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Molecular Dynamics Example
--------------------------
We have 3 implementations of a simple molecular dynamics simulation
of an N body problem in Lennard Jones potential. The first implementation
is a simple :math:`O(N^2)` implementation that can be found in
:code:`md_simple.py`. The second implementation is using nearest neighbor
searching to reduce the complexity to :math:`O(N)` and can be
found in :code:`md_nnps.py`.
We also have two different implementations of nearest neighbor search
algorithms, one using a radix sort on GPU and numpy sort on CPU
and the other using a native counting sort implementation. The counting
sort version is about 30% faster. Both these implementations can be
found in :code:`nnps.py`.
This example has been discussed at length in
`this <http://procbuild.scipy.org/download/prabhuramachandran-compyle>`_
SciPy 2020 paper.
Following commands can be used to reproduce the performance results
shown in the paper.
+------------------+---------------------------------------------------------------+
| Figure 2 | `python performance_comparison.py -c omp_comp --nnps simple` |
+------------------+---------------------------------------------------------------+
| Figure 3 | `python performance_comparison.py -c gpu_comp --nnps simple` |
+------------------+---------------------------------------------------------------+
| Figure 4 & 5 | `python performance_comparison.py -c gpu_comp` |
+------------------+---------------------------------------------------------------+
| Figure 6 & 7 | `python performance_comparison.py -c comp_algo` |
+------------------+---------------------------------------------------------------+
| Figure 8 | `cd 3D && python performance_comparison.py --use-count-sort` |
+------------------+---------------------------------------------------------------+
To generate energy plots for HooMD and Compyle implementations, run the script
:code:`3D/compare_results.py`
Users can use the google colab notebook
`here <https://colab.research.google.com/drive/1SGRiArYXV1LEkZtUeg9j0qQ21MDqQR2U?usp=sharing>`_
to play around with the example.
|
