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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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ZConsParaData* zConsParaData; |
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DoubleData* sampleTime; |
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DoubleData* tolerance; |
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StringData* filename; |
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double COM[3]; |
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|
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//by default, the direction of constraint is z |
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// 0 --> x |
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// 1 --> y |
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// 2 --> z |
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whichDirection = 2; |
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|
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//estimate the force constant of harmonical potential |
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double Kb = 1.986E-3 ; //in kcal/K |
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double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2; |
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zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox); |
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|
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//retrieve sample time of z-contraint |
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data = info->getProperty(ZCONSTIME_ID); |
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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_ID); |
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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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//retrieve tolerance for z-constraint molecuels |
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data = info->getProperty(ZCONSTOL_ID); |
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if(!data) { |
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sprintf( painCave.errMsg, |
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"ZConstraint error: can not get tolerance \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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tolerance = dynamic_cast<DoubleData*>(data); |
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if(!tolerance){ |
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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->zconsTol = tolerance->getData(); |
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} |
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} |
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//retrieve index of z-constraint molecules |
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data = info->getProperty(ZCONSPARADATA_ID); |
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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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zConsParaData = dynamic_cast<ZConsParaData*>(data); |
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if(!zConsParaData){ |
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sprintf( painCave.errMsg, |
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"ZConstraint error: Can not get parameters of zconstraint method 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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parameters = zConsParaData->getData(); |
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//check the range of zconsIndex |
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//and the minimum value of index is the first one (we already sorted the data) |
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//the maximum value of index is the last one |
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int maxIndex; |
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int minIndex; |
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int totalNumMol; |
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minIndex = (*parameters)[0].zconsIndex; |
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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 = (*parameters)[parameters->size() - 1].zconsIndex; |
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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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//if user does not specify the zpos for the zconstraint molecule |
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//its initial z coordinate will be used as default |
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for(int i = 0; i < parameters->size(); i++){ |
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if(!(*parameters)[i].havingZPos){ |
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#ifndef IS_MPI |
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for(int j = 0; j < nMols; j++){ |
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if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
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molecules[j].getCOM(COM); |
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break; |
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} |
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} |
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#else |
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//query which processor current zconstraint molecule belongs to |
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int *MolToProcMap; |
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int whichNode; |
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double initZPos; |
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MolToProcMap = mpiSim->getMolToProcMap(); |
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whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
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//broadcast the zpos of current z-contraint molecule |
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//the node which contain this |
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if (worldRank == whichNode ){ |
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for(int j = 0; j < nMols; j++) |
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if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
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molecules[j].getCOM(COM); |
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break; |
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} |
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} |
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MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
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#endif |
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(*parameters)[i].zPos = COM[whichDirection]; |
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sprintf( painCave.errMsg, |
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"ZConstraint warningr: Does not specify zpos for z-constraint molecule " |
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"initial z coornidate will be used \n"); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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} |
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}//end if (!zConsParaData) |
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}//end if (!data) |
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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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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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zPos.push_back((*parameters)[searchResult].zPos); |
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kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
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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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//determine the states of z-constraint molecules |
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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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zconsMols[i]->getCOM(COM); |
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if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
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states.push_back(zcsFixed); |
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else |
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states.push_back(zcsMoving); |
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} |
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#endif |
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//get total masss of unconstraint molecules |
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double totalMassOfUncons_local; |
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totalMassOfUncons_local = 0; |
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for(int i = 0; i < unconsMols.size(); i++) |
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totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
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#ifndef IS_MPI |
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totalMassOfUncons = totalMassOfUncons_local; |
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#else |
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MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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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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// creat zconsWriter |
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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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zPos.clear(); |
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kz.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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zPos.push_back((*parameters)[index].zPos); |
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kz.push_back((*parameters)[index].kRatio * zForceConst); |
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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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|
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//determine the states of z-constraint molecules |
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for(int i = 0; i < zconsMols.size(); i++){ |
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zconsMols[i]->getCOM(COM); |
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if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
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states.push_back(zcsFixed); |
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else |
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states.push_back(zcsMoving); |
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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 |
410 |
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** Parameter |
411 |
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** Molecule* mol |
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** Return value: |
413 |
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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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*/ |
416 |
|
|
|
417 |
|
|
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
418 |
|
|
{ |
419 |
|
|
int index; |
420 |
|
|
int low; |
421 |
|
|
int high; |
422 |
|
|
int mid; |
423 |
|
|
|
424 |
|
|
index = mol->getGlobalIndex(); |
425 |
|
|
|
426 |
|
|
low = 0; |
427 |
tim |
682 |
high = parameters->size() - 1; |
428 |
tim |
658 |
|
429 |
|
|
//Binary Search (we have sorted the array) |
430 |
|
|
while(low <= high){ |
431 |
|
|
mid = (low + high) /2; |
432 |
tim |
682 |
if ((*parameters)[mid].zconsIndex == index) |
433 |
tim |
658 |
return mid; |
434 |
tim |
682 |
else if ((*parameters)[mid].zconsIndex > index ) |
435 |
tim |
658 |
high = mid -1; |
436 |
|
|
else |
437 |
|
|
low = mid + 1; |
438 |
|
|
} |
439 |
|
|
|
440 |
|
|
return -1; |
441 |
|
|
} |
442 |
|
|
|
443 |
tim |
676 |
template<typename T> void ZConstraint<T>::integrate(){ |
444 |
tim |
658 |
|
445 |
tim |
676 |
//zero out the velocities of center of mass of unconstrained molecules |
446 |
|
|
//and the velocities of center of mass of every single z-constrained molecueles |
447 |
|
|
zeroOutVel(); |
448 |
|
|
|
449 |
|
|
T::integrate(); |
450 |
|
|
|
451 |
tim |
658 |
} |
452 |
tim |
676 |
|
453 |
tim |
658 |
|
454 |
tim |
676 |
/** |
455 |
|
|
* |
456 |
|
|
* |
457 |
|
|
* |
458 |
|
|
* |
459 |
tim |
696 |
*/ |
460 |
tim |
676 |
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
461 |
tim |
693 |
double zsys; |
462 |
tim |
676 |
|
463 |
|
|
T::calcForce(calcPot, calcStress); |
464 |
|
|
|
465 |
|
|
if (checkZConsState()) |
466 |
tim |
696 |
zeroOutVel(); |
467 |
tim |
693 |
|
468 |
|
|
zsys = calcZSys(); |
469 |
|
|
cout << "---------------------------------------------------------------------" <<endl; |
470 |
tim |
696 |
cout << "current time: " << info->getTime() << endl; |
471 |
|
|
cout << "center of mass at z: " << zsys << endl; |
472 |
|
|
//cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
473 |
|
|
cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
474 |
tim |
676 |
|
475 |
tim |
696 |
//cout << "before doZConstraintForce, totalForce is " << calcTotalForce() << endl; |
476 |
|
|
|
477 |
tim |
676 |
//do zconstraint force; |
478 |
|
|
if (haveFixedZMols()) |
479 |
|
|
this->doZconstraintForce(); |
480 |
tim |
696 |
|
481 |
tim |
676 |
//use harmonical poteintial to move the molecules to the specified positions |
482 |
|
|
if (haveMovingZMols()) |
483 |
tim |
693 |
this->doHarmonic(); |
484 |
tim |
696 |
|
485 |
|
|
//cout << "after doHarmonic, totalForce is " << calcTotalForce() << endl; |
486 |
|
|
|
487 |
tim |
676 |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
488 |
tim |
696 |
//cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
489 |
|
|
cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
490 |
tim |
676 |
} |
491 |
|
|
|
492 |
|
|
template<typename T> double ZConstraint<T>::calcZSys() |
493 |
tim |
658 |
{ |
494 |
tim |
676 |
//calculate reference z coordinate for z-constraint molecules |
495 |
|
|
double totalMass_local; |
496 |
|
|
double totalMass; |
497 |
|
|
double totalMZ_local; |
498 |
|
|
double totalMZ; |
499 |
|
|
double massOfCurMol; |
500 |
|
|
double COM[3]; |
501 |
tim |
696 |
|
502 |
tim |
676 |
totalMass_local = 0; |
503 |
|
|
totalMZ_local = 0; |
504 |
|
|
|
505 |
|
|
for(int i = 0; i < nMols; i++){ |
506 |
|
|
massOfCurMol = molecules[i].getTotalMass(); |
507 |
|
|
molecules[i].getCOM(COM); |
508 |
|
|
|
509 |
|
|
totalMass_local += massOfCurMol; |
510 |
|
|
totalMZ_local += massOfCurMol * COM[whichDirection]; |
511 |
tim |
696 |
|
512 |
tim |
676 |
} |
513 |
tim |
696 |
|
514 |
tim |
676 |
|
515 |
|
|
#ifdef IS_MPI |
516 |
|
|
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
517 |
|
|
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
518 |
tim |
696 |
#else |
519 |
tim |
676 |
totalMass = totalMass_local; |
520 |
|
|
totalMZ = totalMZ_local; |
521 |
tim |
696 |
#endif |
522 |
mmeineke |
671 |
|
523 |
tim |
658 |
double zsys; |
524 |
tim |
676 |
zsys = totalMZ / totalMass; |
525 |
tim |
658 |
|
526 |
tim |
676 |
return zsys; |
527 |
|
|
} |
528 |
|
|
|
529 |
|
|
/** |
530 |
|
|
* |
531 |
|
|
*/ |
532 |
|
|
template<typename T> void ZConstraint<T>::thermalize( void ){ |
533 |
|
|
|
534 |
|
|
T::thermalize(); |
535 |
|
|
zeroOutVel(); |
536 |
|
|
} |
537 |
|
|
|
538 |
|
|
/** |
539 |
|
|
* |
540 |
|
|
* |
541 |
|
|
* |
542 |
|
|
*/ |
543 |
|
|
|
544 |
|
|
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
545 |
|
|
|
546 |
|
|
Atom** fixedZAtoms; |
547 |
|
|
double COMvel[3]; |
548 |
|
|
double vel[3]; |
549 |
tim |
693 |
|
550 |
tim |
676 |
//zero out the velocities of center of mass of fixed z-constrained molecules |
551 |
|
|
|
552 |
tim |
658 |
for(int i = 0; i < zconsMols.size(); i++){ |
553 |
tim |
676 |
|
554 |
|
|
if (states[i] == zcsFixed){ |
555 |
|
|
|
556 |
tim |
693 |
zconsMols[i]->getCOMvel(COMvel); |
557 |
tim |
696 |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
558 |
tim |
693 |
|
559 |
tim |
676 |
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
560 |
|
|
|
561 |
|
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
562 |
|
|
fixedZAtoms[j]->getVel(vel); |
563 |
tim |
693 |
vel[whichDirection] -= COMvel[whichDirection]; |
564 |
|
|
fixedZAtoms[j]->setVel(vel); |
565 |
tim |
676 |
} |
566 |
tim |
693 |
|
567 |
|
|
zconsMols[i]->getCOMvel(COMvel); |
568 |
tim |
696 |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
569 |
tim |
676 |
} |
570 |
|
|
|
571 |
tim |
658 |
} |
572 |
tim |
693 |
|
573 |
tim |
696 |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
574 |
|
|
cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl; |
575 |
tim |
693 |
|
576 |
tim |
676 |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
577 |
|
|
double MVzOfMovingMols_local; |
578 |
|
|
double MVzOfMovingMols; |
579 |
|
|
double totalMassOfMovingZMols_local; |
580 |
|
|
double totalMassOfMovingZMols; |
581 |
|
|
|
582 |
|
|
MVzOfMovingMols_local = 0; |
583 |
|
|
totalMassOfMovingZMols_local = 0; |
584 |
tim |
658 |
|
585 |
tim |
676 |
for(int i =0; i < unconsMols.size(); i++){ |
586 |
|
|
unconsMols[i]->getCOMvel(COMvel); |
587 |
|
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
588 |
|
|
} |
589 |
|
|
|
590 |
tim |
693 |
for(int i = 0; i < zconsMols.size(); i++){ |
591 |
tim |
676 |
if (states[i] == zcsMoving){ |
592 |
|
|
zconsMols[i]->getCOMvel(COMvel); |
593 |
|
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
594 |
|
|
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
595 |
|
|
} |
596 |
|
|
|
597 |
|
|
} |
598 |
|
|
|
599 |
|
|
#ifndef IS_MPI |
600 |
|
|
MVzOfMovingMols = MVzOfMovingMols_local; |
601 |
|
|
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
602 |
tim |
658 |
#else |
603 |
tim |
676 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
604 |
|
|
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
605 |
tim |
658 |
#endif |
606 |
|
|
|
607 |
tim |
676 |
double vzOfMovingMols; |
608 |
|
|
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
609 |
|
|
|
610 |
|
|
//modify the velocites of unconstrained molecules |
611 |
|
|
Atom** unconsAtoms; |
612 |
tim |
658 |
for(int i = 0; i < unconsMols.size(); i++){ |
613 |
tim |
676 |
|
614 |
|
|
unconsAtoms = unconsMols[i]->getMyAtoms(); |
615 |
|
|
for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ |
616 |
|
|
unconsAtoms[j]->getVel(vel); |
617 |
|
|
vel[whichDirection] -= vzOfMovingMols; |
618 |
|
|
unconsAtoms[j]->setVel(vel); |
619 |
|
|
} |
620 |
|
|
|
621 |
|
|
} |
622 |
|
|
|
623 |
|
|
//modify the velocities of moving z-constrained molecuels |
624 |
|
|
Atom** movingZAtoms; |
625 |
tim |
693 |
for(int i = 0; i < zconsMols.size(); i++){ |
626 |
tim |
676 |
|
627 |
|
|
if (states[i] ==zcsMoving){ |
628 |
|
|
|
629 |
|
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
630 |
tim |
693 |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
631 |
tim |
676 |
movingZAtoms[j]->getVel(vel); |
632 |
|
|
vel[whichDirection] -= vzOfMovingMols; |
633 |
tim |
693 |
movingZAtoms[j]->setVel(vel); |
634 |
|
|
} |
635 |
tim |
676 |
|
636 |
tim |
693 |
} |
637 |
tim |
676 |
|
638 |
tim |
693 |
} |
639 |
tim |
676 |
|
640 |
tim |
696 |
cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl; |
641 |
tim |
693 |
|
642 |
tim |
676 |
} |
643 |
|
|
|
644 |
|
|
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
645 |
|
|
|
646 |
|
|
Atom** zconsAtoms; |
647 |
|
|
double totalFZ; |
648 |
|
|
double totalFZ_local; |
649 |
|
|
double COMvel[3]; |
650 |
|
|
double COM[3]; |
651 |
|
|
double force[3]; |
652 |
|
|
|
653 |
|
|
|
654 |
tim |
696 |
|
655 |
tim |
676 |
//constrain the molecules which do not reach the specified positions |
656 |
|
|
|
657 |
|
|
//Zero Out the force of z-contrained molecules |
658 |
|
|
totalFZ_local = 0; |
659 |
|
|
|
660 |
|
|
//calculate the total z-contrained force of fixed z-contrained molecules |
661 |
tim |
682 |
cout << "Fixed Molecules" << endl; |
662 |
tim |
676 |
for(int i = 0; i < zconsMols.size(); i++){ |
663 |
|
|
|
664 |
|
|
if (states[i] == zcsFixed){ |
665 |
|
|
|
666 |
|
|
zconsMols[i]->getCOM(COM); |
667 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
668 |
|
|
|
669 |
|
|
fz[i] = 0; |
670 |
|
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
671 |
|
|
zconsAtoms[j]->getFrc(force); |
672 |
|
|
fz[i] += force[whichDirection]; |
673 |
|
|
} |
674 |
|
|
totalFZ_local += fz[i]; |
675 |
|
|
|
676 |
tim |
696 |
cout << "index: " << indexOfZConsMols[i] |
677 |
|
|
<<"\tcurrent zpos: " << COM[whichDirection] |
678 |
|
|
<< "\tcurrent fz: " <<fz[i] << endl; |
679 |
tim |
676 |
|
680 |
|
|
} |
681 |
|
|
|
682 |
|
|
} |
683 |
tim |
696 |
|
684 |
|
|
// apply negative to fixed z-constrained molecues; |
685 |
|
|
force[0]= 0; |
686 |
|
|
force[1]= 0; |
687 |
|
|
force[2]= 0; |
688 |
tim |
676 |
|
689 |
tim |
696 |
for(int i = 0; i < zconsMols.size(); i++){ |
690 |
|
|
|
691 |
|
|
if (states[i] == zcsFixed){ |
692 |
|
|
|
693 |
|
|
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
694 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
695 |
|
|
|
696 |
|
|
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
697 |
|
|
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
698 |
|
|
zconsAtoms[j]->addFrc(force); |
699 |
|
|
} |
700 |
|
|
|
701 |
|
|
} |
702 |
|
|
|
703 |
|
|
} |
704 |
|
|
|
705 |
|
|
cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
706 |
|
|
<< "total force is " << calcTotalForce() << endl; |
707 |
tim |
676 |
//calculate the number of atoms of moving z-constrained molecules |
708 |
tim |
696 |
int nMovingZAtoms_local; |
709 |
|
|
int nMovingZAtoms; |
710 |
|
|
|
711 |
|
|
nMovingZAtoms_local = 0; |
712 |
tim |
693 |
for(int i = 0; i < zconsMols.size(); i++) |
713 |
tim |
676 |
if(states[i] == zcsMoving) |
714 |
tim |
696 |
nMovingZAtoms_local += zconsMols[i]->getNAtoms(); |
715 |
tim |
693 |
|
716 |
tim |
658 |
#ifdef IS_MPI |
717 |
tim |
676 |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
718 |
tim |
696 |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
719 |
tim |
658 |
#else |
720 |
tim |
676 |
totalFZ = totalFZ_local; |
721 |
tim |
696 |
nMovingZAtoms = nMovingZAtoms_local; |
722 |
tim |
676 |
#endif |
723 |
|
|
|
724 |
|
|
force[0]= 0; |
725 |
|
|
force[1]= 0; |
726 |
|
|
force[2]= 0; |
727 |
tim |
696 |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
728 |
tim |
676 |
|
729 |
tim |
693 |
//modify the forces of unconstrained molecules |
730 |
tim |
696 |
int accessCount = 0; |
731 |
tim |
676 |
for(int i = 0; i < unconsMols.size(); i++){ |
732 |
|
|
|
733 |
|
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
734 |
|
|
|
735 |
|
|
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
736 |
|
|
unconsAtoms[j]->addFrc(force); |
737 |
|
|
|
738 |
|
|
} |
739 |
|
|
|
740 |
tim |
693 |
//modify the forces of moving z-constrained molecules |
741 |
tim |
676 |
for(int i = 0; i < zconsMols.size(); i++) { |
742 |
tim |
696 |
if (states[i] == zcsMoving){ |
743 |
tim |
676 |
|
744 |
tim |
696 |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
745 |
tim |
676 |
|
746 |
tim |
696 |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
747 |
|
|
movingZAtoms[j]->addFrc(force); |
748 |
|
|
} |
749 |
tim |
676 |
} |
750 |
|
|
|
751 |
tim |
696 |
cout << "after substracting z-constraint force from moving molecuels " |
752 |
|
|
<< "total force is " << calcTotalForce() << endl; |
753 |
tim |
676 |
|
754 |
|
|
} |
755 |
|
|
|
756 |
|
|
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
757 |
|
|
double COM[3]; |
758 |
|
|
double diff; |
759 |
tim |
658 |
|
760 |
tim |
676 |
bool changed; |
761 |
|
|
|
762 |
|
|
changed = false; |
763 |
|
|
|
764 |
|
|
for(int i =0; i < zconsMols.size(); i++){ |
765 |
|
|
|
766 |
tim |
658 |
zconsMols[i]->getCOM(COM); |
767 |
tim |
682 |
diff = fabs(COM[whichDirection] - zPos[i]); |
768 |
|
|
if ( diff <= zconsTol && states[i] == zcsMoving){ |
769 |
tim |
676 |
states[i] = zcsFixed; |
770 |
|
|
changed = true; |
771 |
|
|
} |
772 |
tim |
682 |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
773 |
tim |
676 |
states[i] = zcsMoving; |
774 |
|
|
changed = true; |
775 |
|
|
} |
776 |
|
|
|
777 |
tim |
658 |
} |
778 |
|
|
|
779 |
tim |
676 |
return changed; |
780 |
tim |
658 |
} |
781 |
tim |
676 |
|
782 |
|
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
783 |
|
|
for(int i = 0; i < zconsMols.size(); i++) |
784 |
|
|
if (states[i] == zcsFixed) |
785 |
|
|
return true; |
786 |
|
|
|
787 |
|
|
return false; |
788 |
|
|
} |
789 |
|
|
|
790 |
|
|
|
791 |
|
|
/** |
792 |
|
|
* |
793 |
|
|
*/ |
794 |
|
|
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
795 |
|
|
for(int i = 0; i < zconsMols.size(); i++) |
796 |
|
|
if (states[i] == zcsMoving) |
797 |
|
|
return true; |
798 |
|
|
|
799 |
|
|
return false; |
800 |
|
|
|
801 |
tim |
682 |
} |
802 |
|
|
|
803 |
|
|
/** |
804 |
|
|
* |
805 |
|
|
* |
806 |
|
|
*/ |
807 |
|
|
|
808 |
|
|
template<typename T> void ZConstraint<T>::doHarmonic(){ |
809 |
|
|
double force[3]; |
810 |
|
|
double harmonicU; |
811 |
tim |
693 |
double harmonicF; |
812 |
tim |
682 |
double COM[3]; |
813 |
|
|
double diff; |
814 |
tim |
693 |
double totalFZ; |
815 |
tim |
682 |
|
816 |
|
|
force[0] = 0; |
817 |
|
|
force[1] = 0; |
818 |
|
|
force[2] = 0; |
819 |
|
|
|
820 |
tim |
693 |
totalFZ = 0; |
821 |
|
|
|
822 |
tim |
682 |
cout << "Moving Molecules" << endl; |
823 |
|
|
for(int i = 0; i < zconsMols.size(); i++) { |
824 |
|
|
|
825 |
|
|
if (states[i] == zcsMoving){ |
826 |
tim |
693 |
zconsMols[i]->getCOM(COM); |
827 |
tim |
682 |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
828 |
|
|
|
829 |
|
|
diff = COM[whichDirection] -zPos[i]; |
830 |
|
|
|
831 |
|
|
harmonicU = 0.5 * kz[i] * diff * diff; |
832 |
tim |
693 |
info->lrPot += harmonicU; |
833 |
tim |
682 |
|
834 |
tim |
696 |
harmonicF = - kz[i] * diff; |
835 |
tim |
693 |
totalFZ += harmonicF; |
836 |
tim |
696 |
|
837 |
|
|
// |
838 |
|
|
force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
839 |
tim |
682 |
|
840 |
|
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
841 |
|
|
|
842 |
|
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
843 |
|
|
movingZAtoms[j]->addFrc(force); |
844 |
|
|
} |
845 |
|
|
|
846 |
|
|
} |
847 |
tim |
696 |
|
848 |
tim |
693 |
force[0]= 0; |
849 |
|
|
force[1]= 0; |
850 |
|
|
force[2]= 0; |
851 |
|
|
force[whichDirection] = -totalFZ /totNumOfUnconsAtoms; |
852 |
|
|
|
853 |
|
|
//modify the forces of unconstrained molecules |
854 |
|
|
for(int i = 0; i < unconsMols.size(); i++){ |
855 |
|
|
|
856 |
|
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
857 |
|
|
|
858 |
|
|
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
859 |
|
|
unconsAtoms[j]->addFrc(force); |
860 |
|
|
} |
861 |
|
|
|
862 |
tim |
682 |
} |
863 |
tim |
693 |
|
864 |
tim |
696 |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
865 |
tim |
693 |
{ |
866 |
|
|
double MVzOfMovingMols_local; |
867 |
|
|
double MVzOfMovingMols; |
868 |
|
|
double totalMassOfMovingZMols_local; |
869 |
|
|
double totalMassOfMovingZMols; |
870 |
|
|
double COMvel[3]; |
871 |
|
|
|
872 |
|
|
MVzOfMovingMols_local = 0; |
873 |
|
|
totalMassOfMovingZMols_local = 0; |
874 |
|
|
|
875 |
|
|
for(int i =0; i < unconsMols.size(); i++){ |
876 |
|
|
unconsMols[i]->getCOMvel(COMvel); |
877 |
|
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
878 |
|
|
} |
879 |
|
|
|
880 |
|
|
for(int i = 0; i < zconsMols.size(); i++){ |
881 |
|
|
|
882 |
|
|
if (states[i] == zcsMoving){ |
883 |
|
|
zconsMols[i]->getCOMvel(COMvel); |
884 |
|
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
885 |
|
|
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
886 |
|
|
} |
887 |
|
|
|
888 |
|
|
} |
889 |
|
|
|
890 |
|
|
#ifndef IS_MPI |
891 |
|
|
MVzOfMovingMols = MVzOfMovingMols_local; |
892 |
|
|
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
893 |
|
|
#else |
894 |
|
|
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
895 |
|
|
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
896 |
|
|
#endif |
897 |
|
|
|
898 |
|
|
double vzOfMovingMols; |
899 |
|
|
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
900 |
|
|
|
901 |
|
|
return vzOfMovingMols; |
902 |
|
|
} |
903 |
|
|
|
904 |
|
|
|
905 |
tim |
696 |
template<typename T> double ZConstraint<T>::calcSysCOMVel() |
906 |
tim |
693 |
{ |
907 |
|
|
double COMvel[3]; |
908 |
|
|
double tempMVz = 0; |
909 |
|
|
|
910 |
|
|
for(int i =0 ; i < nMols; i++){ |
911 |
tim |
696 |
molecules[i].getCOMvel(COMvel); |
912 |
|
|
tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection]; |
913 |
tim |
693 |
} |
914 |
tim |
696 |
|
915 |
|
|
double massOfZCons_local; |
916 |
|
|
double massOfZCons; |
917 |
|
|
|
918 |
|
|
massOfZCons_local = 0; |
919 |
tim |
693 |
|
920 |
tim |
696 |
for(int i = 0; i < massOfZConsMols.size(); i++){ |
921 |
|
|
massOfZCons_local += massOfZConsMols[i]; |
922 |
|
|
} |
923 |
|
|
#ifndef IS_MPI |
924 |
|
|
massOfZCons = massOfZCons_local; |
925 |
|
|
#else |
926 |
|
|
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
927 |
|
|
#endif |
928 |
|
|
|
929 |
|
|
return tempMVz /(totalMassOfUncons + massOfZCons); |
930 |
tim |
693 |
} |
931 |
tim |
696 |
|
932 |
|
|
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
933 |
|
|
|
934 |
|
|
double force[3]; |
935 |
|
|
double totalForce_local; |
936 |
|
|
double totalForce; |
937 |
|
|
|
938 |
|
|
totalForce_local = 0; |
939 |
|
|
|
940 |
|
|
for(int i = 0; i < nAtoms; i++){ |
941 |
|
|
atoms[i]->getFrc(force); |
942 |
|
|
totalForce_local += force[whichDirection]; |
943 |
|
|
} |
944 |
|
|
|
945 |
|
|
#ifndef IS_MPI |
946 |
|
|
totalForce = totalForce_local; |
947 |
|
|
#else |
948 |
|
|
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
949 |
|
|
#endif |
950 |
|
|
|
951 |
|
|
return totalForce; |
952 |
|
|
|
953 |
|
|
} |