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lammps/src/USER-MISC/compute_stress_mop_profile.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 : Romain Vermorel (LFCR), Laurent Joly (ULyon)
--------------------------------------------------------------------------*/
#include <mpi.h>
#include <cmath>
#include <cstring>
#include <cstdlib>
#include "compute_stress_mop_profile.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "error.h"
#include "memory.h"
using namespace LAMMPS_NS;
enum{X,Y,Z};
enum{LOWER,CENTER,UPPER,COORD};
enum{TOTAL,CONF,KIN};
#define BIG 1000000000
/* ---------------------------------------------------------------------- */
ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 7) error->all(FLERR,"Illegal compute stress/mop/profile command");
MPI_Comm_rank(world,&me);
// set compute mode and direction of plane(s) for pressure calculation
if (strcmp(arg[3],"x")==0) {
dir = X;
} else if (strcmp(arg[3],"y")==0) {
dir = Y;
} else if (strcmp(arg[3],"z")==0) {
dir = Z;
} else error->all(FLERR,"Illegal compute stress/mop/profile command");
// bin parameters
if (strcmp(arg[4],"lower") == 0) originflag = LOWER;
else if (strcmp(arg[4],"center") == 0) originflag = CENTER;
else if (strcmp(arg[4],"upper") == 0) originflag = UPPER;
else originflag = COORD;
if (originflag == COORD)
origin = force->numeric(FLERR,arg[4]);
delta = force->numeric(FLERR,arg[5]);
invdelta = 1.0/delta;
// parse values until one isn't recognized
which = new int[3*(narg-6)];
nvalues = 0;
int i;
int iarg=6;
while (iarg < narg) {
if (strcmp(arg[iarg],"conf") == 0) {
for (i=0; i<3; i++) {
which[nvalues] = CONF;
nvalues++;
}
} else if (strcmp(arg[iarg],"kin") == 0) {
for (i=0; i<3; i++) {
which[nvalues] = KIN;
nvalues++;
}
} else if (strcmp(arg[iarg],"total") == 0) {
for (i=0; i<3; i++) {
which[nvalues] = TOTAL;
nvalues++;
}
} else error->all(FLERR, "Illegal compute stress/mop/profile command"); //break;
iarg++;
}
// check domain related errors
// 3D only
if (domain->dimension < 3)
error->all(FLERR, "Compute stress/mop/profile incompatible with simulation dimension");
// orthogonal simulation box
if (domain->triclinic != 0)
error->all(FLERR, "Compute stress/mop/profile incompatible with triclinic simulation box");
// initialize some variables
nbins = 0;
coord = coordp = NULL;
values_local = values_global = array = NULL;
// bin setup
setup_bins();
// this fix produces a global array
memory->create(array,nbins,1+nvalues,"stress/mop/profile:array");
size_array_rows = nbins;
size_array_cols = 1 + nvalues;
array_flag = 1;
extarray = 0;
}
/* ---------------------------------------------------------------------- */
ComputeStressMopProfile::~ComputeStressMopProfile()
{
delete [] which;
memory->destroy(coord);
memory->destroy(coordp);
memory->destroy(values_local);
memory->destroy(values_global);
memory->destroy(array);
}
/* ---------------------------------------------------------------------- */
void ComputeStressMopProfile::init()
{
// conversion constants
nktv2p = force->nktv2p;
ftm2v = force->ftm2v;
// plane area
area = 1;
int i;
for (i=0; i<3; i++) {
if (i!=dir) area = area*domain->prd[i];
}
// timestep Value
dt = update->dt;
// Error check
// Compute stress/mop/profile requires fixed simulation box
if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
error->all(FLERR, "Compute stress/mop/profile requires a fixed simulation box");
//This compute requires a pair style with pair_single method implemented
if (force->pair == NULL)
error->all(FLERR,"No pair style is defined for compute stress/mop/profile");
if (force->pair->single_enable == 0)
error->all(FLERR,"Pair style does not support compute stress/mop/profile");
// Warnings
if (me==0){
//Compute stress/mop/profile only accounts for pair interactions.
// issue a warning if any intramolecular potential or Kspace is defined.
if (force->bond!=NULL)
error->warning(FLERR,"compute stress/mop/profile does not account for bond potentials");
if (force->angle!=NULL)
error->warning(FLERR,"compute stress/mop/profile does not account for angle potentials");
if (force->dihedral!=NULL)
error->warning(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
if (force->improper!=NULL)
error->warning(FLERR,"compute stress/mop/profile does not account for improper potentials");
if (force->kspace!=NULL)
error->warning(FLERR,"compute stress/mop/profile does not account for kspace contributions");
}
// need an occasional half neighbor list
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
}
/* ---------------------------------------------------------------------- */
void ComputeStressMopProfile::init_list(int /* id */, NeighList *ptr)
{
list = ptr;
}
/* ----------------------------------------------------------------------
compute output array
------------------------------------------------------------------------- */
void ComputeStressMopProfile::compute_array()
{
invoked_array = update->ntimestep;
//Compute pressures on separate procs
compute_pairs();
// sum pressure contributions over all procs
MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues,
MPI_DOUBLE,MPI_SUM,world);
int ibin,m,mo;
for (ibin=0; ibin<nbins; ibin++) {
array[ibin][0] = coord[ibin][0];
mo=1;
m = 0;
while (m<nvalues) {
array[ibin][m+mo] = values_global[ibin][m];
m++;
}
}
}
/*------------------------------------------------------------------------
compute pressure contribution of local proc
-------------------------------------------------------------------------*/
void ComputeStressMopProfile::compute_pairs()
{
int i,j,m,ii,jj,inum,jnum,itype,jtype,ibin;
double delx,dely,delz;
double rsq,fpair,factor_coul,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
double pos,pos1;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
// zero out arrays for one sample
for (m = 0; m < nbins; m++) {
for (i = 0; i < nvalues; i++) values_local[m][i] = 0.0;
}
// invoke half neighbor list (will copy or build if necessary)
neighbor->build_one(list);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
// parse values
double xi[3];
double vi[3];
double fi[3];
double xj[3];
m = 0;
while (m<nvalues) {
if (which[m] == CONF || which[m] == TOTAL) {
// Compute configurational contribution to pressure
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xi[0] = atom->x[i][0];
xi[1] = atom->x[i][1];
xi[2] = atom->x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
// skip if neither I nor J are in group
if (!(mask[i] & groupbit || mask[j] & groupbit)) continue;
xj[0] = atom->x[j][0];
xj[1] = atom->x[j][1];
xj[2] = atom->x[j][2];
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
delz = xi[2] - xj[2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq >= cutsq[itype][jtype]) continue;
if (newton_pair || j < nlocal) {
for (ibin=0;ibin<nbins;ibin++) {
pos = coord[ibin][0];
pos1 = coordp[ibin][0];
//check if ij pair is accross plane, add contribution to pressure
if ( ((xi[dir]>pos) && (xj[dir]<pos))
|| ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p;
values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
} else if ( ((xi[dir]<pos) && (xj[dir]>pos))
|| ((xi[dir]<pos1) && (xj[dir]>pos1)) ) {
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
values_local[ibin][m] -= fpair*(xi[0]-xj[0])/area*nktv2p;
values_local[ibin][m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
values_local[ibin][m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
}
}
} else {
for (ibin=0;ibin<nbins;ibin++) {
pos = coord[ibin][0];
pos1 = coordp[ibin][0];
//check if ij pair is accross plane, add contribution to pressure
if ( ((xi[dir]>pos) && (xj[dir]<pos))
|| ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p;
values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
}
}
}
}
}
}
// compute kinetic contribution to pressure
// counts local particles transfers across the plane
if (which[m] == KIN || which[m] == TOTAL){
double sgn;
for (int i = 0; i < nlocal; i++){
// skip if I is not in group
if (mask[i] & groupbit){
itype = type[i];
//coordinates at t
xi[0] = atom->x[i][0];
xi[1] = atom->x[i][1];
xi[2] = atom->x[i][2];
//velocities at t
vi[0] = atom->v[i][0];
vi[1] = atom->v[i][1];
vi[2] = atom->v[i][2];
//forces at t
fi[0] = atom->f[i][0];
fi[1] = atom->f[i][1];
fi[2] = atom->f[i][2];
//coordinates at t-dt (based on Velocity-Verlet alg.)
xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v;
xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
for (ibin=0;ibin<nbins;ibin++) {
pos = coord[ibin][0];
pos1 = coordp[ibin][0];
if (((xi[dir]-pos)*(xj[dir]-pos)*(xi[dir]-pos1)*(xj[dir]-pos1)<0)){
sgn = copysign(1.0,vi[dir]);
//approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
double vcross[3];
vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt;
vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt;
vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt;
values_local[ibin][m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
values_local[ibin][m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
values_local[ibin][m+2] += mass[itype]*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
}
}
}
}
}
m+=3;
}
}
/* ----------------------------------------------------------------------
setup 1d bins and their extent and coordinates
called at init()
------------------------------------------------------------------------- */
void ComputeStressMopProfile::setup_bins()
{
int i,n;
double lo = 0.0, hi = 0.0;
double *boxlo,*boxhi;
boxlo = domain->boxlo;
boxhi = domain->boxhi;
if (originflag == LOWER) origin = boxlo[dir];
else if (originflag == UPPER) origin = boxhi[dir];
else if (originflag == CENTER)
origin = 0.5 * (boxlo[dir] + boxhi[dir]);
if (origin < boxlo[dir]) {
error->all(FLERR,"Origin of bins for compute stress/mop/profile is out of bounds" );
} else {
n = static_cast<int> ((origin - boxlo[dir]) * invdelta);
lo = origin - n*delta;
}
if (origin < boxhi[dir]) {
n = static_cast<int> ((boxhi[dir] - origin) * invdelta);
hi = origin + n*delta;
} else {
error->all(FLERR,"Origin of bins for compute stress/mop/profile is out of bounds" );
}
offset = lo;
nbins = static_cast<int> ((hi-lo) * invdelta + 1.5);
//allocate bin arrays
memory->create(coord,nbins,1,"stress/mop/profile:coord");
memory->create(coordp,nbins,1,"stress/mop/profile:coordp");
memory->create(values_local,nbins,nvalues,"stress/mop/profile:values_local");
memory->create(values_global,nbins,nvalues,"stress/mop/profile:values_global");
// set bin coordinates
for (i = 0; i < nbins; i++) {
coord[i][0] = offset + i*delta;
if ( coord[i][0] < (domain->boxlo[dir]+domain->prd_half[dir]) ) {
coordp[i][0] = coord[i][0] + domain->prd[dir];
} else {
coordp[i][0] = coord[i][0] - domain->prd[dir];
}
}
}
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