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]  Vardeman & Gezelter, in progress (2009).                        
 */

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

    for (StuntDouble* sd = seleMan_.beginSelected(k); 
         sd != NULL; sd = seleMan_.nextSelected(k)) {
      count++;
    }
    
    if (counts_.size() < count) counts_.resize(count);
    counts_[count]++;
  }
   
  int nProcessed = nFrames /step_;

  vector<int>::iterator it;
  unsigned long int n;
  unsigned long int nsum = 0;
  unsigned long int n2sum = 0;
  for (it = counts_.begin(); it != counts_.end(); ++it) {
    n = (*it);
    nsum += n;
    n2sum += n*n;
  }

  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\tcount(N)\n";
      
      for (int i = 0; i < counts_.size(); ++i) {
        ofs << i <<"\t" << counts_[i]<< std::endl;
      }        
    } else {
      
      sprintf(painCave.errMsg, "ObjectCount: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }
    ofs.close();
  }
  
}


Revision:	1513
Committed:	Tue Oct 19 18:40:54 2010 UTC (15 years ago) by gezelter
File size:	4941 byte(s)
Log Message:	Adding an object count option to staticProps
#	User	Rev	Content
1	gezelter	1513	/*
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			* [4] Vardeman & Gezelter, in progress (2009).
40			*/
41
42			#include <algorithm>
43			#include <functional>
44			#include "applications/staticProps/ObjectCount.hpp"
45			#include "utils/simError.h"
46			#include "io/DumpReader.hpp"
47			#include "primitives/Molecule.hpp"
48			#include "utils/NumericConstant.hpp"
49			namespace OpenMD {
50
51			ObjectCount::ObjectCount(SimInfo* info, const std::string& filename,
52			const std::string& sele)
53			: StaticAnalyser(info, filename), selectionScript_(sele),
54			evaluator_(info), seleMan_(info) {
55
56			setOutputName(getPrefix(filename) + ".counts");
57
58			evaluator_.loadScriptString(sele);
59
60			if (!evaluator_.isDynamic()) {
61			seleMan_.setSelectionSet(evaluator_.evaluate());
62			}
63			}
64
65			void ObjectCount::process() {
66			Molecule* mol;
67			RigidBody* rb;
68			SimInfo::MoleculeIterator mi;
69			Molecule::RigidBodyIterator rbIter;
70
71			DumpReader reader(info_, dumpFilename_);
72			int nFrames = reader.getNFrames();
73			for (int i = 0; i < nFrames; i += step_) {
74			reader.readFrame(i);
75			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
76
77			for (mol = info_->beginMolecule(mi); mol != NULL;
78			mol = info_->nextMolecule(mi)) {
79			//change the positions of atoms which belong to the rigidbodies
80			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
81			rb = mol->nextRigidBody(rbIter)) {
82			rb->updateAtoms();
83			}
84			}
85
86			if (evaluator_.isDynamic()) {
87			seleMan_.setSelectionSet(evaluator_.evaluate());
88			}
89
90			int count = 0;
91			int k;
92
93			for (StuntDouble* sd = seleMan_.beginSelected(k);
94			sd != NULL; sd = seleMan_.nextSelected(k)) {
95			count++;
96			}
97
98			if (counts_.size() < count) counts_.resize(count);
99			counts_[count]++;
100			}
101
102			int nProcessed = nFrames /step_;
103
104			vector<int>::iterator it;
105			unsigned long int n;
106			unsigned long int nsum = 0;
107			unsigned long int n2sum = 0;
108			for (it = counts_.begin(); it != counts_.end(); ++it) {
109			n = (*it);
110			nsum += n;
111			n2sum += n*n;
112			}
113
114			nAvg = nsum / nProcessed;
115			n2Avg = n2sum / nProcessed;
116			sDev = sqrt(n2Avg - nAvg*nAvg);
117			writeCounts();
118			}
119
120			void ObjectCount::writeCounts() {
121			std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
122			if (ofs.is_open()) {
123			ofs << "#counts\n";
124			ofs << "#selection: (" << selectionScript_ << ")\n";
125			ofs << "# <N> = "<< nAvg << "\n";
126			ofs << "# <N^2> = " << n2Avg << "\n";
127			ofs << "# sqrt(<N^2> - <N>^2) = " << sDev << "\n";
128			ofs << "# N\tcount(N)\n";
129
130			for (int i = 0; i < counts_.size(); ++i) {
131			ofs << i <<"\t" << counts_[i]<< std::endl;
132			}
133			} else {
134
135			sprintf(painCave.errMsg, "ObjectCount: unable to open %s\n", outputFilename_.c_str());
136			painCave.isFatal = 1;
137			simError();
138			}
139			ofs.close();
140			}
141
142			}
143
144