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Comparing trunk/src/applications/staticProps/RadialDistrFunc.cpp (file contents):
Revision 348 by tim, Tue Feb 15 17:24:12 2005 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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>
#	Line 44 | Line 45
45		#include "RadialDistrFunc.hpp"
46		#include "io/DumpReader.hpp"
47		#include "primitives/Molecule.hpp"
47	–	namespace oopse {
48
49	<	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), seleMan1_(info), seleMan2_(info){
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);
60	>	evaluator1_.loadScriptString(sele1);
61	>	evaluator2_.loadScriptString(sele2);
62
63	<	if (!evaluator1_.isDynamic()) {
64	<	seleMan1_.setSelectionSet(evaluator1_.evaluate());
65	<	}
66	<	if (!evaluator2_.isDynamic()) {
67	<	seleMan2_.setSelectionSet(evaluator2_.evaluate());
68	<	}
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 of real pairs
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	<
82	<	BitSet bs = seleMan1_.getSelectionSet();
83	<	bs &= seleMan2_.getSelectionSet();
84	<	int nIntersect = bs.countBits();
72	<
73	<	nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
74	<	}
81	>	int nIntersect = common_.getSelectionCount();
82	>
83	>	nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
84	>	}
85
86	<	}
86	>	}
87
88	<	void RadialDistrFunc::process() {
88	>	void RadialDistrFunc::process() {
89		Molecule* mol;
90		RigidBody* rb;
91		SimInfo::MoleculeIterator mi;
#	Line 85 | Line 95 | void RadialDistrFunc::process() {
95
96		DumpReader reader(info_, dumpFilename_);
97		int nFrames = reader.getNFrames();
98	<	nProcessed_ = nFrames / step_ + 1;
98	>	nProcessed_ = nFrames / step_;
99	>
100		for (int i = 0; i < nFrames; i += step_) {
101	<	reader.readFrame(i);
102	<	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
101	>	reader.readFrame(i);
102	>	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
103
104	<	if (evaluator1_.isDynamic()) {
105	<	seleMan1_.setSelectionSet(evaluator1_.evaluate());
106	<	}
107	<	if (evaluator2_.isDynamic()) {
108	<	seleMan2_.setSelectionSet(evaluator2_.evaluate());
109	<	}
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; mol = info_->nextMolecule(mi)) {
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; rb = mol->nextRigidBody(rbIter)) {
118	<	rb->updateAtoms();
119	<	}
120	<	}
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	<	initalizeHistogram();
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	<	StuntDouble* sd1;
147	<	int j;
148	<	for (sd1 = seleMan1_.beginSelected(j); sd1 != NULL; sd1 = seleMan1_.nextSelected(j)) {
149	<
150	<	StuntDouble* sd2;
151	<	int k;
152	<	for (sd2 = seleMan2_.beginSelected(k); sd2 != NULL; sd2 = seleMan2_.nextSelected(k)) {
153	<	if (sd1 != sd2) {
154	<	collectHistogram(sd1, sd2);
155	<	}
156	<	}
157	<	}
158	<
159	<	processHistogram();
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	<	}
168	>	}
169
170	<	int RadialDistrFunc::getNRealPairs() {
171	<	if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) {
172	<	//if one of the selection is static,  need to recompute it
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	<	int nSelected1 = seleMan1_.getSelectionCount();
183	<	int nSelected2 = seleMan2_.getSelectionCount();
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	<	BitSet bs = seleMan1_.getSelectionSet();
192	<	bs &= seleMan2_.getSelectionSet();
193	<	int nIntersect = bs.countBits();
191	>	void RadialDistrFunc::processOverlapping( SelectionManager& sman) {
192	>	StuntDouble* sd1;
193	>	StuntDouble* sd2;
194	>	int i;
195	>	int j;
196
197	<	nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
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	<
146	<	return nRealPairs_;
209	>	}
210		}
148	–
149	–	}

Comparing trunk/src/applications/staticProps/RadialDistrFunc.cpp (property svn:keywords):
Revision 348 by tim, Tue Feb 15 17:24:12 2005 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

#	Line 0 | Line 1
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