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.
      //
      // |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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 6 months ago) by gezelter
File size:	6925 byte(s)
Log Message:	updated copyright notices
#	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	namespace OpenMD {
49
50	RadialDistrFunc::RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
51	: StaticAnalyser(info, filename),
52	selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
53	seleMan1_(info), seleMan2_(info), common_(info), sele1_minus_common_(info), sele2_minus_common_(info){
54
55	evaluator1_.loadScriptString(sele1);
56	evaluator2_.loadScriptString(sele2);
57
58	if (!evaluator1_.isDynamic()) {
59	seleMan1_.setSelectionSet(evaluator1_.evaluate());
60	validateSelection1(seleMan1_);
61	}
62	if (!evaluator2_.isDynamic()) {
63	seleMan2_.setSelectionSet(evaluator2_.evaluate());
64	validateSelection2(seleMan2_);
65	}
66
67	if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) {
68	//if all selections are static, we can precompute the number of real pairs
69	common_ = seleMan1_ & seleMan2_;
70	sele1_minus_common_ = seleMan1_ - common_;
71	sele2_minus_common_ = seleMan2_ - common_;
72
73	int nSelected1 = seleMan1_.getSelectionCount();
74	int nSelected2 = seleMan2_.getSelectionCount();
75	int nIntersect = common_.getSelectionCount();
76
77	nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
78	}
79
80	}
81
82	void RadialDistrFunc::process() {
83	Molecule* mol;
84	RigidBody* rb;
85	SimInfo::MoleculeIterator mi;
86	Molecule::RigidBodyIterator rbIter;
87
88	preProcess();
89
90	DumpReader reader(info_, dumpFilename_);
91	int nFrames = reader.getNFrames();
92	nProcessed_ = nFrames / step_;
93
94	for (int i = 0; i < nFrames; i += step_) {
95	reader.readFrame(i);
96	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
97
98	if (evaluator1_.isDynamic()) {
99	seleMan1_.setSelectionSet(evaluator1_.evaluate());
100	validateSelection1(seleMan1_);
101	}
102	if (evaluator2_.isDynamic()) {
103	seleMan2_.setSelectionSet(evaluator2_.evaluate());
104	validateSelection2(seleMan2_);
105	}
106
107	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
108
109	//change the positions of atoms which belong to the rigidbodies
110	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
111	rb->updateAtoms();
112	}
113	}
114
115	initalizeHistogram();
116
117
118
119	//selections may overlap.
120	//
121	// \|s1 -c \| c \|
122	// \| c \|s2 - c\|
123	//
124	// s1 : number of selected stuntdoubles in selection1
125	// s2 : number of selected stuntdoubles in selection2
126	// c : number of intersect stuntdouble between selection1 and selection2
127	//when loop over the pairs, we can divide the looping into 3 stages
128	//stage 1 : [s1-c] [s2]
129	//stage 2 : [c] [s2 - c]
130	//stage 3 : [c] [c]
131	//stage 1 and stage 2 are completly non-overlapping
132	//stage 3 are completely overlapping
133
134	if (evaluator1_.isDynamic() \|\| evaluator2_.isDynamic()) {
135	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
142	nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
143	}
144	processNonOverlapping(sele1_minus_common_, seleMan2_);
145	processNonOverlapping(common_, sele2_minus_common_);
146	processOverlapping(common_);
147
148	processHistogram();
149
150	}
151
152	postProcess();
153
154	writeRdf();
155	}
156
157	void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) {
158	StuntDouble* sd1;
159	StuntDouble* sd2;
160	int i;
161	int j;
162
163	for (sd1 = sman1.beginSelected(i); sd1 != NULL; sd1 = sman1.nextSelected(i)) {
164
165	for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) {
166	collectHistogram(sd1, sd2);
167	}
168	}
169
170	}
171
172	void RadialDistrFunc::processOverlapping( SelectionManager& sman) {
173	StuntDouble* sd1;
174	StuntDouble* sd2;
175	int i;
176	int j;
177
178	//basically, it is the same as below loop
179	//for (int i = 0; i < n; ++i )
180	// for (int j = i + 1; j < n; ++j) {}
181
182	for (sd1 = sman.beginSelected(i); sd1 != NULL; sd1 = sman.nextSelected(i)) {
183	for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL; sd2 = sman.nextSelected(j)) {
184	collectHistogram(sd1, sd2);
185	}
186	}
187
188	}
189
190	}