mirror of
https://github.com/cosmo-sims/monofonIC.git
synced 2024-09-19 17:03:45 +02:00
Move the writing of header and other general properties to rank 0 only in the SWIFT i/o plugin
This commit is contained in:
Matthieu Schaller
parent
5aa59719da
commit
a3e6581902
1 changed files with 105 additions and 105 deletions
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@ -38,14 +38,15 @@ class swift_output_plugin : public output_plugin
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{
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protected:
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int num_files_, num_simultaneous_writers_;
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int num_ranks_, this_rank_;
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int num_files_;
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real_t lunit_, vunit_, munit_;
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real_t boxsize_, hubble_param_, astart_, zstart_;
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bool blongids_, bdobaryons_;
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std::string this_fname_;
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std::array<uint32_t,7> npart_, npartTotal_, npartTotalHighWord_;
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std::array<uint64_t,7> npart_;
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std::array<uint32_t,7> npartTotal_, npartTotalHighWord_;
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std::array<double,7> mass_;
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double time_;
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@ -54,11 +55,12 @@ public:
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explicit swift_output_plugin(config_file &cf, std::unique_ptr<cosmology::calculator> &pcc)
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: output_plugin(cf, pcc, "SWIFT")
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{
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// SWIFT uses a single file as IC */
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num_files_ = 1;
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#ifdef USE_MPI
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// use as many output files as we have MPI tasks
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MPI_Comm_size(MPI_COMM_WORLD, &num_files_);
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#endif
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this_rank_ = 0;
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num_files_ = 1;
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real_t astart = 1.0 / (1.0 + cf_.get_value<double>("setup", "zstart"));
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const double rhoc = 27.7519737; // in h^2 1e10 M_sol / Mpc^3
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@ -83,32 +85,28 @@ public:
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}
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time_ = astart;
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this_fname_ = fname_;
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#ifdef USE_MPI
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int thisrank = 0;
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MPI_Comm_rank(MPI_COMM_WORLD, &thisrank);
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if (num_files_ > 1)
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this_fname_ += "." + std::to_string(thisrank);
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MPI_Comm_rank(MPI_COMM_WORLD, &this_rank_);
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MPI_Comm_size(MPI_COMM_WORLD, &num_ranks_);
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#endif
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// Now that we modified the filename for MPI support, propagate the change to the super-class
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// as it does operations on the file behind our back.
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fname_ = this_fname_;
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// Only ranks 0 writes the header
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if (this_rank_ != 0) return;
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// delete output file if it exists
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unlink(this_fname_.c_str());
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unlink(fname_.c_str());
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// create output HDF5 file
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HDFCreateFile(this_fname_);
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HDFCreateFile(fname_);
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// Write UNITS header using the physical constants assumed internally by SWIFT
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HDFCreateGroup(this_fname_, "Units");
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HDFWriteGroupAttribute(this_fname_, "Units", "Unit mass in cgs (U_M)", 1.98841e43); // 10^10 Msun in grams
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HDFWriteGroupAttribute(this_fname_, "Units", "Unit length in cgs (U_L)", 3.08567758149e24); // 1 Mpc in cm
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HDFWriteGroupAttribute(this_fname_, "Units", "Unit time in cgs (U_t)", 3.08567758149e19); // so that unit vel is 1 km/s
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HDFWriteGroupAttribute(this_fname_, "Units", "Unit current in cgs (U_I)", 1.0); // 1 Ampere
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HDFWriteGroupAttribute(this_fname_, "Units", "Unit temperature in cgs (U_T)", 1.0); // 1 Kelvin
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HDFCreateGroup(fname_, "Units");
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HDFWriteGroupAttribute(fname_, "Units", "Unit mass in cgs (U_M)", 1.98841e43); // 10^10 Msun in grams
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HDFWriteGroupAttribute(fname_, "Units", "Unit length in cgs (U_L)", 3.08567758149e24); // 1 Mpc in cm
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HDFWriteGroupAttribute(fname_, "Units", "Unit time in cgs (U_t)", 3.08567758149e19); // so that unit vel is 1 km/s
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HDFWriteGroupAttribute(fname_, "Units", "Unit current in cgs (U_I)", 1.0); // 1 Ampere
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HDFWriteGroupAttribute(fname_, "Units", "Unit temperature in cgs (U_T)", 1.0); // 1 Kelvin
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// Write MUSIC configuration header
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int order = cf_.get_value<int>("setup", "LPTorder");
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@ -122,32 +120,32 @@ public:
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int do_baryonsVrel = cf_.get_value<bool>("setup", "DoBaryonVrel");
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int L = cf_.get_value<int>("setup", "GridRes");
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HDFCreateGroup(this_fname_, "ICs_parameters");
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Code", std::string("MUSIC2 - monofonIC"));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Git Revision", std::string(GIT_REV));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Git Tag", std::string(GIT_TAG));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Git Branch", std::string(GIT_BRANCH));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Precision", std::string(CMAKE_PRECISION_STR));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Convolutions", std::string(CMAKE_CONVOLVER_STR));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "PLT", std::string(CMAKE_PLT_STR));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "LPT Order", order);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Particle Load", load);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Transfer Function", tf);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Cosmology Parameter Set", cosmo_set);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Random Generator", rng);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Mode Fixing", do_fixing);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Mode inversion", do_invert);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Baryons", do_baryons);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Baryons Relative Velocity", do_baryonsVrel);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Grid Resolution", L);
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HDFCreateGroup(fname_, "ICs_parameters");
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Code", std::string("MUSIC2 - monofonIC"));
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Git Revision", std::string(GIT_REV));
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Git Tag", std::string(GIT_TAG));
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Git Branch", std::string(GIT_BRANCH));
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Precision", std::string(CMAKE_PRECISION_STR));
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Convolutions", std::string(CMAKE_CONVOLVER_STR));
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "PLT", std::string(CMAKE_PLT_STR));
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "LPT Order", order);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Particle Load", load);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Transfer Function", tf);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Cosmology Parameter Set", cosmo_set);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Random Generator", rng);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Mode Fixing", do_fixing);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Mode inversion", do_invert);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Baryons", do_baryons);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Baryons Relative Velocity", do_baryonsVrel);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Grid Resolution", L);
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if (tf == "CLASS") {
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double ztarget = cf_.get_value<double>("cosmology", "ztarget");
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Target Redshift", ztarget);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Target Redshift", ztarget);
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}
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if (rng == "PANPHASIA") {
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std::string desc = cf_.get_value<std::string>("random", "descriptor");
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Descriptor", desc);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Descriptor", desc);
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}
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}
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@ -155,56 +153,27 @@ public:
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~swift_output_plugin()
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{
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if (!std::uncaught_exception())
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{
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HDFCreateGroup(this_fname_, "Header");
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HDFWriteGroupAttribute(fname_, "Header", "Dimension", 3);
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HDFWriteGroupAttribute(fname_, "Header", "BoxSize", boxsize_ / hubble_param_); // in Mpc, not Mpc/h
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HDFWriteGroupAttribute(this_fname_, "Header", "NumPart_Total", from_7array<unsigned>(npartTotal_));
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HDFWriteGroupAttribute(this_fname_, "Header", "NumPart_Total_HighWord", from_7array<unsigned>(npartTotalHighWord_));
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HDFWriteGroupAttribute(this_fname_, "Header", "NumPart_ThisFile", from_7array<unsigned>(npart_));
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HDFWriteGroupAttribute(this_fname_, "Header", "MassTable", from_7array<double>(mass_));
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HDFWriteGroupAttribute(this_fname_, "Header", "Time", from_value<double>(time_));
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HDFWriteGroupAttribute(this_fname_, "Header", "Redshift", from_value<double>(zstart_));
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HDFWriteGroupAttribute(this_fname_, "Header", "Flag_Entropy_ICs", from_value<int>(0));
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{
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if (this_rank_ == 0) {
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// Write Standard Gadget / SWIFT hdf5 header
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HDFCreateGroup(fname_, "Header");
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HDFWriteGroupAttribute(fname_, "Header", "Dimension", 3);
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HDFWriteGroupAttribute(fname_, "Header", "BoxSize", boxsize_ / hubble_param_); // in Mpc, not Mpc/h
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HDFWriteGroupAttribute(fname_, "Header", "NumPart_Total", from_7array<unsigned>(npartTotal_));
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HDFWriteGroupAttribute(fname_, "Header", "NumPart_Total_HighWord", from_7array<unsigned>(npartTotalHighWord_));
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HDFWriteGroupAttribute(fname_, "Header", "NumPart_ThisFile", from_7array<uint64_t>(npart_));
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HDFWriteGroupAttribute(fname_, "Header", "MassTable", from_7array<double>(mass_));
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HDFWriteGroupAttribute(fname_, "Header", "Time", from_value<double>(time_));
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HDFWriteGroupAttribute(fname_, "Header", "Redshift", from_value<double>(zstart_));
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HDFWriteGroupAttribute(fname_, "Header", "Flag_Entropy_ICs", from_value<int>(0));
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HDFWriteGroupAttribute(fname_, "Header", "NumFilesPerSnapshot", from_value<int>(num_files_));
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HDFWriteGroupAttribute(this_fname_, "Header", "NumFilesPerSnapshot", from_value<int>(num_files_));
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// write GAS internal energy and smoothing length if baryons are enabled
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if( bdobaryons_ )
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{
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const double gamma = cf_.get_value_safe<double>("cosmology", "gamma", 5.0 / 3.0);
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const double YHe = pcc_->cosmo_param_["YHe"];
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//const double Omega0 = cf_.get_value<double>("cosmology", "Omega_m");
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const double omegab = pcc_->cosmo_param_["Omega_b"];
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const double Tcmb0 = pcc_->cosmo_param_["Tcmb"];
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// compute gas internal energy
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const double npol = (fabs(1.0 - gamma) > 1e-7) ? 1.0 / (gamma - 1.) : 1.0;
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const double unitv = 1e5;
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const double adec = 1.0 / (160. * std::pow(omegab * hubble_param_ * hubble_param_ / 0.022, 2.0 / 5.0));
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const double Tini = astart_ < adec ? Tcmb0 / astart_ : Tcmb0 / astart_ / astart_ * adec;
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const double mu = (Tini > 1.e4) ? 4.0 / (8. - 5. * YHe) : 4.0 / (1. + 3. * (1. - YHe));
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const double ceint = 1.3806e-16 / 1.6726e-24 * Tini * npol / mu / unitv / unitv;
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music::ilog.Print("Swift : Calculated initial gas temperature: %.2f K/mu", Tini / mu);
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music::ilog.Print("Swift : set initial internal energy to %.2e km^2/s^2", ceint);
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std::vector<write_real_t> data( npart_[0], ceint );
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HDFWriteDataset(this_fname_, "PartType0/InternalEnergy", data);
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const double h = boxsize_ / hubble_param_ / cf_.get_value<double>("setup","GridRes");
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music::ilog.Print("Swift : set initial smoothing length to mean inter-part separation: %.2f Mpc", h);
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data.assign( npart_[0], h);
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HDFWriteDataset(this_fname_, "PartType0/SmoothingLength", data);
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music::ilog << "Wrote SWIFT IC file(s) to " << fname_ << std::endl;
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}
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music::ilog << "Wrote SWIFT IC file(s) to " << this_fname_ << std::endl;
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}
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}
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@ -247,46 +216,77 @@ public:
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void write_particle_data(const particle::container &pc, const cosmo_species &s, double Omega_species)
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{
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int sid = get_species_idx(s);
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assert(sid != -1);
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npart_[sid] = (pc.get_local_num_particles());
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npart_[sid] = (pc.get_global_num_particles());
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npartTotal_[sid] = (uint32_t)(pc.get_global_num_particles());
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npartTotalHighWord_[sid] = (uint32_t)((pc.get_global_num_particles()) >> 32);
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if( pc.bhas_individual_masses_ )
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mass_[sid] = 0.0;
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else
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mass_[sid] = Omega_species * munit_ / pc.get_global_num_particles();
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HDFCreateGroup(this_fname_, std::string("PartType") + std::to_string(sid));
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HDFCreateGroup(fname_, std::string("PartType") + std::to_string(sid));
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//... write positions and velocities.....
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if (this->has_64bit_reals())
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{
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HDFWriteDatasetVector(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), pc.positions64_);
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HDFWriteDatasetVector(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), pc.velocities64_);
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HDFWriteDatasetVector(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), pc.positions64_);
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HDFWriteDatasetVector(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), pc.velocities64_);
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}
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else
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{
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HDFWriteDatasetVector(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), pc.positions32_);
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HDFWriteDatasetVector(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), pc.velocities32_);
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HDFWriteDatasetVector(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), pc.positions32_);
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HDFWriteDatasetVector(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), pc.velocities32_);
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}
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//... write ids.....
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if (this->has_64bit_ids())
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HDFWriteDataset(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), pc.ids64_);
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HDFWriteDataset(fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), pc.ids64_);
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else
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HDFWriteDataset(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), pc.ids32_);
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HDFWriteDataset(fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), pc.ids32_);
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//... write masses.....
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if( pc.bhas_individual_masses_ ){
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if (this->has_64bit_reals()){
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HDFWriteDataset(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), pc.mass64_);
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HDFWriteDataset(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), pc.mass64_);
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}else{
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HDFWriteDataset(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), pc.mass32_);
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HDFWriteDataset(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), pc.mass32_);
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}
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}
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// write GAS internal energy and smoothing length if baryons are enabled
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if( bdobaryons_ && s == cosmo_species::baryon) {
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const double gamma = cf_.get_value_safe<double>("cosmology", "gamma", 5.0 / 3.0);
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const double YHe = pcc_->cosmo_param_["YHe"];
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//const double Omega0 = cf_.get_value<double>("cosmology", "Omega_m");
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const double omegab = pcc_->cosmo_param_["Omega_b"];
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const double Tcmb0 = pcc_->cosmo_param_["Tcmb"];
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// compute gas internal energy
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const double npol = (fabs(1.0 - gamma) > 1e-7) ? 1.0 / (gamma - 1.) : 1.0;
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const double unitv = 1e5;
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const double adec = 1.0 / (160. * std::pow(omegab * hubble_param_ * hubble_param_ / 0.022, 2.0 / 5.0));
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const double Tini = astart_ < adec ? Tcmb0 / astart_ : Tcmb0 / astart_ / astart_ * adec;
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const double mu = (Tini > 1.e4) ? 4.0 / (8. - 5. * YHe) : 4.0 / (1. + 3. * (1. - YHe));
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const double ceint = 1.3806e-16 / 1.6726e-24 * Tini * npol / mu / unitv / unitv;
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music::ilog.Print("Swift : Calculated initial gas temperature: %.2f K/mu", Tini / mu);
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music::ilog.Print("Swift : set initial internal energy to %.2e km^2/s^2", ceint);
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std::vector<write_real_t> data( npart_[0], ceint );
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HDFWriteDataset(fname_, std::string("PartType") + std::to_string(sid) + std::string("/InternalEnergy"), data);
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const double h = boxsize_ / hubble_param_ / cf_.get_value<double>("setup","GridRes");
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music::ilog.Print("Swift : set initial smoothing length to mean inter-part separation: %.2f Mpc", h);
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data.assign( npart_[0], h);
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HDFWriteDataset(fname_, std::string("PartType") + std::to_string(sid) + std::string("/SmoothingLength"), data);
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}
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}
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};
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