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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include <algorithm> |
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|
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#include "RadialDistrFunc.hpp" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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|
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namespace OpenMD { |
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|
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RadialDistrFunc::RadialDistrFunc(SimInfo* info, |
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const std::string& filename, |
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const std::string& sele1, |
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const std::string& sele2) |
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: StaticAnalyser(info, filename), selectionScript1_(sele1), |
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selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
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seleMan1_(info), seleMan2_(info), common_(info), |
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sele1_minus_common_(info), sele2_minus_common_(info) { |
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|
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evaluator1_.loadScriptString(sele1); |
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evaluator2_.loadScriptString(sele2); |
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|
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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validateSelection1(seleMan1_); |
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} |
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if (!evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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validateSelection2(seleMan2_); |
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} |
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|
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if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) { |
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// If all selections are static, we can precompute the number |
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// of real pairs. |
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common_ = seleMan1_ & seleMan2_; |
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sele1_minus_common_ = seleMan1_ - common_; |
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sele2_minus_common_ = seleMan2_ - common_; |
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|
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int nSelected1 = seleMan1_.getSelectionCount(); |
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int nSelected2 = seleMan2_.getSelectionCount(); |
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int nIntersect = common_.getSelectionCount(); |
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|
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nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
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} |
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|
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} |
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|
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void RadialDistrFunc::process() { |
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Molecule* mol; |
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RigidBody* rb; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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|
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preProcess(); |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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nProcessed_ = nFrames / step_; |
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|
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for (int i = 0; i < nFrames; i += step_) { |
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reader.readFrame(i); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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if (evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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validateSelection1(seleMan1_); |
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} |
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if (evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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validateSelection2(seleMan2_); |
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} |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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|
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// Change the positions of atoms which belong to the RigidBodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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} |
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|
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initializeHistogram(); |
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|
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// Selections may overlap, and we need a bit of logic to deal |
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// with this. |
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// |
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// | s1 | |
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// | s1 -c | c | |
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// | c | s2 - c | |
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// | s2 | |
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// |
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// s1 : Set of StuntDoubles in selection1 |
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// s2 : Set of StuntDoubles in selection2 |
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// c : Intersection of selection1 and selection2 |
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// |
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// When we loop over the pairs, we can divide the looping into 3 |
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// stages: |
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// |
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// Stage 1 : [s1-c] [s2] |
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// Stage 2 : [c] [s2 - c] |
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// Stage 3 : [c] [c] |
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// Stages 1 and 2 are completely non-overlapping. |
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// Stage 3 is completely overlapping. |
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|
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if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) { |
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common_ = seleMan1_ & seleMan2_; |
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sele1_minus_common_ = seleMan1_ - common_; |
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sele2_minus_common_ = seleMan2_ - common_; |
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int nSelected1 = seleMan1_.getSelectionCount(); |
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int nSelected2 = seleMan2_.getSelectionCount(); |
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int nIntersect = common_.getSelectionCount(); |
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|
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nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
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} |
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|
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processNonOverlapping(sele1_minus_common_, seleMan2_); |
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processNonOverlapping(common_, sele2_minus_common_); |
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processOverlapping(common_); |
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|
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processHistogram(); |
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|
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} |
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|
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postProcess(); |
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|
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writeRdf(); |
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} |
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|
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void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, |
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SelectionManager& sman2) { |
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StuntDouble* sd1; |
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StuntDouble* sd2; |
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int i; |
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int j; |
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|
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// This is the same as a non-overlapping pairwise loop structure: |
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// for (int i = 0; i < ni ; ++i ) { |
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// for (int j = 0; j < nj; ++j) {} |
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// } |
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|
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for (sd1 = sman1.beginSelected(i); sd1 != NULL; |
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sd1 = sman1.nextSelected(i)) { |
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for (sd2 = sman2.beginSelected(j); sd2 != NULL; |
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sd2 = sman2.nextSelected(j)) { |
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collectHistogram(sd1, sd2); |
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} |
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} |
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} |
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|
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void RadialDistrFunc::processOverlapping( SelectionManager& sman) { |
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StuntDouble* sd1; |
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StuntDouble* sd2; |
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int i; |
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int j; |
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|
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// This is the same as a pairwise loop structure: |
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// for (int i = 0; i < n-1 ; ++i ) { |
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// for (int j = i + 1; j < n; ++j) {} |
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// } |
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|
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for (sd1 = sman.beginSelected(i); sd1 != NULL; |
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sd1 = sman.nextSelected(i)) { |
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for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL; |
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sd2 = sman.nextSelected(j)) { |
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collectHistogram(sd1, sd2); |
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} |
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} |
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} |
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} |
