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pair_srp.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Timothy Sirk (ARL), Pieter in't Veld (BASF)
This pair style srp command calculates a segmental repulsive force
between bonds. This is useful for preventing the crossing of bonds if
soft non-bonded potentials are used, such as DPD polymer chains.
See the doc page for pair_style srp command for usage instructions.
There is an example script for this package in examples/USER/srp.
Please contact Timothy Sirk for questions (tim.sirk@us.army.mil).
------------------------------------------------------------------------- */
#include <stdlib.h>
#include "pair_srp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "fix_srp.h"
#include "thermo.h"
#include "output.h"
#include <string.h>
#include "citeme.h"
using namespace LAMMPS_NS;
#define SMALL 1.0e-10
#define BIG 1e10
#define ONETWOBIT 0x40000000
static const char cite_srp[] =
"@Article{Sirk2012\n"
" author = {T. Sirk and Y. Sliozberg and J. Brennan and M. Lisal and J. Andzelm},\n"
" title = {An enhanced entangled polymer model for dissipative particle dynamics},\n"
" journal = {J.~Chem.~Phys.},\n"
" year = 2012,\n"
" volume = 136,\n"
" pages = {134903}\n"
"}\n\n";
static int srp_instance = 0;
/* ----------------------------------------------------------------------
set size of pair comms in constructor
---------------------------------------------------------------------- */
PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
if (lmp->citeme) lmp->citeme->add(cite_srp);
nextra = 1;
segment = NULL;
// generate unique fix-id for this pair style instance
fix_id = strdup("XX_FIX_SRP");
fix_id[0] = '0' + srp_instance / 10;
fix_id[1] = '0' + srp_instance % 10;
++srp_instance;
// create fix SRP instance here, as it has to
// be executed before all other fixes
char **fixarg = new char*[3];
fixarg[0] = fix_id;
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "SRP";
modify->add_fix(3,fixarg);
f_srp = (FixSRP *) modify->fix[modify->nfix-1];
delete [] fixarg;
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairSRP::allocate()
{
allocated = 1;
// particles of bptype inserted by fix srp
// bptype is the highest numbered atom type
int n = bptype;
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
memory->create(cut, n + 1, n + 1, "pair:cut");
memory->create(a0, n + 1, n + 1, "pair:a0");
// setflag for atom types
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
maxcount = 0;
}
/* ----------------------------------------------------------------------
free
------------------------------------------------------------------------- */
PairSRP::~PairSRP()
{
if (allocated)
{
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(a0);
memory->destroy(segment);
}
// check nfix in case all fixes have already been deleted
if (modify->nfix) modify->delete_fix(fix_id);
free(fix_id);
}
/* ----------------------------------------------------------------------
compute bond-bond repulsions
------------------------------------------------------------------------- */
void PairSRP::compute(int eflag, int vflag)
{
// setup energy and virial
if (eflag || vflag)
ev_setup(eflag, vflag);
else
evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int i0, i1, j0, j1;
int i,j,ii,jj,inum,jnum;
double dijsq, dij;
int *ilist,*jlist,*numneigh,**firstneigh;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
double dx,dy,dz,ti,tj;
double wd, lever0, lever1, evdwl, fpair;
double fxlever0, fylever0, fzlever0, fxlever1, fylever1, fzlever1;
double fx, fy, fz;
evdwl = 0.0;
// mapping global to local for atoms inside bond particles
// exclude 1-2 neighs if requested
if (neighbor->ago == 0){
remapBonds(nall);
if(exclude) onetwoexclude(ilist, inum, jlist, numneigh, firstneigh);
}
// this pair style only used with hybrid
// due to exclusions
// each atom i is type bptype
// each neigh j is type bptype
// using midpoint distance option
if(midpoint){
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
jnum = numneigh[i];
// two atoms inside bond particle
i0 = segment[i][0];
j0 = segment[i][1];
for (jj = 0; jj < jnum; jj++) {
jlist = firstneigh[i];
j = jlist[jj];
// enforce 1-2 exclusions
if( (sbmask(j) & exclude) )
continue;
j &= NEIGHMASK;
//retrieve atoms from bond particle
i1 = segment[j][0];
j1 = segment[j][1];
// midpt dist bond 0 and 1
dx = 0.5*(x[i0][0] - x[i1][0] + x[j0][0] - x[j1][0]);
dy = 0.5*(x[i0][1] - x[i1][1] + x[j0][1] - x[j1][1]);
dz = 0.5*(x[i0][2] - x[i1][2] + x[j0][2] - x[j1][2]);
dijsq = dx*dx + dy*dy + dz*dz;
if (dijsq < cutsq[bptype][bptype]){
dij = sqrt(dijsq);
if (dij < SMALL)
continue; // dij can be 0.0 with soft potentials
wd = 1.0 - dij / cut[bptype][bptype];
fpair = 0.5 * a0[bptype][bptype] * wd / dij; // 0.5 factor for lever rule
// force for bond 0, beads 0,1
//force between bonds
fx = fpair * dx;
fy = fpair * dy;
fz = fpair * dz;
f[i0][0] += fx; //keep force sign for bond 0
f[i0][1] += fy;
f[i0][2] += fz;
f[j0][0] += fx;
f[j0][1] += fy;
f[j0][2] += fz;
f[i1][0] -= fx; //flip force sign for bond 1
f[i1][1] -= fy;
f[i1][2] -= fz;
f[j1][0] -= fx;
f[j1][1] -= fy;
f[j1][2] -= fz;
// ************************************************* //
if (eflag){
evdwl = 0.5 * a0[bptype][bptype] * cut[bptype][bptype] * wd * wd;
}
if (evflag){
ev_tally(i0,i1,nlocal,1,0.5*evdwl,0.0,fpair,dx,dy,dz);
ev_tally(j0,j1,nlocal,1,0.5*evdwl,0.0,fpair,dx,dy,dz);
}
if (vflag_fdotr) virial_fdotr_compute();
}
}
}
}
else{
// using min distance option
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
jnum = numneigh[i];
i0 = segment[i][0];
j0 = segment[i][1];
for (jj = 0; jj < jnum; jj++) {
jlist = firstneigh[i];
j = jlist[jj];
// enforce 1-2 exclusions
if( (sbmask(j) & exclude) )
continue;
j &= NEIGHMASK;
i1 = segment[j][0];
j1 = segment[j][1];
getMinDist(x, dx, dy, dz, ti, tj, i0, j0, i1, j1);
dijsq = dx*dx + dy*dy + dz*dz;
if (dijsq < cutsq[bptype][bptype]){
dij = sqrt(dijsq);
if (dij < SMALL)
continue; // dij can be 0.0 with soft potentials
wd = 1.0 - dij / cut[bptype][bptype];
fpair = a0[bptype][bptype] * wd / dij;
// force for bond 0, beads 0,1
lever0 = 0.5 + ti; // assign force according to lever rule
lever1 = 0.5 + tj; // assign force according to lever rule
//force between bonds
fx = fpair * dx;
fy = fpair * dy;
fz = fpair * dz;
//decompose onto atoms
fxlever0 = fx * lever0;
fylever0 = fy * lever0;
fzlever0 = fz * lever0;
fxlever1 = fx * lever1;
fylever1 = fy * lever1;
fzlever1 = fz * lever1;
f[i0][0] += fxlever0; //keep force sign for bond 0
f[i0][1] += fylever0;
f[i0][2] += fzlever0;
f[j0][0] += (fx - fxlever0);
f[j0][1] += (fy - fylever0);
f[j0][2] += (fz - fzlever0);
f[i1][0] -= fxlever1; //flip force sign for bond 1
f[i1][1] -= fylever1;
f[i1][2] -= fzlever1;
f[j1][0] -= (fx - fxlever1);
f[j1][1] -= (fy - fylever1);
f[j1][2] -= (fz - fzlever1);
// ************************************************* //
if (eflag){
evdwl = 0.5 * a0[bptype][bptype] * cut[bptype][bptype] * wd * wd;
}
if (evflag){
ev_tally(i0,i1,nlocal,1,0.5*evdwl,0.0,0.5*fpair,dx,dy,dz);
ev_tally(j0,j1,nlocal,1,0.5*evdwl,0.0,0.5*fpair,dx,dy,dz);
}
if (vflag_fdotr) virial_fdotr_compute();
}
}
}
}
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairSRP::settings(int narg, char **arg)
{
if (narg < 3 || narg > 7)
error->all(FLERR,"Illegal pair_style command");
if (atom->tag_enable == 0)
error->all(FLERR,"Pair_style srp requires atom IDs");
cut_global = force->numeric(FLERR,arg[0]);
// wildcard
if (strcmp(arg[1],"*") == 0)
btype = 0;
else {
btype = force->inumeric(FLERR,arg[1]);
if ((btype > atom->nbondtypes) || (btype <= 0))
error->all(FLERR,"Illegal pair_style command");
}
// settings
midpoint = 0;
min = 0;
if (strcmp(arg[2],"min") == 0) min = 1;
else if (strcmp(arg[2],"mid") == 0) midpoint = 1;
else
error->all(FLERR,"Illegal pair_style command");
int iarg = 3;
// default exclude 1-2
// scaling for 1-2, etc not supported
exclude = 1;
// use last atom type by default for bond particles
bptype = atom->ntypes;
while (iarg < narg) {
if (strcmp(arg[iarg],"exclude") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair srp command");
if (strcmp(arg[iarg+1],"yes") == 0)
exclude = 1;
if (strcmp(arg[iarg+1],"no") == 0){
if (min) error->all(FLERR,"Illegal exclude option in pair srp command");
exclude = 0;
}
iarg += 2;
} else if (strcmp(arg[iarg],"bptype") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair srp command");
bptype = force->inumeric(FLERR,arg[iarg+1]);
if ((bptype < 1) || (bptype > atom->ntypes))
error->all(FLERR,"Illegal bond particle type for srp");
iarg += 2;
} else error->all(FLERR,"Illegal pair srp command");
}
// reset cutoffs if explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= bptype; i++)
for (j = i+1; j <= bptype; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs
------------------------------------------------------------------------- */
void PairSRP::coeff(int narg, char **arg)
{
if (narg < 3 || narg > 4)
error->all(FLERR,"PairSRP: Incorrect args for pair coeff");
if (!allocated) allocate();
// set ij bond-bond cutoffs
int ilo, ihi, jlo, jhi;
force->bounds(arg[0], bptype, ilo, ihi);
force->bounds(arg[1], bptype, jlo, jhi);
double a0_one = force->numeric(FLERR,arg[2]);
double cut_one = cut_global;
if (narg == 4) cut_one = force->numeric(FLERR,arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++)
{
for (int j = MAX(jlo,i); j <= jhi; j++)
{
a0[i][j] = a0_one;
cut[i][j] = cut_one;
cutsq[i][j] = cut_one * cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->warning(FLERR,"PairSRP: No pair coefficients were set");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairSRP::init_style()
{
if (!force->newton_pair)
error->all(FLERR,"PairSRP: Pair srp requires newton pair on");
// verify that fix SRP is still defined and has not been changed.
int ifix = modify->find_fix(fix_id);
if (f_srp != (FixSRP *)modify->fix[ifix])
error->all(FLERR,"Fix SRP has been changed unexpectedly");
if (comm->me == 0) {
if (screen) fprintf(screen,"Using type %d for bond particles\n",bptype);
if (logfile) fprintf(logfile,"Using type %d for bond particles\n",bptype);
}
// set bond and bond particle types in fix srp
// bonds of this type will be represented by bond particles
// if bond type is 0, then all bonds have bond particles
// btype = bond type
char c0[20];
char* arg0[2];
sprintf(c0, "%d", btype);
arg0[0] = (char *) "btype";
arg0[1] = c0;
f_srp->modify_params(2, arg0);
// bptype = bond particle type
sprintf(c0, "%d", bptype);
arg0[0] = (char *) "bptype";
arg0[1] = c0;
f_srp->modify_params(2, arg0);
// bond particles do not contribute to energy or virial
// bond particles do not belong to group all
// but thermo normalization is by nall
// therefore should turn off normalization
int me;
MPI_Comm_rank(world,&me);
char *arg1[2];
arg1[0] = (char *) "norm";
arg1[1] = (char *) "no";
output->thermo->modify_params(2, arg1);
if (me == 0)
error->message(FLERR,"Thermo normalization turned off by pair srp");
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairSRP::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"PairSRP: All pair coeffs are not set");
cut[j][i] = cut[i][j];
a0[j][i] = a0[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
find min distance for bonds i0/j0 and i1/j1
------------------------------------------------------------------------- */
inline void PairSRP::getMinDist(double** &x, double &dx, double &dy, double &dz, double &ti, double &tj, int &i0, int &j0, int &i1, int &j1)
{
// move these outside the loop
double diffx0, diffy0, diffz0, diffx1, diffy1, diffz1, dPx, dPy, dPz, RiRi, RiRj, RjRj;
double denom, termx0, termy0, termz0, num0, termx1, termy1, termz1, num1;
// compute midpt dist from 1st atom, 1st bond
diffx0 = x[j0][0] - x[i0][0]; // x,y,z from bond 0
diffy0 = x[j0][1] - x[i0][1];
diffz0 = x[j0][2] - x[i0][2];
// compute midpt dist from 1st atom, 2nd bond
diffx1 = x[j1][0] - x[i1][0];
diffy1 = x[j1][1] - x[i1][1];
diffz1 = x[j1][2] - x[i1][2];
// midpoint distance
dPx = 0.5*(diffx0-diffx1) + x[i0][0]-x[i1][0];
dPy = 0.5*(diffy0-diffy1) + x[i0][1]-x[i1][1];
dPz = 0.5*(diffz0-diffz1) + x[i0][2]-x[i1][2];
// Ri^2 Rj^2
RiRi = diffx0*diffx0 + diffy0*diffy0 + diffz0*diffz0;
RiRj = diffx0*diffx1 + diffy0*diffy1 + diffz0*diffz1;
RjRj = diffx1*diffx1 + diffy1*diffy1 + diffz1*diffz1;
denom = RiRj*RiRj - RiRi*RjRj;
// handle case of parallel lines
// reduce to midpt distance
if (fabs(denom) < SMALL){
if(denom < 0) denom = -BIG;
else denom = BIG;
}
// calc ti
termx0 = RiRj*diffx1 - RjRj*diffx0;
termy0 = RiRj*diffy1 - RjRj*diffy0;
termz0 = RiRj*diffz1 - RjRj*diffz0;
num0 = dPx*termx0 + dPy*termy0 + dPz*termz0;
ti = num0 / denom;
if (ti > 0.5) ti = 0.5;
if (ti < -0.5) ti = -0.5;
// calc tj
termx1 = RiRj*diffx0 - RiRi*diffx1;
termy1 = RiRj*diffy0 - RiRi*diffy1;
termz1 = RiRj*diffz0 - RiRi*diffz1;
num1 = dPx*termx1 + dPy*termy1 + dPz*termz1;
tj = -num1/ denom;
if (tj > 0.5) tj = 0.5;
if (tj < -0.5) tj = -0.5;
// min dist
dx = dPx - ti*diffx0 + tj*diffx1;
dy = dPy - ti*diffy0 + tj*diffy1;
dz = dPz - ti*diffz0 + tj*diffz1;
}
/* --------------------------------------------------------
map global id of atoms in stored by each bond particle
------------------------------------------------------- */
inline void PairSRP::remapBonds(int &nall)
{
if(nall > maxcount){
memory->grow(segment, nall, 2, "pair:segment");
maxcount = nall;
}
// loop over all bond particles
// each bond paricle holds two bond atoms
// map global ids of bond atoms to local ids
// might not be able to map both bond atoms of j, if j is outside neighcut
// these are not on neighlist, so are not used
int tmp;
srp = f_srp->array_atom;
for (int i = 0; i < nall; i++) {
if(atom->type[i] == bptype){
// tmp is local id
// tmp == -1 is ok
tmp = atom->map((int)srp[i][0]);
segment[i][0] = domain->closest_image(i,tmp);
// repeat with other id
tmp = atom->map((int)srp[i][1]);
segment[i][1] = domain->closest_image(i,tmp);
}
}
}
/* --------------------------------------------------------
add exclusions for 1-2 neighs, if requested
more complex exclusions or scaling probably not needed
------------------------------------------------------- */
inline void PairSRP::onetwoexclude(int* &ilist, int &inum, int* &jlist, int* &numneigh, int** &firstneigh)
{
int i0, i1, j0, j1;
int i,j,ii,jj,jnum;
// encode neighs with exclusions
// only need 1-2 info for normal uses of srp
// add 1-3, etc later if ever needed
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
jnum = numneigh[i];
// two atoms inside bond particle
i0 = segment[i][0];
j0 = segment[i][1];
for (jj = 0; jj < jnum; jj++) {
jlist = firstneigh[i];
j = jlist[jj];
j &= NEIGHMASK;
//two atoms inside bond particle
i1 = segment[j][0];
j1 = segment[j][1];
// check for a 1-2 neigh
if(i0 == i1 || i0 == j1 || i1 == j0 || j0 == j1){
j |= ONETWOBIT;
jlist[jj] = j;
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairSRP::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g\n",i,a0[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairSRP::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g %g\n",i,j,a0[i][j],cut[i][j]);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairSRP::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&a0[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairSRP::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
printf(" i %d j %d \n",i,j);
fread(&a0[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairSRP::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&bptype,sizeof(int),1,fp);
fwrite(&btype,sizeof(int),1,fp);
fwrite(&min,sizeof(int),1,fp);
fwrite(&midpoint,sizeof(int),1,fp);
fwrite(&exclude,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairSRP::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&bptype,sizeof(int),1,fp);
fread(&btype,sizeof(int),1,fp);
fread(&min,sizeof(int),1,fp);
fread(&midpoint,sizeof(int),1,fp);
fread(&exclude,sizeof(int),1,fp);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
}

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