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());
    }

    if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) {
        //if all selections are static,  we can precompute the number of real pairs    

        int nSelected1 = seleMan1_->getSelectionCount();
        int nSelected2 = seleMan2_->getSelectionCount();

        BitSet bs = seleMan1_.getSelectionSet();
        bs &= seleMan2_.getSelectionSet();
        int nIntersect = bs.countBits();

        nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
    }
    
}

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)) {
                if (sd1 != sd2) {
                    collectHistogram(sd1, sd2);
                }
            }            
        }

        processHistogram();
        
    }

    postProcess();

    writeRdf();
}

int RadialDistrFunc::getNRealPairs() {
    if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) {
        //if one of the selection is static,  need to recompute it    

        int nSelected1 = seleMan1_->getSelectionCount();
        int nSelected2 = seleMan2_->getSelectionCount();

        BitSet bs = seleMan1_.getSelectionSet();
        bs &= seleMan2_.getSelectionSet();
        int nIntersect = bs.countBits();

        nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
    }

    return nRealPairs_
}

}
Revision:	347
Committed:	Tue Feb 15 17:11:35 2005 UTC (20 years, 2 months ago) by tim
Original Path:	*trunk/src/applications/staticProps/RadialDistrFunc.cpp*
File size:	5454 byte(s)
Log Message:	(1) adding #ifdef __RWSTD to make sun compiler happy (2) fix pair density calculation problem when two selections intersect with each other
#	User	Rev	Content
1	tim	306	/*
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	311	#include "io/DumpReader.hpp"
46			#include "primitives/Molecule.hpp"
47	tim	306	namespace oopse {
48
49	tim	310	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	311	selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){
52	tim	306
53			evaluator1_.loadScriptString(sele1);
54			evaluator2_.loadScriptString(sele2);
55
56	tim	311	if (!evaluator1_.isDynamic()) {
57			seleMan1_.setSelectionSet(evaluator1_.evaluate());
58	tim	306	}
59	tim	311	if (!evaluator2_.isDynamic()) {
60			seleMan2_.setSelectionSet(evaluator2_.evaluate());
61	tim	306	}
62
63	tim	347	if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) {
64			//if all selections are static, we can precompute the number of real pairs
65
66			int nSelected1 = seleMan1_->getSelectionCount();
67			int nSelected2 = seleMan2_->getSelectionCount();
68
69			BitSet bs = seleMan1_.getSelectionSet();
70			bs &= seleMan2_.getSelectionSet();
71			int nIntersect = bs.countBits();
72
73			nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
74			}
75
76	tim	306	}
77
78			void RadialDistrFunc::process() {
79	tim	311	Molecule* mol;
80			RigidBody* rb;
81			SimInfo::MoleculeIterator mi;
82			Molecule::RigidBodyIterator rbIter;
83	tim	318
84	tim	306	preProcess();
85
86			DumpReader reader(info_, dumpFilename_);
87	tim	311	int nFrames = reader.getNFrames();
88	tim	307	nProcessed_ = nFrames / step_ + 1;
89	tim	306	for (int i = 0; i < nFrames; i += step_) {
90	tim	311	reader.readFrame(i);
91	tim	306	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
92
93	tim	311	if (evaluator1_.isDynamic()) {
94			seleMan1_.setSelectionSet(evaluator1_.evaluate());
95	tim	306	}
96	tim	311	if (evaluator2_.isDynamic()) {
97			seleMan2_.setSelectionSet(evaluator2_.evaluate());
98	tim	306	}
99
100	tim	311	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
101
102			//change the positions of atoms which belong to the rigidbodies
103			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
104			rb->updateAtoms();
105			}
106			}
107
108	tim	306	initalizeHistogram();
109
110			StuntDouble* sd1;
111			int j;
112	tim	311	for (sd1 = seleMan1_.beginSelected(j); sd1 != NULL; sd1 = seleMan1_.nextSelected(j)) {
113	tim	306
114			StuntDouble* sd2;
115			int k;
116	tim	311	for (sd2 = seleMan2_.beginSelected(k); sd2 != NULL; sd2 = seleMan2_.nextSelected(k)) {
117	tim	347	if (sd1 != sd2) {
118			collectHistogram(sd1, sd2);
119			}
120	tim	306	}
121			}
122
123			processHistogram();
124
125			}
126
127			postProcess();
128
129	tim	307	writeRdf();
130	tim	306	}
131
132	tim	347	int RadialDistrFunc::getNRealPairs() {
133			if (evaluator1_.isDynamic() \|\| evaluator2_.isDynamic()) {
134			//if one of the selection is static, need to recompute it
135
136			int nSelected1 = seleMan1_->getSelectionCount();
137			int nSelected2 = seleMan2_->getSelectionCount();
138
139			BitSet bs = seleMan1_.getSelectionSet();
140			bs &= seleMan2_.getSelectionSet();
141			int nIntersect = bs.countBits();
142
143			nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
144			}
145
146			return nRealPairs_
147	tim	306	}
148	tim	347
149			}