def write_my_displacement_file(self, xdatdict, mydir="", fname="XDATCAR"):
"""Write a displacement file.
Args:
xdatdict <dict>: Dictionary of XDATCAR (see read_my_xdatcar)
mydir <str>: Directory in which to write.
Use ingredient directory if null.
fname <str>: filename (default DYNMAT)
"""
if mydir == "":
mydir = self.keywords['name']
xdatwrite=MASTFile()
xdatwrite.data=list()
xdatwrite.data.append(xdatdict['descline'])
if not (xdatdict['scale'] == ""):
xdatwrite.data.append(xdatdict['scale'])
xdatwrite.data.append(xdatdict['latta'])
xdatwrite.data.append(xdatdict['lattb'])
xdatwrite.data.append(xdatdict['lattc'])
xdatwrite.data.append(xdatdict['specline'])
xdatwrite.data.append(xdatdict['numline'])
if not (xdatdict['type'] == ""):
xdatwrite.data.append(xdatdict['type'])
configlist = xdatdict['configs'].keys()
configlist.sort()
for cfg in configlist:
xdatwrite.data.append("Konfig=%1i\n" % cfg)
xdatwrite.data.extend(xdatdict['configs'][cfg])
xdatwrite.to_file(os.path.join(mydir, fname))
def write_my_dynamical_matrix_file(self, dyndict, mydir="", fname="DYNMAT"):
"""Write a dynamical matrix file based on a dictionary.
Args:
dyndict <dict>: Dictionary of dynmat (see read_my_dynmat)
mydir <str>: Directory in which to write;
use ingredient directory if null
fname <str>: filename (default DYNMAT)
"""
if mydir == "":
mydir = self.keywords['name']
dynwrite=MASTFile()
dynwrite.data=list()
firstline=str(dyndict['numspec']) + " " + str(dyndict['numatoms']) + " " + str(dyndict['numdisp']) + "\n"
dynwrite.data.append(firstline)
dynwrite.data.append(dyndict['massline'])
atomlist=dyndict['atoms'].keys()
atomlist.sort()
for atom in atomlist:
displist = dyndict['atoms'][atom].keys()
displist.sort()
for disp in displist:
thirdline = str(atom) + " " + str(disp) + " " + dyndict['atoms'][atom][disp]['displine'] + "\n"
dynwrite.data.append(thirdline)
for line in dyndict['atoms'][atom][disp]['dynmat']:
dynwrite.data.append(line)
dynwrite.to_file(os.path.join(mydir, fname))
def write_my_dynmat_without_disp_or_mass(self, dyndict, mydir="", fname="DYNMAT"):
"""Write a dynamical matrix file without the displacement indicators 1, 2, 3
and without the masses line, and with first line having only
the total number of displacements, for PHON.
Args:
dyndict <dict>: Dictionary of dynmat (see read_my_dynmat)
mydir <str>: Directory in which to write; use
ingredient directory if null
fname <str>: filename (default DYNMAT)
"""
if mydir == "":
mydir = self.keywords['name']
dynwrite=MASTFile()
dynwrite.data=list()
firstline=str(dyndict['numdisp']) + "\n"
dynwrite.data.append(firstline)
atomlist=dyndict['atoms'].keys()
atomlist.sort()
for atom in atomlist:
displist = dyndict['atoms'][atom].keys()
displist.sort()
for disp in displist:
thirdline = str(atom) + " " + dyndict['atoms'][atom][disp]['displine'] + "\n"
dynwrite.data.append(thirdline)
for line in dyndict['atoms'][atom][disp]['dynmat']:
dynwrite.data.append(line)
dynwrite.to_file(os.path.join(mydir, fname))
def create_input_files(self, datasets_dict):
"""Create independently looped input files.
Args:
datasets_dict <dict of list>
Returns:
createdfiles <list of str>: list of newly-created file names
Creates an input file for each entry.
"""
ifname = self.keywords['inputfile']
dirstem = os.path.dirname(ifname)
basename = os.path.basename(ifname).split('.')[0]
createdfiles = list()
if dirstem == "":
dirstem = os.getcwd()
dkeys = datasets_dict.keys()
dkeys.sort()
dct = 1
for didx in dkeys:
newfile = MASTFile()
newfile.data = list(datasets_dict[didx])
newname = "%s/loop_%s_%s.inp" % (dirstem, basename,
str(dct).zfill(2))
newfile.to_file(newname)
#createdfiles.append(os.path.basename(newname))
createdfiles.append(newname)
dct = dct + 1
return createdfiles
def create_input_files(self, datasets_dict):
"""Create independently looped input files.
Args:
datasets_dict <dict of list>
Returns:
createdfiles <list of str>: list of newly-created file names
Creates an input file for each entry.
"""
ifname = self.keywords['inputfile']
dirstem = os.path.dirname(ifname)
basename = os.path.basename(ifname).split('.')[0]
createdfiles=list()
if dirstem == "":
dirstem = os.getcwd()
dkeys = datasets_dict.keys()
dkeys.sort()
dct=1
for didx in dkeys:
newfile = MASTFile()
newfile.data = list(datasets_dict[didx])
newname="%s/loop_%s_%s.inp" % (dirstem, basename, str(dct).zfill(2))
newfile.to_file(newname)
#createdfiles.append(os.path.basename(newname))
createdfiles.append(newname)
dct=dct+1
return createdfiles
def clear_submission_list():
"""Clear all entries from the submission list at
$MAST_CONTROL/submitlist
"""
submitlist=os.path.join(mast_control, "submitlist")
if not os.path.isfile(submitlist):
print "No submission list at %s" % submitlist
return
submitfile=MASTFile(submitlist)
submitfile.data=list()
submitfile.data.append("\n")
submitfile.to_file(submitlist)
def clear_submission_list():
"""Clear all entries from the submission list at
$MAST_CONTROL/submitlist
"""
submitlist = os.path.join(mast_control, "submitlist")
if not os.path.isfile(submitlist):
print "No submission list at %s" % submitlist
return
submitfile = MASTFile(submitlist)
submitfile.data = list()
submitfile.data.append("\n")
submitfile.to_file(submitlist)
def write_script(self, dirname="", fname=""):
"""Write the python input script, created from the *.inp input file.
Args:
dirname <str>: directory in which to write
fname <str>: filename to write
Returns:
filename <str>: Full file name of the input script created.
"""
mylines = self.print_input_options()
if dirname == "":
dirname = os.getcwd()
if fname == "":
fname = 'input.py'
filename = os.path.join(dirname, fname)
inputpy = MASTFile()
inputpy.data = mylines
inputpy.to_file(filename)
return filename
def write_submit_script(keywords):
"""This script example is built on the following ingredient keywords,
and may require significant customization.
mast_processors
mast_ppn
mast_queue
mast_nodes
mast_exec
mast_walltime
mast_memory
"""
import os
#set defaults
name = os.path.basename(keywords['name'])
try:
mast_processors = str(keywords['program_keys']['mast_processors'])
except KeyError:
mast_processors = "8"
try:
mast_ppn = str(keywords['program_keys']['mast_ppn'])
except KeyError:
mast_ppn = "8"
try:
mast_queue = str(keywords['program_keys']['mast_queue'])
except KeyError:
mast_queue = 'default'
try:
mast_nodes = str(keywords['program_keys']['mast_nodes'])
except KeyError:
mast_nodes = "1"
try:
mast_exec = str(keywords['program_keys']['mast_exec'])
except KeyError:
mast_exec = "mpiexec vasp"
try:
mast_walltime = str(
keywords['program_keys']['mast_walltime']) + ":00:00"
except KeyError:
mast_walltime = "24:00:00"
try:
mast_memory = str(keywords['program_keys']['mast_memory'])
except KeyError:
mast_memory = "1000"
#create submission script
newkey = dict()
newkey['mast_memory'] = mast_memory
newkey['mast_exec'] = mast_exec
newkey['mast_walltime'] = mast_walltime
newkey['mast_queue'] = mast_queue
newkey['mast_ppn'] = mast_ppn
newkey['mast_nodes'] = mast_nodes
newkey['mast_processors'] = mast_processors
newkey['mast_name'] = name
my_template = MASTFile("%s/submit/platforms/%s/submit_template.sh" %
(mast_install, mast_platform))
newdata = list()
for myline in my_template.data:
for mykey in newkey.keys():
querykey = "?" + mykey + "?"
if querykey in myline:
myline = myline.replace(querykey, newkey[mykey])
newdata.append(myline)
filled_template = MASTFile()
filled_template.data = list(newdata)
filled_template.to_file("%s/submit.sh" %
keywords['name']) #use full path here
return
def write_submit_script(keywords):
"""This script example is built on the following ingredient keywords,
and may require significant customization.
mast_processors
mast_ppn
mast_queue
mast_nodes
mast_exec
mast_walltime
mast_memory
"""
import os
#set defaults
name = os.path.basename(keywords['name'])
try:
mast_processors = str(keywords['program_keys']['mast_processors'])
except KeyError:
mast_processors = "8"
try:
mast_ppn = str(keywords['program_keys']['mast_ppn'])
except KeyError:
mast_ppn = "8"
try:
mast_queue = str(keywords['program_keys']['mast_queue'])
except KeyError:
mast_queue = 'default'
try:
mast_nodes = str(keywords['program_keys']['mast_nodes'])
except KeyError:
mast_nodes = "1"
try:
mast_exec = str(keywords['program_keys']['mast_exec'])
except KeyError:
mast_exec = "mpiexec vasp"
try:
mast_walltime = str(keywords['program_keys']['mast_walltime']) + ":00:00"
except KeyError:
mast_walltime = "24:00:00"
try:
mast_memory = str(keywords['program_keys']['mast_memory'])
except KeyError:
mast_memory = "1000"
#create submission script
newkey = dict()
newkey['mast_memory'] = mast_memory
newkey['mast_exec'] = mast_exec
newkey['mast_walltime'] = mast_walltime
newkey['mast_queue'] = mast_queue
newkey['mast_ppn'] = mast_ppn
newkey['mast_nodes'] = mast_nodes
newkey['mast_processors'] = mast_processors
newkey['mast_name'] = name
my_template = MASTFile("%s/submit/platforms/%s/submit_template.sh" % (mast_install, mast_platform))
newdata = list()
for myline in my_template.data:
for mykey in newkey.keys():
querykey = "?" + mykey + "?"
if querykey in myline:
myline = myline.replace(querykey, newkey[mykey])
newdata.append(myline)
filled_template = MASTFile()
filled_template.data = list(newdata)
filled_template.to_file("%s/submit.sh" % keywords['name']) #use full path here
return
