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Use current structure instead of output to update previous structure #483

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merged 3 commits into from
Jan 6, 2022
Merged

Use current structure instead of output to update previous structure #483

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e713094
Use current structure instead of output to update previous structure
samwaseda Dec 17, 2021
d74d6e6
Codacy
samwaseda Dec 17, 2021
3d3cb15
add calc_mode exception
samwaseda Dec 20, 2021
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29 changes: 5 additions & 24 deletions pyiron_atomistics/atomistics/job/interactive.py
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,6 @@ def run_if_interactive(self):
self.interactive_initialize_interface()
if self._structure_previous is None:
self._structure_previous = self.structure.copy()
self._update_previous_structure()
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if self._structure_current is not None:
if (
len(self._structure_current) != len(self._structure_previous)
Expand All @@ -134,6 +133,7 @@ def run_if_interactive(self):
else:
self._logger.debug("Generic library: structure changed!")
self.interactive_structure_setter(self._structure_current)
self._update_previous_structure()

def interactive_index_organizer(self):
index_merge_lst = self._interactive_species_lst.tolist() + list(
Expand All @@ -156,7 +156,7 @@ def interactive_index_organizer(self):
self.interactive_indices_setter(self._structure_current.indices)

def interactive_cell_organizer(self):
if not np.allclose(
if self._generic_input["calc_mode"] != 'static' or not np.allclose(
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This is not necessary for calc_minimize() only calc_minimize(pressure=0) right? And analogously it is not necessary for nvt and nve but npt.

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Is the information about nvt, nve etc. included in the input?

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Not yet but we could include it in https://github.com/pyiron/pyiron_atomistics/blob/master/pyiron_atomistics/atomistics/job/atomistic.py#L226

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So we could go ahead with this version for now, right? I don't think communicating the cell size would significantly change something.

self._structure_current.cell,
self._structure_previous.cell,
rtol=1e-15, atol=1e-15,
Expand All @@ -168,7 +168,7 @@ def interactive_cell_organizer(self):
del self.interactive_input_functions['cell']

def interactive_positions_organizer(self):
if not np.allclose(
if self._generic_input["calc_mode"] != 'static' or not np.allclose(
self._structure_current.positions,
self._structure_previous.positions,
rtol=1e-15,
Expand Down Expand Up @@ -266,27 +266,8 @@ def interactive_volume_getter(self):
return self.initial_structure.get_volume()

def _update_previous_structure(self):
"""
Update the previous structure to the last step configuration
Args:
wrap_atoms (bool):
"""
try:
indices = self.output.indices[-1]
positions = self.output.positions[-1]
cell = self.output.cells[-1]
except IndexError:
return
if len(self._interactive_species_lst) == 0:
el_lst = [el.Abbreviation for el in self.structure.species]
else:
el_lst = self._interactive_species_lst.tolist()
self._structure_previous = self._structure_previous.__class__(
positions=positions,
cell=cell,
indices=indices,
species=[self._periodic_table.element(el) for el in el_lst],
)
"""Update the previous structure to the last step configuration."""
self._structure_previous = self.structure.copy()
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@staticmethod
def _extend_species_elements(struct_species, species_array):
Expand Down