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added output to gadget2 particle files

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This commit is contained in:
Oliver Hahn 2019-05-09 21:41:54 +02:00
parent 9549f5f195
commit 17f2f7e8b6
6 changed files with 2141 additions and 377 deletions
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11
example.conf
View file

@ -1,11 +1,18 @@
[setup]
LPTorder = 3
GridRes = 128
BoxLength = 300
Dplus0 = 1.0
BoxLength = 100
zstart = 1.0
H0 = 70.0
Omega_m = 0.3
Omega_L = 0.7
Omega_b = 0.0455
[output]
fname_hdf5 = output.hdf5
fbase_analysis = output
format = gadget2
filename = ics_gadget.dat
[cosmology]
transfer = eisenstein

685
include/grid_fft.hh
View file

@ -1,4 +1,4 @@
#pragma once
#pragma once
#include <cmath>
#include <array>
@ -17,374 +17,395 @@ enum space_t
template <typename data_t>
class Grid_FFT
{
protected:
protected:
#if defined(USE_MPI)
const MPI_Datatype MPI_data_t_type = (typeid(data_t) == typeid(double)) ? MPI_DOUBLE
: (typeid(data_t) == typeid(float)) ? MPI_FLOAT
: (typeid(data_t) == typeid(std::complex<float>)) ? MPI_COMPLEX
: (typeid(data_t) == typeid(std::complex<double>)) ? MPI_DOUBLE_COMPLEX : MPI_INT;
const MPI_Datatype MPI_data_t_type = (typeid(data_t) == typeid(double)) ? MPI_DOUBLE
: (typeid(data_t) == typeid(float)) ? MPI_FLOAT
: (typeid(data_t) == typeid(std::complex<float>)) ? MPI_COMPLEX
: (typeid(data_t) == typeid(std::complex<double>)) ? MPI_DOUBLE_COMPLEX : MPI_INT;
#endif
public:
std::array<size_t,3> n_, nhalf_;
std::array<size_t,4> sizes_;
size_t npr_, npc_;
size_t ntot_;
std::array<real_t,3> length_, kfac_, dx_;
std::array<size_t, 3> n_, nhalf_;
std::array<size_t, 4> sizes_;
size_t npr_, npc_;
size_t ntot_;
std::array<real_t, 3> length_, kfac_, dx_;
space_t space_;
data_t *data_;
ccomplex_t *cdata_;
space_t space_;
data_t *data_;
ccomplex_t *cdata_;
bounding_box<size_t> global_range_;
bounding_box<size_t> global_range_;
fftw_plan_t plan_, iplan_;
fftw_plan_t plan_, iplan_;
real_t fft_norm_fac_;
real_t fft_norm_fac_;
ptrdiff_t local_0_start_, local_1_start_;
ptrdiff_t local_0_size_, local_1_size_;
ptrdiff_t local_0_start_, local_1_start_;
ptrdiff_t local_0_size_, local_1_size_;
Grid_FFT(const std::array<size_t, 3> &N, const std::array<real_t, 3> &L, space_t initialspace = rspace_id)
: n_(N), length_(L), space_(initialspace), data_(nullptr), cdata_(nullptr) //, RV_(*this), KV_(*this)
{
for(int i=0; i<3; ++i){
kfac_[i] = 2.0 * M_PI / length_[i];
dx_[i] = length_[i] / n_[i];
}
//invalidated = true;
this->Setup();
}
Grid_FFT(const Grid_FFT<data_t> &g)
: n_(g.n_), length_(g.length_), space_(g.space_), data_(nullptr), cdata_(nullptr)
{
for (int i = 0; i < 3; ++i)
{
kfac_[i] = g.kfac_[i];
dx_[i] = g.dx_[i];
}
//invalidated = true;
this->Setup();
for (size_t i = 0; i < ntot_; ++i ){
data_[i] = g.data_[i];
}
}
~Grid_FFT()
{
if( data_!=nullptr){
fftw_free( data_ );
}
}
void Setup();
size_t size( size_t i ) const{ return sizes_[i]; }
void zero() {
for( size_t i=0; i<ntot_; ++i ) data_[i] = 0.0;
}
data_t &relem(size_t i, size_t j, size_t k)
{
size_t idx = (i * sizes_[1] + j) * sizes_[3] + k;
return data_[idx];
}
const data_t &relem(size_t i, size_t j, size_t k) const
{
size_t idx = (i * sizes_[1] + j) * sizes_[3] + k;
return data_[idx];
}
ccomplex_t &kelem(size_t i, size_t j, size_t k)
{
size_t idx = (i * sizes_[1] + j) * sizes_[3] + k;
return cdata_[idx];
}
const ccomplex_t &kelem(size_t i, size_t j, size_t k) const
{
size_t idx = (i * sizes_[1] + j) * sizes_[3] + k;
return cdata_[idx];
}
ccomplex_t &kelem(size_t idx) { return cdata_[idx]; }
const ccomplex_t &kelem(size_t idx) const { return cdata_[idx]; }
data_t &relem(size_t idx) { return data_[idx]; }
const data_t &relem(size_t idx) const { return data_[idx]; }
size_t get_idx( size_t i, size_t j, size_t k ) const
{
return (i * sizes_[1] + j) * sizes_[3] + k;
}
template <typename ft>
vec3<ft> get_r(const size_t& i, const size_t& j, const size_t& k) const
{
vec3<ft> rr;
#if defined(USE_MPI)
rr[0] = real_t(i + local_0_start_) * dx_[0];
#else
rr[0] = real_t(i) * dx_[0];
#endif
rr[1] = real_t(j) * dx_[1];
rr[2] = real_t(k) * dx_[2];
return rr;
}
template <typename ft>
vec3<ft> get_k(const size_t &i, const size_t &j, const size_t &k) const
{
vec3<ft> kk;
#if defined(USE_MPI)
auto ip = i+local_1_start_;
kk[0] = (real_t(j) - real_t(j > nhalf_[0])*n_[0]) * kfac_[0];
kk[1] = (real_t(ip) - real_t(ip > nhalf_[1])*n_[1]) * kfac_[1];
#else
kk[0] = (real_t(i) - real_t(i > nhalf_[0]) * n_[0]) * kfac_[0];
kk[1] = (real_t(j) - real_t(j > nhalf_[1]) * n_[1]) * kfac_[1];
#endif
kk[2] = (real_t(k) - real_t(k>nhalf_[2])*n_[2])* kfac_[2];
return kk;
}
template <typename functional>
void apply_function_k(const functional &f)
{
#pragma omp parallel for
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
auto &elem = this->kelem(i, j, k);
elem = f(elem);
}
}
}
}
template <typename functional>
void apply_function_r(const functional &f)
{
#pragma omp parallel for
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
auto &elem = this->relem(i, j, k);
elem = f(elem);
}
}
}
}
double compute_2norm(void)
{
real_t sum1{0.0};
#pragma omp parallel for reduction(+ : sum1)
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
const auto re = std::real(this->relem(i, j, k));
const auto im = std::imag(this->relem(i, j, k));
sum1 += re*re+im*im;
}
}
}
sum1 /= sizes_[0] * sizes_[1] * sizes_[2];
return sum1;
}
double std( void )
{
real_t sum1{0.0}, sum2{0.0};
#pragma omp parallel for reduction(+:sum1,sum2)
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
const auto elem = std::real(this->relem(i, j, k));
sum1 += elem;
sum2 += elem*elem;
}
}
}
sum1 /= sizes_[0] * sizes_[1] * sizes_[2];
sum2 /= sizes_[0] * sizes_[1] * sizes_[2];
return std::sqrt( sum2 - sum1*sum1 );
}
double mean(void)
{
real_t sum1{0.0};
#pragma omp parallel for reduction(+ : sum1)
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
const auto elem = std::real(this->relem(i, j, k));
sum1 += elem;
}
}
}
sum1 /= sizes_[0] * sizes_[1] * sizes_[2];
return sum1;
}
template <typename functional, typename grid_t>
void assign_function_of_grids_r(const functional &f, const grid_t &g)
{
assert(g.size(0) == size(0) && g.size(1) == size(1));// && g.size(2) == size(2) );
#pragma omp parallel for
for (size_t i = 0; i < sizes_[0]; ++i)
Grid_FFT(const std::array<size_t, 3> &N, const std::array<real_t, 3> &L, space_t initialspace = rspace_id)
: n_(N), length_(L), space_(initialspace), data_(nullptr), cdata_(nullptr) //, RV_(*this), KV_(*this)
{
for (size_t j = 0; j < sizes_[1]; ++j)
for (int i = 0; i < 3; ++i)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
auto &elem = this->relem(i, j, k);
const auto &elemg = g.relem(i, j, k);
kfac_[i] = 2.0 * M_PI / length_[i];
dx_[i] = length_[i] / n_[i];
}
//invalidated = true;
this->Setup();
}
elem = f(elemg);
Grid_FFT(const Grid_FFT<data_t> &g)
: n_(g.n_), length_(g.length_), space_(g.space_), data_(nullptr), cdata_(nullptr)
{
for (int i = 0; i < 3; ++i)
{
kfac_[i] = g.kfac_[i];
dx_[i] = g.dx_[i];
}
//invalidated = true;
this->Setup();
for (size_t i = 0; i < ntot_; ++i)
{
data_[i] = g.data_[i];
}
}
~Grid_FFT()
{
if (data_ != nullptr)
{
fftw_free(data_);
}
}
const Grid_FFT<data_t>* get_grid( size_t ilevel ) const { return this; }
bool is_in_mask( size_t ilevel, size_t i, size_t j, size_t k ) const { return true; }
bool is_refined( size_t ilevel, size_t i, size_t j, size_t k ) const { return false; }
size_t levelmin() const {return 7;}
size_t levelmax() const {return 7;}
void Setup();
size_t size(size_t i) const { return sizes_[i]; }
void zero()
{
for (size_t i = 0; i < ntot_; ++i)
data_[i] = 0.0;
}
data_t &relem(size_t i, size_t j, size_t k)
{
size_t idx = (i * sizes_[1] + j) * sizes_[3] + k;
return data_[idx];
}
const data_t &relem(size_t i, size_t j, size_t k) const
{
size_t idx = (i * sizes_[1] + j) * sizes_[3] + k;
return data_[idx];
}
ccomplex_t &kelem(size_t i, size_t j, size_t k)
{
size_t idx = (i * sizes_[1] + j) * sizes_[3] + k;
return cdata_[idx];
}
const ccomplex_t &kelem(size_t i, size_t j, size_t k) const
{
size_t idx = (i * sizes_[1] + j) * sizes_[3] + k;
return cdata_[idx];
}
ccomplex_t &kelem(size_t idx) { return cdata_[idx]; }
const ccomplex_t &kelem(size_t idx) const { return cdata_[idx]; }
data_t &relem(size_t idx) { return data_[idx]; }
const data_t &relem(size_t idx) const { return data_[idx]; }
size_t get_idx(size_t i, size_t j, size_t k) const
{
return (i * sizes_[1] + j) * sizes_[3] + k;
}
template <typename ft>
vec3<ft> get_r(const size_t &i, const size_t &j, const size_t &k) const
{
vec3<ft> rr;
#if defined(USE_MPI)
rr[0] = real_t(i + local_0_start_) * dx_[0];
#else
rr[0] = real_t(i) * dx_[0];
#endif
rr[1] = real_t(j) * dx_[1];
rr[2] = real_t(k) * dx_[2];
return rr;
}
void cell_pos( int ilevel, size_t i, size_t j, size_t k, double* x ) const {
x[0] = double(i)/size(0);
x[1] = double(j)/size(1);
x[2] = double(k)/size(2);
}
size_t count_leaf_cells( int, int ) const {
return n_[0]*n_[1]*n_[2];
}
template <typename ft>
vec3<ft> get_k(const size_t &i, const size_t &j, const size_t &k) const
{
vec3<ft> kk;
#if defined(USE_MPI)
auto ip = i + local_1_start_;
kk[0] = (real_t(j) - real_t(j > nhalf_[0]) * n_[0]) * kfac_[0];
kk[1] = (real_t(ip) - real_t(ip > nhalf_[1]) * n_[1]) * kfac_[1];
#else
kk[0] = (real_t(i) - real_t(i > nhalf_[0]) * n_[0]) * kfac_[0];
kk[1] = (real_t(j) - real_t(j > nhalf_[1]) * n_[1]) * kfac_[1];
#endif
kk[2] = (real_t(k) - real_t(k > nhalf_[2]) * n_[2]) * kfac_[2];
return kk;
}
template <typename functional>
void apply_function_k(const functional &f)
{
#pragma omp parallel for
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
auto &elem = this->kelem(i, j, k);
elem = f(elem);
}
}
}
}
}
template <typename functional>
void apply_function_r(const functional &f)
{
#pragma omp parallel for
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
auto &elem = this->relem(i, j, k);
elem = f(elem);
}
}
}
}
template <typename functional, typename grid1_t, typename grid2_t>
void assign_function_of_grids_r(const functional &f, const grid1_t &g1, const grid2_t &g2)
{
assert(g1.size(0) == size(0) && g1.size(1) == size(1));// && g1.size(2) == size(2));
assert(g2.size(0) == size(0) && g2.size(1) == size(1));// && g2.size(2) == size(2));
double compute_2norm(void)
{
real_t sum1{0.0};
#pragma omp parallel for reduction(+ \
: sum1)
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
const auto re = std::real(this->relem(i, j, k));
const auto im = std::imag(this->relem(i, j, k));
sum1 += re * re + im * im;
}
}
}
sum1 /= sizes_[0] * sizes_[1] * sizes_[2];
return sum1;
}
double std(void)
{
real_t sum1{0.0}, sum2{0.0};
#pragma omp parallel for reduction(+ \
: sum1, sum2)
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
const auto elem = std::real(this->relem(i, j, k));
sum1 += elem;
sum2 += elem * elem;
}
}
}
sum1 /= sizes_[0] * sizes_[1] * sizes_[2];
sum2 /= sizes_[0] * sizes_[1] * sizes_[2];
return std::sqrt(sum2 - sum1 * sum1);
}
double mean(void)
{
real_t sum1{0.0};
#pragma omp parallel for reduction(+ \
: sum1)
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
const auto elem = std::real(this->relem(i, j, k));
sum1 += elem;
}
}
}
sum1 /= sizes_[0] * sizes_[1] * sizes_[2];
return sum1;
}
template <typename functional, typename grid_t>
void assign_function_of_grids_r(const functional &f, const grid_t &g)
{
assert(g.size(0) == size(0) && g.size(1) == size(1)); // && g.size(2) == size(2) );
#pragma omp parallel for
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
//auto idx = this->get_idx(i,j,k);
auto &elem = this->relem(i,j,k);
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
auto &elem = this->relem(i, j, k);
const auto &elemg = g.relem(i, j, k);
const auto &elemg1 = g1.relem(i,j,k);
const auto &elemg2 = g2.relem(i,j,k);
elem = f(elemg);
}
}
}
}
elem = f(elemg1,elemg2);
}
}
}
}
template <typename functional, typename grid1_t, typename grid2_t, typename grid3_t>
void assign_function_of_grids_r(const functional &f, const grid1_t &g1, const grid2_t &g2, const grid3_t &g3)
{
assert(g1.size(0) == size(0) && g1.size(1) == size(1));// && g1.size(2) == size(2));
assert(g2.size(0) == size(0) && g2.size(1) == size(1));// && g2.size(2) == size(2));
assert(g3.size(0) == size(0) && g3.size(1) == size(1));// && g3.size(2) == size(2));
template <typename functional, typename grid1_t, typename grid2_t>
void assign_function_of_grids_r(const functional &f, const grid1_t &g1, const grid2_t &g2)
{
assert(g1.size(0) == size(0) && g1.size(1) == size(1)); // && g1.size(2) == size(2));
assert(g2.size(0) == size(0) && g2.size(1) == size(1)); // && g2.size(2) == size(2));
#pragma omp parallel for
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
//auto idx = this->get_idx(i,j,k);
auto &elem = this->relem(i, j, k);
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
//auto idx = this->get_idx(i,j,k);
auto &elem = this->relem(i, j, k);
const auto &elemg1 = g1.relem(i, j, k);
const auto &elemg2 = g2.relem(i, j, k);
const auto &elemg3 = g3.relem(i, j, k);
const auto &elemg1 = g1.relem(i, j, k);
const auto &elemg2 = g2.relem(i, j, k);
elem = f(elemg1, elemg2, elemg3);
}
}
}
}
elem = f(elemg1, elemg2);
}
}
}
}
template< typename functional >
void apply_function_k_dep( const functional& f )
{
#pragma omp parallel for
for( size_t i = 0; i < sizes_[0]; ++i )
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
auto& elem = this->kelem(i,j,k);
elem = f(elem,this->get_k<real_t>(i,j,k));
}
}
}
}
template <typename functional, typename grid1_t, typename grid2_t, typename grid3_t>
void assign_function_of_grids_r(const functional &f, const grid1_t &g1, const grid2_t &g2, const grid3_t &g3)
{
assert(g1.size(0) == size(0) && g1.size(1) == size(1)); // && g1.size(2) == size(2));
assert(g2.size(0) == size(0) && g2.size(1) == size(1)); // && g2.size(2) == size(2));
assert(g3.size(0) == size(0) && g3.size(1) == size(1)); // && g3.size(2) == size(2));
template <typename functional>
void apply_function_r_dep( const functional& f)
{
#pragma omp parallel for
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
auto &elem = this->relem(i, j, k);
elem = f(elem, this->get_r<real_t>(i, j, k));
}
}
}
}
#pragma omp parallel for
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
//auto idx = this->get_idx(i,j,k);
auto &elem = this->relem(i, j, k);
void FourierTransformBackward(bool do_transform = true);
const auto &elemg1 = g1.relem(i, j, k);
const auto &elemg2 = g2.relem(i, j, k);
const auto &elemg3 = g3.relem(i, j, k);
void FourierTransformForward(bool do_transform = true);
elem = f(elemg1, elemg2, elemg3);
}
}
}
}
void ApplyNorm(void);
template <typename functional>
void apply_function_k_dep(const functional &f)
{
#pragma omp parallel for
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
auto &elem = this->kelem(i, j, k);
elem = f(elem, this->get_k<real_t>(i, j, k));
}
}
}
}
void FillRandomReal( unsigned long int seed = 123456ul );
template <typename functional>
void apply_function_r_dep(const functional &f)
{
#pragma omp parallel for
for (size_t i = 0; i < sizes_[0]; ++i)
{
for (size_t j = 0; j < sizes_[1]; ++j)
{
for (size_t k = 0; k < sizes_[2]; ++k)
{
auto &elem = this->relem(i, j, k);
elem = f(elem, this->get_r<real_t>(i, j, k));
}
}
}
}
void Write_to_HDF5(std::string fname, std::string datasetname);
void FourierTransformBackward(bool do_transform = true);
void ComputePowerSpectrum(std::vector<double> &bin_k, std::vector<double> &bin_P, std::vector<double> &bin_eP, int nbins);
void FourierTransformForward(bool do_transform = true);
void Compute_PDF(std::string ofname, int nbins = 1000, double scale = 1.0, double rhomin = 1e-3, double rhomax = 1e3);
void ApplyNorm(void);
void zero_DC_mode(void)
{
void FillRandomReal(unsigned long int seed = 123456ul);
void Write_to_HDF5(std::string fname, std::string datasetname);
void ComputePowerSpectrum(std::vector<double> &bin_k, std::vector<double> &bin_P, std::vector<double> &bin_eP, int nbins);
void Compute_PDF(std::string ofname, int nbins = 1000, double scale = 1.0, double rhomin = 1e-3, double rhomax = 1e3);
void zero_DC_mode(void)
{
#ifdef USE_MPI
if (CONFIG::MPI_task_rank == 0)
if (CONFIG::MPI_task_rank == 0)
#endif
cdata_[0] = (data_t)0.0;
}
cdata_[0] = (data_t)0.0;
}
};
template <typename data_t>

169
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@ -0,0 +1,169 @@
/*
output.hh - This file is part of MUSIC -
a code to generate multi-scale initial conditions
for cosmological simulations
Copyright (C) 2010 Oliver Hahn
*/
#ifndef __OUTPUT_HH
#define __OUTPUT_HH
#include <string>
#include <map>
#include "general.hh"
#include "grid_fft.hh"
#include "config_file.hh"
/*!
* @class output_plugin
* @brief abstract base class for output plug-ins
*
* This class provides the abstract base class for all output plug-ins.
* All output plug-ins need to derive from it and implement the purely
* virtual member functions.
*/
class output_plugin
{
public:
using grid_hierarchy = Grid_FFT<real_t>;
protected:
//! reference to the ConfigFile object that holds all configuration options
ConfigFile& cf_;
//! output file or directory name
std::string fname_;
//! minimum refinement level
// unsigned levelmin_;
//! maximum refinement level
// unsigned levelmax_;
std::vector<unsigned>
offx_, //!< vector describing the x-offset of each level
offy_, //!< vector describing the y-offset of each level
offz_, //!< vector describing the z-offset of each level
sizex_, //!< vector describing the extent in x of each level
sizey_, //!< vector describing the extent in y of each level
sizez_; //!< vector describing the extent in z of each level
//! quick access function to query properties of the refinement grid from the configuration options
/*! @param name name of the config property
* @param icomp component index (0=x, 1=y, 2=z)
* @param oit output iterator (e.g. std::back_inserter for vectors)
*/
template< typename output_iterator >
void query_grid_prop( std::string name, int icomp, output_iterator oit )
{
char str[128];
//for( unsigned i=levelmin_; i<=levelmax_; ++i )
unsigned i=0;
{
sprintf( str, "%s(%u,%d)", name.c_str(), i, icomp );
*oit = 0; //cf_.GetValue<unsigned>( "setup", str );
++oit;
}
}
public:
//! constructor
explicit output_plugin( ConfigFile& cf )
: cf_(cf)
{
fname_ = cf.GetValue<std::string>("output","filename");
// levelmin_ = cf.GetValue<unsigned>( "setup", "levelmin" );
// levelmax_ = cf.GetValue<unsigned>( "setup", "levelmax" );
query_grid_prop( "offset", 0, std::back_inserter(offx_) );
query_grid_prop( "offset", 1, std::back_inserter(offy_) );
query_grid_prop( "offset", 2, std::back_inserter(offz_) );
query_grid_prop( "size", 0, std::back_inserter(sizex_) );
query_grid_prop( "size", 1, std::back_inserter(sizey_) );
query_grid_prop( "size", 2, std::back_inserter(sizez_) );
}
//! destructor
virtual ~output_plugin()
{ }
//! purely virtual prototype to write the masses for each dark matter particle
virtual void write_dm_mass( const grid_hierarchy& gh ) = 0;
//! purely virtual prototype to write the dark matter density field
virtual void write_dm_density( const grid_hierarchy& gh ) = 0;
//! purely virtual prototype to write the dark matter gravitational potential (from which displacements are computed in 1LPT)
virtual void write_dm_potential( const grid_hierarchy& gh ) = 0;
//! purely virtual prototype to write dark matter particle velocities
virtual void write_dm_velocity( int coord, const grid_hierarchy& gh ) = 0;
//! purely virtual prototype to write dark matter particle positions
virtual void write_dm_position( int coord, const grid_hierarchy& gh ) = 0;
//! purely virtual prototype to write the baryon velocities
virtual void write_gas_velocity( int coord, const grid_hierarchy& gh ) = 0;
//! purely virtual prototype to write the baryon coordinates
virtual void write_gas_position( int coord, const grid_hierarchy& gh ) = 0;
//! purely virtual prototype to write the baryon density field
virtual void write_gas_density( const grid_hierarchy& gh ) = 0;
//! purely virtual prototype to write the baryon gravitational potential (from which displacements are computed in 1LPT)
virtual void write_gas_potential( const grid_hierarchy& gh ) = 0;
//! purely virtual prototype for all things to be done at the very end
virtual void finalize( void ) = 0;
};
/*!
* @brief implements abstract factory design pattern for output plug-ins
*/
struct output_plugin_creator
{
//! create an instance of a plug-in
virtual output_plugin * create( ConfigFile& cf ) const = 0;
//! destroy an instance of a plug-in
virtual ~output_plugin_creator() { }
};
//! maps the name of a plug-in to a pointer of the factory pattern
std::map< std::string, output_plugin_creator *>& get_output_plugin_map();
//! print a list of all registered output plug-ins
void print_output_plugins();
/*!
* @brief concrete factory pattern for output plug-ins
*/
template< class Derived >
struct output_plugin_creator_concrete : public output_plugin_creator
{
//! register the plug-in by its name
output_plugin_creator_concrete( const std::string& plugin_name )
{
get_output_plugin_map()[ plugin_name ] = this;
}
//! create an instance of the plug-in
output_plugin * create( ConfigFile& cf ) const
{
return new Derived( cf );
}
};
//! failsafe version to select the output plug-in
output_plugin *select_output_plugin( ConfigFile& cf );
#endif // __OUTPUT_HH

186
src/main.cc
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@ -11,6 +11,7 @@
#include <transfer_function_plugin.hh>
#include <random_plugin.hh>
#include <output_plugin.hh>
#include <cosmology_calculator.hh>
namespace CONFIG{
@ -24,6 +25,7 @@ bool FFTW_threads_ok = false;
RNG_plugin *the_random_number_generator;
TransferFunction_plugin *the_transfer_function;
output_plugin *the_output_plugin;
int main( int argc, char** argv )
{
@ -66,7 +68,7 @@ int main( int argc, char** argv )
// print_region_generator_plugins();
print_TransferFunction_plugins();
// print_RNG_plugins();
// print_output_plugins();
print_output_plugins();
csoca::elog << "In order to run, you need to specify a parameter file!" << std::endl;
exit(0);
@ -79,40 +81,41 @@ int main( int argc, char** argv )
const size_t ngrid = the_config.GetValue<size_t>("setup", "GridRes");
const real_t boxlen = the_config.GetValue<double>("setup", "BoxLength");
const real_t zstart = the_config.GetValue<double>("setup", "zstart");
const int LPTorder = the_config.GetValueSafe<double>("setup","LPTorder",100);
const real_t astart = 1.0/(1.0+zstart);
const real_t volfac(std::pow(boxlen / ngrid / 2.0 / M_PI, 1.5));
const real_t phifac = 1.0 / boxlen / boxlen; // to have potential in box units
const real_t deriv_fac = 1.0 ;//boxlen;
real_t Dplus0 = the_config.GetValue<real_t>("setup", "Dplus0");
// real_t Dplus0 = the_config.GetValue<real_t>("setup", "Dplus0");
// real_t Ddot0 = 1.0;
const bool bDoFixing = false;
//...
const std::string fname_hdf5 = the_config.GetValueSafe<std::string>("output", "fname_hdf5", "output.hdf5");
//////////////////////////////////////////////////////////////////////////////////////////////
std::unique_ptr<CosmologyCalculator>
the_cosmo_calc;
try
{
the_random_number_generator = select_RNG_plugin(the_config);
the_transfer_function = select_TransferFunction_plugin(the_config);
the_output_plugin = select_output_plugin(the_config);
the_cosmo_calc = std::make_unique<CosmologyCalculator>(the_config, the_transfer_function);
//double pnorm = the_cosmo_calc->ComputePNorm();
//Dplus = the_cosmo_calc->CalcGrowthFactor(astart) / the_cosmo_calc->CalcGrowthFactor(1.0);
csoca::ilog << "power spectrum is output for D+ =" << Dplus0 << std::endl;
// double pnorm = the_cosmo_calc->ComputePNorm();
// csoca::ilog << "power spectrum is output for D+ =" << Dplus0 << std::endl;
//csoca::ilog << "power spectrum normalisation is " << pnorm << std::endl;
//csoca::ilog << "power spectrum normalisation is " << pnorm*Dplus*Dplus << std::endl;
// write power spectrum to a file
std::ofstream ofs("input_powerspec.txt");
for( double k=1e-4; k<1e4; k*=1.1 ){
ofs << std::setw(16) << k
<< std::setw(16) << std::pow(the_cosmo_calc->GetAmplitude(k, total) * Dplus0, 2.0)
<< std::setw(16) << std::pow(the_cosmo_calc->GetAmplitude(k, total), 2.0)
<< std::endl;
}
}catch(...){
csoca::elog << "Problem during initialisation. See error(s) above. Exiting..." << std::endl;
#if defined(USE_MPI)
@ -120,6 +123,30 @@ int main( int argc, char** argv )
#endif
return 1;
}
const real_t Dplus0 = the_cosmo_calc->CalcGrowthFactor(astart) / the_cosmo_calc->CalcGrowthFactor(1.0);
const real_t vfac = the_cosmo_calc->CalcVFact(astart);
{
// write power spectrum to a file
std::ofstream ofs("input_powerspec.txt");
for( double k=1e-4; k<1e4; k*=1.1 ){
ofs << std::setw(16) << k
<< std::setw(16) << std::pow(the_cosmo_calc->GetAmplitude(k, total) * Dplus0, 2.0)
<< std::setw(16) << std::pow(the_cosmo_calc->GetAmplitude(k, total), 2.0)
<< std::endl;
}
}
// compute growth factors of the respective orders
const double g1 = -Dplus0;
const double g2 = -3.0/7.0*Dplus0*Dplus0;
const double g3a = -1.0/3.0*Dplus0*Dplus0*Dplus0;
const double g3b = 10.0/21.*Dplus0*Dplus0*Dplus0;
const double vfac1 = vfac;
const double vfac2 = 2*vfac1;
const double vfac3 = 3*vfac1;
//--------------------------------------------------------------------
// Create arrays
Grid_FFT<real_t> phi({ngrid, ngrid, ngrid}, {boxlen, boxlen, boxlen});
@ -136,6 +163,8 @@ int main( int argc, char** argv )
phi.apply_function_k_dep([&](auto x, auto k) -> ccomplex_t {
real_t kmod = k.norm();
if( bDoFixing ) x = x / std::abs(x); //std::exp(ccomplex_t(0, iphase * PhaseRotation));
else x = x;
ccomplex_t delta = x * the_cosmo_calc->GetAmplitude(kmod, total);
return -delta / (kmod * kmod) * phifac / volfac;
});
@ -295,16 +324,29 @@ int main( int argc, char** argv )
phi3b.zero_DC_mode();
///////////////////////////////////////////////////////////////////////
// we store the densities here if we compute them
Grid_FFT<real_t> &delta = phi_xx;
Grid_FFT<real_t> &delta2 = phi_xy;
Grid_FFT<real_t> &delta3a = phi_xz;
Grid_FFT<real_t> &delta3b = phi_yy;
Grid_FFT<real_t> &delta3 = phi_yz;
delta.FourierTransformForward(false);
delta2.FourierTransformForward(false);
delta3a.FourierTransformForward(false);
delta3b.FourierTransformForward(false);
// we store displacements and velocities here if we compute them
Grid_FFT<real_t> &Psix = phi_xx;
Grid_FFT<real_t> &Psiy = phi_xy;
Grid_FFT<real_t> &Psiz = phi_xz;
Grid_FFT<real_t> &Vx = phi_yy;
Grid_FFT<real_t> &Vy = phi_yz;
Grid_FFT<real_t> &Vz = phi_zz;
const bool compute_densities = false;
phi_xx.FourierTransformForward(false);
phi_xy.FourierTransformForward(false);
phi_xz.FourierTransformForward(false);
phi_yy.FourierTransformForward(false);
phi_yz.FourierTransformForward(false);
phi_zz.FourierTransformForward(false);
#pragma omp parallel for
for (size_t i = 0; i < phi.size(0); ++i)
@ -317,36 +359,94 @@ int main( int argc, char** argv )
size_t idx = phi.get_idx(i,j,k);
auto laplace = -kk.norm_squared();
delta.kelem(idx) = laplace * phi.kelem(idx) / phifac;
delta2.kelem(idx) = laplace * phi2.kelem(idx) / phifac;
delta3a.kelem(idx) = laplace * phi3a.kelem(idx) / phifac;
delta3b.kelem(idx) = laplace * phi3b.kelem(idx) / phifac;
// scale potentials with respective order growth factors
phi.kelem(idx) *= g1;
phi2.kelem(idx) *= g2;
phi3a.kelem(idx) *= g3a;
phi3b.kelem(idx) *= g3b;
if( compute_densities ){
// compute densities associated to respective potentials as well
delta.kelem(idx) = laplace * phi.kelem(idx) / phifac;
delta2.kelem(idx) = laplace * phi2.kelem(idx) / phifac;
delta3a.kelem(idx) = laplace * phi3a.kelem(idx) / phifac;
delta3b.kelem(idx) = laplace * phi3b.kelem(idx) / phifac;
delta3.kelem(idx) = delta3a.kelem(idx) + delta3b.kelem(idx);
}else{
auto phitot = phi.kelem(idx) + ((LPTorder>1)?phi2.kelem(idx):0.0) + ((LPTorder>2)? phi3a.kelem(idx) + phi3b.kelem(idx) : 0.0);
auto phitot_v = vfac1 * phi.kelem(idx) + ((LPTorder>1)? vfac2 * phi2.kelem(idx) : 0.0) + ((LPTorder>2)? vfac3 * (phi3a.kelem(idx) + phi3b.kelem(idx)) : 0.0);
Psix.kelem(idx) = ccomplex_t(0.0,1.0) * kk[0]* boxlen * ( phitot );
Psiy.kelem(idx) = ccomplex_t(0.0,1.0) * kk[1]* boxlen * ( phitot );
Psiz.kelem(idx) = ccomplex_t(0.0,1.0) * kk[2]* boxlen * ( phitot );
Vx.kelem(idx) = ccomplex_t(0.0,1.0) * kk[0]* boxlen * ( phitot_v );
Vy.kelem(idx) = ccomplex_t(0.0,1.0) * kk[1]* boxlen * ( phitot_v );
Vz.kelem(idx) = ccomplex_t(0.0,1.0) * kk[2]* boxlen * ( phitot_v );
}
}
}
}
///////////////////////////////////////////////////////////////////////
phi.FourierTransformBackward();
phi2.FourierTransformBackward();
phi3a.FourierTransformBackward();
phi3b.FourierTransformBackward();
delta.FourierTransformBackward();
delta2.FourierTransformBackward();
delta3a.FourierTransformBackward();
delta3b.FourierTransformBackward();
//... write output .....
unlink(fname_hdf5.c_str());
phi.Write_to_HDF5(fname_hdf5, "phi");
phi2.Write_to_HDF5(fname_hdf5, "phi2");
phi3a.Write_to_HDF5(fname_hdf5, "phi3a");
phi3b.Write_to_HDF5(fname_hdf5, "phi3b");
delta.Write_to_HDF5(fname_hdf5, "delta");
delta2.Write_to_HDF5(fname_hdf5, "delta2");
delta3a.Write_to_HDF5(fname_hdf5, "delta3a");
delta3b.Write_to_HDF5(fname_hdf5, "delta3b");
if( compute_densities ){
phi.FourierTransformBackward();
phi2.FourierTransformBackward();
phi3a.FourierTransformBackward();
phi3b.FourierTransformBackward();
delta.FourierTransformBackward();
delta2.FourierTransformBackward();
delta3a.FourierTransformBackward();
delta3b.FourierTransformBackward();
delta3.FourierTransformBackward();
unlink(fname_hdf5.c_str());
phi.Write_to_HDF5(fname_hdf5, "phi");
phi2.Write_to_HDF5(fname_hdf5, "phi2");
phi3a.Write_to_HDF5(fname_hdf5, "phi3a");
phi3b.Write_to_HDF5(fname_hdf5, "phi3b");
delta.Write_to_HDF5(fname_hdf5, "delta");
delta2.Write_to_HDF5(fname_hdf5, "delta2");
delta3a.Write_to_HDF5(fname_hdf5, "delta3a");
delta3b.Write_to_HDF5(fname_hdf5, "delta3b");
delta3.Write_to_HDF5(fname_hdf5, "delta3");
}else{
Psix.FourierTransformBackward();
Psiy.FourierTransformBackward();
Psiz.FourierTransformBackward();
Vx.FourierTransformBackward();
Vy.FourierTransformBackward();
Vz.FourierTransformBackward();
// Psix.Write_to_HDF5(fname_hdf5, "Psix");
// Psiy.Write_to_HDF5(fname_hdf5, "Psiy");
// Psiz.Write_to_HDF5(fname_hdf5, "Psiz");
// Vx.Write_to_HDF5(fname_hdf5, "Vx");
// Vy.Write_to_HDF5(fname_hdf5, "Vy");
// Vz.Write_to_HDF5(fname_hdf5, "Vz");
the_output_plugin->write_dm_mass(Psix);
the_output_plugin->write_dm_density(Psix);
the_output_plugin->write_dm_position(0, Psix );
the_output_plugin->write_dm_position(1, Psiy );
the_output_plugin->write_dm_position(2, Psiz );
the_output_plugin->write_dm_velocity(0, Vx );
the_output_plugin->write_dm_velocity(1, Vy );
the_output_plugin->write_dm_velocity(2, Vz );
the_output_plugin->finalize();
delete the_output_plugin;
}

60
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@ -0,0 +1,60 @@
/*
output.cc - This file is part of MUSIC -
a code to generate multi-scale initial conditions
for cosmological simulations
Copyright (C) 2010 Oliver Hahn
*/
#include "output_plugin.hh"
std::map< std::string, output_plugin_creator *>&
get_output_plugin_map()
{
static std::map< std::string, output_plugin_creator* > output_plugin_map;
return output_plugin_map;
}
void print_output_plugins()
{
std::map< std::string, output_plugin_creator *>& m = get_output_plugin_map();
std::map< std::string, output_plugin_creator *>::iterator it;
it = m.begin();
std::cout << " - Available output plug-ins:\n";
while( it!=m.end() )
{
if( (*it).second )
std::cout << "\t\'" << (*it).first << "\'\n";
++it;
}
}
output_plugin *select_output_plugin( ConfigFile& cf )
{
std::string formatname = cf.GetValue<std::string>( "output", "format" );
output_plugin_creator *the_output_plugin_creator
= get_output_plugin_map()[ formatname ];
if( !the_output_plugin_creator )
{
std::cerr << " - Error: output plug-in \'" << formatname << "\' not found." << std::endl;
print_output_plugins();
throw std::runtime_error("Unknown output plug-in");
}else
std::cout << " - Selecting output plug-in \'" << formatname << "\'..." << std::endl;
output_plugin *the_output_plugin
= the_output_plugin_creator->create( cf );
return the_output_plugin;
}

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