419 lines
12 KiB
C++
419 lines
12 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Loukas D. Peristeras (Scienomics SARL)
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[ based on dihedral_charmm.cpp Paul Crozier (SNL) ]
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------------------------------------------------------------------------- */
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#include "dihedral_fourier.h"
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#include <mpi.h>
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#include <cmath>
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#include "atom.h"
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#include "comm.h"
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#include "neighbor.h"
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#include "force.h"
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#include "update.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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#include "utils.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define TOLERANCE 0.05
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/* ---------------------------------------------------------------------- */
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DihedralFourier::DihedralFourier(LAMMPS *lmp) : Dihedral(lmp)
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{
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writedata = 1;
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}
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/* ---------------------------------------------------------------------- */
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DihedralFourier::~DihedralFourier()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(nterms);
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for (int i=1; i<= atom->ndihedraltypes; i++) {
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if ( k[i] ) delete [] k[i];
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if ( multiplicity[i] ) delete [] multiplicity[i];
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if ( shift[i] ) delete [] shift[i];
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if ( cos_shift[i] ) delete [] cos_shift[i];
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if ( sin_shift[i] ) delete [] sin_shift[i];
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}
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delete [] k;
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delete [] multiplicity;
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delete [] shift;
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delete [] cos_shift;
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delete [] sin_shift;
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}
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}
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/* ---------------------------------------------------------------------- */
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void DihedralFourier::compute(int eflag, int vflag)
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{
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int i1,i2,i3,i4,i,j,m,n,type;
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double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
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double edihedral,f1[3],f2[3],f3[3],f4[3];
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double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
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double df,df1_,ddf1_,fg,hg,fga,hgb,gaa,gbb;
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double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
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double c,s,p_,sx2,sy2,sz2;
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ev_init(eflag,vflag);
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double **x = atom->x;
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double **f = atom->f;
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int **dihedrallist = neighbor->dihedrallist;
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int ndihedrallist = neighbor->ndihedrallist;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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for (n = 0; n < ndihedrallist; n++) {
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i1 = dihedrallist[n][0];
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i2 = dihedrallist[n][1];
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i3 = dihedrallist[n][2];
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i4 = dihedrallist[n][3];
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type = dihedrallist[n][4];
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// 1st bond
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vb1x = x[i1][0] - x[i2][0];
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vb1y = x[i1][1] - x[i2][1];
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vb1z = x[i1][2] - x[i2][2];
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// 2nd bond
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vb2x = x[i3][0] - x[i2][0];
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vb2y = x[i3][1] - x[i2][1];
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vb2z = x[i3][2] - x[i2][2];
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vb2xm = -vb2x;
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vb2ym = -vb2y;
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vb2zm = -vb2z;
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// 3rd bond
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vb3x = x[i4][0] - x[i3][0];
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vb3y = x[i4][1] - x[i3][1];
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vb3z = x[i4][2] - x[i3][2];
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ax = vb1y*vb2zm - vb1z*vb2ym;
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ay = vb1z*vb2xm - vb1x*vb2zm;
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az = vb1x*vb2ym - vb1y*vb2xm;
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bx = vb3y*vb2zm - vb3z*vb2ym;
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by = vb3z*vb2xm - vb3x*vb2zm;
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bz = vb3x*vb2ym - vb3y*vb2xm;
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rasq = ax*ax + ay*ay + az*az;
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rbsq = bx*bx + by*by + bz*bz;
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rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
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rg = sqrt(rgsq);
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rginv = ra2inv = rb2inv = 0.0;
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if (rg > 0) rginv = 1.0/rg;
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if (rasq > 0) ra2inv = 1.0/rasq;
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if (rbsq > 0) rb2inv = 1.0/rbsq;
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rabinv = sqrt(ra2inv*rb2inv);
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c = (ax*bx + ay*by + az*bz)*rabinv;
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s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
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// error check
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if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
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int me;
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MPI_Comm_rank(world,&me);
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if (screen) {
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char str[128];
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sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
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TAGINT_FORMAT " " TAGINT_FORMAT " "
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TAGINT_FORMAT " " TAGINT_FORMAT,
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me,update->ntimestep,
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atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
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error->warning(FLERR,str,0);
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fprintf(screen," 1st atom: %d %g %g %g\n",
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me,x[i1][0],x[i1][1],x[i1][2]);
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fprintf(screen," 2nd atom: %d %g %g %g\n",
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me,x[i2][0],x[i2][1],x[i2][2]);
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fprintf(screen," 3rd atom: %d %g %g %g\n",
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me,x[i3][0],x[i3][1],x[i3][2]);
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fprintf(screen," 4th atom: %d %g %g %g\n",
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me,x[i4][0],x[i4][1],x[i4][2]);
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}
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}
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if (c > 1.0) c = 1.0;
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if (c < -1.0) c = -1.0;
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// force and energy
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// p = sum(i=1,nterms) k_i*(1+cos(n_i*phi-d_i)
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// dp = dp / dphi
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edihedral = 0.0;
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df = 0.0;
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for (j=0; j<nterms[type]; j++)
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{
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m = multiplicity[type][j];
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p_ = 1.0;
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ddf1_ = df1_ = 0.0;
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for (i = 0; i < m; i++) {
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ddf1_ = p_*c - df1_*s;
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df1_ = p_*s + df1_*c;
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p_ = ddf1_;
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}
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p_ = p_*cos_shift[type][j] + df1_*sin_shift[type][j];
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df1_ = df1_*cos_shift[type][j] - ddf1_*sin_shift[type][j];
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df1_ *= -m;
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p_ += 1.0;
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if (m == 0) {
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p_ = 1.0 + cos_shift[type][j];
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df1_ = 0.0;
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}
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if (eflag) edihedral += k[type][j] * p_;
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df += (-k[type][j] * df1_);
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}
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fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
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hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
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fga = fg*ra2inv*rginv;
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hgb = hg*rb2inv*rginv;
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gaa = -ra2inv*rg;
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gbb = rb2inv*rg;
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dtfx = gaa*ax;
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dtfy = gaa*ay;
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dtfz = gaa*az;
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dtgx = fga*ax - hgb*bx;
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dtgy = fga*ay - hgb*by;
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dtgz = fga*az - hgb*bz;
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dthx = gbb*bx;
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dthy = gbb*by;
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dthz = gbb*bz;
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sx2 = df*dtgx;
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sy2 = df*dtgy;
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sz2 = df*dtgz;
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f1[0] = df*dtfx;
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f1[1] = df*dtfy;
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f1[2] = df*dtfz;
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f2[0] = sx2 - f1[0];
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f2[1] = sy2 - f1[1];
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f2[2] = sz2 - f1[2];
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f4[0] = df*dthx;
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f4[1] = df*dthy;
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f4[2] = df*dthz;
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f3[0] = -sx2 - f4[0];
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f3[1] = -sy2 - f4[1];
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f3[2] = -sz2 - f4[2];
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// apply force to each of 4 atoms
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if (newton_bond || i1 < nlocal) {
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f[i1][0] += f1[0];
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f[i1][1] += f1[1];
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f[i1][2] += f1[2];
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}
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if (newton_bond || i2 < nlocal) {
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f[i2][0] += f2[0];
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f[i2][1] += f2[1];
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f[i2][2] += f2[2];
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}
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if (newton_bond || i3 < nlocal) {
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f[i3][0] += f3[0];
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f[i3][1] += f3[1];
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f[i3][2] += f3[2];
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}
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if (newton_bond || i4 < nlocal) {
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f[i4][0] += f4[0];
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f[i4][1] += f4[1];
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f[i4][2] += f4[2];
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}
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if (evflag)
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ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
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vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DihedralFourier::allocate()
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{
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allocated = 1;
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int n = atom->ndihedraltypes;
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memory->create(nterms,n+1,"dihedral:nterms");
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k = new double * [n+1];
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multiplicity = new int * [n+1];
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shift = new double * [n+1];
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cos_shift = new double * [n+1];
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sin_shift = new double * [n+1];
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for (int i = 1; i <= n; i++) {
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k[i] = shift[i] = cos_shift[i] = sin_shift[i] = 0;
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multiplicity[i] = 0;
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}
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memory->create(setflag,n+1,"dihedral:setflag");
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for (int i = 1; i <= n; i++) setflag[i] = 0;
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}
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/* ----------------------------------------------------------------------
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set coeffs for one type
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------------------------------------------------------------------------- */
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void DihedralFourier::coeff(int narg, char **arg)
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{
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if (narg < 4) error->all(FLERR,"Incorrect args for dihedral coefficients");
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if (!allocated) allocate();
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int ilo,ihi;
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force->bounds(FLERR,arg[0],atom->ndihedraltypes,ilo,ihi);
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// require integer values of shift for backwards compatibility
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// arbitrary phase angle shift could be allowed, but would break
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// backwards compatibility and is probably not needed
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double k_one;
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int multiplicity_one;
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double shift_one;
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int nterms_one = force->inumeric(FLERR,arg[1]);
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if (nterms_one < 1)
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error->all(FLERR,"Incorrect number of terms arg for dihedral coefficients");
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if (2+3*nterms_one < narg)
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error->all(FLERR,"Incorrect number of arguments for dihedral coefficients");
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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nterms[i] = nterms_one;
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k[i] = new double [nterms_one];
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multiplicity[i] = new int [nterms_one];
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shift[i] = new double [nterms_one];
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cos_shift[i] = new double [nterms_one];
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sin_shift[i] = new double [nterms_one];
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for (int j = 0; j<nterms_one; j++) {
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int offset = 1+3*j;
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k_one = force->numeric(FLERR,arg[offset+1]);
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multiplicity_one = force->inumeric(FLERR,arg[offset+2]);
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shift_one = force->numeric(FLERR,arg[offset+3]);
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k[i][j] = k_one;
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multiplicity[i][j] = multiplicity_one;
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shift[i][j] = shift_one;
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cos_shift[i][j] = cos(MY_PI*shift_one/180.0);
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sin_shift[i][j] = sin(MY_PI*shift_one/180.0);
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}
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setflag[i] = 1;
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count++;
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}
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if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
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}
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/* ----------------------------------------------------------------------
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proc 0 writes out coeffs to restart file
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------------------------------------------------------------------------- */
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void DihedralFourier::write_restart(FILE *fp)
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{
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fwrite(&nterms[1],sizeof(int),atom->ndihedraltypes,fp);
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for(int i = 1; i <= atom->ndihedraltypes; i++) {
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fwrite(k[i],sizeof(double),nterms[i],fp);
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fwrite(multiplicity[i],sizeof(int),nterms[i],fp);
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fwrite(shift[i],sizeof(double),nterms[i],fp);
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 reads coeffs from restart file, bcasts them
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------------------------------------------------------------------------- */
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void DihedralFourier::read_restart(FILE *fp)
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{
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allocate();
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if (comm->me == 0)
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utils::sfread(FLERR,&nterms[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
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MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world);
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// allocate
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for (int i=1; i<=atom->ndihedraltypes; i++) {
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k[i] = new double [nterms[i]];
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multiplicity[i] = new int [nterms[i]];
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shift[i] = new double [nterms[i]];
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cos_shift[i] = new double [nterms[i]];
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sin_shift[i] = new double [nterms[i]];
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}
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if (comm->me == 0) {
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for (int i=1; i<=atom->ndihedraltypes; i++) {
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utils::sfread(FLERR,k[i],sizeof(double),nterms[i],fp,NULL,error);
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utils::sfread(FLERR,multiplicity[i],sizeof(int),nterms[i],fp,NULL,error);
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utils::sfread(FLERR,shift[i],sizeof(double),nterms[i],fp,NULL,error);
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}
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}
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for (int i=1; i<=atom->ndihedraltypes; i++) {
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MPI_Bcast(k[i],nterms[i],MPI_DOUBLE,0,world);
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MPI_Bcast(multiplicity[i],nterms[i],MPI_INT,0,world);
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MPI_Bcast(shift[i],nterms[i],MPI_DOUBLE,0,world);
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}
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for (int i=1; i <= atom->ndihedraltypes; i++) {
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setflag[i] = 1;
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for (int j = 0; j < nterms[i]; j++) {
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cos_shift[i][j] = cos(MY_PI*shift[i][j]/180.0);
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sin_shift[i][j] = sin(MY_PI*shift[i][j]/180.0);
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to data file
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------------------------------------------------------------------------- */
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void DihedralFourier::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->ndihedraltypes; i++)
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{
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fprintf(fp,"%d %d",i,nterms[i]);
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for(int j = 0; j < nterms[i]; j++)
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fprintf(fp," %g %d %g",k[i][j],multiplicity[i][j],shift[i][j]);
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fprintf(fp,"\n");
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}
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}
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