Change the backend library from openbabel to RDKit

0.3.0 (2012-03-31)
~~~~~~~~~~~~~~~~~~

* 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
 
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pygamess-0.4.1.1.tar.gz (md5) Source 2017-09-16 7KB