forked from lijiext/lammps
346 lines
8.6 KiB
C++
346 lines
8.6 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: Paul Crozier (SNL)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdlib.h"
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#include "string.h"
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#include "fix_spring.h"
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#include "atom.h"
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#include "update.h"
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#include "respa.h"
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#include "domain.h"
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#include "error.h"
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#include "group.h"
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using namespace LAMMPS_NS;
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#define SMALL 1.0e-10
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#define MIN(A,B) ((A) < (B)) ? (A) : (B)
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#define MAX(A,B) ((A) > (B)) ? (A) : (B)
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enum{TETHER,COUPLE};
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/* ---------------------------------------------------------------------- */
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FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 9) error->all("Illegal fix spring command");
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scalar_flag = 1;
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vector_flag = 1;
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size_vector = 4;
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global_freq = 1;
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extscalar = 1;
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extvector = 1;
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group2 = NULL;
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if (strcmp(arg[3],"tether") == 0) {
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if (narg != 9) error->all("Illegal fix spring command");
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styleflag = TETHER;
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k_spring = atof(arg[4]);
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xflag = yflag = zflag = 1;
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if (strcmp(arg[5],"NULL") == 0) xflag = 0;
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else xc = atof(arg[5]);
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if (strcmp(arg[6],"NULL") == 0) yflag = 0;
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else yc = atof(arg[6]);
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if (strcmp(arg[7],"NULL") == 0) zflag = 0;
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else zc = atof(arg[7]);
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r0 = atof(arg[8]);
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if (r0 < 0) error->all("R0 < 0 for fix spring command");
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} else if (strcmp(arg[3],"couple") == 0) {
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if (narg != 10) error->all("Illegal fix spring command");
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styleflag = COUPLE;
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int n = strlen(arg[4]) + 1;
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group2 = new char[n];
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strcpy(group2,arg[4]);
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igroup2 = group->find(arg[4]);
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if (igroup2 == -1)
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error->all("Fix spring couple group ID does not exist");
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if (igroup2 == igroup)
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error->all("Two groups cannot be the same in fix spring couple");
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group2bit = group->bitmask[igroup2];
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k_spring = atof(arg[5]);
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xflag = yflag = zflag = 1;
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if (strcmp(arg[6],"NULL") == 0) xflag = 0;
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else xc = atof(arg[6]);
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if (strcmp(arg[7],"NULL") == 0) yflag = 0;
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else yc = atof(arg[7]);
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if (strcmp(arg[8],"NULL") == 0) zflag = 0;
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else zc = atof(arg[8]);
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r0 = atof(arg[9]);
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if (r0 < 0) error->all("R0 < 0 for fix spring command");
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} else error->all("Illegal fix spring command");
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ftotal[0] = ftotal[1] = ftotal[2] = ftotal[3] = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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FixSpring::~FixSpring()
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{
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delete [] group2;
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}
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/* ---------------------------------------------------------------------- */
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int FixSpring::setmask()
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{
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int mask = 0;
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mask |= POST_FORCE;
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mask |= THERMO_ENERGY;
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mask |= POST_FORCE_RESPA;
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mask |= MIN_POST_FORCE;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixSpring::init()
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{
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// recheck that group 2 has not been deleted
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if (group2) {
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igroup2 = group->find(group2);
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if (igroup2 == -1)
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error->all("Fix spring couple group ID does not exist");
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group2bit = group->bitmask[igroup2];
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}
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masstotal = group->mass(igroup);
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if (styleflag == COUPLE) masstotal2 = group->mass(igroup2);
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if (strcmp(update->integrate_style,"respa") == 0)
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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}
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/* ---------------------------------------------------------------------- */
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void FixSpring::setup(int vflag)
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{
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if (strcmp(update->integrate_style,"verlet") == 0)
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post_force(vflag);
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else {
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((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
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post_force_respa(vflag,nlevels_respa-1,0);
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((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixSpring::min_setup(int vflag)
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{
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post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixSpring::post_force(int vflag)
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{
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if (styleflag == TETHER) spring_tether();
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else spring_couple();
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}
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/* ---------------------------------------------------------------------- */
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void FixSpring::spring_tether()
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{
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double xcm[3];
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group->xcm(igroup,masstotal,xcm);
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// fx,fy,fz = components of k * (r-r0) / masstotal
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double dx,dy,dz,fx,fy,fz,r,dr;
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dx = xcm[0] - xc;
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dy = xcm[1] - yc;
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dz = xcm[2] - zc;
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if (!xflag) dx = 0.0;
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if (!yflag) dy = 0.0;
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if (!zflag) dz = 0.0;
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r = sqrt(dx*dx + dy*dy + dz*dz);
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r = MAX(r,SMALL);
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dr = r - r0;
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fx = k_spring*dx*dr/r;
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fy = k_spring*dy*dr/r;
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fz = k_spring*dz*dr/r;
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ftotal[0] = -fx;
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ftotal[1] = -fy;
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ftotal[2] = -fz;
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ftotal[3] = sqrt(fx*fx + fy*fy + fz*fz);
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if (dr < 0.0) ftotal[3] = -ftotal[3];
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espring = 0.5*k_spring * dr*dr;
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fx /= masstotal;
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fy /= masstotal;
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fz /= masstotal;
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// apply restoring force to atoms in group
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double **f = atom->f;
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int *mask = atom->mask;
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int *type = atom->type;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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double massone;
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if (rmass) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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massone = rmass[i];
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f[i][0] -= fx*massone;
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f[i][1] -= fy*massone;
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f[i][2] -= fz*massone;
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}
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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massone = mass[type[i]];
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f[i][0] -= fx*massone;
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f[i][1] -= fy*massone;
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f[i][2] -= fz*massone;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixSpring::spring_couple()
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{
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double xcm[3],xcm2[3];
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group->xcm(igroup,masstotal,xcm);
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group->xcm(igroup2,masstotal2,xcm2);
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// fx,fy,fz = components of k * (r-r0) / masstotal
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// fx2,fy2,fz2 = components of k * (r-r0) / masstotal2
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double dx,dy,dz,fx,fy,fz,fx2,fy2,fz2,r,dr;
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dx = xcm2[0] - xcm[0] - xc;
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dy = xcm2[1] - xcm[1] - yc;
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dz = xcm2[2] - xcm[2] - zc;
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if (!xflag) dx = 0.0;
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if (!yflag) dy = 0.0;
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if (!zflag) dz = 0.0;
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r = sqrt(dx*dx + dy*dy + dz*dz);
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r = MAX(r,SMALL);
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dr = r - r0;
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fx = k_spring*dx*dr/r;
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fy = k_spring*dy*dr/r;
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fz = k_spring*dz*dr/r;
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ftotal[0] = fx;
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ftotal[1] = fy;
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ftotal[2] = fz;
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ftotal[3] = sqrt(fx*fx + fy*fy + fz*fz);
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if (dr < 0.0) ftotal[3] = -ftotal[3];
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espring = 0.5*k_spring * dr*dr;
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fx2 = fx/masstotal2;
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fy2 = fy/masstotal2;
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fz2 = fz/masstotal2;
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fx /= masstotal;
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fy /= masstotal;
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fz /= masstotal;
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// apply restoring force to atoms in group
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// f = -k*(r-r0)*mass/masstotal
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double **f = atom->f;
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int *mask = atom->mask;
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int *type = atom->type;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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double massone;
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if (rmass) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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massone = rmass[i];
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f[i][0] += fx*massone;
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f[i][1] += fy*massone;
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f[i][2] += fz*massone;
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}
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if (mask[i] & group2bit) {
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massone = rmass[i];
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f[i][0] -= fx2*massone;
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f[i][1] -= fy2*massone;
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f[i][2] -= fz2*massone;
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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massone = mass[type[i]];
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f[i][0] += fx*massone;
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f[i][1] += fy*massone;
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f[i][2] += fz*massone;
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}
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if (mask[i] & group2bit) {
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massone = mass[type[i]];
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f[i][0] -= fx2*massone;
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f[i][1] -= fy2*massone;
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f[i][2] -= fz2*massone;
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixSpring::post_force_respa(int vflag, int ilevel, int iloop)
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{
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if (ilevel == nlevels_respa-1) post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixSpring::min_post_force(int vflag)
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{
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post_force(vflag);
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}
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/* ----------------------------------------------------------------------
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energy of stretched spring
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------------------------------------------------------------------------- */
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double FixSpring::compute_scalar()
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{
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return espring;
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}
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/* ----------------------------------------------------------------------
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return components of total spring force on fix group
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------------------------------------------------------------------------- */
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double FixSpring::compute_vector(int n)
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{
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return ftotal[n];
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}
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