Potential energy from rotations

[khavernathy]

[khavernathy]

Ewald force should include k-space (reciprocal space) contribution
http://www.pages.drexel.edu/~cfa22/msim/node49.html

[khavernathy]

name md_NVE_example
mode md ! mc or md
checkpoints_option off

input_atoms input.pdb ! PDB ONLY

potential_form lj
com_option off ! center of mass

carbasis 25 25 25 90 90 90

ensemble nve

! MOLECULAR DYNAMICS ONLY ===============================
md_pbc on
md_dt 0.2 ! fs
md_ft 2 ns
md_corrtime 1000 ! steps
!md_init_vel 0 ! A / fs^2
md_mode molecular
md_rotations off

[khavernathy]

ATOM 1 HT h2o M 1 -1.752770 7.859250 -4.727420 default 0.4170
ATOM 2 OT h2o M 1 -1.871140 8.575620 -4.113410 default -0.8340
ATOM 3 HT h2o M 1 -1.746980 9.388710 -4.590600 default 0.4170
ATOM 4 HT h2o M 2 -2.090070 6.957620 -4.921120 default 0.4170
ATOM 5 OT h2o M 2 -2.854070 7.014120 -5.484420 default -0.8340
ATOM 6 HT h2o M 2 -3.625470 6.980620 -4.929320 default 0.4170
ATOM 7 HT h2o M 3 -2.665930 6.111700 -3.476070 default 0.4170
ATOM 8 OT h2o M 3 -1.816200 5.786300 -3.199900 default -0.8340
ATOM 9 HT h2o M 3 -1.744820 4.883110 -3.488810 default 0.4170
ATOM 10 HT h2o M 4 -0.068850 6.740530 -2.796270 default 0.4170
ATOM 11 OT h2o M 4 -0.817170 7.262010 -2.527460 default -0.8340
ATOM 12 HT h2o M 4 -1.348260 7.424680 -3.299340 default 0.4170

[khavernathy]

quaternion dynamics tests

lj, no rotations, conserves in nve.

file.zip

[khavernathy]

LJES issue fixed via ae0614c
Actually, 0800139
k-space force needed to be doubled to compensate for half Ewald sphere

Now, need to add LJES routine to GPU CUDA
...done; matches cpu force.

NOW rotations...

[khavernathy]

theta should maybe define angular position w/respect to ORIGINAL position; not previous.

so theta is recursive by integration function but the actual rotation should be performed on original relative coordinates r-r_com

[khavernathy]

or,

U_rotation = torque dot theta , add this to normal potential?