https://github.com/deepmodeling/openlam
https://github.com/deepmodeling/openlam
Last synced: 5 months ago
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- Host: GitHub
- URL: https://github.com/deepmodeling/openlam
- Owner: deepmodeling
- License: lgpl-2.1
- Created: 2024-04-22T06:31:11.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-11-08T08:31:42.000Z (8 months ago)
- Last Synced: 2024-11-08T09:30:20.789Z (8 months ago)
- Language: Python
- Size: 55.7 KB
- Stars: 14
- Watchers: 9
- Forks: 5
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# A crystal structure optimization tool built on top of ASE
## Installation
After cloning this project, install `lam-crystal-philately` with common dependencies (including requirements for workflows) by
```
pip install .
```
To install additional dependencies for DP
```
pip install ".[dp]"
```
or mace
```
pip install ".[mace]"
```
Download the latest DP model for structure optimization by
```
wget https://bohrium-api.dp.tech/ds-dl/lam-crystal-model-01oe-v4.zip
unzip lam-crystal-model-01oe-v4.zip
```
## Structure Optimization
### Python API
```
from pathlib import Path
from lam_optimize.main import relax_run
from lam_optimize.relaxer import Relaxer
cif_folder_path = Path("/cifs")
relaxer = Relaxer("mace") # using default mace model
# relaxer = Relaxer(Path("dp.pth")) # using DP model
res_df = relax_run(
cif_folder_path,
relaxer
)
```
You should see something similar to this:
The resulting dataframe should contain the following columns:
To get the optimized structure (if converged), do the following:
```
from pymatgen.core import Structure
Structure.from_dict(df['final_structure'][0])
```
### Commandline tool
To optimize structures using DP model
```
lam-opt relax -i examples/data -m
```
or using mace
```
lam-opt relax -i examples/data -t mace
```
To submit a workflow for optimizing structures on parallel
```
lam-opt submit examples/wf.json -i part0 part1 -m
```
where the arguments after `-i` should be a list of directories containing cifs.
## Single Point Evaluation
```
from lam_optimize.main import single_point
single_point(Path(fpth), relaxer)
```
This returns the potential energy and forces for a given `.cif` structure.
# Query crystal structures from OpenLAM Database
Set environmental variable `BOHRIUM_ACCESS_KEY` which is generated from https://bohrium.dp.tech/settings/user
```
export BOHRIUM_ACCESS_KEY=xxx
```
Query crystal structures from OpenLAM Database using Python API (The method `query_by_page` is deprecated! Use `query_by_offset` instead.)
```python
from lam_optimize import CrystalStructure
data = CrystalStructure.query_by_offset()
```
The method `query_by_offset` accept following arguments as query conditions
```python
formula: Optional[str] = None
min_energy: Optional[float] = None
max_energy: Optional[float] = None
min_submission_time: Optional[datetime.datetime] = None
max_submission_time: Optional[datetime.datetime] = None
offset: int = 0
limit: int = 10
```
The structure of the returned data is like
```
{'nextStartId': 18, 'items': [, , , , , , , , , ]}
```
Except for `nextStartId` (used as `offset` in the next query), `items` is a list of `CrystalStructure` objects
```python
class CrystalStructure:
formula: str
structure: pymatgen.core.Structure
energy: float
submission_time: datetime.datetime
```
The method `query` merging paged results is also provided
```python
structures = CrystalStructure.query(formula="Sr2YSbO6")
```
which returns a list of `CrystalStructure` objects.
NOTE: Calling non-paging method without query condition will be extremely slow.
# Query hull from OpenLAM Database
Set environmental variable `BOHRIUM_ACCESS_KEY` which is generated from https://bohrium.dp.tech/settings/user
```
export BOHRIUM_ACCESS_KEY=xxx
```
Query hull by composition from OpenLAM Database using Python API
```python
from lam_optimize.utils import query_hull_by_composition
hull = query_hull_by_composition(["Ac", "Ag", "Bi", "As", "Rh", "Cl", "O"])
```
You can calculate energy above hull using the hull
```python
from lam_optimize.utils import get_e_above_hull
ehull = get_e_above_hull(structure, hull, 0.123)
```