def run_zeopp(self):
"""It performs the full zeopp calculation for all components."""
if self.ctx.mode == 'standalone' or self.ctx.mode == 'geom_only':
zeopp_inputs = self.exposed_inputs(ZeoppCalculation, 'zeopp')
dict_merge(
zeopp_inputs, {
'metadata': {
'label': "ZeoppResSaVolpoBlock",
},
'structure': self.inputs.structure,
'atomic_radii': self.inputs.zeopp.atomic_radii,
})
for key, value in self.ctx.components.get_dict().items():
comp = value['name']
dict_merge(
zeopp_inputs, {
'parameters':
ZeoppParameters(
dict=self.ctx.components[key]['zeopp']),
'metadata': {
'call_link_label': 'run_zeopp_' + comp
}
})
running = self.submit(ZeoppCalculation, **zeopp_inputs)
zeopp_label = "zeopp_{}".format(comp)
self.report(
"Running zeo++ res, sa, volpo, and block calculation<{}>".
format(running.id))
self.to_context(**{zeopp_label: running})
def run_isotherms(self):
"""Compute isotherms at different temperatures."""
# create inputs: exposed are code and metadata
inputs = self.exposed_inputs(HTSWorkChain)
inputs['raspa_base']['raspa']['block_pocket'] = {}
inputs['geometric'] = self.ctx.geom
for comp in self.ctx.comps:
if self.ctx.geom['geometric_output'][comp]['Number_of_blocking_spheres'] > 0:
inputs['raspa_base']["raspa"]["block_pocket"][comp + "_block_file"] = self.ctx.geom_only.outputs['block_files__' + comp + '_block_file']
# Update the parameters with only one temperature and submit
for index, temp in enumerate(self.inputs.parameters['temperature_list']):
self.ctx.parameters_singletemp = get_parameters_singletemp(index, self.inputs.parameters)
dict_merge(
inputs, {
'metadata': {
'label': "Isotherm_{}".format(index),
'call_link_label': 'run_isotherm_{}'.format(index),
},
'parameters': self.ctx.parameters_singletemp
}
)
running = self.submit(HTSWorkChain, **inputs)
self.ctx.current_T_index += 1
self.to_context(**{'isotherm_{}'.format(index): running})
def run_zeopp_res(self):
"""
It performs the zeopp pore diameter calculation.
"""
zeopp_input = self.exposed_inputs(ZeoppCalculation, 'zeopp')
self.ctx.zeopp_param['zeopp_res'] = self.ctx.default_zeopp_params
dict_merge(
zeopp_input, {
'metadata': {
'label': "Zeopp Pore Diameter Calculation",
'call_link_label': 'run_zeopp_res'
},
'structure':
self.inputs.structure,
'atomic_radii':
self.inputs.zeopp.atomic_radii,
'parameters':
modify_zeopp_parameters(self.ctx.parameters, **
self.ctx.zeopp_param)
})
res = self.submit(ZeoppCalculation, **zeopp_input)
self.report(
"pk: <{}> | Submitted Zeo++ Pore Diameter Calculation".format(
res.pk))
return ToContext(zeopp_res=res)
def run_geometric(self):
"""Perform Zeo++ block and VOLPO calculation with IsothermWC."""
# create inputs: exposed are code and metadata
inputs = self.exposed_inputs(HTSWorkChain)
dict_merge(
inputs, {
'metadata': {
'label': "IsothermGeometric",
'call_link_label': 'run_geometric',
},
}
)
running = self.submit(HTSWorkChain, **inputs)
self.report("Computing common gemetric properties")
return ToContext(geom_only=running)
def run_zeopp(self):
"""It performs the full zeopp calculation for all components."""
zeopp_inputs = self.exposed_inputs(ZeoppCalculation, 'zeopp')
dict_merge(
zeopp_inputs, {
'metadata': {
'label': "ZeoppResSaVolpoBlock",
'call_link_label': 'run_zeopp'
},
'structure':
self.inputs.structure,
'atomic_radii':
self.inputs.zeopp.atomic_radii,
'parameters':
ZeoppParameters(dict=self.ctx.components['comp1']['zeopp']),
})
running = self.submit(ZeoppCalculation, **zeopp_inputs)
self.report(
"Running zeo++ res, sa, volpo, and block calculation<{}>".format(
running.id))
return ToContext(zeopp=running)
def run_zeopp_visvoro(self):
"""
It performs the visVoro calculation.
"""
zeopp_input = self.exposed_inputs(ZeoppCalculation, 'zeopp')
dict_merge(
zeopp_input, {
'metadata': {
'label': "Zeopp Pore Diameter Calculation",
},
'structure': self.inputs.structure,
})
zeopp_input['structure'] = self.inputs.structure
zeopp_input['metadata']['label'] = "Zeopp visVoro Calculation"
self.ctx.components = update_components(
self.inputs.components,
self.ctx.zeopp_res.outputs.output_parameters)
# All together submission!
for key in self.ctx.components.keys():
self.ctx.zeopp_param[
'zeopp_visvoro'] = self.ctx.default_zeopp_params
self.ctx.zeopp_param['probe'] = Str(key)
self.ctx.zeopp_param['components'] = self.ctx.components
dict_merge(
zeopp_input, {
'metadata': {
'call_link_label': 'run_zeopp_visvoro_' + key
},
'parameters':
modify_zeopp_parameters(self.ctx.parameters, **
self.ctx.zeopp_param)
})
visvoro = self.submit(ZeoppCalculation, **zeopp_input)
zeopp_label = "zeopp_{}".format(key)
self.to_context(**{zeopp_label: visvoro})