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lammps/src/BPM/bond_bpm_rotational.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Joel Clemmer (SNL)
------------------------------------------------------------------------- */
#include "bond_bpm_rotational.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_bond_history.h"
#include "force.h"
#include "math_const.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include "neighbor.h"
#include "update.h"
#include <cmath>
#include <cstring>
static constexpr double EPSILON = 1e-10;
using namespace LAMMPS_NS;
using MathConst::MY_SQRT2;
/* ---------------------------------------------------------------------- */
static double acos_limit(double c)
{
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
return acos(c);
}
/* ---------------------------------------------------------------------- */
BondBPMRotational::BondBPMRotational(LAMMPS *_lmp) :
BondBPM(_lmp), Kr(nullptr), Ks(nullptr), Kt(nullptr), Kb(nullptr), gnorm(nullptr),
gslide(nullptr), groll(nullptr), gtwist(nullptr), Fcr(nullptr), Fcs(nullptr), Tct(nullptr),
Tcb(nullptr)
{
partial_flag = 1;
smooth_flag = 1;
normalize_flag = 0;
writedata = 0;
nhistory = 4;
id_fix_bond_history = utils::strdup("HISTORY_BPM_ROTATIONAL");
single_extra = 7;
svector = new double[7];
}
/* ---------------------------------------------------------------------- */
BondBPMRotational::~BondBPMRotational()
{
delete[] svector;
if (allocated) {
memory->destroy(setflag);
memory->destroy(Kr);
memory->destroy(Ks);
memory->destroy(Kt);
memory->destroy(Kb);
memory->destroy(Fcr);
memory->destroy(Fcs);
memory->destroy(Tct);
memory->destroy(Tcb);
memory->destroy(gnorm);
memory->destroy(gslide);
memory->destroy(groll);
memory->destroy(gtwist);
}
}
/* ----------------------------------------------------------------------
Store data for a single bond - if bond added after LAMMPS init (e.g. pour)
------------------------------------------------------------------------- */
double BondBPMRotational::store_bond(int n, int i, int j)
{
double delx, dely, delz, r, rinv;
double **x = atom->x;
tagint *tag = atom->tag;
double **bondstore = fix_bond_history->bondstore;
if (tag[i] < tag[j]) {
delx = x[i][0] - x[j][0];
dely = x[i][1] - x[j][1];
delz = x[i][2] - x[j][2];
} else {
delx = x[j][0] - x[i][0];
dely = x[j][1] - x[i][1];
delz = x[j][2] - x[i][2];
}
r = sqrt(delx * delx + dely * dely + delz * delz);
rinv = 1.0 / r;
bondstore[n][0] = r;
bondstore[n][1] = delx * rinv;
bondstore[n][2] = dely * rinv;
bondstore[n][3] = delz * rinv;
if (i < atom->nlocal) {
for (int m = 0; m < atom->num_bond[i]; m++) {
if (atom->bond_atom[i][m] == tag[j]) {
fix_bond_history->update_atom_value(i, m, 0, r);
fix_bond_history->update_atom_value(i, m, 1, delx * rinv);
fix_bond_history->update_atom_value(i, m, 2, dely * rinv);
fix_bond_history->update_atom_value(i, m, 3, delz * rinv);
}
}
}
if (j < atom->nlocal) {
for (int m = 0; m < atom->num_bond[j]; m++) {
if (atom->bond_atom[j][m] == tag[i]) {
fix_bond_history->update_atom_value(j, m, 0, r);
fix_bond_history->update_atom_value(j, m, 1, delx * rinv);
fix_bond_history->update_atom_value(j, m, 2, dely * rinv);
fix_bond_history->update_atom_value(j, m, 3, delz * rinv);
}
}
}
return r;
}
/* ----------------------------------------------------------------------
Store data for all bonds called once
------------------------------------------------------------------------- */
void BondBPMRotational::store_data()
{
int i, j, m, type;
double delx, dely, delz, r, rinv;
double **x = atom->x;
int **bond_type = atom->bond_type;
tagint *tag = atom->tag;
for (i = 0; i < atom->nlocal; i++) {
for (m = 0; m < atom->num_bond[i]; m++) {
type = bond_type[i][m];
//Skip if bond was turned off
if (type <= 0) continue;
// map to find index n for tag
j = atom->map(atom->bond_atom[i][m]);
if (j == -1) error->one(FLERR, "Atom missing in BPM bond");
// Save orientation as pointing towards small tag
if (tag[i] < tag[j]) {
delx = x[i][0] - x[j][0];
dely = x[i][1] - x[j][1];
delz = x[i][2] - x[j][2];
} else {
delx = x[j][0] - x[i][0];
dely = x[j][1] - x[i][1];
delz = x[j][2] - x[i][2];
}
// Get closest image in case bonded with ghost
domain->minimum_image(FLERR, delx, dely, delz);
r = sqrt(delx * delx + dely * dely + delz * delz);
rinv = 1.0 / r;
fix_bond_history->update_atom_value(i, m, 0, r);
fix_bond_history->update_atom_value(i, m, 1, delx * rinv);
fix_bond_history->update_atom_value(i, m, 2, dely * rinv);
fix_bond_history->update_atom_value(i, m, 3, delz * rinv);
}
}
fix_bond_history->post_neighbor();
}
/* ----------------------------------------------------------------------
Calculate forces using formulation in:
1) Y. Wang Acta Geotechnica 2009
2) P. Mora & Y. Wang Advances in Geomcomputing 2009
---------------------------------------------------------------------- */
double BondBPMRotational::elastic_forces(int i1, int i2, int type, double r_mag, double r0_mag,
double r_mag_inv, double * /*rhat*/, double *r, double *r0,
double *force1on2, double *torque1on2, double *torque2on1)
{
double breaking, temp, r0_dot_rb, c, gamma;
double psi, theta, cos_phi, sin_phi;
double mag_in_plane, mag_out_plane;
double Fs_mag, Tt_mag, Tb_mag;
double q1[4], q2[4];
double q2inv[4], mq[4], mqinv[4], qp21[4], q21[4], qtmp[4];
double rb[3], rb_x_r0[3], s[3], t[3];
double Fr, Fs[3], Fsp[3], F_rot[3], Ftmp[3];
double Ts[3], Tb[3], Tt[3], Tbp[3], Ttp[3], Tsp[3], T_rot[3], Ttmp[3];
double **quat = atom->quat;
double r0_mag_inv = 1.0 / r0_mag;
double Kr_type = Kr[type];
double Ks_type = Ks[type];
if (normalize_flag) {
Kr_type *= r0_mag_inv;
Ks_type *= r0_mag_inv;
}
q1[0] = quat[i1][0];
q1[1] = quat[i1][1];
q1[2] = quat[i1][2];
q1[3] = quat[i1][3];
q2[0] = quat[i2][0];
q2[1] = quat[i2][1];
q2[2] = quat[i2][2];
q2[3] = quat[i2][3];
// Calculate normal forces, rb = bond vector in particle 1's frame
MathExtra::qconjugate(q2, q2inv);
MathExtra::quatrotvec(q2inv, r, rb);
Fr = Kr_type * (r_mag - r0_mag);
MathExtra::scale3(Fr * r_mag_inv, rb, F_rot);
// Calculate forces due to tangential displacements (no rotation)
r0_dot_rb = MathExtra::dot3(r0, rb);
c = r0_dot_rb * r_mag_inv * r0_mag_inv;
gamma = acos_limit(c);
MathExtra::cross3(rb, r0, rb_x_r0);
MathExtra::cross3(rb, rb_x_r0, s);
MathExtra::norm3(s);
MathExtra::scale3(Ks_type * r_mag * gamma, s, Fs);
// Calculate torque due to tangential displacements
MathExtra::cross3(r0, rb, t);
MathExtra::norm3(t);
MathExtra::scale3(0.5 * r_mag * Ks_type * r_mag * gamma, t, Ts);
// Relative rotation force/torque
// Use representation of X'Y'Z' rotations from Wang, Mora 2009
temp = r_mag + rb[2];
if (temp < 0.0) temp = 0.0;
mq[0] = MY_SQRT2 * 0.5 * sqrt(temp * r_mag_inv);
temp = sqrt(rb[0] * rb[0] + rb[1] * rb[1]);
if (temp != 0.0) {
mq[1] = -MY_SQRT2 * 0.5 / temp;
temp = r_mag - rb[2];
if (temp < 0.0) temp = 0.0;
mq[1] *= sqrt(temp * r_mag_inv);
mq[2] = -mq[1];
mq[1] *= rb[1];
mq[2] *= rb[0];
} else {
// If aligned along z axis, x,y terms zero (r_mag-rb[2] = 0)
mq[1] = 0.0;
mq[2] = 0.0;
}
mq[3] = 0.0;
// qp21 = opposite of r^\circ_21 in Wang
// q21 = opposite of r_21 in Wang
MathExtra::quatquat(q2inv, q1, qp21);
MathExtra::qconjugate(mq, mqinv);
MathExtra::quatquat(mqinv, qp21, qtmp);
MathExtra::quatquat(qtmp, mq, q21);
temp = sqrt(q21[0] * q21[0] + q21[3] * q21[3]);
if (temp != 0.0) {
psi = 2.0 * acos_limit(q21[0] / temp);
} else {
psi = 0.0;
}
// Map negative rotations
if (q21[3] < 0.0) // sin = q21[3]/temp
psi = -psi;
if (q21[3] == 0.0) psi = 0.0;
c = q21[0] * q21[0] - q21[1] * q21[1] - q21[2] * q21[2] + q21[3] * q21[3];
theta = acos_limit(c);
// Separately calculate magnitude of quaternion in x-y and out of x-y planes
// to avoid dividing by zero
mag_out_plane = (q21[0] * q21[0] + q21[3] * q21[3]);
mag_in_plane = (q21[1] * q21[1] + q21[2] * q21[2]);
if (mag_in_plane == 0.0) {
// No rotation => no bending/shear torque or extra shear force
// achieve by setting cos/sin = 0
cos_phi = 0.0;
sin_phi = 0.0;
} else if (mag_out_plane == 0.0) {
// Calculate angle in plane
cos_phi = q21[2] / sqrt(mag_in_plane);
sin_phi = -q21[1] / sqrt(mag_in_plane);
} else {
// Default equations in Mora, Wang 2009
cos_phi = q21[1] * q21[3] + q21[0] * q21[2];
sin_phi = q21[2] * q21[3] - q21[0] * q21[1];
cos_phi /= sqrt(mag_out_plane * mag_in_plane);
sin_phi /= sqrt(mag_out_plane * mag_in_plane);
}
Tbp[0] = -Kb[type] * theta * sin_phi;
Tbp[1] = Kb[type] * theta * cos_phi;
Tbp[2] = 0.0;
Ttp[0] = 0.0;
Ttp[1] = 0.0;
Ttp[2] = Kt[type] * psi;
Fsp[0] = -0.5 * Ks_type * r_mag * theta * cos_phi;
Fsp[1] = -0.5 * Ks_type * r_mag * theta * sin_phi;
Fsp[2] = 0.0;
Tsp[0] = 0.25 * Ks_type * r_mag * r_mag * theta * sin_phi;
Tsp[1] = -0.25 * Ks_type * r_mag * r_mag * theta * cos_phi;
Tsp[2] = 0.0;
// Rotate forces/torques back to 1st particle's frame
MathExtra::quatrotvec(mq, Fsp, Ftmp);
MathExtra::quatrotvec(mq, Tsp, Ttmp);
for (int m = 0; m < 3; m++) {
Fs[m] += Ftmp[m];
Ts[m] += Ttmp[m];
}
MathExtra::quatrotvec(mq, Tbp, Tb);
MathExtra::quatrotvec(mq, Ttp, Tt);
// Sum forces and calculate magnitudes
F_rot[0] += Fs[0];
F_rot[1] += Fs[1];
F_rot[2] += Fs[2];
MathExtra::quatrotvec(q2, F_rot, force1on2);
T_rot[0] = Ts[0] + Tt[0] + Tb[0];
T_rot[1] = Ts[1] + Tt[1] + Tb[1];
T_rot[2] = Ts[2] + Tt[2] + Tb[2];
MathExtra::quatrotvec(q2, T_rot, torque1on2);
T_rot[0] = Ts[0] - Tt[0] - Tb[0];
T_rot[1] = Ts[1] - Tt[1] - Tb[1];
T_rot[2] = Ts[2] - Tt[2] - Tb[2];
MathExtra::quatrotvec(q2, T_rot, torque2on1);
Fs_mag = MathExtra::len3(Fs);
Tt_mag = MathExtra::len3(Tt);
Tb_mag = MathExtra::len3(Tb);
breaking = Fr / Fcr[type] + Fs_mag / Fcs[type] + Tb_mag / Tcb[type] + Tt_mag / Tct[type];
if (breaking < 0.0) breaking = 0.0;
return breaking;
}
/* ----------------------------------------------------------------------
Calculate damping using formulation in
Y. Wang, F. Alonso-Marroquin, W. Guo 2015
Note: n points towards 1 vs pointing towards 2
---------------------------------------------------------------------- */
void BondBPMRotational::damping_forces(int i1, int i2, int type, double *rhat, double *r,
double *force1on2, double *torque1on2, double *torque2on1)
{
double v1dotr, v2dotr, w1dotr, w2dotr;
double s1[3], s2[3], tdamp[3], tmp[3];
double vn1[3], vn2[3], vt1[3], vt2[3], vroll[3];
double wxn1[3], wxn2[3], wn1[3], wn2[3];
double **v = atom->v;
double **omega = atom->omega;
// Damp normal velocity difference
v1dotr = MathExtra::dot3(v[i1], rhat);
v2dotr = MathExtra::dot3(v[i2], rhat);
MathExtra::scale3(v1dotr, rhat, vn1);
MathExtra::scale3(v2dotr, rhat, vn2);
MathExtra::sub3(vn1, vn2, tmp);
MathExtra::scale3(gnorm[type], tmp);
MathExtra::add3(force1on2, tmp, force1on2);
// Damp tangential objective velocities
MathExtra::sub3(v[i1], vn1, vt1);
MathExtra::sub3(v[i2], vn2, vt2);
MathExtra::sub3(vt2, vt1, tmp);
MathExtra::scale3(0.5, tmp);
MathExtra::cross3(omega[i1], r, s1);
MathExtra::scale3(-0.5, s1);
MathExtra::sub3(s1, tmp, s1); // Eq 12
MathExtra::cross3(omega[i2], r, s2);
MathExtra::scale3(0.5, s2);
MathExtra::add3(s2, tmp, s2); // Eq 13
MathExtra::sub3(s1, s2, tmp);
MathExtra::scale3(gslide[type], tmp);
MathExtra::add3(force1on2, tmp, force1on2);
// Apply corresponding torque
MathExtra::cross3(r, tmp, tdamp);
MathExtra::scale3(0.5, tdamp);
MathExtra::add3(torque1on2, tdamp, torque1on2);
MathExtra::add3(torque2on1, tdamp, torque2on1);
// Damp rolling
MathExtra::cross3(omega[i1], rhat, wxn1);
MathExtra::cross3(omega[i2], rhat, wxn2);
MathExtra::sub3(wxn1, wxn2, vroll); // Eq. 31
MathExtra::cross3(r, vroll, tdamp);
MathExtra::scale3(0.5 * groll[type], tdamp);
MathExtra::add3(torque1on2, tdamp, torque1on2);
MathExtra::scale3(-1.0, tdamp);
MathExtra::add3(torque2on1, tdamp, torque2on1);
// Damp twist
w1dotr = MathExtra::dot3(omega[i1], rhat);
w2dotr = MathExtra::dot3(omega[i2], rhat);
MathExtra::scale3(w1dotr, rhat, wn1);
MathExtra::scale3(w2dotr, rhat, wn2);
MathExtra::sub3(wn1, wn2, tdamp); // Eq. 38
MathExtra::scale3(0.5 * gtwist[type], tdamp);
MathExtra::add3(torque1on2, tdamp, torque1on2);
MathExtra::scale3(-1.0, tdamp);
MathExtra::add3(torque2on1, tdamp, torque2on1);
}
/* ---------------------------------------------------------------------- */
void BondBPMRotational::compute(int eflag, int vflag)
{
if (!fix_bond_history->stored_flag) {
fix_bond_history->stored_flag = true;
store_data();
}
if (hybrid_flag) fix_bond_history->compress_history();
int i1, i2, itmp, n, type;
double r[3], r0[3], rhat[3];
double rsq, r0_mag, r_mag, r_mag_inv;
double breaking, smooth;
double force1on2[3], torque1on2[3], torque2on1[3];
ev_init(eflag, vflag);
double **x = atom->x;
double **f = atom->f;
double **torque = atom->torque;
tagint *tag = atom->tag;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
double **bondstore = fix_bond_history->bondstore;
const bool allow_breaks = (update->setupflag == 0) && break_flag;
for (n = 0; n < nbondlist; n++) {
// skip bond if already broken
if (bondlist[n][2] <= 0) continue;
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
r0_mag = bondstore[n][0];
// Ensure pair is always ordered such that r0 points in
// a consistent direction and to ensure numerical operations
// are identical to minimize the possibility that a bond straddling
// an mpi grid (newton off) doesn't break on one proc but not the other
if (tag[i2] < tag[i1]) {
itmp = i1;
i1 = i2;
i2 = itmp;
}
// If bond hasn't been set - should be initialized to zero
if (r0_mag < EPSILON || std::isnan(r0_mag)) r0_mag = store_bond(n, i1, i2);
r0[0] = bondstore[n][1];
r0[1] = bondstore[n][2];
r0[2] = bondstore[n][3];
MathExtra::scale3(r0_mag, r0);
// Note this is the reverse of Mora & Wang
MathExtra::sub3(x[i1], x[i2], r);
rsq = MathExtra::lensq3(r);
r_mag = sqrt(rsq);
r_mag_inv = 1.0 / r_mag;
MathExtra::scale3(r_mag_inv, r, rhat);
// ------------------------------------------------------//
// Calculate forces, check if bond breaks
// ------------------------------------------------------//
breaking = elastic_forces(i1, i2, type, r_mag, r0_mag, r_mag_inv, rhat, r, r0, force1on2,
torque1on2, torque2on1);
if ((breaking >= 1.0) && allow_breaks) {
bondlist[n][2] = 0;
process_broken(i1, i2);
continue;
}
damping_forces(i1, i2, type, rhat, r, force1on2, torque1on2, torque2on1);
if (smooth_flag) {
smooth = breaking * breaking;
smooth = 1.0 - smooth * smooth;
} else {
smooth = 1.0;
}
// ------------------------------------------------------//
// Apply forces and torques to particles
// ------------------------------------------------------//
MathExtra::scale3(smooth, force1on2);
if (newton_bond || i1 < nlocal) {
f[i1][0] -= force1on2[0];
f[i1][1] -= force1on2[1];
f[i1][2] -= force1on2[2];
MathExtra::scale3(smooth, torque2on1);
torque[i1][0] += torque2on1[0];
torque[i1][1] += torque2on1[1];
torque[i1][2] += torque2on1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += force1on2[0];
f[i2][1] += force1on2[1];
f[i2][2] += force1on2[2];
MathExtra::scale3(smooth, torque1on2);
torque[i2][0] += torque1on2[0];
torque[i2][1] += torque1on2[1];
torque[i2][2] += torque1on2[2];
}
if (evflag)
ev_tally_xyz(i1, i2, nlocal, newton_bond, 0.0, -force1on2[0], -force1on2[1],
-force1on2[2], r[0], r[1], r[2]);
}
if (hybrid_flag) fix_bond_history->uncompress_history();
}
/* ---------------------------------------------------------------------- */
void BondBPMRotational::allocate()
{
allocated = 1;
const int np1 = atom->nbondtypes + 1;
memory->create(Kr, np1, "bond:Kr");
memory->create(Ks, np1, "bond:Ks");
memory->create(Kt, np1, "bond:Kt");
memory->create(Kb, np1, "bond:Kb");
memory->create(Fcr, np1, "bond:Fcr");
memory->create(Fcs, np1, "bond:Fcs");
memory->create(Tct, np1, "bond:Tct");
memory->create(Tcb, np1, "bond:Tcb");
memory->create(gnorm, np1, "bond:gnorm");
memory->create(gslide, np1, "bond:gslide");
memory->create(groll, np1, "bond:groll");
memory->create(gtwist, np1, "bond:gtwist");
memory->create(setflag, np1, "bond:setflag");
for (int i = 1; i < np1; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void BondBPMRotational::coeff(int narg, char **arg)
{
if (narg != 13) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21));
if (!allocated) allocate();
int ilo, ihi;
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
double Kr_one = utils::numeric(FLERR, arg[1], false, lmp);
double Ks_one = utils::numeric(FLERR, arg[2], false, lmp);
double Kt_one = utils::numeric(FLERR, arg[3], false, lmp);
double Kb_one = utils::numeric(FLERR, arg[4], false, lmp);
double Fcr_one = utils::numeric(FLERR, arg[5], false, lmp);
double Fcs_one = utils::numeric(FLERR, arg[6], false, lmp);
double Tct_one = utils::numeric(FLERR, arg[7], false, lmp);
double Tcb_one = utils::numeric(FLERR, arg[8], false, lmp);
double gnorm_one = utils::numeric(FLERR, arg[9], false, lmp);
double gslide_one = utils::numeric(FLERR, arg[10], false, lmp);
double groll_one = utils::numeric(FLERR, arg[11], false, lmp);
double gtwist_one = utils::numeric(FLERR, arg[12], false, lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
Kr[i] = Kr_one;
Ks[i] = Ks_one;
Kt[i] = Kt_one;
Kb[i] = Kb_one;
Fcr[i] = Fcr_one;
Fcs[i] = Fcs_one;
Tct[i] = Tct_one;
Tcb[i] = Tcb_one;
gnorm[i] = gnorm_one;
gslide[i] = gslide_one;
groll[i] = groll_one;
gtwist[i] = gtwist_one;
setflag[i] = 1;
count++;
if (Fcr[i] / Kr[i] > max_stretch) max_stretch = Fcr[i] / Kr[i];
}
if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21));
}
/* ----------------------------------------------------------------------
check for correct settings and create fix
------------------------------------------------------------------------- */
void BondBPMRotational::init_style()
{
BondBPM::init_style();
if (!atom->quat_flag || !atom->radius_flag || !atom->omega_flag)
error->all(FLERR, "Bond bpm/rotational requires atom style bpm/sphere");
if (comm->ghost_velocity == 0)
error->all(FLERR, "Bond bpm/rotational requires ghost atoms store velocity");
if (domain->dimension == 2)
error->warning(FLERR, "Bond style bpm/rotational not intended for 2d use");
}
/* ---------------------------------------------------------------------- */
void BondBPMRotational::settings(int narg, char **arg)
{
BondBPM::settings(narg, arg);
int iarg;
for (std::size_t i = 0; i < leftover_iarg.size(); i++) {
iarg = leftover_iarg[i];
if (strcmp(arg[iarg], "smooth") == 0) {
if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for smooth");
smooth_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
i += 1;
} else if (strcmp(arg[iarg], "normalize") == 0) {
if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for normalize");
normalize_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
i += 1;
} else {
error->all(FLERR, "Illegal bond bpm command, invalid argument {}", arg[iarg]);
}
}
if (smooth_flag && !break_flag)
error->all(FLERR, "Illegal bond bpm command, must turn off smoothing with break no option");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void BondBPMRotational::write_restart(FILE *fp)
{
BondBPM::write_restart(fp);
write_restart_settings(fp);
fwrite(&Kr[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&Ks[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&Kt[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&Kb[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&Fcr[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&Fcs[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&Tct[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&Tcb[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&gnorm[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&gslide[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&groll[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&gtwist[1], sizeof(double), atom->nbondtypes, fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void BondBPMRotational::read_restart(FILE *fp)
{
BondBPM::read_restart(fp);
read_restart_settings(fp);
allocate();
if (comm->me == 0) {
utils::sfread(FLERR, &Kr[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
utils::sfread(FLERR, &Ks[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
utils::sfread(FLERR, &Kt[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
utils::sfread(FLERR, &Kb[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
utils::sfread(FLERR, &Fcr[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
utils::sfread(FLERR, &Fcs[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
utils::sfread(FLERR, &Tct[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
utils::sfread(FLERR, &Tcb[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
utils::sfread(FLERR, &gnorm[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
utils::sfread(FLERR, &gslide[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
utils::sfread(FLERR, &groll[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
utils::sfread(FLERR, &gtwist[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
}
MPI_Bcast(&Kr[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&Ks[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&Kt[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&Kb[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&Fcr[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&Fcs[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&Tct[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&Tcb[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&gnorm[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&gslide[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&groll[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&gtwist[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void BondBPMRotational::write_restart_settings(FILE *fp)
{
fwrite(&smooth_flag, sizeof(int), 1, fp);
fwrite(&normalize_flag, sizeof(int), 1, fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void BondBPMRotational::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
utils::sfread(FLERR, &smooth_flag, sizeof(int), 1, fp, nullptr, error);
utils::sfread(FLERR, &normalize_flag, sizeof(int), 1, fp, nullptr, error);
}
MPI_Bcast(&smooth_flag, 1, MPI_INT, 0, world);
MPI_Bcast(&normalize_flag, 1, MPI_INT, 0, world);
}
/* ---------------------------------------------------------------------- */
double BondBPMRotational::single(int type, double rsq, int i, int j, double &fforce)
{
if (type <= 0) return 0.0;
int flipped = 0;
if (atom->tag[j] < atom->tag[i]) {
int itmp = i;
i = j;
j = itmp;
flipped = 1;
}
double r0_mag, r_mag, r_mag_inv;
double r0[3], r[3], rhat[3];
for (int n = 0; n < atom->num_bond[i]; n++) {
if (atom->bond_atom[i][n] == atom->tag[j]) {
r0_mag = fix_bond_history->get_atom_value(i, n, 0);
r0[0] = fix_bond_history->get_atom_value(i, n, 1);
r0[1] = fix_bond_history->get_atom_value(i, n, 2);
r0[2] = fix_bond_history->get_atom_value(i, n, 3);
}
}
double **x = atom->x;
MathExtra::scale3(r0_mag, r0);
MathExtra::sub3(x[i], x[j], r);
r_mag = sqrt(rsq);
r_mag_inv = 1.0 / r_mag;
MathExtra::scale3(r_mag_inv, r, rhat);
double force1on2[3], torque1on2[3], torque2on1[3];
double breaking = elastic_forces(i, j, type, r_mag, r0_mag, r_mag_inv, rhat, r, r0, force1on2,
torque1on2, torque2on1);
damping_forces(i, j, type, rhat, r, force1on2, torque1on2, torque2on1);
fforce = MathExtra::dot3(force1on2, rhat);
fforce *= -1;
double smooth = 1.0;
if (smooth_flag) {
smooth = breaking * breaking;
smooth = 1.0 - smooth * smooth;
fforce *= smooth;
}
// set single_extra quantities
MathExtra::scale3(smooth, force1on2);
svector[0] = r0_mag;
if (flipped) {
svector[1] = -r0[0];
svector[2] = -r0[1];
svector[3] = -r0[2];
svector[4] = force1on2[0];
svector[5] = force1on2[1];
svector[6] = force1on2[2];
} else {
svector[1] = r0[0];
svector[2] = r0[1];
svector[3] = r0[2];
svector[4] = -force1on2[0];
svector[5] = -force1on2[1];
svector[6] = -force1on2[2];
}
return 0.0;
}
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