| 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). |
| 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> |
| 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(); |
| 93 |
|
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 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)) { |
| 95 |
< |
count++; |
| 98 |
> |
if (counts_.size() <= count) { |
| 99 |
> |
counts_.resize(count, 0); |
| 100 |
|
} |
| 101 |
< |
|
| 98 |
< |
if (counts_.size() < count) counts_.resize(count); |
| 101 |
> |
|
| 102 |
|
counts_[count]++; |
| 103 |
+ |
|
| 104 |
+ |
nsum += count; |
| 105 |
+ |
n2sum += count * count; |
| 106 |
|
} |
| 107 |
|
|
| 108 |
|
int nProcessed = nFrames /step_; |
| 109 |
|
|
| 104 |
– |
vector<int>::iterator it; |
| 105 |
– |
unsigned long int n; |
| 106 |
– |
unsigned long int nsum = 0; |
| 107 |
– |
unsigned long int n2sum = 0; |
| 108 |
– |
for (it = counts_.begin(); it != counts_.end(); ++it) { |
| 109 |
– |
n = (*it); |
| 110 |
– |
nsum += n; |
| 111 |
– |
n2sum += n*n; |
| 112 |
– |
} |
| 113 |
– |
|
| 110 |
|
nAvg = nsum / nProcessed; |
| 111 |
|
n2Avg = n2sum / nProcessed; |
| 112 |
|
sDev = sqrt(n2Avg - nAvg*nAvg); |
| 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()); |
