def ics_get_ptorsions(ics_st, adj_list, xcc, epslin=5.0):
'''epslin in degrees'''
ics_pt = []
for at2, at3 in ics_st:
x2 = fncs.xyz(xcc, at2)
x3 = fncs.xyz(xcc, at3)
bondedto2 = list(adj_list[at2])
bondedto3 = list(adj_list[at3])
bondedto2.remove(at3)
bondedto3.remove(at2)
if len(bondedto2) == 0: continue
if len(bondedto3) == 0: continue
for at1 in bondedto2:
x1 = fncs.xyz(xcc, at1)
for at4 in bondedto3:
if at1 == at4: continue
x4 = fncs.xyz(xcc, at4)
# the two angles
angA = fncs.rad2deg(fncs.angle(x1, x2, x3))
angB = fncs.rad2deg(fncs.angle(x2, x3, x4))
# linear?
booleanA = angA < epslin or angA > 180 - epslin
booleanB = angB < epslin or angB > 180 - epslin
if booleanA or booleanB: continue
ptorsion = (at1, at2, at3, at4)
ics_pt.append(ptorsion)
return ics_pt
def wilson_getBC(xcc, all_ics):
numics = count_ics(all_ics)
ics_st, ics_ab, ics_lb, ics_it, ics_pt = unmerge_ics(all_ics)
# unit bond vectors
natoms = fncs.howmanyatoms(xcc)
bvecs = wilson_bvecs(xcc)
# initialize matrices
wilsonB = [[0.0 for row in range(numics)] for col in range(3 * natoms)]
wilsonB, wilsonC = [], []
# B and C: stretchings
for atoms in ics_st:
row_B, matrix_C = wilson_stretch(bvecs, atoms, natoms)
wilsonB += row_B
wilsonC += matrix_C
# B and C: angular bendings
for atoms in ics_ab:
row_B, matrix_C = wilson_abend(bvecs, atoms, natoms)
wilsonB += row_B
wilsonC += matrix_C
# B and C: linear bendings
for atoms in ics_lb:
i, j, k = atoms
r_m = np.array(fncs.xyz(xcc, i))
r_o = np.array(fncs.xyz(xcc, j))
r_n = np.array(fncs.xyz(xcc, k))
row_B, matrix_C = wilson_lbend(r_m, r_o, r_n, atoms, natoms)
wilsonB += row_B
wilsonC += matrix_C
# B and C: torsions (proper and improper)
for atoms in ics_it + ics_pt:
row_B, matrix_C = wilson_torsion(bvecs, atoms, natoms)
wilsonB += row_B
wilsonC += matrix_C
return np.matrix(wilsonB), [np.matrix(ll) for ll in wilsonC]
def distance_2fragments(frg1, frg2, xcc):
min_dist = float("inf")
pair = (None, None)
for at1 in frg1:
x1 = fncs.xyz(xcc, at1)
for at2 in frg2:
x2 = fncs.xyz(xcc, at2)
dist = fncs.distance(x1, x2)
if dist < min_dist:
min_dist = dist
pair = (at1, at2)
return min_dist, pair
def ics_classify_bends(xcc, ic_3ats, eps_lin=5.0):
ics_lb = []
ics_ab = []
thetas = {}
for at1, at2, at3 in ic_3ats:
x1 = fncs.xyz(xcc, at1)
x2 = fncs.xyz(xcc, at2)
x3 = fncs.xyz(xcc, at3)
theta = abs(fncs.rad2deg(fncs.angle(x1, x2, x3)))
if theta < eps_lin or theta > 180 - eps_lin:
ics_lb.append((at1, at2, at3))
else:
ics_ab.append((at1, at2, at3))
thetas[(at1, at2, at3)] = theta
return ics_lb, ics_ab, thetas
def rst2xyz(rst, xyz, onlyhess=True, Eref=None):
tpath, tcommon, drst = read_rst(rst)
thelist = [(data[0], label) for (label, data) in drst.items()]
thelist.sort()
(ch, mtp, atonums, masses, mu) = tcommon
symbols = fncs.atonums2symbols(atonums)
natoms = len(symbols)
string = ""
for s_i, label in thelist:
s_i, E_i, xms_i, gms_i, Fms_i, v0_i, v1_i, t_i = drst[label]
if onlyhess and Fms_i is None: continue
if Eref is not None:
E_i = (E_i - Eref) * KCALMOL
energy = "%+.4f kcal/mol" % E_i
else:
energy = "%+.6f hartree" % E_i
string += " %i\n" % natoms
string += " * E = %s ; s = %7.4f (%s)\n" % (energy, s_i, label)
xcc_i = fncs.ms2cc_x(xms_i, masses, mu)
for idx, symbol in enumerate(symbols):
x, y, z = fncs.xyz(xcc_i, idx)
x *= ANGSTROM
y *= ANGSTROM
z *= ANGSTROM
string += " %2s %+10.6f %+10.6f %+10.6f\n" % (symbol, x, y, z)
write_file(xyz, string)
def ics_value(xcc, ic):
''' ic = (ic_type,ic_atoms)'''
if type(ic) == type("string"):
ic_type, ic_atoms = string2ic(ic)
else:
ic_type, ic_atoms = ic
if ic_type == "st":
return fncs.distance(*(fncs.xyz(xcc, at) for at in ic_atoms))
if ic_type == "ab":
return fncs.angle(*(fncs.xyz(xcc, at) for at in ic_atoms))
if ic_type == "lb":
return fncs.angle(*(fncs.xyz(xcc, at) for at in ic_atoms))
if ic_type == "it":
return fncs.dihedral(*(fncs.xyz(xcc, at) for at in ic_atoms))
if ic_type == "pt":
return fncs.dihedral(*(fncs.xyz(xcc, at) for at in ic_atoms))
def wilson_bvecs(xcc):
'''
This functions calculates the distance
between each pair of atoms (dij) and also
the unit bond vector eij = (rj - ri)/dij
'''
nat = fncs.howmanyatoms(xcc)
bond_vectors = {}
for ii in range(nat):
ri = np.array(fncs.xyz(xcc, ii))
for jj in range(ii + 1, nat):
rj = np.array(fncs.xyz(xcc, jj))
eij = rj - ri
dij = np.linalg.norm(eij)
eij = eij / dij
bond_vectors[(ii, jj)] = (eij, dij)
bond_vectors[(jj, ii)] = (-eij, dij)
return bond_vectors
def puckering_rjs(xvec, atoms_in_ring):
''' JACS 1975, 97:6, 1354-1358; eq (4) '''
gc = np.array(fncs.get_centroid(xvec, atoms_in_ring))
list_Rj = []
for at in atoms_in_ring:
rj = np.array(fncs.xyz(xvec, at))
Rj = rj - gc
list_Rj.append(Rj)
return list_Rj, gc
def write_molden(filename, xcc, symbs, freqs, evecs):
'''evecs NOT in mass-scaled!'''
natoms = len(symbs)
nfreqs = len(freqs)
STRING = "[Molden Format]\n"
STRING += "[FR-COORD] # Coordinates in bohr\n"
for at in range(natoms):
symbol = symbs[at]
x, y, z = fncs.xyz(xcc, at)
STRING += " %2s %+11.6f %+11.6f %+11.6f \n" % (symbol, x, y, z)
if freqs not in [None, []]:
STRING += "[FREQ] # Frequencies in cm^-1\n"
for idx in range(nfreqs):
freq = fncs.afreq2cm(freqs[idx])
STRING += " %9.4f\n" % freq
if evecs not in [None, []]:
STRING += "[FR-NORM-COORD] # Displacements in bohr\n"
for idx in range(nfreqs):
STRING += "vibration %i\n" % (idx + 1)
evec = evecs[idx]
for at in range(natoms):
vx, vy, vz = fncs.xyz(evec, at)
STRING += " %+9.3f %+9.3f %+9.3f\n" % (vx, vy, vz)
write_file(filename, STRING)
def write_gtsfile(xcc,
atonums,
ch,
mtp,
E,
pgroup,
rotsigma,
gcc,
Fcc,
gtsfile,
freqs=None,
level=""):
if gcc is None: gcc = []
if Fcc is None: Fcc = []
if freqs is None: freqs = []
nat = len(atonums)
str_gts = ""
# Write atomic numbers and cartesian coordinates
if level != "": str_gts += "# level: %s\n" % level
str_gts += "# Atomic number and non-scaled cartesian coordinates [bohr]\n"
str_gts += "start_cc\n"
for at in range(nat):
atonum = atonums[at]
xx, yy, zz = fncs.xyz(xcc, at)
str_gts += " %03i %+15.8E %+15.8E %+15.8E\n" % (atonum, xx, yy,
zz)
str_gts += "end_cc\n\n"
# Write basic data
str_gts += "# Charge, multiplicity, energy [hartree],\n"
str_gts += "# point group and rotational symmetry number\n"
str_gts += "start_basic\n"
str_gts += " charge %i\n" % ch
str_gts += " multiplicity %i\n" % mtp
str_gts += " energy %-+16.8f # Total energy in hartree\n" % E
str_gts += " pointgroup %-5s # Point group\n" % pgroup
str_gts += " rotsigma %-5i # Rotational sigma\n" % rotsigma
str_gts += "end_basic\n\n"
# Write cartesian gradiend
if len(gcc) != 0:
str_gts += "# Non-scaled cartesian gradient [hartree/bohr]\n"
str_gts += "start_grad\n"
for at in range(nat):
gxx, gyy, gzz = fncs.xyz(gcc, at)
str_gts += " %+15.8E %+15.8E %+15.8E\n" % (gxx, gyy, gzz)
str_gts += "end_grad\n\n"
# Write force constant matrix (i.e. hessian matrix)
if len(Fcc) != 0:
if len(Fcc) == 3 * nat: # not in triangular form
Fcc = matrix2lowt(Fcc)
str_gts += "# Low triangular part of force constant (hessian) matrix [hartree/bohr^2]\n"
str_gts += "# i.e.: F_11, F_21, F_22, F_13, F_23, F_33...\n"
str_gts += "start_hess\n"
for idx in range(0, len(Fcc), 5):
line = " ".join(["%+15.8E" % Fij for Fij in Fcc[idx:idx + 5]])
str_gts += " %s\n" % line
str_gts += "end_hess\n\n"
# Write freqs
elif len(freqs) != 0:
str_gts += "start_freqs\n"
for idx in range(0, len(freqs), 5):
line = " ".join(["%7.2f" % (freq) for freq in freqs[idx:idx + 5]])
str_gts += " %s\n" % line
str_gts += "end_freqs\n\n"
# write
write_file(gtsfile, str_gts)
def info_string(self,ib=0):
root_mass = sum(fncs.symbols2masses(self._symbols))
string = "mol. formula : %s\n"%self._mform
string += "num atoms : %i\n"%self._natoms
string += "num vib dof : %i\n"%self._nvdof
string += "charge : %i\n"%self._ch
string += "multiplicity : %i\n"%self._mtp
string += "electronic energy (V0): %.8f hartree\n"%self._V0
string += "total mass [root] : %.4f amu\n"%(root_mass *AMU)
string += "total mass : %.4f amu\n"%(self._mass*AMU)
if self._pgroup is not None: string += "point group : %s\n"%(self._pgroup)
if self._rotsigma is not None: string += "rot sym num : %i\n"%(self._rotsigma)
string += "Cartesian coordinates (Angstrom):\n"
for at,symbol in enumerate(self._symbols):
mass = self._masses[at]*AMU
x,y,z = fncs.xyz(self._xcc,at)
x *= ANGSTROM
y *= ANGSTROM
z *= ANGSTROM
string += " %2s %+10.6f %+10.6f %+10.6f [%7.3f amu]\n"%(symbol,x,y,z,mass)
#if True:
try:
str2 = "moments and product of inertia (au):\n"
if len(self._imoms) == 1:
str2 += " %+10.3E\n"%self._imoms[0]
if len(self._imoms) == 3:
prodinert = self._imoms[0]*self._imoms[1]*self._imoms[2]
dataline = (self._imoms[0],self._imoms[1],self._imoms[2],prodinert)
str2 += " %+10.3E %+10.3E %+10.3E [%10.3E]\n"%dataline
string += str2
except: pass
try:
str2 = "vibrational frequencies [1/cm] (scaled by %.3f):\n"%self._fscal
for idx in range(0,len(self._ccfreqs),6):
str2 += " %s\n"%(" ".join("%8.2f"%fncs.afreq2cm(freq) \
for freq in self._ccfreqs[idx:idx+6]))
if len(self._ccfreqs) != 0: string += str2
except: pass
try:
str2 = "individual zero-point energies [kcal/mol]:\n"
for idx in range(0,len(self._cczpes),6):
str2 += " %s\n"%(" ".join("%8.2f"%(zpe*KCALMOL) \
for zpe in self._cczpes[idx:idx+6]))
zpe_au = self._cczpe
zpe_kcal = self._cczpe * KCALMOL
zpe_eV = self._cczpe * EV
zpe_cm = self._cczpe * H2CM
str2 += "vibrational zero-point energy (ZPE): %+14.8f hartree = \n"%zpe_au
str2 += " %+14.2f kcal/mol = \n"%zpe_kcal
str2 += " %+14.2f eV = \n"%zpe_eV
str2 += " %+14.2f cm^-1 \n"%zpe_cm
#str2 += "zero-point energy (zpe) : %+14.8f hartree = %.2f kcal/mol = %.3f eV\n"%(zpe_au,zpe_kcal,zpe_eV)
str2 += "electronic energy + ZPE (V1) : %+14.8f hartree\n"%self._ccV1
if self._cczpe != 0.0: string += str2
except: pass
# add blank spaces
string = "\n".join([" "*ib+line for line in string.split("\n")])
return string