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"
#if defined(HAVE_QHULL)
#include "math/ConvexHull.hpp"
#include "math/AlphaHull.hpp"
#endif
#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");

  osq.open(getOutputFileName().c_str());
  
  evaluator_.loadScriptString(sele);
  if (!evaluator_.isDynamic()) {
    seleMan_.setSelectionSet(evaluator_.evaluate());
  }
  frameCounter_ = 0;
}

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

  AlphaHull* thishull = new AlphaHull(2.0);
  //ConvexHull* thishull = new ConvexHull();
  
  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();
    RealType time = currentSnapshot_->getTime();
    
    // Clear pos vector between each frame.
    theAtoms_.clear();
    
    if (evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
    
    // update the positions of atoms which belong to the rigid bodies
    
    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);      
    }
    
    /* variant below for signle atoms, not StuntDoubles:
    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_);
    RealType volume = thishull->getVolume();

    osq.precision(7);
    if (osq.is_open()){
      osq << time << "\t" << volume << std::endl;      
    }
  }
  osq.close();

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

}
Revision:	1942
Committed:	Tue Nov 5 18:33:42 2013 UTC (11 years, 5 months ago) by gezelter
File size:	5154 byte(s)
Log Message:	Fixed some warning messages and NanoVolume issues.
#	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	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38	gezelter	1782	* [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	gezelter	1879	#if defined(HAVE_QHULL)
51	chuckv	1181	#include "math/ConvexHull.hpp"
52	chuckv	1402	#include "math/AlphaHull.hpp"
53	gezelter	1879	#endif
54	chuckv	1181	#include "utils/simError.h"
55			#include "io/DumpReader.hpp"
56			#include "primitives/Molecule.hpp"
57			#include "utils/NumericConstant.hpp"
58
59	gezelter	1390	using namespace OpenMD;
60	chuckv	1181
61			NanoVolume::NanoVolume(SimInfo* info,
62			const std::string& filename,
63			const std::string& sele)
64	gezelter	1942	: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info),
65			seleMan_(info) {
66
67	chuckv	1194	setOutputName(getPrefix(filename) + ".avol");
68	gezelter	1942
69			osq.open(getOutputFileName().c_str());
70	chuckv	1181
71			evaluator_.loadScriptString(sele);
72			if (!evaluator_.isDynamic()) {
73			seleMan_.setSelectionSet(evaluator_.evaluate());
74			}
75	chuckv	1188	frameCounter_ = 0;
76	chuckv	1181	}
77
78			void NanoVolume::process() {
79	gezelter	1382	#if defined(HAVE_QHULL)
80	chuckv	1181	Molecule* mol;
81			RigidBody* rb;
82			SimInfo::MoleculeIterator mi;
83			Molecule::RigidBodyIterator rbIter;
84			StuntDouble* sd;
85			Vector3d vec;
86	gezelter	1942	int i;
87	chuckv	1181
88	gezelter	1942	AlphaHull* thishull = new AlphaHull(2.0);
89			//ConvexHull* thishull = new ConvexHull();
90
91	chuckv	1181	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	gezelter	1942	RealType time = currentSnapshot_->getTime();
102	chuckv	1181
103			// Clear pos vector between each frame.
104	chuckv	1293	theAtoms_.clear();
105	chuckv	1181
106			if (evaluator_.isDynamic()) {
107			seleMan_.setSelectionSet(evaluator_.evaluate());
108			}
109
110	gezelter	1942	// update the positions of atoms which belong to the rigid bodies
111	chuckv	1181
112			for (mol = info_->beginMolecule(mi); mol != NULL;
113			mol = info_->nextMolecule(mi)) {
114			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
115			rb = mol->nextRigidBody(rbIter)) {
116			rb->updateAtoms();
117			}
118			}
119
120			// outer loop is over the selected StuntDoubles:
121	chuckv	1304
122	chuckv	1181	for (sd = seleMan_.beginSelected(i); sd != NULL;
123	gezelter	1942	sd = seleMan_.nextSelected(i)) {
124			theAtoms_.push_back(sd);
125	chuckv	1181	}
126	chuckv	1304
127	gezelter	1942	/* variant below for signle atoms, not StuntDoubles:
128	chuckv	1293	for (mol = info_->beginMolecule(mi); mol != NULL;
129	gezelter	1942	mol = info_->nextMolecule(mi)) {
130			for (atom = mol->beginAtom(ai); atom != NULL;
131			atom = mol->nextAtom(ai)) {
132			theAtoms_.push_back(atom);
133			}
134			}
135	chuckv	1304	*/
136	gezelter	1942
137	chuckv	1181	// Generate convex hull for this frame.
138	chuckv	1293	thishull->computeHull(theAtoms_);
139	gezelter	1942	RealType volume = thishull->getVolume();
140	chuckv	1194
141	gezelter	1942	osq.precision(7);
142			if (osq.is_open()){
143			osq << time << "\t" << volume << std::endl;
144			}
145	chuckv	1194	}
146			osq.close();
147	gezelter	1942
148	cpuglis	1195	#else
149	gezelter	1382	sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n");
150	cpuglis	1195	painCave.isFatal = 1;
151			simError();
152			#endif
153	chuckv	1207
154	chuckv	1181	}