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PYGAMD: Python GPU-Accelerated Molecular Dynamics Software
Molecular dynamics is an essential tool in the scientific research on colloids, polymers, biomolecules, and etc. PYGAMD is a platform based on Python3 Numba where users can define their models and methods by themselves. The simulation models could be ranging from all-atom to coarse-grained scales.
Installation
Access codes on GitHub!
pygamd:
python3 setup.py install
Requirements:
Python3 including numba, numpy, cupy, and pybind11 packages
NVIDIA CUDA Toolkit = 11
Python = 3.9
Citation
Python = 3.9
Citation
To cite PYGAMD in your publications:
感谢吕中元课题组提供PYGAMD软件。
Thanks to Zhongyuan Lu group for providing PYGAMD software in our research work.
Documentation
Online manual could be read here: https://pygamd-v1.readthedocs.io/en/latest/. Tutorials written by jupyter notebook are given here: https://nbviewer.jupyter.org/github/youliangzhu/pygamd-v1/tree/main/tutorials/index.ipynb. More examples could be found here: https://github.com/youliangzhu/pygamd-v1/tree/main/examples.
Example: DPD simulation of diblock copolymer
(1) First step: generate configuration
import molgen
mol1=molgen.Molecule(10)#particle number
mol1.setParticleTypes("A,A,A,A,A,B,B,B,B,B")#type
mol1.setTopology("0-1,1-2,2-3,3-4,4-5,5-6,6-7,7-8,8-9")#topology
mol1.setBondLength(0.75)#bond length
mol1.setMass(1.0)#mass
gen=molgen.Generators(20,20,20) # box size in x, y, and z direction
gen.addMolecule(mol1,2400)#molecule, the number of molecules
gen.outPutMST("A5B5") #file name
(2) Second step: run simulation
import pygamd
mst = pygamd.snapshot.read("A5B5.mst")
app = pygamd.application.dynamics(info=mst, dt=0.04)
fn = pygamd.force.dpd(info=mst, rcut=1.0)
fn.setParams(type_i="A", type_j="A", alpha=25.0, sigma=3.0)
fn.setParams(type_i="B", type_j="B", alpha=25.0, sigma=3.0)
fn.setParams(type_i="A", type_j="B", alpha=40.0, sigma=3.0)
app.add(fn)
fb = pygamd.force.bond(info=mst, func='harmonic')
fb.setParams(bond_type = 'A-A', param=[4.0, 0.0])# param=[k, r0]
fb.setParams(bond_type = 'A-B', param=[4.0, 0.0])# param=[k, r0]
fb.setParams(bond_type = 'B-B', param=[4.0, 0.0])# param=[k, r0]
app.add(fb)
inn = pygamd.integration.gwvv(info=mst, group='all')
app.add(inn)
dm = pygamd.dump.mst(info=mst, group=['A', 'B'], file='p.mst', period=10000)
app.add(dm)
di = pygamd.dump.data(info=mst, group='all', file='data.log', period=100)
app.add(di)
app.run(500000)
Contributing
We welcome contributions to PYGAMD. Whether it is reporting a bug, starting a discussion by asking a question, or proposing/requesting a new feature, please go by creating a new issue here (https://github.com/youliangzhu/pygamd-v1/issues/) or writing an email to the author Dr. You-Liang Zhu (Email: ylzhu@pygamd.com) so that we can talk about it. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
