def XPOL(L):
coord = L[0] + '.xyz'
main = L[1] # name of main fragment
N = int(L[2]) #no. of atoms in main fragment
scaling = float(L[3])
main_charge = int(L[4])
main_mult = int(L[5])
job = L[6]
root = L[7]
n = separate.separate(coord, main, N) # n is no. of water molecules
#replace_by_Q.replace_by_Q('uracil.xyz')
for i in range(n):
charge_water.pointcharge('Water' + str(i + 1) + '.xyz')
for i in range(n):
pc_water.pc_water(i + 1, n)
gen_main_pc.gen_main_pc(main, n)
#for i in range (n):
# gen_water_pc.gen_water_pc(i+1)
make_input.make_input(main + '.xyz', main + '.pc', main_charge, main_mult)
#for i in range (n):
# make_input.make_input('Water'+str(i+1)+'.xyz','Water'+str(i+1)+'.pc')
submit.submit(main + '_pc')
#for i in range (n):
# submit.submit('Water'+str(i+1)+'_pc')
En = energy.energy(main + '_pc.out')
print En
replace_by_Q.replace_by_Q(main + '.xyz', main +
'_pc.out') #update uracil charges from 1st iter
for i in range(n):
gen_water_pc.gen_water_pc(
i + 1, main,
N) #gen. pc files for water using updated uracil charges
for i in range(n):
make_input.make_input('Water' + str(i + 1) + '.xyz',
'Water' + str(i + 1) + '.pc')
for i in range(n):
submit.submit('Water' + str(i + 1) + '_pc')
Eo = 0
j = 0
epsilon = 0.000001
while (abs(Eo - En) >= epsilon):
j += 1
#print abs(Eo-En)
print 'Starting iteration no. ' + str(j)
Eo = En
replace_by_Q.replace_by_Q(main + '.xyz',
main + '_pc.out') #update uracil charges
for i in range(n):
replace_by_Q.replace_by_Q('Water' + str(i + 1) + '.xyz',
'Water' + str(i + 1) +
'_pc.out') #update water charges
for i in range(n):
pc_water.pc_water(i + 1, n)
gen_main_pc.gen_main_pc(main, n) #gen. uracil pc file
for i in range(n):
gen_water_pc.gen_water_pc(i + 1, main, N) #gen. water pc file
make_input.make_input(
main + '.xyz', main + '.pc', main_charge,
main_mult) #make input files with updated charges
for i in range(n):
make_input.make_input('Water' + str(i + 1) + '.xyz',
'Water' + str(i + 1) + '.pc')
submit.submit(main + '_pc') #submit input files
for i in range(n):
submit.submit('Water' + str(i + 1) + '_pc')
En = energy.energy(main + '_pc.out')
print "Energy of " + main + " after iteration " + str(
j) + " is " + str(En)
print "delta E = " + str(abs(Eo - En))
# print 'Converged energy = '+str(En)+'\n\n'
# print 'Scaling the water point charges'
# for i in range(n):
# replace_by_Q.replace_by_Q('Water'+str(i+1)+'.xyz','Water'+str(i+1)+'_pc.out',scaling)
# for i in range (n):
# pc_water.pc_water(i+1,n)
# gen_main_pc.gen_main_pc(main,n)#gen. main fragment pc file
print 'Submitting EOM file'
make_DLPNO_input.make_DLPNO_input(main + '.xyz', main + '.pc', job)
submit.submit(main + '_' + job + '_EOM_pc')
submit_CHELPG.submit(main + '_' + job + '_EOM_pc.root' + str(root) + '.' +
job)
#Regenerating water charges from EE/IP/EA calc. of main frag.
replace_by_Q_EOM.replace_by_Q_EOM(
main + '.xyz',
main + '_' + job + '_EOM_pc.root' + str(root) + '.' + job + '.out')
for i in range(n):
gen_water_pc.gen_water_pc(
i + 1, main,
N) #gen. pc files for water using updated uracil charges
for i in range(n):
make_input.make_input('Water' + str(i + 1) + '.xyz',
'Water' + str(i + 1) + '.pc')
for i in range(n):
submit.submit('Water' + str(i + 1) + '_pc')
for i in range(n):
replace_by_Q.replace_by_Q('Water' + str(i + 1) + '.xyz',
'Water' + str(i + 1) +
'_pc.out') #update water charges
#Now we have final water charges
gen_main_pc.gen_main_pc(main, n) #gen. main fragment pc file
print 'Final files generated'
print 'Submitting ' + job + ' file'
# make_DLPNO_input.make_DLPNO_input(main+'.xyz',main+'.pc')
# submit.submit(main+'_IP_DLPNO_pc')
# print 'IP values obtained'
make_DLPNO_input.make_DLPNO_input(main + '.xyz', main + '.pc', job)
submit.submit(main + '_' + job + '_EOM_pc')
return
def XPOL_n(L, iter_no):
coord = L[0] + '.xyz'
main = L[1] # name of main fragment
N = int(L[2]) #no. of atoms in main fragment
scaling = float(L[3])
main_charge = int(L[4])
main_mult = int(L[5])
job = L[6]
root = int(L[7])
f = open(main + '_time.txt', 'w')
f.close()
n = separate.separate(coord, main, N) # n is no. of water molecules
#replace_by_Q.replace_by_Q('uracil.xyz')
for i in range(n):
charge_water.pointcharge('Water' + str(i + 1) + '.xyz')
for i in range(n):
pc_water.pc_water(i + 1, n)
for k in range(iter_no):
gen_main_pc.gen_main_pc(main, n)
make_input.make_input(main + '.xyz', main + '.pc', main_charge,
main_mult)
submit.submit(main + '_pc')
time = comp_time.comp_time(main + '_pc.out') #comp. time calc.
s = 'Time taken for iteration number ' + str(
k + 1) + ' for main fragment :\n'
s += time + '\n\n'
f = open(main + '_time.txt', 'a')
f.write(s)
f.close()
En = energy.energy(main + '_pc.out')
f = open(main + '_energy.txt', 'a')
s = 'Energy after iteration no. ' + str(k +
1) + ' : ' + str(En) + '\n\n'
f.write(s)
f.close()
replace_by_Q.replace_by_Q(
main + '.xyz',
main + '_pc.out') #update uracil charges from 1st iter
for i in range(n):
gen_water_pc.gen_water_pc(
i + 1, main,
N) #gen. pc files for water using updated uracil charges
for i in range(n):
make_input.make_input('Water' + str(i + 1) + '.xyz',
'Water' + str(i + 1) + '.pc')
for i in range(n):
submit.submit('Water' + str(i + 1) + '_pc')
time = comp_time.comp_time('Water' + str(i + 1) +
'_pc.out') #comp. time calc.
s = 'Time taken for iteration number ' + str(
k + 1) + ' for water mol. no. ' + str(i + 1) + ' :\n'
s += time + '\n\n'
f = open(main + '_time.txt', 'a')
f.write(s)
f.close()
for i in range(n):
replace_by_Q.replace_by_Q('Water' + str(i + 1) + '.xyz',
'Water' + str(i + 1) +
'_pc.out') #update water charges
for i in range(n):
pc_water.pc_water(i + 1, n)
gen_main_pc.gen_main_pc(main, n) #gen. uracil pc file
# for i in range (n):
# gen_water_pc.gen_water_pc(i+1,main,N)#gen. water pc file
# make_input.make_input(main+'.xyz',main+'.pc',main_charge,main_mult)#make input files with updated charges
# for i in range (n):
# make_input.make_input('Water'+str(i+1)+'.xyz','Water'+str(i+1)+'.pc')
# submit.submit(main+'_pc')#submit input files
# for i in range (n):
# submit.submit('Water'+str(i+1)+'_pc')
# En = energy.energy(main+'_pc.out')
# print "Energy of "+main+" after iteration "+str(j)+" is "+str(En)
# print "delta E = " + str(abs(Eo-En))
## print 'Converged energy = '+str(En)+'\n\n'
## print 'Scaling the water point charges'
## for i in range(n):
## replace_by_Q.replace_by_Q('Water'+str(i+1)+'.xyz','Water'+str(i+1)+'_pc.out',scaling)
## for i in range (n):
## pc_water.pc_water(i+1,n)
## gen_main_pc.gen_main_pc(main,n)#gen. main fragment pc file
#############
# print 'Submitting EOM file'
# make_CIS_input.make_DLPNO_input(main+'.xyz',main+'.pc',job)
# submit.submit(main+'_'+job+'_CIS_pc')
#############
# submit_CHELPG.submit(main+'_'+job+'_CIS_pc-iroot'+str(root)+'.csp')
#Regenerating water charges from EE/IP/EA calc. of main frag.
# replace_by_Q_EOM.replace_by_Q_EOM(main+'.xyz',main+'_'+job+'_CIS_pc.root'+str(root)+'.'+job+'.out')
# for i in range (n):
# gen_water_pc.gen_water_pc(i+1,main,N)#gen. pc files for water using updated uracil charges
# for i in range (n):
# make_input.make_input('Water'+str(i+1)+'.xyz','Water'+str(i+1)+'.pc')
# for i in range (n):
# submit.submit('Water'+str(i+1)+'_pc')
# for i in range(n):
# replace_by_Q.replace_by_Q('Water'+str(i+1)+'.xyz','Water'+str(i+1)+'_pc.out')#update water charges
#Now we have final water charges
# gen_main_pc.gen_main_pc(main,n)#gen. main fragment pc file
# print 'Final files generated'
# print 'Submitting '+job+' file'
# make_DLPNO_input.make_DLPNO_input(main+'.xyz',main+'.pc')
# submit.submit(main+'_IP_DLPNO_pc')
# print 'IP values obtained'
# make_CIS_input.make_DLPNO_input(main+'.xyz',main+'.pc',job)
# submit.submit(main+'_'+job+'_CIS_pc')
# append_IROOT.append_IROOT(main+'_'+job+'_EOM_pc.out',main,root)
return En
n = separate.separate(N)
#replace_by_Q.replace_by_Q('uracil.xyz')
for i in range(n):
charge_water.pointcharge('Water' + str(i + 1) + '.xyz')
for i in range(n):
pc_water.pc_water(i + 1, n)
gen_uracil_pc.gen_uracil_pc(n)
#for i in range (n):
# gen_water_pc.gen_water_pc(i+1)
make_input.make_input('uracil.xyz', 'uracil.pc')
#for i in range (n):
# make_input.make_input('Water'+str(i+1)+'.xyz','Water'+str(i+1)+'.pc')
submit.submit('uracil_pc')
#for i in range (n):
# submit.submit('Water'+str(i+1)+'_pc')
En = energy.energy('uracil_pc.out')
print En
replace_by_Q.replace_by_Q(
'uracil.xyz', 'uracil_pc.out') #update uracil charges from 1st iter