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This is a very basic NVE moleculer dynamics program that will be used for the course I teach in the spring.
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This program borrows heavily from David Keffer's "The Working Person's Guide to Molecular Dynamics Simulations", although I have written the program in a different language and also expanded/replaced certain parts of the program.
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The idea for the class is that students will start with this basic serial version of the code and then add parallel support with PThreads, OpenMP, MPI, CUDA, or whatever.
- bin/: binary built to this directory.
- images/: photo gallery of simulation snapshots.
- inc/: contains header files with function prototypes, struct definitions, etc.
- obj/: object files stored in this directory.
- src/: source files.
- Makefile: automated build script.
- simulate.sh: shell script with examples for running program.
To build simply type:
make
If this is your first time to build the program you should see:
$ make
gcc -Iinc -lm -Wall -c src/atoms.c -o obj/atoms.o
gcc -Iinc -lm -Wall -c src/cl_parse.c -o obj/cl_parse.o
gcc -Iinc -lm -Wall -c src/energy_force.c -o obj/energy_force.o
gcc -Iinc -lm -Wall -c src/initialization.c -o obj/initialization.o
gcc -Iinc -lm -Wall -c src/integrator.c -o obj/integrator.o
gcc -Iinc -lm -Wall -c src/mddriver.c -o obj/mddriver.o
gcc -Iinc -lm -Wall -c src/params.c -o obj/params.o
gcc -Iinc -lm -Wall -c src/print_traj.c -o obj/print_traj.o
gcc -Iinc -lm -Wall -c src/props.c -o obj/props.o
gcc -Iinc -lm -Wall -c src/timer.c -o obj/timer.o
gcc -lm obj/atoms.o obj/cl_parse.o obj/energy_force.o obj/initialization.o obj/integrator.o obj/mddriver.o obj/params.o obj/print_traj.o obj/props.o obj/timer.o -o bin/run_md
If you have not edited any files since last running make, then you should see:
$ make
make: `bin/run_md' is up to date.
Make automates the build process, so if you only edit a single source file, only that source file will be recompiled. If you want to blow away all the object files and the program binary, you can run:
$ make cleanall
while
$ make clean
will remove just the binary in bin/.
To run from the project root directory simply type:
bin/run_md
This will run the program with default parameters. To see a list of command-line options and a list of defaults, pass --help as a command-line argument:
$ bin/run_md --help
Usage: ./run_md [-N <n_particles>] [-ts <n_timesteps>] [-xyz <xyz_file_output_frequency>] [-o <thermo_output_frequency>]
Defaults:
n_particles: 100
n_timesteps: 10000
xyz_file_output_fequency: 100
thermo_output_frequency: 100
The project root directory also contains a Bash script for running a number of pre-determined simulations. To run with the default parameters simply type:
bash simulate.sh
Below is an example of the output from a simulation with the default parameters using GCC 4.4.7 with no optimization on a Intel Xeon E5620 @ 2.40GHz.
[frenchwr@vmps10 md]$ bash simulate.sh
running: bin/run_md -N 125
=======Command line arguments=======
N_atoms: 125
n_timesteps: 10000
xyz_file_output_frequency: 100
thermo_output_frequency: 100
====================================
box length: 2.419e+01 Angstrom
density: 8.832e-03 molecules/Ang^3
Beginning simulation....
Timestep KE PE TotE Temp Pressure
0 3.883e-01 -8.432e-01 -4.54901e-01 150.00 -7.240e-05
100 2.790e-01 -7.329e-01 -4.53904e-01 107.78 -7.789e-06
200 3.488e-01 -8.022e-01 -4.53412e-01 134.75 -1.379e-05
300 3.913e-01 -8.446e-01 -4.53270e-01 151.15 -1.782e-05
400 3.670e-01 -8.203e-01 -4.53274e-01 141.76 -3.988e-06
500 3.754e-01 -8.286e-01 -4.53236e-01 145.01 -7.795e-06
600 3.850e-01 -8.383e-01 -4.53259e-01 148.73 -8.743e-06
700 3.775e-01 -8.308e-01 -4.53237e-01 145.83 -1.073e-06
800 4.006e-01 -8.539e-01 -4.53247e-01 154.75 -5.536e-06
900 3.634e-01 -8.167e-01 -4.53250e-01 140.38 8.770e-06
1000 3.879e-01 -8.412e-01 -4.53294e-01 149.84 -2.372e-06
1100 3.943e-01 -8.476e-01 -4.53267e-01 152.33 -6.303e-06
1200 3.781e-01 -8.314e-01 -4.53226e-01 146.07 -2.062e-06
1300 3.886e-01 -8.419e-01 -4.53277e-01 150.13 -3.920e-06
1400 3.756e-01 -8.289e-01 -4.53264e-01 145.09 4.032e-06
1500 3.950e-01 -8.483e-01 -4.53284e-01 152.57 -7.619e-06
1600 3.804e-01 -8.336e-01 -4.53252e-01 146.93 -4.261e-06
1700 3.877e-01 -8.410e-01 -4.53306e-01 149.78 -7.130e-06
1800 3.795e-01 -8.329e-01 -4.53360e-01 146.61 6.970e-06
1900 4.003e-01 -8.536e-01 -4.53320e-01 154.63 -1.702e-06
2000 3.875e-01 -8.408e-01 -4.53274e-01 149.68 5.651e-06
2100 4.062e-01 -8.595e-01 -4.53301e-01 156.91 -3.320e-06
2200 3.882e-01 -8.415e-01 -4.53267e-01 149.97 4.631e-06
2300 3.997e-01 -8.530e-01 -4.53264e-01 154.42 -2.549e-06
2400 4.112e-01 -8.645e-01 -4.53298e-01 158.84 -7.109e-06
2500 4.067e-01 -8.600e-01 -4.53296e-01 157.12 -1.185e-06
2600 4.078e-01 -8.611e-01 -4.53295e-01 157.55 -2.100e-06
2700 4.009e-01 -8.542e-01 -4.53266e-01 154.87 -6.252e-07
2800 4.122e-01 -8.655e-01 -4.53313e-01 159.24 7.340e-07
2900 3.936e-01 -8.469e-01 -4.53310e-01 152.03 1.425e-06
3000 3.914e-01 -8.447e-01 -4.53338e-01 151.18 5.180e-06
3100 4.077e-01 -8.610e-01 -4.53313e-01 157.48 6.553e-07
3200 3.946e-01 -8.479e-01 -4.53281e-01 152.43 2.449e-06
3300 3.893e-01 -8.425e-01 -4.53243e-01 150.37 -4.636e-06
3400 4.093e-01 -8.625e-01 -4.53203e-01 158.12 -1.571e-05
3500 3.628e-01 -8.160e-01 -4.53259e-01 140.14 4.630e-06
3600 3.925e-01 -8.457e-01 -4.53248e-01 151.61 -7.838e-06
3700 3.749e-01 -8.282e-01 -4.53250e-01 144.82 -5.539e-06
3800 3.874e-01 -8.406e-01 -4.53239e-01 149.64 -2.888e-08
3900 4.067e-01 -8.599e-01 -4.53220e-01 157.09 -5.110e-06
4000 4.027e-01 -8.559e-01 -4.53243e-01 155.54 -4.423e-06
4100 3.806e-01 -8.338e-01 -4.53242e-01 147.01 6.911e-06
4200 3.929e-01 -8.461e-01 -4.53235e-01 151.77 -6.156e-06
4300 3.868e-01 -8.401e-01 -4.53255e-01 149.43 -5.675e-06
4400 3.915e-01 -8.447e-01 -4.53232e-01 151.23 -5.125e-06
4500 3.948e-01 -8.480e-01 -4.53245e-01 152.51 -2.586e-07
4600 3.795e-01 -8.327e-01 -4.53226e-01 146.60 2.143e-06
4700 3.847e-01 -8.379e-01 -4.53249e-01 148.60 -5.358e-06
4800 3.860e-01 -8.392e-01 -4.53235e-01 149.09 7.694e-07
4900 3.899e-01 -8.431e-01 -4.53258e-01 150.59 -3.229e-06
5000 3.829e-01 -8.362e-01 -4.53322e-01 147.92 8.065e-07
5100 3.987e-01 -8.520e-01 -4.53291e-01 154.00 -2.326e-06
5200 3.938e-01 -8.471e-01 -4.53247e-01 152.14 3.772e-06
5300 3.791e-01 -8.323e-01 -4.53232e-01 146.45 6.586e-06
5400 3.723e-01 -8.257e-01 -4.53305e-01 143.83 4.653e-06
5500 4.049e-01 -8.582e-01 -4.53289e-01 156.41 -4.113e-06
5600 3.983e-01 -8.515e-01 -4.53253e-01 153.84 -6.733e-06
5700 3.691e-01 -8.223e-01 -4.53198e-01 142.58 -2.884e-06
5800 3.875e-01 -8.407e-01 -4.53179e-01 149.68 -1.105e-05
5900 3.932e-01 -8.464e-01 -4.53210e-01 151.87 -1.305e-05
6000 3.713e-01 -8.246e-01 -4.53263e-01 143.43 -6.830e-07
6100 3.772e-01 -8.305e-01 -4.53275e-01 145.71 -2.825e-06
6200 3.830e-01 -8.362e-01 -4.53247e-01 147.94 -1.005e-05
6300 3.893e-01 -8.425e-01 -4.53222e-01 150.39 -1.361e-05
6400 3.716e-01 -8.249e-01 -4.53231e-01 143.56 -1.096e-05
6500 3.685e-01 -8.217e-01 -4.53238e-01 142.34 -1.192e-05
6600 3.746e-01 -8.278e-01 -4.53249e-01 144.69 -1.545e-05
6700 3.664e-01 -8.196e-01 -4.53227e-01 141.53 -1.215e-05
6800 3.573e-01 -8.105e-01 -4.53258e-01 138.00 -4.989e-06
6900 3.700e-01 -8.233e-01 -4.53256e-01 142.94 -9.059e-06
7000 3.713e-01 -8.246e-01 -4.53278e-01 143.43 -1.882e-06
7100 3.985e-01 -8.518e-01 -4.53257e-01 153.95 -7.574e-06
7200 3.984e-01 -8.517e-01 -4.53299e-01 153.91 -7.369e-06
7300 3.848e-01 -8.381e-01 -4.53301e-01 148.65 2.548e-06
7400 3.888e-01 -8.421e-01 -4.53328e-01 150.20 -3.761e-06
7500 3.859e-01 -8.392e-01 -4.53286e-01 149.06 -5.358e-06
7600 3.845e-01 -8.378e-01 -4.53288e-01 148.52 -5.018e-06
7700 3.688e-01 -8.222e-01 -4.53382e-01 142.47 4.063e-06
7800 3.971e-01 -8.504e-01 -4.53355e-01 153.38 -1.063e-05
7900 3.769e-01 -8.302e-01 -4.53262e-01 145.61 -5.815e-06
8000 3.921e-01 -8.454e-01 -4.53275e-01 151.48 -9.699e-06
8100 4.077e-01 -8.609e-01 -4.53248e-01 157.48 -9.742e-06
8200 3.975e-01 -8.508e-01 -4.53256e-01 153.56 -6.213e-06
8300 3.933e-01 -8.466e-01 -4.53227e-01 151.94 -1.480e-05
8400 3.794e-01 -8.327e-01 -4.53269e-01 146.57 -1.214e-05
8500 3.884e-01 -8.416e-01 -4.53245e-01 150.03 -1.574e-05
8600 3.645e-01 -8.177e-01 -4.53195e-01 140.80 6.260e-07
8700 4.011e-01 -8.543e-01 -4.53228e-01 154.94 -1.170e-06
8800 3.558e-01 -8.090e-01 -4.53201e-01 137.44 1.323e-05
8900 4.105e-01 -8.637e-01 -4.53233e-01 158.56 -5.024e-06
9000 3.994e-01 -8.527e-01 -4.53275e-01 154.28 -5.071e-06
9100 3.709e-01 -8.242e-01 -4.53266e-01 143.29 4.368e-06
9200 3.877e-01 -8.410e-01 -4.53269e-01 149.78 -4.374e-06
9300 3.713e-01 -8.245e-01 -4.53239e-01 143.43 6.201e-06
9400 3.858e-01 -8.390e-01 -4.53186e-01 149.04 -7.370e-06
9500 3.856e-01 -8.389e-01 -4.53262e-01 148.95 -1.216e-05
9600 3.871e-01 -8.404e-01 -4.53272e-01 149.55 -7.571e-06
9700 3.911e-01 -8.443e-01 -4.53223e-01 151.06 -6.837e-06
9800 3.860e-01 -8.392e-01 -4.53197e-01 149.13 -7.472e-07
9900 4.124e-01 -8.656e-01 -4.53237e-01 159.31 -9.298e-06
10000 3.943e-01 -8.476e-01 -4.53270e-01 152.33 2.394e-06
Simulation Complete!
Total simulation time: 8.014 secs
Force/energy time: 7.910 secs (98.70%)
Position/velocity update time: 0.086 secs ( 1.07%)
Thermo/trajectory output time: 0.016 secs ( 0.20%)
Copy the traj.xyz file to your local machine and visualize the simulation with free software like Visual Molecular Dynamic (http://www.ks.uiuc.edu/Research/vmd/). Here are a few example snapshots:
