mirror of https://github.com/pfloos/quack
322 lines
13 KiB
Python
Executable File
322 lines
13 KiB
Python
Executable File
#!/usr/bin/env python2
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import sys
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from termcolor import colored
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import shlex
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from subprocess import Popen, PIPE
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import itertools
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import re
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import numpy as np
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import os
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from shutil import copy2
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import matplotlib.pyplot as plt
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import json
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from math import *
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from collections import OrderedDict
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import csv
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import argparse
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def GetDuckDir():
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return os.path.dirname(os.path.realpath(__file__))
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def nNucl(molbaselines):
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return float(molbaselines[1].split()[0])
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def isMononucle(molbaselines):
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return nNucl(molbaselines)==1
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def openfileindir(path,readwrite):
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mydir=os.path.dirname(path)
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if not os.path.exists(mydir) and mydir!="":
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os.makedirs(mydir)
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return open(path,readwrite)
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def outfile(Outdic,item,index=None):
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itemdata=Outdic[item]
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if itemdata["Enabled"]:
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fmt=itemdata["Format"]
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if index is not None:
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filename=fmt.format(index)
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else:
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filename=fmt
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if "Parent" in Outdic:
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path=os.path.join(Outdic["Parent"],filename)
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else:
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path=filename
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return openfileindir(path,'w')
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else:
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return
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def runDuck(mol,basis,x,molbaselines,molbase,basisbase):
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#gennerate molecule file
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currdir=os.getcwd()
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os.chdir(GetDuckDir())
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molname='.'.join([mol,str(x)])
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lstw=list()
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for i,line in enumerate(molbaselines):
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if i<3:
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lstw.append(line)
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else:
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if isMononucle(molbaselines):
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if i==3:
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lstw.append(' '.join([str(x)]+line.split()[1:]))
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else:
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v=[float(abs(x))/float(2),float(-abs(x)/float(2))]
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val=v[i-3]
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lstw.append(' '.join([line.split()[0],'0.','0.',str(val)]))
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junkfiles=list()
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with open(molbase+molname,'w') as n:
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junkfiles.append(n.name)
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n.write(os.linesep.join(lstw))
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#Copy basis
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basisfile=basisbase+'.'.join([mol,basis])
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newbasisfile=basisbase+'.'.join([molname,basis])
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copy2(basisfile,newbasisfile)
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junkfiles.append(newbasisfile)
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#start child process Goduck
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cmd=" ".join(["./GoDuck",molname, basis])
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Duck=Popen(shlex.split(cmd),stdout=PIPE)
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(DuckOut, DuckErr) = Duck.communicate()
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excode=Duck.wait()
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for junk in junkfiles:
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os.remove(junk)
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os.chdir(currdir)
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return (excode,DuckOut,DuckErr)
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def addvalue(dic,key,x,y):
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if key not in dic:
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dic[key]=list()
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dic[key].append(y)
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print(key)
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print(x,y)
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def main(mol):
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#get basepath for files
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molbase='examples/molecule.'
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basisbase=molbase.replace('molecule','basis')
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with open('PyOptions.json','r') as jfile:
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options=json.loads(jfile.read())
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basis=str(options['Basis'])
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#Get mehtod to analyse
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methodsdic=options['Methods']
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#Get datas to analyse in this method
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scandic=options['Scan']
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scan=np.arange(scandic['Start'],scandic['Stop']+scandic['Step'],scandic['Step'])
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print(scan)
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mymethods=dict()
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alllabels=list()
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for method,methoddatas in methodsdic.iteritems():
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if methoddatas['Enabled']:
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mymethods[method]=methoddatas
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for label,labeldatas in methoddatas['Labels'].iteritems():
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if type(labeldatas) is dict:
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enabled=labeldatas['Enabled']
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else:
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enabled=labeldatas
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if enabled and label not in alllabels:
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alllabels.append(label)
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graphdic=dict()
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errorconvstring="Convergence failed"
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with open(os.path.join(GetDuckDir(),molbase+mol),'r') as b:
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molbaselines=b.read().splitlines()
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if isMononucle(molbaselines):
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print('monoatomic system: variation of the nuclear charge')
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else:
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print('polyatomic system: variation is on the distance')
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for x in scan:
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(DuckExit,DuckOut,DuckErr)=runDuck(mol,basis,x,molbaselines,molbase,basisbase)
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#print DuckOut on file or not
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if "Outputs" in options:
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outdat=options["Outputs"]
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if 'DuckOutput' in outdat:
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outopt=outdat["DuckOutput"]
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if outopt['Enabled']:
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if outopt['Multiple']:
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duckoutf=outfile(outopt,"DuckOutput",x)
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else:
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if x==scan[0]:
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duckoutf=outfile(outdat,"DuckOutput")
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duckoutf.write('Z' if isMononucle(molbaselines) else 'Distance'+' '+str(x)+os.linesep+os.linesep)
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duckoutf.write(DuckOut)
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if outopt['Multiple']:
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duckoutf.close()
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print("GoDuk exit code " + str(DuckExit))
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if DuckExit !=0:
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#if GoDuck is not happy
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print(DuckErr)
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sys.exit(-1)
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#get all data for the method
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for method,methoddatas in mymethods.iteritems():
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isnan=False
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if '{0}' in method:
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if "index" in methoddatas:
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methodheaders=[method.format(str(x)) for x in methoddatas['Index']]
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else:
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try:
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print(method)
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reglist=re.findall('(\d+)'.join([re.escape(s) for s in method.split('{0}')]),DuckOut)
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print(reglist)
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final=max([(int(i[0]) if type(i) is tuple else int(i)) for i in reglist])
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print(final)
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methodheaders=[method.format(str(final))]
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except:
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isnan=True
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methodheaders=[None]
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method=method.replace('{0}','')
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else:
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methodheaders=list([method])
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for methodheader in methodheaders:
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if len(methodheaders)!=1:
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method=methodheader
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lbldic=methoddatas['Labels']
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print(methodheader)
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if methodheader is None:
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methodtxt=''
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else:
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it=itertools.dropwhile(lambda line: methodheader + ' calculation' not in line , DuckOut.splitlines())
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it=itertools.takewhile(lambda line: 'Total CPU time for ' not in line, it)
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methodtxt=os.linesep.join(it)
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if errorconvstring in methodtxt:
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print(colored(' '.join([method, errorconvstring, '!!!!!']),'red'))
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isnan=True
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if methodtxt=='':
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print(colored('No data' +os.linesep+ 'RHF scf not converged or method not enabled','red'))
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isnan=True
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#find the expected values
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for label,labeldatas in lbldic.iteritems():
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if type(labeldatas) is dict:
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indexed=('Index' in labeldatas)
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enabled=labeldatas['Enabled']
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graph=labeldatas['Graph'] if 'Graph' in labeldatas else 1
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else:
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enabled=labeldatas
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graph=1
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indexed=False
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if enabled:
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if graph not in graphdic:
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graphdic[graph]=OrderedDict()
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y=graphdic[graph]
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if not indexed:
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v=np.nan
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print(method)
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print(label)
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if not isnan:
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try:
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m=re.search('\s+'.join([re.escape(w) for w in label.split()]) + "\s+(?:"+re.escape("(eV):")+"\s+)?(?:=\s+)?(-?\d+.?\d*)",methodtxt)
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v=m.group(1)
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except:
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v=np.nan
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addvalue(y,(method,label),x,v)
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else:
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startindex=-1
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columnindex=-1
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linedtxt=methodtxt.split(os.linesep)
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for n,line in enumerate(linedtxt):
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if all(x in line for x in ['|',' '+label+' ','#']):
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startindex=n+2
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columnindex=[s.strip() for s in line.split('|')].index(label)
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break
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with open(os.path.join(GetDuckDir(),'input','molecule'),'r') as molfile:
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molfile.readline()
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line=molfile.readline()
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nel=int(line.split()[1])
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print(nel)
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HOMO=int(nel/2)
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HO=HOMO
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LUMO=HOMO+1
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BV=LUMO
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for i in labeldatas['Index']:
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v=np.nan
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if type(i) is str or type(i) is unicode:
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ival=eval(i)
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if type(ival) is not int:
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print('Index '+ str(i) + 'must be integer')
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sys.exit(-2)
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else:
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ival=i
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v=np.nan
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if not isnan:
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try:
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if startindex!=-1 and columnindex!=-1:
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line=linedtxt[startindex+ival-1]
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v=float(line.split('|')[columnindex].split()[0])
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print(method)
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print(label)
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print(i)
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else:
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v=np.nan
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except:
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v=np.nan
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key=(method,label,i)
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addvalue(y,key,x,v)
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tpl=(x,scan.tolist().index(x)+1,len(y[key]))
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print(tpl)
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if tpl[1]-tpl[2]:
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sys.exit()
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#define graph grid
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maxgraph=max(graphdic.keys())
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maxrow=int(round(sqrt(maxgraph)))
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maxcol=int(ceil(float(maxgraph)/float(maxrow)))
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#define label ls
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for graph,y in graphdic.iteritems():
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datas=list()
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datas.append(["#x"]+scan.tolist())
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if len(y.keys())!=0:
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plt.subplot(maxrow,maxcol,graph)
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plt.xlabel('Z' if isMononucle(molbaselines) else 'Distance '+mol)
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ylbls=list([basis])
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for i in range(0,2):
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lst=list(set([key[i] for key in y.keys()]))
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if len(lst)==1:
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ylbls.append(lst[0])
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plt.ylabel(' '.join(ylbls))
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print('Legend')
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print(list(y.keys()))
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for key,values in y.iteritems():
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legend=list()
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for el in key[0:2]:
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if el not in ylbls:
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legend.append(el)
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if len(key)>2:
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legend.append(str(key[2]))
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#plot curves
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lbl=' '.join(legend)
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plt.plot(scan,y[key],'-o',label=lbl)
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#print("min",x[y.index(min(y))]/2)
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#generate legends
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plt.legend()
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dataout=False
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if "Outputs" in options:
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outputs=options['Outputs']
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if "DataOutput" in outputs:
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DataOutput=outputs['DataOutput']
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dataout=DataOutput['Enabled']
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if dataout:
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fmtlegendf='{0}({1})'
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datas.append([fmtlegendf.format("y",lbl)]+y[key])
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if dataout:
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csvdatas=zip(*datas)
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with outfile(outputs,"DataOutput",graph) as csvf:
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writer = csv.writer(csvf, delimiter=' ')
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writer.writerow(['#']+ylbls)
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writer.writerows(csvdatas)
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#show graph
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if "Outputs" in options:
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outputs=options['Outputs']
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if "FigureOutput" in outputs:
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figout=outputs["FigureOutput"]
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if figout["Enabled"]:
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plt.savefig(figout['Path'])
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plt.show()
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if __name__ == '__main__':
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parser=argparse.ArgumentParser()
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parser.add_argument("mol",nargs='?', help="molecule to compute",type=str)
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parser.add_argument("-c,--copy", help="Copy sample option file",action="store_true",dest="copy")
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args = parser.parse_args()
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if len(sys.argv)==1:
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parser.print_help()
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else:
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if args.copy:
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copy2(os.path.join(GetDuckDir(),"PyOptions.template.json"),"PyOptions.json")
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if args.mol is not None:
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os.system("vim PyOptions.json")
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if args.mol is not None:
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main(args.mol)
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