Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/BODY/body_nparticle.cpp
0f3e4182e869lammm-master-deprecated

Last Change
Raw File

body_nparticle.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 <stdlib.h>
#include "body_nparticle.h"
#include "math_extra.h"
#include "atom_vec_body.h"
#include "atom.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define EPSILON 1.0e-7
enum{SPHERE,LINE}; // also in DumpImage
/* ---------------------------------------------------------------------- */
BodyNparticle::BodyNparticle(LAMMPS *lmp, int narg, char **arg) :
Body(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Invalid body nparticle command");
int nmin = force->inumeric(FLERR,arg[1]);
int nmax = force->inumeric(FLERR,arg[2]);
if (nmin <= 0 || nmin > nmax)
error->all(FLERR,"Invalid body nparticle command");
size_forward = 0;
size_border = 1 + 3*nmax;
// NOTE: need to set appropriate nnbin param for dcp
icp = new MyPoolChunk<int>(1,1);
dcp = new MyPoolChunk<double>(3*nmin,3*nmax);
memory->create(imflag,nmax,"body/nparticle:imflag");
memory->create(imdata,nmax,4,"body/nparticle:imdata");
}
/* ---------------------------------------------------------------------- */
BodyNparticle::~BodyNparticle()
{
delete icp;
delete dcp;
memory->destroy(imflag);
memory->destroy(imdata);
}
/* ---------------------------------------------------------------------- */
int BodyNparticle::nsub(AtomVecBody::Bonus *bonus)
{
return bonus->ivalue[0];
}
/* ---------------------------------------------------------------------- */
double *BodyNparticle::coords(AtomVecBody::Bonus *bonus)
{
return bonus->dvalue;
}
/* ---------------------------------------------------------------------- */
int BodyNparticle::pack_border_body(AtomVecBody::Bonus *bonus, double *buf)
{
int nsub = bonus->ivalue[0];
buf[0] = nsub;
memcpy(&buf[1],bonus->dvalue,3*nsub*sizeof(double));
return 1+3*nsub;
}
/* ---------------------------------------------------------------------- */
int BodyNparticle::unpack_border_body(AtomVecBody::Bonus *bonus, double *buf)
{
int nsub = static_cast<int> (buf[0]);
bonus->ivalue[0] = nsub;
memcpy(bonus->dvalue,&buf[1],3*nsub*sizeof(double));
return 1+3*nsub;
}
/* ----------------------------------------------------------------------
populate bonus data structure with data file values
------------------------------------------------------------------------- */
void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
int *ifile, double *dfile)
{
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
// set ninteger, ndouble in bonus and allocate 2 vectors of ints, doubles
if (ninteger != 1)
error->one(FLERR,"Incorrect # of integer values in "
"Bodies section of data file");
int nsub = ifile[0];
if (nsub < 1)
error->one(FLERR,"Incorrect integer value in "
"Bodies section of data file");
if (ndouble != 6 + 3*nsub)
error->one(FLERR,"Incorrect # of floating-point values in "
"Bodies section of data file");
bonus->ninteger = 1;
bonus->ivalue = icp->get(bonus->iindex);
bonus->ivalue[0] = nsub;
bonus->ndouble = 3*nsub;
bonus->dvalue = dcp->get(bonus->ndouble,bonus->dindex);
// diagonalize inertia tensor
double tensor[3][3];
tensor[0][0] = dfile[0];
tensor[1][1] = dfile[1];
tensor[2][2] = dfile[2];
tensor[0][1] = tensor[1][0] = dfile[3];
tensor[0][2] = tensor[2][0] = dfile[4];
tensor[1][2] = tensor[2][1] = dfile[5];
double *inertia = bonus->inertia;
double evectors[3][3];
int ierror = MathExtra::jacobi(tensor,inertia,evectors);
if (ierror) error->one(FLERR,
"Insufficient Jacobi rotations for body nparticle");
// if any principal moment < scaled EPSILON, set to 0.0
double max;
max = MAX(inertia[0],inertia[1]);
max = MAX(max,inertia[2]);
if (inertia[0] < EPSILON*max) inertia[0] = 0.0;
if (inertia[1] < EPSILON*max) inertia[1] = 0.0;
if (inertia[2] < EPSILON*max) inertia[2] = 0.0;
// exyz_space = principal axes in space frame
double ex_space[3],ey_space[3],ez_space[3];
ex_space[0] = evectors[0][0];
ex_space[1] = evectors[1][0];
ex_space[2] = evectors[2][0];
ey_space[0] = evectors[0][1];
ey_space[1] = evectors[1][1];
ey_space[2] = evectors[2][1];
ez_space[0] = evectors[0][2];
ez_space[1] = evectors[1][2];
ez_space[2] = evectors[2][2];
// enforce 3 evectors as a right-handed coordinate system
// flip 3rd vector if needed
double cross[3];
MathExtra::cross3(ex_space,ey_space,cross);
if (MathExtra::dot3(cross,ez_space) < 0.0) MathExtra::negate3(ez_space);
// create initial quaternion
MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus->quat);
// bonus->dvalue = sub-particle displacements in body frame
double delta[3];
int j = 6;
int k = 0;
for (int i = 0; i < nsub; i++) {
delta[0] = dfile[j];
delta[1] = dfile[j+1];
delta[2] = dfile[j+2];
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
delta,&bonus->dvalue[k]);
j += 3;
k += 3;
}
}
/* ----------------------------------------------------------------------
return radius of body particle defined by ifile/dfile params
params are ordered as in data file
called by Molecule class which needs single body size
------------------------------------------------------------------------- */
double BodyNparticle::radius_body(int ninteger, int ndouble,
int *ifile, double *dfile)
{
int nsub = ifile[0];
if (nsub < 1)
error->one(FLERR,"Incorrect integer value in "
"Bodies section of data file");
if (ndouble != 6 + 3*nsub)
error->one(FLERR,"Incorrect # of floating-point values in "
"Bodies section of data file");
// sub-particle coords are relative to body center at (0,0,0)
// offset = 6 for sub-particle coords
double onerad;
double maxrad = 0.0;
double delta[3];
int offset = 6;
for (int i = 0; i < nsub; i++) {
delta[0] = dfile[offset];
delta[1] = dfile[offset+1];
delta[2] = dfile[offset+2];
offset += 3;
onerad = MathExtra::len3(delta);
maxrad = MAX(maxrad,onerad);
}
return maxrad;
}
/* ---------------------------------------------------------------------- */
int BodyNparticle::noutcol()
{
return 3;
}
/* ---------------------------------------------------------------------- */
int BodyNparticle::noutrow(int ibonus)
{
return avec->bonus[ibonus].ivalue[0];
}
/* ---------------------------------------------------------------------- */
void BodyNparticle::output(int ibonus, int m, double *values)
{
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
double p[3][3];
MathExtra::quat_to_mat(bonus->quat,p);
MathExtra::matvec(p,&bonus->dvalue[3*m],values);
double *x = atom->x[bonus->ilocal];
values[0] += x[0];
values[1] += x[1];
values[2] += x[2];
}
/* ---------------------------------------------------------------------- */
int BodyNparticle::image(int ibonus, double flag1, double flag2,
int *&ivec, double **&darray)
{
double p[3][3];
double *x;
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
int n = bonus->ivalue[0];
for (int i = 0; i < n; i++) {
imflag[i] = SPHERE;
MathExtra::quat_to_mat(bonus->quat,p);
MathExtra::matvec(p,&bonus->dvalue[3*i],imdata[i]);
x = atom->x[bonus->ilocal];
imdata[i][0] += x[0];
imdata[i][1] += x[1];
imdata[i][2] += x[2];
imdata[i][3] = flag1;
}
ivec = imflag;
darray = imdata;
return n;
}
c4science · Help