def check_POSCAR(self, config):
'''
First line must like [1,0]32 to match the elements in POSCAR, 0 could not ignored.
'''
# To check the sum of occupancies
for m in range(len(self.site_ratios)):
sum_occupancy = 0
for n in range(len(self.occupancies[m])):
sum_occupancy += self.occupancies[m][n]
if abs(sum_occupancy - 1) > 1e-10:
print(
'The sum of occupancies in %s is NOT equal to 1, please check!'
% self.occupancies[m])
return (False)
# To check config and occupancy
temp_struct = Structure.from_file(self.poscarfile)
namelist_elements = []
numlist_elements = []
for e, a in temp_struct.composition.items():
namelist_elements.append(e)
numlist_elements.append(a) # [8.0, 24.0]
num_element_firstline = 0
for ocs in self.occupancies:
num_element_firstline += len(ocs)
if len(numlist_elements) != num_element_firstline:
print(
'The number of element kind(%s) in first line of POASCAR is NOT same one in the structure(%s), maybe "0" occupancy should be added.'
% (num_element_firstline, len(numlist_elements)))
return (False)
index = 0
for m in range(len(self.site_ratios)):
if len(config[m]) < len(self.occupancies[m]):
num_occupancy = 0
for n in range(len(self.occupancies[m])):
num_occupancy += self.occupancies[m][n] * self.site_ratios[
m]
if abs(num_occupancy - numlist_elements[index]) > 1e-10:
print(
'The sum of sites in %s%s is NOT equal to %s(Element: %s), please check!'
% (self.occupancies[m], self.site_ratios[m],
numlist_elements[index], namelist_elements[index]))
return (False)
index += len(self.occupancies[m])
else:
for n in range(len(self.occupancies[m])):
if abs(numlist_elements[index] - self.occupancies[m][n] *
self.site_ratios[m]) > 1e-10:
print(
'The sites in %s * %s is NOT equal to %s(Element: %s), please check!'
% (self.occupancies[m][n], self.site_ratios[m],
numlist_elements[index],
namelist_elements[index]))
return (False)
index += 1
return (True)
def run(args):
"""
Run dfttk
Currently, only support get_wf_gibbs
Parameters
STR_FOLDER = args.STRUCTURE_FOLDER
folder/file containing structures
MATCH_PATTERN = args.MATCH_PATTERN
Match patterns for structure file, e.g. *POSCAR
RECURSIVE = args.RECURSIVE
recursive or not
WORKFLOW = args.WORKFLOW
workflow, current only get_wf_gibbs
LAUNCH = args.LAUNCH
Launch to lpad or not
MAX_JOB = args.MAX_JOB
Max job to submit
SETTINGS = args.SETTINGS
Settings file
WRITE_OUT_WF = args.WRITE_OUT_WF
Write out wf file or not
"""
STR_FOLDER = args.STRUCTURE_FOLDER # folder/file containing structures
MATCH_PATTERN = args.MATCH_PATTERN # Match patterns for structure file, e.g. *POSCAR
RECURSIVE = args.RECURSIVE # recursive or not
WORKFLOW = args.WORKFLOW # workflow, current only get_wf_gibbs
PHONON = args.PHONON # run phonon
LAUNCH = args.LAUNCH # Launch to lpad or not
MAX_JOB = args.MAX_JOB # Max job to submit
SETTINGS = args.SETTINGS # Settings file
WRITE_OUT_WF = args.WRITE_OUT_WF # Write out wf file or not
TAG = args.TAG # Metadata from the command line
APPEND = args.APPEND # Append calculations, e.g. appending volumes or phonon or born
db_file = args.db_file # user supplier db_file such as db.json
if not db_file:
if os.path.exists('db.json'):
db_file = 'db.json'
elif not os.path.exists(db_file):
db_file = None
## Initial wfs and metadatas
wfs = []
metadatas = {}
if APPEND:
if TAG:
metadatas = {
os.path.join(os.path.abspath('./'), 'POSCAR'): {
'tag': TAG
}
}
elif os.path.exists('METADATAS.yaml'):
metadatas = loadfn('METADATAS.yaml')
else:
raise ValueError(
'For APPEND model, please provide TAG with -tag or provide METADATAS.yaml file'
)
for keyi in metadatas:
(STR_PATH, STR_FILENAME_WITH_EXT) = os.path.split(keyi)
(STR_FILENAME, STR_EXT) = os.path.splitext(STR_FILENAME_WITH_EXT)
user_settings = get_user_settings(STR_FILENAME_WITH_EXT,
STR_PATH=STR_PATH,
NEW_SETTING=SETTINGS)
metadata = user_settings.get('metadata', {})
metadata.update(metadatas[keyi])
user_settings.update({'metadata': metadata})
structure = get_eq_structure_by_metadata(metadata=metadata,
db_file=db_file)
if structure is None:
raise FileNotFoundError(
'There is no static results under current metadata tag({})'
.format(metadata['tag']))
if PHONON:
user_settings.update({'phonon': True})
phonon_supercell_matrix = user_settings.get(
'phonon_supercell_matrix', None)
if phonon_supercell_matrix is None:
user_settings.update({"phonon_supercell_matrix": "atoms"})
wf = get_wf_single(structure,
WORKFLOW=WORKFLOW,
settings=user_settings,
db_file=db_file)
wf = Customizing_Workflows(wf,
powerups_options=user_settings.get(
'powerups', None))
if isinstance(wf, list):
wfs = wfs + wf
else:
wfs.append(wf)
if WRITE_OUT_WF:
dfttk_wf_filename = os.path.join(
STR_PATH, "dfttk_wf-" + STR_FILENAME_WITH_EXT + ".yaml")
dumpfn(wf, dfttk_wf_filename)
else:
if os.path.exists('METADATAS.yaml'):
metadatas = loadfn('METADATAS.yaml')
## Get the file names of files
STR_FILES = get_structure_file(STR_FOLDER=STR_FOLDER,
RECURSIVE=RECURSIVE,
MATCH_PATTERN=MATCH_PATTERN)
## generat the wf
for STR_FILE in STR_FILES:
(STR_PATH, STR_FILENAME_WITH_EXT) = os.path.split(STR_FILE)
(STR_FILENAME, STR_EXT) = os.path.splitext(STR_FILENAME_WITH_EXT)
str_filename = STR_FILENAME.lower()
if (str_filename.endswith("-" + SETTINGS.lower())
or str_filename.startswith(SETTINGS.lower() + "-")
or (str_filename == SETTINGS.lower())):
print(
STR_FILE +
" is a setting file, not structure file, and skipped when reading the structure."
)
elif STR_FILE == os.path.abspath(__file__):
#This is current file
pass
else:
flag_run = False
try:
structure = Structure.from_file(STR_FILE)
flag_run = True
except Exception as e:
warnings.warn("The name or the contant of " + STR_FILE + " is not supported by dfttk, and skipped. " + \
"Ref. https://pymatgen.org/pymatgen.core.structure.html#pymatgen.core.structure.IStructure.from_file")
if flag_run:
user_settings = get_user_settings(STR_FILENAME_WITH_EXT,
STR_PATH=STR_PATH,
NEW_SETTING=SETTINGS)
metadatai = metadatas.get(STR_FILE, None)
if metadatai:
user_settings.update({'metadata': metadatai})
if PHONON:
user_settings.update({'phonon': True})
phonon_supercell_matrix = user_settings.get(
'phonon_supercell_matrix', None)
if phonon_supercell_matrix is None:
user_settings.update(
{"phonon_supercell_matrix": "atoms"})
wf = get_wf_single(structure,
WORKFLOW=WORKFLOW,
settings=user_settings)
wf = Customizing_Workflows(
wf,
powerups_options=user_settings.get('powerups', None))
metadatas[STR_FILE] = wf.as_dict()["metadata"]
wfs.append(wf)
if WRITE_OUT_WF:
dfttk_wf_filename = os.path.join(
STR_PATH,
"dfttk_wf-" + STR_FILENAME_WITH_EXT + ".yaml")
dumpfn(wf.to_dict(), dfttk_wf_filename)
#Write Out the metadata for POST and continue purpose
dumpfn(metadatas, "METADATAS.yaml")
"""
_fws = []
for wflow in wfs:
revised_wflow = Customizing_Workflows(wflow,user_settings={})
_fws.append(revised_wflow)
fws = _fws
"""
if LAUNCH:
from fireworks import LaunchPad
lpad = LaunchPad.auto_load()
for wflow in wfs:
lpad.add_wf(wflow)
if MAX_JOB:
# Not False or Empty
if MAX_JOB == 1:
os.system("qlaunch singleshot")
else:
os.system("qlaunch rapidfire -m " + str(MAX_JOB))
modify_incar_params = { 'Full relax': {'incar_update': {"LAECHG":False,"LCHARG":False,"LWAVE":False}},
'PreStatic': {'incar_update': {"LAECHG":False,"LCHARG":False,"LWAVE":False}},
'PS2': {'incar_update': {"LAECHG":False,"LCHARG":False,"LWAVE":False}},
'static': {'incar_update': {"LAECHG":False,"LCHARG":False,"LWAVE":False}},
"""
modify_incar_params={}
#dict, dict of class ModifyKpoints with keywords in Workflow name, similar with modify_incar_params
modify_kpoints_params={}
#bool, print(True) or not(False) some informations, used for debug
verbose=False
###################### DO NOT CHANGE THE FOLLOWING LINES ##############################
from pymatgen.ext.matproj import MPRester, Structure
from dfttk.wflows import get_wf_gibbs
structure = Structure.from_file(TEMPLATE_STRUCTURE_FILENAME)
if magmom:
structure.add_site_property('magmom', magmom)
if not db_file:
from fireworks.fw_config import config_to_dict
from monty.serialization import loadfn
db_file = loadfn(config_to_dict()["FWORKER_LOC"])["env"]["db_file"]
wf = get_wf_gibbs(structure, num_deformations=num_deformations, deformation_fraction=deformation_fraction,
phonon=phonon, phonon_supercell_matrix=phonon_supercell_matrix, t_min=t_min, t_max=t_max,
t_step=t_step, tolerance=tolerance, volume_spacing_min=volume_spacing_min,vasp_cmd=vasp_cmd,
db_file=db_file, metadata=metadata, name='EV_QHA', symmetry_tolerance=symmetry_tolerance,
run_isif2=run_isif2, pass_isif4=pass_isif4, passinitrun=passinitrun, relax_path=relax_path,
modify_incar_params=modify_incar_params, modify_kpoints_params=modify_kpoints_params,
def check_symmetry(tol_energy=0.025,
tol_strain=0.05,
tol_bond=0.10,
site_properties=None):
'''
Check symmetry for vasp run. This should be run for each vasp run
Parameter
---------
tol_energy: float
The tolerance of energy
tol_strain: float
The tolerance of strain
tol_bond: float
The tolerance of bond
Return
symm_data: dict
It will store the initial structure/final_structure, isif, initial_energy_per_atom,
final_energy_per_atom, symmetry_checks_passed, tolerances, failures, number_of_failures
------
'''
# Get relevant files as pmg objects
incar = Incar.from_file("INCAR")
outcar = Outcar('OUTCAR')
vasprun = Vasprun("vasprun.xml")
inp_struct = Structure.from_file("POSCAR")
out_struct = Structure.from_file("CONTCAR")
if site_properties:
if 'magmom' in site_properties:
in_mag = incar.as_dict()['MAGMOM']
inp_struct.add_site_property('magmom', in_mag)
out_mag = [m['tot'] for m in outcar.magnetization]
if len(out_mag) == 0:
out_mag = copy.deepcopy(in_mag)
out_struct.add_site_property('magmom', out_mag)
site_properties.pop('magmom')
for site_property in site_properties:
inp_struct.add_site_property(site_property,
site_properties[site_property])
out_struct.add_site_property(site_property,
site_properties[site_property])
current_isif = incar['ISIF']
initial_energy = float(
vasprun.ionic_steps[0]['e_wo_entrp']) / len(inp_struct)
final_energy = float(vasprun.final_energy) / len(out_struct)
# perform all symmetry breaking checks
failures = []
energy_difference = np.abs(final_energy - initial_energy)
if energy_difference > tol_energy:
fail_dict = {
'reason': 'energy',
'tolerance': tol_energy,
'value': energy_difference,
}
failures.append(fail_dict)
strain_norm = get_non_isotropic_strain(inp_struct.lattice.matrix,
out_struct.lattice.matrix)
if strain_norm > tol_strain:
fail_dict = {
'reason': 'strain',
'tolerance': tol_strain,
'value': strain_norm,
}
failures.append(fail_dict)
bond_distance_change = get_bond_distance_change(inp_struct, out_struct)
if bond_distance_change > tol_bond:
fail_dict = {
'reason': 'bond distance',
'tolerance': tol_bond,
'value': bond_distance_change,
}
failures.append(fail_dict)
symm_data = {
"initial_structure": inp_struct.as_dict(),
"final_structure": out_struct.as_dict(),
"isif": current_isif,
"initial_energy_per_atom": initial_energy,
"final_energy_per_atom": final_energy,
"real_value": {
"energy": energy_difference,
"strain": strain_norm,
"bond": bond_distance_change
},
"tolerances": {
"energy": tol_energy,
"strain": tol_strain,
"bond": tol_bond,
},
"failures": failures,
"number_of_failures": len(failures),
"symmetry_checks_passed": len(failures) == 0,
}
return symm_data