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fix_bond_swap.cpp
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Wed, Nov 6, 05:35

fix_bond_swap.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_bond_swap.h"
#include "atom.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "group.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "compute.h"
#include "random_mars.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
#include "update.h"
using namespace LAMMPS_NS;
using namespace FixConst;
static const char cite_fix_bond_swap[] =
"neighbor multi command:\n\n"
"@Article{Auhl03,\n"
" author = {R. Auhl, R. Everaers, G. S. Grest, K. Kremer, S. J. Plimpton},\n"
" title = {Equilibration of long chain polymer melts in computer simulations},\n"
" journal = {J.~Chem.~Phys.},\n"
" year = 2003,\n"
" volume = 119,\n"
" pages = {12718--12728}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
FixBondSwap::FixBondSwap(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
tflag(0), alist(NULL), id_temp(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_bond_swap);
if (narg != 7) error->all(FLERR,"Illegal fix bond/swap command");
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix bond/swap command");
force_reneighbor = 1;
next_reneighbor = -1;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 0;
fraction = force->numeric(FLERR,arg[4]);
double cutoff = force->numeric(FLERR,arg[5]);
cutsq = cutoff*cutoff;
// initialize Marsaglia RNG with processor-unique seed
int seed = force->inumeric(FLERR,arg[6]);
random = new RanMars(lmp,seed + comm->me);
// error check
if (atom->molecular != 1)
error->all(FLERR,"Cannot use fix bond/swap with non-molecular systems");
// create a new compute temp style
// id = fix-ID + temp, compute group = fix group
int n = strlen(id) + 6;
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
// initialize atom list
nmax = 0;
alist = NULL;
naccept = foursome = 0;
}
/* ---------------------------------------------------------------------- */
FixBondSwap::~FixBondSwap()
{
delete random;
// delete temperature if fix created it
if (tflag) modify->delete_compute(id_temp);
delete [] id_temp;
memory->destroy(alist);
}
/* ---------------------------------------------------------------------- */
int FixBondSwap::setmask()
{
int mask = 0;
mask |= POST_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixBondSwap::init()
{
// require an atom style with molecule IDs
if (atom->molecule == NULL)
error->all(FLERR,
"Must use atom style with molecule IDs with fix bond/swap");
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix bond/swap does not exist");
temperature = modify->compute[icompute];
// pair and bonds must be defined
// no dihedral or improper potentials allowed
// special bonds must be 0 1 1
if (force->pair == NULL || force->bond == NULL)
error->all(FLERR,"Fix bond/swap requires pair and bond styles");
if (force->pair->single_enable == 0)
error->all(FLERR,"Pair style does not support fix bond/swap");
if (force->angle == NULL && atom->nangles > 0 && comm->me == 0)
error->warning(FLERR,"Fix bond/swap will ignore defined angles");
if (force->dihedral || force->improper)
error->all(FLERR,"Fix bond/swap cannot use dihedral or improper styles");
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
force->special_lj[3] != 1.0)
error->all(FLERR,"Fix bond/swap requires special_bonds = 0,1,1");
// need a half neighbor list, built every Nevery steps
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->occasional = 1;
// zero out stats
naccept = foursome = 0;
angleflag = 0;
if (force->angle) angleflag = 1;
}
/* ---------------------------------------------------------------------- */
void FixBondSwap::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ----------------------------------------------------------------------
look for and perform swaps
NOTE: used to do this every pre_neighbor(), but think that is a bug
b/c was doing it after exchange() and before neighbor->build()
which is when neigh lists are actually out-of-date or even bogus,
now do it based on user-specified Nevery, and trigger reneigh
if any swaps performed, like fix bond/create
------------------------------------------------------------------------- */
void FixBondSwap::post_integrate()
{
int i,j,ii,jj,m,inum,jnum;
int inext,iprev,ilast,jnext,jprev,jlast,ibond,iangle,jbond,jangle;
int ibondtype,jbondtype,iangletype,inextangletype,jangletype,jnextangletype;
tagint itag,inexttag,iprevtag,ilasttag,jtag,jnexttag,jprevtag,jlasttag;
tagint i1,i2,i3,j1,j2,j3;
int *ilist,*jlist,*numneigh,**firstneigh;
double delta,factor;
if (update->ntimestep % nevery) return;
// compute current temp for Boltzmann factor test
double t_current = temperature->compute_scalar();
// local ptrs to atom arrays
tagint *tag = atom->tag;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *num_angle = atom->num_angle;
tagint **angle_atom1 = atom->angle_atom1;
tagint **angle_atom2 = atom->angle_atom2;
tagint **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int newton_bond = force->newton_bond;
int nlocal = atom->nlocal;
type = atom->type;
x = atom->x;
neighbor->build_one(list,1);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// randomize list of my owned atoms that are in fix group
// grow atom list if necessary
if (atom->nmax > nmax) {
memory->destroy(alist);
nmax = atom->nmax;
memory->create(alist,nmax,"bondswap:alist");
}
int neligible = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit)
alist[neligible++] = i;
}
int tmp;
for (i = 0; i < neligible; i++) {
j = static_cast<int> (random->uniform() * neligible);
tmp = alist[i];
alist[i] = alist[j];
alist[j] = tmp;
}
// examine ntest of my eligible atoms for potential swaps
// atom i is randomly selected via atom list
// look at all j neighbors of atom i
// atom j must be on-processor (j < nlocal)
// atom j must be in fix group
// i and j must be same distance from chain end (mol[i] = mol[j])
// NOTE: must use extra parens in if test on mask[j] & groupbit
int ntest = static_cast<int> (fraction * neligible);
int accept = 0;
for (int itest = 0; itest < ntest; itest++) {
i = alist[itest];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
if (j >= nlocal) continue;
if ((mask[j] & groupbit) == 0) continue;
if (molecule[i] != molecule[j]) continue;
// look at all bond partners of atoms i and j
// use num_bond for this, not special list, so also find bondtypes
// inext,jnext = bonded atoms
// inext,jnext must be on-processor (inext,jnext < nlocal)
// inext,jnext must be same dist from chain end (mol[inext] = mol[jnext])
// since swaps may occur between two ends of a single chain, insure
// the 4 atoms are unique (no duplicates): inext != jnext, inext != j
// all 4 old and new bonds must have length < cutoff
for (ibond = 0; ibond < num_bond[i]; ibond++) {
inext = atom->map(bond_atom[i][ibond]);
if (inext >= nlocal || inext < 0) continue;
ibondtype = bond_type[i][ibond];
for (jbond = 0; jbond < num_bond[j]; jbond++) {
jnext = atom->map(bond_atom[j][jbond]);
if (jnext >= nlocal || jnext < 0) continue;
jbondtype = bond_type[j][jbond];
if (molecule[inext] != molecule[jnext]) continue;
if (inext == jnext || inext == j) continue;
if (dist_rsq(i,inext) >= cutsq) continue;
if (dist_rsq(j,jnext) >= cutsq) continue;
if (dist_rsq(i,jnext) >= cutsq) continue;
if (dist_rsq(j,inext) >= cutsq) continue;
// if angles are enabled:
// find other atoms i,inext,j,jnext are in angles with
// and angletypes: i/j angletype, i/j nextangletype
// use num_angle for this, not special list, so also find angletypes
// 4 atoms consecutively along 1st chain: iprev,i,inext,ilast
// 4 atoms consecutively along 2nd chain: jprev,j,jnext,jlast
// prev or last atom can be non-existent at end of chain
// set prev/last = -1 in this case
// if newton bond = 0, then angles are stored by all 4 atoms
// so require that iprev,ilast,jprev,jlast be owned by this proc
// so all copies of angles can be updated if a swap takes place
if (angleflag) {
itag = tag[i];
inexttag = tag[inext];
jtag = tag[j];
jnexttag = tag[jnext];
iprev = -1;
for (iangle = 0; iangle < num_angle[i]; iangle++) {
i1 = angle_atom1[i][iangle];
i2 = angle_atom2[i][iangle];
i3 = angle_atom3[i][iangle];
if (i2 == itag && i3 == inexttag) iprev = atom->map(i1);
else if (i1 == inexttag && i2 == itag) iprev = atom->map(i3);
if (iprev >= 0) {
iangletype = angle_type[i][iangle];
break;
}
}
if (!newton_bond && iprev >= nlocal) continue;
ilast = -1;
for (iangle = 0; iangle < num_angle[inext]; iangle++) {
i1 = angle_atom1[inext][iangle];
i2 = angle_atom2[inext][iangle];
i3 = angle_atom3[inext][iangle];
if (i1 == itag && i2 == inexttag) ilast = atom->map(i3);
else if (i2 == inexttag && i3 == itag) ilast = atom->map(i1);
if (ilast >= 0) {
inextangletype = angle_type[inext][iangle];
break;
}
}
if (!newton_bond && ilast >= nlocal) continue;
jprev = -1;
for (jangle = 0; jangle < num_angle[j]; jangle++) {
j1 = angle_atom1[j][jangle];
j2 = angle_atom2[j][jangle];
j3 = angle_atom3[j][jangle];
if (j2 == jtag && j3 == jnexttag) jprev = atom->map(j1);
else if (j1 == jnexttag && j2 == jtag) jprev = atom->map(j3);
if (jprev >= 0) {
jangletype = angle_type[j][jangle];
break;
}
}
if (!newton_bond && jprev >= nlocal) continue;
jlast = -1;
for (jangle = 0; jangle < num_angle[jnext]; jangle++) {
j1 = angle_atom1[jnext][jangle];
j2 = angle_atom2[jnext][jangle];
j3 = angle_atom3[jnext][jangle];
if (j1 == jtag && j2 == jnexttag) jlast = atom->map(j3);
else if (j2 == jnexttag && j3 == jtag) jlast = atom->map(j1);
if (jlast >= 0) {
jnextangletype = angle_type[jnext][jangle];
break;
}
}
if (!newton_bond && jlast >= nlocal) continue;
}
// valid foursome found between 2 chains:
// chains = iprev-i-inext-ilast and jprev-j-jnext-jlast
// prev or last values are -1 if do not exist due to end of chain
// OK to call angle_eng with -1 atom, since just return 0.0
// current energy of foursome =
// E_nb(i,j) + E_nb(i,jnext) + E_nb(inext,j) + E_nb(inext,jnext) +
// E_bond(i,inext) + E_bond(j,jnext) +
// E_angle(iprev,i,inext) + E_angle(i,inext,ilast) +
// E_angle(jprev,j,jnext) + E_angle(j,jnext,jlast)
// new energy of foursome with swapped bonds =
// E_nb(i,j) + E_nb(i,inext) + E_nb(j,jnext) + E_nb(inext,jnext) +
// E_bond(i,jnext) + E_bond(j,inext) +
// E_angle(iprev,i,jnext) + E_angle(i,jnext,jlast) +
// E_angle(jprev,j,inext) + E_angle(j,inext,ilast)
// energy delta = add/subtract differing terms between 2 formulas
foursome++;
delta = pair_eng(i,inext) + pair_eng(j,jnext) -
pair_eng(i,jnext) - pair_eng(inext,j);
delta += bond_eng(ibondtype,i,jnext) + bond_eng(jbondtype,j,inext) -
bond_eng(ibondtype,i,inext) - bond_eng(jbondtype,j,jnext);
if (angleflag)
delta += angle_eng(iangletype,iprev,i,jnext) +
angle_eng(jnextangletype,i,jnext,jlast) +
angle_eng(jangletype,jprev,j,inext) +
angle_eng(inextangletype,j,inext,ilast) -
angle_eng(iangletype,iprev,i,inext) -
angle_eng(inextangletype,i,inext,ilast) -
angle_eng(jangletype,jprev,j,jnext) -
angle_eng(jnextangletype,j,jnext,jlast);
// if delta <= 0, accept swap
// if delta > 0, compute Boltzmann factor with current temperature
// only accept if greater than random value
// whether accept or not, exit test loop
if (delta < 0.0) accept = 1;
else {
factor = exp(-delta/force->boltz/t_current);
if (random->uniform() < factor) accept = 1;
}
goto done;
}
}
}
}
done:
// trigger immediate reneighboring if any swaps occurred
int accept_any;
MPI_Allreduce(&accept,&accept_any,1,MPI_INT,MPI_SUM,world);
if (accept_any) next_reneighbor = update->ntimestep;
if (!accept) return;
naccept++;
// change bond partners of affected atoms
// on atom i: bond i-inext changes to i-jnext
// on atom j: bond j-jnext changes to j-inext
// on atom inext: bond inext-i changes to inext-j
// on atom jnext: bond jnext-j changes to jnext-i
for (ibond = 0; ibond < num_bond[i]; ibond++)
if (bond_atom[i][ibond] == tag[inext]) bond_atom[i][ibond] = tag[jnext];
for (jbond = 0; jbond < num_bond[j]; jbond++)
if (bond_atom[j][jbond] == tag[jnext]) bond_atom[j][jbond] = tag[inext];
for (ibond = 0; ibond < num_bond[inext]; ibond++)
if (bond_atom[inext][ibond] == tag[i]) bond_atom[inext][ibond] = tag[j];
for (jbond = 0; jbond < num_bond[jnext]; jbond++)
if (bond_atom[jnext][jbond] == tag[j]) bond_atom[jnext][jbond] = tag[i];
// set global tags of 4 atoms in bonds
itag = tag[i];
inexttag = tag[inext];
jtag = tag[j];
jnexttag = tag[jnext];
// change 1st special neighbors of affected atoms: i,j,inext,jnext
// don't need to change 2nd/3rd special neighbors for any atom
// since special bonds = 0 1 1 means they are never used
for (m = 0; m < nspecial[i][0]; m++)
if (special[i][m] == inexttag) special[i][m] = jnexttag;
for (m = 0; m < nspecial[j][0]; m++)
if (special[j][m] == jnexttag) special[j][m] = inexttag;
for (m = 0; m < nspecial[inext][0]; m++)
if (special[inext][m] == itag) special[inext][m] = jtag;
for (m = 0; m < nspecial[jnext][0]; m++)
if (special[jnext][m] == jtag) special[jnext][m] = itag;
// done if no angles
if (!angleflag) return;
// set global tags of 4 additional atoms in angles, 0 if no angle
if (iprev >= 0) iprevtag = tag[iprev];
else iprevtag = 0;
if (ilast >= 0) ilasttag = tag[ilast];
else ilasttag = 0;
if (jprev >= 0) jprevtag = tag[jprev];
else jprevtag = 0;
if (jlast >= 0) jlasttag = tag[jlast];
else jlasttag = 0;
// change angle partners of affected atoms
// must check if each angle is stored as a-b-c or c-b-a
// on atom i:
// angle iprev-i-inext changes to iprev-i-jnext
// angle i-inext-ilast changes to i-jnext-jlast
// on atom j:
// angle jprev-j-jnext changes to jprev-j-inext
// angle j-jnext-jlast changes to j-inext-ilast
// on atom inext:
// angle iprev-i-inext changes to jprev-j-inext
// angle i-inext-ilast changes to j-inext-ilast
// on atom jnext:
// angle jprev-j-jnext changes to iprev-i-jnext
// angle j-jnext-jlast changes to i-jnext-jlast
for (iangle = 0; iangle < num_angle[i]; iangle++) {
i1 = angle_atom1[i][iangle];
i2 = angle_atom2[i][iangle];
i3 = angle_atom3[i][iangle];
if (i1 == iprevtag && i2 == itag && i3 == inexttag)
angle_atom3[i][iangle] = jnexttag;
else if (i1 == inexttag && i2 == itag && i3 == iprevtag)
angle_atom1[i][iangle] = jnexttag;
else if (i1 == itag && i2 == inexttag && i3 == ilasttag) {
angle_atom2[i][iangle] = jnexttag;
angle_atom3[i][iangle] = jlasttag;
} else if (i1 == ilasttag && i2 == inexttag && i3 == itag) {
angle_atom1[i][iangle] = jlasttag;
angle_atom2[i][iangle] = jnexttag;
}
}
for (jangle = 0; jangle < num_angle[j]; jangle++) {
j1 = angle_atom1[j][jangle];
j2 = angle_atom2[j][jangle];
j3 = angle_atom3[j][jangle];
if (j1 == jprevtag && j2 == jtag && j3 == jnexttag)
angle_atom3[j][jangle] = inexttag;
else if (j1 == jnexttag && j2 == jtag && j3 == jprevtag)
angle_atom1[j][jangle] = inexttag;
else if (j1 == jtag && j2 == jnexttag && j3 == jlasttag) {
angle_atom2[j][jangle] = inexttag;
angle_atom3[j][jangle] = ilasttag;
} else if (j1 == jlasttag && j2 == jnexttag && j3 == jtag) {
angle_atom1[j][jangle] = ilasttag;
angle_atom2[j][jangle] = inexttag;
}
}
for (iangle = 0; iangle < num_angle[inext]; iangle++) {
i1 = angle_atom1[inext][iangle];
i2 = angle_atom2[inext][iangle];
i3 = angle_atom3[inext][iangle];
if (i1 == iprevtag && i2 == itag && i3 == inexttag) {
angle_atom1[inext][iangle] = jprevtag;
angle_atom2[inext][iangle] = jtag;
} else if (i1 == inexttag && i2 == itag && i3 == iprevtag) {
angle_atom2[inext][iangle] = jtag;
angle_atom3[inext][iangle] = jprevtag;
} else if (i1 == itag && i2 == inexttag && i3 == ilasttag)
angle_atom1[inext][iangle] = jtag;
else if (i1 == ilasttag && i2 == inexttag && i3 == itag)
angle_atom3[inext][iangle] = jtag;
}
for (jangle = 0; jangle < num_angle[jnext]; jangle++) {
j1 = angle_atom1[jnext][jangle];
j2 = angle_atom2[jnext][jangle];
j3 = angle_atom3[jnext][jangle];
if (j1 == jprevtag && j2 == jtag && j3 == jnexttag) {
angle_atom1[jnext][jangle] = iprevtag;
angle_atom2[jnext][jangle] = itag;
} else if (j1 == jnexttag && j2 == jtag && j3 == jprevtag) {
angle_atom2[jnext][jangle] = itag;
angle_atom3[jnext][jangle] = iprevtag;
} else if (j1 == jtag && j2 == jnexttag && j3 == jlasttag)
angle_atom1[jnext][jangle] = itag;
else if (j1 == jlasttag && j2 == jnexttag && j3 == jtag)
angle_atom3[jnext][jangle] = itag;
}
// done if newton bond set
if (newton_bond) return;
// change angles stored by iprev,ilast,jprev,jlast
// on atom iprev: angle iprev-i-inext changes to iprev-i-jnext
// on atom jprev: angle jprev-j-jnext changes to jprev-j-inext
// on atom ilast: angle i-inext-ilast changes to j-inext-ilast
// on atom jlast: angle j-jnext-jlast changes to i-jnext-jlast
for (iangle = 0; iangle < num_angle[iprev]; iangle++) {
i1 = angle_atom1[iprev][iangle];
i2 = angle_atom2[iprev][iangle];
i3 = angle_atom3[iprev][iangle];
if (i1 == iprevtag && i2 == itag && i3 == inexttag)
angle_atom3[iprev][iangle] = jnexttag;
else if (i1 == inexttag && i2 == itag && i3 == iprevtag)
angle_atom1[iprev][iangle] = jnexttag;
}
for (jangle = 0; jangle < num_angle[jprev]; jangle++) {
j1 = angle_atom1[jprev][jangle];
j2 = angle_atom2[jprev][jangle];
j3 = angle_atom3[jprev][jangle];
if (j1 == jprevtag && j2 == jtag && j3 == jnexttag)
angle_atom3[jprev][jangle] = inexttag;
else if (j1 == jnexttag && j2 == jtag && j3 == jprevtag)
angle_atom1[jprev][jangle] = inexttag;
}
for (iangle = 0; iangle < num_angle[ilast]; iangle++) {
i1 = angle_atom1[ilast][iangle];
i2 = angle_atom2[ilast][iangle];
i3 = angle_atom3[ilast][iangle];
if (i1 == itag && i2 == inexttag && i3 == ilasttag)
angle_atom1[ilast][iangle] = jtag;
else if (i1 == ilasttag && i2 == inexttag && i3 == itag)
angle_atom3[ilast][iangle] = jtag;
}
for (jangle = 0; jangle < num_angle[jlast]; jangle++) {
j1 = angle_atom1[jlast][jangle];
j2 = angle_atom2[jlast][jangle];
j3 = angle_atom3[jlast][jangle];
if (j1 == jtag && j2 == jnexttag && j3 == jlasttag)
angle_atom1[jlast][jangle] = itag;
else if (j1 == jlasttag && j2 == jnexttag && j3 == jtag)
angle_atom3[jlast][jangle] = itag;
}
}
/* ---------------------------------------------------------------------- */
int FixBondSwap::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
if (tflag) {
modify->delete_compute(id_temp);
tflag = 0;
}
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,"Fix_modify temperature ID does not "
"compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
return 2;
}
return 0;
}
/* ----------------------------------------------------------------------
compute squared distance between atoms I,J
must use minimum_image since J was found thru atom->map()
------------------------------------------------------------------------- */
double FixBondSwap::dist_rsq(int i, int j)
{
double delx = x[i][0] - x[j][0];
double dely = x[i][1] - x[j][1];
double delz = x[i][2] - x[j][2];
domain->minimum_image(delx,dely,delz);
return (delx*delx + dely*dely + delz*delz);
}
/* ----------------------------------------------------------------------
return pairwise interaction energy between atoms I,J
will always be full non-bond interaction, so factors = 1 in single() call
------------------------------------------------------------------------- */
double FixBondSwap::pair_eng(int i, int j)
{
double tmp;
double rsq = dist_rsq(i,j);
return force->pair->single(i,j,type[i],type[j],rsq,1.0,1.0,tmp);
}
/* ---------------------------------------------------------------------- */
double FixBondSwap::bond_eng(int btype, int i, int j)
{
double tmp;
double rsq = dist_rsq(i,j);
return force->bond->single(btype,rsq,i,j,tmp);
}
/* ---------------------------------------------------------------------- */
double FixBondSwap::angle_eng(int atype, int i, int j, int k)
{
// test for non-existent angle at end of chain
if (i == -1 || k == -1) return 0.0;
return force->angle->single(atype,i,j,k);
}
/* ----------------------------------------------------------------------
return bond swapping stats
n = 1 is # of swaps
n = 2 is # of attempted swaps
------------------------------------------------------------------------- */
double FixBondSwap::compute_vector(int n)
{
double one,all;
if (n == 0) one = naccept;
else one = foursome;
MPI_Allreduce(&one,&all,1,MPI_DOUBLE,MPI_SUM,world);
return all;
}
/* ----------------------------------------------------------------------
memory usage of alist
------------------------------------------------------------------------- */
double FixBondSwap::memory_usage()
{
double bytes = nmax * sizeof(int);
return bytes;
}

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