Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/RIGID/compute_rigid_local.cpp
503cd8206557lammm-master-deprecated

Last Change
Raw File

compute_rigid_local.cpp
View Options

/* ----------------------------------------------------------------------
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 <string.h>
#include "compute_rigid_local.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "modify.h"
#include "fix_rigid_small.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
enum{ID,MOL,MASS,X,Y,Z,XU,YU,ZU,VX,VY,VZ,FX,FY,FZ,IX,IY,IZ,
TQX,TQY,TQZ,OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
QUATW,QUATI,QUATJ,QUATK,INERTIAX,INERTIAY,INERTIAZ};
/* ---------------------------------------------------------------------- */
ComputeRigidLocal::ComputeRigidLocal(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 5) error->all(FLERR,"Illegal compute rigid/local command");
local_flag = 1;
nvalues = narg - 4;
if (nvalues == 1) size_local_cols = 0;
else size_local_cols = nvalues;
int n = strlen(arg[3]) + 1;
idrigid = new char[n];
strcpy(idrigid,arg[3]);
rstyle = new int[nvalues];
nvalues = 0;
for (int iarg = 4; iarg < narg; iarg++) {
if (strcmp(arg[iarg],"id") == 0) rstyle[nvalues++] = ID;
else if (strcmp(arg[iarg],"mol") == 0) rstyle[nvalues++] = MOL;
else if (strcmp(arg[iarg],"mass") == 0) rstyle[nvalues++] = MASS;
else if (strcmp(arg[iarg],"x") == 0) rstyle[nvalues++] = X;
else if (strcmp(arg[iarg],"y") == 0) rstyle[nvalues++] = Y;
else if (strcmp(arg[iarg],"z") == 0) rstyle[nvalues++] = Z;
else if (strcmp(arg[iarg],"xu") == 0) rstyle[nvalues++] = XU;
else if (strcmp(arg[iarg],"yu") == 0) rstyle[nvalues++] = YU;
else if (strcmp(arg[iarg],"zu") == 0) rstyle[nvalues++] = ZU;
else if (strcmp(arg[iarg],"vx") == 0) rstyle[nvalues++] = VX;
else if (strcmp(arg[iarg],"vy") == 0) rstyle[nvalues++] = VY;
else if (strcmp(arg[iarg],"vz") == 0) rstyle[nvalues++] = VZ;
else if (strcmp(arg[iarg],"fx") == 0) rstyle[nvalues++] = FX;
else if (strcmp(arg[iarg],"fy") == 0) rstyle[nvalues++] = FY;
else if (strcmp(arg[iarg],"fz") == 0) rstyle[nvalues++] = FZ;
else if (strcmp(arg[iarg],"ix") == 0) rstyle[nvalues++] = IX;
else if (strcmp(arg[iarg],"iy") == 0) rstyle[nvalues++] = IY;
else if (strcmp(arg[iarg],"iz") == 0) rstyle[nvalues++] = IZ;
else if (strcmp(arg[iarg],"tqx") == 0) rstyle[nvalues++] = TQX;
else if (strcmp(arg[iarg],"tqy") == 0) rstyle[nvalues++] = TQY;
else if (strcmp(arg[iarg],"tqz") == 0) rstyle[nvalues++] = TQZ;
else if (strcmp(arg[iarg],"omegax") == 0) rstyle[nvalues++] = OMEGAX;
else if (strcmp(arg[iarg],"omegay") == 0) rstyle[nvalues++] = OMEGAY;
else if (strcmp(arg[iarg],"omegaz") == 0) rstyle[nvalues++] = OMEGAZ;
else if (strcmp(arg[iarg],"angmomx") == 0) rstyle[nvalues++] = ANGMOMX;
else if (strcmp(arg[iarg],"angmomy") == 0) rstyle[nvalues++] = ANGMOMY;
else if (strcmp(arg[iarg],"angmomz") == 0) rstyle[nvalues++] = ANGMOMZ;
else if (strcmp(arg[iarg],"quatw") == 0) rstyle[nvalues++] = QUATW;
else if (strcmp(arg[iarg],"quati") == 0) rstyle[nvalues++] = QUATI;
else if (strcmp(arg[iarg],"quatj") == 0) rstyle[nvalues++] = QUATJ;
else if (strcmp(arg[iarg],"quatk") == 0) rstyle[nvalues++] = QUATK;
else if (strcmp(arg[iarg],"inertiax") == 0) rstyle[nvalues++] = INERTIAX;
else if (strcmp(arg[iarg],"inertiay") == 0) rstyle[nvalues++] = INERTIAY;
else if (strcmp(arg[iarg],"inertiaz") == 0) rstyle[nvalues++] = INERTIAZ;
else error->all(FLERR,"Invalid keyword in compute rigid/local command");
}
nmax = 0;
vector = NULL;
array = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeRigidLocal::~ComputeRigidLocal()
{
memory->destroy(vector);
memory->destroy(array);
delete [] idrigid;
delete [] rstyle;
}
/* ---------------------------------------------------------------------- */
void ComputeRigidLocal::init()
{
// set fixrigid
int ifix = modify->find_fix(idrigid);
if (ifix < 0)
error->all(FLERR,"FixRigidSmall ID for compute rigid/local does not exist");
fixrigid = (FixRigidSmall *) modify->fix[ifix];
int flag = 0;
if (strstr(fixrigid->style,"rigid/") == NULL) flag = 1;
if (strstr(fixrigid->style,"/small") == NULL) flag = 1;
if (flag)
error->all(FLERR,"Compute rigid/local does not use fix rigid/small fix");
// do initial memory allocation so that memory_usage() is correct
ncount = compute_rigid(0);
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
}
/* ---------------------------------------------------------------------- */
void ComputeRigidLocal::compute_local()
{
invoked_local = update->ntimestep;
// count local entries and compute bond info
ncount = compute_rigid(0);
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
ncount = compute_rigid(1);
}
/* ----------------------------------------------------------------------
count rigid bodies and compute rigid info on this proc
if flag is set, compute requested info about rigid body
owning atom of rigid body must be in group
------------------------------------------------------------------------- */
int ComputeRigidLocal::compute_rigid(int flag)
{
int i,m,n,ibody;
double *ptr;
FixRigidSmall::Body *body;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;
m = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
ibody = fixrigid->bodyown[i];
if (ibody < 0) continue;
body = &fixrigid->body[ibody];
if (flag) {
if (nvalues == 1) ptr = &vector[m];
else ptr = array[m];
for (n = 0; n < nvalues; n++) {
switch (rstyle[n]) {
case ID:
ptr[n] = tag[body->ilocal];
break;
case MOL:
ptr[n] = molecule[body->ilocal];
break;
case MASS:
ptr[n] = body->mass;
break;
case X:
ptr[n] = body->xcm[0];
break;
case Y:
ptr[n] = body->xcm[1];
break;
case Z:
ptr[n] = body->xcm[2];
break;
case XU:
ptr[n] = body->xcm[0] +
((body->image & IMGMASK) - IMGMAX) * xprd;
break;
case YU:
ptr[n] = body->xcm[1] +
((body->image >> IMGBITS & IMGMASK) - IMGMAX) * yprd;
break;
case ZU:
ptr[n] = body->xcm[2] +
((body->image >> IMG2BITS) - IMGMAX) * zprd;
break;
case VX:
ptr[n] = body->vcm[0];
break;
case VY:
ptr[n] = body->vcm[1];
break;
case VZ:
ptr[n] = body->vcm[2];
break;
case FX:
ptr[n] = body->fcm[0];
break;
case FY:
ptr[n] = body->fcm[1];
break;
case FZ:
ptr[n] = body->fcm[2];
break;
case IX:
ptr[n] = (body->image & IMGMASK) - IMGMAX;
break;
case IY:
ptr[n] = (body->image >> IMGBITS & IMGMASK) - IMGMAX;
break;
case IZ:
ptr[n] = (body->image >> IMG2BITS) - IMGMAX;
break;
case TQX:
ptr[n] = body->torque[0];
break;
case TQY:
ptr[n] = body->torque[1];
break;
case TQZ:
ptr[n] = body->torque[2];
break;
case OMEGAX:
ptr[n] = body->omega[0];
break;
case OMEGAY:
ptr[n] = body->omega[1];
break;
case OMEGAZ:
ptr[n] = body->omega[2];
break;
case ANGMOMX:
ptr[n] = body->angmom[0];
break;
case ANGMOMY:
ptr[n] = body->angmom[1];
break;
case ANGMOMZ:
ptr[n] = body->angmom[2];
break;
case QUATW:
ptr[n] = body->quat[0];
break;
case QUATI:
ptr[n] = body->quat[1];
break;
case QUATJ:
ptr[n] = body->quat[2];
break;
case QUATK:
ptr[n] = body->quat[3];
break;
case INERTIAX:
ptr[n] = body->inertia[0];
break;
case INERTIAY:
ptr[n] = body->inertia[1];
break;
case INERTIAZ:
ptr[n] = body->inertia[2];
break;
}
}
}
m++;
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeRigidLocal::reallocate(int n)
{
// grow vector or array
while (nmax < n) nmax += DELTA;
if (nvalues == 1) {
memory->destroy(vector);
memory->create(vector,nmax,"rigid/local:vector");
vector_local = vector;
} else {
memory->destroy(array);
memory->create(array,nmax,nvalues,"rigid/local:array");
array_local = array;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeRigidLocal::memory_usage()
{
double bytes = nmax*nvalues * sizeof(double);
return bytes;
}
c4science · Help