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Silo test utils changes to support specsets and matset xforms tweaks #1342

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Jan 9, 2025
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Silo test utils changes to support specsets and matset xforms tweaks #1342

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17 changes: 11 additions & 6 deletions src/libs/blueprint/conduit_blueprint_mesh_matset_xforms.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1554,7 +1554,6 @@ to_silo(const conduit::Node &specset,
CONDUIT_ERROR("blueprint::mesh::specset::to_silo passed matset node "
"must be a valid matset tree or a valid intermediate silo "
"representation of a matset.");
// TODO well, not entirely true...
}

// need to check if passed matset is already in the silo rep
Expand Down Expand Up @@ -1639,6 +1638,9 @@ to_silo(const conduit::Node &specset,
// to avoid writing unneeded data
// that could be expensive though

// The function silo_write_specset() in conduit_relay_io_silo.cpp
// depends on this being a float64. If we change this here,
// we must also change it there.
std::vector<float64> species_mf;

// need to iterate across all species for all materials at once
Expand Down Expand Up @@ -1696,12 +1698,15 @@ to_silo(const conduit::Node &specset,
// So if mat0 has 2 species and mat1 has 3 species, then
// the 1-index start of mat2 will be 2 + 3 + 1 = 6.

int sum = 1;
for (index_t i = 0; i < mat_index; i ++)
const int local_index = [&]()
{
sum += nmatspec[i];
}
const int &local_index = sum;
int sum = 1;
for (index_t i = 0; i < mat_index; i ++)
{
sum += nmatspec[i];
}
return sum;
}();

// we save the final index for this zone
return outer_index + local_index;
Expand Down
170 changes: 151 additions & 19 deletions src/tests/relay/silo_test_utils.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -75,13 +75,13 @@ silo_name_changer(const std::string &mmesh_name,
while(topo_itr.has_next())
{
Node &n_topo = topo_itr.next();
std::string topo_name = topo_itr.name();
std::string new_topo_name = mmesh_name + "_" + topo_name;
const std::string topo_name = topo_itr.name();
const std::string new_topo_name = mmesh_name + "_" + topo_name;

old_to_new_names[topo_name] = new_topo_name;

std::string coordset_name = n_topo["coordset"].as_string();
std::string new_coordset_name = mmesh_name + "_" + topo_name;
const std::string coordset_name = n_topo["coordset"].as_string();
const std::string new_coordset_name = mmesh_name + "_" + topo_name;

// change the coordset this topo refers to
save_mesh["topologies"][topo_name]["coordset"].reset();
Expand Down Expand Up @@ -124,9 +124,9 @@ silo_name_changer(const std::string &mmesh_name,
while (matset_itr.has_next())
{
Node &n_matset = matset_itr.next();
std::string matset_name = matset_itr.name();
const std::string matset_name = matset_itr.name();

std::string old_topo_name = n_matset["topology"].as_string();
const std::string old_topo_name = n_matset["topology"].as_string();

if (old_to_new_names.find(old_topo_name) == old_to_new_names.end())
{
Expand All @@ -135,14 +135,14 @@ silo_name_changer(const std::string &mmesh_name,
// But our job in this function is just to rename things, so we
// will just skip.
}
std::string new_topo_name = old_to_new_names[old_topo_name];
const std::string new_topo_name = old_to_new_names[old_topo_name];

// use new topo name
n_matset["topology"].reset();
n_matset["topology"] = new_topo_name;

// come up with new matset name
std::string new_matset_name = mmesh_name + "_" + matset_name;
const std::string new_matset_name = mmesh_name + "_" + matset_name;

old_to_new_names[matset_name] = new_matset_name;

Expand All @@ -151,38 +151,107 @@ silo_name_changer(const std::string &mmesh_name,
}
}

if (save_mesh.has_child("specsets"))
{
auto specset_itr = save_mesh["specsets"].children();
while (specset_itr.has_next())
{
Node &n_specset = specset_itr.next();
const std::string specset_name = specset_itr.name();

const std::string old_matset_name = n_specset["matset"].as_string();

if (old_to_new_names.find(old_matset_name) == old_to_new_names.end())
{
continue;
// If this is the case, we probably need to delete this specset.
// But our job in this function is just to rename things, so we
// will just skip.
}

// TODO I assume the specset is multi_buffer full
// we have no way to check for now
// and multi_buffer full is the only allowed specset variety
// later, we will need to add functionality here

const std::string &new_matset_name = old_to_new_names[old_matset_name];
const Node &n_matset = save_mesh["matsets"][new_matset_name];
const int num_zones = blueprint::mesh::matset::count_zones_from_matset(n_matset);
Node &matset_values = n_specset["matset_values"];

// we must modify the specset; see note below
for (int zone_id = 0; zone_id < num_zones; zone_id ++)
{
auto mat_itr = matset_values.children();
while (mat_itr.has_next())
{
Node &mat = mat_itr.next();
const std::string matname = mat_itr.name();
if (! blueprint::mesh::matset::is_material_in_zone(n_matset, matname, zone_id))
{
// if this material is not present in the zone, then we need
// to change the species mass fractions to all zero to pass
// the diff, since Silo read will set everything to zero
// for multi_buffer full.

auto spec_itr = mat.children();
while (spec_itr.has_next())
{
Node &spec = spec_itr.next();
const std::string specname = spec_itr.name();
float64_accessor mass_fractions = spec.value();
mass_fractions.set(zone_id, 0.0);
}
}
}
}

// use new matset name
n_specset["matset"].reset();
n_specset["matset"] = new_matset_name;

// come up with new specset name
const std::string new_specset_name = mmesh_name + "_" + specset_name;

old_to_new_names[specset_name] = new_specset_name;

// rename the specset
save_mesh["specsets"].rename_child(specset_name, new_specset_name);
}
}

if (save_mesh.has_child("fields"))
{
auto field_itr = save_mesh["fields"].children();
while (field_itr.has_next())
{
Node &n_field = field_itr.next();
std::string field_name = field_itr.name();
const std::string field_name = field_itr.name();

std::string old_topo_name = n_field["topology"].as_string();
const std::string old_topo_name = n_field["topology"].as_string();
if (old_to_new_names.find(old_topo_name) == old_to_new_names.end())
{
continue;
// If this is the case, we probably need to delete this field.
// But our job in this function is just to rename things, so we
// will just skip.
}
std::string new_topo_name = old_to_new_names[old_topo_name];
const std::string new_topo_name = old_to_new_names[old_topo_name];
// use new topo name
n_field["topology"].reset();
n_field["topology"] = new_topo_name;

if (n_field.has_child("matset"))
{
std::string old_matset_name = n_field["matset"].as_string();
const std::string old_matset_name = n_field["matset"].as_string();
if (old_to_new_names.find(old_matset_name) == old_to_new_names.end())
{
continue;
// If this is the case, we probably need to delete this field.
// But our job in this function is just to rename things, so we
// will just skip.
}
std::string new_matset_name = old_to_new_names[old_matset_name];
const std::string new_matset_name = old_to_new_names[old_matset_name];
// use new matset name
n_field["matset"].reset();
n_field["matset"] = new_matset_name;
Expand All @@ -204,7 +273,7 @@ silo_name_changer(const std::string &mmesh_name,
while (val_itr.has_next())
{
val_itr.next();
std::string comp_name = val_itr.name();
const std::string comp_name = val_itr.name();

// rename vector components
n_field["values"].rename_child(comp_name, std::to_string(child_index));
Expand Down Expand Up @@ -243,11 +312,10 @@ overlink_name_changer(conduit::Node &save_mesh)
// we assume 1 coordset and 1 topo
Node &coordsets = save_mesh["coordsets"];
Node &topologies = save_mesh["topologies"];


// we assume only 1 child for each
std::string coordset_name = coordsets.children().next().name();
std::string topo_name = topologies.children().next().name();
const std::string coordset_name = coordsets.children().next().name();
const std::string topo_name = topologies.children().next().name();

// add default labels if they don't exist already
if (! save_mesh["coordsets"][coordset_name].has_child("labels") &&
Expand Down Expand Up @@ -281,7 +349,7 @@ overlink_name_changer(conduit::Node &save_mesh)
{
// we assume 1 adjset
Node &n_adjset = save_mesh["adjsets"].children().next();
std::string adjset_name = n_adjset.name();
const std::string adjset_name = n_adjset.name();

// use new topo name
n_adjset["topology"].reset();
Expand All @@ -301,7 +369,7 @@ overlink_name_changer(conduit::Node &save_mesh)
// one per topo. But if you want the diff to pass for tests, you
// really can only have one. So we assume one.
Node &n_matset = save_mesh["matsets"].children().next();
std::string matset_name = n_matset.name();
const std::string matset_name = n_matset.name();

// use new topo name
n_matset["topology"].reset();
Expand All @@ -311,6 +379,69 @@ overlink_name_changer(conduit::Node &save_mesh)
save_mesh["matsets"].rename_child(matset_name, "MMATERIAL");
}

if (save_mesh.has_child("specsets"))
{
int species_id = 0;

auto specset_itr = save_mesh["specsets"].children();
while (specset_itr.has_next())
{
Node &n_specset = specset_itr.next();
const std::string specset_name = specset_itr.name();

// TODO I assume the specset is multi_buffer full
// we have no way to check for now
// and multi_buffer full is the only allowed specset variety
// later, we will need to add functionality here

const Node &n_matset = save_mesh["matsets"]["MMATERIAL"];
const int num_zones = blueprint::mesh::matset::count_zones_from_matset(n_matset);
Node &matset_values = n_specset["matset_values"];

// we must modify the specset; see note below
for (int zone_id = 0; zone_id < num_zones; zone_id ++)
{
auto mat_itr = matset_values.children();
while (mat_itr.has_next())
{
Node &mat = mat_itr.next();
const std::string matname = mat_itr.name();
if (! blueprint::mesh::matset::is_material_in_zone(n_matset, matname, zone_id))
{
// if this material is not present in the zone, then we need
// to change the species mass fractions to all zero to pass
// the diff, since Silo read will set everything to zero
// for multi_buffer full.

auto spec_itr = mat.children();
while (spec_itr.has_next())
{
Node &spec = spec_itr.next();
const std::string specname = spec_itr.name();
float64_accessor mass_fractions = spec.value();
mass_fractions.set(zone_id, 0.0);
}
}
}
}

// use new matset name
n_specset["matset"].reset();
n_specset["matset"] = "MMATERIAL";

// rename the specset
if (species_id == 0)
{
save_mesh["specsets"].rename_child(specset_name, "MSPECIES");
}
else
{
save_mesh["specsets"].rename_child(specset_name, "MSPECIES" + std::to_string(species_id));
}
species_id ++;
}
}

if (save_mesh.has_child("fields"))
{
auto field_itr = save_mesh["fields"].children();
Expand Down Expand Up @@ -388,6 +519,7 @@ add_matset_to_spiral(Node &n_mesh, const int ndomains)
//-----------------------------------------------------------------------------
void
vector_field_to_scalars_braid(Node &n_mesh, const std::string &dim)
// TODO generalize this approach so that it works for all fields as part of overlink_name_changer
{
Node &field_vel = n_mesh["fields"]["vel"];

Expand Down
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