def softlink_a_file(self, childpath, filename):
"""Softlink a parent file to a matching name in the child folder.
Args:
childpath <str>: path to child ingredient
filename <str>: file name (e.g. "CHGCAR")
"""
parentpath = self.keywords['name']
dirutil.lock_directory(childpath)
import subprocess
#print "cwd: ", os.getcwd()
#print parentpath
#print childpath
if os.path.isfile("%s/%s" % (parentpath, filename)):
if not os.path.isfile("%s/%s" % (childpath, filename)):
curpath = os.getcwd()
os.chdir(childpath)
mylink = subprocess.Popen("ln -s %s/%s %s" %
(parentpath, filename, filename),
shell=True)
mylink.wait()
os.chdir(curpath)
else:
self.logger.warning(
"%s already exists in %s. Parent %s not softlinked." %
(filename, childpath, filename))
else:
raise MASTError(
self.__class__.__name__,
"No file in parent path %s named %s. Cannot create softlink." %
(parentpath, filename))
dirutil.unlock_directory(childpath)
def _vasp_poscar_setup(self):
"""Set up the POSCAR file for a single VASP run.
"""
name = self.keywords['name']
pospath = os.path.join(name, "POSCAR")
if os.path.isfile(pospath):
my_poscar = Poscar.from_file(pospath)
#parent should have given a structure
else: #this is an originating run; mast should give it a structure
if self.keywords['structure'] is not None:
my_poscar = Poscar(self.keywords['structure'])
else:
pf = os.path.join(os.path.dirname(name),'POSCAR_%s'%os.path.basename(name))
if os.path.isfile(pf):
my_poscar = Poscar.from_file(pf)
workdir=os.path.dirname(name)
sdir=os.path.join(workdir,"structure_index_files")
if os.path.exists(sdir):
mystr=my_poscar.structure
manname="manifest___"
myatomindex=AtomIndex(structure_index_directory=sdir)
newstr=myatomindex.graft_new_coordinates_from_manifest(mystr, manname, "")
self.logger.info("Getting original coordinates from manifest.")
new_pos=Poscar(newstr)
my_poscar=new_pos
self.logger.info("No POSCAR found from a parent; base structure used for %s" % self.keywords['name'])
if 'mast_coordinates' in self.keywords['program_keys'].keys():
sxtend = StructureExtensions(struc_work1=my_poscar.structure, name=self.keywords['name'])
coordstrucs=self.get_coordinates_only_structure_from_input()
newstruc = sxtend.graft_coordinates_onto_structure(coordstrucs[0])
my_poscar.structure=newstruc.copy()
dirutil.lock_directory(name)
my_poscar.write_file(pospath)
dirutil.unlock_directory(name)
return my_poscar
def _vasp_potcar_setup(self, my_poscar):
"""Set up the POTCAR file."""
name = self.keywords['name']
if 'mast_xc' in self.keywords['program_keys'].keys():
myxc = self.keywords['program_keys']['mast_xc'].upper() #Uppercase
else:
raise MASTError("vasp_checker, _vasp_potcar_setup","Exchange correlation functional needs to be specified in ingredients keyword mast_xc")
if ('mast_pp_setup' in self.keywords['program_keys'].keys()):
sites = my_poscar.site_symbols
setup = self.keywords['program_keys']['mast_pp_setup']
pp_sites = list()
for site in sites:
try:
pp_sites.append(setup[site])
except KeyError:
pp_sites.append(site)
my_potcar = Potcar(symbols=pp_sites, functional=myxc, sym_potcar_map=None)
else:
my_potcar = Potcar(symbols=my_poscar.site_symbols, functional=myxc, sym_potcar_map=None)
dirutil.lock_directory(name)
my_potcar.write_file(name + "/POTCAR")
dirutil.unlock_directory(name)
return my_potcar
def copy_a_file(self, childpath, pfname, cfname):
"""Copy a parent file to an arbitrary name in the child folder.
Args:
childpath <str>: path to child ingredient
pfname <str>: file name in parent folder (e.g. "CONTCAR")
cfname <str>: file name for child folder (e.g. "POSCAR")
"""
parentpath = self.keywords['name']
dirutil.lock_directory(childpath)
self.logger.info("Attempting copy of %s/%s into %s/%s" %
(parentpath, pfname, childpath, cfname))
if os.path.isfile("%s/%s" % (parentpath, pfname)):
if not os.path.isfile("%s/%s" % (childpath, cfname)):
shutil.copy("%s/%s" % (parentpath, pfname),
"%s/%s" % (childpath, cfname))
else:
self.logger.warning(
"%s already exists in %s. Parent file %s not copied from %s into child %s."
% (cfname, childpath, pfname, parentpath, cfname))
else:
raise MASTError(
self.__class__.__name__,
"No file in parent path %s named %s. Cannot copy into child path as %s."
% (parentpath, pfname, cfname))
dirutil.unlock_directory(childpath)
def _vasp_kpoints_setup(self):
"""Parse mast_kpoints string, which should take the format:
number, number, number designation
examples: "3x3x3 M", "1x1x1 G". If no designation is given,
Monkhorst-Pack is assumed.
"""
name = self.keywords['name']
tryname = os.path.join(name, "KPOINTS")
if os.path.isfile(tryname):
#KPOINTS already exists. Do not overwrite.
my_kpoints = Kpoints.from_file(tryname)
return my_kpoints
if not (self.metafile.read_data('kpoints')==None):
kpoints = self.metafile.read_data('kpoints').split()
kmesh = (int(kpoints[0].split('x')[0]),int(kpoints[0].split('x')[1]),int(kpoints[0].split('x')[2]))
try: desig = kpoints[1].upper()
except IndexError: desig = 'M'
try: kshift = (float(kpoints[2]),float(kpoints[3]),float(kpoints[4]))
except IndexError: kshift = (0.0,0.0,0.0)
else:
if 'mast_kpoints' in self.keywords['program_keys'].keys():
kpoints = self.keywords['program_keys']['mast_kpoints']
else:
raise MASTError(self.__class__.__name__,"k-point instructions need to be set either in ingredients keyword mast_kpoints or scaling section in structure ingredient: No k-point settings for the ingredient %s"% name)
if len(kpoints) == 3:
desig = "M"
elif 'line' in str(kpoints[1]):
desig = 'L'
else:
desig = kpoints[3].upper()
if not desig == 'L':
kmesh = (int(kpoints[0]),int(kpoints[1]),int(kpoints[2]))
kshift = (0,0,0)
if desig == "M":
my_kpoints = Kpoints.monkhorst_automatic(kpts=kmesh,shift=kshift)
elif desig == "G":
my_kpoints = Kpoints.gamma_automatic(kpts=kmesh,shift=kshift)
elif desig == 'L':
my_kpoints='Line Mode\n'+'\n'.join(' '.join(kpoints).split(','))+'\n'
fp=open(name+'/KPOINTS','w')
fp.write(my_kpoints)
else:
raise MASTError(self.__class__.__name__,"kpoint designation " + desig + " not recognized.")
dirutil.lock_directory(name)
if not desig=='L':
my_kpoints.write_file(name + "/KPOINTS")
dirutil.unlock_directory(name)
return my_kpoints
def to_file(self, file_path):
"""Writes data to a file (overwrites existing file)."""
#TTM+2 10/7/11 add error checking in case of no path
if (file_path == "") or (file_path == None):
raise MASTError(self.__class__.__name__,
"Refusing to copy to empty path.")
if self.data == []:
raise MASTError(self.__class__.__name__,
"Empty file not copied to " + file_path)
dirutil.lock_directory(os.path.dirname(file_path))
writef = open(file_path, 'wb')
for line in self.data:
writef.write(line)
writef.close()
dirutil.unlock_directory(os.path.dirname(file_path))
def to_file(self,file_path):
"""Writes data to a file (overwrites existing file)."""
#TTM+2 10/7/11 add error checking in case of no path
if (file_path == "") or (file_path == None):
raise MASTError(self.__class__.__name__,
"Refusing to copy to empty path.")
if self.data == []:
raise MASTError(self.__class__.__name__,
"Empty file not copied to " + file_path)
dirutil.lock_directory(os.path.dirname(file_path))
writef = open(file_path,'wb')
for line in self.data:
writef.write(line)
writef.close()
dirutil.unlock_directory(os.path.dirname(file_path))
def _vasp_incar_setup(self, my_potcar, my_poscar):
"""Set up the INCAR, including MAGMOM string, ENCUT, and NELECT."""
name=self.keywords['name']
myd = dict()
myd = self._vasp_incar_get_non_mast_keywords()
try:
myd.pop("IMAGES")
except KeyError:
pass
if 'mast_multiplyencut' in self.keywords['program_keys'].keys():
mymult = float(self.keywords['program_keys']['mast_multiplyencut'])
else:
mymult = 1.5
if 'ENCUT' in myd.keys():
pass
else:
myd['ENCUT']=self._get_max_enmax_from_potcar(my_potcar)*mymult
if 'mast_setmagmom' in self.keywords['program_keys'].keys():
magstr = str(self.keywords['program_keys']['mast_setmagmom'])
magmomstr=""
maglist = magstr.split()
numatoms = sum(my_poscar.natoms)
if len(maglist) < numatoms:
magct=0
while magct < len(maglist):
magmomstr = magmomstr + str(my_poscar.natoms[magct]) + "*" + maglist[magct] + " "
magct = magct + 1
else:
magmomstr = magstr
myd['MAGMOM']=magmomstr
if 'mast_charge' in self.keywords['program_keys'].keys():
myelectrons = self.get_total_electrons(my_poscar, my_potcar)
newelectrons=0.0
try:
adjustment = float(self.keywords['program_keys']['mast_charge'])
except (ValueError, TypeError):
raise MASTError("vasp_checker, vasp_incar_setup","Could not parse adjustment")
#newelectrons = myelectrons + adjustment
newelectrons = myelectrons - adjustment
myd['NELECT']=str(newelectrons)
if self.metafile.read_data('nbands'):
myd['NBANDS']=self.metafile.read_data('nbands')
my_incar = Incar(myd)
dirutil.lock_directory(name)
my_incar.write_file(name + "/INCAR")
dirutil.unlock_directory(name)
return my_incar
def add_selective_dynamics_to_structure_file(self, sdarray):
"""Add selective dynamics to a structure file.
In the case of VASP, the structure file is
POSCAR-like
Args:
sdarray <numpy array of bool>: Numpy array of
booleans for T F F etc.
"""
name = self.keywords['name']
pname = os.path.join(name,"POSCAR")
phposcar = Poscar.from_file(pname)
phposcar.selective_dynamics = sdarray
dirutil.lock_directory(name)
os.rename(pname, pname + "_no_sd")
phposcar.write_file(pname)
dirutil.unlock_directory(name)
return
def set_up_neb_folders(self, image_structures):
"""Set up NEB folders.
Args:
image_structures <list of Structure>: List
of image structures
"""
imct = 0
myname = self.keywords['name']
if 'mast_coordinates' in self.keywords['program_keys'].keys():
coordstrucs = self.get_coordinates_only_structure_from_input()
newstrucs = list()
sidx = 0 #ex. coordstrucs 0, 1, 2 for 3 images
while sidx < self.keywords['program_keys']['mast_neb_settings'][
'images']:
sxtend = StructureExtensions(
struc_work1=image_structures[sidx + 1].copy(),
name=self.keywords['name'])
newstrucs.append(
sxtend.graft_coordinates_onto_structure(coordstrucs[sidx]))
sidx = sidx + 1
while imct < len(image_structures):
imposcar = Poscar(image_structures[imct])
num_str = str(imct).zfill(2)
impath = os.path.join(myname, num_str)
impospath = os.path.join(myname, "POSCAR_" + num_str)
if 'mast_coordinates' in self.keywords['program_keys'].keys():
if imct == 0: #skip endpoint
pass
elif imct == len(image_structures) - 1: #skip other endpt
pass
else:
imposcar.structure = newstrucs[imct - 1].copy()
dirutil.lock_directory(myname)
self.write_poscar_with_zero_velocities(imposcar, impospath)
dirutil.unlock_directory(myname)
try:
os.makedirs(impath)
except OSError:
self.logger.warning("Directory at %s already exists." % impath)
return None
dirutil.lock_directory(impath)
self.write_poscar_with_zero_velocities(
imposcar, os.path.join(impath, "POSCAR"))
dirutil.unlock_directory(impath)
imct = imct + 1
return
def copy_a_file(self, childpath, pfname, cfname):
"""Copy a parent file to an arbitrary name in the child folder.
Args:
childpath <str>: path to child ingredient
pfname <str>: file name in parent folder (e.g. "CONTCAR")
cfname <str>: file name for child folder (e.g. "POSCAR")
"""
parentpath = self.keywords['name']
dirutil.lock_directory(childpath)
self.logger.info("Attempting copy of %s/%s into %s/%s" % (parentpath, pfname, childpath, cfname))
if os.path.isfile("%s/%s" % (parentpath, pfname)):
if not os.path.isfile("%s/%s" % (childpath, cfname)):
shutil.copy("%s/%s" % (parentpath, pfname),"%s/%s" % (childpath, cfname))
else:
self.logger.warning("%s already exists in %s. Parent file %s not copied from %s into child %s." % (cfname,childpath,pfname,parentpath,cfname))
else:
raise MASTError(self.__class__.__name__,"No file in parent path %s named %s. Cannot copy into child path as %s." % (parentpath, pfname, cfname))
dirutil.unlock_directory(childpath)
def set_up_neb_folders(self, image_structures):
"""Set up NEB folders.
Args:
image_structures <list of Structure>: List
of image structures
"""
imct=0
myname = self.keywords['name']
if 'mast_coordinates' in self.keywords['program_keys'].keys():
coordstrucs=self.get_coordinates_only_structure_from_input()
newstrucs=list()
sidx = 0 #ex. coordstrucs 0, 1, 2 for 3 images
while sidx < self.keywords['program_keys']['mast_neb_settings']['images']:
sxtend = StructureExtensions(struc_work1=image_structures[sidx+1].copy(), name=self.keywords['name'])
newstrucs.append(sxtend.graft_coordinates_onto_structure(coordstrucs[sidx]))
sidx = sidx + 1
while imct < len(image_structures):
imposcar = Poscar(image_structures[imct])
num_str = str(imct).zfill(2)
impath = os.path.join(myname, num_str)
impospath = os.path.join(myname, "POSCAR_" + num_str)
if 'mast_coordinates' in self.keywords['program_keys'].keys():
if imct == 0: #skip endpoint
pass
elif imct == len(image_structures)-1: #skip other endpt
pass
else:
imposcar.structure=newstrucs[imct-1].copy()
dirutil.lock_directory(myname)
imposcar.write_file(impospath)
dirutil.unlock_directory(myname)
try:
os.makedirs(impath)
except OSError:
self.logger.warning("Directory at %s already exists." % impath)
return None
dirutil.lock_directory(impath)
imposcar.write_file(os.path.join(impath, "POSCAR"))
dirutil.unlock_directory(impath)
imct = imct + 1
return
def forward_extra_restart_files(self, childpath):
"""Forward extra restart files:
For VASP, this entails a softlink to WAVECAR and
CHGCAR.
Args:
childpath <str>: path to child ingredient
"""
raise MASTError(self.__class__.__name__,"This function is obsolete. Use softlink_charge_density_file, softlink_wavefunction_file, forward_charge_density_file, and/or forward_wavefunction_file")
parentpath = self.keywords['name']
dirutil.lock_directory(childpath)
import subprocess
#print "cwd: ", os.getcwd()
curpath = os.getcwd()
os.chdir(childpath)
#print parentpath
#print childpath
mylink=subprocess.Popen("ln -s %s/WAVECAR WAVECAR" % parentpath, shell=True)
mylink.wait()
mylink2=subprocess.Popen("ln -s %s/CHGCAR CHGCAR" % parentpath, shell=True)
mylink2.wait()
os.chdir(curpath)
dirutil.unlock_directory(childpath)
def _phon_poscar_setup(self):
"""Set up a PHON POSCAR file. Strip out the "elements" line (that is,
use VASP version 4 format. Also strip out anything beneath the atoms
line.
"""
name = self.keywords["name"]
pospath = os.path.join(name, "POSCAR")
prepath = os.path.join(name, "POSCAR_prePHON")
if os.path.isfile(pospath): # Already done. Return.
return
my_poscar = Poscar.from_file(prepath)
my_poscar.selective_dynamics = None # unset SD if it is set
my_poscar.velocities = None # unset velocities
dirutil.lock_directory(name)
my_poscar.write_file(pospath)
dirutil.unlock_directory(name)
# pick up a copy and strip out the elements line.
mypfile = MASTFile(pospath)
myline6 = mypfile.get_line_number(6)
if myline6.strip().split()[0].isalpha:
mypfile.modify_file_by_line_number(6, "D")
mypfile.to_file(pospath)
return
def _phon_poscar_setup(self):
"""Set up a PHON POSCAR file. Strip out the "elements" line (that is,
use VASP version 4 format. Also strip out anything beneath the atoms
line.
"""
name = self.keywords['name']
pospath = os.path.join(name, "POSCAR")
prepath = os.path.join(name, "POSCAR_prePHON")
if os.path.isfile(pospath): #Already done. Return.
return
my_poscar = Poscar.from_file(prepath)
my_poscar.selective_dynamics=None #unset SD if it is set
my_poscar.velocities=None #unset velocities
dirutil.lock_directory(name)
my_poscar.write_file(pospath)
dirutil.unlock_directory(name)
#pick up a copy and strip out the elements line.
mypfile = MASTFile(pospath)
myline6=mypfile.get_line_number(6)
if myline6.strip().split()[0].isalpha:
mypfile.modify_file_by_line_number(6,"D")
mypfile.to_file(pospath)
return
def softlink_a_file(self, childpath, filename):
"""Softlink a parent file to a matching name in the child folder.
Args:
childpath <str>: path to child ingredient
filename <str>: file name (e.g. "CHGCAR")
"""
parentpath = self.keywords['name']
dirutil.lock_directory(childpath)
import subprocess
#print "cwd: ", os.getcwd()
#print parentpath
#print childpath
if os.path.isfile("%s/%s" % (parentpath, filename)):
if not os.path.isfile("%s/%s" % (childpath, filename)):
curpath = os.getcwd()
os.chdir(childpath)
mylink=subprocess.Popen("ln -s %s/%s %s" % (parentpath,filename,filename), shell=True)
mylink.wait()
os.chdir(curpath)
else:
self.logger.warning("%s already exists in %s. Parent %s not softlinked." % (filename,childpath,filename))
else:
raise MASTError(self.__class__.__name__,"No file in parent path %s named %s. Cannot create softlink." % (parentpath, filename))
dirutil.unlock_directory(childpath)
def lock_directory(self):
return dirutil.lock_directory(self.keywords['name'])
def lock_directory(self):
return dirutil.lock_directory(self.keywords['name'])