46 |
|
|
47 |
|
namespace oopse { |
48 |
|
|
49 |
< |
GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins) |
49 |
> |
GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins) |
50 |
|
: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){ |
51 |
|
|
52 |
< |
deltaR_ = len_ /nRBins_; |
52 |
> |
deltaR_ = len_ /nRBins_; |
53 |
|
|
54 |
< |
histogram_.resize(nRBins_); |
55 |
< |
avgGofr_.resize(nRBins_); |
54 |
> |
histogram_.resize(nRBins_); |
55 |
> |
avgGofr_.resize(nRBins_); |
56 |
|
|
57 |
< |
setOutputName(getPrefix(filename) + ".gofr"); |
58 |
< |
} |
57 |
> |
setOutputName(getPrefix(filename) + ".gofr"); |
58 |
> |
} |
59 |
|
|
60 |
|
|
61 |
< |
void GofR::preProcess() { |
61 |
> |
void GofR::preProcess() { |
62 |
|
std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0); |
63 |
< |
} |
63 |
> |
} |
64 |
|
|
65 |
< |
void GofR::initalizeHistogram() { |
65 |
> |
void GofR::initalizeHistogram() { |
66 |
|
std::fill(histogram_.begin(), histogram_.end(), 0); |
67 |
< |
} |
67 |
> |
} |
68 |
|
|
69 |
|
|
70 |
< |
void GofR::processHistogram() { |
70 |
> |
void GofR::processHistogram() { |
71 |
|
|
72 |
|
int nPairs = getNPairs(); |
73 |
< |
double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
74 |
< |
double pairDensity = nPairs /volume * 2.0; |
75 |
< |
double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
73 |
> |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
74 |
> |
RealType pairDensity = nPairs /volume * 2.0; |
75 |
> |
RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
76 |
|
|
77 |
|
for(int i = 0 ; i < histogram_.size(); ++i){ |
78 |
|
|
79 |
< |
double rLower = i * deltaR_; |
80 |
< |
double rUpper = rLower + deltaR_; |
81 |
< |
double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
82 |
< |
double nIdeal = volSlice * pairConstant; |
79 |
> |
RealType rLower = i * deltaR_; |
80 |
> |
RealType rUpper = rLower + deltaR_; |
81 |
> |
RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
82 |
> |
RealType nIdeal = volSlice * pairConstant; |
83 |
|
|
84 |
< |
avgGofr_[i] += histogram_[i] / nIdeal; |
84 |
> |
avgGofr_[i] += histogram_[i] / nIdeal; |
85 |
|
} |
86 |
|
|
87 |
< |
} |
87 |
> |
} |
88 |
|
|
89 |
< |
void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
89 |
> |
void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
90 |
|
|
91 |
|
if (sd1 == sd2) { |
92 |
< |
return; |
92 |
> |
return; |
93 |
|
} |
94 |
|
|
95 |
|
Vector3d pos1 = sd1->getPos(); |
96 |
|
Vector3d pos2 = sd2->getPos(); |
97 |
< |
Vector3d r12 = pos1 - pos2; |
97 |
> |
Vector3d r12 = pos2 - pos1; |
98 |
|
currentSnapshot_->wrapVector(r12); |
99 |
|
|
100 |
< |
double distance = r12.length(); |
100 |
> |
RealType distance = r12.length(); |
101 |
|
|
102 |
|
if (distance < len_) { |
103 |
< |
int whichBin = distance / deltaR_; |
104 |
< |
histogram_[whichBin] += 2; |
103 |
> |
int whichBin = distance / deltaR_; |
104 |
> |
histogram_[whichBin] += 2; |
105 |
|
} |
106 |
< |
} |
106 |
> |
} |
107 |
|
|
108 |
|
|
109 |
< |
void GofR::writeRdf() { |
109 |
> |
void GofR::writeRdf() { |
110 |
|
std::ofstream rdfStream(outputFilename_.c_str()); |
111 |
|
if (rdfStream.is_open()) { |
112 |
< |
rdfStream << "#radial distribution function\n"; |
113 |
< |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
114 |
< |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
115 |
< |
rdfStream << "#r\tcorrValue\n"; |
116 |
< |
for (int i = 0; i < avgGofr_.size(); ++i) { |
117 |
< |
double r = deltaR_ * (i + 0.5); |
118 |
< |
rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n"; |
119 |
< |
} |
112 |
> |
rdfStream << "#radial distribution function\n"; |
113 |
> |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
114 |
> |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
115 |
> |
rdfStream << "#r\tcorrValue\n"; |
116 |
> |
for (int i = 0; i < avgGofr_.size(); ++i) { |
117 |
> |
RealType r = deltaR_ * (i + 0.5); |
118 |
> |
rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n"; |
119 |
> |
} |
120 |
|
|
121 |
|
} else { |
122 |
|
|
123 |
< |
sprintf(painCave.errMsg, "GofR: unable to open %s\n", outputFilename_.c_str()); |
124 |
< |
painCave.isFatal = 1; |
125 |
< |
simError(); |
123 |
> |
sprintf(painCave.errMsg, "GofR: unable to open %s\n", outputFilename_.c_str()); |
124 |
> |
painCave.isFatal = 1; |
125 |
> |
simError(); |
126 |
|
} |
127 |
|
|
128 |
|
rdfStream.close(); |
129 |
< |
} |
129 |
> |
} |
130 |
|
|
131 |
|
} |
132 |
|
|