mdsea is a stand-alone Python molecular dynamics library equipped with a flexible simulation engine and multiple analysis tools, including integrated beautiful visualization in 1, 2, and 3 dimensions.
mdsea requires Python >= 3.6. The
minimal requirements for this project will be automatically
installed with setup.py.
To install mdsea you need to get the source and execute the setup.py
script
git clone https://github.com/TPVasconcelos/mdsea.git
cd mdsea
python setup.py installIn order to install the complete set of requirements and be able to make the most use of mdsea, run
pip install -r requirements.txtTo render 3D animation with Blender, you will need to download and install it on your machine first. If you want mdsea to render mp4 animation files for you, you will also need to install ffmpeg.
You can find the test scripts inside the /tests directory.
You should start by running
cd tests
python initsetup.pywhich will run a default simulation and store in in
./simfiles/_mdsea_testsimulation/*. You can then run tests for the
multiple visualization tools (/tests/vis_*.py) - See bellow how to run
the Blender tests! - The /tests/cleanup.py script will remove the
/simfiles/_mdsea_testsimulation directory.
Blender uses its own python interpreter, so you will need to install mdsea there as well. Find out where the python binary is stored and execute the following command. e.g. on macOS:
cd mdsea
/path/to/blender.app/Contents/Resources/2.XX/python/bin/python setup.py install --forceTo run the tests, execute
cd tests
/path/to/blender.app/Contents/MacOS/blender --python vis_blender.pyI'd also suggest that you add
alias blender=/path/to/blender.app/Contents/MacOS/blender
to .bash_profile and .profile.
echo "alias blender=/path/to/blender.app/Contents/MacOS/blender" >> ~/.profile
echo "alias blender=/path/to/blender.app/Contents/MacOS/blender" >> ~/.bash_profileIn
Blender’s documentation
they only state the alias in ~/.profile but this is only read by
login shells. On the other hand, ~/.bash_profile is read by
interactive shells (like the one linked to Terminal).
from mdsea.core import SysManager
from mdsea.helpers import setup_logging
from mdsea.potentials import Potential
from mdsea.simulator import ContinuousPotentialSolver
setup_logging(level="DEBUG")
# Instantiate system manager ---
sm = SysManager.new(
simid="_mdsea_docs_example",
ndim=2,
num_particles=6 ** 2,
steps=500,
vol_fraction=0.2,
radius_particle=0.5,
)
# Instantiate simulation ---
sim = ContinuousPotentialSolver(sm, pot=Potential.lennardjones(1, 1))
# Run the simulation ---
sim.run_simulation()
# Run 2D animation with matplotlib ---
from mdsea.vis.matplotlib import MLPAnimationScatter
anim = MLPAnimationScatter(sm, frame_step=6, colorspeed=True)
anim.anim()The output should look something like this (you can ignore the warning):
[INFO:mdsea.core] New simulation: {'id': '_mdsea_docs_example', 'path': 'simfiles/_mdsea_docs_example'}
[WARNING:mdsea.core] A ValueError ('Not a location (invalid object ID)') was catched while trying to update a dataset. However, we noticed that the datafile in question wasn't open. We'll try to fix this and retry...
[INFO:mdsea.simulator] ProgresBar (Simulator): {'step': '28/500', 'percentage': 6, 'ETA': '1s'}
[INFO:mdsea.simulator] ProgresBar (Simulator): {'step': '73/500', 'percentage': 15, 'ETA': '1s'}
[INFO:mdsea.simulator] ProgresBar (Simulator): {'step': '128/500', 'percentage': 26, 'ETA': '1s'}
...
[INFO:mdsea.simulator] ProgresBar (Simulator): {'step': '428/500', 'percentage': 86, 'ETA': '0s'}
[INFO:mdsea.simulator] ProgresBar (Simulator): {'step': '473/500', 'percentage': 95, 'ETA': '0s'}
[INFO:mdsea.simulator] ProgresBar (Simulator): {'status': 'finished', 'lifetime': '1.1s'}
[INFO:mdsea.vis.mpl] Plotting anim_loop...
1D Simulation:
2D Simulation:
3D Simulation with Blender's Cycles rendering engine:
