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Merge pull request #6052 from gassmoeller/tests_for_multiple_particle…
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…_worlds

Tests for multiple particle worlds
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@tjhei
tjhei authored Oct 4, 2024
2 parents 136fe5d + f540ce9 commit 532b6aa
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Showing 43 changed files with 1,249 additions and 73 deletions.
45 changes: 26 additions & 19 deletions include/aspect/postprocess/particles.h
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Expand Up @@ -213,36 +213,38 @@ namespace aspect
std::vector<std::string> output_formats;

/**
* A list of pairs (time, pvtu_filename) that have so far been written
* and that we will pass to DataOutInterface::write_pvd_record
* A map between particle world name and list of pairs of
* (time, pvtu_filename) that have so far been written.
* We will pass these lists to DataOutInterface::write_pvd_record
* to create a description file that can make the association
* between simulation time and corresponding file name (this
* is done because there is no way to store the simulation
* time inside the .pvtu or .vtu files).
* time inside the .pvtu or .vtu files). We store one list
* per particle world, because each particle world will
* have its own output directory and description file.
*/
std::vector<std::pair<double,std::string>> times_and_pvtu_file_names;
std::map<std::string,std::vector<std::pair<double,std::string>>> times_and_pvtu_file_names;

/**
* A corresponding variable that we use for the .visit files created
* by DataOutInterface::write_visit_record. The second part of a
* pair contains all files that together form a time step.
*/
std::vector<std::pair<double,std::vector<std::string>>> times_and_vtu_file_names;

/**
* A list of list of filenames, sorted by timestep, that correspond to
* what has been created as output. This is used to create a descriptive
* A map between particle world name and list of list of
* filenames that corresponds to
* what has been created as output. This list is sorted by
* filename and is used to create a descriptive
* .visit file for the entire simulation.
* We store one list per particle world, because each particle
* world will have its own output directory and description file.
*/
std::vector<std::vector<std::string>> output_file_names_by_timestep;
std::map<std::string,std::vector<std::vector<std::string>>> output_file_names_by_timestep;

/**
* A set of data related to XDMF file sections describing the HDF5
* heavy data files created. These contain things such as the
* dimensions and names of data written at all steps during the
* simulation.
* A map between particle world name and a list of data for
* the XDMF file sections describing the HDF5 files created.
* These XDMF data contain things such as the dimensions
* and names of data written at all steps during the simulation.
* We store one list per particle world, because each particle
* world will have its own output directory and description file.
*/
std::vector<XDMFEntry> xdmf_entries;
std::map<std::string,std::vector<XDMFEntry>> xdmf_entries;

/**
* VTU file output supports grouping files from several CPUs into one
Expand Down Expand Up @@ -305,11 +307,16 @@ namespace aspect
*
* @param data_out The DataOut object that was used to write the
* solutions.
* @param description_file_prefix The stem of the filename to be written.
* @param solution_file_directory The directory where the solution files
* are written.
* @param solution_file_prefix The stem of the filename to be written.
* @param filenames List of filenames for the current output from all
* processors.
*/
void write_description_files (const internal::ParticleOutput<dim> &data_out,
const std::string &description_file_prefix,
const std::string &solution_file_directory,
const std::string &solution_file_prefix,
const std::vector<std::string> &filenames);
};
Expand Down
2 changes: 1 addition & 1 deletion source/particle/world.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -755,7 +755,7 @@ namespace aspect
void
World<dim>::declare_parameters (ParameterHandler &prm)
{
constexpr unsigned int number_of_particle_worlds = 1;
constexpr unsigned int number_of_particle_worlds = ASPECT_MAX_NUM_PARTICLE_WORLDS;
for (unsigned int world_index = 0; world_index < number_of_particle_worlds; ++world_index)
{
if (world_index == 0)
Expand Down
111 changes: 59 additions & 52 deletions source/postprocess/particles.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -259,6 +259,8 @@ namespace aspect
template <int dim>
void
Particles<dim>::write_description_files (const internal::ParticleOutput<dim> &data_out,
const std::string &description_file_prefix,
const std::string &solution_file_directory,
const std::string &solution_file_prefix,
const std::vector<std::string> &filenames)
{
Expand All @@ -267,23 +269,23 @@ namespace aspect
this->get_time());
const std::string pvtu_filename = (solution_file_prefix +
".pvtu");
std::ofstream pvtu_file (this->get_output_directory() + "particles/" +
std::ofstream pvtu_file (this->get_output_directory() + solution_file_directory +
pvtu_filename);
data_out.write_pvtu_record (pvtu_file, filenames);

// now also generate a .pvd file that matches simulation
// time and corresponding .pvtu record
times_and_pvtu_file_names.emplace_back(time_in_years_or_seconds, "particles/"+pvtu_filename);
times_and_pvtu_file_names[description_file_prefix].emplace_back(time_in_years_or_seconds, solution_file_directory + pvtu_filename);

const std::string pvd_filename = (this->get_output_directory() + "particles.pvd");
const std::string pvd_filename = (this->get_output_directory() + description_file_prefix + ".pvd");
std::ofstream pvd_file (pvd_filename);

DataOutBase::write_pvd_record (pvd_file, times_and_pvtu_file_names);
DataOutBase::write_pvd_record (pvd_file, times_and_pvtu_file_names[description_file_prefix]);

// finally, do the same for VisIt via the .visit file for this
// time step, as well as for all time steps together
const std::string visit_filename = (this->get_output_directory()
+ "particles/"
+ solution_file_directory
+ solution_file_prefix
+ ".visit");
std::ofstream visit_file (visit_filename);
Expand All @@ -297,19 +299,19 @@ namespace aspect
filenames_with_path.reserve(filenames.size());
for (const auto &filename : filenames)
{
filenames_with_path.push_back("particles/" + filename);
filenames_with_path.push_back(solution_file_directory + filename);
}

output_file_names_by_timestep.push_back (filenames_with_path);
output_file_names_by_timestep[description_file_prefix].push_back (filenames_with_path);
}

std::ofstream global_visit_file (this->get_output_directory() +
"particles.visit");
description_file_prefix + ".visit");

std::vector<std::pair<double, std::vector<std::string>>> times_and_output_file_names;
for (unsigned int timestep=0; timestep<times_and_pvtu_file_names.size(); ++timestep)
times_and_output_file_names.emplace_back(times_and_pvtu_file_names[timestep].first,
output_file_names_by_timestep[timestep]);
for (unsigned int timestep=0; timestep<times_and_pvtu_file_names[description_file_prefix].size(); ++timestep)
times_and_output_file_names.emplace_back(times_and_pvtu_file_names[description_file_prefix][timestep].first,
output_file_names_by_timestep[description_file_prefix][timestep]);
DataOutBase::write_visit_record (global_visit_file, times_and_output_file_names);
}

Expand All @@ -330,54 +332,55 @@ namespace aspect
for (unsigned int particle_world = 0; particle_world < this->n_particle_worlds(); ++particle_world)
{
const Particle::World<dim> &world = this->get_particle_world(particle_world);
statistics.add_value("Number of advected particles",world.n_global_particles());

// If it's not time to generate an output file
// return early with the number of particles that were advected
if (this->get_time() < last_output_time + output_interval)
{
write_output = false;
if (particle_world > 0)
{
number_of_advected_particles += ", ";
}
number_of_advected_particles += Utilities::int_to_string(world.n_global_particles());
const std::string statistics_column_name = (particle_world == 0 ?
"Number of advected particles" :
"Number of advected particles (World " + Utilities::int_to_string(particle_world+1) + ")");

continue;
}
statistics.add_value(statistics_column_name,world.n_global_particles());

// If we do not write output
// return early with the number of particles that were advected
if (output_formats.size() == 0 || output_formats[0] == "none")
if (particle_world > 0)
{
// Up the next time we need output. This is relevant to correctly
// write output after a restart if the format is changed.
set_last_output_time (this->get_time());
number_of_advected_particles += ", ";
}
number_of_advected_particles += Utilities::int_to_string(world.n_global_particles());
}

write_output = false;
if (particle_world > 0)
{
number_of_advected_particles += ", ";
}
number_of_advected_particles += Utilities::int_to_string(world.n_global_particles());
// If it's not time to generate an output file
// return early with the number of particles that were advected
if (this->get_time() < last_output_time + output_interval)
{
write_output = false;
}

continue;
}
// If we do not write output
// return early with the number of particles that were advected
if (output_formats.size() == 0 || output_formats[0] == "none")
{
// Up the next time we need output. This is relevant to correctly
// write output after a restart if the format is changed.
set_last_output_time (this->get_time());

write_output = false;
}

Assert(write_output, ExcMessage("Trying to write output while it was set to not do so."));
if (write_output == false)
return std::make_pair("Number of advected particles", number_of_advected_particles);

if (output_file_number == numbers::invalid_unsigned_int)
output_file_number = 0;
else
++output_file_number;
if (output_file_number == numbers::invalid_unsigned_int)
output_file_number = 0;
else
++output_file_number;

for (unsigned int particle_world = 0; particle_world < this->n_particle_worlds(); ++particle_world)
{
const Particle::World<dim> &world = this->get_particle_world(particle_world);
std::string particles_output_base_name = "particles";
if (particle_world > 0)
{
particles_output_base_name += "-" + Utilities::int_to_string(particle_world+1);
}


// Create the particle output
const bool output_hdf5 = std::find(output_formats.begin(), output_formats.end(),"hdf5") != output_formats.end();
internal::ParticleOutput<dim> data_out;
Expand Down Expand Up @@ -415,8 +418,8 @@ namespace aspect
particle_file_name,
time_in_years_or_seconds,
this->get_mpi_communicator());
xdmf_entries.push_back(new_xdmf_entry);
data_out.write_xdmf_file(xdmf_entries, this->get_output_directory() + xdmf_filename,
xdmf_entries[particles_output_base_name].push_back(new_xdmf_entry);
data_out.write_xdmf_file(xdmf_entries[particles_output_base_name], this->get_output_directory() + xdmf_filename,
this->get_mpi_communicator());
}
else if (output_format == "vtu")
Expand All @@ -433,7 +436,11 @@ namespace aspect
filenames.push_back (particle_file_prefix
+ "." + Utilities::int_to_string(i, 4)
+ ".vtu");
write_description_files (data_out, particle_file_prefix, filenames);
write_description_files (data_out,
particles_output_base_name,
particles_output_base_name + "/",
particle_file_prefix,
filenames);
}

const unsigned int n_processes = Utilities::MPI::n_mpi_processes(this->get_mpi_communicator());
Expand Down Expand Up @@ -548,14 +555,14 @@ namespace aspect
screen_output = particle_output;

// record the file base file name in the output file
statistics.add_value ("Particle file name",
const std::string statistics_column_name = (particle_world == 0 ?
"Particle file name" :
"Particle file name (" + Utilities::int_to_string(particle_world+1) + ")");
statistics.add_value (statistics_column_name,
particle_output);
}

if (write_output)
return std::make_pair("Writing particle output:", screen_output);
else
return std::make_pair("Number of advected particles:", number_of_advected_particles);
return std::make_pair("Writing particle output:", screen_output);
}


Expand Down
2 changes: 1 addition & 1 deletion source/simulator/parameters.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -359,7 +359,7 @@ namespace aspect
"Name of the world builder file. If empty, the world builder is not initialized.");

prm.declare_entry ("Number of particle worlds", "1",
Patterns::Integer(0,1),
Patterns::Integer(0, ASPECT_MAX_NUM_PARTICLE_WORLDS),
"The number of particle worlds to be created. The maximum number of particle worlds "
"is set by the CMake variable `ASPECT_MAX_NUM_PARTICLE_WORLDS` and is by default 2.");

Expand Down
107 changes: 107 additions & 0 deletions tests/particle_multiple_worlds.prm
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Original file line number Diff line number Diff line change
@@ -0,0 +1,107 @@
# Test that we can activate multiple particle worlds with
# different particle properties and output directories.

# MPI: 2

set Dimension = 2
set End time = 70
set Use years in output instead of seconds = false
set Number of particle worlds = 2

subsection Geometry model
set Model name = box

subsection Box
set X extent = 0.9142
set Y extent = 1.0000
end
end

subsection Boundary velocity model
set Tangential velocity boundary indicators = left, right
set Zero velocity boundary indicators = bottom, top
end

subsection Material model
set Model name = simple

subsection Simple model
set Reference density = 1010
set Viscosity = 1e2
set Thermal expansion coefficient = 0
set Density differential for compositional field 1 = -10
end
end

subsection Gravity model
set Model name = vertical

subsection Vertical
set Magnitude = 10
end
end

subsection Initial temperature model
set Model name = function

subsection Function
set Function expression = 0
end
end

subsection Compositional fields
set Number of fields = 1
set Names of fields = anomaly
end

subsection Initial composition model
set Model name = function

subsection Function
set Variable names = x,z
set Function constants = pi=3.1415926
set Function expression = 0.5*(1+tanh((0.2+0.02*cos(pi*x/0.9142)-z)/0.02))
end
end

subsection Mesh refinement
set Initial adaptive refinement = 0
set Strategy = composition
set Initial global refinement = 4
set Time steps between mesh refinement = 0
end

subsection Postprocess
set List of postprocessors = velocity statistics, composition statistics, particles

subsection Particles
set Time between data output = 70
set Data output format = gnuplot
end
end

subsection Particles
set List of particle properties = initial composition

subsection Generator
subsection Probability density function
set Number of particles = 10
end
end
end

subsection Particles 2
set List of particle properties = function

subsection Function
set Variable names = x,z
set Function constants = pi=3.1415926
set Function expression = 0.5*(1+tanh((0.2+0.02*cos(pi*x/0.9142)-z)/0.02))
end

subsection Generator
subsection Probability density function
set Number of particles = 10
end
end
end
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