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lammps/src/min_fire.cpp

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/* ----------------------------------------------------------------------
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, CNRS and
Erik Bitzek, FAU Erlangen-Nuernberg
------------------------------------------------------------------------- */
#include <cmath>
#include "min_fire.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
/* ---------------------------------------------------------------------- */
MinFire::MinFire(LAMMPS *lmp) : Min(lmp) {}
/* ---------------------------------------------------------------------- */
void MinFire::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 MinFire::setup_style()
{
double **v = atom->v;
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 \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;
flagv0 = 1;
}
/* ----------------------------------------------------------------------
set current vector lengths and pointers
called after atoms have migrated
------------------------------------------------------------------------- */
void MinFire::reset_vectors()
{
// atomic dof
nvec = 3 * atom->nlocal;
if (nvec) xvec = atom->x[0];
if (nvec) fvec = atom->f[0];
}
/* ---------------------------------------------------------------------- */
int MinFire::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 * dt * v[i][0];
x[i][1] -= 0.5 * dt * v[i][1];
x[i][2] -= 0.5 * dt * v[i][2];
}
}
for (int i = 0; i < nlocal; i++)
v[i][0] = v[i][1] = v[i][2] = 0.0;
flagv0 = 1;
}
// evaluates velocties to estimate wether dtv has to be limited
// required when v have been reset
if (flagv0) {
dtf = dt * force->ftm2v;
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];
}
}
}
// 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);
// reset velocities when necessary
if (flagv0) {
for (int i = 0; i < nlocal; i++)
v[i][0] = v[i][1] = v[i][2] = 0.0;
}
// 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++;
}
// velocities have been evaluated
flagv0 = 0;
// 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
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;
}
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