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Added some support for double precision gadget snapshot

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This commit is contained in:
Guilhem Lavaux 2015-02-26 10:36:52 +01:00
parent b7392204ad
commit 0b40de23d0
6 changed files with 102 additions and 67 deletions
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6
python/_cosmo_power.pyx
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@ -44,7 +44,7 @@ cdef extern from "cosmopower.hpp" namespace "CosmoTool":
void setFunction(CosmoFunction) void setFunction(CosmoFunction)
void updateCosmology() void updateCosmology()
void updatePhysicalCosmology() void updatePhysicalCosmology()
void normalize(double) void normalize(double,double)
void setNormalization(double) void setNormalization(double)
double power(double) double power(double)
@ -75,7 +75,7 @@ cdef class CosmologyPower:
self.power.updateCosmology() self.power.updateCosmology()
def normalize(self,s8,k_max=-1): def normalize(self,s8,k_min=-1,k_max=-1):
"""normalize(self, sigma8) """normalize(self, sigma8)
Compute the normalization of the power spectrum using sigma8. Compute the normalization of the power spectrum using sigma8.
@ -84,7 +84,7 @@ cdef class CosmologyPower:
sigma8 (float): standard deviation of density field smoothed at 8 Mpc/h sigma8 (float): standard deviation of density field smoothed at 8 Mpc/h
""" """
self.power.SIGMA8 = s8 self.power.SIGMA8 = s8
self.power.normalize(k_max) self.power.normalize(k_min, k_max)
def setFunction(self,funcname): def setFunction(self,funcname):

17
src/cosmopower.cpp
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@ -123,6 +123,9 @@ double CosmoPower::powerEfstathiou(double k)
void CosmoPower::updateHuWigglesConsts() void CosmoPower::updateHuWigglesConsts()
{ {
double f_b = OMEGA_B / OMEGA_0;
double f_c = OMEGA_C / OMEGA_0;
double k_silk = 1.6 * pow(OMEGA_B * h * h, 0.52) * pow(OmegaEff, 0.73) * (1 + pow(10.4 * OmegaEff, -0.95)); double k_silk = 1.6 * pow(OMEGA_B * h * h, 0.52) * pow(OmegaEff, 0.73) * (1 + pow(10.4 * OmegaEff, -0.95));
double z_eq = 2.50e4 * OmegaEff * pow(Theta_27, -4); double z_eq = 2.50e4 * OmegaEff * pow(Theta_27, -4);
//double s = 44.5 * log(9.83 / OmegaEff) / (sqrt(1 + 10 * pow(OMEGA_B * h * h, 0.75))); //double s = 44.5 * log(9.83 / OmegaEff) / (sqrt(1 + 10 * pow(OMEGA_B * h * h, 0.75)));
@ -139,14 +142,14 @@ void CosmoPower::updateHuWigglesConsts()
double a1 = pow(46.9 * OmegaEff, 0.670) * (1 + pow(32.1 * OmegaEff, -0.532)); double a1 = pow(46.9 * OmegaEff, 0.670) * (1 + pow(32.1 * OmegaEff, -0.532));
double a2 = pow(12.0 * OmegaEff, 0.424) * (1 + pow(45.0 * OmegaEff, -0.582)); double a2 = pow(12.0 * OmegaEff, 0.424) * (1 + pow(45.0 * OmegaEff, -0.582));
double alpha_c = pow(a1, -OMEGA_B/ OMEGA_0) * pow(a2, -pow(OMEGA_B / OMEGA_0, 3)); double alpha_c = pow(a1, -f_b) * pow(a2, -pow(f_b, 3));
double b1_betac = 0.944 * 1/(1 + pow(458 * OmegaEff, -0.708)); double b1_betac = 0.944 * 1/(1 + pow(458 * OmegaEff, -0.708));
double b2_betac = pow(0.395 * OmegaEff, -0.0266); double b2_betac = pow(0.395 * OmegaEff, -0.0266);
double beta_c = 1/ ( 1 + b1_betac * (pow(OMEGA_C / OMEGA_0, b2_betac) - 1) ); double beta_c = 1/ ( 1 + b1_betac * (pow(f_c, b2_betac) - 1) );
double alpha_b = 2.07 * k_eq * s * pow(1 + R_d, -0.75) * powG((1 + z_eq)/(1 + z_d)); double alpha_b = 2.07 * k_eq * s * pow(1 + R_d, -0.75) * powG((1 + z_eq)/(1 + z_d));
double beta_b = 0.5 + OMEGA_B / OMEGA_0 + (3 - 2 * OMEGA_B / OMEGA_0) * sqrt(pow(17.2 * OmegaEff, 2) + 1); double beta_b = 0.5 + f_b + (3 - 2 * f_b) * sqrt(pow(17.2 * OmegaEff, 2) + 1);
double beta_node = 8.41 * pow(OmegaEff, 0.435); double beta_node = 8.41 * pow(OmegaEff, 0.435);
ehu.k_silk = k_silk; ehu.k_silk = k_silk;
@ -262,16 +265,18 @@ double CosmoPower::integrandNormalize(double x)
return power(k)*k*k*f*f/(x*x); return power(k)*k*k*f*f/(x*x);
} }
void CosmoPower::normalize(double k_max) void CosmoPower::normalize(double k_min, double k_max)
{ {
double normVal = 0; double normVal = 0;
double abserr; double abserr;
gsl_integration_workspace *w = gsl_integration_workspace_alloc(NUM_ITERATION); gsl_integration_workspace *w = gsl_integration_workspace_alloc(NUM_ITERATION);
gsl_function f; gsl_function f;
double x_min = 0; double x_min = 0, x_max = 1;
if (k_max > 0) if (k_max > 0)
x_min = 1/(1+k_max); x_min = 1/(1+k_max);
if (k_min > 0)
x_max = 1/(1+k_min);
f.function = gslPowSpecNorm; f.function = gslPowSpecNorm;
f.params = this; f.params = this;
@ -286,7 +291,7 @@ void CosmoPower::normalize(double k_max)
} }
// gsl_integration_qagiu(&f, 0, 0, TOLERANCE, NUM_ITERATION, w, &normVal, &abserr); // gsl_integration_qagiu(&f, 0, 0, TOLERANCE, NUM_ITERATION, w, &normVal, &abserr);
gsl_integration_qag(&f, x_min, 1, 0, TOLERANCE, NUM_ITERATION, GSL_INTEG_GAUSS61, w, &normVal, &abserr); gsl_integration_qag(&f, x_min, x_max, 0, TOLERANCE, NUM_ITERATION, GSL_INTEG_GAUSS61, w, &normVal, &abserr);
gsl_integration_workspace_free(w); gsl_integration_workspace_free(w);
normVal /= (2*M_PI*M_PI); normVal /= (2*M_PI*M_PI);

2
src/cosmopower.hpp
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@ -92,7 +92,7 @@ namespace CosmoTool {
void updateCosmology(); void updateCosmology();
void updatePhysicalCosmology(); void updatePhysicalCosmology();
void normalize(double k_max = -1); void normalize(double k_min = -1, double k_max = -1);
void setNormalization(double A_K); void setNormalization(double A_K);
void updateHuWigglesConsts(); void updateHuWigglesConsts();

72
src/loadGadget.cpp
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@ -38,6 +38,8 @@ knowledge of the CeCILL license and that you accept its terms.
#include <assert.h> #include <assert.h>
#include <stdio.h> #include <stdio.h>
#include <stdlib.h> #include <stdlib.h>
#include <boost/function.hpp>
#include <boost/bind.hpp>
#include "load_data.hpp" #include "load_data.hpp"
#include "loadGadget.hpp" #include "loadGadget.hpp"
#include "fortran.hpp" #include "fortran.hpp"
@ -65,6 +67,13 @@ void loadGadgetHeader(UnformattedRead *f, GadgetHeader& h, SimuData *data, int i
data->Omega_M = h.Omega0 = f->readReal64(); data->Omega_M = h.Omega0 = f->readReal64();
data->Omega_Lambda = h.OmegaLambda = f->readReal64(); data->Omega_Lambda = h.OmegaLambda = f->readReal64();
data->Hubble = h.HubbleParam = f->readReal64(); data->Hubble = h.HubbleParam = f->readReal64();
(int)f->readInt32(); // stellarage
(int)f->readInt32(); // metals
for (int i = 0; i < 6; i++)
h.npartTotal[i] |= ((unsigned long)f->readInt32()) << 32;
(int)f->readInt32(); // entropy instead of u
h.flag_doubleprecision = f->readInt32();
f->endCheckpoint(true); f->endCheckpoint(true);
ssize_t NumPart = 0, NumPartTotal = 0; ssize_t NumPart = 0, NumPartTotal = 0;
@ -77,6 +86,12 @@ void loadGadgetHeader(UnformattedRead *f, GadgetHeader& h, SimuData *data, int i
data->TotalNumPart = NumPartTotal; data->TotalNumPart = NumPartTotal;
} }
template<typename T>
T myRead64(UnformattedRead *f) { return f->readReal64(); }
template<typename T>
T myRead32(UnformattedRead *f) { return f->readReal32(); }
SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
int loadflags, int GadgetFormat, int loadflags, int GadgetFormat,
SimuFilter filter) SimuFilter filter)
@ -86,6 +101,9 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
UnformattedRead *f; UnformattedRead *f;
GadgetHeader h; GadgetHeader h;
float velmul; float velmul;
boost::function0<double> readToDouble;
boost::function0<float> readToSingle;
long float_size;
if (id >= 0) { if (id >= 0) {
int k = snprintf(0, 0, "%s.%d", fname, id)+1; int k = snprintf(0, 0, "%s.%d", fname, id)+1;
@ -124,9 +142,18 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
velmul = 1/(h.time); velmul = 1/(h.time);
else { else {
cerr << "unknown gadget format" << endl; cerr << "unknown gadget format" << endl;
abort(); abort();
}
if (h.flag_doubleprecision) {
readToDouble = boost::bind(myRead64<double>, f);
readToSingle = boost::bind(myRead64<float>, f);
float_size = sizeof(double);
} else {
readToDouble = boost::bind(myRead32<double>, f);
readToSingle = boost::bind(myRead32<float>, f);
float_size = sizeof(float);
} }
NumPart = data->NumPart; NumPart = data->NumPart;
NumPartTotal = data->TotalNumPart; NumPartTotal = data->TotalNumPart;
} }
@ -144,28 +171,28 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
data->type = new int[data->NumPart]; data->type = new int[data->NumPart];
for (int k = 0; k < 6; k++) for (int k = 0; k < 6; k++)
for (int n = 0; n < h.npart[k]; n++,p++) for (int n = 0; n < h.npart[k]; n++,p++)
data->type[p] = k; data->type[p] = k;
} }
if (loadflags & NEED_POSITION) { if (loadflags & NEED_POSITION) {
for (int i = 0; i < 3; i++) { for (int i = 0; i < 3; i++) {
data->Pos[i] = new float[data->NumPart]; data->Pos[i] = new float[data->NumPart];
if (data->Pos[i] == 0) { if (data->Pos[i] == 0) {
delete data; delete data;
return 0; return 0;
}
} }
}
try try
{ {
f->beginCheckpoint(); f->beginCheckpoint();
for(int k = 0, p = 0; k < 6; k++) { for(int k = 0, p = 0; k < 6; k++) {
for(int n = 0; n < h.npart[k]; n++) { for(int n = 0; n < h.npart[k]; n++) {
data->Pos[0][p] = f->readReal32(); data->Pos[0][p] = readToSingle();
data->Pos[1][p] = f->readReal32(); data->Pos[1][p] = readToSingle();
data->Pos[2][p] = f->readReal32(); data->Pos[2][p] = readToSingle();
p++; p++;
} }
} }
@ -173,15 +200,16 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
} }
catch (const InvalidUnformattedAccess& e) catch (const InvalidUnformattedAccess& e)
{ {
cerr << "Invalid format while reading positions" << endl; cerr << "Invalid format while reading positions" << endl;
delete f; delete f;
delete data; delete data;
return 0; return 0;
} }
} else { } else {
long float_size = (h.flag_doubleprecision) ? sizeof(double) : sizeof(float);
// Skip positions // Skip positions
f->skip(NumPart * 3 * sizeof(float) + 2*4); f->skip(NumPart * 3 * float_size + 2*4);
} }
if (loadflags & NEED_VELOCITY) { if (loadflags & NEED_VELOCITY) {
@ -202,9 +230,9 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
for(int k = 0, p = 0; k < 6; k++) { for(int k = 0, p = 0; k < 6; k++) {
for(int n = 0; n < h.npart[k]; n++) { for(int n = 0; n < h.npart[k]; n++) {
// THIS IS GADGET 1 // THIS IS GADGET 1
data->Vel[0][p] = f->readReal32()*velmul; data->Vel[0][p] = readToSingle()*velmul;
data->Vel[1][p] = f->readReal32()*velmul; data->Vel[1][p] = readToSingle()*velmul;
data->Vel[2][p] = f->readReal32()*velmul; data->Vel[2][p] = readToSingle()*velmul;
p++; p++;
} }
} }
@ -222,7 +250,7 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
/// // TODO: FIX THE UNITS OF THESE FUNKY VELOCITIES !!! /// // TODO: FIX THE UNITS OF THESE FUNKY VELOCITIES !!!
} else { } else {
// Skip velocities // Skip velocities
f->skip(NumPart*3*sizeof(float)+2*4); f->skip(NumPart*3*float_size+2*4);
} }
// Skip ids // Skip ids
@ -280,7 +308,7 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
if (h.mass[k] == 0) { if (h.mass[k] == 0) {
for(int n = 0; n < h.npart[k]; n++) for(int n = 0; n < h.npart[k]; n++)
{ {
data->Mass[l++] = f->readReal32(); data->Mass[l++] = readToSingle();
} }
} else { } else {
for(int n = 0; n < h.npart[k]; n++) for(int n = 0; n < h.npart[k]; n++)

66
src/loadSimu.hpp
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@ -46,6 +46,7 @@ namespace CosmoTool
static const int NEED_VELOCITY = 4; static const int NEED_VELOCITY = 4;
static const int NEED_TYPE = 8; static const int NEED_TYPE = 8;
static const int NEED_MASS = 16; static const int NEED_MASS = 16;
static const int NEED_DOUBLE_PRECISION = 32;
struct SimuParticle struct SimuParticle
{ {
@ -88,49 +89,46 @@ namespace CosmoTool
SimuData() : Mass(0), Id(0),NumPart(0),type(0),noAuto(false) { Pos[0]=Pos[1]=Pos[2]=0; Vel[0]=Vel[1]=Vel[2]=0; } SimuData() : Mass(0), Id(0),NumPart(0),type(0),noAuto(false) { Pos[0]=Pos[1]=Pos[2]=0; Vel[0]=Vel[1]=Vel[2]=0; }
~SimuData() ~SimuData()
{ {
if (!noAuto) { if (!noAuto) {
for (int j = 0; j < 3; j++) for (int j = 0; j < 3; j++) {
{ if (Pos[j])
if (Pos[j]) delete[] Pos[j];
delete[] Pos[j]; if (Vel[j])
if (Vel[j]) delete[] Vel[j];
delete[] Vel[j]; }
} if (type)
if (type) delete[] type;
delete[] type; if (Id)
if (Id) delete[] Id;
delete[] Id; if (Mass)
if (Mass) delete[] Mass;
delete[] Mass; }
} for (AttributeMap::iterator i = attributes.begin();
for (AttributeMap::iterator i = attributes.begin(); i != attributes.end();
i != attributes.end(); ++i) {
++i) if (i->second.second)
{ i->second.second(i->second.first);
if (i->second.second) }
i->second.second(i->second.first);
}
} }
template<typename T> template<typename T>
T *as(const std::string& n) T *as(const std::string& n)
{ {
AttributeMap::iterator i = attributes.find(n); AttributeMap::iterator i = attributes.find(n);
if (i == attributes.end()) if (i == attributes.end())
return 0; return 0;
return reinterpret_cast<T *>(i->second.first); return reinterpret_cast<T *>(i->second.first);
} }
void new_attribute(const std::string& n, void *p, FreeFunction free_func) void new_attribute(const std::string& n, void *p, FreeFunction free_func)
{ {
AttributeMap::iterator i = attributes.find(n); AttributeMap::iterator i = attributes.find(n);
if (i != attributes.end()) if (i != attributes.end()) {
{ if (i->second.second)
if (i->second.second) i->second.second(i->second.first);
i->second.second(i->second.first); }
} attributes[n] = std::make_pair(p, free_func);
attributes[n] = std::make_pair(p, free_func);
} }
}; };

6
src/load_data.hpp
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@ -55,7 +55,11 @@ namespace CosmoTool {
double Omega0; double Omega0;
double OmegaLambda; double OmegaLambda;
double HubbleParam; double HubbleParam;
char fill[256- 6*4- 6*8- 2*8- 2*4- 6*4- 2*4 - 4*8]; /* fills to 256 Bytes */ int flag_doubleprecision;
int flag_ic_info;
float lpt_scalingfactor;
char fill[18]; /*!< fills to 256 Bytes */
char names[15][2];
}; };
struct ParticleState struct ParticleState