def mergejobfiles(jobfiles,
outputfile,
checkids=False,
ignorejobsidentifier=False):
if type(jobfiles) == str:
jobfiles = [jobfiles]
root = lxml.Element("jobs")
for jobfile in jobfiles:
numberofjobs = 0
ignoredjobs = 0
smallroot = XmlParser(jobfile)
for entry in smallroot.iter('job'):
if ignorejobsidentifier != False:
status = entry.find("status").text
if status in ignorejobsidentifier:
ignoredjobs += 1
continue
numberofjobs += 1
if checkids:
jobid = int(entry.find("id").text)
for entry in root.iter('job'):
jid = int(entry.find("id").text)
if jobid == jid:
print "Job {} from {} has the same ID as a job parsed before. Exiting..".format(
jobid, jobfile)
sys.exit()
root.append(entry)
print "Found {} jobs in file {}".format(numberofjobs, jobfile)
if ignorejobsidentifier != False:
if type(ignorejobsidentifier) == str:
ignorejobsidentifier = [ignorejobsidentifier]
print "which are not of type:{}".format(
" ".join(ignorejobsidentifier))
print "Ignored jobs: {}".format(ignoredjobs)
XmlWriter(root, outputfile)
def mergejobfiles(jobfiles,outputfile,checkids=False,ignorejobsidentifier=False):
if type(jobfiles)==str:
jobfiles=[jobfiles]
root=lxml.Element("jobs")
for jobfile in jobfiles:
numberofjobs=0
ignoredjobs=0
smallroot=XmlParser(jobfile)
for entry in smallroot.iter('job'):
if ignorejobsidentifier!=False:
status=entry.find("status").text
if status in ignorejobsidentifier:
ignoredjobs+=1
continue
numberofjobs+=1
if checkids:
jobid=int(entry.find("id").text)
for entry in root.iter('job'):
jid=int(entry.find("id").text)
if jobid==jid:
print "Job {} from {} has the same ID as a job parsed before. Exiting..".format(jobid,jobfile)
sys.exit()
root.append(entry)
print "Found {} jobs in file {}".format(numberofjobs,jobfile)
if ignorejobsidentifier!=False:
if type(ignorejobsidentifier)==str:
ignorejobsidentifier=[ignorejobsidentifier]
print "which are not of type:{}".format(" ".join(ignorejobsidentifier))
print "Ignored jobs: {}".format(ignoredjobs)
XmlWriter(root,outputfile)
def readexcitonxml_egwbse(filename):
results = []
root = XmlParser(filename)
for job in root.iter('job'):
output = job.find("output")
segment = output.find("segment")
gwbse = segment.find("GWBSE")
mol = readexcitonxml_molecule(gwbse)
mol.setId(int(segment.get("id")))
mol.setName(segment.get("type"))
results.append(mol)
return results
def makefolder(self):
#print self.path
copyfromtemplate(self.foldername)
root=XmlParser("{}/exciton.xml".format(self.foldername))
exciton=root.find("exciton")
exciton.find("tasks").text="input"
XmlWriter(root,"{}/exciton.xml".format(self.foldername))
with cd(self.foldername):
sp.call("xtp_tools -e exciton -o exciton.xml > exciton.log",shell=True)
self.modcomfile("system.com")
exciton.find("tasks").text="dft,parse,gwbse"
XmlWriter(root,"{}/exciton.xml".format(self.foldername))
def makefolder(self):
#print self.path
copyfromtemplate(self.foldername)
root = XmlParser("{}/exciton.xml".format(self.foldername))
exciton = root.find("exciton")
gwbseengine = exciton.find("gwbse_engine")
gwbseengine.find("tasks").text = "input"
XmlWriter(root, "{}/exciton.xml".format(self.foldername))
with cd(self.foldername):
sp.call("xtp_tools -e exciton -o exciton.xml > exciton.log",
shell=True)
self.modcomfile("system.com")
gwbseengine.find("tasks").text = "dft,parse,gwbse"
XmlWriter(root, "{}/exciton.xml".format(self.foldername))
def readexcitoncoulingclassical(filename):
root = XmlParser(filename)
results = []
for pair in root:
Coupling = pair[0]
results.append(float(Coupling.get("jABstatic")))
return results
def readexcitoncouplingxml(filename, states):
root = XmlParser(filename)
resultlist = []
for pair in root:
types = pair[0]
couplings = []
for state in states:
results = None
if state[0] == "s":
results = types.find("singlets")
elif state[0] == "t":
results = types.find("triplets")
else:
print "state not known"
number = int(state[1:])
#print number
for coupling in results:
noA = int(coupling.get("excitonA"))
noB = int(coupling.get("excitonB"))
if noA + 1 == number and noB + 1 == number:
couplings.append((float(coupling.text)))
break
resultlist.append(couplings)
return resultlist
def splittjobfile(jobfile,jobfiles,ignorejobsidentifier=False):
root=XmlParser(jobfile)
numberofjobs=0
ignoredjobs=0
for entry in root.iter('job'):
if ignorejobsidentifier!=False:
status=entry.find("status").text
if status in ignorejobsidentifier:
root.remove(entry)
ignoredjobs+=1
continue
numberofjobs+=1
print "Found {} jobs in in file {}".format(numberofjobs,jobfile)
if ignorejobsidentifier!=False:
if type(ignorejobsidentifier)==str:
ignorejobsidentifier=[ignorejobsidentifier]
print "which are not of type:{}".format(" ".join(ignorejobsidentifier))
print "Ignored jobs: {}".format(ignoredjobs)
numberoffiles=len(jobfiles)
jobsperfile=numberofjobs/numberoffiles
remaining=numberofjobs%numberoffiles
jobsperfilelist=[]
roots=[]
for i in range(numberoffiles):
roots.append(lxml.Element("jobs"))
if remaining>0:
jobsperfilelist.append(jobsperfile+1)
remaining-=1
else:
jobsperfilelist.append(jobsperfile)
i=0
j=1
for entry in root.iter('job'):
if j>jobsperfilelist[i]:
i+=1
j=1
j+=1
roots[i].append(entry)
print "Split up jobfile into {} files with".format(numberoffiles)
print "with: {} jobs each".format(" ".join(map(str,jobsperfilelist)))
for outputfile,root in zip(jobfiles,roots):
XmlWriter(root,outputfile)
def resetjobfile(jobfile,assigned=True,failed=True):
root=XmlParser(jobfile)
piece=""
if assigned and failed:
piece="ASSIGNED and FAILED"
elif assigned:
piece="ASSIGNED"
elif failed:
piece="FAILED"
else:
piece="No Entry"
print "Resetting for file {}: {} to AVAILABLE".format(jobfile,piece)
for entry in root.iter('job'):
status=entry.find("status").text
if assigned==True and status=="ASSIGNED":
entry.find("status").text="AVAILABLE"
elif failed==True and status=="FAILED":
entry.find("status").text="AVAILABLE"
XmlWriter(root,jobfile)
def infojobfile(jobfile):
complete=0
available=0
assigned=0
failed=0
root=XmlParser(jobfile)
for entry in root.iter('job'):
status=entry.find("status").text
if status=="ASSIGNED":
assigned+=1
elif status=="AVAILABLE":
available+=1
elif status=="COMPLETE":
complete+=1
elif status=="FAILED":
failed+=1
else:
jobid=entry.find("id").text
print "WARNING: Job status {} for job id:{} in file {} not known".format(status,jobid,jobfile)
total=complete+available+assigned+failed
return total,complete,available,assigned,failed
def resetjobfile(jobfile, assigned=True, failed=True, complete=False):
root = XmlParser(jobfile)
piece = ""
if assigned:
piece += "ASSIGNED "
if failed:
piece += "FAILED "
if complete:
piece += "COMPLETE "
if piece == "":
piece = "No Entry"
print "Resetting for file {}: {} to AVAILABLE".format(jobfile, piece)
for entry in root.iter('job'):
status = entry.find("status").text
if assigned == True and status == "ASSIGNED":
entry.find("status").text = "AVAILABLE"
elif failed == True and status == "FAILED":
entry.find("status").text = "AVAILABLE"
elif complete == True and status == "COMPLETE":
entry.find("status").text = "AVAILABLE"
XmlWriter(root, jobfile)
def infojobfile(jobfile):
complete = 0
available = 0
assigned = 0
failed = 0
root = XmlParser(jobfile)
for entry in root.iter('job'):
status = entry.find("status").text
if status == "ASSIGNED":
assigned += 1
elif status == "AVAILABLE":
available += 1
elif status == "COMPLETE":
complete += 1
elif status == "FAILED":
failed += 1
else:
jobid = entry.find("id").text
print "WARNING: Job status {} for job id:{} in file {} not known".format(
status, jobid, jobfile)
total = complete + available + assigned + failed
return total, complete, available, assigned, failed
def readcouplingxml(filename):
root = XmlParser(filename)
Je = []
Jh = []
for pair in root:
homoA = int(pair.get("homoA"))
homoB = int(pair.get("homoB"))
for overlap in pair:
orbA = int(overlap.get("orbA"))
orbB = int(overlap.get("orbB"))
if orbA == homoA and orbB == homoB:
Je.append((float(overlap.text)))
elif orbA == homoA + 1 and orbB == homoB + 1:
Jh.append((float(overlap.text)))
return [Je, Jh]
def splittjobfile(jobfile, jobfiles, ignorejobsidentifier=False):
root = XmlParser(jobfile)
numberofjobs = 0
ignoredjobs = 0
for entry in root.iter('job'):
if ignorejobsidentifier != False:
status = entry.find("status").text
if status in ignorejobsidentifier:
root.remove(entry)
ignoredjobs += 1
continue
numberofjobs += 1
print "Found {} jobs in in file {}".format(numberofjobs, jobfile)
if ignorejobsidentifier != False:
if type(ignorejobsidentifier) == str:
ignorejobsidentifier = [ignorejobsidentifier]
print "which are not of type:{}".format(" ".join(ignorejobsidentifier))
print "Ignored jobs: {}".format(ignoredjobs)
numberoffiles = len(jobfiles)
jobsperfile = numberofjobs / numberoffiles
remaining = numberofjobs % numberoffiles
jobsperfilelist = []
roots = []
for i in range(numberoffiles):
roots.append(lxml.Element("jobs"))
if remaining > 0:
jobsperfilelist.append(jobsperfile + 1)
remaining -= 1
else:
jobsperfilelist.append(jobsperfile)
i = 0
j = 1
for entry in root.iter('job'):
if j > jobsperfilelist[i]:
i += 1
j = 1
j += 1
roots[i].append(entry)
print "Split up jobfile into {} files with".format(numberoffiles)
print "with: {} jobs each".format(" ".join(map(str, jobsperfilelist)))
for outputfile, root in zip(jobfiles, roots):
XmlWriter(root, outputfile)
def readexcitonxml(filename):
root = XmlParser(filename)
return readexcitonxml_molecule(root)
required=True,
help="Name of jobfile")
parser.add_argument("--min",
type=int,
default=-14,
help="Minimum log10(J2) to still count")
args = parser.parse_args()
if type(args.jobfiles) == str:
args.jobfiles = [args.jobfiles]
for i, jobfile in enumerate(args.jobfiles):
job = []
toosmall = 0
print "Reading in {}".format(jobfile)
root = XmlParser(jobfile)
for entry in root.iter('job'):
status = entry.find("status").text
if status == "COMPLETE":
coupling = entry.find("output")[0][0].get("jABstatic")
j2 = float(coupling)**2
#if j2>10**args.min:
job.append(j2)
#else:
#toosmall+=1
job = np.array(job)
if i == 0:
total = job
else:
total += job
parser.add_argument("--state",type=str,help="State to give tag to, only required for ewald")
parser.add_argument("--format",type=str,required=True,help="Format string into which the id is placed e.g. Molecule_{}_n2s1.mps")
parser.add_argument("--id",nargs="+",type=int,default=[1, 2],help="only rewrite first or second segment of pair,iexcitoncl")
parser.add_argument("--compare", action='store_const', const=1, default=0,help="Only replace mps files where segtype can be found in formatstring")
args=parser.parse_args()
filetype= os.path.splitext(args.jobfile)[1][1:]
if filetype=="jobs":
root=XmlParser(args.jobfile)
print "read in "
for inputs in root.iterfind('.//input'):
for i,segment in enumerate(inputs):
if i+1 not in args.id:
continue
if args.compare:
segtype=segment.get('type')
if segtype not in args.format:
continue
segid=segment.get("id")
mpsfile=os.path.join(args.path,(args.format).format(segid))
segment.set('mps_file',mpsfile)
print "writing"
with open(args.jobfile, 'w') as f:
f.write(lxml.tostring(root, pretty_print=True))
nargs="+",
type=int,
default=[1, 2],
help="only rewrite first or second segment of pair,iexcitoncl")
parser.add_argument(
"--compare",
action='store_const',
const=1,
default=0,
help="Only replace mps files where segtype can be found in formatstring")
args = parser.parse_args()
filetype = os.path.splitext(args.jobfile)[1][1:]
if filetype == "jobs":
root = XmlParser(args.jobfile)
print "read in "
for inputs in root.iterfind('.//input'):
for i, segment in enumerate(inputs):
if i + 1 not in args.id:
continue
if args.compare:
segtype = segment.get('type')
if segtype not in args.format:
continue
segid = segment.get("id")
mpsfile = os.path.join(args.path, (args.format).format(segid))
segment.set('mps_file', mpsfile)
print "writing"
with open(args.jobfile, 'w') as f:
f.write(lxml.tostring(root, pretty_print=True))
parser.add_argument("--run",
action='store_const',
const=1,
default=0,
help="Run jobs")
parser.add_argument("--read",
action='store_const',
const=1,
default=0,
help="Readout outputfiles")
args = parser.parse_args()
BohrtoAngstroem = 0.5291772109
b2a3 = BohrtoAngstroem**3
root = XmlParser(args.options)
h = float(root.find("fieldstrength").text)
tags = (root.find("tags").text).split()
if h < 10E-5:
print "Aborting. Field strength is too small"
sys.exit()
def copyfromtemplate(path):
base = os.path.realpath('.')
#print base
template = os.path.join(base, "TEMPLATE")
#print template
from __tools__ import MyParser
from __tools__ import XmlParser
from __tools__ import XmlWriter
import lxml.etree as lxml
parser = MyParser(description="Delete Entries from Jobfile")
parser.add_argument("--jobfile", "-j", type=str, required=True, help="jobfile")
parser.add_argument("--output",
"-o",
type=str,
default="joboutput.xml",
help="jobfile")
parser.add_argument("--exclude",
type=str,
nargs="+",
help="Tags to exclude from jobfile e,h,n,s,t")
args = parser.parse_args()
print "Removing states with tags including: {} ".format(" ".join(args.exclude))
root = XmlParser(args.jobfile)
for entry in root.iter('job'):
status = entry.find("tag").text
for eex in args.exclude:
if eex in status:
root.remove(entry)
break
print "Writing to {}".format(args.output)
XmlWriter(root, args.output)
parser=MyParser(description="Environment to split a jobfile into many and submit to cluster")
parser.add_argument("--options","-o",type=str,required=True,help="optionfile")
parser.add_argument("--submit",action='store_const', const=1, default=0,help="Submit to cluster")
parser.add_argument("--setup",action='store_const', const=1, default=0,help="Setup")
parser.add_argument("--merge",action='store_const', const=1, default=0,help="Merge jobfiles")
parser.add_argument("--info",action='store_const', const=1, default=0,help="Display info about each jobfile")
parser.add_argument("--reset",type=str, nargs="+",default=False,help="Reset FAILED and or ASSIGNED to AVAILABLE")
parser.add_argument("--exclude",type=int, nargs="+", default=False,help="Exclude certain jobs from action,give the numbers of the jobs")
parser.add_argument("--include",type=int, nargs="+", default=False,help="Limit action to only the jobs, give the numbers of the jobs")
args=parser.parse_args()
if args.exclude!=False and args.include!=False:
print "ERROR: Excluding and Including at the same time does not work. Choose different options!"
sys.exit()
root=XmlParser(args.options)
queue=root.find("queue").text
procs=int(root.find("procs").text)
tag=root.find("tag").text
jobfile=root.find("jobfile").text
calculator=root.find("calculator").text
optionfile=root.find("optfile").text
sql=root.find("sqlfile").text
threads=int(root.find("threads").text)
cache=int(root.find("cache").text)
rsync=(root.find("rsync").text)
numberofjobs=int(root.find("clusterjobs").text)
workdir=root.find("workdir").text
nargs="+",
default=False,
help="Exclude certain jobs from action,give the numbers of the jobs")
parser.add_argument(
"--include",
type=int,
nargs="+",
default=False,
help="Limit action to only the jobs, give the numbers of the jobs")
args = parser.parse_args()
if args.exclude != False and args.include != False:
print "ERROR: Excluding and Including at the same time does not work. Choose different options!"
sys.exit()
root = XmlParser(args.options)
queue = root.find("queue").text
procs = int(root.find("procs").text)
tag = root.find("tag").text
jobfile = root.find("jobfile").text
calculator = root.find("calculator").text
optionfile = root.find("optfile").text
sql = root.find("sqlfile").text
threads = int(root.find("threads").text)
cache = int(root.find("cache").text)
rsync = (root.find("rsync").text)
numberofjobs = int(root.find("clusterjobs").text)
workdir = root.find("workdir").text
modules = root.find("modules").text
source = root.find("source").text
from __tools__ import RepresentsInt
from __exciton__ import readexcitonlogfile
parser=MyParser(description="Enviroment to do numerical polarisation calculations with gwbse and gaussian")
parser.add_argument("--template","-t",type=str,required=True,help="Folder, from which to take votca-optionfiles from")
parser.add_argument("--options","-o",type=str,required=True,help="optionfile")
parser.add_argument("--setup", action='store_const', const=1, default=0,help="Setup folders")
parser.add_argument("--run", action='store_const', const=1, default=0,help="Run jobs")
parser.add_argument("--read", action='store_const', const=1, default=0,help="Readout outputfiles")
args=parser.parse_args()
BohrtoAngstroem=0.5291772109
b2a3=BohrtoAngstroem**3
root=XmlParser(args.options)
h=float(root.find("fieldstrength").text)
tags=(root.find("tags").text).split()
if h< 10E-5:
print "Aborting. Field strength is too small"
sys.exit()
def copyfromtemplate(path):
base=os.path.realpath('.')
#print base
template=os.path.join(base, "TEMPLATE")