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poltype.py.0.1
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#!/usr/bin/python
##################################################################
#
# Title: Poltype
# Description: Atomic typer for the polarizable AMOEBA force field
#
# Copyright: Copyright (c) Johnny C. Wu,
# Gaurav Chattree, & Pengyu Ren 2010-2011
#
# Poltype is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 3
# as published by the Free Software Foundation.
#
# Poltype is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# if not, write to:
# Free Software Foundation, Inc.
# 59 Temple Place, Suite 330
# Boston, MA 02111-1307 USA
#
##################################################################
import os
import sys
import time
import string
from collections import deque
from types import *
import re
import getopt
import tempfile
import shutil
import pprint
import subprocess
import inspect
from socket import gethostname
from math import *
import numpy
from scipy import optimize
import matplotlib
matplotlib.use('Agg')
import pylab as plt
import openbabel
import valence
# Implementation Notes
# 1) Minimize Structure
# 2) Run SP Calculations
# 3) Run GDMA DONE (electrostatic-param.pl)
# 4) Run poledit (to extract atom types) DONE (electrostatic-param.pl)
# 4) Run avgmpoles.pl
# Default starting index of atom type
prmstartidx = 401
# These values can be edited. Affect speed of QM calculations.
numproc = 1
maxmem = "700MB"
maxdisk = "100GB"
# Initilize directories
gausdir = None
gdmadir = None
tinkerdir = None
scratchdir = "/scratch"
paramfname = sys.path[0] + "/amoeba_v2_new.prm"
paramhead = sys.path[0] + "/amoeba_v2_new_head.prm"
obdatadir = sys.path[0] + "/datadir"
amoeba_conv_spec_fname = "amoeba_t5_t4.txt"
# Initilize executables
babelexe = "babel"
gausexe = "g09"
formchkexe = "formchk"
cubegenexe = "cubegen"
gdmaexe = "gdma"
eleparmexe = sys.path[0] + "/electrostatic-param.pl"
groupsymexe = sys.path[0] + "/groupsym.exe"
avgmpolesexe = sys.path[0] + "/avgmpoles.pl"
peditexe = "poledit.x"
potentialexe = "potential.x"
valenceexe = "valence.x"
minimizeexe = "minimize.x"
analyzeexe = "analyze.x"
superposeexe = "superpose.x"
#peditexe = "poledit"
#potentialexe = "potential"
#valenceexe = "valence"
#minimizeexe = "minimize"
#analyzeexe = "analyze"
#superposeexe = "superpose"
# Initialize constants, basis sets
defopbendval = 0.20016677990819662
Hartree2kcal_mol = 627.5095
optbasisset = "6-31G*"
dmabasisset = "6-311G**"
popbasisset = "6-31G*"
espbasisset = "6-311++G(2d,2p)"
m06lbasisset = "6-311++G**"
# Initialize some global variables such as arrays and booleans
qmonly = False
espfit = True
parmtors = True
uniqidx = False
torkeyfname = None
nfoldlist = range(1,4)
foldoffsetlist = [ 0.0, 180.0, 0.0, 0.0, 0.0, 0.0 ]
torlist = []
rotbndlist = []
mm_tor_count = 1
output_format = 5
toromit_list = []
omittorsion2 = False
do_tor_qm_opt = False
# Poltype begins with the 'main' method which is found towards the bottom of the program
def call_subsystem(cmdstr, iscritical=False):
"""
Intent: Run 'cmdstr' on the command line
Input:
cmdstr: command string to be run on command line
Output:
Description: -
"""
now = time.strftime("%c",time.localtime())
logfh.write(now + " Calling: " + cmdstr + "\n")
logfh.flush()
os.fsync(logfh.fileno())
p = subprocess.Popen(cmdstr, shell=True,
stdout=logfh, stderr=logfh)
if p.wait() != 0:
now = time.strftime("%c",time.localtime())
logfh.write(now + " ERROR: " + cmdstr + "\n")
logfh.flush()
os.fsync(logfh.fileno())
if iscritical:
sys.exit(1)
return p.wait()
def which(program,pathlist=os.environ["PATH"]):
"""
Intent: Check if the 'program' is in the user's path
Input:
program: Program name
pathlist: members of the user's path
Output:
program: path to program
exe_file: path to program
None: program was not found
Referenced By: initialize
Description: -
"""
def is_exe(fpath):
return os.path.exists(fpath) and os.access(fpath, os.X_OK)
fpath, fname = os.path.split(program)
if fpath:
if is_exe(program):
return program
else:
for path in pathlist.split(os.pathsep):
exe_file = os.path.join(path, program)
if is_exe(exe_file):
return exe_file
return None
def rotate_list(l1):
deq = deque(l1)
deq.rotate(-1)
return list(deq)
def parse_options(argv):
"""
Intent: Set up variables based on arguments supplied by user
Input:
argv: command line arguments supplied by user
Output:
Referenced By: main
Description:
"""
global molecprefix
global qmonly
global molstructfname
global chkname
global fname
global gausfname
global gausoptfname
global gdmafname
global comfname
global prmstartidx
global numproc
global maxmem
global maxdisk
# global gausdir
global espfit
global parmtors
global uniqidx
global torkeyfname
global optbasisset
global dmabasisset
global popbasisset
global espbasisset
global comoptfname
global chkoptfname
global fckoptfname
global logoptfname
global compopfname
global chkpopfname
global fckpopfname
global logpopfname
global comdmafname
global chkdmafname
global fckdmafname
global logdmafname
global comespfname
global chkespfname
global fckespfname
global logespfname
global output_format
global paramhead
global omittorsion2
global do_tor_qm_opt
try:
opts, xargs = getopt.getopt(argv[1:],'hqn:m:M:a:s:p:d:u:',["help","qmonly","optbasisset=","dmabasisset=","popbasisset=","espbasisset=","m06lbasisset=","optlog=","dmalog=","esplog=","dmafck=","espfck=","numproc=","maxmem=","maxdisk=","atmidx=","structure=","prefix=","gdmaout=","gbindir=","qm-scratch-dir=","omit-espfit","omit-torsion","test-tor-key=","uniqidx","tinker4format","omit-torsion2","do-tor-qm-opt"])
except getopt.GetoptError, err:
print str(err)
usage()
sys.exit(2)
for o, a in opts:
if o in ("-s", "--structure"):
molstructfname = a
elif o in ("-n", "--numproc"):
numproc = a
elif o in ("-m", "--maxmem"):
maxmem = a
elif o in ("-M", "--maxdisk"):
maxdisk = a
elif o in ("-a", "--atmidx"):
prmstartidx = int(a)
elif o in ("--optbasisset"):
optbasisset = a
elif o in ("--dmabasisset"):
dmabasisset = a
elif o in ("--popbasisset"):
popbasisset = a
elif o in ("--espbasisset"):
espbasisset = a
elif o in ("--m06lbasisset"):
m06lbasisset = a
elif o in ("--optlog"):
logoptfname = a
elif o in ("--dmalog"):
logdmafname = a
elif o in ("--esplog"):
logespfname = a
elif o in ("--dmafck"):
fckdmafname = a
elif o in ("--espfck"):
fckespfname = a
elif o in ("--dmachk"):
chkdmafname = a
elif o in ("--espchk"):
chkespfname = a
elif o in ("-f", "--formchk"):
fname = a
elif o in ("-d", "--gdmaout"):
gdmafname = a
elif o in ("-u", "--gbindir"):
gausdir = a
elif o in ("-q", "--qmonly"):
qmonly = True
elif o in ("--omit-espfit"):
espfit = False
elif o in ("--omit-torsion"):
parmtors = False
elif o in ("--omit-torsion2"):
omittorsion2 = True
elif o in ("--do-tor-qm-opt"):
do_tor_qm_opt = True
elif o in ("--test-tor-key"):
torkeyfname = a
elif o in ("--uniqidx"):
uniqidx = True
elif o in ("-h", "--help"):
usage()
sys.exit(2)
elif o in ("--version"):
printversion()
sys.exit(2)
elif o in ("--tinker4format"):
output_format = 4
paramhead = sys.path[0] + "/amoeba_v2_new_head_tinker_4.prm"
else:
assert False, "unhandled option"
assert globals().has_key("molstructfname"), "Molecule structure file (-s) needs to be defined."
class PrettyFloat(float):
def __repr__(self):
return '%.3f' % self
def pretty_floats(obj):
if isinstance(obj, float):
return PrettyFloat(obj)
if isinstance(obj, openbabel.OBAtom):
return obj.GetIdx()
elif isinstance(obj, dict):
return dict((k, pretty_floats(v)) for k, v in obj.items())
elif isinstance(obj, (list, tuple, numpy.ndarray)):
return map(pretty_floats, obj)
return obj
def dispvar(label, *vars):
"""
Intent: Output variable to stdout
"""
print label + ': ',
for var in vars:
print pretty_floats(var),
print ""
def print_error(errstrarr,kill=None):
now = time.strftime("%c",time.localtime())
sys.stderr.write('ERROR (%s): ' % now)
logfh.write('ERROR (%s): ' % now)
if isinstance(errstrarr, (list,tuple)):
for errstr in errstrarr:
sys.stderr.write(str(pretty_floats(errstr)) + '\n')
logfh.write(str(pretty_floats(errstr)) + '\n')
else:
sys.stderr.write(str(pretty_floats(errstrarr)) + '\n')
logfh.write(str(pretty_floats(errstrarr)) + '\n')
if kill is not None:
if isinstance(kill,int):
sys.exit(kill)
else:
sys.exit(255)
def write_arr_to_file(fname, array_list):
"""
Intent: Write out information in array to file
Input:
fname: file name
array_list: array with data to be printed
Output:
file is written to 'filename'
Referenced By: fit_rot_bond_tors, eval_rot_bond_parms
Description: -
"""
outfh = open(fname,'w')
rows = zip(*array_list)
for cols in rows:
for ele in cols:
outfh.write("%10.4f" % ele)
outfh.write("\n")
def initialize ():
"""
Intent: Initialize all paths to needed executables
Input:
Output:
Referenced By: main
Description: -
"""
global gausdir
global gausexe
global formchkexe
global cubegenexe
global tinkerdir
global peditexe
global potentialexe
global valenceexe
global minimizeexe
global analyzeexe
global superposeexe
global gdmaexe
if (gausdir is not None):
if which(os.path.join(gausdir,"g09")) is not None:
gausexe = os.path.join(gausdir,"g09")
formchkexe = os.path.join(gausdir,formchkexe)
cubegenexe = os.path.join(gausdir,cubegenexe)
elif which(os.path.join(gausdir,"g03")) is not None:
gausexe = os.path.join(gausdir,"g03")
formchkexe = os.path.join(gausdir,formchkexe)
cubegenexe = os.path.join(gausdir,cubegenexe)
else:
print "ERROR: Invalid Gaussian directory: ", gausdir
sys.exit(1)
else:
if which("g09") is not None:
gausexe = "g09"
elif which("g03") is not None:
gausexe = "g03"
else:
print "ERROR: Cannot find Gaussian executable in $PATH. Please install Gaussian or specify Gaussian directory with --gbindir flag."
sys.exit(1)
if ("TINKERDIR" in os.environ):
tinkerdir = os.environ["TINKERDIR"]
promof = open(tinkerdir+"/promo.f")
latestversion = False
for line in promof:
if "6.2" in line:
latestversion = True
break
promof.close()
if(not latestversion):
print "ERROR: Not latest version of tinker (6.2)"
sys.exit(1)
peditexe = os.path.join(tinkerdir,peditexe)
potentialexe = os.path.join(tinkerdir,potentialexe)
valenceexe = os.path.join(tinkerdir,valenceexe)
minimizeexe = os.path.join(tinkerdir,minimizeexe)
analyzeexe = os.path.join(tinkerdir,analyzeexe)
superposeexe = os.path.join(tinkerdir,superposeexe)
if (not which(analyzeexe)):
print "ERROR: Cannot find TINKER analyze executable"
sys.exit(2)
if ("GDMADIR" in os.environ):
gdmadir = os.environ["GDMADIR"]
gdmaexe = os.path.join(gdmadir,gdmaexe)
if (not which(gdmaexe)):
print "ERROR: Cannot find GDMA executable"
sys.exit(2)
if ("GAUSS_SCRDIR" in os.environ):
scratchdir = os.environ["GAUSS_SCRDIR"]
vfs = os.statvfs(scratchdir)
gbfree = (vfs.f_bavail * vfs.f_frsize) / (1024*1024*1024)
if(float(maxdisk[:-2]) > gbfree):
print "ERROR: maxdisk greater than free space in scratch directory"
sys.exit(2)
if (not which(scratchdir)):
print "ERROR: Cannot find Gaussian scratch directory"
sys.exit(2)
#os.putenv('BABEL_DATADIR',obdatadir)
def init_filenames ():
"""
Intent: Initialize file names
Input:
Output:
Referenced By: main
Description: -
"""
global logfname
global molecprefix
global molstructfname
global chkname
global fname
global gausfname
global gausoptfname
global gdmafname
global keyfname
global xyzfname
global peditinfile
global valinfile
global superposeinfile
global espgrdfname
global qmespfname
global qmesp2fname
global grpfname
global key2fname
global key3fname
global key4fname
global key5fname
global xyzoutfile
global valoutfname
global scrtmpdir
global tmpxyzfile
global tmpkeyfile
molecprefix = os.path.splitext(molstructfname)[0]
logfname = assign_filenames ( "logfname" , "-poltype.log")
chkname = assign_filenames ( "chkname" , ".chk")
fname = assign_filenames ( "fname" , ".fchk")
gausfname = assign_filenames ( "gausfname" , ".log")
gausoptfname = assign_filenames ( "gausoptfname" , "-opt.log")
gdmafname = assign_filenames ( "gdmafname" , ".gdmaout")
keyfname = assign_filenames ( "keyfname" , ".key")
xyzfname = assign_filenames ( "xyzfname" , ".xyz")
peditinfile = assign_filenames ( "peditinfile" , "-peditin.txt")
valinfile = assign_filenames ( "valinfile" , "-valin.txt")
superposeinfile = assign_filenames ( "superposeinfile" , "-superin.txt")
espgrdfname = assign_filenames ( "espgrdfname" , ".grid")
qmespfname = assign_filenames ( "qmespfname" , ".cube")
#qmesp2fname = assign_filenames ( "qmesp2fname" , ".cube_2")
qmesp2fname = assign_filenames ( "qmesp2fname" , ".pot")
grpfname = assign_filenames ( "grpfname" , "-groups.txt")
key2fname = assign_filenames ( "key2fname" , ".key_2")
key3fname = assign_filenames ( "key3fname" , ".key_3")
key4fname = assign_filenames ( "key4fname" , ".key_4")
key5fname = assign_filenames ( "key5fname" , ".key_5")
xyzoutfile = assign_filenames ( "xyzoutfile" , ".xyz_2")
valoutfname = assign_filenames ( "valoutfname" , "sp.valout")
scrtmpdir = scratchdir + '/Gau-' + molecprefix
tmpxyzfile = 'ttt.xyz'
tmpkeyfile = 'ttt.key'
def assign_filenames (filename,suffix):
global molecprefix
if globals().has_key(filename):
return eval(filename)
else:
return molecprefix + suffix
def printversion ():
print os.path.basename(sys.argv[0]) + \
''': Version 1.0.2'''
def copyright ():
print '''
Poltype -- Polarizable atom typer of small molecules for the
AMOEBA polarizable force field
Please cite:
Wu, J.C.; Chattree, G.; Ren, P.Y.; Automation of AMOEBA polarizable force field
parameterization for small molecules. Theor Chem Acc. (Accepted).
Version 1.1.4 June 2015
Copyright (c) Johnny Wu and Pengyu Ren 2011
All Rights Reserved
######################################################################################
'''
def usage ():
print '''poltype:
-h, --help -- displays this help message
-s, --structure -- Gaussian checkpoint file
-a, --atmidx -- Starting index of atom type
-m MEMORY , --maxmem --
-M, --maxdisk
-q, --qmonly
--optbasisset
--dmabasisset
--espbasisset
--m06lbasisset
--omit-espfit
--omit-torsion
--version -- displays version of script'''
def load_structfile(structfname):
"""
Intent: load 'structfname' as an OBMol structure
Input:
structfname: structure file name
Output:
tmpmol: OBMol object with information loaded from structfname
Referenced By: run_gaussian, tor_opt_sp, compute_qm_tor_energy, compute_mm_tor_energy
Description: -
"""
strctext = os.path.splitext(structfname)[1]
tmpconv = openbabel.OBConversion()
if strctext in '.fchk':
tmpconv.SetInFormat('fchk')
elif strctext in '.log':
tmpconv.SetInFormat('g03')
else:
inFormat = openbabel.OBConversion.FormatFromExt(structfname)
tmpconv.SetInFormat(inFormat)
tmpmol = openbabel.OBMol()
tmpconv.ReadFile(tmpmol, structfname)
return tmpmol
#def verify_topology (newmol, refmol):
#for atm in openbabel.OBMolAtomIter(refmol):
# newatm = newmol.
#return True
def rebuild_bonds(newmol, refmol):
for b in openbabel.OBMolBondIter(refmol):
beg = b.GetBeginAtomIdx()
end = b.GetEndAtomIdx()
if not newmol.GetBond(beg,end):
newmol.AddBond(beg,end, b.GetBO(), b.GetFlags())
return True
def get_class_number(idx):
"""
Intent: Given an atom idx, return the atom's class number
"""
maxidx = max(symmetryclass)
return prmstartidx + (maxidx - symmetryclass[idx - 1])
def get_class_key(a, b, c, d):
"""
Intent: Given a set of atom idx's, return the class key for the set (the class numbers of the atoms appended together)
"""
cla = get_class_number(a)
clb = get_class_number(b)
clc = get_class_number(c)
cld = get_class_number(d)
if ((clb > clc) or (clb == clc and cla > cld)):
return '%d %d %d %d' % (cld, clc, clb, cla)
return '%d %d %d %d' % (cla, clb, clc, cld)
def get_uniq_rotbnd(a, b, c, d):
"""
Intent: Return the atom idx's defining a rotatable bond in the order of the class key
found by 'get_class_key'
"""
cla = get_class_number(a)
clb = get_class_number(b)
clc = get_class_number(c)
cld = get_class_number(d)
tmpkey = '%d %d %d %d' % (cla,clb,clc,cld)
if (get_class_key(a,b,c,d) == tmpkey):
return (a, b, c, d)
return (d, c, b, a)
def obatom2idx(obatoms):
"""
Intent: Given a list of OBAtom objects, return a list of their corresponding idx's
Referenced By: get_torlist_opt_angle
"""
atmidxlist = []
for obatm in obatoms:
atmidxlist.append(obatm.GetIdx())
return atmidxlist
def save_structfile(molstruct, structfname):
"""
Intent: Output the data in the OBMol structure to a file (such as *.xyz)
Input:
molstruct: OBMol structure
structfname: output file name
Output:
file is output to structfname
Referenced By: tor_opt_sp, compute_mm_tor_energy
Description: -
"""
strctext = os.path.splitext(structfname)[1]
tmpconv = openbabel.OBConversion()
if strctext in '.xyz':
tmpfh = open(structfname, "w")
maxidx = max(symmetryclass)
iteratom = openbabel.OBMolAtomIter(molstruct)
etab = openbabel.OBElementTable()
tmpfh.write('%6d %s\n' % (molstruct.NumAtoms(), molstruct.GetTitle()))
for ia in iteratom:
tmpfh.write( '%6d %2s %13.6f %11.6f %11.6f %5d' % (ia.GetIdx(), etab.GetSymbol(ia.GetAtomicNum()), ia.x(), ia.y(), ia.z(), prmstartidx + (maxidx - symmetryclass[ia.GetIdx() - 1])))
iteratomatom = openbabel.OBAtomAtomIter(ia)
neighbors = []
for iaa in iteratomatom:
neighbors.append(iaa.GetIdx())
neighbors = sorted(neighbors)
for iaa in neighbors:
tmpfh.write('%5d' % iaa)
tmpfh.write('\n')
else:
inFormat = openbabel.OBConversion.FormatFromExt(structfname)
tmpconv.SetOutFormat(inFormat)
return tmpconv.WriteFile(molstruct, structfname)
def rads(degrees):
"""
Intent: Convert degrees to radians
"""
if type(degrees) == ListType:
return [ deg * pi / 180 for deg in degrees ]
else:
return degrees * pi / 180
def getCan(x):
"""
Intent: For a given atom, output it's canonical label if it exists
Input:
x: atom in question
Output:
canonical label if it exists, -1 if not
"""
if (str(type(mol.GetAtom(x))).find("OBAtom") >= 0):
return canonicallabel[x-1]
else:
return -1
def get_symm_class(x):
"""
Intent: For a given atom, output it's symmetry class if it exists
Input:
x: atom in question
Output:
symmetry class if it exists, -1 if not
"""
if (str(type(mol.GetAtom(x))).find("OBAtom") >= 0):
return symmetryclass[x-1]
else:
return -1
def prepend_keyfile(keyfilename):
"""
Intent: Adds a header to the key file given by 'keyfilename'
"""
tmpfname = keyfilename + "_tmp"
tmpfh = open(tmpfname, "w")
keyfh = open(keyfilename, "r")
tmpfh.write("parameters " + paramhead + "\n")
tmpfh.write("bondterm none\n")
tmpfh.write("angleterm none\n")
tmpfh.write("torsionterm none\n")
tmpfh.write("vdwterm none\n")
tmpfh.write("fix-monopole\n")
tmpfh.write("potential-offset 1.0\n\n")
for line in keyfh:
tmpfh.write(line)
shutil.move(tmpfname, keyfilename)
def scale_multipoles (symmclass, mpolelines,scalelist):
"""
Intent: Scale multipoles based on value in scalelist
"""
symmclass = int(symmclass)
if scalelist[symmclass][2]:
qp1 = float(mpolelines[2])
qp1 = map(float, mpolelines[2].split())
qp1 = [ scalelist[symmclass][2] * x for x in qp1 ]
mpolelines[2] = '%46.5f\n' % qp1[0]
qp2 = map(float, mpolelines[3].split())
qp2 = [ scalelist[symmclass][2] * x for x in qp2 ]
mpolelines[3] = '%46.5f %10.5f\n' % tuple(qp2)
qp3 = map(float, mpolelines[4].split())
qp3 = [ scalelist[symmclass][2] * x for x in qp3 ]
mpolelines[4] = '%46.5f %10.5f %10.5f\n' % tuple(qp3)
return mpolelines
def rm_esp_terms_keyfile(keyfilename):
"""
Intent: Remove unnecessary terms from the key file
"""
tmpfname = keyfilename + "_tmp"
cmdstr = "sed -e \'/\(.* none$\|^#\|^fix\|^potential-offset\)/d\' " + keyfilename + " > " + tmpfname
call_subsystem(cmdstr)
shutil.move(tmpfname, keyfilename)
# Removes redundant multipole definitions created after potential fitting
keyfh = open(keyfilename)
lines = keyfh.readlines()
newlines = []
tmpfh = open(tmpfname, "w")
mpolelines = 0
for ln1 in range(len(lines)):
if mpolelines > 0:
mpolelines -= 1
continue
if 'multipole' in lines[ln1]:
nllen = len(newlines)
for ln2 in range(len(newlines)):
if len(lines[ln1].split()) <= 1 or len(lines[ln2].split()) <= 1:
continue
if lines[ln1].split()[0] in newlines[ln2].split()[0] and \
lines[ln1].split()[0] in 'multipole' and \
lines[ln1].split()[1] in newlines[ln2].split()[1]:
newlines[ln2] = lines[ln1]
newlines[ln2+1] = lines[ln1+1]
newlines[ln2+2] = lines[ln1+2]
newlines[ln2+3] = lines[ln1+3]
newlines[ln2+4] = lines[ln1+4]
mpolelines = 4
break
if mpolelines == 0:
newlines.append(lines[ln1])
else:
newlines.append(lines[ln1])
for nline in newlines:
tmpfh.write(nline)
tmpfh.close()
keyfh.close()
shutil.move(tmpfname, keyfilename)
def post_proc_localframes(keyfilename, lfzerox):
"""
Intent: This method runs after the tinker tool Poledit has run and created an
initial *.key file. The local frames for each multipole are "post processed".
Zeroed out x-components of the local frame are set back to their original values
If certain multipole values were not zeroed out by poltype this method zeroes them out
Input:
keyfilename: string containing file name of *.key file
lfzerox: array containing a boolean about whether the x-component of the local frame
for a given atom should be zeroed or not. Filled in method 'gen_peditin'.
'lfzerox' is true for atoms that are only bound to one other atom (valence = 1)
that have more than one possible choice for the x-component of their local frame
Output: *.key file is edited
Referenced By: main
Description:
1. Move the original *.key file to *.keyb
2. Create new empty file *.key
3. Iterate through the lines of *.keyb.
a. If poledit wrote out the local frame with an x-component missing or as 0
Then rewrite it with the original x-component (lf2) found in gen_peditin
b. If poledit did not zero out the local frame x-component for an atom but
lfzerox is true, zero out the necessary multipole components manually
4. Write the edited multipole information to *.key
"""
# mv *.key to *.keyb
tmpfname = keyfilename + "b"
shutil.move(keyfilename, tmpfname)
keyfh = open(tmpfname)
lines = keyfh.readlines()
newlines = []
# open *.key which is currently empty
tmpfh = open(keyfilename, "w")
mpolelines = 0
# iterate over lines in the *.key file
for ln1 in range(len(lines)):
# skip over the lines containing multipole values
if mpolelines > 0:
mpolelines -= 1
continue
elif 'multipole' in lines[ln1]:
# Check what poledit wrote as localframe2
tmplst = lines[ln1].split()
if len(tmplst) == 5:
(keywd,atmidx,lf1,lf2,chg) = tmplst
elif len(tmplst) == 4:
(keywd,atmidx,lf1,chg) = tmplst
lf2 = '0'
# If poledit set lf2 to 0, then replace it with the lf2 found in gen_peditin
if int(lf2) == 0:
lf2 = localframe2[int(atmidx) - 1]
lines[ln1] = '%s %5s %4s %4d %21s\n' % (keywd,
atmidx, lf1, lf2, chg)
# manually zero out components of the multipole if they were not done by poledit
elif lfzerox[int(atmidx) - 1]:
tmpmp = map(float, lines[ln1+1].split())
tmpmp[0] = 0.
lines[ln1+1] = '%46.5f %10.5f %10.5f\n' % tuple(tmpmp)
tmpmp = map(float, lines[ln1+4].split())
tmpmp[0] = 0.
lines[ln1+4] = '%46.5f %10.5f %10.5f\n' % tuple(tmpmp)
newlines.extend(lines[ln1:ln1+5])
mpolelines = 4
# append any lines unrelated to multipoles as is
else:
newlines.append(lines[ln1])
# write out the new lines to *.key
for nline in newlines:
tmpfh.write(nline)
tmpfh.close()
keyfh.close()
def post_process_mpoles(keyfilename, scalelist):
"""
Intent: Iterate through multipoles in 'keyfilename' and scale them if necessary
Calls 'scale_multipoles'
Input:
keyfilename: file name for key file
scalelist: structure containing scaling information. Found in process_types
Output: new *.key file
Referenced By: main
Description:
1. Move old keyfile to tmpfname
2. open an empty key file
3. iterate through tmpfname scaling the multipoles if necessary
4. output new multipoles to the new key file
"""
tmpfname = keyfilename + "b"
shutil.move(keyfilename, tmpfname)
keyfh = open(tmpfname)
lines = keyfh.readlines()
newlines = []
tmpfh = open(keyfilename, "w")
mpolelines = 0
for ln1 in range(len(lines)):
if mpolelines > 0:
mpolelines -= 1
continue
elif 'multipole' in lines[ln1]:
(keywd,symcls,lf1,lf2,chg) = lines[ln1].split()
newlines.extend(scale_multipoles(symcls,lines[ln1:ln1+5],scalelist))
mpolelines = 4
else:
newlines.append(lines[ln1])
for nline in newlines:
tmpfh.write(nline)
tmpfh.close()
keyfh.close()
def append_basisset (comfname, spacedformulastr,basissetstr):
"""
Intent: Append terms to *.com file if necessary
Input:
comfname: com file name
spacedformulastr: stoichoimetric molecular formula in spaced form (e.g. C 4 H 6 O 1)
basissetstr: basis set string
Output:
comfname is possibly appended to
Referenced By: gen_optcomfile, gen_comfile, tor_opt_sp
Description:
"""
if ('I ' in spacedformulastr):
fh = open(comfname, "a")
fh.write(' ' + re.sub(r'(\d+|I)\s+',r'', spacedformulastr) + '0\n')
fh.write(' %s\n' % basissetstr)
fh.write(' ****\n')
# if re.search('6-31',basissetstr,re.I):
fh.write(' I 0 \n')
fh.write(' S 5 1.00\n')
fh.write(' 444750.000 0.0008900 \n')
fh.write(' 66127.0000 0.0069400 \n')
fh.write(' 14815.0000 0.0360900 \n')
fh.write(' 4144.90000 0.1356800 \n')
fh.write(' 1361.20000 0.3387800 \n')
fh.write(' S 2 1.00\n')
fh.write(' 508.440000 0.4365900 \n')
fh.write(' 209.590000 0.1837500 \n')
fh.write(' S 1 1.00\n')
fh.write(' 81.9590000 1.0000000 \n')
fh.write(' S 1 1.00\n')
fh.write(' 36.8050000 1.0000000 \n')
fh.write(' S 1 1.00\n')
fh.write(' 13.4950000 1.0000000 \n')
fh.write(' S 1 1.00\n')
fh.write(' 6.88590000 1.0000000 \n')
fh.write(' S 1 1.00\n')
fh.write(' 2.55200000 1.0000000 \n')
fh.write(' S 1 1.00\n')
fh.write(' 1.20880000 1.0000000 \n')
fh.write(' S 1 1.00\n')
fh.write(' 0.27340000 1.0000000 \n')
fh.write(' S 1 1.00\n')
fh.write(' 0.10090000 1.0000000 \n')
fh.write(' P 4 1.00\n')
fh.write(' 2953.60000 0.0122100 \n')
fh.write(' 712.610000 0.0858700 \n')
fh.write(' 236.710000 0.2949300 \n')
fh.write(' 92.6310000 0.4784900 \n')
fh.write(' P 1 1.00\n')
fh.write(' 39.7320000 1.0000000 \n')
fh.write(' P 1 1.00\n')
fh.write(' 17.2730000 1.0000000 \n')
fh.write(' P 1 1.00\n')
fh.write(' 7.95700000 1.0000000 \n')
fh.write(' P 1 1.00\n')
fh.write(' 3.15290000 1.0000000 \n')
fh.write(' P 1 1.00\n')
fh.write(' 1.33280000 1.0000000 \n')
fh.write(' P 1 1.00\n')
fh.write(' 0.49470000 1.0000000 \n')
fh.write(' P 1 1.00\n')
fh.write(' 0.21600000 1.0000000 \n')
fh.write(' P 1 1.00\n')
fh.write(' 0.08293000 1.0000000 \n')
fh.write(' D 3 1.00\n')
fh.write(' 261.950000 0.0314400 \n')
fh.write(' 76.7340000 0.1902800 \n')
fh.write(' 27.5510000 0.4724700 \n')
fh.write(' D 1 1.00\n')
fh.write(' 10.6060000 1.0000000 \n')
fh.write(' D 1 1.00\n')
fh.write(' 3.42170000 1.0000000 \n')
fh.write(' D 1 1.00\n')
fh.write(' 1.13700000 1.0000000 \n')
fh.write(' D 1 1.00\n')
fh.write(' 0.30200000 1.0000000 \n')
fh.write(' ****\n\n')
fh.close()
def is_qm_normal_termination(logfname):
"""
Intent: Checks the *.log file for normal termination
"""
if os.path.isfile(logfname):
for line in open(logfname):
if "Normal termination" in line:
logfh.write("Normal termination: %s\n" % logfname)
return True
return False
def gen_opt_str(optimizeoptlist):
optstr = "#opt"
if optimizeoptlist:
optstr += "=(" + ','.join(optimizeoptlist) + ")"
return optstr