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        "author": "Abel Carreras",
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        "description": "[![Build Status](https://travis-ci.org/abelcarreras/aiida-lammps.svg?branch=master)](https://travis-ci.org/abelcarreras/aiida-lammps)\n\n# AiiDA LAMMPS plugin\n\nThis a LAMMPS plugin for [AiiDA](http://aiida-core.readthedocs.io/).\nThis plugin contains 4 code types:\n\n- `lammps.forces`: Atomic single-point forces calculation\n- `lammps.optimize`: Crystal structure optimization\n- `lammps.md`: Molecular dynamics calculation\n- `lammps.combinate`: DynaPhoPy calculation using LAMMPS MD trajectory (currently untested)\n\nNote: `lammps.combinate` requires `aiida-phonopy` (https://github.com/abelcarreras/aiida-phonopy)\nplugin to work, DynaPhoPy can be found in: https://github.com/abelcarreras/aiida-phonopy\n\n- [AiiDA LAMMPS plugin](#AiiDA-LAMMPS-plugin)\n  - [Built-in Potential Support](#Built-in-Potential-Support)\n  - [Examples](#Examples)\n    - [Code Setup](#Code-Setup)\n    - [Structure Setup](#Structure-Setup)\n    - [Potential Setup](#Potential-Setup)\n    - [Force Calculation](#Force-Calculation)\n    - [Optimisation Calculation](#Optimisation-Calculation)\n    - [MD Calculation](#MD-Calculation)\n\n## Built-in Potential Support\n\n- EAM\n- Lennad Jones\n- Tersoff\n- ReaxFF\n\n## Examples\n\nMore example calculations are found in the folder **/examples**,\nand there are many test examples in **/aiida_lammps/tests/test_calculations**.\n\n### Code Setup\n\n```python\nfrom aiida_lammps.tests.utils import (\n    get_or_create_local_computer, get_or_create_code)\nfrom aiida_lammps.tests.utils import lammps_version\n\ncomputer_local = get_or_create_local_computer('work_directory', 'localhost')\ncode_lammps_force = get_or_create_code('lammps.force', computer_local, 'lammps')\ncode_lammps_opt = get_or_create_code('lammps.optimize', computer_local, 'lammps')\ncode_lammps_md = get_or_create_code('lammps.md', computer_local, 'lammps')\n\nmeta_options = {\n    \"resources\": {\n        \"num_machines\": 1,\n        \"num_mpiprocs_per_machine\": 1}\n}\n```\n\n### Structure Setup\n\n```python\nfrom aiida.plugins import DataFactory\nimport numpy as np\n\ncell = [[3.1900000572, 0, 0],\n        [-1.5950000286, 2.762621076, 0],\n        [0.0, 0, 5.1890001297]]\n\npositions = [(0.6666669, 0.3333334, 0.0000000),\n             (0.3333331, 0.6666663, 0.5000000),\n             (0.6666669, 0.3333334, 0.3750000),\n             (0.3333331, 0.6666663, 0.8750000)]\n\nsymbols = names = ['Ga', 'Ga', 'N', 'N']\n\nstructure = DataFactory('structure')(cell=cell)\nfor position, symbol, name in zip(positions, symbols, names):\n    position = np.dot(position, cell).tolist()\n    structure.append_atom(\n        position=position, symbols=symbol, name=name)\n\nstructure\n```\n\n```console\n<StructureData: uuid: 96f9c02b-77c7-4889-9de2-dbda27bb03fa (unstored)>\n```\n\n### Potential Setup\n\n```python\npair_style = 'tersoff'\npotential_dict = {\n    'Ga Ga Ga': '1.0 0.007874 1.846 1.918000 0.75000 -0.301300 1.0 1.0 1.44970 410.132 2.87 0.15 1.60916 535.199',\n    'N  N  N': '1.0 0.766120 0.000 0.178493 0.20172 -0.045238 1.0 1.0 2.38426 423.769 2.20 0.20 3.55779 1044.77',\n    'Ga Ga N': '1.0 0.001632 0.000 65.20700 2.82100 -0.518000 1.0 0.0 0.00000 0.00000 2.90 0.20 0.00000 0.00000',\n    'Ga N  N': '1.0 0.001632 0.000 65.20700 2.82100 -0.518000 1.0 1.0 2.63906 3864.27 2.90 0.20 2.93516 6136.44',\n    'N  Ga Ga': '1.0 0.001632 0.000 65.20700 2.82100 -0.518000 1.0 1.0 2.63906 3864.27 2.90 0.20 2.93516 6136.44',\n    'N  Ga N ': '1.0 0.766120 0.000 0.178493 0.20172 -0.045238 1.0 0.0 0.00000 0.00000 2.20 0.20 0.00000 0.00000',\n    'N  N  Ga': '1.0 0.001632 0.000 65.20700 2.82100 -0.518000 1.0 0.0 0.00000 0.00000 2.90 0.20 0.00000 0.00000',\n    'Ga N  Ga': '1.0 0.007874 1.846 1.918000 0.75000 -0.301300 1.0 0.0 0.00000 0.00000 2.87 0.15 0.00000 0.00000'}\npotential = DataFactory(\"lammps.potential\")(\n    structure=structure, type=pair_style, data=potential_dict\n)\npotential.attributes\n```\n\n```python\n{'kind_elements': ['Ga', 'N'],\n 'potential_type': 'tersoff',\n 'atom_style': 'atomic',\n 'default_units': 'metal',\n 'potential_md5': 'b3b7d45ae7b92eba05ed99ffe69810d0',\n 'input_lines_md5': '3145644a408a6d464e80866b833115a2'}\n```\n\n### Force Calculation\n\n```python\nfrom aiida.engine import run_get_node\nparameters = DataFactory('dict')(dict={\n    'lammps_version': lammps_version(),\n    'output_variables': [\"temp\", \"etotal\", \"pe\", \"ke\"],\n    'thermo_keywords': []\n})\nbuilder = code_lammps_force.get_builder()\nbuilder.metadata.options = meta_options\nbuilder.structure = structure\nbuilder.potential = potential\nbuilder.parameters = parameters\nresult, calc_node = run_get_node(builder)\n```\n\n```console\n$ verdi process list -D desc -a -l 1\n  PK  Created    Process label     Process State    Process status\n----  ---------  ----------------  ---------------  ----------------\n2480  32s ago    ForceCalculation  Finished [0]\n\nTotal results: 1\n\nInfo: last time an entry changed state: 28s ago (at 02:02:36 on 2019-06-21)\n\n$ verdi process show 2480\nProperty       Value\n-------------  ------------------------------------\ntype           CalcJobNode\npk             2480\nuuid           c754f044-b190-4505-b121-776b79d2d1c8\nlabel\ndescription\nctime          2019-06-21 02:02:32.894858+00:00\nmtime          2019-06-21 02:02:33.297377+00:00\nprocess state  Finished\nexit status    0\ncomputer       [2] localhost\n\nInputs        PK  Type\n----------  ----  ------------------\ncode        1351  Code\nparameters  2479  Dict\npotential   2478  EmpiricalPotential\nstructure   2477  StructureData\n\nOutputs          PK  Type\n-------------  ----  ----------\narrays         2483  ArrayData\nremote_folder  2481  RemoteData\nresults        2484  Dict\nretrieved      2482  FolderData\n```\n\n```python\ncalc_node.outputs.results.attributes\n```\n\n```python\n{'parser_version': '0.4.0b3',\n 'parser_class': 'ForceParser',\n 'errors': [],\n 'warnings': '',\n 'distance_units': 'Angstroms',\n 'force_units': 'eV/Angstrom',\n 'energy_units': 'eV',\n 'energy': -18.1098859130104,\n 'final_variables': {'ke': 0.0,\n  'pe': -18.1098859130104,\n  'etotal': -18.1098859130104,\n  'temp': 0.0},\n 'units_style': 'metal'}\n```\n\n```python\ncalc_node.outputs.arrays.attributes\n```\n\n```python\n{'array|forces': [1, 4, 3]}\n```\n\n### Optimisation Calculation\n\n```python\nfrom aiida.engine import run_get_node\nparameters = DataFactory('dict')(dict={\n    'lammps_version': lammps_version(),\n    'output_variables': [\"temp\", \"etotal\", \"pe\", \"ke\"],\n    'thermo_keywords': [],\n    'units': 'metal',\n    'relax': {\n        'type': 'iso',\n        'pressure': 0.0,\n        'vmax': 0.001,\n    },\n    \"minimize\": {\n        'style': 'cg',\n        'energy_tolerance': 1.0e-25,\n        'force_tolerance': 1.0e-25,\n        'max_evaluations': 100000,\n        'max_iterations': 50000}\n})\nbuilder = code_lammps_opt.get_builder()\nbuilder.metadata.options = meta_options\nbuilder.structure = structure\nbuilder.potential = potential\nbuilder.parameters = parameters\nresult, calc_node = run_get_node(builder)\n```\n\n```console\n$ verdi process list -D desc -a -l 1\n  PK  Created    Process label        Process State    Process status\n----  ---------  -------------------  ---------------  ----------------\n2486  1m ago     OptimizeCalculation  \u23f9 Finished [0]\n\nTotal results: 1\n\nInfo: last time an entry changed state: 1m ago (at 02:09:54 on 2019-06-21)\n\n$ verdi process show 2486\nProperty       Value\n-------------  ------------------------------------\ntype           CalcJobNode\npk             2486\nuuid           5c64433d-6337-4352-a0a8-0acb4083a0c3\nlabel\ndescription\nctime          2019-06-21 02:09:50.872336+00:00\nmtime          2019-06-21 02:09:51.128639+00:00\nprocess state  Finished\nexit status    0\ncomputer       [2] localhost\n\nInputs        PK  Type\n----------  ----  ------------------\ncode        1344  Code\nparameters  2485  Dict\npotential   2478  EmpiricalPotential\nstructure   2477  StructureData\n\nOutputs          PK  Type\n-------------  ----  -------------\narrays         2490  ArrayData\nremote_folder  2487  RemoteData\nresults        2491  Dict\nretrieved      2488  FolderData\nstructure      2489  StructureData\n```\n\n```python\ncalc_node.outputs.results.attributes\n```\n\n```python\n{'parser_version': '0.4.0b3',\n 'parser_class': 'OptimizeParser',\n 'errors': [],\n 'warnings': '',\n 'stress_units': 'bars',\n 'distance_units': 'Angstroms',\n 'force_units': 'eV/Angstrom',\n 'energy_units': 'eV',\n 'energy': -18.1108516231423,\n 'final_variables': {'ke': 0.0,\n  'pe': -18.1108516231423,\n  'etotal': -18.1108516231423,\n  'temp': 0.0},\n 'units_style': 'metal'}\n```\n\n```python\ncalc_node.outputs.arrays.attributes\n```\n\n```python\n{'array|positions': [56, 4, 3],\n 'array|stress': [3, 3],\n 'array|forces': [56, 4, 3]}\n```\n\n### MD Calculation\n\n```python\nfrom aiida.engine import submit\nparameters = DataFactory('dict')(dict={\n    'lammps_version': lammps_version(),\n    'output_variables': [\"temp\", \"etotal\", \"pe\", \"ke\"],\n    'thermo_keywords': [],\n    'units': 'metal',\n    'timestep': 0.001,\n    'integration': {\n        'style': 'nvt',\n        'constraints': {\n            'temp': [300, 300, 0.5]\n        }\n    },\n    \"neighbor\": [0.3, \"bin\"],\n    \"neigh_modify\": {\"every\": 1, \"delay\": 0, \"check\": False},\n    'equilibrium_steps': 100,\n    'total_steps': 1000,\n    'dump_rate': 10,\n    'restart': 100\n})\nbuilder = code_lammps_md.get_builder()\nbuilder.metadata.options = meta_options\nbuilder.structure = structure\nbuilder.potential = potential\nbuilder.parameters = parameters\nresult, calc_node = run_get_node(builder)\n```\n\n```console\n$ verdi process list -D desc -a -l 1\n  PK  Created    Process label    Process State    Process status\n----  ---------  ---------------  ---------------  ----------------\n2493  12s ago    MdCalculation    \u23f9 Finished [0]\n\nTotal results: 1\n\nInfo: last time an entry changed state: 4s ago (at 02:15:02 on 2019-06-21)\n\n$ verdi process show 2493\nProperty       Value\n-------------  ------------------------------------\ntype           CalcJobNode\npk             2493\nuuid           351b4721-10ff-406c-8f1c-951317091524\nlabel\ndescription\nctime          2019-06-21 02:14:54.986384+00:00\nmtime          2019-06-21 02:14:55.282272+00:00\nprocess state  Finished\nexit status    0\ncomputer       [2] localhost\n\nInputs        PK  Type\n----------  ----  ------------------\ncode        1540  Code\nparameters  2492  Dict\npotential   2478  EmpiricalPotential\nstructure   2477  StructureData\n\nOutputs            PK  Type\n---------------  ----  --------------\nremote_folder    2494  RemoteData\nresults          2496  Dict\nretrieved        2495  FolderData\nsystem_data      2498  ArrayData\ntrajectory_data  2497  TrajectoryData\n```\n\n```python\ncalc_node.outputs.results.attributes\n```\n\n```python\n{'parser_version': '0.4.0b3',\n 'parser_class': 'MdParser',\n 'errors': [],\n 'warnings': '',\n 'time_units': 'picoseconds',\n 'distance_units': 'Angstroms',\n 'energy': -17.8464193488116,\n 'units_style': 'metal'}\n```\n\n```python\ncalc_node.outputs.system_data.attributes\n```\n\n```python\n{'units_style': 'metal',\n 'array|step': [100],\n 'array|ke': [100],\n 'array|pe': [100],\n 'array|etotal': [100],\n 'array|temp': [100]}\n```\n\n```python\ncalc_node.outputs.trajectory_data.attributes\n```\n\n```python\n{'array|times': [101],\n 'array|cells': [101, 3, 3],\n 'array|steps': [101],\n 'array|positions': [101, 4, 3],\n 'symbols': ['Ga', 'Ga', 'N', 'N']}\n```\n\n\n",
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