remove fix to delete large files

hippynn/molecular_dynamics/md.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 from functools import singledispatchmethod
+from copy import copy
 
 import numpy as np
 import torch
@@ -9,7 +10,6 @@
 from ..graphs import Predictor
 from ..layers.pairs.periodic import wrap_systems_torch
 
-
 class Variable:
     """
     Tracks the state of a quantity (eg. position, cell, species,
@@ -307,10 +307,12 @@ def pre_step(self, dt):
 
         self.variable.data["position"] = self.variable.data["position"] + self.variable.data["velocity"] * dt
 
-        try:
-            _, self.variable.data["position"], *_ = wrap_systems_torch(coords=self.variable.data["position"], cell=self.variable.data["cell"], cutoff=0) # cutoff only used for discarded outputs; can be set arbitrarily
-        except KeyError:
-            pass
+        if "cell" in self.variable.data.keys():
+            _, self.variable.data["position"], *_ = wrap_systems_torch(coords=self.variable.data["position"], cell=self.variable.data["cell"], cutoff=0) # cutoff only impacts unused outputs; can be set arbitrarily
+            try:
+                self.variable.data["unwrapped_position"] = self.variable.data["unwrapped_position"] + self.variable.data["velocity"] * dt
+            except KeyError:
+                self.variable.data["unwrapped_position"] = copy(self.variable.data["position"])
 
     def post_step(self, dt, model_outputs):
         """Updates to variables performed during each step of MD simulation after HIPNN model evaluation
@@ -406,6 +408,7 @@ def model(self, model):
                     + f" Entries in the 'model_input_map' should have the form 'hipnn-db_name: variable-data-key' where 'hipnn-db_name'"
                     + f" refers to the db_name of an input for the hippynn Predictor model,"
                     + f" and 'variable-data-key' corresponds to a key in the 'data' dictionary of one of the Variables."
+                    + f" Currently assigned db_names are: {variable_data_db_names}."
                 )
         self._model = model
 
@@ -482,6 +485,9 @@ def _update_data(self, model_outputs: dict):
             except KeyError:
                 self._data[f"output_{key}"] = [value.cpu().detach()[0]]
 
+            for key, value in variable._data.items():
+                print(variable.name, key, value.shape)
+
 
     def run(self, dt: float, n_steps: int, record_every: int = None):
         """Run `n_steps` of MD algorithm.