--- trunk/src/applications/staticProps/RadialDistrFunc.cpp 2005/02/17 18:30:54 361 +++ trunk/src/applications/staticProps/RadialDistrFunc.cpp 2012/08/22 18:43:27 1785 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 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. @@ -37,6 +28,16 @@ * 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 @@ -44,27 +45,33 @@ #include "RadialDistrFunc.hpp" #include "io/DumpReader.hpp" #include "primitives/Molecule.hpp" -namespace oopse { -RadialDistrFunc:: RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) - : info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1), - selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), - seleMan1_(info), seleMan2_(info), common_(info), sele1_minus_common_(info), sele2_minus_common_(info){ +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); + evaluator1_.loadScriptString(sele1); + evaluator2_.loadScriptString(sele2); - if (!evaluator1_.isDynamic()) { + if (!evaluator1_.isDynamic()) { seleMan1_.setSelectionSet(evaluator1_.evaluate()); validateSelection1(seleMan1_); - } - if (!evaluator2_.isDynamic()) { + } + 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 + 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_; @@ -73,12 +80,12 @@ RadialDistrFunc:: RadialDistrFunc(SimInfo* info int nSelected2 = seleMan2_.getSelectionCount(); int nIntersect = common_.getSelectionCount(); - nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; - } + nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; + } -} + } -void RadialDistrFunc::process() { + void RadialDistrFunc::process() { Molecule* mol; RigidBody* rb; SimInfo::MoleculeIterator mi; @@ -91,102 +98,113 @@ void RadialDistrFunc::process() { nProcessed_ = nFrames / step_; for (int i = 0; i < nFrames; i += step_) { - reader.readFrame(i); - currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); + 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_); - } + 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)) { + 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(); - } - } + // Change the positions of atoms which belong to the RigidBodies + for (rb = mol->beginRigidBody(rbIter); rb != NULL; + rb = mol->nextRigidBody(rbIter)) { + rb->updateAtoms(); + } + } - initalizeHistogram(); - - + initializeHistogram(); - //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 + // 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(); + 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_); + nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; + } + + processNonOverlapping(sele1_minus_common_, seleMan2_); + processNonOverlapping(common_, sele2_minus_common_); + processOverlapping(common_); + + processHistogram(); - - processHistogram(); - } postProcess(); writeRdf(); -} + } -void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) { + 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)) { + // 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 (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) { - collectHistogram(sd1, sd2); - } + 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) { + 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) {} + // 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); - } + 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); + } } - + } } - -}