mirror of
https://gitlab.com/scemama/resultsFile.git
synced 2025-01-03 01:55:53 +01:00
Python3
This commit is contained in:
parent
b502a622cc
commit
53b075a839
@ -41,9 +41,9 @@ if "q5CostFile" in all:
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for mod in all:
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try:
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exec 'from '+mod+' import *'
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exec('from '+mod+' import *')
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except:
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print "Error importing module", mod
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print("Error importing module", mod)
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pass
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@ -26,7 +26,7 @@
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import include
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from . import include
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eval(include.code)
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import struct
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@ -54,13 +54,13 @@ class gamessFile(resultsFile):
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local_vars = list(local_vars)
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defined_vars = list(gamessFile_defined_vars)
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exec get_data('date',"EXECUTION OF GAMESS BEGUN",'4:') in locals()
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exec get_data('machine',"Files used on the master node",'6:7') in locals()
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exec get_data('version',"GAMESS VERSION",'4:8') in locals()
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exec get_data('num_proc',"MEMDDI DISTRIBUTED OVER",'3:4',"int") in locals()
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exec get_data('num_elec',"NUMBER OF ELECTRONS", '4:5',"int") in locals()
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exec get_data('charge',"CHARGE OF MOLECULE", '4:5',"float") in locals()
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exec get_data('nuclear_energy',"THE NUCLEAR REPULSION ENERGY", '5:6',"float") in locals()
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exec(get_data('date',"EXECUTION OF GAMESS BEGUN",'4:'), locals())
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exec(get_data('machine',"Files used on the master node",'6:7'), locals())
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exec(get_data('version',"GAMESS VERSION",'4:8'), locals())
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exec(get_data('num_proc',"MEMDDI DISTRIBUTED OVER",'3:4',"int"), locals())
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exec(get_data('num_elec',"NUMBER OF ELECTRONS", '4:5',"int"), locals())
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exec(get_data('charge',"CHARGE OF MOLECULE", '4:5',"float"), locals())
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exec(get_data('nuclear_energy',"THE NUCLEAR REPULSION ENERGY", '5:6',"float"), locals())
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def get_multiplicity(self):
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if self._multiplicity is None:
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@ -272,7 +272,7 @@ class gamessFile(resultsFile):
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tokens = line.split()[0::2]
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values = line.split()[1::2]
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if len(tokens) != len(values):
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print "error: ",line
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print("error: ",line)
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sys.exit(0)
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except IndexError:
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pass
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@ -407,7 +407,7 @@ class gamessFile(resultsFile):
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buffer = self.text[pos].split()
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label = buffer[1]
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assert label == i.name
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f = map(float,buffer[2:])
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f = list(map(float,buffer[2:]))
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self._gradient_energy.append(f)
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pos +=1
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except IndexError:
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@ -698,7 +698,7 @@ class gamessFile(resultsFile):
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"xxxxyz", "xyyyyz", "xyzzzz", "xxxyyy", "xxxzzz", \
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"yyyzzz", "xxxyyz", "xxxyzz", "xxyyyz", "xyyyzz", \
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"xxyzzz", "xyyzzz" ]
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map(normalize_basis_name,mylist)
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list(map(normalize_basis_name,mylist))
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for i in mylist[:-1]:
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basis[k][0] = i
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basis.insert(k,list(basis[k]))
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@ -1451,17 +1451,17 @@ class gamessFile(resultsFile):
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for i, j in local_vars:
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if i not in defined_vars:
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exec build_get_funcs(i) in locals()
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exec build_property(i,j) in locals()
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exec(build_get_funcs(i), locals())
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exec(build_property(i,j), locals())
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del to_remove, i, j
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atom_to_ao_range = property(fget=get_atom_to_ao_range)
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for i in "two_e_int_mo_filename two_e_int_ao_filename".split():
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exec """
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exec("""
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def get_%(i)s(self): return self._%(i)s
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def set_%(i)s(self,value): self._%(i)s = value
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%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals()
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%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals())
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class two_e_int_array(object):
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@ -1499,7 +1499,7 @@ def set_%(i)s(self,value): self._%(i)s = value
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Nint = rec.pop(0)
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while (index >= Nint):
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index -= Nint
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rec = self._file.next()
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rec = next(self._file)
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Nint = rec.pop(0)
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rec_i = rec[:4*Nint]
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@ -1524,29 +1524,29 @@ def set_%(i)s(self,value): self._%(i)s = value
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def gamess_write_contrl(res,file, runtyp="ENERGY",guess="HUCKEL",
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exetyp="RUN",scftyp=None,moread=False,NoSym=False,units="BOHR"):
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print >>file, " $CONTRL"
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print >>file, " EXETYP=",exetyp
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print >>file, " COORD= UNIQUE", " UNITS=",units
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print >>file, " RUNTYP=", runtyp
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print(" $CONTRL", file=file)
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print(" EXETYP=",exetyp, file=file)
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print(" COORD= UNIQUE", " UNITS=",units, file=file)
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print(" RUNTYP=", runtyp, file=file)
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if NoSym:
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print >>file, " NOSYM=1"
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print(" NOSYM=1", file=file)
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if scftyp is None:
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if res.num_alpha == res.num_beta:
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scftyp="RHF"
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else:
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scftyp="ROHF"
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print >>file, " SCFTYP=", scftyp
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print >>file, " MULT=", res.multiplicity
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print >>file, " ICHARG=",str(int(res.charge))
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print >>file, " $END"
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print >>file, ""
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print >>file, " $GUESS"
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print(" SCFTYP=", scftyp, file=file)
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print(" MULT=", res.multiplicity, file=file)
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print(" ICHARG=",str(int(res.charge)), file=file)
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print(" $END", file=file)
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print("", file=file)
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print(" $GUESS", file=file)
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if moread:
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print >>file, " GUESS=MOREAD"
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print >>file, " NORB=",len(res.mo_sets[res.mo_types[-1]])
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print(" GUESS=MOREAD", file=file)
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print(" NORB=",len(res.mo_sets[res.mo_types[-1]]), file=file)
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else:
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print >>file, " GUESS=HUCKEL"
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print >>file, " $END"
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print(" GUESS=HUCKEL", file=file)
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print(" $END", file=file)
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def gamess_write_vec(res, file):
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@ -1556,8 +1556,8 @@ def gamess_write_vec(res, file):
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# motypelist = [motype]
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# for motype in motypelist:
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motype = res.mo_types[-1]
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print >>file, motype, "MOs"
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print >>file, " $VEC"
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print(motype, "MOs", file=file)
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print(" $VEC", file=file)
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moset = res.mo_sets[motype]
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moindex = res.closed_mos + res.active_mos + \
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res.virtual_mos
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@ -1578,13 +1578,13 @@ def gamess_write_vec(res, file):
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fields.append ( "%15.8E"%v.pop(0) )
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except IndexError:
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pass
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print >>file, ''.join(fields)
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print(''.join(fields), file=file)
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line += 1
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print >>file, " $END"
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print(" $END", file=file)
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def gamess_write_data(res, file):
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print >>file, " $DATA"
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print >>file, res.title
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print(" $DATA", file=file)
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print(res.title, file=file)
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try:
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point_group = res.point_group
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N = point_group[1]
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@ -1594,10 +1594,10 @@ def gamess_write_data(res, file):
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except TypeError:
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point_group = 'C1'
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N = '1'
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print >>file, point_group
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print(point_group, file=file)
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for at in res.geometry:
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print >>file, "%10s %3.1f %15.8f %15.8f %15.8f" % tuple( \
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[at.name.ljust(10), at.charge]+list(at.coord) )
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print("%10s %3.1f %15.8f %15.8f %15.8f" % tuple( \
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[at.name.ljust(10), at.charge]+list(at.coord) ), file=file)
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for contr in at.basis:
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sym = contr.sym
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if sym == 's' :
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@ -1632,13 +1632,13 @@ def gamess_write_data(res, file):
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else:
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doPrint = False
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if doPrint:
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print >>file, "%4s%8d"%(sym, len(contr.prim))
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print("%4s%8d"%(sym, len(contr.prim)), file=file)
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for i, p in enumerate(contr.prim):
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if not isinstance(p,gaussian):
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raise TypeError("Basis function is not a gaussian")
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print >>file, "%6d%26.10f%12.8f"%(i+1,p.expo,contr.coef[i])
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print >>file, ""
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print >>file, " $END"
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print("%6d%26.10f%12.8f"%(i+1,p.expo,contr.coef[i]), file=file)
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print("", file=file)
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print(" $END", file=file)
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def gamess_write_integrals(res,file):
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filename = file.name.replace('.inp','.moints')
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@ -26,7 +26,7 @@
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import include
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from . import include
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eval(include.code)
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import struct
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@ -343,7 +343,7 @@ class gaussianFile(resultsFile):
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if self._basis is None:
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gfprint=False
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gfinput=False
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buffer = map(lambda x: x.lower(),self.options[1][0].split())
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buffer = [x.lower() for x in self.options[1][0].split()]
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if 'gfprint' in buffer: gfprint=True
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elif 'gfinput' in buffer: gfinput=True
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@ -409,7 +409,7 @@ class gaussianFile(resultsFile):
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if line[0].startswith('==============='):
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pos = end
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else:
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print "GFPRINT should be present in the gaussian keywords."
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print("GFPRINT should be present in the gaussian keywords.")
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return None
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Nmax = basis_read[len(basis_read)-1][0]
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basis = [None for i in range(Nmax)]
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@ -473,7 +473,7 @@ class gaussianFile(resultsFile):
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mylist = [ "G0", "G1+", "G1-", "G2+", "G2-", "G3+", "G3-",
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"H4+", "H4-", "H5+", "H5-", "I6+", "I6-" ]
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mylist = map(normalize_basis_name,mylist)
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mylist = list(map(normalize_basis_name,mylist))
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for i in mylist[:-1]:
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basis[k][0] = i
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basis.insert(k,list(basis[k]))
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@ -904,8 +904,8 @@ class gaussianFile(resultsFile):
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for i, j in local_vars:
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if i not in defined_vars:
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exec build_get_funcs(i) in locals()
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exec build_property(i,j) in locals()
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exec(build_get_funcs(i), locals())
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exec(build_property(i,j), locals())
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del to_remove, i, j
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@ -944,7 +944,7 @@ class gaussianFile(resultsFile):
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Nint = rec.pop(0)
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while (index >= Nint):
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index -= Nint
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rec = self._file.next()
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rec = next(self._file)
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Nint = rec.pop(0)
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rec_i = rec[:4*Nint]
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@ -969,7 +969,7 @@ class gaussianFile(resultsFile):
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def write_vec(res, file):
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for motype in res.mo_types:
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print >>file, " $VEC"
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print(" $VEC", file=file)
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moset = res.mo_sets[motype]
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for idx,mo in enumerate(moset):
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v = list(mo.vector)
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@ -984,24 +984,24 @@ def write_vec(res, file):
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fields.append ( linum )
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for n in range(5):
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fields.append ( "%15.8E"%v.pop(0) )
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print >>file, ''.join(fields)
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print(''.join(fields), file=file)
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line += 1
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print >>file, " $END"
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print(" $END", file=file)
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def write_data(res, file):
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print >>file, " $DATA"
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print >>file, res.title
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print(" $DATA", file=file)
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print(res.title, file=file)
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point_group = res.point_group
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N = point_group[1]
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if N != '1':
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point_group = point_group[0]+'N'+point_group[2:]
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point_group += ' '+N
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print >>file, point_group
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print(point_group, file=file)
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if N != '1':
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print >>file, ""
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print("", file=file)
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for at in res.geometry:
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print >>file, "%10s %3.1f %15.8f %15.8f %15.8f" % tuple( \
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[at.name.ljust(10), at.charge]+list(at.coord) )
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print("%10s %3.1f %15.8f %15.8f %15.8f" % tuple( \
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[at.name.ljust(10), at.charge]+list(at.coord) ), file=file)
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for contr in at.basis:
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sym = contr.sym
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if sym == 's' :
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@ -1024,13 +1024,13 @@ def write_data(res, file):
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else:
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doPrint = False
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if doPrint:
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print >>file, "%4s%8d"%(sym, len(contr.prim))
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print("%4s%8d"%(sym, len(contr.prim)), file=file)
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for i, p in enumerate(contr.prim):
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if not isinstance(p,gaussian):
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raise TypeError("Basis function is not a gaussian")
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print >>file, "%6d%26.10f%12.8f"%(i+1,p.expo,contr.coef[i])
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print >>file, ""
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print >>file, " $END"
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print("%6d%26.10f%12.8f"%(i+1,p.expo,contr.coef[i]), file=file)
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print("", file=file)
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print(" $END", file=file)
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@ -26,7 +26,7 @@
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import include
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from . import include
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eval(include.code)
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import struct
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@ -54,10 +54,10 @@ class molproFile(resultsFile):
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local_vars = list(local_vars)
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defined_vars = list(molproFile_defined_vars)
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exec get_data('date',"DATE: ",'-3:-2') in locals()
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exec get_data('point_group',"Point group",'2:') in locals()
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exec get_data('version'," Version",'1:2') in locals()
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exec get_data('nuclear_energy',"NUCLEAR REPULSION ENERGY", '3:4',"float") in locals()
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exec(get_data('date',"DATE: ",'-3:-2'), locals())
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exec(get_data('point_group',"Point group",'2:'), locals())
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exec(get_data('version'," Version",'1:2'), locals())
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exec(get_data('nuclear_energy',"NUCLEAR REPULSION ENERGY", '3:4',"float"), locals())
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def get_num_elec(self):
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if self._num_elec is None:
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@ -181,7 +181,7 @@ class molproFile(resultsFile):
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program = regexp.findall(line)
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if program != []:
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if program[0] in methods_with_orbitals:
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while program[0] in occ.keys():
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while program[0] in list(occ.keys()):
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program[0] += 'x'
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occ[program[0]] = []
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progFound=True
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@ -483,10 +483,10 @@ class molproFile(resultsFile):
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file = open('basis.molpro','w')
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molpro_write_input(self,file)
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file.close()
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print >>sys.stderr, """
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print("""
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Warning: there is a bug in the molpro output. Run the 'basis.molpro'
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input file with molpro to generate a correct output for the basis set.
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"""
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""", file=sys.stderr)
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return self._basis
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def get_mo_types(self):
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@ -584,7 +584,7 @@ input file with molpro to generate a correct output for the basis set.
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v.sym = self.symmetries[ int(buffer[0].split('.')[1])-1 ][0]
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v.eigenvalue = float(buffer[2])
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if v.eigenvalue == 999999.9999:
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print "Warning line", iline+1, ": '**********' in orbital eigenvalues"
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print("Warning line", iline+1, ": '**********' in orbital eigenvalues")
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for l,s in enumerate(self.num_orb_sym):
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if l < symcount-1 :
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bf += s[0]
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@ -604,7 +604,7 @@ input file with molpro to generate a correct output for the basis set.
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try:
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x2 = k*float(x)
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except ValueError:
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print "Error line", iline+1, ": orbital coefficients"
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print("Error line", iline+1, ": orbital coefficients")
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sys.exit(1)
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v.vector.append(x2)
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bf+=1
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@ -708,7 +708,7 @@ input file with molpro to generate a correct output for the basis set.
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ncoreold=0
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nactold=0
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mo2=""
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for ((ncore,nact),next) in zip(zip(ncore0,nact0),next0):
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for ((ncore,nact),next) in zip(list(zip(ncore0,nact0)),next0):
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for i in range(ncore):
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tempcsf_a.append(ncoreold+i)
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tempcsf_b.append(ncoreold+i)
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@ -748,7 +748,7 @@ input file with molpro to generate a correct output for the basis set.
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def get_closed_mos(self):
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if self._closed_mos is None:
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result = []
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occ = filter(lambda x: x>0., self.occ_num[self.determinants_mo_type])
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occ = [x for x in self.occ_num[self.determinants_mo_type] if x>0.]
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maxmo = len(occ)
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for orb in range(maxmo):
|
||||
present = True
|
||||
@ -765,7 +765,7 @@ input file with molpro to generate a correct output for the basis set.
|
||||
def get_virtual_mos(self):
|
||||
if self._virtual_mos is None:
|
||||
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])
|
||||
for orb in range(maxmo):
|
||||
present = False
|
||||
@ -821,7 +821,7 @@ input file with molpro to generate a correct output for the basis set.
|
||||
|
||||
# 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 = []
|
||||
for i, j in local_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:
|
||||
if i not in defined_vars:
|
||||
exec build_get_funcs(i) in locals()
|
||||
exec build_property(i,j) in locals()
|
||||
exec(build_get_funcs(i), locals())
|
||||
exec(build_property(i,j), locals())
|
||||
del to_remove, i, j
|
||||
|
||||
# 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):
|
||||
|
||||
print >>file, " ***,", res.title
|
||||
print(" ***,", res.title, file=file)
|
||||
geom = res.geometry
|
||||
print >>file, """
|
||||
print("""
|
||||
print,basis;
|
||||
print,orbitals;
|
||||
gprint,civector;
|
||||
@ -850,17 +850,17 @@ def molpro_write_input(res,file):
|
||||
|
||||
geomtyp=xyz
|
||||
geometry={
|
||||
""", len(geom)
|
||||
print >>file, res.title
|
||||
""", len(geom), file=file)
|
||||
print(res.title, file=file)
|
||||
i=1
|
||||
for at in geom:
|
||||
coord = []
|
||||
for x in at.coord: coord.append(x*a0)
|
||||
print >>file, "%10s %15.8f %15.8f %15.8f" % tuple( \
|
||||
[(at.name+str(i)).ljust(10) ]+coord )
|
||||
print("%10s %15.8f %15.8f %15.8f" % tuple( \
|
||||
[(at.name+str(i)).ljust(10) ]+coord ), file=file)
|
||||
i+=1
|
||||
print >>file, "}\n"
|
||||
print >>file, "basis={"
|
||||
print("}\n", file=file)
|
||||
print("basis={", file=file)
|
||||
lines = []
|
||||
for idx,at in enumerate(geom):
|
||||
# Find atom
|
||||
@ -925,11 +925,11 @@ def molpro_write_input(res,file):
|
||||
if line not in lines:
|
||||
lines.append(line)
|
||||
for line in lines:
|
||||
print >>file, line
|
||||
print >>file, "}\n",
|
||||
print(line, file=file)
|
||||
print("}\n", end=' ', file=file)
|
||||
|
||||
print >>file, "rhf;"
|
||||
print >>file, "---"
|
||||
print("rhf;", file=file)
|
||||
print("---", file=file)
|
||||
|
||||
fileTypes.append(molproFile)
|
||||
|
||||
|
||||
@ -26,7 +26,7 @@
|
||||
|
||||
|
||||
|
||||
import include
|
||||
from . import include
|
||||
eval(include.code)
|
||||
|
||||
import struct
|
||||
@ -336,8 +336,8 @@ class wfnFile(resultsFile):
|
||||
|
||||
for i, j in local_vars:
|
||||
if i not in defined_vars:
|
||||
exec build_get_funcs(i) in locals()
|
||||
exec build_property(i,j) in locals()
|
||||
exec(build_get_funcs(i), locals())
|
||||
exec(build_property(i,j), locals())
|
||||
del to_remove, i, j
|
||||
|
||||
|
||||
@ -381,9 +381,9 @@ basis_correspond['f+2'] = 16
|
||||
basis_correspond['f+3'] = 17
|
||||
|
||||
def wfn_write(res,file,MO_type=None):
|
||||
print >>file, " "+res.title.strip()
|
||||
print >>file, "GAUSSIAN %14d MOL ORBITALS %6d PRIMITIVES %8d NUCLEI" \
|
||||
%(len(res.closed_mos+res.active_mos), len(res.uncontracted_basis), len(res.geometry)),
|
||||
print(" "+res.title.strip(), file=file)
|
||||
print("GAUSSIAN %14d MOL ORBITALS %6d PRIMITIVES %8d NUCLEI" \
|
||||
%(len(res.closed_mos+res.active_mos), len(res.uncontracted_basis), len(res.geometry)), end=' ', file=file)
|
||||
|
||||
# write geom
|
||||
geom = res.geometry
|
||||
@ -394,8 +394,8 @@ def wfn_write(res,file,MO_type=None):
|
||||
name = atom.name
|
||||
for d in string.digits:
|
||||
name = name.replace(d,'')
|
||||
print >>file, "\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),
|
||||
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), end=' ', file=file)
|
||||
|
||||
# write basis
|
||||
basis = res.uncontracted_basis
|
||||
@ -415,23 +415,23 @@ def wfn_write(res,file,MO_type=None):
|
||||
k=0
|
||||
for c in center:
|
||||
if k%20 == 0:
|
||||
print "\nCENTRE ASSIGNMENTS ",
|
||||
print "%2d"%(c),
|
||||
print("\nCENTRE ASSIGNMENTS ", end=' ')
|
||||
print("%2d"%(c), end=' ')
|
||||
k+=1
|
||||
k=0
|
||||
for t in type:
|
||||
if k%20 == 0:
|
||||
print "\nTYPE ASSIGNMENTS ",
|
||||
print "%2d"%(t),
|
||||
print("\nTYPE ASSIGNMENTS ", end=' ')
|
||||
print("%2d"%(t), end=' ')
|
||||
k+=1
|
||||
k=0
|
||||
for e in expo:
|
||||
if k%5 == 0:
|
||||
print "\nEXPONENTS ",
|
||||
print ("%13.7e"%(e)).replace('e','D'),
|
||||
print("\nEXPONENTS ", end=' ')
|
||||
print(("%13.7e"%(e)).replace('e','D'), end=' ')
|
||||
k+=1
|
||||
|
||||
print '\n',
|
||||
print('\n', end=' ')
|
||||
|
||||
# MOs
|
||||
if MO_type is None:
|
||||
@ -439,7 +439,7 @@ def wfn_write(res,file,MO_type=None):
|
||||
try:
|
||||
allMOs = res.uncontracted_mo_sets[MO_type]
|
||||
except KeyError:
|
||||
print "MO type not present in "+res.filename
|
||||
print("MO type not present in "+res.filename)
|
||||
return
|
||||
mos = []
|
||||
occ = res.occ_num[MO_type]
|
||||
@ -449,22 +449,22 @@ def wfn_write(res,file,MO_type=None):
|
||||
for i,orb2 in enumerate(mos):
|
||||
if occ[orb2[2]] > 0.:
|
||||
orb = orb2[1]
|
||||
print "MO %4d MO 0.0 OCC NO = %9.7f ORB. ENERGY =%12.6f" \
|
||||
%(i+1, occ[orb2[2]], orb.eigenvalue),
|
||||
print("MO %4d MO 0.0 OCC NO = %9.7f ORB. ENERGY =%12.6f" \
|
||||
%(i+1, occ[orb2[2]], orb.eigenvalue), end=' ')
|
||||
k=0
|
||||
for c in orb.vector:
|
||||
if k%5 == 0:
|
||||
print "\n",
|
||||
print "%15.8e"%(c),
|
||||
print("\n", end=' ')
|
||||
print("%15.8e"%(c), end=' ')
|
||||
k+=1
|
||||
print "\n",
|
||||
print "END DATA"
|
||||
print("\n", end=' ')
|
||||
print("END DATA")
|
||||
idx = res.mo_types.index(MO_type)
|
||||
try:
|
||||
print " THE HF ENERGY =%20.12f THE VIRIAL(-V/T)="%(res.energies[idx]),
|
||||
print "%12.8f"%(res.virials[idx])
|
||||
print(" THE HF ENERGY =%20.12f THE VIRIAL(-V/T)="%(res.energies[idx]), end=' ')
|
||||
print("%12.8f"%(res.virials[idx]))
|
||||
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):
|
||||
if "basis" in file.mo_sets.keys() :
|
||||
if "basis" in list(file.mo_sets.keys()) :
|
||||
MoType = "basis"
|
||||
else:
|
||||
MoType = None
|
||||
|
||||
@ -26,7 +26,7 @@
|
||||
|
||||
|
||||
|
||||
import include
|
||||
from . import include
|
||||
eval(include.code)
|
||||
|
||||
import struct
|
||||
@ -316,7 +316,7 @@ class xmvbFile(resultsFile):
|
||||
if len(bf) > 0:
|
||||
basis_read.append( [index,sym,bf,iatom] )
|
||||
else:
|
||||
print "GFPRINT should be present in the gaussian keywords."
|
||||
print("GFPRINT should be present in the gaussian keywords.")
|
||||
return None
|
||||
Nmax = basis_read[len(basis_read)-1][0]
|
||||
basis = [None for i in range(Nmax)]
|
||||
@ -373,7 +373,7 @@ class xmvbFile(resultsFile):
|
||||
# "XXXXYZ", "YYYYXZ", "ZZZZXY", "XXXYYY", "XXXZZZ", \
|
||||
# "YYYZZZ", "XXXYYZ", "XXXZZY", "YYYXXZ", "YYYZZX", \
|
||||
# "ZZZXXY", "ZZZYYX" ]
|
||||
mylist = map(normalize_basis_name,mylist)
|
||||
mylist = list(map(normalize_basis_name,mylist))
|
||||
for i in mylist[:-1]:
|
||||
basis[k][0] = i
|
||||
basis.insert(k,list(basis[k]))
|
||||
@ -718,8 +718,8 @@ class xmvbFile(resultsFile):
|
||||
|
||||
for i, j in local_vars:
|
||||
if i not in defined_vars:
|
||||
exec build_get_funcs(i) in locals()
|
||||
exec build_property(i,j) in locals()
|
||||
exec(build_get_funcs(i), locals())
|
||||
exec(build_property(i,j), locals())
|
||||
del to_remove, i, j
|
||||
|
||||
|
||||
|
||||
@ -36,9 +36,9 @@ all = [ "resultsFile", "getFile", "lib", "Modules" ]
|
||||
|
||||
for mod in all:
|
||||
try:
|
||||
exec 'from '+mod+' import *'
|
||||
exec('from '+mod+' import *')
|
||||
except:
|
||||
print "Error importing module", mod
|
||||
print("Error importing module", mod)
|
||||
pass
|
||||
|
||||
|
||||
|
||||
@ -26,7 +26,7 @@
|
||||
|
||||
|
||||
|
||||
from resultsFile import *
|
||||
from .resultsFile import *
|
||||
import sys
|
||||
|
||||
# Find fileType
|
||||
@ -44,7 +44,7 @@ def getFile(name):
|
||||
pass
|
||||
|
||||
if fileType is None:
|
||||
print "File type not recognized."
|
||||
print("File type not recognized.")
|
||||
sys.exit(1)
|
||||
|
||||
return file
|
||||
|
||||
@ -38,9 +38,9 @@ all = [ i[:-3] for i in os.listdir(wd) if i.endswith(".py") ]
|
||||
|
||||
for mod in all:
|
||||
try:
|
||||
exec 'from '+mod+' import *'
|
||||
exec('from '+mod+' import *')
|
||||
except:
|
||||
print "Error importing module", mod
|
||||
print("Error importing module", mod)
|
||||
pass
|
||||
|
||||
|
||||
|
||||
@ -26,7 +26,7 @@
|
||||
|
||||
|
||||
|
||||
from library import *
|
||||
from .library import *
|
||||
from math import *
|
||||
|
||||
class atom(object):
|
||||
@ -62,10 +62,10 @@ class atom(object):
|
||||
return 0
|
||||
|
||||
for i in "name charge coord basis".split():
|
||||
exec """
|
||||
exec("""
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
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):
|
||||
@ -213,5 +213,5 @@ for line in atomDataText.splitlines():
|
||||
|
||||
if __name__ == '__main__':
|
||||
for s in atomData:
|
||||
print s
|
||||
print(s)
|
||||
|
||||
|
||||
@ -27,7 +27,7 @@
|
||||
|
||||
|
||||
#import pdb
|
||||
from library import *
|
||||
from .library import *
|
||||
from math import *
|
||||
import sys
|
||||
|
||||
@ -97,10 +97,10 @@ class primitive(object):
|
||||
|
||||
norm = property (get_norm,None,doc="Sqrt( Integral f^2(R) dR ).")
|
||||
for i in "center expo sym".split():
|
||||
exec """
|
||||
exec("""
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
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 ddfact2(n):
|
||||
if n%2 == 0: print 'error in ddfact2'
|
||||
if n%2 == 0: print('error in ddfact2')
|
||||
res=1.
|
||||
for i in range(1,n+1,2):
|
||||
res*=float(i)
|
||||
@ -228,7 +228,7 @@ def xyz_from_lm(l,m):
|
||||
absm = abs(m)
|
||||
nb2 = absm
|
||||
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
|
||||
if m>=0:
|
||||
nb2_start = mod_absm_2
|
||||
@ -241,8 +241,8 @@ def xyz_from_lm(l,m):
|
||||
for n1 in range(nb2_start,nb2+1,2):
|
||||
k = (absm-n1)/2
|
||||
factor = (-1.)**k * binom(absm,n1) * norm
|
||||
for t in xrange(nb1+1):
|
||||
for n2 in xrange(t+1):
|
||||
for t in range(nb1+1):
|
||||
for n2 in range(t+1):
|
||||
coe = clmt[t] * factor * binom(t,n2)
|
||||
ipw = ( n1+2*n2 , absm-n1+2*(t-n2), l-2*t-absm )
|
||||
done = False
|
||||
@ -402,10 +402,10 @@ class contraction(object):
|
||||
|
||||
|
||||
for i in "center prim sym coef".split():
|
||||
exec """
|
||||
exec("""
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
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 ).")
|
||||
|
||||
@ -425,9 +425,9 @@ except ImportError:
|
||||
|
||||
if __name__ == '__main__':
|
||||
for l in range(6):
|
||||
print '---'
|
||||
print('---')
|
||||
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)
|
||||
|
||||
if __name__ == '__main__':
|
||||
@ -441,13 +441,13 @@ if __name__ == '__main__':
|
||||
b.center = [0.,0.,0.]
|
||||
x = spheToCart(a)
|
||||
y = spheToCart(a)
|
||||
print x
|
||||
print(x)
|
||||
sys.exit(0)
|
||||
print GoverlapCart(a,b)
|
||||
print GoverlapCartNorm2(a,b)
|
||||
print ''
|
||||
print(GoverlapCart(a,b))
|
||||
print(GoverlapCartNorm2(a,b))
|
||||
print('')
|
||||
for i in range(0,10):
|
||||
print rintgauss(i)
|
||||
print(rintgauss(i))
|
||||
sys.exit(0)
|
||||
c = gaussian()
|
||||
c.sym = 's'
|
||||
@ -458,7 +458,7 @@ if __name__ == '__main__':
|
||||
d.append(0.190362765893, b)
|
||||
d.append(0.852162022245, c)
|
||||
d.normalize()
|
||||
print d
|
||||
print(d)
|
||||
sys.exit(0)
|
||||
a = gaussian()
|
||||
a.sym = 'x'
|
||||
@ -471,14 +471,14 @@ if __name__ == '__main__':
|
||||
c = contraction()
|
||||
c.append(1.,a)
|
||||
c.append(2.,b)
|
||||
print c.value( (1.,1.,0.) )
|
||||
print b.overlap(a)
|
||||
print a.overlap(b)
|
||||
print a.norm
|
||||
print c.norm, c.coef
|
||||
print(c.value( (1.,1.,0.) ))
|
||||
print(b.overlap(a))
|
||||
print(a.overlap(b))
|
||||
print(a.norm)
|
||||
print(c.norm, c.coef)
|
||||
c.normalize()
|
||||
print c.norm, c.coef
|
||||
print(c.norm, c.coef)
|
||||
c.normalize()
|
||||
print c.norm, c.coef
|
||||
print Goverlap(a,b)
|
||||
print(c.norm, c.coef)
|
||||
print(Goverlap(a,b))
|
||||
|
||||
|
||||
@ -26,7 +26,7 @@
|
||||
|
||||
|
||||
|
||||
from library import *
|
||||
from .library import *
|
||||
|
||||
class CSF(object):
|
||||
"""Class for an configuration state function."""
|
||||
@ -69,8 +69,8 @@ class CSF(object):
|
||||
self._coefficients.append( c )
|
||||
|
||||
for i in "determinants coefficients".split():
|
||||
exec """
|
||||
exec("""
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
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())
|
||||
|
||||
|
||||
@ -27,7 +27,7 @@
|
||||
|
||||
|
||||
import struct
|
||||
from library import *
|
||||
from .library import *
|
||||
import sys
|
||||
|
||||
class fortranBinary(object):
|
||||
@ -51,7 +51,7 @@ Behaves like an array of records.
|
||||
def seek(self,index):
|
||||
self.file.seek(index)
|
||||
|
||||
def next(self):
|
||||
def __next__(self):
|
||||
if self.form is None:
|
||||
raise TypeError
|
||||
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")
|
||||
# form = xproperty ( '_form', doc="Format to read the binary record")
|
||||
for i in "recl mode name file form".split():
|
||||
exec """
|
||||
exec("""
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
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__':
|
||||
f = fortranBinary(sys.argv[1],"rb")
|
||||
f.form = 'l'+4*15000*'h'+15000*'d'
|
||||
print f.name
|
||||
print f.mode
|
||||
print f[0]
|
||||
print f[10]
|
||||
print f[0]
|
||||
print(f.name)
|
||||
print(f.mode)
|
||||
print(f[0])
|
||||
print(f[10])
|
||||
print(f[0])
|
||||
|
||||
@ -26,7 +26,7 @@
|
||||
|
||||
|
||||
|
||||
from library import *
|
||||
from .library import *
|
||||
from math import *
|
||||
|
||||
class integral(object):
|
||||
@ -56,19 +56,19 @@ class integral(object):
|
||||
return 0
|
||||
|
||||
for i in "indices value".split():
|
||||
exec """
|
||||
exec("""
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
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__':
|
||||
i = integral()
|
||||
i.indices = [1,4]
|
||||
i.value = 1.5
|
||||
print i
|
||||
print(i)
|
||||
j = integral()
|
||||
j.indices = [4,3,2,1]
|
||||
j.value = 2.5
|
||||
print j
|
||||
print i<j
|
||||
print(j)
|
||||
print(i<j)
|
||||
|
||||
@ -35,10 +35,10 @@ def prettyPrint(obj,shift=" "):
|
||||
prettyPrint(k)
|
||||
elif isinstance(obj,dict):
|
||||
for k in obj:
|
||||
print k
|
||||
print(k)
|
||||
prettyPrint(obj[k])
|
||||
else:
|
||||
print str(obj)
|
||||
print(str(obj))
|
||||
|
||||
def xproperty(fget, fset=None, fdel=None, doc=None):
|
||||
"""Automatically defines the properties if the functions don't exist."""
|
||||
|
||||
@ -26,7 +26,7 @@
|
||||
|
||||
|
||||
|
||||
from library import *
|
||||
from .library import *
|
||||
from math import *
|
||||
|
||||
class orbital(object):
|
||||
@ -96,10 +96,10 @@ class orbital(object):
|
||||
return result
|
||||
|
||||
for i in "eigenvalue vector basis set sym".split():
|
||||
exec """
|
||||
exec("""
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
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[2].eigenvalue = 3.
|
||||
for i in l:
|
||||
print i.eigenvalue
|
||||
print(i.eigenvalue)
|
||||
l.sort()
|
||||
print ""
|
||||
print("")
|
||||
for i in l:
|
||||
print i.eigenvalue
|
||||
print(i.eigenvalue)
|
||||
l[0].vector = [1., 0., 0.]
|
||||
l[1].vector = [0., 1., 0.]
|
||||
l[2].vector = [0., 1., 1.]
|
||||
print l[0].is_ortho(l[1])
|
||||
print l[1].is_ortho(l[2])
|
||||
print l[1].dot(l[2])
|
||||
print l[1].dot(l[0])
|
||||
print l[1].norm()
|
||||
print l[2].norm()
|
||||
print(l[0].is_ortho(l[1]))
|
||||
print(l[1].is_ortho(l[2]))
|
||||
print(l[1].dot(l[2]))
|
||||
print(l[1].dot(l[0]))
|
||||
print(l[1].norm())
|
||||
print(l[2].norm())
|
||||
|
||||
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user