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#include "Integrator.hpp" |
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#include "simError.h" |
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#include <cmath> |
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template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
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: T(theInfo, the_ff), fz(NULL), |
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indexOfZConsMols(NULL) |
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{ |
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//get properties from SimInfo |
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GenericData* data; |
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IndexData* index; |
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DoubleData* sampleTime; |
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StringData* filename; |
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//retrieve index of z-constraint molecules |
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data = info->getProperty("zconsindex"); |
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if(!data) { |
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sprintf( painCave.errMsg, |
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"ZConstraint error: If you use an ZConstraint\n" |
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" , you must set index of z-constraint molecules.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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else{ |
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index = dynamic_cast<IndexData*>(data); |
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if(!index){ |
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sprintf( painCave.errMsg, |
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"ZConstraint error: Can not get property from SimInfo\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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else{ |
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indexOfAllZConsMols = index->getIndexData(); |
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//the maximum value of index is the last one(we sorted the index data in SimSetup.cpp) |
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int maxIndex; |
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int minIndex; |
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int totalNumMol; |
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minIndex = indexOfAllZConsMols[0]; |
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if(minIndex < 0){ |
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sprintf( painCave.errMsg, |
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"ZConstraint error: index is out of range\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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maxIndex = indexOfAllZConsMols[indexOfAllZConsMols.size() - 1]; |
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#ifndef IS_MPI |
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totalNumMol = nMols; |
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#else |
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totalNumMol = mpiSim->getTotNmol(); |
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#endif |
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if(maxIndex > totalNumMol - 1){ |
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sprintf( painCave.errMsg, |
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"ZConstraint error: index is out of range\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} |
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//retrieve sample time of z-contraint |
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data = info->getProperty("zconstime"); |
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if(!data) { |
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sprintf( painCave.errMsg, |
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"ZConstraint error: If you use an ZConstraint\n" |
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" , you must set sample time.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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else{ |
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sampleTime = dynamic_cast<DoubleData*>(data); |
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if(!sampleTime){ |
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sprintf( painCave.errMsg, |
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"ZConstraint error: Can not get property from SimInfo\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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else{ |
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this->zconsTime = sampleTime->getData(); |
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} |
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} |
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//retrieve output filename of z force |
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data = info->getProperty("zconsfilename"); |
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if(!data) { |
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sprintf( painCave.errMsg, |
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"ZConstraint error: If you use an ZConstraint\n" |
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" , you must set output filename of z-force.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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else{ |
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filename = dynamic_cast<StringData*>(data); |
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if(!filename){ |
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sprintf( painCave.errMsg, |
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"ZConstraint error: Can not get property from SimInfo\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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else{ |
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this->zconsOutput = filename->getData(); |
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} |
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} |
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#ifdef IS_MPI |
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update(); |
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#else |
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int searchResult; |
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double COM[3]; |
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for(int i = 0; i < nMols; i++){ |
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searchResult = isZConstraintMol(&molecules[i]); |
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if(searchResult > -1){ |
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zconsMols.push_back(&molecules[i]); |
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massOfZConsMols.push_back(molecules[i].getTotalMass()); |
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molecules[i].getCOM(COM); |
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} |
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else |
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{ |
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unconsMols.push_back(&molecules[i]); |
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massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
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} |
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} |
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fz = new double[zconsMols.size()]; |
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indexOfZConsMols = new int [zconsMols.size()]; |
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if(!fz || !indexOfZConsMols){ |
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sprintf( painCave.errMsg, |
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"Memory allocation failure in class Zconstraint\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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for(int i = 0; i < zconsMols.size(); i++) |
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indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
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#endif |
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//get total number of unconstrained atoms |
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int nUnconsAtoms_local; |
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nUnconsAtoms_local = 0; |
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for(int i = 0; i < unconsMols.size(); i++) |
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nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
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#ifndef IS_MPI |
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totNumOfUnconsAtoms = nUnconsAtoms_local; |
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#else |
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MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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#endif |
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fzOut = new ZConsWriter(zconsOutput.c_str()); |
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if(!fzOut){ |
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sprintf( painCave.errMsg, |
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"Memory allocation failure in class Zconstraint\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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template<typename T> ZConstraint<T>::~ZConstraint() |
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{ |
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if(fz) |
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delete[] fz; |
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if(indexOfZConsMols) |
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delete[] indexOfZConsMols; |
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if(fzOut) |
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delete fzOut; |
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} |
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#ifdef IS_MPI |
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template<typename T> void ZConstraint<T>::update() |
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{ |
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double COM[3]; |
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int index; |
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zconsMols.clear(); |
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massOfZConsMols.clear(); |
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unconsMols.clear(); |
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massOfUnconsMols.clear(); |
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//creat zconsMol and unconsMol lists |
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for(int i = 0; i < nMols; i++){ |
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index = isZConstraintMol(&molecules[i]); |
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if(index > -1){ |
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zconsMols.push_back(&molecules[i]); |
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massOfZConsMols.push_back(molecules[i].getTotalMass()); |
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molecules[i].getCOM(COM); |
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} |
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else |
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{ |
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unconsMols.push_back(&molecules[i]); |
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massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
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} |
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} |
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//The reason to declare fz and indexOfZconsMols as pointer to array is |
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// that we want to make the MPI communication simple |
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if(fz) |
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delete[] fz; |
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if(indexOfZConsMols) |
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delete[] indexOfZConsMols; |
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if (zconsMols.size() > 0){ |
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fz = new double[zconsMols.size()]; |
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indexOfZConsMols = new int[zconsMols.size()]; |
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if(!fz || !indexOfZConsMols){ |
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sprintf( painCave.errMsg, |
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"Memory allocation failure in class Zconstraint\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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for(int i = 0; i < zconsMols.size(); i++){ |
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indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
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} |
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} |
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else{ |
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fz = NULL; |
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indexOfZConsMols = NULL; |
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} |
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} |
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#endif |
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/** Function Name: isZConstraintMol |
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** Parameter |
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** Molecule* mol |
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** Return value: |
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** -1, if the molecule is not z-constraint molecule, |
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** other non-negative values, its index in indexOfAllZConsMols vector |
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*/ |
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template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
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{ |
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int index; |
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int low; |
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int high; |
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int mid; |
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index = mol->getGlobalIndex(); |
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low = 0; |
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high = indexOfAllZConsMols.size() - 1; |
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//Binary Search (we have sorted the array) |
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while(low <= high){ |
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mid = (low + high) /2; |
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if (indexOfAllZConsMols[mid] == index) |
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return mid; |
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else if (indexOfAllZConsMols[mid] > index ) |
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high = mid -1; |
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else |
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low = mid + 1; |
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} |
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return -1; |
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} |
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/** |
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* Description: |
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* Reset the z coordinates |
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*/ |
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template<typename T> void ZConstraint<T>::integrate(){ |
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//zero out the velocities of center of mass of unconstrained molecules |
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//and the velocities of center of mass of every single z-constrained molecueles |
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zeroOutVel(); |
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T::integrate(); |
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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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*/ |
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template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
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T::calcForce(calcPot, calcStress); |
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if (checkZConsState()) |
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zeroOutVel(); |
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//do zconstraint force; |
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if (haveFixedZMols()) |
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this->doZconstraintForce(); |
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//use harmonical poteintial to move the molecules to the specified positions |
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if (haveMovingZMols()) |
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//this->doHarmonic(); |
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fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
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} |
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template<typename T> double ZConstraint<T>::calcZSys() |
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{ |
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//calculate reference z coordinate for z-constraint molecules |
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double totalMass_local; |
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double totalMass; |
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double totalMZ_local; |
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double totalMZ; |
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double massOfUncons_local; |
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double massOfCurMol; |
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double COM[3]; |
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totalMass_local = 0; |
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totalMass = 0; |
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totalMZ_local = 0; |
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totalMZ = 0; |
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massOfUncons_local = 0; |
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for(int i = 0; i < nMols; i++){ |
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massOfCurMol = molecules[i].getTotalMass(); |
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molecules[i].getCOM(COM); |
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totalMass_local += massOfCurMol; |
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totalMZ_local += massOfCurMol * COM[whichDirection]; |
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if(isZConstraintMol(&molecules[i]) == -1){ |
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massOfUncons_local += massOfCurMol; |
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} |
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} |
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#ifdef IS_MPI |
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MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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#else |
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totalMass = totalMass_local; |
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totalMZ = totalMZ_local; |
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totalMassOfUncons = massOfUncons_local; |
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#endif |
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mmeineke |
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double zsys; |
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zsys = totalMZ / totalMass; |
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return zsys; |
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} |
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/** |
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* |
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*/ |
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template<typename T> void ZConstraint<T>::thermalize( void ){ |
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T::thermalize(); |
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zeroOutVel(); |
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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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template<typename T> void ZConstraint<T>::zeroOutVel(){ |
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421 |
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Atom** fixedZAtoms; |
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double COMvel[3]; |
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double vel[3]; |
424 |
tim |
658 |
|
425 |
tim |
676 |
//zero out the velocities of center of mass of fixed z-constrained molecules |
426 |
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427 |
tim |
658 |
for(int i = 0; i < zconsMols.size(); i++){ |
428 |
tim |
676 |
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if (states[i] == zcsFixed){ |
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|
|
zconsMols[i]->getCOMvel(COMvel); |
432 |
|
|
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
433 |
|
|
|
434 |
|
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
435 |
|
|
fixedZAtoms[j]->getVel(vel); |
436 |
|
|
vel[whichDirection] -= COMvel[whichDirection]; |
437 |
|
|
fixedZAtoms[j]->setVel(vel); |
438 |
|
|
} |
439 |
|
|
|
440 |
|
|
} |
441 |
|
|
|
442 |
tim |
658 |
} |
443 |
tim |
676 |
|
444 |
|
|
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
445 |
|
|
double MVzOfMovingMols_local; |
446 |
|
|
double MVzOfMovingMols; |
447 |
|
|
double totalMassOfMovingZMols_local; |
448 |
|
|
double totalMassOfMovingZMols; |
449 |
|
|
|
450 |
|
|
MVzOfMovingMols_local = 0; |
451 |
|
|
totalMassOfMovingZMols_local = 0; |
452 |
tim |
658 |
|
453 |
tim |
676 |
for(int i =0; i < unconsMols.size(); i++){ |
454 |
|
|
unconsMols[i]->getCOMvel(COMvel); |
455 |
|
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
456 |
|
|
} |
457 |
|
|
|
458 |
|
|
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
459 |
|
|
|
460 |
|
|
if (states[i] == zcsMoving){ |
461 |
|
|
zconsMols[i]->getCOMvel(COMvel); |
462 |
|
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
463 |
|
|
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
464 |
|
|
} |
465 |
|
|
|
466 |
|
|
} |
467 |
|
|
|
468 |
|
|
#ifndef IS_MPI |
469 |
|
|
MVzOfMovingMols = MVzOfMovingMols_local; |
470 |
|
|
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
471 |
tim |
658 |
#else |
472 |
tim |
676 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
473 |
|
|
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
474 |
tim |
658 |
#endif |
475 |
|
|
|
476 |
tim |
676 |
double vzOfMovingMols; |
477 |
|
|
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
478 |
|
|
|
479 |
|
|
//modify the velocites of unconstrained molecules |
480 |
|
|
Atom** unconsAtoms; |
481 |
tim |
658 |
for(int i = 0; i < unconsMols.size(); i++){ |
482 |
tim |
676 |
|
483 |
|
|
unconsAtoms = unconsMols[i]->getMyAtoms(); |
484 |
|
|
for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ |
485 |
|
|
unconsAtoms[j]->getVel(vel); |
486 |
|
|
vel[whichDirection] -= vzOfMovingMols; |
487 |
|
|
unconsAtoms[j]->setVel(vel); |
488 |
|
|
} |
489 |
|
|
|
490 |
|
|
} |
491 |
|
|
|
492 |
|
|
//modify the velocities of moving z-constrained molecuels |
493 |
|
|
Atom** movingZAtoms; |
494 |
|
|
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
495 |
|
|
|
496 |
|
|
if (states[i] ==zcsMoving){ |
497 |
|
|
|
498 |
|
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
499 |
|
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
500 |
|
|
movingZAtoms[j]->getVel(vel); |
501 |
|
|
vel[whichDirection] -= vzOfMovingMols; |
502 |
|
|
movingZAtoms[j]->setVel(vel); |
503 |
|
|
} |
504 |
|
|
|
505 |
|
|
} |
506 |
|
|
|
507 |
tim |
658 |
} |
508 |
tim |
676 |
|
509 |
|
|
} |
510 |
|
|
|
511 |
|
|
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
512 |
|
|
|
513 |
|
|
Atom** zconsAtoms; |
514 |
|
|
double totalFZ; |
515 |
|
|
double totalFZ_local; |
516 |
|
|
double COMvel[3]; |
517 |
|
|
double COM[3]; |
518 |
|
|
double force[3]; |
519 |
|
|
double zsys; |
520 |
|
|
|
521 |
|
|
int nMovingZMols_local; |
522 |
|
|
int nMovingZMols; |
523 |
|
|
|
524 |
|
|
//constrain the molecules which do not reach the specified positions |
525 |
|
|
|
526 |
|
|
zsys = calcZSys(); |
527 |
|
|
cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
528 |
|
|
|
529 |
|
|
//Zero Out the force of z-contrained molecules |
530 |
|
|
totalFZ_local = 0; |
531 |
|
|
|
532 |
|
|
//calculate the total z-contrained force of fixed z-contrained molecules |
533 |
|
|
for(int i = 0; i < zconsMols.size(); i++){ |
534 |
|
|
|
535 |
|
|
if (states[i] == zcsFixed){ |
536 |
|
|
|
537 |
|
|
zconsMols[i]->getCOM(COM); |
538 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
539 |
|
|
|
540 |
|
|
fz[i] = 0; |
541 |
|
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
542 |
|
|
zconsAtoms[j]->getFrc(force); |
543 |
|
|
fz[i] += force[whichDirection]; |
544 |
|
|
} |
545 |
|
|
totalFZ_local += fz[i]; |
546 |
|
|
|
547 |
|
|
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
548 |
|
|
|
549 |
|
|
} |
550 |
|
|
|
551 |
|
|
} |
552 |
|
|
|
553 |
|
|
//calculate the number of atoms of moving z-constrained molecules |
554 |
|
|
nMovingZMols_local = 0; |
555 |
|
|
for(int i = 0; zconsMols.size(); i++){ |
556 |
|
|
if(states[i] == zcsMoving) |
557 |
|
|
nMovingZMols_local += massOfZConsMols[i]; |
558 |
|
|
} |
559 |
tim |
658 |
#ifdef IS_MPI |
560 |
tim |
676 |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
561 |
|
|
MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
562 |
tim |
658 |
#else |
563 |
tim |
676 |
totalFZ = totalFZ_local; |
564 |
|
|
nMovingZMols = nMovingZMols_local; |
565 |
|
|
#endif |
566 |
|
|
|
567 |
|
|
force[0]= 0; |
568 |
|
|
force[1]= 0; |
569 |
|
|
force[2]= 0; |
570 |
|
|
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols); |
571 |
|
|
|
572 |
|
|
//modify the velocites of unconstrained molecules |
573 |
|
|
for(int i = 0; i < unconsMols.size(); i++){ |
574 |
|
|
|
575 |
|
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
576 |
|
|
|
577 |
|
|
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
578 |
|
|
unconsAtoms[j]->addFrc(force); |
579 |
|
|
|
580 |
|
|
} |
581 |
|
|
|
582 |
|
|
//modify the velocities of moving z-constrained molecules |
583 |
|
|
for(int i = 0; i < zconsMols.size(); i++) { |
584 |
|
|
if (states[i] == zcsMoving){ |
585 |
|
|
|
586 |
|
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
587 |
|
|
|
588 |
|
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
589 |
|
|
movingZAtoms[j]->addFrc(force); |
590 |
|
|
} |
591 |
|
|
} |
592 |
|
|
|
593 |
|
|
// apply negative to fixed z-constrained molecues; |
594 |
|
|
force[0]= 0; |
595 |
|
|
force[1]= 0; |
596 |
|
|
force[2]= 0; |
597 |
|
|
|
598 |
|
|
for(int i = 0; i < zconsMols.size(); i++){ |
599 |
|
|
|
600 |
|
|
if (states[i] == zcsFixed){ |
601 |
|
|
|
602 |
|
|
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
603 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
604 |
|
|
|
605 |
|
|
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
606 |
|
|
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
607 |
|
|
zconsAtoms[j]->addFrc(force); |
608 |
|
|
} |
609 |
|
|
|
610 |
|
|
} |
611 |
|
|
|
612 |
|
|
} |
613 |
|
|
|
614 |
|
|
} |
615 |
|
|
|
616 |
|
|
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
617 |
|
|
double COM[3]; |
618 |
|
|
double diff; |
619 |
tim |
658 |
|
620 |
tim |
676 |
bool changed; |
621 |
|
|
|
622 |
|
|
changed = false; |
623 |
|
|
|
624 |
|
|
for(int i =0; i < zconsMols.size(); i++){ |
625 |
|
|
|
626 |
tim |
658 |
zconsMols[i]->getCOM(COM); |
627 |
tim |
676 |
diff = fabs(COM[whichDirection] - ZPos[i]); |
628 |
|
|
if ( diff <= ztol && states[i] == zcsMoving){ |
629 |
|
|
states[i] = zcsFixed; |
630 |
|
|
changed = true; |
631 |
|
|
} |
632 |
|
|
else if ( diff > ztol && states[i] == zcsFixed){ |
633 |
|
|
states[i] = zcsMoving; |
634 |
|
|
changed = true; |
635 |
|
|
} |
636 |
|
|
|
637 |
tim |
658 |
} |
638 |
|
|
|
639 |
tim |
676 |
return changed; |
640 |
tim |
658 |
} |
641 |
tim |
676 |
|
642 |
|
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
643 |
|
|
for(int i = 0; i < zconsMols.size(); i++) |
644 |
|
|
if (states[i] == zcsFixed) |
645 |
|
|
return true; |
646 |
|
|
|
647 |
|
|
return false; |
648 |
|
|
} |
649 |
|
|
|
650 |
|
|
|
651 |
|
|
/** |
652 |
|
|
* |
653 |
|
|
*/ |
654 |
|
|
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
655 |
|
|
for(int i = 0; i < zconsMols.size(); i++) |
656 |
|
|
if (states[i] == zcsMoving) |
657 |
|
|
return true; |
658 |
|
|
|
659 |
|
|
return false; |
660 |
|
|
|
661 |
|
|
} |