def kmc_savedata(kmcof, data):
# Molecules and same length
molecules = sorted(data[0][2].keys())
len1 = max([len(string) for string in molecules + ["time", "-" * 10]])
ss = "%%%is" % len1
# string for gnuplot data file
string = ""
string += "# Time in ps; populations in molecules\n"
string += "\n\n"
# string for gnuplot string
gpstr = "datafile='%s'\n" % kmcof
gpstr += "plot\\\n"
# data for each temperature
for ii, (stemp, xvalues, yvalues) in enumerate(data):
# add line in gnuplot script
gpstr += " datafile index %i using 1:2 with points,\\\n" % ii
# add data in gnuplot file
string += "# T = %s K\n" % stemp
string += "#" + ss % "time" + " ".join([ss % mol
for mol in molecules]) + "\n"
for jj, time in enumerate(xvalues):
time = 1e12 * SECOND * time
string += " %10.3E " % time
for molecule in molecules:
pop = yvalues[molecule][jj] / NA
string += " %10.3E " % pop
string += "\n"
string += "\n\n"
# write files
write_file(kmcof, string)
write_file("plotkmc.gp", gpstr)
def write_alldata(filename, ltemp, dall):
variables = [
"gibbs", "pfn", "anh", "zct", "sct", "cvt", "cagtst", "cagcvt", "rcons"
]
# write variables in order
string = ""
for variable in variables:
if variable not in dall.keys(): continue
string += "#-------------------------#\n"
string += "# Adding data for: %6s #\n" % variable
string += "#-------------------------#\n"
for key, data in sorted(dall[variable].items()):
string += "start_%s %s\n" % (variable, key)
if variable == "pfn":
V0, V1 = data[0:2]
data = data[2]
string += " %.8f\n" % V0
string += " %.8f\n" % V1
if variable == "gibbs":
string += "".join(" %7.2f %.8f\n" % (T, value)
for T, value in zip(ltemp, data))
else:
string += "".join(" %7.2f %.5E\n" % (T, value)
for T, value in zip(ltemp, data))
string += "end_%s\n\n" % variable
write_file(filename, string)
def write_frozen(filename,frozen_xcc,frozen_symbols):
if len(frozen_symbols) == 0: return
string = ""
for idx,symbol in enumerate(frozen_symbols):
x,y,z = xyz(frozen_xcc,idx)
string += " %-2s %+9.5f %+9.5f %+9.5f\n"%(symbol,x,y,z)
write_file(filename,string)
def write_chem(dchem,filename=PN.IFILE5):
string = PH.INFO_pifchem+"\n"
# nice formatting
ml1,ml2,ml3,ml4 = 3,3,3,3
for rcname,(Rs,TS,Ps) in dchem.items():
if TS is None: TS = ""
l1 = len(rcname)
l2 = len(" + ".join(Rs))
l3 = len(TS)
l4 = len(" + ".join(Ps))
if l1 > ml1: ml1 = l1
if l2 > ml2: ml2 = l2
if l3 > ml3: ml3 = l3
if l4 > ml4: ml4 = l4
# remove blanks in string
string = "\n".join([line.strip() for line in string.split("\n")])
# add to string
for label,(Rs,TS,Ps) in sorted(dchem.items()):
Rs = " + ".join(Rs)
Ps = " + ".join(Ps)
if TS is None: TS = " "
# nice formating
label = ("%%-%is"%ml1)%label
Rs = ("%%-%is"%ml2)%Rs
TS = ("%%-%is"%ml3)%TS
Ps = ("%%-%is"%ml4)%Ps
# add to string
string += "%s : %s --> %s --> %s\n"%(label,Rs,TS,Ps)
string += "\n"
write_file(filename,string)
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 write_dlevel(ddlevel,filename=PN.IFILE7):
string = ""
ml = max([len(ctc) for ctc in ddlevel.keys()]+[1])
for key,points in sorted(ddlevel.items()):
string += "%%-%is "%ml%key
if len(points) != 0:
string += "{%s}"%",".join(points)
string += "\n"
write_file(filename,string)
def write_track(dict_track,filename=PN.IFILE0):
if dict_track == {}:
string = "# NO DATA INSIDE %s\n"%PN.UFOLDER
else:
# lengths
mlkey = max([len(key) for key in dict_track.keys() ])
mlval = max([len(val) for val in dict_track.values()])
# format of each line
lformat = "%%%is --> %%%is\n"%(mlkey,mlval)
string = "".join([lformat%(ifile,ffile) for ifile,ffile in sorted(dict_track.items())])
write_file(filename,string)
def write_ctc(dctc,dimasses={},filename=PN.IFILE1):
string = ""
#------------------------#
# write info in dimasses #
#------------------------#
if dimasses != {}:
string += "#------------------------------------------#\n"
string += "# Definition of the isotopic masses #\n"
string += "#------------------------------------------#\n"
string += "start_isomass\n"
toloop = sorted([(imass,label) for label,imass in dimasses.items()])
for imass,label in toloop:
imass *= AMU
string += " %-5s = %12.7f\n"%(label,imass)
string += "end_isomass\n"
string += "\n"
#------------------------#
# write info in dctc #
#------------------------#
string0 = ""
string1 = ""
stringn = ""
for name,ctc in sorted(dctc.items()):
string_ctc = "start_ctc %s\n"%name
for line in ctc.get_piflines().split("\n"):
if line == "": continue
string_ctc+= " "+line+"\n"
string_ctc += "end_ctc\n\n"
if int(ctc._type) == 0: string0 += string_ctc
elif int(ctc._type) == 1: string1 += string_ctc
else : stringn += string_ctc
# Generate string with all data
if string0 != "":
string += "#------------------------------------------#\n"
string += "# Cluster of torsional conformers: MINIMA #\n"
string += "#------------------------------------------#\n"
string += string0
if string1 != "":
string += "#------------------------------------------#\n"
string += "# Cluster of torsional conformers: SADDLES #\n"
string += "#------------------------------------------#\n"
string += string1
if stringn != "":
string += "#------------------------------------------#\n"
string += "# Cluster of torsional conformers: OTHERS #\n"
string += "#------------------------------------------#\n"
string += stringn
string += PH.INFO_pifstruc
write_file(filename,string)
def write_kmc(kmctuple, filename=PN.IFILE6):
ipopulations, rateconstants, numbersteps, volume, timeunits, excess = kmctuple
# get l1 and l2 for nice formatting
try:
l1 = max(len(ctc) for ctc in ipopulations.keys()) + 7
except:
l1 = 7
try:
l2 = max(len(reac) for reac in rateconstants.keys()) + 3
except:
l2 = 3
# Write step for printing
string = "# KMC Parameters\n"
string += "psteps %-5i # print data each nstp steps\n" % numbersteps
string += "volume %8.2E # simulation volume (mL)\n" % (volume * ML)
if timeunits in "fs,ps,mcs,ms,s,min,hr".split(","):
string += "timeunits %-5s # units for time variable\n" % timeunits
else:
string += "timeunits %-5s # units for time variable\n" % "ps"
string += "\n"
# Concentration of each species
string += "# Initial (non-zero) populations (number of molecules)\n"
for specie, ipop in sorted(ipopulations.items()):
specie = "pop(%s)_0" % specie
string += ("%%-%is %%.2e" % l1) % (specie, ipop)
if specie in excess: string += " excess"
string += "\n"
string += "\n"
# Type of rate constant to use
string += "# Selection of the rate constant to use\n"
for reaction, (rctype, weight, rcdata) in sorted(rateconstants.items()):
reaction = "k(%s)" % reaction
if weight == 1:
string += ("%%-%is %%s " % l2) % (reaction, rctype.lower())
else:
string += ("%%-%is*%%i %%s " % l2) % (reaction, weight,
rctype.lower())
if rcdata is not None:
string += " ".join(["%.3e" % coef for coef in rcdata])
string += "\n"
string += "\n"
write_file(filename, string)
def write_tes(dtesLL, dtesHL, filename=PN.IFILE4):
dstring = {}
for case, dtes in [("LL", dtesLL), ("HL", dtesHL)]:
# loop for each software
for software in sorted(dtes.keys()):
# initialize dictionary
dstring[software] = dstring.get(software, {})
dstring[software][case] = dstring[software].get(case, "")
# block case?
if case == "LL": blockkey = "meppoint"
if case == "HL": blockkey = "highlevel"
# generate string
string = ""
for ctc in sorted(dtes[software].keys()):
string += "#- - - - - - - - - - - - - -#\n"
string += "start_%s %s %s\n" % (blockkey, ctc, software)
string += dtes[software][ctc]
string += "end_%s\n" % blockkey
string += "#- - - - - - - - - - - - - -#\n"
string += "\n"
dstring[software][case] += string
# Final string
final_string = ""
for software in dstring.keys():
final_string += "#===========================%-10s=#\n" % ("=" * 10)
final_string += "# INPUT FILE TEMPLATES FOR: %-10s #\n" % (
software.upper())
final_string += "#===========================%-10s=#\n" % ("=" * 10)
final_string += "\n"
for case in dstring[software].keys():
if case == "LL":
final_string += "#-------------------------#\n"
final_string += "# MEP POINT CALCULATIONS #\n"
final_string += "#-------------------------#\n"
if case == "HL":
final_string += "#-------------------------#\n"
final_string += "# HIGH-LEVEL CALCULATIONS #\n"
final_string += "#-------------------------#\n"
final_string += "\n"
final_string += dstring[software][case]
final_string += "\n"
write_file(filename, final_string)
def write_alldata(filename,ltemp,dall):
variables = ["gibbs1cm3","gibbs1bar","pfn","ctr","anh","zct","sct","cvt","cagtst","cagcvt","cfs","rcons"]
# write variables in order
string = ""
for variable in variables:
if variable not in dall.keys(): continue
string += "#-------------------------#\n"
string += "# Adding data for: %6s #\n"%variable
string += "#-------------------------#\n"
# add info about variable
if variable == "gibbs1cm3": string += "# Gibbs free energy in hartree (ref: 1 molec/cc)\n"
if variable == "gibbs1bar": string += "# Gibbs free energy in hartree (ref: 1 bar)\n"
if variable == "pfn" : string += "# V0, V0+zpe and partition functions\n"
if variable == "ctr" : string += "# transl, rovib and elec partition functions\n"
if variable == "anh" : string += "# anharmonicity\n"
if variable == "zct" : string += "# ZCT transmission coefficient\n"
if variable == "sct" : string += "# SCT transmission coefficient\n"
if variable == "cagtst" : string += "# CAG/TST coefficient\n"
if variable == "cagcvt" : string += "# CAG/CVT coefficient\n"
if variable == "cvt" : string += "# CVT coefficient\n"
if variable == "cfs" : string += "# TST correction factors/coefficients\n"
if variable == "rcons" : string += "# Rate constants (in au)\n"
for key,data in sorted(dall[variable].items()):
if data is None: continue
string += "start_%s %s\n"%(variable,key)
if variable == "pfn":
V0,V1 = data[0:2]
data = data[2]
string += " %.8f\n"%V0
string += " %.8f\n"%V1
string += "".join(" %7.2f %.5E\n"%(T,value) for T,value in zip(ltemp,data))
elif variable == "ctr":
PIB,RRHO,ELE = data
for idx,T in enumerate(ltemp):
string += " %7.2f %.5E %.5E %.5E\n"%(T,PIB[idx],RRHO[idx],ELE[idx])
elif variable in ["gibbs1cm3","gibbs1bar"]:
string += "".join(" %7.2f %.8f\n"%(T,value) for T,value in zip(ltemp,data))
else:
for T,val in zip(ltemp,data): string += " %7.2f %s\n"%(T,fncs.eformat(val,5))
#string += "".join(" %7.2f %.5E\n"%(T,val) for T,val in zip(ltemp,data))
string += "end_%s\n\n"%variable
write_file(filename,string)
def write_highlevelfile(filename,dhighlvl):
# if exists, read it before
dhighlvl_0 = read_highlevelfile(filename)
# update with new
for key,value in dhighlvl.items():
# new key
if key not in dhighlvl_0.keys():
dhighlvl_0[key] = value
continue
# old key and "sp"
if type(value) == float:
dhighlvl_0[key] = value
continue
# old key and path points
for slabel,E in value.items():
dhighlvl_0[key][slabel] = E
# save with correct name and del
dhighlvl = dhighlvl_0
del dhighlvl_0
# for nice formatting
ml = max([len(key) for key in dhighlvl.keys()])
# write string (two parts: one for sp, one for MEP points)
string_sp = ""
string_path = ""
for key,value in sorted(dhighlvl.items()):
key = "%%-%is"%ml%key
# stationary points
if type(value) == float:
string_sp += "%s %-6s %-+14.8f\n"%(key,"sp",value)
# path points
if type(value) == dict:
for slabel,E in sorted(value.items()):
string_path += "%s %-6s %-+14.8f\n"%(key,slabel,E)
string_path += "\n"
string = string_sp + "\n" + string_path
write_file(filename,string)
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 write_path(dpath,filename=PN.IFILE3):
string = "\n"
for target,pathvars in sorted(dpath.items()):
string += pathvars.string4pif(target)
string += "\n"
write_file(filename,string)
def write_temp(Tlist,filename=PN.IFILE2):
string = ""
for idx in range(0,len(Tlist),7):
line = " ".join(["%7.2f"%T for T in Tlist[idx:idx+7]])
string += " " + line + "\n"
write_file(filename,string)
