def get_dsoft():
'''
This functions is in charge of reading the file
mesc.txt where the available softwares are listed
'''
# defined here:
if False:
dsoft = {'clhbrpot': 'mpilgrim.itf_asurf', \
'gaussian': 'mpilgrim.itf_gau' ,\
'orca' : 'mpilgrim.itf_orca' \
}
# read from file
if True:
TXTFILE = os.path.dirname(os.path.realpath(__file__)) + "/mesc.txt"
# read file
lines = read_file(TXTFILE)
lines = clean_lines(lines, "#", True)
# get info from lines
dsoft = {}
for line in lines:
if line == "\n": continue
software, module = line.split()
dsoft[software] = module
# return dictionary
return dsoft
def file2lines(filename):
if not os.path.exists(filename):
lines = []
status = -1
else:
lines = read_file(filename)
lines = clean_lines(lines,"#",True)
lines = [line for line in lines if line != "\n"]
if lines == []: status = 0
else : status = 1
return lines, status
def read_ispe(filename):
'''
read input file for ispe
'''
# read lines
lines = ff.read_file(filename)
lines = fncs.clean_lines(lines, strip=True)
# initialize data
ispe_xy = []
VR, VP = None, None
tension = 0.0
# find data in lines
for line in lines:
if line == "\n": continue
label, val = line.split()
val = float(val)
if label.lower() == "tension": tension = val
elif label.lower() == "reac": VR = val
elif label.lower() == "prod": VP = val
else: ispe_xy.append((label, val))
return ispe_xy, tension, VR, VP
def set_EXE():
global EXE
txt = os.path.dirname(os.path.realpath(__file__))+"/paths.txt"
# Defined in this file
if 'EXE' in globals():
return
# Try to export it from bashrc
elif "OrcaExe" in os.environ:
# in .bashrc: export OrcaExe="$MYHOME/Software/orca_4_0_1_2/orca"
EXE = os.environ["OrcaExe"]
return
# Export it from file
elif os.path.exists(txt):
lines = read_file(txt)
lines = clean_lines(lines,"#",True)
for line in lines:
if line == "\n": continue
name, path = line.split()
if name == "orca":
EXE = path
return
# Not found
else: raise Exc.ExeNotDef(Exception)
def read_rst(rstfile):
if not os.path.exists(rstfile):
return None, None, {}
lines = read_file(rstfile)
lines = fncs.clean_lines(lines, "#", True)
if len(lines) == 0:
return None, None, {}
# pathinfo lines
lines_path = fncs.extract_lines(lines, "start_pathinfo", "end_pathinfo")
for line in lines_path:
if line.startswith("path "): path = line.split()[1].lower()
if line.startswith("mtype "): path = line.split()[1].lower()
if line.startswith("mu "): mu = float(line.split()[1]) / AMU
if line.startswith("ds "): ds = float(line.split()[1])
if line.startswith("hsteps "): hsteps = int(line.split()[1])
if line.startswith("cubic "):
cubic = line.split()[1].lower()
if cubic != "no": cubic = float(cubic)
else: cubic = None
# structinfo lines
lines_struct = fncs.extract_lines(lines, "start_structinfo",
"end_structinfo")
bool1 = False
bool2 = False
atonums = []
masses = []
for line in lines_struct:
if line.startswith("atonums"):
bool1, bool2 = True, False
continue
elif line.startswith("masslist") or line.startswith("masses"):
bool1, bool2 = False, True
continue
elif line.startswith("ch "):
bool1, bool2 = False, False
ch = int(line.split()[1])
elif line.startswith("mtp "):
bool1, bool2 = False, False
mtp = int(line.split()[1])
if bool1: atonums += [int(atonum) for atonum in line.split()]
if bool2: masses += [float(mass) / AMU for mass in line.split()]
# tuples of common data and of path
tcommon = (ch, mtp, atonums, masses, mu)
tpath = (path, mu, ds, hsteps, cubic)
# initialize structures
drst = {}
mins = +float("inf")
maxs = -float("inf")
record = False
lines = iter(lines)
# Read structures
for line in lines:
if "==>" in line:
record = True
t_value = None
data_line = line.split()[1:]
meplabel = data_line[0]
if meplabel.endswith("bw"):
meplabel = "bw" + meplabel.split("bw")[0]
if meplabel.endswith("fw"):
meplabel = "fw" + meplabel.split("fw")[0]
variables = data_line[1].split("-")
mepsvalue = float(data_line[2])
Vmep = float(data_line[3])
if len(data_line) == 5: t_value = float(data_line[4])
xms, gms, Fms, v0, v1 = None, None, None, None, None
# Read geometry
if "x" in variables:
xms = []
while True:
line = next(lines)
if "---" in line: break
xms += line.split()
xms = [float(xx) for xx in xms]
#xcc = ms2cc_x(xms,masses,mu)
# Read gradient
if "g" in variables:
gms = []
while True:
line = next(lines)
if "---" in line: break
gms += line.split()
gms = [float(gg) for gg in gms]
#gcc = ms2cc_g(gms,masses,mu)
# Read hessian
if "F" in variables:
Fms = []
while True:
line = next(lines)
if "---" in line: break
Fms += line.split()
Fms = [float(FF) for FF in Fms]
Fms = fncs.lowt2matrix(Fms)
#Fcc = ms2cc_F(Fms,masses,mu)
# Read v0
if "v0" in variables:
v0 = []
while True:
line = next(lines)
if "---" in line: break
v0 += line.split()
v0 = [float(xx) for xx in v0]
# Read v1
if "v1" in variables:
v1 = []
while True:
line = next(lines)
if "---" in line: break
v1 += line.split()
v1 = [float(xx) for xx in v1]
# Generate Structure
drst[meplabel] = (mepsvalue, Vmep, xms, gms, Fms, v0, v1, t_value)
# limit values
if mepsvalue < mins: mins = mepsvalue
if mepsvalue > maxs: maxs = mepsvalue
return tpath, tcommon, drst
