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), common_(info), sele1_minus_common_(info), sele2_minus_common_(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    
        common_ = seleMan1_ & seleMan2_;
        sele1_minus_common_ = seleMan1_ - common_;
        sele2_minus_common_ = seleMan2_ - common_;      

        int nSelected1 = seleMan1_.getSelectionCount();
        int nSelected2 = seleMan2_.getSelectionCount();
        int nIntersect = common_.getSelectionCount();
        
        nPairs_ = 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_;

    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();


        //selections may overlap.
        //
        // |s1 -c | c |
        //            | c |s2 - c|
        //
        // s1 : number of selected stuntdoubles in selection1
        // s2 : number of selected stuntdoubles in selection2
        // c   : number of intersect stuntdouble between selection1 and selection2
        //when loop over the pairs, we can divide the looping into 3 stages
        //stage 1 :     [s1-c]      [s2]
        //stage 2 :     [c]            [s2 - c]
        //stage 3 :     [c]            [c]
        //stage 1 and stage 2 are completly non-overlapping
        //stage 3 are completely overlapping

        if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) {

            common_ = seleMan1_ & seleMan2_;
            sele1_minus_common_ = seleMan1_ - common_;
            sele2_minus_common_ = seleMan2_ - common_;            
            int nSelected1 = seleMan1_.getSelectionCount();
            int nSelected2 = seleMan2_.getSelectionCount();
            int nIntersect = common_.getSelectionCount();
            
            nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;                      
        }

        processNonOverlapping(sele1_minus_common_, seleMan2_);
        processNonOverlapping(common_, sele2_minus_common_);        
        processOverlapping(common_);
        
        
        processHistogram();
        
    }

    postProcess();

    writeRdf();
}

void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) {
    StuntDouble* sd1;
    StuntDouble* sd2;
    int i;    
    int j;
    
    for (sd1 = sman1.beginSelected(i); sd1 != NULL; sd1 = sman1.nextSelected(i)) {

        for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) {
            collectHistogram(sd1, sd2);
        }            
    }

}

void RadialDistrFunc::processOverlapping( SelectionManager& sman) {
    StuntDouble* sd1;
    StuntDouble* sd2;
    int i;    
    int j;

    //basically, it is the same as below loop
    //for (int i = 0;  i < n; ++i )
    //  for (int j = i + 1; j < n; ++j) {}
    
    for (sd1 = sman.beginSelected(i); sd1 != NULL; sd1 = sman.nextSelected(i)) {                    
        for (j  = i, sd2 = sman.nextSelected(j); sd2 != NULL; sd2 = sman.nextSelected(j)) {
            collectHistogram(sd1, sd2);
        }            
    }

}

}
Revision:	353
Committed:	Wed Feb 16 19:36:30 2005 UTC (20 years, 8 months ago) by tim
File size:	6977 byte(s)
Log Message:	change the suffix of output files;fix the problem of counting in staticProps
#	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	353	selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
52			seleMan1_(info), seleMan2_(info), common_(info), sele1_minus_common_(info), sele2_minus_common_(info){
53	tim	306
54			evaluator1_.loadScriptString(sele1);
55			evaluator2_.loadScriptString(sele2);
56
57	tim	311	if (!evaluator1_.isDynamic()) {
58			seleMan1_.setSelectionSet(evaluator1_.evaluate());
59	tim	306	}
60	tim	311	if (!evaluator2_.isDynamic()) {
61			seleMan2_.setSelectionSet(evaluator2_.evaluate());
62	tim	306	}
63
64	tim	347	if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) {
65			//if all selections are static, we can precompute the number of real pairs
66	tim	353	common_ = seleMan1_ & seleMan2_;
67			sele1_minus_common_ = seleMan1_ - common_;
68			sele2_minus_common_ = seleMan2_ - common_;
69	tim	347
70	tim	348	int nSelected1 = seleMan1_.getSelectionCount();
71			int nSelected2 = seleMan2_.getSelectionCount();
72	tim	353	int nIntersect = common_.getSelectionCount();
73
74			nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
75	tim	347	}
76
77	tim	306	}
78
79			void RadialDistrFunc::process() {
80	tim	311	Molecule* mol;
81			RigidBody* rb;
82			SimInfo::MoleculeIterator mi;
83			Molecule::RigidBodyIterator rbIter;
84	tim	318
85	tim	306	preProcess();
86
87			DumpReader reader(info_, dumpFilename_);
88	tim	311	int nFrames = reader.getNFrames();
89	tim	351	nProcessed_ = nFrames / step_;
90
91	tim	306	for (int i = 0; i < nFrames; i += step_) {
92	tim	311	reader.readFrame(i);
93	tim	306	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
94
95	tim	311	if (evaluator1_.isDynamic()) {
96			seleMan1_.setSelectionSet(evaluator1_.evaluate());
97	tim	306	}
98	tim	311	if (evaluator2_.isDynamic()) {
99			seleMan2_.setSelectionSet(evaluator2_.evaluate());
100	tim	306	}
101
102	tim	311	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
103
104			//change the positions of atoms which belong to the rigidbodies
105			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
106			rb->updateAtoms();
107			}
108			}
109
110	tim	306	initalizeHistogram();
111
112
113	tim	353
114			//selections may overlap.
115			//
116			// \|s1 -c \| c \|
117			// \| c \|s2 - c\|
118			//
119			// s1 : number of selected stuntdoubles in selection1
120			// s2 : number of selected stuntdoubles in selection2
121			// c : number of intersect stuntdouble between selection1 and selection2
122			//when loop over the pairs, we can divide the looping into 3 stages
123			//stage 1 : [s1-c] [s2]
124			//stage 2 : [c] [s2 - c]
125			//stage 3 : [c] [c]
126			//stage 1 and stage 2 are completly non-overlapping
127			//stage 3 are completely overlapping
128
129			if (evaluator1_.isDynamic() \|\| evaluator2_.isDynamic()) {
130
131			common_ = seleMan1_ & seleMan2_;
132			sele1_minus_common_ = seleMan1_ - common_;
133			sele2_minus_common_ = seleMan2_ - common_;
134			int nSelected1 = seleMan1_.getSelectionCount();
135			int nSelected2 = seleMan2_.getSelectionCount();
136			int nIntersect = common_.getSelectionCount();
137
138			nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
139	tim	306	}
140
141	tim	353	processNonOverlapping(sele1_minus_common_, seleMan2_);
142			processNonOverlapping(common_, sele2_minus_common_);
143			processOverlapping(common_);
144
145
146	tim	306	processHistogram();
147
148			}
149
150			postProcess();
151
152	tim	307	writeRdf();
153	tim	306	}
154
155	tim	353	void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) {
156			StuntDouble* sd1;
157			StuntDouble* sd2;
158			int i;
159			int j;
160
161			for (sd1 = sman1.beginSelected(i); sd1 != NULL; sd1 = sman1.nextSelected(i)) {
162	tim	347
163	tim	353	for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) {
164			collectHistogram(sd1, sd2);
165			}
166			}
167	tim	347
168	tim	353	}
169	tim	347
170	tim	353	void RadialDistrFunc::processOverlapping( SelectionManager& sman) {
171			StuntDouble* sd1;
172			StuntDouble* sd2;
173			int i;
174			int j;
175
176			//basically, it is the same as below loop
177			//for (int i = 0; i < n; ++i )
178			// for (int j = i + 1; j < n; ++j) {}
179
180			for (sd1 = sman.beginSelected(i); sd1 != NULL; sd1 = sman.nextSelected(i)) {
181			for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL; sd2 = sman.nextSelected(j)) {
182			collectHistogram(sd1, sd2);
183			}
184	tim	347	}
185
186	tim	306	}
187	tim	347
188			}