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lammps/src/fix_wall_region.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.
------------------------------------------------------------------------- */
#include "fix_wall_region.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h"
#include "domain.h"
#include "region.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{LJ93,LJ126,LJ1043,COLLOID,HARMONIC,MORSE};
/* ---------------------------------------------------------------------- */
FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
idregion(NULL)
{
if (narg < 8) error->all(FLERR,"Illegal fix wall/region command");
scalar_flag = 1;
vector_flag = 1;
size_vector = 3;
global_freq = 1;
extscalar = 1;
extvector = 1;
respa_level_support = 1;
ilevel_respa = 0;
virial_flag = 1;
// parse args
iregion = domain->find_region(arg[3]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix wall/region does not exist");
int n = strlen(arg[3]) + 1;
idregion = new char[n];
strcpy(idregion,arg[3]);
if (strcmp(arg[4],"lj93") == 0) style = LJ93;
else if (strcmp(arg[4],"lj126") == 0) style = LJ126;
else if (strcmp(arg[4],"lj1043") == 0) style = LJ1043;
else if (strcmp(arg[4],"colloid") == 0) style = COLLOID;
else if (strcmp(arg[4],"harmonic") == 0) style = HARMONIC;
else if (strcmp(arg[4],"morse") == 0) style = MORSE;
else error->all(FLERR,"Illegal fix wall/region command");
if (style != COLLOID) dynamic_group_allow = 1;
if (style == MORSE) {
if (narg != 9)
error->all(FLERR,"Illegal fix wall/region command");
epsilon = force->numeric(FLERR,arg[5]);
alpha = force->numeric(FLERR,arg[6]);
sigma = force->numeric(FLERR,arg[7]);
cutoff = force->numeric(FLERR,arg[8]);
} else {
if (narg != 8)
error->all(FLERR,"Illegal fix wall/region command");
epsilon = force->numeric(FLERR,arg[5]);
sigma = force->numeric(FLERR,arg[6]);
cutoff = force->numeric(FLERR,arg[7]);
}
if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region cutoff <= 0.0");
eflag = 0;
ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
}
/* ---------------------------------------------------------------------- */
FixWallRegion::~FixWallRegion()
{
delete [] idregion;
}
/* ---------------------------------------------------------------------- */
int FixWallRegion::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::init()
{
// set index and check validity of region
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for fix wall/region does not exist");
// error checks for style COLLOID
// insure all particles in group are extended particles
if (style == COLLOID) {
if (!atom->sphere_flag)
error->all(FLERR,"Fix wall/region colloid requires atom style sphere");
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int flag = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (radius[i] == 0.0) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"Fix wall/region colloid requires extended particles");
}
// setup coefficients for each style
if (style == LJ93) {
coeff1 = 6.0/5.0 * epsilon * pow(sigma,9.0);
coeff2 = 3.0 * epsilon * pow(sigma,3.0);
coeff3 = 2.0/15.0 * epsilon * pow(sigma,9.0);
coeff4 = epsilon * pow(sigma,3.0);
double rinv = 1.0/cutoff;
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
offset = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv;
} else if (style == LJ126) {
coeff1 = 48.0 * epsilon * pow(sigma,12.0);
coeff2 = 24.0 * epsilon * pow(sigma,6.0);
coeff3 = 4.0 * epsilon * pow(sigma,12.0);
coeff4 = 4.0 * epsilon * pow(sigma,6.0);
double r2inv = 1.0/(cutoff*cutoff);
double r6inv = r2inv*r2inv*r2inv;
offset = r6inv*(coeff3*r6inv - coeff4);
} else if (style == LJ1043) {
coeff1 = MY_2PI * 2.0/5.0 * epsilon * pow(sigma,10.0);
coeff2 = MY_2PI * epsilon * pow(sigma,4.0);
coeff3 = MY_2PI * pow(2.0,1/2.0) / 3 * epsilon * pow(sigma,3.0);
coeff4 = 0.61 / pow(2.0,1/2.0) * sigma;
coeff5 = coeff1 * 10.0;
coeff6 = coeff2 * 4.0;
coeff7 = coeff3 * 3.0;
double rinv = 1.0/cutoff;
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
offset = coeff1*r4inv*r4inv*r2inv - coeff2*r4inv -
coeff3*pow(cutoff+coeff4,-3.0);
} else if (style == MORSE) {
coeff1 = 2 * epsilon * alpha;
double alpha_dr = -alpha * (cutoff - sigma);
offset = epsilon * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
} else if (style == COLLOID) {
coeff1 = -4.0/315.0 * epsilon * pow(sigma,6.0);
coeff2 = -2.0/3.0 * epsilon;
coeff3 = epsilon * pow(sigma,6.0)/7560.0;
coeff4 = epsilon/6.0;
double rinv = 1.0/cutoff;
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
offset = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv;
}
if (strstr(update->integrate_style,"respa")) {
ilevel_respa = ((Respa *) update->integrate)->nlevels-1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
}
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);
post_force_respa(vflag,ilevel_respa,0);
((Respa *) update->integrate)->copy_f_flevel(ilevel_respa);
}
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::post_force(int vflag)
{
int i,m,n;
double rinv,fx,fy,fz,tooclose;
double delx, dely, delz, v[6];
double **x = atom->x;
double **f = atom->f;
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
Region *region = domain->regions[iregion];
region->prematch();
int onflag = 0;
// energy and virial setup
eflag = 0;
if (vflag) v_setup(vflag);
else evflag = 0;
// region->match() insures particle is in region or on surface, else error
// if returned contact dist r = 0, is on surface, also an error
// in COLLOID case, r <= radius is an error
// initilize ewall after region->prematch(),
// so a dynamic region can access last timestep values
ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (!region->match(x[i][0],x[i][1],x[i][2])) {
onflag = 1;
continue;
}
if (style == COLLOID) tooclose = radius[i];
else tooclose = 0.0;
n = region->surface(x[i][0],x[i][1],x[i][2],cutoff);
for (m = 0; m < n; m++) {
if (region->contact[m].r <= tooclose) {
onflag = 1;
continue;
} else rinv = 1.0/region->contact[m].r;
if (style == LJ93) lj93(region->contact[m].r);
else if (style == LJ126) lj126(region->contact[m].r);
else if (style == LJ1043) lj1043(region->contact[m].r);
else if (style == MORSE) morse(region->contact[m].r);
else if (style == COLLOID) colloid(region->contact[m].r,radius[i]);
else harmonic(region->contact[m].r);
delx = region->contact[m].delx;
dely = region->contact[m].dely;
delz = region->contact[m].delz;
fx = fwall * delx * rinv;
fy = fwall * dely * rinv;
fz = fwall * delz * rinv;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
ewall[1] -= fx;
ewall[2] -= fy;
ewall[3] -= fz;
ewall[0] += eng;
if (evflag) {
v[0] = fx*delx;
v[1] = fy*dely;
v[2] = fz*delz;
v[3] = fx*dely;
v[4] = fx*delz;
v[5] = fy*delz;
v_tally(i, v);
}
}
}
if (onflag) error->one(FLERR,"Particle outside surface of region "
"used in fix wall/region");
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::post_force_respa(int vflag, int ilevel, int /* iloop */)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::min_post_force(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
energy of wall interaction
------------------------------------------------------------------------- */
double FixWallRegion::compute_scalar()
{
// only sum across procs one time
if (eflag == 0) {
MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
eflag = 1;
}
return ewall_all[0];
}
/* ----------------------------------------------------------------------
components of force on wall
------------------------------------------------------------------------- */
double FixWallRegion::compute_vector(int n)
{
// only sum across procs one time
if (eflag == 0) {
MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
eflag = 1;
}
return ewall_all[n+1];
}
/* ----------------------------------------------------------------------
LJ 9/3 interaction for particle with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void FixWallRegion::lj93(double r)
{
double rinv = 1.0/r;
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
double r10inv = r4inv*r4inv*r2inv;
fwall = coeff1*r10inv - coeff2*r4inv;
eng = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv - offset;
}
/* ----------------------------------------------------------------------
LJ 12/6 interaction for particle with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void FixWallRegion::lj126(double r)
{
double rinv = 1.0/r;
double r2inv = rinv*rinv;
double r6inv = r2inv*r2inv*r2inv;
fwall = r6inv*(coeff1*r6inv - coeff2) * rinv;
eng = r6inv*(coeff3*r6inv - coeff4) - offset;
}
/* ----------------------------------------------------------------------
LJ 10/4/3 interaction for particle with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void FixWallRegion::lj1043(double r)
{
double rinv = 1.0/r;
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
double r10inv = r4inv*r4inv*r2inv;
fwall = coeff5*r10inv*rinv - coeff6*r4inv*rinv -
coeff7*pow(r+coeff4,-4.0);
eng = coeff1*r10inv - coeff2*r4inv -
coeff3*pow(r+coeff4,-3.0) - offset;
}
/* ----------------------------------------------------------------------
Morse interaction for particle with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void FixWallRegion::morse(double r)
{
double dr = r - sigma;
double dexp = exp(-alpha * dr);
fwall = coeff1 * (dexp*dexp - dexp) / r;
eng = epsilon * (dexp*dexp - 2.0*dexp) - offset;
}
/* ----------------------------------------------------------------------
colloid interaction for finite-size particle of rad with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void FixWallRegion::colloid(double r, double rad)
{
double new_coeff2 = coeff2*rad*rad*rad;
double diam = 2.0*rad;
double rad2 = rad*rad;
double rad4 = rad2*rad2;
double rad8 = rad4*rad4;
double delta2 = rad2 - r*r;
double rinv = 1.0/delta2;
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
double r8inv = r4inv*r4inv;
fwall = coeff1*(rad8*rad + 27.0*rad4*rad2*rad*pow(r,2.0)
+ 63.0*rad4*rad*pow(r,4.0)
+ 21.0*rad2*rad*pow(r,6.0))*r8inv - new_coeff2*r2inv;
double r2 = 0.5*diam - r;
double rinv2 = 1.0/r2;
double r2inv2 = rinv2*rinv2;
double r4inv2 = r2inv2*r2inv2;
double r3 = r + 0.5*diam;
double rinv3 = 1.0/r3;
double r2inv3 = rinv3*rinv3;
double r4inv3 = r2inv3*r2inv3;
eng = coeff3*((-3.5*diam+r)*r4inv2*r2inv2*rinv2
+ (3.5*diam+r)*r4inv3*r2inv3*rinv3) -
coeff4*((-diam*r+r2*r3*(log(-r2)-log(r3)))*
(-rinv2)*rinv3) - offset;
}
/* ----------------------------------------------------------------------
harmonic interaction for particle with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void FixWallRegion::harmonic(double r)
{
double dr = cutoff - r;
fwall = 2.0*epsilon*dr;
eng = epsilon*dr*dr;
}
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