| 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 |
#include <functional> |
| 45 |
#include "applications/staticProps/ObjectCount.hpp" |
| 46 |
#include "utils/simError.h" |
| 47 |
#include "io/DumpReader.hpp" |
| 48 |
#include "primitives/Molecule.hpp" |
| 49 |
#include "utils/NumericConstant.hpp" |
| 50 |
namespace OpenMD { |
| 51 |
|
| 52 |
ObjectCount::ObjectCount(SimInfo* info, const std::string& filename, |
| 53 |
const std::string& sele) |
| 54 |
: StaticAnalyser(info, filename), selectionScript_(sele), |
| 55 |
evaluator_(info), seleMan_(info) { |
| 56 |
|
| 57 |
setOutputName(getPrefix(filename) + ".counts"); |
| 58 |
|
| 59 |
evaluator_.loadScriptString(sele); |
| 60 |
|
| 61 |
if (!evaluator_.isDynamic()) { |
| 62 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 63 |
} |
| 64 |
} |
| 65 |
|
| 66 |
void ObjectCount::process() { |
| 67 |
Molecule* mol; |
| 68 |
RigidBody* rb; |
| 69 |
SimInfo::MoleculeIterator mi; |
| 70 |
Molecule::RigidBodyIterator rbIter; |
| 71 |
|
| 72 |
counts_.clear(); |
| 73 |
counts_.resize(10, 0); |
| 74 |
DumpReader reader(info_, dumpFilename_); |
| 75 |
int nFrames = reader.getNFrames(); |
| 76 |
unsigned long int nsum = 0; |
| 77 |
unsigned long int n2sum = 0; |
| 78 |
|
| 79 |
for (int i = 0; i < nFrames; i += step_) { |
| 80 |
reader.readFrame(i); |
| 81 |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 82 |
|
| 83 |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 84 |
mol = info_->nextMolecule(mi)) { |
| 85 |
//change the positions of atoms which belong to the rigidbodies |
| 86 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 87 |
rb = mol->nextRigidBody(rbIter)) { |
| 88 |
rb->updateAtoms(); |
| 89 |
} |
| 90 |
} |
| 91 |
|
| 92 |
if (evaluator_.isDynamic()) { |
| 93 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 94 |
} |
| 95 |
|
| 96 |
unsigned int count = seleMan_.getSelectionCount(); |
| 97 |
|
| 98 |
if (counts_.size() <= count) { |
| 99 |
counts_.resize(count, 0); |
| 100 |
} |
| 101 |
|
| 102 |
counts_[count]++; |
| 103 |
|
| 104 |
nsum += count; |
| 105 |
n2sum += count * count; |
| 106 |
} |
| 107 |
|
| 108 |
int nProcessed = nFrames /step_; |
| 109 |
|
| 110 |
nAvg = nsum / nProcessed; |
| 111 |
n2Avg = n2sum / nProcessed; |
| 112 |
sDev = sqrt(n2Avg - nAvg*nAvg); |
| 113 |
writeCounts(); |
| 114 |
} |
| 115 |
|
| 116 |
void ObjectCount::writeCounts() { |
| 117 |
std::ofstream ofs(outputFilename_.c_str(), std::ios::binary); |
| 118 |
if (ofs.is_open()) { |
| 119 |
ofs << "#counts\n"; |
| 120 |
ofs << "#selection: (" << selectionScript_ << ")\n"; |
| 121 |
ofs << "# <N> = "<< nAvg << "\n"; |
| 122 |
ofs << "# <N^2> = " << n2Avg << "\n"; |
| 123 |
ofs << "# sqrt(<N^2> - <N>^2) = " << sDev << "\n"; |
| 124 |
ofs << "# N\tcounts[N]\n"; |
| 125 |
for (unsigned int i = 0; i < counts_.size(); ++i) { |
| 126 |
ofs << i << "\t" << counts_[i] << "\n"; |
| 127 |
} |
| 128 |
|
| 129 |
} else { |
| 130 |
|
| 131 |
sprintf(painCave.errMsg, "ObjectCount: unable to open %s\n", outputFilename_.c_str()); |
| 132 |
painCave.isFatal = 1; |
| 133 |
simError(); |
| 134 |
} |
| 135 |
ofs.close(); |
| 136 |
} |
| 137 |
|
| 138 |
} |
| 139 |
|
| 140 |
|
