ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/applications/staticProps/ObjectCount.cpp
Revision: 1513
Committed: Tue Oct 19 18:40:54 2010 UTC (14 years, 6 months ago) by gezelter
File size: 4941 byte(s)
Log Message:
Adding an object count option to staticProps

File Contents

# 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    

Properties

Name Value
svn:eol-style native
svn:executable *