blist = get_blist(mol, atids)
all_list = get_all_list(mol, blist, atids, 8.0)
natids = {}
for i in range(0, len(atids)):
natids[atids[i]] = i + 1
#crds after optimization
if options.softversion in ['g03', 'g09']:
crds = get_crds_from_fchk(options.hessfile, len(atids))
elif options.softversion == 'gms':
crds = get_crds_from_gms(options.hessfile)
#Whole Hessian Matrix
if options.softversion in ['g03', 'g09']:
fcmatrix = get_matrix_from_fchk(options.hessfile, 3*len(atids))
elif options.softversion == 'gms':
fcmatrix = get_matrix_from_gms(options.hessfile, 3*len(atids))
for i in all_list.bondlist:
at1 = i[0]
at2 = i[1]
nat1 = natids[at1]
nat2 = natids[at2]
if options.bondavg is True:
dis, fcfinal, stdv = get_bond_fc_with_sem(crds, fcmatrix, nat1, nat2, options.scalef, 1)
else:
dis, fcfinal = get_bond_fc_with_sem(crds, fcmatrix, nat1, nat2, options.scalef, 0)
print('### Bond force constant between ' + \
blist = get_blist(mol, atids)
all_list = get_all_list(mol, blist, atids, 8.0)
natids = {}
for i in range(0, len(atids)):
natids[atids[i]] = i + 1
#crds after optimization
if options.softversion in ['g03', 'g09']:
crds = get_crds_from_fchk(options.hessfile, len(atids))
elif options.softversion == 'gms':
crds = get_crds_from_gms(options.hessfile)
#Whole Hessian Matrix
if options.softversion in ['g03', 'g09']:
fcmatrix = get_matrix_from_fchk(options.hessfile, 3 * len(atids))
elif options.softversion == 'gms':
fcmatrix = get_matrix_from_gms(options.hessfile, 3 * len(atids))
for i in all_list.bondlist:
at1 = i[0]
at2 = i[1]
nat1 = natids[at1]
nat2 = natids[at2]
if options.bondavg is True:
dis, fcfinal, stdv = get_bond_fc_with_sem(crds, fcmatrix, nat1, nat2,
options.scalef, 1)
else:
dis, fcfinal = get_bond_fc_with_sem(crds, fcmatrix, nat1, nat2,
options.scalef, 0)
def gene_by_QM_fitting_sem(smpdbf, ionids, stfpf, pref, finf, chkfname,
logfile, g0x, scalef, bondavg, angavg):
print("==================Using the Seminario method to solve the problem.")
mol, atids, resids = get_atominfo_fpdb(smpdbf)
blist = get_mc_blist(mol, atids, ionids, stfpf)
alist = get_alist(mol, blist)
#crds after optimization
if g0x in ['g03', 'g09']:
crds = get_crds_from_fchk(chkfname, len(atids))
elif g0x == 'gms':
crds = get_crds_from_gms(logfile)
#Whole Hessian Matrix
if g0x in ['g03', 'g09']:
fcmatrix = get_matrix_from_fchk(chkfname, 3*len(atids))
elif g0x == 'gms':
fcmatrix = get_matrix_from_gms(logfile, 3*len(atids))
natids = {}
for i in range(0, len(atids)):
natids[atids[i]] = i + 1
attypdict = get_attypdict(stfpf, atids)
missbondtyps, missangtyps = get_misstyps(pref)
finalparmdict = {}
#for bond
print("=======================Generate the bond parameters===============")
for misbond in missbondtyps:
bondlen = []
bfconst = []
for bond in blist:
at1 = bond[0]
at2 = bond[1]
bondtyp = (attypdict[at1], attypdict[at2])
"The unit in fchk file is a.u. so the distance is in Bohr."
if bondtyp == misbond or bondtyp[::-1] == misbond:
nat1 = natids[at1]
nat2 = natids[at2]
if bondavg == 1:
dis, fcfinal, stdv = get_bond_fc_with_sem(crds, fcmatrix, nat1, nat2, scalef, bondavg)
print('### Bond force constant between ' + \
mol.atoms[at1].resname + str(mol.atoms[at1].resid) + '@' + mol.atoms[at1].atname + ' and ' + \
mol.atoms[at2].resname + str(mol.atoms[at2].resid) + '@' + mol.atoms[at2].atname + ' : ' + \
str(round(fcfinal, 1)) + ' with StdDev ' + str(round(stdv, 1)))
elif bondavg == 0:
dis, fcfinal = get_bond_fc_with_sem(crds, fcmatrix, nat1, nat2, scalef, bondavg)
bondlen.append(dis)
bfconst.append(fcfinal)
#Get average bond parameters
misbondat12 = misbond[0] + '-' + misbond[1]
bond_para = avg_bond_para(misbondat12, bondlen, bfconst)
#get the force constant
finalparmdict[misbondat12] = bond_para
#for angle
print("=======================Generate the angle parameters==============")
for misang in missangtyps:
angvals = []
afconst = []
for ang in alist:
at1 = ang[0]
at2 = ang[1]
at3 = ang[2]
angtyp = (attypdict[at1], attypdict[at2], attypdict[at3])
if angtyp == misang or angtyp[::-1] == misang:
nat1 = natids[at1]
nat2 = natids[at2]
nat3 = natids[at3]
if angavg == 1:
angval, fcfinal, stdv = get_ang_fc_with_sem(crds, fcmatrix, nat1, nat2, nat3, scalef, angavg)
print('### Angle force constant between ' + \
mol.atoms[at1].resname + str(mol.atoms[at1].resid) + '@' + mol.atoms[at1].atname + ', ' + \
mol.atoms[at2].resname + str(mol.atoms[at2].resid) + '@' + mol.atoms[at2].atname + ' and ' + \
mol.atoms[at3].resname + str(mol.atoms[at3].resid) + '@' + mol.atoms[at3].atname + ' : ' + \
str(round(fcfinal, 2)) + ' with StdDev ' + str(round(stdv, 2)))
elif angavg == 0:
angval, fcfinal = get_ang_fc_with_sem(crds, fcmatrix, nat1, nat2, nat3, scalef, angavg)
angvals.append(angval)
afconst.append(fcfinal)
#Get average angle parameters
misangat123 = misang[0] + '-' + misang[1] + '-' + misang[2]
ang_para = avg_angle_para(misangat123, angvals, afconst)
finalparmdict[misangat123] = ang_para
#Print out the final frcmod file
print_frcmod_file(pref, finf, finalparmdict, 'Seminario')
def gene_by_QM_fitting_sem(smpdbf, ionids, stfpf, pref, finf, chkfname,
logfile, g0x, scalef, bondavg, angavg):
print("==================Using the Seminario method to solve the problem.")
mol, atids, resids = get_atominfo_fpdb(smpdbf)
blist = get_mc_blist(mol, atids, ionids, stfpf)
alist = get_alist(mol, blist)
#crds after optimization
if g0x in ['g03', 'g09']:
crds = get_crds_from_fchk(chkfname, len(atids))
elif g0x == 'gms':
crds = get_crds_from_gms(logfile)
#Whole Hessian Matrix
if g0x in ['g03', 'g09']:
fcmatrix = get_matrix_from_fchk(chkfname, 3 * len(atids))
elif g0x == 'gms':
fcmatrix = get_matrix_from_gms(logfile, 3 * len(atids))
natids = {}
for i in range(0, len(atids)):
natids[atids[i]] = i + 1
attypdict = get_attypdict(stfpf, atids)
missbondtyps, missangtyps = get_misstyps(pref)
finalparmdict = {}
#for bond
print("=======================Generate the bond parameters===============")
for misbond in missbondtyps:
bondlen = []
bfconst = []
for bond in blist:
at1 = bond[0]
at2 = bond[1]
bondtyp = (attypdict[at1], attypdict[at2])
"The unit in fchk file is a.u. so the distance is in Bohr."
if bondtyp == misbond or bondtyp[::-1] == misbond:
nat1 = natids[at1]
nat2 = natids[at2]
if bondavg == 1:
dis, fcfinal, stdv = get_bond_fc_with_sem(
crds, fcmatrix, nat1, nat2, scalef, bondavg)
print('### Bond force constant between ' + \
mol.atoms[at1].resname + str(mol.atoms[at1].resid) + '@' + mol.atoms[at1].atname + ' and ' + \
mol.atoms[at2].resname + str(mol.atoms[at2].resid) + '@' + mol.atoms[at2].atname + ' : ' + \
str(round(fcfinal, 1)) + ' with StdDev ' + str(round(stdv, 1)))
elif bondavg == 0:
dis, fcfinal = get_bond_fc_with_sem(
crds, fcmatrix, nat1, nat2, scalef, bondavg)
bondlen.append(dis)
bfconst.append(fcfinal)
#Get average bond parameters
misbondat12 = misbond[0] + '-' + misbond[1]
bond_para = avg_bond_para(misbondat12, bondlen, bfconst)
#get the force constant
finalparmdict[misbondat12] = bond_para
#for angle
print("=======================Generate the angle parameters==============")
for misang in missangtyps:
angvals = []
afconst = []
for ang in alist:
at1 = ang[0]
at2 = ang[1]
at3 = ang[2]
angtyp = (attypdict[at1], attypdict[at2], attypdict[at3])
if angtyp == misang or angtyp[::-1] == misang:
nat1 = natids[at1]
nat2 = natids[at2]
nat3 = natids[at3]
if angavg == 1:
angval, fcfinal, stdv = get_ang_fc_with_sem(
crds, fcmatrix, nat1, nat2, nat3, scalef, angavg)
print('### Angle force constant between ' + \
mol.atoms[at1].resname + str(mol.atoms[at1].resid) + '@' + mol.atoms[at1].atname + ', ' + \
mol.atoms[at2].resname + str(mol.atoms[at2].resid) + '@' + mol.atoms[at2].atname + ' and ' + \
mol.atoms[at3].resname + str(mol.atoms[at3].resid) + '@' + mol.atoms[at3].atname + ' : ' + \
str(round(fcfinal, 2)) + ' with StdDev ' + str(round(stdv, 2)))
elif angavg == 0:
angval, fcfinal = get_ang_fc_with_sem(
crds, fcmatrix, nat1, nat2, nat3, scalef, angavg)
angvals.append(angval)
afconst.append(fcfinal)
#Get average angle parameters
misangat123 = misang[0] + '-' + misang[1] + '-' + misang[2]
ang_para = avg_angle_para(misangat123, angvals, afconst)
finalparmdict[misangat123] = ang_para
#Print out the final frcmod file
print_frcmod_file(pref, finf, finalparmdict, 'Seminario')
def get_all_fc_with_sem(mol, atids, hessf, prog, scalef, bondavg, avg13,
angavg):
"""Generate all the force constants with Z-matrix method"""
print_method_title('S')
# Get the new atom ids
natids = {}
for i in xrange(0, len(atids)):
natids[atids[i]] = i + 1
# Get the connection list
blist = get_blist(mol, atids)
all_list = get_all_list(mol, blist, atids, 8.0)
# Crds after optimization
if prog in ['g03', 'g09']:
crds = get_crds_from_fchk(hessf, len(atids))
elif prog == 'gms':
crds = get_crds_from_gms(hessf)
# Whole Hessian Matrix
if prog in ['g03', 'g09']:
fcmatrix = get_matrix_from_fchk(hessf, 3 * len(atids))
elif prog == 'gms':
fcmatrix = get_matrix_from_gms(hessf, 3 * len(atids))
# Print the bond part
if bondavg is True:
print_bond_title_wsd()
else:
print_bond_title()
for i in all_list.bondlist:
at1 = i[0]
at2 = i[1]
nat1 = natids[at1]
nat2 = natids[at2]
at1_rep = atom_rep(mol, at1)
at2_rep = atom_rep(mol, at2)
if bondavg is True:
dis, fcfinal, stdv = get_bond_fc_with_sem(crds, fcmatrix, nat1,
nat2, scalef, 1)
print_bond_inf_wsd(at1_rep, at2_rep, fcfinal, stdv, dis)
else:
dis, fcfinal = get_bond_fc_with_sem(crds, fcmatrix, nat1, nat2,
scalef, 0)
print_bond_inf(at1_rep, at2_rep, fcfinal, dis)
# Print the 1-3 part
if avg13 is True:
print_13_title_wsd()
else:
print_13_title()
for i in all_list.anglist:
at1 = i[0]
at3 = i[2]
nat1 = natids[at1]
nat3 = natids[at3]
at1_rep = atom_rep(mol, at1)
at3_rep = atom_rep(mol, at3)
if avg13 is True:
dis, fcfinal, stdv = get_bond_fc_with_sem(crds, fcmatrix, nat1,
nat3, scalef, 1)
print_13_inf_wsd(at1_rep, at3_rep, fcfinal, stdv, dis)
else:
dis, fcfinal = get_bond_fc_with_sem(crds, fcmatrix, nat1, nat3,
scalef, 0)
print_13_inf(at1_rep, at3_rep, fcfinal, dis)
# Print the Angle part
if angavg is True:
print_angle_title_wsd()
else:
print_angle_title()
for i in all_list.anglist:
at1 = i[0]
at2 = i[1]
at3 = i[2]
nat1 = natids[at1]
nat2 = natids[at2]
nat3 = natids[at3]
at1_rep = atom_rep(mol, at1)
at2_rep = atom_rep(mol, at2)
at3_rep = atom_rep(mol, at3)
if angavg is True:
angval, fcfinal, stdv = get_ang_fc_with_sem(
crds, fcmatrix, nat1, nat2, nat3, scalef, 1)
print_angle_inf_wsd(at1_rep, at2_rep, at3_rep, fcfinal, stdv,
angval)
else:
angval, fcfinal = get_ang_fc_with_sem(crds, fcmatrix, nat1, nat2,
nat3, scalef, 0)
print_angle_inf(at1_rep, at2_rep, at3_rep, fcfinal, angval)
# Print the Dihedral part
print_dih_title()
for i in all_list.dihlist:
at1 = i[0]
at2 = i[1]
at3 = i[2]
at4 = i[3]
nat1 = natids[at1]
nat2 = natids[at2]
nat3 = natids[at3]
nat4 = natids[at4]
at1_rep = atom_rep(mol, at1)
at2_rep = atom_rep(mol, at2)
at3_rep = atom_rep(mol, at3)
at4_rep = atom_rep(mol, at4)
dihval, fcfinal = get_dih_fc_with_sem(crds, fcmatrix, nat1, nat2, nat3,
nat4, scalef)
print_dih_inf(at1_rep, at2_rep, at3_rep, at4_rep, fcfinal, dihval)
# Print the Improper part
print_imp_title()
for i in all_list.implist:
at1 = i[0]
at2 = i[1]
at3 = i[2] #Central atom
at4 = i[3]
nat1 = natids[at1]
nat2 = natids[at2]
nat3 = natids[at3]
nat4 = natids[at4]
at1_rep = atom_rep(mol, at1)
at2_rep = atom_rep(mol, at2)
at3_rep = atom_rep(mol, at3)
at4_rep = atom_rep(mol, at4)
if mol.atoms[at1].element == mol.atoms[at2].element:
fcfinal, dis = get_imp_fc_with_sem(
crds, fcmatrix, nat3, nat1, nat2, nat4,
scalef) #Treat the central atom first
print_imp_inf(at1_rep, at2_rep, at3_rep, at4_rep, fcfinal, dis)
elif mol.atoms[at1].element == mol.atoms[at4].element:
fcfinal, dis = get_imp_fc_with_sem(
crds, fcmatrix, nat3, nat1, nat4, nat2,
scalef) #Treat the central atom first
print_imp_inf(at1_rep, at4_rep, at3_rep, at2_rep, fcfinal, dis)
elif mol.atoms[at2].element == mol.atoms[at4].element:
fcfinal, dis = get_imp_fc_with_sem(
crds, fcmatrix, nat3, nat2, nat4, nat1,
scalef) #Treat the central atom first
print_imp_inf(at4_rep, at2_rep, at3_rep, at1_rep, fcfinal, dis)
else:
fcfinal, dis = get_imp_fc_with_sem(
crds, fcmatrix, nat3, nat1, nat2, nat4,
scalef) #Treat the central atom first
print_imp_inf(at1_rep, at2_rep, at3_rep, at4_rep, fcfinal, dis)
