applications/staticProps/RadialDistrFunc.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. 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.
 */

#include <algorithm>

#include "RadialDistrFunc.hpp"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
namespace oopse {

RadialDistrFunc::        RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
        : info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1), 
          selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){
          
    evaluator1_.loadScriptString(sele1);
    evaluator2_.loadScriptString(sele2);

    if (!evaluator1_.isDynamic()) {
            seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }
    if (!evaluator2_.isDynamic()) {
            seleMan2_.setSelectionSet(evaluator2_.evaluate());
    }

}

void RadialDistrFunc::process() {
    Molecule* mol;
    RigidBody* rb;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    
    preProcess();
    
    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    nProcessed_ = nFrames / step_ + 1;
    for (int i = 0; i < nFrames; i += step_) {
        reader.readFrame(i);
        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();

        if (evaluator1_.isDynamic()) {
            seleMan1_.setSelectionSet(evaluator1_.evaluate());
        }
        if (evaluator2_.isDynamic()) {
            seleMan2_.setSelectionSet(evaluator2_.evaluate());
        }

        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();
            }
        }
        
        initalizeHistogram();

        StuntDouble* sd1;
        int j;
        for (sd1 = seleMan1_.beginSelected(j); sd1 != NULL; sd1 = seleMan1_.nextSelected(j)) {

            StuntDouble* sd2;
            int k;
            for (sd2 = seleMan2_.beginSelected(k); sd2 != NULL; sd2 = seleMan2_.nextSelected(k)) {
                collectHistogram(sd1, sd2);
            }            
        }

        processHistogram();
        
    }

    postProcess();

    writeRdf();
}

}
Revision:	2002
Committed:	Sun Feb 13 06:57:48 2005 UTC (19 years, 5 months ago) by tim
File size:	4370 byte(s)
Log Message:	adding dynamicProps
#	User	Rev	Content
1	tim	1990	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include <algorithm>
43
44			#include "RadialDistrFunc.hpp"
45	tim	1995	#include "io/DumpReader.hpp"
46			#include "primitives/Molecule.hpp"
47	tim	1990	namespace oopse {
48
49	tim	1994	RadialDistrFunc:: RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
50			: info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1),
51	tim	1995	selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){
52	tim	1990
53			evaluator1_.loadScriptString(sele1);
54			evaluator2_.loadScriptString(sele2);
55
56	tim	1995	if (!evaluator1_.isDynamic()) {
57			seleMan1_.setSelectionSet(evaluator1_.evaluate());
58	tim	1990	}
59	tim	1995	if (!evaluator2_.isDynamic()) {
60			seleMan2_.setSelectionSet(evaluator2_.evaluate());
61	tim	1990	}
62
63			}
64
65			void RadialDistrFunc::process() {
66	tim	1995	Molecule* mol;
67			RigidBody* rb;
68			SimInfo::MoleculeIterator mi;
69			Molecule::RigidBodyIterator rbIter;
70	tim	2002
71	tim	1990	preProcess();
72
73			DumpReader reader(info_, dumpFilename_);
74	tim	1995	int nFrames = reader.getNFrames();
75	tim	1991	nProcessed_ = nFrames / step_ + 1;
76	tim	1990	for (int i = 0; i < nFrames; i += step_) {
77	tim	1995	reader.readFrame(i);
78	tim	1990	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
79
80	tim	1995	if (evaluator1_.isDynamic()) {
81			seleMan1_.setSelectionSet(evaluator1_.evaluate());
82	tim	1990	}
83	tim	1995	if (evaluator2_.isDynamic()) {
84			seleMan2_.setSelectionSet(evaluator2_.evaluate());
85	tim	1990	}
86
87	tim	1995	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
88
89			//change the positions of atoms which belong to the rigidbodies
90			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
91			rb->updateAtoms();
92			}
93			}
94
95	tim	1990	initalizeHistogram();
96
97			StuntDouble* sd1;
98			int j;
99	tim	1995	for (sd1 = seleMan1_.beginSelected(j); sd1 != NULL; sd1 = seleMan1_.nextSelected(j)) {
100	tim	1990
101			StuntDouble* sd2;
102			int k;
103	tim	1995	for (sd2 = seleMan2_.beginSelected(k); sd2 != NULL; sd2 = seleMan2_.nextSelected(k)) {
104	tim	1990	collectHistogram(sd1, sd2);
105			}
106			}
107
108			processHistogram();
109
110			}
111
112			postProcess();
113
114	tim	1991	writeRdf();
115	tim	1990	}
116
117			}