def compare_old_and_new_change_status_files():
"""Compare old and new status files from $MAST_CONTROL
and $MAST_SCRATCH.
Write an indication whether the status files have changed,
not changed. Use "archived" if a recipe has been archived or is
missing from SCRATCH for some other reason.
"""
rdict = dict()
mastcontrol = dirutil.get_mast_control_path()
mastscratch = dirutil.get_mast_scratch_path()
recipedirs = dirutil.immediate_subdirs(
os.path.join(mastcontrol, "changestatusfiles"))
for recipedir in recipedirs:
mystatus = "unknown"
rdict[recipedir] = dict()
changelist = list()
if not os.path.exists(os.path.join(mastscratch, recipedir)):
mystatus = "archived"
else:
ingreddirs = dirutil.immediate_subdirs(
os.path.join(mastcontrol, "changestatusfiles", recipedir))
for ingreddir in ingreddirs:
scratchstatusfile = MASTFile(
os.path.join(mastscratch, recipedir, ingreddir,
"change_status.txt"))
controlstatusfile = MASTFile(
os.path.join(mastcontrol, "changestatusfiles", recipedir,
ingreddir, "change_status.txt"))
if scratchstatusfile.data == controlstatusfile.data:
mystatus = "unchanged"
else:
mystatus = "changed"
rdict[recipedir][ingreddir] = "send"
rdict[recipedir]["MAIN"] = mystatus
return rdict
def get_new_change_status_files():
"""Compare old and new status files from $MAST_CONTROL
and $MAST_SCRATCH.
Write an indication whether the status files have changed,
not changed. Use "archived" if a recipe has been archived or is
missing from SCRATCH for some other reason.
"""
rdict = dict()
mastcontrol = dirutil.get_mast_control_path()
mastscratch = dirutil.get_mast_scratch_path()
olddirs = list()
recipedirs = dirutil.immediate_subdirs(
os.path.join(mastcontrol, "changestatusfiles"))
for recipedir in recipedirs:
ingreddirs = dirutil.immediate_subdirs(
os.path.join(mastcontrol, "changestatusfiles", recipedir))
for ingreddir in ingreddirs:
olddirs.append("%s/%s" % (recipedir, ingreddir))
srecdirs = dirutil.immediate_subdirs(mastscratch)
for srecdir in srecdirs:
singreddirs = dirutil.immediate_subdirs(
os.path.join(mastscratch, srecdir))
for singreddir in singreddirs:
csfile = os.path.join(mastscratch, srecdir, singreddir,
"change_status.txt")
if os.path.isfile(csfile):
if not "%s/%s" % (srecdir, singreddir) in olddirs:
if not srecdir in rdict.keys():
rdict[srecdir] = dict()
rdict[srecdir]["MAIN"] = "changed"
rdict[srecdir][singreddir] = "send"
return rdict
def save_old_change_status_files():
"""Save off old status files from $MAST_SCRATCH
into $MAST_CONTROL
"""
mastcontrol = dirutil.get_mast_control_path()
if not os.path.exists(os.path.join(mastcontrol, "changestatusfiles")):
os.mkdir(os.path.join(mastcontrol, "changestatusfiles"))
mastscratch = dirutil.get_mast_scratch_path()
recipedirs = dirutil.immediate_subdirs(mastscratch)
for recipedir in recipedirs:
ingreddirs = dirutil.immediate_subdirs(
os.path.join(mastscratch, recipedir))
for ingreddir in ingreddirs:
csfile = os.path.join(mastscratch, recipedir, ingreddir,
"change_status.txt")
if os.path.isfile(csfile):
changestatusfile = MASTFile(csfile)
trydir = os.path.join(mastcontrol, "changestatusfiles",
recipedir)
if not os.path.exists(trydir):
os.mkdir(trydir)
trydir2 = os.path.join(trydir, ingreddir)
if not os.path.exists(trydir2):
os.mkdir(trydir2)
changestatusfile.to_file("%s/change_status.txt" % trydir2)
return True
def compare_old_and_new_change_status_files():
"""Compare old and new status files from $MAST_CONTROL
and $MAST_SCRATCH.
Write an indication whether the status files have changed,
not changed. Use "archived" if a recipe has been archived or is
missing from SCRATCH for some other reason.
"""
rdict=dict()
mastcontrol=dirutil.get_mast_control_path()
mastscratch=dirutil.get_mast_scratch_path()
recipedirs=dirutil.immediate_subdirs(os.path.join(mastcontrol,"changestatusfiles"))
for recipedir in recipedirs:
mystatus="unknown"
rdict[recipedir]=dict()
changelist=list()
if not os.path.exists(os.path.join(mastscratch,recipedir)):
mystatus="archived"
else:
ingreddirs = dirutil.immediate_subdirs(os.path.join(mastcontrol,"changestatusfiles",recipedir))
for ingreddir in ingreddirs:
scratchstatusfile = MASTFile(os.path.join(mastscratch,recipedir,ingreddir,"change_status.txt"))
controlstatusfile = MASTFile(os.path.join(mastcontrol,"changestatusfiles",recipedir,ingreddir,"change_status.txt"))
if scratchstatusfile.data == controlstatusfile.data:
mystatus="unchanged"
else:
mystatus="changed"
rdict[recipedir][ingreddir]="send"
rdict[recipedir]["MAIN"]=mystatus
return rdict
def get_new_change_status_files():
"""Compare old and new status files from $MAST_CONTROL
and $MAST_SCRATCH.
Write an indication whether the status files have changed,
not changed. Use "archived" if a recipe has been archived or is
missing from SCRATCH for some other reason.
"""
rdict=dict()
mastcontrol=dirutil.get_mast_control_path()
mastscratch=dirutil.get_mast_scratch_path()
olddirs=list()
recipedirs=dirutil.immediate_subdirs(os.path.join(mastcontrol,"changestatusfiles"))
for recipedir in recipedirs:
ingreddirs = dirutil.immediate_subdirs(os.path.join(mastcontrol,"changestatusfiles",recipedir))
for ingreddir in ingreddirs:
olddirs.append("%s/%s" % (recipedir, ingreddir))
srecdirs = dirutil.immediate_subdirs(mastscratch)
for srecdir in srecdirs:
singreddirs = dirutil.immediate_subdirs(os.path.join(mastscratch,srecdir))
for singreddir in singreddirs:
csfile = os.path.join(mastscratch, srecdir, singreddir, "change_status.txt")
if os.path.isfile(csfile):
if not "%s/%s" % (srecdir, singreddir) in olddirs:
if not srecdir in rdict.keys():
rdict[srecdir]=dict()
rdict[srecdir]["MAIN"]="changed"
rdict[srecdir][singreddir]="send"
return rdict
def save_ingredient_files(listfilename="",whichfilename=""):
"""Save off old files from ingredients in $MAST_SCRATCH
into $MAST_CONTROL
Args:
listfilename <str>: File name for the list of files to be saved
whichfilename <str>: Short file name to be saved (identical file
for all recipes)
"""
if listfilename == "":
raise NameError("No list file name given.")
if whichfilename == "":
raise NameError("No file name given for which files to save.")
mastcontrol=dirutil.get_mast_control_path()
if not os.path.exists(os.path.join(mastcontrol,listfilename)):
os.mkdir(os.path.join(mastcontrol,listfilename))
mastscratch=dirutil.get_mast_scratch_path()
recipedirs=dirutil.immediate_subdirs(mastscratch)
for recipedir in recipedirs:
recipefulldir=os.path.join(mastscratch,recipedir)
ingreddirs=dirutil.immediate_subdirs(recipefulldir)
for ingreddir in ingreddirs:
statfilepath = os.path.join(recipefulldir, ingreddir, whichfilename)
if os.path.exists(statfilepath):
statusfile = MASTFile(statfilepath)
trydir = os.path.join(mastcontrol,listfilename,recipedir,ingreddir)
if not os.path.exists(trydir):
os.mkdir(trydir)
statusfile.to_file("%s/%s" % (trydir, whichfilename))
return True
def compare_old_and_new_status_files():
"""Compare old and new status files from $MAST_CONTROL
and $MAST_SCRATCH.
Write an indication whether the status files have changed,
not changed. Use "archived" if a recipe has been archived or is
missing from SCRATCH for some other reason.
"""
rdict=dict()
mastcontrol=dirutil.get_mast_control_path()
mastscratch=dirutil.get_mast_scratch_path()
recipedirs=dirutil.immediate_subdirs(os.path.join(mastcontrol,"statusfiles"))
for recipedir in recipedirs:
mystatus="unknown"
rdict[recipedir]=dict()
changelist=list()
if not os.path.exists(os.path.join(mastscratch,recipedir)):
mystatus="archived"
else:
scratchstatusfile = MASTFile(os.path.join(mastscratch,recipedir,"status.txt"))
controlstatusfile = MASTFile(os.path.join(mastcontrol,"statusfiles",recipedir,"status.txt"))
if scratchstatusfile.data == controlstatusfile.data:
mystatus="unchanged"
else:
mystatus="changed"
myidx=0
while myidx < len(scratchstatusfile.data):
oldline = controlstatusfile.data[myidx]
newline = scratchstatusfile.data[myidx]
if "#" in oldline:
pass
else:
ingred = oldline.split(":")[0].strip()
oldstatus = oldline.split(":")[1].strip()
newstatus = newline.split(":")[1].strip()
if (oldstatus == "P") and (newstatus == "P"):
rdict[recipedir][ingred]="AVOID"
elif (oldstatus == "C") and (newstatus == "C"):
rdict[recipedir][ingred]="AVOID"
else:
rdict[recipedir][ingred]="send"
myidx = myidx + 1
rdict[recipedir]["MAIN"]=mystatus
recipedirs=dirutil.immedate_subdirs(os.path.join(mastcontrol,"changestatusfiles"))
for recipedir in recipedirs:
ingreddirs=dirutil.immediate_subdirs(os.path.join(mastcontrol,"changestatusfiles",recipedir))
for ingreddir in ingreddirs:
oldchangestatus=MASTFile(os.path.join(mastcontrol,"changestatusfiles",recipedir,ingreddir,"change_status.txt"))
newchangestatus=MASTFile(os.path.join(mastscratch,recipedir,ingreddir,"change_status.txt"))
if not (oldchangestatus.data == newchangestatus.data):
rdict[recipedir]["MAIN"]="changed"
rdict[recipedir][ingreddir]="send"
rchangefile = MASTFile()
for rdir in rdict.keys():
for key, value in rdict[rdir].iteritems():
rchangefile.data.append("%s:%s:%s\n" % (rdir,key,value))
rchangefile.to_file(os.path.join(mastcontrol,"recipechangefile.txt"))
return True
def main(ingname=""):
"""Get the energy from an ingredient.
Args:
ingname <str>: Ingredient name, full path
Returns:
<string>: "energy (eV);<energy as a string>", ex:
"energy (eV); 3.0"
Returns last E0 energy for a VASP run.
Returns last E0 energy for all images for a VASP neb.
Returns "N/A" otherwise.
"""
trymeta = "%s/metadata.txt" % ingname
if os.path.isfile(trymeta):
mymeta = Metadata(metafile=trymeta)
myprogram = mymeta.read_data("program")
else:
myprogram = "None"
if 'induce' in ingname: #skip inducedefect ingredients
myprogram = "None"
if 'vasp' in myprogram:
if os.path.isdir("%s/01" % ingname):
estr = "energies (eV)"
for subdir in dirutil.immediate_subdirs(ingname):
mychecker = VaspChecker(name="%s/%s" % (ingname, subdir))
estr = estr + ";%3.3f" % mychecker.get_energy_from_energy_file()
return estr
else:
mychecker = VaspChecker(name=ingname)
return "energy (eV);%3.3f" % mychecker.get_energy_from_energy_file()
else:
return "energy (eV);N/A"
def main(ingname=""):
"""Get the energy from an ingredient.
Args:
ingname <str>: Ingredient name, full path
Returns:
<string>: "energy (eV);<energy as a string>", ex:
"energy (eV); 3.0"
Returns last E0 energy for a VASP run.
Returns last E0 energy for all images for a VASP neb.
Returns "N/A" otherwise.
"""
trymeta = "%s/metadata.txt" % ingname
if os.path.isfile(trymeta):
mymeta = Metadata(metafile=trymeta)
myprogram = mymeta.read_data("program")
else:
myprogram = "None"
if 'induce' in ingname: #skip inducedefect ingredients
myprogram = "None"
if 'vasp' in myprogram:
if os.path.isdir("%s/01" % ingname):
estr = "energies (eV)"
for subdir in dirutil.immediate_subdirs(ingname):
mychecker = VaspChecker(name="%s/%s" % (ingname, subdir))
estr = estr + ";%3.3f" % mychecker.get_energy_from_energy_file(
)
return estr
else:
mychecker = VaspChecker(name=ingname)
return "energy (eV);%3.3f" % mychecker.get_energy_from_energy_file(
)
else:
return "energy (eV);N/A"
def compare_old_and_new_status_files():
"""Compare old and new status files from $MAST_CONTROL
and $MAST_SCRATCH.
Write an indication whether the status files have changed,
not changed. Use "archived" if a recipe has been archived or is
missing from SCRATCH for some other reason.
"""
rdict = dict()
mastcontrol = dirutil.get_mast_control_path()
mastscratch = dirutil.get_mast_scratch_path()
recipedirs = dirutil.immediate_subdirs(
os.path.join(mastcontrol, "statusfiles"))
for recipedir in recipedirs:
mystatus = "unknown"
rdict[recipedir] = dict()
changelist = list()
if not os.path.exists(os.path.join(mastscratch, recipedir)):
mystatus = "archived"
else:
scratchstatusfile = MASTFile(
os.path.join(mastscratch, recipedir, "status.txt"))
controlstatusfile = MASTFile(
os.path.join(mastcontrol, "statusfiles", recipedir,
"status.txt"))
if scratchstatusfile.data == controlstatusfile.data:
mystatus = "unchanged"
else:
mystatus = "changed"
myidx = 0
while myidx < len(scratchstatusfile.data):
oldline = controlstatusfile.data[myidx]
newline = scratchstatusfile.data[myidx]
if "#" in oldline:
pass
else:
ingred = oldline.split(":")[0].strip()
oldstatus = oldline.split(":")[1].strip()
newstatus = newline.split(":")[1].strip()
if (oldstatus == "P") and (newstatus == "P"):
rdict[recipedir][ingred] = "AVOID"
elif (oldstatus == "C") and (newstatus == "C"):
rdict[recipedir][ingred] = "AVOID"
else:
rdict[recipedir][ingred] = "send"
myidx = myidx + 1
rdict[recipedir]["MAIN"] = mystatus
rchangefile = MASTFile()
for rdir in rdict.keys():
for key, value in rdict[rdir].iteritems():
rchangefile.data.append("%s:%s:%s\n" % (rdir, key, value))
rchangefile.to_file(os.path.join(mastcontrol, "recipechangefile.txt"))
return True
def save_old_change_status_files():
"""Save off old status files from $MAST_SCRATCH
into $MAST_CONTROL
"""
mastcontrol=dirutil.get_mast_control_path()
if not os.path.exists(os.path.join(mastcontrol,"changestatusfiles")):
os.mkdir(os.path.join(mastcontrol,"changestatusfiles"))
mastscratch=dirutil.get_mast_scratch_path()
recipedirs=dirutil.immediate_subdirs(mastscratch)
for recipedir in recipedirs:
ingreddirs=dirutil.immediate_subdirs(os.path.join(mastscratch,recipedir))
for ingreddir in ingreddirs:
csfile = os.path.join(mastscratch,recipedir,ingreddir,"change_status.txt")
if os.path.isfile(csfile):
changestatusfile = MASTFile(csfile)
trydir = os.path.join(mastcontrol,"changestatusfiles",recipedir)
if not os.path.exists(trydir):
os.mkdir(trydir)
trydir2 = os.path.join(trydir, ingreddir)
if not os.path.exists(trydir2):
os.mkdir(trydir2)
changestatusfile.to_file("%s/change_status.txt" % trydir2)
return True
def get_new_mast_error_files():
"""Get new MAST_ERROR files.
"""
rdict = dict()
mastcontrol = dirutil.get_mast_control_path()
mastscratch = dirutil.get_mast_scratch_path()
olddirs = list()
srecdirs = dirutil.immediate_subdirs(mastscratch)
for srecdir in srecdirs:
merrfile = os.path.join(mastscratch, srecdir, "MAST_ERROR")
if os.path.isfile(merrfile):
if not srecdir in rdict.keys():
rdict[srecdir] = dict()
rdict[srecdir]["MAIN"] = "changed"
return rdict
def get_new_mast_error_files():
"""Get new MAST_ERROR files.
"""
rdict=dict()
mastcontrol=dirutil.get_mast_control_path()
mastscratch=dirutil.get_mast_scratch_path()
olddirs=list()
srecdirs = dirutil.immediate_subdirs(mastscratch)
for srecdir in srecdirs:
merrfile = os.path.join(mastscratch, srecdir, "MAST_ERROR")
if os.path.isfile(merrfile):
if not srecdir in rdict.keys():
rdict[srecdir] = dict()
rdict[srecdir]["MAIN"]="changed"
return rdict
def save_old_status_files():
"""Save off old status files from $MAST_SCRATCH
into $MAST_CONTROL
"""
mastcontrol=dirutil.get_mast_control_path()
if not os.path.exists(os.path.join(mastcontrol,"statusfiles")):
os.mkdir(os.path.join(mastcontrol,"statusfiles"))
mastscratch=dirutil.get_mast_scratch_path()
recipedirs=dirutil.immediate_subdirs(mastscratch)
for recipedir in recipedirs:
statusfile = MASTFile(os.path.join(mastscratch,recipedir,"status.txt"))
trydir = os.path.join(mastcontrol,"statusfiles",recipedir)
if not os.path.exists(trydir):
os.mkdir(trydir)
statusfile.to_file("%s/status.txt" % trydir)
return True
def save_old_status_files():
"""Save off old status files from $MAST_SCRATCH
into $MAST_CONTROL
"""
mastcontrol = dirutil.get_mast_control_path()
if not os.path.exists(os.path.join(mastcontrol, "statusfiles")):
os.mkdir(os.path.join(mastcontrol, "statusfiles"))
mastscratch = dirutil.get_mast_scratch_path()
recipedirs = dirutil.immediate_subdirs(mastscratch)
for recipedir in recipedirs:
statusfile = MASTFile(
os.path.join(mastscratch, recipedir, "status.txt"))
trydir = os.path.join(mastcontrol, "statusfiles", recipedir)
if not os.path.exists(trydir):
os.mkdir(trydir)
statusfile.to_file("%s/status.txt" % trydir)
return True
def update_atom_index_for_complete(self):
"""Update atom index files with positions for the
completed ingredient.
"""
proceed=False
mydir = self.keywords['name']
workdir=os.path.dirname(mydir)
sdir=os.path.join(workdir,"structure_index_files")
if os.path.exists(sdir):
proceed=True
if not proceed:
self.logger.warning("Called update atom index for ingredient %s, but no atom indices exist." % self.keywords['name'])
return
mymeta=Metadata(metafile="%s/metadata.txt" % mydir)
phonon_label = mymeta.read_data("phonon_label")
if not (phonon_label == None): #Don't update atom indices for phonons
self.logger.debug("Skipping atom index update for phonon calculation %s" % self.keywords['name'])
return
scaling_label=mymeta.read_data("scaling_label")
defect_label=mymeta.read_data("defect_label")
neb_label=mymeta.read_data("neb_label")
if scaling_label == None:
scaling_label = ""
if defect_label == None:
defect_label = ""
if neb_label == None:
neb_label = ""
if neb_label == "":
mystr=Poscar.from_file("%s/CONTCAR" % self.keywords["name"]).structure
ing_label=os.path.basename(mydir)
manname="manifest_%s_%s_%s" % (scaling_label, defect_label, neb_label)
myatomindex=AtomIndex(structure_index_directory=sdir)
myatomindex.update_atom_indices_from_structure(mystr, ing_label, manname)
else:
nebdirs = dirutil.immediate_subdirs(self.keywords["name"])
for mysubdir in nebdirs:
if os.path.isfile("%s/%s/CONTCAR" % (self.keywords["name"],mysubdir)):
mystr=Poscar.from_file("%s/%s/CONTCAR" % (self.keywords["name"], mysubdir)).structure
ing_label=os.path.join(os.path.basename(mydir), mysubdir)
for defect_label in neb_label.split("-"):
manname="manifest_%s_%s_%s" % (scaling_label, defect_label, neb_label)
myatomindex=AtomIndex(structure_index_directory=sdir)
myatomindex.update_atom_indices_from_structure(mystr, ing_label, manname)
return