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tim |
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#include "Integrator.hpp"
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#include "simError.h"
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#include <math.h>
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const double INFINITE_TIME = 10e30;
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template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo,
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ForceFields* the_ff): T(theInfo, the_ff),
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fzOut(NULL),
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curZconsTime(0),
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forcePolicy(NULL),
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usingSMD(false),
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hasZConsGap(false){
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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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DoubleData* gap;
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DoubleData* fixtime;
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StringData* policy;
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StringData* filename;
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IntData* smdFlag;
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double COM[3];
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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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//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])) /
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2;
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zForceConst = Kb * info->target_temp / (halfOfLargestBox * halfOfLargestBox);
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//creat force Subtraction policy
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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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"ZConstraint Warning: User does not set force Subtraction policy, "
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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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if (!policy){
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sprintf(painCave.errMsg,
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"ZConstraint Error: Convertion from GenericData to StringData failure, "
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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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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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else{
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sprintf(painCave.errMsg,
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"ZConstraint Warning: unknown force Subtraction policy, "
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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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}
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}
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//retrieve sample time of z-contraint
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data = info->getProperty(ZCONSTIME_ID);
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if (!data){
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sprintf(painCave.errMsg,
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"ZConstraint error: If you use an ZConstraint\n"
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" , you must set sample time.\n");
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painCave.isFatal = 1;
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simError();
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}
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else{
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sampleTime = dynamic_cast<DoubleData*>(data);
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if (!sampleTime){
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sprintf(painCave.errMsg,
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"ZConstraint error: Can not get property from SimInfo\n");
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painCave.isFatal = 1;
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simError();
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}
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else{
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this->zconsTime = sampleTime->getData();
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}
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}
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//retrieve output filename of z force
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data = info->getProperty(ZCONSFILENAME_ID);
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if (!data){
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sprintf(painCave.errMsg,
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"ZConstraint error: If you use an ZConstraint\n"
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" , you must set output filename of z-force.\n");
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painCave.isFatal = 1;
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simError();
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}
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else{
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filename = dynamic_cast<StringData*>(data);
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if (!filename){
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sprintf(painCave.errMsg,
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"ZConstraint error: Can not get property from SimInfo\n");
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painCave.isFatal = 1;
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simError();
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}
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else{
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this->zconsOutput = filename->getData();
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}
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}
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//retrieve tolerance for z-constraint molecuels
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data = info->getProperty(ZCONSTOL_ID);
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if (!data){
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sprintf(painCave.errMsg, "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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//quick hack here
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data = info->getProperty(ZCONSGAP_ID);
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if (data){
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gap = dynamic_cast<DoubleData*>(data);
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if (!gap){
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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->hasZConsGap = true;
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this->zconsGap = gap->getData();
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}
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}
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tim |
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tim |
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data = info->getProperty(ZCONSFIXTIME_ID);
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if (data){
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fixtime = dynamic_cast<DoubleData*>(data);
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tim |
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if (!fixtime){
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sprintf(painCave.errMsg,
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"ZConstraint error: Can not get zconsFixTime 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->zconsFixTime = fixtime->getData();
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}
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}
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else if(hasZConsGap){
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sprintf(painCave.errMsg,
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"ZConstraint error: must set fixtime if already set zconsGap\n");
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painCave.isFatal = 1;
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simError();
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}
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tim |
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tim |
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data = info->getProperty(ZCONSUSINGSMD_ID);
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if (data){
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smdFlag = dynamic_cast<IntData*>(data);
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if (!smdFlag){
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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->usingSMD= smdFlag->getData() ? true : false;
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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, "ZConstraint error: index is out of range\n");
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painCave.isFatal = 1;
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simError();
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}
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maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
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#ifndef IS_MPI
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totalNumMol = nMols;
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#else
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totalNumMol = mpiSim->getTotNmol();
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#endif
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if (maxIndex > totalNumMol - 1){
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sprintf(painCave.errMsg, "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 < (int) (parameters->size()); i++){
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if (!(*parameters)[i].havingZPos){
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#ifndef IS_MPI
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for (int j = 0; j < nMols; j++){
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if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
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molecules[j].getCOM(COM);
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break;
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}
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}
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#else
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//query which processor current zconstraint molecule belongs to
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int* MolToProcMap;
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int whichNode;
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MolToProcMap = mpiSim->getMolToProcMap();
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whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
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//broadcast the zpos of current z-contraint molecule
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//the node which contain this
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if (worldRank == whichNode){
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for (int j = 0; j < nMols; j++)
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if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
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molecules[j].getCOM(COM);
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break;
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}
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}
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MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode,
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MPI_COMM_WORLD);
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#endif
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292 |
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(*parameters)[i].zPos = COM[whichDirection];
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sprintf(painCave.errMsg,
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"ZConstraint warning: 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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307 |
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#ifdef IS_MPI
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308 |
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update();
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309 |
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#else
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310 |
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int searchResult;
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311 |
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312 |
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for (int i = 0; i < nMols; i++){
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313 |
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searchResult = isZConstraintMol(&molecules[i]);
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314 |
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if (searchResult > -1){
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316 |
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zconsMols.push_back(&molecules[i]);
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317 |
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massOfZConsMols.push_back(molecules[i].getTotalMass());
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318 |
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319 |
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zPos.push_back((*parameters)[searchResult].zPos);
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320 |
tim |
1093 |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
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321 |
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322 |
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if(usingSMD)
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323 |
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cantVel.push_back((*parameters)[searchResult].cantVel);
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324 |
tim |
1091 |
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}
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326 |
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else{
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327 |
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unconsMols.push_back(&molecules[i]);
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328 |
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massOfUnconsMols.push_back(molecules[i].getTotalMass());
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329 |
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}
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330 |
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}
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331 |
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332 |
tim |
1093 |
fz.resize(zconsMols.size());
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333 |
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curZPos.resize(zconsMols.size());
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334 |
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indexOfZConsMols.resize(zconsMols.size());
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335 |
tim |
1091 |
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336 |
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//determine the states of z-constraint molecules
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337 |
tim |
1093 |
for (size_t i = 0; i < zconsMols.size(); i++){
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338 |
tim |
1091 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
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339 |
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340 |
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zconsMols[i]->getCOM(COM);
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341 |
tim |
1093 |
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342 |
tim |
1091 |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){
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343 |
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states.push_back(zcsFixed);
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344 |
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345 |
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if (hasZConsGap)
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346 |
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endFixTime.push_back(info->getTime() + zconsFixTime);
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347 |
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}
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348 |
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else{
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349 |
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states.push_back(zcsMoving);
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350 |
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351 |
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if (hasZConsGap)
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endFixTime.push_back(INFINITE_TIME);
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}
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354 |
tim |
1093 |
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355 |
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if(usingSMD)
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356 |
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cantPos.push_back(COM[whichDirection]);
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357 |
tim |
1091 |
}
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358 |
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359 |
tim |
1141 |
if(usingSMD)
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360 |
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prevCantPos = cantPos;
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361 |
tim |
1091 |
#endif
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362 |
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363 |
tim |
1093 |
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364 |
tim |
1091 |
//get total masss of unconstraint molecules
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365 |
|
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double totalMassOfUncons_local;
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366 |
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totalMassOfUncons_local = 0;
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367 |
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368 |
tim |
1093 |
for (size_t i = 0; i < unconsMols.size(); i++)
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369 |
tim |
1091 |
totalMassOfUncons_local += unconsMols[i]->getTotalMass();
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370 |
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371 |
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#ifndef IS_MPI
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372 |
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totalMassOfUncons = totalMassOfUncons_local;
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373 |
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#else
|
374 |
|
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MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,
|
375 |
|
|
MPI_SUM, MPI_COMM_WORLD);
|
376 |
|
|
#endif
|
377 |
|
|
|
378 |
|
|
//get total number of unconstrained atoms
|
379 |
|
|
int nUnconsAtoms_local;
|
380 |
|
|
nUnconsAtoms_local = 0;
|
381 |
|
|
for (int i = 0; i < (int) (unconsMols.size()); i++)
|
382 |
|
|
nUnconsAtoms_local += unconsMols[i]->getNAtoms();
|
383 |
|
|
|
384 |
|
|
#ifndef IS_MPI
|
385 |
|
|
totNumOfUnconsAtoms = nUnconsAtoms_local;
|
386 |
|
|
#else
|
387 |
|
|
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT, MPI_SUM,
|
388 |
|
|
MPI_COMM_WORLD);
|
389 |
|
|
#endif
|
390 |
|
|
|
391 |
|
|
forcePolicy->update();
|
392 |
|
|
}
|
393 |
|
|
|
394 |
|
|
template<typename T> ZConstraint<T>::~ZConstraint(){
|
395 |
|
|
|
396 |
|
|
if (fzOut){
|
397 |
|
|
delete fzOut;
|
398 |
|
|
}
|
399 |
|
|
|
400 |
|
|
if (forcePolicy){
|
401 |
|
|
delete forcePolicy;
|
402 |
|
|
}
|
403 |
|
|
}
|
404 |
|
|
|
405 |
|
|
|
406 |
|
|
/**
|
407 |
|
|
*
|
408 |
|
|
*/
|
409 |
|
|
|
410 |
|
|
#ifdef IS_MPI
|
411 |
|
|
template<typename T> void ZConstraint<T>::update(){
|
412 |
|
|
double COM[3];
|
413 |
|
|
int index;
|
414 |
|
|
|
415 |
|
|
zconsMols.clear();
|
416 |
|
|
massOfZConsMols.clear();
|
417 |
|
|
zPos.clear();
|
418 |
|
|
kz.clear();
|
419 |
tim |
1093 |
cantPos.clear();
|
420 |
|
|
cantVel.clear();
|
421 |
tim |
1091 |
|
422 |
|
|
unconsMols.clear();
|
423 |
|
|
massOfUnconsMols.clear();
|
424 |
|
|
|
425 |
|
|
|
426 |
|
|
//creat zconsMol and unconsMol lists
|
427 |
|
|
for (int i = 0; i < nMols; i++){
|
428 |
|
|
index = isZConstraintMol(&molecules[i]);
|
429 |
|
|
|
430 |
|
|
if (index > -1){
|
431 |
|
|
zconsMols.push_back(&molecules[i]);
|
432 |
|
|
zPos.push_back((*parameters)[index].zPos);
|
433 |
|
|
kz.push_back((*parameters)[index].kRatio * zForceConst);
|
434 |
tim |
1093 |
massOfZConsMols.push_back(molecules[i].getTotalMass());
|
435 |
|
|
|
436 |
|
|
if(usingSMD)
|
437 |
|
|
cantVel.push_back((*parameters)[index].cantVel);
|
438 |
tim |
1091 |
|
439 |
|
|
}
|
440 |
|
|
else{
|
441 |
|
|
unconsMols.push_back(&molecules[i]);
|
442 |
|
|
massOfUnconsMols.push_back(molecules[i].getTotalMass());
|
443 |
|
|
}
|
444 |
|
|
}
|
445 |
|
|
|
446 |
tim |
1093 |
fz.resize(zconsMols.size());
|
447 |
|
|
curZPos.resize(zconsMols.size());
|
448 |
|
|
indexOfZConsMols.resize(zconsMols.size());
|
449 |
|
|
|
450 |
|
|
for (size_t i = 0; i < zconsMols.size(); i++){
|
451 |
|
|
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
|
452 |
tim |
1091 |
}
|
453 |
tim |
1093 |
|
454 |
tim |
1091 |
//determine the states of z-constraint molecules
|
455 |
|
|
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
456 |
tim |
1093 |
|
457 |
tim |
1091 |
zconsMols[i]->getCOM(COM);
|
458 |
tim |
1093 |
|
459 |
tim |
1091 |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){
|
460 |
|
|
states.push_back(zcsFixed);
|
461 |
|
|
|
462 |
|
|
if (hasZConsGap)
|
463 |
|
|
endFixTime.push_back(info->getTime() + zconsFixTime);
|
464 |
|
|
}
|
465 |
|
|
else{
|
466 |
|
|
states.push_back(zcsMoving);
|
467 |
|
|
|
468 |
|
|
if (hasZConsGap)
|
469 |
|
|
endFixTime.push_back(INFINITE_TIME);
|
470 |
|
|
}
|
471 |
tim |
1093 |
|
472 |
|
|
if(usingSMD)
|
473 |
|
|
cantPos.push_back(COM[whichDirection]);
|
474 |
tim |
1091 |
}
|
475 |
tim |
1141 |
|
476 |
|
|
if(usingSMD)
|
477 |
|
|
prevCantPos = cantPos;
|
478 |
|
|
|
479 |
tim |
1091 |
//
|
480 |
|
|
forcePolicy->update();
|
481 |
|
|
}
|
482 |
|
|
|
483 |
|
|
#endif
|
484 |
|
|
|
485 |
|
|
/**
|
486 |
|
|
* Function Name: isZConstraintMol
|
487 |
|
|
* Parameter
|
488 |
|
|
* Molecule* mol
|
489 |
|
|
* Return value:
|
490 |
|
|
* -1, if the molecule is not z-constraint molecule,
|
491 |
|
|
* other non-negative values, its index in indexOfAllZConsMols vector
|
492 |
|
|
*/
|
493 |
|
|
|
494 |
|
|
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol){
|
495 |
|
|
int index;
|
496 |
|
|
int low;
|
497 |
|
|
int high;
|
498 |
|
|
int mid;
|
499 |
|
|
|
500 |
|
|
index = mol->getGlobalIndex();
|
501 |
|
|
|
502 |
|
|
low = 0;
|
503 |
|
|
high = parameters->size() - 1;
|
504 |
|
|
|
505 |
|
|
//Binary Search (we have sorted the array)
|
506 |
|
|
while (low <= high){
|
507 |
|
|
mid = (low + high) / 2;
|
508 |
|
|
if ((*parameters)[mid].zconsIndex == index)
|
509 |
|
|
return mid;
|
510 |
|
|
else if ((*parameters)[mid].zconsIndex > index)
|
511 |
|
|
high = mid - 1;
|
512 |
|
|
else
|
513 |
|
|
low = mid + 1;
|
514 |
|
|
}
|
515 |
|
|
|
516 |
|
|
return -1;
|
517 |
|
|
}
|
518 |
|
|
|
519 |
|
|
template<typename T> void ZConstraint<T>::integrate(){
|
520 |
|
|
// creat zconsWriter
|
521 |
|
|
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);
|
522 |
|
|
|
523 |
|
|
if (!fzOut){
|
524 |
|
|
sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n");
|
525 |
|
|
painCave.isFatal = 1;
|
526 |
|
|
simError();
|
527 |
|
|
}
|
528 |
|
|
|
529 |
|
|
//zero out the velocities of center of mass of unconstrained molecules
|
530 |
|
|
//and the velocities of center of mass of every single z-constrained molecueles
|
531 |
|
|
zeroOutVel();
|
532 |
|
|
|
533 |
|
|
curZconsTime = zconsTime + info->getTime();
|
534 |
|
|
|
535 |
|
|
T::integrate();
|
536 |
|
|
}
|
537 |
|
|
|
538 |
|
|
|
539 |
|
|
/**
|
540 |
|
|
*
|
541 |
|
|
*
|
542 |
|
|
*
|
543 |
|
|
*
|
544 |
|
|
*/
|
545 |
|
|
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
|
546 |
|
|
double zsys;
|
547 |
|
|
double COM[3];
|
548 |
|
|
double force[3];
|
549 |
|
|
double zSysCOMVel;
|
550 |
|
|
|
551 |
|
|
T::calcForce(calcPot, calcStress);
|
552 |
|
|
|
553 |
|
|
|
554 |
|
|
if (hasZConsGap){
|
555 |
|
|
updateZPos();
|
556 |
|
|
}
|
557 |
|
|
|
558 |
|
|
if (checkZConsState()){
|
559 |
|
|
zeroOutVel();
|
560 |
|
|
forcePolicy->update();
|
561 |
|
|
}
|
562 |
|
|
|
563 |
|
|
zsys = calcZSys();
|
564 |
|
|
zSysCOMVel = calcSysCOMVel();
|
565 |
|
|
#ifdef IS_MPI
|
566 |
|
|
if (worldRank == 0){
|
567 |
|
|
#endif
|
568 |
|
|
//cout << "---------------------------------------------------------------------" <<endl;
|
569 |
|
|
//cout << "current time: " << info->getTime() << endl;
|
570 |
|
|
//cout << "center of mass at z: " << zsys << endl;
|
571 |
|
|
//cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
|
572 |
|
|
|
573 |
|
|
#ifdef IS_MPI
|
574 |
|
|
}
|
575 |
|
|
#endif
|
576 |
|
|
|
577 |
|
|
//do zconstraint force;
|
578 |
|
|
if (haveFixedZMols()){
|
579 |
|
|
this->doZconstraintForce();
|
580 |
|
|
}
|
581 |
|
|
|
582 |
tim |
1093 |
//use external force to move the molecules to the specified positions
|
583 |
tim |
1091 |
if (haveMovingZMols()){
|
584 |
tim |
1093 |
if (usingSMD)
|
585 |
|
|
this->doHarmonic(cantPos);
|
586 |
|
|
else
|
587 |
|
|
this->doHarmonic(zPos);
|
588 |
tim |
1091 |
}
|
589 |
|
|
|
590 |
|
|
//write out forces and current positions of z-constraint molecules
|
591 |
|
|
if (info->getTime() >= curZconsTime){
|
592 |
|
|
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
593 |
|
|
zconsMols[i]->getCOM(COM);
|
594 |
|
|
curZPos[i] = COM[whichDirection];
|
595 |
|
|
|
596 |
|
|
//if the z-constraint molecule is still moving, just record its force
|
597 |
|
|
if (states[i] == zcsMoving){
|
598 |
|
|
fz[i] = 0;
|
599 |
|
|
Atom** movingZAtoms;
|
600 |
|
|
movingZAtoms = zconsMols[i]->getMyAtoms();
|
601 |
|
|
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
|
602 |
|
|
movingZAtoms[j]->getFrc(force);
|
603 |
|
|
fz[i] += force[whichDirection];
|
604 |
|
|
}
|
605 |
|
|
}
|
606 |
|
|
}
|
607 |
tim |
1093 |
fzOut->writeFZ(info->getTime(), zconsMols.size(), &indexOfZConsMols[0], &fz[0],
|
608 |
|
|
&curZPos[0], &zPos[0]);
|
609 |
tim |
1091 |
curZconsTime += zconsTime;
|
610 |
|
|
}
|
611 |
|
|
|
612 |
|
|
zSysCOMVel = calcSysCOMVel();
|
613 |
|
|
#ifdef IS_MPI
|
614 |
|
|
if (worldRank == 0){
|
615 |
|
|
#endif
|
616 |
|
|
//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
|
617 |
|
|
#ifdef IS_MPI
|
618 |
|
|
}
|
619 |
|
|
#endif
|
620 |
|
|
}
|
621 |
|
|
|
622 |
|
|
|
623 |
|
|
/**
|
624 |
|
|
*
|
625 |
|
|
*/
|
626 |
|
|
|
627 |
|
|
template<typename T> double ZConstraint<T>::calcZSys(){
|
628 |
|
|
//calculate reference z coordinate for z-constraint molecules
|
629 |
|
|
double totalMass_local;
|
630 |
|
|
double totalMass;
|
631 |
|
|
double totalMZ_local;
|
632 |
|
|
double totalMZ;
|
633 |
|
|
double massOfCurMol;
|
634 |
|
|
double COM[3];
|
635 |
|
|
|
636 |
|
|
totalMass_local = 0;
|
637 |
|
|
totalMZ_local = 0;
|
638 |
|
|
|
639 |
|
|
for (int i = 0; i < nMols; i++){
|
640 |
|
|
massOfCurMol = molecules[i].getTotalMass();
|
641 |
|
|
molecules[i].getCOM(COM);
|
642 |
|
|
|
643 |
|
|
totalMass_local += massOfCurMol;
|
644 |
|
|
totalMZ_local += massOfCurMol * COM[whichDirection];
|
645 |
|
|
}
|
646 |
|
|
|
647 |
|
|
|
648 |
|
|
#ifdef IS_MPI
|
649 |
|
|
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM,
|
650 |
|
|
MPI_COMM_WORLD);
|
651 |
|
|
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
|
652 |
|
|
#else
|
653 |
|
|
totalMass = totalMass_local;
|
654 |
|
|
totalMZ = totalMZ_local;
|
655 |
|
|
#endif
|
656 |
|
|
|
657 |
|
|
double zsys;
|
658 |
|
|
zsys = totalMZ / totalMass;
|
659 |
|
|
|
660 |
|
|
return zsys;
|
661 |
|
|
}
|
662 |
|
|
|
663 |
|
|
/**
|
664 |
|
|
*
|
665 |
|
|
*/
|
666 |
|
|
template<typename T> void ZConstraint<T>::thermalize(void){
|
667 |
|
|
T::thermalize();
|
668 |
|
|
zeroOutVel();
|
669 |
|
|
}
|
670 |
|
|
|
671 |
|
|
/**
|
672 |
|
|
*
|
673 |
|
|
*/
|
674 |
|
|
|
675 |
|
|
template<typename T> void ZConstraint<T>::zeroOutVel(){
|
676 |
|
|
Atom** fixedZAtoms;
|
677 |
|
|
double COMvel[3];
|
678 |
|
|
double vel[3];
|
679 |
|
|
double zSysCOMVel;
|
680 |
|
|
|
681 |
|
|
//zero out the velocities of center of mass of fixed z-constrained molecules
|
682 |
|
|
|
683 |
|
|
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
684 |
|
|
if (states[i] == zcsFixed){
|
685 |
|
|
zconsMols[i]->getCOMvel(COMvel);
|
686 |
|
|
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
|
687 |
|
|
|
688 |
|
|
fixedZAtoms = zconsMols[i]->getMyAtoms();
|
689 |
|
|
|
690 |
|
|
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
|
691 |
|
|
fixedZAtoms[j]->getVel(vel);
|
692 |
|
|
vel[whichDirection] -= COMvel[whichDirection];
|
693 |
|
|
fixedZAtoms[j]->setVel(vel);
|
694 |
|
|
}
|
695 |
|
|
|
696 |
|
|
zconsMols[i]->getCOMvel(COMvel);
|
697 |
|
|
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
|
698 |
|
|
}
|
699 |
|
|
}
|
700 |
|
|
|
701 |
|
|
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
|
702 |
|
|
|
703 |
|
|
zSysCOMVel = calcSysCOMVel();
|
704 |
|
|
#ifdef IS_MPI
|
705 |
|
|
if (worldRank == 0){
|
706 |
|
|
#endif
|
707 |
|
|
//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;
|
708 |
|
|
#ifdef IS_MPI
|
709 |
|
|
}
|
710 |
|
|
#endif
|
711 |
|
|
|
712 |
|
|
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
|
713 |
|
|
double MVzOfMovingMols_local;
|
714 |
|
|
double MVzOfMovingMols;
|
715 |
|
|
double totalMassOfMovingZMols_local;
|
716 |
|
|
double totalMassOfMovingZMols;
|
717 |
|
|
|
718 |
|
|
MVzOfMovingMols_local = 0;
|
719 |
|
|
totalMassOfMovingZMols_local = 0;
|
720 |
|
|
|
721 |
|
|
for (int i = 0; i < (int) (unconsMols.size()); i++){
|
722 |
|
|
unconsMols[i]->getCOMvel(COMvel);
|
723 |
|
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
|
724 |
|
|
}
|
725 |
|
|
|
726 |
|
|
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
727 |
|
|
if (states[i] == zcsMoving){
|
728 |
|
|
zconsMols[i]->getCOMvel(COMvel);
|
729 |
|
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
|
730 |
|
|
totalMassOfMovingZMols_local += massOfZConsMols[i];
|
731 |
|
|
}
|
732 |
|
|
}
|
733 |
|
|
|
734 |
|
|
#ifndef IS_MPI
|
735 |
|
|
MVzOfMovingMols = MVzOfMovingMols_local;
|
736 |
|
|
totalMassOfMovingZMols = totalMassOfMovingZMols_local;
|
737 |
|
|
#else
|
738 |
|
|
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,
|
739 |
|
|
MPI_SUM, MPI_COMM_WORLD);
|
740 |
|
|
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,
|
741 |
|
|
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
|
742 |
|
|
#endif
|
743 |
|
|
|
744 |
|
|
double vzOfMovingMols;
|
745 |
|
|
vzOfMovingMols = MVzOfMovingMols /
|
746 |
|
|
(totalMassOfUncons + totalMassOfMovingZMols);
|
747 |
|
|
|
748 |
|
|
//modify the velocites of unconstrained molecules
|
749 |
|
|
Atom** unconsAtoms;
|
750 |
|
|
for (int i = 0; i < (int) (unconsMols.size()); i++){
|
751 |
|
|
unconsAtoms = unconsMols[i]->getMyAtoms();
|
752 |
|
|
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
|
753 |
|
|
unconsAtoms[j]->getVel(vel);
|
754 |
|
|
vel[whichDirection] -= vzOfMovingMols;
|
755 |
|
|
unconsAtoms[j]->setVel(vel);
|
756 |
|
|
}
|
757 |
|
|
}
|
758 |
|
|
|
759 |
|
|
//modify the velocities of moving z-constrained molecuels
|
760 |
|
|
Atom** movingZAtoms;
|
761 |
|
|
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
762 |
|
|
if (states[i] == zcsMoving){
|
763 |
|
|
movingZAtoms = zconsMols[i]->getMyAtoms();
|
764 |
|
|
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
|
765 |
|
|
movingZAtoms[j]->getVel(vel);
|
766 |
|
|
vel[whichDirection] -= vzOfMovingMols;
|
767 |
|
|
movingZAtoms[j]->setVel(vel);
|
768 |
|
|
}
|
769 |
|
|
}
|
770 |
|
|
}
|
771 |
|
|
|
772 |
|
|
|
773 |
|
|
zSysCOMVel = calcSysCOMVel();
|
774 |
|
|
#ifdef IS_MPI
|
775 |
|
|
if (worldRank == 0){
|
776 |
|
|
#endif
|
777 |
|
|
//cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;
|
778 |
|
|
#ifdef IS_MPI
|
779 |
|
|
}
|
780 |
|
|
#endif
|
781 |
|
|
}
|
782 |
|
|
|
783 |
|
|
/**
|
784 |
|
|
*
|
785 |
|
|
*/
|
786 |
|
|
|
787 |
|
|
template<typename T> void ZConstraint<T>::doZconstraintForce(){
|
788 |
|
|
Atom** zconsAtoms;
|
789 |
|
|
double totalFZ;
|
790 |
|
|
double totalFZ_local;
|
791 |
|
|
double COM[3];
|
792 |
|
|
double force[3];
|
793 |
|
|
|
794 |
|
|
//constrain the molecules which do not reach the specified positions
|
795 |
|
|
|
796 |
|
|
//Zero Out the force of z-contrained molecules
|
797 |
|
|
totalFZ_local = 0;
|
798 |
|
|
|
799 |
|
|
//calculate the total z-contrained force of fixed z-contrained molecules
|
800 |
|
|
|
801 |
|
|
//cout << "before zero out z-constraint force on fixed z-constraint molecuels "
|
802 |
|
|
// << "total force is " << calcTotalForce() << endl;
|
803 |
|
|
|
804 |
|
|
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
805 |
|
|
if (states[i] == zcsFixed){
|
806 |
|
|
zconsMols[i]->getCOM(COM);
|
807 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms();
|
808 |
|
|
|
809 |
|
|
fz[i] = 0;
|
810 |
|
|
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
|
811 |
|
|
zconsAtoms[j]->getFrc(force);
|
812 |
|
|
fz[i] += force[whichDirection];
|
813 |
|
|
}
|
814 |
|
|
totalFZ_local += fz[i];
|
815 |
|
|
|
816 |
|
|
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
|
817 |
|
|
// <<"\tcurrent zpos: " << COM[whichDirection]
|
818 |
|
|
// << "\tcurrent fz: " <<fz[i] << endl;
|
819 |
|
|
}
|
820 |
|
|
}
|
821 |
|
|
|
822 |
|
|
//calculate total z-constraint force
|
823 |
|
|
#ifdef IS_MPI
|
824 |
|
|
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
|
825 |
|
|
#else
|
826 |
|
|
totalFZ = totalFZ_local;
|
827 |
|
|
#endif
|
828 |
|
|
|
829 |
|
|
|
830 |
|
|
// apply negative to fixed z-constrained molecues;
|
831 |
|
|
force[0] = 0;
|
832 |
|
|
force[1] = 0;
|
833 |
|
|
force[2] = 0;
|
834 |
|
|
|
835 |
|
|
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
836 |
|
|
if (states[i] == zcsFixed){
|
837 |
|
|
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
|
838 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms();
|
839 |
|
|
|
840 |
|
|
for (int j = 0; j < nAtomOfCurZConsMol; j++){
|
841 |
|
|
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
|
842 |
|
|
force[whichDirection] = -forcePolicy->getZFOfFixedZMols(zconsMols[i],
|
843 |
|
|
zconsAtoms[j],
|
844 |
|
|
fz[i]);
|
845 |
|
|
zconsAtoms[j]->addFrc(force);
|
846 |
|
|
}
|
847 |
|
|
}
|
848 |
|
|
}
|
849 |
|
|
|
850 |
|
|
//cout << "after zero out z-constraint force on fixed z-constraint molecuels "
|
851 |
|
|
// << "total force is " << calcTotalForce() << endl;
|
852 |
|
|
|
853 |
|
|
|
854 |
|
|
force[0] = 0;
|
855 |
|
|
force[1] = 0;
|
856 |
|
|
force[2] = 0;
|
857 |
|
|
|
858 |
|
|
//modify the forces of unconstrained molecules
|
859 |
|
|
for (int i = 0; i < (int) (unconsMols.size()); i++){
|
860 |
|
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
|
861 |
|
|
|
862 |
|
|
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
|
863 |
|
|
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
|
864 |
|
|
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],
|
865 |
|
|
totalFZ);
|
866 |
|
|
unconsAtoms[j]->addFrc(force);
|
867 |
|
|
}
|
868 |
|
|
}
|
869 |
|
|
|
870 |
|
|
//modify the forces of moving z-constrained molecules
|
871 |
|
|
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
872 |
|
|
if (states[i] == zcsMoving){
|
873 |
|
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
|
874 |
|
|
|
875 |
|
|
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
|
876 |
|
|
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
|
877 |
|
|
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],
|
878 |
|
|
totalFZ);
|
879 |
|
|
movingZAtoms[j]->addFrc(force);
|
880 |
|
|
}
|
881 |
|
|
}
|
882 |
|
|
}
|
883 |
|
|
// cout << "after substracting z-constraint force from moving molecuels "
|
884 |
|
|
// << "total force is " << calcTotalForce() << endl;
|
885 |
|
|
}
|
886 |
|
|
|
887 |
|
|
/**
|
888 |
|
|
*
|
889 |
|
|
*
|
890 |
|
|
*/
|
891 |
|
|
|
892 |
tim |
1093 |
template<typename T> void ZConstraint<T>::doHarmonic(vector<double>& resPos){
|
893 |
tim |
1091 |
double force[3];
|
894 |
|
|
double harmonicU;
|
895 |
|
|
double harmonicF;
|
896 |
|
|
double COM[3];
|
897 |
|
|
double diff;
|
898 |
|
|
double totalFZ_local;
|
899 |
|
|
double totalFZ;
|
900 |
|
|
|
901 |
|
|
force[0] = 0;
|
902 |
|
|
force[1] = 0;
|
903 |
|
|
force[2] = 0;
|
904 |
|
|
|
905 |
|
|
totalFZ_local = 0;
|
906 |
|
|
|
907 |
|
|
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
908 |
|
|
if (states[i] == zcsMoving){
|
909 |
|
|
zconsMols[i]->getCOM(COM);
|
910 |
|
|
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
|
911 |
|
|
// << "\tcurrent zpos: " << COM[whichDirection] << endl;
|
912 |
|
|
|
913 |
tim |
1093 |
diff = COM[whichDirection] - resPos[i];
|
914 |
tim |
1091 |
|
915 |
|
|
harmonicU = 0.5 * kz[i] * diff * diff;
|
916 |
|
|
info->lrPot += harmonicU;
|
917 |
|
|
|
918 |
|
|
harmonicF = -kz[i] * diff;
|
919 |
|
|
totalFZ_local += harmonicF;
|
920 |
|
|
|
921 |
|
|
//adjust force
|
922 |
|
|
|
923 |
|
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
|
924 |
|
|
|
925 |
|
|
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
|
926 |
|
|
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
|
927 |
|
|
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i],
|
928 |
|
|
movingZAtoms[j],
|
929 |
|
|
harmonicF);
|
930 |
|
|
movingZAtoms[j]->addFrc(force);
|
931 |
|
|
}
|
932 |
|
|
}
|
933 |
|
|
}
|
934 |
|
|
|
935 |
|
|
#ifndef IS_MPI
|
936 |
|
|
totalFZ = totalFZ_local;
|
937 |
|
|
#else
|
938 |
|
|
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
|
939 |
|
|
#endif
|
940 |
|
|
|
941 |
|
|
//cout << "before substracting harmonic force from moving molecuels "
|
942 |
|
|
// << "total force is " << calcTotalForce() << endl;
|
943 |
|
|
|
944 |
|
|
force[0] = 0;
|
945 |
|
|
force[1] = 0;
|
946 |
|
|
force[2] = 0;
|
947 |
|
|
|
948 |
|
|
//modify the forces of unconstrained molecules
|
949 |
|
|
for (int i = 0; i < (int) (unconsMols.size()); i++){
|
950 |
|
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
|
951 |
|
|
|
952 |
|
|
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
|
953 |
|
|
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
|
954 |
|
|
force[whichDirection] = -forcePolicy->getHFOfUnconsMols(unconsAtoms[j],
|
955 |
|
|
totalFZ);
|
956 |
|
|
unconsAtoms[j]->addFrc(force);
|
957 |
|
|
}
|
958 |
|
|
}
|
959 |
|
|
|
960 |
|
|
//cout << "after substracting harmonic force from moving molecuels "
|
961 |
|
|
// << "total force is " << calcTotalForce() << endl;
|
962 |
|
|
}
|
963 |
|
|
|
964 |
|
|
/**
|
965 |
|
|
*
|
966 |
|
|
*/
|
967 |
|
|
|
968 |
|
|
template<typename T> bool ZConstraint<T>::checkZConsState(){
|
969 |
|
|
double COM[3];
|
970 |
|
|
double diff;
|
971 |
|
|
|
972 |
|
|
int changed_local;
|
973 |
|
|
int changed;
|
974 |
|
|
|
975 |
|
|
changed_local = 0;
|
976 |
|
|
|
977 |
|
|
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
978 |
|
|
zconsMols[i]->getCOM(COM);
|
979 |
|
|
diff = fabs(COM[whichDirection] - zPos[i]);
|
980 |
|
|
if (diff <= zconsTol && states[i] == zcsMoving){
|
981 |
|
|
states[i] = zcsFixed;
|
982 |
|
|
changed_local = 1;
|
983 |
|
|
|
984 |
tim |
1141 |
if(usingSMD)
|
985 |
|
|
prevCantPos = cantPos;
|
986 |
|
|
|
987 |
tim |
1091 |
if (hasZConsGap)
|
988 |
|
|
endFixTime[i] = info->getTime() + zconsFixTime;
|
989 |
|
|
}
|
990 |
|
|
else if (diff > zconsTol && states[i] == zcsFixed){
|
991 |
|
|
states[i] = zcsMoving;
|
992 |
|
|
changed_local = 1;
|
993 |
|
|
|
994 |
tim |
1141 |
if(usingSMD)
|
995 |
|
|
cantPos = prevCantPos;
|
996 |
|
|
|
997 |
tim |
1091 |
if (hasZConsGap)
|
998 |
|
|
endFixTime[i] = INFINITE_TIME;
|
999 |
|
|
}
|
1000 |
|
|
}
|
1001 |
|
|
|
1002 |
|
|
#ifndef IS_MPI
|
1003 |
|
|
changed = changed_local;
|
1004 |
|
|
#else
|
1005 |
|
|
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
|
1006 |
|
|
#endif
|
1007 |
|
|
|
1008 |
|
|
return (changed > 0);
|
1009 |
|
|
}
|
1010 |
|
|
|
1011 |
|
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){
|
1012 |
|
|
int havingFixed_local;
|
1013 |
|
|
int havingFixed;
|
1014 |
|
|
|
1015 |
|
|
havingFixed_local = 0;
|
1016 |
|
|
|
1017 |
|
|
for (int i = 0; i < (int) (zconsMols.size()); i++)
|
1018 |
|
|
if (states[i] == zcsFixed){
|
1019 |
|
|
havingFixed_local = 1;
|
1020 |
|
|
break;
|
1021 |
|
|
}
|
1022 |
|
|
|
1023 |
|
|
#ifndef IS_MPI
|
1024 |
|
|
havingFixed = havingFixed_local;
|
1025 |
|
|
#else
|
1026 |
|
|
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM,
|
1027 |
|
|
MPI_COMM_WORLD);
|
1028 |
|
|
#endif
|
1029 |
|
|
|
1030 |
|
|
return (havingFixed > 0);
|
1031 |
|
|
}
|
1032 |
|
|
|
1033 |
|
|
|
1034 |
|
|
/**
|
1035 |
|
|
*
|
1036 |
|
|
*/
|
1037 |
|
|
template<typename T> bool ZConstraint<T>::haveMovingZMols(){
|
1038 |
|
|
int havingMoving_local;
|
1039 |
|
|
int havingMoving;
|
1040 |
|
|
|
1041 |
|
|
havingMoving_local = 0;
|
1042 |
|
|
|
1043 |
|
|
for (int i = 0; i < (int) (zconsMols.size()); i++)
|
1044 |
|
|
if (states[i] == zcsMoving){
|
1045 |
|
|
havingMoving_local = 1;
|
1046 |
|
|
break;
|
1047 |
|
|
}
|
1048 |
|
|
|
1049 |
|
|
#ifndef IS_MPI
|
1050 |
|
|
havingMoving = havingMoving_local;
|
1051 |
|
|
#else
|
1052 |
|
|
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM,
|
1053 |
|
|
MPI_COMM_WORLD);
|
1054 |
|
|
#endif
|
1055 |
|
|
|
1056 |
|
|
return (havingMoving > 0);
|
1057 |
|
|
}
|
1058 |
|
|
|
1059 |
|
|
/**
|
1060 |
|
|
*
|
1061 |
|
|
*/
|
1062 |
|
|
|
1063 |
|
|
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel(){
|
1064 |
|
|
double MVzOfMovingMols_local;
|
1065 |
|
|
double MVzOfMovingMols;
|
1066 |
|
|
double totalMassOfMovingZMols_local;
|
1067 |
|
|
double totalMassOfMovingZMols;
|
1068 |
|
|
double COMvel[3];
|
1069 |
|
|
|
1070 |
|
|
MVzOfMovingMols_local = 0;
|
1071 |
|
|
totalMassOfMovingZMols_local = 0;
|
1072 |
|
|
|
1073 |
|
|
for (int i = 0; i < unconsMols.size(); i++){
|
1074 |
|
|
unconsMols[i]->getCOMvel(COMvel);
|
1075 |
|
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
|
1076 |
|
|
}
|
1077 |
|
|
|
1078 |
|
|
for (int i = 0; i < zconsMols.size(); i++){
|
1079 |
|
|
if (states[i] == zcsMoving){
|
1080 |
|
|
zconsMols[i]->getCOMvel(COMvel);
|
1081 |
|
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
|
1082 |
|
|
totalMassOfMovingZMols_local += massOfZConsMols[i];
|
1083 |
|
|
}
|
1084 |
|
|
}
|
1085 |
|
|
|
1086 |
|
|
#ifndef IS_MPI
|
1087 |
|
|
MVzOfMovingMols = MVzOfMovingMols_local;
|
1088 |
|
|
totalMassOfMovingZMols = totalMassOfMovingZMols_local;
|
1089 |
|
|
#else
|
1090 |
|
|
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,
|
1091 |
|
|
MPI_SUM, MPI_COMM_WORLD);
|
1092 |
|
|
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,
|
1093 |
|
|
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
|
1094 |
|
|
#endif
|
1095 |
|
|
|
1096 |
|
|
double vzOfMovingMols;
|
1097 |
|
|
vzOfMovingMols = MVzOfMovingMols /
|
1098 |
|
|
(totalMassOfUncons + totalMassOfMovingZMols);
|
1099 |
|
|
|
1100 |
|
|
return vzOfMovingMols;
|
1101 |
|
|
}
|
1102 |
|
|
|
1103 |
|
|
/**
|
1104 |
|
|
*
|
1105 |
|
|
*/
|
1106 |
|
|
|
1107 |
|
|
template<typename T> double ZConstraint<T>::calcSysCOMVel(){
|
1108 |
|
|
double COMvel[3];
|
1109 |
|
|
double tempMVz_local;
|
1110 |
|
|
double tempMVz;
|
1111 |
|
|
double massOfZCons_local;
|
1112 |
|
|
double massOfZCons;
|
1113 |
|
|
|
1114 |
|
|
|
1115 |
|
|
tempMVz_local = 0;
|
1116 |
|
|
|
1117 |
|
|
for (int i = 0 ; i < nMols; i++){
|
1118 |
|
|
molecules[i].getCOMvel(COMvel);
|
1119 |
|
|
tempMVz_local += molecules[i].getTotalMass() * COMvel[whichDirection];
|
1120 |
|
|
}
|
1121 |
|
|
|
1122 |
|
|
massOfZCons_local = 0;
|
1123 |
|
|
|
1124 |
|
|
for (int i = 0; i < (int) (massOfZConsMols.size()); i++){
|
1125 |
|
|
massOfZCons_local += massOfZConsMols[i];
|
1126 |
|
|
}
|
1127 |
|
|
#ifndef IS_MPI
|
1128 |
|
|
massOfZCons = massOfZCons_local;
|
1129 |
|
|
tempMVz = tempMVz_local;
|
1130 |
|
|
#else
|
1131 |
|
|
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE, MPI_SUM,
|
1132 |
|
|
MPI_COMM_WORLD);
|
1133 |
|
|
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
|
1134 |
|
|
#endif
|
1135 |
|
|
|
1136 |
|
|
return tempMVz / (totalMassOfUncons + massOfZCons);
|
1137 |
|
|
}
|
1138 |
|
|
|
1139 |
|
|
/**
|
1140 |
|
|
*
|
1141 |
|
|
*/
|
1142 |
|
|
|
1143 |
|
|
template<typename T> double ZConstraint<T>::calcTotalForce(){
|
1144 |
|
|
double force[3];
|
1145 |
|
|
double totalForce_local;
|
1146 |
|
|
double totalForce;
|
1147 |
|
|
|
1148 |
|
|
totalForce_local = 0;
|
1149 |
|
|
|
1150 |
|
|
for (int i = 0; i < nAtoms; i++){
|
1151 |
|
|
atoms[i]->getFrc(force);
|
1152 |
|
|
totalForce_local += force[whichDirection];
|
1153 |
|
|
}
|
1154 |
|
|
|
1155 |
|
|
#ifndef IS_MPI
|
1156 |
|
|
totalForce = totalForce_local;
|
1157 |
|
|
#else
|
1158 |
|
|
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE, MPI_SUM,
|
1159 |
|
|
MPI_COMM_WORLD);
|
1160 |
|
|
#endif
|
1161 |
|
|
|
1162 |
|
|
return totalForce;
|
1163 |
|
|
}
|
1164 |
|
|
|
1165 |
|
|
/**
|
1166 |
|
|
*
|
1167 |
|
|
*/
|
1168 |
|
|
|
1169 |
|
|
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
|
1170 |
|
|
//calculate the number of atoms of moving z-constrained molecules
|
1171 |
|
|
int nMovingZAtoms_local;
|
1172 |
|
|
int nMovingZAtoms;
|
1173 |
|
|
|
1174 |
|
|
nMovingZAtoms_local = 0;
|
1175 |
|
|
for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)
|
1176 |
|
|
if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){
|
1177 |
|
|
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
|
1178 |
|
|
}
|
1179 |
|
|
|
1180 |
|
|
#ifdef IS_MPI
|
1181 |
|
|
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM,
|
1182 |
|
|
MPI_COMM_WORLD);
|
1183 |
|
|
#else
|
1184 |
|
|
nMovingZAtoms = nMovingZAtoms_local;
|
1185 |
|
|
#endif
|
1186 |
|
|
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
|
1187 |
|
|
}
|
1188 |
|
|
|
1189 |
|
|
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol,
|
1190 |
|
|
Atom* atom,
|
1191 |
|
|
double totalForce){
|
1192 |
|
|
return totalForce / mol->getNAtoms();
|
1193 |
|
|
}
|
1194 |
|
|
|
1195 |
|
|
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom,
|
1196 |
|
|
double totalForce){
|
1197 |
|
|
return totalForce / totNumOfMovingAtoms;
|
1198 |
|
|
}
|
1199 |
|
|
|
1200 |
|
|
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol,
|
1201 |
|
|
Atom* atom,
|
1202 |
|
|
double totalForce){
|
1203 |
|
|
return totalForce / mol->getNAtoms();
|
1204 |
|
|
}
|
1205 |
|
|
|
1206 |
|
|
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom,
|
1207 |
|
|
double totalForce){
|
1208 |
|
|
return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
|
1209 |
|
|
}
|
1210 |
|
|
|
1211 |
|
|
/**
|
1212 |
|
|
*
|
1213 |
|
|
*/
|
1214 |
|
|
|
1215 |
|
|
template<typename T> void ZConstraint<T>::PolicyByMass::update(){
|
1216 |
|
|
//calculate the number of atoms of moving z-constrained molecules
|
1217 |
|
|
double massOfMovingZAtoms_local;
|
1218 |
|
|
double massOfMovingZAtoms;
|
1219 |
|
|
|
1220 |
|
|
massOfMovingZAtoms_local = 0;
|
1221 |
|
|
for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)
|
1222 |
|
|
if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){
|
1223 |
|
|
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
|
1224 |
|
|
}
|
1225 |
|
|
|
1226 |
|
|
#ifdef IS_MPI
|
1227 |
|
|
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,
|
1228 |
|
|
MPI_SUM, MPI_COMM_WORLD);
|
1229 |
|
|
#else
|
1230 |
|
|
massOfMovingZAtoms = massOfMovingZAtoms_local;
|
1231 |
|
|
#endif
|
1232 |
|
|
totMassOfMovingAtoms = massOfMovingZAtoms +
|
1233 |
|
|
zconsIntegrator->totalMassOfUncons;
|
1234 |
|
|
}
|
1235 |
|
|
|
1236 |
|
|
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol,
|
1237 |
|
|
Atom* atom,
|
1238 |
|
|
double totalForce){
|
1239 |
|
|
return totalForce * atom->getMass() / mol->getTotalMass();
|
1240 |
|
|
}
|
1241 |
|
|
|
1242 |
|
|
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols(Atom* atom,
|
1243 |
|
|
double totalForce){
|
1244 |
|
|
return totalForce * atom->getMass() / totMassOfMovingAtoms;
|
1245 |
|
|
}
|
1246 |
|
|
|
1247 |
|
|
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol,
|
1248 |
|
|
Atom* atom,
|
1249 |
|
|
double totalForce){
|
1250 |
|
|
return totalForce * atom->getMass() / mol->getTotalMass();
|
1251 |
|
|
}
|
1252 |
|
|
|
1253 |
|
|
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom,
|
1254 |
|
|
double totalForce){
|
1255 |
|
|
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
|
1256 |
|
|
}
|
1257 |
|
|
|
1258 |
|
|
template<typename T> void ZConstraint<T>::updateZPos(){
|
1259 |
|
|
double curTime;
|
1260 |
tim |
1093 |
double COM[3];
|
1261 |
|
|
|
1262 |
tim |
1091 |
curTime = info->getTime();
|
1263 |
|
|
|
1264 |
|
|
for (size_t i = 0; i < zconsMols.size(); i++){
|
1265 |
tim |
1093 |
|
1266 |
tim |
1091 |
if (states[i] == zcsFixed && curTime >= endFixTime[i]){
|
1267 |
|
|
zPos[i] += zconsGap;
|
1268 |
tim |
1093 |
|
1269 |
|
|
if (usingSMD){
|
1270 |
|
|
zconsMols[i]->getCOM(COM);
|
1271 |
|
|
cantPos[i] = COM[whichDirection];
|
1272 |
|
|
}
|
1273 |
|
|
|
1274 |
tim |
1091 |
}
|
1275 |
tim |
1093 |
|
1276 |
tim |
1091 |
}
|
1277 |
tim |
1093 |
|
1278 |
tim |
1091 |
}
|
1279 |
tim |
1093 |
|
1280 |
|
|
template<typename T> void ZConstraint<T>::updateCantPos(){
|
1281 |
|
|
double curTime;
|
1282 |
|
|
double dt;
|
1283 |
|
|
|
1284 |
|
|
curTime = info->getTime();
|
1285 |
|
|
dt = info->dt;
|
1286 |
|
|
|
1287 |
|
|
for (size_t i = 0; i < zconsMols.size(); i++){
|
1288 |
|
|
if (states[i] == zcsMoving){
|
1289 |
|
|
cantPos[i] += cantVel[i] * dt;
|
1290 |
|
|
}
|
1291 |
|
|
}
|
1292 |
|
|
|
1293 |
|
|
}
|