Merge pull request #1601 from pyiron/Increase-lammps-parsing-robustness

Increase lammps parsing robustness
pyiron · Nov 13, 2024 · 745b602 · 745b602
2 parents a4e3bbb + 9252df1
commit 745b602
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Showing 2 changed files with 19 additions and 6 deletions.
diff --git a/pyiron_atomistics/lammps/base.py b/pyiron_atomistics/lammps/base.py
@@ -13,6 +13,7 @@
 import pandas
 from pyiron_base import state
 from pyiron_snippets.deprecate import deprecate
+from pyiron_snippets.logger import logger
 
 from pyiron_atomistics.atomistics.job.atomistic import AtomisticGenericJob
 from pyiron_atomistics.lammps.control import LammpsControl
@@ -427,17 +428,22 @@ def save_output(
             data_dict=output_dict,
             group_name="output",
         )
-        final_structure = self.structure.copy()
-        final_structure.indices = hdf_dict["output/generic/indices"][-1]
-        final_structure.positions = hdf_dict["output/generic/positions"][-1]
-        final_structure.cell = hdf_dict["output/generic/cells"][-1]
-        if final_structure is not None:
+        if len(self.structure) == len(hdf_dict["output/generic/indices"][-1]):
+            final_structure = self.structure.copy()
+            final_structure.indices = hdf_dict["output/generic/indices"][-1]
+            final_structure.positions = hdf_dict["output/generic/positions"][-1]
+            final_structure.cell = hdf_dict["output/generic/cells"][-1]
             hdf_dict.update(
                 {
                     "output/structure/" + k: v
                     for k, v in final_structure.to_dict().items()
                 }
             )
+        else:
+            logger.warning(
+                "The number of atoms changed during the simulation. This can be a sign of massive issues in your simulation.\n"
+                "Not storing 'output/structure' to HDF"
+            )
         self.project_hdf5.write_dict_to_hdf(data_dict=hdf_dict)
 
     def convergence_check(self):

diff --git a/pyiron_atomistics/lammps/output.py b/pyiron_atomistics/lammps/output.py
@@ -10,6 +10,7 @@
 import numpy as np
 import pandas as pd
 from pyiron_base import extract_data_from_file
+from pyiron_snippets.logger import logger
 
 from pyiron_atomistics.lammps.structure import UnfoldingPrism
 from pyiron_atomistics.lammps.units import UnitConverter
@@ -75,7 +76,10 @@ def parse_lammps_output(
 
     for k, v in dump_dict.items():
         if len(v) > 0:
-            hdf_generic[k] = convert_units(np.array(v), label=k)
+            try:
+                hdf_generic[k] = convert_units(np.array(v), label=k)
+            except ValueError:
+                hdf_generic[k] = [convert_units(np.array(val), label=k) for val in v]
 
     if df is not None and pressure_dict is not None and generic_keys_lst is not None:
         for k, v in df.items():
@@ -328,6 +332,9 @@ def _collect_output_log(
                 if l.startswith("Loop") or l.startswith("ERROR"):
                     read_thermo = False
                     continue
+                elif l.startswith("WARNING:"):
+                    logger.warning(f"A warning was found in the log:\n{l}")
+                    continue
                 thermo_lines += l
 
             if l.startswith("Step"):