def _storeConfigurations(self):
"Store Configuration files"
self._updateStatus("prepare-configs")
#pfnlist = []
# Save 4 config files
for type in FILETYPE:
inputs = self.clerk.getQEConfigurations(where = "taskid='%s' and type='%s'" % \
(self.taskid, type))
if len(inputs) == 0:
return
# assert input.type == type
input = latestInput(inputs)
fn = input.type
#pfn = packname(input.id, fn) # E.g. 44XXJJG2filecrys
#pfnlist.append(pfn)
# Read text and store it in different location.
# Not very efficient but will work for file of size < 1Mb
text = readRecordFile(self.dds, input, fn)
writeRecordFile(self.dds, self._job, fn, text) # -> qejobs directory
self.dds.remember(self._job, fn) # Change object and filename?
self._files.append(fn)
# Main config file
text = EPSC_IN_TEXT #% pfnlist # Should be 4 element list
writeRecordFile(self.dds, self._job, EPSC_IN, text) # -> qejobs directory
self.dds.remember(self._job, EPSC_IN) # Change object and filename?
self._files.append(EPSC_IN)
def _storePosFile(self):
"Stores positions to cp.pos file"
str = ""
for ts in range(len(self._pos)):
str += " %s %s\n" % (self._step[ts], self._time[ts])
for atom in self._pos[ts]:
str += " %s %s %s\n" % (atom[0], atom[1], atom[2])
str = str.rstrip("\n")
writeRecordFile(self.dds, self._job, POSFILE, str)
self.dds.remember(self._job, POSFILE) # Important step
self._files.append(POSFILE)
def _storeVelFile(self):
"Stores velocities to cp.vel file"
str = ""
for ts in range(len(self._vel)):
str += " %s %s\n" % (self._step[ts], self._time[ts])
for atom in self._vel[ts]:
str += " %s %s %s\n" % (atom[0], atom[1], atom[2])
str = str.rstrip("\n")
writeRecordFile(self.dds, self._job, VELFILE, str)
self.dds.remember(self._job, VELFILE) # Important step
self._files.append(VELFILE)
def _createRunScript(self):
"Creates run script"
self._updateStatus("prepare-controls")
server = self.clerk.getServers(id = self._job.serverid)
self._task = self.clerk.getQETasks(id = self.taskid)
if self._task.type == "trajectory": # Special case for trajectory task
args = self._trajectoryArgs()
else:
args = self._commandArgs()
cmds = [ "#!/bin/env bash", # Suppose there is bash available
"export ESPRESSO_TMPDIR=%s/" % self._outdir(server),
" ".join(args)
]
writeRecordFile(self.dds, self._job, RUNSCRIPT, "\n".join(cmds)) # -> qejobs directory
self.dds.remember(self._job, RUNSCRIPT) # Important step during which the .__dds_nodelist* files are created
self._files.append(RUNSCRIPT)
def _createRunScript(self):
"Creates run script"
self._updateStatus("prepare-controls")
server = self.clerk.getServers(id = self._job.serverid)
self._task = self.clerk.getQETasks(id = self.taskid)
dest = self.dds.abspath(self._job, server=server) # Important
# This is a nasty HACK!
# EPSC simulation if NOT ever intended for usage other than on desktop!
cmds = [ "#!/bin/env bash", # Suppose there is bash available
"",
"dest='%s'" % dest, # Destination directory in qejobs (on computational cluster)
"",
"epsc3path=`which %s`" % EPSC_BIN,
"cp $epsc3path $dest", # Copy binary to destination directory
"cd $dest", # Go to this directory
"./%s > %s" % (EPSC_BIN, EPSC_OUT)] # Execute binary
writeRecordFile(self.dds, self._job, RUNSCRIPT, "\n".join(cmds)) # -> qejobs directory
self.dds.remember(self._job, RUNSCRIPT) # Important step during which the .__dds_nodelist* files are created
self._files.append(RUNSCRIPT)
def _storeConfigurations(self):
"Store Configuration files"
self._updateStatus("prepare-configs")
inputs = self.clerk.getQEConfigurations(where = "taskid='%s'" % self.taskid)
dds = self.dds
if len(inputs) <= 0:
return
input = inputs[0] # Take the first input record
fn = defaultInputName(input.type)
pfn = packname(input.id, fn) # E.g. 44XXJJG2pw.in
# Read text and store it in different location.
# Not very efficient but will work for file of size < 1Mb
text = readRecordFile(dds, input, fn)
writeRecordFile(dds, self._job, pfn, text) # -> qejobs directory
dds.remember(self._job, pfn) # Change object and filename?
self._files.append(pfn)