nomad-schema-plugin-simulation-workflow 1.0.6__tar.gz → 1.0.8__tar.gz

{nomad_schema_plugin_simulation_workflow-1.0.6/nomad_schema_plugin_simulation_workflow.egg-info → nomad_schema_plugin_simulation_workflow-1.0.8}/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: 1.0.8
 Summary: Simulation workflow schema plugin for NOMAD.
 Author: The NOMAD Authors
 License: Apache-2.0
@@ -10,11 +10,12 @@ 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
 
-[![DOI](https://zenodo.org/badge/744481756.svg)](https://zenodo.org/doi/10.5281/zenodo.13844195)
+[![DOI](https://zenodo.org/badge/744481756.svg)](https://zenodo.org/badge/latestdoi/744481756)
 
 This is a collection of schemas for various types of simulation workflows.
 

{nomad_schema_plugin_simulation_workflow-1.0.6 → nomad_schema_plugin_simulation_workflow-1.0.8}/README.md

@@ -1,4 +1,4 @@
-[![DOI](https://zenodo.org/badge/744481756.svg)](https://zenodo.org/doi/10.5281/zenodo.13844195)
+[![DOI](https://zenodo.org/badge/744481756.svg)](https://zenodo.org/badge/latestdoi/744481756)
 
 This is a collection of schemas for various types of simulation workflows.
 

{nomad_schema_plugin_simulation_workflow-1.0.6 → nomad_schema_plugin_simulation_workflow-1.0.8/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: 1.0.8
 Summary: Simulation workflow schema plugin for NOMAD.
 Author: The NOMAD Authors
 License: Apache-2.0
@@ -10,11 +10,12 @@ 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
 
-[![DOI](https://zenodo.org/badge/744481756.svg)](https://zenodo.org/doi/10.5281/zenodo.13844195)
+[![DOI](https://zenodo.org/badge/744481756.svg)](https://zenodo.org/badge/latestdoi/744481756)
 
 This is a collection of schemas for various types of simulation workflows.
 

nomad_schema_plugin_simulation_workflow-1.0.8/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-1.0.8}/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-1.0.8}/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.'
@@ -1234,13 +1245,14 @@ class ThermostatParameters(ArchiveSection):
             'andersen',
             'berendsen',
             'brownian',
+            'dissipative_particle_dynamics',
             'langevin_goga',
+            'langevin_leap_frog',
             'langevin_schneider',
             'nose_hoover',
             'velocity_rescaling',
             'velocity_rescaling_langevin',
             'velocity_rescaling_woodcock',
-            'langevin_leap_frog',
         ),
         shape=[],
         description="""
@@ -1264,10 +1276,16 @@ class ThermostatParameters(ArchiveSection):
 
         | `"brownian"`           | Brownian Dynamics |
 
+        | `"dissipative_particle_dynamics"` | R.D. Groot and P.B. Warren
+        [J. Chem. Phys. **107**(11), 4423-4435 (1997)](https://doi.org/10.1063/1.474784) |
+
         | `"langevin_goga"`           | N. Goga, A. J. Rzepiela, A. H. de Vries,
         S. J. Marrink, and H. J. C. Berendsen, [J. Chem. Theory Comput. **8**, 3637 (2012)]
         (https://doi.org/10.1021/ct3000876) |
 
+        | `"langevin_leap_frog"` | J.A. Izaguirre, C.R. Sweet, and V.S. Pande
+        [Pac Symp Biocomput. **15**, 240-251 (2010)](https://doi.org/10.1142/9789814295291_0026) |
+
         | `"langevin_schneider"`           | T. Schneider and E. Stoll,
         [Phys. Rev. B **17**, 1302](https://doi.org/10.1103/PhysRevB.17.1302) |
 
@@ -1283,9 +1301,6 @@ class ThermostatParameters(ArchiveSection):
 
         | `"velocity_rescaling_woodcock"` | L. V. Woodcock,
         [Chem. Phys. Lett. **10**, 257 (1971)](https://doi.org/10.1016/0009-2614(71)80281-6) |
-
-        | `"langevin_leap_frog"` | J.A. Izaguirre, C.R. Sweet, and V.S. Pande
-        [Pac Symp Biocomput. **15**, 240-251 (2010)](https://doi.org/10.1142/9789814295291_0026) |
         """,
     )
 

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