#! /usr/bin/env python import sys import re import numpy as np import readarc fileprefix = sys.argv[1] cutoff = float(sys.argv[2]) filename = fileprefix + '.arc' ljoname = fileprefix + '.ljo' arc = readarc.readarc(filename) n = arc[0] atomname = arc[1] x = arc[2] y = arc[3] z = arc[4] atomtype = arc[5] bonds = arc[6] ljofile = open(ljoname, 'r') nsolatoms = int(re.split('\s+',ljofile.readline().strip())[0]) ljofile.close() newatomname = [] newx = [] newy = [] newz = []
import os import sys import math import re import readarc import numpy as np fileprefix = sys.argv[1] keywords = '$rem\nJOBTYPE SP\nEXCHANGE omegaB97X-D\nBASIS GENERAL\nPURECART 2222\nEFP TRUE\nCHELPG TRUE\n$end\n\n' arcname = fileprefix + '.arc' ljoname = fileprefix + '.ljo' arc = readarc.readarc(arcname) ljofile = open(ljoname, 'r') nsolatoms = int(re.split('\s+',ljofile.readline().strip())[0]) charge = re.split('\s+',ljofile.readline().strip())[0] ljofile.close() n = arc[0] x = arc[2] y = arc[3] z = arc[4] atomtype = arc[5] symbols = {900:'C', 901:'C', 902:'C', 910:'H', 911:'H', 912:'H', 920:'Cl', 921:'Cl', 922:'Cl', 930:'O', 931:'O', 932:'O', 940:'H', 941:'H', 942:'H', 55:'O', 56:'H', 57:''}
weight_e = 15.19562 weight_f = 1.293817 weight_t = 1.0 fileprefix = sys.argv[1] atom_tinker = {901:'C', 911:'H', 921:'Cl', 55:'O', 56:'H', 57:''} atom_gauss = {1:'H', 6:'C', 8:'O', 17:'Cl'} mass = {'H':1.008,'C':12.000,'O':15.999,'Cl':35.453} arcname = fileprefix + '.arc' keyname = fileprefix + '.key' ljoname = fileprefix + '.ljo' outname = fileprefix + '.out' arcdata = readarc.readarc(arcname) n = arcdata[0] x = arcdata[2] y = arcdata[3] z = arcdata[4] atomtype = arcdata[5] bonds = arcdata[6] keydata = readkey.readkey(keyname) prm_sigma = keydata[0] prm_ep = keydata[1] prm_ch = keydata[2] conv = keydata[3] ljofile = open(ljoname, 'r')