| 42 |
|
#include <algorithm> |
| 43 |
|
|
| 44 |
|
#include "RadialDistrFunc.hpp" |
| 45 |
< |
|
| 45 |
> |
#include "io/DumpReader.hpp" |
| 46 |
> |
#include "primitives/Molecule.hpp" |
| 47 |
|
namespace oopse { |
| 48 |
|
|
| 49 |
< |
RadialDistrFunc:: RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len) |
| 50 |
< |
: info_(info), currentSnapshot_(NULL), dumpFilename_(filename), len_(len), nbins_(50), step_(1), |
| 51 |
< |
selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info){ |
| 49 |
> |
RadialDistrFunc:: RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
| 50 |
> |
: info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1), |
| 51 |
> |
selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){ |
| 52 |
|
|
| 53 |
|
evaluator1_.loadScriptString(sele1); |
| 54 |
|
evaluator2_.loadScriptString(sele2); |
| 55 |
|
|
| 56 |
< |
if (!evaluator1_->isDynamic()) { |
| 57 |
< |
seleMan1_.setSelectionSet(evaluator1_->evaluate()); |
| 56 |
> |
if (!evaluator1_.isDynamic()) { |
| 57 |
> |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 58 |
|
} |
| 59 |
< |
if (!evaluator2_->isDynamic()) { |
| 60 |
< |
seleMan2_.setSelectionSet(evaluator2_->evaluate()); |
| 59 |
> |
if (!evaluator2_.isDynamic()) { |
| 60 |
> |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
| 61 |
|
} |
| 62 |
|
|
| 63 |
< |
delta_ = len_ /nbins_; |
| 63 |
> |
if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) { |
| 64 |
> |
//if all selections are static, we can precompute the number of real pairs |
| 65 |
> |
|
| 66 |
> |
int nSelected1 = seleMan1_.getSelectionCount(); |
| 67 |
> |
int nSelected2 = seleMan2_.getSelectionCount(); |
| 68 |
> |
|
| 69 |
> |
BitSet bs = seleMan1_.getSelectionSet(); |
| 70 |
> |
bs &= seleMan2_.getSelectionSet(); |
| 71 |
> |
int nIntersect = bs.countBits(); |
| 72 |
> |
|
| 73 |
> |
nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
| 74 |
> |
} |
| 75 |
> |
|
| 76 |
|
} |
| 77 |
|
|
| 78 |
|
void RadialDistrFunc::process() { |
| 79 |
< |
|
| 79 |
> |
Molecule* mol; |
| 80 |
> |
RigidBody* rb; |
| 81 |
> |
SimInfo::MoleculeIterator mi; |
| 82 |
> |
Molecule::RigidBodyIterator rbIter; |
| 83 |
> |
|
| 84 |
|
preProcess(); |
| 85 |
|
|
| 86 |
|
DumpReader reader(info_, dumpFilename_); |
| 87 |
< |
int nFrames = reader->getNFrames(); |
| 88 |
< |
nProcessed_ = nFrames / step_ + 1; |
| 87 |
> |
int nFrames = reader.getNFrames(); |
| 88 |
> |
nProcessed_ = nFrames / step_; |
| 89 |
> |
|
| 90 |
|
for (int i = 0; i < nFrames; i += step_) { |
| 91 |
< |
reader->readFrame(i); |
| 91 |
> |
reader.readFrame(i); |
| 92 |
|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 93 |
|
|
| 94 |
< |
if (evaluator1_->isDynamic()) { |
| 95 |
< |
seleMan1_.setSelectionSet(evaluator1_->evaluate()); |
| 94 |
> |
if (evaluator1_.isDynamic()) { |
| 95 |
> |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 96 |
|
} |
| 97 |
< |
if (evaluator2_->isDynamic()) { |
| 98 |
< |
seleMan2_.setSelectionSet(evaluator2_->evaluate()); |
| 97 |
> |
if (evaluator2_.isDynamic()) { |
| 98 |
> |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
| 99 |
|
} |
| 100 |
|
|
| 101 |
+ |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 102 |
+ |
|
| 103 |
+ |
//change the positions of atoms which belong to the rigidbodies |
| 104 |
+ |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 105 |
+ |
rb->updateAtoms(); |
| 106 |
+ |
} |
| 107 |
+ |
} |
| 108 |
+ |
|
| 109 |
|
initalizeHistogram(); |
| 110 |
|
|
| 111 |
|
StuntDouble* sd1; |
| 112 |
|
int j; |
| 113 |
< |
for (sd1 = seleMan1_->beginSelected(j); sd1 != NULL; sd1 = seleMan1_->nextSelected(j)) { |
| 113 |
> |
for (sd1 = seleMan1_.beginSelected(j); sd1 != NULL; sd1 = seleMan1_.nextSelected(j)) { |
| 114 |
|
|
| 115 |
|
StuntDouble* sd2; |
| 116 |
|
int k; |
| 117 |
< |
for (sd2 = seleMan2_->beginSelected(k); sd2 != NULL; sd2 = seleMan2_->nextSelected(k)) { |
| 118 |
< |
collectHistogram(sd1, sd2); |
| 117 |
> |
for (sd2 = seleMan2_.beginSelected(k); sd2 != NULL; sd2 = seleMan2_.nextSelected(k)) { |
| 118 |
> |
if (sd1 != sd2) { |
| 119 |
> |
collectHistogram(sd1, sd2); |
| 120 |
> |
} |
| 121 |
|
} |
| 122 |
|
} |
| 123 |
|
|
| 130 |
|
writeRdf(); |
| 131 |
|
} |
| 132 |
|
|
| 133 |
+ |
int RadialDistrFunc::getNRealPairs() { |
| 134 |
+ |
if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) { |
| 135 |
+ |
//if one of the selection is dynamic, need to recompute it |
| 136 |
+ |
|
| 137 |
+ |
int nSelected1 = seleMan1_.getSelectionCount(); |
| 138 |
+ |
int nSelected2 = seleMan2_.getSelectionCount(); |
| 139 |
+ |
|
| 140 |
+ |
BitSet bs = seleMan1_.getSelectionSet(); |
| 141 |
+ |
bs &= seleMan2_.getSelectionSet(); |
| 142 |
+ |
int nIntersect = bs.countBits(); |
| 143 |
+ |
|
| 144 |
+ |
nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
| 145 |
+ |
} |
| 146 |
+ |
|
| 147 |
+ |
return nRealPairs_; |
| 148 |
|
} |
| 149 |
+ |
|
| 150 |
+ |
} |
