diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 96a5569..b79eb0a 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.9.9 +current_version = 0.9.10 commit = True tag = False diff --git a/CITATION.cff b/CITATION.cff index 7379d69..a10dede 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -19,4 +19,4 @@ url: 'https://atomrdf.pyscal.org' license: "MIT" repository-code: https://github.com/pyscal/atomRDF type: software -version: 0.9.9 +version: 0.9.10 diff --git a/atomrdf/network/patch.py b/atomrdf/network/patch.py index c2cf052..483b5de 100644 --- a/atomrdf/network/patch.py +++ b/atomrdf/network/patch.py @@ -25,6 +25,15 @@ def patch_terms(iri, rn): elif iri == "http://purls.helmholtz-metadaten.de/cmso/hasValue": rn = ["float", "double", "int", "str"] + elif iri == "http://purls.helmholtz-metadaten.de/cmso/hasRepetition_x": + rn = ["float", "double", "int"] + + elif iri == "http://purls.helmholtz-metadaten.de/cmso/hasRepetition_y": + rn = ["float", "double", "int"] + + elif iri == "http://purls.helmholtz-metadaten.de/cmso/hasRepetition_z": + rn = ["float", "double", "int"] + elif iri == "http://purls.helmholtz-metadaten.de/asmo/hasValue": rn = ["float", "double", "int", "str"] diff --git a/atomrdf/properties.py b/atomrdf/properties.py index c12de0d..0725538 100644 --- a/atomrdf/properties.py +++ b/atomrdf/properties.py @@ -234,6 +234,12 @@ def get_crystal_structure_name(system): return None return system.atoms._lattice +def get_repetitions(system): + if system._structure_dict is None: + return [None, None, None] + if "repetitions" in system._structure_dict.keys(): + return system._structure_dict["repetitions"] + return [None, None, None] def get_bravais_lattice(system): """ diff --git a/atomrdf/structure.py b/atomrdf/structure.py index dc89c69..d9ae5d0 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -23,10 +23,12 @@ from pyscal3.atoms import AttrSetter, Atoms import pyscal3.core as pc from pyscal3.core import structure_dict, element_dict +from pyscal3.formats.ase import convert_snap + import pyscal3.operations.input as inputmethods import pyscal3.operations.serialize as serialize -from pyscal3.formats.ase import convert_snap import pyscal3.operations.visualize as visualize +import pyscal3.operations.operations as operations import atomrdf.json_io as json_io import atomrdf.properties as prp @@ -102,6 +104,8 @@ def _make_crystal( return_structure_dict=True, primitive=primitive, ) + if 'repetitions' not in sdict.keys(): + sdict['repetitions'] = repetitions s = System(graph=graph, names=names) s.box = box @@ -169,6 +173,10 @@ def _make_general_lattice( element=element, return_structure_dict=True, ) + + if 'repetitions' not in sdict.keys(): + sdict['repetitions'] = repetitions + s = System(graph=graph, names=names) s.box = box s.atoms = atoms @@ -365,6 +373,7 @@ def _make_dislocation( 'DislocationCharacter': angle_deg, } + # here we dont add repetitions, since we cannot guarantee atom_dict = {"positions": positions, "types": types, "species": species} atom_obj = Atoms() atom_obj.from_dict(atom_dict) @@ -606,6 +615,10 @@ def _make_grain_boundary_inbuilt( atoms, box, sdict = gb.populate_grain_boundary( element, repetitions=repetitions, overlap=overlap ) + + if 'repetitions' not in sdict.keys(): + sdict['repetitions'] = repetitions + s = System(graph=graph, names=names) s.box = box s.atoms = atoms @@ -797,6 +810,16 @@ def __init__( mapdict['selection'] = update_wrapper(partial(self._plot_system, plot_style='selection'), self._plot_system) self.show._add_attribute(mapdict) + self.modify = AttrSetter() + mapdict = {} + mapdict["repeat"] = self.repeat + mapdict["delete"] = self.delete + mapdict["transform_to_cubic_cell"] = update_wrapper(partial(operations.extract_cubic_representation, self), operations.extract_cubic_representation) + mapdict["remap_to_box"] = update_wrapper(partial(operations.remap_to_box, self), operations.remap_to_box) + mapdict["remap_position_to_box"] = update_wrapper(partial(operations.remap_position_to_box, self), operations.remap_position_to_box) + mapdict["embed_in_cubic_box"] = update_wrapper(partial(operations.embed_in_cubic_box, self), operations.embed_in_cubic_box) + self.modify._add_attribute(mapdict) + self.schema = AttrSetter() mapdict = { "material": { @@ -818,6 +841,7 @@ def __init__( "length": partial(prp.get_simulation_cell_length, self), "vector": partial(prp.get_simulation_cell_vector, self), "angle": partial(prp.get_simulation_cell_angle, self), + "repetitions": partial(prp.get_repetitions, self), }, "atom_attribute": { "position": partial(prp.get_position, self), @@ -887,6 +911,31 @@ def duplicate(self, only_essential=False): return new_system + def repeat(self, repetitions): + """ + Repeat the system in each direction by the specified number of times. + + Parameters + ---------- + repetitions : tuple + The number of times to repeat the system in each direction. + + Returns + ------- + None + + Notes + ----- + The system is repeated in each direction by the specified number of times. + """ + new_system = self.duplicate() + new_system = operations.repeat(new_system, repetitions) + if new_system._structure_dict is None: + new_system._structure_dict = {} + new_system._structure_dict["repetitions"] = repetitions + new_system.to_graph() + return new_system + def delete(self, ids=None, indices=None, condition=None, selection=False, copy_structure=False): """ Delete atoms from the structure. @@ -1019,8 +1068,7 @@ def delete(self, ids=None, indices=None, condition=None, selection=False, copy_s sys.graph.add((sys.sample, PROV.wasGeneratedBy, activity)) return sys - - + def add_property_mappings(self, output_property, mapping_quantity=None): if self.graph is None: return @@ -1679,6 +1727,11 @@ def _add_simulation_cell(self): ), ) ) + + repetitions = self.schema.simulation_cell.repetitions() + self.graph.add((simulation_cell, CMSO.hasRepetition_x, Literal(repetitions[0], datatype=XSD.integer))) + self.graph.add((simulation_cell, CMSO.hasRepetition_y, Literal(repetitions[1], datatype=XSD.integer))) + self.graph.add((simulation_cell, CMSO.hasRepetition_z, Literal(repetitions[2], datatype=XSD.integer))) self.simulation_cell = simulation_cell def _add_simulation_cell_properties(self): diff --git a/examples/01_getting_started.ipynb b/examples/01_getting_started.ipynb index 2ae3289..6b9fee7 100644 --- a/examples/01_getting_started.ipynb +++ b/examples/01_getting_started.ipynb @@ -31,20 +31,7 @@ "metadata": { "tags": [] }, - "outputs": [ - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "e14fde86d50d405b855fda6dc6114c40", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "from atomrdf import KnowledgeGraph, System" ] @@ -113,7 +100,7 @@ }, { "cell_type": "code", - "execution_count": 4, + 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+ "\n", "cmso.SimulationCellAngle->cmso.Angle\n", - "\n", - "\n", - "subClassOf\n", - "\n", - "\n", - "\n", - "cmso.LatticeVector\n", - "\n", - "cmso.LatticeVector\n", - "\n", - "\n", - "\n", - "cmso.LatticeVector->cmso.Vector\n", - "\n", - "\n", - "subClassOf\n", + "\n", + "\n", + "subClassOf\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 7, @@ -3322,22 +4888,6 @@ "id": "7613387a", "metadata": {}, "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "a1\n", - "a1 True\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/home/srmnitc/miniconda3/envs/workflow-rdf/lib/python3.11/site-packages/atomrdf/graph.py:1043: UserWarning: The results\n", - " warnings.warn('The results')\n" - ] - }, { "data": { "text/html": [ @@ -3367,7 +4917,7 @@ " \n", "
\n", " 0\n", - " sample:6a11acf5-e81f-47ff-85f3-fa29f6ed17e2\n", + " sample:c9036dea-a6f0-41c0-8882-7d0069efdf53\n", " Pm-3m\n", " 4\n", "
\n", @@ -3377,7 +4927,7 @@ ], "text/plain": [ " AtomicScaleSample hasSpaceGroupSymbolvalue \\\n", - "0 sample:6a11acf5-e81f-47ff-85f3-fa29f6ed17e2 Pm-3m \n", + "0 sample:c9036dea-a6f0-41c0-8882-7d0069efdf53 Pm-3m \n", "\n", " hasNumberOfAtomsvalue \n", "0 4 " @@ -3402,7 +4952,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 15, "id": "08f1d892-64a8-40ce-af52-657ef4f59baf", "metadata": {}, "outputs": [ @@ -3434,7 +4984,7 @@ " \n", "
\n", " 0\n", - " sample:d94ae612-c21c-4029-8637-ec449ad78bd8\n", + " sample:59baf144-09ed-453b-af1c-d8028868e5d7\n", " bcc\n", "
\n", " \n", @@ -3443,10 +4993,10 @@ ], "text/plain": [ " AtomicScaleSample hasAltNamevalue\n", - "0 sample:d94ae612-c21c-4029-8637-ec449ad78bd8 bcc" + "0 sample:59baf144-09ed-453b-af1c-d8028868e5d7 bcc" ] }, - "execution_count": 18, + "execution_count": 15, "metadata": {}, "output_type": "execute_result" } @@ -3467,7 +5017,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 16, "id": "efde861c-b9dd-4b97-861b-a330bbd95de0", "metadata": {}, "outputs": [], @@ -3485,7 +5035,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 17, "id": "0cb6b043-abb3-41ca-bee7-fb3bf1e7e615", "metadata": { "tags": [] @@ -3497,7 +5047,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 18, "id": "ae884716-a31b-4170-b4d4-9cf8309a6d74", "metadata": { "tags": [] @@ -3507,16 +5057,16 @@ "name": "stdout", "output_type": "stream", "text": [ - "bcc.data (written by ASE) \n", + "(written by ASE)\n", + "\n", + "2 atoms\n", + "1 atom types\n", "\n", - "2 \t atoms \n", - "1 atom types\n", "0.0 2.8700000000000001 xlo xhi\n", "0.0 2.8700000000000001 ylo yhi\n", "0.0 2.8700000000000001 zlo zhi\n", "\n", - "\n", - "Atoms \n", + "Atoms # atomic\n", "\n", " 1 1 0 0 \n", " 0\n", @@ -3539,7 +5089,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 19, "id": "7ba5d551-f85b-4c33-be37-b997feffd7d7", "metadata": { "tags": [] @@ -3551,23 +5101,12 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 20, "id": "f4a90cbe-cf6a-4285-a0d2-b7525726c6dc", "metadata": { "tags": [] }, - "outputs": [ - { - "data": { - "text/plain": [ - "Atoms(symbols='Fe2', pbc=True, cell=[2.87, 2.87, 2.87])" - ] - }, - "execution_count": 23, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "aseobj" ] diff --git a/setup.py b/setup.py index e47349d..ff182b1 100644 --- a/setup.py +++ b/setup.py @@ -6,7 +6,7 @@ setup( name='atomrdf', - version='0.9.9', + version='0.9.10', author='Abril Azocar Guzman, Sarath Menon', author_email='sarath.menon@pyscal.org', description='Ontology based structural manipulation and quering',