def perform_workflow(self, from_scratch=False):
#TODO: Make the directory structure more organic (avoid duplicate
# "initial_structure.vasp" files e.g.)
##relaxation_dir = os.path.join(self.run_location, 'acc_std_relax')
relaxation_dir = os.path.join(self.run_location)
### if from_scratch, delete the relaxation folder, if it exists
##if from_scratch and os.path.isdir(relaxation_dir):
## shutil.rmtree(relaxation_dir)
### create a "relaxation" folder, if one doesn't already exist
##os.makedirs(relaxation_dir, exist_ok=True)
relaxation_settings = DEFAULT_VASP_INCAR_SETTINGS['acc_std_relax']
relaxation_settings.update(self.custom_calculation_settings.get('acc_std_relax', {}))
initial_structure = self.initial_structure
with files_and_folders.change_working_dir(relaxation_dir):
if not from_scratch:
previous_outcar = os.path.join(relaxation_dir, 'OUTCAR')
previous_contcar = os.path.join(relaxation_dir, 'CONTCAR')
previous_poscar = os.path.join(relaxation_dir, 'POSCAR')
if os.path.isfile(previous_outcar) and os.path.getsize(previous_outcar):
files_and_folders.backup_files()
if os.path.isfile(previous_contcar) and os.path.getsize(previous_contcar):
initial_structure = io.read_poscar(previous_contcar)
elif os.path.isfile(previous_poscar) and os.path.getsize(previous_poscar):
initial_structure = io.read_poscar(previous_poscar)
vcd, converged = self.do_relaxation(structure=initial_structure,
settings=relaxation_settings,
mpi_call=self.mpi_call,
**self.kwargs)
with open('acc_std_relax_data.json', 'w') as fw:
json.dump(vcd.as_dict(), fw, indent=2)
if not converged:
msg = 'Error while performing the relaxation run(s)'
raise KelpieWorkflowError(msg)
def perform_workflow(self, from_scratch=False):
relaxation_dir = os.path.join(self.run_location, 'relaxation')
# if from_scratch, delete the "relaxation" folder, if it exists
if from_scratch and os.path.isdir(relaxation_dir):
shutil.rmtree(relaxation_dir)
# create a "relaxation" folder, if one doesn't already exist
os.makedirs(relaxation_dir, exist_ok=True)
relaxation_settings = DEFAULT_VASP_INCAR_SETTINGS['relaxation']
relaxation_settings.update(self.custom_calculation_settings.get('relaxation', {}))
initial_structure = self.initial_structure
with files_and_folders.change_working_dir(relaxation_dir):
if not from_scratch:
previous_outcar = os.path.join(relaxation_dir, 'OUTCAR')
previous_contcar = os.path.join(relaxation_dir, 'CONTCAR')
previous_poscar = os.path.join(relaxation_dir, 'POSCAR')
if os.path.isfile(previous_outcar) and os.path.getsize(previous_outcar):
files_and_folders.backup_files()
if os.path.isfile(previous_contcar) and os.path.getsize(previous_contcar):
initial_structure = io.read_poscar(previous_contcar)
elif os.path.isfile(previous_poscar) and os.path.getsize(previous_poscar):
initial_structure = io.read_poscar(previous_poscar)
vcd, converged = self.do_relaxation(structure=initial_structure,
settings=relaxation_settings,
mpi_call=self.mpi_call,
**self.kwargs)
with open('relaxation_data.json', 'w') as fw:
json.dump(vcd.as_dict(), fw, indent=2)
if not converged:
msg = 'Error while performing the relaxation run(s)'
raise KelpieWorkflowError(msg)
relaxation_output_structure = os.path.join(relaxation_dir, 'CONTCAR')
initial_structure = io.read_poscar(relaxation_output_structure)
static_dir = os.path.join(self.run_location, 'static')
os.makedirs(static_dir, exist_ok=True)
static_settings = DEFAULT_VASP_INCAR_SETTINGS['static']
static_settings.update(self.custom_calculation_settings.get('static', {}))
files_and_folders.copy_files(src_folder='relaxation',
dest_folder='static',
list_of_filenames=['CHGCAR'])
with files_and_folders.change_working_dir(static_dir):
vcd, converged = self.do_static(structure=initial_structure,
settings=static_settings,
mpi_call=self.mpi_call,
**self.kwargs)
with open('static_data.json', 'w') as fw:
json.dump(vcd.as_dict(), fw, indent=2)
if not converged:
msg = 'Error while performing the final static run'
raise KelpieWorkflowError(msg)
def do_static(self, structure=None, settings=None, mpi_call=None, **kwargs):
# propagate "n_attempts" to keep track of the number of VASP runs
# if this is the first do_relaxation() call, initialize "n_attempts"
if not hasattr(kwargs, 'n_attempts'):
kwargs['n_attempts'] = 0
# write input files with the given structure and settings
ig = VaspInputGenerator(structure=structure,
calculation_settings=settings,
**kwargs)
ig.write_vasp_input_files()
# use the MPI call specified to run VASP
vasp_process = self.run_vasp(mpi_call)
# did the VASP run OK?
if vasp_process.returncode != 0:
msg = 'Something went wrong with the MPI VASP run'
raise KelpieWorkflowError(msg)
# increase "n_attempts": the number of VASP runs
kwargs['n_attempts'] += 1
# parse VASP output files to check for convergence
vcd = VaspCalculationData(vasprunxml_file='vasprun.xml',
vasp_outcar_file='OUTCAR')
converged = vcd.is_fully_converged(scf_thresh=settings.get('ediff'))
# if the calculation has converged or the maximum number of attempts
# has been reached, return the most recent calculation data
max_nattempts = kwargs.get('max_nattempts', 2)
if converged or kwargs['n_attempts'] >= max_nattempts:
return vcd, converged
# if not try to fix any errors and/or convergence issues
# get all runtime errors reported by VASP
with open('stdout.txt', 'r') as fr:
vasp_stdout = fr.read()
vasp_errors = self.get_vasp_errors(vasp_stdout=vasp_stdout)
if not vcd.is_number_of_bands_converged():
vasp_errors.add('bands')
# try to address any errors encountered above
# except when VASP didn't run at all: request user intervention
if any([e in vasp_errors for e in ['empty_stdout', 'input_error']]):
msg = 'Error running VASP. Problem with the INCAR?'
raise KelpieWorkflowError(msg)
new_sett = self.address_vasp_errors(errors=vasp_errors,
current_sett=settings,
calc_data=vcd)
settings.update(new_sett)
# restart the static calculation
files_and_folders.backup_files()
return self.do_static(structure=structure,
settings=settings,
mpi_call=mpi_call,
**kwargs)
def perform_workflow(self, from_scratch=False):
calc_dir = os.path.join(self.run_location)
calc_settings = DEFAULT_VASP_INCAR_SETTINGS['sc_forces']
calc_settings.update(self.custom_calculation_settings.get('sc_forces', {}))
initial_structure = self.initial_structure
with files_and_folders.change_working_dir(calc_dir):
if not from_scratch:
previous_outcar = os.path.join(calc_dir, 'OUTCAR')
if os.path.isfile(previous_outcar) and os.path.getsize(previous_outcar):
files_and_folders.backup_files()
vcd, converged = self.do_static(structure=initial_structure,
settings=calc_settings,
mpi_call=self.mpi_call,
**self.kwargs)
with open('sc_forces_data.json', 'w') as fw:
json.dump(vcd.as_dict(), fw, indent=2)
if not converged:
msg = 'Error during (scf) calculation of forces'
raise KelpieWorkflowError(msg)