410 lines
12 KiB
C++
410 lines
12 KiB
C++
/* ----------------------------------------------------------------------
|
|
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: Philipp Kloza (University of Cambridge)
|
|
pak37@cam.ac.uk
|
|
------------------------------------------------------------------------- */
|
|
|
|
#include "angle_mesocnt.h"
|
|
|
|
#include "atom.h"
|
|
#include "comm.h"
|
|
#include "domain.h"
|
|
#include "error.h"
|
|
#include "force.h"
|
|
#include "math_const.h"
|
|
#include "memory.h"
|
|
#include "modify.h"
|
|
#include "neighbor.h"
|
|
#include "update.h"
|
|
|
|
#include <cmath>
|
|
#include <cstring>
|
|
|
|
using namespace LAMMPS_NS;
|
|
using MathConst::DEG2RAD;
|
|
using MathConst::MY_2PI;
|
|
using MathConst::MY_PI;
|
|
using MathConst::RAD2DEG;
|
|
|
|
static constexpr double SMALL = 0.001;
|
|
static constexpr double A_CC = 1.421;
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
AngleMesoCNT::AngleMesoCNT(LAMMPS *_lmp) : Angle(_lmp)
|
|
{
|
|
buckling = nullptr;
|
|
kh = nullptr;
|
|
kb = nullptr;
|
|
thetab = nullptr;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
AngleMesoCNT::~AngleMesoCNT()
|
|
{
|
|
if (allocated && !copymode) {
|
|
memory->destroy(setflag);
|
|
memory->destroy(buckling);
|
|
memory->destroy(kh);
|
|
memory->destroy(kb);
|
|
memory->destroy(thetab);
|
|
memory->destroy(theta0);
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void AngleMesoCNT::compute(int eflag, int vflag)
|
|
{
|
|
int i1, i2, i3, n, type;
|
|
double delx1, dely1, delz1, delx2, dely2, delz2;
|
|
double eangle, f1[3], f3[3];
|
|
double dtheta, tk;
|
|
double rsq1, rsq2, r1, r2, c, s, a, a11, a12, a22;
|
|
|
|
eangle = 0.0;
|
|
ev_init(eflag, vflag);
|
|
|
|
double **x = atom->x;
|
|
double **f = atom->f;
|
|
int **anglelist = neighbor->anglelist;
|
|
int nanglelist = neighbor->nanglelist;
|
|
int nlocal = atom->nlocal;
|
|
int newton_bond = force->newton_bond;
|
|
|
|
int flag, cols;
|
|
int index = atom->find_custom("buckled", flag, cols);
|
|
int *buckled = atom->ivector[index];
|
|
|
|
for (n = 0; n < nanglelist; n++) {
|
|
i1 = anglelist[n][0];
|
|
i2 = anglelist[n][1];
|
|
i3 = anglelist[n][2];
|
|
type = anglelist[n][3];
|
|
|
|
// 1st bond
|
|
|
|
delx1 = x[i1][0] - x[i2][0];
|
|
dely1 = x[i1][1] - x[i2][1];
|
|
delz1 = x[i1][2] - x[i2][2];
|
|
|
|
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];
|
|
|
|
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) - theta0[type];
|
|
|
|
// harmonic bending
|
|
if (!buckling[type] || fabs(dtheta) < thetab[type]) {
|
|
tk = kh[type] * dtheta;
|
|
if (eflag) eangle = tk * dtheta;
|
|
a = -2.0 * tk * s;
|
|
|
|
buckled[i2] = 0;
|
|
}
|
|
// bending buckling
|
|
else {
|
|
if (eflag)
|
|
eangle = kb[type] * fabs(dtheta) + thetab[type] * (kh[type] * thetab[type] - kb[type]);
|
|
a = kb[type] * s;
|
|
|
|
buckled[i2] = 1;
|
|
}
|
|
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];
|
|
}
|
|
|
|
if (evflag)
|
|
ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2,
|
|
delz2);
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void AngleMesoCNT::allocate()
|
|
{
|
|
allocated = 1;
|
|
const int np1 = atom->nangletypes + 1;
|
|
|
|
memory->create(buckling, np1, "angle:buckling");
|
|
memory->create(kh, np1, "angle:kh");
|
|
memory->create(kb, np1, "angle:kb");
|
|
memory->create(thetab, np1, "angle:thetab");
|
|
memory->create(theta0, np1, "angle:theta0");
|
|
|
|
memory->create(setflag, np1, "angle:setflag");
|
|
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
set coeffs for one or more types
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AngleMesoCNT::coeff(int narg, char **arg)
|
|
{
|
|
if (narg < 1) utils::missing_cmd_args(FLERR, "angle_coeff", error);
|
|
|
|
int buckling_one;
|
|
if (strcmp(arg[1], "buckling") == 0)
|
|
buckling_one = 1;
|
|
else if (strcmp(arg[1], "harmonic") == 0)
|
|
buckling_one = 0;
|
|
else
|
|
error->all(FLERR,
|
|
"Unknown first argument {} for angle coefficients, must be 'buckling' or 'harmonic'",
|
|
arg[1]);
|
|
|
|
// units, eV to energy unit conversion
|
|
|
|
double ang = force->angstrom;
|
|
double eunit;
|
|
if (strcmp(update->unit_style, "real") == 0)
|
|
eunit = 23.06054966;
|
|
else if (strcmp(update->unit_style, "metal") == 0)
|
|
eunit = 1.0;
|
|
else if (strcmp(update->unit_style, "si") == 0)
|
|
eunit = 1.6021765e-19;
|
|
else if (strcmp(update->unit_style, "cgs") == 0)
|
|
eunit = 1.6021765e-12;
|
|
else if (strcmp(update->unit_style, "electron") == 0)
|
|
eunit = 3.674932248e-2;
|
|
else if (strcmp(update->unit_style, "micro") == 0)
|
|
eunit = 1.6021765e-4;
|
|
else if (strcmp(update->unit_style, "nano") == 0)
|
|
eunit = 1.6021765e2;
|
|
else
|
|
error->all(FLERR, "Angle style mesocnt does not support {} units", update->unit_style);
|
|
|
|
// set parameters
|
|
|
|
double kh_one, kb_one, thetab_one;
|
|
if (strcmp(arg[2], "custom") == 0) {
|
|
if (buckling_one) {
|
|
if (narg != 6) error->all(FLERR, "Incorrect number of args for 'custom' angle coefficients");
|
|
kb_one = utils::numeric(FLERR, arg[4], false, lmp);
|
|
thetab_one = utils::numeric(FLERR, arg[5], false, lmp);
|
|
} else if (narg != 4)
|
|
error->all(FLERR, "Incorrect number of args for 'custom' angle coefficients");
|
|
|
|
kh_one = utils::numeric(FLERR, arg[3], false, lmp);
|
|
} else if (strcmp(arg[2], "C") == 0) {
|
|
if (narg != 6)
|
|
error->all(FLERR, "Incorrect number of args for 'C' preset in angle coefficients");
|
|
int n = utils::inumeric(FLERR, arg[3], false, lmp);
|
|
int m = utils::inumeric(FLERR, arg[4], false, lmp);
|
|
double l = utils::numeric(FLERR, arg[5], false, lmp);
|
|
|
|
double r_ang = sqrt(3.0 * (n * n + n * m + m * m)) * A_CC / MY_2PI;
|
|
|
|
// empirical parameters
|
|
|
|
double k = 63.80 * pow(r_ang, 2.93) * eunit * ang;
|
|
kh_one = 0.5 * k / l;
|
|
|
|
if (buckling_one) {
|
|
kb_one = 0.7 * k / (275.0 * ang);
|
|
thetab_one = 180.0 / MY_PI * atan(l / (275.0 * ang));
|
|
}
|
|
} else
|
|
error->all(FLERR, "Unknown {} preset in angle coefficients", arg[2]);
|
|
|
|
// set safe default values for buckling parameters if buckling is disabled
|
|
|
|
if (!buckling_one) {
|
|
kb_one = 0.0;
|
|
thetab_one = 180.0;
|
|
}
|
|
|
|
if (!allocated) allocate();
|
|
|
|
int ilo, ihi;
|
|
utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error);
|
|
|
|
// convert thetab from degrees to radians
|
|
|
|
int count = 0;
|
|
for (int i = ilo; i <= ihi; i++) {
|
|
buckling[i] = buckling_one;
|
|
kh[i] = kh_one;
|
|
kb[i] = kb_one;
|
|
thetab[i] = DEG2RAD * thetab_one;
|
|
theta0[i] = DEG2RAD * 180.0;
|
|
setflag[i] = 1;
|
|
count++;
|
|
}
|
|
|
|
if (count == 0) error->all(FLERR, "Invalid angle type {}", arg[0]);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void AngleMesoCNT::init_style()
|
|
{
|
|
std::string id_fix = "angle_mesocnt_buckled";
|
|
if (!modify->get_fix_by_id(id_fix))
|
|
modify->add_fix(id_fix + " all property/atom i_buckled ghost yes");
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double AngleMesoCNT::equilibrium_angle(int /*i*/)
|
|
{
|
|
return 180.0;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 writes out coeffs to restart file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AngleMesoCNT::write_restart(FILE *fp)
|
|
{
|
|
fwrite(&buckling[1], sizeof(int), atom->nangletypes, fp);
|
|
fwrite(&kh[1], sizeof(double), atom->nangletypes, fp);
|
|
fwrite(&kb[1], sizeof(double), atom->nangletypes, fp);
|
|
fwrite(&thetab[1], sizeof(double), atom->nangletypes, fp);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 reads coeffs from restart file, bcasts them
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AngleMesoCNT::read_restart(FILE *fp)
|
|
{
|
|
allocate();
|
|
|
|
if (comm->me == 0) {
|
|
utils::sfread(FLERR, &buckling[1], sizeof(int), atom->nangletypes, fp, nullptr, error);
|
|
utils::sfread(FLERR, &kh[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
|
|
utils::sfread(FLERR, &kb[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
|
|
utils::sfread(FLERR, &thetab[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
|
|
}
|
|
MPI_Bcast(&buckling[1], atom->nangletypes, MPI_INT, 0, world);
|
|
MPI_Bcast(&kh[1], atom->nangletypes, MPI_DOUBLE, 0, world);
|
|
MPI_Bcast(&kb[1], atom->nangletypes, MPI_DOUBLE, 0, world);
|
|
MPI_Bcast(&thetab[1], atom->nangletypes, MPI_DOUBLE, 0, world);
|
|
|
|
for (int i = 1; i <= atom->nangletypes; i++) {
|
|
theta0[i] = 180.0;
|
|
setflag[i] = 1;
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 writes to data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AngleMesoCNT::write_data(FILE *fp)
|
|
{
|
|
for (int i = 1; i <= atom->nangletypes; i++)
|
|
fprintf(fp, "%d %d %g %g %g\n", i, buckling[i], kh[i], kb[i], RAD2DEG * thetab[i]);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double AngleMesoCNT::single(int type, int i1, int i2, int i3)
|
|
{
|
|
double **x = atom->x;
|
|
|
|
double delx1 = x[i1][0] - x[i2][0];
|
|
double dely1 = x[i1][1] - x[i2][1];
|
|
double delz1 = x[i1][2] - x[i2][2];
|
|
domain->minimum_image(FLERR, delx1, dely1, delz1);
|
|
double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
|
|
|
|
double delx2 = x[i3][0] - x[i2][0];
|
|
double dely2 = x[i3][1] - x[i2][1];
|
|
double delz2 = x[i3][2] - x[i2][2];
|
|
domain->minimum_image(FLERR, delx2, dely2, delz2);
|
|
double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
|
|
|
|
double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
|
|
c /= r1 * r2;
|
|
if (c > 1.0) c = 1.0;
|
|
if (c < -1.0) c = -1.0;
|
|
|
|
double dtheta = acos(c) - theta0[type];
|
|
|
|
// harmonic bending
|
|
if (!buckling[type] || dtheta < thetab[type]) {
|
|
double tk = kh[type] * dtheta;
|
|
return tk * dtheta;
|
|
}
|
|
// bending buckling
|
|
else
|
|
return kb[type] * dtheta + thetab[type] * (kh[type] * thetab[type] - kb[type]);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
return ptr to internal members upon request
|
|
------------------------------------------------------------------------ */
|
|
|
|
void *AngleMesoCNT::extract(const char *str, int &dim)
|
|
{
|
|
dim = 1;
|
|
if (strcmp(str, "theta0") == 0) return (void *) theta0;
|
|
return nullptr;
|
|
}
|