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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include <algorithm>

#include "RadialDistrFunc.hpp"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"

namespace OpenMD {

  RadialDistrFunc::RadialDistrFunc(SimInfo* info, 
                                   const std::string& filename, 
                                   const std::string& sele1, 
                                   const std::string& sele2)
    : StaticAnalyser(info, filename), 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, and we need a bit of logic to deal
      // with this.
      //
      // |     s1    |
      // | s1 -c | c |
      //         | c | s2 - c |
      //         |    s2      |
      //
      // s1 : Set of StuntDoubles in selection1
      // s2 : Set of StuntDoubles in selection2
      // c  : Intersection of selection1 and selection2
      // 
      // When we 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]
      // Stages 1 and 2 are completely non-overlapping.
      // Stage 3 is 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;
    
    // This is the same as a non-overlapping pairwise loop structure:
    // for (int i = 0;  i < ni ; ++i ) {
    //   for (int j = 0; j < nj; ++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;

    // This is the same as a pairwise loop structure:
    // for (int i = 0;  i < n-1 ; ++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:	1757
Committed:	Tue Jun 19 02:11:07 2012 UTC (12 years, 10 months ago) by gezelter
File size:	7431 byte(s)
Log Message:	Possibly fixed the rigid body global indexing issue. Reformatted comments. Started work on the FrameData section of Snapshot.
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	306	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	306	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	306	*/
42
43			#include <algorithm>
44
45			#include "RadialDistrFunc.hpp"
46	tim	311	#include "io/DumpReader.hpp"
47			#include "primitives/Molecule.hpp"
48	gezelter	1757
49	gezelter	1390	namespace OpenMD {
50	tim	306
51	gezelter	1757	RadialDistrFunc::RadialDistrFunc(SimInfo* info,
52			const std::string& filename,
53			const std::string& sele1,
54			const std::string& sele2)
55			: StaticAnalyser(info, filename), selectionScript1_(sele1),
56			selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
57			seleMan1_(info), seleMan2_(info), common_(info),
58			sele1_minus_common_(info), sele2_minus_common_(info) {
59	tim	306
60	gezelter	507	evaluator1_.loadScriptString(sele1);
61			evaluator2_.loadScriptString(sele2);
62	tim	306
63	gezelter	507	if (!evaluator1_.isDynamic()) {
64	tim	361	seleMan1_.setSelectionSet(evaluator1_.evaluate());
65			validateSelection1(seleMan1_);
66	gezelter	507	}
67			if (!evaluator2_.isDynamic()) {
68	tim	361	seleMan2_.setSelectionSet(evaluator2_.evaluate());
69			validateSelection2(seleMan2_);
70	gezelter	507	}
71	tim	306
72	gezelter	507	if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) {
73	gezelter	1757	// If all selections are static, we can precompute the number
74			// of real pairs.
75	tim	353	common_ = seleMan1_ & seleMan2_;
76			sele1_minus_common_ = seleMan1_ - common_;
77			sele2_minus_common_ = seleMan2_ - common_;
78	tim	347
79	tim	348	int nSelected1 = seleMan1_.getSelectionCount();
80			int nSelected2 = seleMan2_.getSelectionCount();
81	tim	353	int nIntersect = common_.getSelectionCount();
82
83	gezelter	1757	nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
84	gezelter	507	}
85
86	tim	347	}
87	tim	306
88	gezelter	507	void RadialDistrFunc::process() {
89	tim	311	Molecule* mol;
90			RigidBody* rb;
91			SimInfo::MoleculeIterator mi;
92			Molecule::RigidBodyIterator rbIter;
93	tim	318
94	tim	306	preProcess();
95
96			DumpReader reader(info_, dumpFilename_);
97	tim	311	int nFrames = reader.getNFrames();
98	tim	351	nProcessed_ = nFrames / step_;
99
100	tim	306	for (int i = 0; i < nFrames; i += step_) {
101	gezelter	507	reader.readFrame(i);
102			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
103	tim	306
104	gezelter	507	if (evaluator1_.isDynamic()) {
105			seleMan1_.setSelectionSet(evaluator1_.evaluate());
106			validateSelection1(seleMan1_);
107			}
108			if (evaluator2_.isDynamic()) {
109			seleMan2_.setSelectionSet(evaluator2_.evaluate());
110			validateSelection2(seleMan2_);
111			}
112	tim	306
113	gezelter	1757	for (mol = info_->beginMolecule(mi); mol != NULL;
114			mol = info_->nextMolecule(mi)) {
115	tim	311
116	gezelter	1757	// Change the positions of atoms which belong to the RigidBodies
117			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
118			rb = mol->nextRigidBody(rbIter)) {
119	gezelter	507	rb->updateAtoms();
120			}
121			}
122	tim	311
123	gezelter	507	initalizeHistogram();
124	tim	353
125	gezelter	1757	// Selections may overlap, and we need a bit of logic to deal
126			// with this.
127	gezelter	507	//
128	gezelter	1757	// \| s1 \|
129			// \| s1 -c \| c \|
130			// \| c \| s2 - c \|
131			// \| s2 \|
132	gezelter	507	//
133	gezelter	1757	// s1 : Set of StuntDoubles in selection1
134			// s2 : Set of StuntDoubles in selection2
135			// c : Intersection of selection1 and selection2
136			//
137			// When we loop over the pairs, we can divide the looping into 3
138			// stages:
139			//
140			// Stage 1 : [s1-c] [s2]
141			// Stage 2 : [c] [s2 - c]
142			// Stage 3 : [c] [c]
143			// Stages 1 and 2 are completely non-overlapping.
144			// Stage 3 is completely overlapping.
145	tim	353
146	gezelter	507	if (evaluator1_.isDynamic() \|\| evaluator2_.isDynamic()) {
147			common_ = seleMan1_ & seleMan2_;
148			sele1_minus_common_ = seleMan1_ - common_;
149			sele2_minus_common_ = seleMan2_ - common_;
150			int nSelected1 = seleMan1_.getSelectionCount();
151			int nSelected2 = seleMan2_.getSelectionCount();
152			int nIntersect = common_.getSelectionCount();
153	tim	353
154	xsun	1213	nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
155	gezelter	507	}
156	gezelter	1757
157	gezelter	507	processNonOverlapping(sele1_minus_common_, seleMan2_);
158	gezelter	1757	processNonOverlapping(common_, sele2_minus_common_);
159	gezelter	507	processOverlapping(common_);
160	xsun	1213
161	gezelter	507	processHistogram();
162	tim	306
163			}
164
165			postProcess();
166
167	tim	307	writeRdf();
168	gezelter	507	}
169	tim	306
170	gezelter	1757	void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1,
171			SelectionManager& sman2) {
172	tim	353	StuntDouble* sd1;
173			StuntDouble* sd2;
174			int i;
175			int j;
176
177	gezelter	1757	// This is the same as a non-overlapping pairwise loop structure:
178			// for (int i = 0; i < ni ; ++i ) {
179			// for (int j = 0; j < nj; ++j) {}
180			// }
181	tim	347
182	gezelter	1757	for (sd1 = sman1.beginSelected(i); sd1 != NULL;
183			sd1 = sman1.nextSelected(i)) {
184			for (sd2 = sman2.beginSelected(j); sd2 != NULL;
185			sd2 = sman2.nextSelected(j)) {
186	gezelter	507	collectHistogram(sd1, sd2);
187	gezelter	1757	}
188	tim	353	}
189	gezelter	507	}
190	tim	347
191	gezelter	507	void RadialDistrFunc::processOverlapping( SelectionManager& sman) {
192	tim	353	StuntDouble* sd1;
193			StuntDouble* sd2;
194			int i;
195			int j;
196
197	gezelter	1757	// This is the same as a pairwise loop structure:
198			// for (int i = 0; i < n-1 ; ++i ) {
199			// for (int j = i + 1; j < n; ++j) {}
200			// }
201	tim	353
202	gezelter	1757	for (sd1 = sman.beginSelected(i); sd1 != NULL;
203			sd1 = sman.nextSelected(i)) {
204			for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL;
205			sd2 = sman.nextSelected(j)) {
206	gezelter	507	collectHistogram(sd1, sd2);
207			}
208	tim	347	}
209	gezelter	507	}
210	tim	347	}