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());
        validateSelection1(seleMan1_);
      }
      if (!evaluator2_.isDynamic()) {
        seleMan2_.setSelectionSet(evaluator2_.evaluate());
        validateSelection2(seleMan2_);
      }

      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());
        validateSelection1(seleMan1_);
      }
      if (evaluator2_.isDynamic()) {
        seleMan2_.setSelectionSet(evaluator2_.evaluate());
        validateSelection2(seleMan2_);
      }

      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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 3 months ago) by gezelter
File size:	6900 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	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	gezelter	2204	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			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	1990
54	gezelter	2204	evaluator1_.loadScriptString(sele1);
55			evaluator2_.loadScriptString(sele2);
56	tim	1990
57	gezelter	2204	if (!evaluator1_.isDynamic()) {
58	tim	2045	seleMan1_.setSelectionSet(evaluator1_.evaluate());
59			validateSelection1(seleMan1_);
60	gezelter	2204	}
61			if (!evaluator2_.isDynamic()) {
62	tim	2045	seleMan2_.setSelectionSet(evaluator2_.evaluate());
63			validateSelection2(seleMan2_);
64	gezelter	2204	}
65	tim	1990
66	gezelter	2204	if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) {
67	tim	2031	//if all selections are static, we can precompute the number of real pairs
68	tim	2037	common_ = seleMan1_ & seleMan2_;
69			sele1_minus_common_ = seleMan1_ - common_;
70			sele2_minus_common_ = seleMan2_ - common_;
71	tim	2031
72	tim	2032	int nSelected1 = seleMan1_.getSelectionCount();
73			int nSelected2 = seleMan2_.getSelectionCount();
74	tim	2037	int nIntersect = common_.getSelectionCount();
75
76			nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
77	gezelter	2204	}
78
79	tim	2031	}
80	tim	1990
81	gezelter	2204	void RadialDistrFunc::process() {
82	tim	1995	Molecule* mol;
83			RigidBody* rb;
84			SimInfo::MoleculeIterator mi;
85			Molecule::RigidBodyIterator rbIter;
86	tim	2002
87	tim	1990	preProcess();
88
89			DumpReader reader(info_, dumpFilename_);
90	tim	1995	int nFrames = reader.getNFrames();
91	tim	2035	nProcessed_ = nFrames / step_;
92
93	tim	1990	for (int i = 0; i < nFrames; i += step_) {
94	gezelter	2204	reader.readFrame(i);
95			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
96	tim	1990
97	gezelter	2204	if (evaluator1_.isDynamic()) {
98			seleMan1_.setSelectionSet(evaluator1_.evaluate());
99			validateSelection1(seleMan1_);
100			}
101			if (evaluator2_.isDynamic()) {
102			seleMan2_.setSelectionSet(evaluator2_.evaluate());
103			validateSelection2(seleMan2_);
104			}
105	tim	1990
106	gezelter	2204	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
107	tim	1995
108	gezelter	2204	//change the positions of atoms which belong to the rigidbodies
109			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
110			rb->updateAtoms();
111			}
112			}
113	tim	1995
114	gezelter	2204	initalizeHistogram();
115	tim	1990
116
117	tim	2037
118	gezelter	2204	//selections may overlap.
119			//
120			// \|s1 -c \| c \|
121			// \| c \|s2 - c\|
122			//
123			// s1 : number of selected stuntdoubles in selection1
124			// s2 : number of selected stuntdoubles in selection2
125			// c : number of intersect stuntdouble between selection1 and selection2
126			//when loop over the pairs, we can divide the looping into 3 stages
127			//stage 1 : [s1-c] [s2]
128			//stage 2 : [c] [s2 - c]
129			//stage 3 : [c] [c]
130			//stage 1 and stage 2 are completly non-overlapping
131			//stage 3 are completely overlapping
132	tim	2037
133	gezelter	2204	if (evaluator1_.isDynamic() \|\| evaluator2_.isDynamic()) {
134	tim	2037
135	gezelter	2204	common_ = seleMan1_ & seleMan2_;
136			sele1_minus_common_ = seleMan1_ - common_;
137			sele2_minus_common_ = seleMan2_ - common_;
138			int nSelected1 = seleMan1_.getSelectionCount();
139			int nSelected2 = seleMan2_.getSelectionCount();
140			int nIntersect = common_.getSelectionCount();
141	tim	2037
142	gezelter	2204	nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
143			}
144	tim	1990
145	gezelter	2204	processNonOverlapping(sele1_minus_common_, seleMan2_);
146			processNonOverlapping(common_, sele2_minus_common_);
147			processOverlapping(common_);
148	tim	2037
149
150	gezelter	2204	processHistogram();
151	tim	1990
152			}
153
154			postProcess();
155
156	tim	1991	writeRdf();
157	gezelter	2204	}
158	tim	1990
159	gezelter	2204	void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) {
160	tim	2037	StuntDouble* sd1;
161			StuntDouble* sd2;
162			int i;
163			int j;
164
165			for (sd1 = sman1.beginSelected(i); sd1 != NULL; sd1 = sman1.nextSelected(i)) {
166	tim	2031
167	gezelter	2204	for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) {
168			collectHistogram(sd1, sd2);
169			}
170	tim	2037	}
171	tim	2031
172	gezelter	2204	}
173	tim	2031
174	gezelter	2204	void RadialDistrFunc::processOverlapping( SelectionManager& sman) {
175	tim	2037	StuntDouble* sd1;
176			StuntDouble* sd2;
177			int i;
178			int j;
179
180			//basically, it is the same as below loop
181			//for (int i = 0; i < n; ++i )
182			// for (int j = i + 1; j < n; ++j) {}
183
184			for (sd1 = sman.beginSelected(i); sd1 != NULL; sd1 = sman.nextSelected(i)) {
185	gezelter	2204	for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL; sd2 = sman.nextSelected(j)) {
186			collectHistogram(sd1, sd2);
187			}
188	tim	2031	}
189
190	gezelter	2204	}
191	tim	2031
192			}