| 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. 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 |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
|
| 42 |
#include <algorithm> |
| 43 |
|
| 44 |
#include "RadialDistrFunc.hpp" |
| 45 |
#include "io/DumpReader.hpp" |
| 46 |
#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){ |
| 52 |
|
| 53 |
evaluator1_.loadScriptString(sele1); |
| 54 |
evaluator2_.loadScriptString(sele2); |
| 55 |
|
| 56 |
if (!evaluator1_.isDynamic()) { |
| 57 |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 58 |
} |
| 59 |
if (!evaluator2_.isDynamic()) { |
| 60 |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
| 61 |
} |
| 62 |
|
| 63 |
} |
| 64 |
|
| 65 |
void RadialDistrFunc::process() { |
| 66 |
Molecule* mol; |
| 67 |
RigidBody* rb; |
| 68 |
SimInfo::MoleculeIterator mi; |
| 69 |
Molecule::RigidBodyIterator rbIter; |
| 70 |
preProcess(); |
| 71 |
|
| 72 |
DumpReader reader(info_, dumpFilename_); |
| 73 |
int nFrames = reader.getNFrames(); |
| 74 |
nProcessed_ = nFrames / step_ + 1; |
| 75 |
for (int i = 0; i < nFrames; i += step_) { |
| 76 |
reader.readFrame(i); |
| 77 |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 78 |
|
| 79 |
if (evaluator1_.isDynamic()) { |
| 80 |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 81 |
} |
| 82 |
if (evaluator2_.isDynamic()) { |
| 83 |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
| 84 |
} |
| 85 |
|
| 86 |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 87 |
|
| 88 |
//change the positions of atoms which belong to the rigidbodies |
| 89 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 90 |
rb->updateAtoms(); |
| 91 |
} |
| 92 |
} |
| 93 |
|
| 94 |
initalizeHistogram(); |
| 95 |
|
| 96 |
StuntDouble* sd1; |
| 97 |
int j; |
| 98 |
for (sd1 = seleMan1_.beginSelected(j); sd1 != NULL; sd1 = seleMan1_.nextSelected(j)) { |
| 99 |
|
| 100 |
StuntDouble* sd2; |
| 101 |
int k; |
| 102 |
for (sd2 = seleMan2_.beginSelected(k); sd2 != NULL; sd2 = seleMan2_.nextSelected(k)) { |
| 103 |
collectHistogram(sd1, sd2); |
| 104 |
} |
| 105 |
} |
| 106 |
|
| 107 |
processHistogram(); |
| 108 |
|
| 109 |
} |
| 110 |
|
| 111 |
postProcess(); |
| 112 |
|
| 113 |
writeRdf(); |
| 114 |
} |
| 115 |
|
| 116 |
} |
