lammpsparser 0.0.6__tar.gz → 0.0.7__tar.gz

{lammpsparser-0.0.6 → lammpsparser-0.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lammpsparser
-Version: 0.0.6
+Version: 0.0.7
 Summary: Vector-oriented LAMMPS interface to rapidly iterate over series of atomistic structures or interatomic potentials.
 Project-URL: Homepage, https://github.com/pyiron/lammpsparser
 Project-URL: Documentation, https://github.com/pyiron/lammpsparser

{lammpsparser-0.0.6 → lammpsparser-0.0.7}/src/lammpsparser/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.0.6'
-__version_tuple__ = version_tuple = (0, 0, 6)
+__version__ = version = '0.0.7'
+__version_tuple__ = version_tuple = (0, 0, 7)
 
 __commit_id__ = commit_id = None

{lammpsparser-0.0.6 → lammpsparser-0.0.7}/src/lammpsparser/compatibility/file.py

@@ -33,6 +33,7 @@ def lammps_file_interface_function(
     write_restart_file: bool = False,
     read_restart_file: bool = False,
     restart_file: str = "restart.out",
+    dump_final_structure: bool = False,
 ):
     """
     A single function to execute a LAMMPS calculation based on the LAMMPS job implemented in pyiron
@@ -85,6 +86,8 @@ def lammps_file_interface_function(
         write_restart_file (bool): enable writing the LAMMPS restart file
         read_restart_file (bool): enable loading the LAMMPS restart file
         restart_file (str): file name of the LAMMPS restart file to copy
+        dump_final_structure (bool): in "md" mode, append a ``write_dump`` command after the ``run`` command to capture
+            the final structure in ``dump.out`` if last step is not a regular dump step. Disabled by default.
         executable_version (str): LAMMPS version to for the execution
         executable_path (str): path to the LAMMPS executable
         input_control_file (str|list|dict): Option to modify the LAMMPS input file directly
@@ -141,14 +144,21 @@ def lammps_file_interface_function(
         else:
             lmp_str_lst.append(line)
 
+    dump_fields = "id type xsu ysu zsu fx fy fz vx vy vz"
+    dump_format = '"%d %d %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g"'
+
     lmp_str_lst += potential_lst
     lmp_str_lst += ["variable dumptime equal {} ".format(calc_kwargs.get("n_print", 1))]
     lmp_str_lst += [
-        "dump 1 all custom ${dumptime} dump.out id type xsu ysu zsu fx fy fz vx vy vz",
-        'dump_modify 1 sort id format line "%d %d %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g"',
+        "dump 1 all custom ${dumptime} dump.out " + dump_fields,
+        "dump_modify 1 sort id format line " + dump_format,
     ]
 
     if calc_mode == "static":
+        if dump_final_structure:
+            raise ValueError(
+                "dump_final_structure is only applicable for molecular dynamics (md) calculations."
+            )
         lmp_str_constraint_lst = [
             k + " " + v
             for k, v in set_selective_dynamics(
@@ -183,7 +193,20 @@ def lammps_file_interface_function(
         if read_restart_file:
             lmp_str_lst += ["reset_timestep 0"]
         lmp_str_lst += ["run {} ".format(n_ionic_steps)]
+        last_step_is_regular_dump = n_ionic_steps % calc_kwargs.get("n_print", 1) == 0
+        if dump_final_structure and not last_step_is_regular_dump:
+            lmp_str_lst += [
+                "write_dump all custom dump.out "
+                + dump_fields
+                + " modify sort id format line "
+                + dump_format
+                + " append yes"
+            ]
     elif calc_mode == "minimize":
+        if dump_final_structure:
+            raise ValueError(
+                "dump_final_structure is only applicable for molecular dynamics (md) calculations."
+            )
         calc_kwargs["units"] = units
         lmp_str_constraint_lst = [
             k + " " + v

{lammpsparser-0.0.6 → lammpsparser-0.0.7}/src/lammpsparser/compatibility/structure.py

@@ -1,5 +1,5 @@
 from collections import OrderedDict
-from typing import Dict, Optional
+from typing import Dict, List, Optional, Union, cast
 
 import numpy as np
 from ase.atoms import Atoms
@@ -17,7 +17,7 @@ class LammpsStructureCompatibility(LammpsStructure):
         atom_type: str = "atomic",
     ):
         super().__init__(bond_dict=bond_dict, units=units, atom_type=atom_type)
-        self._molecule_ids: list[int] = []
+        self._molecule_ids: Optional[List[int]] = []
 
     @property
     def structure(self) -> Optional[Atoms]:
@@ -37,17 +37,28 @@ class LammpsStructureCompatibility(LammpsStructure):
             structure (ase.atoms.Atoms): The structure to serialise.
         """
         self._structure = structure
-        if self.atom_type == "full":
+        if self._atom_type == "full":
             input_str = self.structure_full()
-        elif self.atom_type == "bond":
+        elif self._atom_type == "bond":
             input_str = self.structure_bond()
-        elif self.atom_type == "charge":
+        elif self._atom_type == "charge":
             input_str = self.structure_charge()
-        else:  # self.atom_type == 'atomic'
+        else:  # self._atom_type == 'atomic'
             input_str = self.structure_atomic()
 
         self._string_input = input_str + self._get_velocities_input_string()
 
+    @property
+    def molecule_ids(self) -> Union[List[int], np.ndarray]:
+        """Per-atom molecule IDs; defaults to all atoms in a single molecule."""
+        if self._molecule_ids is None or len(self._molecule_ids) == 0:
+            return np.ones(len(cast(Atoms, self._structure)), dtype=int)
+        return self._molecule_ids
+
+    @molecule_ids.setter
+    def molecule_ids(self, molecule_ids: Optional[List[int]]):
+        self._molecule_ids = molecule_ids
+
     def structure_bond(self):
         """
         Serialise the structure for LAMMPS ``atom_style bond``.
@@ -120,7 +131,7 @@ class LammpsStructureCompatibility(LammpsStructure):
                 bond_type[i, j] = count
                 bond_type[j, i] = count
 
-        if self.structure.bonds is None:
+        if getattr(self.structure, "bonds", None) is None:
             if self.cutoff_radius is None:
                 bonds_lst = get_bonds(structure=self.structure, max_shells=1)
             else:
@@ -182,16 +193,22 @@ class LammpsStructureCompatibility(LammpsStructure):
         coords = self.rotate_positions(self._structure)
 
         # extract electric charges from potential file
-        q_dict = {
-            species_name: self.potential.get_charge(species_name)
-            for species_name in set(self.structure.get_chemical_symbols())
-        }
+        if self.potential is not None:
+            q_dict = {
+                species_name: self.potential.get_charge(species_name)
+                for species_name in set(self.structure.get_chemical_symbols())
+            }
+        else:
+            q_dict = {
+                species_name: 0.0
+                for species_name in set(self.structure.get_chemical_symbols())
+            }
 
         bonds_lst, angles_lst = [], []
         bond_type_lst, angle_type_lst = [], []
         # Using a cutoff distance to draw the bonds instead of the number of neighbors
         # Only if any bonds are defined
-        if len(self._bond_dict.keys()) > 0:
+        if self._bond_dict is not None and len(self._bond_dict.keys()) > 0:
             cutoff_list = list()
             for val in self._bond_dict.values():
                 cutoff_list.append(np.max(val["cutoff_list"]))
@@ -350,7 +367,6 @@ def get_bonds(
         tolerance=2,
         id_list=None,
         width_buffer=1.2,
-        allow_ragged=None,
         mode="ragged",
         norm_order=2,
     )