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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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|
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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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|
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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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|
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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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|
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if(!index){ |
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|
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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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} |
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else{ |
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|
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indexOfAllZConsMols = index->getIndexData(); |
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|
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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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|
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minIndex = indexOfAllZConsMols[0]; |
| 46 |
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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; |
| 50 |
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simError(); |
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} |
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|
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maxIndex = indexOfAllZConsMols[indexOfAllZConsMols.size() - 1]; |
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|
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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 |
| 60 |
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|
| 61 |
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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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} |
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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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|
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if(!data) { |
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|
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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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|
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sampleTime = dynamic_cast<DoubleData*>(data); |
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|
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if(!sampleTime){ |
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|
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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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} |
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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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} |
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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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|
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|
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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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} |
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else{ |
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|
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filename = dynamic_cast<StringData*>(data); |
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|
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if(!filename){ |
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|
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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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} |
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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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|
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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; |
| 138 |
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double COM[3]; |
| 139 |
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|
| 140 |
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for(int i = 0; i < nMols; i++){ |
| 141 |
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|
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searchResult = isZConstraintMol(&molecules[i]); |
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|
| 144 |
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if(searchResult > -1){ |
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|
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zconsMols.push_back(&molecules[i]); |
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massOfZConsMols.push_back(molecules[i].getTotalMass()); |
| 148 |
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|
| 149 |
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molecules[i].getCOM(COM); |
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} |
| 151 |
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else |
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{ |
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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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} |
| 158 |
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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()]; |
| 162 |
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|
| 163 |
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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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|
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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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#endif |
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|
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//get total number of unconstrained atoms |
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int nUnconsAtoms_local; |
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nUnconsAtoms_local = 0; |
| 178 |
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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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|
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#ifndef IS_MPI |
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totNumOfUnconsAtoms = nUnconsAtoms_local; |
| 183 |
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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 |
| 186 |
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|
| 187 |
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|
| 188 |
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|
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fzOut = new ZConsWriter(zconsOutput.c_str()); |
| 190 |
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|
| 191 |
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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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} |
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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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|
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if(indexOfZConsMols) |
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delete[] indexOfZConsMols; |
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|
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if(fzOut) |
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delete fzOut; |
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} |
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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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|
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zconsMols.clear(); |
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massOfZConsMols.clear(); |
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|
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unconsMols.clear(); |
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massOfUnconsMols.clear(); |
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|
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|
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//creat zconsMol and unconsMol lists |
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for(int i = 0; i < nMols; i++){ |
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|
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index = isZConstraintMol(&molecules[i]); |
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|
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if(index > -1){ |
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|
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zconsMols.push_back(&molecules[i]); |
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massOfZConsMols.push_back(molecules[i].getTotalMass()); |
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|
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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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|
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unconsMols.push_back(&molecules[i]); |
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massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
| 242 |
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|
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} |
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} |
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|
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//The reason to declare fz and indexOfZconsMols as pointer to array is |
| 247 |
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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; |
| 250 |
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|
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if(indexOfZConsMols) |
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delete[] indexOfZConsMols; |
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|
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if (zconsMols.size() > 0){ |
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fz = new double[zconsMols.size()]; |
| 256 |
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indexOfZConsMols = new int[zconsMols.size()]; |
| 257 |
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|
| 258 |
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if(!fz || !indexOfZConsMols){ |
| 259 |
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sprintf( painCave.errMsg, |
| 260 |
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"Memory allocation failure in class Zconstraint\n"); |
| 261 |
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painCave.isFatal = 1; |
| 262 |
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simError(); |
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} |
| 264 |
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|
| 265 |
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for(int i = 0; i < zconsMols.size(); i++){ |
| 266 |
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indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
| 267 |
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} |
| 268 |
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|
| 269 |
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} |
| 270 |
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else{ |
| 271 |
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fz = NULL; |
| 272 |
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indexOfZConsMols = NULL; |
| 273 |
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} |
| 274 |
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|
| 275 |
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} |
| 276 |
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|
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#endif |
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|
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/** Function Name: isZConstraintMol |
| 280 |
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** Parameter |
| 281 |
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** Molecule* mol |
| 282 |
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** Return value: |
| 283 |
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** -1, if the molecule is not z-constraint molecule, |
| 284 |
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** other non-negative values, its index in indexOfAllZConsMols vector |
| 285 |
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*/ |
| 286 |
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|
| 287 |
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template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
| 288 |
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{ |
| 289 |
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int index; |
| 290 |
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int low; |
| 291 |
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int high; |
| 292 |
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int mid; |
| 293 |
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|
| 294 |
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index = mol->getGlobalIndex(); |
| 295 |
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|
| 296 |
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low = 0; |
| 297 |
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high = indexOfAllZConsMols.size() - 1; |
| 298 |
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|
| 299 |
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//Binary Search (we have sorted the array) |
| 300 |
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while(low <= high){ |
| 301 |
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mid = (low + high) /2; |
| 302 |
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if (indexOfAllZConsMols[mid] == index) |
| 303 |
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return mid; |
| 304 |
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else if (indexOfAllZConsMols[mid] > index ) |
| 305 |
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high = mid -1; |
| 306 |
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else |
| 307 |
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low = mid + 1; |
| 308 |
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} |
| 309 |
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|
| 310 |
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return -1; |
| 311 |
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} |
| 312 |
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|
| 313 |
< |
/** |
| 314 |
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* Description: |
| 315 |
< |
* Reset the z coordinates |
| 316 |
< |
*/ |
| 317 |
< |
template<typename T> void ZConstraint<T>::integrate(){ |
| 318 |
< |
|
| 319 |
< |
//zero out the velocities of center of mass of unconstrained molecules |
| 320 |
< |
//and the velocities of center of mass of every single z-constrained molecueles |
| 321 |
< |
zeroOutVel(); |
| 322 |
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|
| 323 |
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T::integrate(); |
| 324 |
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|
| 325 |
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} |
| 326 |
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|
| 327 |
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|
| 328 |
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/** |
| 329 |
< |
* |
| 330 |
< |
* |
| 331 |
< |
* |
| 332 |
< |
* |
| 333 |
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*/ |
| 334 |
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|
| 335 |
< |
|
| 336 |
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template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
| 337 |
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|
| 338 |
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T::calcForce(calcPot, calcStress); |
| 339 |
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|
| 340 |
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if (checkZConsState()) |
| 341 |
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zeroOutVel(); |
| 342 |
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|
| 343 |
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//do zconstraint force; |
| 344 |
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if (haveFixedZMols()) |
| 345 |
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this->doZconstraintForce(); |
| 346 |
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|
| 347 |
< |
//use harmonical poteintial to move the molecules to the specified positions |
| 348 |
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if (haveMovingZMols()) |
| 349 |
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//this->doHarmonic(); |
| 350 |
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|
| 351 |
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fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
| 352 |
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|
| 353 |
< |
} |
| 354 |
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|
| 355 |
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template<typename T> double ZConstraint<T>::calcZSys() |
| 356 |
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{ |
| 357 |
< |
//calculate reference z coordinate for z-constraint molecules |
| 358 |
< |
double totalMass_local; |
| 359 |
< |
double totalMass; |
| 360 |
< |
double totalMZ_local; |
| 361 |
< |
double totalMZ; |
| 362 |
< |
double massOfUncons_local; |
| 363 |
< |
double massOfCurMol; |
| 364 |
< |
double COM[3]; |
| 365 |
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|
| 366 |
< |
totalMass_local = 0; |
| 367 |
< |
totalMass = 0; |
| 368 |
< |
totalMZ_local = 0; |
| 369 |
< |
totalMZ = 0; |
| 370 |
< |
massOfUncons_local = 0; |
| 371 |
< |
|
| 372 |
< |
|
| 373 |
< |
for(int i = 0; i < nMols; i++){ |
| 374 |
< |
massOfCurMol = molecules[i].getTotalMass(); |
| 375 |
< |
molecules[i].getCOM(COM); |
| 376 |
< |
|
| 377 |
< |
totalMass_local += massOfCurMol; |
| 378 |
< |
totalMZ_local += massOfCurMol * COM[whichDirection]; |
| 379 |
< |
|
| 380 |
< |
if(isZConstraintMol(&molecules[i]) == -1){ |
| 381 |
< |
|
| 382 |
< |
massOfUncons_local += massOfCurMol; |
| 383 |
< |
} |
| 384 |
< |
|
| 385 |
< |
} |
| 386 |
< |
|
| 387 |
< |
|
| 388 |
< |
#ifdef IS_MPI |
| 389 |
< |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 390 |
< |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 391 |
< |
MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 392 |
< |
#else |
| 393 |
< |
totalMass = totalMass_local; |
| 394 |
< |
totalMZ = totalMZ_local; |
| 395 |
< |
totalMassOfUncons = massOfUncons_local; |
| 396 |
< |
#endif |
| 397 |
< |
|
| 398 |
< |
double zsys; |
| 399 |
< |
zsys = totalMZ / totalMass; |
| 400 |
< |
|
| 401 |
< |
return zsys; |
| 402 |
< |
} |
| 403 |
< |
|
| 404 |
< |
/** |
| 405 |
< |
* |
| 406 |
< |
*/ |
| 407 |
< |
template<typename T> void ZConstraint<T>::thermalize( void ){ |
| 408 |
< |
|
| 409 |
< |
T::thermalize(); |
| 410 |
< |
zeroOutVel(); |
| 411 |
< |
} |
| 412 |
< |
|
| 413 |
< |
/** |
| 414 |
< |
* |
| 415 |
< |
* |
| 416 |
< |
* |
| 417 |
< |
*/ |
| 418 |
< |
|
| 419 |
< |
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
| 420 |
< |
|
| 421 |
< |
Atom** fixedZAtoms; |
| 422 |
< |
double COMvel[3]; |
| 423 |
< |
double vel[3]; |
| 424 |
< |
|
| 425 |
< |
//zero out the velocities of center of mass of fixed z-constrained molecules |
| 426 |
< |
|
| 427 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
| 428 |
< |
|
| 429 |
< |
if (states[i] == zcsFixed){ |
| 430 |
< |
|
| 431 |
< |
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 |
< |
} |
| 443 |
< |
|
| 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 |
< |
|
| 453 |
< |
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 |
< |
#else |
| 472 |
< |
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 |
< |
#endif |
| 475 |
< |
|
| 476 |
< |
double vzOfMovingMols; |
| 477 |
< |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
| 478 |
< |
|
| 479 |
< |
//modify the velocites of unconstrained molecules |
| 480 |
< |
Atom** unconsAtoms; |
| 481 |
< |
for(int i = 0; i < unconsMols.size(); i++){ |
| 482 |
< |
|
| 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 |
< |
} |
| 508 |
< |
|
| 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 |
< |
#ifdef IS_MPI |
| 560 |
< |
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 |
< |
#else |
| 563 |
< |
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 |
< |
|
| 620 |
< |
bool changed; |
| 621 |
< |
|
| 622 |
< |
changed = false; |
| 623 |
< |
|
| 624 |
< |
for(int i =0; i < zconsMols.size(); i++){ |
| 625 |
< |
|
| 626 |
< |
zconsMols[i]->getCOM(COM); |
| 627 |
< |
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 |
< |
} |
| 638 |
< |
|
| 639 |
< |
return changed; |
| 640 |
< |
} |
| 641 |
< |
|
| 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 |
< |
} |
| 1 |
> |
#include "Integrator.hpp" |
| 2 |
> |
#include "simError.h" |
| 3 |
> |
#include <math.h> |
| 4 |
> |
|
| 5 |
> |
const double INFINITE_TIME = 10e30; |
| 6 |
> |
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, |
| 7 |
> |
ForceFields* the_ff): T(theInfo, the_ff), |
| 8 |
> |
fzOut(NULL), |
| 9 |
> |
curZconsTime(0), |
| 10 |
> |
forcePolicy(NULL), |
| 11 |
> |
usingSMD(false), |
| 12 |
> |
hasZConsGap(false){ |
| 13 |
> |
//get properties from SimInfo |
| 14 |
> |
GenericData* data; |
| 15 |
> |
ZConsParaData* zConsParaData; |
| 16 |
> |
DoubleData* sampleTime; |
| 17 |
> |
DoubleData* tolerance; |
| 18 |
> |
DoubleData* gap; |
| 19 |
> |
DoubleData* fixtime; |
| 20 |
> |
StringData* policy; |
| 21 |
> |
StringData* filename; |
| 22 |
> |
IntData* smdFlag; |
| 23 |
> |
double COM[3]; |
| 24 |
> |
|
| 25 |
> |
//by default, the direction of constraint is z |
| 26 |
> |
// 0 --> x |
| 27 |
> |
// 1 --> y |
| 28 |
> |
// 2 --> z |
| 29 |
> |
whichDirection = 2; |
| 30 |
> |
|
| 31 |
> |
//estimate the force constant of harmonical potential |
| 32 |
> |
double Kb = 1.986E-3 ; //in kcal/K |
| 33 |
> |
|
| 34 |
> |
double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) / |
| 35 |
> |
2; |
| 36 |
> |
zForceConst = Kb * info->target_temp / (halfOfLargestBox * halfOfLargestBox); |
| 37 |
> |
|
| 38 |
> |
//creat force Subtraction policy |
| 39 |
> |
data = info->getProperty(ZCONSFORCEPOLICY_ID); |
| 40 |
> |
if (!data){ |
| 41 |
> |
sprintf(painCave.errMsg, |
| 42 |
> |
"ZConstraint Warning: User does not set force Subtraction policy, " |
| 43 |
> |
"PolicyByMass is used\n"); |
| 44 |
> |
painCave.isFatal = 0; |
| 45 |
> |
simError(); |
| 46 |
> |
|
| 47 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
| 48 |
> |
} |
| 49 |
> |
else{ |
| 50 |
> |
policy = dynamic_cast<StringData*>(data); |
| 51 |
> |
|
| 52 |
> |
if (!policy){ |
| 53 |
> |
sprintf(painCave.errMsg, |
| 54 |
> |
"ZConstraint Error: Convertion from GenericData to StringData failure, " |
| 55 |
> |
"PolicyByMass is used\n"); |
| 56 |
> |
painCave.isFatal = 0; |
| 57 |
> |
simError(); |
| 58 |
> |
|
| 59 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
| 60 |
> |
} |
| 61 |
> |
else{ |
| 62 |
> |
if (policy->getData() == "BYNUMBER") |
| 63 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByNumber(this); |
| 64 |
> |
else if (policy->getData() == "BYMASS") |
| 65 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
| 66 |
> |
else{ |
| 67 |
> |
sprintf(painCave.errMsg, |
| 68 |
> |
"ZConstraint Warning: unknown force Subtraction policy, " |
| 69 |
> |
"PolicyByMass is used\n"); |
| 70 |
> |
painCave.isFatal = 0; |
| 71 |
> |
simError(); |
| 72 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
| 73 |
> |
} |
| 74 |
> |
} |
| 75 |
> |
} |
| 76 |
> |
|
| 77 |
> |
|
| 78 |
> |
//retrieve sample time of z-contraint |
| 79 |
> |
data = info->getProperty(ZCONSTIME_ID); |
| 80 |
> |
|
| 81 |
> |
if (!data){ |
| 82 |
> |
sprintf(painCave.errMsg, |
| 83 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
| 84 |
> |
" , you must set sample time.\n"); |
| 85 |
> |
painCave.isFatal = 1; |
| 86 |
> |
simError(); |
| 87 |
> |
} |
| 88 |
> |
else{ |
| 89 |
> |
sampleTime = dynamic_cast<DoubleData*>(data); |
| 90 |
> |
|
| 91 |
> |
if (!sampleTime){ |
| 92 |
> |
sprintf(painCave.errMsg, |
| 93 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 94 |
> |
painCave.isFatal = 1; |
| 95 |
> |
simError(); |
| 96 |
> |
} |
| 97 |
> |
else{ |
| 98 |
> |
this->zconsTime = sampleTime->getData(); |
| 99 |
> |
} |
| 100 |
> |
} |
| 101 |
> |
|
| 102 |
> |
//retrieve output filename of z force |
| 103 |
> |
data = info->getProperty(ZCONSFILENAME_ID); |
| 104 |
> |
if (!data){ |
| 105 |
> |
sprintf(painCave.errMsg, |
| 106 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
| 107 |
> |
" , you must set output filename of z-force.\n"); |
| 108 |
> |
painCave.isFatal = 1; |
| 109 |
> |
simError(); |
| 110 |
> |
} |
| 111 |
> |
else{ |
| 112 |
> |
filename = dynamic_cast<StringData*>(data); |
| 113 |
> |
|
| 114 |
> |
if (!filename){ |
| 115 |
> |
sprintf(painCave.errMsg, |
| 116 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 117 |
> |
painCave.isFatal = 1; |
| 118 |
> |
simError(); |
| 119 |
> |
} |
| 120 |
> |
else{ |
| 121 |
> |
this->zconsOutput = filename->getData(); |
| 122 |
> |
} |
| 123 |
> |
} |
| 124 |
> |
|
| 125 |
> |
//retrieve tolerance for z-constraint molecuels |
| 126 |
> |
data = info->getProperty(ZCONSTOL_ID); |
| 127 |
> |
|
| 128 |
> |
if (!data){ |
| 129 |
> |
sprintf(painCave.errMsg, "ZConstraint error: can not get tolerance \n"); |
| 130 |
> |
painCave.isFatal = 1; |
| 131 |
> |
simError(); |
| 132 |
> |
} |
| 133 |
> |
else{ |
| 134 |
> |
tolerance = dynamic_cast<DoubleData*>(data); |
| 135 |
> |
|
| 136 |
> |
if (!tolerance){ |
| 137 |
> |
sprintf(painCave.errMsg, |
| 138 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 139 |
> |
painCave.isFatal = 1; |
| 140 |
> |
simError(); |
| 141 |
> |
} |
| 142 |
> |
else{ |
| 143 |
> |
this->zconsTol = tolerance->getData(); |
| 144 |
> |
} |
| 145 |
> |
} |
| 146 |
> |
|
| 147 |
> |
//quick hack here |
| 148 |
> |
data = info->getProperty(ZCONSGAP_ID); |
| 149 |
> |
|
| 150 |
> |
if (data){ |
| 151 |
> |
gap = dynamic_cast<DoubleData*>(data); |
| 152 |
> |
|
| 153 |
> |
if (!gap){ |
| 154 |
> |
sprintf(painCave.errMsg, |
| 155 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 156 |
> |
painCave.isFatal = 1; |
| 157 |
> |
simError(); |
| 158 |
> |
} |
| 159 |
> |
else{ |
| 160 |
> |
this->hasZConsGap = true; |
| 161 |
> |
this->zconsGap = gap->getData(); |
| 162 |
> |
} |
| 163 |
> |
} |
| 164 |
> |
|
| 165 |
> |
|
| 166 |
> |
|
| 167 |
> |
data = info->getProperty(ZCONSFIXTIME_ID); |
| 168 |
> |
|
| 169 |
> |
if (data){ |
| 170 |
> |
fixtime = dynamic_cast<DoubleData*>(data); |
| 171 |
> |
if (!fixtime){ |
| 172 |
> |
sprintf(painCave.errMsg, |
| 173 |
> |
"ZConstraint error: Can not get zconsFixTime from SimInfo\n"); |
| 174 |
> |
painCave.isFatal = 1; |
| 175 |
> |
simError(); |
| 176 |
> |
} |
| 177 |
> |
else{ |
| 178 |
> |
this->zconsFixTime = fixtime->getData(); |
| 179 |
> |
} |
| 180 |
> |
} |
| 181 |
> |
else if(hasZConsGap){ |
| 182 |
> |
sprintf(painCave.errMsg, |
| 183 |
> |
"ZConstraint error: must set fixtime if already set zconsGap\n"); |
| 184 |
> |
painCave.isFatal = 1; |
| 185 |
> |
simError(); |
| 186 |
> |
} |
| 187 |
> |
|
| 188 |
> |
|
| 189 |
> |
|
| 190 |
> |
data = info->getProperty(ZCONSUSINGSMD_ID); |
| 191 |
> |
|
| 192 |
> |
if (data){ |
| 193 |
> |
smdFlag = dynamic_cast<IntData*>(data); |
| 194 |
> |
|
| 195 |
> |
if (!smdFlag){ |
| 196 |
> |
sprintf(painCave.errMsg, |
| 197 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 198 |
> |
painCave.isFatal = 1; |
| 199 |
> |
simError(); |
| 200 |
> |
} |
| 201 |
> |
else{ |
| 202 |
> |
this->usingSMD= smdFlag->getData() ? true : false; |
| 203 |
> |
} |
| 204 |
> |
|
| 205 |
> |
} |
| 206 |
> |
|
| 207 |
> |
|
| 208 |
> |
|
| 209 |
> |
//retrieve index of z-constraint molecules |
| 210 |
> |
data = info->getProperty(ZCONSPARADATA_ID); |
| 211 |
> |
if (!data){ |
| 212 |
> |
sprintf(painCave.errMsg, |
| 213 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
| 214 |
> |
" , you must set index of z-constraint molecules.\n"); |
| 215 |
> |
painCave.isFatal = 1; |
| 216 |
> |
simError(); |
| 217 |
> |
} |
| 218 |
> |
else{ |
| 219 |
> |
zConsParaData = dynamic_cast<ZConsParaData*>(data); |
| 220 |
> |
|
| 221 |
> |
if (!zConsParaData){ |
| 222 |
> |
sprintf(painCave.errMsg, |
| 223 |
> |
"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n"); |
| 224 |
> |
painCave.isFatal = 1; |
| 225 |
> |
simError(); |
| 226 |
> |
} |
| 227 |
> |
else{ |
| 228 |
> |
parameters = zConsParaData->getData(); |
| 229 |
> |
|
| 230 |
> |
//check the range of zconsIndex |
| 231 |
> |
//and the minimum value of index is the first one (we already sorted the data) |
| 232 |
> |
//the maximum value of index is the last one |
| 233 |
> |
|
| 234 |
> |
int maxIndex; |
| 235 |
> |
int minIndex; |
| 236 |
> |
int totalNumMol; |
| 237 |
> |
|
| 238 |
> |
minIndex = (*parameters)[0].zconsIndex; |
| 239 |
> |
if (minIndex < 0){ |
| 240 |
> |
sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n"); |
| 241 |
> |
painCave.isFatal = 1; |
| 242 |
> |
simError(); |
| 243 |
> |
} |
| 244 |
> |
|
| 245 |
> |
maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
| 246 |
> |
|
| 247 |
> |
#ifndef IS_MPI |
| 248 |
> |
totalNumMol = nMols; |
| 249 |
> |
#else |
| 250 |
> |
totalNumMol = mpiSim->getTotNmol(); |
| 251 |
> |
#endif |
| 252 |
> |
|
| 253 |
> |
if (maxIndex > totalNumMol - 1){ |
| 254 |
> |
sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n"); |
| 255 |
> |
painCave.isFatal = 1; |
| 256 |
> |
simError(); |
| 257 |
> |
} |
| 258 |
> |
|
| 259 |
> |
//if user does not specify the zpos for the zconstraint molecule |
| 260 |
> |
//its initial z coordinate will be used as default |
| 261 |
> |
for (int i = 0; i < (int) (parameters->size()); i++){ |
| 262 |
> |
if (!(*parameters)[i].havingZPos){ |
| 263 |
> |
#ifndef IS_MPI |
| 264 |
> |
for (int j = 0; j < nMols; j++){ |
| 265 |
> |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
| 266 |
> |
molecules[j].getCOM(COM); |
| 267 |
> |
break; |
| 268 |
> |
} |
| 269 |
> |
} |
| 270 |
> |
#else |
| 271 |
> |
//query which processor current zconstraint molecule belongs to |
| 272 |
> |
int* MolToProcMap; |
| 273 |
> |
int whichNode; |
| 274 |
> |
|
| 275 |
> |
MolToProcMap = mpiSim->getMolToProcMap(); |
| 276 |
> |
whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
| 277 |
> |
|
| 278 |
> |
//broadcast the zpos of current z-contraint molecule |
| 279 |
> |
//the node which contain this |
| 280 |
> |
|
| 281 |
> |
if (worldRank == whichNode){ |
| 282 |
> |
for (int j = 0; j < nMols; j++) |
| 283 |
> |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
| 284 |
> |
molecules[j].getCOM(COM); |
| 285 |
> |
break; |
| 286 |
> |
} |
| 287 |
> |
} |
| 288 |
> |
|
| 289 |
> |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode, |
| 290 |
> |
MPI_COMM_WORLD); |
| 291 |
> |
#endif |
| 292 |
> |
|
| 293 |
> |
(*parameters)[i].zPos = COM[whichDirection]; |
| 294 |
> |
|
| 295 |
> |
sprintf(painCave.errMsg, |
| 296 |
> |
"ZConstraint warning: Does not specify zpos for z-constraint molecule " |
| 297 |
> |
"initial z coornidate will be used \n"); |
| 298 |
> |
painCave.isFatal = 0; |
| 299 |
> |
simError(); |
| 300 |
> |
} |
| 301 |
> |
} |
| 302 |
> |
}//end if (!zConsParaData) |
| 303 |
> |
|
| 304 |
> |
}//end if (!data) |
| 305 |
> |
|
| 306 |
> |
// |
| 307 |
> |
#ifdef IS_MPI |
| 308 |
> |
update(); |
| 309 |
> |
#else |
| 310 |
> |
int searchResult; |
| 311 |
> |
|
| 312 |
> |
for (int i = 0; i < nMols; i++){ |
| 313 |
> |
searchResult = isZConstraintMol(&molecules[i]); |
| 314 |
> |
|
| 315 |
> |
if (searchResult > -1){ |
| 316 |
> |
zconsMols.push_back(&molecules[i]); |
| 317 |
> |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
| 318 |
> |
|
| 319 |
> |
zPos.push_back((*parameters)[searchResult].zPos); |
| 320 |
> |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
| 321 |
> |
|
| 322 |
> |
if(usingSMD) |
| 323 |
> |
cantVel.push_back((*parameters)[searchResult].cantVel); |
| 324 |
> |
|
| 325 |
> |
} |
| 326 |
> |
else{ |
| 327 |
> |
unconsMols.push_back(&molecules[i]); |
| 328 |
> |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
| 329 |
> |
} |
| 330 |
> |
} |
| 331 |
> |
|
| 332 |
> |
fz.resize(zconsMols.size()); |
| 333 |
> |
curZPos.resize(zconsMols.size()); |
| 334 |
> |
indexOfZConsMols.resize(zconsMols.size()); |
| 335 |
> |
|
| 336 |
> |
//determine the states of z-constraint molecules |
| 337 |
> |
for (size_t i = 0; i < zconsMols.size(); i++){ |
| 338 |
> |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
| 339 |
> |
|
| 340 |
> |
zconsMols[i]->getCOM(COM); |
| 341 |
> |
|
| 342 |
> |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){ |
| 343 |
> |
states.push_back(zcsFixed); |
| 344 |
> |
|
| 345 |
> |
if (hasZConsGap) |
| 346 |
> |
endFixTime.push_back(info->getTime() + zconsFixTime); |
| 347 |
> |
} |
| 348 |
> |
else{ |
| 349 |
> |
states.push_back(zcsMoving); |
| 350 |
> |
|
| 351 |
> |
if (hasZConsGap) |
| 352 |
> |
endFixTime.push_back(INFINITE_TIME); |
| 353 |
> |
} |
| 354 |
> |
|
| 355 |
> |
if(usingSMD) |
| 356 |
> |
cantPos.push_back(COM[whichDirection]); |
| 357 |
> |
} |
| 358 |
> |
|
| 359 |
> |
#endif |
| 360 |
> |
|
| 361 |
> |
|
| 362 |
> |
//get total masss of unconstraint molecules |
| 363 |
> |
double totalMassOfUncons_local; |
| 364 |
> |
totalMassOfUncons_local = 0; |
| 365 |
> |
|
| 366 |
> |
for (size_t i = 0; i < unconsMols.size(); i++) |
| 367 |
> |
totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
| 368 |
> |
|
| 369 |
> |
#ifndef IS_MPI |
| 370 |
> |
totalMassOfUncons = totalMassOfUncons_local; |
| 371 |
> |
#else |
| 372 |
> |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE, |
| 373 |
> |
MPI_SUM, MPI_COMM_WORLD); |
| 374 |
> |
#endif |
| 375 |
> |
|
| 376 |
> |
//get total number of unconstrained atoms |
| 377 |
> |
int nUnconsAtoms_local; |
| 378 |
> |
nUnconsAtoms_local = 0; |
| 379 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++) |
| 380 |
> |
nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
| 381 |
> |
|
| 382 |
> |
#ifndef IS_MPI |
| 383 |
> |
totNumOfUnconsAtoms = nUnconsAtoms_local; |
| 384 |
> |
#else |
| 385 |
> |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT, MPI_SUM, |
| 386 |
> |
MPI_COMM_WORLD); |
| 387 |
> |
#endif |
| 388 |
> |
|
| 389 |
> |
forcePolicy->update(); |
| 390 |
> |
} |
| 391 |
> |
|
| 392 |
> |
template<typename T> ZConstraint<T>::~ZConstraint(){ |
| 393 |
> |
|
| 394 |
> |
if (fzOut){ |
| 395 |
> |
delete fzOut; |
| 396 |
> |
} |
| 397 |
> |
|
| 398 |
> |
if (forcePolicy){ |
| 399 |
> |
delete forcePolicy; |
| 400 |
> |
} |
| 401 |
> |
} |
| 402 |
> |
|
| 403 |
> |
|
| 404 |
> |
/** |
| 405 |
> |
* |
| 406 |
> |
*/ |
| 407 |
> |
|
| 408 |
> |
#ifdef IS_MPI |
| 409 |
> |
template<typename T> void ZConstraint<T>::update(){ |
| 410 |
> |
double COM[3]; |
| 411 |
> |
int index; |
| 412 |
> |
|
| 413 |
> |
zconsMols.clear(); |
| 414 |
> |
massOfZConsMols.clear(); |
| 415 |
> |
zPos.clear(); |
| 416 |
> |
kz.clear(); |
| 417 |
> |
cantPos.clear(); |
| 418 |
> |
cantVel.clear(); |
| 419 |
> |
|
| 420 |
> |
unconsMols.clear(); |
| 421 |
> |
massOfUnconsMols.clear(); |
| 422 |
> |
|
| 423 |
> |
|
| 424 |
> |
//creat zconsMol and unconsMol lists |
| 425 |
> |
for (int i = 0; i < nMols; i++){ |
| 426 |
> |
index = isZConstraintMol(&molecules[i]); |
| 427 |
> |
|
| 428 |
> |
if (index > -1){ |
| 429 |
> |
zconsMols.push_back(&molecules[i]); |
| 430 |
> |
zPos.push_back((*parameters)[index].zPos); |
| 431 |
> |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
| 432 |
> |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
| 433 |
> |
|
| 434 |
> |
if(usingSMD) |
| 435 |
> |
cantVel.push_back((*parameters)[index].cantVel); |
| 436 |
> |
|
| 437 |
> |
} |
| 438 |
> |
else{ |
| 439 |
> |
unconsMols.push_back(&molecules[i]); |
| 440 |
> |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
| 441 |
> |
} |
| 442 |
> |
} |
| 443 |
> |
|
| 444 |
> |
fz.resize(zconsMols.size()); |
| 445 |
> |
curZPos.resize(zconsMols.size()); |
| 446 |
> |
indexOfZConsMols.resize(zconsMols.size()); |
| 447 |
> |
|
| 448 |
> |
for (size_t i = 0; i < zconsMols.size(); i++){ |
| 449 |
> |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
| 450 |
> |
} |
| 451 |
> |
|
| 452 |
> |
//determine the states of z-constraint molecules |
| 453 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
| 454 |
> |
|
| 455 |
> |
zconsMols[i]->getCOM(COM); |
| 456 |
> |
|
| 457 |
> |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){ |
| 458 |
> |
states.push_back(zcsFixed); |
| 459 |
> |
|
| 460 |
> |
if (hasZConsGap) |
| 461 |
> |
endFixTime.push_back(info->getTime() + zconsFixTime); |
| 462 |
> |
} |
| 463 |
> |
else{ |
| 464 |
> |
states.push_back(zcsMoving); |
| 465 |
> |
|
| 466 |
> |
if (hasZConsGap) |
| 467 |
> |
endFixTime.push_back(INFINITE_TIME); |
| 468 |
> |
} |
| 469 |
> |
|
| 470 |
> |
if(usingSMD) |
| 471 |
> |
cantPos.push_back(COM[whichDirection]); |
| 472 |
> |
} |
| 473 |
> |
// |
| 474 |
> |
forcePolicy->update(); |
| 475 |
> |
} |
| 476 |
> |
|
| 477 |
> |
#endif |
| 478 |
> |
|
| 479 |
> |
/** |
| 480 |
> |
* Function Name: isZConstraintMol |
| 481 |
> |
* Parameter |
| 482 |
> |
* Molecule* mol |
| 483 |
> |
* Return value: |
| 484 |
> |
* -1, if the molecule is not z-constraint molecule, |
| 485 |
> |
* other non-negative values, its index in indexOfAllZConsMols vector |
| 486 |
> |
*/ |
| 487 |
> |
|
| 488 |
> |
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol){ |
| 489 |
> |
int index; |
| 490 |
> |
int low; |
| 491 |
> |
int high; |
| 492 |
> |
int mid; |
| 493 |
> |
|
| 494 |
> |
index = mol->getGlobalIndex(); |
| 495 |
> |
|
| 496 |
> |
low = 0; |
| 497 |
> |
high = parameters->size() - 1; |
| 498 |
> |
|
| 499 |
> |
//Binary Search (we have sorted the array) |
| 500 |
> |
while (low <= high){ |
| 501 |
> |
mid = (low + high) / 2; |
| 502 |
> |
if ((*parameters)[mid].zconsIndex == index) |
| 503 |
> |
return mid; |
| 504 |
> |
else if ((*parameters)[mid].zconsIndex > index) |
| 505 |
> |
high = mid - 1; |
| 506 |
> |
else |
| 507 |
> |
low = mid + 1; |
| 508 |
> |
} |
| 509 |
> |
|
| 510 |
> |
return -1; |
| 511 |
> |
} |
| 512 |
> |
|
| 513 |
> |
template<typename T> void ZConstraint<T>::integrate(){ |
| 514 |
> |
// creat zconsWriter |
| 515 |
> |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
| 516 |
> |
|
| 517 |
> |
if (!fzOut){ |
| 518 |
> |
sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n"); |
| 519 |
> |
painCave.isFatal = 1; |
| 520 |
> |
simError(); |
| 521 |
> |
} |
| 522 |
> |
|
| 523 |
> |
//zero out the velocities of center of mass of unconstrained molecules |
| 524 |
> |
//and the velocities of center of mass of every single z-constrained molecueles |
| 525 |
> |
zeroOutVel(); |
| 526 |
> |
|
| 527 |
> |
curZconsTime = zconsTime + info->getTime(); |
| 528 |
> |
|
| 529 |
> |
T::integrate(); |
| 530 |
> |
} |
| 531 |
> |
|
| 532 |
> |
|
| 533 |
> |
/** |
| 534 |
> |
* |
| 535 |
> |
* |
| 536 |
> |
* |
| 537 |
> |
* |
| 538 |
> |
*/ |
| 539 |
> |
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
| 540 |
> |
double zsys; |
| 541 |
> |
double COM[3]; |
| 542 |
> |
double force[3]; |
| 543 |
> |
double zSysCOMVel; |
| 544 |
> |
|
| 545 |
> |
T::calcForce(calcPot, calcStress); |
| 546 |
> |
|
| 547 |
> |
|
| 548 |
> |
if (hasZConsGap){ |
| 549 |
> |
updateZPos(); |
| 550 |
> |
} |
| 551 |
> |
|
| 552 |
> |
if (checkZConsState()){ |
| 553 |
> |
zeroOutVel(); |
| 554 |
> |
forcePolicy->update(); |
| 555 |
> |
} |
| 556 |
> |
|
| 557 |
> |
zsys = calcZSys(); |
| 558 |
> |
zSysCOMVel = calcSysCOMVel(); |
| 559 |
> |
#ifdef IS_MPI |
| 560 |
> |
if (worldRank == 0){ |
| 561 |
> |
#endif |
| 562 |
> |
//cout << "---------------------------------------------------------------------" <<endl; |
| 563 |
> |
//cout << "current time: " << info->getTime() << endl; |
| 564 |
> |
//cout << "center of mass at z: " << zsys << endl; |
| 565 |
> |
//cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
| 566 |
> |
|
| 567 |
> |
#ifdef IS_MPI |
| 568 |
> |
} |
| 569 |
> |
#endif |
| 570 |
> |
|
| 571 |
> |
//do zconstraint force; |
| 572 |
> |
if (haveFixedZMols()){ |
| 573 |
> |
this->doZconstraintForce(); |
| 574 |
> |
} |
| 575 |
> |
|
| 576 |
> |
//use external force to move the molecules to the specified positions |
| 577 |
> |
if (haveMovingZMols()){ |
| 578 |
> |
if (usingSMD) |
| 579 |
> |
this->doHarmonic(cantPos); |
| 580 |
> |
else |
| 581 |
> |
this->doHarmonic(zPos); |
| 582 |
> |
} |
| 583 |
> |
|
| 584 |
> |
//write out forces and current positions of z-constraint molecules |
| 585 |
> |
if (info->getTime() >= curZconsTime){ |
| 586 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
| 587 |
> |
zconsMols[i]->getCOM(COM); |
| 588 |
> |
curZPos[i] = COM[whichDirection]; |
| 589 |
> |
|
| 590 |
> |
//if the z-constraint molecule is still moving, just record its force |
| 591 |
> |
if (states[i] == zcsMoving){ |
| 592 |
> |
fz[i] = 0; |
| 593 |
> |
Atom** movingZAtoms; |
| 594 |
> |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
| 595 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
| 596 |
> |
movingZAtoms[j]->getFrc(force); |
| 597 |
> |
fz[i] += force[whichDirection]; |
| 598 |
> |
} |
| 599 |
> |
} |
| 600 |
> |
} |
| 601 |
> |
fzOut->writeFZ(info->getTime(), zconsMols.size(), &indexOfZConsMols[0], &fz[0], |
| 602 |
> |
&curZPos[0], &zPos[0]); |
| 603 |
> |
curZconsTime += zconsTime; |
| 604 |
> |
} |
| 605 |
> |
|
| 606 |
> |
zSysCOMVel = calcSysCOMVel(); |
| 607 |
> |
#ifdef IS_MPI |
| 608 |
> |
if (worldRank == 0){ |
| 609 |
> |
#endif |
| 610 |
> |
//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
| 611 |
> |
#ifdef IS_MPI |
| 612 |
> |
} |
| 613 |
> |
#endif |
| 614 |
> |
} |
| 615 |
> |
|
| 616 |
> |
|
| 617 |
> |
/** |
| 618 |
> |
* |
| 619 |
> |
*/ |
| 620 |
> |
|
| 621 |
> |
template<typename T> double ZConstraint<T>::calcZSys(){ |
| 622 |
> |
//calculate reference z coordinate for z-constraint molecules |
| 623 |
> |
double totalMass_local; |
| 624 |
> |
double totalMass; |
| 625 |
> |
double totalMZ_local; |
| 626 |
> |
double totalMZ; |
| 627 |
> |
double massOfCurMol; |
| 628 |
> |
double COM[3]; |
| 629 |
> |
|
| 630 |
> |
totalMass_local = 0; |
| 631 |
> |
totalMZ_local = 0; |
| 632 |
> |
|
| 633 |
> |
for (int i = 0; i < nMols; i++){ |
| 634 |
> |
massOfCurMol = molecules[i].getTotalMass(); |
| 635 |
> |
molecules[i].getCOM(COM); |
| 636 |
> |
|
| 637 |
> |
totalMass_local += massOfCurMol; |
| 638 |
> |
totalMZ_local += massOfCurMol * COM[whichDirection]; |
| 639 |
> |
} |
| 640 |
> |
|
| 641 |
> |
|
| 642 |
> |
#ifdef IS_MPI |
| 643 |
> |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM, |
| 644 |
> |
MPI_COMM_WORLD); |
| 645 |
> |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 646 |
> |
#else |
| 647 |
> |
totalMass = totalMass_local; |
| 648 |
> |
totalMZ = totalMZ_local; |
| 649 |
> |
#endif |
| 650 |
> |
|
| 651 |
> |
double zsys; |
| 652 |
> |
zsys = totalMZ / totalMass; |
| 653 |
> |
|
| 654 |
> |
return zsys; |
| 655 |
> |
} |
| 656 |
> |
|
| 657 |
> |
/** |
| 658 |
> |
* |
| 659 |
> |
*/ |
| 660 |
> |
template<typename T> void ZConstraint<T>::thermalize(void){ |
| 661 |
> |
T::thermalize(); |
| 662 |
> |
zeroOutVel(); |
| 663 |
> |
} |
| 664 |
> |
|
| 665 |
> |
/** |
| 666 |
> |
* |
| 667 |
> |
*/ |
| 668 |
> |
|
| 669 |
> |
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
| 670 |
> |
Atom** fixedZAtoms; |
| 671 |
> |
double COMvel[3]; |
| 672 |
> |
double vel[3]; |
| 673 |
> |
double zSysCOMVel; |
| 674 |
> |
|
| 675 |
> |
//zero out the velocities of center of mass of fixed z-constrained molecules |
| 676 |
> |
|
| 677 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
| 678 |
> |
if (states[i] == zcsFixed){ |
| 679 |
> |
zconsMols[i]->getCOMvel(COMvel); |
| 680 |
> |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
| 681 |
> |
|
| 682 |
> |
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
| 683 |
> |
|
| 684 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
| 685 |
> |
fixedZAtoms[j]->getVel(vel); |
| 686 |
> |
vel[whichDirection] -= COMvel[whichDirection]; |
| 687 |
> |
fixedZAtoms[j]->setVel(vel); |
| 688 |
> |
} |
| 689 |
> |
|
| 690 |
> |
zconsMols[i]->getCOMvel(COMvel); |
| 691 |
> |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
| 692 |
> |
} |
| 693 |
> |
} |
| 694 |
> |
|
| 695 |
> |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
| 696 |
> |
|
| 697 |
> |
zSysCOMVel = calcSysCOMVel(); |
| 698 |
> |
#ifdef IS_MPI |
| 699 |
> |
if (worldRank == 0){ |
| 700 |
> |
#endif |
| 701 |
> |
//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
| 702 |
> |
#ifdef IS_MPI |
| 703 |
> |
} |
| 704 |
> |
#endif |
| 705 |
> |
|
| 706 |
> |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
| 707 |
> |
double MVzOfMovingMols_local; |
| 708 |
> |
double MVzOfMovingMols; |
| 709 |
> |
double totalMassOfMovingZMols_local; |
| 710 |
> |
double totalMassOfMovingZMols; |
| 711 |
> |
|
| 712 |
> |
MVzOfMovingMols_local = 0; |
| 713 |
> |
totalMassOfMovingZMols_local = 0; |
| 714 |
> |
|
| 715 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
| 716 |
> |
unconsMols[i]->getCOMvel(COMvel); |
| 717 |
> |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
| 718 |
> |
} |
| 719 |
> |
|
| 720 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
| 721 |
> |
if (states[i] == zcsMoving){ |
| 722 |
> |
zconsMols[i]->getCOMvel(COMvel); |
| 723 |
> |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
| 724 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
| 725 |
> |
} |
| 726 |
> |
} |
| 727 |
> |
|
| 728 |
> |
#ifndef IS_MPI |
| 729 |
> |
MVzOfMovingMols = MVzOfMovingMols_local; |
| 730 |
> |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
| 731 |
> |
#else |
| 732 |
> |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE, |
| 733 |
> |
MPI_SUM, MPI_COMM_WORLD); |
| 734 |
> |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, |
| 735 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 736 |
> |
#endif |
| 737 |
> |
|
| 738 |
> |
double vzOfMovingMols; |
| 739 |
> |
vzOfMovingMols = MVzOfMovingMols / |
| 740 |
> |
(totalMassOfUncons + totalMassOfMovingZMols); |
| 741 |
> |
|
| 742 |
> |
//modify the velocites of unconstrained molecules |
| 743 |
> |
Atom** unconsAtoms; |
| 744 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
| 745 |
> |
unconsAtoms = unconsMols[i]->getMyAtoms(); |
| 746 |
> |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
| 747 |
> |
unconsAtoms[j]->getVel(vel); |
| 748 |
> |
vel[whichDirection] -= vzOfMovingMols; |
| 749 |
> |
unconsAtoms[j]->setVel(vel); |
| 750 |
> |
} |
| 751 |
> |
} |
| 752 |
> |
|
| 753 |
> |
//modify the velocities of moving z-constrained molecuels |
| 754 |
> |
Atom** movingZAtoms; |
| 755 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
| 756 |
> |
if (states[i] == zcsMoving){ |
| 757 |
> |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
| 758 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
| 759 |
> |
movingZAtoms[j]->getVel(vel); |
| 760 |
> |
vel[whichDirection] -= vzOfMovingMols; |
| 761 |
> |
movingZAtoms[j]->setVel(vel); |
| 762 |
> |
} |
| 763 |
> |
} |
| 764 |
> |
} |
| 765 |
> |
|
| 766 |
> |
|
| 767 |
> |
zSysCOMVel = calcSysCOMVel(); |
| 768 |
> |
#ifdef IS_MPI |
| 769 |
> |
if (worldRank == 0){ |
| 770 |
> |
#endif |
| 771 |
> |
//cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
| 772 |
> |
#ifdef IS_MPI |
| 773 |
> |
} |
| 774 |
> |
#endif |
| 775 |
> |
} |
| 776 |
> |
|
| 777 |
> |
/** |
| 778 |
> |
* |
| 779 |
> |
*/ |
| 780 |
> |
|
| 781 |
> |
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
| 782 |
> |
Atom** zconsAtoms; |
| 783 |
> |
double totalFZ; |
| 784 |
> |
double totalFZ_local; |
| 785 |
> |
double COM[3]; |
| 786 |
> |
double force[3]; |
| 787 |
> |
|
| 788 |
> |
//constrain the molecules which do not reach the specified positions |
| 789 |
> |
|
| 790 |
> |
//Zero Out the force of z-contrained molecules |
| 791 |
> |
totalFZ_local = 0; |
| 792 |
> |
|
| 793 |
> |
//calculate the total z-contrained force of fixed z-contrained molecules |
| 794 |
> |
|
| 795 |
> |
//cout << "before zero out z-constraint force on fixed z-constraint molecuels " |
| 796 |
> |
// << "total force is " << calcTotalForce() << endl; |
| 797 |
> |
|
| 798 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
| 799 |
> |
if (states[i] == zcsFixed){ |
| 800 |
> |
zconsMols[i]->getCOM(COM); |
| 801 |
> |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
| 802 |
> |
|
| 803 |
> |
fz[i] = 0; |
| 804 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
| 805 |
> |
zconsAtoms[j]->getFrc(force); |
| 806 |
> |
fz[i] += force[whichDirection]; |
| 807 |
> |
} |
| 808 |
> |
totalFZ_local += fz[i]; |
| 809 |
> |
|
| 810 |
> |
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
| 811 |
> |
// <<"\tcurrent zpos: " << COM[whichDirection] |
| 812 |
> |
// << "\tcurrent fz: " <<fz[i] << endl; |
| 813 |
> |
} |
| 814 |
> |
} |
| 815 |
> |
|
| 816 |
> |
//calculate total z-constraint force |
| 817 |
> |
#ifdef IS_MPI |
| 818 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 819 |
> |
#else |
| 820 |
> |
totalFZ = totalFZ_local; |
| 821 |
> |
#endif |
| 822 |
> |
|
| 823 |
> |
|
| 824 |
> |
// apply negative to fixed z-constrained molecues; |
| 825 |
> |
force[0] = 0; |
| 826 |
> |
force[1] = 0; |
| 827 |
> |
force[2] = 0; |
| 828 |
> |
|
| 829 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
| 830 |
> |
if (states[i] == zcsFixed){ |
| 831 |
> |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
| 832 |
> |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
| 833 |
> |
|
| 834 |
> |
for (int j = 0; j < nAtomOfCurZConsMol; j++){ |
| 835 |
> |
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
| 836 |
> |
force[whichDirection] = -forcePolicy->getZFOfFixedZMols(zconsMols[i], |
| 837 |
> |
zconsAtoms[j], |
| 838 |
> |
fz[i]); |
| 839 |
> |
zconsAtoms[j]->addFrc(force); |
| 840 |
> |
} |
| 841 |
> |
} |
| 842 |
> |
} |
| 843 |
> |
|
| 844 |
> |
//cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
| 845 |
> |
// << "total force is " << calcTotalForce() << endl; |
| 846 |
> |
|
| 847 |
> |
|
| 848 |
> |
force[0] = 0; |
| 849 |
> |
force[1] = 0; |
| 850 |
> |
force[2] = 0; |
| 851 |
> |
|
| 852 |
> |
//modify the forces of unconstrained molecules |
| 853 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
| 854 |
> |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
| 855 |
> |
|
| 856 |
> |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
| 857 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
| 858 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j], |
| 859 |
> |
totalFZ); |
| 860 |
> |
unconsAtoms[j]->addFrc(force); |
| 861 |
> |
} |
| 862 |
> |
} |
| 863 |
> |
|
| 864 |
> |
//modify the forces of moving z-constrained molecules |
| 865 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
| 866 |
> |
if (states[i] == zcsMoving){ |
| 867 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
| 868 |
> |
|
| 869 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
| 870 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
| 871 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j], |
| 872 |
> |
totalFZ); |
| 873 |
> |
movingZAtoms[j]->addFrc(force); |
| 874 |
> |
} |
| 875 |
> |
} |
| 876 |
> |
} |
| 877 |
> |
// cout << "after substracting z-constraint force from moving molecuels " |
| 878 |
> |
// << "total force is " << calcTotalForce() << endl; |
| 879 |
> |
} |
| 880 |
> |
|
| 881 |
> |
/** |
| 882 |
> |
* |
| 883 |
> |
* |
| 884 |
> |
*/ |
| 885 |
> |
|
| 886 |
> |
template<typename T> void ZConstraint<T>::doHarmonic(vector<double>& resPos){ |
| 887 |
> |
double force[3]; |
| 888 |
> |
double harmonicU; |
| 889 |
> |
double harmonicF; |
| 890 |
> |
double COM[3]; |
| 891 |
> |
double diff; |
| 892 |
> |
double totalFZ_local; |
| 893 |
> |
double totalFZ; |
| 894 |
> |
|
| 895 |
> |
force[0] = 0; |
| 896 |
> |
force[1] = 0; |
| 897 |
> |
force[2] = 0; |
| 898 |
> |
|
| 899 |
> |
totalFZ_local = 0; |
| 900 |
> |
|
| 901 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
| 902 |
> |
if (states[i] == zcsMoving){ |
| 903 |
> |
zconsMols[i]->getCOM(COM); |
| 904 |
> |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
| 905 |
> |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
| 906 |
> |
|
| 907 |
> |
diff = COM[whichDirection] - resPos[i]; |
| 908 |
> |
|
| 909 |
> |
harmonicU = 0.5 * kz[i] * diff * diff; |
| 910 |
> |
info->lrPot += harmonicU; |
| 911 |
> |
|
| 912 |
> |
harmonicF = -kz[i] * diff; |
| 913 |
> |
totalFZ_local += harmonicF; |
| 914 |
> |
|
| 915 |
> |
//adjust force |
| 916 |
> |
|
| 917 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
| 918 |
> |
|
| 919 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
| 920 |
> |
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
| 921 |
> |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], |
| 922 |
> |
movingZAtoms[j], |
| 923 |
> |
harmonicF); |
| 924 |
> |
movingZAtoms[j]->addFrc(force); |
| 925 |
> |
} |
| 926 |
> |
} |
| 927 |
> |
} |
| 928 |
> |
|
| 929 |
> |
#ifndef IS_MPI |
| 930 |
> |
totalFZ = totalFZ_local; |
| 931 |
> |
#else |
| 932 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 933 |
> |
#endif |
| 934 |
> |
|
| 935 |
> |
//cout << "before substracting harmonic force from moving molecuels " |
| 936 |
> |
// << "total force is " << calcTotalForce() << endl; |
| 937 |
> |
|
| 938 |
> |
force[0] = 0; |
| 939 |
> |
force[1] = 0; |
| 940 |
> |
force[2] = 0; |
| 941 |
> |
|
| 942 |
> |
//modify the forces of unconstrained molecules |
| 943 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
| 944 |
> |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
| 945 |
> |
|
| 946 |
> |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
| 947 |
> |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
| 948 |
> |
force[whichDirection] = -forcePolicy->getHFOfUnconsMols(unconsAtoms[j], |
| 949 |
> |
totalFZ); |
| 950 |
> |
unconsAtoms[j]->addFrc(force); |
| 951 |
> |
} |
| 952 |
> |
} |
| 953 |
> |
|
| 954 |
> |
//cout << "after substracting harmonic force from moving molecuels " |
| 955 |
> |
// << "total force is " << calcTotalForce() << endl; |
| 956 |
> |
} |
| 957 |
> |
|
| 958 |
> |
/** |
| 959 |
> |
* |
| 960 |
> |
*/ |
| 961 |
> |
|
| 962 |
> |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
| 963 |
> |
double COM[3]; |
| 964 |
> |
double diff; |
| 965 |
> |
|
| 966 |
> |
int changed_local; |
| 967 |
> |
int changed; |
| 968 |
> |
|
| 969 |
> |
changed_local = 0; |
| 970 |
> |
|
| 971 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
| 972 |
> |
zconsMols[i]->getCOM(COM); |
| 973 |
> |
diff = fabs(COM[whichDirection] - zPos[i]); |
| 974 |
> |
if (diff <= zconsTol && states[i] == zcsMoving){ |
| 975 |
> |
states[i] = zcsFixed; |
| 976 |
> |
changed_local = 1; |
| 977 |
> |
|
| 978 |
> |
if (hasZConsGap) |
| 979 |
> |
endFixTime[i] = info->getTime() + zconsFixTime; |
| 980 |
> |
} |
| 981 |
> |
else if (diff > zconsTol && states[i] == zcsFixed){ |
| 982 |
> |
states[i] = zcsMoving; |
| 983 |
> |
changed_local = 1; |
| 984 |
> |
|
| 985 |
> |
if (hasZConsGap) |
| 986 |
> |
endFixTime[i] = INFINITE_TIME; |
| 987 |
> |
} |
| 988 |
> |
} |
| 989 |
> |
|
| 990 |
> |
#ifndef IS_MPI |
| 991 |
> |
changed = changed_local; |
| 992 |
> |
#else |
| 993 |
> |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 994 |
> |
#endif |
| 995 |
> |
|
| 996 |
> |
return (changed > 0); |
| 997 |
> |
} |
| 998 |
> |
|
| 999 |
> |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
| 1000 |
> |
int havingFixed_local; |
| 1001 |
> |
int havingFixed; |
| 1002 |
> |
|
| 1003 |
> |
havingFixed_local = 0; |
| 1004 |
> |
|
| 1005 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++) |
| 1006 |
> |
if (states[i] == zcsFixed){ |
| 1007 |
> |
havingFixed_local = 1; |
| 1008 |
> |
break; |
| 1009 |
> |
} |
| 1010 |
> |
|
| 1011 |
> |
#ifndef IS_MPI |
| 1012 |
> |
havingFixed = havingFixed_local; |
| 1013 |
> |
#else |
| 1014 |
> |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM, |
| 1015 |
> |
MPI_COMM_WORLD); |
| 1016 |
> |
#endif |
| 1017 |
> |
|
| 1018 |
> |
return (havingFixed > 0); |
| 1019 |
> |
} |
| 1020 |
> |
|
| 1021 |
> |
|
| 1022 |
> |
/** |
| 1023 |
> |
* |
| 1024 |
> |
*/ |
| 1025 |
> |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
| 1026 |
> |
int havingMoving_local; |
| 1027 |
> |
int havingMoving; |
| 1028 |
> |
|
| 1029 |
> |
havingMoving_local = 0; |
| 1030 |
> |
|
| 1031 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++) |
| 1032 |
> |
if (states[i] == zcsMoving){ |
| 1033 |
> |
havingMoving_local = 1; |
| 1034 |
> |
break; |
| 1035 |
> |
} |
| 1036 |
> |
|
| 1037 |
> |
#ifndef IS_MPI |
| 1038 |
> |
havingMoving = havingMoving_local; |
| 1039 |
> |
#else |
| 1040 |
> |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM, |
| 1041 |
> |
MPI_COMM_WORLD); |
| 1042 |
> |
#endif |
| 1043 |
> |
|
| 1044 |
> |
return (havingMoving > 0); |
| 1045 |
> |
} |
| 1046 |
> |
|
| 1047 |
> |
/** |
| 1048 |
> |
* |
| 1049 |
> |
*/ |
| 1050 |
> |
|
| 1051 |
> |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel(){ |
| 1052 |
> |
double MVzOfMovingMols_local; |
| 1053 |
> |
double MVzOfMovingMols; |
| 1054 |
> |
double totalMassOfMovingZMols_local; |
| 1055 |
> |
double totalMassOfMovingZMols; |
| 1056 |
> |
double COMvel[3]; |
| 1057 |
> |
|
| 1058 |
> |
MVzOfMovingMols_local = 0; |
| 1059 |
> |
totalMassOfMovingZMols_local = 0; |
| 1060 |
> |
|
| 1061 |
> |
for (int i = 0; i < unconsMols.size(); i++){ |
| 1062 |
> |
unconsMols[i]->getCOMvel(COMvel); |
| 1063 |
> |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
| 1064 |
> |
} |
| 1065 |
> |
|
| 1066 |
> |
for (int i = 0; i < zconsMols.size(); i++){ |
| 1067 |
> |
if (states[i] == zcsMoving){ |
| 1068 |
> |
zconsMols[i]->getCOMvel(COMvel); |
| 1069 |
> |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
| 1070 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
| 1071 |
> |
} |
| 1072 |
> |
} |
| 1073 |
> |
|
| 1074 |
> |
#ifndef IS_MPI |
| 1075 |
> |
MVzOfMovingMols = MVzOfMovingMols_local; |
| 1076 |
> |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
| 1077 |
> |
#else |
| 1078 |
> |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE, |
| 1079 |
> |
MPI_SUM, MPI_COMM_WORLD); |
| 1080 |
> |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, |
| 1081 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 1082 |
> |
#endif |
| 1083 |
> |
|
| 1084 |
> |
double vzOfMovingMols; |
| 1085 |
> |
vzOfMovingMols = MVzOfMovingMols / |
| 1086 |
> |
(totalMassOfUncons + totalMassOfMovingZMols); |
| 1087 |
> |
|
| 1088 |
> |
return vzOfMovingMols; |
| 1089 |
> |
} |
| 1090 |
> |
|
| 1091 |
> |
/** |
| 1092 |
> |
* |
| 1093 |
> |
*/ |
| 1094 |
> |
|
| 1095 |
> |
template<typename T> double ZConstraint<T>::calcSysCOMVel(){ |
| 1096 |
> |
double COMvel[3]; |
| 1097 |
> |
double tempMVz_local; |
| 1098 |
> |
double tempMVz; |
| 1099 |
> |
double massOfZCons_local; |
| 1100 |
> |
double massOfZCons; |
| 1101 |
> |
|
| 1102 |
> |
|
| 1103 |
> |
tempMVz_local = 0; |
| 1104 |
> |
|
| 1105 |
> |
for (int i = 0 ; i < nMols; i++){ |
| 1106 |
> |
molecules[i].getCOMvel(COMvel); |
| 1107 |
> |
tempMVz_local += molecules[i].getTotalMass() * COMvel[whichDirection]; |
| 1108 |
> |
} |
| 1109 |
> |
|
| 1110 |
> |
massOfZCons_local = 0; |
| 1111 |
> |
|
| 1112 |
> |
for (int i = 0; i < (int) (massOfZConsMols.size()); i++){ |
| 1113 |
> |
massOfZCons_local += massOfZConsMols[i]; |
| 1114 |
> |
} |
| 1115 |
> |
#ifndef IS_MPI |
| 1116 |
> |
massOfZCons = massOfZCons_local; |
| 1117 |
> |
tempMVz = tempMVz_local; |
| 1118 |
> |
#else |
| 1119 |
> |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE, MPI_SUM, |
| 1120 |
> |
MPI_COMM_WORLD); |
| 1121 |
> |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 1122 |
> |
#endif |
| 1123 |
> |
|
| 1124 |
> |
return tempMVz / (totalMassOfUncons + massOfZCons); |
| 1125 |
> |
} |
| 1126 |
> |
|
| 1127 |
> |
/** |
| 1128 |
> |
* |
| 1129 |
> |
*/ |
| 1130 |
> |
|
| 1131 |
> |
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
| 1132 |
> |
double force[3]; |
| 1133 |
> |
double totalForce_local; |
| 1134 |
> |
double totalForce; |
| 1135 |
> |
|
| 1136 |
> |
totalForce_local = 0; |
| 1137 |
> |
|
| 1138 |
> |
for (int i = 0; i < nAtoms; i++){ |
| 1139 |
> |
atoms[i]->getFrc(force); |
| 1140 |
> |
totalForce_local += force[whichDirection]; |
| 1141 |
> |
} |
| 1142 |
> |
|
| 1143 |
> |
#ifndef IS_MPI |
| 1144 |
> |
totalForce = totalForce_local; |
| 1145 |
> |
#else |
| 1146 |
> |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE, MPI_SUM, |
| 1147 |
> |
MPI_COMM_WORLD); |
| 1148 |
> |
#endif |
| 1149 |
> |
|
| 1150 |
> |
return totalForce; |
| 1151 |
> |
} |
| 1152 |
> |
|
| 1153 |
> |
/** |
| 1154 |
> |
* |
| 1155 |
> |
*/ |
| 1156 |
> |
|
| 1157 |
> |
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
| 1158 |
> |
//calculate the number of atoms of moving z-constrained molecules |
| 1159 |
> |
int nMovingZAtoms_local; |
| 1160 |
> |
int nMovingZAtoms; |
| 1161 |
> |
|
| 1162 |
> |
nMovingZAtoms_local = 0; |
| 1163 |
> |
for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++) |
| 1164 |
> |
if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){ |
| 1165 |
> |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
| 1166 |
> |
} |
| 1167 |
> |
|
| 1168 |
> |
#ifdef IS_MPI |
| 1169 |
> |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, |
| 1170 |
> |
MPI_COMM_WORLD); |
| 1171 |
> |
#else |
| 1172 |
> |
nMovingZAtoms = nMovingZAtoms_local; |
| 1173 |
> |
#endif |
| 1174 |
> |
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
| 1175 |
> |
} |
| 1176 |
> |
|
| 1177 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, |
| 1178 |
> |
Atom* atom, |
| 1179 |
> |
double totalForce){ |
| 1180 |
> |
return totalForce / mol->getNAtoms(); |
| 1181 |
> |
} |
| 1182 |
> |
|
| 1183 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, |
| 1184 |
> |
double totalForce){ |
| 1185 |
> |
return totalForce / totNumOfMovingAtoms; |
| 1186 |
> |
} |
| 1187 |
> |
|
| 1188 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, |
| 1189 |
> |
Atom* atom, |
| 1190 |
> |
double totalForce){ |
| 1191 |
> |
return totalForce / mol->getNAtoms(); |
| 1192 |
> |
} |
| 1193 |
> |
|
| 1194 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, |
| 1195 |
> |
double totalForce){ |
| 1196 |
> |
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
| 1197 |
> |
} |
| 1198 |
> |
|
| 1199 |
> |
/** |
| 1200 |
> |
* |
| 1201 |
> |
*/ |
| 1202 |
> |
|
| 1203 |
> |
template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
| 1204 |
> |
//calculate the number of atoms of moving z-constrained molecules |
| 1205 |
> |
double massOfMovingZAtoms_local; |
| 1206 |
> |
double massOfMovingZAtoms; |
| 1207 |
> |
|
| 1208 |
> |
massOfMovingZAtoms_local = 0; |
| 1209 |
> |
for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++) |
| 1210 |
> |
if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){ |
| 1211 |
> |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
| 1212 |
> |
} |
| 1213 |
> |
|
| 1214 |
> |
#ifdef IS_MPI |
| 1215 |
> |
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE, |
| 1216 |
> |
MPI_SUM, MPI_COMM_WORLD); |
| 1217 |
> |
#else |
| 1218 |
> |
massOfMovingZAtoms = massOfMovingZAtoms_local; |
| 1219 |
> |
#endif |
| 1220 |
> |
totMassOfMovingAtoms = massOfMovingZAtoms + |
| 1221 |
> |
zconsIntegrator->totalMassOfUncons; |
| 1222 |
> |
} |
| 1223 |
> |
|
| 1224 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, |
| 1225 |
> |
Atom* atom, |
| 1226 |
> |
double totalForce){ |
| 1227 |
> |
return totalForce * atom->getMass() / mol->getTotalMass(); |
| 1228 |
> |
} |
| 1229 |
> |
|
| 1230 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols(Atom* atom, |
| 1231 |
> |
double totalForce){ |
| 1232 |
> |
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
| 1233 |
> |
} |
| 1234 |
> |
|
| 1235 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, |
| 1236 |
> |
Atom* atom, |
| 1237 |
> |
double totalForce){ |
| 1238 |
> |
return totalForce * atom->getMass() / mol->getTotalMass(); |
| 1239 |
> |
} |
| 1240 |
> |
|
| 1241 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, |
| 1242 |
> |
double totalForce){ |
| 1243 |
> |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
| 1244 |
> |
} |
| 1245 |
> |
|
| 1246 |
> |
template<typename T> void ZConstraint<T>::updateZPos(){ |
| 1247 |
> |
double curTime; |
| 1248 |
> |
double COM[3]; |
| 1249 |
> |
|
| 1250 |
> |
curTime = info->getTime(); |
| 1251 |
> |
|
| 1252 |
> |
for (size_t i = 0; i < zconsMols.size(); i++){ |
| 1253 |
> |
|
| 1254 |
> |
if (states[i] == zcsFixed && curTime >= endFixTime[i]){ |
| 1255 |
> |
zPos[i] += zconsGap; |
| 1256 |
> |
|
| 1257 |
> |
if (usingSMD){ |
| 1258 |
> |
zconsMols[i]->getCOM(COM); |
| 1259 |
> |
cantPos[i] = COM[whichDirection]; |
| 1260 |
> |
} |
| 1261 |
> |
|
| 1262 |
> |
} |
| 1263 |
> |
|
| 1264 |
> |
} |
| 1265 |
> |
|
| 1266 |
> |
} |
| 1267 |
> |
|
| 1268 |
> |
template<typename T> void ZConstraint<T>::updateCantPos(){ |
| 1269 |
> |
double curTime; |
| 1270 |
> |
double dt; |
| 1271 |
> |
|
| 1272 |
> |
curTime = info->getTime(); |
| 1273 |
> |
dt = info->dt; |
| 1274 |
> |
|
| 1275 |
> |
for (size_t i = 0; i < zconsMols.size(); i++){ |
| 1276 |
> |
if (states[i] == zcsMoving){ |
| 1277 |
> |
cantPos[i] += cantVel[i] * dt; |
| 1278 |
> |
} |
| 1279 |
> |
} |
| 1280 |
> |
|
| 1281 |
> |
} |
