GAMESS

gamess.py

import openbabel as ob
from tempfile import mkstemp, mkdtemp
from os import removedirs, unlink, system, environ
import re
import os.path
import string
from random import choice

def randstr(n):
    """ランダムなファイル名を生成するため"""
    return u''.join(choice('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ') for i in xrange(n))

class Gamess(object):

    def __init__(self):
        self.tempdir = mkdtemp()
        self.gamess  = "/Users/kzfm/gamess/rungms"
        self.jobname = ''
        self.cwd    = os.getcwd()

    def run(self, mol, runtype="energy", basis="6-31G"):
        self.jobname = randstr(6)
        obc = ob.OBConversion()
        obc.SetInFormat("gamout")

        gamin = self.write_file(mol, runtype=runtype, basis=basis)
        gamout = self.tempdir + "/" + self.jobname + ".out"
        os.chdir(self.tempdir)
        os.system("%s %s> %s  2> /dev/null" % (self.gamess, self.jobname, gamout))        

        # エラーが出たのでstringを渡したらなおった
        # TypeError: in method 'OBConversion_ReadFile', argument 3 of type 'std::string'
        new_mol = ob.OBMol()
        s = open(gamout).read()
        next = obc.ReadString(new_mol, s)

        os.chdir(self.cwd)
        unlink(gamin)
        unlink(gamout)
        return new_mol

    def optimize(self, mol, basis="6-31G"):        
        return self.run(mol, runtype="optimize",basis=basis)

    def singlepoint_energy(self, mol, basis="6-31G"):
        return self.run(mol, runtype="energy",basis=basis)


    def header(self, runtype="optimize", basis="6-31G"):

        basis_section = " $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END\n"
        runtype_section = """ $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE $END
 $STATPT OPTTOL=0.0001 NSTEP=20 $END"""

        if basis in ["sto3g", "STO-3G"]:
            basis_section = " $BASIS GBASIS=STO NGAUSS=3 $END\n"
        elif basis in ["631g", "6-31G(d)", "6-31G"]:
            basis_section = " $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END\n"
        elif basis in ["631gdp","6-31G(d,p)"]:
            basis_section = " $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 $END\n"
        elif basis in["631+gdp", "6-31G+(d,p)"]:
            basis_section = " $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 DIFFSP=.TRUE. $END\n"

        if runtype == "energy":
            runtype_section = """ $CONTRL SCFTYP=RHF RUNTYP=ENERGY ECP=SBK $END"""

        section = basis_section + runtype_section
        return section

    def write_file(self, mol, runtype="energy", basis="6-31G"):
        obc = ob.OBConversion()
        obc.SetOutFormat("gamin")

        gamess_input_file = self.tempdir + "/" + self.jobname +".inp"
        gamess_input_str = obc.WriteString(mol)

        h = self.header(runtype=runtype, basis=basis)
        ng = gamess_input_str.replace(" $CONTRL COORD=CART UNITS=ANGS $END",h)

        with open(gamess_input_file, "w") as f:
            f.write(ng)
        return gamess_input_file

    def __del__(self):
        #print "remove " + self.tempdir
        removedirs(self.tempdir)

if __name__ == '__main__':

    g = Gamess()

    obc = ob.OBConversion()
    obc.SetInFormat("mol")

    mol = ob.OBMol()
    next = obc.ReadFile(mol,"test.mol")

    newmol = g.run(mol)

    print [(obatom.GetIdx(), obatom.GetType(), obatom.GetPartialCharge()) for obatom in ob.OBMolAtomIter(newmol)]