| 44 |
|
* |
| 45 |
|
* Created by Charles F. Vardeman II on 11/26/05. |
| 46 |
|
* @author Charles F. Vardeman II |
| 47 |
< |
* @version $Id: RhoZ.cpp,v 1.1 2005-11-30 21:00:39 chuckv Exp $ |
| 47 |
> |
* @version $Id: RhoZ.cpp,v 1.2 2006-01-09 22:14:32 tim Exp $ |
| 48 |
|
* |
| 49 |
|
*/ |
| 50 |
|
|
| 54 |
|
#include <fstream> |
| 55 |
|
#include "applications/staticProps/RhoZ.hpp" |
| 56 |
|
#include "utils/simError.h" |
| 57 |
< |
|
| 57 |
> |
#include "io/DumpReader.hpp" |
| 58 |
> |
#include "primitives/Molecule.hpp" |
| 59 |
|
namespace oopse { |
| 60 |
|
|
| 61 |
< |
RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins) |
| 62 |
< |
: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){ |
| 61 |
> |
RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, int len, int nrbins) |
| 62 |
> |
: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){ |
| 63 |
> |
|
| 64 |
> |
evaluator_.loadScriptString(sele); |
| 65 |
> |
if (!evaluator_.isDynamic()) { |
| 66 |
> |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 67 |
> |
} |
| 68 |
> |
|
| 69 |
|
|
| 70 |
|
deltaR_ = len_ /nRBins_; |
| 71 |
|
|
| 72 |
< |
histogram_.resize(nRBins_); |
| 73 |
< |
avgRhoZ_.resize(nRBins_); |
| 72 |
> |
sliceSDLists_.resize(nRBins_); |
| 73 |
> |
density_.resize(nRBins_); |
| 74 |
|
|
| 75 |
|
setOutputName(getPrefix(filename) + ".RhoZ"); |
| 76 |
|
} |
| 77 |
< |
|
| 78 |
< |
|
| 79 |
< |
void RhoZ::preProcess() { |
| 80 |
< |
std::fill(avgRhoZ_.begin(), avgRhoZ_.end(), 0.0); |
| 81 |
< |
} |
| 82 |
< |
|
| 83 |
< |
void RhoZ::initalizeHistogram() { |
| 84 |
< |
std::fill(histogram_.begin(), histogram_.end(), 0); |
| 85 |
< |
} |
| 86 |
< |
|
| 87 |
< |
|
| 88 |
< |
void RhoZ::processHistogram() { |
| 89 |
< |
|
| 90 |
< |
int nPairs = getNPairs(); |
| 91 |
< |
double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
| 92 |
< |
double pairDensity = nPairs /volume * 2.0; |
| 93 |
< |
double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
| 94 |
< |
|
| 95 |
< |
for(int i = 0 ; i < histogram_.size(); ++i){ |
| 96 |
< |
|
| 97 |
< |
double rLower = i * deltaR_; |
| 98 |
< |
double rUpper = rLower + deltaR_; |
| 99 |
< |
double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
| 100 |
< |
double nIdeal = volSlice * pairConstant; |
| 101 |
< |
|
| 102 |
< |
avgRhoZ_[i] += histogram_[i] / nIdeal; |
| 77 |
> |
|
| 78 |
> |
void RhoZ::process() { |
| 79 |
> |
DumpReader reader(info_, dumpFilename_); |
| 80 |
> |
int nFrames = reader.getNFrames(); |
| 81 |
> |
nProcessed_ = nFrames / step_; |
| 82 |
> |
|
| 83 |
> |
|
| 84 |
> |
for (int istep = 0; istep < nFrames; istep += step_) { |
| 85 |
> |
|
| 86 |
> |
StuntDouble* sd; |
| 87 |
> |
int i; |
| 88 |
> |
reader.readFrame(istep); |
| 89 |
> |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 90 |
> |
|
| 91 |
> |
double sliceVolume = currentSnapshot_->getVolume() /nRBins_; |
| 92 |
> |
//assume simulation box will never change |
| 93 |
> |
//Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 94 |
> |
double halfBoxZ = len_ /2; |
| 95 |
> |
|
| 96 |
> |
if (evaluator_.isDynamic()) { |
| 97 |
> |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 98 |
> |
} |
| 99 |
> |
|
| 100 |
> |
//wrap the stuntdoubles into a cell |
| 101 |
> |
for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
| 102 |
> |
Vector3d pos = sd->getPos(); |
| 103 |
> |
currentSnapshot_->wrapVector(pos); |
| 104 |
> |
sd->setPos(pos); |
| 105 |
> |
} |
| 106 |
> |
|
| 107 |
> |
//determine which atom belong to which slice |
| 108 |
> |
for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
| 109 |
> |
Vector3d pos = sd->getPos(); |
| 110 |
> |
int binNo = (pos.z() + halfBoxZ) /deltaR_; |
| 111 |
> |
sliceSDLists_[binNo].push_back(sd); |
| 112 |
> |
} |
| 113 |
> |
|
| 114 |
> |
//loop over the slices to calculate the densities |
| 115 |
> |
for (std::size_t j = 0; j < sliceSDLists_.size(); ++j) { |
| 116 |
> |
double totalMass = 0; |
| 117 |
> |
for (int k = 0; k < sliceSDLists_[j].size(); ++k) { |
| 118 |
> |
totalMass += sliceSDLists_[j][k]->getMass(); |
| 119 |
> |
} |
| 120 |
> |
density_[j] += totalMass/sliceVolume; |
| 121 |
> |
} |
| 122 |
|
} |
| 123 |
+ |
|
| 124 |
|
|
| 125 |
+ |
writeDensity(); |
| 126 |
+ |
|
| 127 |
|
} |
| 128 |
< |
|
| 129 |
< |
void RhoZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 128 |
> |
|
| 129 |
> |
|
| 130 |
|
|
| 131 |
< |
if (sd1 == sd2) { |
| 103 |
< |
return; |
| 104 |
< |
} |
| 105 |
< |
|
| 106 |
< |
Vector3d pos1 = sd1->getPosZ(); |
| 107 |
< |
Vector3d pos2 = sd2->getPosZ(); |
| 108 |
< |
Vector3d r12 = pos2 - pos1; |
| 109 |
< |
currentSnapshot_->wrapVector(r12); |
| 110 |
< |
|
| 111 |
< |
double distance = r12.length(); |
| 112 |
< |
|
| 113 |
< |
if (distance < len_) { |
| 114 |
< |
int whichBin = distance / deltaR_; |
| 115 |
< |
histogram_[whichBin] += 2; |
| 116 |
< |
} |
| 117 |
< |
} |
| 118 |
< |
|
| 119 |
< |
|
| 120 |
< |
void RhoZ::writeRdf() { |
| 131 |
> |
void RhoZ::writeDensity() { |
| 132 |
|
std::ofstream rdfStream(outputFilename_.c_str()); |
| 133 |
|
if (rdfStream.is_open()) { |
| 134 |
< |
rdfStream << "#radial distribution function\n"; |
| 135 |
< |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 136 |
< |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 137 |
< |
rdfStream << "#r\tcorrValue\n"; |
| 127 |
< |
for (int i = 0; i < avgRhoZ_.size(); ++i) { |
| 134 |
> |
rdfStream << "#RhoZ\n"; |
| 135 |
> |
rdfStream << "#selection: (" << selectionScript_ << ")\t"; |
| 136 |
> |
rdfStream << "#z\tdensity\n"; |
| 137 |
> |
for (int i = 0; i < density_.size(); ++i) { |
| 138 |
|
double r = deltaR_ * (i + 0.5); |
| 139 |
< |
rdfStream << r << "\t" << avgRhoZ_[i]/nProcessed_ << "\n"; |
| 139 |
> |
rdfStream << r << "\t" << density_[i]/nProcessed_ << "\n"; |
| 140 |
|
} |
| 141 |
|
|
| 142 |
|
} else { |
