92 lines
2.0 KiB
Plaintext
92 lines
2.0 KiB
Plaintext
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#!/usr/bin/env python2
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"""
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convert zmatrix and input for spin multiplicity and charge from the SI of
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J. Chem. Phys. 131, 154112 (2009); https://doi.org/10.1063/1.3247288
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into a zmatrix usable by the QP, and spits the correct command to execute
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Usage:
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qp_create_ezfio_from_g09_zmat g09_zmat basis
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Produces the ezfio folder g09_zmat.ezfio
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"""
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import sys
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import os
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import subprocess
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try:
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import qp_path
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except ImportError:
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print "source .quantum_package.rc"
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raise
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try:
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QP_ROOT = os.environ["QP_ROOT"]
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QP_EZFIO = os.environ["QP_EZFIO"]
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except KeyError:
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print "Error: QP_ROOT environment variable not found."
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sys.exit(1)
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else:
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sys.path = [QP_EZFIO + "/Python",
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QP_ROOT + "/install/resultsFile",
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QP_ROOT + "/install",
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QP_ROOT + "/scripts"] + sys.path
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def findall(sub, string):
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"""
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>>> text = "Allowed Hello Hollow"
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>>> tuple(findall('ll', text))
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(1, 10, 16)
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"""
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index = 0 - len(sub)
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try:
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while True:
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index = string.index(sub, index + len(sub))
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yield index
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except ValueError:
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pass
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filepath = sys.argv[1]
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basis = sys.argv[2]
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icount = 0
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zmat = []
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with open(filepath, "r") as fp:
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cipsi = []
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for line in fp:
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if (icount == 0 ):
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a=line.split(',')
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charge = int(a[0])
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spin = int(a[1])
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else:
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a=line.split()
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if(len(a)>0):
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n=a[0].count(',')
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if(n > 6):
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listfind=list(findall(',', a[0]))
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char=a[0]
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a[0]=char[0:listfind[n-1]]
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b=a[0].replace(',', ' ')
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b=b.replace('=', ' ')
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zmat.append(b)
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else:
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b=" "
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zmat.append(b)
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icount += 1
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c = filepath.split('.')
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file_origin = c[0]
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ezfio = file_origin+".ezfio"
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zmat_file = file_origin+".zmt"
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file_zmat = open(zmat_file,"w+")
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for l in zmat:
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file_zmat.write(l +'\n')
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command="qp_create_ezfio -m %s -c %s -b %s -o %s %s" % (spin,charge,basis,ezfio,zmat_file)
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print command
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#os.system(command)
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