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fix_smd.cpp
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Thu, Jun 6, 07:47
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rLAMMPS lammps
fix_smd.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 author: Axel Kohlmeyer (UPenn)
based on fix spring by: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_smd.h"
#include "atom.h"
#include "comm.h"
#include "update.h"
#include "respa.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "group.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum { SMD_NONE=0,
SMD_TETHER=1<<0, SMD_COUPLE=1<<1,
SMD_CVEL=1<<2, SMD_CFOR=1<<3,
SMD_AUTOX=1<<4, SMD_AUTOY=1<<5, SMD_AUTOZ=1<<6};
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
FixSMD::FixSMD(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
styleflag = SMD_NONE;
k_smd = f_smd = v_smd = -1.0;
xflag = yflag = zflag = 1;
xc = yc = zc = 0.0;
xn = yn = zn = 1.0;
pmf = r_old = r_now = r0 = 0.0;
restart_global = 1;
vector_flag = 1;
size_vector = 7;
global_freq = 1;
extvector = 1;
int argoffs=3;
if (strcmp(arg[argoffs],"cvel") == 0) {
if (narg < argoffs+3) error->all(FLERR,"Illegal fix smd command");
styleflag |= SMD_CVEL;
k_smd = force->numeric(FLERR,arg[argoffs+1]);
v_smd = force->numeric(FLERR,arg[argoffs+2]); // to be multiplied by update->dt when used.
argoffs += 3;
} else if (strcmp(arg[argoffs],"cfor") == 0) {
if (narg < argoffs+2) error->all(FLERR,"Illegal fix smd command");
styleflag |= SMD_CFOR;
f_smd = force->numeric(FLERR,arg[argoffs+1]);
argoffs += 2;
} else error->all(FLERR,"Illegal fix smd command");
if (strcmp(arg[argoffs],"tether") == 0) {
if (narg < argoffs+5) error->all(FLERR,"Illegal fix smd command");
styleflag |= SMD_TETHER;
if (strcmp(arg[argoffs+1],"NULL") == 0) xflag = 0;
else xc = force->numeric(FLERR,arg[argoffs+1]);
if (strcmp(arg[argoffs+2],"NULL") == 0) yflag = 0;
else yc = force->numeric(FLERR,arg[argoffs+2]);
if (strcmp(arg[argoffs+3],"NULL") == 0) zflag = 0;
else zc = force->numeric(FLERR,arg[argoffs+3]);
r0 = force->numeric(FLERR,arg[argoffs+4]);
if (r0 < 0) error->all(FLERR,"R0 < 0 for fix smd command");
argoffs += 5;
} else if (strcmp(arg[argoffs],"couple") == 0) {
if (narg < argoffs+6) error->all(FLERR,"Illegal fix smd command");
styleflag |= SMD_COUPLE;
igroup2 = group->find(arg[argoffs+1]);
if (igroup2 == -1)
error->all(FLERR,"Could not find fix smd couple group ID");
if (igroup2 == igroup)
error->all(FLERR,"Two groups cannot be the same in fix smd couple");
group2bit = group->bitmask[igroup2];
if (strcmp(arg[argoffs+2],"NULL") == 0) xflag = 0;
else if (strcmp(arg[argoffs+2],"auto") == 0) styleflag |= SMD_AUTOX;
else xc = force->numeric(FLERR,arg[argoffs+2]);
if (strcmp(arg[argoffs+3],"NULL") == 0) yflag = 0;
else if (strcmp(arg[argoffs+3],"auto") == 0) styleflag |= SMD_AUTOY;
else yc = force->numeric(FLERR,arg[argoffs+3]);
if (strcmp(arg[argoffs+4],"NULL") == 0) zflag = 0;
else if (strcmp(arg[argoffs+4],"auto") == 0) styleflag |= SMD_AUTOZ;
else zc = force->numeric(FLERR,arg[argoffs+4]);
r0 = force->numeric(FLERR,arg[argoffs+5]);
if (r0 < 0) error->all(FLERR,"R0 < 0 for fix smd command");
argoffs +=6;
} else error->all(FLERR,"Illegal fix smd command");
force_flag = 0;
ftotal[0] = ftotal[1] = ftotal[2] = 0.0;
}
/* ---------------------------------------------------------------------- */
int FixSMD::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixSMD::init()
{
double xcm[3], xcm2[3];
masstotal = group->mass(igroup);
group->xcm(igroup,masstotal,xcm);
double dx,dy,dz;
if (styleflag & SMD_TETHER) {
dx = xc - xcm[0];
dy = yc - xcm[1];
dz = zc - xcm[2];
} else { /* SMD_COUPLE */
masstotal2 = group->mass(igroup2);
group->xcm(igroup2,masstotal2,xcm2);
if (styleflag & SMD_AUTOX) dx = xcm2[0] - xcm[0];
else dx = xc;
if (styleflag & SMD_AUTOY) dy = xcm2[1] - xcm[1];
else dy = yc;
if (styleflag & SMD_AUTOZ) dz = xcm2[2] - xcm[2];
else dz = zc;
}
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
r_old = sqrt(dx*dx + dy*dy + dz*dz);
if (r_old > SMALL) {
xn = dx/r_old;
yn = dy/r_old;
zn = dz/r_old;
}
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixSMD::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixSMD::post_force(int vflag)
{
if (styleflag & SMD_TETHER) smd_tether();
else smd_couple();
if (styleflag & SMD_CVEL) r_old += v_smd * update->dt;
}
/* ---------------------------------------------------------------------- */
void FixSMD::smd_tether()
{
double xcm[3];
group->xcm(igroup,masstotal,xcm);
// fx,fy,fz = components of k * (r-r0)
double dx,dy,dz,fx,fy,fz,r,dr;
dx = xcm[0] - xc;
dy = xcm[1] - yc;
dz = xcm[2] - zc;
r_now = sqrt(dx*dx + dy*dy + dz*dz);
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
r = sqrt(dx*dx + dy*dy + dz*dz);
if (styleflag & SMD_CVEL) {
if(r > SMALL) {
dr = r - r0 - r_old;
fx = k_smd*dx*dr/r;
fy = k_smd*dy*dr/r;
fz = k_smd*dz*dr/r;
pmf += (fx*xn + fy*yn + fz*zn) * v_smd * update->dt;
} else {
fx = 0.0;
fy = 0.0;
fz = 0.0;
}
} else {
r_old = r;
fx = f_smd*dx/r;
fy = f_smd*dy/r;
fz = f_smd*dz/r;
}
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
double **f = atom->f;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
double massfrac;
int nlocal = atom->nlocal;
ftotal[0] = ftotal[1] = ftotal[2] = 0.0;
force_flag = 0;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massfrac = rmass[i]/masstotal;
f[i][0] -= fx*massfrac;
f[i][1] -= fy*massfrac;
f[i][2] -= fz*massfrac;
ftotal[0] -= fx*massfrac;
ftotal[1] -= fy*massfrac;
ftotal[2] -= fz*massfrac;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massfrac = mass[type[i]]/masstotal;
f[i][0] -= fx*massfrac;
f[i][1] -= fy*massfrac;
f[i][2] -= fz*massfrac;
ftotal[0] -= fx*massfrac;
ftotal[1] -= fy*massfrac;
ftotal[2] -= fz*massfrac;
}
}
}
/* ---------------------------------------------------------------------- */
void FixSMD::smd_couple()
{
double xcm[3],xcm2[3];
group->xcm(igroup,masstotal,xcm);
group->xcm(igroup2,masstotal2,xcm2);
// renormalize direction of spring
double dx,dy,dz,r,dr;
if (styleflag & SMD_AUTOX) dx = xcm2[0] - xcm[0];
else dx = xn*r_old;
if (styleflag & SMD_AUTOY) dy = xcm2[1] - xcm[1];
else dy = yn*r_old;
if (styleflag & SMD_AUTOZ) dz = xcm2[2] - xcm[2];
else dz = zn*r_old;
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
r = sqrt(dx*dx + dy*dy + dz*dz);
if (r > SMALL) {
xn = dx/r; yn = dy/r; zn = dz/r;
}
double fx,fy,fz;
if (styleflag & SMD_CVEL) {
dx = xcm2[0] - xcm[0];
dy = xcm2[1] - xcm[1];
dz = xcm2[2] - xcm[2];
r_now = sqrt(dx*dx + dy*dy + dz*dz);
dx -= xn*r_old;
dy -= yn*r_old;
dz -= zn*r_old;
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
r = sqrt(dx*dx + dy*dy + dz*dz);
dr = r - r0;
if (r > SMALL) {
double fsign;
fsign = (v_smd<0.0) ? -1.0 : 1.0;
fx = k_smd*dx*dr/r;
fy = k_smd*dy*dr/r;
fz = k_smd*dz*dr/r;
pmf += (fx*xn + fy*yn + fz*zn) * fsign * v_smd * update->dt;
} else {
fx = 0.0;
fy = 0.0;
fz = 0.0;
}
} else {
dx = xcm2[0] - xcm[0];
dy = xcm2[1] - xcm[1];
dz = xcm2[2] - xcm[2];
r_now = sqrt(dx*dx + dy*dy + dz*dz);
r_old = r;
fx = f_smd*xn;
fy = f_smd*yn;
fz = f_smd*zn;
}
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
double **f = atom->f;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
ftotal[0] = ftotal[1] = ftotal[2] = 0.0;
force_flag = 0;
double massfrac;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
massfrac = rmass[i]/masstotal;
f[i][0] += fx*massfrac;
f[i][1] += fy*massfrac;
f[i][2] += fz*massfrac;
ftotal[0] += fx*massfrac;
ftotal[1] += fy*massfrac;
ftotal[2] += fz*massfrac;
}
if (mask[i] & group2bit) {
massfrac = rmass[i]/masstotal2;
f[i][0] -= fx*massfrac;
f[i][1] -= fy*massfrac;
f[i][2] -= fz*massfrac;
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
massfrac = mass[type[i]]/masstotal;
f[i][0] += fx*massfrac;
f[i][1] += fy*massfrac;
f[i][2] += fz*massfrac;
ftotal[0] += fx*massfrac;
ftotal[1] += fy*massfrac;
ftotal[2] += fz*massfrac;
}
if (mask[i] & group2bit) {
massfrac = mass[type[i]]/masstotal2;
f[i][0] -= fx*massfrac;
f[i][1] -= fy*massfrac;
f[i][2] -= fz*massfrac;
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixSMD::write_restart(FILE *fp)
{
#define RESTART_ITEMS 5
double buf[RESTART_ITEMS], fsign;
if (comm->me == 0) {
// make sure we project the force into the direction of the pulling.
fsign = (v_smd<0.0) ? -1.0 : 1.0;
buf[0] = r_old;
buf[1] = xn*fsign;
buf[2] = yn*fsign;
buf[3] = zn*fsign;
buf[4] = pmf;
int size = RESTART_ITEMS*sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(&buf[0],sizeof(double),RESTART_ITEMS,fp);
}
}
/* ---------------------------------------------------------------------- */
void FixSMD::restart(char *buf)
{
double *list = (double *)buf;
r_old = list[0];
xn=list[1];
yn=list[2];
zn=list[3];
pmf=list[4];
}
/* ---------------------------------------------------------------------- */
void FixSMD::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ----------------------------------------------------------------------
return components of total smd force on fix group
------------------------------------------------------------------------- */
double FixSMD::compute_vector(int n)
{
// only sum across procs one time
if (force_flag == 0) {
MPI_Allreduce(ftotal,ftotal_all,3,MPI_DOUBLE,MPI_SUM,world);
force_flag = 1;
if (styleflag & SMD_CVEL) {
ftotal_all[3]=ftotal_all[0]*xn+ftotal_all[1]*yn+ftotal_all[2]*zn;
ftotal_all[4]=r_old;
} else {
ftotal_all[3]=f_smd;
ftotal_all[4]=r_old;
}
ftotal_all[5]=r_now;
ftotal_all[6]=pmf;
}
return ftotal_all[n];
}
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