def get_my_label(self, label):
"""Get the value of a label in the metadata file.
Args:
label <str>: Label to search for.
Returns:
<str>: Value of the label as a string, stripped.
"""
myname = self.keywords['name']
mymeta = Metadata(metafile=os.path.join(myname, "metadata.txt"))
mylabel = mymeta.search_data(label)
if mylabel == "":
raise MASTError(self.__class__.__name__,
"No metadata for tag %s" % label)
return mylabel[1]
def get_my_label(self, label):
"""Get the value of a label in the metadata file.
Args:
label <str>: Label to search for.
Returns:
<str>: Value of the label as a string, stripped.
"""
myname = self.keywords['name']
mymeta = Metadata(metafile=os.path.join(myname, "metadata.txt"))
mylabel = mymeta.search_data(label)
if mylabel == "":
raise MASTError(self.__class__.__name__,
"No metadata for tag %s" % label)
return mylabel[1]
class RecipeTemplateParser(MASTObj):
"""Class for parsing the template recipe file in the input file and
creating a "personalized" recipe file where any <sys> and <N> from
the recipe template have been filled in according to information
from the input file.
Attributes:
self.input_options <InputOptions>: Input options from input file.
self.template_file <str>: Path to the recipe template file
self.personal_recipe <str>: Path to the personalized recipe.
self.ingredient_list <list of str>: List of ingredients mentioned
in the recipe template file.
self.chunks <list of list>: List of chunks
"""
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.input_options = self.keywords["inputOptions"]
self.template_file = self.keywords["templateFile"]
self.personal_recipe = self.keywords["personalRecipe"]
self.ingredient_list = list()
self.metafile = Metadata(metafile="%s/metadata.txt" % self.keywords["working_directory"])
self.chunks = list()
def parse(self):
""" Parses the template recipe file and creates
the personalized recipe file
"""
if len(self.template_file) == 0:
raise MASTError(self.__class__.__name__, "Recipe contents not provided!")
if self.input_options is None:
raise MASTError(self.__class__.__name__, "Input Options not provided!")
if self.personal_recipe is None:
raise MASTError(self.__class__.__name__, "Personal recipe file not provided!")
# fetch required paramaters
# f_ptr = open(self.template_file, "r")
recipe_contents = list(self.template_file)
# print recipe_contents
o_ptr = open(self.personal_recipe, "a")
system_name = self.input_options.get_item("mast", "system_name", "sys")
n_defects = self.input_options.get_item("defects", "num_defects", 0)
d_defects = self.input_options.get_item("defects", "defects")
n_images = self.input_options.get_item("neb", "images", 0)
d_neblines = self.input_options.get_item("neb", "neblines", {})
recipe_name = None
# print system_name, self.input_options.get_item('mast', 'system_name')
chunkcount = 0
mychunk = list()
modchunk = False
for line in recipe_contents: # f_ptr.readlines():
duplicate = line
if (len(duplicate) - len(duplicate.lstrip(" "))) % 4 != 0:
raise MASTError(
"parsers/recipetemplateparser",
"Recipe at %s contains incorrect number of whitespace chars at the beginning of the line! Please convert all indentations to the appropriate number of groups of four spaces."
% line,
)
if "\t" in line:
raise MASTError(
"parsers/recipetemplateparser",
"The tab character exists in recipe template %s. Please convert all tabs to the appropriate number of groups of four spaces."
% self.template_file,
)
if "{begin}" in line:
self.chunks.append(list(mychunk))
mychunk = list()
elif "{end}" in line:
pass
else:
mychunk.append(line)
if len(mychunk) > 0:
self.chunks.append(list(mychunk))
# for chunk in self.chunks:
# print chunk
input_options_keys = self.input_options.get_sections()
key = "personal_recipe"
expandedlist = list()
if key in input_options_keys:
return expandedlist
else:
for chunk in self.chunks:
expanded = self.parse_chunk(chunk)
expandedlist.extend(expanded)
o_ptr.write("$personal_recipe\n")
o_ptr.writelines(expandedlist)
o_ptr.write("$end\n")
# f_ptr.close()
o_ptr.close()
return expandedlist
# self.chunks[chunkcount]=dict()
# self.chunks[chunkcount]['modify'] = modchunk
# #line = line.strip()
# #line = line.lower()
# processing_lines = []
# #shortcut straight copy + 6
# processing_lines.append(line)
# output_str = "\n".join(processing_lines)
# o_ptr.write("%s\n" % output_str)
# f_ptr.close()
# o_ptr.close()
# print 'in RecipeParser.parse():', list(set(self.ingredient_list))
# return recipe_name
def parse_chunk(self, chunk):
"""Parse a chunk of lines.
Args:
chunk <list>: List of lines
Returns:
expandedchunk <list>: List of lines
"""
origchunk = list(chunk)
expandedchunk = list()
needsdefects = 0
needscharges = 0
needsphonons = 0
needsnebs = 0
needsscaling = 0
for line in chunk:
if "<N>" in line:
needsdefects = 1
if "<B-E>" in line:
needsnebs = 1
if "<P>" in line:
needsphonons = 1
if "<Q>" in line:
needscharges = 1
if "<B>" in line:
needsnebs = 1
if "<E>" in line:
needsnebs = 1
if "<S>" in line:
needsscaling = 1
d_scaling = self.input_options.get_item("scaling")
d_defects = self.input_options.get_item("defects", "defects")
d_nebs = self.input_options.get_item("neb", "nebs")
if needsscaling == 1:
scalingsize = d_scaling.keys()
scalingsize.sort()
else:
scalingsize = ["1x1x1"]
for size in scalingsize:
if needsdefects == 1:
mydefects = d_defects.keys()
mydefects.sort()
for defectname in mydefects:
for charge in d_defects[defectname]["charge"]:
if charge < 0:
mycharge = "q=n" + str(int(math.fabs(charge)))
else:
mycharge = "q=p" + str(int(charge))
if needsphonons == 1:
if len(d_defects[defectname]["phonon"].keys()) > 0:
phononkeys = d_defects[defectname]["phonon"].keys()
phononkeys.sort()
for phonon in phononkeys:
for line in origchunk:
newline = line.replace("<N>", defectname)
if needscharges == 1:
newline = newline.replace("<Q>", mycharge)
if needsscaling == 1:
newline = newline.replace("<S>", size)
newline = newline.replace("<P>", phonon)
expandedchunk.append(newline)
else:
for line in origchunk:
newline = line.replace("<N>", defectname)
if needscharges == 1:
newline = newline.replace("<Q>", mycharge)
if needsscaling == 1:
newline = newline.replace("<S>", size)
expandedchunk.append(newline)
elif needsnebs == 1:
nebkeys = d_nebs.keys()
nebkeys.sort()
for neblabel in nebkeys:
defbegin = neblabel.split("-")[0]
defend = neblabel.split("-")[1]
chargebegin = d_defects[defbegin]["charge"]
chargeend = d_defects[defend]["charge"]
chargeboth = set(chargebegin) & set(chargeend)
for charge in chargeboth:
if charge < 0:
mycharge = "q=n" + str(int(math.fabs(charge)))
else:
mycharge = "q=p" + str(int(charge))
if needsphonons == 1:
if len(d_nebs[neblabel]["phonon"].keys()) > 0:
phononkeys = d_nebs[neblabel]["phonon"].keys()
phononkeys.sort()
for phonon in phononkeys:
for line in origchunk:
newline = line.replace("<B>", defbegin)
newline = newline.replace("<E>", defend)
newline = newline.replace("<B-E>", neblabel)
if needscharges == 1:
newline = newline.replace("<Q>", mycharge)
if needsscaling == 1:
newline = newline.replace("<S>", size)
newline = newline.replace("<P>", phonon)
expandedchunk.append(newline)
else:
for line in origchunk:
newline = line.replace("<B>", defbegin)
newline = newline.replace("<E>", defend)
newline = newline.replace("<B-E>", neblabel)
if needscharges == 1:
newline = newline.replace("<Q>", mycharge)
if needsscaling == 1:
newline = newline.replace("<S>", size)
expandedchunk.append(newline)
elif needsscaling == 1:
for line in origchunk:
newline = line.replace("<S>", size)
expandedchunk.append(newline)
else:
expandedchunk = list(origchunk)
return expandedchunk
# origchunk = list(expandedchunk)
# expandedchunk=list()
# for defectname in self.d_defects:
# for line in origchunk:
# newline = line.replace("<N>", defectname)
# expandedchunk.append(line)
def old_parsing(self):
raise MASTError(self.__class__.__name__, "This function is obsolete.")
for line in linestr:
# validate the input line
if not line or line.startswith("#"):
continue
# collect recipe name
line2 = line.split()
if line2[0].lower() == "recipe":
recipe_name = line2[1]
# collect ingredents
line2 = line.split()
if line2[0].lower() == "ingredient":
self.ingredient_list.append(line2[2])
# replace line params<N>
# step 1 : replace <sys> with system_name
# step 2 : replace <n-n> with appropriate hop combinations
# step 3 : replace <img-n> with appropriate image numbers
# step 4 : replace <n> with appropriate defect numbers
processing_lines.append(line)
# step 1
processing_lines = self.process_system_name(processing_lines, system_name)
# step 4
processing_lines = self.process_defects(processing_lines, n_defects, d_defects)
# step 2
processing_lines = self.process_hop_combinations(processing_lines, d_neblines)
# step 3
processing_lines = self.process_images(processing_lines, n_images)
self.make_metadata_entries(processing_lines)
self.process_phononlines(processing_lines)
# dump the processed lines to file
output_str = "\n".join(processing_lines)
o_ptr.write("%s\n" % output_str)
f_ptr.close()
o_ptr.close()
# print 'in RecipeParser.parse():', list(set(self.ingredient_list))
return recipe_name
def process_system_name(self, processing_lines, system_name):
"""replace <sys> with the system name from the input options
"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
for index in xrange(len(processing_lines)):
processing_lines[index] = processing_lines[index].replace("<sys>", system_name)
return processing_lines
def process_hop_combinations(self, processing_lines, d_neblines):
"""replace <n-n> with neb labels which are keys of the
neblines dict of the input options.
Args:
processing_lines <list of str>: recipe lines to process.
d_neblines <dict of str>: dictionary of NEB lines.
"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
new_lines = []
eval_lines = []
if not d_neblines:
return processing_lines
line = ""
for line in processing_lines:
if "<n-n>" in line:
for neblabel in d_neblines.keys():
n_line = line.replace("<n-n>", neblabel)
eval_lines.append(n_line)
if "ingredient" in n_line and not "<" in n_line:
keyword = n_line.split()[1]
data = "neblabel: %s" % neblabel
self.metafile.write_data(keyword, data)
else:
eval_lines.append(line)
line = ""
for line in eval_lines:
# print "TTM DEBUG line: ", line
if not "neb" in line.split("_"):
# print "TTM DEBUG line safe"
new_lines.append(line)
else:
evalsplit = line.split("child")
if len(evalsplit) == 1:
new_lines.append(line)
else:
childsplit = evalsplit[1].split("_")
parsplit = evalsplit[0].split("_")
okay = 1
for neblabel in d_neblines.keys():
if okay == 1 and (neblabel in childsplit):
parlabels = neblabel.split("-")
# print "TTM DEBUG: parlabels: ",parlabels
# print "TTM DEBUG: parsplit: ",parsplit
if not parlabels[0] in parsplit and not (parlabels[1] in parsplit):
if not neblabel in parsplit: # image static
okay = 0
if okay == 0:
pass
else:
new_lines.append(line)
return new_lines
def process_images(self, processing_lines, n_images):
"""replace <img-n> with the equivalent number of
lines based on the number of images found in the
input_options
"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
new_lines = []
if not n_images:
return processing_lines
for line in processing_lines:
if "<img-n>" in line:
for index in xrange(n_images):
n_line = line.replace("<img-n>", str(index + 1).zfill(2))
if "ingredient" in n_line and not "<" in n_line:
keyword = n_line.split()[1]
data = "name: %s" % keyword
self.metafile.write_data(keyword, data)
new_lines.append(n_line)
else:
new_lines.append(line)
return new_lines
def process_defects(self, processing_lines, n_defects, d_defects):
"""replace <N> with the equivalent number of lines
based on the number of defects given in the
input options
Args:
processing_lines <list of str>: recipe lines to proceess
n_defects <int>: number of defected systems
d_defects <dict>: dictionary of defects, including labels and
positions.
"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
# import inspect
# print 'GRJ DEBUG: %s.%s' % (self.__class__.__name__, inspect.stack()[0][3])
# print d_defects
# print 'GRJ DEBUG: parse_defects() working_directory =', self.keywords['working_directory']
new_lines = list()
if not n_defects:
return processing_lines
for line in processing_lines:
# print 'GRJ DEBUG: line =', line
if ("<n>" in line) or ("<q>" in line):
for defect_key in d_defects.keys():
# print 'GRJ DEBUG: defect_key =', defect_key
# defect_label = defect_key.split('_')[1] #defect_1, etc.
def_line = line.replace("<n>", defect_key)
charge_list = d_defects[defect_key]["charge"]
# print 'GRJ DEBUG: charge_list =', charge_list
# print 'GRJ DEBUG: def_line before charges:', def_line
for charge in charge_list:
if charge < 0:
clabel = "q=n" + str(abs(charge))
else:
clabel = "q=p" + str(charge)
# print 'GRJ DEBUG: clabel =', clabel
new_def_line = def_line.replace("<q>", clabel)
new_lines.append(new_def_line)
# new_lines.append(def_line.replace('<q>', clabel))
if "ingredient" in def_line:
keyword = new_def_line.split()[1]
data = "defect_label: %s, charge: %i" % (defect_key, charge)
# print 'GRJ DEBUG: def_line, keyword, charge', new_def_line, keyword, charge
self.metafile.write_data(keyword, data)
else:
new_lines.append(line)
return new_lines
def process_phononlines(self, processing_lines):
"""add phonon information to the metadata. Does not change line info.
"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
for line in processing_lines:
if "ingredient" in line and "phonon_" in line:
nameval = line.split()[1]
[dataline, dataval] = self.metafile.search_data(nameval)
okay = 0
if not (dataval == None):
datapcs = dataval.split(",")
for datapc in datapcs:
dlabel = datapc.split(":")[0].strip()
dval = datapc.split(":")[1].strip()
if dlabel == "neblabel" or dlabel == "defect_label":
data = "phononlabel: %s" % dval
self.metafile.write_data(nameval, data)
okay = 1
break
if okay == 0:
if "perfect" in line:
data = "phononlabel: perfect"
self.metafile.write_data(nameval, data)
okay = 1
else:
data = "phononlabel: %s" % nameval
self.metafile.write_data(nameval, data)
okay = 1
return
def make_metadata_entries(self, processing_lines):
"""Add metadata entry for all ingredients.
Does not change line information.
"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
for line in processing_lines:
if "ingredient" in line:
nameval = line.split()[1]
data = "name: %s" % nameval
self.metafile.write_data(nameval, data)
return
def get_unique_ingredients(self):
"""fetches the ingredients names"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
return list(set(self.ingredient_list))
def parse_ingredients_section(self, section_name, section_content,
options):
"""Parses the ingredients section and populates the options.
Section takes the form of:
$ingredients
begin ingredients_global
mast_kpoints 3x3x3
mast_xc pbe
end
begin singlepoint
encut 400
end
begin optimize
encut 300
ibrion 2
end
$end
mast_kpoints are parsed out as a 3 index list of integers.
Everything else is parsed out as a string.
Anything in ingredients_global is then appended onto each
individual ingredient.
"""
global_dict = dict()
ingredients_dict = dict()
for line in section_content:
if (line.startswith('begin')):
# Each ingredient section starts with "begin".
# Check for this line, and initialize the individual
# ingredient dictionary
ingredient_name = line.split()[1]
ingredient_dict = dict()
elif (not (line == 'end')):
opt = line.split()
# print opt
if (opt[0] == 'mast_kpoints'):
try:
kpts = map(int, opt[1].split('x'))
if len(opt) > 2:
kpts.append(opt[2])
except ValueError:
kpts = opt[1:]
# Second option after mast_kpoints tells where to
# center the k-point mesh.
# If it's there, we append it onto the k-point grid list.
ingredient_dict[opt[0]] = kpts
elif (opt[0] == 'mast_pp_setup'):
psp_dict = dict()
for key in opt[1:]:
key = key.split('=')
ref = key[0].title()
val = str().join(key[1][0].upper() + key[1][1:])
psp_dict[ref] = val
ingredient_dict[opt[0]] = psp_dict
#elif (opt[0] == 'mast_exec'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'mast_strain'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'ptemp'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'rwigs'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'mast_setmagmom'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
elif (opt[0] == 'mast_coordinates'):
shortsplit = opt[1].split(",")
filesplit = list()
origindir = os.getcwd()
metatry = os.path.join(os.getcwd(), 'metadata.txt')
if os.path.isfile(metatry):
myrecipemeta = Metadata(metafile=metatry)
origindir = myrecipemeta.search_data('origin_dir')[1]
myfiles = dirutil.walkfiles(origindir)
for shortname in shortsplit:
for fullfile in myfiles:
if shortname.strip() in os.path.basename(fullfile):
filesplit.append(fullfile)
if not (len(filesplit) == len(shortsplit)):
raise MASTError(
self.__class__.__name__,
"Not all files given by %s were found in %s." %
(shortsplit, origindir))
ingredient_dict[opt[0]] = filesplit
else:
ingredient_dict[opt[0]] = ' '.join(
opt[1:]) #preserve whole line
#ingredient_dict[opt[0]] = opt[1] #old behavior took only the first part
if (opt[0] == 'mast_program') and (opt[1] == 'vasp'
or opt[1] == 'vasp_neb'):
if os.getenv('VASP_PSP_DIR') == None:
raise MASTError(
self.__class__.__name__,
"Input file specifies program vasp, but no POTCAR directory is set in environment variable VASP_PSP_DIR"
)
elif ('end' in line):
# Each ingredient section ends with "end", if present finish
# that current section and assign
# the neccessary element in the ingredients dictionary and
# create the global dictionary
if (ingredient_name == 'ingredients_global'):
global_dict = ingredient_dict
else:
ingredients_dict[ingredient_name] = ingredient_dict
# Each value in ingredients_dict is a dictionary containing the relevant
# ingredient and option(s).
for ing_key, ing_value in ingredients_dict.items():
options.set_item(section_name, ing_key, ing_value)
options.set_item(section_name, 'global', global_dict)
def parse_structure_section(self, section_name, section_content, options):
"""Parses the structure section and populate the options.
Does not create the structure.
Format is along the lines of:
coord_type fractional
begin coordinates
Ga 0.000000 0.000000 0.000000
Ga 0.500000 0.500000 0.000000
Ga 0.000000 0.500000 0.500000
Ga 0.500000 0.000000 0.500000
As 0.250000 0.250000 0.250000
As 0.750000 0.750000 0.250000
As 0.250000 0.750000 0.750000
As 0.750000 0.250000 0.750000
end
begin lattice
2.0 0.0 0.0
0.0 2.0 0.0
0.0 0.0 2.0
end
Note that coord_type will default to "cartesian" if not specified.
"""
# Initialize with default values
structure_dict = STRUCTURE_KEYWORDS.copy()
subsection_dict = dict()
for myline in section_content:
line = myline.split()
if (line[0] in structure_dict):
structure_dict[line[0]] = line[1]
elif ('begin' in line[0]):
subsection = line[1]
subsection_list = list()
elif ('end' not in line):
lsplit = myline.split()
lineval = list()
for lval in lsplit:
lval.strip()
if len(lval) > 0:
lineval.append(lval)
subsection_list.append(lineval)
elif ('end' in line):
subsection_dict[subsection] = subsection_list
# GRJ: Since we lowercase the whole input file, and filenames may not
# conform to this, we examine the current directory for any files that
# may match and use that. If there are multiple matches, we'll throw
# an error.
if (structure_dict['posfile']
is not None): # Do we have a geometry file?
# TTM for issue #423
posfiletry = os.path.join(os.getcwd(), structure_dict['posfile'])
if os.path.isfile(posfiletry):
self.logger.info("Using posfile %s in directory %s" %
(structure_dict['posfile'], os.getcwd()))
else:
# First build a list of likely files
origindir = os.path.dirname(self.keywords['inputfile'])
if origindir == "":
origindir = os.getcwd()
metatry = os.path.join(os.getcwd(), 'metadata.txt')
if os.path.isfile(metatry):
myrecipemeta = Metadata(metafile=metatry)
origindir = myrecipemeta.search_data('origin_dir')[1]
myfiles = dirutil.walkfiles(origindir)
file_list = list()
for myfile in myfiles:
if structure_dict['posfile'] in myfile:
file_list.append(myfile)
if (len(file_list) > 1):
# If we have multiple files with the same name, but different capitalization, throw an error here
self.logger.warning(
'Found multiple files with the name %s' %
structure_dict['posfile'])
self.logger.warning('Found the files:')
for file in file_list:
self.logger.warning(file)
error = 'Found ambiguous file names'
raise MASTError(self.__class__.__name__, error)
elif len(file_list) == 0:
raise MASTError(
self.__class__.__name__,
"No structure file %s found in %s" %
(structure_dict['posfile'], origindir))
else:
structure_dict['posfile'] = file_list[0]
# print 'in InputParser.parse_structure_section:', subsection_dict
# TM
element_map = dict()
atom_list = list()
for key, value in subsection_dict.items():
if (key == 'coordinates'):
value = np.array(value)
# Here we use .title() to re-capitalize the first letter of all
# the atomic symbols to comply with what
# pymatgen needs
atom_list = [val.title() for val in value[:, 0]]
structure_dict['atom_list'] = atom_list
coordinates = np.array(value[:, 1:], dtype='float')
structure_dict['coordinates'] = coordinates
if (key == 'lattice'):
#print "VALUE: ", value
lattice = np.array(value, dtype='float')
structure_dict['lattice'] = lattice
if (key == 'elementmap'):
for elline in value:
elkey = elline[0].strip().upper() #all caps
elname = elline[1].strip().title() #Title case
element_map[elkey] = elname
structure_dict['element_map'] = element_map
if len(element_map) > 0 and len(atom_list) > 0:
new_atom_list = list()
for atomval in atom_list:
if atomval.upper() in element_map.keys():
new_atom_list.append(element_map[atomval])
else:
new_atom_list.append(atomval)
structure_dict['atom_list'] = new_atom_list
for key, value in structure_dict.items():
options.set_item(section_name, key, value)
class RecipeTemplateParser(MASTObj):
"""Class for parsing the template recipe file in the input file and
creating a "personalized" recipe file where any <sys> and <N> from
the recipe template have been filled in according to information
from the input file.
Attributes:
self.input_options <InputOptions>: Input options from input file.
self.template_file <str>: Path to the recipe template file
self.personal_recipe <str>: Path to the personalized recipe.
self.ingredient_list <list of str>: List of ingredients mentioned
in the recipe template file.
self.chunks <list of list>: List of chunks
"""
def __init__(self, **kwargs):
MASTObj.__init__(self, ALLOWED_KEYS, **kwargs)
self.input_options = self.keywords['inputOptions']
self.template_file = self.keywords['templateFile']
self.personal_recipe = self.keywords['personalRecipe']
self.ingredient_list = list()
self.metafile = Metadata(metafile='%s/metadata.txt' %
self.keywords['working_directory'])
self.chunks = list()
def parse(self):
""" Parses the template recipe file and creates
the personalized recipe file
"""
if len(self.template_file) == 0:
raise MASTError(self.__class__.__name__,
"Recipe contents not provided!")
if self.input_options is None:
raise MASTError(self.__class__.__name__,
"Input Options not provided!")
if self.personal_recipe is None:
raise MASTError(self.__class__.__name__,
"Personal recipe file not provided!")
#fetch required paramaters
#f_ptr = open(self.template_file, "r")
recipe_contents = list(self.template_file)
#print recipe_contents
o_ptr = open(self.personal_recipe, "a")
system_name = self.input_options.get_item("mast", "system_name", "sys")
n_defects = self.input_options.get_item("defects", "num_defects", 0)
d_defects = self.input_options.get_item("defects", "defects")
n_images = self.input_options.get_item("neb", "images", 0)
d_neblines = self.input_options.get_item("neb", "neblines", {})
recipe_name = None
# print system_name, self.input_options.get_item('mast', 'system_name')
chunkcount = 0
mychunk = list()
modchunk = False
for line in recipe_contents: #f_ptr.readlines():
duplicate = line
if ((len(duplicate) - len(duplicate.lstrip(' '))) % 4 != 0):
raise MASTError(
"parsers/recipetemplateparser",
"Recipe at %s contains incorrect number of whitespace chars at the beginning of the line! Please convert all indentations to the appropriate number of groups of four spaces."
% line)
if '\t' in line:
raise MASTError(
"parsers/recipetemplateparser",
"The tab character exists in recipe template %s. Please convert all tabs to the appropriate number of groups of four spaces."
% self.template_file)
if '{begin}' in line:
self.chunks.append(list(mychunk))
mychunk = list()
elif '{end}' in line:
pass
else:
mychunk.append(line)
if len(mychunk) > 0:
self.chunks.append(list(mychunk))
#for chunk in self.chunks:
# print chunk
input_options_keys = self.input_options.get_sections()
key = 'personal_recipe'
expandedlist = list()
if key in input_options_keys:
return expandedlist
else:
for chunk in self.chunks:
expanded = self.parse_chunk(chunk)
expandedlist.extend(expanded)
o_ptr.write("$personal_recipe\n")
o_ptr.writelines(expandedlist)
o_ptr.write("$end\n")
#f_ptr.close()
o_ptr.close()
return expandedlist
#self.chunks[chunkcount]=dict()
#self.chunks[chunkcount]['modify'] = modchunk
# #line = line.strip()
# #line = line.lower()
# processing_lines = []
# #shortcut straight copy + 6
# processing_lines.append(line)
# output_str = "\n".join(processing_lines)
# o_ptr.write("%s\n" % output_str)
#f_ptr.close()
#o_ptr.close()
# print 'in RecipeParser.parse():', list(set(self.ingredient_list))
#return recipe_name
def parse_chunk(self, chunk):
"""Parse a chunk of lines.
Args:
chunk <list>: List of lines
Returns:
expandedchunk <list>: List of lines
"""
origchunk = list(chunk)
expandedchunk = list()
needsdefects = 0
needscharges = 0
needsphonons = 0
needsnebs = 0
needsscaling = 0
for line in chunk:
if "<N>" in line:
needsdefects = 1
if "<B-E>" in line:
needsnebs = 1
if "<P>" in line:
needsphonons = 1
if "<Q>" in line:
needscharges = 1
if "<B>" in line:
needsnebs = 1
if "<E>" in line:
needsnebs = 1
if "<S>" in line:
needsscaling = 1
d_scaling = self.input_options.get_item("scaling")
d_defects = self.input_options.get_item("defects", "defects")
d_nebs = self.input_options.get_item("neb", "nebs")
if needsscaling == 1:
scalingsize = d_scaling.keys()
scalingsize.sort()
else:
scalingsize = ['1x1x1']
for size in scalingsize:
if needsdefects == 1:
mydefects = d_defects.keys()
mydefects.sort()
for defectname in mydefects:
for charge in d_defects[defectname]['charge']:
if charge < 0:
mycharge = 'q=n' + str(int(math.fabs(charge)))
else:
mycharge = 'q=p' + str(int(charge))
if needsphonons == 1:
if len(d_defects[defectname]['phonon'].keys()) > 0:
phononkeys = d_defects[defectname][
'phonon'].keys()
phononkeys.sort()
for phonon in phononkeys:
for line in origchunk:
newline = line.replace(
"<N>", defectname)
if needscharges == 1:
newline = newline.replace(
"<Q>", mycharge)
if needsscaling == 1:
newline = newline.replace(
"<S>", size)
newline = newline.replace(
"<P>", phonon)
expandedchunk.append(newline)
else:
for line in origchunk:
newline = line.replace("<N>", defectname)
if needscharges == 1:
newline = newline.replace("<Q>", mycharge)
if needsscaling == 1:
newline = newline.replace("<S>", size)
expandedchunk.append(newline)
elif needsnebs == 1:
nebkeys = d_nebs.keys()
nebkeys.sort()
for neblabel in nebkeys:
defbegin = neblabel.split('-')[0]
defend = neblabel.split('-')[1]
chargebegin = d_defects[defbegin]['charge']
chargeend = d_defects[defend]['charge']
chargeboth = set(chargebegin) & set(chargeend)
for charge in chargeboth:
if charge < 0:
mycharge = 'q=n' + str(int(math.fabs(charge)))
else:
mycharge = 'q=p' + str(int(charge))
if needsphonons == 1:
if len(d_nebs[neblabel]['phonon'].keys()) > 0:
phononkeys = d_nebs[neblabel]['phonon'].keys()
phononkeys.sort()
for phonon in phononkeys:
for line in origchunk:
newline = line.replace("<B>", defbegin)
newline = newline.replace(
"<E>", defend)
newline = newline.replace(
"<B-E>", neblabel)
if needscharges == 1:
newline = newline.replace(
"<Q>", mycharge)
if needsscaling == 1:
newline = newline.replace(
"<S>", size)
newline = newline.replace(
"<P>", phonon)
expandedchunk.append(newline)
else:
for line in origchunk:
newline = line.replace("<B>", defbegin)
newline = newline.replace("<E>", defend)
newline = newline.replace("<B-E>", neblabel)
if needscharges == 1:
newline = newline.replace("<Q>", mycharge)
if needsscaling == 1:
newline = newline.replace("<S>", size)
expandedchunk.append(newline)
elif needsscaling == 1:
for line in origchunk:
newline = line.replace("<S>", size)
expandedchunk.append(newline)
else:
expandedchunk = list(origchunk)
return expandedchunk
#origchunk = list(expandedchunk)
#expandedchunk=list()
#for defectname in self.d_defects:
# for line in origchunk:
# newline = line.replace("<N>", defectname)
# expandedchunk.append(line)
def old_parsing(self):
raise MASTError(self.__class__.__name__, "This function is obsolete.")
for line in linestr:
#validate the input line
if not line or line.startswith('#'):
continue
#collect recipe name
line2 = line.split()
if (line2[0].lower() == 'recipe'):
recipe_name = line2[1]
#collect ingredents
line2 = line.split()
if (line2[0].lower() == 'ingredient'):
self.ingredient_list.append(line2[2])
#replace line params<N>
#step 1 : replace <sys> with system_name
#step 2 : replace <n-n> with appropriate hop combinations
#step 3 : replace <img-n> with appropriate image numbers
#step 4 : replace <n> with appropriate defect numbers
processing_lines.append(line)
#step 1
processing_lines = self.process_system_name(
processing_lines, system_name)
#step 4
processing_lines = self.process_defects(processing_lines,
n_defects, d_defects)
#step 2
processing_lines = self.process_hop_combinations(
processing_lines, d_neblines)
#step 3
processing_lines = self.process_images(processing_lines, n_images)
self.make_metadata_entries(processing_lines)
self.process_phononlines(processing_lines)
#dump the processed lines to file
output_str = "\n".join(processing_lines)
o_ptr.write("%s\n" % output_str)
f_ptr.close()
o_ptr.close()
# print 'in RecipeParser.parse():', list(set(self.ingredient_list))
return recipe_name
def process_system_name(self, processing_lines, system_name):
"""replace <sys> with the system name from the input options
"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
for index in xrange(len(processing_lines)):
processing_lines[index] = processing_lines[index].replace(
'<sys>', system_name)
return processing_lines
def process_hop_combinations(self, processing_lines, d_neblines):
"""replace <n-n> with neb labels which are keys of the
neblines dict of the input options.
Args:
processing_lines <list of str>: recipe lines to process.
d_neblines <dict of str>: dictionary of NEB lines.
"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
new_lines = []
eval_lines = []
if not d_neblines:
return processing_lines
line = ""
for line in processing_lines:
if "<n-n>" in line:
for neblabel in d_neblines.keys():
n_line = line.replace('<n-n>', neblabel)
eval_lines.append(n_line)
if 'ingredient' in n_line and not '<' in n_line:
keyword = n_line.split()[1]
data = 'neblabel: %s' % neblabel
self.metafile.write_data(keyword, data)
else:
eval_lines.append(line)
line = ""
for line in eval_lines:
#print "TTM DEBUG line: ", line
if not 'neb' in line.split('_'):
#print "TTM DEBUG line safe"
new_lines.append(line)
else:
evalsplit = line.split('child')
if len(evalsplit) == 1:
new_lines.append(line)
else:
childsplit = evalsplit[1].split('_')
parsplit = evalsplit[0].split('_')
okay = 1
for neblabel in d_neblines.keys():
if okay == 1 and (neblabel in childsplit):
parlabels = neblabel.split('-')
#print "TTM DEBUG: parlabels: ",parlabels
#print "TTM DEBUG: parsplit: ",parsplit
if not parlabels[0] in parsplit and not (
parlabels[1] in parsplit):
if not neblabel in parsplit: #image static
okay = 0
if okay == 0:
pass
else:
new_lines.append(line)
return new_lines
def process_images(self, processing_lines, n_images):
"""replace <img-n> with the equivalent number of
lines based on the number of images found in the
input_options
"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
new_lines = []
if not n_images:
return processing_lines
for line in processing_lines:
if '<img-n>' in line:
for index in xrange(n_images):
n_line = line.replace('<img-n>', str(index + 1).zfill(2))
if 'ingredient' in n_line and not '<' in n_line:
keyword = n_line.split()[1]
data = 'name: %s' % keyword
self.metafile.write_data(keyword, data)
new_lines.append(n_line)
else:
new_lines.append(line)
return new_lines
def process_defects(self, processing_lines, n_defects, d_defects):
"""replace <N> with the equivalent number of lines
based on the number of defects given in the
input options
Args:
processing_lines <list of str>: recipe lines to proceess
n_defects <int>: number of defected systems
d_defects <dict>: dictionary of defects, including labels and
positions.
"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
#import inspect
#print 'GRJ DEBUG: %s.%s' % (self.__class__.__name__, inspect.stack()[0][3])
#print d_defects
#print 'GRJ DEBUG: parse_defects() working_directory =', self.keywords['working_directory']
new_lines = list()
if not n_defects:
return processing_lines
for line in processing_lines:
#print 'GRJ DEBUG: line =', line
if ('<n>' in line) or ('<q>' in line):
for defect_key in d_defects.keys():
#print 'GRJ DEBUG: defect_key =', defect_key
#defect_label = defect_key.split('_')[1] #defect_1, etc.
def_line = line.replace("<n>", defect_key)
charge_list = d_defects[defect_key]['charge']
#print 'GRJ DEBUG: charge_list =', charge_list
#print 'GRJ DEBUG: def_line before charges:', def_line
for charge in charge_list:
if (charge < 0):
clabel = 'q=n' + str(abs(charge))
else:
clabel = 'q=p' + str(charge)
#print 'GRJ DEBUG: clabel =', clabel
new_def_line = def_line.replace('<q>', clabel)
new_lines.append(new_def_line)
#new_lines.append(def_line.replace('<q>', clabel))
if 'ingredient' in def_line:
keyword = new_def_line.split()[1]
data = 'defect_label: %s, charge: %i' % (
defect_key, charge)
#print 'GRJ DEBUG: def_line, keyword, charge', new_def_line, keyword, charge
self.metafile.write_data(keyword, data)
else:
new_lines.append(line)
return new_lines
def process_phononlines(self, processing_lines):
"""add phonon information to the metadata. Does not change line info.
"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
for line in processing_lines:
if 'ingredient' in line and 'phonon_' in line:
nameval = line.split()[1]
[dataline, dataval] = self.metafile.search_data(nameval)
okay = 0
if not (dataval == None):
datapcs = dataval.split(',')
for datapc in datapcs:
dlabel = datapc.split(":")[0].strip()
dval = datapc.split(":")[1].strip()
if dlabel == 'neblabel' or dlabel == 'defect_label':
data = 'phononlabel: %s' % dval
self.metafile.write_data(nameval, data)
okay = 1
break
if okay == 0:
if 'perfect' in line:
data = 'phononlabel: perfect'
self.metafile.write_data(nameval, data)
okay = 1
else:
data = 'phononlabel: %s' % nameval
self.metafile.write_data(nameval, data)
okay = 1
return
def make_metadata_entries(self, processing_lines):
"""Add metadata entry for all ingredients.
Does not change line information.
"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
for line in processing_lines:
if 'ingredient' in line:
nameval = line.split()[1]
data = 'name: %s' % nameval
self.metafile.write_data(nameval, data)
return
def get_unique_ingredients(self):
"""fetches the ingredients names"""
raise MASTError(self.__class__.__name__, "This function is obsolete.")
return list(set(self.ingredient_list))
def parse_ingredients_section(self, section_name, section_content, options):
"""Parses the ingredients section and populates the options.
Section takes the form of:
$ingredients
begin ingredients_global
mast_kpoints 3x3x3
mast_xc pbe
end
begin singlepoint
encut 400
end
begin optimize
encut 300
ibrion 2
end
$end
mast_kpoints are parsed out as a 3 index list of integers.
Everything else is parsed out as a string.
Anything in ingredients_global is then appended onto each
individual ingredient.
"""
global_dict = dict()
ingredients_dict = dict()
for line in section_content:
if (line.startswith('begin')):
# Each ingredient section starts with "begin".
# Check for this line, and initialize the individual
# ingredient dictionary
ingredient_name = line.split()[1]
ingredient_dict = dict()
elif (not (line == 'end')):
opt = line.split()
# print opt
if (opt[0] == 'mast_kpoints'):
try:
kpts = map(int, opt[1].split('x'))
if len(opt) > 2:
kpts.append(opt[2])
except ValueError:
kpts = opt[1:]
# Second option after mast_kpoints tells where to
# center the k-point mesh.
# If it's there, we append it onto the k-point grid list.
ingredient_dict[opt[0]] = kpts
elif (opt[0] == 'mast_pp_setup'):
psp_dict = dict()
for key in opt[1:]:
key = key.split('=')
ref = key[0].title()
val = str().join(key[1][0].upper() + key[1][1:])
psp_dict[ref] = val
ingredient_dict[opt[0]] = psp_dict
#elif (opt[0] == 'mast_exec'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'mast_strain'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'ptemp'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'rwigs'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'mast_setmagmom'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
elif (opt[0] == 'mast_coordinates'):
shortsplit = opt[1].split(",")
filesplit=list()
origindir = os.getcwd()
metatry = os.path.join(os.getcwd(), 'metadata.txt')
if os.path.isfile(metatry):
myrecipemeta = Metadata(metafile=metatry)
origindir = myrecipemeta.search_data('origin_dir')[1]
myfiles = dirutil.walkfiles(origindir)
for shortname in shortsplit:
for fullfile in myfiles:
if shortname.strip() in os.path.basename(fullfile):
filesplit.append(fullfile)
if not (len(filesplit) == len(shortsplit)):
raise MASTError(self.__class__.__name__, "Not all files given by %s were found in %s." % (shortsplit, origindir))
ingredient_dict[opt[0]] = filesplit
else:
ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#ingredient_dict[opt[0]] = opt[1] #old behavior took only the first part
if (opt[0] == 'mast_program') and (opt[1] == 'vasp' or opt[1] == 'vasp_neb'):
if os.getenv('VASP_PSP_DIR') == None:
raise MASTError(self.__class__.__name__, "Input file specifies program vasp, but no POTCAR directory is set in environment variable VASP_PSP_DIR")
elif ('end' in line):
# Each ingredient section ends with "end", if present finish
# that current section and assign
# the neccessary element in the ingredients dictionary and
# create the global dictionary
if (ingredient_name == 'ingredients_global'):
global_dict = ingredient_dict
else:
ingredients_dict[ingredient_name] = ingredient_dict
# Each value in ingredients_dict is a dictionary containing the relevant
# ingredient and option(s).
for ing_key, ing_value in ingredients_dict.items():
options.set_item(section_name, ing_key, ing_value)
options.set_item(section_name, 'global', global_dict)
def parse_structure_section(self, section_name, section_content, options):
"""Parses the structure section and populate the options.
Does not create the structure.
Format is along the lines of:
coord_type fractional
begin coordinates
Ga 0.000000 0.000000 0.000000
Ga 0.500000 0.500000 0.000000
Ga 0.000000 0.500000 0.500000
Ga 0.500000 0.000000 0.500000
As 0.250000 0.250000 0.250000
As 0.750000 0.750000 0.250000
As 0.250000 0.750000 0.750000
As 0.750000 0.250000 0.750000
end
begin lattice
2.0 0.0 0.0
0.0 2.0 0.0
0.0 0.0 2.0
end
Note that coord_type will default to "cartesian" if not specified.
"""
# Initialize with default values
structure_dict = STRUCTURE_KEYWORDS.copy()
subsection_dict = dict()
for myline in section_content:
line = myline.split()
if (line[0] in structure_dict):
structure_dict[line[0]] = line[1]
elif ('begin' in line[0]):
subsection = line[1]
subsection_list = list()
elif ('end' not in line):
lsplit = myline.split()
lineval = list()
for lval in lsplit:
lval.strip()
if len(lval) > 0:
lineval.append(lval)
subsection_list.append(lineval)
elif ('end' in line):
subsection_dict[subsection] = subsection_list
# GRJ: Since we lowercase the whole input file, and filenames may not
# conform to this, we examine the current directory for any files that
# may match and use that. If there are multiple matches, we'll throw
# an error.
if (structure_dict['posfile'] is not None): # Do we have a geometry file?
# TTM for issue #423
posfiletry = os.path.join(os.getcwd(), structure_dict['posfile'])
if os.path.isfile(posfiletry):
self.logger.info("Using posfile %s in directory %s" % (structure_dict['posfile'], os.getcwd()))
else:
# First build a list of likely files
origindir = os.path.dirname(self.keywords['inputfile'])
if origindir == "":
origindir = os.getcwd()
metatry = os.path.join(os.getcwd(), 'metadata.txt')
if os.path.isfile(metatry):
myrecipemeta = Metadata(metafile=metatry)
origindir = myrecipemeta.search_data('origin_dir')[1]
myfiles = dirutil.walkfiles(origindir)
file_list=list()
for myfile in myfiles:
if structure_dict['posfile'] in myfile:
file_list.append(myfile)
if (len(file_list) > 1):
# If we have multiple files with the same name, but different capitalization, throw an error here
self.logger.warning('Found multiple files with the name %s' % structure_dict['posfile'])
self.logger.warning('Found the files:')
for file in file_list:
self.logger.warning(file)
error='Found ambiguous file names'
raise MASTError(self.__class__.__name__, error)
elif len(file_list) == 0:
raise MASTError(self.__class__.__name__, "No structure file %s found in %s" % (structure_dict['posfile'], origindir))
else:
structure_dict['posfile'] = file_list[0]
# print 'in InputParser.parse_structure_section:', subsection_dict
# TM
element_map = dict()
atom_list = list()
for key, value in subsection_dict.items():
if (key == 'coordinates'):
value = np.array(value)
# Here we use .title() to re-capitalize the first letter of all
# the atomic symbols to comply with what
# pymatgen needs
atom_list = [val.title() for val in value[:, 0]]
structure_dict['atom_list'] = atom_list
coordinates = np.array(value[:, 1:], dtype='float')
structure_dict['coordinates'] = coordinates
if (key == 'lattice'):
#print "VALUE: ", value
lattice = np.array(value, dtype='float')
structure_dict['lattice'] = lattice
if (key == 'elementmap'):
for elline in value:
elkey = elline[0].strip().upper() #all caps
elname = elline[1].strip().title() #Title case
element_map[elkey]=elname
structure_dict['element_map'] = element_map
if len(element_map) > 0 and len(atom_list) > 0:
new_atom_list = list()
for atomval in atom_list:
if atomval.upper() in element_map.keys():
new_atom_list.append(element_map[atomval])
else:
new_atom_list.append(atomval)
structure_dict['atom_list'] = new_atom_list
for key, value in structure_dict.items():
options.set_item(section_name, key, value)
