93 lines
2.6 KiB
Python
93 lines
2.6 KiB
Python
#!/usr/bin/env python3
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import os
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import sys
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# First argument is the EZFIO file
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# It reads a file EZFIO_point_charges.xyz written in this way:
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# charge x y z (Angstrom)
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# for all charges
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def zip_in_ezfio(ezfio,tmp):
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tmpzip=tmp+".gz"
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cmdzip="gzip -c "+tmp+" > "+tmpzip
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os.system(cmdzip)
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os.system("rm "+tmp)
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cmdmv="mv "+tmpzip+" "+EZFIO+"/nuclei/"+tmpzip
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os.system(cmdmv)
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def mv_in_ezfio(ezfio,tmp):
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cmdmv="mv "+tmp+" "+EZFIO+"/nuclei/"+tmp
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os.system(cmdmv)
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##Getting the EZFIO
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EZFIO=sys.argv[1]
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EZFIO=EZFIO.replace("/", "")
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print(EZFIO)
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# Reading the point charges and convert the Angstrom geometry in Bohr for QP
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f = open(EZFIO+'_point_charges.xyz','r')
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lines = f.readlines()
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convert_angs_to_bohr=1.8897259885789233
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n_charges=0
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coord_x=[]
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coord_y=[]
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coord_z=[]
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charges=[]
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for line in lines:
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data = line.split()
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if(len(data)>0):
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n_charges += 1
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charges.append(str(data[0]))
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coord_x.append(str(convert_angs_to_bohr*float(data[1])))
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coord_y.append(str(convert_angs_to_bohr*float(data[2])))
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coord_z.append(str(convert_angs_to_bohr*float(data[3])))
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# Write the file containing the number of charges and set in EZFIO folder
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tmp="n_pts_charge"
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fncharges = open(tmp,'w')
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fncharges.write(" "+str(n_charges)+'\n')
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fncharges.close()
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mv_in_ezfio(EZFIO,tmp)
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# Write the file containing the charges and set in EZFIO folder
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tmp="pts_charge_z"
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fcharges = open(tmp,'w')
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fcharges.write(" 1\n")
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fcharges.write(" "+str(n_charges)+'\n')
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for i in range(n_charges):
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fcharges.write(charges[i]+'\n')
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fcharges.close()
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zip_in_ezfio(EZFIO,tmp)
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# Write the file containing the charge coordinates and set in EZFIO folder
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tmp="pts_charge_coord"
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fcoord = open(tmp,'w')
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fcoord.write(" 2\n")
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if(n_charges < 10):
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fcoord.write(" "+str(n_charges)+' 3\n')
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elif(n_charges <100):
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fcoord.write(" "+str(n_charges)+' 3\n')
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elif(n_charges <1000):
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fcoord.write(" "+str(n_charges)+' 3\n')
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elif(n_charges <10000):
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fcoord.write(" "+str(n_charges)+' 3\n')
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elif(n_charges <100000):
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fcoord.write(" "+str(n_charges)+' 3\n')
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elif(n_charges <1000000):
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fcoord.write(" "+str(n_charges)+' 3\n')
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elif(n_charges <10000000):
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fcoord.write(" "+str(n_charges)+' 3\n')
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for i in range(n_charges):
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fcoord.write(' '+coord_x[i]+'\n')
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for i in range(n_charges):
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fcoord.write(' '+coord_y[i]+'\n')
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for i in range(n_charges):
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fcoord.write(' '+coord_z[i]+'\n')
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fcoord.close()
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zip_in_ezfio(EZFIO,tmp)
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