mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6650 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
9e5fd0d3f4
commit
c4606286b8
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@ -1,343 +0,0 @@
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/* ----------------------------------------------------------------------
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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: Carsten Svaneborg, science@zqex.dk
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------------------------------------------------------------------------- */
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#include "lmptype.h"
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#include "mpi.h"
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#include "math.h"
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#include "stdlib.h"
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#include "dihedral_cosineshiftexp.h"
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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 "domain.h"
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#include "force.h"
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#include "update.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define TOLERANCE 0.05
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#define SMALL 0.001
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/* ---------------------------------------------------------------------- */
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DihedralCosShiftExp::DihedralCosShiftExp(LAMMPS *lmp) : Dihedral(lmp) {}
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/* ---------------------------------------------------------------------- */
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DihedralCosShiftExp::~DihedralCosShiftExp()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(umin);
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memory->destroy(a);
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memory->destroy(opt1);
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memory->destroy(cost);
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memory->destroy(sint);
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memory->destroy(theta);
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memory->destroy(doExpansion);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DihedralCosShiftExp::compute(int eflag, int vflag)
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{
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int i1,i2,i3,i4,i,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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double cccpsss,cssmscc,exp2;
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edihedral = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = 0;
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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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domain->minimum_image(vb1x,vb1y,vb1z);
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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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domain->minimum_image(vb2x,vb2y,vb2z);
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vb2xm = -vb2x;
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vb2ym = -vb2y;
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vb2zm = -vb2z;
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domain->minimum_image(vb2xm,vb2ym,vb2zm);
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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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domain->minimum_image(vb3x,vb3y,vb3z);
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// c,s calculation
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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 " %d %d %d %d",
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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(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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double aa=a[type];
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double uumin=umin[type];
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cccpsss = c*cost[type]+s*sint[type];
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cssmscc = c*sint[type]-s*cost[type];
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// eflag=1;
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if (doExpansion[type])
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{ // |a|<0.001 so use expansions relative precision <1e-5
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if (eflag) edihedral = -0.125*(1+cccpsss)*(4+aa*(cccpsss-1))*uumin;
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df=0.5*uumin*( cssmscc + 0.5*aa*cccpsss);
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}
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else
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{
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exp2=exp(0.5*aa*(1+cccpsss));
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if (eflag) edihedral = opt1[type]*(1-exp2);
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df= 0.5*opt1[type]*aa* ( exp2*cssmscc );
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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 DihedralCosShiftExp::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(doExpansion, n+1, "dihedral:doExpansion");
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memory->create(umin,n+1,"dihedral:umin");
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memory->create(a,n+1,"dihedral:a");
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memory->create(sint,n+1,"dihedral:sind");
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memory->create(cost,n+1,"dihedral:cosd");
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memory->create(opt1,n+1,"dihedral:opt1");
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memory->create(theta,n+1,"dihedral:opt1");
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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 DihedralCosShiftExp::coeff(int narg, char **arg)
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{
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if (narg != 4) error->all("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(arg[0],atom->ndihedraltypes,ilo,ihi);
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double umin_ = force->numeric(arg[1]);
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double theta0_ = force->numeric(arg[2]);
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double a_ = force->numeric(arg[3]);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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doExpansion[i]=(fabs(a_)<0.001);
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umin[i] = umin_;
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a[i] = a_;
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cost[i] = cos(theta0_*3.14159265/180);
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sint[i] = sin(theta0_*3.14159265/180);
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theta[i] = theta0_*3.14159265/180;
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if (!doExpansion[i]) opt1[i]=umin_/(exp(a_)-1);
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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("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 DihedralCosShiftExp::write_restart(FILE *fp)
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{
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fwrite(&umin[1],sizeof(double),atom->ndihedraltypes,fp);
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fwrite(&a[1],sizeof(double),atom->ndihedraltypes,fp);
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fwrite(&cost[1],sizeof(double),atom->ndihedraltypes,fp);
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fwrite(&sint[1],sizeof(double),atom->ndihedraltypes,fp);
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fwrite(&theta[1],sizeof(double),atom->ndihedraltypes,fp);
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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 DihedralCosShiftExp::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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fread(&umin[1],sizeof(double),atom->ndihedraltypes,fp);
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fread(&a[1],sizeof(double),atom->ndihedraltypes,fp);
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fread(&cost[1],sizeof(double),atom->ndihedraltypes,fp);
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fread(&sint[1],sizeof(double),atom->ndihedraltypes,fp);
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fread(&theta[1],sizeof(double),atom->ndihedraltypes,fp);
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}
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MPI_Bcast(&umin[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&a[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&cost[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&sint[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&theta[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
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for (int i = 1; i <= atom->ndihedraltypes; i++) {
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setflag[i] = 1;
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doExpansion[i]=(fabs(a[i])<0.01);
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if (!doExpansion[i]) opt1[i]=umin[i]/(exp(a[i])-1);
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}
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}
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@ -1,71 +0,0 @@
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/* ----------------------------------------------------------------------
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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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The torsion angle is defined such that a straight bond has costheta=180.
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U(theta,theta0,umin,a) = -Umin[Exp(-a U)-1]/[[Exp(a)-1]]
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with U = (-1-cos[theta-theta0])/2 = -Cos((theta-theta0)/2)^2
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potential has minimum at theta=theta0 where U() = -Umin
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potential has maximum at theta=theta0+180 where U() = 0
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The spring constant around the minimum is controlled by a and
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is given by k = a exp(a) Umin/[ 2(Exp[a]-1) ] for a=0
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the spring constant is k=Umin/2 and the potential reduces to
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the cosineshifted potential.
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The potential is implemented such that for a<0.001 a series
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expansion to linear order is used instead of the expression
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above. This ensures a precision of about 1e-5 or better for
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energies and forces, and ensures the potential is well
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behaved for a=0
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*/
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#ifdef DIHEDRAL_CLASS
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DihedralStyle(cosineshiftexp,DihedralCosShiftExp)
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#else
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#ifndef LMP_DIHEDRAL_COSINESHIFTEDEXP_H
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#define LMP_DIHEDRAL_COSINESHIFTEDEXP_H
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#include "stdio.h"
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#include "dihedral.h"
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namespace LAMMPS_NS {
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class DihedralCosShiftExp : public Dihedral {
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public:
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DihedralCosShiftExp(class LAMMPS *);
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~DihedralCosShiftExp();
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void compute(int, int);
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void coeff(int, char **);
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void write_restart(FILE *);
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void read_restart(FILE *);
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private:
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bool *doExpansion;
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double *umin,*a,*opt1;
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double *sint;
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double *cost;
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double *theta;
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void allocate();
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};
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}
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#endif
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#endif
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