mirror of
https://github.com/pfloos/quack
synced 2024-11-05 13:43:51 +01:00
322 lines
13 KiB
Plaintext
322 lines
13 KiB
Plaintext
|
#!/usr/bin/env python2
|
||
|
|
import sys
|
||
|
|
from termcolor import colored
|
||
|
|
import shlex
|
||
|
|
from subprocess import Popen, PIPE
|
||
|
|
import itertools
|
||
|
|
import re
|
||
|
|
import numpy as np
|
||
|
|
import os
|
||
|
|
from shutil import copy2
|
||
|
|
import matplotlib.pyplot as plt
|
||
|
|
import json
|
||
|
|
from math import *
|
||
|
|
from collections import OrderedDict
|
||
|
|
import csv
|
||
|
|
import argparse
|
||
|
|
def GetDuckDir():
|
||
|
|
return os.path.dirname(os.path.realpath(__file__))
|
||
|
|
|
||
|
|
def nNucl(molbaselines):
|
||
|
|
return float(molbaselines[1].split()[0])
|
||
|
|
|
||
|
|
def isMononucle(molbaselines):
|
||
|
|
return nNucl(molbaselines)==1
|
||
|
|
|
||
|
|
def openfileindir(path,readwrite):
|
||
|
|
mydir=os.path.dirname(path)
|
||
|
|
if not os.path.exists(mydir) and mydir!="":
|
||
|
|
os.makedirs(mydir)
|
||
|
|
return open(path,readwrite)
|
||
|
|
def outfile(Outdic,item,index=None):
|
||
|
|
itemdata=Outdic[item]
|
||
|
|
if itemdata["Enabled"]:
|
||
|
|
fmt=itemdata["Format"]
|
||
|
|
if index is not None:
|
||
|
|
filename=fmt.format(index)
|
||
|
|
else:
|
||
|
|
filename=fmt
|
||
|
|
if "Parent" in Outdic:
|
||
|
|
path=os.path.join(Outdic["Parent"],filename)
|
||
|
|
else:
|
||
|
|
path=filename
|
||
|
|
return openfileindir(path,'w')
|
||
|
|
else:
|
||
|
|
return
|
||
|
|
|
||
|
|
def runDuck(mol,basis,x,molbaselines,molbase,basisbase):
|
||
|
|
#gennerate molecule file
|
||
|
|
currdir=os.getcwd()
|
||
|
|
os.chdir(GetDuckDir())
|
||
|
|
molname='.'.join([mol,str(x)])
|
||
|
|
lstw=list()
|
||
|
|
for i,line in enumerate(molbaselines):
|
||
|
|
if i<3:
|
||
|
|
lstw.append(line)
|
||
|
|
else:
|
||
|
|
if isMononucle(molbaselines):
|
||
|
|
if i==3:
|
||
|
|
lstw.append(' '.join([str(x)]+line.split()[1:]))
|
||
|
|
else:
|
||
|
|
v=[float(abs(x))/float(2),float(-abs(x)/float(2))]
|
||
|
|
val=v[i-3]
|
||
|
|
lstw.append(' '.join([line.split()[0],'0.','0.',str(val)]))
|
||
|
|
junkfiles=list()
|
||
|
|
with open(molbase+molname,'w') as n:
|
||
|
|
junkfiles.append(n.name)
|
||
|
|
n.write(os.linesep.join(lstw))
|
||
|
|
#Copy basis
|
||
|
|
basisfile=basisbase+'.'.join([mol,basis])
|
||
|
|
newbasisfile=basisbase+'.'.join([molname,basis])
|
||
|
|
copy2(basisfile,newbasisfile)
|
||
|
|
junkfiles.append(newbasisfile)
|
||
|
|
#start child process Goduck
|
||
|
|
cmd=" ".join(["./GoDuck",molname, basis])
|
||
|
|
Duck=Popen(shlex.split(cmd),stdout=PIPE)
|
||
|
|
(DuckOut, DuckErr) = Duck.communicate()
|
||
|
|
excode=Duck.wait()
|
||
|
|
for junk in junkfiles:
|
||
|
|
os.remove(junk)
|
||
|
|
os.chdir(currdir)
|
||
|
|
return (excode,DuckOut,DuckErr)
|
||
|
|
|
||
|
|
def addvalue(dic,key,x,y):
|
||
|
|
if key not in dic:
|
||
|
|
dic[key]=list()
|
||
|
|
dic[key].append(y)
|
||
|
|
print(key)
|
||
|
|
print(x,y)
|
||
|
|
|
||
|
|
def main(mol):
|
||
|
|
#get basepath for files
|
||
|
|
molbase='examples/molecule.'
|
||
|
|
basisbase=molbase.replace('molecule','basis')
|
||
|
|
with open('PyOptions.json','r') as jfile:
|
||
|
|
options=json.loads(jfile.read())
|
||
|
|
basis=str(options['Basis'])
|
||
|
|
#Get mehtod to analyse
|
||
|
|
methodsdic=options['Methods']
|
||
|
|
#Get datas to analyse in this method
|
||
|
|
scandic=options['Scan']
|
||
|
|
scan=np.arange(scandic['Start'],scandic['Stop']+scandic['Step'],scandic['Step'])
|
||
|
|
print(scan)
|
||
|
|
mymethods=dict()
|
||
|
|
alllabels=list()
|
||
|
|
for method,methoddatas in methodsdic.iteritems():
|
||
|
|
if methoddatas['Enabled']:
|
||
|
|
mymethods[method]=methoddatas
|
||
|
|
for label,labeldatas in methoddatas['Labels'].iteritems():
|
||
|
|
if type(labeldatas) is dict:
|
||
|
|
enabled=labeldatas['Enabled']
|
||
|
|
else:
|
||
|
|
enabled=labeldatas
|
||
|
|
if enabled and label not in alllabels:
|
||
|
|
alllabels.append(label)
|
||
|
|
graphdic=dict()
|
||
|
|
errorconvstring="Convergence failed"
|
||
|
|
with open(os.path.join(GetDuckDir(),molbase+mol),'r') as b:
|
||
|
|
molbaselines=b.read().splitlines()
|
||
|
|
if isMononucle(molbaselines):
|
||
|
|
print('monoatomic system: variation of the nuclear charge')
|
||
|
|
else:
|
||
|
|
print('polyatomic system: variation is on the distance')
|
||
|
|
for x in scan:
|
||
|
|
(DuckExit,DuckOut,DuckErr)=runDuck(mol,basis,x,molbaselines,molbase,basisbase)
|
||
|
|
#print DuckOut on file or not
|
||
|
|
if "Outputs" in options:
|
||
|
|
outdat=options["Outputs"]
|
||
|
|
if 'DuckOutput' in outdat:
|
||
|
|
outopt=outdat["DuckOutput"]
|
||
|
|
if outopt['Enabled']:
|
||
|
|
if outopt['Multiple']:
|
||
|
|
duckoutf=outfile(outopt,"DuckOutput",x)
|
||
|
|
else:
|
||
|
|
if x==scan[0]:
|
||
|
|
duckoutf=outfile(outdat,"DuckOutput")
|
||
|
|
duckoutf.write('Z' if isMononucle(molbaselines) else 'Distance'+' '+str(x)+os.linesep+os.linesep)
|
||
|
|
duckoutf.write(DuckOut)
|
||
|
|
if outopt['Multiple']:
|
||
|
|
duckoutf.close()
|
||
|
|
print("GoDuk exit code " + str(DuckExit))
|
||
|
|
if DuckExit !=0:
|
||
|
|
#if GoDuck is not happy
|
||
|
|
print(DuckErr)
|
||
|
|
sys.exit(-1)
|
||
|
|
#get all data for the method
|
||
|
|
for method,methoddatas in mymethods.iteritems():
|
||
|
|
isnan=False
|
||
|
|
if '{0}' in method:
|
||
|
|
if "index" in methoddatas:
|
||
|
|
methodheaders=[method.format(str(x)) for x in methoddatas['Index']]
|
||
|
|
else:
|
||
|
|
try:
|
||
|
|
print(method)
|
||
|
|
reglist=re.findall('(\d+)'.join([re.escape(s) for s in method.split('{0}')]),DuckOut)
|
||
|
|
print(reglist)
|
||
|
|
final=max([(int(i[0]) if type(i) is tuple else int(i)) for i in reglist])
|
||
|
|
print(final)
|
||
|
|
methodheaders=[method.format(str(final))]
|
||
|
|
except:
|
||
|
|
isnan=True
|
||
|
|
methodheaders=[None]
|
||
|
|
method=method.replace('{0}','')
|
||
|
|
else:
|
||
|
|
methodheaders=list([method])
|
||
|
|
for methodheader in methodheaders:
|
||
|
|
if len(methodheaders)!=1:
|
||
|
|
method=methodheader
|
||
|
|
lbldic=methoddatas['Labels']
|
||
|
|
print(methodheader)
|
||
|
|
if methodheader is None:
|
||
|
|
methodtxt=''
|
||
|
|
else:
|
||
|
|
it=itertools.dropwhile(lambda line: methodheader + ' calculation' not in line , DuckOut.splitlines())
|
||
|
|
it=itertools.takewhile(lambda line: 'Total CPU time for ' not in line, it)
|
||
|
|
methodtxt=os.linesep.join(it)
|
||
|
|
if errorconvstring in methodtxt:
|
||
|
|
print(colored(' '.join([method, errorconvstring, '!!!!!']),'red'))
|
||
|
|
isnan=True
|
||
|
|
if methodtxt=='':
|
||
|
|
print(colored('No data' +os.linesep+ 'RHF scf not converged or method not enabled','red'))
|
||
|
|
isnan=True
|
||
|
|
#find the expected values
|
||
|
|
for label,labeldatas in lbldic.iteritems():
|
||
|
|
if type(labeldatas) is dict:
|
||
|
|
indexed=('Index' in labeldatas)
|
||
|
|
enabled=labeldatas['Enabled']
|
||
|
|
graph=labeldatas['Graph'] if 'Graph' in labeldatas else 1
|
||
|
|
else:
|
||
|
|
enabled=labeldatas
|
||
|
|
graph=1
|
||
|
|
indexed=False
|
||
|
|
if enabled:
|
||
|
|
if graph not in graphdic:
|
||
|
|
graphdic[graph]=OrderedDict()
|
||
|
|
y=graphdic[graph]
|
||
|
|
if not indexed:
|
||
|
|
v=np.nan
|
||
|
|
print(method)
|
||
|
|
print(label)
|
||
|
|
if not isnan:
|
||
|
|
try:
|
||
|
|
m=re.search('\s+'.join([re.escape(w) for w in label.split()]) + "\s+(?:"+re.escape("(eV):")+"\s+)?(?:=\s+)?(-?\d+.?\d*)",methodtxt)
|
||
|
|
v=m.group(1)
|
||
|
|
except:
|
||
|
|
v=np.nan
|
||
|
|
addvalue(y,(method,label),x,v)
|
||
|
|
else:
|
||
|
|
startindex=-1
|
||
|
|
columnindex=-1
|
||
|
|
linedtxt=methodtxt.split(os.linesep)
|
||
|
|
for n,line in enumerate(linedtxt):
|
||
|
|
if all(x in line for x in ['|',' '+label+' ','#']):
|
||
|
|
startindex=n+2
|
||
|
|
columnindex=[s.strip() for s in line.split('|')].index(label)
|
||
|
|
break
|
||
|
|
with open(os.path.join(GetDuckDir(),'input','molecule'),'r') as molfile:
|
||
|
|
molfile.readline()
|
||
|
|
line=molfile.readline()
|
||
|
|
nel=int(line.split()[1])
|
||
|
|
print(nel)
|
||
|
|
HOMO=int(nel/2)
|
||
|
|
HO=HOMO
|
||
|
|
LUMO=HOMO+1
|
||
|
|
BV=LUMO
|
||
|
|
for i in labeldatas['Index']:
|
||
|
|
v=np.nan
|
||
|
|
if type(i) is str or type(i) is unicode:
|
||
|
|
ival=eval(i)
|
||
|
|
if type(ival) is not int:
|
||
|
|
print('Index '+ str(i) + 'must be integer')
|
||
|
|
sys.exit(-2)
|
||
|
|
else:
|
||
|
|
ival=i
|
||
|
|
v=np.nan
|
||
|
|
if not isnan:
|
||
|
|
try:
|
||
|
|
if startindex!=-1 and columnindex!=-1:
|
||
|
|
line=linedtxt[startindex+ival-1]
|
||
|
|
v=float(line.split('|')[columnindex].split()[0])
|
||
|
|
print(method)
|
||
|
|
print(label)
|
||
|
|
print(i)
|
||
|
|
else:
|
||
|
|
v=np.nan
|
||
|
|
except:
|
||
|
|
v=np.nan
|
||
|
|
key=(method,label,i)
|
||
|
|
addvalue(y,key,x,v)
|
||
|
|
tpl=(x,scan.tolist().index(x)+1,len(y[key]))
|
||
|
|
print(tpl)
|
||
|
|
if tpl[1]-tpl[2]:
|
||
|
|
sys.exit()
|
||
|
|
#define graph grid
|
||
|
|
maxgraph=max(graphdic.keys())
|
||
|
|
maxrow=int(round(sqrt(maxgraph)))
|
||
|
|
maxcol=int(ceil(float(maxgraph)/float(maxrow)))
|
||
|
|
#define label ls
|
||
|
|
for graph,y in graphdic.iteritems():
|
||
|
|
datas=list()
|
||
|
|
datas.append(["#x"]+scan.tolist())
|
||
|
|
if len(y.keys())!=0:
|
||
|
|
plt.subplot(maxrow,maxcol,graph)
|
||
|
|
plt.xlabel('Z' if isMononucle(molbaselines) else 'Distance '+mol)
|
||
|
|
ylbls=list([basis])
|
||
|
|
for i in range(0,2):
|
||
|
|
lst=list(set([key[i] for key in y.keys()]))
|
||
|
|
if len(lst)==1:
|
||
|
|
ylbls.append(lst[0])
|
||
|
|
plt.ylabel(' '.join(ylbls))
|
||
|
|
print('Legend')
|
||
|
|
print(list(y.keys()))
|
||
|
|
for key,values in y.iteritems():
|
||
|
|
legend=list()
|
||
|
|
for el in key[0:2]:
|
||
|
|
if el not in ylbls:
|
||
|
|
legend.append(el)
|
||
|
|
if len(key)>2:
|
||
|
|
legend.append(str(key[2]))
|
||
|
|
#plot curves
|
||
|
|
lbl=' '.join(legend)
|
||
|
|
plt.plot(scan,y[key],'-o',label=lbl)
|
||
|
|
#print("min",x[y.index(min(y))]/2)
|
||
|
|
#generate legends
|
||
|
|
plt.legend()
|
||
|
|
dataout=False
|
||
|
|
if "Outputs" in options:
|
||
|
|
outputs=options['Outputs']
|
||
|
|
if "DataOutput" in outputs:
|
||
|
|
DataOutput=outputs['DataOutput']
|
||
|
|
dataout=DataOutput['Enabled']
|
||
|
|
if dataout:
|
||
|
|
fmtlegendf='{0}({1})'
|
||
|
|
datas.append([fmtlegendf.format("y",lbl)]+y[key])
|
||
|
|
if dataout:
|
||
|
|
csvdatas=zip(*datas)
|
||
|
|
with outfile(outputs,"DataOutput",graph) as csvf:
|
||
|
|
writer = csv.writer(csvf, delimiter=' ')
|
||
|
|
writer.writerow(['#']+ylbls)
|
||
|
|
writer.writerows(csvdatas)
|
||
|
|
#show graph
|
||
|
|
if "Outputs" in options:
|
||
|
|
outputs=options['Outputs']
|
||
|
|
if "FigureOutput" in outputs:
|
||
|
|
figout=outputs["FigureOutput"]
|
||
|
|
if figout["Enabled"]:
|
||
|
|
plt.savefig(figout['Path'])
|
||
|
|
plt.show()
|
||
|
|
if __name__ == '__main__':
|
||
|
|
parser=argparse.ArgumentParser()
|
||
|
|
parser.add_argument("mol",nargs='?', help="molecule to compute",type=str)
|
||
|
|
parser.add_argument("-c,--copy", help="Copy sample option file",action="store_true",dest="copy")
|
||
|
|
args = parser.parse_args()
|
||
|
|
if len(sys.argv)==1:
|
||
|
|
parser.print_help()
|
||
|
|
else:
|
||
|
|
if args.copy:
|
||
|
|
copy2(os.path.join(GetDuckDir(),"PyOptions.template.json"),"PyOptions.json")
|
||
|
|
if args.mol is not None:
|
||
|
|
os.system("vim PyOptions.json")
|
||
|
|
if args.mol is not None:
|
||
|
|
main(args.mol)
|