1 |
#include "integrators/Integrator.hpp"
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2 |
#include "utils/simError.h"
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3 |
#include <math.h>
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4 |
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5 |
const double INFINITE_TIME = 10e30;
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6 |
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo,
|
7 |
ForceFields* the_ff): T(theInfo, the_ff),
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8 |
fzOut(NULL),
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9 |
curZconsTime(0),
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10 |
forcePolicy(NULL),
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11 |
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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DoubleGenericData* sampleTime;
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DoubleGenericData* tolerance;
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DoubleGenericData* gap;
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DoubleGenericData* fixtime;
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StringGenericData* policy;
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StringGenericData* filename;
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IntGenericData* smdFlag;
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23 |
double COM[3];
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24 |
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25 |
//by default, the direction of constraint is z
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26 |
// 0 --> x
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27 |
// 1 --> y
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28 |
// 2 --> z
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29 |
whichDirection = 2;
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30 |
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31 |
//estimate the force constant of harmonical potential
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32 |
double Kb = 1.986E-3 ; //in kcal/K
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33 |
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34 |
double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /
|
35 |
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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41 |
sprintf(painCave.errMsg,
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42 |
"ZConstraint Warning: User does not set force Subtraction policy, "
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43 |
"PolicyByMass is used\n");
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44 |
painCave.isFatal = 0;
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45 |
simError();
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46 |
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forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
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}
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else{
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50 |
policy = dynamic_cast<StringGenericData*>(data);
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51 |
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52 |
if (!policy){
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sprintf(painCave.errMsg,
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"ZConstraint Error: Convertion from GenericData to StringGenericData 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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58 |
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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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80 |
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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<DoubleGenericData*>(data);
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90 |
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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<StringGenericData*>(data);
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113 |
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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<DoubleGenericData*>(data);
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if (!tolerance){
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sprintf(painCave.errMsg,
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138 |
"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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146 |
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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<DoubleGenericData*>(data);
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152 |
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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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164 |
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165 |
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data = info->getProperty(ZCONSFIXTIME_ID);
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168 |
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if (data){
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fixtime = dynamic_cast<DoubleGenericData*>(data);
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171 |
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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185 |
simError();
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}
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187 |
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188 |
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189 |
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data = info->getProperty(ZCONSUSINGSMD_ID);
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191 |
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192 |
if (data){
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smdFlag = dynamic_cast<IntGenericData*>(data);
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194 |
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195 |
if (!smdFlag){
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196 |
sprintf(painCave.errMsg,
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197 |
"ZConstraint error: Can not get property from SimInfo\n");
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198 |
painCave.isFatal = 1;
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199 |
simError();
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200 |
}
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else{
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202 |
this->usingSMD= smdFlag->getData() ? true : false;
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}
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204 |
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205 |
}
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206 |
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207 |
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208 |
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209 |
//retrieve index of z-constraint molecules
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210 |
data = info->getProperty(ZCONSPARADATA_ID);
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211 |
if (!data){
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212 |
sprintf(painCave.errMsg,
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213 |
"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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215 |
painCave.isFatal = 1;
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216 |
simError();
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217 |
}
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218 |
else{
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zConsParaData = dynamic_cast<ZConsParaData*>(data);
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220 |
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221 |
if (!zConsParaData){
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222 |
sprintf(painCave.errMsg,
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223 |
"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n");
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224 |
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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233 |
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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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239 |
if (minIndex < 0){
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240 |
sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n");
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241 |
painCave.isFatal = 1;
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242 |
simError();
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}
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244 |
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maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
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246 |
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#ifndef IS_MPI
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248 |
totalNumMol = nMols;
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#else
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250 |
totalNumMol = mpiSim->getNMolGlobal();
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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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255 |
painCave.isFatal = 1;
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256 |
simError();
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}
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258 |
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259 |
//if user does not specify the zpos for the zconstraint molecule
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260 |
//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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263 |
#ifndef IS_MPI
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264 |
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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272 |
int* MolToProcMap;
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273 |
int whichNode;
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274 |
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MolToProcMap = mpiSim->getMolToProcMap();
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276 |
whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
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277 |
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278 |
//broadcast the zpos of current z-contraint molecule
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//the node which contain this
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280 |
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281 |
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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284 |
molecules[j].getCOM(COM);
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285 |
break;
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286 |
}
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287 |
}
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288 |
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289 |
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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293 |
(*parameters)[i].zPos = COM[whichDirection];
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294 |
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295 |
sprintf(painCave.errMsg,
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296 |
"ZConstraint warning: Does not specify zpos for z-constraint molecule "
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297 |
"initial z coornidate will be used \n");
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298 |
painCave.isFatal = 0;
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299 |
simError();
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300 |
}
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301 |
}
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302 |
}//end if (!zConsParaData)
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303 |
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304 |
}//end if (!data)
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305 |
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306 |
//
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307 |
#ifdef IS_MPI
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308 |
update();
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309 |
#else
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310 |
int searchResult;
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311 |
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312 |
for (int i = 0; i < nMols; i++){
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313 |
searchResult = isZConstraintMol(&molecules[i]);
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314 |
|
315 |
if (searchResult > -1){
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316 |
zconsMols.push_back(&molecules[i]);
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317 |
massOfZConsMols.push_back(molecules[i].getTotalMass());
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318 |
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319 |
zPos.push_back((*parameters)[searchResult].zPos);
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320 |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
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321 |
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322 |
if(usingSMD)
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323 |
cantVel.push_back((*parameters)[searchResult].cantVel);
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324 |
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325 |
}
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326 |
else{
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327 |
unconsMols.push_back(&molecules[i]);
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328 |
massOfUnconsMols.push_back(molecules[i].getTotalMass());
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329 |
}
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330 |
}
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331 |
|
332 |
fz.resize(zconsMols.size());
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333 |
curZPos.resize(zconsMols.size());
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334 |
indexOfZConsMols.resize(zconsMols.size());
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335 |
|
336 |
//determine the states of z-constraint molecules
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337 |
for (size_t i = 0; i < zconsMols.size(); i++){
|
338 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
|
339 |
|
340 |
zconsMols[i]->getCOM(COM);
|
341 |
|
342 |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){
|
343 |
states.push_back(zcsFixed);
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344 |
|
345 |
if (hasZConsGap)
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346 |
endFixTime.push_back(info->getTime() + zconsFixTime);
|
347 |
}
|
348 |
else{
|
349 |
states.push_back(zcsMoving);
|
350 |
|
351 |
if (hasZConsGap)
|
352 |
endFixTime.push_back(INFINITE_TIME);
|
353 |
}
|
354 |
|
355 |
if(usingSMD)
|
356 |
cantPos.push_back(COM[whichDirection]);
|
357 |
}
|
358 |
|
359 |
if(usingSMD)
|
360 |
prevCantPos = cantPos;
|
361 |
#endif
|
362 |
|
363 |
|
364 |
//get total masss of unconstraint molecules
|
365 |
double totalMassOfUncons_local;
|
366 |
totalMassOfUncons_local = 0;
|
367 |
|
368 |
for (size_t i = 0; i < unconsMols.size(); i++)
|
369 |
totalMassOfUncons_local += unconsMols[i]->getTotalMass();
|
370 |
|
371 |
#ifndef IS_MPI
|
372 |
totalMassOfUncons = totalMassOfUncons_local;
|
373 |
#else
|
374 |
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 |
cantPos.clear();
|
420 |
cantVel.clear();
|
421 |
|
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 |
massOfZConsMols.push_back(molecules[i].getTotalMass());
|
435 |
|
436 |
if(usingSMD)
|
437 |
cantVel.push_back((*parameters)[index].cantVel);
|
438 |
|
439 |
}
|
440 |
else{
|
441 |
unconsMols.push_back(&molecules[i]);
|
442 |
massOfUnconsMols.push_back(molecules[i].getTotalMass());
|
443 |
}
|
444 |
}
|
445 |
|
446 |
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 |
}
|
453 |
|
454 |
//determine the states of z-constraint molecules
|
455 |
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
456 |
|
457 |
zconsMols[i]->getCOM(COM);
|
458 |
|
459 |
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 |
|
472 |
if(usingSMD)
|
473 |
cantPos.push_back(COM[whichDirection]);
|
474 |
}
|
475 |
|
476 |
if(usingSMD)
|
477 |
prevCantPos = cantPos;
|
478 |
|
479 |
forcePolicy->update();
|
480 |
}
|
481 |
|
482 |
#endif
|
483 |
|
484 |
/**
|
485 |
* Function Name: isZConstraintMol
|
486 |
* Parameter
|
487 |
* Molecule* mol
|
488 |
* Return value:
|
489 |
* -1, if the molecule is not z-constraint molecule,
|
490 |
* other non-negative values, its index in indexOfAllZConsMols vector
|
491 |
*/
|
492 |
|
493 |
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol){
|
494 |
int index;
|
495 |
int low;
|
496 |
int high;
|
497 |
int mid;
|
498 |
|
499 |
index = mol->getGlobalIndex();
|
500 |
|
501 |
low = 0;
|
502 |
high = parameters->size() - 1;
|
503 |
|
504 |
//Binary Search (we have sorted the array)
|
505 |
while (low <= high){
|
506 |
mid = (low + high) / 2;
|
507 |
if ((*parameters)[mid].zconsIndex == index)
|
508 |
return mid;
|
509 |
else if ((*parameters)[mid].zconsIndex > index)
|
510 |
high = mid - 1;
|
511 |
else
|
512 |
low = mid + 1;
|
513 |
}
|
514 |
|
515 |
return -1;
|
516 |
}
|
517 |
|
518 |
template<typename T> void ZConstraint<T>::integrate(){
|
519 |
// creat zconsWriter
|
520 |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);
|
521 |
|
522 |
if (!fzOut){
|
523 |
sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n");
|
524 |
painCave.isFatal = 1;
|
525 |
simError();
|
526 |
}
|
527 |
|
528 |
//zero out the velocities of center of mass of unconstrained molecules
|
529 |
//and the velocities of center of mass of every single z-constrained molecueles
|
530 |
zeroOutVel();
|
531 |
|
532 |
curZconsTime = zconsTime + info->getTime();
|
533 |
|
534 |
T::integrate();
|
535 |
}
|
536 |
|
537 |
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
|
538 |
double zsys;
|
539 |
double COM[3];
|
540 |
double force[3];
|
541 |
double zSysCOMVel;
|
542 |
|
543 |
T::calcForce(calcPot, calcStress);
|
544 |
|
545 |
|
546 |
if (hasZConsGap){
|
547 |
updateZPos();
|
548 |
}
|
549 |
|
550 |
if (checkZConsState()){
|
551 |
zeroOutVel();
|
552 |
forcePolicy->update();
|
553 |
}
|
554 |
|
555 |
zsys = calcZSys();
|
556 |
zSysCOMVel = calcSysCOMVel();
|
557 |
#ifdef IS_MPI
|
558 |
if (worldRank == 0){
|
559 |
#endif
|
560 |
|
561 |
#ifdef IS_MPI
|
562 |
}
|
563 |
#endif
|
564 |
|
565 |
//do zconstraint force;
|
566 |
if (haveFixedZMols()){
|
567 |
this->doZconstraintForce();
|
568 |
}
|
569 |
|
570 |
//use external force to move the molecules to the specified positions
|
571 |
if (haveMovingZMols()){
|
572 |
if (usingSMD)
|
573 |
this->doHarmonic(cantPos);
|
574 |
else
|
575 |
this->doHarmonic(zPos);
|
576 |
}
|
577 |
|
578 |
//write out forces and current positions of z-constraint molecules
|
579 |
if (info->getTime() >= curZconsTime){
|
580 |
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
581 |
zconsMols[i]->getCOM(COM);
|
582 |
curZPos[i] = COM[whichDirection];
|
583 |
|
584 |
//if the z-constraint molecule is still moving, just record its force
|
585 |
if (states[i] == zcsMoving){
|
586 |
fz[i] = 0;
|
587 |
Atom** movingZAtoms;
|
588 |
movingZAtoms = zconsMols[i]->getMyAtoms();
|
589 |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
|
590 |
movingZAtoms[j]->getFrc(force);
|
591 |
fz[i] += force[whichDirection];
|
592 |
}
|
593 |
}
|
594 |
}
|
595 |
fzOut->writeFZ(info->getTime(), zconsMols.size(), &indexOfZConsMols[0], &fz[0],
|
596 |
&curZPos[0], &zPos[0]);
|
597 |
curZconsTime += zconsTime;
|
598 |
}
|
599 |
|
600 |
zSysCOMVel = calcSysCOMVel();
|
601 |
#ifdef IS_MPI
|
602 |
if (worldRank == 0){
|
603 |
#endif
|
604 |
#ifdef IS_MPI
|
605 |
}
|
606 |
#endif
|
607 |
}
|
608 |
|
609 |
|
610 |
template<typename T> double ZConstraint<T>::calcZSys(){
|
611 |
//calculate reference z coordinate for z-constraint molecules
|
612 |
double totalMass_local;
|
613 |
double totalMass;
|
614 |
double totalMZ_local;
|
615 |
double totalMZ;
|
616 |
double massOfCurMol;
|
617 |
double COM[3];
|
618 |
|
619 |
totalMass_local = 0;
|
620 |
totalMZ_local = 0;
|
621 |
|
622 |
for (int i = 0; i < nMols; i++){
|
623 |
massOfCurMol = molecules[i].getTotalMass();
|
624 |
molecules[i].getCOM(COM);
|
625 |
|
626 |
totalMass_local += massOfCurMol;
|
627 |
totalMZ_local += massOfCurMol * COM[whichDirection];
|
628 |
}
|
629 |
|
630 |
|
631 |
#ifdef IS_MPI
|
632 |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM,
|
633 |
MPI_COMM_WORLD);
|
634 |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
|
635 |
#else
|
636 |
totalMass = totalMass_local;
|
637 |
totalMZ = totalMZ_local;
|
638 |
#endif
|
639 |
|
640 |
double zsys;
|
641 |
zsys = totalMZ / totalMass;
|
642 |
|
643 |
return zsys;
|
644 |
}
|
645 |
|
646 |
template<typename T> void ZConstraint<T>::thermalize(void){
|
647 |
T::thermalize();
|
648 |
zeroOutVel();
|
649 |
}
|
650 |
|
651 |
template<typename T> void ZConstraint<T>::zeroOutVel(){
|
652 |
Atom** fixedZAtoms;
|
653 |
double COMvel[3];
|
654 |
double vel[3];
|
655 |
double zSysCOMVel;
|
656 |
|
657 |
//zero out the velocities of center of mass of fixed z-constrained molecules
|
658 |
|
659 |
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
660 |
if (states[i] == zcsFixed){
|
661 |
zconsMols[i]->getCOMvel(COMvel);
|
662 |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
|
663 |
|
664 |
fixedZAtoms = zconsMols[i]->getMyAtoms();
|
665 |
|
666 |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
|
667 |
vel = fixedZAtoms[j]->getVel();
|
668 |
vel[whichDirection] -= COMvel[whichDirection];
|
669 |
fixedZAtoms[j]->setVel(vel);
|
670 |
}
|
671 |
|
672 |
zconsMols[i]->getCOMvel(COMvel);
|
673 |
}
|
674 |
}
|
675 |
|
676 |
zSysCOMVel = calcSysCOMVel();
|
677 |
#ifdef IS_MPI
|
678 |
if (worldRank == 0){
|
679 |
#endif
|
680 |
#ifdef IS_MPI
|
681 |
}
|
682 |
#endif
|
683 |
|
684 |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
|
685 |
double MVzOfMovingMols_local;
|
686 |
double MVzOfMovingMols;
|
687 |
double totalMassOfMovingZMols_local;
|
688 |
double totalMassOfMovingZMols;
|
689 |
|
690 |
MVzOfMovingMols_local = 0;
|
691 |
totalMassOfMovingZMols_local = 0;
|
692 |
|
693 |
for (int i = 0; i < (int) (unconsMols.size()); i++){
|
694 |
unconsMols[i]->getCOMvel(COMvel);
|
695 |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
|
696 |
}
|
697 |
|
698 |
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
699 |
if (states[i] == zcsMoving){
|
700 |
zconsMols[i]->getCOMvel(COMvel);
|
701 |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
|
702 |
totalMassOfMovingZMols_local += massOfZConsMols[i];
|
703 |
}
|
704 |
}
|
705 |
|
706 |
#ifndef IS_MPI
|
707 |
MVzOfMovingMols = MVzOfMovingMols_local;
|
708 |
totalMassOfMovingZMols = totalMassOfMovingZMols_local;
|
709 |
#else
|
710 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,
|
711 |
MPI_SUM, MPI_COMM_WORLD);
|
712 |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,
|
713 |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
|
714 |
#endif
|
715 |
|
716 |
double vzOfMovingMols;
|
717 |
vzOfMovingMols = MVzOfMovingMols /
|
718 |
(totalMassOfUncons + totalMassOfMovingZMols);
|
719 |
|
720 |
//modify the velocites of unconstrained molecules
|
721 |
Atom** unconsAtoms;
|
722 |
for (int i = 0; i < (int) (unconsMols.size()); i++){
|
723 |
unconsAtoms = unconsMols[i]->getMyAtoms();
|
724 |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
|
725 |
vel = unconsAtoms[j]->getVel();
|
726 |
vel[whichDirection] -= vzOfMovingMols;
|
727 |
unconsAtoms[j]->setVel(vel);
|
728 |
}
|
729 |
}
|
730 |
|
731 |
//modify the velocities of moving z-constrained molecuels
|
732 |
Atom** movingZAtoms;
|
733 |
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
734 |
if (states[i] == zcsMoving){
|
735 |
movingZAtoms = zconsMols[i]->getMyAtoms();
|
736 |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
|
737 |
vel = movingZAtoms[j]->getVel();
|
738 |
vel[whichDirection] -= vzOfMovingMols;
|
739 |
movingZAtoms[j]->setVel(vel);
|
740 |
}
|
741 |
}
|
742 |
}
|
743 |
|
744 |
|
745 |
zSysCOMVel = calcSysCOMVel();
|
746 |
#ifdef IS_MPI
|
747 |
if (worldRank == 0){
|
748 |
#endif
|
749 |
#ifdef IS_MPI
|
750 |
}
|
751 |
#endif
|
752 |
}
|
753 |
|
754 |
|
755 |
template<typename T> void ZConstraint<T>::doZconstraintForce(){
|
756 |
Atom** zconsAtoms;
|
757 |
double totalFZ;
|
758 |
double totalFZ_local;
|
759 |
double COM[3];
|
760 |
double force[3];
|
761 |
|
762 |
//constrain the molecules which do not reach the specified positions
|
763 |
|
764 |
//Zero Out the force of z-contrained molecules
|
765 |
totalFZ_local = 0;
|
766 |
|
767 |
//calculate the total z-contrained force of fixed z-contrained molecules
|
768 |
|
769 |
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
770 |
if (states[i] == zcsFixed){
|
771 |
zconsMols[i]->getCOM(COM);
|
772 |
zconsAtoms = zconsMols[i]->getMyAtoms();
|
773 |
|
774 |
fz[i] = 0;
|
775 |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
|
776 |
zconsAtoms[j]->getFrc(force);
|
777 |
fz[i] += force[whichDirection];
|
778 |
}
|
779 |
totalFZ_local += fz[i];
|
780 |
|
781 |
}
|
782 |
}
|
783 |
|
784 |
//calculate total z-constraint force
|
785 |
#ifdef IS_MPI
|
786 |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
|
787 |
#else
|
788 |
totalFZ = totalFZ_local;
|
789 |
#endif
|
790 |
|
791 |
|
792 |
// apply negative to fixed z-constrained molecues;
|
793 |
force[0] = 0;
|
794 |
force[1] = 0;
|
795 |
force[2] = 0;
|
796 |
|
797 |
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
798 |
if (states[i] == zcsFixed){
|
799 |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
|
800 |
zconsAtoms = zconsMols[i]->getMyAtoms();
|
801 |
|
802 |
for (int j = 0; j < nAtomOfCurZConsMol; j++){
|
803 |
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
|
804 |
force[whichDirection] = -forcePolicy->getZFOfFixedZMols(zconsMols[i],
|
805 |
zconsAtoms[j],
|
806 |
fz[i]);
|
807 |
zconsAtoms[j]->addFrc(force);
|
808 |
}
|
809 |
}
|
810 |
}
|
811 |
|
812 |
force[0] = 0;
|
813 |
force[1] = 0;
|
814 |
force[2] = 0;
|
815 |
|
816 |
//modify the forces of unconstrained molecules
|
817 |
for (int i = 0; i < (int) (unconsMols.size()); i++){
|
818 |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
|
819 |
|
820 |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
|
821 |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
|
822 |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],
|
823 |
totalFZ);
|
824 |
unconsAtoms[j]->addFrc(force);
|
825 |
}
|
826 |
}
|
827 |
|
828 |
//modify the forces of moving z-constrained molecules
|
829 |
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
830 |
if (states[i] == zcsMoving){
|
831 |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
|
832 |
|
833 |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
|
834 |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
|
835 |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],
|
836 |
totalFZ);
|
837 |
movingZAtoms[j]->addFrc(force);
|
838 |
}
|
839 |
}
|
840 |
}
|
841 |
}
|
842 |
|
843 |
|
844 |
template<typename T> void ZConstraint<T>::doHarmonic(vector<double>& resPos){
|
845 |
double force[3];
|
846 |
double harmonicU;
|
847 |
double harmonicF;
|
848 |
double COM[3];
|
849 |
double diff;
|
850 |
double totalFZ_local;
|
851 |
double totalFZ;
|
852 |
|
853 |
force[0] = 0;
|
854 |
force[1] = 0;
|
855 |
force[2] = 0;
|
856 |
|
857 |
totalFZ_local = 0;
|
858 |
|
859 |
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
860 |
if (states[i] == zcsMoving){
|
861 |
zconsMols[i]->getCOM(COM);
|
862 |
|
863 |
diff = COM[whichDirection] - resPos[i];
|
864 |
|
865 |
harmonicU = 0.5 * kz[i] * diff * diff;
|
866 |
info->lrPot += harmonicU;
|
867 |
|
868 |
harmonicF = -kz[i] * diff;
|
869 |
totalFZ_local += harmonicF;
|
870 |
|
871 |
//adjust force
|
872 |
|
873 |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
|
874 |
|
875 |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
|
876 |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i],
|
877 |
movingZAtoms[j],
|
878 |
harmonicF);
|
879 |
movingZAtoms[j]->addFrc(force);
|
880 |
}
|
881 |
}
|
882 |
}
|
883 |
|
884 |
#ifndef IS_MPI
|
885 |
totalFZ = totalFZ_local;
|
886 |
#else
|
887 |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
|
888 |
#endif
|
889 |
|
890 |
force[0] = 0;
|
891 |
force[1] = 0;
|
892 |
force[2] = 0;
|
893 |
|
894 |
//modify the forces of unconstrained molecules
|
895 |
for (int i = 0; i < (int) (unconsMols.size()); i++){
|
896 |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
|
897 |
|
898 |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
|
899 |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
|
900 |
force[whichDirection] = -forcePolicy->getHFOfUnconsMols(unconsAtoms[j],
|
901 |
totalFZ);
|
902 |
unconsAtoms[j]->addFrc(force);
|
903 |
}
|
904 |
}
|
905 |
|
906 |
}
|
907 |
|
908 |
template<typename T> bool ZConstraint<T>::checkZConsState(){
|
909 |
double COM[3];
|
910 |
double diff;
|
911 |
|
912 |
int changed_local;
|
913 |
int changed;
|
914 |
|
915 |
changed_local = 0;
|
916 |
|
917 |
for (int i = 0; i < (int) (zconsMols.size()); i++){
|
918 |
zconsMols[i]->getCOM(COM);
|
919 |
diff = fabs(COM[whichDirection] - zPos[i]);
|
920 |
if (diff <= zconsTol && states[i] == zcsMoving){
|
921 |
states[i] = zcsFixed;
|
922 |
changed_local = 1;
|
923 |
|
924 |
if(usingSMD)
|
925 |
prevCantPos = cantPos;
|
926 |
|
927 |
if (hasZConsGap)
|
928 |
endFixTime[i] = info->getTime() + zconsFixTime;
|
929 |
}
|
930 |
else if (diff > zconsTol && states[i] == zcsFixed){
|
931 |
states[i] = zcsMoving;
|
932 |
changed_local = 1;
|
933 |
|
934 |
if(usingSMD)
|
935 |
cantPos = prevCantPos;
|
936 |
|
937 |
if (hasZConsGap)
|
938 |
endFixTime[i] = INFINITE_TIME;
|
939 |
}
|
940 |
}
|
941 |
|
942 |
#ifndef IS_MPI
|
943 |
changed = changed_local;
|
944 |
#else
|
945 |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
|
946 |
#endif
|
947 |
|
948 |
return (changed > 0);
|
949 |
}
|
950 |
|
951 |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){
|
952 |
int havingFixed_local;
|
953 |
int havingFixed;
|
954 |
|
955 |
havingFixed_local = 0;
|
956 |
|
957 |
for (int i = 0; i < (int) (zconsMols.size()); i++)
|
958 |
if (states[i] == zcsFixed){
|
959 |
havingFixed_local = 1;
|
960 |
break;
|
961 |
}
|
962 |
|
963 |
#ifndef IS_MPI
|
964 |
havingFixed = havingFixed_local;
|
965 |
#else
|
966 |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM,
|
967 |
MPI_COMM_WORLD);
|
968 |
#endif
|
969 |
|
970 |
return (havingFixed > 0);
|
971 |
}
|
972 |
|
973 |
|
974 |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){
|
975 |
int havingMoving_local;
|
976 |
int havingMoving;
|
977 |
|
978 |
havingMoving_local = 0;
|
979 |
|
980 |
for (int i = 0; i < (int) (zconsMols.size()); i++)
|
981 |
if (states[i] == zcsMoving){
|
982 |
havingMoving_local = 1;
|
983 |
break;
|
984 |
}
|
985 |
|
986 |
#ifndef IS_MPI
|
987 |
havingMoving = havingMoving_local;
|
988 |
#else
|
989 |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM,
|
990 |
MPI_COMM_WORLD);
|
991 |
#endif
|
992 |
|
993 |
return (havingMoving > 0);
|
994 |
}
|
995 |
|
996 |
|
997 |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel(){
|
998 |
double MVzOfMovingMols_local;
|
999 |
double MVzOfMovingMols;
|
1000 |
double totalMassOfMovingZMols_local;
|
1001 |
double totalMassOfMovingZMols;
|
1002 |
double COMvel[3];
|
1003 |
|
1004 |
MVzOfMovingMols_local = 0;
|
1005 |
totalMassOfMovingZMols_local = 0;
|
1006 |
|
1007 |
for (int i = 0; i < unconsMols.size(); i++){
|
1008 |
unconsMols[i]->getCOMvel(COMvel);
|
1009 |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
|
1010 |
}
|
1011 |
|
1012 |
for (int i = 0; i < zconsMols.size(); i++){
|
1013 |
if (states[i] == zcsMoving){
|
1014 |
zconsMols[i]->getCOMvel(COMvel);
|
1015 |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
|
1016 |
totalMassOfMovingZMols_local += massOfZConsMols[i];
|
1017 |
}
|
1018 |
}
|
1019 |
|
1020 |
#ifndef IS_MPI
|
1021 |
MVzOfMovingMols = MVzOfMovingMols_local;
|
1022 |
totalMassOfMovingZMols = totalMassOfMovingZMols_local;
|
1023 |
#else
|
1024 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,
|
1025 |
MPI_SUM, MPI_COMM_WORLD);
|
1026 |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,
|
1027 |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
|
1028 |
#endif
|
1029 |
|
1030 |
double vzOfMovingMols;
|
1031 |
vzOfMovingMols = MVzOfMovingMols /
|
1032 |
(totalMassOfUncons + totalMassOfMovingZMols);
|
1033 |
|
1034 |
return vzOfMovingMols;
|
1035 |
}
|
1036 |
|
1037 |
template<typename T> double ZConstraint<T>::calcSysCOMVel(){
|
1038 |
double COMvel[3];
|
1039 |
double tempMVz_local;
|
1040 |
double tempMVz;
|
1041 |
double massOfZCons_local;
|
1042 |
double massOfZCons;
|
1043 |
|
1044 |
|
1045 |
tempMVz_local = 0;
|
1046 |
|
1047 |
for (int i = 0 ; i < nMols; i++){
|
1048 |
molecules[i].getCOMvel(COMvel);
|
1049 |
tempMVz_local += molecules[i].getTotalMass() * COMvel[whichDirection];
|
1050 |
}
|
1051 |
|
1052 |
massOfZCons_local = 0;
|
1053 |
|
1054 |
for (int i = 0; i < (int) (massOfZConsMols.size()); i++){
|
1055 |
massOfZCons_local += massOfZConsMols[i];
|
1056 |
}
|
1057 |
#ifndef IS_MPI
|
1058 |
massOfZCons = massOfZCons_local;
|
1059 |
tempMVz = tempMVz_local;
|
1060 |
#else
|
1061 |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE, MPI_SUM,
|
1062 |
MPI_COMM_WORLD);
|
1063 |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
|
1064 |
#endif
|
1065 |
|
1066 |
return tempMVz / (totalMassOfUncons + massOfZCons);
|
1067 |
}
|
1068 |
|
1069 |
template<typename T> double ZConstraint<T>::calcTotalForce(){
|
1070 |
double force[3];
|
1071 |
double totalForce_local;
|
1072 |
double totalForce;
|
1073 |
|
1074 |
totalForce_local = 0;
|
1075 |
|
1076 |
for (int i = 0; i < nAtoms; i++){
|
1077 |
atoms[i]->getFrc(force);
|
1078 |
totalForce_local += force[whichDirection];
|
1079 |
}
|
1080 |
|
1081 |
#ifndef IS_MPI
|
1082 |
totalForce = totalForce_local;
|
1083 |
#else
|
1084 |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE, MPI_SUM,
|
1085 |
MPI_COMM_WORLD);
|
1086 |
#endif
|
1087 |
|
1088 |
return totalForce;
|
1089 |
}
|
1090 |
|
1091 |
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
|
1092 |
//calculate the number of atoms of moving z-constrained molecules
|
1093 |
int nMovingZAtoms_local;
|
1094 |
int nMovingZAtoms;
|
1095 |
|
1096 |
nMovingZAtoms_local = 0;
|
1097 |
for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)
|
1098 |
if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){
|
1099 |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
|
1100 |
}
|
1101 |
|
1102 |
#ifdef IS_MPI
|
1103 |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM,
|
1104 |
MPI_COMM_WORLD);
|
1105 |
#else
|
1106 |
nMovingZAtoms = nMovingZAtoms_local;
|
1107 |
#endif
|
1108 |
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
|
1109 |
}
|
1110 |
|
1111 |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol,
|
1112 |
Atom* atom,
|
1113 |
double totalForce){
|
1114 |
return totalForce / mol->getNAtoms();
|
1115 |
}
|
1116 |
|
1117 |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom,
|
1118 |
double totalForce){
|
1119 |
return totalForce / totNumOfMovingAtoms;
|
1120 |
}
|
1121 |
|
1122 |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol,
|
1123 |
Atom* atom,
|
1124 |
double totalForce){
|
1125 |
return totalForce / mol->getNAtoms();
|
1126 |
}
|
1127 |
|
1128 |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom,
|
1129 |
double totalForce){
|
1130 |
return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
|
1131 |
}
|
1132 |
|
1133 |
|
1134 |
template<typename T> void ZConstraint<T>::PolicyByMass::update(){
|
1135 |
//calculate the number of atoms of moving z-constrained molecules
|
1136 |
double massOfMovingZAtoms_local;
|
1137 |
double massOfMovingZAtoms;
|
1138 |
|
1139 |
massOfMovingZAtoms_local = 0;
|
1140 |
for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)
|
1141 |
if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){
|
1142 |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
|
1143 |
}
|
1144 |
|
1145 |
#ifdef IS_MPI
|
1146 |
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,
|
1147 |
MPI_SUM, MPI_COMM_WORLD);
|
1148 |
#else
|
1149 |
massOfMovingZAtoms = massOfMovingZAtoms_local;
|
1150 |
#endif
|
1151 |
totMassOfMovingAtoms = massOfMovingZAtoms +
|
1152 |
zconsIntegrator->totalMassOfUncons;
|
1153 |
}
|
1154 |
|
1155 |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol,
|
1156 |
Atom* atom,
|
1157 |
double totalForce){
|
1158 |
return totalForce * atom->getMass() / mol->getTotalMass();
|
1159 |
}
|
1160 |
|
1161 |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols(Atom* atom,
|
1162 |
double totalForce){
|
1163 |
return totalForce * atom->getMass() / totMassOfMovingAtoms;
|
1164 |
}
|
1165 |
|
1166 |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol,
|
1167 |
Atom* atom,
|
1168 |
double totalForce){
|
1169 |
return totalForce * atom->getMass() / mol->getTotalMass();
|
1170 |
}
|
1171 |
|
1172 |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom,
|
1173 |
double totalForce){
|
1174 |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
|
1175 |
}
|
1176 |
|
1177 |
template<typename T> void ZConstraint<T>::updateZPos(){
|
1178 |
double curTime;
|
1179 |
double COM[3];
|
1180 |
|
1181 |
curTime = info->getTime();
|
1182 |
|
1183 |
for (size_t i = 0; i < zconsMols.size(); i++){
|
1184 |
|
1185 |
if (states[i] == zcsFixed && curTime >= endFixTime[i]){
|
1186 |
zPos[i] += zconsGap;
|
1187 |
|
1188 |
if (usingSMD){
|
1189 |
zconsMols[i]->getCOM(COM);
|
1190 |
cantPos[i] = COM[whichDirection];
|
1191 |
}
|
1192 |
|
1193 |
}
|
1194 |
|
1195 |
}
|
1196 |
|
1197 |
}
|
1198 |
|
1199 |
template<typename T> void ZConstraint<T>::updateCantPos(){
|
1200 |
double curTime;
|
1201 |
double dt;
|
1202 |
|
1203 |
curTime = info->getTime();
|
1204 |
dt = info->dt;
|
1205 |
|
1206 |
for (size_t i = 0; i < zconsMols.size(); i++){
|
1207 |
if (states[i] == zcsMoving){
|
1208 |
cantPos[i] += cantVel[i] * dt;
|
1209 |
}
|
1210 |
}
|
1211 |
|
1212 |
}
|