khavernathy/mcmd

Monte Carlo and Molecular Dynamics Simulation Package

mcmd's Issues

non-rigid (constraint,flexible) sorbate potentials/forces

this includes the bonded terms in the potential:

bond-stretching, angle bending, dihedral torsion, inversion

make input arguments case insensitive

yep.

Add option for no-zero-sorbates forced

check for existence of input file (instead of just erroring in options.)

is nose-hoover thermostat good for NVT only?

seems maybe so. investigate via MD uVT ex.

Andersen thermostat works well here but NH doesn't

Investigate polarization energy differerence from MPMC

test cases are 0.0014-0.0015% (Zn-datzbdc + CO2) off.
RD and ES look identical.

refactor force computation for ES

could be made a lot faster with prefactors instead of redundant products..

add RK4 integration for MD

error is order dt^4, slower calc but less deviation from real solution over time.

No-PBC MD (on GPU)

auto-restart feat

Tang-Toennies iterative mixing rules

need to find that paper again and apply in code.

multi-sorbate MD temperature correction

need to accommodate multiple sorbates (with different masses) for temperature calculation.

make trajectory optional

and xyz default instead of pdb.

Octane water mixing example

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?

Multi-sorbate histograms (MD and MC)

Half the polarization A matrix

A will be decomposed into two 1D arrays: the diagonal, and the upper symmetric half

The Map is as follows:

The new req. memory will be

instead of (3N)^2

add quaternion dynamics for rigid molecules in MD

GUI using QML

• 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?)

add exchange/swap movetype in MC

try another random number gen.

GPU polarization

add non-LB mixing rules

Add virial pressure and heat-capacity in MD

p84 frenkel -- NVT pressure
p85 frenkel -- NVE heat capacity

windows 7, 8, 10 installations

make this as easy as possible.

I have done in Win7 with Gygwin and gcc manually installed but ideally this will be streamlined.

Potential energy from rotations

optimization mode

classical via UFF bonding etc. param's

Monte Carlo opt. done;

Now do steepest descent

rigid rotational contribution to temperature

only relevant for rigid-body rotation

apply Nose-Hoover thermostat even when init_vel=0

see molecular_dynamics/nvt example.

add compressibility, bulk mod., calculators for main output

Add multi-sorbate Qst calculator

parallelization for isotherms/isobars

add to NIST materials registry

https://materials.registry.nist.gov/

same for MPMC

nose-hoover thermostat

threading energy tasks for MC

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

MD polarizable force

select random molecule when frozens are input after movables in input .pdb

In the special case of, e.g.
F
F
F
F
M
F

in the input_atoms_pdb file,

displaceMolecule() does an infinite loop.

gravitational md

big mass, no ES, no polar.

mods to restart mode

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.

GEMC (multi-box Monte Carlo)

add MD observable calcs to averages function and stats variables

i.e. average.cpp functions,

and classes.cpp Stats class

Will be cleaner than on-the-fly function in md.cpp

clean unsigned int != int for gdb compilation.

GPU for RD/ES energy in MC

gpu k-space es

must be equal to cpu kspace

Add Tang-Toennies potential

optimize GPU force; match GPU force w/CPU force in all cases

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.

check for existence of input atoms file

i thought this was already done but jobs still run without error

Intel compiler compatibility

check for error in prefactor 5 in polarization force

the p5 term seems to have units K/A^3 instead of K/A.

New sorbate models from literature

Tang-Toennies forces on GPU

Need to evaluate -dU/dr and add to CPU and GPU code for Tang-Toennies MD.