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Merge branch 'master' of bitbucket.org:glavaux/cosmotool

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This commit is contained in:
Guilhem Lavaux 2015-06-07 10:44:54 +02:00
commit 59b1b12be8
14 changed files with 84 additions and 19 deletions
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6
CMakeLists.txt
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@ -39,13 +39,13 @@ MESSAGE(STATUS "Using the target ${CosmoTool_local} to build python module")
include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
IF(YORICK_SUPPORT)
IF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
IF((EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4") OR (INTERNAL_NETCDF))
SET(FOUND_NETCDF4 1)
FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#define NETCDFCPP4 1")
ELSE(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
ELSE((EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4") OR (INTERNAL_NETCDF))
SET(FOUND_NETCDF3 1)
FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#undef NETCDFCPP4")
ENDIF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
ENDIF((EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4") OR (INTERNAL_NETCDF))
ENDIF(YORICK_SUPPORT)
find_program(CYTHON cython)

3
external/external_build.cmake vendored
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@ -5,7 +5,7 @@ OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF)
SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE URL "URL to download FFTW from")
SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.1.4.tar.gz" CACHE URL "URL to download Eigen from")
SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from")
SET(HDF5_URL "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.9/src/hdf5-1.8.9.tar.gz" CACHE STRING "URL to download HDF5 from")
SET(HDF5_URL "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.15/src/hdf5-1.8.15.tar.gz" CACHE STRING "URL to download HDF5 from")
SET(NETCDF_URL "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.1.3.tar.gz" CACHE STRING "URL to download NetCDF from")
SET(BOOST_URL "http://sourceforge.net/projects/boost/files/boost/1.49.0/boost_1_49_0.tar.gz/download" CACHE STRING "URL to download Boost from")
SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to download GSL from ")
@ -142,6 +142,7 @@ if (INTERNAL_BOOST)
)
set(Boost_INCLUDE_DIRS ${BOOST_SOURCE_DIR} CACHE STRING "Boost path" FORCE)
set(Boost_LIBRARIES ${BOOST_SOURCE_DIR}/stage/lib/libboost_python.a CACHE STRING "Boost libraries" FORCE)
set(Boost_FOUND YES)
ELSE (INTERNAL_BOOST)
find_package(Boost 1.53)

13
python/cosmotool/simu.py
View File

@ -1,3 +1,4 @@
import warnings
from _cosmotool import *
class SimulationBare(PySimulationBase):
@ -18,6 +19,10 @@ class SimulationBare(PySimulationBase):
self.Hubble = s.getHubble()
self.Omega_M = s.getOmega_M()
self.Omega_Lambda = s.getOmega_Lambda()
try:
self.masses = s.getMasses().copy() if s.getMasses() is not None else None
except Exception as e:
warnings.warn("Unexpected exception: " + repr(e))
def merge(self, other):
@ -48,6 +53,11 @@ class SimulationBare(PySimulationBase):
self.positions = _safe_merge(self.positions, other.getPositions())
self.velocities = _safe_merge(self.velocities, other.getVelocities())
self.identifiers = _safe_merge0(self.identifiers, other.getIdentifiers())
try:
self.masses = _safe_merge0(self.masses, other.getMasses())
except Exception as e:
warnings.warn("Unexpected exception: " + repr(e));
self.masses = None
def getPositions(self):
return self.positions
@ -58,6 +68,9 @@ class SimulationBare(PySimulationBase):
def getIdentifiers(self):
return self.identifiers
def getMasses(self):
return self.masses
def getTime(self):
return self.time

4
python_sample/icgen/borgicgen.py
View File

@ -93,7 +93,7 @@ def do_supergenerate(density, density_out=None, mulfac=None,zero_fill=False,Pk=N
def build_Pk():
ik = np.fft.fftfreq(Ns, d=L/Ns)*2*np.pi
k = ne.evaluate('sqrt(kx**2 + ky**2 + kz**2)', {'kx':ik[:,None,None], 'ky':ik[None,:,None], 'kz':ik[None,None,:(Ns/2+1)]})
return Pk.compute(k)*(h*L)**3
return Pk.compute(k)*L**3
print np.where(np.isnan(density_out))[0].size
Nz = np.count_nonzero(cond)
@ -185,7 +185,7 @@ def whitify(density, L, cosmo, supergenerate=1, zero_fill=False, func='HU_WIGGLE
def build_Pk():
ik = np.fft.fftfreq(N, d=L/N)*2*np.pi
k = np.sqrt(ik[:,None,None]**2 + ik[None,:,None]**2 + ik[None,None,:(N/2+1)]**2)
return p.compute(k)*cosmo['h']**3*L**3
return p.compute(k)*L**3
Pk = build_Pk()
Pk[0,0,0]=1

5
sample/gadgetToArray.cpp
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@ -66,12 +66,15 @@ int main(int argc, char **argv)
SimuData *p = loadGadgetMulti(fname, 0, 0);
double L0 = p->BoxSize/MPC;
cout << "Will read " << p->TotalNumPart << " particles" << endl;
array_type parts(boost::extents[p->TotalNumPart][7]);
uint64_t q = 0;
try {
for (int cpuid=0;;cpuid++) {
cout << " = CPU " << cpuid << " = " << endl;
p = loadGadgetMulti(fname, cpuid, NEED_POSITION|NEED_VELOCITY|NEED_MASS);
cout << " = DONE LOAD, COPYING IN PLACE" << endl;
for (uint32_t i = 0; i < p->NumPart; i++)
{
for (int j = 0; j < 3; j++)
@ -87,11 +90,13 @@ int main(int argc, char **argv)
parts[q][6] = p->Mass[i];
q++;
}
cout << " = DONE (q=" << q << ")" << endl;
delete p;
}
} catch (const NoSuchFileException& e) {}
cout << " ++ WRITING ++" << endl;
hdf5_write_array(f, "particles", parts);
return 0;

8
sample/simple3DFilter.cpp
View File

@ -123,10 +123,12 @@ int main(int argc, char **argv)
MyCell *allCells_1 = new MyCell[N1_points];
#pragma omp parallel for schedule(static)
for (long i = 0; i < Nres*Nres*Nres; i++)
bins.data()[i] = 0;
cout << "Shuffling data in cells..." << endl;
#pragma omp parallel for schedule(static)
for (int i = 0 ; i < N1_points; i++)
{
for (int j = 0; j < 3; j++)
@ -144,6 +146,7 @@ int main(int argc, char **argv)
if (rx < 0 || rx >= Nres || ry < 0 || ry >= Nres || rz < 0 || rz >= Nres)
continue;
#pragma omp atomic update
bins[rx][ry][rz]++;
}
v1_data.resize(boost::extents[1][1]);
@ -168,7 +171,7 @@ int main(int argc, char **argv)
{
double pz = (rz)*boxsize/Nres-cz;
cout << rz << " / " << Nres << endl;
(cout << rz << " / " << Nres << endl).flush();
for (int ry = 0; ry < Nres; ry++)
{
double py = (ry)*boxsize/Nres-cy;
@ -193,6 +196,7 @@ int main(int argc, char **argv)
smooth1.addGridSite(c);
}
}
(cout << " Done " << rz << endl).flush();
}
}
@ -204,7 +208,7 @@ int main(int argc, char **argv)
bins, interpolated, getMass, rLimit2);
hdf5_write_array(out_f, "density", interpolated);
//out_f.flush();
for (int i = 0; i < 0; i++) {
for (int i = 0; i < 3; i++) {
computeInterpolatedField(&tree1, boxsize, Nres, cx, cy, cz,
bins, interpolated, boost::bind(getVelocity, _1, i), rLimit2);
hdf5_write_array(out_f, str(format("p%d") % i), interpolated);

9
src/CMakeLists.txt
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@ -3,7 +3,6 @@ SET(CosmoTool_SRCS
fortran.cpp
interpolate.cpp
load_data.cpp
loadGadget.cpp
loadRamses.cpp
powerSpectrum.cpp
miniargs.cpp
@ -12,6 +11,14 @@ SET(CosmoTool_SRCS
cic.cpp
)
IF (Boost_FOUND)
include_directories(${Boost_INCLUDE_DIRS})
SET(CosmoTool_SRCS
${CosmoTool_SRCS}
loadGadget.cpp
)
ENDIF (Boost_FOUND)
IF (ENABLE_OPENMP)
ENDIF (ENABLE_OPENMP)

2
src/cosmopower.cpp
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@ -99,7 +99,7 @@ static double powC(double q, double alpha_c)
static double T_tilde_0(double q, double alpha_c, double beta_c)
{
static const double c_E = 2.718282; //M_E;
static const double c_E = M_E;
double a = log(c_E + 1.8 * beta_c * q);
return a / ( a + powC(q, alpha_c) * q * q);
}

18
src/fortran.cpp
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@ -112,7 +112,7 @@ void UnformattedRead::beginCheckpoint()
checkPointRef = (cSize == Check_32bits) ? 4 : 8;
checkPointAccum = 0;
checkPointRef = (cSize == Check_32bits) ? readInt32() : readInt64();
checkPointRef = (cSize == Check_32bits) ? readUint32() : readInt64();
checkPointAccum = 0;
if (f->eof())
@ -144,7 +144,7 @@ void UnformattedRead::endCheckpoint(bool autodrop)
void UnformattedRead::readOrderedBuffer(void *buffer, int size)
throw (InvalidUnformattedAccess)
{
if ((checkPointAccum+size) > checkPointRef)
if ((checkPointAccum+(uint64_t)size) > checkPointRef)
throw InvalidUnformattedAccess();
f->read((char *)buffer, size);
@ -186,6 +186,20 @@ float UnformattedRead::readReal32()
return a.f;
}
uint32_t UnformattedRead::readUint32()
throw (InvalidUnformattedAccess)
{
union
{
char b[4];
uint32_t i;
} a;
readOrderedBuffer(&a, 4);
return a.i;
}
int32_t UnformattedRead::readInt32()
throw (InvalidUnformattedAccess)
{

4
src/fortran.hpp
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@ -73,6 +73,8 @@ namespace CosmoTool
// Todo implement primitive description
void setOrdering(Ordering o);
void setCheckpointSize(CheckpointSize cs);
uint64_t getBlockSize() const { return checkPointRef; }
void beginCheckpoint()
throw (InvalidUnformattedAccess,EndOfFileException);
@ -83,6 +85,8 @@ namespace CosmoTool
throw (InvalidUnformattedAccess);
float readReal32()
throw (InvalidUnformattedAccess);
uint32_t readUint32()
throw (InvalidUnformattedAccess);
int32_t readInt32()
throw (InvalidUnformattedAccess);
int64_t readInt64()

17
src/loadGadget.cpp
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@ -146,10 +146,12 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
}
if (h.flag_doubleprecision) {
cout << "Gadget format with double precision" << endl;
readToDouble = boost::bind(myRead64<double>, f);
readToSingle = boost::bind(myRead64<float>, f);
float_size = sizeof(double);
} else {
cout << "Gadget format with single precision" << endl;
readToDouble = boost::bind(myRead32<double>, f);
readToSingle = boost::bind(myRead32<float>, f);
float_size = sizeof(float);
@ -188,8 +190,19 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
try
{
f->beginCheckpoint();
if (f->getBlockSize() != NumPart*float_size*3) {
// Check that single would work
if (f->getBlockSize() == NumPart*sizeof(float)*3) {
// Change to single
cout << "Change back to single. Buggy header." << endl;
readToDouble = boost::bind(myRead32<double>, f);
readToSingle = boost::bind(myRead32<float>, f);
float_size = sizeof(float);
}
}
for(int k = 0, p = 0; k < 6; k++) {
for(int n = 0; n < h.npart[k]; n++) {
// if ((n%1000000)==0) cout << n << endl;
data->Pos[0][p] = readToSingle();
data->Pos[1][p] = readToSingle();
data->Pos[2][p] = readToSingle();
@ -230,6 +243,7 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
for(int k = 0, p = 0; k < 6; k++) {
for(int n = 0; n < h.npart[k]; n++) {
// THIS IS GADGET 1
// if ((n%1000000)==0) cout << n << endl;
data->Vel[0][p] = readToSingle()*velmul;
data->Vel[1][p] = readToSingle()*velmul;
data->Vel[2][p] = readToSingle()*velmul;
@ -292,6 +306,7 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
if (loadflags & NEED_MASS) {
bool do_load = false;
cout << "=> Mass" << endl;
for (int k = 0; k < 6; k++)
{
do_load = do_load || ((h.mass[k] == 0)&&(h.npart[k]>0));
@ -308,11 +323,13 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
if (h.mass[k] == 0) {
for(int n = 0; n < h.npart[k]; n++)
{
// if ((n%1000000)==0) cout << n << endl;
data->Mass[l++] = readToSingle();
}
} else {
for(int n = 0; n < h.npart[k]; n++)
{
if ((n%1000000)==0) cout << n << endl;
data->Mass[l++] = h.mass[k];
}
}

2
src/load_data.cpp
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@ -41,7 +41,7 @@ knowledge of the CeCILL license and that you accept its terms.
using namespace CosmoTool;
//#define LARGE_CONTROL
#define LITTLE_ENDIAN
//#define LITTLE_ENDIAN
#define NEW(t,n) ((t *)malloc(sizeof(t)*n))
#define SKIP(f) fread(&dummy,sizeof(dummy),1,f);

3
src/sphSmooth.hpp
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@ -60,9 +60,10 @@ namespace CosmoTool
typedef void (*runParticleValue)(ValType& t);
public:
typedef SPHCell *P_SPHCell;
struct SPHState
{
boost::shared_ptr<SPHCell *[]> ngb;
boost::shared_ptr<P_SPHCell[]> ngb;
boost::shared_ptr<CoordType[]> distances;
typename SPHTree::coords currentCenter;
int currentNgb;

9
src/sphSmooth.tcc
View File

@ -48,15 +48,15 @@ SPHSmooth<ValType,Ndims>::fetchNeighbours(const typename SPHTree::coords& c, uin
if (requested > maxNgb)
{
maxNgb = requested;
internal.ngb = boost::shared_ptr<SPHCell*[]>(new SPHCell *[maxNgb]);
internal.ngb = boost::shared_ptr<P_SPHCell[]>(new P_SPHCell[maxNgb]);
internal.distances = boost::shared_ptr<CoordType[]>(new CoordType[maxNgb]);
}
memcpy(internal.currentCenter, c, sizeof(c));
tree->getNearestNeighbours(c, requested, internal.ngb.get(), internal.distances.get());
tree->getNearestNeighbours(c, requested, (SPHCell **)internal.ngb.get(), (CoordType*)internal.distances.get());
internal.currentNgb = 0;
for (uint32_t i = 0; i < requested && internal.ngb[i] != 0; i++,internal.currentNgb++)
for (uint32_t i = 0; i < requested && (internal.ngb)[i] != 0; i++,internal.currentNgb++)
{
internal.distances[i] = sqrt(internal.distances[i]);
d2 = internal.distances[i];
@ -191,9 +191,8 @@ void SPHSmooth<ValType,Ndims>::addGridSite(const typename SPHTree::coords& c)
for (uint32_t i = 0; i < internal.currentNgb; i++)
{
ComputePrecision d = internal.distances[i];
SPHCell& cell = *internal.ngb[i];
SPHCell& cell = *(internal.ngb[i]);
cell.val.weight += getKernel(d/internal.smoothRadius) / r3;
}
}