applications/staticProps/NanoVolume.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.
 *
 *
 *  NanoVolume.cpp
 *
 *  Purpose: To calculate convexhull, hull volume and radius
 *  using the CGAL library.
 *
 *  Created by Charles F. Vardeman II on 14 Dec 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id: NanoVolume.cpp,v 1.3 2007-12-06 19:52:11 chuckv Exp $
 *
 */

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

using namespace oopse;

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

  ConvexHull* hull = new ConvexHull();

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

  pos_.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.
    pos_.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)) {
      
      pos_.push_back(sd->getPos());
      myIndex = sd->getGlobalIndex();
      
    }
    // Generate convex hull for this frame.
    hull->genHull(pos_);
    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();

}
Revision:	1194
Committed:	Thu Dec 6 19:52:11 2007 UTC (17 years, 11 months ago) by chuckv
File size:	4767 byte(s)
Log Message:	Added more chamges to nanovol.
#	User	Rev	Content
1	chuckv	1181	/* 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			* NanoVolume.cpp
42			*
43			* Purpose: To calculate convexhull, hull volume and radius
44			* using the CGAL library.
45			*
46			* Created by Charles F. Vardeman II on 14 Dec 2006.
47			* @author Charles F. Vardeman II
48	chuckv	1194	* @version $Id: NanoVolume.cpp,v 1.3 2007-12-06 19:52:11 chuckv Exp $
49	chuckv	1181	*
50			*/
51
52			#include "applications/staticProps/NanoVolume.hpp"
53			#include "math/ConvexHull.hpp"
54			#include "utils/simError.h"
55			#include "io/DumpReader.hpp"
56			#include "primitives/Molecule.hpp"
57			#include "utils/NumericConstant.hpp"
58
59			using namespace oopse;
60
61			NanoVolume::NanoVolume(SimInfo* info,
62			const std::string& filename,
63			const std::string& sele)
64			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info) {
65	chuckv	1194	setOutputName(getPrefix(filename) + ".avol");
66	chuckv	1181
67			evaluator_.loadScriptString(sele);
68			if (!evaluator_.isDynamic()) {
69			seleMan_.setSelectionSet(evaluator_.evaluate());
70			}
71	chuckv	1188	frameCounter_ = 0;
72			totalVolume_ = 0.0;
73	chuckv	1181	}
74
75			void NanoVolume::process() {
76
77			Molecule* mol;
78			Atom* atom;
79			RigidBody* rb;
80			int myIndex;
81			SimInfo::MoleculeIterator mi;
82			Molecule::RigidBodyIterator rbIter;
83			Molecule::AtomIterator ai;
84			StuntDouble* sd;
85			Vector3d vec;
86			int i,j;
87
88			ConvexHull* hull = new ConvexHull();
89
90			DumpReader reader(info_, dumpFilename_);
91			int nFrames = reader.getNFrames();
92			frameCounter_ = 0;
93
94			pos_.reserve(info_->getNGlobalAtoms());
95
96			for (int istep = 0; istep < nFrames; istep += step_) {
97			reader.readFrame(istep);
98			frameCounter_++;
99			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
100
101			// Clear pos vector between each frame.
102			pos_.clear();
103
104			if (evaluator_.isDynamic()) {
105			seleMan_.setSelectionSet(evaluator_.evaluate());
106			}
107
108			// update the positions of atoms which belong to the rigidbodies
109
110			for (mol = info_->beginMolecule(mi); mol != NULL;
111			mol = info_->nextMolecule(mi)) {
112			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
113			rb = mol->nextRigidBody(rbIter)) {
114			rb->updateAtoms();
115			}
116			}
117
118			// outer loop is over the selected StuntDoubles:
119
120			for (sd = seleMan_.beginSelected(i); sd != NULL;
121			sd = seleMan_.nextSelected(i)) {
122
123			pos_.push_back(sd->getPos());
124			myIndex = sd->getGlobalIndex();
125
126			}
127			// Generate convex hull for this frame.
128			hull->genHull(pos_);
129	chuckv	1188	totalVolume_ += hull->getVolume();
130	chuckv	1181	}
131	chuckv	1188	RealType avgVolume = totalVolume_/(RealType) frameCounter_;
132	chuckv	1194	//std::cout.precision(7);
133			//std::cout << avgVolume << std::endl;
134
135			std::ofstream osq(getOutputFileName().c_str());
136			osq.precision(7);
137			if (osq.is_open()){
138			osq << avgVolume << std::endl;
139
140			}
141			osq.close();
142
143	chuckv	1181	}