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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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|
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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()].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[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
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molecules[i].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 i = 0; i < nMols; i++) |
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if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
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molecules[i].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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for(int i = 0; i < zconsMols.size(); i++) |
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indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
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#endif |
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//get total number of unconstrained atoms |
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int nUnconsAtoms_local; |
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nUnconsAtoms_local = 0; |
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for(int i = 0; i < unconsMols.size(); i++) |
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nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
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#ifndef IS_MPI |
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totNumOfUnconsAtoms = nUnconsAtoms_local; |
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#else |
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MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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#endif |
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checkZConsState(); |
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// |
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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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//The reason to declare fz and indexOfZconsMols as pointer to array is |
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// that we want to make the MPI communication simple |
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if(fz) |
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delete[] fz; |
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if(indexOfZConsMols) |
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delete[] indexOfZConsMols; |
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if (zconsMols.size() > 0){ |
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fz = new double[zconsMols.size()]; |
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indexOfZConsMols = new int[zconsMols.size()]; |
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if(!fz || !indexOfZConsMols){ |
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sprintf( painCave.errMsg, |
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"Memory allocation failure in class Zconstraint\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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for(int i = 0; i < zconsMols.size(); i++){ |
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indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
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} |
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} |
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else{ |
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fz = NULL; |
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indexOfZConsMols = NULL; |
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} |
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} |
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#endif |
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/** Function Name: isZConstraintMol |
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** Parameter |
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** Molecule* mol |
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** Return value: |
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** -1, if the molecule is not z-constraint molecule, |
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** other non-negative values, its index in indexOfAllZConsMols vector |
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*/ |
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template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
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{ |
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int index; |
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int low; |
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int high; |
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int mid; |
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index = mol->getGlobalIndex(); |
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low = 0; |
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high = parameters->size() - 1; |
398 |
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//Binary Search (we have sorted the array) |
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while(low <= high){ |
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mid = (low + high) /2; |
402 |
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if ((*parameters)[mid].zconsIndex == index) |
403 |
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return mid; |
404 |
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else if ((*parameters)[mid].zconsIndex > index ) |
405 |
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high = mid -1; |
406 |
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else |
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low = mid + 1; |
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} |
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410 |
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return -1; |
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} |
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tim |
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/** |
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* Description: |
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* Reset the z coordinates |
416 |
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*/ |
417 |
tim |
676 |
template<typename T> void ZConstraint<T>::integrate(){ |
418 |
tim |
658 |
|
419 |
tim |
676 |
//zero out the velocities of center of mass of unconstrained molecules |
420 |
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//and the velocities of center of mass of every single z-constrained molecueles |
421 |
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zeroOutVel(); |
422 |
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423 |
|
|
T::integrate(); |
424 |
|
|
|
425 |
tim |
658 |
} |
426 |
tim |
676 |
|
427 |
tim |
658 |
|
428 |
tim |
676 |
/** |
429 |
|
|
* |
430 |
|
|
* |
431 |
|
|
* |
432 |
|
|
* |
433 |
tim |
658 |
*/ |
434 |
|
|
|
435 |
tim |
676 |
|
436 |
|
|
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
437 |
|
|
|
438 |
|
|
T::calcForce(calcPot, calcStress); |
439 |
|
|
|
440 |
|
|
if (checkZConsState()) |
441 |
|
|
zeroOutVel(); |
442 |
|
|
|
443 |
|
|
//do zconstraint force; |
444 |
|
|
if (haveFixedZMols()) |
445 |
|
|
this->doZconstraintForce(); |
446 |
|
|
|
447 |
|
|
//use harmonical poteintial to move the molecules to the specified positions |
448 |
|
|
if (haveMovingZMols()) |
449 |
|
|
//this->doHarmonic(); |
450 |
|
|
|
451 |
|
|
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
452 |
|
|
|
453 |
|
|
} |
454 |
|
|
|
455 |
|
|
template<typename T> double ZConstraint<T>::calcZSys() |
456 |
tim |
658 |
{ |
457 |
tim |
676 |
//calculate reference z coordinate for z-constraint molecules |
458 |
|
|
double totalMass_local; |
459 |
|
|
double totalMass; |
460 |
|
|
double totalMZ_local; |
461 |
|
|
double totalMZ; |
462 |
|
|
double massOfUncons_local; |
463 |
|
|
double massOfCurMol; |
464 |
|
|
double COM[3]; |
465 |
|
|
|
466 |
|
|
totalMass_local = 0; |
467 |
|
|
totalMass = 0; |
468 |
|
|
totalMZ_local = 0; |
469 |
|
|
totalMZ = 0; |
470 |
|
|
massOfUncons_local = 0; |
471 |
|
|
|
472 |
|
|
|
473 |
|
|
for(int i = 0; i < nMols; i++){ |
474 |
|
|
massOfCurMol = molecules[i].getTotalMass(); |
475 |
|
|
molecules[i].getCOM(COM); |
476 |
|
|
|
477 |
|
|
totalMass_local += massOfCurMol; |
478 |
|
|
totalMZ_local += massOfCurMol * COM[whichDirection]; |
479 |
|
|
|
480 |
|
|
if(isZConstraintMol(&molecules[i]) == -1){ |
481 |
|
|
|
482 |
|
|
massOfUncons_local += massOfCurMol; |
483 |
|
|
} |
484 |
|
|
|
485 |
|
|
} |
486 |
|
|
|
487 |
|
|
|
488 |
|
|
#ifdef IS_MPI |
489 |
|
|
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
490 |
|
|
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
491 |
|
|
MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
492 |
|
|
#else |
493 |
|
|
totalMass = totalMass_local; |
494 |
|
|
totalMZ = totalMZ_local; |
495 |
|
|
totalMassOfUncons = massOfUncons_local; |
496 |
|
|
#endif |
497 |
mmeineke |
671 |
|
498 |
tim |
658 |
double zsys; |
499 |
tim |
676 |
zsys = totalMZ / totalMass; |
500 |
tim |
658 |
|
501 |
tim |
676 |
return zsys; |
502 |
|
|
} |
503 |
|
|
|
504 |
|
|
/** |
505 |
|
|
* |
506 |
|
|
*/ |
507 |
|
|
template<typename T> void ZConstraint<T>::thermalize( void ){ |
508 |
|
|
|
509 |
|
|
T::thermalize(); |
510 |
|
|
zeroOutVel(); |
511 |
|
|
} |
512 |
|
|
|
513 |
|
|
/** |
514 |
|
|
* |
515 |
|
|
* |
516 |
|
|
* |
517 |
|
|
*/ |
518 |
|
|
|
519 |
|
|
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
520 |
|
|
|
521 |
|
|
Atom** fixedZAtoms; |
522 |
|
|
double COMvel[3]; |
523 |
|
|
double vel[3]; |
524 |
tim |
658 |
|
525 |
tim |
676 |
//zero out the velocities of center of mass of fixed z-constrained molecules |
526 |
|
|
|
527 |
tim |
658 |
for(int i = 0; i < zconsMols.size(); i++){ |
528 |
tim |
676 |
|
529 |
|
|
if (states[i] == zcsFixed){ |
530 |
|
|
|
531 |
|
|
zconsMols[i]->getCOMvel(COMvel); |
532 |
|
|
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
533 |
|
|
|
534 |
|
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
535 |
|
|
fixedZAtoms[j]->getVel(vel); |
536 |
|
|
vel[whichDirection] -= COMvel[whichDirection]; |
537 |
|
|
fixedZAtoms[j]->setVel(vel); |
538 |
|
|
} |
539 |
|
|
|
540 |
|
|
} |
541 |
|
|
|
542 |
tim |
658 |
} |
543 |
tim |
676 |
|
544 |
|
|
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
545 |
|
|
double MVzOfMovingMols_local; |
546 |
|
|
double MVzOfMovingMols; |
547 |
|
|
double totalMassOfMovingZMols_local; |
548 |
|
|
double totalMassOfMovingZMols; |
549 |
|
|
|
550 |
|
|
MVzOfMovingMols_local = 0; |
551 |
|
|
totalMassOfMovingZMols_local = 0; |
552 |
tim |
658 |
|
553 |
tim |
676 |
for(int i =0; i < unconsMols.size(); i++){ |
554 |
|
|
unconsMols[i]->getCOMvel(COMvel); |
555 |
|
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
556 |
|
|
} |
557 |
|
|
|
558 |
|
|
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
559 |
|
|
|
560 |
|
|
if (states[i] == zcsMoving){ |
561 |
|
|
zconsMols[i]->getCOMvel(COMvel); |
562 |
|
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
563 |
|
|
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
564 |
|
|
} |
565 |
|
|
|
566 |
|
|
} |
567 |
|
|
|
568 |
|
|
#ifndef IS_MPI |
569 |
|
|
MVzOfMovingMols = MVzOfMovingMols_local; |
570 |
|
|
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
571 |
tim |
658 |
#else |
572 |
tim |
676 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
573 |
|
|
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
574 |
tim |
658 |
#endif |
575 |
|
|
|
576 |
tim |
676 |
double vzOfMovingMols; |
577 |
|
|
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
578 |
|
|
|
579 |
|
|
//modify the velocites of unconstrained molecules |
580 |
|
|
Atom** unconsAtoms; |
581 |
tim |
658 |
for(int i = 0; i < unconsMols.size(); i++){ |
582 |
tim |
676 |
|
583 |
|
|
unconsAtoms = unconsMols[i]->getMyAtoms(); |
584 |
|
|
for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ |
585 |
|
|
unconsAtoms[j]->getVel(vel); |
586 |
|
|
vel[whichDirection] -= vzOfMovingMols; |
587 |
|
|
unconsAtoms[j]->setVel(vel); |
588 |
|
|
} |
589 |
|
|
|
590 |
|
|
} |
591 |
|
|
|
592 |
|
|
//modify the velocities of moving z-constrained molecuels |
593 |
|
|
Atom** movingZAtoms; |
594 |
|
|
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
595 |
|
|
|
596 |
|
|
if (states[i] ==zcsMoving){ |
597 |
|
|
|
598 |
|
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
599 |
|
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
600 |
|
|
movingZAtoms[j]->getVel(vel); |
601 |
|
|
vel[whichDirection] -= vzOfMovingMols; |
602 |
|
|
movingZAtoms[j]->setVel(vel); |
603 |
|
|
} |
604 |
|
|
|
605 |
|
|
} |
606 |
|
|
|
607 |
tim |
658 |
} |
608 |
tim |
676 |
|
609 |
|
|
} |
610 |
|
|
|
611 |
|
|
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
612 |
|
|
|
613 |
|
|
Atom** zconsAtoms; |
614 |
|
|
double totalFZ; |
615 |
|
|
double totalFZ_local; |
616 |
|
|
double COMvel[3]; |
617 |
|
|
double COM[3]; |
618 |
|
|
double force[3]; |
619 |
|
|
double zsys; |
620 |
|
|
|
621 |
|
|
int nMovingZMols_local; |
622 |
|
|
int nMovingZMols; |
623 |
|
|
|
624 |
|
|
//constrain the molecules which do not reach the specified positions |
625 |
|
|
|
626 |
|
|
zsys = calcZSys(); |
627 |
|
|
cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
628 |
|
|
|
629 |
|
|
//Zero Out the force of z-contrained molecules |
630 |
|
|
totalFZ_local = 0; |
631 |
|
|
|
632 |
|
|
//calculate the total z-contrained force of fixed z-contrained molecules |
633 |
tim |
682 |
cout << "Fixed Molecules" << endl; |
634 |
tim |
676 |
for(int i = 0; i < zconsMols.size(); i++){ |
635 |
|
|
|
636 |
|
|
if (states[i] == zcsFixed){ |
637 |
|
|
|
638 |
|
|
zconsMols[i]->getCOM(COM); |
639 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
640 |
|
|
|
641 |
|
|
fz[i] = 0; |
642 |
|
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
643 |
|
|
zconsAtoms[j]->getFrc(force); |
644 |
|
|
fz[i] += force[whichDirection]; |
645 |
|
|
} |
646 |
|
|
totalFZ_local += fz[i]; |
647 |
|
|
|
648 |
|
|
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
649 |
|
|
|
650 |
|
|
} |
651 |
|
|
|
652 |
|
|
} |
653 |
|
|
|
654 |
|
|
//calculate the number of atoms of moving z-constrained molecules |
655 |
|
|
nMovingZMols_local = 0; |
656 |
|
|
for(int i = 0; zconsMols.size(); i++){ |
657 |
|
|
if(states[i] == zcsMoving) |
658 |
|
|
nMovingZMols_local += massOfZConsMols[i]; |
659 |
|
|
} |
660 |
tim |
658 |
#ifdef IS_MPI |
661 |
tim |
676 |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
662 |
|
|
MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
663 |
tim |
658 |
#else |
664 |
tim |
676 |
totalFZ = totalFZ_local; |
665 |
|
|
nMovingZMols = nMovingZMols_local; |
666 |
|
|
#endif |
667 |
|
|
|
668 |
|
|
force[0]= 0; |
669 |
|
|
force[1]= 0; |
670 |
|
|
force[2]= 0; |
671 |
|
|
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols); |
672 |
|
|
|
673 |
|
|
//modify the velocites of unconstrained molecules |
674 |
|
|
for(int i = 0; i < unconsMols.size(); i++){ |
675 |
|
|
|
676 |
|
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
677 |
|
|
|
678 |
|
|
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
679 |
|
|
unconsAtoms[j]->addFrc(force); |
680 |
|
|
|
681 |
|
|
} |
682 |
|
|
|
683 |
|
|
//modify the velocities of moving z-constrained molecules |
684 |
|
|
for(int i = 0; i < zconsMols.size(); i++) { |
685 |
|
|
if (states[i] == zcsMoving){ |
686 |
|
|
|
687 |
|
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
688 |
|
|
|
689 |
|
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
690 |
|
|
movingZAtoms[j]->addFrc(force); |
691 |
|
|
} |
692 |
|
|
} |
693 |
|
|
|
694 |
|
|
// apply negative to fixed z-constrained molecues; |
695 |
|
|
force[0]= 0; |
696 |
|
|
force[1]= 0; |
697 |
|
|
force[2]= 0; |
698 |
|
|
|
699 |
|
|
for(int i = 0; i < zconsMols.size(); i++){ |
700 |
|
|
|
701 |
|
|
if (states[i] == zcsFixed){ |
702 |
|
|
|
703 |
|
|
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
704 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
705 |
|
|
|
706 |
|
|
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
707 |
|
|
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
708 |
|
|
zconsAtoms[j]->addFrc(force); |
709 |
|
|
} |
710 |
|
|
|
711 |
|
|
} |
712 |
|
|
|
713 |
|
|
} |
714 |
|
|
|
715 |
|
|
} |
716 |
|
|
|
717 |
|
|
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
718 |
|
|
double COM[3]; |
719 |
|
|
double diff; |
720 |
tim |
658 |
|
721 |
tim |
676 |
bool changed; |
722 |
|
|
|
723 |
|
|
changed = false; |
724 |
|
|
|
725 |
|
|
for(int i =0; i < zconsMols.size(); i++){ |
726 |
|
|
|
727 |
tim |
658 |
zconsMols[i]->getCOM(COM); |
728 |
tim |
682 |
diff = fabs(COM[whichDirection] - zPos[i]); |
729 |
|
|
if ( diff <= zconsTol && states[i] == zcsMoving){ |
730 |
tim |
676 |
states[i] = zcsFixed; |
731 |
|
|
changed = true; |
732 |
|
|
} |
733 |
tim |
682 |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
734 |
tim |
676 |
states[i] = zcsMoving; |
735 |
|
|
changed = true; |
736 |
|
|
} |
737 |
|
|
|
738 |
tim |
658 |
} |
739 |
|
|
|
740 |
tim |
676 |
return changed; |
741 |
tim |
658 |
} |
742 |
tim |
676 |
|
743 |
|
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
744 |
|
|
for(int i = 0; i < zconsMols.size(); i++) |
745 |
|
|
if (states[i] == zcsFixed) |
746 |
|
|
return true; |
747 |
|
|
|
748 |
|
|
return false; |
749 |
|
|
} |
750 |
|
|
|
751 |
|
|
|
752 |
|
|
/** |
753 |
|
|
* |
754 |
|
|
*/ |
755 |
|
|
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
756 |
|
|
for(int i = 0; i < zconsMols.size(); i++) |
757 |
|
|
if (states[i] == zcsMoving) |
758 |
|
|
return true; |
759 |
|
|
|
760 |
|
|
return false; |
761 |
|
|
|
762 |
tim |
682 |
} |
763 |
|
|
|
764 |
|
|
/** |
765 |
|
|
* |
766 |
|
|
* |
767 |
|
|
*/ |
768 |
|
|
|
769 |
|
|
template<typename T> void ZConstraint<T>::doHarmonic(){ |
770 |
|
|
double force[3]; |
771 |
|
|
double harmonicU; |
772 |
|
|
double COM[3]; |
773 |
|
|
double diff; |
774 |
|
|
|
775 |
|
|
force[0] = 0; |
776 |
|
|
force[1] = 0; |
777 |
|
|
force[2] = 0; |
778 |
|
|
|
779 |
|
|
cout << "Moving Molecules" << endl; |
780 |
|
|
for(int i = 0; i < zconsMols.size(); i++) { |
781 |
|
|
|
782 |
|
|
if (states[i] == zcsMoving){ |
783 |
|
|
zconsMols[i]->getCOM(COM): |
784 |
|
|
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
785 |
|
|
|
786 |
|
|
diff = COM[whichDirection] -zPos[i]; |
787 |
|
|
|
788 |
|
|
harmonicU = 0.5 * kz[i] * diff * diff; |
789 |
|
|
info->ltPot += harmonicU; |
790 |
|
|
|
791 |
|
|
force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms(); |
792 |
|
|
|
793 |
|
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
794 |
|
|
|
795 |
|
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
796 |
|
|
movingZAtoms[j]->addFrc(force); |
797 |
|
|
} |
798 |
|
|
|
799 |
|
|
} |
800 |
|
|
|
801 |
|
|
} |