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#include "types/MultipoleAdapter.hpp" |
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namespace OpenMD { |
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|
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GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins) |
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: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) { |
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setOutputName(getPrefix(filename) + ".gxyz"); |
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|
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evaluator3_.loadScriptString(sele3); |
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if (!evaluator3_.isDynamic()) { |
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seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
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} |
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|
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deltaR_ = len_ / nRBins_; |
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|
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GofXyz::GofXyz(SimInfo* info, const std::string& filename, |
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const std::string& sele1, const std::string& sele2, |
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const std::string& sele3, RealType len, int nrbins) |
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: RadialDistrFunc(info, filename, sele1, sele2), len_(len), |
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halfLen_(len/2), nRBins_(nrbins), evaluator3_(info), seleMan3_(info) { |
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|
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histogram_.resize(nRBins_); |
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for (int i = 0 ; i < nRBins_; ++i) { |
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histogram_[i].resize(nRBins_); |
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for(int j = 0; j < nRBins_; ++j) { |
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histogram_[i][j].resize(nRBins_); |
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} |
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} |
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|
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} |
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|
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|
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setOutputName(getPrefix(filename) + ".gxyz"); |
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|
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evaluator3_.loadScriptString(sele3); |
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if (!evaluator3_.isDynamic()) { |
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seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
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} |
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|
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deltaR_ = len_ / nRBins_; |
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|
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histogram_.resize(nRBins_); |
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for (int i = 0 ; i < nRBins_; ++i) { |
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histogram_[i].resize(nRBins_); |
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for(int j = 0; j < nRBins_; ++j) { |
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histogram_[i][j].resize(nRBins_); |
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} |
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} |
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} |
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|
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void GofXyz::preProcess() { |
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for (int i = 0 ; i < nRBins_; ++i) { |
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histogram_[i].resize(nRBins_); |
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} |
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} |
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} |
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void GofXyz::initializeHistogram() { |
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//calculate the center of mass of the molecule of selected stuntdouble in selection1 |
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// Calculate the center of mass of the molecule of selected |
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// StuntDouble in selection1 |
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|
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if (!evaluator3_.isDynamic()) { |
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seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
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} |
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assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount()); |
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//dipole direction of selection3 and position of selection3 will be used to determine the y-z plane |
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//v1 = s3 -s1, |
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//z = origin.dipole |
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//x = v1 X z |
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//y = z X x |
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// The Dipole direction of selection3 and position of selection3 will |
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// be used to determine the y-z plane |
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// v1 = s3 -s1, |
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// z = origin.dipole |
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// x = v1 X z |
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// y = z X x |
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rotMats_.clear(); |
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int i; |
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//rdfStream << "#g(x, y, z)\n"; |
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//rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
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//rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
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//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
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//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " |
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// << len_ << "deltaR = " << deltaR_ <<"\n"; |
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for (unsigned int i = 0; i < histogram_.size(); ++i) { |
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for(unsigned int j = 0; j < histogram_[i].size(); ++j) { |
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for(unsigned int k = 0;k < histogram_[i][j].size(); ++k) { |
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rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), |
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sizeof(histogram_[i][j][k] )); |
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rdfStream.write(reinterpret_cast<char *>( &histogram_[i][j][k] ), |
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sizeof( histogram_[i][j][k] )); |
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} |
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} |
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} |
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|
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} else { |
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|
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sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str()); |
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> |
sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", |
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outputFilename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
