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fix_restrain.cpp
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Mon, Nov 11, 06:47

fix_restrain.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: Craig Tenney (University of Notre Dame)
support for bond and angle restraints by Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include "fix_restrain.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "domain.h"
#include "comm.h"
#include "respa.h"
#include "input.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{BOND,ANGLE,DIHEDRAL};
#define TOLERANCE 0.05
#define SMALL 0.001
#define DELTA 1
/* ---------------------------------------------------------------------- */
FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal fix restrain command");
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
// parse args
nrestrain = maxrestrain = 0;
rstyle = NULL;
ids = NULL;
kstart = kstop = NULL;
target = cos_target = sin_target = NULL;
int iarg = 3;
while (iarg < narg) {
if (nrestrain == maxrestrain) {
maxrestrain += DELTA;
memory->grow(rstyle,maxrestrain,"restrain:rstyle");
memory->grow(ids,maxrestrain,4,"restrain:ids");
memory->grow(kstart,maxrestrain,"restrain:kstart");
memory->grow(kstop,maxrestrain,"restrain:kstop");
memory->grow(target,maxrestrain,"restrain:target");
memory->grow(cos_target,maxrestrain,"restrain:cos_target");
memory->grow(sin_target,maxrestrain,"restrain:sin_target");
}
if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+6 > narg) error->all(FLERR,"Illegal fix restrain command");
rstyle[nrestrain] = BOND;
ids[nrestrain][0] = force->inumeric(FLERR,arg[iarg+1]);
ids[nrestrain][1] = force->inumeric(FLERR,arg[iarg+2]);
kstart[nrestrain] = force->numeric(FLERR,arg[iarg+3]);
kstop[nrestrain] = force->numeric(FLERR,arg[iarg+4]);
target[nrestrain] = force->numeric(FLERR,arg[iarg+5]);
iarg += 6;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+7 > narg) error->all(FLERR,"Illegal fix restrain command");
rstyle[nrestrain] = ANGLE;
ids[nrestrain][0] = force->inumeric(FLERR,arg[iarg+1]);
ids[nrestrain][1] = force->inumeric(FLERR,arg[iarg+2]);
ids[nrestrain][2] = force->inumeric(FLERR,arg[iarg+3]);
kstart[nrestrain] = force->numeric(FLERR,arg[iarg+4]);
kstop[nrestrain] = force->numeric(FLERR,arg[iarg+5]);
target[nrestrain] = force->numeric(FLERR,arg[iarg+6]);
target[nrestrain] *= MY_PI / 180.0;
iarg += 7;
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+8 > narg) error->all(FLERR,"Illegal fix restrain command");
rstyle[nrestrain] = DIHEDRAL;
ids[nrestrain][0] = force->inumeric(FLERR,arg[iarg+1]);
ids[nrestrain][1] = force->inumeric(FLERR,arg[iarg+2]);
ids[nrestrain][2] = force->inumeric(FLERR,arg[iarg+3]);
ids[nrestrain][3] = force->inumeric(FLERR,arg[iarg+4]);
kstart[nrestrain] = force->numeric(FLERR,arg[iarg+5]);
kstop[nrestrain] = force->numeric(FLERR,arg[iarg+6]);
target[nrestrain] = force->numeric(FLERR,arg[iarg+7]);
target[nrestrain] *= MY_PI / 180.0;
cos_target[nrestrain] = cos(target[nrestrain]);
sin_target[nrestrain] = sin(target[nrestrain]);
iarg += 8;
} else error->all(FLERR,"Illegal fix restrain command");
nrestrain++;
}
// require atom map to lookup atom IDs
if (atom->map_style == 0)
error->all(FLERR,"Fix restrain requires an atom map, see atom_modify");
}
/* ---------------------------------------------------------------------- */
FixRestrain::~FixRestrain()
{
memory->destroy(rstyle);
memory->destroy(ids);
memory->destroy(kstart);
memory->destroy(kstop);
memory->destroy(target);
memory->destroy(cos_target);
memory->destroy(sin_target);
}
/* ---------------------------------------------------------------------- */
int FixRestrain::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixRestrain::init()
{
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixRestrain::setup(int vflag)
{
if (strcmp(update->integrate_style,"verlet") == 0)
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 FixRestrain::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixRestrain::post_force(int vflag)
{
energy = 0.0;
for (int m = 0; m < nrestrain; m++)
if (rstyle[m] == BOND) restrain_bond(m);
else if (rstyle[m] == ANGLE) restrain_angle(m);
else if (rstyle[m] == DIHEDRAL) restrain_dihedral(m);
}
/* ---------------------------------------------------------------------- */
void FixRestrain::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixRestrain::min_post_force(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
apply harmonic bond restraints
---------------------------------------------------------------------- */
void FixRestrain::restrain_bond(int m)
{
int i1,i2;
double delx,dely,delz,fbond;
double rsq,r,dr,rk;
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
double k = kstart[m] + delta * (kstop[m] - kstart[m]);
i1 = atom->map(ids[m][0]);
i2 = atom->map(ids[m][1]);
// newton_bond on: only processor owning i2 computes restraint
// newton_bond off: only processors owning either of i1,i2 computes restraint
if (newton_bond) {
if (i2 == -1 || i2 >= nlocal) return;
if (i1 == -1) {
char str[128];
sprintf(str,
"Restrain atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
ids[m][0],ids[m][1],
comm->me,update->ntimestep);
error->one(FLERR,str);
}
} else {
if ((i1 == -1 || i1 >= nlocal) && (i2 == -1 || i2 >= nlocal)) return;
if (i1 == -1 || i2 == -1) {
char str[128];
sprintf(str,
"Restrain atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
ids[m][0],ids[m][1],
comm->me,update->ntimestep);
error->one(FLERR,str);
}
}
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
dr = r - target[m];
rk = k * dr;
// force & energy
if (r > 0.0) fbond = -2.0*rk/r;
else fbond = 0.0;
energy = rk*dr;
// apply force to each of 2 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
}
}
/* ----------------------------------------------------------------------
apply harmonic angle restraints
---------------------------------------------------------------------- */
void FixRestrain::restrain_angle(int m)
{
int i1,i2,i3;
double delx1,dely1,delz1,delx2,dely2,delz2;
double f1[3],f3[3];
double dtheta,tk;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
double k = kstart[m] + delta * (kstop[m] - kstart[m]);
i1 = atom->map(ids[m][0]);
i2 = atom->map(ids[m][1]);
i3 = atom->map(ids[m][2]);
// newton_bond on: only processor owning i2 computes restraint
// newton_bond off: only processors owning any of i1-i3 computes restraint
if (newton_bond) {
if (i2 == -1 || i2 >= nlocal) return;
if (i1 == -1 || i3 == -1) {
char str[128];
sprintf(str,
"Restrain atoms %d %d %d missing on proc %d at step "
BIGINT_FORMAT,
ids[m][0],ids[m][1],ids[m][2],
comm->me,update->ntimestep);
error->one(FLERR,str);
}
} else {
if ((i1 == -1 || i1 >= nlocal) && (i2 == -1 || i2 >= nlocal) &&
(i3 == -1 || i3 >= nlocal)) return;
if (i1 == -1 || i2 == -1 || i3 == -1) {
char str[128];
sprintf(str,
"Restrain atoms %d %d %d missing on proc %d at step "
BIGINT_FORMAT,
ids[m][0],ids[m][1],ids[m][2],
comm->me,update->ntimestep);
error->one(FLERR,str);
}
}
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(delx2,dely2,delz2);
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
// force & energy
dtheta = acos(c) - target[m];
tk = k * dtheta;
energy = tk*dtheta;
a = -2.0 * tk * s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
f3[0] = a22*delx2 + a12*delx1;
f3[1] = a22*dely2 + a12*dely1;
f3[2] = a22*delz2 + a12*delz1;
// apply force to each of 3 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
}
/* ----------------------------------------------------------------------
apply dihedral restraints
adopted from dihedral_charmm
---------------------------------------------------------------------- */
void FixRestrain::restrain_dihedral(int m)
{
int i1,i2,i3,i4,i,mult;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,p,sx2,sy2,sz2;
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
double k = kstart[m] + delta * (kstop[m] - kstart[m]);
i1 = atom->map(ids[m][0]);
i2 = atom->map(ids[m][1]);
i3 = atom->map(ids[m][2]);
i4 = atom->map(ids[m][3]);
// newton_bond on: only processor owning i2 computes restraint
// newton_bond off: only processors owning any of i1-i4 computes restraint
if (newton_bond) {
if (i2 == -1 || i2 >= nlocal) return;
if (i1 == -1 || i3 == -1 || i4 == -1) {
char str[128];
sprintf(str,
"Restrain atoms %d %d %d %d missing on proc %d at step "
BIGINT_FORMAT,
ids[m][0],ids[m][1],ids[m][2],ids[m][3],
comm->me,update->ntimestep);
error->one(FLERR,str);
}
} else {
if ((i1 == -1 || i1 >= nlocal) && (i2 == -1 || i2 >= nlocal) &&
(i3 == -1 || i3 >= nlocal) && (i4 == -1 || i3 >= nlocal)) return;
if (i1 == -1 || i2 == -1 || i3 == -1 || i4 == -1) {
char str[128];
sprintf(str,
"Restrain atoms %d %d %d %d missing on proc %d at step "
BIGINT_FORMAT,
ids[m][0],ids[m][1],ids[m][2],ids[m][3],
comm->me,update->ntimestep);
error->one(FLERR,str);
}
}
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
domain->minimum_image(vb1x,vb1y,vb1z);
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
domain->minimum_image(vb2xm,vb2ym,vb2zm);
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
ax = vb1y*vb2zm - vb1z*vb2ym;
ay = vb1z*vb2xm - vb1x*vb2zm;
az = vb1x*vb2ym - vb1y*vb2xm;
bx = vb3y*vb2zm - vb3z*vb2ym;
by = vb3z*vb2xm - vb3x*vb2zm;
bz = vb3x*vb2ym - vb3y*vb2xm;
rasq = ax*ax + ay*ay + az*az;
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
rginv = ra2inv = rb2inv = 0.0;
if (rg > 0) rginv = 1.0/rg;
if (rasq > 0) ra2inv = 1.0/rasq;
if (rbsq > 0) rb2inv = 1.0/rbsq;
rabinv = sqrt(ra2inv*rb2inv);
c = (ax*bx + ay*by + az*bz)*rabinv;
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,"Restrain problem: %d " BIGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
mult = 1; // multiplicity
p = 1.0;
df1 = 0.0;
for (i = 0; i < mult; i++) {
ddf1 = p*c - df1*s;
df1 = p*s + df1*c;
p = ddf1;
}
p = p*cos_target[m] + df1*sin_target[m];
df1 = df1*cos_target[m] - ddf1*sin_target[m];
df1 *= -mult;
p += 1.0;
energy = k * p;
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
fga = fg*ra2inv*rginv;
hgb = hg*rb2inv*rginv;
gaa = -ra2inv*rg;
gbb = rb2inv*rg;
dtfx = gaa*ax;
dtfy = gaa*ay;
dtfz = gaa*az;
dtgx = fga*ax - hgb*bx;
dtgy = fga*ay - hgb*by;
dtgz = fga*az - hgb*bz;
dthx = gbb*bx;
dthy = gbb*by;
dthz = gbb*bz;
df = -k * df1;
sx2 = df*dtgx;
sy2 = df*dtgy;
sz2 = df*dtgz;
f1[0] = df*dtfx;
f1[1] = df*dtfy;
f1[2] = df*dtfz;
f2[0] = sx2 - f1[0];
f2[1] = sy2 - f1[1];
f2[2] = sz2 - f1[2];
f4[0] = df*dthx;
f4[1] = df*dthy;
f4[2] = df*dthz;
f3[0] = -sx2 - f4[0];
f3[1] = -sy2 - f4[1];
f3[2] = -sz2 - f4[2];
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
}
/* ----------------------------------------------------------------------
potential energy of added force
------------------------------------------------------------------------- */
double FixRestrain::compute_scalar()
{
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
return energy_all;
}

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