git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4906 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
192
src/min_fire.cpp
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192
src/min_fire.cpp
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@ -0,0 +1,192 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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||||||
|
certain rights in this software. This software is distributed under
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||||||
|
the GNU General Public License.
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|
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "min_fire.h"
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#include "atom.h"
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#include "force.h"
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#include "update.h"
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#include "output.h"
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#include "timer.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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// same as in other min classes
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enum{MAXITER,MAXEVAL,ETOL,FTOL,DOWNHILL,ZEROALPHA,ZEROFORCE,ZEROQUAD};
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#define MIN(A,B) ((A) < (B)) ? (A) : (B)
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#define MAX(A,B) ((A) > (B)) ? (A) : (B)
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#define DELAYSTEP 5
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#define DT_GROW 1.1
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#define DT_SHRINK 0.5
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#define ALPHA0 0.1
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#define ALPHA_SHRINK 0.99
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#define TMAX 10.0
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/* ---------------------------------------------------------------------- */
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MinFire::MinFire(LAMMPS *lmp) : Min(lmp) {}
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/* ---------------------------------------------------------------------- */
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void MinFire::init_style()
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{
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dt = update->dt;
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}
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/* ---------------------------------------------------------------------- */
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void MinFire::setup_style()
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{
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double **v = atom->v;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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v[i][0] = v[i][1] = v[i][2] = 0.0;
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}
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/* ----------------------------------------------------------------------
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set current vector lengths and pointers
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called after atoms have migrated
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------------------------------------------------------------------------- */
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void MinFire::reset_vectors()
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{
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// atomic dof
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nvec = 3 * atom->nlocal;
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if (nvec) xvec = atom->x[0];
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if (nvec) fvec = atom->f[0];
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}
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/* ---------------------------------------------------------------------- */
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int MinFire::iterate(int maxiter)
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{
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int ntimestep;
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double vmax,vdotf,vdotfall,vdotv,vdotvall,fdotf,fdotfall;
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double scale1,scale2;
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double dtvone,dtv,dtfm;
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alpha_final = 0.0;
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double alpha = ALPHA0;
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double dtmax = TMAX * dt;
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int last_negative = update->ntimestep;
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for (int iter = 0; iter < maxiter; iter++) {
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ntimestep = ++update->ntimestep;
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niter++;
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// vdotfall = v dot f
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double **v = atom->v;
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double **f = atom->f;
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int nlocal = atom->nlocal;
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vdotf = 0.0;
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for (int i = 0; i < nlocal; i++)
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vdotf += v[i][0]*f[i][0] + v[i][1]*f[i][1] + v[i][2]*f[i][2];
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MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,world);
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// if (v dot f) > 0:
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// v = (1-alpha) v + alpha |v| Fhat
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// |v| = length of v, Fhat = unit f
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// if more than DELAYSTEP since v dot f was negative:
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// increase timestep and decrease alpha
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if (vdotfall > 0.0) {
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vdotv = 0.0;
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for (int i = 0; i < nlocal; i++)
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vdotv += v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
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MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world);
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fdotf = 0.0;
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for (int i = 0; i < nlocal; i++)
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fdotf += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
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MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,world);
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scale1 = 1.0 - alpha;
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if (fdotfall == 0.0) scale2 = 0.0;
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else scale2 = alpha * sqrt(vdotvall/fdotfall);
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for (int i = 0; i < nlocal; i++) {
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v[i][0] = scale1*v[i][0] + scale2*f[i][0];
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v[i][1] = scale1*v[i][1] + scale2*f[i][1];
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v[i][2] = scale1*v[i][2] + scale2*f[i][2];
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}
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if (ntimestep - last_negative > DELAYSTEP) {
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dt = MIN(dt*DT_GROW,dtmax);
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alpha *= ALPHA_SHRINK;
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}
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// else (v dot f) <= 0:
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// decrease timestep, reset alpha, set v = 0
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} else {
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last_negative = ntimestep;
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dt *= DT_SHRINK;
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alpha = ALPHA0;
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for (int i = 0; i < nlocal; i++)
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v[i][0] = v[i][1] = v[i][2] = 0.0;
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}
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// limit timestep so no particle moves further than dmax
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double *mass = atom->mass;
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int *type = atom->type;
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dtvone = dt;
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for (int i = 0; i < nlocal; i++) {
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vmax = MAX(fabs(v[i][0]),fabs(v[i][1]));
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vmax = MAX(vmax,fabs(v[i][2]));
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if (dtvone*vmax > dmax) dtvone = dmax/vmax;
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}
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MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world);
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// Euler integration step
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double **x = atom->x;
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for (int i = 0; i < nlocal; i++) {
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dtfm = dtv / mass[type[i]];
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x[i][0] += dtv * v[i][0];
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x[i][1] += dtv * v[i][1];
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x[i][2] += dtv * v[i][2];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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}
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eprevious = ecurrent;
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ecurrent = energy_force(0);
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neval++;
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// force tolerance criterion
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//fdotf = fnorm_sqr();
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//if (fdotf < update->ftol*update->ftol) return FTOL;
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// output for thermo, dump, restart files
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if (output->next == ntimestep) {
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timer->stamp();
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output->write(ntimestep);
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timer->stamp(TIME_OUTPUT);
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}
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}
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return MAXITER;
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}
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43
src/min_fire.h
Normal file
43
src/min_fire.h
Normal file
@ -0,0 +1,43 @@
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/* ----------------------------------------------------------------------
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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.
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|
------------------------------------------------------------------------- */
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#ifdef MINIMIZE_CLASS
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MinimizeStyle(fire,MinFire)
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#else
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#ifndef LMP_MIN_FIRE_H
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#define LMP_MIN_FIRE_H
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#include "min.h"
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namespace LAMMPS_NS {
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class MinFire : public Min {
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public:
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MinFire(class LAMMPS *);
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~MinFire() {}
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void init_style();
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void setup_style();
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void reset_vectors();
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|
int iterate(int);
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|
private:
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|
double dt;
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};
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}
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#endif
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#endif
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159
src/min_quickmin.cpp
Normal file
159
src/min_quickmin.cpp
Normal file
@ -0,0 +1,159 @@
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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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include "math.h"
|
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|
#include "min_quickmin.h"
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|
#include "atom.h"
|
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|
#include "force.h"
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|
#include "update.h"
|
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|
#include "output.h"
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|
#include "timer.h"
|
||||||
|
#include "error.h"
|
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|
|
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|
using namespace LAMMPS_NS;
|
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|
|
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|
// same as in other min classes
|
||||||
|
|
||||||
|
enum{MAXITER,MAXEVAL,ETOL,FTOL,DOWNHILL,ZEROALPHA,ZEROFORCE,ZEROQUAD};
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|
|
||||||
|
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
|
||||||
|
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
MinQuickmin::MinQuickmin(LAMMPS *lmp) : Min(lmp) {}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void MinQuickmin::init_style()
|
||||||
|
{
|
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|
dt = update->dt;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void MinQuickmin::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 MinQuickmin::reset_vectors()
|
||||||
|
{
|
||||||
|
// atomic dof
|
||||||
|
|
||||||
|
nvec = 3 * atom->nlocal;
|
||||||
|
if (nvec) xvec = atom->x[0];
|
||||||
|
if (nvec) fvec = atom->f[0];
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
int MinQuickmin::iterate(int maxiter)
|
||||||
|
{
|
||||||
|
int ntimestep;
|
||||||
|
double vmax,vdotf,vdotfall,fdotf,fdotfall,scale;
|
||||||
|
double dtvone,dtv,dtfm;
|
||||||
|
|
||||||
|
alpha_final = 0.0;
|
||||||
|
|
||||||
|
for (int iter = 0; iter < maxiter; iter++) {
|
||||||
|
ntimestep = ++update->ntimestep;
|
||||||
|
niter++;
|
||||||
|
|
||||||
|
// zero velocity if anti-parallel to force
|
||||||
|
// else project velocity in direction of force
|
||||||
|
|
||||||
|
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);
|
||||||
|
|
||||||
|
if (vdotfall < 0.0) {
|
||||||
|
for (int i = 0; i < nlocal; i++)
|
||||||
|
v[i][0] = v[i][1] = v[i][2] = 0.0;
|
||||||
|
|
||||||
|
} else {
|
||||||
|
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);
|
||||||
|
if (fdotfall == 0.0) scale = 0.0;
|
||||||
|
else scale = vdotfall/fdotfall;
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
v[i][0] = scale * f[i][0];
|
||||||
|
v[i][1] = scale * f[i][1];
|
||||||
|
v[i][2] = scale * f[i][2];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// limit timestep so no particle moves further than dmax
|
||||||
|
|
||||||
|
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);
|
||||||
|
|
||||||
|
// Euler integration step
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
dtfm = dtv / 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++;
|
||||||
|
|
||||||
|
// force tolerance criterion
|
||||||
|
|
||||||
|
//fdotf = fnorm_sqr();
|
||||||
|
//if (fdotf < update->ftol*update->ftol) return FTOL;
|
||||||
|
|
||||||
|
// output for thermo, dump, restart files
|
||||||
|
|
||||||
|
if (output->next == ntimestep) {
|
||||||
|
timer->stamp();
|
||||||
|
output->write(ntimestep);
|
||||||
|
timer->stamp(TIME_OUTPUT);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return MAXITER;
|
||||||
|
}
|
||||||
43
src/min_quickmin.h
Normal file
43
src/min_quickmin.h
Normal file
@ -0,0 +1,43 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef MINIMIZE_CLASS
|
||||||
|
|
||||||
|
MinimizeStyle(quickmin,MinQuickmin)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_MIN_QUICKMIN_H
|
||||||
|
#define LMP_MIN_QUICKMIN_H
|
||||||
|
|
||||||
|
#include "min.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class MinQuickmin : public Min {
|
||||||
|
public:
|
||||||
|
MinQuickmin(class LAMMPS *);
|
||||||
|
~MinQuickmin() {}
|
||||||
|
void init_style();
|
||||||
|
void setup_style();
|
||||||
|
void reset_vectors();
|
||||||
|
int iterate(int);
|
||||||
|
|
||||||
|
private:
|
||||||
|
double dt;
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
357
src/temper.cpp
357
src/temper.cpp
@ -1,357 +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 author: Mark Sears (SNL)
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#include "math.h"
|
|
||||||
#include "stdlib.h"
|
|
||||||
#include "string.h"
|
|
||||||
#include "temper.h"
|
|
||||||
#include "universe.h"
|
|
||||||
#include "domain.h"
|
|
||||||
#include "atom.h"
|
|
||||||
#include "update.h"
|
|
||||||
#include "integrate.h"
|
|
||||||
#include "modify.h"
|
|
||||||
#include "compute.h"
|
|
||||||
#include "force.h"
|
|
||||||
#include "output.h"
|
|
||||||
#include "thermo.h"
|
|
||||||
#include "fix.h"
|
|
||||||
#include "random_park.h"
|
|
||||||
#include "finish.h"
|
|
||||||
#include "timer.h"
|
|
||||||
#include "memory.h"
|
|
||||||
#include "error.h"
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
|
||||||
|
|
||||||
// #define TEMPER_DEBUG 1
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
Temper::Temper(LAMMPS *lmp) : Pointers(lmp) {}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
Temper::~Temper()
|
|
||||||
{
|
|
||||||
MPI_Comm_free(&roots);
|
|
||||||
if (ranswap) delete ranswap;
|
|
||||||
delete ranboltz;
|
|
||||||
delete [] set_temp;
|
|
||||||
delete [] temp2world;
|
|
||||||
delete [] world2temp;
|
|
||||||
delete [] world2root;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
perform tempering with inter-world swaps
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void Temper::command(int narg, char **arg)
|
|
||||||
{
|
|
||||||
if (universe->nworlds == 1)
|
|
||||||
error->all("Must have more than one processor partition to temper");
|
|
||||||
if (domain->box_exist == 0)
|
|
||||||
error->all("Temper command before simulation box is defined");
|
|
||||||
if (narg != 6 && narg != 7) error->universe_all("Illegal temper command");
|
|
||||||
|
|
||||||
int nsteps = atoi(arg[0]);
|
|
||||||
nevery = atoi(arg[1]);
|
|
||||||
double temp = atof(arg[2]);
|
|
||||||
|
|
||||||
for (whichfix = 0; whichfix < modify->nfix; whichfix++)
|
|
||||||
if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
|
|
||||||
if (whichfix == modify->nfix)
|
|
||||||
error->universe_all("Tempering fix ID is not defined");
|
|
||||||
|
|
||||||
seed_swap = atoi(arg[4]);
|
|
||||||
seed_boltz = atoi(arg[5]);
|
|
||||||
|
|
||||||
my_set_temp = universe->iworld;
|
|
||||||
if (narg == 7) my_set_temp = atoi(arg[6]);
|
|
||||||
|
|
||||||
// swap frequency must evenly divide total # of timesteps
|
|
||||||
|
|
||||||
if (nevery == 0) error->universe_all("Invalid frequency in temper command");
|
|
||||||
nswaps = nsteps/nevery;
|
|
||||||
if (nswaps*nevery != nsteps)
|
|
||||||
error->universe_all("Non integer # of swaps in temper command");
|
|
||||||
|
|
||||||
// fix style must be appropriate for temperature control
|
|
||||||
|
|
||||||
if ((strcmp(modify->fix[whichfix]->style,"nvt") != 0) &&
|
|
||||||
(strcmp(modify->fix[whichfix]->style,"langevin") != 0) &&
|
|
||||||
(strcmp(modify->fix[whichfix]->style,"temp/berendsen") != 0) &&
|
|
||||||
(strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0))
|
|
||||||
error->universe_all("Tempering temperature fix is not valid");
|
|
||||||
|
|
||||||
// setup for long tempering run
|
|
||||||
|
|
||||||
update->whichflag = 1;
|
|
||||||
update->nsteps = nsteps;
|
|
||||||
update->beginstep = update->firststep = update->ntimestep;
|
|
||||||
update->endstep = update->laststep = update->firststep + nsteps;
|
|
||||||
|
|
||||||
lmp->init();
|
|
||||||
|
|
||||||
// local storage
|
|
||||||
|
|
||||||
me_universe = universe->me;
|
|
||||||
MPI_Comm_rank(world,&me);
|
|
||||||
nworlds = universe->nworlds;
|
|
||||||
iworld = universe->iworld;
|
|
||||||
boltz = force->boltz;
|
|
||||||
|
|
||||||
// pe_compute = ptr to thermo_pe compute
|
|
||||||
// notify compute it will be called at first swap
|
|
||||||
|
|
||||||
int id = modify->find_compute("thermo_pe");
|
|
||||||
if (id < 0) error->all("Tempering could not find thermo_pe compute");
|
|
||||||
Compute *pe_compute = modify->compute[id];
|
|
||||||
pe_compute->addstep(update->ntimestep + nevery);
|
|
||||||
|
|
||||||
// create MPI communicator for root proc from each world
|
|
||||||
|
|
||||||
int color;
|
|
||||||
if (me == 0) color = 0;
|
|
||||||
else color = 1;
|
|
||||||
MPI_Comm_split(universe->uworld,color,0,&roots);
|
|
||||||
|
|
||||||
// RNGs for swaps and Boltzmann test
|
|
||||||
// warm up Boltzmann RNG
|
|
||||||
|
|
||||||
if (seed_swap) ranswap = new RanPark(lmp,seed_swap);
|
|
||||||
else ranswap = NULL;
|
|
||||||
ranboltz = new RanPark(lmp,seed_boltz + me_universe);
|
|
||||||
for (int i = 0; i < 100; i++) ranboltz->uniform();
|
|
||||||
|
|
||||||
// world2root[i] = global proc that is root proc of world i
|
|
||||||
|
|
||||||
world2root = new int[nworlds];
|
|
||||||
if (me == 0)
|
|
||||||
MPI_Allgather(&me_universe,1,MPI_INT,world2root,1,MPI_INT,roots);
|
|
||||||
MPI_Bcast(world2root,nworlds,MPI_INT,0,world);
|
|
||||||
|
|
||||||
// create static list of set temperatures
|
|
||||||
// allgather tempering arg "temp" across root procs
|
|
||||||
// bcast from each root to other procs in world
|
|
||||||
|
|
||||||
set_temp = new double[nworlds];
|
|
||||||
if (me == 0) MPI_Allgather(&temp,1,MPI_DOUBLE,set_temp,1,MPI_DOUBLE,roots);
|
|
||||||
MPI_Bcast(set_temp,nworlds,MPI_DOUBLE,0,world);
|
|
||||||
|
|
||||||
// create world2temp only on root procs from my_set_temp
|
|
||||||
// create temp2world on root procs from world2temp,
|
|
||||||
// then bcast to all procs within world
|
|
||||||
|
|
||||||
world2temp = new int[nworlds];
|
|
||||||
temp2world = new int[nworlds];
|
|
||||||
if (me == 0) {
|
|
||||||
MPI_Allgather(&my_set_temp,1,MPI_INT,world2temp,1,MPI_INT,roots);
|
|
||||||
for (int i = 0; i < nworlds; i++) temp2world[world2temp[i]] = i;
|
|
||||||
}
|
|
||||||
MPI_Bcast(temp2world,nworlds,MPI_INT,0,world);
|
|
||||||
|
|
||||||
// if restarting tempering, reset temp target of Fix to current my_set_temp
|
|
||||||
|
|
||||||
if (narg == 7) {
|
|
||||||
double new_temp = set_temp[my_set_temp];
|
|
||||||
modify->fix[whichfix]->reset_target(new_temp);
|
|
||||||
}
|
|
||||||
|
|
||||||
// setup tempering runs
|
|
||||||
|
|
||||||
int i,which,partner,swap,partner_set_temp,partner_world;
|
|
||||||
double pe,pe_partner,boltz_factor,new_temp;
|
|
||||||
MPI_Status status;
|
|
||||||
|
|
||||||
if (me_universe == 0 && universe->uscreen)
|
|
||||||
fprintf(universe->uscreen,"Setting up tempering ...\n");
|
|
||||||
|
|
||||||
update->integrate->setup();
|
|
||||||
|
|
||||||
if (me_universe == 0) {
|
|
||||||
if (universe->uscreen) {
|
|
||||||
fprintf(universe->uscreen,"Step");
|
|
||||||
for (int i = 0; i < nworlds; i++)
|
|
||||||
fprintf(universe->uscreen," T%d",i);
|
|
||||||
fprintf(universe->uscreen,"\n");
|
|
||||||
}
|
|
||||||
if (universe->ulogfile) {
|
|
||||||
fprintf(universe->ulogfile,"Step");
|
|
||||||
for (int i = 0; i < nworlds; i++)
|
|
||||||
fprintf(universe->ulogfile," T%d",i);
|
|
||||||
fprintf(universe->ulogfile,"\n");
|
|
||||||
}
|
|
||||||
print_status();
|
|
||||||
}
|
|
||||||
|
|
||||||
timer->barrier_start(TIME_LOOP);
|
|
||||||
|
|
||||||
for (int iswap = 0; iswap < nswaps; iswap++) {
|
|
||||||
|
|
||||||
// run for nevery timesteps
|
|
||||||
|
|
||||||
update->integrate->run(nevery);
|
|
||||||
|
|
||||||
// compute PE
|
|
||||||
// notify compute it will be called at next swap
|
|
||||||
|
|
||||||
pe = pe_compute->compute_scalar();
|
|
||||||
pe_compute->addstep(update->ntimestep + nevery);
|
|
||||||
|
|
||||||
// which = which of 2 kinds of swaps to do (0,1)
|
|
||||||
|
|
||||||
if (!ranswap) which = iswap % 2;
|
|
||||||
else if (ranswap->uniform() < 0.5) which = 0;
|
|
||||||
else which = 1;
|
|
||||||
|
|
||||||
// partner_set_temp = which set temp I am partnering with for this swap
|
|
||||||
|
|
||||||
if (which == 0) {
|
|
||||||
if (my_set_temp % 2 == 0) partner_set_temp = my_set_temp + 1;
|
|
||||||
else partner_set_temp = my_set_temp - 1;
|
|
||||||
} else {
|
|
||||||
if (my_set_temp % 2 == 1) partner_set_temp = my_set_temp + 1;
|
|
||||||
else partner_set_temp = my_set_temp - 1;
|
|
||||||
}
|
|
||||||
|
|
||||||
// partner = proc ID to swap with
|
|
||||||
// if partner = -1, then I am not a proc that swaps
|
|
||||||
|
|
||||||
partner = -1;
|
|
||||||
if (me == 0 && partner_set_temp >= 0 && partner_set_temp < nworlds) {
|
|
||||||
partner_world = temp2world[partner_set_temp];
|
|
||||||
partner = world2root[partner_world];
|
|
||||||
}
|
|
||||||
|
|
||||||
// swap with a partner, only root procs in each world participate
|
|
||||||
// hi proc sends PE to low proc
|
|
||||||
// lo proc make Boltzmann decision on whether to swap
|
|
||||||
// lo proc communicates decision back to hi proc
|
|
||||||
|
|
||||||
swap = 0;
|
|
||||||
if (partner != -1) {
|
|
||||||
if (me_universe > partner)
|
|
||||||
MPI_Send(&pe,1,MPI_DOUBLE,partner,0,universe->uworld);
|
|
||||||
else
|
|
||||||
MPI_Recv(&pe_partner,1,MPI_DOUBLE,partner,0,universe->uworld,&status);
|
|
||||||
|
|
||||||
if (me_universe < partner) {
|
|
||||||
boltz_factor = (pe - pe_partner) *
|
|
||||||
(1.0/(boltz*set_temp[my_set_temp]) -
|
|
||||||
1.0/(boltz*set_temp[partner_set_temp]));
|
|
||||||
if (boltz_factor >= 0.0) swap = 1;
|
|
||||||
else if (ranboltz->uniform() < exp(boltz_factor)) swap = 1;
|
|
||||||
}
|
|
||||||
|
|
||||||
if (me_universe < partner)
|
|
||||||
MPI_Send(&swap,1,MPI_INT,partner,0,universe->uworld);
|
|
||||||
else
|
|
||||||
MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,&status);
|
|
||||||
|
|
||||||
#ifdef TEMPER_DEBUG
|
|
||||||
if (me_universe < partner)
|
|
||||||
printf("SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
|
|
||||||
me_universe,partner,swap,my_set_temp,partner_set_temp,
|
|
||||||
pe,pe_partner,boltz_factor,exp(boltz_factor));
|
|
||||||
#endif
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
// bcast swap result to other procs in my world
|
|
||||||
|
|
||||||
MPI_Bcast(&swap,1,MPI_INT,0,world);
|
|
||||||
|
|
||||||
// rescale kinetic energy via velocities if move is accepted
|
|
||||||
|
|
||||||
if (swap) scale_velocities(partner_set_temp,my_set_temp);
|
|
||||||
|
|
||||||
// if my world swapped, all procs in world reset temp target of Fix
|
|
||||||
|
|
||||||
if (swap) {
|
|
||||||
new_temp = set_temp[partner_set_temp];
|
|
||||||
modify->fix[whichfix]->reset_target(new_temp);
|
|
||||||
}
|
|
||||||
|
|
||||||
// update my_set_temp and temp2world on every proc
|
|
||||||
// root procs update their value if swap took place
|
|
||||||
// allgather across root procs
|
|
||||||
// bcast within my world
|
|
||||||
|
|
||||||
if (swap) my_set_temp = partner_set_temp;
|
|
||||||
if (me == 0) {
|
|
||||||
MPI_Allgather(&my_set_temp,1,MPI_INT,world2temp,1,MPI_INT,roots);
|
|
||||||
for (i = 0; i < nworlds; i++) temp2world[world2temp[i]] = i;
|
|
||||||
}
|
|
||||||
MPI_Bcast(temp2world,nworlds,MPI_INT,0,world);
|
|
||||||
|
|
||||||
// print out current swap status
|
|
||||||
|
|
||||||
if (me_universe == 0) print_status();
|
|
||||||
}
|
|
||||||
|
|
||||||
timer->barrier_stop(TIME_LOOP);
|
|
||||||
|
|
||||||
update->integrate->cleanup();
|
|
||||||
|
|
||||||
Finish finish(lmp);
|
|
||||||
finish.end(1);
|
|
||||||
|
|
||||||
update->whichflag = 0;
|
|
||||||
update->firststep = update->laststep = 0;
|
|
||||||
update->beginstep = update->endstep = 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
scale kinetic energy via velocities a la Sugita
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void Temper::scale_velocities(int t_partner, int t_me)
|
|
||||||
{
|
|
||||||
double sfactor = sqrt(set_temp[t_partner]/set_temp[t_me]);
|
|
||||||
|
|
||||||
double **v = atom->v;
|
|
||||||
int nlocal = atom->nlocal;
|
|
||||||
|
|
||||||
for (int i = 0; i < nlocal; i++) {
|
|
||||||
v[i][0] = v[i][0]*sfactor;
|
|
||||||
v[i][1] = v[i][1]*sfactor;
|
|
||||||
v[i][2] = v[i][2]*sfactor;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
proc 0 prints current tempering status
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void Temper::print_status()
|
|
||||||
{
|
|
||||||
if (universe->uscreen) {
|
|
||||||
fprintf(universe->uscreen,"%d ",update->ntimestep);
|
|
||||||
for (int i = 0; i < nworlds; i++)
|
|
||||||
fprintf(universe->uscreen,"%d ",world2temp[i]);
|
|
||||||
fprintf(universe->uscreen,"\n");
|
|
||||||
}
|
|
||||||
if (universe->ulogfile) {
|
|
||||||
fprintf(universe->ulogfile,"%d ",update->ntimestep);
|
|
||||||
for (int i = 0; i < nworlds; i++)
|
|
||||||
fprintf(universe->ulogfile,"%d ",world2temp[i]);
|
|
||||||
fprintf(universe->ulogfile,"\n");
|
|
||||||
fflush(universe->ulogfile);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
59
src/temper.h
59
src/temper.h
@ -1,59 +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.
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#ifdef COMMAND_CLASS
|
|
||||||
|
|
||||||
CommandStyle(temper,Temper)
|
|
||||||
|
|
||||||
#else
|
|
||||||
|
|
||||||
#ifndef LMP_TEMPER_H
|
|
||||||
#define LMP_TEMPER_H
|
|
||||||
|
|
||||||
#include "pointers.h"
|
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
|
||||||
|
|
||||||
class Temper : protected Pointers {
|
|
||||||
public:
|
|
||||||
Temper(class LAMMPS *);
|
|
||||||
~Temper();
|
|
||||||
void command(int, char **);
|
|
||||||
|
|
||||||
private:
|
|
||||||
int me,me_universe; // my proc ID in world and universe
|
|
||||||
int iworld,nworlds; // world info
|
|
||||||
double boltz; // copy from output->boltz
|
|
||||||
MPI_Comm roots; // MPI comm with 1 root proc from each world
|
|
||||||
class RanPark *ranswap,*ranboltz; // RNGs for swapping and Boltz factor
|
|
||||||
int nevery; // # of timesteps between swaps
|
|
||||||
int nswaps; // # of tempering swaps to perform
|
|
||||||
int seed_swap; // 0 = toggle swaps, n = RNG for swap direction
|
|
||||||
int seed_boltz; // seed for Boltz factor comparison
|
|
||||||
int whichfix; // index of temperature fix to use
|
|
||||||
int fixstyle; // what kind of temperature fix is used
|
|
||||||
|
|
||||||
int my_set_temp; // which set temp I am simulating
|
|
||||||
double *set_temp; // static list of replica set temperatures
|
|
||||||
int *temp2world; // temp2world[i] = world simulating set temp i
|
|
||||||
int *world2temp; // world2temp[i] = temp simulated by world i
|
|
||||||
int *world2root; // world2root[i] = root proc of world i
|
|
||||||
|
|
||||||
void scale_velocities(int, int);
|
|
||||||
void print_status();
|
|
||||||
};
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
#endif
|
|
||||||
#endif
|
|
||||||
Reference in New Issue
Block a user