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Python3

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This commit is contained in:
Anthony Scemama 2020-01-27 20:29:00 +01:00
parent b502a622cc
commit 53b075a839
16 changed files with 192 additions and 192 deletions
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4
resultsFile/Modules/__init__.py
View File

@ -41,9 +41,9 @@ if "q5CostFile" in all:
for mod in all: for mod in all:
try: try:
exec 'from '+mod+' import *' exec('from '+mod+' import *')
except: except:
print "Error importing module", mod print("Error importing module", mod)
pass pass

88
resultsFile/Modules/gamessFile.py
View File

@ -26,7 +26,7 @@
import include from . import include
eval(include.code) eval(include.code)
import struct import struct
@ -54,13 +54,13 @@ class gamessFile(resultsFile):
local_vars = list(local_vars) local_vars = list(local_vars)
defined_vars = list(gamessFile_defined_vars) defined_vars = list(gamessFile_defined_vars)
exec get_data('date',"EXECUTION OF GAMESS BEGUN",'4:') in locals() exec(get_data('date',"EXECUTION OF GAMESS BEGUN",'4:'), locals())
exec get_data('machine',"Files used on the master node",'6:7') in locals() exec(get_data('machine',"Files used on the master node",'6:7'), locals())
exec get_data('version',"GAMESS VERSION",'4:8') in locals() exec(get_data('version',"GAMESS VERSION",'4:8'), locals())
exec get_data('num_proc',"MEMDDI DISTRIBUTED OVER",'3:4',"int") in locals() exec(get_data('num_proc',"MEMDDI DISTRIBUTED OVER",'3:4',"int"), locals())
exec get_data('num_elec',"NUMBER OF ELECTRONS", '4:5',"int") in locals() exec(get_data('num_elec',"NUMBER OF ELECTRONS", '4:5',"int"), locals())
exec get_data('charge',"CHARGE OF MOLECULE", '4:5',"float") in locals() exec(get_data('charge',"CHARGE OF MOLECULE", '4:5',"float"), locals())
exec get_data('nuclear_energy',"THE NUCLEAR REPULSION ENERGY", '5:6',"float") in locals() exec(get_data('nuclear_energy',"THE NUCLEAR REPULSION ENERGY", '5:6',"float"), locals())
def get_multiplicity(self): def get_multiplicity(self):
if self._multiplicity is None: if self._multiplicity is None:
@ -272,7 +272,7 @@ class gamessFile(resultsFile):
tokens = line.split()[0::2] tokens = line.split()[0::2]
values = line.split()[1::2] values = line.split()[1::2]
if len(tokens) != len(values): if len(tokens) != len(values):
print "error: ",line print("error: ",line)
sys.exit(0) sys.exit(0)
except IndexError: except IndexError:
pass pass
@ -407,7 +407,7 @@ class gamessFile(resultsFile):
buffer = self.text[pos].split() buffer = self.text[pos].split()
label = buffer[1] label = buffer[1]
assert label == i.name assert label == i.name
f = map(float,buffer[2:]) f = list(map(float,buffer[2:]))
self._gradient_energy.append(f) self._gradient_energy.append(f)
pos +=1 pos +=1
except IndexError: except IndexError:
@ -698,7 +698,7 @@ class gamessFile(resultsFile):
"xxxxyz", "xyyyyz", "xyzzzz", "xxxyyy", "xxxzzz", \ "xxxxyz", "xyyyyz", "xyzzzz", "xxxyyy", "xxxzzz", \
"yyyzzz", "xxxyyz", "xxxyzz", "xxyyyz", "xyyyzz", \ "yyyzzz", "xxxyyz", "xxxyzz", "xxyyyz", "xyyyzz", \
"xxyzzz", "xyyzzz" ] "xxyzzz", "xyyzzz" ]
map(normalize_basis_name,mylist) list(map(normalize_basis_name,mylist))
for i in mylist[:-1]: for i in mylist[:-1]:
basis[k][0] = i basis[k][0] = i
basis.insert(k,list(basis[k])) basis.insert(k,list(basis[k]))
@ -1451,17 +1451,17 @@ class gamessFile(resultsFile):
for i, j in local_vars: for i, j in local_vars:
if i not in defined_vars: if i not in defined_vars:
exec build_get_funcs(i) in locals() exec(build_get_funcs(i), locals())
exec build_property(i,j) in locals() exec(build_property(i,j), locals())
del to_remove, i, j del to_remove, i, j
atom_to_ao_range = property(fget=get_atom_to_ao_range) atom_to_ao_range = property(fget=get_atom_to_ao_range)
for i in "two_e_int_mo_filename two_e_int_ao_filename".split(): for i in "two_e_int_mo_filename two_e_int_ao_filename".split():
exec """ exec("""
def get_%(i)s(self): return self._%(i)s def get_%(i)s(self): return self._%(i)s
def set_%(i)s(self,value): self._%(i)s = value def set_%(i)s(self,value): self._%(i)s = value
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals() %(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals())
class two_e_int_array(object): class two_e_int_array(object):
@ -1499,7 +1499,7 @@ def set_%(i)s(self,value): self._%(i)s = value
Nint = rec.pop(0) Nint = rec.pop(0)
while (index >= Nint): while (index >= Nint):
index -= Nint index -= Nint
rec = self._file.next() rec = next(self._file)
Nint = rec.pop(0) Nint = rec.pop(0)
rec_i = rec[:4*Nint] rec_i = rec[:4*Nint]
@ -1524,29 +1524,29 @@ def set_%(i)s(self,value): self._%(i)s = value
def gamess_write_contrl(res,file, runtyp="ENERGY",guess="HUCKEL", def gamess_write_contrl(res,file, runtyp="ENERGY",guess="HUCKEL",
exetyp="RUN",scftyp=None,moread=False,NoSym=False,units="BOHR"): exetyp="RUN",scftyp=None,moread=False,NoSym=False,units="BOHR"):
print >>file, " $CONTRL" print(" $CONTRL", file=file)
print >>file, " EXETYP=",exetyp print(" EXETYP=",exetyp, file=file)
print >>file, " COORD= UNIQUE", " UNITS=",units print(" COORD= UNIQUE", " UNITS=",units, file=file)
print >>file, " RUNTYP=", runtyp print(" RUNTYP=", runtyp, file=file)
if NoSym: if NoSym:
print >>file, " NOSYM=1" print(" NOSYM=1", file=file)
if scftyp is None: if scftyp is None:
if res.num_alpha == res.num_beta: if res.num_alpha == res.num_beta:
scftyp="RHF" scftyp="RHF"
else: else:
scftyp="ROHF" scftyp="ROHF"
print >>file, " SCFTYP=", scftyp print(" SCFTYP=", scftyp, file=file)
print >>file, " MULT=", res.multiplicity print(" MULT=", res.multiplicity, file=file)
print >>file, " ICHARG=",str(int(res.charge)) print(" ICHARG=",str(int(res.charge)), file=file)
print >>file, " $END" print(" $END", file=file)
print >>file, "" print("", file=file)
print >>file, " $GUESS" print(" $GUESS", file=file)
if moread: if moread:
print >>file, " GUESS=MOREAD" print(" GUESS=MOREAD", file=file)
print >>file, " NORB=",len(res.mo_sets[res.mo_types[-1]]) print(" NORB=",len(res.mo_sets[res.mo_types[-1]]), file=file)
else: else:
print >>file, " GUESS=HUCKEL" print(" GUESS=HUCKEL", file=file)
print >>file, " $END" print(" $END", file=file)
def gamess_write_vec(res, file): def gamess_write_vec(res, file):
@ -1556,8 +1556,8 @@ def gamess_write_vec(res, file):
# motypelist = [motype] # motypelist = [motype]
# for motype in motypelist: # for motype in motypelist:
motype = res.mo_types[-1] motype = res.mo_types[-1]
print >>file, motype, "MOs" print(motype, "MOs", file=file)
print >>file, " $VEC" print(" $VEC", file=file)
moset = res.mo_sets[motype] moset = res.mo_sets[motype]
moindex = res.closed_mos + res.active_mos + \ moindex = res.closed_mos + res.active_mos + \
res.virtual_mos res.virtual_mos
@ -1578,13 +1578,13 @@ def gamess_write_vec(res, file):
fields.append ( "%15.8E"%v.pop(0) ) fields.append ( "%15.8E"%v.pop(0) )
except IndexError: except IndexError:
pass pass
print >>file, ''.join(fields) print(''.join(fields), file=file)
line += 1 line += 1
print >>file, " $END" print(" $END", file=file)
def gamess_write_data(res, file): def gamess_write_data(res, file):
print >>file, " $DATA" print(" $DATA", file=file)
print >>file, res.title print(res.title, file=file)
try: try:
point_group = res.point_group point_group = res.point_group
N = point_group[1] N = point_group[1]
@ -1594,10 +1594,10 @@ def gamess_write_data(res, file):
except TypeError: except TypeError:
point_group = 'C1' point_group = 'C1'
N = '1' N = '1'
print >>file, point_group print(point_group, file=file)
for at in res.geometry: for at in res.geometry:
print >>file, "%10s %3.1f %15.8f %15.8f %15.8f" % tuple( \ print("%10s %3.1f %15.8f %15.8f %15.8f" % tuple( \
[at.name.ljust(10), at.charge]+list(at.coord) ) [at.name.ljust(10), at.charge]+list(at.coord) ), file=file)
for contr in at.basis: for contr in at.basis:
sym = contr.sym sym = contr.sym
if sym == 's' : if sym == 's' :
@ -1632,13 +1632,13 @@ def gamess_write_data(res, file):
else: else:
doPrint = False doPrint = False
if doPrint: if doPrint:
print >>file, "%4s%8d"%(sym, len(contr.prim)) print("%4s%8d"%(sym, len(contr.prim)), file=file)
for i, p in enumerate(contr.prim): for i, p in enumerate(contr.prim):
if not isinstance(p,gaussian): if not isinstance(p,gaussian):
raise TypeError("Basis function is not a gaussian") raise TypeError("Basis function is not a gaussian")
print >>file, "%6d%26.10f%12.8f"%(i+1,p.expo,contr.coef[i]) print("%6d%26.10f%12.8f"%(i+1,p.expo,contr.coef[i]), file=file)
print >>file, "" print("", file=file)
print >>file, " $END" print(" $END", file=file)
def gamess_write_integrals(res,file): def gamess_write_integrals(res,file):
filename = file.name.replace('.inp','.moints') filename = file.name.replace('.inp','.moints')

40
resultsFile/Modules/gaussianFile.py
View File

@ -26,7 +26,7 @@
import include from . import include
eval(include.code) eval(include.code)
import struct import struct
@ -343,7 +343,7 @@ class gaussianFile(resultsFile):
if self._basis is None: if self._basis is None:
gfprint=False gfprint=False
gfinput=False gfinput=False
buffer = map(lambda x: x.lower(),self.options[1][0].split()) buffer = [x.lower() for x in self.options[1][0].split()]
if 'gfprint' in buffer: gfprint=True if 'gfprint' in buffer: gfprint=True
elif 'gfinput' in buffer: gfinput=True elif 'gfinput' in buffer: gfinput=True
@ -409,7 +409,7 @@ class gaussianFile(resultsFile):
if line[0].startswith('==============='): if line[0].startswith('==============='):
pos = end pos = end
else: else:
print "GFPRINT should be present in the gaussian keywords." print("GFPRINT should be present in the gaussian keywords.")
return None return None
Nmax = basis_read[len(basis_read)-1][0] Nmax = basis_read[len(basis_read)-1][0]
basis = [None for i in range(Nmax)] basis = [None for i in range(Nmax)]
@ -473,7 +473,7 @@ class gaussianFile(resultsFile):
mylist = [ "G0", "G1+", "G1-", "G2+", "G2-", "G3+", "G3-", mylist = [ "G0", "G1+", "G1-", "G2+", "G2-", "G3+", "G3-",
"H4+", "H4-", "H5+", "H5-", "I6+", "I6-" ] "H4+", "H4-", "H5+", "H5-", "I6+", "I6-" ]
mylist = map(normalize_basis_name,mylist) mylist = list(map(normalize_basis_name,mylist))
for i in mylist[:-1]: for i in mylist[:-1]:
basis[k][0] = i basis[k][0] = i
basis.insert(k,list(basis[k])) basis.insert(k,list(basis[k]))
@ -904,8 +904,8 @@ class gaussianFile(resultsFile):
for i, j in local_vars: for i, j in local_vars:
if i not in defined_vars: if i not in defined_vars:
exec build_get_funcs(i) in locals() exec(build_get_funcs(i), locals())
exec build_property(i,j) in locals() exec(build_property(i,j), locals())
del to_remove, i, j del to_remove, i, j
@ -944,7 +944,7 @@ class gaussianFile(resultsFile):
Nint = rec.pop(0) Nint = rec.pop(0)
while (index >= Nint): while (index >= Nint):
index -= Nint index -= Nint
rec = self._file.next() rec = next(self._file)
Nint = rec.pop(0) Nint = rec.pop(0)
rec_i = rec[:4*Nint] rec_i = rec[:4*Nint]
@ -969,7 +969,7 @@ class gaussianFile(resultsFile):
def write_vec(res, file): def write_vec(res, file):
for motype in res.mo_types: for motype in res.mo_types:
print >>file, " $VEC" print(" $VEC", file=file)
moset = res.mo_sets[motype] moset = res.mo_sets[motype]
for idx,mo in enumerate(moset): for idx,mo in enumerate(moset):
v = list(mo.vector) v = list(mo.vector)
@ -984,24 +984,24 @@ def write_vec(res, file):
fields.append ( linum ) fields.append ( linum )
for n in range(5): for n in range(5):
fields.append ( "%15.8E"%v.pop(0) ) fields.append ( "%15.8E"%v.pop(0) )
print >>file, ''.join(fields) print(''.join(fields), file=file)
line += 1 line += 1
print >>file, " $END" print(" $END", file=file)
def write_data(res, file): def write_data(res, file):
print >>file, " $DATA" print(" $DATA", file=file)
print >>file, res.title print(res.title, file=file)
point_group = res.point_group point_group = res.point_group
N = point_group[1] N = point_group[1]
if N != '1': if N != '1':
point_group = point_group[0]+'N'+point_group[2:] point_group = point_group[0]+'N'+point_group[2:]
point_group += ' '+N point_group += ' '+N
print >>file, point_group print(point_group, file=file)
if N != '1': if N != '1':
print >>file, "" print("", file=file)
for at in res.geometry: for at in res.geometry:
print >>file, "%10s %3.1f %15.8f %15.8f %15.8f" % tuple( \ print("%10s %3.1f %15.8f %15.8f %15.8f" % tuple( \
[at.name.ljust(10), at.charge]+list(at.coord) ) [at.name.ljust(10), at.charge]+list(at.coord) ), file=file)
for contr in at.basis: for contr in at.basis:
sym = contr.sym sym = contr.sym
if sym == 's' : if sym == 's' :
@ -1024,13 +1024,13 @@ def write_data(res, file):
else: else:
doPrint = False doPrint = False
if doPrint: if doPrint:
print >>file, "%4s%8d"%(sym, len(contr.prim)) print("%4s%8d"%(sym, len(contr.prim)), file=file)
for i, p in enumerate(contr.prim): for i, p in enumerate(contr.prim):
if not isinstance(p,gaussian): if not isinstance(p,gaussian):
raise TypeError("Basis function is not a gaussian") raise TypeError("Basis function is not a gaussian")
print >>file, "%6d%26.10f%12.8f"%(i+1,p.expo,contr.coef[i]) print("%6d%26.10f%12.8f"%(i+1,p.expo,contr.coef[i]), file=file)
print >>file, "" print("", file=file)
print >>file, " $END" print(" $END", file=file)

56
resultsFile/Modules/molproFile.py
View File

@ -26,7 +26,7 @@
import include from . import include
eval(include.code) eval(include.code)
import struct import struct
@ -54,10 +54,10 @@ class molproFile(resultsFile):
local_vars = list(local_vars) local_vars = list(local_vars)
defined_vars = list(molproFile_defined_vars) defined_vars = list(molproFile_defined_vars)
exec get_data('date',"DATE: ",'-3:-2') in locals() exec(get_data('date',"DATE: ",'-3:-2'), locals())
exec get_data('point_group',"Point group",'2:') in locals() exec(get_data('point_group',"Point group",'2:'), locals())
exec get_data('version'," Version",'1:2') in locals() exec(get_data('version'," Version",'1:2'), locals())
exec get_data('nuclear_energy',"NUCLEAR REPULSION ENERGY", '3:4',"float") in locals() exec(get_data('nuclear_energy',"NUCLEAR REPULSION ENERGY", '3:4',"float"), locals())
def get_num_elec(self): def get_num_elec(self):
if self._num_elec is None: if self._num_elec is None:
@ -181,7 +181,7 @@ class molproFile(resultsFile):
program = regexp.findall(line) program = regexp.findall(line)
if program != []: if program != []:
if program[0] in methods_with_orbitals: if program[0] in methods_with_orbitals:
while program[0] in occ.keys(): while program[0] in list(occ.keys()):
program[0] += 'x' program[0] += 'x'
occ[program[0]] = [] occ[program[0]] = []
progFound=True progFound=True
@ -483,10 +483,10 @@ class molproFile(resultsFile):
file = open('basis.molpro','w') file = open('basis.molpro','w')
molpro_write_input(self,file) molpro_write_input(self,file)
file.close() file.close()
print >>sys.stderr, """ print("""
Warning: there is a bug in the molpro output. Run the 'basis.molpro' Warning: there is a bug in the molpro output. Run the 'basis.molpro'
input file with molpro to generate a correct output for the basis set. input file with molpro to generate a correct output for the basis set.
""" """, file=sys.stderr)
return self._basis return self._basis
def get_mo_types(self): def get_mo_types(self):
@ -584,7 +584,7 @@ input file with molpro to generate a correct output for the basis set.
v.sym = self.symmetries[ int(buffer[0].split('.')[1])-1 ][0] v.sym = self.symmetries[ int(buffer[0].split('.')[1])-1 ][0]
v.eigenvalue = float(buffer[2]) v.eigenvalue = float(buffer[2])
if v.eigenvalue == 999999.9999: if v.eigenvalue == 999999.9999:
print "Warning line", iline+1, ": '**********' in orbital eigenvalues" print("Warning line", iline+1, ": '**********' in orbital eigenvalues")
for l,s in enumerate(self.num_orb_sym): for l,s in enumerate(self.num_orb_sym):
if l < symcount-1 : if l < symcount-1 :
bf += s[0] bf += s[0]
@ -604,7 +604,7 @@ input file with molpro to generate a correct output for the basis set.
try: try:
x2 = k*float(x) x2 = k*float(x)
except ValueError: except ValueError:
print "Error line", iline+1, ": orbital coefficients" print("Error line", iline+1, ": orbital coefficients")
sys.exit(1) sys.exit(1)
v.vector.append(x2) v.vector.append(x2)
bf+=1 bf+=1
@ -708,7 +708,7 @@ input file with molpro to generate a correct output for the basis set.
ncoreold=0 ncoreold=0
nactold=0 nactold=0
mo2="" mo2=""
for ((ncore,nact),next) in zip(zip(ncore0,nact0),next0): for ((ncore,nact),next) in zip(list(zip(ncore0,nact0)),next0):
for i in range(ncore): for i in range(ncore):
tempcsf_a.append(ncoreold+i) tempcsf_a.append(ncoreold+i)
tempcsf_b.append(ncoreold+i) tempcsf_b.append(ncoreold+i)
@ -748,7 +748,7 @@ input file with molpro to generate a correct output for the basis set.
def get_closed_mos(self): def get_closed_mos(self):
if self._closed_mos is None: if self._closed_mos is None:
result = [] result = []
occ = filter(lambda x: x>0., self.occ_num[self.determinants_mo_type]) occ = [x for x in self.occ_num[self.determinants_mo_type] if x>0.]
maxmo = len(occ) maxmo = len(occ)
for orb in range(maxmo): for orb in range(maxmo):
present = True present = True
@ -765,7 +765,7 @@ input file with molpro to generate a correct output for the basis set.
def get_virtual_mos(self): def get_virtual_mos(self):
if self._virtual_mos is None: if self._virtual_mos is None:
result = [] result = []
occ = filter(lambda x: x>0., self.occ_num[self.determinants_mo_type]) occ = [x for x in self.occ_num[self.determinants_mo_type] if x>0.]
maxmo = len(self.mo_sets[self.determinants_mo_type]) maxmo = len(self.mo_sets[self.determinants_mo_type])
for orb in range(maxmo): for orb in range(maxmo):
present = False present = False
@ -821,7 +821,7 @@ input file with molpro to generate a correct output for the basis set.
# Properties # Properties
# ---------- # ----------
exec build_property("num_orb_sym","Number of SALCAO/sym") in locals() exec(build_property("num_orb_sym","Number of SALCAO/sym"), locals())
to_remove = [] to_remove = []
for i, j in local_vars: for i, j in local_vars:
if i in resultsFile_defined_vars: if i in resultsFile_defined_vars:
@ -831,8 +831,8 @@ input file with molpro to generate a correct output for the basis set.
for i, j in local_vars: for i, j in local_vars:
if i not in defined_vars: if i not in defined_vars:
exec build_get_funcs(i) in locals() exec(build_get_funcs(i), locals())
exec build_property(i,j) in locals() exec(build_property(i,j), locals())
del to_remove, i, j del to_remove, i, j
# Output Routines # Output Routines
@ -840,9 +840,9 @@ input file with molpro to generate a correct output for the basis set.
def molpro_write_input(res,file): def molpro_write_input(res,file):
print >>file, " ***,", res.title print(" ***,", res.title, file=file)
geom = res.geometry geom = res.geometry
print >>file, """ print("""
print,basis; print,basis;
print,orbitals; print,orbitals;
gprint,civector; gprint,civector;
@ -850,17 +850,17 @@ def molpro_write_input(res,file):
geomtyp=xyz geomtyp=xyz
geometry={ geometry={
""", len(geom) """, len(geom), file=file)
print >>file, res.title print(res.title, file=file)
i=1 i=1
for at in geom: for at in geom:
coord = [] coord = []
for x in at.coord: coord.append(x*a0) for x in at.coord: coord.append(x*a0)
print >>file, "%10s %15.8f %15.8f %15.8f" % tuple( \ print("%10s %15.8f %15.8f %15.8f" % tuple( \
[(at.name+str(i)).ljust(10) ]+coord ) [(at.name+str(i)).ljust(10) ]+coord ), file=file)
i+=1 i+=1
print >>file, "}\n" print("}\n", file=file)
print >>file, "basis={" print("basis={", file=file)
lines = [] lines = []
for idx,at in enumerate(geom): for idx,at in enumerate(geom):
# Find atom # Find atom
@ -925,11 +925,11 @@ def molpro_write_input(res,file):
if line not in lines: if line not in lines:
lines.append(line) lines.append(line)
for line in lines: for line in lines:
print >>file, line print(line, file=file)
print >>file, "}\n", print("}\n", end=' ', file=file)
print >>file, "rhf;" print("rhf;", file=file)
print >>file, "---" print("---", file=file)
fileTypes.append(molproFile) fileTypes.append(molproFile)

52
resultsFile/Modules/wfnFile.py
View File

@ -26,7 +26,7 @@
import include from . import include
eval(include.code) eval(include.code)
import struct import struct
@ -336,8 +336,8 @@ class wfnFile(resultsFile):
for i, j in local_vars: for i, j in local_vars:
if i not in defined_vars: if i not in defined_vars:
exec build_get_funcs(i) in locals() exec(build_get_funcs(i), locals())
exec build_property(i,j) in locals() exec(build_property(i,j), locals())
del to_remove, i, j del to_remove, i, j
@ -381,9 +381,9 @@ basis_correspond['f+2'] = 16
basis_correspond['f+3'] = 17 basis_correspond['f+3'] = 17
def wfn_write(res,file,MO_type=None): def wfn_write(res,file,MO_type=None):
print >>file, " "+res.title.strip() print(" "+res.title.strip(), file=file)
print >>file, "GAUSSIAN %14d MOL ORBITALS %6d PRIMITIVES %8d NUCLEI" \ print("GAUSSIAN %14d MOL ORBITALS %6d PRIMITIVES %8d NUCLEI" \
%(len(res.closed_mos+res.active_mos), len(res.uncontracted_basis), len(res.geometry)), %(len(res.closed_mos+res.active_mos), len(res.uncontracted_basis), len(res.geometry)), end=' ', file=file)
# write geom # write geom
geom = res.geometry geom = res.geometry
@ -394,8 +394,8 @@ def wfn_write(res,file,MO_type=None):
name = atom.name name = atom.name
for d in string.digits: for d in string.digits:
name = name.replace(d,'') name = name.replace(d,'')
print >>file, "\n%3s %4d (CENTRE%3d) %12.8f%12.8f%12.8f CHARGE = %4.1f" \ print("\n%3s %4d (CENTRE%3d) %12.8f%12.8f%12.8f CHARGE = %4.1f" \
%(name, i+1, i+1, atom.coord[0]*f, atom.coord[1]*f, atom.coord[2]*f, atom.charge), %(name, i+1, i+1, atom.coord[0]*f, atom.coord[1]*f, atom.coord[2]*f, atom.charge), end=' ', file=file)
# write basis # write basis
basis = res.uncontracted_basis basis = res.uncontracted_basis
@ -415,23 +415,23 @@ def wfn_write(res,file,MO_type=None):
k=0 k=0
for c in center: for c in center:
if k%20 == 0: if k%20 == 0:
print "\nCENTRE ASSIGNMENTS ", print("\nCENTRE ASSIGNMENTS ", end=' ')
print "%2d"%(c), print("%2d"%(c), end=' ')
k+=1 k+=1
k=0 k=0
for t in type: for t in type:
if k%20 == 0: if k%20 == 0:
print "\nTYPE ASSIGNMENTS ", print("\nTYPE ASSIGNMENTS ", end=' ')
print "%2d"%(t), print("%2d"%(t), end=' ')
k+=1 k+=1
k=0 k=0
for e in expo: for e in expo:
if k%5 == 0: if k%5 == 0:
print "\nEXPONENTS ", print("\nEXPONENTS ", end=' ')
print ("%13.7e"%(e)).replace('e','D'), print(("%13.7e"%(e)).replace('e','D'), end=' ')
k+=1 k+=1
print '\n', print('\n', end=' ')
# MOs # MOs
if MO_type is None: if MO_type is None:
@ -439,7 +439,7 @@ def wfn_write(res,file,MO_type=None):
try: try:
allMOs = res.uncontracted_mo_sets[MO_type] allMOs = res.uncontracted_mo_sets[MO_type]
except KeyError: except KeyError:
print "MO type not present in "+res.filename print("MO type not present in "+res.filename)
return return
mos = [] mos = []
occ = res.occ_num[MO_type] occ = res.occ_num[MO_type]
@ -449,22 +449,22 @@ def wfn_write(res,file,MO_type=None):
for i,orb2 in enumerate(mos): for i,orb2 in enumerate(mos):
if occ[orb2[2]] > 0.: if occ[orb2[2]] > 0.:
orb = orb2[1] orb = orb2[1]
print "MO %4d MO 0.0 OCC NO = %9.7f ORB. ENERGY =%12.6f" \ print("MO %4d MO 0.0 OCC NO = %9.7f ORB. ENERGY =%12.6f" \
%(i+1, occ[orb2[2]], orb.eigenvalue), %(i+1, occ[orb2[2]], orb.eigenvalue), end=' ')
k=0 k=0
for c in orb.vector: for c in orb.vector:
if k%5 == 0: if k%5 == 0:
print "\n", print("\n", end=' ')
print "%15.8e"%(c), print("%15.8e"%(c), end=' ')
k+=1 k+=1
print "\n", print("\n", end=' ')
print "END DATA" print("END DATA")
idx = res.mo_types.index(MO_type) idx = res.mo_types.index(MO_type)
try: try:
print " THE HF ENERGY =%20.12f THE VIRIAL(-V/T)="%(res.energies[idx]), print(" THE HF ENERGY =%20.12f THE VIRIAL(-V/T)="%(res.energies[idx]), end=' ')
print "%12.8f"%(res.virials[idx]) print("%12.8f"%(res.virials[idx]))
except TypeError: except TypeError:
print " THE HF ENERGY =%20.12f THE VIRIAL(-V/T)=%12.8f"%(0.,0.) print(" THE HF ENERGY =%20.12f THE VIRIAL(-V/T)=%12.8f"%(0.,0.))
@ -472,7 +472,7 @@ def wfn_write(res,file,MO_type=None):
def write_wfnFile(file,out=sys.stdout): def write_wfnFile(file,out=sys.stdout):
if "basis" in file.mo_sets.keys() : if "basis" in list(file.mo_sets.keys()) :
MoType = "basis" MoType = "basis"
else: else:
MoType = None MoType = None

10
resultsFile/Modules/xmvbFile.py
View File

@ -26,7 +26,7 @@
import include from . import include
eval(include.code) eval(include.code)
import struct import struct
@ -316,7 +316,7 @@ class xmvbFile(resultsFile):
if len(bf) > 0: if len(bf) > 0:
basis_read.append( [index,sym,bf,iatom] ) basis_read.append( [index,sym,bf,iatom] )
else: else:
print "GFPRINT should be present in the gaussian keywords." print("GFPRINT should be present in the gaussian keywords.")
return None return None
Nmax = basis_read[len(basis_read)-1][0] Nmax = basis_read[len(basis_read)-1][0]
basis = [None for i in range(Nmax)] basis = [None for i in range(Nmax)]
@ -373,7 +373,7 @@ class xmvbFile(resultsFile):
# "XXXXYZ", "YYYYXZ", "ZZZZXY", "XXXYYY", "XXXZZZ", \ # "XXXXYZ", "YYYYXZ", "ZZZZXY", "XXXYYY", "XXXZZZ", \
# "YYYZZZ", "XXXYYZ", "XXXZZY", "YYYXXZ", "YYYZZX", \ # "YYYZZZ", "XXXYYZ", "XXXZZY", "YYYXXZ", "YYYZZX", \
# "ZZZXXY", "ZZZYYX" ] # "ZZZXXY", "ZZZYYX" ]
mylist = map(normalize_basis_name,mylist) mylist = list(map(normalize_basis_name,mylist))
for i in mylist[:-1]: for i in mylist[:-1]:
basis[k][0] = i basis[k][0] = i
basis.insert(k,list(basis[k])) basis.insert(k,list(basis[k]))
@ -718,8 +718,8 @@ class xmvbFile(resultsFile):
for i, j in local_vars: for i, j in local_vars:
if i not in defined_vars: if i not in defined_vars:
exec build_get_funcs(i) in locals() exec(build_get_funcs(i), locals())
exec build_property(i,j) in locals() exec(build_property(i,j), locals())
del to_remove, i, j del to_remove, i, j

4
resultsFile/__init__.py
View File

@ -36,9 +36,9 @@ all = [ "resultsFile", "getFile", "lib", "Modules" ]
for mod in all: for mod in all:
try: try:
exec 'from '+mod+' import *' exec('from '+mod+' import *')
except: except:
print "Error importing module", mod print("Error importing module", mod)
pass pass

4
resultsFile/getFile.py
View File

@ -26,7 +26,7 @@
from resultsFile import * from .resultsFile import *
import sys import sys
# Find fileType # Find fileType
@ -44,7 +44,7 @@ def getFile(name):
pass pass
if fileType is None: if fileType is None:
print "File type not recognized." print("File type not recognized.")
sys.exit(1) sys.exit(1)
return file return file

4
resultsFile/lib/__init__.py
View File

@ -38,9 +38,9 @@ all = [ i[:-3] for i in os.listdir(wd) if i.endswith(".py") ]
for mod in all: for mod in all:
try: try:
exec 'from '+mod+' import *' exec('from '+mod+' import *')
except: except:
print "Error importing module", mod print("Error importing module", mod)
pass pass

8
resultsFile/lib/atom.py
View File

@ -26,7 +26,7 @@
from library import * from .library import *
from math import * from math import *
class atom(object): class atom(object):
@ -62,10 +62,10 @@ class atom(object):
return 0 return 0
for i in "name charge coord basis".split(): for i in "name charge coord basis".split():
exec """ exec("""
def get_%(i)s(self): return self._%(i)s def get_%(i)s(self): return self._%(i)s
def set_%(i)s(self,value): self._%(i)s = value def set_%(i)s(self,value): self._%(i)s = value
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals() %(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals())
class atomDataElement(object): class atomDataElement(object):
@ -213,5 +213,5 @@ for line in atomDataText.splitlines():
if __name__ == '__main__': if __name__ == '__main__':
for s in atomData: for s in atomData:
print s print(s)

50
resultsFile/lib/basis.py
View File

@ -27,7 +27,7 @@
#import pdb #import pdb
from library import * from .library import *
from math import * from math import *
import sys import sys
@ -97,10 +97,10 @@ class primitive(object):
norm = property (get_norm,None,doc="Sqrt( Integral f^2(R) dR ).") norm = property (get_norm,None,doc="Sqrt( Integral f^2(R) dR ).")
for i in "center expo sym".split(): for i in "center expo sym".split():
exec """ exec("""
def get_%(i)s(self): return self._%(i)s def get_%(i)s(self): return self._%(i)s
def set_%(i)s(self,value): self._%(i)s = value def set_%(i)s(self,value): self._%(i)s = value
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals() %(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals())
#----------------------- #-----------------------
@ -132,7 +132,7 @@ def binom(n,m):
def rintgauss(n): def rintgauss(n):
def ddfact2(n): def ddfact2(n):
if n%2 == 0: print 'error in ddfact2' if n%2 == 0: print('error in ddfact2')
res=1. res=1.
for i in range(1,n+1,2): for i in range(1,n+1,2):
res*=float(i) res*=float(i)
@ -228,7 +228,7 @@ def xyz_from_lm(l,m):
absm = abs(m) absm = abs(m)
nb2 = absm nb2 = absm
nb1 = (l-absm)/2 nb1 = (l-absm)/2
clmt = [ (-0.25)**t * binom(l,t) * binom(l-t,absm+t) for t in xrange(nb1+1) ] clmt = [ (-0.25)**t * binom(l,t) * binom(l-t,absm+t) for t in range(nb1+1) ]
mod_absm_2 = absm % 2 mod_absm_2 = absm % 2
if m>=0: if m>=0:
nb2_start = mod_absm_2 nb2_start = mod_absm_2
@ -241,8 +241,8 @@ def xyz_from_lm(l,m):
for n1 in range(nb2_start,nb2+1,2): for n1 in range(nb2_start,nb2+1,2):
k = (absm-n1)/2 k = (absm-n1)/2
factor = (-1.)**k * binom(absm,n1) * norm factor = (-1.)**k * binom(absm,n1) * norm
for t in xrange(nb1+1): for t in range(nb1+1):
for n2 in xrange(t+1): for n2 in range(t+1):
coe = clmt[t] * factor * binom(t,n2) coe = clmt[t] * factor * binom(t,n2)
ipw = ( n1+2*n2 , absm-n1+2*(t-n2), l-2*t-absm ) ipw = ( n1+2*n2 , absm-n1+2*(t-n2), l-2*t-absm )
done = False done = False
@ -402,10 +402,10 @@ class contraction(object):
for i in "center prim sym coef".split(): for i in "center prim sym coef".split():
exec """ exec("""
def get_%(i)s(self): return self._%(i)s def get_%(i)s(self): return self._%(i)s
def set_%(i)s(self,value): self._%(i)s = value def set_%(i)s(self,value): self._%(i)s = value
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals() %(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals())
norm = property (get_norm,None,doc="Sqrt( Integral f^2(R) dR ).") norm = property (get_norm,None,doc="Sqrt( Integral f^2(R) dR ).")
@ -425,9 +425,9 @@ except ImportError:
if __name__ == '__main__': if __name__ == '__main__':
for l in range(6): for l in range(6):
print '---' print('---')
for m in range(-l,l+1): for m in range(-l,l+1):
print "%3d %3d :"%(l,m), xyz_from_lm(l,m) print("%3d %3d :"%(l,m), xyz_from_lm(l,m))
sys.exit(0) sys.exit(0)
if __name__ == '__main__': if __name__ == '__main__':
@ -441,13 +441,13 @@ if __name__ == '__main__':
b.center = [0.,0.,0.] b.center = [0.,0.,0.]
x = spheToCart(a) x = spheToCart(a)
y = spheToCart(a) y = spheToCart(a)
print x print(x)
sys.exit(0) sys.exit(0)
print GoverlapCart(a,b) print(GoverlapCart(a,b))
print GoverlapCartNorm2(a,b) print(GoverlapCartNorm2(a,b))
print '' print('')
for i in range(0,10): for i in range(0,10):
print rintgauss(i) print(rintgauss(i))
sys.exit(0) sys.exit(0)
c = gaussian() c = gaussian()
c.sym = 's' c.sym = 's'
@ -458,7 +458,7 @@ if __name__ == '__main__':
d.append(0.190362765893, b) d.append(0.190362765893, b)
d.append(0.852162022245, c) d.append(0.852162022245, c)
d.normalize() d.normalize()
print d print(d)
sys.exit(0) sys.exit(0)
a = gaussian() a = gaussian()
a.sym = 'x' a.sym = 'x'
@ -471,14 +471,14 @@ if __name__ == '__main__':
c = contraction() c = contraction()
c.append(1.,a) c.append(1.,a)
c.append(2.,b) c.append(2.,b)
print c.value( (1.,1.,0.) ) print(c.value( (1.,1.,0.) ))
print b.overlap(a) print(b.overlap(a))
print a.overlap(b) print(a.overlap(b))
print a.norm print(a.norm)
print c.norm, c.coef print(c.norm, c.coef)
c.normalize() c.normalize()
print c.norm, c.coef print(c.norm, c.coef)
c.normalize() c.normalize()
print c.norm, c.coef print(c.norm, c.coef)
print Goverlap(a,b) print(Goverlap(a,b))

6
resultsFile/lib/csf.py
View File

@ -26,7 +26,7 @@
from library import * from .library import *
class CSF(object): class CSF(object):
"""Class for an configuration state function.""" """Class for an configuration state function."""
@ -69,8 +69,8 @@ class CSF(object):
self._coefficients.append( c ) self._coefficients.append( c )
for i in "determinants coefficients".split(): for i in "determinants coefficients".split():
exec """ exec("""
def get_%(i)s(self): return self._%(i)s def get_%(i)s(self): return self._%(i)s
def set_%(i)s(self,value): self._%(i)s = value def set_%(i)s(self,value): self._%(i)s = value
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals() %(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals())

18
resultsFile/lib/fortranBinary.py
View File

@ -27,7 +27,7 @@
import struct import struct
from library import * from .library import *
import sys import sys
class fortranBinary(object): class fortranBinary(object):
@ -51,7 +51,7 @@ Behaves like an array of records.
def seek(self,index): def seek(self,index):
self.file.seek(index) self.file.seek(index)
def next(self): def __next__(self):
if self.form is None: if self.form is None:
raise TypeError raise TypeError
data = self.file.read(4) # Rec length at the beginning of record data = self.file.read(4) # Rec length at the beginning of record
@ -102,18 +102,18 @@ Behaves like an array of records.
# file = property ( get_file, doc="Binary file") # file = property ( get_file, doc="Binary file")
# form = xproperty ( '_form', doc="Format to read the binary record") # form = xproperty ( '_form', doc="Format to read the binary record")
for i in "recl mode name file form".split(): for i in "recl mode name file form".split():
exec """ exec("""
def get_%(i)s(self): return self._%(i)s def get_%(i)s(self): return self._%(i)s
def set_%(i)s(self,value): self._%(i)s = value def set_%(i)s(self,value): self._%(i)s = value
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals() %(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals())
if __name__ == '__main__': if __name__ == '__main__':
f = fortranBinary(sys.argv[1],"rb") f = fortranBinary(sys.argv[1],"rb")
f.form = 'l'+4*15000*'h'+15000*'d' f.form = 'l'+4*15000*'h'+15000*'d'
print f.name print(f.name)
print f.mode print(f.mode)
print f[0] print(f[0])
print f[10] print(f[10])
print f[0] print(f[0])

12
resultsFile/lib/integral.py
View File

@ -26,7 +26,7 @@
from library import * from .library import *
from math import * from math import *
class integral(object): class integral(object):
@ -56,19 +56,19 @@ class integral(object):
return 0 return 0
for i in "indices value".split(): for i in "indices value".split():
exec """ exec("""
def get_%(i)s(self): return self._%(i)s def get_%(i)s(self): return self._%(i)s
def set_%(i)s(self,value): self._%(i)s = value def set_%(i)s(self,value): self._%(i)s = value
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals() %(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals())
if __name__ == '__main__': if __name__ == '__main__':
i = integral() i = integral()
i.indices = [1,4] i.indices = [1,4]
i.value = 1.5 i.value = 1.5
print i print(i)
j = integral() j = integral()
j.indices = [4,3,2,1] j.indices = [4,3,2,1]
j.value = 2.5 j.value = 2.5
print j print(j)
print i<j print(i<j)

4
resultsFile/lib/library.py
View File

@ -35,10 +35,10 @@ def prettyPrint(obj,shift=" "):
prettyPrint(k) prettyPrint(k)
elif isinstance(obj,dict): elif isinstance(obj,dict):
for k in obj: for k in obj:
print k print(k)
prettyPrint(obj[k]) prettyPrint(obj[k])
else: else:
print str(obj) print(str(obj))
def xproperty(fget, fset=None, fdel=None, doc=None): def xproperty(fget, fset=None, fdel=None, doc=None):
"""Automatically defines the properties if the functions don't exist.""" """Automatically defines the properties if the functions don't exist."""

24
resultsFile/lib/orbital.py
View File

@ -26,7 +26,7 @@
from library import * from .library import *
from math import * from math import *
class orbital(object): class orbital(object):
@ -96,10 +96,10 @@ class orbital(object):
return result return result
for i in "eigenvalue vector basis set sym".split(): for i in "eigenvalue vector basis set sym".split():
exec """ exec("""
def get_%(i)s(self): return self._%(i)s def get_%(i)s(self): return self._%(i)s
def set_%(i)s(self,value): self._%(i)s = value def set_%(i)s(self,value): self._%(i)s = value
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals() %(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals())
@ -114,20 +114,20 @@ if __name__ == '__main__':
l[1].eigenvalue = 1. l[1].eigenvalue = 1.
l[2].eigenvalue = 3. l[2].eigenvalue = 3.
for i in l: for i in l:
print i.eigenvalue print(i.eigenvalue)
l.sort() l.sort()
print "" print("")
for i in l: for i in l:
print i.eigenvalue print(i.eigenvalue)
l[0].vector = [1., 0., 0.] l[0].vector = [1., 0., 0.]
l[1].vector = [0., 1., 0.] l[1].vector = [0., 1., 0.]
l[2].vector = [0., 1., 1.] l[2].vector = [0., 1., 1.]
print l[0].is_ortho(l[1]) print(l[0].is_ortho(l[1]))
print l[1].is_ortho(l[2]) print(l[1].is_ortho(l[2]))
print l[1].dot(l[2]) print(l[1].dot(l[2]))
print l[1].dot(l[0]) print(l[1].dot(l[0]))
print l[1].norm() print(l[1].norm())
print l[2].norm() print(l[2].norm())