git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6790 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
401
src/fix_restrain.cpp
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401
src/fix_restrain.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: Craig Tenney (University of Notre Dame)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "stdlib.h"
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#include "fix_restrain.h"
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#include "atom.h"
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#include "force.h"
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#include "update.h"
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#include "domain.h"
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#include "comm.h"
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#include "respa.h"
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#include "input.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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enum{DIHEDRAL};
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#define TOLERANCE 0.05
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/* ---------------------------------------------------------------------- */
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FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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int iarg = 6;
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if (narg < iarg) error->all("Illegal fix restrain command");
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scalar_flag = 1;
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global_freq = 1;
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extscalar = 1;
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time_depend = 1;
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// parse standard arguments
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int n_atoms;
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k_start = force->numeric(arg[3]);
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k_stop = force->numeric(arg[4]);
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if (strcmp(arg[5], "dihedral") == 0) {
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rstyle = DIHEDRAL;
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n_atoms = 4;
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} else error->all("Illegal fix restrain command");
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n_bonds = (narg - iarg) / (n_atoms + 1);
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if (narg != iarg + n_bonds * (n_atoms + 1))
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error->all("Illegal fix restrain command");
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// allocate arrays
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memory->create(atom_id,n_bonds,n_atoms,"restrain:atom_id");
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memory->create(target,n_bonds,"restrain:taret");
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// grab atom_ids and restraint target values
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int ibond = 0;
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while (iarg < narg) {
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for (int i = 0; i < n_atoms; i++) {
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atom_id[ibond][i] = force->inumeric(arg[iarg]);
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iarg++;
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}
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target[ibond] = force->numeric(arg[iarg]);
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iarg++;
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ibond++;
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}
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// special treatment for dihedral restraints
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if (rstyle == DIHEDRAL) {
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double PI = 4.0*atan(1.0);
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cos_shift = (double *)
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memory->smalloc(n_bonds * sizeof(double), "restrain:cos_shift");
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sin_shift = (double *)
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memory->smalloc(n_bonds * sizeof(double), "restrain:sin_shift");
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for (ibond = 0; ibond < n_bonds; ibond++) {
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double my_arg = PI * (180.0 + target[ibond]) / 180.0;
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cos_shift[ibond] = cos(my_arg);
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sin_shift[ibond] = sin(my_arg);
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}
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}
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// require atom map to lookup atom IDs
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if (atom->map_style == 0)
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error->all("Fix restrain requires an atom map, see atom_modify");
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}
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/* ---------------------------------------------------------------------- */
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FixRestrain::~FixRestrain()
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{
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memory->destroy(atom_id);
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memory->destroy(target);
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if (rstyle == DIHEDRAL) {
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memory->sfree(cos_shift);
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memory->sfree(sin_shift);
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}
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}
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/* ---------------------------------------------------------------------- */
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int FixRestrain::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 FixRestrain::init()
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{
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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 FixRestrain::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 FixRestrain::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 FixRestrain::post_force(int vflag)
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{
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energy = 0.0;
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if (rstyle == DIHEDRAL) restrain_dihedral();
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}
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/* ---------------------------------------------------------------------- */
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void FixRestrain::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 FixRestrain::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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apply dihedral restraints
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adopted from dihedral_charmm
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---------------------------------------------------------------------- */
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void FixRestrain::restrain_dihedral()
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{
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int i1,i2,i3,i4,i,m,n;
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double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
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double 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 **x = atom->x;
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double **f = atom->f;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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double delta = update->ntimestep - update->beginstep;
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delta /= update->endstep - update->beginstep;
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double k_step = k_start + delta * (k_stop - k_start);
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for (n = 0; n < n_bonds; n++) {
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i1 = atom->map(atom_id[n][0]);
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i2 = atom->map(atom_id[n][1]);
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i3 = atom->map(atom_id[n][2]);
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i4 = atom->map(atom_id[n][3]);
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// insure exactly one processor computes restraint
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if (newton_bond) {
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if (i2 == -1 || i2 >= nlocal) continue;
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if (i1 == -1 || i3 == -1 || i4 == -1) {
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char str[128];
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sprintf(str,
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"Restrain atoms %d %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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atom_id[n][0],atom_id[n][1],atom_id[n][2],atom_id[n][3],
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comm->me,update->ntimestep);
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error->one(str);
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}
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} else {
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if ((i1 == -1 || i1 >= nlocal) && (i2 == -1 || i2 >= nlocal) &&
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(i3 == -1 || i3 >= nlocal) && (i4 == -1 || i3 >= nlocal)) continue;
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if (i1 == -1 || i2 == -1 || i3 == -1 || i4 == -1) {
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char str[128];
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sprintf(str,
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"Restrain atoms %d %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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atom_id[n][0],atom_id[n][1],atom_id[n][2],atom_id[n][3],
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comm->me,update->ntimestep);
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error->one(str);
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}
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}
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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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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,"Restrain problem: %d %d %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);
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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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m = 1; //multiplicity
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p = 1.0;
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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[n] + df1*sin_shift[n];
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df1 = df1*cos_shift[n] - ddf1*sin_shift[n];
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df1 *= -m;
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p += 1.0;
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energy = k_step * p;
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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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df = -k_step * df1;
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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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}
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}
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/* ----------------------------------------------------------------------
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potential energy of added force
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------------------------------------------------------------------------- */
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double FixRestrain::compute_scalar()
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{
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MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
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return energy_all;
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}
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