def status(self):
from os import path
from time import time
from aBuild.utility import grep
import os
ctime = time()
with chdir(self.directory):
outcar = self._check_file_exists('OUTCAR')
incar = self._check_file_exists('INCAR')
kpoints = self._check_file_exists('KPOINTS')
potcar = self._check_file_exists('POTCAR')
poscar = self._check_file_exists('POSCAR')
if not (incar and kpoints and potcar and poscar):
return 'not setup'
if incar:
relax = grep('INCAR', 'IBRION')
if '-1' not in relax or relax is []:
static = True
else:
static = False
else:
msg.warn("No INCAR found. That seems odd..")
outcarfinishtags = self._check_tag_exists(
'OUTCAR',
'------------------------ aborting loop because EDIFF is reached ----------------------------------------\n'
) or self._check_tag_exists('OUTCAR', ' writing wavefunctions')
if outcar:
time = path.getmtime('OUTCAR')
sgrcon = grep('OUTCAR', 'SGRCON')
if (ctime - time) < 60:
folderstat = 'running'
else:
if static and self._check_tag_exists(
'OUTCAR',
'------------------------ aborting loop because EDIFF is reached ----------------------------------------\n'
):
print('Tripped 1')
folderstat = 'done'
elif self._check_tag_exists('OUTCAR',
' writing wavefunctions'):
print('Tripped 2')
folderstat = 'done'
else:
folderstat = 'running'
else:
folderstat = 'not started'
# if outcar:
#if 'OUTCAR' in files:
print("Folder Stat {}".format(folderstat))
return folderstat
def _check_tag_exists(self,file,tag):
from aBuild.utility import grep
lines = grep(file,tag)
if lines == []:
return False
else:
return True
def setup_select(self):
from os import path, remove
from shutil import copy
from glob import glob
from aBuild.utility import sed, grep, tail, cat
from aBuild.fitting.mtp import MTP
from math import ceil
# 1. Concatenate all of the candidate.cfg_# into one candidate.cfg
# and remove all of the other ones.
# 2. Concatenate all of the selection.log_* files into one file.
# 3. Concatenate all of the relaxed.cfg_# into one file. This file should
# get bigger and bigger with each iteration (Hopefully), but we don't ever
# want to delete one of these files.
# 4. Save the old new_training.cfg
# 5. Build a submission script.
# Find what iteration we are currently on.
candIterationFiles = glob(path.join(self.root,
"candidate_iteration_*"))
relaxedIterationFiles = glob(
path.join(self.root, "relaxed_iteration_*"))
unrelaxedIterationFiles = glob(
path.join(self.root, "unrelaxed_iteration_*"))
if len(candIterationFiles) != len(relaxedIterationFiles) or len(
candIterationFiles) != len(unrelaxedIterationFiles):
msg.fatal(
" I can't figure out what iteration we're on based on the files present. Have a look at all of the *_iteration_* files"
)
if candIterationFiles != []:
iteration = len(candIterationFiles) + 1
else:
iteration = 1
# 1. Bring all of the candidate.cfg_* files together into one
candFiles = glob(path.join(self.root, "candidate.cfg_*"))
if candFiles != []:
cat(candFiles, path.join(self.root, "candidate.temp"), remove=True)
# Save a record
copy(
path.join(self.root, 'candidate.temp'),
path.join(self.root,
"candidate_iteration_" + str(iteration) + ".cfg"))
# Prepare to select, which needs this file.
copy(path.join(self.root, 'candidate.temp'),
path.join(self.root, "candidate.cfg"))
remove(path.join(self.root, 'candidate.temp'))
else:
msg.info("Can't find candidate.cfg_* files to concatenate")
candidatesFile = path.join(self.root, 'candidate.cfg')
grepResults = grep(candidatesFile, 'begin', '-in')
nCandidates = len(grepResults)
print(nCandidates, 'Found this many candidates')
# Sometimes the candidate.cfg file is really big and it is best to split it up into 2 or 3 files and select in quasi-parallel fashion
if nCandidates > 1e6:
with open(candidatesFile, 'r') as f:
for i, l in enumerate(f):
pass
nLines = i + 1
nFiles = ceil(nCandidates / 1e6)
nConfigs = ceil(nCandidates / nFiles)
msg.info("Found lots of candidates, splitting into multiple files")
start = 1
for fileNo in range(1, nFiles + 1):
print("Building candidate file no: {}".format(fileNo))
if fileNo < nFiles:
end = int(grepResults[nConfigs * fileNo].split(':')[0]) - 1
sed(
'-n',
str(start) + ',' + str(end) + ' p', candidatesFile,
"> " +
path.join(self.root,
'candidate_part_' + str(fileNo) + '.cfg'))
else:
tail(
candidatesFile, nLines - end + 1, "> " +
path.join(self.root,
'candidate_part_' + str(fileNo) + '.cfg'))
self.settings["execution"]["mem_per_cpu"] = '72'
self.select_add(
self.settings["execution"],
exeCommand=
'mlp_release_version select-add pot.mtp train.cfg candidate_part_'
+ str(fileNo) + '.cfg new_training_' + str(fileNo) +
'.cfg',
jobfile='jobscript_select_' + str(fileNo) + '.sh')
start = end + 1
# 2. selection.log_*
logFiles = glob(path.join(self.root, "selection.log_*"))
if logFiles != []:
cat(logFiles, path.join(self.root, "selection.temp"), remove=True)
copy(
path.join(self.root, 'selection.temp'),
path.join(self.root,
"selection_iteration_" + str(iteration) + ".log"))
remove(path.join(self.root, 'selection.temp'))
else:
msg.info("Can't find selection.log_* files to concatenate")
# 3. relaxed.cfg_*
relaxedFiles = glob(path.join(self.root, "relaxed.cfg_*"))
if relaxedFiles != []:
cat(relaxedFiles,
path.join(self.root, "relaxed.temp"),
remove=True)
copy(
path.join(self.root, 'relaxed.temp'),
path.join(self.root,
"relaxed_iteration_" + str(iteration) + ".cfg"))
remove(path.join(self.root, 'relaxed.temp'))
else:
msg.info("Can't find relaxed.cfg_* files to concatenate")
# 4. unrelaxed.cfg_*
unrelaxedFiles = glob(path.join(self.root, "unrelaxed.cfg_*"))
if unrelaxedFiles != []:
cat(unrelaxedFiles,
path.join(self.root, "unrelaxed.temp"),
remove=True)
# Save a record of this iteration. May consider copying this file to to-relax.cfg next time we relax
copy(
path.join(self.root, 'unrelaxed.temp'),
path.join(self.root,
"unrelaxed_iteration_" + str(iteration) + ".cfg"))
remove(path.join(self.root, 'unrelaxed.temp'))
else:
msg.info("Can't find unrelaxed.cfg_* files to concatenate")
# 5. relax_log.txt_*
relaxLogFiles = glob(path.join(self.root, "relax_log.txt_*"))
if relaxLogFiles != []:
cat(relaxLogFiles,
path.join(self.root, "relax_log.temp"),
remove=True)
copy(
path.join(self.root, 'relax_log.temp'),
path.join(self.root,
"relax_log_iteration_" + str(iteration) + ".txt"))
remove(path.join(self.root, 'relax_log.temp'))
else:
msg.info("Can't find relax_log.txt_* files to concatenate")
#6. save the new_training.cfg
if path.isfile(path.join(self.root, 'new_training.cfg')):
copy(
path.join(self.root, 'new_training.cfg'),
path.join(
self.root,
"new_training_iteration_" + str(iteration - 1) + ".cfg"))
remove(path.join(self.root, 'new_training.cfg'))
# 7. Build job submission script.
self.select_add(self.settings["execution"])
def status(self):
from os import path
from time import time
from aBuild.utility import grep
import os
fTagStatic = '------------------------ aborting loop because EDIFF is reached ----------------------------------------\n'
fTagRelax = ' writing wavefunctions'
ctime = time()
print('checking directory {}'.format(self.directory))
with chdir(self.directory):
outcar = self._check_file_exists('OUTCAR')
incar = self._check_file_exists('INCAR')
kpoints = self._check_file_exists('KPOINTS')
potcar = self._check_file_exists('POTCAR')
poscar = self._check_file_exists('POSCAR')
output = self._check_file_exists('vasp_output')
oszicar = self._check_file_exists('OSZICAR')
inputs = incar and kpoints and potcar and poscar
''' Check to see if the input files are present
if they aren't, no need to proceed, just return
'not setup'
'''
if not inputs:
return 'not setup'
''' If the OUTCAR file is present, we know that we're
either running, finished successfully, or finished
with errors!
'''
elif outcar: # OUTCAR present
sgrcon = grep('vasp_output','SGRCON')
tooclose = grep('vasp_output','HOPE')
finalenergyline = grep('OUTCAR','free energy')
generalerror = grep('vasp_output','ERROR')
# Check to make sure I've converged electonically.
if grep('OSZICAR','DAV:') != []:
electronicIteration = int(grep('OSZICAR','DAV:')[-1].split()[1])
else:
electronicIteration = 0
if grep('INCAR','nsw') != []:
nsw = int(grep('INCAR','nsw')[0].split('=')[1])
if nsw == 0:
nsw = 1
else:
nsw = 1
if grep('OSZICAR','F=') != []:
ionicIteration = int(grep('OSZICAR','F=')[-1].split()[0])
else:
ionicIteration = 1
if grep('INCAR','nelm') != []:
maxelectronic = grep('INCAR','nelm')[0].split('=')[1]
else:
maxelectronic = 60
if ionicIteration == nsw and int(electronicIteration) == int(maxelectronic):
return 'unconverged'
''' Let's first check to see if this is a static
calculation or a relaxation because the tag
to check for is different.'''
if incar:
relax = grep('INCAR','IBRION')
if '-1' not in relax or relax is []:
static = True
else:
static = False
else:
return 'not setup'
''' Check finish tag for static calc'''
if static and self._check_tag_exists('OUTCAR', fTagStatic): #finish tag found
if finalenergyline != []: #Let's double check
return 'done'
else: # Apparently not, why?
return 'idk'
''' Check finish tag for relax calc'''
elif self._check_tag_exists('OUTCAR',fTagRelax): #Looks like it's done
if finalenergyline != []: # Let's double check
return 'done'
else: # Apparently not, why?
return 'idk'
else:
''' Check how long since the last file write. If it was recent
then we're probably running.'''
time = path.getmtime('OUTCAR')
if (ctime - time) < 3600: # If the OUTCAR was modified in the last hour
# the calculation is probably still running.
return 'running'
elif sgrcon:
return 'sgrcon'
elif generalerror:
return 'error'
elif tooclose:
return 'warning'
else:
return 'too long'
else:
return 'not started'
if output:
warning = grep('output','RRRRR') != [] or grep('output','AAAAAA') != []
if warning:
return 'warning'
return folderstat