mirror of https://gitlab.com/scemama/eplf
181 lines
4.7 KiB
Python
Executable File
181 lines
4.7 KiB
Python
Executable File
#!/usr/bin/env python
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import sys,os,time
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wd = os.path.dirname(__file__)
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sys.path += [ wd+"../EZFIO/Python" ]
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sys.path += [ "/home/scemama/resultsFile" ]
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from resultsFile import *
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# Check command line
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if len(sys.argv) == 2:
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State=0
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elif len(sys.argv) == 3:
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State=int(sys.argv[2])
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else:
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print "usage: "+sys.argv[0]+" file.out"
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sys.exit(2)
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firstArg = sys.argv[1]
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file = getFile(firstArg)
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print firstArg, 'recognized as', str(file).split('.')[-1].split()[0]
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from ezfio import ezfio
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def write_ezfioFile(res,filename):
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ezfio.set_file(filename)
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# Electrons
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ezfio.set_electrons_elec_alpha_num(res.num_alpha)
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ezfio.set_electrons_elec_beta_num(res.num_beta)
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# Nuclei
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ezfio.set_nuclei_nucl_num(len(res.geometry))
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charge = []
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coord = []
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coord_x = []
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coord_y = []
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coord_z = []
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for a in res.geometry:
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charge.append(a.charge)
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if res.units == 'BOHR':
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coord_x.append(a.coord[0])
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coord_y.append(a.coord[1])
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coord_z.append(a.coord[2])
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else:
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coord_x.append(a.coord[0]/a0)
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coord_y.append(a.coord[1]/a0)
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coord_z.append(a.coord[2]/a0)
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ezfio.set_nuclei_nucl_charge(charge)
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ezfio.set_nuclei_nucl_coord(coord_x+coord_y+coord_z)
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# AO Basis
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import string
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is_cartesian = True
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at = []
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num_prim = []
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magnetic_number = []
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angular_number = []
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power_x = []
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power_y = []
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power_z = []
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coefficient = []
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exponent = []
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for b in res.basis:
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if '+' in b.sym or '-' in b.sym:
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is_cartesian = False
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names = ["s","p","d","f","g","h","i","j"]
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for b in res.basis:
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c = b.center
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for i,atom in enumerate(res.geometry):
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if atom.coord == c:
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at.append(i+1)
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num_prim.append(len(b.prim))
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if is_cartesian:
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s = b.sym
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power_x.append( string.count(s,"x") )
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power_y.append( string.count(s,"y") )
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power_z.append( string.count(s,"z") )
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else:
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magnetic_number.append(names.index(b.sym[0]))
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angular_number.append(int(b.sym[1:]))
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coefficient.append( b.coef )
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exponent.append( [ p.expo for p in b.prim ] )
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if not is_cartesian:
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print 'Only cartesian basis functions work...'
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sys.exit(0)
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ezfio.set_ao_basis_ao_num(len(res.basis))
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ezfio.set_ao_basis_ao_nucl(at)
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ezfio.set_ao_basis_ao_prim_num(num_prim)
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ezfio.set_ao_basis_ao_power(power_x+power_y+power_z)
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prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
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len_res_basis = len(res.basis)
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for i in range(len(res.basis)):
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coefficient[i] += [ 0. for j in range(len(coefficient[i]),prim_num_max) ]
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exponent[i] += [ 0. for j in range(len(exponent[i]),prim_num_max) ]
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coefficient = reduce(lambda x, y: x+y, coefficient, [])
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exponent = reduce(lambda x, y: x+y, exponent, [])
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coef = []
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expo = []
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for i in range(prim_num_max):
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for j in range(i,len(coefficient),prim_num_max):
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coef.append ( coefficient[j] )
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expo.append ( exponent[j] )
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ezfio.set_ao_basis_ao_coef(coef)
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ezfio.set_ao_basis_ao_expo(expo)
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# MOs
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NumOrbSym = [ s[1] for s in res.symmetries ]
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mo_tot_num = sum(NumOrbSym)
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ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
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if res.occ_num is not None:
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ezfio.set_mo_basis_mo_occ(res.occ_num)
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MoTag = res.mo_types[-1]
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mo = res.mo_sets[MoTag]
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if len(mo) < mo_tot_num:
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newmo = orbital()
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newmo.eigenvalue = 0.
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newmo.vector = [0. for i in range(mo_tot_num)]
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while len(mo) < mo_tot_num:
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mo.append(newmo)
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Energies = [ m.eigenvalue for m in mo ]
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ezfio.set_mo_basis_mo_energy(Energies)
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if res.occ_num is not None:
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OccNum = res.occ_num[MoTag]
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while len(OccNum) < mo_tot_num:
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OccNum.append(0.)
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ezfio.set_mo_basis_mo_occ(OccNum)
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cls = [ "v" for i in mo ]
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for i in res.closed_mos:
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cls[i] = 'c'
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for i in res.active_mos:
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cls[i] = 'a'
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ezfio.set_mo_basis_mo_classif(cls)
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MoMatrix = []
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for m in mo:
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for coef in m.vector:
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MoMatrix.append(coef)
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while len(MoMatrix) < len(mo[0].vector)**2:
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MoMatrix.append(0.)
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ezfio.set_mo_basis_mo_coef(MoMatrix)
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# Determinants
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closed_mos = res.closed_mos
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nactive = ezfio.get_mo_basis_mo_active_num()
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dets_a = []
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dets_b = []
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for d in res.determinants:
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dnew_a = []
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dnew_b = []
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for x in d['alpha']:
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if x not in closed_mos:
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dnew_a.append(x+1)
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for x in d['beta']:
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if x not in closed_mos:
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dnew_b.append(x+1)
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for x in range(nactive-len(dnew_b)):
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dnew_b.append(0)
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dets_a.append( dnew_a )
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dets_b.append( dnew_b )
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coef = reduce(lambda x, y: x+y,res.det_coefficients,[])
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if len(dets_a[0]) > 0:
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ezfio.set_determinants_det_num(len(dets_a))
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ezfio.set_determinants_det_coef(coef)
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ezfio.set_determinants_det_occ(dets_a+dets_b)
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else:
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ezfio.set_determinants_det_num(1)
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ezfio.set_determinants_det_coef([1.])
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ezfio.set_determinants_det_occ(dets_a+dets_b)
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write_ezfioFile(file,firstArg+".ezfio")
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