applications/staticProps/NanoVolume.cpp

/* Copyright (c) 2006, 2009, 2010 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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *
 *  NanoVolume.cpp
 *
 *  Created by Charles F. Vardeman II on 14 Dec 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id$
 *
 */

#include "applications/staticProps/NanoVolume.hpp"
#include "math/ConvexHull.hpp"
#include "math/AlphaHull.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"

using namespace OpenMD;

NanoVolume::NanoVolume(SimInfo* info,
                       const std::string& filename,
                       const std::string& sele)
  : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info) {
  setOutputName(getPrefix(filename) + ".avol");
  
  evaluator_.loadScriptString(sele);
  if (!evaluator_.isDynamic()) {
    seleMan_.setSelectionSet(evaluator_.evaluate());
  }
  frameCounter_ = 0;
  totalVolume_ = 0.0;
}

void NanoVolume::process() {
#if defined(HAVE_QHULL)
  Molecule* mol;
  Atom* atom;
  RigidBody* rb;
  int myIndex;
  SimInfo::MoleculeIterator mi;
  Molecule::RigidBodyIterator rbIter;
  Molecule::AtomIterator ai;
  StuntDouble* sd;
  Vector3d vec;
  int i,j;

#ifdef HAVE_QHULL
   //ConvexHull* thishull = new ConvexHull();
   AlphaHull* thishull = new AlphaHull(2.0);
#endif

  DumpReader reader(info_, dumpFilename_);
  int nFrames = reader.getNFrames();
  frameCounter_ = 0;

  theAtoms_.reserve(info_->getNGlobalAtoms());

  for (int istep = 0; istep < nFrames; istep += step_) {
    reader.readFrame(istep);
    frameCounter_++;
    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
    
    // Clear pos vector between each frame.
    theAtoms_.clear();
    
    if (evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
    
    // update the positions of atoms which belong to the rigidbodies
    
    for (mol = info_->beginMolecule(mi); mol != NULL;
         mol = info_->nextMolecule(mi)) {
      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
           rb = mol->nextRigidBody(rbIter)) {   
        rb->updateAtoms();
      }
    }
    
    // outer loop is over the selected StuntDoubles:
    
    for (sd = seleMan_.beginSelected(i); sd != NULL;
            sd = seleMan_.nextSelected(i)) {
      
     theAtoms_.push_back(sd);
      myIndex = sd->getGlobalIndex();
      
    }
    
    /*
    for (mol = info_->beginMolecule(mi); mol != NULL; 
                 mol = info_->nextMolecule(mi)) {
              for (atom = mol->beginAtom(ai); atom != NULL; 
                   atom = mol->nextAtom(ai)) {
                     theAtoms_.push_back(atom);
              }
            }
    */
    // Generate convex hull for this frame.
    thishull->computeHull(theAtoms_);
  //  totalVolume_ += hull->getVolume();                
  }
  //RealType avgVolume = totalVolume_/(RealType) frameCounter_;
  //std::cout.precision(7);
  //std::cout  << avgVolume << std::endl;
/*
  std::ofstream osq(getOutputFileName().c_str());
  osq.precision(7);
  if (osq.is_open()){
      osq << avgVolume << std::endl;

  }
  osq.close();
*/
#else
  sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n");
  painCave.isFatal = 1;
  simError();  

#endif

}
Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	5332 byte(s)
Log Message:	Fixed a widespread typo in the license
#	User	Rev	Content
1	chuckv	1402	/* Copyright (c) 2006, 2009, 2010 The University of Notre Dame. All Rights Reserved.
2	chuckv	1181	*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
9	chuckv	1181	* notice, this list of conditions and the following disclaimer.
10			*
11	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
12	chuckv	1181	* notice, this list of conditions and the following disclaimer in the
13			* documentation and/or other materials provided with the
14			* distribution.
15			*
16			* This software is provided "AS IS," without a warranty of any
17			* kind. All express or implied conditions, representations and
18			* warranties, including any implied warranty of merchantability,
19			* fitness for a particular purpose or non-infringement, are hereby
20			* excluded. The University of Notre Dame and its licensors shall not
21			* be liable for any damages suffered by licensee as a result of
22			* using, modifying or distributing the software or its
23			* derivatives. In no event will the University of Notre Dame or its
24			* licensors be liable for any lost revenue, profit or data, or for
25			* direct, indirect, special, consequential, incidental or punitive
26			* damages, however caused and regardless of the theory of liability,
27			* arising out of the use of or inability to use software, even if the
28			* University of Notre Dame has been advised of the possibility of
29			* such damages.
30			*
31	gezelter	1390	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32			* research, please cite the appropriate papers when you publish your
33			* work. Good starting points are:
34			*
35			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39			* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40	chuckv	1181	*
41			* NanoVolume.cpp
42			*
43			* Created by Charles F. Vardeman II on 14 Dec 2006.
44			* @author Charles F. Vardeman II
45	gezelter	1442	* @version $Id$
46	chuckv	1181	*
47			*/
48
49			#include "applications/staticProps/NanoVolume.hpp"
50			#include "math/ConvexHull.hpp"
51	chuckv	1402	#include "math/AlphaHull.hpp"
52	chuckv	1181	#include "utils/simError.h"
53			#include "io/DumpReader.hpp"
54			#include "primitives/Molecule.hpp"
55			#include "utils/NumericConstant.hpp"
56
57	gezelter	1390	using namespace OpenMD;
58	chuckv	1181
59			NanoVolume::NanoVolume(SimInfo* info,
60			const std::string& filename,
61			const std::string& sele)
62			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info) {
63	chuckv	1194	setOutputName(getPrefix(filename) + ".avol");
64	chuckv	1181
65			evaluator_.loadScriptString(sele);
66			if (!evaluator_.isDynamic()) {
67			seleMan_.setSelectionSet(evaluator_.evaluate());
68			}
69	chuckv	1188	frameCounter_ = 0;
70			totalVolume_ = 0.0;
71	chuckv	1181	}
72
73			void NanoVolume::process() {
74	gezelter	1382	#if defined(HAVE_QHULL)
75	chuckv	1181	Molecule* mol;
76			Atom* atom;
77			RigidBody* rb;
78			int myIndex;
79			SimInfo::MoleculeIterator mi;
80			Molecule::RigidBodyIterator rbIter;
81			Molecule::AtomIterator ai;
82			StuntDouble* sd;
83			Vector3d vec;
84			int i,j;
85
86	chuckv	1199	#ifdef HAVE_QHULL
87	chuckv	1404	//ConvexHull* thishull = new ConvexHull();
88			AlphaHull* thishull = new AlphaHull(2.0);
89	chuckv	1199	#endif
90	chuckv	1181
91			DumpReader reader(info_, dumpFilename_);
92			int nFrames = reader.getNFrames();
93			frameCounter_ = 0;
94
95	chuckv	1293	theAtoms_.reserve(info_->getNGlobalAtoms());
96	chuckv	1181
97			for (int istep = 0; istep < nFrames; istep += step_) {
98			reader.readFrame(istep);
99			frameCounter_++;
100			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
101
102			// Clear pos vector between each frame.
103	chuckv	1293	theAtoms_.clear();
104	chuckv	1181
105			if (evaluator_.isDynamic()) {
106			seleMan_.setSelectionSet(evaluator_.evaluate());
107			}
108
109			// update the positions of atoms which belong to the rigidbodies
110
111			for (mol = info_->beginMolecule(mi); mol != NULL;
112			mol = info_->nextMolecule(mi)) {
113			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
114			rb = mol->nextRigidBody(rbIter)) {
115			rb->updateAtoms();
116			}
117			}
118
119			// outer loop is over the selected StuntDoubles:
120	chuckv	1304
121	chuckv	1181	for (sd = seleMan_.beginSelected(i); sd != NULL;
122	chuckv	1293	sd = seleMan_.nextSelected(i)) {
123	chuckv	1181
124	chuckv	1304	theAtoms_.push_back(sd);
125	chuckv	1181	myIndex = sd->getGlobalIndex();
126
127			}
128	chuckv	1304
129			/*
130	chuckv	1293	for (mol = info_->beginMolecule(mi); mol != NULL;
131			mol = info_->nextMolecule(mi)) {
132			for (atom = mol->beginAtom(ai); atom != NULL;
133			atom = mol->nextAtom(ai)) {
134			theAtoms_.push_back(atom);
135			}
136			}
137	chuckv	1304	*/
138	chuckv	1181	// Generate convex hull for this frame.
139	chuckv	1293	thishull->computeHull(theAtoms_);
140	chuckv	1207	// totalVolume_ += hull->getVolume();
141	chuckv	1181	}
142	chuckv	1207	//RealType avgVolume = totalVolume_/(RealType) frameCounter_;
143	chuckv	1194	//std::cout.precision(7);
144			//std::cout << avgVolume << std::endl;
145	chuckv	1207	/*
146	chuckv	1194	std::ofstream osq(getOutputFileName().c_str());
147			osq.precision(7);
148			if (osq.is_open()){
149			osq << avgVolume << std::endl;
150
151			}
152			osq.close();
153	chuckv	1207	*/
154	cpuglis	1195	#else
155	gezelter	1382	sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n");
156	cpuglis	1195	painCave.isFatal = 1;
157			simError();
158	chuckv	1207
159	cpuglis	1195	#endif
160	chuckv	1207
161	chuckv	1181	}