applications/staticProps/ObjectCount.cpp

/*
 * Copyright (c) 2005 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include <algorithm>
#include <functional>
#include "applications/staticProps/ObjectCount.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
namespace OpenMD {

  ObjectCount::ObjectCount(SimInfo* info, const std::string& filename, 
                           const std::string& sele)
    : StaticAnalyser(info, filename), selectionScript_(sele), 
      evaluator_(info), seleMan_(info)   {
    
    setOutputName(getPrefix(filename) + ".counts");
    
    evaluator_.loadScriptString(sele);
    
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }            
  }

void ObjectCount::process() {
  Molecule* mol;
  RigidBody* rb;
  SimInfo::MoleculeIterator mi;
  Molecule::RigidBodyIterator rbIter;
  
  counts_.clear();
  counts_.resize(10, 0);
  DumpReader reader(info_, dumpFilename_);    
  int nFrames = reader.getNFrames();
  unsigned long int nsum = 0;
  unsigned long int n2sum = 0;

  for (int i = 0; i < nFrames; i += step_) {
    reader.readFrame(i);
    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
      //change the positions of atoms which belong to the rigidbodies
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        rb->updateAtoms();        
      }      
    }
    
    if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
    }
        
    int count = seleMan_.getSelectionCount();

    if (counts_.size() <= count)  {
      counts_.resize(count, 0);
    }

    counts_[count]++;

    nsum += count;
    n2sum += count * count;
  }
   
  int nProcessed = nFrames /step_;

  nAvg = nsum / nProcessed;
  n2Avg = n2sum / nProcessed;
  sDev = sqrt(n2Avg - nAvg*nAvg);
  writeCounts();   
}
  
  void ObjectCount::writeCounts() {
    std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
    if (ofs.is_open()) {
      ofs << "#counts\n";
      ofs << "#selection: (" << selectionScript_ << ")\n";
      ofs << "# <N> = "<< nAvg << "\n";
      ofs << "# <N^2> = " << n2Avg << "\n";
      ofs << "# sqrt(<N^2> - <N>^2)  = " << sDev << "\n";
      ofs << "# N\tcounts[N]\n";
      for (int i = 0; i < counts_.size(); ++i) {
        ofs << i << "\t" << counts_[i] << "\n";
      }
      
    } else {
      
      sprintf(painCave.errMsg, "ObjectCount: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }
    ofs.close();
  }
  
}


Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	4828 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	1629	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31			*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1629	*/
42
43			#include <algorithm>
44			#include <functional>
45			#include "applications/staticProps/ObjectCount.hpp"
46			#include "utils/simError.h"
47			#include "io/DumpReader.hpp"
48			#include "primitives/Molecule.hpp"
49			#include "utils/NumericConstant.hpp"
50			namespace OpenMD {
51
52			ObjectCount::ObjectCount(SimInfo* info, const std::string& filename,
53			const std::string& sele)
54			: StaticAnalyser(info, filename), selectionScript_(sele),
55			evaluator_(info), seleMan_(info) {
56
57			setOutputName(getPrefix(filename) + ".counts");
58
59			evaluator_.loadScriptString(sele);
60
61			if (!evaluator_.isDynamic()) {
62			seleMan_.setSelectionSet(evaluator_.evaluate());
63			}
64			}
65
66			void ObjectCount::process() {
67			Molecule* mol;
68			RigidBody* rb;
69			SimInfo::MoleculeIterator mi;
70			Molecule::RigidBodyIterator rbIter;
71
72			counts_.clear();
73			counts_.resize(10, 0);
74			DumpReader reader(info_, dumpFilename_);
75			int nFrames = reader.getNFrames();
76			unsigned long int nsum = 0;
77			unsigned long int n2sum = 0;
78
79			for (int i = 0; i < nFrames; i += step_) {
80			reader.readFrame(i);
81			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
82
83			for (mol = info_->beginMolecule(mi); mol != NULL;
84			mol = info_->nextMolecule(mi)) {
85			//change the positions of atoms which belong to the rigidbodies
86			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
87			rb = mol->nextRigidBody(rbIter)) {
88			rb->updateAtoms();
89			}
90			}
91
92			if (evaluator_.isDynamic()) {
93			seleMan_.setSelectionSet(evaluator_.evaluate());
94			}
95
96			int count = seleMan_.getSelectionCount();
97
98			if (counts_.size() <= count) {
99			counts_.resize(count, 0);
100			}
101
102			counts_[count]++;
103
104			nsum += count;
105			n2sum += count * count;
106			}
107
108			int nProcessed = nFrames /step_;
109
110			nAvg = nsum / nProcessed;
111			n2Avg = n2sum / nProcessed;
112			sDev = sqrt(n2Avg - nAvg*nAvg);
113			writeCounts();
114			}
115
116			void ObjectCount::writeCounts() {
117			std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
118			if (ofs.is_open()) {
119			ofs << "#counts\n";
120			ofs << "#selection: (" << selectionScript_ << ")\n";
121			ofs << "# <N> = "<< nAvg << "\n";
122			ofs << "# <N^2> = " << n2Avg << "\n";
123			ofs << "# sqrt(<N^2> - <N>^2) = " << sDev << "\n";
124			ofs << "# N\tcounts[N]\n";
125			for (int i = 0; i < counts_.size(); ++i) {
126			ofs << i << "\t" << counts_[i] << "\n";
127			}
128
129			} else {
130
131			sprintf(painCave.errMsg, "ObjectCount: unable to open %s\n", outputFilename_.c_str());
132			painCave.isFatal = 1;
133			simError();
134			}
135			ofs.close();
136			}
137
138			}
139
140