nomad-schema-plugin-simulation-workflow 1.0.6__tar.gz → 1.0.7__tar.gz

{nomad_schema_plugin_simulation_workflow-1.0.6/nomad_schema_plugin_simulation_workflow.egg-info → nomad_schema_plugin_simulation_workflow-1.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nomad-schema-plugin-simulation-workflow
-Version: 1.0.6
+Version: 1.0.7
 Summary: Simulation workflow schema plugin for NOMAD.
 Author: The NOMAD Authors
 License: Apache-2.0
@@ -10,7 +10,8 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: nomad-lab>=1.3.6.dev1
 Requires-Dist: nomad-schema-plugin-run>=1.0.1
-Requires-Dist: mdanalysis<3.0.0,>=2.7.0
+Requires-Dist: mdanalysis<3.0.0,>=2.8.0; python_full_version >= "3.10"
+Requires-Dist: mdanalysis<2.8; python_full_version < "3.10"
 Requires-Dist: scipy>=1.7.1
 Requires-Dist: networkx>=2.6.3
 

{nomad_schema_plugin_simulation_workflow-1.0.6 → nomad_schema_plugin_simulation_workflow-1.0.7/nomad_schema_plugin_simulation_workflow.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nomad-schema-plugin-simulation-workflow
-Version: 1.0.6
+Version: 1.0.7
 Summary: Simulation workflow schema plugin for NOMAD.
 Author: The NOMAD Authors
 License: Apache-2.0
@@ -10,7 +10,8 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: nomad-lab>=1.3.6.dev1
 Requires-Dist: nomad-schema-plugin-run>=1.0.1
-Requires-Dist: mdanalysis<3.0.0,>=2.7.0
+Requires-Dist: mdanalysis<3.0.0,>=2.8.0; python_full_version >= "3.10"
+Requires-Dist: mdanalysis<2.8; python_full_version < "3.10"
 Requires-Dist: scipy>=1.7.1
 Requires-Dist: networkx>=2.6.3
 

nomad_schema_plugin_simulation_workflow-1.0.7/nomad_schema_plugin_simulation_workflow.egg-info/requires.txt

@@ -0,0 +1,10 @@
+nomad-lab>=1.3.6.dev1
+nomad-schema-plugin-run>=1.0.1
+scipy>=1.7.1
+networkx>=2.6.3
+
+[:python_full_version < "3.10"]
+mdanalysis<2.8
+
+[:python_full_version >= "3.10"]
+mdanalysis<3.0.0,>=2.8.0

{nomad_schema_plugin_simulation_workflow-1.0.6 → nomad_schema_plugin_simulation_workflow-1.0.7}/pyproject.toml

@@ -12,7 +12,8 @@ license = { text = "Apache-2.0" }
 dependencies = [
     "nomad-lab>=1.3.6.dev1",
     "nomad-schema-plugin-run>=1.0.1",
-    "mdanalysis>=2.7.0,<3.0.0",
+    "mdanalysis>=2.8.0,<3.0.0 ; python_full_version >= '3.10'",
+    "mdanalysis<2.8 ; python_full_version < '3.10'",
     "scipy>=1.7.1",
     "networkx>=2.6.3",
 ]

{nomad_schema_plugin_simulation_workflow-1.0.6 → nomad_schema_plugin_simulation_workflow-1.0.7}/simulationworkflowschema/molecular_dynamics.py

@@ -68,6 +68,11 @@ class BeadGroup(object):
     def __init__(self, atoms, compound='fragments'):
         """Initialize with an AtomGroup instance.
         Will split based on keyword 'compounds' (residues or fragments).
+
+        self._atoms: AtomGroup (total number of atoms)
+        self.compound: str (dictates type of grouping)
+        self._nbeads: int (total number of beads)
+        self.positions: list (total number of "compounds")
         """
         self._atoms = atoms
         self.compound = compound
@@ -84,8 +89,10 @@ class BeadGroup(object):
     def positions(self):
         # cache positions for current frame
         if self.universe.trajectory.frame != self.__last_frame:
-            self._cache['positions'] = self._atoms.center_of_mass(
-                unwrap=True, compound=self.compound
+            self._cache['positions'] = (
+                self._atoms.center_of_mass(unwrap=True, compound=self.compound)
+                if self._nbeads != 0
+                else []
             )
             self.__last_frame = self.universe.trajectory.frame
         return self._cache['positions']
@@ -560,9 +567,13 @@ def _get_molecular_bead_groups(
     bead_groups = {}
     for moltype in moltypes:
         ags_by_moltype = universe.select_atoms('moltype ' + moltype)
-        ags_by_moltype = ags_by_moltype[
-            ags_by_moltype.masses > abs(1e-2)
-        ]  # remove any virtual/massless sites (needed for, e.g., 4-bead water models)
+        if ags_by_moltype.n_atoms == 0:
+            continue
+
+        if ags_by_moltype.masses is not None:
+            ags_by_moltype = ags_by_moltype[
+                ags_by_moltype.masses > abs(1e-2)
+            ]  # remove any virtual/massless sites (needed for, e.g., 4-bead water models)
         bead_groups[moltype] = BeadGroup(ags_by_moltype, compound='fragments')
 
     return bead_groups
@@ -619,7 +630,7 @@ def calc_molecular_rdf(
     del_list = [
         i_moltype
         for i_moltype, moltype in enumerate(moltypes)
-        if bead_groups[moltype]._nbeads > max_mols
+        if len(bead_groups[moltype].positions) > max_mols
     ]
     moltypes = np.delete(moltypes, del_list).tolist()
 
@@ -972,7 +983,7 @@ def calc_molecular_mean_squared_displacements(
     moltypes = [moltype for moltype in bead_groups.keys()]
     del_list = []
     for i_moltype, moltype in enumerate(moltypes):
-        if bead_groups[moltype]._nbeads > max_mols:
+        if len(bead_groups[moltype].positions) > max_mols:
             if max_mols > 50000:
                 LOGGER.warn(
                     'Calculating mean squared displacements for more than 50k molecules.'

nomad_schema_plugin_simulation_workflow-1.0.6/nomad_schema_plugin_simulation_workflow.egg-info/requires.txt

@@ -1,5 +0,0 @@
-nomad-lab>=1.3.6.dev1
-nomad-schema-plugin-run>=1.0.1
-mdanalysis<3.0.0,>=2.7.0
-scipy>=1.7.1
-networkx>=2.6.3