def main():
"""Quantum Chemistry Interface - Fesigned to simplify the use of QC packages
Quantum Chemistry Interface has been designed to simplify quantum chemistry
calculations for organic chemists, it provides a common interface to quantum
chemistry packages, automatically handles creating input file and reading
output files, furthermore it is capable of automatically calculating
reaction thermodynamic quantities given basic reaction path info. QCI
understands the PBS system so is ideal for use on many clusters
When the script is run you must call it with the 3 positional arguments
described below, these tell the script how to name your job, and where the
files relating to each job are found. Both the job and step names can accept
a list of names to automatically create batch jobs. Warning: Batch modes can
radpidly create a large number of job, be careful if there is limits to job
submission on your cluster.
Furthermore you must provide a flag indicating which mode the script should
run in. Currently the options are new (creates a new job, no batch mode),
submit (submits jobs to the queue), analyse (extracts data from jobs),
reaction, (extracts thermochemistry for reactions)
It is invisioned that the project name should hold a braod description of
a series of calulations, the job name should hold a description of the
substitution pattern, and the step name should hold a description of the
reaction step.
For example in a series of calculations studying H atom loss from
substituted methane moecules you might start with the starting material,
methane.
projectName: - Hloss
jobName: - H
stepname: - SM
qci Hloss H SM -n -c 0 -m 1 -x methane.xyz
The values not specifically passed are taken from the config file
Next you would calculate the transition state for loss of H atom
projectName: - Hloss
jobName: - H
stepName -HlossTS
qci Hloss H HlossTS -n -ts -c 0 -m 1 -x HlossTS.xyz
Notice we have to explictly tell qci we are looking for a TS state
Next we need to make the product job for methyl radical
projectName: - Hloss
jobName: - H
stepName: - Product
qci Hloss H Product -n -c 0 -m 2 -x methylradical.xyz
We have now created the input files for this reaction, we can submit to the
queue using a batch mode by passing a list of stepnames
qci Hloss H "SM HlossTS Product" -s -w 4:00:00
This will submit the jobs we created in the previous commands.
Once this jobs are complete we can analyse the job to check the geometery
has converged to the correct structure, again we can use a batch mode here
qci Hloss H "SM HlossTS Product" -a
This will print the most important infomaition from the output file
If all the jobs have finished correctly, and freqency calculations
were requested it is now possible to calculate reaction paramters.
qci Hloss H "SM HlossTS Product+H" -re
Reaction mode requires a list of reaction steps, it is assumed that odd
numbered steps are starting materials and products, and that even steps are
transition states connecting them. If a step has more than one molecule you
ask qci to sum their enthalpies by giving a list seperated by + signs, with
no spaces.
Positional Args:
projectName -- Set name of project
jobName -- Set name of job. Accepts a list of names for batch modes
stepName -- Set name of Step. Accepts a list of name for batch modes
Optional Args:
Modes:
new/-n -- Creates inputfile files from options selected
submit/-s -- Creates pbsfile and submits job to queue. Batch mode
analyse/-a -- Reads output file with cclib to extract chemical data.
Batch mode
reaction/-re -- Calculates therodynamics quantites for reaction
given list in form "SM TS Prod TS2 Prod2 ... TSN
ProdN" where each word is a step name
Chemical Options:
tstate/-ts -- Mark job as a transition state. Default = False
charge/-c -- Set charge for molecule. Default from config file
mult/-m -- Set multiplicity for moecule. Default from config file
basis/-b -- Set basis set for calculation. Default from config file
functional/-f -- Set functional for system. Default from config file
xyz/-x -- Set location to read .xyz file for coordinates. No default
pcm/-p -- Set PCM simulation on and select solvent. Deafult = false
type/-t -- Set type of job, currently either OPT and FREQ.
Default = OPT
engine/-e -- Set which QC packake to use for calculation.
Default from config file
PBS Options:
walltime/-w -- Set allowed excution time. Default from config file
nodes/-n -- Set number of nodes to be used. Default from config file
cpus/-cp -- Set number of cpus per node. Default from config file
ram/-r -- Set amount of ram per node. Default from config file
queue/-q -- Set queue for job. Default from config file
"""
logging.basicConfig(filename="qcfoc.log", level=logging.DEBUG)
logging.info("Started")
confparser = SafeConfigParser()
confparser.read("conf/qcfoc.conf")
argparser = argparse.ArgumentParser(description="Quantum Chemistry Interface", version="0.1")
argparser.add_argument("projectName", action="store", help="Set name of project")
argparser.add_argument(
"jobName", action="store", help=("Set name of job. Accepts a list " "of names for batch modes")
)
argparser.add_argument(
"stepName", action="store", help=("Set name of Step. Accepts a list" "of name for batch modes")
)
argparser.add_argument(
"--new", "-n", action="store_true", default=False, help="Creates inputfile files from options selecte"
)
argparser.add_argument(
"--submit",
"-s",
action="store_true",
default=False,
help=("Creates pbsfile and submits" "job to queue. Batch mode"),
)
argparser.add_argument(
"--analyse",
"-a",
action="store_true",
default=False,
help=("Creates pbsfile and submits " "job to queue. Batch mode"),
)
argparser.add_argument(
"--reaction",
"-re",
action="store_true",
default=False,
help=("Calcuates reaction thermochem given reaction" "profile in stepname in form of" "SM TS Prod1+Prod2"),
)
argparser.add_argument(
"--irc", "-irc", action="store_true", default=False, help="Checks if IRC jobs give correct SM + Prod"
)
argparser.add_argument(
"--fragment",
"-fr",
action="store",
default=None,
help=("Automatically subtitute" "atom with fragment. pass" 'as "AtomNo Frag"'),
)
argparser.add_argument(
"--tstate",
"-ts",
action="store_true",
default=False,
help=("Flag to mark job as a " "transition state. Default = False"),
)
argparser.add_argument(
"--charge",
"-c",
action="store",
default=confparser.get("default_options", "charge"),
help=("Set charge for molecule. Default from config" "file"),
type=int,
)
argparser.add_argument(
"--mult",
"-m",
action="store",
default=confparser.get("default_options", "mult"),
help=("Set multiplicity for moecule. Default" "from config file"),
type=int,
)
argparser.add_argument(
"--basis",
"-b",
action="store",
default=confparser.get("default_options", "basis"),
help=("Set basis set for calculation. Default" "from config file"),
)
argparser.add_argument(
"--functional",
"-f",
action="store",
default=confparser.get("default_options", "functional"),
help=("Set functional for calculation. Default" "from config file"),
)
argparser.add_argument(
"--xyz", "-x", action="store", help=("Set location to read .xyz file for coordinates." "No default")
)
argparser.add_argument(
"--symmetry",
"-sym",
action="store",
default=confparser.get("default_options", "sym"),
help=("Molecular point group. Default" "from config file"),
)
argparser.add_argument(
"--pcm",
"-p",
action="store",
default=None,
help=("Set PCM solvent simulation on and select solvent." "Deafult = false"),
)
argparser.add_argument(
"--type",
"-t",
action="store",
default="OPT",
choices=("OPT", "FREQ", "IRC"),
help=("Set type of job, " "currently supported" "OPT and FREQ." "Default = OPT"),
)
argparser.add_argument(
"--engine",
"-e",
action="store",
default=confparser.get("default_options", "engine"),
choices=("GAU", "GAMESS"),
help=("Set which quantum " "chemistry packake to " "use for calculation. " "Default from config " "file"),
)
argparser.add_argument(
"--walltime",
"-w",
action="store",
default=confparser.get("default_options", "walltime"),
help=("Set max allowed excution time. Default " "from config file"),
)
argparser.add_argument(
"--nodes",
"-no",
action="store",
default=confparser.get("default_options", "nodes"),
help=("Set number of nodes to be used." "Default from config file"),
)
argparser.add_argument(
"--cpus",
"-cp",
action="store",
default=confparser.get("default_options", "cpus"),
help=("Set number of cpus per node. Default " "from config file"),
)
argparser.add_argument(
"--ram",
"-r",
action="store",
default=confparser.get("default_options", "ram"),
help=("Set amount of ram per node. Default" "from config file"),
)
argparser.add_argument(
"--queue",
"-q",
action="store",
default=confparser.get("default_options", "queue"),
help="Set queue for job. Default from config file",
)
args = argparser.parse_args()
# Call subroutines for making Gaussian new jobs
if args.new is True:
if args.engine == "GAU":
try:
if args.fragment is not None:
j = classes.gau_step(
args.projectName,
args.jobName,
args.stepName,
ts=args.tstate,
charge=args.charge,
mult=args.mult,
xyz=args.xyz,
fragatom=args.fragment.split()[0],
frag=args.fragment.split()[1],
)
else:
j = classes.gau_step(
args.projectName,
args.jobName,
args.stepName,
ts=args.tstate,
charge=args.charge,
mult=args.mult,
xyz=args.xyz,
)
except IOError, error:
exit("IOError: %s for job %s-%s-%s" % (error, args.projectName, args.jobName, args.stepName))
try:
j.write_inputfile(args.basis, args.functional, args.nodes, args.cpus, args.ram, args.pcm, args.type)
print "Wrote inputfile for: %s-%s-%s" % (args.projectName, args.jobName, args.stepName)
except IOError, error:
exit("IOError: %s for job %s-%s-%s" % (error, args.projectName, args.jobName, args.stepName))
except IOError, error:
exit("IOError: %s for job %s-%s-%s" % (error, args.projectName, args.jobName, args.stepName))
try:
j.write_inputfile(
args.basis, args.functional, args.nodes, args.cpus, args.ram, args.pcm, args.type, args.symmetry
)
print "Wrote inputfile for: %s-%s-%s" % (args.projectName, args.jobName, args.stepName)
except IOError, error:
exit("IOError: %s for job %s-%s-%s" % (error, args.projectName, args.jobName, args.stepName))
# Call subroutines for sumbitting jobs
if args.submit is True:
for job in args.jobName.split():
for step in args.stepName.split():
if args.engine == "GAU":
j = classes.gau_step(args.projectName, job, step)
elif args.engine == "GAMESS":
j = classes.gamess_step(args.projectName, job, step)
try:
j.write_pbsfile(args.walltime, args.nodes, args.cpus, args.queue)
except IOError, error:
exit("IOError: %s for job %s-%s-%s" % (error, args.projectName, job, step))
j.submit_job()
# Call subroutines for Analysing job
if args.analyse is True:
for job in args.jobName.split():
for step in args.stepName.split():
if args.engine == "GAU":
j = classes.gau_step(args.projectName, job, step)
elif args.engine == "GAMESS":
