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0d8f549e33048b08eea480b45a1ab673550e88bc
lammps/src/fix_wall_region.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
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 "atom.h"
#include "domain.h"
#include "error.h"
#include "math_const.h"
#include "math_special.h"
#include "region.h"
#include "respa.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
using MathConst::MY_2PI;
using MathConst::MY_SQRT2;
using MathSpecial::powint;
enum { LJ93, LJ126, LJ1043, COLLOID, HARMONIC, MORSE };
/* ---------------------------------------------------------------------- */
FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), idregion(nullptr), region(nullptr)
{
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;
energy_global_flag = 1;
virial_global_flag = virial_peratom_flag = 1;
respa_level_support = 1;
ilevel_respa = 0;
// parse args
region = domain->get_region_by_id(arg[3]);
if (!region) error->all(FLERR, "Region {} for fix wall/region does not exist", arg[3]);
idregion = utils::strdup(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 = utils::numeric(FLERR, arg[5], false, lmp);
alpha = utils::numeric(FLERR, arg[6], false, lmp);
sigma = utils::numeric(FLERR, arg[7], false, lmp);
cutoff = utils::numeric(FLERR, arg[8], false, lmp);
} else {
if (narg != 8) error->all(FLERR, "Illegal fix wall/region command");
epsilon = utils::numeric(FLERR, arg[5], false, lmp);
sigma = utils::numeric(FLERR, arg[6], false, lmp);
cutoff = utils::numeric(FLERR, arg[7], false, lmp);
}
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 |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::init()
{
// set index and check validity of region
region = domain->get_region_by_id(idregion);
if (!region) error->all(FLERR, "Region {} for fix wall/region does not exist", idregion);
// error checks for style COLLOID
// ensure all particles in group are extended particles
if (style == COLLOID) {
if (!atom->radius_flag) error->all(FLERR, "Fix wall/region colloid requires atom attribute radius");
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 only extended particles");
}
// setup coefficients for each style
if (style == LJ93) {
coeff1 = 6.0 / 5.0 * epsilon * powint(sigma, 9);
coeff2 = 3.0 * epsilon * powint(sigma, 3);
coeff3 = 2.0 / 15.0 * epsilon * powint(sigma, 9);
coeff4 = epsilon * powint(sigma, 3);
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 * powint(sigma, 12);
coeff2 = 24.0 * epsilon * powint(sigma, 6);
coeff3 = 4.0 * epsilon * powint(sigma, 12);
coeff4 = 4.0 * epsilon * powint(sigma, 6);
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 * powint(sigma, 10);
coeff2 = MY_2PI * epsilon * powint(sigma, 4);
coeff3 = MY_2PI * MY_SQRT2 / 3.0 * epsilon * powint(sigma, 3);
coeff4 = 0.61 / MY_SQRT2 * 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 * powint(cutoff + coeff4, -3);
} 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 * powint(sigma, 6);
coeff2 = -2.0 / 3.0 * epsilon;
coeff3 = epsilon * powint(sigma, 6) / 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 (utils::strmatch(update->integrate_style, "^respa")) {
ilevel_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels - 1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level, ilevel_respa);
}
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::setup(int vflag)
{
if (utils::strmatch(update->integrate_style, "^respa")) {
auto respa = dynamic_cast<Respa *>(update->integrate);
respa->copy_flevel_f(ilevel_respa);
post_force_respa(vflag, ilevel_respa, 0);
respa->copy_f_flevel(ilevel_respa);
} else {
post_force(vflag);
}
}
/* ---------------------------------------------------------------------- */
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->prematch();
int onflag = 0;
// virial setup
v_init(vflag);
// region->match() ensures 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
eflag = 0;
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 * powint(r + coeff4, -4);
eng = coeff1 * r10inv - coeff2 * r4inv - coeff3 * powint(r + coeff4, -3) - 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);
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 * r * r + 63.0 * rad4 * rad * powint(r, 4) +
21.0 * rad2 * rad * powint(r, 6)) *
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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