Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/lib/voro++/src/pre_container.cc
706c4ccdaefdefficient_neuronet

Last Change
Raw File

pre_container.cc
View Options

// Voro++, a 3D cell-based Voronoi library
//
// Author : Chris H. Rycroft (LBL / UC Berkeley)
// Email : chr@alum.mit.edu
// Date : August 30th 2011
/** \file pre_container.cc
* \brief Function implementations for the pre_container and related classes.
*/
#include <cmath>
#include "config.hh"
#include "pre_container.hh"
namespace voro {
/** The class constructor sets up the geometry of container, initializing the
* minimum and maximum coordinates in each direction. It allocates an initial
* chunk into which to store particle information.
* \param[in] (ax_,bx_) the minimum and maximum x coordinates.
* \param[in] (ay_,by_) the minimum and maximum y coordinates.
* \param[in] (az_,bz_) the minimum and maximum z coordinates.
* \param[in] (xperiodic_,yperiodic_,zperiodic_ ) flags setting whether the
* container is periodic in each
* coordinate direction.
* \param[in] ps_ the number of floating point entries to store for each
* particle. */
pre_container_base::pre_container_base(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
bool xperiodic_,bool yperiodic_,bool zperiodic_,int ps_) :
ax(ax_), bx(bx_), ay(ay_), by(by_), az(az_), bz(bz_),
xperiodic(xperiodic_), yperiodic(yperiodic_), zperiodic(zperiodic_), ps(ps_),
index_sz(init_chunk_size), pre_id(new int*[index_sz]), end_id(pre_id),
pre_p(new double*[index_sz]), end_p(pre_p) {
ch_id=*end_id=new int[pre_container_chunk_size];
l_id=end_id+index_sz;e_id=ch_id+pre_container_chunk_size;
ch_p=*end_p=new double[ps*pre_container_chunk_size];
}
/** The destructor frees the dynamically allocated memory. */
pre_container_base::~pre_container_base() {
delete [] *end_p;
delete [] *end_id;
while (end_id!=pre_id) {
end_p--;
delete [] *end_p;
end_id--;
delete [] *end_id;
}
delete [] pre_p;
delete [] pre_id;
}
/** Makes a guess at the optimal grid of blocks to use, computing in
* a way that
* \param[out] (nx,ny,nz) the number of blocks to use. */
void pre_container_base::guess_optimal(int &nx,int &ny,int &nz) {
double dx=bx-ax,dy=by-ay,dz=bz-az;
double ilscale=pow(total_particles()/(optimal_particles*dx*dy*dz),1/3.0);
nx=int(dx*ilscale+1);
ny=int(dy*ilscale+1);
nz=int(dz*ilscale+1);
}
/** Stores a particle ID and position, allocating a new memory chunk if
* necessary. For coordinate directions in which the container is not periodic,
* the routine checks to make sure that the particle is within the container
* bounds. If the particle is out of bounds, it is not stored.
* \param[in] n the numerical ID of the inserted particle.
* \param[in] (x,y,z) the position vector of the inserted particle. */
void pre_container::put(int n,double x,double y,double z) {
if((xperiodic||(x>=ax&&x<=bx))&&(yperiodic||(y>=ay&&y<=by))&&(zperiodic||(z>=az&&z<=bz))) {
if(ch_id==e_id) new_chunk();
*(ch_id++)=n;
*(ch_p++)=x;*(ch_p++)=y;*(ch_p++)=z;
}
#if VOROPP_REPORT_OUT_OF_BOUNDS ==1
else fprintf(stderr,"Out of bounds: (x,y,z)=(%g,%g,%g)\n",x,y,z);
#endif
}
/** Stores a particle ID and position, allocating a new memory chunk if necessary.
* \param[in] n the numerical ID of the inserted particle.
* \param[in] (x,y,z) the position vector of the inserted particle.
* \param[in] r the radius of the particle. */
void pre_container_poly::put(int n,double x,double y,double z,double r) {
if((xperiodic||(x>=ax&&x<=bx))&&(yperiodic||(y>=ay&&y<=by))&&(zperiodic||(z>=az&&z<=bz))) {
if(ch_id==e_id) new_chunk();
*(ch_id++)=n;
*(ch_p++)=x;*(ch_p++)=y;*(ch_p++)=z;*(ch_p++)=r;
}
#if VOROPP_REPORT_OUT_OF_BOUNDS ==1
else fprintf(stderr,"Out of bounds: (x,y,z)=(%g,%g,%g)\n",x,y,z);
#endif
}
/** Transfers the particles stored within the class to a container class.
* \param[in] con the container class to transfer to. */
void pre_container::setup(container &con) {
int **c_id=pre_id,*idp,*ide,n;
double **c_p=pre_p,*pp,x,y,z;
while(c_id<end_id) {
idp=*(c_id++);ide=idp+pre_container_chunk_size;
pp=*(c_p++);
while(idp<ide) {
n=*(idp++);x=*(pp++);y=*(pp++);z=*(pp++);
con.put(n,x,y,z);
}
}
idp=*c_id;
pp=*c_p;
while(idp<ch_id) {
n=*(idp++);x=*(pp++);y=*(pp++);z=*(pp++);
con.put(n,x,y,z);
}
}
/** Transfers the particles stored within the class to a container_poly class.
* \param[in] con the container_poly class to transfer to. */
void pre_container_poly::setup(container_poly &con) {
int **c_id=pre_id,*idp,*ide,n;
double **c_p=pre_p,*pp,x,y,z,r;
while(c_id<end_id) {
idp=*(c_id++);ide=idp+pre_container_chunk_size;
pp=*(c_p++);
while(idp<ide) {
n=*(idp++);x=*(pp++);y=*(pp++);z=*(pp++);r=*(pp++);
con.put(n,x,y,z,r);
}
}
idp=*c_id;
pp=*c_p;
while(idp<ch_id) {
n=*(idp++);x=*(pp++);y=*(pp++);z=*(pp++);r=*(pp++);
con.put(n,x,y,z,r);
}
}
/** Transfers the particles stored within the class to a container class, also
* recording the order in which particles were stored.
* \param[in] vo the ordering class to use.
* \param[in] con the container class to transfer to. */
void pre_container::setup(particle_order &vo,container &con) {
int **c_id=pre_id,*idp,*ide,n;
double **c_p=pre_p,*pp,x,y,z;
while(c_id<end_id) {
idp=*(c_id++);ide=idp+pre_container_chunk_size;
pp=*(c_p++);
while(idp<ide) {
n=*(idp++);x=*(pp++);y=*(pp++);z=*(pp++);
con.put(vo,n,x,y,z);
}
}
idp=*c_id;
pp=*c_p;
while(idp<ch_id) {
n=*(idp++);x=*(pp++);y=*(pp++);z=*(pp++);
con.put(vo,n,x,y,z);
}
}
/** Transfers the particles stored within the class to a container_poly class,
* also recording the order in which particles were stored.
* \param[in] vo the ordering class to use.
* \param[in] con the container_poly class to transfer to. */
void pre_container_poly::setup(particle_order &vo,container_poly &con) {
int **c_id=pre_id,*idp,*ide,n;
double **c_p=pre_p,*pp,x,y,z,r;
while(c_id<end_id) {
idp=*(c_id++);ide=idp+pre_container_chunk_size;
pp=*(c_p++);
while(idp<ide) {
n=*(idp++);x=*(pp++);y=*(pp++);z=*(pp++);r=*(pp++);
con.put(vo,n,x,y,z,r);
}
}
idp=*c_id;
pp=*c_p;
while(idp<ch_id) {
n=*(idp++);x=*(pp++);y=*(pp++);z=*(pp++);r=*(pp++);
con.put(vo,n,x,y,z,r);
}
}
/** Import a list of particles from an open file stream into the container.
* Entries of four numbers (Particle ID, x position, y position, z position)
* are searched for. If the file cannot be successfully read, then the routine
* causes a fatal error.
* \param[in] fp the file handle to read from. */
void pre_container::import(FILE *fp) {
int i,j;
double x,y,z;
while((j=fscanf(fp,"%d %lg %lg %lg",&i,&x,&y,&z))==4) put(i,x,y,z);
if(j!=EOF) voro_fatal_error("File import error",VOROPP_FILE_ERROR);
}
/** Import a list of particles from an open file stream, also storing the order
* of that the particles are read. Entries of four numbers (Particle ID, x
* position, y position, z position) are searched for. If the file cannot be
* successfully read, then the routine causes a fatal error.
* \param[in] fp the file handle to read from. */
void pre_container_poly::import(FILE *fp) {
int i,j;
double x,y,z,r;
while((j=fscanf(fp,"%d %lg %lg %lg %lg",&i,&x,&y,&z,&r))==5) put(i,x,y,z,r);
if(j!=EOF) voro_fatal_error("File import error",VOROPP_FILE_ERROR);
}
/** Allocates a new chunk of memory for storing particles. */
void pre_container_base::new_chunk() {
end_id++;end_p++;
if(end_id==l_id) extend_chunk_index();
ch_id=*end_id=new int[pre_container_chunk_size];
e_id=ch_id+pre_container_chunk_size;
ch_p=*end_p=new double[ps*pre_container_chunk_size];
}
/** Extends the index of chunks. */
void pre_container_base::extend_chunk_index() {
index_sz<<=1;
if(index_sz>max_chunk_size)
voro_fatal_error("Absolute memory limit on chunk index reached",VOROPP_MEMORY_ERROR);
#if VOROPP_VERBOSE >=2
fprintf(stderr,"Pre-container chunk index scaled up to %d\n",index_sz);
#endif
int **n_id=new int*[index_sz],**p_id=n_id,**c_id=pre_id;
double **n_p=new double*[index_sz],**p_p=n_p,**c_p=pre_p;
while(c_id<end_id) {
*(p_id++)=*(c_id++);
*(p_p++)=*(c_p++);
}
delete [] pre_id;pre_id=n_id;end_id=p_id;l_id=pre_id+index_sz;
delete [] pre_p;pre_p=n_p;end_p=p_p;
}
}
c4science · Help