| 34 |
|
* |
| 35 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 36 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 37 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 37 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 38 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 39 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#include "applications/staticProps/NanoLength.hpp" |
| 54 |
|
NanoLength::NanoLength(SimInfo* info, |
| 55 |
|
const std::string& filename, |
| 56 |
|
const std::string& sele) |
| 57 |
< |
: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info) { |
| 57 |
> |
: StaticAnalyser(info, filename), selectionScript_(sele), seleMan_(info), |
| 58 |
> |
evaluator_(info) { |
| 59 |
> |
|
| 60 |
|
setOutputName(getPrefix(filename) + ".length"); |
| 61 |
|
|
| 62 |
|
osq.open(getOutputFileName().c_str()); |
| 63 |
< |
|
| 63 |
> |
|
| 64 |
|
evaluator_.loadScriptString(sele); |
| 65 |
|
if (!evaluator_.isDynamic()) { |
| 66 |
|
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 67 |
|
} |
| 68 |
|
frameCounter_ = 0; |
| 69 |
< |
} |
| 69 |
> |
} |
| 70 |
|
|
| 71 |
|
void NanoLength::process() { |
| 72 |
|
Molecule* mol; |
| 70 |
– |
Atom* atom; |
| 73 |
|
RigidBody* rb; |
| 72 |
– |
int myIndex; |
| 74 |
|
SimInfo::MoleculeIterator mi; |
| 75 |
|
Molecule::RigidBodyIterator rbIter; |
| 75 |
– |
Molecule::AtomIterator ai; |
| 76 |
|
StuntDouble* sd; |
| 77 |
|
Vector3d vec; |
| 78 |
< |
int i,j; |
| 78 |
> |
int i; |
| 79 |
|
|
| 80 |
|
DumpReader reader(info_, dumpFilename_); |
| 81 |
|
int nFrames = reader.getNFrames(); |
| 120 |
|
osq << time << "\t" << rodLength << std::endl; |
| 121 |
|
} |
| 122 |
|
} |
| 123 |
+ |
osq.close(); |
| 124 |
|
} |
| 125 |
|
|
| 126 |
|
RealType NanoLength::getLength(std::vector<StuntDouble*> atoms) { |
