src/math/ConvexHull.cpp

/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 *
 *  ConvexHull.cpp
 *
 *  Purpose: To calculate convexhull, hull volume libqhull.
 *
 *  Created by Charles F. Vardeman II on 11 Dec 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id: ConvexHull.cpp,v 1.4 2007-05-30 19:51:07 chuckv Exp $
 *
 */

#include <iostream>
#include <fstream>
#include "math/ConvexHull.hpp"

using namespace oopse;

ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt FA") {
}

bool ConvexHull::genHull(std::vector<Vector3d> pos) {
  FILE *outfile = stdout;
  FILE *errfile = stderr;
  facetT *facet;
  int exitcode;
  boolT ismalloc = False;
  int curlong,totlong;
  
  int numpoints = pos.size();
 
  coordT* points;
  points = (coordT*) malloc(sizeof(coordT) * (numpoints*dim_)); 

  for (int i=0; i<numpoints; i++) {
    points[dim_ * i] = pos[i][0];
    points[dim_ * i + 1] = pos[i][1];
    points[dim_ * i + 2] = pos[i][2];           
  }
  
  
  qh_initflags (const_cast<char *>(options_.c_str()));
  qh_init_B (points, numpoints, dim_, ismalloc);
  qh_qhull();
  qh_check_output();
  
  
  qh_getarea(qh facet_list);
  volume_ = qh totvol;                                                  
  area_ = qh totarea;                                           
  
  
  qh_freeqhull(!qh_ALL);
  qh_memfreeshort (&curlong, &totlong);
  if (curlong || totlong)
    fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
             totlong, curlong);
  
  
  return true;
}


RealType ConvexHull::getVolume() {
  return volume_;
}

void ConvexHull::geomviewHull(const std::string& geomFileName) {
  
  std::ofstream newGeomFile;
  
  //create new .md file based on old .md file
  newGeomFile.open(geomFileName.c_str());
  
  
  newGeomFile.close();
}
Revision:	3143
Committed:	Wed May 30 19:51:07 2007 UTC (17 years, 11 months ago) by chuckv
File size:	3720 byte(s)
Log Message:	Pos copied into a malloc array now.
#	User	Rev	Content
1	chuckv	3083	/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
2			*
3			* The University of Notre Dame grants you ("Licensee") a
4			* non-exclusive, royalty free, license to use, modify and
5			* redistribute this software in source and binary code form, provided
6			* that the following conditions are met:
7			*
8			* 1. Acknowledgement of the program authors must be made in any
9			* publication of scientific results based in part on use of the
10			* program. An acceptable form of acknowledgement is citation of
11			* the article in which the program was described (Matthew
12			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
13			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
14			* Parallel Simulation Engine for Molecular Dynamics,"
15			* J. Comput. Chem. 26, pp. 252-271 (2005))
16			*
17			* 2. Redistributions of source code must retain the above copyright
18			* notice, this list of conditions and the following disclaimer.
19			*
20			* 3. Redistributions in binary form must reproduce the above copyright
21			* notice, this list of conditions and the following disclaimer in the
22			* documentation and/or other materials provided with the
23			* distribution.
24			*
25			* This software is provided "AS IS," without a warranty of any
26			* kind. All express or implied conditions, representations and
27			* warranties, including any implied warranty of merchantability,
28			* fitness for a particular purpose or non-infringement, are hereby
29			* excluded. The University of Notre Dame and its licensors shall not
30			* be liable for any damages suffered by licensee as a result of
31			* using, modifying or distributing the software or its
32			* derivatives. In no event will the University of Notre Dame or its
33			* licensors be liable for any lost revenue, profit or data, or for
34			* direct, indirect, special, consequential, incidental or punitive
35			* damages, however caused and regardless of the theory of liability,
36			* arising out of the use of or inability to use software, even if the
37			* University of Notre Dame has been advised of the possibility of
38			* such damages.
39			*
40			*
41			* ConvexHull.cpp
42			*
43	chuckv	3137	* Purpose: To calculate convexhull, hull volume libqhull.
44	chuckv	3083	*
45			* Created by Charles F. Vardeman II on 11 Dec 2006.
46			* @author Charles F. Vardeman II
47	chuckv	3143	* @version $Id: ConvexHull.cpp,v 1.4 2007-05-30 19:51:07 chuckv Exp $
48	chuckv	3083	*
49			*/
50
51			#include <iostream>
52			#include <fstream>
53	chuckv	3141	#include "math/ConvexHull.hpp"
54	chuckv	3083
55			using namespace oopse;
56
57	chuckv	3141	ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt FA") {
58			}
59	chuckv	3083
60	chuckv	3141	bool ConvexHull::genHull(std::vector<Vector3d> pos) {
61			FILE *outfile = stdout;
62			FILE *errfile = stderr;
63			facetT *facet;
64			int exitcode;
65			boolT ismalloc = False;
66			int curlong,totlong;
67
68			int numpoints = pos.size();
69	chuckv	3143
70			coordT* points;
71			points = (coordT) malloc(sizeof(coordT) (numpoints*dim_));
72
73	chuckv	3141	for (int i=0; i<numpoints; i++) {
74	chuckv	3143	points[dim_ * i] = pos[i][0];
75			points[dim_ * i + 1] = pos[i][1];
76			points[dim_ * i + 2] = pos[i][2];
77	chuckv	3141	}
78
79
80			qh_initflags (const_cast<char *>(options_.c_str()));
81	chuckv	3143	qh_init_B (points, numpoints, dim_, ismalloc);
82	chuckv	3141	qh_qhull();
83			qh_check_output();
84
85
86
87			qh_getarea(qh facet_list);
88			volume_ = qh totvol;
89			area_ = qh totarea;
90
91
92
93			qh_freeqhull(!qh_ALL);
94			qh_memfreeshort (&curlong, &totlong);
95			if (curlong \|\| totlong)
96			fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
97			totlong, curlong);
98
99
100			return true;
101	chuckv	3083	}
102
103	chuckv	3137
104	chuckv	3141	RealType ConvexHull::getVolume() {
105			return volume_;
106	chuckv	3083	}
107
108	chuckv	3141	void ConvexHull::geomviewHull(const std::string& geomFileName) {
109
110	chuckv	3083	std::ofstream newGeomFile;
111	chuckv	3141
112	chuckv	3083	//create new .md file based on old .md file
113			newGeomFile.open(geomFileName.c_str());
114	chuckv	3141
115
116	chuckv	3083	newGeomFile.close();
117			}