def fukuiPlusMartinez(self):
print "-----------------------------------------------------------------"
print "\nProcessing Chi plus.... \n\n"
occ_orb = sp.get_orbitals(self.lines)[0]
all_orb = sp.get_orbitals(self.lines)[2]
molecule = self.fchkFile.split("_")[0]
chiplus=[]
denvirt=0.0
# Compute the denominator of chiplus
start = int(len(occ_orb))
for j in range(start,len(all_orb)):
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,len(all_orb)):
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"+" fukuiPlusIAP.cub")
cub_final = "fukuiPlusIAP.cub"
return cub_final
def all_symm_orbs_energ(lines):
occ_energ_symm = {}
virt_energ_symm = {}
blocks = get_blocks(lines)
for blockNum in range(0,len(blocks)):
# Get the dictcionary with the number of orbitals and respective symmetries
Occ_dict_num = sp.get_symm_orbs(blocks[blockNum])[0]
Virt_dict_num = sp.get_symm_orbs(blocks[blockNum])[1]
#Get the orbital energies:
occ_energ = sp.get_orbitals(blocks[blockNum])[0]
virt_energ = sp.get_orbitals(blocks[blockNum])[1]
all_orbs = sp.get_orbitals(blocks[blockNum])[2]
#In the first block initialize the symm_orbital dictcionary
if blockNum == 0:
for itemNum in range(1,len(occ_energ)+1):
symm = Occ_dict_num[itemNum]
occ_energ_symm[symm] = []
for itemNum in range(len(occ_energ)+1, len(all_orbs)+1):
symm = Virt_dict_num[itemNum]
virt_energ_symm[symm] = []
# Appending the orbital energies of that point in the IRC with the orbtial enengies
for itemNum in range(1,len(occ_energ)+1):
symm = str(Occ_dict_num[itemNum])
occ_energ_symm[symm].append(occ_energ[itemNum-1])
for itemNum in range(len(occ_energ)+1, len(all_orbs)+1):
#print itemNum
symm = str(Virt_dict_num[itemNum])
virt_energ_symm[symm].append(virt_energ[itemNum-len(occ_energ)-1])
all_energ_symm = dict(occ_energ_symm.items() + virt_energ_symm.items())
return(all_energ_symm, occ_energ_symm, virt_energ_symm)
def LUMO(self):
virt_energy_list = sp.get_orbitals(self.lines)[1]
occ_energy_list = sp.get_orbitals(self.lines)[0]
lumo_energy = virt_energy_list[0]
lumo_number = int(len(occ_energy_list)) + 1
lumo = cubman.generate_cube(lumo_number,self.fchkpath, "LUMO.cube",True)
print "LUMO: "+str(lumo_number) + " "+lumo_energy
return lumo
def fukuiMinusMartinez(self):
print "Processing Chi minus.... \n\n"
occ_orb = sp.get_orbitals(self.lines)[0]
molecule = self.fchkFile.split("_")[0]
chiminus=[]
denocc=0.0
# Compute the denominator of chimins
for j in range(1,len(occ_orb)):
denocc=denocc+float(occ_orb[j])-float(occ_orb[0])
# Compute the division to get total chiminus
for i in range(0,len(occ_orb)):
chiminus_i = (float(occ_orb[i])-float(occ_orb[0]))/denocc
chiminus.append(chiminus_i)
# Calculo del cubo perteneciente al orbital i-esimo
if i==0:
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>0:
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"+" fukuiMinusIAP.cub")
os.system("rm *cub_sq")
cub_final = "fukuiMinusIAP.cub"
return cub_final
def H**O(self):
occ_energy_list = sp.get_orbitals(self.lines)[0]
homo_energy = occ_energy_list[-1]
homo_number = len(occ_energy_list)
h**o = cubman.generate_cube(homo_number,self.fchkpath, "H**O.cube",True)
print "H**O: "+str(homo_number) + " "+homo_energy
return h**o
def localHyperSoftnessFMOA(self):
occ_energy_list = sp.get_orbitals(self.lines)[0]
HOMO_enr = occ_energy_list[-1]
virt_energy_list = sp.get_orbitals(self.lines)[1]
LUMO_energy = virt_energy_list[0]
hard = float(HOMO_enr) - float(LUMO_energy)
print "HARDNESS: " + str(hard)
if not os.path.exists("lhsFMOA"):
os.makedirs("lhsFMOA")
os.chdir("lhsFMOA")
print "CALCULATING THE DUAL DESCRIPTOR"
dual = cubman.substract_cube(self.LUMO(), self.H**O())
os.system("mv "+dual+" dualFMOA.cub")
print "MULTIPlYING THE DUAL DESCRIPTOR"
HS = cubman.mult_cube("dualFMOA.cub", 1.0/(hard*hard))
os.system("mv "+HS+" lhsFMOA.cub")
os.chdir("../")
def allCubes(self):
all_orbs = sp.get_orbitals(self.lines)[2]
for orbNum in range(1,len(all_orbs)+1):
cubman.generate_cube(orbNum, self.fchkpath,"cube_"+str(orbNum)+".cub")
def all_orbs(lines):
all_orbs = []
blocks = get_blocks(lines)
for blockNum in range(0,len(blocks)):
all_orbs.append(sp.get_orbitals(blocks[blockNum]))
return all_orbs
