Energy landscape
================
[](https://pypi.python.org/pypi/atooms-landscape/)
[](https://pypi.python.org/pypi/atooms-landscape/)
[](https://en.wikipedia.org/wiki/GNU_General_Public_License)
[](https://mybinder.org/v2/git/https%3A%2F%2Fframagit.org%2Fatooms%2Flandscape/HEAD?labpath=docs%2Findex.ipynb)
[](https://framagit.org/atooms/landscape/badges/master/pipeline.svg)
[](https://framagit.org/atooms/landscape/-/commits/master)
Energy landscape analysis tools built with atooms.
Quick start
-----------
Find the minimum of the potential energy surface (PES) of a Lennard-Jones trimer
```python
from atooms.landscape import conjugate_gradient
from atooms.system import Particle, Cell, System
from atooms.models.f90 import Interaction
system = System()
system.particle = [Particle(species=1, position=[0., 0., 0.]),
Particle(species=1, position=[0.5, 1., -.1]),
Particle(species=1, position=[1.1, 0.1, 0.1])]
system.cell = Cell([10., 10., 10.])
system.interaction = Interaction('lennard_jones')
result = conjugate_gradient(system)
distance = sum(system.particle[0].distance(system.particle[1])**2)**0.5
assert abs(distance - 1.12246) < 1e-5
```
Features
--------
- Optimization methods to find **local minima** of the PES
- Steepest descent
- Conjugate gradients
- l-BFGS
- Fast inertial relaxation engine (FIRE)
- Optimization methods to find **stationary points** of the PES
- Eigenvector-following
- Square-force minimization
- Normal modes analysis
Documentation
-------------
Check out the [tutorial](https://atooms.frama.io/landscape/tutorial) for more examples and the [public API](https://atooms.frama.io/landscape/api/landscape) for full details.
Org-mode and jupyter notebooks are available under `docs/`. You can run the tutorial interactively on [Binder]( https://mybinder.org/v2/git/https%3A%2F%2Fframagit.org%2Fatooms%2Flandscape/HEAD?labpath=docs%2Findex.ipynb).
Installation
------------
From pypi
```
pip install atooms-landscape
```
You can clone the code repository and install from source
```
git clone https://framagit.org/atooms/landscape.git
cd landscape
make install
```
Contributing
------------
Contributions to the project are welcome. If you wish to contribute, check out [these guidelines](https://framagit.org/atooms/atooms/-/blob/master/CONTRIBUTING.md).
Authors
-------
Daniele Coslovich: https://www.units.it/daniele.coslovich/
Thanks go to Ginevra Lautizi for her contribution to code testing.
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"description": "Energy landscape\n================\n\n[](https://pypi.python.org/pypi/atooms-landscape/)\n[](https://pypi.python.org/pypi/atooms-landscape/)\n[](https://en.wikipedia.org/wiki/GNU_General_Public_License)\n[](https://mybinder.org/v2/git/https%3A%2F%2Fframagit.org%2Fatooms%2Flandscape/HEAD?labpath=docs%2Findex.ipynb)\n[](https://framagit.org/atooms/landscape/badges/master/pipeline.svg)\n[](https://framagit.org/atooms/landscape/-/commits/master)\n\nEnergy landscape analysis tools built with atooms.\n\nQuick start\n-----------\n\nFind the minimum of the potential energy surface (PES) of a Lennard-Jones trimer\n```python\nfrom atooms.landscape import conjugate_gradient\nfrom atooms.system import Particle, Cell, System\nfrom atooms.models.f90 import Interaction\n\nsystem = System()\nsystem.particle = [Particle(species=1, position=[0., 0., 0.]),\n Particle(species=1, position=[0.5, 1., -.1]),\n Particle(species=1, position=[1.1, 0.1, 0.1])]\nsystem.cell = Cell([10., 10., 10.])\nsystem.interaction = Interaction('lennard_jones')\nresult = conjugate_gradient(system)\ndistance = sum(system.particle[0].distance(system.particle[1])**2)**0.5\nassert abs(distance - 1.12246) < 1e-5\n```\n\nFeatures\n--------\n- Optimization methods to find **local minima** of the PES\n - Steepest descent\n - Conjugate gradients\n - l-BFGS\n - Fast inertial relaxation engine (FIRE)\n- Optimization methods to find **stationary points** of the PES\n - Eigenvector-following\n - Square-force minimization\n- Normal modes analysis\n\nDocumentation\n-------------\n\nCheck out the [tutorial](https://atooms.frama.io/landscape/tutorial) for more examples and the [public API](https://atooms.frama.io/landscape/api/landscape) for full details.\n\nOrg-mode and jupyter notebooks are available under `docs/`. You can run the tutorial interactively on [Binder]( https://mybinder.org/v2/git/https%3A%2F%2Fframagit.org%2Fatooms%2Flandscape/HEAD?labpath=docs%2Findex.ipynb).\n\nInstallation\n------------\nFrom pypi\n```\npip install atooms-landscape\n```\n\nYou can clone the code repository and install from source\n```\ngit clone https://framagit.org/atooms/landscape.git\ncd landscape\nmake install\n```\n\nContributing\n------------\nContributions to the project are welcome. If you wish to contribute, check out [these guidelines](https://framagit.org/atooms/atooms/-/blob/master/CONTRIBUTING.md).\n\nAuthors\n-------\nDaniele Coslovich: https://www.units.it/daniele.coslovich/\n\nThanks go to Ginevra Lautizi for her contribution to code testing.\n\n",
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