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lammps/src/MOLECULE/dihedral_multi_harmonic.cpp
Axel Kohlmeyer 61fd2ba25c apply clang-format to have some files with changes
2024-08-22 11:40:26 -04:00

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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: Mathias Puetz (SNL) and friends
------------------------------------------------------------------------- */
#include "dihedral_multi_harmonic.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neighbor.h"
#include <cmath>
using namespace LAMMPS_NS;
static constexpr double TOLERANCE = 0.05;
static constexpr double SMALL = 0.001;
/* ---------------------------------------------------------------------- */
DihedralMultiHarmonic::DihedralMultiHarmonic(LAMMPS *_lmp) : Dihedral(_lmp)
{
writedata = 1;
born_matrix_enable = 1;
}
/* ---------------------------------------------------------------------- */
DihedralMultiHarmonic::~DihedralMultiHarmonic()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(a1);
memory->destroy(a2);
memory->destroy(a3);
memory->destroy(a4);
memory->destroy(a5);
}
}
/* ---------------------------------------------------------------------- */
void DihedralMultiHarmonic::compute(int eflag, int vflag)
{
int i1, i2, i3, i4, n, type;
double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm;
double edihedral, f1[3], f2[3], f3[3], f4[3];
double sb1, sb2, sb3, rb1, rb3, c0, b1mag2, b1mag, b2mag2;
double b2mag, b3mag2, b3mag, ctmp, r12c1, c1mag, r12c2;
double c2mag, sc1, sc2, s1, s12, c, p, pd, a, a11, a22;
double a33, a12, a13, a23, sx2, sy2, sz2;
double s2, sin2;
edihedral = 0.0;
ev_init(eflag, vflag);
double **x = atom->x;
double **f = atom->f;
int **dihedrallist = neighbor->dihedrallist;
int ndihedrallist = neighbor->ndihedrallist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < ndihedrallist; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
// c0 calculation
sb1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z);
sb2 = 1.0 / (vb2x * vb2x + vb2y * vb2y + vb2z * vb2z);
sb3 = 1.0 / (vb3x * vb3x + vb3y * vb3y + vb3z * vb3z);
rb1 = sqrt(sb1);
rb3 = sqrt(sb3);
c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * rb1 * rb3;
// 1st and 2nd angle
b1mag2 = vb1x * vb1x + vb1y * vb1y + vb1z * vb1z;
b1mag = sqrt(b1mag2);
b2mag2 = vb2x * vb2x + vb2y * vb2y + vb2z * vb2z;
b2mag = sqrt(b2mag2);
b3mag2 = vb3x * vb3x + vb3y * vb3y + vb3z * vb3z;
b3mag = sqrt(b3mag2);
ctmp = vb1x * vb2x + vb1y * vb2y + vb1z * vb2z;
r12c1 = 1.0 / (b1mag * b2mag);
c1mag = ctmp * r12c1;
ctmp = vb2xm * vb3x + vb2ym * vb3y + vb2zm * vb3z;
r12c2 = 1.0 / (b2mag * b3mag);
c2mag = ctmp * r12c2;
// cos and sin of 2 angles and final c
sin2 = MAX(1.0 - c1mag * c1mag, 0.0);
sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0 / sc1;
sin2 = MAX(1.0 - c2mag * c2mag, 0.0);
sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0 / sc2;
s1 = sc1 * sc1;
s2 = sc2 * sc2;
s12 = sc1 * sc2;
c = (c0 + c1mag * c2mag) * s12;
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4);
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
// force & energy
// p = sum (i=1,5) a_i * c**(i-1)
// pd = dp/dc
p = a1[type] + c * (a2[type] + c * (a3[type] + c * (a4[type] + c * a5[type])));
pd = a2[type] + c * (2.0 * a3[type] + c * (3.0 * a4[type] + c * 4.0 * a5[type]));
if (eflag) edihedral = p;
a = pd;
c = c * a;
s12 = s12 * a;
a11 = c * sb1 * s1;
a22 = -sb2 * (2.0 * c0 * s12 - c * (s1 + s2));
a33 = c * sb3 * s2;
a12 = -r12c1 * (c1mag * c * s1 + c2mag * s12);
a13 = -rb1 * rb3 * s12;
a23 = r12c2 * (c2mag * c * s2 + c1mag * s12);
sx2 = a12 * vb1x + a22 * vb2x + a23 * vb3x;
sy2 = a12 * vb1y + a22 * vb2y + a23 * vb3y;
sz2 = a12 * vb1z + a22 * vb2z + a23 * vb3z;
f1[0] = a11 * vb1x + a12 * vb2x + a13 * vb3x;
f1[1] = a11 * vb1y + a12 * vb2y + a13 * vb3y;
f1[2] = a11 * vb1z + a12 * vb2z + a13 * vb3z;
f2[0] = -sx2 - f1[0];
f2[1] = -sy2 - f1[1];
f2[2] = -sz2 - f1[2];
f4[0] = a13 * vb1x + a23 * vb2x + a33 * vb3x;
f4[1] = a13 * vb1y + a23 * vb2y + a33 * vb3y;
f4[2] = a13 * vb1z + a23 * vb2z + a33 * vb3z;
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];
}
if (evflag)
ev_tally(i1, i2, i3, i4, nlocal, newton_bond, edihedral, f1, f3, f4, vb1x, vb1y, vb1z, vb2x,
vb2y, vb2z, vb3x, vb3y, vb3z);
}
}
/* ---------------------------------------------------------------------- */
void DihedralMultiHarmonic::allocate()
{
allocated = 1;
const int np1 = atom->ndihedraltypes + 1;
memory->create(a1, np1, "dihedral:a1");
memory->create(a2, np1, "dihedral:a2");
memory->create(a3, np1, "dihedral:a3");
memory->create(a4, np1, "dihedral:a4");
memory->create(a5, np1, "dihedral:a5");
memory->create(setflag, np1, "dihedral:setflag");
for (int i = 1; i < np1; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void DihedralMultiHarmonic::coeff(int narg, char **arg)
{
if (narg != 6) error->all(FLERR, "Incorrect args for dihedral coefficients");
if (!allocated) allocate();
int ilo, ihi;
utils::bounds(FLERR, arg[0], 1, atom->ndihedraltypes, ilo, ihi, error);
double a1_one = utils::numeric(FLERR, arg[1], false, lmp);
double a2_one = utils::numeric(FLERR, arg[2], false, lmp);
double a3_one = utils::numeric(FLERR, arg[3], false, lmp);
double a4_one = utils::numeric(FLERR, arg[4], false, lmp);
double a5_one = utils::numeric(FLERR, arg[5], false, lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
a1[i] = a1_one;
a2[i] = a2_one;
a3[i] = a3_one;
a4[i] = a4_one;
a5[i] = a5_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralMultiHarmonic::write_restart(FILE *fp)
{
fwrite(&a1[1], sizeof(double), atom->ndihedraltypes, fp);
fwrite(&a2[1], sizeof(double), atom->ndihedraltypes, fp);
fwrite(&a3[1], sizeof(double), atom->ndihedraltypes, fp);
fwrite(&a4[1], sizeof(double), atom->ndihedraltypes, fp);
fwrite(&a5[1], sizeof(double), atom->ndihedraltypes, fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralMultiHarmonic::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
utils::sfread(FLERR, &a1[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
utils::sfread(FLERR, &a2[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
utils::sfread(FLERR, &a3[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
utils::sfread(FLERR, &a4[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
utils::sfread(FLERR, &a5[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
}
MPI_Bcast(&a1[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&a2[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&a3[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&a4[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&a5[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void DihedralMultiHarmonic::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp, "%d %g %g %g %g %g\n", i, a1[i], a2[i], a3[i], a4[i], a5[i]);
}
/* ---------------------------------------------------------------------- */
void DihedralMultiHarmonic::born_matrix(int nd, int i1, int i2, int i3, int i4, double &du,
double &du2)
{
double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm;
double sb1, sb3, rb1, rb3, c0, b1mag2, b1mag, b2mag2;
double b2mag, b3mag2, b3mag, ctmp, r12c1, c1mag, r12c2;
double c2mag, sc1, sc2, s12, c;
double sin2;
double **x = atom->x;
int **dihedrallist = neighbor->dihedrallist;
int type = dihedrallist[nd][4];
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
// c0 calculation
sb1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z);
sb3 = 1.0 / (vb3x * vb3x + vb3y * vb3y + vb3z * vb3z);
rb1 = sqrt(sb1);
rb3 = sqrt(sb3);
c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * rb1 * rb3;
// 1st and 2nd angle
b1mag2 = vb1x * vb1x + vb1y * vb1y + vb1z * vb1z;
b1mag = sqrt(b1mag2);
b2mag2 = vb2x * vb2x + vb2y * vb2y + vb2z * vb2z;
b2mag = sqrt(b2mag2);
b3mag2 = vb3x * vb3x + vb3y * vb3y + vb3z * vb3z;
b3mag = sqrt(b3mag2);
ctmp = vb1x * vb2x + vb1y * vb2y + vb1z * vb2z;
r12c1 = 1.0 / (b1mag * b2mag);
c1mag = ctmp * r12c1;
ctmp = vb2xm * vb3x + vb2ym * vb3y + vb2zm * vb3z;
r12c2 = 1.0 / (b2mag * b3mag);
c2mag = ctmp * r12c2;
// cos and sin of 2 angles and final c
sin2 = MAX(1.0 - c1mag * c1mag, 0.0);
sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0 / sc1;
sin2 = MAX(1.0 - c2mag * c2mag, 0.0);
sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0 / sc2;
s12 = sc1 * sc2;
c = (c0 + c1mag * c2mag) * s12;
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4);
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
du = a2[type] + c * (2.0 * a3[type] + c * (3.0 * a4[type] + c * 4.0 * a5[type]));
du2 = 2.0 * a3[type] + 6.0 * c * (a4[type] + 2.0 * a5[type] * c);
}
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