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Sph.cpp
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Sph.cpp
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/*
* Routines to implement SPH.
* Main author: James Wadsley, as first implemented in GASOLINE.
* See Wadsley, J.~W., Stadel, J., Quinn, T.\ 2004.\ Gasoline: a flexible,
* parallel implementation of TreeSPH.\ New Astronomy 9, 137-158.
*/
#include "ParallelGravity.h"
#include "DataManager.h"
#include "smooth.h"
#include "Sph.h"
#include "SphUtils.h"
#include "physconst.h"
#ifndef MAXPATHLEN
#define MAXPATHLEN PATH_MAX
#endif
#include <float.h>
///
/// @brief initialize SPH quantities
///
/// Initial calculation of densities and internal energies, and cooling rates.
///
void
Main::initSph()
{
if(param.bDoGas) {
ckout << "Calculating densities/divv ...";
// The following smooths all GAS, and also marks neighbors of
// actives, and those who have actives as neighbors
// Starting is true
DenDvDxSmoothParams pDen(TYPE_GAS, 0, param.csm, dTime, 0,
param.bConstantDiffusion, 1, bHaveAlpha,
param.dConstAlphaMax);
double startTime = CkWallTimer();
double dfBall2OverSoft2 = 4.0*param.dhMinOverSoft*param.dhMinOverSoft;
treeProxy.startSmooth(&pDen, 1, param.nSmooth, dfBall2OverSoft2,
CkCallbackResumeThread());
ckout << " took " << (CkWallTimer() - startTime) << " seconds."
<< endl;
if(verbosity > 1 && !param.bConcurrentSph)
memoryStatsCache();
double dTuFac = param.dGasConst/(param.dConstGamma-1)
/param.dMeanMolWeight;
double z = 1.0/csmTime2Exp(param.csm, dTime) - 1.0;
if(param.bGasCooling) {
// Update cooling on the datamanager
dMProxy.CoolingSetTime(z, dTime, CkCallbackResumeThread());
if(!bIsRestarting) // Energy is already OK from checkpoint.
treeProxy.InitEnergy(dTuFac, z, dTime, CkCallbackResumeThread());
}
if(verbosity) CkPrintf("Initializing SPH forces\n");
nActiveSPH = nTotalSPH;
doSph(0, 0);
double duDelta[MAXRUNG+1];
double dStartTime[MAXRUNG+1];
for(int iRung = 0; iRung <= MAXRUNG; iRung++) {
duDelta[iRung] = 0.5e-7*param.dDelta;
dStartTime[iRung] = dTime;
}
treeProxy.updateuDot(0, duDelta, dStartTime, param.bGasCooling, 0, 1,
CkCallbackResumeThread());
}
}
// see below for definition.
bool arrayFileExists(const std::string filename, const int64_t count) ;
#include <sys/stat.h>
///
/// @brief Initialize cooling constants and integration data structures.
///
void Main::initCooling()
{
#ifndef COOLING_NONE
dMProxy.initCooling(param.dGmPerCcUnit, param.dComovingGmPerCcUnit,
param.dErgPerGmUnit, param.dSecUnit, param.dKpcUnit,
param.CoolParam, CkCallbackResumeThread());
/* Read in tables from files as necessary */
int cntTable = 0;
int nTableRows;
int nTableColumns;
char TableFileSuffix[20];
for (;;) {
CoolTableReadInfo(¶m.CoolParam, cntTable, &nTableColumns,
TableFileSuffix);
if (!nTableColumns) break;
cntTable++;
nTableRows = ReadASCII(TableFileSuffix, nTableColumns, NULL);
if (nTableRows) {
CkAssert(sizeof(double)*nTableRows*nTableColumns <= CL_NMAXBYTETABLE );
double *dTableData = (double *)malloc(sizeof(double)*nTableRows*nTableColumns);
CkAssert( dTableData != NULL );
nTableRows = ReadASCII(TableFileSuffix, nTableColumns, dTableData);
dMProxy.dmCoolTableRead(dTableData,nTableRows*nTableColumns,
CkCallbackResumeThread());
free(dTableData);
}
}
treeProxy.initCoolingData(CkCallbackResumeThread());
if(!bIsRestarting) { // meaning not restarting from a checkpoint.
struct stat s;
int err = stat(basefilename.c_str(), &s);
if(err != -1 && S_ISDIR(s.st_mode)) {
// The file is a directory; assume NChilada
int64_t nGas = 0;
nGas = ncGetCount(basefilename + "/gas/coolontime");
if(nGas == nTotalSPH) {
CkPrintf("Reading coolontime\n");
coolontimeOutputParams pCoolOnOut(basefilename, 6, 0.0);
treeProxy.readFloatBinary(pCoolOnOut, param.bParaRead,
CkCallbackResumeThread());
}
}
else {
if(arrayFileExists(basefilename + ".coolontime", nTotalParticles)) {
CkPrintf("Reading coolontime\n");
coolontimeOutputParams pCoolOnOut(basefilename, 0, 0.0);
treeProxy.readTipsyArray(pCoolOnOut, CkCallbackResumeThread());
}
}
}
#endif
}
/**
* Initialized Cooling Read-only data on the DataManager, which
* doesn't migrate.
*/
void
DataManager::initCooling(double dGmPerCcUnit, double dComovingGmPerCcUnit,
double dErgPerGmUnit, double dSecUnit, double dKpcUnit,
COOLPARAM inParam, const CkCallback& cb)
{
#ifndef COOLING_NONE
clInitConstants(Cool, dGmPerCcUnit, dComovingGmPerCcUnit, dErgPerGmUnit,
dSecUnit, dKpcUnit, inParam);
CoolInitRatesTable(Cool,inParam);
#endif
contribute(cb);
}
/**
* Per thread initialization
*/
void
TreePiece::initCoolingData(const CkCallback& cb)
{
#ifndef COOLING_NONE
bGasCooling = 1;
dm = (DataManager*)CkLocalNodeBranch(dataManagerID);
CoolData = CoolDerivsInit(dm->Cool);
#endif
contribute(cb);
}
void
DataManager::dmCoolTableRead(double *dTableData, int nData, const CkCallback& cb)
{
#ifndef COOLING_NONE
CoolTableRead(Cool, nData*sizeof(double), (void *) dTableData);
#endif
contribute(cb);
}
///
/// @brief function from PKDGRAV to read an ASCII table
///
/// @param extension Appended to outName to determine file name to
/// read.
/// @param nDataPerLine Number of columns in the table.
/// @param dDataOut pointer to array in which to store the table.
/// Note if dDataOut is NULL it just counts the number of valid input
/// lines.
///
int Main::ReadASCII(char *extension, int nDataPerLine, double *dDataOut)
{
FILE *fp;
int i,ret;
char achIn[160];
double *dData;
if (dDataOut == NULL)
dData = (double *)malloc(sizeof(double)*nDataPerLine);
else
dData = dDataOut;
CkAssert(nDataPerLine > 0 && nDataPerLine <= 10);
char achFile[MAXPATHLEN];
sprintf(achFile, "%s.%s", param.achOutName, extension);
fp = fopen(achFile,"r");
if (!fp) {
CkPrintf("WARNING: Could not open .%s input file:%s\n",
extension,achFile);
return 0;
}
i = 0;
while (1) {
if (!fgets(achIn,160,fp)) goto Done;
switch (nDataPerLine) {
case 1:
ret = sscanf(achIn,"%lf",dData);
break;
case 2:
ret = sscanf(achIn,"%lf %lf",dData,dData+1);
break;
case 3:
ret = sscanf(achIn,"%lf %lf %lf",dData,dData+1,dData+2);
break;
case 4:
ret = sscanf(achIn,"%lf %lf %lf %lf",dData,dData+1,dData+2,dData+3);
break;
case 5:
ret = sscanf(achIn,"%lf %lf %lf %lf %lf",dData,dData+1,dData+2,dData+3,dData+4);
break;
case 6:
ret = sscanf(achIn,"%lf %lf %lf %lf %lf %lf",dData,dData+1,dData+2,dData+3,dData+4,dData+5);
break;
case 7:
ret = sscanf(achIn,"%lf %lf %lf %lf %lf %lf %lf",
dData,dData+1,dData+2,dData+3,dData+4,dData+5,dData+6);
break;
case 8:
ret = sscanf(achIn,"%lf %lf %lf %lf %lf %lf %lf %lf",
dData,dData+1,dData+2,dData+3,dData+4,dData+5,dData+6,dData+7);
break;
case 9:
ret = sscanf(achIn,"%lf %lf %lf %lf %lf %lf %lf %lf %lf",
dData,dData+1,dData+2,dData+3,dData+4,dData+5,dData+6,dData+7,dData+8);
break;
case 10:
ret = sscanf(achIn,"%lf %lf %lf %lf %lf %lf %lf %lf %lf %lf",
dData,dData+1,dData+2,dData+3,dData+4,dData+5,dData+6,dData+7,dData+8,dData+9);
break;
default:
ret = EOF;
CkAssert(0);
}
if (ret != nDataPerLine) goto Done;
++i;
if (dDataOut != NULL) dData += nDataPerLine;
}
Done:
fclose(fp);
if (dDataOut != NULL && verbosity)
printf("Read %i lines from %s\n",i,achFile);
if (dDataOut == NULL) free(dData);
return i;
}
/*
* Update the cooling functions to the current time.
* This is on the DataManager to avoid duplication of effort.
*/
void
DataManager::CoolingSetTime(double z, // redshift
double dTime, // Time
const CkCallback& cb)
{
#ifndef COOLING_NONE
CoolSetTime( Cool, dTime, z );
#endif
contribute(cb);
}
/**
* @brief DataManager::SetStarCM saves the total mass and center of mass of the
* star(s) to the COOL struct Cool, making them available to the cool particles
* @param dCenterOfMass Array(length 4) which contains the star(s) center of
* mass as the first 3 entries and the total star mass as the final entry
* @param cb Callback
*/
void DataManager::SetStarCM(double dCenterOfMass[4], const CkCallback& cb) {
#ifndef COOLING_NONE
#ifdef COOLING_PLANET
CoolSetStarCM(Cool, dCenterOfMass);
#endif
#endif
contribute(cb);
}
/**
* @brief utility for checking array files
*/
bool
arrayFileExists(const std::string filename, const int64_t count)
{
FILE *fp = CmiFopen(filename.c_str(), "r");
if(fp != NULL) {
// Check if its a binary file
unsigned int iDum;
XDR xdrs;
xdrstdio_create(&xdrs, fp, XDR_DECODE);
xdr_u_int(&xdrs,&iDum);
xdr_destroy(&xdrs);
if(iDum == count) { // Assume a valid binary array file
fclose(fp);
return true;
}
fseek(fp, 0, SEEK_SET);
int64_t nIOrd;
fscanf(fp, "%ld", &nIOrd);
CkAssert(nIOrd == count); // Valid ASCII file.
fclose(fp);
return true;
}
return false;
}
/// @brief Set total metals based on Ox and Fe mass fractions
void
TreePiece::resetMetals(const CkCallback& cb)
{
for(unsigned int i = 1; i <= myNumParticles; ++i) {
GravityParticle *p = &myParticles[i];
// Use total metals to Fe and O based on Asplund et al 2009
if (p->isGas())
p->fMetals() = 1.06*p->fMFracIron() + 2.09*p->fMFracOxygen();
if (p->isStar())
p->fStarMetals() = 1.06*p->fStarMFracIron()
+ 2.09*p->fStarMFracOxygen();
}
contribute(cb);
}
#include <sys/stat.h>
/**
* @brief Read in array files for complete gas information.
*/
void
Main::restartGas()
{
if(verbosity)
CkPrintf("Restarting Gas Simulation with array files.\n");
struct stat s;
int err = stat(basefilename.c_str(), &s);
if(err != -1 && S_ISDIR(s.st_mode)) {
// The file is a directory; assume NChilada
int64_t nGas = 0;
int64_t nDark = 0;
int64_t nStar = 0;
if(nTotalSPH > 0)
nGas = ncGetCount(basefilename + "/gas/iord");
if(nTotalDark > 0)
nDark = ncGetCount(basefilename + "/dark/iord");
if(nTotalStar > 0)
nStar = ncGetCount(basefilename + "/star/iord");
if(nGas + nDark + nStar == nTotalParticles) {
IOrderOutputParams pIOrdOut(basefilename, 6, 0.0);
treeProxy.readFloatBinary(pIOrdOut, param.bParaRead,
CkCallbackResumeThread());
CkReductionMsg *msg;
treeProxy.getMaxIOrds(CkCallbackResumeThread((void*&)msg));
CmiInt8 *maxIOrds = (CmiInt8 *)msg->getData();
nMaxOrderGas = maxIOrds[0];
nMaxOrderDark = maxIOrds[1];
nMaxOrder = maxIOrds[2];
delete msg;
}
else
CkError("WARNING: no iorder file, or wrong format for restart\n");
if(nTotalStar > 0)
nStar = ncGetCount(basefilename + "/star/igasorder");
if(nStar == nTotalStar) {
IGasOrderOutputParams pIOrdOut(basefilename, 6, 0.0);
treeProxy.readFloatBinary(pIOrdOut, param.bParaRead,
CkCallbackResumeThread());
}
else
CkError("WARNING: no igasorder file, or wrong format for restart\n");
if(param.bFeedback) {
if(nTotalSPH > 0)
nGas = ncGetCount(basefilename + "/gas/ESNRate");
if(nTotalStar > 0)
nStar = ncGetCount(basefilename + "/star/ESNRate");
if(nGas + nStar == nTotalSPH + nTotalStar) {
ESNRateOutputParams pESNROut(basefilename, 6, 0.0);
treeProxy.readFloatBinary(pESNROut, param.bParaRead,
CkCallbackResumeThread());
}
else
CkError("WARNING: no ESNRate file, or wrong format for restart\n");
if(nTotalSPH > 0)
nGas = ncGetCount(basefilename + "/gas/OxMassFrac");
if(nTotalStar > 0)
nStar = ncGetCount(basefilename + "/star/OxMassFrac");
if(nGas + nStar == nTotalSPH + nTotalStar) {
OxOutputParams pOxOut(basefilename, 6, 0.0);
treeProxy.readFloatBinary(pOxOut, param.bParaRead,
CkCallbackResumeThread());
}
else
CkError("WARNING: no OxMassFrac file, or wrong format for restart\n");
if(nTotalSPH > 0)
nGas = ncGetCount(basefilename + "/gas/FeMassFrac");
if(nTotalStar > 0)
nStar = ncGetCount(basefilename + "/star/FeMassFrac");
if(nGas + nStar == nTotalSPH + nTotalStar) {
FeOutputParams pFeOut(basefilename, 6, 0.0);
treeProxy.readFloatBinary(pFeOut, param.bParaRead,
CkCallbackResumeThread());
}
else
CkError("WARNING: no FeMassFrac file, or wrong format for restart\n");
treeProxy.resetMetals(CkCallbackResumeThread());
if(nTotalStar > 0)
nStar = ncGetCount(basefilename + "/star/massform");
if(nStar == nTotalStar) {
MFormOutputParams pMFOut(basefilename, 6, 0.0);
treeProxy.readFloatBinary(pMFOut, param.bParaRead,
CkCallbackResumeThread());
}
else
CkError("WARNING: no massform file, or wrong format for restart\n");
}
#ifdef CULLENALPHA
if(nTotalSPH > 0) {
nGas = ncGetCount(basefilename + "/gas/alpha");
if(nGas == nTotalSPH) {
AlphaOutputParams pAlphaOut(basefilename, 6, 0.0);
treeProxy.readFloatBinary(pAlphaOut, param.bParaRead,
CkCallbackResumeThread());
bHaveAlpha = 1;
}
else
CkError("WARNING: no alpha file, or wrong format for restart\n");
}
#endif
#ifndef COOLING_NONE
if(param.bGasCooling && nTotalSPH > 0) {
bool bFoundCoolArray = false;
// read ionization fractions
nGas = ncGetCount(basefilename + "/gas/" + COOL_ARRAY0_EXT);
if(nGas == nTotalSPH) {
Cool0OutputParams pCool0Out(basefilename, 6, 0.0);
treeProxy.readFloatBinary(pCool0Out, param.bParaRead,
CkCallbackResumeThread());
bFoundCoolArray = true;
}
else
CkError("WARNING: no CoolArray0 file, or wrong format for restart\n");
nGas = ncGetCount(basefilename + "/gas/" + COOL_ARRAY1_EXT);
if(nGas == nTotalSPH) {
Cool1OutputParams pCool1Out(basefilename, 6, 0.0);
treeProxy.readFloatBinary(pCool1Out, param.bParaRead,
CkCallbackResumeThread());
bFoundCoolArray = true;
}
else
CkError("WARNING: no CoolArray1 file, or wrong format for restart\n");
nGas = ncGetCount(basefilename + "/gas/" + COOL_ARRAY2_EXT);
if(nGas == nTotalSPH) {
Cool2OutputParams pCool2Out(basefilename, 6, 0.0);
treeProxy.readFloatBinary(pCool2Out, param.bParaRead,
CkCallbackResumeThread());
bFoundCoolArray = true;
}
else
CkError("WARNING: no CoolArray2 file, or wrong format for restart\n");
nGas = ncGetCount(basefilename + "/gas/" + COOL_ARRAY3_EXT);
if(nGas == nTotalSPH) {
Cool3OutputParams pCool3Out(basefilename, 6, 0.0);
treeProxy.readFloatBinary(pCool3Out, param.bParaRead,
CkCallbackResumeThread());
bFoundCoolArray = true;
}
else
CkError("WARNING: no CoolArray3 file, or wrong format for restart\n");
double dTuFac = param.dGasConst/(param.dConstGamma-1)
/param.dMeanMolWeight;
if(bFoundCoolArray) {
// reset thermal energy with ionization fractions
treeProxy.RestartEnergy(dTuFac, CkCallbackResumeThread());
}
else {
double z = 1.0/csmTime2Exp(param.csm, dTime) - 1.0;
dMProxy.CoolingSetTime(z, dTime, CkCallbackResumeThread());
treeProxy.InitEnergy(dTuFac, z, dTime, CkCallbackResumeThread());
}
}
#endif
} else {
// Assume TIPSY arrays
// read iOrder
if(arrayFileExists(basefilename + ".iord", nTotalParticles)) {
CkReductionMsg *msg;
IOrderOutputParams pIOrdOut(basefilename, 0, 0.0);
treeProxy.readTipsyArray(pIOrdOut, CkCallbackResumeThread());
treeProxy.getMaxIOrds(CkCallbackResumeThread((void*&)msg));
CmiInt8 *maxIOrds = (CmiInt8 *)msg->getData();
nMaxOrderGas = maxIOrds[0];
nMaxOrderDark = maxIOrds[1];
nMaxOrder = maxIOrds[2];
delete msg;
}
else
CkError("WARNING: no iOrder file for restart\n");
// read iGasOrder
if(arrayFileExists(basefilename + ".igasorder", nTotalParticles)) {
IGasOrderOutputParams pIOrdOut(basefilename, 0, 0.0);
treeProxy.readTipsyArray(pIOrdOut, CkCallbackResumeThread());
}
else {
CkError("WARNING: no igasorder file for restart\n");
}
if(param.bFeedback) {
if(arrayFileExists(basefilename + ".ESNRate", nTotalParticles)) {
ESNRateOutputParams pESNROut(basefilename, 0, 0.0);
treeProxy.readTipsyArray(pESNROut, CkCallbackResumeThread());
}
if(arrayFileExists(basefilename + ".OxMassFrac", nTotalParticles)) {
OxOutputParams pOxOut(basefilename, 0, 0.0);
treeProxy.readTipsyArray(pOxOut, CkCallbackResumeThread());
}
if(arrayFileExists(basefilename + ".FeMassFrac", nTotalParticles)) {
FeOutputParams pFeOut(basefilename, 0, 0.0);
treeProxy.readTipsyArray(pFeOut, CkCallbackResumeThread());
}
treeProxy.resetMetals(CkCallbackResumeThread());
if(arrayFileExists(basefilename + ".massform", nTotalParticles)) {
MFormOutputParams pMFOut(basefilename, 0, 0.0);
treeProxy.readTipsyArray(pMFOut, CkCallbackResumeThread());
}
}
#ifdef CULLENALPHA
if(arrayFileExists(basefilename + ".alpha", nTotalParticles)) {
AlphaOutputParams pAlphaOut(basefilename, 0, 0.0);
treeProxy.readTipsyArray(pAlphaOut, CkCallbackResumeThread());
bHaveAlpha = 1;
}
else
CkError("WARNING: no alpha file, or wrong format for restart\n");
#endif
#ifndef COOLING_NONE
if(param.bGasCooling) {
bool bFoundCoolArray = false;
// read ionization fractions
if(arrayFileExists(basefilename + "." + COOL_ARRAY0_EXT, nTotalParticles)) {
Cool0OutputParams pCool0Out(basefilename, 0, 0.0);
treeProxy.readTipsyArray(pCool0Out, CkCallbackResumeThread());
bFoundCoolArray = true;
}
else {
CkError("WARNING: no CoolArray0 file for restart\n");
}
if(arrayFileExists(basefilename + "." + COOL_ARRAY1_EXT, nTotalParticles)) {
Cool1OutputParams pCool1Out(basefilename, 0, 0.0);
treeProxy.readTipsyArray(pCool1Out, CkCallbackResumeThread());
bFoundCoolArray = true;
}
else {
CkError("WARNING: no CoolArray1 file for restart\n");
}
if(arrayFileExists(basefilename + "." + COOL_ARRAY2_EXT, nTotalParticles)) {
Cool2OutputParams pCool2Out(basefilename, 0, 0.0);
treeProxy.readTipsyArray(pCool2Out, CkCallbackResumeThread());
bFoundCoolArray = true;
}
else {
CkError("WARNING: no CoolArray2 file for restart\n");
}
if(arrayFileExists(basefilename + "." + COOL_ARRAY3_EXT, nTotalParticles)) {
Cool3OutputParams pCool3Out(basefilename, 0, 0.0);
treeProxy.readTipsyArray(pCool3Out, CkCallbackResumeThread());
bFoundCoolArray = true;
}
else {
CkError("WARNING: no CoolArray3 file for restart\n");
}
double dTuFac = param.dGasConst/(param.dConstGamma-1)
/param.dMeanMolWeight;
if(bFoundCoolArray) {
// reset thermal energy with ionization fractions
treeProxy.RestartEnergy(dTuFac, CkCallbackResumeThread());
}
else {
double z = 1.0/csmTime2Exp(param.csm, dTime) - 1.0;
dMProxy.CoolingSetTime(z, dTime, CkCallbackResumeThread());
treeProxy.InitEnergy(dTuFac, z, dTime, CkCallbackResumeThread());
}
}
#endif
}
}
/*
* Initialize energy on restart
*/
void TreePiece::RestartEnergy(double dTuFac, // T to internal energy
const CkCallback& cb)
{
#ifndef COOLING_NONE
COOL *cl;
dm = (DataManager*)CkLocalNodeBranch(dataManagerID);
cl = dm->Cool;
#endif
for(unsigned int i = 1; i <= myNumParticles; ++i) {
GravityParticle *p = &myParticles[i];
if (p->isGas()) {
#ifndef COOLING_NONE
#ifndef COOLING_GRACKLE
double T;
T = p->u() / dTuFac;
PERBARYON Y;
CoolPARTICLEtoPERBARYON(cl, &Y, &p->CoolParticle());
p->u() = clThermalEnergy(Y.Total,T)*cl->diErgPerGmUnit;
#endif
#endif
p->uPred() = p->u();
}
}
contribute(cb);
}
/**
* @brief Perform the SPH force calculation.
* @param activeRung Timestep rung (and above) on which to perform
* SPH
* @param bNeedDensity Does the density calculation need to be done?
* Defaults to 1
*/
void
Main::doSph(int activeRung, int bNeedDensity)
{
if(bNeedDensity) {
double dfBall2OverSoft2 = 4.0*param.dhMinOverSoft*param.dhMinOverSoft;
if (param.bFastGas && nActiveSPH < nTotalSPH*param.dFracFastGas) {
ckout << "Calculating densities/divv on Actives ...";
// This also marks neighbors of actives
DenDvDxSmoothParams pDen(TYPE_GAS, activeRung, param.csm, dTime, 1,
param.bConstantDiffusion, 0, 0,
param.dConstAlphaMax);
double startTime = CkWallTimer();
treeProxy.startSmooth(&pDen, 1, param.nSmooth, dfBall2OverSoft2,
CkCallbackResumeThread());
ckout << " took " << (CkWallTimer() - startTime) << " seconds."
<< endl;
ckout << "Marking Neighbors ...";
// This marks particles with actives as neighbors
MarkSmoothParams pMark(TYPE_GAS, activeRung);
startTime = CkWallTimer();
treeProxy.startMarkSmooth(&pMark, CkCallbackResumeThread());
ckout << " took " << (CkWallTimer() - startTime) << " seconds."
<< endl;
ckout << "Density of Neighbors ...";
// This does neighbors (but not actives), It also does no
// additional marking
DenDvDxNeighborSmParams pDenN(TYPE_GAS, activeRung, param.csm, dTime,
param.bConstantDiffusion,
param.dConstAlphaMax);
startTime = CkWallTimer();
treeProxy.startSmooth(&pDenN, 1, param.nSmooth, dfBall2OverSoft2,
CkCallbackResumeThread());
ckout << " took " << (CkWallTimer() - startTime) << " seconds."
<< endl;
}
else {
ckout << "Calculating densities/divv ...";
// The following smooths all GAS, and also marks neighbors of
// actives, and those who have actives as neighbors.
DenDvDxSmoothParams pDen(TYPE_GAS, activeRung, param.csm, dTime, 0,
param.bConstantDiffusion, 0, 0,
param.dConstAlphaMax);
double startTime = CkWallTimer();
treeProxy.startSmooth(&pDen, 1, param.nSmooth, dfBall2OverSoft2,
CkCallbackResumeThread());
ckout << " took " << (CkWallTimer() - startTime) << " seconds."
<< endl;
if(verbosity > 1 && !param.bConcurrentSph)
memoryStatsCache();
}
}
treeProxy.sphViscosityLimiter(param.iViscosityLimiter, activeRung,
CkCallbackResumeThread());
double a = csmTime2Exp(param.csm,dTime);
double dDtCourantFac = param.dEtaCourant*a*2.0/1.6;
if(param.bGasCooling)
treeProxy.getCoolingGasPressure(param.dConstGamma,
param.dConstGamma-1,
dDtCourantFac,
param.dResolveJeans/csmTime2Exp(param.csm, dTime),
CkCallbackResumeThread());
else
treeProxy.getAdiabaticGasPressure(param.dConstGamma,
param.dConstGamma-1,
dDtCourantFac,
CkCallbackResumeThread());
ckout << "Calculating pressure gradients ...";
PressureSmoothParams pPressure(TYPE_GAS, activeRung, param.csm, dTime,
param.dConstAlpha, param.dConstBeta,
param.dThermalDiffusionCoeff, param.dMetalDiffusionCoeff,
param.dEtaCourant, param.dEtaDiffusion);
double startTime = CkWallTimer();
treeProxy.startReSmooth(&pPressure, CkCallbackResumeThread());
ckout << " took " << (CkWallTimer() - startTime) << " seconds."
<< endl;
treeProxy.ballMax(activeRung, 1.0+param.ddHonHLimit,
CkCallbackResumeThread());
}
/*
* Initialize energy and ionization state for cooling particles
*/
void TreePiece::InitEnergy(double dTuFac, // T to internal energy
double z, // redshift
double dTime,
const CkCallback& cb)
{
#ifndef COOLING_NONE
COOL *cl;
dm = (DataManager*)CkLocalNodeBranch(dataManagerID);
cl = dm->Cool;
#endif
for(unsigned int i = 1; i <= myNumParticles; ++i) {
GravityParticle *p = &myParticles[i];
if (TYPETest(p, TYPE_GAS) && p->rung >= activeRung) {
#ifndef COOLING_NONE
double T,E;
T = p->u() / dTuFac;
CoolInitEnergyAndParticleData(cl, &p->CoolParticle(), &E,
p->fDensity, T, p->fMetals() );
p->u() = E;
#endif
p->uPred() = p->u();
}
}
// Use shadow array to avoid reduction conflict
smoothProxy[thisIndex].ckLocal()->contribute(cb);
}
/**
* @brief Update the cooling rate (uDot)
*
* @param activeRung (minimum) rung being updated
* @param duDelta array of timesteps of length MAXRUNG+1
* @param dStartTime array of start times of length MAXRUNG+1
* @param bCool Whether cooling is on
* @param bUpdateState Whether the ionization factions need updating
* @param bAll Do all rungs below activeRung
* @param cb Callback.
*/
void TreePiece::updateuDot(int activeRung,
double duDelta[MAXRUNG+1], // timesteps
double dStartTime[MAXRUNG+1],
int bCool, // select equation of state
int bUpdateState, // update ionization fractions
int bAll, // update all rungs below activeRung
const CkCallback& cb)
{
#ifndef COOLING_NONE
double dt; // time in seconds
for(unsigned int i = 1; i <= myNumParticles; ++i) {
GravityParticle *p = &myParticles[i];
if (TYPETest(p, TYPE_GAS)
&& (p->rung == activeRung || (bAll && p->rung >= activeRung))) {
dt = CoolCodeTimeToSeconds(dm->Cool, duDelta[p->rung] );
double ExternalHeating = p->PdV();
ExternalHeating += p->fESNrate();
if ( bCool ) {
COOLPARTICLE cp = p->CoolParticle();
double E = p->u();
double r[3]; // For conversion to C
p->position.array_form(r);
double dtUse = dt;
if(dStartTime[p->rung] + 0.5*duDelta[p->rung]
< p->fTimeCoolIsOffUntil()) {
/* This flags cooling shutoff (e.g., from SNe) to
the cooling functions. */
dtUse = -dt;
p->uDot() = ExternalHeating;
}
CoolIntegrateEnergyCode(dm->Cool, CoolData, &cp, &E,
ExternalHeating, p->fDensity,
p->fMetals(), r, dtUse);
CkAssert(E > 0.0);
if(dtUse > 0 || ExternalHeating*duDelta[p->rung] + p->u() < 0)
// linear interpolation over interval
p->uDot() = (E - p->u())/duDelta[p->rung];
if (bUpdateState) p->CoolParticle() = cp;
}
else {
p->uDot() = ExternalHeating;
}
}
}
#endif
// Use shadow array to avoid reduction conflict
smoothProxy[thisIndex].ckLocal()->contribute(cb);
}
/* Set a maximum ball for inverse Nearest Neighbor searching */
void TreePiece::ballMax(int activeRung, double dhFac, const CkCallback& cb)
{
for(unsigned int i = 1; i <= myNumParticles; ++i) {
if (TYPETest(&myParticles[i], TYPE_GAS)) {
myParticles[i].fBallMax() = myParticles[i].fBall*dhFac;
}
}
// Use shadow array to avoid reduction conflict
smoothProxy[thisIndex].ckLocal()->contribute(cb);
}
int DenDvDxSmoothParams::isSmoothActive(GravityParticle *p)
{
if(bActiveOnly && p->rung < activeRung)
return 0; // not active
return (TYPETest(p, iType));
}
// Non-active neighbors of Actives
int DenDvDxNeighborSmParams::isSmoothActive(GravityParticle *p)
{
if(p->rung < activeRung && TYPETest(p, iType)
&& TYPETest(p, TYPE_NbrOfACTIVE))
return 1;
return 0;
}
// Only do actives
int MarkSmoothParams::isSmoothActive(GravityParticle *p)
{
if(p->rung < activeRung)
return 0; // not active
return (TYPETest(p, iType));
}
/// A remote neighbor particle is active.
void MarkSmoothParams::combSmoothCache(GravityParticle *p1,
ExternalSmoothParticle *p2)
{
p1->iType |= p2->iType;
}
void DenDvDxSmoothParams::initSmoothParticle(GravityParticle *p)
{
TYPEReset(p, TYPE_NbrOfACTIVE);
}
void DenDvDxSmoothParams::initTreeParticle(GravityParticle *p)
{
TYPEReset(p, TYPE_NbrOfACTIVE);
}
void DenDvDxSmoothParams::postTreeParticle(GravityParticle *p)
{
#ifdef CULLENALPHA
if(p->isGas())
p->dvds_old() = p->dvdsOnSFull();
#endif
}
void DenDvDxSmoothParams::initSmoothCache(GravityParticle *p)
{
}
void DenDvDxSmoothParams::combSmoothCache(GravityParticle *p1,
ExternalSmoothParticle *p2)
{
p1->iType |= p2->iType;
}
/* Gather only version */
void DenDvDxSmoothParams::fcnSmooth(GravityParticle *p, int nSmooth,
pqSmoothNode *nnList)
{
double ih2,ih, r2,rs,rs1,fDensity,fNorm,fNorm1,vFac;
double dvxdx, dvxdy, dvxdz, dvydx, dvydy, dvydz, dvzdx, dvzdy, dvzdz;
double dvx,dvy,dvz,dx,dy,dz,trace,grx,gry,grz;
#ifdef CULLENALPHA
double R_CD, R_CDN; ///< R in CD limiter, and
/// normalization for R.
double maxVSignal; ///< Maximum signal velocity
R_CD = 0.0; R_CDN = 0; maxVSignal = 0.0;
#endif
double divvnorm = 0.0;
GravityParticle *q;
int i;
unsigned int qiActive;
ih2 = invH2(p);
ih = sqrt(ih2);
vFac = 1./(a*a); /* converts v to xdot */
fNorm = M_1_PI*ih2*sqrt(ih2);
fDensity = 0.0;
dvxdx = 0; dvxdy = 0; dvxdz= 0;
dvydx = 0; dvydy = 0; dvydz= 0;
dvzdx = 0; dvzdy = 0; dvzdz= 0;
grx = 0; gry = 0; grz= 0;
qiActive = 0;
for (i=0;i<nSmooth;++i) {
double fDist2 = nnList[i].fKey;
r2 = fDist2*ih2;
q = nnList[i].p;
if(q == NULL)
CkAbort("NULL neighbor in DenDvDxSmooth");
if (p->rung >= activeRung)
TYPESet(q,TYPE_NbrOfACTIVE); /* important for SPH */
if(q->rung >= activeRung)
qiActive = 1;
rs = KERNEL(r2, nSmooth);
fDensity += rs*q->mass;
rs1 = DKERNEL(r2);
rs1 *= q->mass;
dx = nnList[i].dx.x; /* NB: dx = px - qx */
dy = nnList[i].dx.y;
dz = nnList[i].dx.z;
dvx = (-p->vPred().x + q->vPred().x)*vFac;
dvy = (-p->vPred().y + q->vPred().y)*vFac;
dvz = (-p->vPred().z + q->vPred().z)*vFac;
dvxdx += dvx*dx*rs1;
dvxdy += dvx*dy*rs1;
dvxdz += dvx*dz*rs1;
dvydx += dvy*dx*rs1;
dvydy += dvy*dy*rs1;
dvydz += dvy*dz*rs1;
dvzdx += dvz*dx*rs1;
dvzdy += dvz*dy*rs1;
dvzdz += dvz*dz*rs1;
divvnorm += (dx*dx+dy*dy+dz*dz)*rs1;
/* Grad P estimate */
/* This used to be:
grx += (-p->uPred + q->uPred)*dx*rs1; But that is
rho grad u*/
grx += (q->uPred())*dx*rs1;
gry += (q->uPred())*dy*rs1;
grz += (q->uPred())*dz*rs1;
#ifdef CULLENALPHA
// Special weighting function to reduce noise in R
// calculation. See discussion after eq. 29 in
// Wadsley et al 2017.
double R_wt = (1-r2*r2*0.0625)* q->mass;
R_CD += q->dvds_old() * R_wt;
R_CDN += R_wt;
// Convention here dvdx = vxq-vxp, dx = xp-xq so
// dvdotdr = -dvx*dx ...
double dvdotdr = -(dvx*dx + dvy*dy + dvz*dz)
+ fDist2*H; // vFac already in there
double cavg = (p->c() + q->c())*0.5;
double vSig = cavg - (dvdotdr < 0 ? dvdotdr/sqrt(fDist2) : 0);
if (vSig > maxVSignal) maxVSignal = vSig;
#endif
}
if (qiActive)
TYPESet(p,TYPE_NbrOfACTIVE);
p->fDensity = fNorm*fDensity;
trace = dvxdx+dvydy+dvzdz;
// keep Norm positive consistent w/ std 1/rho norm
fNorm1 = (divvnorm != 0 ? 3.0/fabs(divvnorm) : 0.0);
#if defined(DIFFUSION) || defined(CULLENALPHA)
double onethirdtrace = (1./3.)*trace;
/* Build Traceless Strain Tensor (not yet normalized) */
double sxx = dvxdx - onethirdtrace; /* pure compression/expansion doesn't diffuse */
double syy = dvydy - onethirdtrace;
double szz = dvzdz - onethirdtrace;
double sxy = 0.5*(dvxdy + dvydx); /* pure rotation doesn't diffuse */
double sxz = 0.5*(dvxdz + dvzdx);
double syz = 0.5*(dvydz + dvzdy);
#endif
#ifdef DIFFUSION
/* diff coeff., nu ~ C L^2 S (add C via dMetalDiffusionConstant, assume L ~ h) */