Loading .vscode/settings.json 0 → 100644 +6 −0 Changes for .vscode/settings.json: 6 added lines, 0 removed lines. Original line number Diff line number Diff line { "files.associations": { "cmath": "cpp", "complex": "cpp" } } No newline at end of file src/min_adaptglok.cpp +54 −17 Changes for src/min_adaptglok.cpp: 54 added lines, 17 removed lines. Original line number Diff line number Diff line Loading @@ -33,6 +33,7 @@ using namespace LAMMPS_NS; #define ALPHA0 0.25 #define ALPHA_SHRINK 0.99 #define TMAX 2.0 #define TMIN 0.02 // as harcoded in IMD: 1/50 /* ---------------------------------------------------------------------- */ Loading @@ -46,9 +47,15 @@ void MinAdaptGlok::init() Min::init(); dt = update->dt; // GUENOLE - save the global timestep dtdef = dt; dtmax = TMAX * dt; dtmin = TMIN * dt; alpha = ALPHA0; last_negative = update->ntimestep; ntimestep_start = update->ntimestep; } /* ---------------------------------------------------------------------- */ Loading Loading @@ -101,6 +108,9 @@ int MinAdaptGlok::iterate(int maxiter) double **v = atom->v; double **f = atom->f; int nlocal = atom->nlocal; double *rmass = atom->rmass; double *mass = atom->mass; int *type = atom->type; vdotf = 0.0; for (int i = 0; i < nlocal; i++) Loading Loading @@ -149,13 +159,13 @@ int MinAdaptGlok::iterate(int maxiter) } scale1 = 1.0 - alpha; if (fdotfall == 0.0) scale2 = 0.0; if (fdotfall == 0.0) scale2 = alpha; else scale2 = alpha * sqrt(vdotvall/fdotfall); for (int i = 0; i < nlocal; i++) { v[i][0] = scale1*v[i][0] + scale2*f[i][0]; v[i][1] = scale1*v[i][1] + scale2*f[i][1]; v[i][2] = scale1*v[i][2] + scale2*f[i][2]; } //for (int i = 0; i < nlocal; i++) { // v[i][0] = scale1*v[i][0] + scale2*f[i][0]; // v[i][1] = scale1*v[i][1] + scale2*f[i][1]; // v[i][2] = scale1*v[i][2] + scale2*f[i][2]; //} if (ntimestep - last_negative > DELAYSTEP) { dt = MIN(dt*DT_GROW,dtmax); Loading @@ -167,31 +177,38 @@ int MinAdaptGlok::iterate(int maxiter) } else { // Limit decrease of timestep if (ntimestep - last_negative > DELAYSTEP) { if (ntimestep - ntimestep_start > DELAYSTEP) { if (dt > dtmin) dt *= DT_SHRINK; alpha = ALPHA0; if (dt > dtmax / 50.0) { dt *= DT_SHRINK; } } last_negative = ntimestep; double **x = atom->x; for (int i = 0; i < nlocal; i++) { x[i][0] -= 0.5 * dtv * v[i][0]; x[i][1] -= 0.5 * dtv * v[i][1]; x[i][2] -= 0.5 * dtv * v[i][2]; } for (int i = 0; i < nlocal; i++) v[i][0] = v[i][1] = v[i][2] = 0.0; } // limit timestep so no particle moves further than dmax double *rmass = atom->rmass; double *mass = atom->mass; int *type = atom->type; dtvone = dt; ke = 0.0; for (int i = 0; i < nlocal; i++) { vmax = MAX(fabs(v[i][0]),fabs(v[i][1])); vmax = MAX(vmax,fabs(v[i][2])); if (dtvone*vmax > dmax) dtvone = dmax/vmax; ke += mass[type[i]] * (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]); } MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world); MPI_Allreduce(&ke,&keall,1,MPI_DOUBLE,MPI_SUM,world); fprintf(screen,"vdotfall %f %f\n",vdotfall,keall); // min dtv over replicas, if necessary // this communicator would be invalid for multiprocess replicas Loading Loading @@ -220,12 +237,19 @@ int MinAdaptGlok::iterate(int maxiter) } else { for (int i = 0; i < nlocal; i++) { dtfm = dtf / mass[type[i]]; x[i][0] += dtv * v[i][0]; x[i][1] += dtv * v[i][1]; x[i][2] += dtv * v[i][2]; //fprintf(screen,"mass %f\n",mass[type[i]]); v[i][0] += dtfm * f[i][0]; v[i][1] += dtfm * f[i][1]; v[i][2] += dtfm * f[i][2]; if (vdotfall > 0.0) { // we perform the mixing AFTER the timeintegration v[i][0] = scale1*v[i][0] + scale2*f[i][0]; v[i][1] = scale1*v[i][1] + scale2*f[i][1]; v[i][2] = scale1*v[i][2] + scale2*f[i][2]; } x[i][0] += dtv * v[i][0]; x[i][1] += dtv * v[i][1]; x[i][2] += dtv * v[i][2]; } } Loading Loading @@ -258,7 +282,13 @@ int MinAdaptGlok::iterate(int maxiter) if (update->ftol > 0.0) { fdotf = fnorm_sqr(); if (update->multireplica == 0) { if (fdotf < update->ftol*update->ftol) return FTOL; if (fdotf < update->ftol*update->ftol) { // GUENOLE - reset the global timestep to the default value //update->dt = dtdef; return FTOL; } } else { if (fdotf < update->ftol*update->ftol) flag = 0; else flag = 1; Loading @@ -270,11 +300,18 @@ int MinAdaptGlok::iterate(int maxiter) // output for thermo, dump, restart files if (output->next == ntimestep) { // GUENOLE - update of the global timestep for thermo output update->dt = dt; timer->stamp(); output->write(ntimestep); timer->stamp(Timer::OUTPUT); } } // GUENOLE - reset the global timestep to the default value //update->dt = dtdef; return MAXITER; } src/min_adaptglok.h +2 −2 Changes for src/min_adaptglok.h: 2 added lines, 2 removed lines. Original line number Diff line number Diff line Loading @@ -34,9 +34,9 @@ class MinAdaptGlok : public Min { int iterate(int); private: double dt,dtmax; double dt,dtmax,dtmin,dtdef,ke,keall; double alpha; bigint last_negative; bigint last_negative,ntimestep_start; }; } Loading test/fdotfall.txt 0 → 100644 +616 −0 Changes for test/fdotfall.txt: 616 added lines, 0 removed lines. 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View file Loading
.vscode/settings.json 0 → 100644 +6 −0 Changes for .vscode/settings.json: 6 added lines, 0 removed lines. Original line number Diff line number Diff line { "files.associations": { "cmath": "cpp", "complex": "cpp" } } No newline at end of file
src/min_adaptglok.cpp +54 −17 Changes for src/min_adaptglok.cpp: 54 added lines, 17 removed lines. Original line number Diff line number Diff line Loading @@ -33,6 +33,7 @@ using namespace LAMMPS_NS; #define ALPHA0 0.25 #define ALPHA_SHRINK 0.99 #define TMAX 2.0 #define TMIN 0.02 // as harcoded in IMD: 1/50 /* ---------------------------------------------------------------------- */ Loading @@ -46,9 +47,15 @@ void MinAdaptGlok::init() Min::init(); dt = update->dt; // GUENOLE - save the global timestep dtdef = dt; dtmax = TMAX * dt; dtmin = TMIN * dt; alpha = ALPHA0; last_negative = update->ntimestep; ntimestep_start = update->ntimestep; } /* ---------------------------------------------------------------------- */ Loading Loading @@ -101,6 +108,9 @@ int MinAdaptGlok::iterate(int maxiter) double **v = atom->v; double **f = atom->f; int nlocal = atom->nlocal; double *rmass = atom->rmass; double *mass = atom->mass; int *type = atom->type; vdotf = 0.0; for (int i = 0; i < nlocal; i++) Loading Loading @@ -149,13 +159,13 @@ int MinAdaptGlok::iterate(int maxiter) } scale1 = 1.0 - alpha; if (fdotfall == 0.0) scale2 = 0.0; if (fdotfall == 0.0) scale2 = alpha; else scale2 = alpha * sqrt(vdotvall/fdotfall); for (int i = 0; i < nlocal; i++) { v[i][0] = scale1*v[i][0] + scale2*f[i][0]; v[i][1] = scale1*v[i][1] + scale2*f[i][1]; v[i][2] = scale1*v[i][2] + scale2*f[i][2]; } //for (int i = 0; i < nlocal; i++) { // v[i][0] = scale1*v[i][0] + scale2*f[i][0]; // v[i][1] = scale1*v[i][1] + scale2*f[i][1]; // v[i][2] = scale1*v[i][2] + scale2*f[i][2]; //} if (ntimestep - last_negative > DELAYSTEP) { dt = MIN(dt*DT_GROW,dtmax); Loading @@ -167,31 +177,38 @@ int MinAdaptGlok::iterate(int maxiter) } else { // Limit decrease of timestep if (ntimestep - last_negative > DELAYSTEP) { if (ntimestep - ntimestep_start > DELAYSTEP) { if (dt > dtmin) dt *= DT_SHRINK; alpha = ALPHA0; if (dt > dtmax / 50.0) { dt *= DT_SHRINK; } } last_negative = ntimestep; double **x = atom->x; for (int i = 0; i < nlocal; i++) { x[i][0] -= 0.5 * dtv * v[i][0]; x[i][1] -= 0.5 * dtv * v[i][1]; x[i][2] -= 0.5 * dtv * v[i][2]; } for (int i = 0; i < nlocal; i++) v[i][0] = v[i][1] = v[i][2] = 0.0; } // limit timestep so no particle moves further than dmax double *rmass = atom->rmass; double *mass = atom->mass; int *type = atom->type; dtvone = dt; ke = 0.0; for (int i = 0; i < nlocal; i++) { vmax = MAX(fabs(v[i][0]),fabs(v[i][1])); vmax = MAX(vmax,fabs(v[i][2])); if (dtvone*vmax > dmax) dtvone = dmax/vmax; ke += mass[type[i]] * (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]); } MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world); MPI_Allreduce(&ke,&keall,1,MPI_DOUBLE,MPI_SUM,world); fprintf(screen,"vdotfall %f %f\n",vdotfall,keall); // min dtv over replicas, if necessary // this communicator would be invalid for multiprocess replicas Loading Loading @@ -220,12 +237,19 @@ int MinAdaptGlok::iterate(int maxiter) } else { for (int i = 0; i < nlocal; i++) { dtfm = dtf / mass[type[i]]; x[i][0] += dtv * v[i][0]; x[i][1] += dtv * v[i][1]; x[i][2] += dtv * v[i][2]; //fprintf(screen,"mass %f\n",mass[type[i]]); v[i][0] += dtfm * f[i][0]; v[i][1] += dtfm * f[i][1]; v[i][2] += dtfm * f[i][2]; if (vdotfall > 0.0) { // we perform the mixing AFTER the timeintegration v[i][0] = scale1*v[i][0] + scale2*f[i][0]; v[i][1] = scale1*v[i][1] + scale2*f[i][1]; v[i][2] = scale1*v[i][2] + scale2*f[i][2]; } x[i][0] += dtv * v[i][0]; x[i][1] += dtv * v[i][1]; x[i][2] += dtv * v[i][2]; } } Loading Loading @@ -258,7 +282,13 @@ int MinAdaptGlok::iterate(int maxiter) if (update->ftol > 0.0) { fdotf = fnorm_sqr(); if (update->multireplica == 0) { if (fdotf < update->ftol*update->ftol) return FTOL; if (fdotf < update->ftol*update->ftol) { // GUENOLE - reset the global timestep to the default value //update->dt = dtdef; return FTOL; } } else { if (fdotf < update->ftol*update->ftol) flag = 0; else flag = 1; Loading @@ -270,11 +300,18 @@ int MinAdaptGlok::iterate(int maxiter) // output for thermo, dump, restart files if (output->next == ntimestep) { // GUENOLE - update of the global timestep for thermo output update->dt = dt; timer->stamp(); output->write(ntimestep); timer->stamp(Timer::OUTPUT); } } // GUENOLE - reset the global timestep to the default value //update->dt = dtdef; return MAXITER; }
src/min_adaptglok.h +2 −2 Changes for src/min_adaptglok.h: 2 added lines, 2 removed lines. Original line number Diff line number Diff line Loading @@ -34,9 +34,9 @@ class MinAdaptGlok : public Min { int iterate(int); private: double dt,dtmax; double dt,dtmax,dtmin,dtdef,ke,keall; double alpha; bigint last_negative; bigint last_negative,ntimestep_start; }; } Loading
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