# gamda: GPU-Accelerated Molecular Dynamics Analysis
gamda, a python library which utilizes the CUDA-enable GPU to accelerate the analysis of molecular dynamics (MD)
# Dependency
1. cupy
cupy is the backend of the CUDA kernels for analysis
2. MDAnalysis
MDAnalysis is used to handle the reading of MD trajectories and the selection of atoms
# Installation
## from pypi
```
pip install gamda
```
## from gitee
```
git clone https://gitee.com/gao_hyp_xyj_admin/gamda.git
cd gamda
pip install .
```
# Unittest
```
git clone https://gitee.com/gao_hyp_xyj_admin/gamda.git
cd gamda
cd unittest
python -m unittest
```
# Usage
A simple exampe:
```
# Here, we create a xyz file as an example
with open("test.xyz", "w") as f:
f.write("3\n3\nO 1.11 2.22 3.33\nH 3.33 2.22 1.11\nH 2.22 2.22 2.22")
# Import the package
import gamda
import numpy as np
# Import the desired observable
from gamda.observable import PositionZ
# Import the disired analyzer
from gamda.analyzer import Histogrammer
# gamda.Universe is a subclass of MDAnalysis.Universe
u = gamda.Universe("test.xyz")
# Get your AtomGroup in host (CPU)
ag = u.select_atoms("element H")
# Get your AtomGroup in device (GPU)
dag = u.get_dag("atom", ag)
# Initialize your observable
z = PositionZ("z", dag, gamda.Argument("z", np.float32(0)))
# Initialize your analyzer and add it to the universe
zdf = Histogrammer("zdf", 0, 4, 4, z)
u.add_analyzer(zdf)
# Print the source code
print(u.source_code)
# Run
u.run()
# Free the memory
u.free()
del u
# Normalize the result and save
zdf.normalize()
zdf.save("test_zdf.txt")
```
# Reference
1. cupy
- https://github.com/cupy/cupy
2. MDAnalysis
- N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319–2327. doi:10.1002/jcc.21787
- R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 98-105, Austin, TX, 2016. SciPy. doi:10.25080/Majora-629e541a-00e
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"description": "# gamda: GPU-Accelerated Molecular Dynamics Analysis\r\n\r\ngamda, a python library which utilizes the CUDA-enable GPU to accelerate the analysis of molecular dynamics (MD)\r\n\r\n# Dependency\r\n\r\n1. cupy\r\n\r\ncupy is the backend of the CUDA kernels for analysis\r\n\r\n2. MDAnalysis\r\n\r\nMDAnalysis is used to handle the reading of MD trajectories and the selection of atoms\r\n\r\n# Installation\r\n\r\n## from pypi\r\n\r\n```\r\npip install gamda\r\n```\r\n\r\n## from gitee\r\n\r\n```\r\ngit clone https://gitee.com/gao_hyp_xyj_admin/gamda.git\r\ncd gamda\r\npip install .\r\n```\r\n\r\n# Unittest\r\n\r\n```\r\ngit clone https://gitee.com/gao_hyp_xyj_admin/gamda.git\r\ncd gamda\r\ncd unittest\r\npython -m unittest\r\n```\r\n\r\n# Usage\r\n\r\nA simple exampe:\r\n\r\n```\r\n# Here, we create a xyz file as an example\r\nwith open(\"test.xyz\", \"w\") as f:\r\n f.write(\"3\\n3\\nO 1.11 2.22 3.33\\nH 3.33 2.22 1.11\\nH 2.22 2.22 2.22\")\r\n\r\n# Import the package\r\nimport gamda\r\nimport numpy as np\r\n\r\n# Import the desired observable\r\nfrom gamda.observable import PositionZ\r\n\r\n# Import the disired analyzer\r\nfrom gamda.analyzer import Histogrammer\r\n\r\n# gamda.Universe is a subclass of MDAnalysis.Universe\r\nu = gamda.Universe(\"test.xyz\")\r\n\r\n# Get your AtomGroup in host (CPU)\r\nag = u.select_atoms(\"element H\")\r\n\r\n# Get your AtomGroup in device (GPU)\r\ndag = u.get_dag(\"atom\", ag)\r\n\r\n# Initialize your observable\r\nz = PositionZ(\"z\", dag, gamda.Argument(\"z\", np.float32(0)))\r\n\r\n# Initialize your analyzer and add it to the universe\r\nzdf = Histogrammer(\"zdf\", 0, 4, 4, z)\r\nu.add_analyzer(zdf)\r\n\r\n# Print the source code\r\nprint(u.source_code)\r\n\r\n# Run\r\nu.run()\r\n\r\n# Free the memory\r\nu.free()\r\ndel u\r\n\r\n# Normalize the result and save\r\nzdf.normalize()\r\nzdf.save(\"test_zdf.txt\")\r\n\r\n```\r\n\r\n# Reference\r\n\r\n1. cupy\r\n - https://github.com/cupy/cupy\r\n2. MDAnalysis\r\n - N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319\u20132327. doi:10.1002/jcc.21787\r\n - R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 98-105, Austin, TX, 2016. SciPy. doi:10.25080/Majora-629e541a-00e\r\n",
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