def execute(ifile,ofile,err,folder=None):
# Add folder to names
if folder is not None:
if not folder.endswith("/"): folder = folder + "/"
ifile = folder + ifile
ofile = folder + ofile
err = folder + err
# Execution file?
set_EXE()
check_EXE()
# Exception
exception = Exc.CalcFails(Exception)
exception._var = ofile
# Execute Gaussian
command = "%s <%s 1>%s 2>%s"%(EXE,ifile,ofile,err)
# Try up to NN times
NN = 5
for ii in range(NN):
try : status = os.system(command)
except: status = 0
# interrupted by ctrl+c (status = 2?)
if status == 2: raise KeyboardInterrupt
# Get log status
logstatus = log_status(ofile)
# Act according log status
# (a) Normal termination
if logstatus == 1 : break
# (b) empty file, no file or open-new-file error
elif logstatus in (-1,0,2):
time.sleep(1)
continue
# (c) other type of error
else: raise exception
return status
def pilgrim_spc(xcc,symbols,bhessian,mname,eargs):
# expand extra-args
if len(eargs) == 1:
spc_template = eargs[0]
folder, clean = None, False
elif len(eargs) == 2:
spc_template, folder = eargs
clean = False
elif len(eargs) == 3:
spc_template, folder, clean = eargs
# no template??
if spc_template is None: raise Exc.NoTemplateGiven(Exception)
# create folder
if folder is not None:
if not os.path.exists(folder): os.mkdir(folder)
# Calculate gradient&hessian or just gradient
if bhessian: inkey3 = "! EnGrad Freq "
else : inkey3 = "! EnGrad "
# names of files
wname, ifile, ofile, engrad, hess, gbw, err = ITF.iofiles(mname,folder)
# Input
string_ifile = ""
for line in spc_template.split("\n"):
if key1 in line:
line = ""
for idx,symbol in enumerate(symbols):
x,y,z = fncs.xyz(xcc,idx)
linedata = (symbol,x*pc.ANGSTROM,y*pc.ANGSTROM,z*pc.ANGSTROM)
line += "%2s %+11.6f %+11.6f %+11.6f\n"%linedata
if key2 in line:
pos = line.find(key2)
line = line[0:pos] + wname + line[pos+len(key2):]
if key3 in line:
pos = line.find(key3)
line = line[0:pos] + inkey3 + line[pos+len(key3):]
# Add \n to line
if not line.endswith("\n"): line += "\n"
string_ifile += line
ff.write_file(ifile,string_ifile)
# Send calculation
status = ITF.execute(ifile,ofile,err)
# # Sleep 0.5 seconds, so Orca can write the files
# time.sleep(0.5)
# Check output
exception = Exc.CalcFails(Exception)
exception._var = ofile
if not ITF.normal_termination(ofile): raise exception
# Read data
xcc, atonums, ch, mtp, E, gcc, Fcc, masses, clevel = ff.read_orca(ofile)
# Remove files
if clean:
files = os.listdir(folder)
files = [fff for fff in files if fff.startswith(name) ]
files = [fff for fff in files if not fff.endswith(".inp") ]
files = [fff for fff in files if not fff.endswith(".out") ]
files = [fff for fff in files if not fff.endswith(".engrad")]
files = [fff for fff in files if not fff.endswith(".hess") ]
for fff in files: os.remove(folder+fff)
return xcc, atonums, ch, mtp, E, gcc, Fcc, masses
def genfchk(chk,fchk,err,folder=None):
# Add folder to names
if folder is not None:
if not folder.endswith("/"): folder = folder + "/"
chk = folder + chk
fchk = folder + fchk
err = folder + err
# fchk tool?
set_FCHK()
check_FCHK()
# Exception
exception = Exc.CalcFails(Exception)
exception._var = chk
# Execute fchk tool
command = "%s %s %s 1>%s 2>&1"%(FCHK,chk,fchk,err)
try : status = os.system(command)
except: raise exception
return status
def execute(ifile,ofile,err,folder=None):
# Add folder to names
if folder is not None:
if not folder.endswith("/"): folder = folder + "/"
ifile = folder + ifile
ofile = folder + ofile
err = folder + err
# Execution file?
set_EXE()
check_EXE()
# Exception
exception = Exc.CalcFails(Exception)
exception._var = ofile
# Execute command
command = "%s %s 1>%s 2>%s"%(EXE,ifile,ofile,err)
try : status = os.system(command)
except: raise exception
return status
def pilgrim_spc(xcc, symbols, bhessian, mname, eargs):
# initialize
folder = None
clean = False
oniomH = []
oniomM = []
oniomL = []
frozen = ([], [])
# expand extra-args
if len(eargs) == 1:
spc_template = eargs[0]
elif len(eargs) == 2:
spc_template, folder = eargs
elif len(eargs) == 3:
spc_template, folder, clean = eargs
elif len(eargs) == 5:
spc_template, folder, clean, frozen, oniom_layers = eargs
oniomH, oniomM, oniomL = oniom_layers
# no template??
if spc_template is None: raise Exc.NoTemplateGiven(Exception)
# create folder
if folder is not None:
if not os.path.exists(folder): os.mkdir(folder)
# Calculate gradient&hessian or just gradient
if bhessian: inkey3 = "freq=noraman "
else: inkey3 = "force "
# names of files
wname, ifile, ofile, chk, fchk, err = ITF.iofiles(mname, folder)
# Input
string_ifile = ""
for line in spc_template.split("\n"):
if key1 in line:
line = ""
for idx, symbol in enumerate(symbols):
x, y, z = fncs.xyz(xcc, idx)
if idx in oniomH: layer = " H"
elif idx in oniomM: layer = " M"
elif idx in oniomL: layer = " L"
else: layer = " "
linedata = (symbol, x * pc.ANGSTROM, y * pc.ANGSTROM,
z * pc.ANGSTROM, layer)
line += "%2s %+11.6f %+11.6f %+11.6f %s\n" % linedata
# add frozen atoms
frozen_symbols, frozen_xcc = frozen
for idx, symbol in enumerate(frozen_symbols):
x, y, z = fncs.xyz(frozen_xcc, idx)
# oniom layer?
at = len(symbols) + idx
if at in oniomH: layer = " H"
elif at in oniomM: layer = " M"
elif at in oniomL: layer = " L"
else: layer = " "
linedata = (symbol, x * pc.ANGSTROM, y * pc.ANGSTROM,
z * pc.ANGSTROM, layer)
line += "%2s -1 %+11.6f %+11.6f %+11.6f %s\n" % linedata
if key2 in line:
pos = line.find(key2)
line = line[0:pos] + wname + line[pos + len(key2):]
if key3 in line:
pos = line.find(key3)
line = line[0:pos] + inkey3 + line[pos + len(key3):]
# Add \n to line
if not line.endswith("\n"): line += "\n"
string_ifile += line
ff.write_file(ifile, string_ifile)
# Send calculation
status = ITF.execute(ifile, ofile, err)
# Check output
exception = Exc.CalcFails(Exception)
exception._var = ofile
if not ITF.normal_termination(ofile): raise exception
# (a) chk exists!
if os.path.exists(chk):
# Generate fchk
status = ITF.genfchk(chk, fchk, err)
# Read data
xcc, atonums, ch, mtp, E, gcc, Fcc, masses, clevel = ff.read_fchk(fchk)
# (b) chk does not exist!
else:
xcc, atonums, ch, mtp, E, gcc, Fcc, masses, clevel = ITF.read_gauout(
ofile)
# Remove files
if clean:
files = os.listdir(folder)
files = [fff for fff in files if fff.startswith(name)]
files = [fff for fff in files if not fff.endswith(".gjf")]
files = [fff for fff in files if not fff.endswith(".log")]
files = [fff for fff in files if not fff.endswith(".out")]
files = [fff for fff in files if not fff.endswith(".chk")]
files = [fff for fff in files if not fff.endswith(".fchk")]
for fff in files:
os.remove(folder + fff)
return xcc, atonums, ch, mtp, E, gcc, Fcc, masses
def pilgrim_spc(xcc, symbols, bhessian, mname, eargs):
# expand extra-args
if len(eargs) == 1:
spc_template = eargs[0]
folder, clean = None, False
elif len(eargs) == 2:
spc_template, folder = eargs
clean = False
elif len(eargs) == 3:
spc_template, folder, clean = eargs
elif len(eargs) == 5:
spc_template, folder, clean, frozen, oniom_layers = eargs
# no template??
if spc_template is None: raise Exc.NoTemplateGiven(Exception)
# lines for GRADIENT (if any)
gradient_lines = None
if key4a in spc_template and key4b in spc_template:
gradient_lines = spc_template.split(key4a)[1].split(key4b)[0]
spc_template = spc_template.replace(gradient_lines,
"").replace(key4b, "")
gradient_lines = gradient_lines.strip()
# lines for HESSIAN (if any)
hessian_lines = None
if key5a in spc_template and key5b in spc_template:
hessian_lines = spc_template.split(key5a)[1].split(key5b)[0]
spc_template = spc_template.replace(hessian_lines,
"").replace(key5b, "")
hessian_lines = hessian_lines.strip()
# create folder
if folder is not None:
if not os.path.exists(folder): os.mkdir(folder)
# names of files
wname, ifile, ofile, engrad, hess, gbw, err = ITF.iofiles(mname, folder)
# Input
string_ifile = ""
for line in spc_template.split("\n"):
if key1 in line:
line = ""
for idx, symbol in enumerate(symbols):
x, y, z = fncs.xyz(xcc, idx)
linedata = (symbol, x * pc.ANGSTROM, y * pc.ANGSTROM,
z * pc.ANGSTROM)
line += "%2s %+11.6f %+11.6f %+11.6f\n" % linedata
if key2 in line:
pos = line.find(key2)
line = line[0:pos] + wname + line[pos + len(key2):]
#--------------------------------#
# Gradient & Hessian computation #
#--------------------------------#
# (a) via key3
if key3 in line:
if bhessian: inkey3 = "! EnGrad Freq "
else: inkey3 = "! EnGrad "
pos = line.find(key3)
line = line[0:pos] + inkey3 + line[pos + len(key3):]
# (b) via key4 & key5
if key4a in line:
line = line.replace(key4a, gradient_lines)
if key5a in line:
if bhessian: line = line.replace(key5a, hessian_lines)
else: continue
#--------------------------------#
# Add \n to line
if not line.endswith("\n"): line += "\n"
string_ifile += line
with open(ifile, 'w') as asdf:
asdf.write(string_ifile)
# Send calculation
status = ITF.execute(ifile, ofile, err)
# # Sleep 0.5 seconds, so Orca can write the files
# time.sleep(0.5)
# Check output
exception = Exc.CalcFails(Exception)
exception._var = ofile
if not ITF.normal_termination(ofile): raise exception
# Read data
xcc, atonums, ch, mtp, E, gcc, Fcc, masses, clevel = ITF.read_orca(ofile)
# Remove files
if clean:
files = os.listdir(folder)
files = [fff for fff in files if fff.startswith(name)]
files = [fff for fff in files if not fff.endswith(".inp")]
files = [fff for fff in files if not fff.endswith(".out")]
files = [fff for fff in files if not fff.endswith(".engrad")]
files = [fff for fff in files if not fff.endswith(".hess")]
for fff in files:
os.remove(folder + fff)
return xcc, atonums, ch, mtp, E, gcc, Fcc, masses