def all_distances(lines):
all_dist = []
blocks = get_blocks(lines)
for blockNum in range(0,len(blocks)):
xyz = sp.get_xyz(blocks[blockNum])
dis = sp.bonddistance(xyz)
all_dist.append(dis)
return all_dist
def all_angles(lines):
all_angles = []
blocks = get_blocks(lines)
for blockNum in range(0,len(blocks)):
xyz = sp.get_xyz(blocks[blockNum])
ang = sp.angles(xyz)
all_angles.append(ang)
return all_angles
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
def get_all_xyz(lines):
xyz = []
blocks = get_blocks(lines)
for blockNum in range(0,len(blocks)):
xyz.append(sp.get_xyz(blocks[blockNum]))
return xyz
def atoms(self): return sp.get_xyz(self.lines)[0]