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License: GNU General Public License v3.0
Monte Carlo and Molecular Dynamics Simulation Package
License: GNU General Public License v3.0
the p5 term seems to have units K/A^3 instead of K/A.
seems maybe so. investigate via MD uVT ex.
Andersen thermostat works well here but NH doesn't
make this as easy as possible.
I have done in Win7 with Gygwin and gcc manually installed but ideally this will be streamlined.
This needs a thorough check.
Consolidate pair distance calculator to 1x instead of 3x for polarized force.
Likewise consolidate local (accumulated) force vector to save time by avoiding atomicAdd()
LJ should (probably) check mixing before computing r.
see molecular_dynamics/nvt example.
classical via UFF bonding etc. param's
Monte Carlo opt. done;
Now do steepest descent
i thought this was already done but jobs still run without error
and xyz default instead of pdb.
i.e. average.cpp functions,
and classes.cpp Stats class
Will be cleaner than on-the-fly function in md.cpp
p84 frenkel -- NVT pressure
p85 frenkel -- NVE heat capacity
need to find that paper again and apply in code.
big mass, no ES, no polar.
this includes the bonded terms in the potential:
bond-stretching, angle bending, dihedral torsion, inversion
only relevant for rigid-body rotation
detect if input_atoms_xyz was used, otherwise restart.pdb will overwrite the .xyz
i.e.
if xyz input is used, also print restart.xyz (and use that for restart.)
Also update SA temperature in input for restart mode.
Also investigate restart overwrites of runlog.
I was testing the code, but the octane water cuda example, even though it ran, didn't show any movement on the octane molecules. Is this behaviour in any way intended, or I'm missing something?
Additionally, where can I find a list of commands and input formats aside from the examples and the source code? On the MPMC wiki, assuming this is written based on that? If using a PDB, how are the atom connections infered? Any note on PQR files?
could be made a lot faster with prefactors instead of redundant products..
In the special case of, e.g.
F
F
F
F
M
F
in the input_atoms_pdb file,
displaceMolecule() does an infinite loop.
make initial read function to set graphing variables etc at startup.
make viz for atoms
dropdown menu for input generator
Mac Apple Store app (via Qt)
Ubuntu App Store app (via Qt?)
need to accommodate multiple sorbates (with different masses) for temperature calculation.
https://materials.registry.nist.gov/
same for MPMC
must be equal to cpu kspace
stuff.zip
http://bisqwit.iki.fi/story/howto/openmp/
Initial:
RD avg = -16295.29771 +- 0.00000 K (90.06 %)
ES avg = -1105.17625 +- 0.00000 K (6.11 %)
Polar avg = -694.20377 +- 0.00000 K (3.84 %)
Total potential avg = -18094.67774 +- 0.00000 K
Time for 1000 steps (100 corrtime)
182.579 s total walltime (linux comp: 156.722 s)/// mpmc: 305.507
0.1825 step/sec (linux comp: 0.1567)/// mpmc: 0.305
bash compile omp linux
yep.
error is order dt^4, slower calc but less deviation from real solution over time.
Need to evaluate -dU/dr and add to CPU and GPU code for Tang-Toennies MD.
test cases are 0.0014-0.0015% (Zn-datzbdc + CO2) off.
RD and ES look identical.
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