git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8142 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/USER-MISC/improper_cossq.cpp
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315
src/USER-MISC/improper_cossq.cpp
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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: Georgios G. Vogiatzis (CoMSE, NTU Athens)
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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 "improper_cossq.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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#include "math_const.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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#define SMALL 0.001
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/* ---------------------------------------------------------------------- */
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ImproperCossq::ImproperCossq(LAMMPS *lmp) : Improper(lmp) {}
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/* ---------------------------------------------------------------------- */
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ImproperCossq::~ImproperCossq()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(k);
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memory->destroy(chi);
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}
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}
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/* ---------------------------------------------------------------------- */
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void ImproperCossq::compute(int eflag, int vflag)
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{
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int i1,i2,i3,i4,m,n,type;
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double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z ;
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double eimproper,f1[3],f2[3],f3[3],f4[3];
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double rjisq, rji, rlksq, rlk, cosphi, angfac;
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double cjiji, clkji, clklk, cfact1, cfact2, cfact3;
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eimproper = 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 **improperlist = neighbor->improperlist;
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int nimproperlist = neighbor->nimproperlist;
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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 < nimproperlist; n++) {
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/* Ask the improper list for the atom types. */
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i1 = improperlist[n][0];
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i2 = improperlist[n][1];
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i3 = improperlist[n][2];
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i4 = improperlist[n][3];
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type = improperlist[n][4];
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/* separation vector between i1 and i2, (i2-i1) */
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vb1x = x[i2][0] - x[i1][0];
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vb1y = x[i2][1] - x[i1][1];
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vb1z = x[i2][2] - x[i1][2];
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domain->minimum_image(vb1x,vb1y,vb1z);
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rjisq = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z ;
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rji = sqrt(rjisq);
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/* separation vector between i2 and i3 (i3-i2) */
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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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/* separation vector between i3 and i4, (i4-i3) */
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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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rlksq = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z ;
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rlk = sqrt(rlksq);
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cosphi = (vb3x*vb1x + vb3y*vb1y + vb3z*vb1z)/(rji * rlk);
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/* Check that cos(phi) is in the correct limits. */
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if (cosphi > 1.0 + TOLERANCE || cosphi < (-1.0 - TOLERANCE))
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{
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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,"Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
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me,update->ntimestep,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",me,x[i1][0],x[i1][1],x[i1][2]);
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fprintf(screen," 2nd atom: %d %g %g %g\n",me,x[i2][0],x[i2][1],x[i2][2]);
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fprintf(screen," 3rd atom: %d %g %g %g\n",me,x[i3][0],x[i3][1],x[i3][2]);
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fprintf(screen," 4th atom: %d %g %g %g\n",me,x[i4][0],x[i4][1],x[i4][2]);
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}
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}
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/* Apply corrections to round-off errors. */
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if (cosphi > 1.0) cosphi -= SMALL;
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if (cosphi < -1.0) cosphi += SMALL;
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/* Calculate the angle: */
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double torangle = acos(cosphi);
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cosphi = cos(torangle - chi[type]);
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if (eflag) eimproper = 0.5 * k[type] * cosphi * cosphi;
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/*
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printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
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printf("The ji vector: %f, %f, %f.\nThe lk vector: %f, %f, %f.\n", vb1x,vb1y,vb1z,vb3x,vb3y,vb3z);
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printf("The cosine of the angle: %-1.16e.\n", cosphi);
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printf("The energy of the improper: %-1.16e with prefactor %-1.16e.\n", eimproper, 0.5*k[type]);
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*/
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/* Work out forces. */
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angfac = - k[type] * cosphi;
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cjiji = rjisq;
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clklk = rlksq;
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/*CLKJI = RXLK * RXJI + RYLK * RYJI + RZLK * RZJI */
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clkji = vb3x*vb1x + vb3y*vb1y + vb3z*vb1z;
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/*CFACT1 = CLKLK * CJIJI
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CFACT1 = SQRT(CFACT1)
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CFACT1 = ANGFAC / CFACT1*/
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cfact1 = angfac / sqrt(clklk * cjiji);
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/*CFACT2 = CLKJI / CLKLK*/
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cfact2 = clkji / clklk;
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/*CFACT3 = CLKJI / CJIJI*/
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cfact3 = clkji / cjiji;
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/*FIX = -RXLK + CFACT3 * RXJI
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FIY = -RYLK + CFACT3 * RYJI
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FIZ = -RZLK + CFACT3 * RZJI*/
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f1[0] = - vb3x + cfact3 * vb1x;
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f1[1] = - vb3y + cfact3 * vb1y;
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f1[2] = - vb3z + cfact3 * vb1z;
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/*FJX = -FIX
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FJY = -FIY
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FJZ = -FIZ*/
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f2[0] = - f1[0];
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f2[1] = - f1[1];
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f2[2] = - f1[2];
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/*FKX = CFACT2 * RXLK - RXJI
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FKY = CFACT2 * RYLK - RYJI
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FKZ = CFACT2 * RZLK - RZJI*/
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f3[0] = cfact2 * vb3x - vb1x;
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f3[1] = cfact2 * vb3y - vb1y;
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f3[2] = cfact2 * vb3z - vb1z;
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/*FLX = -FKX
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FLY = -FKY
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FLZ = -FKZ*/
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f4[0] = - f3[0];
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f4[1] = - f3[1];
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f4[2] = - f3[2];
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/*FIX = FIX * CFACT1
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FIY = FIY * CFACT1
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FIZ = FIZ * CFACT1*/
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f1[0] *= cfact1;
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f1[1] *= cfact1;
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f1[2] *= cfact1;
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/*FJX = FJX * CFACT1
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FJY = FJY * CFACT1
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FJZ = FJZ * CFACT1*/
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f2[0] *= cfact1;
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f2[1] *= cfact1;
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f2[2] *= cfact1;
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/*FKX = FKX * CFACT1
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FKY = FKY * CFACT1
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FKZ = FKZ * CFACT1*/
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f3[0] *= cfact1;
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f3[1] *= cfact1;
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f3[2] *= cfact1;
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/*FLX = FLX * CFACT1
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FLY = FLY * CFACT1
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FLZ = FLZ * CFACT1*/
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f4[0] *= cfact1;
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f4[1] *= cfact1;
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f4[2] *= cfact1;
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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,eimproper,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 ImproperCossq::allocate()
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{
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allocated = 1;
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int n = atom->nimpropertypes;
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memory->create(k,n+1,"improper:k");
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memory->create(chi,n+1,"improper:chi");
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memory->create(setflag,n+1,"improper: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 ImproperCossq::coeff(int narg, char **arg)
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{
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/* Check whether there exist sufficient number of arguments.
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0: type of improper to be applied to
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1: energetic constant
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2: equilibrium angle in degrees */
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if (narg != 3) error->all(FLERR,"Incorrect args for cossq improper coefficients");
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if (!allocated) allocate();
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int ilo,ihi;
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force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
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double k_one = force->numeric(arg[1]);
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double chi_one = force->numeric(arg[2]);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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k[i] = k_one;
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chi[i] = ((chi_one * MY_PI)/180.0);
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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 improper 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 ImproperCossq::write_restart(FILE *fp)
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{
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fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp);
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fwrite(&chi[1],sizeof(double),atom->nimpropertypes,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 ImproperCossq::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(&k[1],sizeof(double),atom->nimpropertypes,fp);
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fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
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}
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MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
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for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
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}
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