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aiida-lammps-0.8.0
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مشاهده بیشترتوضیحات
AiiDA plugin for LAMMPS
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | aiida-lammps-0.8.0 |
| نام | aiida-lammps |
| نسخه کتابخانه | 0.8.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Abel Carreras, Chris Sewell |
| ایمیل نویسنده | abelcarreras83@gmail.com |
| آدرس صفحه اصلی | https://github.com/aiidaplugins/aiida-lammps |
| آدرس اینترنتی | https://pypi.org/project/aiida-lammps/ |
| مجوز | MIT license |
[](https://github.com/aiidaplugins/aiida-lammps)
[](https://codecov.io/gh/aiidaplugins/aiida-lammps)
[](https://pypi.python.org/pypi/aiida-lammps/)
[](https://github.com/ambv/black)
# AiiDA LAMMPS plugin
This a LAMMPS plugin for [AiiDA](http://aiida-core.readthedocs.io/).
This plugin contains 4 code types:
- `lammps.forces`: Atomic single-point forces calculation
- `lammps.optimize`: Crystal structure optimization
- `lammps.md`: Molecular dynamics calculation
- `lammps.combinate`: DynaPhoPy calculation using LAMMPS MD trajectory (currently untested)
Note: `lammps.combinate` requires `aiida-phonopy` (https://github.com/abelcarreras/aiida-phonopy)
plugin to work, DynaPhoPy can be found in: https://github.com/abelcarreras/aiida-phonopy
- [AiiDA LAMMPS plugin](#aiida-lammps-plugin)
- [Installation](#installation)
- [Built-in Potential Support](#built-in-potential-support)
- [Examples](#examples)
- [Code Setup](#code-setup)
- [Structure Setup](#structure-setup)
- [Potential Setup](#potential-setup)
- [Force Calculation](#force-calculation)
- [Optimisation Calculation](#optimisation-calculation)
- [MD Calculation](#md-calculation)
- [Development](#development)
- [Coding Style Requirements](#coding-style-requirements)
- [Testing](#testing)
## Installation
To install from pypi:
```shell
pip install aiida-lammps
```
## Built-in Potential Support
- EAM
- Lennad Jones
- Tersoff
- ReaxFF
## Examples
More example calculations are found in the folder **/examples**,
and there are many test examples in **/aiida_lammps/tests/test_calculations**.
### Code Setup
```python
from aiida_lammps.tests.utils import (
get_or_create_local_computer, get_or_create_code)
from aiida_lammps.tests.utils import lammps_version
computer_local = get_or_create_local_computer('work_directory', 'localhost')
code_lammps_force = get_or_create_code('lammps.force', computer_local, 'lammps')
code_lammps_opt = get_or_create_code('lammps.optimize', computer_local, 'lammps')
code_lammps_md = get_or_create_code('lammps.md', computer_local, 'lammps')
meta_options = {
"resources": {
"num_machines": 1,
"num_mpiprocs_per_machine": 1}
}
```
### Structure Setup
```python
from aiida.plugins import DataFactory
import numpy as np
cell = [[3.1900000572, 0, 0],
[-1.5950000286, 2.762621076, 0],
[0.0, 0, 5.1890001297]]
positions = [(0.6666669, 0.3333334, 0.0000000),
(0.3333331, 0.6666663, 0.5000000),
(0.6666669, 0.3333334, 0.3750000),
(0.3333331, 0.6666663, 0.8750000)]
symbols = names = ['Ga', 'Ga', 'N', 'N']
structure = DataFactory('structure')(cell=cell)
for position, symbol, name in zip(positions, symbols, names):
position = np.dot(position, cell).tolist()
structure.append_atom(
position=position, symbols=symbol, name=name)
structure
```
```console
<StructureData: uuid: 96f9c02b-77c7-4889-9de2-dbda27bb03fa (unstored)>
```
### Potential Setup
```python
pair_style = 'tersoff'
potential_dict = {
'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': '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',
'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',
'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 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 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 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',
'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'}
potential = DataFactory("lammps.potential")(
structure=structure, type=pair_style, data=potential_dict
)
potential.attributes
```
```python
{'kind_elements': ['Ga', 'N'],
'potential_type': 'tersoff',
'atom_style': 'atomic',
'default_units': 'metal',
'potential_md5': 'b3b7d45ae7b92eba05ed99ffe69810d0',
'input_lines_md5': '3145644a408a6d464e80866b833115a2'}
```
### Force Calculation
```python
from aiida.engine import run_get_node
parameters = DataFactory('dict')(dict={
'lammps_version': lammps_version(),
'output_variables': ["temp", "etotal", "pe", "ke"],
'thermo_keywords': []
})
builder = code_lammps_force.get_builder()
builder.metadata.options = meta_options
builder.structure = structure
builder.potential = potential
builder.parameters = parameters
result, calc_node = run_get_node(builder)
```
```console
$ verdi process list -D desc -a -l 1
PK Created Process label Process State Process status
---- --------- ---------------- --------------- ----------------
2480 32s ago ForceCalculation Finished [0]
Total results: 1
Info: last time an entry changed state: 28s ago (at 02:02:36 on 2019-06-21)
$ verdi process show 2480
Property Value
------------- ------------------------------------
type CalcJobNode
pk 2480
uuid c754f044-b190-4505-b121-776b79d2d1c8
label
description
ctime 2019-06-21 02:02:32.894858+00:00
mtime 2019-06-21 02:02:33.297377+00:00
process state Finished
exit status 0
computer [2] localhost
Inputs PK Type
---------- ---- ------------------
code 1351 Code
parameters 2479 Dict
potential 2478 EmpiricalPotential
structure 2477 StructureData
Outputs PK Type
------------- ---- ----------
arrays 2483 ArrayData
remote_folder 2481 RemoteData
results 2484 Dict
retrieved 2482 FolderData
```
```python
calc_node.outputs.results.attributes
```
```python
{'parser_version': '0.4.0b3',
'parser_class': 'ForceParser',
'errors': [],
'warnings': '',
'distance_units': 'Angstroms',
'force_units': 'eV/Angstrom',
'energy_units': 'eV',
'energy': -18.1098859130104,
'final_variables': {'ke': 0.0,
'pe': -18.1098859130104,
'etotal': -18.1098859130104,
'temp': 0.0},
'units_style': 'metal'}
```
```python
calc_node.outputs.arrays.attributes
```
```python
{'array|forces': [1, 4, 3]}
```
### Optimisation Calculation
```python
from aiida.engine import run_get_node
parameters = DataFactory('dict')(dict={
'lammps_version': lammps_version(),
'output_variables': ["temp", "etotal", "pe", "ke"],
'thermo_keywords': [],
'units': 'metal',
'relax': {
'type': 'iso',
'pressure': 0.0,
'vmax': 0.001,
},
"minimize": {
'style': 'cg',
'energy_tolerance': 1.0e-25,
'force_tolerance': 1.0e-25,
'max_evaluations': 100000,
'max_iterations': 50000}
})
builder = code_lammps_opt.get_builder()
builder.metadata.options = meta_options
builder.structure = structure
builder.potential = potential
builder.parameters = parameters
result, calc_node = run_get_node(builder)
```
```console
$ verdi process list -D desc -a -l 1
PK Created Process label Process State Process status
---- --------- ------------------- --------------- ----------------
2486 1m ago OptimizeCalculation ⏹ Finished [0]
Total results: 1
Info: last time an entry changed state: 1m ago (at 02:09:54 on 2019-06-21)
$ verdi process show 2486
Property Value
------------- ------------------------------------
type CalcJobNode
pk 2486
uuid 5c64433d-6337-4352-a0a8-0acb4083a0c3
label
description
ctime 2019-06-21 02:09:50.872336+00:00
mtime 2019-06-21 02:09:51.128639+00:00
process state Finished
exit status 0
computer [2] localhost
Inputs PK Type
---------- ---- ------------------
code 1344 Code
parameters 2485 Dict
potential 2478 EmpiricalPotential
structure 2477 StructureData
Outputs PK Type
------------- ---- -------------
arrays 2490 ArrayData
remote_folder 2487 RemoteData
results 2491 Dict
retrieved 2488 FolderData
structure 2489 StructureData
```
```python
calc_node.outputs.results.attributes
```
```python
{'parser_version': '0.4.0b3',
'parser_class': 'OptimizeParser',
'errors': [],
'warnings': '',
'stress_units': 'bars',
'distance_units': 'Angstroms',
'force_units': 'eV/Angstrom',
'energy_units': 'eV',
'energy': -18.1108516231423,
'final_variables': {'ke': 0.0,
'pe': -18.1108516231423,
'etotal': -18.1108516231423,
'temp': 0.0},
'units_style': 'metal'}
```
```python
calc_node.outputs.arrays.attributes
```
```python
{'array|positions': [56, 4, 3],
'array|stress': [3, 3],
'array|forces': [56, 4, 3]}
```
### MD Calculation
```python
from aiida.engine import submit
parameters = DataFactory('dict')(dict={
'lammps_version': lammps_version(),
'output_variables': ["temp", "etotal", "pe", "ke"],
'thermo_keywords': [],
'units': 'metal',
'timestep': 0.001,
'integration': {
'style': 'nvt',
'constraints': {
'temp': [300, 300, 0.5]
}
},
"neighbor": [0.3, "bin"],
"neigh_modify": {"every": 1, "delay": 0, "check": False},
'equilibrium_steps': 100,
'total_steps': 1000,
'dump_rate': 10,
'restart': 100
})
builder = code_lammps_md.get_builder()
builder.metadata.options = meta_options
builder.structure = structure
builder.potential = potential
builder.parameters = parameters
result, calc_node = run_get_node(builder)
```
```console
$ verdi process list -D desc -a -l 1
PK Created Process label Process State Process status
---- --------- --------------- --------------- ----------------
2493 12s ago MdCalculation ⏹ Finished [0]
Total results: 1
Info: last time an entry changed state: 4s ago (at 02:15:02 on 2019-06-21)
$ verdi process show 2493
Property Value
------------- ------------------------------------
type CalcJobNode
pk 2493
uuid 351b4721-10ff-406c-8f1c-951317091524
label
description
ctime 2019-06-21 02:14:54.986384+00:00
mtime 2019-06-21 02:14:55.282272+00:00
process state Finished
exit status 0
computer [2] localhost
Inputs PK Type
---------- ---- ------------------
code 1540 Code
parameters 2492 Dict
potential 2478 EmpiricalPotential
structure 2477 StructureData
Outputs PK Type
--------------- ---- --------------
remote_folder 2494 RemoteData
results 2496 Dict
retrieved 2495 FolderData
system_data 2498 ArrayData
trajectory_data 2497 TrajectoryData
```
```python
calc_node.outputs.results.attributes
```
```python
{'parser_version': '0.4.0b3',
'parser_class': 'MdParser',
'errors': [],
'warnings': '',
'time_units': 'picoseconds',
'distance_units': 'Angstroms',
'energy': -17.8464193488116,
'units_style': 'metal'}
```
```python
calc_node.outputs.system_data.attributes
```
```python
{'units_style': 'metal',
'array|step': [100],
'array|ke': [100],
'array|pe': [100],
'array|etotal': [100],
'array|temp': [100]}
```
```python
calc_node.outputs.trajectory_data.attributes
```
```python
{'array|times': [101],
'array|cells': [101, 3, 3],
'array|steps': [101],
'array|positions': [101, 4, 3],
'symbols': ['Ga', 'Ga', 'N', 'N']}
```
## Development
### Coding Style Requirements
The code is formatted and linted using [pre-commit](https://pre-commit.com/), which runs in an isolated, virtual environment:
```shell
>> pip install pre-commit
>> pre-commit run --all
```
or to automate runs, triggered before each commit:
```shell
>> pre-commit install
```
### Testing
the test suite can be run in an isolated, virtual environment using `tox` (see `tox.ini` in the repo):
```shell
>> pip install tox
>> tox -e py37
```
or directly:
```shell
>> pip install -e .[testing]
>> reentry scan -r aiida
>> pytest -v
```
The tests require that both PostgreSQL and RabbitMQ are running.
If you wish to run an isolated RabbitMQ instance, see the `docker-compose.yml` file in the repo.
Some tests require that a `lammps` executable be present.
The easiest way to achieve this is to use Conda:
```shell
>> conda install lammps==2019.06.05
# this will install lmp_serial and lmp_mpi
```
You can specify a different executable name for LAMMPS with:
```shell
>> tox -e py37 -- --lammps-exec lmp_exec
```
To output the results of calcjob executions to a specific directory:
```shell
>> pytest --lammps-workdir "test_workdir"
```
نیازمندی
| مقدار | نام |
|---|---|
| <2.0.0,>=1.4.0 | aiida-core |
| <4.0.0,>=3.12.0 | ase |
| - | importlib-resources |
| - | jsonschema |
| - | numpy |
| - | packaging |
| - | python-dateutil |
| ~=2.6 | pre-commit |
| - | dynaphopy |
| >=17.4.0 | attrs |
| - | pgtest |
| - | pytest |
| - | pytest-cov |
| - | coverage |
| - | pytest-timeout |
| - | pytest-regressions |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl aiida-lammps-0.8.0:
pip install aiida-lammps-0.8.0.whl
نصب پکیج tar.gz aiida-lammps-0.8.0:
pip install aiida-lammps-0.8.0.tar.gz