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Change fire to fire/old and fire2 to fire. Implement normstyle in fire. Update author affiliation.

This commit is contained in:
Julien Guénolé 2020-01-28 14:51:23 +01:00
parent ea24ec8d6a
commit 197ba62cd9
5 changed files with 566 additions and 564 deletions
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339
src/min_fire.cpp
View File

@ -11,16 +11,26 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "min_fire.h" /* ----------------------------------------------------------------------
#include <mpi.h> Contributing authors: Julien Guénolé, CNRS and
Erik Bitzek, FAU Erlangen-Nuernberg
------------------------------------------------------------------------- */
#include <cmath> #include <cmath>
#include "min_fire.h"
#include "universe.h" #include "universe.h"
#include "atom.h" #include "atom.h"
#include "error.h"
#include "force.h" #include "force.h"
#include "update.h" #include "update.h"
#include "output.h" #include "output.h"
#include "timer.h" #include "timer.h"
#include "error.h"
#include "variable.h"
#include "modify.h"
#include "compute.h"
#include "domain.h"
#include "neighbor.h"
#include "comm.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -28,13 +38,6 @@ using namespace LAMMPS_NS;
#define EPS_ENERGY 1.0e-8 #define EPS_ENERGY 1.0e-8
#define DELAYSTEP 5
#define DT_GROW 1.1
#define DT_SHRINK 0.5
#define ALPHA0 0.1
#define ALPHA_SHRINK 0.99
#define TMAX 10.0
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
MinFire::MinFire(LAMMPS *lmp) : Min(lmp) {} MinFire::MinFire(LAMMPS *lmp) : Min(lmp) {}
@ -45,10 +48,18 @@ void MinFire::init()
{ {
Min::init(); Min::init();
// simple parameters validation
if (tmax < tmin) error->all(FLERR,"tmax has to be larger than tmin");
if (dtgrow < 1.0) error->all(FLERR,"dtgrow has to be larger than 1.0");
if (dtshrink > 1.0) error->all(FLERR,"dtshrink has to be smaller than 1.0");
dt = update->dt; dt = update->dt;
dtmax = TMAX * dt; dtmax = tmax * dt;
alpha = ALPHA0; dtmin = tmin * dt;
last_negative = update->ntimestep; alpha = alpha0;
last_negative = ntimestep_start = update->ntimestep;
vdotf_negatif = 0;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -58,6 +69,22 @@ void MinFire::setup_style()
double **v = atom->v; double **v = atom->v;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
// print the parameters used within fire into the log
const char *s1[] = {"eulerimplicit","verlet","leapfrog","eulerexplicit"};
const char *s2[] = {"no","yes"};
if (comm->me == 0 && logfile) {
fprintf(logfile," Parameters for fire: \n"
" dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin "
" integrator halfstepback relaxbox relaxbox_mod relaxbox_rate ptol \n"
" %4g %9i %6g %8g %6g %11g %4g %4g %13s %12s \n",
dmax, delaystep, dtgrow, dtshrink, alpha0, alphashrink, tmax, tmin,
s1[integrator], s2[halfstepback_flag]);
}
// initialize the velocities
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
v[i][0] = v[i][1] = v[i][2] = 0.0; v[i][0] = v[i][1] = v[i][2] = 0.0;
} }
@ -88,6 +115,39 @@ int MinFire::iterate(int maxiter)
alpha_final = 0.0; alpha_final = 0.0;
// Leap Frog integration initialization
if (integrator == 2) {
double **f = atom->f;
double **v = atom->v;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int nlocal = atom->nlocal;
energy_force(0);
neval++;
dtf = -0.5 * dt * force->ftm2v;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / rmass[i];
v[i][0] = dtfm * f[i][0];
v[i][1] = dtfm * f[i][1];
v[i][2] = dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / mass[type[i]];
v[i][0] = dtfm * f[i][0];
v[i][1] = dtfm * f[i][1];
v[i][2] = dtfm * f[i][2];
}
}
}
for (int iter = 0; iter < maxiter; iter++) { for (int iter = 0; iter < maxiter; iter++) {
if (timer->check_timeout(niter)) if (timer->check_timeout(niter))
@ -96,11 +156,17 @@ int MinFire::iterate(int maxiter)
ntimestep = ++update->ntimestep; ntimestep = ++update->ntimestep;
niter++; niter++;
// vdotfall = v dot f // pointers
int nlocal = atom->nlocal;
double **v = atom->v; double **v = atom->v;
double **f = atom->f; double **f = atom->f;
int nlocal = atom->nlocal; double **x = atom->x;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
// vdotfall = v dot f
vdotf = 0.0; vdotf = 0.0;
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
@ -118,11 +184,14 @@ int MinFire::iterate(int maxiter)
// if (v dot f) > 0: // if (v dot f) > 0:
// v = (1-alpha) v + alpha |v| Fhat // v = (1-alpha) v + alpha |v| Fhat
// |v| = length of v, Fhat = unit f // |v| = length of v, Fhat = unit f
// if more than DELAYSTEP since v dot f was negative: // Only: (1-alpha) and alpha |v| Fhat is calculated here
// increase timestep and decrease alpha // the modificatin of v is made wihtin the integration, after v update
// if more than delaystep since v dot f was negative:
// increase timestep, update global timestep and decrease alpha
if (vdotfall > 0.0) { if (vdotfall > 0.0) {
vdotv = 0.0; vdotv = 0.0;
vdotf_negatif = 0;
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
vdotv += v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]; vdotv += v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world);
@ -149,36 +218,59 @@ int MinFire::iterate(int maxiter)
} }
scale1 = 1.0 - alpha; scale1 = 1.0 - alpha;
if (fdotfall == 0.0) scale2 = 0.0; if (fdotfall <= 1e-20) scale2 = 0.0;
else scale2 = alpha * sqrt(vdotvall/fdotfall); else scale2 = alpha * sqrt(vdotvall/fdotfall);
for (int i = 0; i < nlocal; i++) {
v[i][0] = scale1*v[i][0] + scale2*f[i][0]; if (ntimestep - last_negative > delaystep) {
v[i][1] = scale1*v[i][1] + scale2*f[i][1]; dt = MIN(dt*dtgrow,dtmax);
v[i][2] = scale1*v[i][2] + scale2*f[i][2]; update->dt = dt;
alpha *= alphashrink;
} }
if (ntimestep - last_negative > DELAYSTEP) { // else (v dot f) <= 0
dt = MIN(dt*DT_GROW,dtmax); // if more than delaystep since starting the relaxation:
alpha *= ALPHA_SHRINK; // reset alpha
} // if dt*dtshrink > dtmin:
// decrease timestep
// else (v dot f) <= 0: // update global timestep (for thermo output)
// decrease timestep, reset alpha, set v = 0 // half step back within the dynamics: x(t) = x(t-0.5*dt)
// reset velocities: v = 0
} else { } else {
last_negative = ntimestep; last_negative = ntimestep;
dt *= DT_SHRINK; int delayflag = 1;
alpha = ALPHA0; if (ntimestep - ntimestep_start < delaystep && delaystep_start_flag)
delayflag = 0;
if (delayflag) {
alpha = alpha0;
if (dt*dtshrink >= dtmin) {
dt *= dtshrink;
update->dt = dt;
}
}
// stopping criterion while stuck in a local bassin of the PES
vdotf_negatif++;
if (max_vdotf_negatif > 0 && vdotf_negatif > max_vdotf_negatif)
return MAXVDOTF;
// inertia correction
if (halfstepback_flag) {
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++) for (int i = 0; i < nlocal; i++)
v[i][0] = v[i][1] = v[i][2] = 0.0; v[i][0] = v[i][1] = v[i][2] = 0.0;
} }
// limit timestep so no particle moves further than dmax // limit timestep so no particle moves further than dmax
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
dtvone = dt; dtvone = dt;
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
@ -186,6 +278,7 @@ int MinFire::iterate(int maxiter)
vmax = MAX(vmax,fabs(v[i][2])); vmax = MAX(vmax,fabs(v[i][2]));
if (dtvone*vmax > dmax) dtvone = dmax/vmax; if (dtvone*vmax > dmax) dtvone = dmax/vmax;
} }
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world); MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world);
// min dtv over replicas, if necessary // min dtv over replicas, if necessary
@ -196,43 +289,161 @@ int MinFire::iterate(int maxiter)
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld); MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld);
} }
dtf = dtv * force->ftm2v; // Dynamic integration scheme:
// 0: semi-implicit Euler
// 1: velocity Verlet
// 2: leapfrog (initial half step before the iteration loop)
// 3: explicit Euler
// Euler integration step // Semi-implicit Euler OR Leap Frog integration
double **x = atom->x; if (integrator == 0 || integrator == 2) {
if (rmass) { dtf = dtv * force->ftm2v;
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / rmass[i]; if (rmass) {
x[i][0] += dtv * v[i][0]; for (int i = 0; i < nlocal; i++) {
x[i][1] += dtv * v[i][1]; dtfm = dtf / rmass[i];
x[i][2] += dtv * v[i][2]; v[i][0] += dtfm * f[i][0];
v[i][0] += dtfm * f[i][0]; v[i][1] += dtfm * f[i][1];
v[i][1] += dtfm * f[i][1]; v[i][2] += dtfm * f[i][2];
v[i][2] += dtfm * f[i][2]; if (vdotfall > 0.0) {
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];
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / 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) {
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];
}
} }
} else {
for (int i = 0; i < nlocal; i++) { eprevious = ecurrent;
dtfm = dtf / mass[type[i]]; ecurrent = energy_force(0);
x[i][0] += dtv * v[i][0]; neval++;
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2]; // Velocity Verlet integration
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1]; } else if (integrator == 1) {
v[i][2] += dtfm * f[i][2];
dtf = 0.5 * dtv * force->ftm2v;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / rmass[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) {
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];
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / 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) {
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];
}
} }
eprevious = ecurrent;
ecurrent = energy_force(0);
neval++;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
}
// Standard Euler integration
} else if (integrator == 3) {
dtf = dtv * force->ftm2v;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / rmass[i];
if (vdotfall > 0.0) {
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];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / mass[type[i]];
if (vdotfall > 0.0) {
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];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
}
eprevious = ecurrent;
ecurrent = energy_force(0);
neval++;
} }
eprevious = ecurrent;
ecurrent = energy_force(0);
neval++;
// energy tolerance criterion // energy tolerance criterion
// only check after DELAYSTEP elapsed since velocties reset to 0 // only check after delaystep elapsed since velocties reset to 0
// sync across replicas if running multi-replica minimization // sync across replicas if running multi-replica minimization
// reset the timestep to the initial value
if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) { if (update->etol > 0.0 && ntimestep-last_negative > delaystep) {
if (update->multireplica == 0) { if (update->multireplica == 0) {
if (fabs(ecurrent-eprevious) < if (fabs(ecurrent-eprevious) <
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)) update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
@ -243,12 +454,14 @@ int MinFire::iterate(int maxiter)
flag = 0; flag = 0;
else flag = 1; else flag = 1;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld); MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
if (flagall == 0) return ETOL; if (flagall == 0)
return ETOL;
} }
} }
// force tolerance criterion // force tolerance criterion
// sync across replicas if running multi-replica minimization // sync across replicas if running multi-replica minimization
// reset the timestep to the initial value
fdotf = 0.0; fdotf = 0.0;
if (update->ftol > 0.0) { if (update->ftol > 0.0) {

5
src/min_fire.h
View File

@ -34,9 +34,10 @@ class MinFire : public Min {
int iterate(int); int iterate(int);
private: private:
double dt,dtmax; double dt,dtmax,dtmin;
double alpha; double alpha;
bigint last_negative; bigint last_negative,ntimestep_start;
int vdotf_negatif;
}; };
} }

490
src/min_fire2.cpp
View File

@ -1,490 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Julien Guénolé, RWTH Aachen University and
Erik Bitzek, FAU Erlangen-Nuernberg
------------------------------------------------------------------------- */
#include <cmath>
#include "min_fire2.h"
#include "universe.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "output.h"
#include "timer.h"
#include "error.h"
#include "variable.h"
#include "modify.h"
#include "compute.h"
#include "domain.h"
#include "neighbor.h"
#include "comm.h"
using namespace LAMMPS_NS;
// EPS_ENERGY = minimum normalization for energy tolerance
#define EPS_ENERGY 1.0e-8
/* ---------------------------------------------------------------------- */
MinFire2::MinFire2(LAMMPS *lmp) : Min(lmp) {}
/* ---------------------------------------------------------------------- */
void MinFire2::init()
{
Min::init();
// simple parameters validation
if (tmax < tmin) error->all(FLERR,"tmax has to be larger than tmin");
if (dtgrow < 1.0) error->all(FLERR,"dtgrow has to be larger than 1.0");
if (dtshrink > 1.0) error->all(FLERR,"dtshrink has to be smaller than 1.0");
dt = update->dt;
dtmax = tmax * dt;
dtmin = tmin * dt;
alpha = alpha0;
last_negative = ntimestep_start = update->ntimestep;
vdotf_negatif = 0;
}
/* ---------------------------------------------------------------------- */
void MinFire2::setup_style()
{
double **v = atom->v;
int nlocal = atom->nlocal;
// print the parameters used within fire2 into the log
const char *s1[] = {"eulerimplicit","verlet","leapfrog","eulerexplicit"};
const char *s2[] = {"no","yes"};
if (comm->me == 0 && logfile) {
fprintf(logfile," Parameters for fire2: \n"
" dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin "
" integrator halfstepback relaxbox relaxbox_mod relaxbox_rate ptol \n"
" %4g %9i %6g %8g %6g %11g %4g %4g %13s %12s \n",
dmax, delaystep, dtgrow, dtshrink, alpha0, alphashrink, tmax, tmin,
s1[integrator], s2[halfstepback_flag]);
}
// initialize the velocities
for (int i = 0; i < nlocal; i++)
v[i][0] = v[i][1] = v[i][2] = 0.0;
}
/* ----------------------------------------------------------------------
set current vector lengths and pointers
called after atoms have migrated
------------------------------------------------------------------------- */
void MinFire2::reset_vectors()
{
// atomic dof
nvec = 3 * atom->nlocal;
if (nvec) xvec = atom->x[0];
if (nvec) fvec = atom->f[0];
}
/* ---------------------------------------------------------------------- */
int MinFire2::iterate(int maxiter)
{
bigint ntimestep;
double vmax,vdotf,vdotfall,vdotv,vdotvall,fdotf,fdotfall;
double scale1,scale2;
double dtvone,dtv,dtf,dtfm;
int flag,flagall;
alpha_final = 0.0;
// Leap Frog integration initialization
if (integrator == 2) {
double **f = atom->f;
double **v = atom->v;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int nlocal = atom->nlocal;
energy_force(0);
neval++;
dtf = -0.5 * dt * force->ftm2v;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / rmass[i];
v[i][0] = dtfm * f[i][0];
v[i][1] = dtfm * f[i][1];
v[i][2] = dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / mass[type[i]];
v[i][0] = dtfm * f[i][0];
v[i][1] = dtfm * f[i][1];
v[i][2] = dtfm * f[i][2];
}
}
}
for (int iter = 0; iter < maxiter; iter++) {
if (timer->check_timeout(niter))
return TIMEOUT;
ntimestep = ++update->ntimestep;
niter++;
// pointers
int nlocal = atom->nlocal;
double **v = atom->v;
double **f = atom->f;
double **x = atom->x;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
// vdotfall = v dot f
vdotf = 0.0;
for (int i = 0; i < nlocal; i++)
vdotf += v[i][0]*f[i][0] + v[i][1]*f[i][1] + v[i][2]*f[i][2];
MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,world);
// sum vdotf over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
vdotf = vdotfall;
MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
}
// if (v dot f) > 0:
// v = (1-alpha) v + alpha |v| Fhat
// |v| = length of v, Fhat = unit f
// Only: (1-alpha) and alpha |v| Fhat is calculated here
// the modificatin of v is made wihtin the integration, after v update
// if more than delaystep since v dot f was negative:
// increase timestep, update global timestep and decrease alpha
if (vdotfall > 0.0) {
vdotv = 0.0;
vdotf_negatif = 0;
for (int i = 0; i < nlocal; i++)
vdotv += v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world);
// sum vdotv over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
vdotv = vdotvall;
MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
}
fdotf = 0.0;
for (int i = 0; i < nlocal; i++)
fdotf += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,world);
// sum fdotf over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
fdotf = fdotfall;
MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
}
scale1 = 1.0 - alpha;
if (fdotfall <= 1e-20) scale2 = 0.0;
else scale2 = alpha * sqrt(vdotvall/fdotfall);
if (ntimestep - last_negative > delaystep) {
dt = MIN(dt*dtgrow,dtmax);
update->dt = dt;
alpha *= alphashrink;
}
// else (v dot f) <= 0
// if more than delaystep since starting the relaxation:
// reset alpha
// if dt*dtshrink > dtmin:
// decrease timestep
// update global timestep (for thermo output)
// half step back within the dynamics: x(t) = x(t-0.5*dt)
// reset velocities: v = 0
} else {
last_negative = ntimestep;
int delayflag = 1;
if (ntimestep - ntimestep_start < delaystep && delaystep_start_flag)
delayflag = 0;
if (delayflag) {
alpha = alpha0;
if (dt*dtshrink >= dtmin) {
dt *= dtshrink;
update->dt = dt;
}
}
// stopping criterion while stuck in a local bassin of the PES
vdotf_negatif++;
if (max_vdotf_negatif > 0 && vdotf_negatif > max_vdotf_negatif)
return MAXVDOTF;
// inertia correction
if (halfstepback_flag) {
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
dtvone = dt;
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;
}
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world);
// min dtv over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
dtvone = dtv;
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld);
}
// Dynamic integration scheme:
// 0: semi-implicit Euler
// 1: velocity Verlet
// 2: leapfrog (initial half step before the iteration loop)
// 3: explicit Euler
// Semi-implicit Euler OR Leap Frog integration
if (integrator == 0 || integrator == 2) {
dtf = dtv * force->ftm2v;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / rmass[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) {
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];
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / 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) {
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];
}
}
eprevious = ecurrent;
ecurrent = energy_force(0);
neval++;
// Velocity Verlet integration
} else if (integrator == 1) {
dtf = 0.5 * dtv * force->ftm2v;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / rmass[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) {
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];
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / 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) {
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];
}
}
eprevious = ecurrent;
ecurrent = energy_force(0);
neval++;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
}
// Standard Euler integration
} else if (integrator == 3) {
dtf = dtv * force->ftm2v;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / rmass[i];
if (vdotfall > 0.0) {
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];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / mass[type[i]];
if (vdotfall > 0.0) {
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];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
}
eprevious = ecurrent;
ecurrent = energy_force(0);
neval++;
}
// energy tolerance criterion
// only check after delaystep elapsed since velocties reset to 0
// sync across replicas if running multi-replica minimization
// reset the timestep to the initial value
if (update->etol > 0.0 && ntimestep-last_negative > delaystep) {
if (update->multireplica == 0) {
if (fabs(ecurrent-eprevious) <
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
return ETOL;
} else {
if (fabs(ecurrent-eprevious) <
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
flag = 0;
else flag = 1;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
if (flagall == 0)
return ETOL;
}
}
// force tolerance criterion
// sync across replicas if running multi-replica minimization
// reset the timestep to the initial value
if (update->ftol > 0.0) {
fdotf = fnorm_sqr();
if (update->multireplica == 0) {
if (fdotf < update->ftol*update->ftol)
return FTOL;
} else {
if (fdotf < update->ftol*update->ftol) flag = 0;
else flag = 1;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
if (flagall == 0)
return FTOL;
}
}
// output for thermo, dump, restart files
if (output->next == ntimestep) {
timer->stamp();
output->write(ntimestep);
timer->stamp(Timer::OUTPUT);
}
}
return MAXITER;
}

279
src/min_fire_old.cpp Normal file
View File

@ -0,0 +1,279 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "min_fire_old.h"
#include <mpi.h>
#include <cmath>
#include "universe.h"
#include "atom.h"
#include "error.h"
#include "force.h"
#include "update.h"
#include "output.h"
#include "timer.h"
using namespace LAMMPS_NS;
// EPS_ENERGY = minimum normalization for energy tolerance
#define EPS_ENERGY 1.0e-8
#define DELAYSTEP 5
#define DT_GROW 1.1
#define DT_SHRINK 0.5
#define ALPHA0 0.1
#define ALPHA_SHRINK 0.99
#define TMAX 10.0
/* ---------------------------------------------------------------------- */
MinFireOld::MinFireOld(LAMMPS *lmp) : Min(lmp) {}
/* ---------------------------------------------------------------------- */
void MinFireOld::init()
{
Min::init();
dt = update->dt;
dtmax = TMAX * dt;
alpha = ALPHA0;
last_negative = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
void MinFireOld::setup_style()
{
double **v = atom->v;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
v[i][0] = v[i][1] = v[i][2] = 0.0;
}
/* ----------------------------------------------------------------------
set current vector lengths and pointers
called after atoms have migrated
------------------------------------------------------------------------- */
void MinFireOld::reset_vectors()
{
// atomic dof
nvec = 3 * atom->nlocal;
if (nvec) xvec = atom->x[0];
if (nvec) fvec = atom->f[0];
}
/* ---------------------------------------------------------------------- */
int MinFireOld::iterate(int maxiter)
{
bigint ntimestep;
double vmax,vdotf,vdotfall,vdotv,vdotvall,fdotf,fdotfall;
double scale1,scale2;
double dtvone,dtv,dtf,dtfm;
int flag,flagall;
alpha_final = 0.0;
for (int iter = 0; iter < maxiter; iter++) {
if (timer->check_timeout(niter))
return TIMEOUT;
ntimestep = ++update->ntimestep;
niter++;
// vdotfall = v dot f
double **v = atom->v;
double **f = atom->f;
int nlocal = atom->nlocal;
vdotf = 0.0;
for (int i = 0; i < nlocal; i++)
vdotf += v[i][0]*f[i][0] + v[i][1]*f[i][1] + v[i][2]*f[i][2];
MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,world);
// sum vdotf over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
vdotf = vdotfall;
MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
}
// if (v dot f) > 0:
// v = (1-alpha) v + alpha |v| Fhat
// |v| = length of v, Fhat = unit f
// if more than DELAYSTEP since v dot f was negative:
// increase timestep and decrease alpha
if (vdotfall > 0.0) {
vdotv = 0.0;
for (int i = 0; i < nlocal; i++)
vdotv += v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world);
// sum vdotv over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
vdotv = vdotvall;
MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
}
fdotf = 0.0;
for (int i = 0; i < nlocal; i++)
fdotf += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,world);
// sum fdotf over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
fdotf = fdotfall;
MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
}
scale1 = 1.0 - alpha;
if (fdotfall == 0.0) scale2 = 0.0;
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];
}
if (ntimestep - last_negative > DELAYSTEP) {
dt = MIN(dt*DT_GROW,dtmax);
alpha *= ALPHA_SHRINK;
}
// else (v dot f) <= 0:
// decrease timestep, reset alpha, set v = 0
} else {
last_negative = ntimestep;
dt *= DT_SHRINK;
alpha = ALPHA0;
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;
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;
}
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world);
// min dtv over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
dtvone = dtv;
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld);
}
dtf = dtv * force->ftm2v;
// Euler integration step
double **x = atom->x;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtf / rmass[i];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
} 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];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
}
eprevious = ecurrent;
ecurrent = energy_force(0);
neval++;
// energy tolerance criterion
// only check after DELAYSTEP elapsed since velocties reset to 0
// sync across replicas if running multi-replica minimization
if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) {
if (update->multireplica == 0) {
if (fabs(ecurrent-eprevious) <
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
return ETOL;
} else {
if (fabs(ecurrent-eprevious) <
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
flag = 0;
else flag = 1;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
if (flagall == 0) return ETOL;
}
}
// force tolerance criterion
// sync across replicas if running multi-replica minimization
fdotf = 0.0;
if (update->ftol > 0.0) {
if (normstyle == MAX) fdotf = fnorm_max(); // max force norm
else if (normstyle == INF) fdotf = fnorm_inf(); // inf force norm
else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm
else error->all(FLERR,"Illegal min_modify command");
if (update->multireplica == 0) {
if (fdotf < update->ftol*update->ftol) return FTOL;
} else {
if (fdotf < update->ftol*update->ftol) flag = 0;
else flag = 1;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
if (flagall == 0) return FTOL;
}
}
// output for thermo, dump, restart files
if (output->next == ntimestep) {
timer->stamp();
output->write(ntimestep);
timer->stamp(Timer::OUTPUT);
}
}
return MAXITER;
}

17
src/min_fire2.h → src/min_fire_old.h
View File

@ -13,31 +13,30 @@
#ifdef MINIMIZE_CLASS #ifdef MINIMIZE_CLASS
MinimizeStyle(fire2,MinFire2) MinimizeStyle(fire/old,MinFireOld)
#else #else
#ifndef LMP_MIN_FIRE2_H #ifndef LMP_MIN_FIRE_OLD_H
#define LMP_MIN_FIRE2_H #define LMP_MIN_FIRE_OLD_H
#include "min.h" #include "min.h"
namespace LAMMPS_NS { namespace LAMMPS_NS {
class MinFire2 : public Min { class MinFireOld : public Min {
public: public:
MinFire2(class LAMMPS *); MinFireOld(class LAMMPS *);
~MinFire2() {} ~MinFireOld() {}
void init(); void init();
void setup_style(); void setup_style();
void reset_vectors(); void reset_vectors();
int iterate(int); int iterate(int);
private: private:
double dt,dtmax,dtmin; double dt,dtmax;
double alpha; double alpha;
bigint last_negative,ntimestep_start; bigint last_negative;
int vdotf_negatif;
}; };
} }