lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   http://lammps.sandia.gov, Sandia National Laboratories
   Steve Plimpton, sjplimp@sandia.gov

   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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */

#include <cmath>
#include "dihedral_class2_omp.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "timer.h"
#include "force.h"
#include "update.h"
#include "error.h"

#include "suffix.h"
using namespace LAMMPS_NS;

#define TOLERANCE 0.05
#define SMALL     0.0000001

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

DihedralClass2OMP::DihedralClass2OMP(class LAMMPS *lmp)
  : DihedralClass2(lmp), ThrOMP(lmp,THR_DIHEDRAL)
{
  suffix_flag |= Suffix::OMP;
}

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

void DihedralClass2OMP::compute(int eflag, int vflag)
{
  ev_init(eflag,vflag);

  const int nall = atom->nlocal + atom->nghost;
  const int nthreads = comm->nthreads;
  const int inum = neighbor->ndihedrallist;

#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
  {
    int ifrom, ito, tid;

    loop_setup_thr(ifrom, ito, tid, inum, nthreads);
    ThrData *thr = fix->get_thr(tid);
    thr->timer(Timer::START);
    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);

    if (inum > 0) {
      if (evflag) {
        if (eflag) {
          if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
          else eval<1,1,0>(ifrom, ito, thr);
        } else {
          if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
          else eval<1,0,0>(ifrom, ito, thr);
        }
      } else {
        if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
        else eval<0,0,0>(ifrom, ito, thr);
      }
    }
    thr->timer(Timer::BOND);
    reduce_thr(this, eflag, vflag, thr);
  } // end of omp parallel region
}

template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
{

  int i1,i2,i3,i4,i,j,k,n,type;
  double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
  double edihedral;
  double r1mag2,r1,r2mag2,r2,r3mag2,r3;
  double sb1,rb1,sb2,rb2,sb3,rb3,c0,r12c1;
  double r12c2,costh12,costh13,costh23,sc1,sc2,s1,s2,c;
  double cosphi,phi,sinphi,a11,a22,a33,a12,a13,a23,sx1,sx2;
  double sx12,sy1,sy2,sy12,sz1,sz2,sz12,dphi1,dphi2,dphi3;
  double de_dihedral,t1,t2,t3,t4,cos2phi,cos3phi,bt1,bt2;
  double bt3,sumbte,db,sumbtf,at1,at2,at3,da,da1,da2,r1_0;
  double r3_0,dr1,dr2,tk1,tk2,s12,sin2;
  double dcosphidr[4][3],dphidr[4][3],dbonddr[3][4][3],dthetadr[2][4][3];
  double fabcd[4][3];

  edihedral = 0.0;

  const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
  dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
  const int5_t * _noalias const dihedrallist = (int5_t *) neighbor->dihedrallist[0];
  const int nlocal = atom->nlocal;

  for (n = nfrom; n < nto; n++) {
    i1 = dihedrallist[n].a;
    i2 = dihedrallist[n].b;
    i3 = dihedrallist[n].c;
    i4 = dihedrallist[n].d;
    type = dihedrallist[n].t;

    // 1st bond

    vb1x = x[i1].x - x[i2].x;
    vb1y = x[i1].y - x[i2].y;
    vb1z = x[i1].z - x[i2].z;

    // 2nd bond

    vb2x = x[i3].x - x[i2].x;
    vb2y = x[i3].y - x[i2].y;
    vb2z = x[i3].z - x[i2].z;

    vb2xm = -vb2x;
    vb2ym = -vb2y;
    vb2zm = -vb2z;

    // 3rd bond

    vb3x = x[i4].x - x[i3].x;
    vb3y = x[i4].y - x[i3].y;
    vb3z = x[i4].z - x[i3].z;

    // distances

    r1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
    r1 = sqrt(r1mag2);
    r2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
    r2 = sqrt(r2mag2);
    r3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
    r3 = sqrt(r3mag2);

    sb1 = 1.0/r1mag2;
    rb1 = 1.0/r1;
    sb2 = 1.0/r2mag2;
    rb2 = 1.0/r2;
    sb3 = 1.0/r3mag2;
    rb3 = 1.0/r3;

    c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;

    // angles

    r12c1 = rb1*rb2;
    r12c2 = rb2*rb3;
    costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
    costh13 = c0;
    costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;

    // cos and sin of 2 angles and final c

    sin2 = MAX(1.0 - costh12*costh12,0.0);
    sc1 = sqrt(sin2);
    if (sc1 < SMALL) sc1 = SMALL;
    sc1 = 1.0/sc1;

    sin2 = MAX(1.0 - costh23*costh23,0.0);
    sc2 = sqrt(sin2);
    if (sc2 < SMALL) sc2 = SMALL;
    sc2 = 1.0/sc2;

    s1 = sc1 * sc1;
    s2 = sc2 * sc2;
    s12 = sc1 * sc2;
    c = (c0 + costh12*costh23) * s12;

    // error check

    if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
      int me = comm->me;

      if (screen) {
        char str[128];
        sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " "
                TAGINT_FORMAT " " TAGINT_FORMAT " "
                TAGINT_FORMAT " " TAGINT_FORMAT,
                me,thr->get_tid(),update->ntimestep,
                atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
        error->warning(FLERR,str,0);
        fprintf(screen,"  1st atom: %d %g %g %g\n",
                me,x[i1].x,x[i1].y,x[i1].z);
        fprintf(screen,"  2nd atom: %d %g %g %g\n",
                me,x[i2].x,x[i2].y,x[i2].z);
        fprintf(screen,"  3rd atom: %d %g %g %g\n",
                me,x[i3].x,x[i3].y,x[i3].z);
        fprintf(screen,"  4th atom: %d %g %g %g\n",
                me,x[i4].x,x[i4].y,x[i4].z);
      }
    }

    if (c > 1.0) c = 1.0;
    if (c < -1.0) c = -1.0;
    cosphi = c;
    phi = acos(c);

    sinphi = sqrt(1.0 - c*c);
    sinphi = MAX(sinphi,SMALL);

    a11 = -c*sb1*s1;
    a22 = sb2 * (2.0*costh13*s12 - c*(s1+s2));
    a33 = -c*sb3*s2;
    a12 = r12c1 * (costh12*c*s1 + costh23*s12);
    a13 = rb1*rb3*s12;
    a23 = r12c2 * (-costh23*c*s2 - costh12*s12);

    sx1  = a11*vb1x + a12*vb2x + a13*vb3x;
    sx2  = a12*vb1x + a22*vb2x + a23*vb3x;
    sx12 = a13*vb1x + a23*vb2x + a33*vb3x;
    sy1  = a11*vb1y + a12*vb2y + a13*vb3y;
    sy2  = a12*vb1y + a22*vb2y + a23*vb3y;
    sy12 = a13*vb1y + a23*vb2y + a33*vb3y;
    sz1  = a11*vb1z + a12*vb2z + a13*vb3z;
    sz2  = a12*vb1z + a22*vb2z + a23*vb3z;
    sz12 = a13*vb1z + a23*vb2z + a33*vb3z;

    // set up d(cos(phi))/d(r) and dphi/dr arrays

    dcosphidr[0][0] = -sx1;
    dcosphidr[0][1] = -sy1;
    dcosphidr[0][2] = -sz1;
    dcosphidr[1][0] = sx2 + sx1;
    dcosphidr[1][1] = sy2 + sy1;
    dcosphidr[1][2] = sz2 + sz1;
    dcosphidr[2][0] = sx12 - sx2;
    dcosphidr[2][1] = sy12 - sy2;
    dcosphidr[2][2] = sz12 - sz2;
    dcosphidr[3][0] = -sx12;
    dcosphidr[3][1] = -sy12;
    dcosphidr[3][2] = -sz12;

    for (i = 0; i < 4; i++)
      for (j = 0; j < 3; j++)
        dphidr[i][j] = -dcosphidr[i][j] / sinphi;

    // energy

    dphi1 = phi - phi1[type];
    dphi2 = 2.0*phi - phi2[type];
    dphi3 = 3.0*phi - phi3[type];

    if (EFLAG) edihedral = k1[type]*(1.0 - cos(dphi1)) +
                 k2[type]*(1.0 - cos(dphi2)) +
                 k3[type]*(1.0 - cos(dphi3));

    de_dihedral = k1[type]*sin(dphi1) + 2.0*k2[type]*sin(dphi2) +
      3.0*k3[type]*sin(dphi3);

    // torsion forces on all 4 atoms

    for (i = 0; i < 4; i++)
      for (j = 0; j < 3; j++)
        fabcd[i][j] = de_dihedral*dphidr[i][j];

    // set up d(bond)/d(r) array
    // dbonddr(i,j,k) = bond i, atom j, coordinate k

    for (i = 0; i < 3; i++)
      for (j = 0; j < 4; j++)
        for (k = 0; k < 3; k++)
          dbonddr[i][j][k] = 0.0;

    // bond1

    dbonddr[0][0][0] = vb1x / r1;
    dbonddr[0][0][1] = vb1y / r1;
    dbonddr[0][0][2] = vb1z / r1;
    dbonddr[0][1][0] = -vb1x / r1;
    dbonddr[0][1][1] = -vb1y / r1;
    dbonddr[0][1][2] = -vb1z / r1;

    // bond2

    dbonddr[1][1][0] = vb2x / r2;
    dbonddr[1][1][1] = vb2y / r2;
    dbonddr[1][1][2] = vb2z / r2;
    dbonddr[1][2][0] = -vb2x / r2;
    dbonddr[1][2][1] = -vb2y / r2;
    dbonddr[1][2][2] = -vb2z / r2;

    // bond3

    dbonddr[2][2][0] = vb3x / r3;
    dbonddr[2][2][1] = vb3y / r3;
    dbonddr[2][2][2] = vb3z / r3;
    dbonddr[2][3][0] = -vb3x / r3;
    dbonddr[2][3][1] = -vb3y / r3;
    dbonddr[2][3][2] = -vb3z / r3;

    // set up d(theta)/d(r) array
    // dthetadr(i,j,k) = angle i, atom j, coordinate k

    for (i = 0; i < 2; i++)
      for (j = 0; j < 4; j++)
        for (k = 0; k < 3; k++)
          dthetadr[i][j][k] = 0.0;

    t1 = costh12 / r1mag2;
    t2 = costh23 / r2mag2;
    t3 = costh12 / r2mag2;
    t4 = costh23 / r3mag2;

    // angle12

    dthetadr[0][0][0] = sc1 * ((t1 * vb1x) - (vb2x * r12c1));
    dthetadr[0][0][1] = sc1 * ((t1 * vb1y) - (vb2y * r12c1));
    dthetadr[0][0][2] = sc1 * ((t1 * vb1z) - (vb2z * r12c1));

    dthetadr[0][1][0] = sc1 * ((-t1 * vb1x) + (vb2x * r12c1) +
                               (-t3 * vb2x) + (vb1x * r12c1));
    dthetadr[0][1][1] = sc1 * ((-t1 * vb1y) + (vb2y * r12c1) +
                               (-t3 * vb2y) + (vb1y * r12c1));
    dthetadr[0][1][2] = sc1 * ((-t1 * vb1z) + (vb2z * r12c1) +
                               (-t3 * vb2z) + (vb1z * r12c1));

    dthetadr[0][2][0] = sc1 * ((t3 * vb2x) - (vb1x * r12c1));
    dthetadr[0][2][1] = sc1 * ((t3 * vb2y) - (vb1y * r12c1));
    dthetadr[0][2][2] = sc1 * ((t3 * vb2z) - (vb1z * r12c1));

    // angle23

    dthetadr[1][1][0] = sc2 * ((t2 * vb2x) + (vb3x * r12c2));
    dthetadr[1][1][1] = sc2 * ((t2 * vb2y) + (vb3y * r12c2));
    dthetadr[1][1][2] = sc2 * ((t2 * vb2z) + (vb3z * r12c2));

    dthetadr[1][2][0] = sc2 * ((-t2 * vb2x) - (vb3x * r12c2) +
                               (t4 * vb3x) + (vb2x * r12c2));
    dthetadr[1][2][1] = sc2 * ((-t2 * vb2y) - (vb3y * r12c2) +
                               (t4 * vb3y) + (vb2y * r12c2));
    dthetadr[1][2][2] = sc2 * ((-t2 * vb2z) - (vb3z * r12c2) +
                               (t4 * vb3z) + (vb2z * r12c2));

    dthetadr[1][3][0] = -sc2 * ((t4 * vb3x) + (vb2x * r12c2));
    dthetadr[1][3][1] = -sc2 * ((t4 * vb3y) + (vb2y * r12c2));
    dthetadr[1][3][2] = -sc2 * ((t4 * vb3z) + (vb2z * r12c2));

    // mid-bond/torsion coupling
    // energy on bond2 (middle bond)

    cos2phi = cos(2.0*phi);
    cos3phi = cos(3.0*phi);

    bt1 = mbt_f1[type] * cosphi;
    bt2 = mbt_f2[type] * cos2phi;
    bt3 = mbt_f3[type] * cos3phi;
    sumbte = bt1 + bt2 + bt3;
    db = r2 - mbt_r0[type];
    if (EFLAG) edihedral += db * sumbte;

    // force on bond2

    bt1 = -mbt_f1[type] * sinphi;
    bt2 = -2.0 * mbt_f2[type] * sin(2.0*phi);
    bt3 = -3.0 * mbt_f3[type] * sin(3.0*phi);
    sumbtf = bt1 + bt2 + bt3;

    for (i = 0; i < 4; i++)
      for (j = 0; j < 3; j++)
        fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[1][i][j];

    // end-bond/torsion coupling
    // energy on bond1 (first bond)

    bt1 = ebt_f1_1[type] * cosphi;
    bt2 = ebt_f2_1[type] * cos2phi;
    bt3 = ebt_f3_1[type] * cos3phi;
    sumbte = bt1 + bt2 + bt3;

    db = r1 - ebt_r0_1[type];
    if (EFLAG) edihedral += db * (bt1+bt2+bt3);

    // force on bond1

    bt1 = ebt_f1_1[type] * sinphi;
    bt2 = 2.0 * ebt_f2_1[type] * sin(2.0*phi);
    bt3 = 3.0 * ebt_f3_1[type] * sin(3.0*phi);
    sumbtf = bt1 + bt2 + bt3;

    for (i = 0; i < 4; i++)
      for (j = 0; j < 3; j++)
        fabcd[i][j] -= db*sumbtf*dphidr[i][j] + sumbte*dbonddr[0][i][j];

    // end-bond/torsion coupling
    // energy on bond3 (last bond)

    bt1 = ebt_f1_2[type] * cosphi;
    bt2 = ebt_f2_2[type] * cos2phi;
    bt3 = ebt_f3_2[type] * cos3phi;
    sumbte = bt1 + bt2 + bt3;

    db = r3 - ebt_r0_2[type];
    if (EFLAG) edihedral += db * (bt1+bt2+bt3);

    // force on bond3

    bt1 = -ebt_f1_2[type] * sinphi;
    bt2 = -2.0 * ebt_f2_2[type] * sin(2.0*phi);
    bt3 = -3.0 * ebt_f3_2[type] * sin(3.0*phi);
    sumbtf = bt1 + bt2 + bt3;

    for (i = 0; i < 4; i++)
      for (j = 0; j < 3; j++)
        fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[2][i][j];

    // angle/torsion coupling
    // energy on angle1

    at1 = at_f1_1[type] * cosphi;
    at2 = at_f2_1[type] * cos2phi;
    at3 = at_f3_1[type] * cos3phi;
    sumbte = at1 + at2 + at3;

    da = acos(costh12) - at_theta0_1[type];
    if (EFLAG) edihedral += da * (at1+at2+at3);

    // force on angle1

    bt1 = at_f1_1[type] * sinphi;
    bt2 = 2.0 * at_f2_1[type] * sin(2.0*phi);
    bt3 = 3.0 * at_f3_1[type] * sin(3.0*phi);
    sumbtf = bt1 + bt2 + bt3;

    for (i = 0; i < 4; i++)
      for (j = 0; j < 3; j++)
        fabcd[i][j] -= da*sumbtf*dphidr[i][j] + sumbte*dthetadr[0][i][j];

    // energy on angle2

    at1 = at_f1_2[type] * cosphi;
    at2 = at_f2_2[type] * cos2phi;
    at3 = at_f3_2[type] * cos3phi;
    sumbte = at1 + at2 + at3;

    da = acos(costh23) - at_theta0_2[type];
    if (EFLAG) edihedral += da * (at1+at2+at3);

    // force on angle2

    bt1 = -at_f1_2[type] * sinphi;
    bt2 = -2.0 * at_f2_2[type] * sin(2.0*phi);
    bt3 = -3.0 * at_f3_2[type] * sin(3.0*phi);
    sumbtf = bt1 + bt2 + bt3;

    for (i = 0; i < 4; i++)
      for (j = 0; j < 3; j++)
        fabcd[i][j] += da*sumbtf*dphidr[i][j] + sumbte*dthetadr[1][i][j];

    // angle/angle/torsion coupling

    da1 = acos(costh12) - aat_theta0_1[type];
    da2 = acos(costh23) - aat_theta0_2[type];

    if (EFLAG) edihedral += aat_k[type]*da1*da2*cosphi;

    for (i = 0; i < 4; i++)
      for (j = 0; j < 3; j++)
        fabcd[i][j] -= aat_k[type] *
          (cosphi * (da2*dthetadr[0][i][j] - da1*dthetadr[1][i][j]) +
           sinphi * da1*da2*dphidr[i][j]);

    // bond1/bond3 coupling

    if (fabs(bb13t_k[type]) > SMALL) {

      r1_0 = bb13t_r10[type];
      r3_0 = bb13t_r30[type];
      dr1 = r1 - r1_0;
      dr2 = r3 - r3_0;
      tk1 = -bb13t_k[type] * dr1 / r3;
      tk2 = -bb13t_k[type] * dr2 / r1;

      if (EFLAG) edihedral += bb13t_k[type]*dr1*dr2;

      fabcd[0][0] += tk2 * vb1x;
      fabcd[0][1] += tk2 * vb1y;
      fabcd[0][2] += tk2 * vb1z;

      fabcd[1][0] -= tk2 * vb1x;
      fabcd[1][1] -= tk2 * vb1y;
      fabcd[1][2] -= tk2 * vb1z;

      fabcd[2][0] -= tk1 * vb3x;
      fabcd[2][1] -= tk1 * vb3y;
      fabcd[2][2] -= tk1 * vb3z;

      fabcd[3][0] += tk1 * vb3x;
      fabcd[3][1] += tk1 * vb3y;
      fabcd[3][2] += tk1 * vb3z;
    }

    // apply force to each of 4 atoms

    if (NEWTON_BOND || i1 < nlocal) {
      f[i1].x += fabcd[0][0];
      f[i1].y += fabcd[0][1];
      f[i1].z += fabcd[0][2];
    }

    if (NEWTON_BOND || i2 < nlocal) {
      f[i2].x += fabcd[1][0];
      f[i2].y += fabcd[1][1];
      f[i2].z += fabcd[1][2];
    }

    if (NEWTON_BOND || i3 < nlocal) {
      f[i3].x += fabcd[2][0];
      f[i3].y += fabcd[2][1];
      f[i3].z += fabcd[2][2];
    }

    if (NEWTON_BOND || i4 < nlocal) {
      f[i4].x += fabcd[3][0];
      f[i4].y += fabcd[3][1];
      f[i4].z += fabcd[3][2];
    }

    if (EVFLAG)
      ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,edihedral,
                   fabcd[0],fabcd[2],fabcd[3],
                   vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
  }
}