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MMK Memory [WIP] #114

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MMK Memory [WIP] #114

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eaf1877
Add memory too mmk
SamTov May 25, 2023
695b619
Merge branch 'main' into SamTov_MMK_memory
SamTov May 25, 2023
6bcae1b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 25, 2023
4099ca4
Merge branch 'main' into SamTov_MMK_memory
SamTov May 27, 2023
e4ae599
Merge branch 'main' into SamTov_MMK_memory
PythonFZ Jun 26, 2023
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19 changes: 17 additions & 2 deletions ipsuite/configuration_comparison/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -140,6 +140,7 @@ class ConfigurationComparison(base.IPSNode):

reference: base.protocol.HasOrIsAtoms = zntrack.zn.deps()
analyte: base.protocol.HasOrIsAtoms = zntrack.zn.deps()
memory: int = zntrack.zn.params()
similarities = zntrack.zn.plots()
soap: typing.Union[dict, SOAPParameter] = zntrack.zn.params(SOAPParameter())
result: typing.List[float] = zntrack.zn.outs()
Expand All @@ -153,6 +154,7 @@ def __init__(
analyte=None,
soap: dict = None,
use_jit: bool = True,
memory: int = 100,
**kwargs
):
"""Initialize the ConfigurationComparison node.
Expand All @@ -172,6 +174,8 @@ def __init__(
Parameter to use for the SOAP descriptor.
use_jit: bool
use jit compilation.
memory: int
How far back to look in the MMK vector.
kwargs: dict
additional keyword arguments
"""
Expand All @@ -193,6 +197,7 @@ def __init__(
self.remove_database = True
self.disable_tqdm = False
self.use_jit = use_jit
self.memory = memory

def save_representation(self):
"""Save the SOAP descriptor representation as hdf5 file to save RAM.
Expand Down Expand Up @@ -291,7 +296,12 @@ def run(self):
for max_index, _atoms in enumerate(self.analyte):
if max_index == 0:
continue
reference_soap = representation_file["soap"][:max_index]
if max_index <= self.memory:
reference_soap = representation_file["soap"][:max_index]
else:
reference_soap = representation_file["soap"][
max_index - self.memory : max_index
]
analyte_soap = representation_file["soap"][max_index]
comparison = self.compare(reference_soap, analyte_soap)
self.result.append(float(comparison.numpy()))
Expand All @@ -306,7 +316,12 @@ def run(self):
disable=self.disable_tqdm,
) as pbar:
for max_index, _atoms in enumerate(self.analyte):
reference_soap = representation_file["soap_reference"]
if max_index <= self.memory:
reference_soap = representation_file["soap"][:max_index]
else:
reference_soap = representation_file["soap"][
max_index - self.memory : max_index
]
analyte_soap = representation_file["soap_analyte"][max_index]
comparison = self.compare(reference_soap, analyte_soap)
self.result.append(float(comparison.numpy()))
Expand Down