def load_model(self, model, name=None):
"""
Loads record contents from a given model.
Parameters
----------
model : str or DataModelDict
The model contents of the record to load.
name : str, optional
The name to assign to the record. Often inferred from other
attributes if not given.
"""
# Load universal and subset content
super().load_model(model, name=name)
calc = self.model[self.modelroot]
# Load calculation-specific content
run_params = calc['calculation']['run-parameter']
self.thermosteps = run_params['thermosteps']
self.dumpsteps = run_params['dumpsteps']
self.runsteps = run_params['runsteps']
self.equilsteps = run_params['equilsteps']
self.randomseed = run_params['randomseed']
# Load phase-state info
self.temperature = uc.value_unit(calc['phase-state']['temperature'])
# Load results
if self.status == 'finished':
self.__nsamples = calc['number-of-measurements']
self.__natoms = calc['number-of-atoms']
mps = calc['measured-phase-state']
self.__measured_temperature = uc.value_unit(mps['temperature'])
self.__measured_temperature_std = uc.error_unit(mps['temperature'])
self.__measured_pressure_xx = uc.value_unit(mps['pressure-xx'])
self.__measured_pressure_xx_std = uc.error_unit(mps['pressure-xx'])
self.__measured_pressure_yy = uc.value_unit(mps['pressure-yy'])
self.__measured_pressure_yy_std = uc.error_unit(mps['pressure-yy'])
self.__measured_pressure_zz = uc.value_unit(mps['pressure-zz'])
self.__measured_pressure_zz_std = uc.error_unit(mps['pressure-zz'])
self.__potential_energy = uc.value_unit(mps['potential-energy'])
self.__potential_energy_std = uc.error_unit(
mps['potential-energy'])
self.__total_energy = uc.value_unit(mps['total-energy'])
self.__total_energy_std = uc.error_unit(mps['total-energy'])
dr = calc['diffusion-rate']
self.__d = uc.value_unit(dr['total'])
self.__dx = uc.value_unit(dr['x-direction'])
self.__dy = uc.value_unit(dr['y-direction'])
self.__dz = uc.value_unit(dr['z-direction'])
def todict(self, full=True, flat=False):
"""
Converts the structured content to a simpler dictionary.
Parameters
----------
full : bool, optional
Flag used by the calculation records. A True value will include
terms for both the calculation's input and results, while a value
of False will only include input terms (Default is True).
flat : bool, optional
Flag affecting the format of the dictionary terms. If True, the
dictionary terms are limited to having only str, int, and float
values, which is useful for comparisons. If False, the term
values can be of any data type, which is convenient for analysis.
(Default is False).
Returns
-------
dict
A dictionary representation of the record's content.
"""
calc = self.content[self.contentroot]
params = {}
params['key'] = calc['key']
params['script'] = calc['calculation']['script']
params['iprPy_version'] = calc['calculation']['iprPy-version']
params['LAMMPS_version'] = calc['calculation']['LAMMPS-version']
params['thermosteps'] = calc['calculation']['run-parameter'][
'thermosteps']
params['runsteps'] = calc['calculation']['run-parameter']['runsteps']
params['randomseed'] = calc['calculation']['run-parameter'][
'randomseed']
sizemults = calc['calculation']['run-parameter']['size-multipliers']
params['potential_LAMMPS_key'] = calc['potential-LAMMPS']['key']
params['potential_LAMMPS_id'] = calc['potential-LAMMPS']['id']
params['potential_key'] = calc['potential-LAMMPS']['potential']['key']
params['potential_id'] = calc['potential-LAMMPS']['potential']['id']
params['load_file'] = calc['system-info']['artifact']['file']
params['load_style'] = calc['system-info']['artifact']['format']
params['load_options'] = calc['system-info']['artifact'][
'load_options']
params['family'] = calc['system-info']['family']
symbols = aslist(calc['system-info']['symbol'])
params['pointdefect_key'] = calc['point-defect']['key']
params['pointdefect_id'] = calc['point-defect']['id']
params['temperature'] = uc.value_unit(
calc['phase-state']['temperature'])
if flat is True:
params['a_mult1'] = sizemults['a'][0]
params['a_mult2'] = sizemults['a'][1]
params['b_mult1'] = sizemults['b'][0]
params['b_mult2'] = sizemults['b'][1]
params['c_mult1'] = sizemults['c'][0]
params['c_mult2'] = sizemults['c'][1]
params['symbols'] = ' '.join(symbols)
else:
params['sizemults'] = np.array(
[sizemults['a'], sizemults['b'], sizemults['c']])
params['symbols'] = symbols
params['status'] = calc.get('status', 'finished')
params['error'] = calc.get('error', np.nan)
if full is True and params['status'] == 'finished':
params['measured_temperature'] = uc.value_unit(
calc['measured-phase-state']['temperature'])
params['measured_pressure_xx'] = uc.value_unit(
calc['measured-phase-state']['pressure-xx'])
params['measured_pressure_xx_std'] = uc.error_unit(
calc['measured-phase-state']['pressure-xx'])
params['measured_pressure_yy'] = uc.value_unit(
calc['measured-phase-state']['pressure-yy'])
params['measured_pressure_yy_std'] = uc.error_unit(
calc['measured-phase-state']['pressure-yy'])
params['measured_pressure_zz'] = uc.value_unit(
calc['measured-phase-state']['pressure-zz'])
params['measured_pressure_zz_std'] = uc.error_unit(
calc['measured-phase-state']['pressure-zz'])
params['measured_potential_energy'] = uc.value_unit(
calc['measured-phase-state']['potential-energy'])
params['measured_potential_energy_std'] = uc.error_unit(
calc['measured-phase-state']['potential-energy'])
params['d'] = uc.value_unit(calc['diffusion-rate']['total'])
params['dx'] = uc.value_unit(calc['diffusion-rate']['x-direction'])
params['dy'] = uc.value_unit(calc['diffusion-rate']['y-direction'])
params['dz'] = uc.value_unit(calc['diffusion-rate']['z-direction'])
params['natoms'] = calc['number-of-atoms']
return params
def todict(self, full=True, flat=False):
"""
Converts the structured content to a simpler dictionary.
Parameters
----------
full : bool, optional
Flag used by the calculation records. A True value will include
terms for both the calculation's input and results, while a value
of False will only include input terms (Default is True).
flat : bool, optional
Flag affecting the format of the dictionary terms. If True, the
dictionary terms are limited to having only str, int, and float
values, which is useful for comparisons. If False, the term
values can be of any data type, which is convenient for analysis.
(Default is False).
Returns
-------
dict
A dictionary representation of the record's content.
"""
# Extract universal content
params = super().todict(full=full, flat=flat)
calc = self.content[self.contentroot]
# Extract potential info
subset('lammps_potential').todict(calc, params, full=full, flat=flat)
# Extract system info
subset('atomman_systemload').todict(calc, params, full=full, flat=flat)
subset('atomman_systemmanipulate').todict(calc, params, full=full, flat=flat)
params['temperature'] = uc.value_unit(calc['phase-state']['temperature'])
params['pressure_xx'] = uc.value_unit(calc['phase-state']['pressure-xx'])
params['pressure_yy'] = uc.value_unit(calc['phase-state']['pressure-yy'])
params['pressure_zz'] = uc.value_unit(calc['phase-state']['pressure-zz'])
params['pressure_xy'] = uc.value_unit(calc['phase-state']['pressure-xy'])
params['pressure_xz'] = uc.value_unit(calc['phase-state']['pressure-xz'])
params['pressure_yz'] = uc.value_unit(calc['phase-state']['pressure-yz'])
if full is True and params['status'] == 'finished':
params['lx'] = uc.value_unit(calc['measured-box-parameter']['lx'])
params['lx_std'] = uc.error_unit(calc['measured-box-parameter']['lx'])
params['ly'] = uc.value_unit(calc['measured-box-parameter']['ly'])
params['ly_std'] = uc.error_unit(calc['measured-box-parameter']['ly'])
params['lz'] = uc.value_unit(calc['measured-box-parameter']['lz'])
params['lz_std'] = uc.error_unit(calc['measured-box-parameter']['lz'])
params['xy'] = uc.value_unit(calc['measured-box-parameter']['xy'])
params['xy_std'] = uc.error_unit(calc['measured-box-parameter']['xy'])
params['xz'] = uc.value_unit(calc['measured-box-parameter']['xz'])
params['xz_std'] = uc.error_unit(calc['measured-box-parameter']['xz'])
params['yz'] = uc.value_unit(calc['measured-box-parameter']['yz'])
params['yz_std'] = uc.error_unit(calc['measured-box-parameter']['yz'])
params['E_cohesive'] = uc.value_unit(calc['cohesive-energy'])
params['E_cohesive_std'] = uc.error_unit(calc['cohesive-energy'])
params['measured_temperature'] = uc.value_unit(calc['measured-phase-state']['temperature'])
params['measured_pressure_xx'] = uc.value_unit(calc['measured-phase-state']['pressure-xx'])
params['measured_pressure_xx_std'] = uc.error_unit(calc['measured-phase-state']['pressure-xx'])
params['measured_pressure_yy'] = uc.value_unit(calc['measured-phase-state']['pressure-yy'])
params['measured_pressure_yy_std'] = uc.error_unit(calc['measured-phase-state']['pressure-yy'])
params['measured_pressure_zz'] = uc.value_unit(calc['measured-phase-state']['pressure-zz'])
params['measured_pressure_zz_std'] = uc.error_unit(calc['measured-phase-state']['pressure-zz'])
params['measured_pressure_xy'] = uc.value_unit(calc['measured-phase-state']['pressure-xy'])
params['measured_pressure_xy_std'] = uc.error_unit(calc['measured-phase-state']['pressure-xy'])
params['measured_pressure_xz'] = uc.value_unit(calc['measured-phase-state']['pressure-xz'])
params['measured_pressure_xz_std'] = uc.error_unit(calc['measured-phase-state']['pressure-xz'])
params['measured_pressure_yz'] = uc.value_unit(calc['measured-phase-state']['pressure-yz'])
params['measured_pressure_xyz_std'] = uc.error_unit(calc['measured-phase-state']['pressure-yz'])
return params
def todict(self, full=True, flat=False):
"""
Converts the structured content to a simpler dictionary.
Parameters
----------
full : bool, optional
Flag used by the calculation records. A True value will include
terms for both the calculation's input and results, while a value
of False will only include input terms (Default is True).
flat : bool, optional
Flag affecting the format of the dictionary terms. If True, the
dictionary terms are limited to having only str, int, and float
values, which is useful for comparisons. If False, the term
values can be of any data type, which is convenient for analysis.
(Default is False).
Returns
-------
dict
A dictionary representation of the record's content.
"""
calc = self.content[self.contentroot]
params = {}
params['key'] = calc['key']
params['script'] = calc['calculation']['script']
params['iprPy_version'] = calc['calculation']['iprPy-version']
params['LAMMPS_version'] = calc['calculation']['LAMMPS-version']
params['thermosteps']= calc['calculation']['run-parameter']['thermosteps']
params['runsteps'] = calc['calculation']['run-parameter']['runsteps']
params['randomseed'] = calc['calculation']['run-parameter']['randomseed']
sizemults = calc['calculation']['run-parameter']['size-multipliers']
params['potential_LAMMPS_key'] = calc['potential-LAMMPS']['key']
params['potential_LAMMPS_id'] = calc['potential-LAMMPS']['id']
params['potential_key'] = calc['potential-LAMMPS']['potential']['key']
params['potential_id'] = calc['potential-LAMMPS']['potential']['id']
params['load_file'] = calc['system-info']['artifact']['file']
params['load_style'] = calc['system-info']['artifact']['format']
params['load_options'] = calc['system-info']['artifact']['load_options']
params['family'] = calc['system-info']['family']
symbols = aslist(calc['system-info']['symbol'])
params['pointdefect_key'] = calc['point-defect']['key']
params['pointdefect_id'] = calc['point-defect']['id']
params['temperature'] = uc.value_unit(calc['phase-state']['temperature'])
if flat is True:
params['a_mult1'] = sizemults['a'][0]
params['a_mult2'] = sizemults['a'][1]
params['b_mult1'] = sizemults['b'][0]
params['b_mult2'] = sizemults['b'][1]
params['c_mult1'] = sizemults['c'][0]
params['c_mult2'] = sizemults['c'][1]
params['symbols'] = ' '.join(symbols)
else:
params['sizemults'] = np.array([sizemults['a'], sizemults['b'], sizemults['c']])
params['symbols'] = symbols
params['status'] = calc.get('status', 'finished')
params['error'] = calc.get('error', np.nan)
if full is True and params['status'] == 'finished':
params['measured_temperature'] = uc.value_unit(calc['measured-phase-state']['temperature'])
params['measured_pressure_xx'] = uc.value_unit(calc['measured-phase-state']['pressure-xx'])
params['measured_pressure_xx_std'] = uc.error_unit(calc['measured-phase-state']['pressure-xx'])
params['measured_pressure_yy'] = uc.value_unit(calc['measured-phase-state']['pressure-yy'])
params['measured_pressure_yy_std'] = uc.error_unit(calc['measured-phase-state']['pressure-yy'])
params['measured_pressure_zz'] = uc.value_unit(calc['measured-phase-state']['pressure-zz'])
params['measured_pressure_zz_std'] = uc.error_unit(calc['measured-phase-state']['pressure-zz'])
params['measured_potential_energy'] = uc.value_unit(calc['measured-phase-state']['potential-energy'])
params['measured_potential_energy_std'] = uc.error_unit(calc['measured-phase-state']['potential-energy'])
params['d'] = uc.value_unit(calc['diffusion-rate']['total'])
params['dx'] = uc.value_unit(calc['diffusion-rate']['x-direction'])
params['dy'] = uc.value_unit(calc['diffusion-rate']['y-direction'])
params['dz'] = uc.value_unit(calc['diffusion-rate']['z-direction'])
params['natoms'] = calc['number-of-atoms']
return params
