def get_data_from_maintext(mtext):
key_geom1 = 'Z-Matrix orientation'
key_geom2 = 'Input orientation'
key_geom3 = 'Standard orientation'
key_force = " Forces ("
key_zmat = 'Final structure in terms of initial Z-matrix:'
key_end = "------------------"
key_1bar = "\\"
key_oniom = "ONIOM: extrapolated energy"
# (a) Find cartesian coordinates
if key_geom1 in mtext: geom = mtext.split(key_geom1)[-1]
elif key_geom2 in mtext: geom = mtext.split(key_geom2)[-1]
elif key_geom3 in mtext: geom = mtext.split(key_geom3)[-1]
else : geom = None
if geom is not None:
# convert to list of lines and get the lines associated to geometry
geom = "\n".join(geom.split("\n")[5:])
idx = geom.find(key_end)
geom = geom[:idx].strip()
# convert to list of floats
geom = [line.split() for line in geom.split("\n") if line.strip() != ""]
xcc = [[float(x),float(y),float(z)] for (_,atnum,_,x,y,z) in geom]
xcc = flatten_llist(xcc)
else: xcc = None
# (b) Find forces --> gradient
if key_force in mtext:
force = mtext.split(key_force)[-1]
# convert to list of lines and get the lines associated to forces
force = "\n".join(force.split("\n")[3:])
idx = force.find(key_end)
force = force[:idx]
# convert to list of floats
force = [line.split() for line in force.split("\n") if line.strip() != ""]
gcc = [[-float(gx),-float(gy),-float(gz)] for (_,atnum,gx,gy,gz) in force]
gcc = flatten_llist(gcc)
else: gcc = None
# (c) Find z-matrix
if key_zmat in mtext:
lines_zmat = mtext.split(key_zmat)[-1].strip().split("\n")
for idx,line in enumerate(lines_zmat):
line = line.strip()
if line == "" or key_1bar in line:
idx1 = idx
break
zmat = [line.strip() for line in lines_zmat[:idx1] if "Variables:" not in line]
else: zmat = None
# (d) ONIOM energy?
E_ONIOM = None
for line in mtext.split("\n")[::-1]:
if key_oniom in line:
E_ONIOM = float(line.split()[-1])
break
# Convert xcc to bohr
if xcc is not None: xcc = [xi/ANGSTROM for xi in xcc]
# Return data
return xcc, gcc, zmat, E_ONIOM
def write_molden_allconfs(dataconfs,Eref,allsymbols,folder):
print(tvars.IBS2+"Generating xyz file with all geometries...")
print(tvars.IBS2+" filename: %s"%(folder+tvars.ALLCONFS))
string = ""
for idx,conftuple in enumerate(dataconfs):
vec,V0,V1,G,weight,Qrv,ifreq,zmat,zmatvals,log = conftuple
# convert to xyz
V0_rel = (V0-Eref)*pc.KCALMOL
description = " * E = %+7.3f kcal/mol ; (%i) %s"%(V0_rel,idx+1,str(vec))
symbols = [symbol for symbol in allsymbols if symbol.upper() not in ("X","XX")]
natoms = len(symbols)
xcc = intl.zmat2xcc(zmat,zmatvals)
# remove dummy atoms (if there is any)
xcc = fncs.flatten_llist( [fncs.xyz(xcc,idx) for idx,symbol in enumerate(allsymbols) \
if symbol.upper() not in ("X","XX")])
# add to string
string += string4xyzfile(xcc,symbols,info=description)
with open(folder+tvars.ALLCONFS,'w') as asdf: asdf.write(string)
print("")
def get_data_from_archive(summary):
# Keywords to look for
key_hag = "#"
key_1bar ='\\'
key_2bar ='\\\\'
key_ver ='Version'
key_en1 ='State='
key_en2 ='RMSD='
key_imag ='NImag='
# logical variables
Lzmat = False
Lxyz = False
Lhess = False
# (a) the command line
idx1 = summary.find(key_hag,0)+len(key_hag)
idx2 = summary.find(key_2bar,idx1)
commands = summary[idx1:idx2]
# (b) the comment line
idx3 = summary.find(key_2bar,idx2)+len(key_2bar)
idx4 = summary.find(key_2bar,idx3)
comment = summary[idx3:idx4]
# (c) charge and multiplicity
idx5 = summary.find(key_2bar,idx4)+len(key_2bar)
idx6 = summary.find(key_1bar,idx5)
ch,mtp = [int(value) for value in summary[idx5:idx6].split(",")]
# (d) z-matrix or Cartesian coordinates
idx7 = summary.find(key_ver,idx6)
geom = [string for string in summary[idx6+len(key_1bar):idx7].split(key_1bar) if string != ""]
if len(geom[0]) <= 4:
Lzmat = True
zmat = list(geom)
symbols = [line.split(",")[0] for line in zmat if "=" not in line]
xcc = None
else:
Lxyz = True
zmat = None
symbols = [line.split(",")[0] for line in geom]
# sometimes, this line has 5 elements instead of 4
# for this reason, coordinates are extracted with [-3:]
# instead of [1:]
xyz = [line.split(",")[-3:] for line in geom]
xyz = [[float(x),float(y),float(z)] for (x,y,z) in xyz]
xcc = flatten_llist(xyz)
# (e) Energy and other info
idx8a = summary.find(key_ver,idx7)
idx8b = summary.find(key_en1,idx7)
idx8 = max(idx8a,idx8b)
idx9 = summary.find(key_1bar,idx8)+len(key_1bar)
idx10 = summary.find(key_en2,idx9)
str_energies = summary[idx9:idx10].replace(key_1bar," ")
energies = str_energies.split()
energies = [line.split("=") for line in energies]
# remove S**2 (for open-shell)
energies = [(float(energy),level.strip()) for level,energy in energies if not level.strip().startswith("S2")]
# (f) Hessian matrix
Lhess = key_imag in summary
if Lhess:
idx11=summary.find(key_imag,0)+len(key_imag)
idx12=summary.find(key_2bar,idx11)
num_imag = int(summary[idx11:idx12])
idx12 += len(key_2bar)
idx13=summary.find(key_2bar,idx12)
# low-triangle hessian
Fcc = [float(value) for value in summary[idx12:idx13].split(",")]
else:
num_imag = -1
Fcc = None
# (g) Gradient may appera after hessian matrix
if Lhess:
idx13 += len(key_2bar)
idx14=summary.find(key_2bar,idx13)
gcc = [float(value) for value in summary[idx13:idx14].split(",")]
else:
gcc = None
# Convert xcc to bohr
if xcc is not None: xcc = [xi/ANGSTROM for xi in xcc]
return commands,comment,ch,mtp,symbols,xcc,gcc,Fcc,energies,num_imag,zmat
def read_gauout(filename):
# check extension
end_out = (filename.lower()).endswith(".out")
end_log = (filename.lower()).endswith(".log")
if (not end_out) and (not end_log):
raise Exc.FileType(Exception)
key = 'GINC'
fin = '@'
str_end = 'Normal termination'
str_atoms = 'NAtoms'
str_geom1a = 'Z-Matrix orientation'
str_geom1b = 'Input orientation'
str_geom2 = 'Standard orientation'
str_nosym = 'Nosym'
str_zmat = 'Final structure in terms of initial Z-matrix'
start_archives = []
end_archives = []
str_endfiles = []
latom = []
idx_last_zmat = -1
list_zmat_backup = []
# More then one archive file for instance Link1
filex = open(filename, 'r')
nlin = 0
for linea in filex:
nlin += 1
if str_end in linea: str_endfiles.append(nlin)
if key in linea: start_archives.append(nlin)
if fin in linea: end_archives.append(nlin)
if str_atoms in linea:
latom = linea.split()
filex.close()
# It does not consider an archive file right after the main archive file
# For some reason gaussian sometimes print one archive after the other
str_tmp = str_endfiles[:]
num_tmp = len(str_tmp)
if num_tmp > 1:
for i in range(num_tmp - 1, 0, -1):
if abs(str_tmp[i - 1] - str_tmp[i]) < 300:
del str_endfiles[i]
del start_archives[i]
del end_archives[i]
#
#
number_archives = len(start_archives)
if number_archives == 0: return -1
str_beginfiles = str_endfiles[:]
str_beginfiles.insert(0, 0)
str_beginfiles.pop()
natoms = int(latom[1])
if number_archives == 1 and start_archives[0] == 0: return
str_geom1s = []
str_geom2s = []
str_nosyms = []
str_zmats = []
for i in range(number_archives):
str_geom1s.append(0)
str_geom2s.append(0)
str_nosyms.append(0)
str_zmats.append(0)
start_archive = start_archives[i]
end_archive = end_archives[i]
pos_beginfile = str_beginfiles[i]
pos_endfile = str_endfiles[i]
filex = open(filename, 'r')
nlin = 0
for linea in filex:
nlin += 1
if nlin >= pos_beginfile and nlin <= pos_endfile:
if str_nosym.lower() in linea.lower(): str_nosyms[i] = nlin
if str_geom1a in linea or str_geom1b in linea:
str_geom1s[i] = nlin
if str_geom2 in linea: str_geom2s[i] = nlin
if str_zmat in linea: str_zmats[i] = nlin
filex.close()
# position of the geometries
pos_nosym = str_nosyms[i]
pos_geom1 = str_geom1s[i]
pos_geom2 = str_geom2s[i]
pos_zmat1 = str_zmats[i]
num_imag,charge,mult,commands,list_level,list_energy,atomic_number,ccgeom,list_zmat,\
hess_data,hess_full,grad=\
archive(filename,natoms,start_archive,end_archive,\
pos_beginfile,pos_endfile,pos_nosym,pos_geom1,pos_geom2,pos_zmat1)
# Saves the last available z-matrix
if str_zmats[i] != 0:
idx_last_zmat = i
list_zmat_backup = list_zmat[:]
# atomic mass
atomic_mass = atonums2masses(atomic_number)
ccgeom = flatten_llist(ccgeom)
energy = list_energy[-1]
level = list_level[-1]
# from Angstrom to Bohr
ccgeom = [xx / ANGSTROM for xx in ccgeom]
return ccgeom, atomic_number, charge, mult, energy, grad, hess_data, atomic_mass, level