lammps/src/YAFF/improper_distharm.cpp

// clang-format off
/* ----------------------------------------------------------------------
   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: Steven Vandenbrande, heavily based on the
   improper_distance code by Paolo Raiteri (Curtin University)
------------------------------------------------------------------------- */

#include "improper_distharm.h"

#include <cmath>
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "memory.h"
#include "error.h"


using namespace LAMMPS_NS;

#define TOLERANCE 0.05
#define SMALL     0.001

/* ---------------------------------------------------------------------- */

ImproperDistHarm::ImproperDistHarm(LAMMPS *lmp) : Improper(lmp)
{
  // the fourth atom in the quadruplet is the atom of symmetry

  symmatoms[3] = 1;
}

/* ---------------------------------------------------------------------- */

ImproperDistHarm::~ImproperDistHarm()
{
  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(k);
    memory->destroy(chi);
  }
}

/* ---------------------------------------------------------------------- */

void ImproperDistHarm::compute(int eflag, int vflag)
{
  int i1,i2,i3,i4,n,type;
  double xab, yab, zab; // bond 1-2
  double xac, yac, zac; // bond 1-3
  double xad, yad, zad; // bond 1-4
  double xbc, ybc, zbc; // bond 2-3
  double xbd, ybd, zbd; // bond 2-4
  double xcd, ycd, zcd; // bond 3-4
  double xna, yna, zna, rna; // normal
  double da;

  double eimproper,f1[3],f2[3],f3[3],f4[3];
  double domega,a;

  eimproper = 0.0;
  ev_init(eflag,vflag);

  double **x = atom->x;
  double **f = atom->f;
  int **improperlist = neighbor->improperlist;
  int nimproperlist = neighbor->nimproperlist;
  int nlocal = atom->nlocal;
  int newton_bond = force->newton_bond;

  for (n = 0; n < nimproperlist; n++) {
    i1 = improperlist[n][0];
    i2 = improperlist[n][1];
    i3 = improperlist[n][2];
    i4 = improperlist[n][3];
    type = improperlist[n][4];

    // geometry of 4-body
    // 4 is the central atom
    // 1-2-3 are ment to be equivalent
    // I need the bonds between 2-3 and 3-4 to get the plane normal
    // Then I need the bond 1-4 to project it onto the normal to the plane

    // bond 1->2
    xab = x[i2][0] - x[i1][0];
    yab = x[i2][1] - x[i1][1];
    zab = x[i2][2] - x[i1][2];
    domain->minimum_image(xab,yab,zab);

    // bond 1->3
    xac = x[i3][0] - x[i1][0];
    yac = x[i3][1] - x[i1][1];
    zac = x[i3][2] - x[i1][2];
    domain->minimum_image(xac,yac,zac);

    // bond 1->4
    xad = x[i4][0] - x[i1][0];
    yad = x[i4][1] - x[i1][1];
    zad = x[i4][2] - x[i1][2];
    domain->minimum_image(xad,yad,zad);

    // bond 2-3
    xbc = x[i3][0] - x[i2][0];
    ybc = x[i3][1] - x[i2][1];
    zbc = x[i3][2] - x[i2][2];
    domain->minimum_image(xbc,ybc,zbc);

    // bond 2-4
    xbd = x[i4][0] - x[i2][0];
    ybd = x[i4][1] - x[i2][1];
    zbd = x[i4][2] - x[i2][2];
    domain->minimum_image(xbd,ybd,zbd);

    // bond 3-4
    xcd = x[i4][0] - x[i3][0];
    ycd = x[i4][1] - x[i3][1];
    zcd = x[i4][2] - x[i3][2];
    domain->minimum_image(xcd,ycd,zcd);

    xna =   ybc*zcd - zbc*ycd;
    yna = -(xbc*zcd - zbc*xcd);
    zna =   xbc*ycd - ybc*xcd;
    rna = 1.0 / sqrt(xna*xna+yna*yna+zna*zna);
    xna *= rna;
    yna *= rna;
    zna *= rna;

    da = -(xna*xad + yna*yad + zna*zad);


    domega = k[type]*(da - chi[type])*(da - chi[type]);
    a =  2.0* k[type]*(da - chi[type]);

    if (eflag) eimproper = domega;

    f1[0] = a*( -xna);
    f1[1] = a*( -yna);
    f1[2] = a*( -zna);
    f4[0] = a*(  xna);
    f4[1] = a*(  yna);
    f4[2] = a*(  zna);

    f2[0] =  a*( yad*zcd - zad*ycd )*rna + a*da*rna*( yna*zcd - zna*ycd);
    f2[1] =  a*( zad*xcd - xad*zcd )*rna + a*da*rna*( zna*xcd - xna*zcd);
    f2[2] =  a*( xad*ycd - yad*xcd )*rna + a*da*rna*( xna*ycd - yna*xcd);

    f3[0] = - a*( yad*zcd - zad*ycd )*rna - a*da*rna*( yna*zcd - zna*ycd);
    f3[1] = - a*( zad*xcd - xad*zcd )*rna - a*da*rna*( zna*xcd - xna*zcd);
    f3[2] = - a*( xad*ycd - yad*xcd )*rna - a*da*rna*( xna*ycd - yna*xcd);

    f3[0] +=  -a*( yad*zbc - zad*ybc )*rna - a*da*rna*( yna*zbc - zna*ybc);
    f3[1] +=  -a*( zad*xbc - xad*zbc )*rna - a*da*rna*( zna*xbc - xna*zbc);
    f3[2] +=  -a*( xad*ybc - yad*xbc )*rna - a*da*rna*( xna*ybc - yna*xbc);
    f4[0] += a*( yad*zbc - zad*ybc )*rna + a*da*rna*( yna*zbc - zna*ybc);
    f4[1] += a*( zad*xbc - xad*zbc )*rna + a*da*rna*( zna*xbc - xna*zbc);
    f4[2] += a*( xad*ybc - yad*xbc )*rna + a*da*rna*( xna*ybc - yna*xbc);

    // 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,eimproper,f2,f3,f4,
       xab,yab,zab,xac,yac,zac,xad-xac,yad-yac,zad-zac);
  }
}

/* ---------------------------------------------------------------------- */

void ImproperDistHarm::allocate()
{
  allocated = 1;
  int n = atom->nimpropertypes;

  memory->create(k,n+1,"improper:k");
  memory->create(chi,n+1,"improper:chi");

  memory->create(setflag,n+1,"improper:setflag");
  for (int i = 1; i <= n; i++) setflag[i] = 0;
}

/* ----------------------------------------------------------------------
   set coeffs for one type
------------------------------------------------------------------------- */

void ImproperDistHarm::coeff(int narg, char **arg)
{
//  if (which > 0) return;
  if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients");
  if (!allocated) allocate();

  int ilo,ihi;
  utils::bounds(FLERR,arg[0],1,atom->nimpropertypes,ilo,ihi,error);

  double k_one = utils::numeric(FLERR,arg[1],false,lmp);
  double chi_one = utils::numeric(FLERR,arg[2],false,lmp);

  // convert chi from degrees to radians

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    k[i] = k_one;
    //chi[i] = chi_one/180.0 * PI;
    chi[i] = chi_one;
    setflag[i] = 1;
    count++;
  }

  if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients");
}

/* ----------------------------------------------------------------------
   proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */

void ImproperDistHarm::write_restart(FILE *fp)
{
  fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp);
  fwrite(&chi[1],sizeof(double),atom->nimpropertypes,fp);
}

/* ----------------------------------------------------------------------
   proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */

void ImproperDistHarm::read_restart(FILE *fp)
{
  allocate();

  if (comm->me == 0) {
    utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,nullptr,error);
    utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,nullptr,error);
  }
  MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
  MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);

  for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}