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Finalized boxrelax option

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This commit is contained in:
Julien Guénolé
2017-08-16 16:54:49 +02:00
parent a2cf4e98b7
commit 6345e6b760
4 changed files with 146 additions and 15 deletions
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33
src/min.cpp
View File

@ -64,8 +64,11 @@ Min::Min(LAMMPS *lmp) : Pointers(lmp)
tmin = 0.02;
integrator = 0;
halfstepback_flag = 1;
relaxbox_mod = 1000000;
relaxbox_rate = 0.33;
relaxbox_flag = 0;
ptol = 1e-5;
p_flag[0] = p_flag[1] = p_flag[2] = 0;
elist_global = elist_atom = NULL;
vlist_global = vlist_atom = NULL;
@ -699,14 +702,32 @@ void Min::modify_params(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"relaxbox") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
if (strcmp(arg[iarg+1],"no") == 0) relaxbox_flag = 0;
else if (strcmp(arg[iarg+1],"iso") == 0) relaxbox_flag = 1;
else if (strcmp(arg[iarg+1],"axial") == 0) relaxbox_flag = 2;
else error->all(FLERR,"Illegal min_modify command");
if (strcmp(arg[iarg+1],"no") == 0) {
relaxbox_flag = 0;
} else if (strcmp(arg[iarg+1],"iso") == 0) {
relaxbox_flag = 1;
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) p_flag[2] = 0;
} else if (strcmp(arg[iarg+1],"aniso") == 0) {
relaxbox_flag = 2;
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) p_flag[2] = 0;
} else if (strcmp(arg[iarg+1],"x") == 0) {
relaxbox_flag = 2;
p_flag[0] = 1;
} else if (strcmp(arg[iarg+1],"y") == 0) {
relaxbox_flag = 2;
p_flag[1] = 1;
} else if (strcmp(arg[iarg+1],"z") == 0) {
relaxbox_flag = 2;
p_flag[2] = 1;
if (dimension == 2)
error->all(FLERR,"Invalid min_modify command for a 2d simulation");
} else error->all(FLERR,"Illegal min_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"relaxbox_modulus") == 0) {
} else if (strcmp(arg[iarg],"relaxbox_mod") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
relaxbox_modulus = force->numeric(FLERR,arg[iarg+1]);
relaxbox_mod = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"relaxbox_rate") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");

6
src/min.h
View File

@ -65,10 +65,12 @@ class Min : protected Pointers {
double tmax,tmin; // timestep multiplicators max, min
int integrator; // Newton integration: euler, leapfrog, verlet...
int halfstepback_flag; // half step backward when v.f <= 0.0
double relaxbox_modulus; // Bulk modulus used for box relax
double relaxbox_mod; // Bulk modulus used for box relax
double relaxbox_rate; // for box relaxation to 0 pressure
int relaxbox_flag; // 1: box relaxation iso; 2: axial
int relaxbox_flag; // 1: box relaxation iso; 2: aniso
double ptol; // pressure threshold for boxrelax
int p_flag[3];
int dimension;
int nelist_global,nelist_atom; // # of PE,virial computes to check
int nvlist_global,nvlist_atom;

120
src/min_adaptglok.cpp
View File

@ -20,6 +20,10 @@
#include "output.h"
#include "timer.h"
#include "error.h"
#include "variable.h"
#include "modify.h"
#include "compute.h"
#include "domain.h"
using namespace LAMMPS_NS;
@ -37,15 +41,35 @@ void MinAdaptGlok::init()
{
Min::init();
if (tmax < tmin) error->all(FLERR,"tmax cannot be smaller than tmin");
if (dtgrow < 1.0) error->all(FLERR,"dtgrow cannot be smaller than 1.0");
if (dtshrink > 1.0) error->all(FLERR,"dtshrink cannot be greater than 1.0");
// 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");
if (relaxbox_mod < 0.0)
error->all(FLERR,"relaxbox_mod has to be positif");
// require periodicity in boxrelax dimensions
if (p_flag[0] && domain->xperiodic == 0)
error->all(FLERR,"Cannot use boxrelax on a non-periodic dimension");
if (p_flag[1] && domain->yperiodic == 0)
error->all(FLERR,"Cannot use boxrelax on a non-periodic dimension");
if (p_flag[2] && domain->zperiodic == 0)
error->all(FLERR,"Cannot use boxrelax on a non-periodic dimension");
dt = dtinit = update->dt;
dtmax = tmax * dt;
dtmin = tmin * dt;
alpha = alpha0;
last_negative = ntimestep_start = update->ntimestep;
if (relaxbox_flag){
int icompute = modify->find_compute("thermo_temp");
temperature = modify->compute[icompute];
icompute = modify->find_compute("thermo_press");
pressure = modify->compute[icompute];
}
}
/* ---------------------------------------------------------------------- */
@ -73,6 +97,67 @@ void MinAdaptGlok::reset_vectors()
if (nvec) fvec = atom->f[0];
}
/* ----------------------------------------------------------------------
save current box state for converting atoms to lamda coords
------------------------------------------------------------------------- */
void MinAdaptGlok::save_box_state()
{
boxlo[0] = domain->boxlo[0];
boxlo[1] = domain->boxlo[1];
boxlo[2] = domain->boxlo[2];
for (int i = 0; i < 6; i++)
h_inv[i] = domain->h_inv[i];
}
/* ----------------------------------------------------------------------
deform the simulation box and remap the particles
------------------------------------------------------------------------- */
void MinAdaptGlok::relax_box()
{
int i,n;
// rescale simulation box and scale atom coords for all atoms
double **x = atom->x;
double epsilon;
double *current_pressure_v;
int *mask = atom->mask;
n = atom->nlocal + atom->nghost;
save_box_state();
// convert pertinent atoms and rigid bodies to lamda coords
domain->x2lamda(n);
// ensure the virial is tallied, update the flag
pressure->addstep(update->ntimestep);
update->vflag_global = update->ntimestep;
// compute pressure and change simulation box
pressure->compute_scalar();
pressure->compute_vector();
epsilon = pressure->scalar / relaxbox_mod;
for (int i = 0; i < 3; i++) {
if (relaxbox_flag == 2) epsilon = pressure->vector[i] / relaxbox_mod;
domain->boxhi[i] += p_flag[i] * domain->boxhi[i] * epsilon * relaxbox_rate;
}
// reset global and local box to new size/shape
domain->set_global_box();
domain->set_local_box();
// convert atoms and back to box coords
domain->lamda2x(n);
save_box_state();
}
/* ---------------------------------------------------------------------- */
int MinAdaptGlok::iterate(int maxiter)
@ -126,6 +211,10 @@ int MinAdaptGlok::iterate(int maxiter)
ntimestep = ++update->ntimestep;
niter++;
// Relax the simulation box
if (relaxbox_flag) relax_box();
// pointers
int nlocal = atom->nlocal;
@ -394,6 +483,21 @@ int MinAdaptGlok::iterate(int maxiter)
}
// Pressure relaxation criterion
// set pflag = 0 if relaxbox is activated and pressure > ptol
// pflag = 0 will hinder the energy or force criterion
pflag = 1;
if (relaxbox_flag == 1){
pressure->compute_scalar();
if (fabs(pressure->scalar) > ptol) pflag = 0;
}else if (relaxbox_flag == 2){
pressure->compute_vector();
for (int i = 0; i < 3; i++)
if (fabs(pressure->vector[i]) * p_flag[i] > ptol) pflag = 0;
}
// energy tolerance criterion
// only check after delaystep elapsed since velocties reset to 0
// sync across replicas if running multi-replica minimization
@ -402,13 +506,15 @@ int MinAdaptGlok::iterate(int maxiter)
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)){
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)
&& pflag) {
update->dt = dtinit;
return ETOL;
}
} else {
if (fabs(ecurrent-eprevious) <
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)
&& pflag)
flag = 0;
else flag = 1;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
@ -426,12 +532,12 @@ int MinAdaptGlok::iterate(int maxiter)
if (update->ftol > 0.0) {
fdotf = fnorm_sqr();
if (update->multireplica == 0) {
if (fdotf < update->ftol*update->ftol) {
if (fdotf < update->ftol*update->ftol && pflag) {
update->dt = dtinit;
return FTOL;
}
} else {
if (fdotf < update->ftol*update->ftol) flag = 0;
if (fdotf < update->ftol*update->ftol && pflag) flag = 0;
else flag = 1;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
if (flagall == 0) {

2
src/min_adaptglok.h
View File

@ -31,6 +31,8 @@ class MinAdaptGlok : public Min {
void init();
void setup_style();
void reset_vectors();
void save_box_state();
void relax_box();
int iterate(int);
private: