| 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] Vardeman & Gezelter, in progress (2009). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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> |
| 52 |
|
ObjectCount::ObjectCount(SimInfo* info, const std::string& filename, |
| 53 |
|
const std::string& sele) |
| 54 |
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: StaticAnalyser(info, filename), selectionScript_(sele), |
| 55 |
< |
evaluator_(info), seleMan_(info) { |
| 55 |
> |
seleMan_(info), evaluator_(info) { |
| 56 |
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|
| 57 |
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setOutputName(getPrefix(filename) + ".counts"); |
| 58 |
|
|
| 63 |
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} |
| 64 |
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} |
| 65 |
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|
| 66 |
< |
void ObjectCount::process() { |
| 67 |
< |
Molecule* mol; |
| 68 |
< |
RigidBody* rb; |
| 69 |
< |
SimInfo::MoleculeIterator mi; |
| 70 |
< |
Molecule::RigidBodyIterator rbIter; |
| 66 |
> |
void ObjectCount::process() { |
| 67 |
> |
Molecule* mol; |
| 68 |
> |
RigidBody* rb; |
| 69 |
> |
SimInfo::MoleculeIterator mi; |
| 70 |
> |
Molecule::RigidBodyIterator rbIter; |
| 71 |
|
|
| 72 |
< |
DumpReader reader(info_, dumpFilename_); |
| 73 |
< |
int nFrames = reader.getNFrames(); |
| 74 |
< |
for (int i = 0; i < nFrames; i += step_) { |
| 75 |
< |
reader.readFrame(i); |
| 76 |
< |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 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 |
< |
} |
| 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()) { |
| 92 |
> |
if (evaluator_.isDynamic()) { |
| 93 |
|
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 94 |
< |
} |
| 94 |
> |
} |
| 95 |
|
|
| 96 |
< |
int count = 0; |
| 91 |
< |
int k; |
| 96 |
> |
unsigned int count = seleMan_.getSelectionCount(); |
| 97 |
|
|
| 98 |
< |
for (StuntDouble* sd = seleMan_.beginSelected(k); |
| 99 |
< |
sd != NULL; sd = seleMan_.nextSelected(k)) { |
| 100 |
< |
count++; |
| 98 |
> |
if (counts_.size() <= count) { |
| 99 |
> |
counts_.resize(count, 0); |
| 100 |
> |
} |
| 101 |
> |
|
| 102 |
> |
counts_[count]++; |
| 103 |
> |
|
| 104 |
> |
nsum += count; |
| 105 |
> |
n2sum += count * count; |
| 106 |
|
} |
| 97 |
– |
|
| 98 |
– |
if (counts_.size() < count) counts_.resize(count); |
| 99 |
– |
counts_[count]++; |
| 100 |
– |
} |
| 107 |
|
|
| 108 |
< |
int nProcessed = nFrames /step_; |
| 108 |
> |
int nProcessed = nFrames /step_; |
| 109 |
|
|
| 110 |
< |
vector<int>::iterator it; |
| 111 |
< |
unsigned long int n; |
| 112 |
< |
unsigned long int nsum = 0; |
| 113 |
< |
unsigned long int n2sum = 0; |
| 108 |
< |
for (it = counts_.begin(); it != counts_.end(); ++it) { |
| 109 |
< |
n = (*it); |
| 110 |
< |
nsum += n; |
| 111 |
< |
n2sum += n*n; |
| 110 |
> |
nAvg = nsum / nProcessed; |
| 111 |
> |
n2Avg = n2sum / nProcessed; |
| 112 |
> |
sDev = sqrt(n2Avg - nAvg*nAvg); |
| 113 |
> |
writeCounts(); |
| 114 |
|
} |
| 113 |
– |
|
| 114 |
– |
nAvg = nsum / nProcessed; |
| 115 |
– |
n2Avg = n2sum / nProcessed; |
| 116 |
– |
sDev = sqrt(n2Avg - nAvg*nAvg); |
| 117 |
– |
writeCounts(); |
| 118 |
– |
} |
| 115 |
|
|
| 116 |
|
void ObjectCount::writeCounts() { |
| 117 |
|
std::ofstream ofs(outputFilename_.c_str(), std::ios::binary); |
| 121 |
|
ofs << "# <N> = "<< nAvg << "\n"; |
| 122 |
|
ofs << "# <N^2> = " << n2Avg << "\n"; |
| 123 |
|
ofs << "# sqrt(<N^2> - <N>^2) = " << sDev << "\n"; |
| 124 |
< |
ofs << "# N\tcount(N)\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 |
|
|
| 130 |
– |
for (int i = 0; i < counts_.size(); ++i) { |
| 131 |
– |
ofs << i <<"\t" << counts_[i]<< std::endl; |
| 132 |
– |
} |
| 129 |
|
} else { |
| 130 |
|
|
| 131 |
< |
sprintf(painCave.errMsg, "ObjectCount: unable to open %s\n", outputFilename_.c_str()); |
| 131 |
> |
sprintf(painCave.errMsg, "ObjectCount: unable to open %s\n", |
| 132 |
> |
outputFilename_.c_str()); |
| 133 |
|
painCave.isFatal = 1; |
| 134 |
|
simError(); |
| 135 |
|
} |
