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timings, energy, virial tallying

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This commit is contained in:
Steve Plimpton
2022-05-18 08:49:31 -06:00
parent dbcc08ba00
commit df2ecf5bf8
12 changed files with 230 additions and 244 deletions
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7
src/AMOEBA/amoeba_charge_transfer.cpp
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@ -148,6 +148,7 @@ void PairAmoeba::charge_transfer()
// increment the internal virial tensor components
if (vflag_global) {
vxx = xr * frcx;
vxy = yr * frcx;
vxz = zr * frcx;
@ -161,12 +162,6 @@ void PairAmoeba::charge_transfer()
virqxfer[3] -= vxy;
virqxfer[4] -= vxz;
virqxfer[5] -= vyz;
// energy = e
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
}
}
}

11
src/AMOEBA/amoeba_dispersion.cpp
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@ -212,6 +212,7 @@ void PairAmoeba::dispersion_real()
// increment the internal virial tensor components
if (vflag_global) {
vxx = xr * dedx;
vyx = yr * dedx;
vzx = zr * dedx;
@ -225,12 +226,6 @@ void PairAmoeba::dispersion_real()
virdisp[3] -= vyx;
virdisp[4] -= vzx;
virdisp[5] -= vzy;
// energy = e
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
}
}
}
@ -350,6 +345,7 @@ void PairAmoeba::dispersion_kspace()
struc2 = gridfft[n]*gridfft[n] + gridfft[n+1]*gridfft[n+1];
e = -(term1 / denom) * struc2;
edisp += e;
if (vflag_global) {
vterm = 3.0 * (fac1*erfcterm*h + fac3*expterm) * struc2/denom;
virdisp[0] -= h1*h1*vterm - e;
virdisp[1] -= h2*h2*vterm - e;
@ -357,6 +353,7 @@ void PairAmoeba::dispersion_kspace()
virdisp[3] -= h1*h2*vterm;
virdisp[4] -= h1*h3*vterm;
virdisp[5] -= h2*h3*vterm;
}
} else term1 = 0.0;
// NOTE: pre-calc this division only once
gridfft[n] *= -(term1/denom);
@ -418,8 +415,10 @@ void PairAmoeba::dispersion_kspace()
if (me == 0) {
edisp -= term;
if (vflag_global) {
virdisp[0] -= term;
virdisp[1] -= term;
virdisp[2] -= term;
}
}
}

7
src/AMOEBA/amoeba_hal.cpp
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@ -188,6 +188,7 @@ void PairAmoeba::hal()
// increment the internal virial tensor components
if (vflag_global) {
vxx = xr * dedx;
vyx = yr * dedx;
vzx = zr * dedx;
@ -201,12 +202,6 @@ void PairAmoeba::hal()
virhal[3] -= vyx;
virhal[4] -= vzx;
virhal[5] -= vzy;
// energy = e
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
}
}
}

15
src/AMOEBA/amoeba_multipole.cpp
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@ -497,6 +497,7 @@ void PairAmoeba::multipole_real()
// increment the virial due to pairwise Cartesian forces
if (vflag_global) {
vxx = -xr * frcx;
vxy = -0.5 * (yr*frcx+xr*frcy);
vxz = -0.5 * (zr*frcx+xr*frcz);
@ -510,12 +511,6 @@ void PairAmoeba::multipole_real()
virmpole[3] -= vxy;
virmpole[4] -= vxz;
virmpole[5] -= vyz;
// energy = e
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
}
}
}
@ -530,6 +525,8 @@ void PairAmoeba::multipole_real()
for (i = 0; i < nlocal; i++) {
torque2force(i,tq[i],fix,fiy,fiz,f);
if (!vflag_global) continue;
iz = zaxis2local[i];
ix = xaxis2local[i];
iy = yaxis2local[i];
@ -768,6 +765,7 @@ void PairAmoeba::multipole_kspace()
// augment the permanent multipole virial contributions
if (vflag_global) {
for (i = 0; i < nlocal; i++) {
vxx = vxx - cmp[i][1]*cphi[i][1] - 2.0*cmp[i][4]*cphi[i][4] -
cmp[i][7]*cphi[i][7] - cmp[i][8]*cphi[i][8];
@ -785,6 +783,7 @@ void PairAmoeba::multipole_kspace()
vzz = vzz - cmp[i][3]*cphi[i][3] - 2.0*cmp[i][6]*cphi[i][6] -
cmp[i][8]*cphi[i][8] - cmp[i][9]*cphi[i][9];
}
}
// resolve site torques then increment forces and virial
@ -804,6 +803,7 @@ void PairAmoeba::multipole_kspace()
torque2force(i,tem,fix,fiy,fiz,f);
if (vflag_global) {
iz = zaxis2local[i];
ix = xaxis2local[i];
iy = yaxis2local[i];
@ -828,9 +828,11 @@ void PairAmoeba::multipole_kspace()
yix*fix[2] + yiy*fiy[2] + yiz*fiz[2]);
vzz += zix*fix[2] + ziy*fiy[2] + ziz*fiz[2];
}
}
// increment total internal virial tensor components
if (vflag_global) {
virmpole[0] -= vxx;
virmpole[1] -= vyy;
virmpole[2] -= vzz;
@ -838,6 +840,7 @@ void PairAmoeba::multipole_kspace()
virmpole[4] -= vxz;
virmpole[5] -= vyz;
}
}
/* ----------------------------------------------------------------------
damppole generates coefficients for the charge penetration

13
src/AMOEBA/amoeba_polar.cpp
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@ -100,6 +100,8 @@ void PairAmoeba::polar()
torque2force(i,tep,fix,fiy,fiz,f);
if (!vflag_global) continue;
iz = zaxis2local[i];
ix = xaxis2local[i];
iy = yaxis2local[i];
@ -1139,6 +1141,7 @@ void PairAmoeba::polar_real()
// increment the virial due to pairwise Cartesian forces
if (vflag_global) {
vxx = xr * frcx;
vxy = 0.5 * (yr*frcx+xr*frcy);
vxz = 0.5 * (zr*frcx+xr*frcz);
@ -1152,12 +1155,6 @@ void PairAmoeba::polar_real()
virpolar[3] -= vxy;
virpolar[4] -= vxz;
virpolar[5] -= vyz;
// energy = e
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
}
}
}
@ -1191,6 +1188,8 @@ void PairAmoeba::polar_real()
torque2force(i,tep,fix,fiy,fiz,f);
if (!vflag_global) continue;
iz = zaxis2local[i];
ix = xaxis2local[i];
iy = yaxis2local[i];
@ -2163,6 +2162,7 @@ void PairAmoeba::polar_kspace()
// increment the total internal virial tensor components
if (vflag_global) {
virpolar[0] -= vxx;
virpolar[1] -= vyy;
virpolar[2] -= vzz;
@ -2170,3 +2170,4 @@ void PairAmoeba::polar_kspace()
virpolar[4] -= vxz;
virpolar[5] -= vyz;
}
}

18
src/AMOEBA/amoeba_repulsion.cpp
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@ -354,6 +354,7 @@ void PairAmoeba::repulsion()
// increment the virial due to pairwise Cartesian forces
if (vflag_global) {
vxx = -xr * frcx;
vxy = -0.5 * (yr*frcx+xr*frcy);
vxz = -0.5 * (zr*frcx+xr*frcz);
@ -367,19 +368,10 @@ void PairAmoeba::repulsion()
virrepulse[3] -= vxy;
virrepulse[4] -= vxz;
virrepulse[5] -= vyz;
// energy = e
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
}
}
}
// DEBUG
//fclose(fp);
// reverse comm to sum torque from ghost atoms to owned atoms
crstyle = TORQUE;
@ -390,6 +382,8 @@ void PairAmoeba::repulsion()
for (i = 0; i < nlocal; i++) {
torque2force(i,tq[i],fix,fiy,fiz,f);
if (!vflag_global) continue;
iz = zaxis2local[i];
ix = xaxis2local[i];
iy = yaxis2local[i];
@ -420,12 +414,6 @@ void PairAmoeba::repulsion()
virrepulse[3] -= vxy;
virrepulse[4] -= vxz;
virrepulse[5] -= vyz;
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
}
}
}

101
src/AMOEBA/pair_amoeba.cpp
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@ -49,8 +49,6 @@ enum{GEAR,ASPC,LSQR};
#define DELTASTACK 16
#define UIND_DEBUG 0 // also in amoeba_induce.cpp
/* ---------------------------------------------------------------------- */
PairAmoeba::PairAmoeba(LAMMPS *lmp) : Pair(lmp)
@ -67,10 +65,16 @@ PairAmoeba::PairAmoeba(LAMMPS *lmp) : Pair(lmp)
me = comm->me;
nprocs = comm->nprocs;
// force field settings
// pair style settings
one_coeff = 1;
single_enable = 0;
no_virial_fdotr_compute = 1;
nextra = 6;
pvector = new double[nextra];
// force field settings
amoeba = 1;
hippo = 0;
@ -165,6 +169,8 @@ PairAmoeba::PairAmoeba(LAMMPS *lmp) : Pair(lmp)
PairAmoeba::~PairAmoeba()
{
delete [] pvector;
// check nfix in case all fixes have already been deleted
if (modify->nfix) {
@ -275,26 +281,12 @@ PairAmoeba::~PairAmoeba()
}
delete [] factors;
// DEBUG
if (me == 0 && UIND_DEBUG) fclose(fp_uind);
}
/* ---------------------------------------------------------------------- */
void PairAmoeba::compute(int eflag, int vflag)
{
// DEBUG timer init
if (update->ntimestep <= 1) {
time_init = time_hal = time_repulse = time_disp = time_mpole = 0.0;
time_induce = time_polar = time_qxfer = 0.0;
}
double evdwl;
evdwl = 0.0;
ev_init(eflag,vflag);
// zero energy/virial components
@ -358,6 +350,13 @@ void PairAmoeba::compute(int eflag, int vflag)
// end of one-time initializations
// -------------------------------------------------------------------
// initialize timers on first compute() call after setup
if (update->ntimestep <= update->beginstep+1) {
time_init = time_hal = time_repulse = time_disp = time_mpole = 0.0;
time_induce = time_polar = time_qxfer = 0.0;
}
double time0,time1,time2,time3,time4,time5,time6,time7,time8;
MPI_Barrier(world);
@ -462,29 +461,27 @@ void PairAmoeba::compute(int eflag, int vflag)
// charge transfer, pairwise
if (hippo && qxfer_flag) charge_transfer();
time8 = MPI_Wtime();
// energy, force, virial summations
// store energy components for output by compute pair command
eng_vdwl = ehal + erepulse + edisp + empole + epolar + eqxfer;
pvector[0] = ehal;
pvector[2] = erepulse;
pvector[3] = edisp;
pvector[4] = empole;
pvector[5] = epolar;
pvector[6] = eqxfer;
double **f = atom->f;
nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
// energy & virial summations
eng_vdwl = ehal + edisp;
eng_coul = erepulse + empole + epolar + eqxfer;
for (int i = 0; i < 6; i++)
virial[i] = virhal[i] + virrepulse[i] + virdisp[i] +
virpolar[i] + virmpole[i] + virqxfer[i];
// virial computation
// NOTE: how does this work for AMOEBA ?
// do all terms get summed this way, or only pairwise
// it is 2x what summed virial[6] above is
// if (vflag_fdotr) virial_fdotr_compute();
// timing information
// accumulate timing information
time_init += time1 - time0;
time_hal += time2 - time1;
@ -494,11 +491,14 @@ void PairAmoeba::compute(int eflag, int vflag)
time_induce += time6 - time5;
time_polar += time7 - time6;
time_qxfer += time8 - time7;
}
// timing output
if (update->ntimestep < update->laststep) return;
/* ----------------------------------------------------------------------
print out AMOEBA/HIPPO timing info at end of run
------------------------------------------------------------------------- */
void PairAmoeba::finish()
{
double ave;
MPI_Allreduce(&time_init,&ave,1,MPI_DOUBLE,MPI_SUM,world);
time_init = ave/nprocs;
@ -524,32 +524,32 @@ void PairAmoeba::compute(int eflag, int vflag)
MPI_Allreduce(&time_qxfer,&ave,1,MPI_DOUBLE,MPI_SUM,world);
time_qxfer = ave/nprocs;
double time_amtot = time_init + time_hal + time_repulse + time_disp +
double time_total = time_init + time_hal + time_repulse + time_disp +
time_mpole + time_induce + time_polar + time_qxfer;
if (me == 0) {
utils::logmesg(lmp,"\nAMEOBA/HIPPO timing info:\n");
utils::logmesg(lmp,"\nAMEOBA/HIPPO timing breakdown:\n");
utils::logmesg(lmp," Init time: {:.6g} {:.6g}\n",
time_init,time_init/time_amtot);
time_init,time_init/time_total);
if (amoeba)
utils::logmesg(lmp," Hal time: {:.6g} {:.6g}\n",
time_hal,time_hal/time_amtot*100);
time_hal,time_hal/time_total*100);
if (hippo)
utils::logmesg(lmp," Repls time: {:.6g} {:.6g}\n",
time_repulse,time_repulse/time_amtot*100);
utils::logmesg(lmp," Repulse time: {:.6g} {:.6g}\n",
time_repulse,time_repulse/time_total*100);
if (hippo)
utils::logmesg(lmp," Disp time: {:.6g} {:.6g}\n",
time_disp,time_disp/time_amtot*100);
time_disp,time_disp/time_total*100);
utils::logmesg(lmp," Mpole time: {:.6g} {:.6g}\n",
time_mpole,time_mpole/time_amtot*100);
time_mpole,time_mpole/time_total*100);
utils::logmesg(lmp," Induce time: {:.6g} {:.6g}\n",
time_induce,time_induce/time_amtot*100);
time_induce,time_induce/time_total*100);
utils::logmesg(lmp," Polar time: {:.6g} {:.6g}\n",
time_polar,time_polar/time_amtot*100);
time_polar,time_polar/time_total*100);
if (hippo)
utils::logmesg(lmp," Qxfer time: {:.6g} {:.6g}\n",
time_qxfer,time_qxfer/time_amtot*100);
utils::logmesg(lmp," Total time: {:.6g}\n\n",time_amtot);
time_qxfer,time_qxfer/time_total*100);
utils::logmesg(lmp," Total time: {:.6g}\n",time_total);
}
}
@ -1016,15 +1016,6 @@ void PairAmoeba::init_style()
// request neighbor lists
int irequest = neighbor->request(this,instance_me);
// open debug output files
// names are hard-coded
if (me == 0) {
char fname[32];
sprintf(fname,"tmp.uind.kspace.%d",nprocs);
if (UIND_DEBUG) fp_uind = fopen(fname,"w");
}
}
/* ----------------------------------------------------------------------

1
src/AMOEBA/pair_amoeba.h
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@ -46,6 +46,7 @@ class PairAmoeba : public Pair {
void coeff(int, char **);
void init_style();
double init_one(int, int);
void finish();
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);

5
src/finish.cpp
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@ -28,6 +28,7 @@
#include "neigh_request.h"
#include "neighbor.h" // IWYU pragma: keep
#include "output.h"
#include "pair.h"
#include "thermo.h"
#include "timer.h" // IWYU pragma: keep
#include "universe.h"
@ -214,6 +215,10 @@ void Finish::end(int flag)
}
}
// pair_style timing stats if provided
if (force->pair) force->pair->finish();
// PRD stats
if (prdflag) {

1
src/pair.h
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@ -169,6 +169,7 @@ class Pair : protected Pointers {
return 0.0;
}
virtual void finish() {}
virtual void settings(int, char **) = 0;
virtual void coeff(int, char **) = 0;

6
src/pair_hybrid.cpp
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@ -192,6 +192,12 @@ void PairHybrid::compute(int eflag, int vflag)
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairHybrid::finish()
{
for (int m = 0; m < nstyles; m++) styles[m]->finish();
}
/* ---------------------------------------------------------------------- */

1
src/pair_hybrid.h
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@ -46,6 +46,7 @@ class PairHybrid : public Pair {
void init_style() override;
double init_one(int, int) override;
void setup() override;
void finish();
void write_restart(FILE *) override;
void read_restart(FILE *) override;
double single(int, int, int, int, double, double, double, double &) override;