| 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). |
| 40 |
< |
* |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/* Calculates Rho(theta) */ |
| 44 |
|
|
| 45 |
|
#include <algorithm> |
| 46 |
< |
#include <fstream> |
| 46 |
> |
#include <fstream> |
| 47 |
|
#include "applications/staticProps/pAngle.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
|
#include "io/DumpReader.hpp" |
| 50 |
|
#include "primitives/Molecule.hpp" |
| 51 |
+ |
#include "brains/Thermo.hpp" |
| 52 |
+ |
|
| 53 |
|
namespace OpenMD { |
| 54 |
|
|
| 55 |
|
pAngle::pAngle(SimInfo* info, const std::string& filename, |
| 76 |
|
Molecule::RigidBodyIterator rbIter; |
| 77 |
|
int i; |
| 78 |
|
|
| 79 |
+ |
Thermo thermo(info_); |
| 80 |
|
DumpReader reader(info_, dumpFilename_); |
| 81 |
|
int nFrames = reader.getNFrames(); |
| 82 |
|
nProcessed_ = nFrames/step_; |
| 97 |
|
} |
| 98 |
|
} |
| 99 |
|
|
| 100 |
< |
Vector3d CenterOfMass = info_->getCom(); |
| 100 |
> |
Vector3d CenterOfMass = thermo.getCom(); |
| 101 |
|
|
| 102 |
|
if (evaluator_.isDynamic()) { |
| 103 |
|
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 104 |
|
} |
| 105 |
|
|
| 103 |
– |
|
| 106 |
|
int runningTot = 0; |
| 107 |
|
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 108 |
|
sd = seleMan_.nextSelected(i)) { |
| 109 |
< |
|
| 109 |
> |
|
| 110 |
|
Vector3d pos = sd->getPos(); |
| 111 |
|
|
| 112 |
|
Vector3d r1 = CenterOfMass - pos; |
| 134 |
|
void pAngle::processHistogram() { |
| 135 |
|
|
| 136 |
|
int atot = 0; |
| 137 |
< |
for(int i = 0; i < count_.size(); ++i) |
| 137 |
> |
for(unsigned int i = 0; i < count_.size(); ++i) |
| 138 |
|
atot += count_[i]; |
| 139 |
|
|
| 140 |
< |
for(int i = 0; i < count_.size(); ++i) { |
| 141 |
< |
histogram_[i] = double(count_[i]) / double(atot); |
| 140 |
> |
for(unsigned int i = 0; i < count_.size(); ++i) { |
| 141 |
> |
histogram_[i] = double(count_[i] / double(atot)); |
| 142 |
|
} |
| 143 |
|
} |
| 144 |
|
|
| 152 |
|
rdfStream << "#selection: (" << selectionScript_ << ")\n"; |
| 153 |
|
rdfStream << "#cos(theta)\tp(cos(theta))\n"; |
| 154 |
|
RealType dct = 2.0 / histogram_.size(); |
| 155 |
< |
for (int i = 0; i < histogram_.size(); ++i) { |
| 155 |
> |
for (unsigned int i = 0; i < histogram_.size(); ++i) { |
| 156 |
|
RealType ct = -1.0 + (2.0 * i + 1) / (histogram_.size()); |
| 157 |
|
rdfStream << ct << "\t" << histogram_[i]/dct << "\n"; |
| 158 |
|
} |
