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/*****************************************************************************
TRAVIS - Trajectory Analyzer and Visualizer
http://www.travis-analyzer.de/
Copyright (c) 2009-2020 Martin Brehm
2012-2020 Martin Thomas
2016-2020 Sascha Gehrke
Please cite: J. Chem. Phys. 2020, 152 (16), 164105. (DOI 10.1063/5.0005078 )
J. Chem. Inf. Model. 2011, 51 (8), 2007-2023. (DOI 10.1021/ci200217w )
---------------------------------------------------------------------------
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
// 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.hh
* \brief Header file for the pre_container and related classes. */
#ifndef VOROPP_PRE_CONTAINER_HH
#define VOROPP_PRE_CONTAINER_HH
// This must always be the first include directive
#include "config.h"
#include "v_c_loops.h"
#include "v_container.h"
/** \brief A class for storing an arbitrary number of particles, prior to setting
* up a container geometry.
*
* The pre_container_base class can dynamically import and store an arbitrary
* number of particles. Once the particles have been read in, an appropriate
* container class can be set up with the optimal grid size, and the particles
* can be transferred.
*
* The pre_container_base class is not intended for direct use, but forms the
* base of the pre_container and pre_container_poly classes, that add routines
* depending on whether particle radii need to be tracked or not. */
class pre_container_base {
public:
/** The minimum x coordinate of the container. */
const double ax;
/** The maximum x coordinate of the container. */
const double bx;
/** The minimum y coordinate of the container. */
const double ay;
/** The maximum y coordinate of the container. */
const double by;
/** The minimum z coordinate of the container. */
const double az;
/** The maximum z coordinate of the container. */
const double bz;
/** A boolean value that determines if the x coordinate in
* periodic or not. */
const bool xperiodic;
/** A boolean value that determines if the y coordinate in
* periodic or not. */
const bool yperiodic;
/** A boolean value that determines if the z coordinate in
* periodic or not. */
const bool zperiodic;
void guess_optimal(int &nx,int &ny,int &nz);
pre_container_base(double ax_,double bx_,double ay_,double by_,double az_,double bz_,bool xperiodic_,bool yperiodic_,bool zperiodic_,int ps_);
~pre_container_base();
/** Calculates and returns the total number of particles stored
* within the class.
* \return The number of particles. */
inline int total_particles() {
return (int)((end_id-pre_id)*pre_container_chunk_size+(ch_id-*end_id));
}
protected:
/** The number of doubles associated with a single particle
* (three for the standard container, four when radius
* information is stored). */
const int ps;
void new_chunk();
void extend_chunk_index();
/** The size of the chunk index. */
int index_sz;
/** A pointer to the chunk index to store the integer particle
* IDs. */
int **pre_id;
/** A pointer to the last allocated integer ID chunk. */
int **end_id;
/** A pointer to the end of the integer ID chunk index, used to
* determine when the chunk index is full. */
int **l_id;
/** A pointer to the next available slot on the current
* particle ID chunk. */
int *ch_id;
/** A pointer to the end of the current integer chunk. */
int *e_id;
/** A pointer to the chunk index to store the floating point
* information associated with particles. */
double **pre_p;
/** A pointer to the last allocated chunk of floating point
* information. */
double **end_p;
/** A pointer to the next available slot on the current
* floating point chunk. */
double *ch_p;
};
/** \brief A class for storing an arbitrary number of particles with radius
* information, prior to setting up a container geometry.
*
* The pre_container_poly class is an extension of the pre_container_base class
* for cases when particle radius information is available. */
class pre_container_poly : public pre_container_base {
public:
/** The class constructor sets up the geometry of container,
* initializing the minimum and maximum coordinates in each
* direction.
* \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. */
pre_container_poly(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
bool xperiodic_,bool yperiodic_,bool zperiodic_)
: pre_container_base(ax_,bx_,ay_,by_,az_,bz_,xperiodic_,yperiodic_,zperiodic_,4) {};
void put(int n,double x,double y,double z,double r);
void import(FILE *fp=stdin);
/** Imports particles from a file.
* \param[in] filename the name of the file to read from. */
inline void import(const char* filename) {
FILE *fp=safe_fopen(filename,"r");
import(fp);
fclose(fp);
}
void setup(container_periodic_poly &con);
// void setup(particle_order &vo,container_periodic_poly &con);
};
#endif
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