From 9e124822be14fb6d1a26a0ef7379000bbf037e51 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Wed, 17 Apr 2024 09:17:42 +0200 Subject: [PATCH 1/5] add warning for structure read in --- atomrdf/structure.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/atomrdf/structure.py b/atomrdf/structure.py index e0015d3..5bdbed7 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -11,6 +11,7 @@ import json import shutil import tarfile +import warnings import pyscal3.structure_creator as pcs from pyscal3.grain_boundary import GrainBoundary @@ -149,7 +150,7 @@ def _read_structure(filename, datadict['positions'] = basis_positions s = System(filename, format=format, species=species, - graph=graph, names=names) + graph=graph, names=names, warn_read_in=False) s.lattice_properties = datadict s.to_graph() return s @@ -191,8 +192,12 @@ def __init__(self, filename = None, species = None, source=None, graph=None, - names=False): + names=False, + warn_read_in=True): + if (filename is not None) and warn_read_in: + warnings.warn('To provide additional information, use the System.read.file method') + super().__init__(filename = filename, format = format, compressed = compressed, From e1729a6d661a77e3ad2cdeca428bbfb58765987d Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Wed, 17 Apr 2024 09:31:52 +0200 Subject: [PATCH 2/5] update list checker --- atomrdf/graph.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/atomrdf/graph.py b/atomrdf/graph.py index f69a47e..1490b63 100644 --- a/atomrdf/graph.py +++ b/atomrdf/graph.py @@ -136,7 +136,13 @@ def add_structure(self, structure): def _is_valid(self, input_list): valid = False + flat_list = [] for x in input_list: + if isinstance(x,list): + flat_list.extend(x) + else: + flat_list.append(x) + for x in flat_list: if x is not None: valid = True break From 22356c9a799473d36b73d0cf5639e4ad1797e573 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Wed, 17 Apr 2024 09:44:29 +0200 Subject: [PATCH 3/5] add docstrings --- atomrdf/structure.py | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/atomrdf/structure.py b/atomrdf/structure.py index 5bdbed7..1a767b5 100644 --- a/atomrdf/structure.py +++ b/atomrdf/structure.py @@ -137,6 +137,45 @@ def _read_structure(filename, basis_box=None, basis_positions=None, ): + """ + Read in structure from file or ase object + + Parameters + ---------- + filename: string + name of file + + format: optional, string + format of the file + + graph: optional + if provided, the structure will be added to the graph + + names: bool, optional + if True, human readable names instead of random ids will be created. + + species: list, optional + if provided lammps types will be matched to species. For example, if types 1 and 2 exist + in the input file, and species = ['Li', 'Al'] is given, type 1 will be matched to 'Li' and + type 2 will be matched to 'Al' + + lattice: str, optional + currently supported lattices are {simple_cubic, bcc, fcc, hcp, dhcp, diamond, a15, l12, b2} + if provided, information such as the unit cell, basis positions, space groups, etc are automatically added + + lattice_constant: float, optional + specify the lattice constant of the system + + basis_box: 3x3 list, optional + specify the basis unit cell. Not required if lattice is provided + + basis_positions: nX3 list, optional + specify the relative positions of atoms in the unit cell. Not required if lattice is provided + + Returns + ------- + Structure + """ datadict = {} if lattice is not None: if lattice in structure_dict.keys(): From 91699936f1b58141cd0cc1f698e2f256007732bc Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Wed, 17 Apr 2024 09:47:36 +0200 Subject: [PATCH 4/5] add example --- examples/07_read_in.ipynb | 1295 +++++++++++++++++++++++++++++++++++++ examples/conf.dump | 11 + 2 files changed, 1306 insertions(+) create mode 100644 examples/07_read_in.ipynb create mode 100644 examples/conf.dump diff --git a/examples/07_read_in.ipynb b/examples/07_read_in.ipynb new file mode 100644 index 0000000..d821208 --- /dev/null +++ b/examples/07_read_in.ipynb @@ -0,0 +1,1295 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "d3ff083a-cdf1-468a-9b2b-8279abcd5966", + "metadata": {}, + "source": [ + "# Reading in structures" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "8bef733f-c0b5-4c92-88fa-6d12114172f9", + "metadata": {}, + "outputs": [], + "source": [ + "from atomrdf import System, KnowledgeGraph" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "50c53e9a-1029-49e6-9cb0-2b8171475c6a", + "metadata": {}, + "outputs": [], + "source": [ + "kg = KnowledgeGraph()" + ] + }, + { + "cell_type": "markdown", + "id": "58b32ff8-2255-4969-98a3-1ce683258aa5", + "metadata": {}, + "source": [ + "Read in a structure file, `System.read.ase` can also be used for ASE objects" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "0beed8c2-ede7-4b7b-b98a-d0d8b236565f", + "metadata": {}, + "outputs": [], + "source": [ + "struct = System.read.file('conf.dump', graph=kg)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "13b457c1-2051-451d-8d98-6ee436959cf1", + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellAngle\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellAngle\n", + "\n", + "\n", + "\n", + "0b3ecf7d-ba31-4ae0-8528-b96ef6eebecf\n", + "\n", + "90.0\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellAngle->0b3ecf7d-ba31-4ae0-8528-b96ef6eebecf\n", + "\n", + "\n", + "cmso.hasAngle_alpha\n", + "\n", + "\n", + "\n", + "64b798f7-8517-4d20-8695-8ea5f101560a\n", + "\n", + "90.0\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellAngle->64b798f7-8517-4d20-8695-8ea5f101560a\n", + "\n", + "\n", + "cmso.hasAngle_gamma\n", + "\n", + "\n", + "\n", + "7098dd9b-e885-4c24-89e4-833a1ee3cb14\n", + "\n", + "90.0\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellAngle->7098dd9b-e885-4c24-89e4-833a1ee3cb14\n", + "\n", + "\n", + "cmso.hasAngle_beta\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_2\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_2\n", + "\n", + "\n", + "\n", + "8d4ca55f-4a93-4969-8a3a-6fe3a7d88033\n", + "\n", + "0.0\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_2->8d4ca55f-4a93-4969-8a3a-6fe3a7d88033\n", + "\n", + "\n", + "cmso.hasComponent_x\n", + "\n", + "\n", + "\n", + "cea5101e-27dd-41e5-9080-2ec2f22f6796\n", + "\n", + "0.0\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_2->cea5101e-27dd-41e5-9080-2ec2f22f6796\n", + "\n", + "\n", + "cmso.hasComponent_z\n", + "\n", + "\n", + "\n", + "adbab075-ffe8-43c0-9534-3eee8f90c8a0\n", + "\n", + "2.87\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_2->adbab075-ffe8-43c0-9534-3eee8f90c8a0\n", + "\n", + "\n", + "cmso.hasComponent_y\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellLength\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellLength\n", + "\n", + "\n", + "\n", + "a275fc02-c0d9-447c-8b40-b31121f35e37\n", + "\n", + "2.87\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellLength->a275fc02-c0d9-447c-8b40-b31121f35e37\n", + "\n", + "\n", + "cmso.hasLength_z\n", + "\n", + "\n", + "\n", + "14a2c71c-53fb-493d-86c7-771ac7205d4c\n", + "\n", + "2.87\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellLength->14a2c71c-53fb-493d-86c7-771ac7205d4c\n", + "\n", + "\n", + "cmso.hasLength_x\n", + "\n", + "\n", + "\n", + "389d9dd9-ad70-4927-9669-f2800757270e\n", + "\n", + "2.87\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellLength->389d9dd9-ad70-4927-9669-f2800757270e\n", + "\n", + "\n", + "cmso.hasLength_y\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_1\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_1\n", + "\n", + "\n", + "\n", + "7885adbc-cbdb-4d95-a5dd-2b56d1733c01\n", + "\n", + "2.87\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_1->7885adbc-cbdb-4d95-a5dd-2b56d1733c01\n", + "\n", + "\n", + "cmso.hasComponent_x\n", + "\n", + "\n", + "\n", + "b65f5bac-c633-4828-a451-46b9e1abab52\n", + "\n", + "0.0\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_1->b65f5bac-c633-4828-a451-46b9e1abab52\n", + "\n", + "\n", + "cmso.hasComponent_z\n", + "\n", + "\n", + "\n", + "f405fbd6-982a-4804-8578-e7e49de4c30e\n", + "\n", + "0.0\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_1->f405fbd6-982a-4804-8578-e7e49de4c30e\n", + "\n", + "\n", + "cmso.hasComponent_y\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Species\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Species\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357->sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Species\n", + "\n", + "\n", + "cmso.hasAttribute\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCell\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCell\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357->sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCell\n", + "\n", + "\n", + "cmso.hasSimulationCell\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Material\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Material\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357->sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Material\n", + "\n", + "\n", + "cmso.hasMaterial\n", + "\n", + "\n", + "\n", + "0a7bebd1-050a-46d0-8608-87f70f927ea1\n", + "\n", + "2\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357->0a7bebd1-050a-46d0-8608-87f70f927ea1\n", + "\n", + "\n", + "cmso.hasNumberOfAtoms\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Position\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Position\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357->sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Position\n", + "\n", + "\n", + "cmso.hasAttribute\n", + "\n", + "\n", + "\n", + "b86241b0-167c-4642-8811-a7cf1e24933d\n", + "\n", + "B61Ddba3-9327-436A-88Eb-040Ff918E42B\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Species->b86241b0-167c-4642-8811-a7cf1e24933d\n", + "\n", + "\n", + "cmso.hasIdentifier\n", + "\n", + "\n", + "\n", + "afeb4912-7a84-47f5-8c60-d31d88d66714\n", + "\n", + "Species\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Species->afeb4912-7a84-47f5-8c60-d31d88d66714\n", + "\n", + "\n", + "cmso.hasName\n", + "\n", + "\n", + "\n", + "efbfe627-1ef3-4d71-a7a5-02127a585450\n", + "\n", + "Rdf_Structure_Store/A3D602E4-2C41-446C-85Db-9Aa4E75Cc357.Json\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Species->efbfe627-1ef3-4d71-a7a5-02127a585450\n", + "\n", + "\n", + "cmso.hasPath\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_3\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_3\n", + "\n", + "\n", + "\n", + "690aa9fe-37c2-484f-8000-f2f87a54762c\n", + "\n", + "0.0\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_3->690aa9fe-37c2-484f-8000-f2f87a54762c\n", + "\n", + "\n", + "cmso.hasComponent_y\n", + "\n", + "\n", + "\n", + "970a1358-50a8-4543-b184-6284c1ba0679\n", + "\n", + "2.87\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_3->970a1358-50a8-4543-b184-6284c1ba0679\n", + "\n", + "\n", + "cmso.hasComponent_z\n", + "\n", + "\n", + "\n", + "c015f8ce-f0e9-4015-ae64-42badd8ca339\n", + "\n", + "0.0\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_3->c015f8ce-f0e9-4015-ae64-42badd8ca339\n", + "\n", + "\n", + "cmso.hasComponent_x\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCell->sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellAngle\n", + "\n", + "\n", + "cmso.hasAngle\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCell->sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_2\n", + "\n", + "\n", + "cmso.hasVector\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCell->sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellLength\n", + "\n", + "\n", + "cmso.hasLength\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCell->sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_1\n", + "\n", + "\n", + "cmso.hasVector\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCell->sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCellVector_3\n", + "\n", + "\n", + "cmso.hasVector\n", + "\n", + "\n", + "\n", + "6ffcce78-7fcb-4592-82c6-567c4ff72872\n", + "\n", + "23.64\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_SimulationCell->6ffcce78-7fcb-4592-82c6-567c4ff72872\n", + "\n", + "\n", + "cmso.hasVolume\n", + "\n", + "\n", + "\n", + "2671977c-2b3e-4b3c-a601-35557d06df02\n", + "\n", + "E215E6C9-06Bf-4042-B17D-Deb2B2E73E90\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Position->2671977c-2b3e-4b3c-a601-35557d06df02\n", + "\n", + "\n", + "cmso.hasIdentifier\n", + "\n", + "\n", + "\n", + "8e2c2c45-5a98-4e43-bf96-6fd324a4867f\n", + "\n", + "Rdf_Structure_Store/A3D602E4-2C41-446C-85Db-9Aa4E75Cc357.Json\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Position->8e2c2c45-5a98-4e43-bf96-6fd324a4867f\n", + "\n", + "\n", + "cmso.hasPath\n", + "\n", + "\n", + "\n", + "fba96551-03b1-44c6-91b2-2d92453529a1\n", + "\n", + "Position\n", + "\n", + "\n", + "\n", + "sample_a3d602e4-2c41-446c-85db-9aa4e75cc357_Position->fba96551-03b1-44c6-91b2-2d92453529a1\n", + "\n", + "\n", + "cmso.hasName\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "kg.visualise(hide_types=True, layout='dot')" + ] + }, + { + "cell_type": "markdown", + "id": "0b8fdca8-e857-4cb5-97f0-106aeb139a27", + "metadata": {}, + "source": [ + "Providing extra information" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "5d6c808a-07e7-4eca-8a46-9e2965046269", + "metadata": {}, + "outputs": [], + "source": [ + "kg = KnowledgeGraph()" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "88c44dbf-da7e-411f-9147-6011130825d9", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "\u001b[0;31mSignature:\u001b[0m\n", + "\u001b[0mSystem\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\u001b[0m\n", + "\u001b[0;34m\u001b[0m \u001b[0mfilename\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", + "\u001b[0;34m\u001b[0m \u001b[0mformat\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'lammps-dump'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", + "\u001b[0;34m\u001b[0m \u001b[0mgraph\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", + "\u001b[0;34m\u001b[0m \u001b[0mnames\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", + "\u001b[0;34m\u001b[0m \u001b[0mspecies\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", + "\u001b[0;34m\u001b[0m \u001b[0mlattice\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", + "\u001b[0;34m\u001b[0m \u001b[0mlattice_constant\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", + "\u001b[0;34m\u001b[0m \u001b[0mbasis_box\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", + "\u001b[0;34m\u001b[0m \u001b[0mbasis_positions\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", + "\u001b[0;34m\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mDocstring:\u001b[0m\n", + "Read in structure from file or ase object\n", + "\n", + "Parameters\n", + "----------\n", + "filename: string\n", + " name of file\n", + "\n", + "format: optional, string\n", + " format of the file\n", + "\n", + "graph: optional\n", + " if provided, the structure will be added to the graph\n", + "\n", + "names: bool, optional\n", + " if True, human readable names instead of random ids will be created.\n", + "\n", + "species: list, optional\n", + " if provided lammps types will be matched to species. For example, if types 1 and 2 exist\n", + " in the input file, and species = ['Li', 'Al'] is given, type 1 will be matched to 'Li' and\n", + " type 2 will be matched to 'Al'\n", + "\n", + "lattice: str, optional\n", + " currently supported lattices are {simple_cubic, bcc, fcc, hcp, dhcp, diamond, a15, l12, b2}\n", + " if provided, information such as the unit cell, basis positions, space groups, etc are automatically added\n", + "\n", + "lattice_constant: float, optional\n", + " specify the lattice constant of the system\n", + "\n", + "basis_box: 3x3 list, optional\n", + " specify the basis unit cell. Not required if lattice is provided\n", + "\n", + "basis_positions: nX3 list, optional\n", + " specify the relative positions of atoms in the unit cell. Not required if lattice is provided\n", + "\n", + "Returns\n", + "-------\n", + "Structure\n", + "\u001b[0;31mFile:\u001b[0m ~/miniconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/atomrdf/structure.py\n", + "\u001b[0;31mType:\u001b[0m function" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "System.read.file?" + ] + }, + { + "cell_type": "markdown", + "id": "dbd6907a-3180-4cc8-9576-46ce4ca8959b", + "metadata": {}, + "source": [ + "The file is a bcc structure, with lattice constant of 2.861" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "5b9355f0-7066-4239-8570-7b6dd59cb985", + "metadata": {}, + "outputs": [], + "source": [ + "struct = System.read.file('conf.dump', graph=kg, lattice='bcc', lattice_constant=2.861)" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "8e106f28-2320-4b76-8c30-06c7317e4bcd", + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCell\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCell\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellLength\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellLength\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCell->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellLength\n", + "\n", + "\n", + "cmso.hasLength\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellAngle\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellAngle\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCell->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellAngle\n", + "\n", + "\n", + "cmso.hasAngle\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_2\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_2\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCell->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_2\n", + "\n", + "\n", + "cmso.hasVector\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_1\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_1\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCell->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_1\n", + "\n", + "\n", + "cmso.hasVector\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_3\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_3\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCell->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_3\n", + "\n", + "\n", + "cmso.hasVector\n", + "\n", + "\n", + "\n", + "d78eae62-ab6e-41c8-b640-0c9f6f408c17\n", + "\n", + "23.64\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCell->d78eae62-ab6e-41c8-b640-0c9f6f408c17\n", + "\n", + "\n", + "cmso.hasVolume\n", + "\n", + "\n", + "\n", + "2a82d5bb-f050-4cae-9718-8c86ce7c6cd1\n", + "\n", + "2.87\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellLength->2a82d5bb-f050-4cae-9718-8c86ce7c6cd1\n", + "\n", + "\n", + "cmso.hasLength_z\n", + "\n", + "\n", + "\n", + "4b0bc553-ec0e-437b-86e1-745ce47a90ba\n", + "\n", + "2.87\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellLength->4b0bc553-ec0e-437b-86e1-745ce47a90ba\n", + "\n", + "\n", + "cmso.hasLength_x\n", + "\n", + "\n", + "\n", + "ecf21316-b4db-45fb-a552-f3eb0ef69f42\n", + "\n", + "2.87\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellLength->ecf21316-b4db-45fb-a552-f3eb0ef69f42\n", + "\n", + "\n", + "cmso.hasLength_y\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_UnitCell\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_UnitCell\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_LatticeParameter\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_LatticeParameter\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_UnitCell->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_LatticeParameter\n", + "\n", + "\n", + "cmso.hasLatticeParameter\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_LatticeAngle\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_LatticeAngle\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_UnitCell->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_LatticeAngle\n", + "\n", + "\n", + "cmso.hasAngle\n", + "\n", + "\n", + "\n", + "wiki.Q851536\n", + "\n", + "wiki.Q851536\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_UnitCell->wiki.Q851536\n", + "\n", + "\n", + "cmso.hasBravaisLattice\n", + "\n", + "\n", + "\n", + "1870ab0e-7209-49de-8a93-9b51c0b49ffa\n", + "\n", + "2.861\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_LatticeParameter->1870ab0e-7209-49de-8a93-9b51c0b49ffa\n", + "\n", + "\n", + "cmso.hasLength_x\n", + "\n", + "\n", + "\n", + "3f16b76d-2ebb-4dea-9b52-120ac7138948\n", + "\n", + "2.861\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_LatticeParameter->3f16b76d-2ebb-4dea-9b52-120ac7138948\n", + "\n", + "\n", + "cmso.hasLength_z\n", + "\n", + "\n", + "\n", + "5af9919e-8c3e-4945-a105-30d6eab2d121\n", + "\n", + "2.861\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_LatticeParameter->5af9919e-8c3e-4945-a105-30d6eab2d121\n", + "\n", + "\n", + "cmso.hasLength_y\n", + "\n", + "\n", + "\n", + "ae76ff7e-f1a8-4fc0-a3d5-b7b228c2277b\n", + "\n", + "90.0\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellAngle->ae76ff7e-f1a8-4fc0-a3d5-b7b228c2277b\n", + "\n", + "\n", + "cmso.hasAngle_alpha\n", + "\n", + "\n", + "\n", + "54423a75-7e58-408b-9775-17c13ac19b02\n", + "\n", + "90.0\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellAngle->54423a75-7e58-408b-9775-17c13ac19b02\n", + "\n", + "\n", + "cmso.hasAngle_gamma\n", + "\n", + "\n", + "\n", + "bb69b509-2475-403f-8e9f-eb807823bbbc\n", + "\n", + "90.0\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellAngle->bb69b509-2475-403f-8e9f-eb807823bbbc\n", + "\n", + "\n", + "cmso.hasAngle_beta\n", + "\n", + "\n", + "\n", + "5554ebdc-ca4e-4f6c-961e-fdbac80f8506\n", + "\n", + "0.0\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_2->5554ebdc-ca4e-4f6c-961e-fdbac80f8506\n", + "\n", + "\n", + "cmso.hasComponent_z\n", + "\n", + "\n", + "\n", + "a266cb8f-48a5-43a2-9a62-e4ec248ca86f\n", + "\n", + "2.87\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_2->a266cb8f-48a5-43a2-9a62-e4ec248ca86f\n", + "\n", + "\n", + "cmso.hasComponent_y\n", + "\n", + "\n", + "\n", + "2f8ae35e-9662-442b-a960-6ee7f0fc4394\n", + "\n", + "0.0\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_2->2f8ae35e-9662-442b-a960-6ee7f0fc4394\n", + "\n", + "\n", + "cmso.hasComponent_x\n", + "\n", + "\n", + "\n", + "18805995-10ed-413c-8617-0f8dae4d6078\n", + "\n", + "0.0\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_1->18805995-10ed-413c-8617-0f8dae4d6078\n", + "\n", + "\n", + "cmso.hasComponent_y\n", + "\n", + "\n", + "\n", + "04adbe98-037f-408b-8d2d-be9c15286f06\n", + "\n", + "2.87\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_1->04adbe98-037f-408b-8d2d-be9c15286f06\n", + "\n", + "\n", + "cmso.hasComponent_x\n", + "\n", + "\n", + "\n", + "446cf7a8-a6ec-4433-bff7-0bfc9a1fa243\n", + "\n", + "0.0\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_1->446cf7a8-a6ec-4433-bff7-0bfc9a1fa243\n", + "\n", + "\n", + "cmso.hasComponent_z\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCell\n", + "\n", + "\n", + "cmso.hasSimulationCell\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Species\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Species\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Species\n", + "\n", + "\n", + "cmso.hasAttribute\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Position\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Position\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Position\n", + "\n", + "\n", + "cmso.hasAttribute\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Material\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Material\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Material\n", + "\n", + "\n", + "cmso.hasMaterial\n", + "\n", + "\n", + "\n", + "9a58cf4d-acb4-4cf6-bcc4-745e27417a48\n", + "\n", + "2\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6->9a58cf4d-acb4-4cf6-bcc4-745e27417a48\n", + "\n", + "\n", + "cmso.hasNumberOfAtoms\n", + "\n", + "\n", + "\n", + "bd042717-d141-4dcb-90be-0e694cf6f513\n", + "\n", + "84C6E983-9053-4F31-81A2-99206Ecd6B9A\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Species->bd042717-d141-4dcb-90be-0e694cf6f513\n", + "\n", + "\n", + "cmso.hasIdentifier\n", + "\n", + "\n", + "\n", + "262fbdcc-0cb8-4216-88cf-f443662af8b3\n", + "\n", + "Species\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Species->262fbdcc-0cb8-4216-88cf-f443662af8b3\n", + "\n", + "\n", + "cmso.hasName\n", + "\n", + "\n", + "\n", + "a847b81e-8e6e-4467-b9bf-f27c7aa19bb8\n", + "\n", + "Rdf_Structure_Store/018978Ce-Cd81-46Bc-B8A3-5Abd0B43Eeb6.Json\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Species->a847b81e-8e6e-4467-b9bf-f27c7aa19bb8\n", + "\n", + "\n", + "cmso.hasPath\n", + "\n", + "\n", + "\n", + "4debc369-6941-4a3e-9910-27d14c94b328\n", + "\n", + "Position\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Position->4debc369-6941-4a3e-9910-27d14c94b328\n", + "\n", + "\n", + "cmso.hasName\n", + "\n", + "\n", + "\n", + "7a79039c-9804-43de-98e7-b10c160c4380\n", + "\n", + "11E14A5A-Dca4-4651-92E6-Df0359149933\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Position->7a79039c-9804-43de-98e7-b10c160c4380\n", + "\n", + "\n", + "cmso.hasIdentifier\n", + "\n", + "\n", + "\n", + "2380b303-61ed-4a5c-a36a-d3fbd4785319\n", + "\n", + "Rdf_Structure_Store/018978Ce-Cd81-46Bc-B8A3-5Abd0B43Eeb6.Json\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Position->2380b303-61ed-4a5c-a36a-d3fbd4785319\n", + "\n", + "\n", + "cmso.hasPath\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SpaceGroup\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SpaceGroup\n", + "\n", + "\n", + "\n", + "641a9c02-5578-41b1-bf44-c3879116e6e8\n", + "\n", + "229\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SpaceGroup->641a9c02-5578-41b1-bf44-c3879116e6e8\n", + "\n", + "\n", + "cmso.hasSpaceGroupNumber\n", + "\n", + "\n", + "\n", + "18dfb1da-571a-48c6-a664-6cd11865cd87\n", + "\n", + "Im-3M\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SpaceGroup->18dfb1da-571a-48c6-a664-6cd11865cd87\n", + "\n", + "\n", + "cmso.hasSpaceGroupSymbol\n", + "\n", + "\n", + "\n", + "57c29e05-c0a3-4ac3-85c2-69e69f4a7b71\n", + "\n", + "0.0\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_3->57c29e05-c0a3-4ac3-85c2-69e69f4a7b71\n", + "\n", + "\n", + "cmso.hasComponent_x\n", + "\n", + "\n", + "\n", + "8ddac36a-5dbf-432f-aa1b-0d1b07a3cf33\n", + "\n", + "0.0\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_3->8ddac36a-5dbf-432f-aa1b-0d1b07a3cf33\n", + "\n", + "\n", + "cmso.hasComponent_y\n", + "\n", + "\n", + "\n", + "d987be97-3067-4cc0-838a-84eea8a4864a\n", + "\n", + "2.87\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SimulationCellVector_3->d987be97-3067-4cc0-838a-84eea8a4864a\n", + "\n", + "\n", + "cmso.hasComponent_z\n", + "\n", + "\n", + "\n", + "faeb5ec5-5779-4071-81a2-83443b6e48cc\n", + "\n", + "90.0\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_LatticeAngle->faeb5ec5-5779-4071-81a2-83443b6e48cc\n", + "\n", + "\n", + "cmso.hasAngle_gamma\n", + "\n", + "\n", + "\n", + "48ed2700-78b8-44ce-881b-9ba013a1dadc\n", + "\n", + "90.0\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_LatticeAngle->48ed2700-78b8-44ce-881b-9ba013a1dadc\n", + "\n", + "\n", + "cmso.hasAngle_beta\n", + "\n", + "\n", + "\n", + "50438cb7-b003-428a-9339-75843ea5c3ad\n", + "\n", + "90.0\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_LatticeAngle->50438cb7-b003-428a-9339-75843ea5c3ad\n", + "\n", + "\n", + "cmso.hasAngle_alpha\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_CrystalStructure\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_CrystalStructure\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_Material->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_CrystalStructure\n", + "\n", + "\n", + "cmso.hasStructure\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_CrystalStructure->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_UnitCell\n", + "\n", + "\n", + "cmso.hasUnitCell\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_CrystalStructure->sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_SpaceGroup\n", + "\n", + "\n", + "cmso.hasSpaceGroup\n", + "\n", + "\n", + "\n", + "c324f4ca-2f2d-424a-a869-773b4261f3bb\n", + "\n", + "Bcc\n", + "\n", + "\n", + "\n", + "sample_018978ce-cd81-46bc-b8a3-5abd0b43eeb6_CrystalStructure->c324f4ca-2f2d-424a-a869-773b4261f3bb\n", + "\n", + "\n", + "cmso.hasAltName\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "kg.visualise(hide_types=True, layout='dot')" + ] + }, + { + "cell_type": "markdown", + "id": "96c4a15b-0ee6-422b-8d40-b8900cf9b4d5", + "metadata": {}, + "source": [ + "Infomation such as space group symbols and numbers, lattice angles, and so on are automatically added" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.8" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/examples/conf.dump b/examples/conf.dump new file mode 100644 index 0000000..37ab323 --- /dev/null +++ b/examples/conf.dump @@ -0,0 +1,11 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS pp pp pp +0.0 2.87 +0.0 2.87 +0.0 2.87 +ITEM: ATOMS x y z type id +0.0 0.0 0.0 1 1 +1.435 1.435 1.435 1 2 From 271e4734b8005a17992b1637727dbb45a0c76419 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Wed, 17 Apr 2024 09:47:41 +0200 Subject: [PATCH 5/5] =?UTF-8?q?Bump=20version:=200.5.2=20=E2=86=92=200.5.3?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- CITATION.cff | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index f9b37e4..ed7ad00 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.5.2 +current_version = 0.5.3 commit = True tag = False diff --git a/CITATION.cff b/CITATION.cff index 63dba64..7af0537 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -20,4 +20,4 @@ url: 'https://atomrdf.pyscal.org' license: "MIT" repository-code: https://github.com/pyscal/atomRDF type: software -version: 0.5.2 +version: 0.5.3 diff --git a/setup.py b/setup.py index 612ef77..26e132e 100644 --- a/setup.py +++ b/setup.py @@ -6,7 +6,7 @@ setup( name='atomrdf', - version='0.5.2', + version='0.5.3', author='Abril Azocar Guzman, Sarath Menon', author_email='sarath.menon@pyscal.org', description='Ontology based structural manipulation and quering',