def readline_and_strip_and_skip(f, line, z):
line1 = line.strip()
line_lt = line1.split(',')
while line:
if (not line1):
line = f.readline()
line1 = line.strip()
line_lt = line1.split(',')
elif line1 and line1[0] == '!':
line = f.readline()
line1 = line.strip()
line_lt = line1.split(',')
elif line1 and line1[0] != '!' and z != ele.atomicnumber_reg(
line_lt[1]):
line = f.readline()
line1 = line.strip()
line_lt = line1.split(',')
elif line1 and line1[0] != '!' and z == ele.atomicnumber_reg(
line_lt[1]) and line_lt[0] == 'ecp':
line = f.readline()
line1 = line.strip()
line_lt = line1.split(',')
else:
return (line, line1)
else:
return (line, line1)
def read_molpro_library_basis(basis, f, am, z, basis_contr_lt):
while True:
line = f.readline()
#error control
if len(line) == 0:
print 'There is no such element in this file! \n 1. Continue 2. Exit \n'
Ctrl_local_exit = raw_input('')
if Ctrl_local_exit == '2':
sys.exit(1)
elif Ctrl_local_exit == '1':
f.close()
f = file(Usr_in_basis_name, 'r')
Gbl_Z = raw_input(
'Please input what is the atomic number of the element that you want: '
)
z = int(Gbl_Z)
else:
print 'Wrong input, error exit!'
sys.exit(1)
#end of error control
line_lt = line.split(' ')
line_lt = filter(None, line_lt)
if line[0] != '!' and line[0] != '*' and len(
line_lt) > 2 and z == ele.atomicnumber_reg(line_lt[0]):
basis.molpro_library_basis_in(f, line, am, basis_contr_lt)
f.close()
return True
def molpro_library_basis_in(self,The_File,line,am,contr):
linelt=line.split(' ')
linelt=filter(None,linelt)
while line and self.Z==ele.atomicnumber_reg(linelt[0]):
if linelt[1] in am:
i='spdfghiklmn'.index(linelt[1])
line=self.molpro_library_basis_in_AG(The_File,line,self.LT_EXP_COE_LT[i],linelt[1],contr)
for j in range(0,len(self.LT_EXP_COE_LT[i])):
self.LT_EXP_LT[i].append(self.LT_EXP_COE_LT[i][j][0])
self.LT_COE_LT[i].append(self.LT_EXP_COE_LT[i][j][1:])
tmp_lt=map(list,zip(*self.LT_COE_LT[i]))
del self.LT_COE_LT[i][:]
self.LT_COE_LT[i].extend(tmp_lt)
linelt=line.split(' ')
linelt=filter(None,linelt)
else:
line=The_File.readline()
linelt=line.split(' ')
linelt=filter(None,linelt)
while line and self.Z!=ele.atomicnumber_reg(linelt[0]):
line=The_File.readline()
linelt=line.split(' ')
linelt=filter(None,linelt)
def molpro_regular_basis_in(self,The_File,linein,line_lt,lbr_am):
'''Read molpro_regular basis set file'''
line=linein
if line and ele.atomicnumber_reg(line_lt[1])==self.Z:
if line_lt[0]=='s':
line=self.molpro_regular_basis_in_AG(The_File,line,self.LT_EXP_S,self.LT_COE_S,self.LT_EXP_COE_S,'s')
return line
elif line_lt[0]=='p':
line=self.molpro_regular_basis_in_AG(The_File,line,self.LT_EXP_P,self.LT_COE_P,self.LT_EXP_COE_P,'p')
return line
elif line_lt[0]=='d':
line=self.molpro_regular_basis_in_AG(The_File,line,self.LT_EXP_D,self.LT_COE_D,self.LT_EXP_COE_D,'d')
return line
elif line_lt[0]=='f':
line=self.molpro_regular_basis_in_AG(The_File,line,self.LT_EXP_F,self.LT_COE_F,self.LT_EXP_COE_F,'f')
return line
elif line_lt[0]=='g':
line=self.molpro_regular_basis_in_AG(The_File,line,self.LT_EXP_G,self.LT_COE_G,self.LT_EXP_COE_G,'g')
return line
elif line_lt[0]=='h':
line=self.molpro_regular_basis_in_AG(The_File,line,self.LT_EXP_H,self.LT_COE_H,self.LT_EXP_COE_H,'h')
return line
elif line_lt[0]=='i':
line=self.molpro_regular_basis_in_AG(The_File,line,self.LT_EXP_I,self.LT_COE_I,self.LT_EXP_COE_I,'i')
return line
elif line_lt[0]=='k':
line=self.molpro_regular_basis_in_AG(The_File,line,self.LT_EXP_K,self.LT_COE_K,self.LT_EXP_COE_K,'k')
return line
elif line_lt[0]=='l':
line=self.molpro_regular_basis_in_AG(The_File,line,self.LT_EXP_L,self.LT_COE_L,self.LT_EXP_COE_L,'l')
return line
elif line_lt[0]=='m':
line=self.molpro_regular_basis_in_AG(The_File,line,self.LT_EXP_M,self.LT_COE_M,self.LT_EXP_COE_M,'m')
return line
elif line_lt[0]=='n':
line=self.molpro_regular_basis_in_AG(The_File,line,self.LT_EXP_N,self.LT_COE_N,self.LT_EXP_COE_N,'n')
return line
else:
return line
else:
return line
#end of error control
try:
if basis:
pass
except NameError:
basis = Classes.Basis_set(z)
pre_am = ''
while line and line_lt[1]:
if not Nest.is_number(line_lt[2]):
library_basis_sc_lt = line_lt
library_basis_lt = library_basis_sc_lt[:3]
library_basis_contr_lt = library_basis_sc_lt[3:]
lbr_am = library_basis_lt[0]
pre_am = lbr_am
lbr_element = library_basis_lt[1]
lbr_element_atomicnumber = ele.atomicnumber_reg(
lbr_element)
lbr_basis_name = library_basis_lt[2].lower()
try:
fd = file(
Usr_in_basis_name_default_dir + lbr_basis_name +
'.libmol', 'r')
except IOError:
lbr_basis_name = lbr_basis_name.replace('-', '_')
try:
fd = file(
Usr_in_basis_name_default_dir +
lbr_basis_name + '.libmol', 'r')
except IOError:
print Usr_in_basis_name_default_dir + lbr_basis_name + '.libmol' + ' does not exist! Select a solution: ' + ' \n 1. Continue (Manually specify the default library file ) 2. Exit \n'
Ctrl_local_exit = raw_input('')
if Ctrl_local_exit == '2':
def molpro_regular_basis_in_AG(self,f,tmpline,basislt_EXP,basislt_COE,basislt_EXP_COE,AM):
'''Read molpro_regular basis set file for each angular momentum.'''
killslash_lt=tmpline.split('\n')
tmpline1=killslash_lt[0]
print self.element_name
print AM
while tmpline1 and tmpline1[0]==AM:
tmpline1_lt=tmpline1.split(',')
if ele.atomicnumber_reg(tmpline1_lt[1])!=self.Z:
tmpline=f.readline()
if basislt_COE:
num1=len(basislt_COE[0])
else:
num1=0
break
if tmpline1_lt[0]==AM:
# read in exp
for item in tmpline1_lt[2:]:
basislt_EXP.append(float(item))
tmpline=f.readline()
killslash_lt=tmpline.split('\n')
tmpline1=killslash_lt[0]
num2=len(basislt_EXP)
#skip the comment lines
while tmpline1 and tmpline1[0]=='!':
tmpline=f.readline()
killslash_lt=tmpline.split('\n')
tmpline1=killslash_lt[0]
while tmpline1 and tmpline1[0]=='c':
# read in coeff s
tmpline1_lt=tmpline1.split(',')
coe_mark_lt=tmpline1_lt[1].split('.')
coe_tmp=[]
for item in tmpline1_lt[2:]:
coe_tmp.append(float(item))
for count_i in range(1,int(coe_mark_lt[0])):
coe_tmp.insert(0,0)
for count_i in range(int(coe_mark_lt[1]),num2):
coe_tmp.append(0)
basislt_COE.append(coe_tmp)
tmpline=f.readline()
killslash_lt=tmpline.split('\n')
tmpline1=killslash_lt[0]
# skip the comment lines
while tmpline1 and tmpline1[0]=='!':
tmpline=f.readline()
killslash_lt=tmpline.split('\n')
tmpline1=killslash_lt[0]
if basislt_COE:
num1=len(basislt_COE[0])
else:
num1=0
if num1!=num2:
for count_i in range(0,num2-num1):
for item in basislt_COE:
item.append(0)
coe_tmp=[]
for count_j in range(0,num1+count_i):
coe_tmp.append(0)
coe_tmp.append(1)
basislt_COE.append(coe_tmp)
tmp_lt=map(list,zip(*basislt_COE))
del basislt_EXP_COE[:]
for i,item in enumerate(tmp_lt):
item=[item]
for j,jtem in enumerate(tmp_lt):
if i==j:
basislt_EXP_COE.append(item+jtem)
return tmpline