def main(ingname=""):
"""Get the U value from an ingredient.
Args:
ingname <str>: Ingredient name, full path
Returns:
<string>: "LDAUU, LDAUJ (eV);x x x, x x x", ex:
"LDAUU, LDAUJ (eV); 0 5 0, 0 1 0"
"""
trymeta = "%s/metadata.txt" % ingname
frontstr = "LDAUU, LDAUJ (eV);"
if os.path.isfile(trymeta):
mymeta = Metadata(metafile=trymeta)
myprogram = mymeta.read_data("program")
else:
myprogram = "None"
if myprogram in ['vasp','vasp_neb']:
if os.path.isdir("%s/01" % ingname):
tryfile = "%s/01/OUTCAR" % ingname
else:
tryfile = "%s/OUTCAR" % ingname
grepldauu = fileutil.grepme(tryfile, "LDAUU")
if grepldauu == []:
return "%s N/A" % frontstr
ldauuparse = grepldauu[0].split("=")[1].strip()
grepldauj = fileutil.grepme(tryfile, "LDAUJ")
ldaujparse = grepldauj[0].split("=")[1].strip()
return "%s %s, %s" % (frontstr, ldauuparse, ldaujparse)
else:
return "%s N/A" % frontstr
def main(ingname=""):
"""Get the U value from an ingredient.
Args:
ingname <str>: Ingredient name, full path
Returns:
<string>: "LDAUU, LDAUJ (eV);x x x, x x x", ex:
"LDAUU, LDAUJ (eV); 0 5 0, 0 1 0"
"""
trymeta = "%s/metadata.txt" % ingname
frontstr = "LDAUU, LDAUJ (eV);"
if os.path.isfile(trymeta):
mymeta = Metadata(metafile=trymeta)
myprogram = mymeta.read_data("program")
else:
myprogram = "None"
if myprogram in ['vasp', 'vasp_neb']:
if os.path.isdir("%s/01" % ingname):
tryfile = "%s/01/OUTCAR" % ingname
else:
tryfile = "%s/OUTCAR" % ingname
grepldauu = fileutil.grepme(tryfile, "LDAUU")
if grepldauu == []:
return "%s N/A" % frontstr
ldauuparse = grepldauu[0].split("=")[1].strip()
grepldauj = fileutil.grepme(tryfile, "LDAUJ")
ldaujparse = grepldauj[0].split("=")[1].strip()
return "%s %s, %s" % (frontstr, ldauuparse, ldaujparse)
else:
return "%s N/A" % frontstr
def get_citations(recipedir):
"""Use mast_exec lines from the recipe directory in order
to assign a CITATIONS section to the SUMMARY.txt file.
Args:
recipedir <str>: Recipe directory
Returns:
linelist <list of str>: Lines to add to SUMMARY.txt
"""
mylist = list()
mylist = ['mast', 'pymatgen',
'spglib'] #need to use; removed python as standard
myinput = os.path.join(recipedir, "input.inp")
mastexecs = fileutil.grepme(myinput, "mast_exec")
for mastexec in mastexecs:
if 'vasp' in mastexec.lower():
mylist.append('vasp')
mastxcs = fileutil.grepme(myinput, "mast_xc")
if len(mastxcs) >= 1:
mylist.append('vasp_pps')
for mastxc in mastxcs:
if ("pw" in mastxc.lower()) or ("paw" in mastxc.lower()):
mylist.append('vasp_paw')
mastprogs = fileutil.grepme(myinput, "mast_program")
if len(mastprogs) >= 1:
for mastprog in mastprogs:
if ("vasp_neb" in mastprog.lower()):
mylist.append('vaspneb')
if "tst" in mastexec.lower():
mylist.append('vaspneb')
#if 'phon' in mastexec.lower():
# mylist.append('phon')
if 'structopt' in mastexec.lower():
mylist.append('structopt')
mastwrites = fileutil.grepme(myinput, "mast_write_method")
for mastwrite in mastwrites:
if 'pathfinder' in mastexec.lower():
mylist.append('pathfinder')
citationpath = os.path.join(dirutil.get_mast_install_path(), "summary",
"citation_files")
citationfiles = os.listdir(citationpath)
linelist = list()
uniquelist = list()
for mylistitem in mylist:
if not mylistitem in uniquelist:
uniquelist.append(mylistitem)
#print "UNIQUELIST: ", uniquelist
for listitem in uniquelist:
for citationfile in citationfiles:
if citationfile[:-3] == listitem: #all except number
cfpath = os.path.join(citationpath, citationfile)
cffile = MASTFile(cfpath)
linelist.extend(cffile.data)
return linelist
def get_citations(recipedir):
"""Use mast_exec lines from the recipe directory in order
to assign a CITATIONS section to the SUMMARY.txt file.
Args:
recipedir <str>: Recipe directory
Returns:
linelist <list of str>: Lines to add to SUMMARY.txt
"""
mylist=list()
mylist=['mast','pymatgen','spglib'] #need to use; removed python as standard
myinput = os.path.join(recipedir, "input.inp")
mastexecs = fileutil.grepme(myinput, "mast_exec")
for mastexec in mastexecs:
if 'vasp' in mastexec.lower():
mylist.append('vasp')
mastxcs = fileutil.grepme(myinput, "mast_xc")
if len(mastxcs) >= 1:
mylist.append('vasp_pps')
for mastxc in mastxcs:
if ("pw" in mastxc.lower()) or ("paw" in mastxc.lower()):
mylist.append('vasp_paw')
mastprogs = fileutil.grepme(myinput, "mast_program")
if len(mastprogs) >= 1:
for mastprog in mastprogs:
if ("vasp_neb" in mastprog.lower()):
mylist.append('vaspneb')
if "tst" in mastexec.lower():
mylist.append('vaspneb')
#if 'phon' in mastexec.lower():
# mylist.append('phon')
if 'structopt' in mastexec.lower():
mylist.append('structopt')
mastwrites = fileutil.grepme(myinput, "mast_write_method")
for mastwrite in mastwrites:
if 'pathfinder' in mastexec.lower():
mylist.append('pathfinder')
citationpath = os.path.join(dirutil.get_mast_install_path(),
"summary","citation_files")
citationfiles = os.listdir(citationpath)
linelist = list()
uniquelist=list()
for mylistitem in mylist:
if not mylistitem in uniquelist:
uniquelist.append(mylistitem)
#print "UNIQUELIST: ", uniquelist
for listitem in uniquelist:
for citationfile in citationfiles:
if citationfile[:-3] == listitem: #all except number
cfpath = os.path.join(citationpath, citationfile)
cffile = MASTFile(cfpath)
linelist.extend(cffile.data)
return linelist
def check(self):
ifile = "%s/INCAR" % self.ingpath
if os.path.isfile(ifile):
myincar = pymatgen.io.vaspio.Incar.from_file(ifile)
else:
self.logger.warning("No INCAR file found at %s" % ifile)
return False
nsw = myincar.get('NSW', 0)
if nsw == 0:
self.logger.info("NSW is 0 or not set.")
return False
ofile = "%s/OUTCAR" % self.ingpath
if not (os.path.isfile(ofile)):
ofile = "%s/01/OUTCAR" % self.ingpath
if not (os.path.isfile(ofile)):
self.logger.error("No OUTCAR file at %s or %s/01." %
(self.ingpath, self.ingpath))
return False
myiters = fileutil.grepme(ofile, "Iter")
if len(myiters) == 0:
self.logger.warning("No Iterations in OUTCAR at %s" % ofile)
return False
lastentry = myiters[-1]
ionichalf = lastentry.split('(')[0]
lastiter = ionichalf.split()[-1]
lastiter = int(lastiter)
if lastiter >= nsw:
self.logger.info("Last ionic step %s is at NSW %s" %
(lastiter, nsw))
return True
return False
def main(ingname=""):
"""Get the last volume value from an ingredient.
Args:
ingname <str>: Ingredient name, full path
Returns:
<string>: "Last volume (Angstroms^3);0.000", ex:
"Last volume (Angstroms^3); 324.456"
"""
trymeta = "%s/metadata.txt" % ingname
frontstr = "Last volume (Angstroms^3);"
if os.path.isfile(trymeta):
mymeta = Metadata(metafile=trymeta)
myprogram = mymeta.read_data("program")
else:
myprogram = "None"
if myprogram in ['vasp', 'vasp_neb']:
if os.path.isdir("%s/01" % ingname):
tryfile = "%s/01/OUTCAR" % ingname
else:
tryfile = "%s/OUTCAR" % ingname
grepvol = fileutil.grepme(tryfile, "volume of cell")
if grepvol == []:
return "%s N/A" % frontstr
myvol = grepvol[-1].split(":")[1].strip()
return "%s %s" % (frontstr, myvol)
else:
return "%s N/A" % frontstr
def main(ingname=""):
"""Get the last pressure value from an ingredient.
Args:
ingname <str>: Ingredient name, full path
Returns:
<string>: "Last pressure (kbar);0.00", ex:
"Last pressure (kbar);-23.55"
"""
trymeta = "%s/metadata.txt" % ingname
frontstr = "Last pressure (kbar);"
if os.path.isfile(trymeta):
mymeta = Metadata(metafile=trymeta)
myprogram = mymeta.read_data("program")
else:
myprogram = "None"
if myprogram in ['vasp', 'vasp_neb']:
if os.path.isdir("%s/01" % ingname):
tryfile = "%s/01/OUTCAR" % ingname
else:
tryfile = "%s/OUTCAR" % ingname
greppress = fileutil.grepme(tryfile, "external pressure")
#"external pressure = -1.97 kB Pullay stress = 0.00 kB"
if greppress == []:
return "%s N/A" % frontstr
mypress = greppress[-1].strip().split()[3]
return "%s %s" % (frontstr, mypress)
else:
return "%s N/A" % frontstr
def check(self):
ifile = "%s/INCAR" % self.ingpath
if os.path.isfile(ifile):
myincar = pymatgen.io.vaspio.Incar.from_file(ifile)
else:
self.logger.warning("No INCAR file found at %s" % ifile)
return False
nsw = myincar.get('NSW',0)
if nsw == 0:
self.logger.info("NSW is 0 or not set.")
return False
ofile = "%s/OUTCAR" % self.ingpath
if not (os.path.isfile(ofile)):
ofile = "%s/01/OUTCAR" % self.ingpath
if not (os.path.isfile(ofile)):
self.logger.error("No OUTCAR file at %s or %s/01." % (self.ingpath, self.ingpath))
return False
myiters = fileutil.grepme(ofile, "Iter")
if len(myiters) == 0:
self.logger.warning("No Iterations in OUTCAR at %s" % ofile)
return False
lastentry = myiters[-1]
ionichalf = lastentry.split('(')[0]
lastiter = ionichalf.split()[-1]
lastiter = int(lastiter)
if lastiter >= nsw:
self.logger.info("Last ionic step %s is at NSW %s" % (lastiter, nsw))
return True
return False
def main(ingname=""):
"""Get the last pressure value from an ingredient.
Args:
ingname <str>: Ingredient name, full path
Returns:
<string>: "Last pressure (kbar);0.00", ex:
"Last pressure (kbar);-23.55"
"""
trymeta = "%s/metadata.txt" % ingname
frontstr = "Last pressure (kbar);"
if os.path.isfile(trymeta):
mymeta = Metadata(metafile=trymeta)
myprogram = mymeta.read_data("program")
else:
myprogram = "None"
if myprogram in ['vasp','vasp_neb']:
if os.path.isdir("%s/01" % ingname):
tryfile = "%s/01/OUTCAR" % ingname
else:
tryfile = "%s/OUTCAR" % ingname
greppress = fileutil.grepme(tryfile, "external pressure")
#"external pressure = -1.97 kB Pullay stress = 0.00 kB"
if greppress == []:
return "%s N/A" % frontstr
mypress = greppress[-1].strip().split()[3]
return "%s %s" % (frontstr, mypress)
else:
return "%s N/A" % frontstr
def main(ingname=""):
"""Get the last volume value from an ingredient.
Args:
ingname <str>: Ingredient name, full path
Returns:
<string>: "Last volume (Angstroms^3);0.000", ex:
"Last volume (Angstroms^3); 324.456"
"""
trymeta = "%s/metadata.txt" % ingname
frontstr = "Last volume (Angstroms^3);"
if os.path.isfile(trymeta):
mymeta = Metadata(metafile=trymeta)
myprogram = mymeta.read_data("program")
else:
myprogram = "None"
if myprogram in ['vasp','vasp_neb']:
if os.path.isdir("%s/01" % ingname):
tryfile = "%s/01/OUTCAR" % ingname
else:
tryfile = "%s/OUTCAR" % ingname
grepvol = fileutil.grepme(tryfile, "volume of cell")
if grepvol == []:
return "%s N/A" % frontstr
myvol = grepvol[-1].split(":")[1].strip()
return "%s %s" % (frontstr, myvol)
else:
return "%s N/A" % frontstr
def get_fermi_energy(self, directory):
"""Returns the Fermi energy from a directory"""
abspath = '%s/%s/' % (self.recdir, directory)
if ('OUTCAR' in os.listdir(abspath)):
grepfermi = fileutil.grepme("%s/OUTCAR" % abspath, "E-fermi")
lastfermi = grepfermi[-1]
fermi = float(lastfermi.split()[2])
print "TTM DEBUG LAST FERMI: ", fermi
return fermi
#print "TTM DEBUG: OUTCAR efermi: ", Outcar('%s/OUTCAR' % abspath).efermi
#return Outcar('%s/OUTCAR' % abspath).efermi
elif ('vasprun.xml' in os.listdir(abspath)):
return Vasprun('%s/vasprun.xml' % abspath).efermi
def get_fermi_energy(self, directory):
"""Returns the Fermi energy from a directory"""
abspath = '%s/%s/' % (self.recdir, directory)
if ('OUTCAR' in os.listdir(abspath)):
grepfermi = fileutil.grepme("%s/OUTCAR" % abspath, "E-fermi")
lastfermi=grepfermi[-1]
fermi = float(lastfermi.split()[2])
print "TTM DEBUG LAST FERMI: ", fermi
return fermi
#print "TTM DEBUG: OUTCAR efermi: ", Outcar('%s/OUTCAR' % abspath).efermi
#return Outcar('%s/OUTCAR' % abspath).efermi
elif ('vasprun.xml' in os.listdir(abspath)):
return Vasprun('%s/vasprun.xml' % abspath).efermi
def get_v(self,vdir,vdir_num,vdir_denom):
"""Obtaining the attempt frequencies.
Args:
vdir <list of dict>: vdir={'v0':*,'v1':*,...}, * is the list like [<local_min>,<saddle>]
vdir_num <dict>: vdir_num={'E0':<local_min>,...}
Edir_denum <dict>: Edir_denom={'E0':<saddle>,...}
"""
v = dict()
v_num = dict()
v_denom = dict()
for freq in vdir.keys():
if len(vdir[freq])==1: v[freq] = vdir[freq][0]
else:
if os.path.isfile(vdir_num[freq]+'_FREQ') and os.path.isfile(vdir_num[freq]+'_FREQ'): # Reading data from FREQ files
fn=open(vdir_num[freq]+'_FREQ','r')
nthzlist=self.getinfo(fn.readline())
i=0
num_num=0
v_num[freq]=1.0
while i<len(nthzlist):
if abs(float(nthzlist[i]))>0.1:
v_num[freq]=v_num[freq]*float(nthzlist[i])
num_num+=1
i+=1
fd=open(vdir_denom[freq]+'_FREQ','r')
dthzlist=self.getinfo(fd.readline())
j=0
denom_num=0
v_denom[freq]=1.0
while j<len(dthzlist):
if abs(float(dthzlist[j]))>0.1:
v_denom[freq]=v_denom[freq]*float(dthzlist[j])
denom_num+=1
j+=1
if not num_num==denom_num+1:
print 'WARNING: Numbers of non-zero frequencies at local minimum and at saddle point do not match! Please double-check the FREQ files of %s and %s'%(vdir_num[freq],vdir_denom[freq])
else: # Reading data from OUTCAR files
nthzlist = fileutil.grepme(vdir_num[freq]+'_OUTCAR', "2PiTHz")
num_num=len(nthzlist)
dthzlist = fileutil.grepme(vdir_denom[freq]+'_OUTCAR', "2PiTHz")
denom_num=len(dthzlist)
im_num=0
im_denom=0
if denom_num==num_num:
for i in range(num_num):
if 'f/i' in dthzlist[i]: im_denom+=1
if 'f/i' in nthzlist[i]: im_num+=1
if not im_num==0:
print 'WARNING: Imaginary frequency found in the local minimum! Please check the OUTCAR of %s!'%vdir_num[freq]
elif im_denom==0:
print 'WARNING: No imaginary frequency found in the saddle point! Please check the OUTCAR of %s!'%vdir_denom[freq]
elif im_denom>1:
print 'WARNING: More than 1 imaginary frequencies found in the saddle point! Please check the OUTCAR of %s!'%vdir_denom[freq]
else:
print 'WARNING: Numbers of frequencies at local minimum and at saddle point are not equal! Please check the OUTCAR of %s and %s!'%(vdir_num[freq],vdir_denom[freq])
v_num[freq]=v_denom[freq]=1.0
for i in range(num_num):
if not 'f/i' in nthzlist[i]:
v_num[freq]*=float(self.getinfo(nthzlist[i])[3])
for i in range(denom_num):
if not 'f/i' in dthzlist[i]:
v_denom[freq]*=float(self.getinfo(dthzlist[i])[3])
v[freq]=v_num[freq]/v_denom[freq]
return v
i+=1
fd=open(vdir_denom[freq]+'_FREQ','r')
dthzlist=self.getinfo(fd.readline())
j=0
denom_num=0
v_denom[freq]=1.0
while j<len(dthzlist):
if abs(float(dthzlist[j]))>0.1:
v_denom[freq]=v_denom[freq]*float(dthzlist[j])
denom_num+=1
j+=1
if not num_num==denom_num+1:
print 'WARNING: Numbers of non-zero frequencies at local minimum and at saddle point do not match! Please double-check the FREQ files of %s and %s'%(vdir_num[freq],vdir_denom[freq])
else: # Reading data from OUTCAR files
nthzlist = fileutil.grepme(vdir_num[freq]+'_OUTCAR', "2PiTHz")
num_num=len(nthzlist)
dthzlist = fileutil.grepme(vdir_denom[freq]+'_OUTCAR', "2PiTHz")
denom_num=len(dthzlist)
im_num=0
im_denom=0
if denom_num==num_num:
for i in range(num_num):
if 'f/i' in dthzlist[i]: im_denom+=1
if 'f/i' in nthzlist[i]: im_num+=1
if not im_num==0:
print 'WARNING: Imaginary frequency found in the local minimum! Please check the OUTCAR of %s!'%vdir_num[freq]
elif im_denom==0:
print 'WARNING: No imaginary frequency found in the saddle point! Please check the OUTCAR of %s!'%vdir_denom[freq]
elif im_denom>1:
print 'WARNING: More than 1 imaginary frequencies found in the saddle point! Please check the OUTCAR of %s!'%vdir_denom[freq]
