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();
        }
      }
        
      initializeHistogram();
        
      // 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:	1785
Committed:	Wed Aug 22 18:43:27 2012 UTC (12 years, 8 months ago) by jmichalk
File size:	7432 byte(s)
Log Message:	Trunk: The changes in this commit are confined to applications/staticProps and for the most part deal with a misspelling of initialize. The one other change took place in StaticProps.cpp and deals with the default treatment of sele2. It had previously been set to 'select all' which seems to go against what would be desired by not specifying it with regard to proper operations of many of the analysis programs ( g of r's especially)
#	Content
1	/*
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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include <algorithm>
44
45	#include "RadialDistrFunc.hpp"
46	#include "io/DumpReader.hpp"
47	#include "primitives/Molecule.hpp"
48
49	namespace OpenMD {
50
51	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
60	evaluator1_.loadScriptString(sele1);
61	evaluator2_.loadScriptString(sele2);
62
63	if (!evaluator1_.isDynamic()) {
64	seleMan1_.setSelectionSet(evaluator1_.evaluate());
65	validateSelection1(seleMan1_);
66	}
67	if (!evaluator2_.isDynamic()) {
68	seleMan2_.setSelectionSet(evaluator2_.evaluate());
69	validateSelection2(seleMan2_);
70	}
71
72	if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) {
73	// If all selections are static, we can precompute the number
74	// of real pairs.
75	common_ = seleMan1_ & seleMan2_;
76	sele1_minus_common_ = seleMan1_ - common_;
77	sele2_minus_common_ = seleMan2_ - common_;
78
79	int nSelected1 = seleMan1_.getSelectionCount();
80	int nSelected2 = seleMan2_.getSelectionCount();
81	int nIntersect = common_.getSelectionCount();
82
83	nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
84	}
85
86	}
87
88	void RadialDistrFunc::process() {
89	Molecule* mol;
90	RigidBody* rb;
91	SimInfo::MoleculeIterator mi;
92	Molecule::RigidBodyIterator rbIter;
93
94	preProcess();
95
96	DumpReader reader(info_, dumpFilename_);
97	int nFrames = reader.getNFrames();
98	nProcessed_ = nFrames / step_;
99
100	for (int i = 0; i < nFrames; i += step_) {
101	reader.readFrame(i);
102	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
103
104	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
113	for (mol = info_->beginMolecule(mi); mol != NULL;
114	mol = info_->nextMolecule(mi)) {
115
116	// Change the positions of atoms which belong to the RigidBodies
117	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
118	rb = mol->nextRigidBody(rbIter)) {
119	rb->updateAtoms();
120	}
121	}
122
123	initializeHistogram();
124
125	// Selections may overlap, and we need a bit of logic to deal
126	// with this.
127	//
128	// \| s1 \|
129	// \| s1 -c \| c \|
130	// \| c \| s2 - c \|
131	// \| s2 \|
132	//
133	// 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
146	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
154	nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
155	}
156
157	processNonOverlapping(sele1_minus_common_, seleMan2_);
158	processNonOverlapping(common_, sele2_minus_common_);
159	processOverlapping(common_);
160
161	processHistogram();
162
163	}
164
165	postProcess();
166
167	writeRdf();
168	}
169
170	void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1,
171	SelectionManager& sman2) {
172	StuntDouble* sd1;
173	StuntDouble* sd2;
174	int i;
175	int j;
176
177	// 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
182	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	collectHistogram(sd1, sd2);
187	}
188	}
189	}
190
191	void RadialDistrFunc::processOverlapping( SelectionManager& sman) {
192	StuntDouble* sd1;
193	StuntDouble* sd2;
194	int i;
195	int j;
196
197	// 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
202	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	collectHistogram(sd1, sd2);
207	}
208	}
209	}
210	}