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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 *
 *
 *  NanoVolume.cpp
 *
 *  Created by Charles F. Vardeman II on 14 Dec 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id: NanoVolume.cpp,v 1.10 2009-11-25 20:01:59 gezelter Exp $
 *
 */

#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:	1402
Committed:	Fri Jan 8 17:15:27 2010 UTC (15 years, 3 months ago) by chuckv
File size:	5332 byte(s)
Log Message:	Added preliminary code for Alpha Hull calculation using qhull. Added preliminary support to SMIPD to support Alpha Hull. Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. Preliminary changes for shadow hamiltonian integrator. Chages to md files so they will work in openMD.
#	Content
1	/* Copyright (c) 2006, 2009, 2010 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. Redistributions of source code must retain the above copyright
9	* notice, this list of conditions and the following disclaimer.
10	*
11	* 2. Redistributions in binary form must reproduce the above copyright
12	* 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	* 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	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38	* [4] Vardeman & Gezelter, in progress (2009).
39	*
40	*
41	* NanoVolume.cpp
42	*
43	* Created by Charles F. Vardeman II on 14 Dec 2006.
44	* @author Charles F. Vardeman II
45	* @version $Id: NanoVolume.cpp,v 1.10 2009-11-25 20:01:59 gezelter Exp $
46	*
47	*/
48
49	#include "applications/staticProps/NanoVolume.hpp"
50	#include "math/ConvexHull.hpp"
51	#include "math/AlphaHull.hpp"
52	#include "utils/simError.h"
53	#include "io/DumpReader.hpp"
54	#include "primitives/Molecule.hpp"
55	#include "utils/NumericConstant.hpp"
56
57	using namespace OpenMD;
58
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	setOutputName(getPrefix(filename) + ".avol");
64
65	evaluator_.loadScriptString(sele);
66	if (!evaluator_.isDynamic()) {
67	seleMan_.setSelectionSet(evaluator_.evaluate());
68	}
69	frameCounter_ = 0;
70	totalVolume_ = 0.0;
71	}
72
73	void NanoVolume::process() {
74	#if defined(HAVE_QHULL)
75	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	#ifdef HAVE_QHULL
87	// ConvexHull* thishull = new ConvexHull();
88	AlphaHull* thishull = new AlphaHull(2.0);
89	#endif
90
91	DumpReader reader(info_, dumpFilename_);
92	int nFrames = reader.getNFrames();
93	frameCounter_ = 0;
94
95	theAtoms_.reserve(info_->getNGlobalAtoms());
96
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	theAtoms_.clear();
104
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
121	for (sd = seleMan_.beginSelected(i); sd != NULL;
122	sd = seleMan_.nextSelected(i)) {
123
124	theAtoms_.push_back(sd);
125	myIndex = sd->getGlobalIndex();
126
127	}
128
129	/*
130	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	*/
138	// Generate convex hull for this frame.
139	thishull->computeHull(theAtoms_);
140	// totalVolume_ += hull->getVolume();
141	}
142	//RealType avgVolume = totalVolume_/(RealType) frameCounter_;
143	//std::cout.precision(7);
144	//std::cout << avgVolume << std::endl;
145	/*
146	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	*/
154	#else
155	sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n");
156	painCave.isFatal = 1;
157	simError();
158
159	#endif
160
161	}