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tim |
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#include "Integrator.hpp" |
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#include "simError.h" |
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gezelter |
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#include <math.h> |
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tim |
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template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
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mmeineke |
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: T(theInfo, the_ff), indexOfZConsMols(NULL), fz(NULL), curZPos(NULL), |
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fzOut(NULL), curZconsTime(0), forcePolicy(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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tim |
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StringData* policy; |
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StringData* filename; |
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tim |
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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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tim |
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|
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tim |
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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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tim |
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|
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tim |
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//creat force Subtraction policy |
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tim |
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data = info->getProperty(ZCONSFORCEPOLICY_ID); |
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if(!data){ |
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sprintf( painCave.errMsg, |
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tim |
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"ZConstraint Warning: User does not set force Subtraction policy, " |
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tim |
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"PolicyByMass is used\n"); |
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painCave.isFatal = 0; |
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simError(); |
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forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
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} |
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else{ |
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policy = dynamic_cast<StringData*>(data); |
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tim |
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|
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if(!policy){ |
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tim |
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sprintf( painCave.errMsg, |
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"ZConstraint Error: Convertion from GenericData to StringData failure, " |
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tim |
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"PolicyByMass is used\n"); |
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tim |
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painCave.isFatal = 0; |
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simError(); |
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tim |
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forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
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} |
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else{ |
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if(policy->getData() == "BYNUMBER") |
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forcePolicy = (ForceSubtractionPolicy*) new PolicyByNumber(this); |
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else if(policy->getData() == "BYMASS") |
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forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
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tim |
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else{ |
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tim |
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sprintf( painCave.errMsg, |
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tim |
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"ZConstraint Warning: unknown force Subtraction policy, " |
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tim |
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"PolicyByMass is used\n"); |
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tim |
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painCave.isFatal = 0; |
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simError(); |
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tim |
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forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
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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_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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|
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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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tim |
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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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tim |
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tim |
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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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tim |
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|
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tim |
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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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tim |
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} |
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tim |
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|
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tim |
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maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
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tim |
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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 |
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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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mmeineke |
787 |
for(int i = 0; i < (int)(parameters->size()); i++){ |
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tim |
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|
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tim |
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if(!(*parameters)[i].havingZPos){ |
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tim |
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#ifndef IS_MPI |
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tim |
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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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tim |
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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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mmeineke |
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|
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tim |
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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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tim |
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|
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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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tim |
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|
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MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
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tim |
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#endif |
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tim |
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(*parameters)[i].zPos = COM[whichDirection]; |
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tim |
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|
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tim |
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sprintf( painCave.errMsg, |
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tim |
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"ZConstraint warning: Does not specify zpos for z-constraint molecule " |
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tim |
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"initial z coornidate will be used \n"); |
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tim |
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painCave.isFatal = 0; |
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simError(); |
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} |
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} |
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tim |
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}//end if (!zConsParaData) |
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}//end if (!data) |
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// |
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tim |
658 |
#ifdef IS_MPI |
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update(); |
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#else |
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int searchResult; |
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tim |
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|
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tim |
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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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tim |
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|
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zPos.push_back((*parameters)[searchResult].zPos); |
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mmeineke |
723 |
// cout << "index: "<< (*parameters)[searchResult].zconsIndex |
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// <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
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tim |
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|
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tim |
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kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
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tim |
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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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tim |
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curZPos = new double[zconsMols.size()]; |
297 |
tim |
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indexOfZConsMols = new int [zconsMols.size()]; |
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299 |
tim |
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if(!fz || !curZPos || !indexOfZConsMols){ |
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tim |
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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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tim |
693 |
//determine the states of z-constraint molecules |
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mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
308 |
tim |
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indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
309 |
tim |
693 |
|
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tim |
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zconsMols[i]->getCOM(COM); |
311 |
tim |
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if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
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tim |
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states.push_back(zcsFixed); |
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else |
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states.push_back(zcsMoving); |
315 |
tim |
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} |
316 |
tim |
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#endif |
318 |
tim |
676 |
|
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tim |
693 |
//get total masss of unconstraint molecules |
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double totalMassOfUncons_local; |
321 |
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totalMassOfUncons_local = 0; |
322 |
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323 |
mmeineke |
787 |
for(int i = 0; i < (int)(unconsMols.size()); i++) |
324 |
tim |
693 |
totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
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#ifndef IS_MPI |
327 |
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totalMassOfUncons = totalMassOfUncons_local; |
328 |
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#else |
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tim |
701 |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, |
330 |
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MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
331 |
tim |
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#endif |
332 |
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333 |
tim |
676 |
//get total number of unconstrained atoms |
334 |
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int nUnconsAtoms_local; |
335 |
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nUnconsAtoms_local = 0; |
336 |
mmeineke |
787 |
for(int i = 0; i < (int)(unconsMols.size()); i++) |
337 |
tim |
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nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
338 |
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339 |
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#ifndef IS_MPI |
340 |
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totNumOfUnconsAtoms = nUnconsAtoms_local; |
341 |
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#else |
342 |
tim |
701 |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, |
343 |
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MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
344 |
tim |
693 |
#endif |
345 |
tim |
676 |
|
346 |
tim |
699 |
forcePolicy->update(); |
347 |
tim |
658 |
} |
348 |
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349 |
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template<typename T> ZConstraint<T>::~ZConstraint() |
350 |
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{ |
351 |
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if(fz) |
352 |
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delete[] fz; |
353 |
tim |
699 |
|
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if(curZPos) |
355 |
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delete[] curZPos; |
356 |
tim |
658 |
|
357 |
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if(indexOfZConsMols) |
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delete[] indexOfZConsMols; |
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360 |
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if(fzOut) |
361 |
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delete fzOut; |
362 |
tim |
701 |
|
363 |
tim |
699 |
if(forcePolicy) |
364 |
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delete forcePolicy; |
365 |
tim |
658 |
} |
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tim |
701 |
|
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/** |
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* |
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*/ |
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tim |
658 |
#ifdef IS_MPI |
373 |
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template<typename T> void ZConstraint<T>::update() |
374 |
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{ |
375 |
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double COM[3]; |
376 |
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int index; |
377 |
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378 |
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zconsMols.clear(); |
379 |
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massOfZConsMols.clear(); |
380 |
tim |
682 |
zPos.clear(); |
381 |
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kz.clear(); |
382 |
tim |
658 |
|
383 |
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unconsMols.clear(); |
384 |
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massOfUnconsMols.clear(); |
385 |
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386 |
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387 |
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//creat zconsMol and unconsMol lists |
388 |
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for(int i = 0; i < nMols; i++){ |
389 |
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390 |
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index = isZConstraintMol(&molecules[i]); |
391 |
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392 |
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if(index > -1){ |
393 |
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394 |
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zconsMols.push_back(&molecules[i]); |
395 |
tim |
682 |
zPos.push_back((*parameters)[index].zPos); |
396 |
tim |
701 |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
397 |
tim |
658 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
398 |
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399 |
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molecules[i].getCOM(COM); |
400 |
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} |
401 |
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else |
402 |
|
|
{ |
403 |
|
|
|
404 |
|
|
unconsMols.push_back(&molecules[i]); |
405 |
|
|
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
406 |
|
|
|
407 |
|
|
} |
408 |
|
|
} |
409 |
tim |
693 |
|
410 |
|
|
//determine the states of z-constraint molecules |
411 |
mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
412 |
tim |
701 |
zconsMols[i]->getCOM(COM); |
413 |
tim |
693 |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
414 |
tim |
701 |
states.push_back(zcsFixed); |
415 |
|
|
else |
416 |
|
|
states.push_back(zcsMoving); |
417 |
tim |
693 |
} |
418 |
|
|
|
419 |
tim |
658 |
|
420 |
|
|
//The reason to declare fz and indexOfZconsMols as pointer to array is |
421 |
|
|
// that we want to make the MPI communication simple |
422 |
|
|
if(fz) |
423 |
|
|
delete[] fz; |
424 |
tim |
701 |
|
425 |
tim |
699 |
if(curZPos) |
426 |
|
|
delete[] curZPos; |
427 |
tim |
658 |
|
428 |
|
|
if(indexOfZConsMols) |
429 |
|
|
delete[] indexOfZConsMols; |
430 |
|
|
|
431 |
|
|
if (zconsMols.size() > 0){ |
432 |
|
|
fz = new double[zconsMols.size()]; |
433 |
tim |
701 |
curZPos = new double[zconsMols.size()]; |
434 |
tim |
658 |
indexOfZConsMols = new int[zconsMols.size()]; |
435 |
|
|
|
436 |
tim |
699 |
if(!fz || !curZPos || !indexOfZConsMols){ |
437 |
tim |
658 |
sprintf( painCave.errMsg, |
438 |
|
|
"Memory allocation failure in class Zconstraint\n"); |
439 |
|
|
painCave.isFatal = 1; |
440 |
|
|
simError(); |
441 |
|
|
} |
442 |
|
|
|
443 |
mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
444 |
tim |
658 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
445 |
|
|
} |
446 |
|
|
|
447 |
|
|
} |
448 |
|
|
else{ |
449 |
|
|
fz = NULL; |
450 |
tim |
701 |
curZPos = NULL; |
451 |
tim |
658 |
indexOfZConsMols = NULL; |
452 |
|
|
} |
453 |
tim |
701 |
|
454 |
tim |
699 |
// |
455 |
|
|
forcePolicy->update(); |
456 |
tim |
658 |
|
457 |
|
|
} |
458 |
|
|
|
459 |
|
|
#endif |
460 |
|
|
|
461 |
tim |
701 |
/** |
462 |
|
|
* Function Name: isZConstraintMol |
463 |
|
|
* Parameter |
464 |
|
|
* Molecule* mol |
465 |
|
|
* Return value: |
466 |
|
|
* -1, if the molecule is not z-constraint molecule, |
467 |
|
|
* other non-negative values, its index in indexOfAllZConsMols vector |
468 |
tim |
658 |
*/ |
469 |
|
|
|
470 |
|
|
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
471 |
|
|
{ |
472 |
|
|
int index; |
473 |
|
|
int low; |
474 |
|
|
int high; |
475 |
|
|
int mid; |
476 |
|
|
|
477 |
|
|
index = mol->getGlobalIndex(); |
478 |
|
|
|
479 |
|
|
low = 0; |
480 |
tim |
682 |
high = parameters->size() - 1; |
481 |
tim |
658 |
|
482 |
|
|
//Binary Search (we have sorted the array) |
483 |
|
|
while(low <= high){ |
484 |
|
|
mid = (low + high) /2; |
485 |
tim |
682 |
if ((*parameters)[mid].zconsIndex == index) |
486 |
tim |
658 |
return mid; |
487 |
tim |
682 |
else if ((*parameters)[mid].zconsIndex > index ) |
488 |
tim |
658 |
high = mid -1; |
489 |
|
|
else |
490 |
|
|
low = mid + 1; |
491 |
|
|
} |
492 |
|
|
|
493 |
|
|
return -1; |
494 |
|
|
} |
495 |
|
|
|
496 |
tim |
676 |
template<typename T> void ZConstraint<T>::integrate(){ |
497 |
tim |
738 |
|
498 |
|
|
// creat zconsWriter |
499 |
|
|
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
500 |
tim |
658 |
|
501 |
tim |
738 |
if(!fzOut){ |
502 |
|
|
sprintf( painCave.errMsg, |
503 |
|
|
"Memory allocation failure in class Zconstraint\n"); |
504 |
|
|
painCave.isFatal = 1; |
505 |
|
|
simError(); |
506 |
|
|
} |
507 |
|
|
|
508 |
tim |
676 |
//zero out the velocities of center of mass of unconstrained molecules |
509 |
|
|
//and the velocities of center of mass of every single z-constrained molecueles |
510 |
|
|
zeroOutVel(); |
511 |
mmeineke |
711 |
|
512 |
|
|
curZconsTime = zconsTime + info->getTime(); |
513 |
tim |
676 |
|
514 |
|
|
T::integrate(); |
515 |
|
|
|
516 |
tim |
658 |
} |
517 |
tim |
676 |
|
518 |
tim |
658 |
|
519 |
tim |
676 |
/** |
520 |
|
|
* |
521 |
|
|
* |
522 |
|
|
* |
523 |
|
|
* |
524 |
tim |
696 |
*/ |
525 |
tim |
676 |
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
526 |
tim |
693 |
double zsys; |
527 |
tim |
699 |
double COM[3]; |
528 |
|
|
double force[3]; |
529 |
tim |
702 |
double zSysCOMVel; |
530 |
tim |
676 |
|
531 |
|
|
T::calcForce(calcPot, calcStress); |
532 |
|
|
|
533 |
tim |
738 |
if (checkZConsState()){ |
534 |
|
|
zeroOutVel(); |
535 |
mmeineke |
711 |
forcePolicy->update(); |
536 |
tim |
699 |
} |
537 |
mmeineke |
711 |
|
538 |
tim |
693 |
zsys = calcZSys(); |
539 |
tim |
702 |
zSysCOMVel = calcSysCOMVel(); |
540 |
|
|
#ifdef IS_MPI |
541 |
|
|
if(worldRank == 0){ |
542 |
|
|
#endif |
543 |
tim |
738 |
//cout << "---------------------------------------------------------------------" <<endl; |
544 |
|
|
//cout << "current time: " << info->getTime() << endl; |
545 |
|
|
//cout << "center of mass at z: " << zsys << endl; |
546 |
|
|
//cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
547 |
tim |
676 |
|
548 |
tim |
702 |
#ifdef IS_MPI |
549 |
|
|
} |
550 |
|
|
#endif |
551 |
tim |
696 |
|
552 |
tim |
676 |
//do zconstraint force; |
553 |
|
|
if (haveFixedZMols()) |
554 |
|
|
this->doZconstraintForce(); |
555 |
tim |
733 |
|
556 |
tim |
676 |
//use harmonical poteintial to move the molecules to the specified positions |
557 |
|
|
if (haveMovingZMols()) |
558 |
tim |
693 |
this->doHarmonic(); |
559 |
tim |
696 |
|
560 |
tim |
699 |
//write out forces and current positions of z-constraint molecules |
561 |
tim |
701 |
if(info->getTime() >= curZconsTime){ |
562 |
mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
563 |
tim |
699 |
zconsMols[i]->getCOM(COM); |
564 |
tim |
701 |
curZPos[i] = COM[whichDirection]; |
565 |
tim |
699 |
|
566 |
tim |
701 |
//if the z-constraint molecule is still moving, just record its force |
567 |
|
|
if(states[i] == zcsMoving){ |
568 |
tim |
699 |
fz[i] = 0; |
569 |
tim |
701 |
Atom** movingZAtoms; |
570 |
|
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
571 |
|
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
572 |
tim |
699 |
movingZAtoms[j]->getFrc(force); |
573 |
|
|
fz[i] += force[whichDirection]; |
574 |
tim |
701 |
} |
575 |
|
|
} |
576 |
|
|
} |
577 |
tim |
699 |
fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); |
578 |
tim |
701 |
curZconsTime += zconsTime; |
579 |
tim |
699 |
} |
580 |
tim |
702 |
|
581 |
|
|
zSysCOMVel = calcSysCOMVel(); |
582 |
|
|
#ifdef IS_MPI |
583 |
|
|
if(worldRank == 0){ |
584 |
|
|
#endif |
585 |
tim |
738 |
//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
586 |
tim |
702 |
#ifdef IS_MPI |
587 |
|
|
} |
588 |
|
|
#endif |
589 |
tim |
676 |
} |
590 |
tim |
701 |
|
591 |
|
|
|
592 |
|
|
/** |
593 |
|
|
* |
594 |
|
|
*/ |
595 |
tim |
676 |
|
596 |
|
|
template<typename T> double ZConstraint<T>::calcZSys() |
597 |
tim |
658 |
{ |
598 |
tim |
676 |
//calculate reference z coordinate for z-constraint molecules |
599 |
|
|
double totalMass_local; |
600 |
|
|
double totalMass; |
601 |
|
|
double totalMZ_local; |
602 |
|
|
double totalMZ; |
603 |
|
|
double massOfCurMol; |
604 |
|
|
double COM[3]; |
605 |
tim |
701 |
|
606 |
tim |
676 |
totalMass_local = 0; |
607 |
|
|
totalMZ_local = 0; |
608 |
|
|
|
609 |
|
|
for(int i = 0; i < nMols; i++){ |
610 |
|
|
massOfCurMol = molecules[i].getTotalMass(); |
611 |
|
|
molecules[i].getCOM(COM); |
612 |
|
|
|
613 |
|
|
totalMass_local += massOfCurMol; |
614 |
|
|
totalMZ_local += massOfCurMol * COM[whichDirection]; |
615 |
tim |
696 |
|
616 |
tim |
676 |
} |
617 |
tim |
696 |
|
618 |
tim |
676 |
|
619 |
|
|
#ifdef IS_MPI |
620 |
tim |
701 |
MPI_Allreduce(&totalMass_local, &totalMass, 1, |
621 |
|
|
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
622 |
|
|
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, |
623 |
|
|
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
624 |
tim |
696 |
#else |
625 |
tim |
676 |
totalMass = totalMass_local; |
626 |
|
|
totalMZ = totalMZ_local; |
627 |
tim |
696 |
#endif |
628 |
mmeineke |
671 |
|
629 |
tim |
658 |
double zsys; |
630 |
tim |
676 |
zsys = totalMZ / totalMass; |
631 |
tim |
658 |
|
632 |
tim |
676 |
return zsys; |
633 |
|
|
} |
634 |
|
|
|
635 |
|
|
/** |
636 |
|
|
* |
637 |
|
|
*/ |
638 |
|
|
template<typename T> void ZConstraint<T>::thermalize( void ){ |
639 |
|
|
|
640 |
|
|
T::thermalize(); |
641 |
|
|
zeroOutVel(); |
642 |
|
|
} |
643 |
|
|
|
644 |
|
|
/** |
645 |
|
|
* |
646 |
|
|
*/ |
647 |
|
|
|
648 |
|
|
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
649 |
|
|
|
650 |
|
|
Atom** fixedZAtoms; |
651 |
|
|
double COMvel[3]; |
652 |
|
|
double vel[3]; |
653 |
tim |
701 |
double zSysCOMVel; |
654 |
tim |
693 |
|
655 |
tim |
676 |
//zero out the velocities of center of mass of fixed z-constrained molecules |
656 |
|
|
|
657 |
mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
658 |
tim |
676 |
|
659 |
tim |
701 |
if (states[i] == zcsFixed){ |
660 |
tim |
676 |
|
661 |
tim |
701 |
zconsMols[i]->getCOMvel(COMvel); |
662 |
tim |
738 |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
663 |
tim |
693 |
|
664 |
tim |
676 |
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
665 |
tim |
701 |
|
666 |
tim |
676 |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
667 |
|
|
fixedZAtoms[j]->getVel(vel); |
668 |
tim |
701 |
vel[whichDirection] -= COMvel[whichDirection]; |
669 |
|
|
fixedZAtoms[j]->setVel(vel); |
670 |
tim |
676 |
} |
671 |
tim |
693 |
|
672 |
tim |
701 |
zconsMols[i]->getCOMvel(COMvel); |
673 |
|
|
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
674 |
tim |
676 |
} |
675 |
tim |
701 |
|
676 |
tim |
658 |
} |
677 |
tim |
693 |
|
678 |
tim |
701 |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
679 |
tim |
699 |
|
680 |
tim |
701 |
zSysCOMVel = calcSysCOMVel(); |
681 |
tim |
699 |
#ifdef IS_MPI |
682 |
tim |
701 |
if(worldRank == 0){ |
683 |
tim |
699 |
#endif |
684 |
tim |
738 |
//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
685 |
tim |
699 |
#ifdef IS_MPI |
686 |
|
|
} |
687 |
|
|
#endif |
688 |
tim |
701 |
|
689 |
tim |
676 |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
690 |
|
|
double MVzOfMovingMols_local; |
691 |
|
|
double MVzOfMovingMols; |
692 |
|
|
double totalMassOfMovingZMols_local; |
693 |
|
|
double totalMassOfMovingZMols; |
694 |
|
|
|
695 |
|
|
MVzOfMovingMols_local = 0; |
696 |
|
|
totalMassOfMovingZMols_local = 0; |
697 |
tim |
658 |
|
698 |
mmeineke |
787 |
for(int i =0; i < (int)(unconsMols.size()); i++){ |
699 |
tim |
676 |
unconsMols[i]->getCOMvel(COMvel); |
700 |
|
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
701 |
|
|
} |
702 |
|
|
|
703 |
mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
704 |
tim |
676 |
if (states[i] == zcsMoving){ |
705 |
|
|
zconsMols[i]->getCOMvel(COMvel); |
706 |
|
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
707 |
tim |
701 |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
708 |
tim |
676 |
} |
709 |
tim |
701 |
|
710 |
tim |
676 |
} |
711 |
|
|
|
712 |
|
|
#ifndef IS_MPI |
713 |
|
|
MVzOfMovingMols = MVzOfMovingMols_local; |
714 |
|
|
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
715 |
tim |
658 |
#else |
716 |
tim |
676 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
717 |
|
|
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
718 |
tim |
658 |
#endif |
719 |
|
|
|
720 |
tim |
676 |
double vzOfMovingMols; |
721 |
|
|
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
722 |
|
|
|
723 |
|
|
//modify the velocites of unconstrained molecules |
724 |
|
|
Atom** unconsAtoms; |
725 |
mmeineke |
787 |
for(int i = 0; i < (int)(unconsMols.size()); i++){ |
726 |
tim |
676 |
|
727 |
|
|
unconsAtoms = unconsMols[i]->getMyAtoms(); |
728 |
|
|
for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ |
729 |
|
|
unconsAtoms[j]->getVel(vel); |
730 |
|
|
vel[whichDirection] -= vzOfMovingMols; |
731 |
|
|
unconsAtoms[j]->setVel(vel); |
732 |
|
|
} |
733 |
|
|
|
734 |
|
|
} |
735 |
|
|
|
736 |
|
|
//modify the velocities of moving z-constrained molecuels |
737 |
|
|
Atom** movingZAtoms; |
738 |
mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
739 |
tim |
676 |
|
740 |
|
|
if (states[i] ==zcsMoving){ |
741 |
|
|
|
742 |
|
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
743 |
tim |
701 |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
744 |
tim |
676 |
movingZAtoms[j]->getVel(vel); |
745 |
|
|
vel[whichDirection] -= vzOfMovingMols; |
746 |
tim |
701 |
movingZAtoms[j]->setVel(vel); |
747 |
|
|
} |
748 |
|
|
|
749 |
tim |
693 |
} |
750 |
tim |
676 |
|
751 |
tim |
693 |
} |
752 |
tim |
676 |
|
753 |
tim |
701 |
|
754 |
|
|
zSysCOMVel = calcSysCOMVel(); |
755 |
tim |
699 |
#ifdef IS_MPI |
756 |
tim |
701 |
if(worldRank == 0){ |
757 |
tim |
699 |
#endif |
758 |
tim |
738 |
//cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
759 |
tim |
699 |
#ifdef IS_MPI |
760 |
|
|
} |
761 |
|
|
#endif |
762 |
tim |
693 |
|
763 |
tim |
676 |
} |
764 |
|
|
|
765 |
tim |
701 |
/** |
766 |
|
|
* |
767 |
|
|
*/ |
768 |
|
|
|
769 |
tim |
676 |
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
770 |
|
|
|
771 |
|
|
Atom** zconsAtoms; |
772 |
|
|
double totalFZ; |
773 |
|
|
double totalFZ_local; |
774 |
|
|
double COM[3]; |
775 |
|
|
double force[3]; |
776 |
|
|
|
777 |
tim |
701 |
//constrain the molecules which do not reach the specified positions |
778 |
tim |
676 |
|
779 |
|
|
//Zero Out the force of z-contrained molecules |
780 |
|
|
totalFZ_local = 0; |
781 |
|
|
|
782 |
|
|
//calculate the total z-contrained force of fixed z-contrained molecules |
783 |
tim |
738 |
|
784 |
|
|
//cout << "before zero out z-constraint force on fixed z-constraint molecuels " |
785 |
|
|
// << "total force is " << calcTotalForce() << endl; |
786 |
tim |
699 |
|
787 |
mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
788 |
tim |
701 |
|
789 |
tim |
676 |
if (states[i] == zcsFixed){ |
790 |
tim |
701 |
|
791 |
tim |
676 |
zconsMols[i]->getCOM(COM); |
792 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
793 |
|
|
|
794 |
|
|
fz[i] = 0; |
795 |
|
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
796 |
|
|
zconsAtoms[j]->getFrc(force); |
797 |
|
|
fz[i] += force[whichDirection]; |
798 |
tim |
701 |
} |
799 |
tim |
676 |
totalFZ_local += fz[i]; |
800 |
|
|
|
801 |
tim |
726 |
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
802 |
|
|
// <<"\tcurrent zpos: " << COM[whichDirection] |
803 |
tim |
738 |
// << "\tcurrent fz: " <<fz[i] << endl; |
804 |
tim |
676 |
|
805 |
tim |
726 |
|
806 |
tim |
676 |
} |
807 |
tim |
701 |
|
808 |
tim |
676 |
} |
809 |
tim |
699 |
|
810 |
|
|
//calculate total z-constraint force |
811 |
|
|
#ifdef IS_MPI |
812 |
|
|
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
813 |
|
|
#else |
814 |
|
|
totalFZ = totalFZ_local; |
815 |
|
|
#endif |
816 |
|
|
|
817 |
tim |
701 |
|
818 |
tim |
696 |
// apply negative to fixed z-constrained molecues; |
819 |
|
|
force[0]= 0; |
820 |
|
|
force[1]= 0; |
821 |
|
|
force[2]= 0; |
822 |
tim |
676 |
|
823 |
mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
824 |
tim |
696 |
|
825 |
|
|
if (states[i] == zcsFixed){ |
826 |
tim |
701 |
|
827 |
tim |
696 |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
828 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
829 |
|
|
|
830 |
|
|
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
831 |
tim |
726 |
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
832 |
|
|
force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
833 |
tim |
696 |
zconsAtoms[j]->addFrc(force); |
834 |
|
|
} |
835 |
tim |
701 |
|
836 |
tim |
696 |
} |
837 |
tim |
701 |
|
838 |
tim |
696 |
} |
839 |
|
|
|
840 |
tim |
738 |
//cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
841 |
|
|
// << "total force is " << calcTotalForce() << endl; |
842 |
|
|
|
843 |
tim |
699 |
|
844 |
tim |
676 |
force[0]= 0; |
845 |
|
|
force[1]= 0; |
846 |
|
|
force[2]= 0; |
847 |
|
|
|
848 |
tim |
693 |
//modify the forces of unconstrained molecules |
849 |
mmeineke |
787 |
for(int i = 0; i < (int)(unconsMols.size()); i++){ |
850 |
tim |
676 |
|
851 |
|
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
852 |
|
|
|
853 |
tim |
699 |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
854 |
tim |
726 |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
855 |
|
|
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
856 |
tim |
676 |
unconsAtoms[j]->addFrc(force); |
857 |
tim |
699 |
} |
858 |
tim |
676 |
|
859 |
|
|
} |
860 |
|
|
|
861 |
tim |
693 |
//modify the forces of moving z-constrained molecules |
862 |
mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++) { |
863 |
tim |
696 |
if (states[i] == zcsMoving){ |
864 |
tim |
701 |
|
865 |
tim |
696 |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
866 |
tim |
676 |
|
867 |
tim |
699 |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
868 |
tim |
726 |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
869 |
|
|
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
870 |
tim |
696 |
movingZAtoms[j]->addFrc(force); |
871 |
tim |
699 |
} |
872 |
tim |
696 |
} |
873 |
tim |
676 |
} |
874 |
tim |
738 |
// cout << "after substracting z-constraint force from moving molecuels " |
875 |
|
|
// << "total force is " << calcTotalForce() << endl; |
876 |
tim |
676 |
|
877 |
|
|
} |
878 |
|
|
|
879 |
tim |
701 |
/** |
880 |
|
|
* |
881 |
|
|
* |
882 |
|
|
*/ |
883 |
|
|
|
884 |
|
|
template<typename T> void ZConstraint<T>::doHarmonic(){ |
885 |
|
|
double force[3]; |
886 |
|
|
double harmonicU; |
887 |
|
|
double harmonicF; |
888 |
|
|
double COM[3]; |
889 |
|
|
double diff; |
890 |
|
|
double totalFZ_local; |
891 |
|
|
double totalFZ; |
892 |
|
|
|
893 |
|
|
force[0] = 0; |
894 |
|
|
force[1] = 0; |
895 |
|
|
force[2] = 0; |
896 |
|
|
|
897 |
|
|
totalFZ_local = 0; |
898 |
|
|
|
899 |
mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++) { |
900 |
tim |
701 |
|
901 |
|
|
if (states[i] == zcsMoving){ |
902 |
|
|
zconsMols[i]->getCOM(COM); |
903 |
mmeineke |
723 |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
904 |
|
|
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
905 |
tim |
726 |
|
906 |
|
|
diff = COM[whichDirection] -zPos[i]; |
907 |
tim |
701 |
|
908 |
|
|
harmonicU = 0.5 * kz[i] * diff * diff; |
909 |
tim |
726 |
info->lrPot += harmonicU; |
910 |
tim |
701 |
|
911 |
|
|
harmonicF = - kz[i] * diff; |
912 |
|
|
totalFZ_local += harmonicF; |
913 |
|
|
|
914 |
|
|
//adjust force |
915 |
|
|
|
916 |
|
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
917 |
|
|
|
918 |
|
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
919 |
tim |
726 |
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
920 |
|
|
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
921 |
tim |
701 |
movingZAtoms[j]->addFrc(force); |
922 |
|
|
} |
923 |
|
|
} |
924 |
|
|
|
925 |
|
|
} |
926 |
|
|
|
927 |
|
|
#ifndef IS_MPI |
928 |
|
|
totalFZ = totalFZ_local; |
929 |
|
|
#else |
930 |
|
|
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
931 |
|
|
#endif |
932 |
|
|
|
933 |
tim |
763 |
//cout << "before substracting harmonic force from moving molecuels " |
934 |
|
|
// << "total force is " << calcTotalForce() << endl; |
935 |
tim |
738 |
|
936 |
tim |
701 |
force[0]= 0; |
937 |
|
|
force[1]= 0; |
938 |
|
|
force[2]= 0; |
939 |
|
|
|
940 |
|
|
//modify the forces of unconstrained molecules |
941 |
mmeineke |
787 |
for(int i = 0; i < (int)(unconsMols.size()); i++){ |
942 |
tim |
701 |
|
943 |
|
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
944 |
|
|
|
945 |
|
|
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
946 |
tim |
726 |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
947 |
|
|
force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
948 |
tim |
701 |
unconsAtoms[j]->addFrc(force); |
949 |
|
|
} |
950 |
|
|
} |
951 |
|
|
|
952 |
tim |
763 |
//cout << "after substracting harmonic force from moving molecuels " |
953 |
|
|
// << "total force is " << calcTotalForce() << endl; |
954 |
tim |
738 |
|
955 |
tim |
701 |
} |
956 |
|
|
|
957 |
|
|
/** |
958 |
|
|
* |
959 |
|
|
*/ |
960 |
|
|
|
961 |
tim |
676 |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
962 |
|
|
double COM[3]; |
963 |
|
|
double diff; |
964 |
tim |
658 |
|
965 |
tim |
699 |
int changed_local; |
966 |
|
|
int changed; |
967 |
tim |
701 |
|
968 |
tim |
699 |
changed_local = 0; |
969 |
tim |
676 |
|
970 |
mmeineke |
787 |
for(int i =0; i < (int)(zconsMols.size()); i++){ |
971 |
tim |
676 |
|
972 |
tim |
658 |
zconsMols[i]->getCOM(COM); |
973 |
tim |
682 |
diff = fabs(COM[whichDirection] - zPos[i]); |
974 |
|
|
if ( diff <= zconsTol && states[i] == zcsMoving){ |
975 |
tim |
676 |
states[i] = zcsFixed; |
976 |
tim |
701 |
changed_local = 1; |
977 |
tim |
676 |
} |
978 |
tim |
682 |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
979 |
tim |
676 |
states[i] = zcsMoving; |
980 |
tim |
701 |
changed_local = 1; |
981 |
tim |
676 |
} |
982 |
|
|
|
983 |
tim |
658 |
} |
984 |
|
|
|
985 |
tim |
699 |
#ifndef IS_MPI |
986 |
|
|
changed =changed_local; |
987 |
|
|
#else |
988 |
|
|
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
989 |
|
|
#endif |
990 |
tim |
726 |
|
991 |
mmeineke |
711 |
return (changed > 0); |
992 |
tim |
726 |
|
993 |
tim |
658 |
} |
994 |
tim |
676 |
|
995 |
|
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
996 |
tim |
699 |
|
997 |
|
|
int havingFixed_local; |
998 |
|
|
int havingFixed; |
999 |
|
|
|
1000 |
|
|
havingFixed_local = 0; |
1001 |
|
|
|
1002 |
mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++) |
1003 |
tim |
699 |
if (states[i] == zcsFixed){ |
1004 |
|
|
havingFixed_local = 1; |
1005 |
tim |
701 |
break; |
1006 |
tim |
699 |
} |
1007 |
tim |
676 |
|
1008 |
tim |
699 |
#ifndef IS_MPI |
1009 |
|
|
havingFixed = havingFixed_local; |
1010 |
|
|
#else |
1011 |
|
|
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1012 |
|
|
#endif |
1013 |
|
|
|
1014 |
tim |
726 |
return (havingFixed > 0); |
1015 |
tim |
676 |
} |
1016 |
|
|
|
1017 |
|
|
|
1018 |
|
|
/** |
1019 |
|
|
* |
1020 |
|
|
*/ |
1021 |
|
|
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
1022 |
tim |
699 |
|
1023 |
|
|
int havingMoving_local; |
1024 |
|
|
int havingMoving; |
1025 |
|
|
|
1026 |
|
|
havingMoving_local = 0; |
1027 |
|
|
|
1028 |
mmeineke |
787 |
for(int i = 0; i < (int)(zconsMols.size()); i++) |
1029 |
tim |
699 |
if (states[i] == zcsMoving){ |
1030 |
|
|
havingMoving_local = 1; |
1031 |
tim |
701 |
break; |
1032 |
tim |
699 |
} |
1033 |
tim |
676 |
|
1034 |
tim |
699 |
#ifndef IS_MPI |
1035 |
|
|
havingMoving = havingMoving_local; |
1036 |
|
|
#else |
1037 |
|
|
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1038 |
|
|
#endif |
1039 |
|
|
|
1040 |
tim |
726 |
return (havingMoving > 0); |
1041 |
tim |
676 |
|
1042 |
tim |
682 |
} |
1043 |
|
|
|
1044 |
|
|
/** |
1045 |
tim |
701 |
* |
1046 |
|
|
*/ |
1047 |
tim |
682 |
|
1048 |
tim |
696 |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1049 |
tim |
693 |
{ |
1050 |
|
|
double MVzOfMovingMols_local; |
1051 |
|
|
double MVzOfMovingMols; |
1052 |
|
|
double totalMassOfMovingZMols_local; |
1053 |
|
|
double totalMassOfMovingZMols; |
1054 |
|
|
double COMvel[3]; |
1055 |
|
|
|
1056 |
|
|
MVzOfMovingMols_local = 0; |
1057 |
|
|
totalMassOfMovingZMols_local = 0; |
1058 |
|
|
|
1059 |
|
|
for(int i =0; i < unconsMols.size(); i++){ |
1060 |
|
|
unconsMols[i]->getCOMvel(COMvel); |
1061 |
|
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1062 |
|
|
} |
1063 |
|
|
|
1064 |
|
|
for(int i = 0; i < zconsMols.size(); i++){ |
1065 |
|
|
|
1066 |
|
|
if (states[i] == zcsMoving){ |
1067 |
|
|
zconsMols[i]->getCOMvel(COMvel); |
1068 |
|
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1069 |
tim |
701 |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1070 |
tim |
693 |
} |
1071 |
tim |
701 |
|
1072 |
tim |
693 |
} |
1073 |
|
|
|
1074 |
|
|
#ifndef IS_MPI |
1075 |
|
|
MVzOfMovingMols = MVzOfMovingMols_local; |
1076 |
|
|
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
1077 |
|
|
#else |
1078 |
|
|
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1079 |
|
|
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1080 |
|
|
#endif |
1081 |
|
|
|
1082 |
|
|
double vzOfMovingMols; |
1083 |
|
|
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
1084 |
|
|
|
1085 |
|
|
return vzOfMovingMols; |
1086 |
|
|
} |
1087 |
|
|
|
1088 |
tim |
701 |
/** |
1089 |
|
|
* |
1090 |
|
|
*/ |
1091 |
tim |
693 |
|
1092 |
tim |
696 |
template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1093 |
tim |
693 |
{ |
1094 |
|
|
double COMvel[3]; |
1095 |
tim |
699 |
double tempMVz_local; |
1096 |
|
|
double tempMVz; |
1097 |
|
|
double massOfZCons_local; |
1098 |
|
|
double massOfZCons; |
1099 |
|
|
|
1100 |
|
|
|
1101 |
|
|
tempMVz_local = 0; |
1102 |
|
|
|
1103 |
tim |
693 |
for(int i =0 ; i < nMols; i++){ |
1104 |
tim |
696 |
molecules[i].getCOMvel(COMvel); |
1105 |
tim |
701 |
tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1106 |
tim |
693 |
} |
1107 |
tim |
696 |
|
1108 |
|
|
massOfZCons_local = 0; |
1109 |
tim |
701 |
|
1110 |
mmeineke |
787 |
for(int i = 0; i < (int)(massOfZConsMols.size()); i++){ |
1111 |
tim |
696 |
massOfZCons_local += massOfZConsMols[i]; |
1112 |
|
|
} |
1113 |
|
|
#ifndef IS_MPI |
1114 |
|
|
massOfZCons = massOfZCons_local; |
1115 |
tim |
699 |
tempMVz = tempMVz_local; |
1116 |
tim |
696 |
#else |
1117 |
|
|
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1118 |
tim |
699 |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1119 |
tim |
696 |
#endif |
1120 |
|
|
|
1121 |
|
|
return tempMVz /(totalMassOfUncons + massOfZCons); |
1122 |
tim |
693 |
} |
1123 |
tim |
696 |
|
1124 |
tim |
701 |
/** |
1125 |
|
|
* |
1126 |
|
|
*/ |
1127 |
|
|
|
1128 |
tim |
696 |
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1129 |
|
|
|
1130 |
|
|
double force[3]; |
1131 |
|
|
double totalForce_local; |
1132 |
|
|
double totalForce; |
1133 |
|
|
|
1134 |
|
|
totalForce_local = 0; |
1135 |
|
|
|
1136 |
|
|
for(int i = 0; i < nAtoms; i++){ |
1137 |
|
|
atoms[i]->getFrc(force); |
1138 |
|
|
totalForce_local += force[whichDirection]; |
1139 |
|
|
} |
1140 |
|
|
|
1141 |
|
|
#ifndef IS_MPI |
1142 |
|
|
totalForce = totalForce_local; |
1143 |
|
|
#else |
1144 |
|
|
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1145 |
|
|
#endif |
1146 |
|
|
|
1147 |
|
|
return totalForce; |
1148 |
|
|
|
1149 |
|
|
} |
1150 |
tim |
699 |
|
1151 |
|
|
/** |
1152 |
|
|
* |
1153 |
|
|
*/ |
1154 |
|
|
|
1155 |
|
|
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1156 |
|
|
//calculate the number of atoms of moving z-constrained molecules |
1157 |
|
|
int nMovingZAtoms_local; |
1158 |
|
|
int nMovingZAtoms; |
1159 |
tim |
701 |
|
1160 |
tim |
699 |
nMovingZAtoms_local = 0; |
1161 |
mmeineke |
787 |
for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++) |
1162 |
tim |
699 |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1163 |
tim |
701 |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1164 |
tim |
699 |
|
1165 |
|
|
#ifdef IS_MPI |
1166 |
|
|
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1167 |
|
|
#else |
1168 |
|
|
nMovingZAtoms = nMovingZAtoms_local; |
1169 |
|
|
#endif |
1170 |
|
|
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1171 |
|
|
} |
1172 |
|
|
|
1173 |
tim |
701 |
template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1174 |
tim |
699 |
return totalForce / mol->getNAtoms(); |
1175 |
|
|
} |
1176 |
|
|
|
1177 |
|
|
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1178 |
|
|
return totalForce / totNumOfMovingAtoms; |
1179 |
|
|
} |
1180 |
|
|
|
1181 |
|
|
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1182 |
|
|
return totalForce / mol->getNAtoms(); |
1183 |
|
|
} |
1184 |
|
|
|
1185 |
|
|
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1186 |
|
|
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1187 |
|
|
} |
1188 |
|
|
|
1189 |
|
|
/** |
1190 |
|
|
* |
1191 |
|
|
*/ |
1192 |
|
|
|
1193 |
|
|
template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1194 |
|
|
//calculate the number of atoms of moving z-constrained molecules |
1195 |
|
|
double massOfMovingZAtoms_local; |
1196 |
|
|
double massOfMovingZAtoms; |
1197 |
tim |
701 |
|
1198 |
tim |
699 |
massOfMovingZAtoms_local = 0; |
1199 |
mmeineke |
787 |
for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++) |
1200 |
tim |
699 |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1201 |
tim |
701 |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1202 |
tim |
699 |
|
1203 |
|
|
#ifdef IS_MPI |
1204 |
|
|
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1205 |
|
|
#else |
1206 |
|
|
massOfMovingZAtoms = massOfMovingZAtoms_local; |
1207 |
|
|
#endif |
1208 |
tim |
738 |
totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons; |
1209 |
tim |
699 |
} |
1210 |
|
|
|
1211 |
|
|
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1212 |
|
|
return totalForce * atom->getMass() / mol->getTotalMass(); |
1213 |
|
|
} |
1214 |
|
|
|
1215 |
|
|
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1216 |
|
|
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1217 |
|
|
} |
1218 |
|
|
|
1219 |
|
|
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1220 |
|
|
return totalForce * atom->getMass() / mol->getTotalMass(); |
1221 |
|
|
} |
1222 |
|
|
|
1223 |
|
|
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1224 |
|
|
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1225 |
|
|
} |
1226 |
|
|
|