def highlevel_mep(ctc, itc, keyHL_sp, software, dtesHL, dhighlvl, points):
# key for dhighlvl
keyHL_path = "%s.%s.path" % (ctc, itc)
# initialize dictE
dictE = {}
# folder for calculation and file name
TMP = PN.TMPHLi % PN.struckey(ctc, itc)
# template and function for calculation
tes = dtesHL.get(software, {}).get(ctc, None)
spc_fnc = get_spc_fnc(software)
# extra-arguments for spc_fnc
clean = False # do not delete files
bhess = False # do not calculate hessian (no needed actually)
eargs = (tes, TMP, clean)
# rst file
rstfile = PN.get_rst(ctc, itc)
tpath2, tcommon2, drst = ff.read_rst(rstfile)
if drst == {}:
yield None, keyHL_path, (None, None), None, "emptyrst"
return
ch, mtp, atonums, masses, mu = tcommon2
symbols = fncs.atonums2symbols(atonums)
# define points
allpoints = sorted_points(drst, hess=False)
for point in points:
if point.startswith("auto"):
auto, nbw, nfw = point.split("_")
points = auto_points(drst, allpoints, int(nbw), int(nfw))
break
# loop in points
for point_i in points:
# name for files
mname = "%s.%s.%s" % (ctc, itc, point_i)
# get label
label_i, s_i = find_label_in_rst(point_i, drst)
# tuple for identify
tuple_ID = (s_i, label_i)
# not in drst?
if label_i is None:
yield point_i, keyHL_path, tuple_ID, None, "noinrst"
# already calculated
elif label_i in dhighlvl.get(keyHL_path, {}).keys():
yield point_i, keyHL_path, tuple_ID, dhighlvl[keyHL_path][
label_i], "already"
# HL-calculation
else:
if s_i == 0.0:
Ehl_sp = dhighlvl.get(keyHL_sp, None)
if Ehl_sp is not None:
yield point_i, keyHL_path, tuple_ID, Ehl_sp, "saddlefromsp"
continue
# get xcc from rst
xms = drst[label_i][2]
xcc = fncs.ms2cc_x(xms, masses, mu)
# calculation
try:
out_spc = spc_fnc(xcc, symbols, bhess, mname, eargs)
yield point_i, keyHL_path, tuple_ID, out_spc[4], "calculated"
except:
yield point_i, keyHL_path, tuple_ID, None, "fail"
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 %+12.8f %+12.8f %+12.8f\n" % (symbol, x, y, z)
with open(xyz, 'w') as asdf:
asdf.write(string)
def prepare(self):
# check atnums
if self._atnums is not None and type(self._atnums[0]) == str:
self._symbols = list(self._atnums)
# check symbols
if self._symbols is not None and type(self._symbols[0]) == int:
self._atnums = list(self._symbols)
# Get both atnums and symbols if None
if self._atnums is None: self._atnums = fncs.symbols2atonums(self._symbols)
if self._symbols is None: self._symbols = fncs.atonums2symbols(self._atnums)
# check masses
if self._masses is None:
self._masses = fncs.atonums2masses(self._atnums)
# derivated magnitudes
self.genderivates()
# check Fcc
if self._Fcc not in (None,[]) and len(self._Fcc) != 3*self._natoms:
self._Fcc = fncs.lowt2matrix(self._Fcc)