def virt_orbtitals(self):
all_orbs = irclib.all_orbs(self.lines)
val_orbs = op.num_valence_orbs(self.atoms())
epsilon = []
Epsilon = {}
num_orbs = len(all_orbs[0][1])
Epsilon["Reaction Coordinate"] = self.rxCoord()
end = val_orbs
start = 1
for j in range(start,end):
for coord in range(0,len(all_orbs)):
epsilon.append(all_orbs[coord][1][j])
Epsilon[str(j)] = epsilon
epsilon = []
return Epsilon
def fukuiPlusMartinezVal(self):
print "-----------------------------------------------------------------"
print "\nProcessing Chi plus Valence.... \n\n"
occ_orb = sp.get_orbitals(self.lines)[0]
all_orb = sp.get_orbitals(self.lines)[2]
atom_list = sp.get_xyz(self.lines)[0]
valence_orbs = op.num_valence_orbs(atom_list)
molecule = self.fchkFile.split("_")[0]
chiplus=[]
denvirt=0.0
# Compute the denominator of chiplus
start = int(len(occ_orb))
end = start + int(valence_orbs)
for j in range(start,end):
ek_ej = float(all_orb[-1])-float(all_orb[j])
denvirt= denvirt + ek_ej
# Compute the division to get total chiplus
for i in range(start,end):
print i
chiplus_i=(float(all_orb[-1])-float(all_orb[i]))/denvirt
chiplus.append(chiplus_i)
if i==start:
cub_sum="F_plus_"+molecule+".cub"
input1="cubegen 0 MO="+str(i+1)+" "+self.fchkFile+" "+cub_sum+" 0 h"
commands.getstatusoutput(input1)
cubman.sq_cube(cub_sum)
cubman.mult_cube(cub_sum+"_sq",chiplus_i)
if i>start:
cub_out=molecule+"_"+str(i+1)+".cub"
input1="cubegen 0 MO="+str(i+1)+" "+self.fchkFile+" "+cub_out+" 0 h"
commands.getstatusoutput(input1)
cubman.sq_cube(cub_out)
cubman.mult_cube(cub_out+"_sq",chiplus_i)
cubman.sum_total(cub_sum+"_sq"+"_mult",cub_out+"_sq"+"_mult")
os.system("mv "+cub_sum+"_sq_mult"+" fukuiPlusIAPval.cub")
cub_final = "fukuiPlusIAPval.cub"
return cub_final
def fukuiMinusMartinezVal(self):
print "Processing Chi minus.... \n\n"
occ_orb = sp.get_orbitals(self.lines)[0]
atom_list = sp.get_xyz(self.lines)[0]
valence_orbs = op.num_valence_orbs(atom_list)
molecule = self.fchkFile.split("_")[0]
chiminus=[]
denocc=0.0
start = int(len(occ_orb)) - int(valence_orbs)
# Compute the denominator of chimins
for j in range(start,len(occ_orb)):
denocc=denocc+float(occ_orb[j])-float(occ_orb[start])
# Compute the division to get total chiminus
for i in range(start,len(occ_orb)):
chiminus_i = (float(occ_orb[i])-float(occ_orb[start]))/denocc
chiminus.append(chiminus_i)
# Calculo del cubo perteneciente al orbital i-esimo
if i==start:
print "Computing cube for orbital "+str(i)
cub_sum="F_minus_"+molecule+".cub"
input1="cubegen 0 MO="+str(i+1)+" "+self.fchkFile+" "+cub_sum+" 0 h"
commands.getstatusoutput(input1)
cubman.sq_cube(cub_sum)
cubman.mult_cube(cub_sum+"_sq",chiminus_i)
if i>start:
print "Computing cube for orbital "+str(i)
cub_out=molecule+"_"+str(i+1)+".cub"
input1="cubegen 0 MO="+str(i+1)+" "+self.fchkFile+" "+cub_out+" 0 h"
commands.getstatusoutput(input1)
cubman.sq_cube(cub_out)
cubman.mult_cube(cub_out+"_sq",chiminus_i)
cubman.sum_total(cub_sum+"_sq"+"_mult",cub_out+"_sq"+"_mult")
os.system("mv "+cub_sum+"_sq_mult"+" fukuiMinusIAPval.cub")
os.system("rm *cub_sq")
cub_final = "fukuiMinusIAPval.cub"
return cub_final