From ceaf98e8f6a553020cbf05f18a422cd3b6723a39 Mon Sep 17 00:00:00 2001
From: Nils-Arne Dreier <dreier@dkrz.de>
Date: Fri, 6 Sep 2024 10:54:57 +0200
Subject: [PATCH] refactor: build 2d_domain in separate file
---
src/2d_domain.cpp | 75 +++++++++++++++++++++++++++++++++++++++
src/CMakeLists.txt | 2 +-
src/catalyst_adapter.cpp | 76 +++-------------------------------------
3 files changed, 80 insertions(+), 73 deletions(-)
create mode 100644 src/2d_domain.cpp
diff --git a/src/2d_domain.cpp b/src/2d_domain.cpp
new file mode 100644
index 0000000..8649b7e
--- /dev/null
+++ b/src/2d_domain.cpp
@@ -0,0 +1,75 @@
+#include <comin.h>
+#include <catalyst.hpp>
+
+conduit_cpp::Node catalyst_adapter_2d_domain(int jg){
+ conduit_cpp::Node channel;
+ // now, create the mesh.
+ channel["type"] = "mesh";
+
+ double *vlon, *vlat;
+ int nverts = comin_descrdata_get_domain_verts_nverts(jg);
+ int nverts_arr[2];
+ comin_descrdata_get_domain_verts_vlon(jg, &vlon, nverts_arr);
+ comin_descrdata_get_domain_verts_vlat(jg, &vlat, nverts_arr);
+ channel["data/coordsets/coords/type"] = "explicit";
+ channel["data/coordsets/coords/values/x"].set_external(vlon, nverts);
+ channel["data/coordsets/coords/values/y"].set_external(vlat, nverts);
+ channel["data/coordsets/coords/values/z"].set(std::vector<double>(nverts, 1.0));
+
+ channel["data/topologies/mesh/type"] = "unstructured";
+ channel["data/topologies/mesh/coordset"] = "coords";
+ channel["data/topologies/mesh/elements/shape"] = "tri";
+
+ int* vertex_idx = NULL;
+ int* vertex_blk = NULL;
+ int vertex_idx_size[3];
+ int ncells = comin_descrdata_get_domain_cells_ncells(jg);
+ comin_descrdata_get_domain_cells_vertex_idx(jg, &vertex_idx, vertex_idx_size);
+ comin_descrdata_get_domain_cells_vertex_blk(jg, &vertex_blk, vertex_idx_size);
+ int offset = vertex_idx_size[0]*vertex_idx_size[1];
+ std::vector<int> vidx(3*ncells);
+ for(int c=0; c<ncells; ++c){
+ vidx[3*c+0] = (vertex_idx[c+0*offset] - 1) + nverts_arr[0]*(vertex_blk[c+0*offset] - 1);
+ vidx[3*c+1] = (vertex_idx[c+1*offset] - 1) + nverts_arr[0]*(vertex_blk[c+1*offset] - 1);
+ vidx[3*c+2] = (vertex_idx[c+2*offset] - 1) + nverts_arr[0]*(vertex_blk[c+2*offset] - 1);
+ }
+ channel["data/topologies/mesh/elements/connectivity"].set(vidx);
+
+ // add all 2d variables
+ for(void* it = comin_var_get_descr_list_head();
+ it != nullptr;
+ it = comin_var_get_descr_list_next(it)){
+ t_comin_var_descriptor var_desc;
+ comin_var_get_descr_list_var_desc(it, &var_desc);
+ int zaxis_id = -1;
+ comin_metadata_get_integer(var_desc, "zaxis_id", &zaxis_id);
+ if(var_desc.id == jg &&
+ zaxis_id == COMIN_ZAXIS_2D){
+ channel["data/fields/" + std::string(var_desc.name) + "/association"] = "element";
+ channel["data/fields/" + std::string(var_desc.name) + "/topology"] = "mesh";
+ channel["data/fields/" + std::string(var_desc.name) + "/volume_dependend"] = false;
+ int ep = EP_ATM_WRITE_OUTPUT_BEFORE;
+ void* handle = comin_var_get(1, &ep, var_desc, COMIN_FLAG_READ);
+ channel["data/fields/" + std::string(var_desc.name) + "/values"]
+ .set_external(comin_var_get_ptr(handle), ncells);
+ }
+ }
+
+ // add some special fields
+ channel["data/fields/mpi_rank/association"] = "element";
+ channel["data/fields/mpi_rank/topology"] = "mesh";
+ channel["data/fields/mpi_rank/volume_dependend"] = false;
+ channel["data/fields/mpi_rank/values"]
+ .set(std::vector<int>(ncells, comin_parallel_get_host_mpi_rank()));
+
+ channel["data/fields/decomp_domain/association"] = "element";
+ channel["data/fields/decomp_domain/topology"] = "mesh";
+ channel["data/fields/decomp_domain/volume_dependend"] = false;
+ int* decomp_domain_ptr = nullptr;
+ int arr_size2[2];
+ comin_descrdata_get_domain_cells_decomp_domain(jg, &decomp_domain_ptr, arr_size2);
+ channel["data/fields/decomp_domain/values"]
+ .set_external(decomp_domain_ptr, ncells);
+
+ return channel;
+}
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c1ce8c3..4bad5b4 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,2 +1,2 @@
-add_library(catalyst_adapter MODULE catalyst_adapter.cpp)
+add_library(catalyst_adapter MODULE catalyst_adapter.cpp 2d_domain.cpp)
target_link_libraries(catalyst_adapter PRIVATE ComIn::ComIn catalyst::catalyst)
diff --git a/src/catalyst_adapter.cpp b/src/catalyst_adapter.cpp
index 0dd235d..3b1cc15 100644
--- a/src/catalyst_adapter.cpp
+++ b/src/catalyst_adapter.cpp
@@ -8,6 +8,7 @@
void catalyst_adapter_secondary_constructor();
void catalyst_adapter_execute();
void catalyst_adapter_destruct();
+conduit_cpp::Node catalyst_adapter_2d_domain(int jg);
static conduit_cpp::Node catalyst_exec_params;
@@ -40,80 +41,11 @@ extern "C"{ // avoid name-mangling
}
void catalyst_adapter_secondary_constructor(){
-
// prepare the execute node
for(int jg = 1; jg<=comin_descrdata_get_global_n_dom(); ++jg){
- std::cout << "dom: " << jg << std::endl;
- auto channel = catalyst_exec_params[std::string("catalyst/channels/2d_domain")+std::to_string(jg)];
- // now, create the mesh.
- channel["type"] = "mesh";
-
-
- double *vlon, *vlat;
- int nverts = comin_descrdata_get_domain_verts_nverts(jg);
- int nverts_arr[2];
- comin_descrdata_get_domain_verts_vlon(jg, &vlon, nverts_arr);
- comin_descrdata_get_domain_verts_vlat(jg, &vlat, nverts_arr);
- channel["data/coordsets/coords/type"] = "explicit";
- channel["data/coordsets/coords/values/x"].set_external(vlon, nverts);
- channel["data/coordsets/coords/values/y"].set_external(vlat, nverts);
- channel["data/coordsets/coords/values/z"].set(std::vector<double>(nverts, 1.0));
-
- channel["data/topologies/mesh/type"] = "unstructured";
- channel["data/topologies/mesh/coordset"] = "coords";
- channel["data/topologies/mesh/elements/shape"] = "tri";
-
- int* vertex_idx = NULL;
- int* vertex_blk = NULL;
- int vertex_idx_size[3];
- int ncells = comin_descrdata_get_domain_cells_ncells(jg);
- comin_descrdata_get_domain_cells_vertex_idx(jg, &vertex_idx, vertex_idx_size);
- comin_descrdata_get_domain_cells_vertex_blk(jg, &vertex_blk, vertex_idx_size);
- int offset = vertex_idx_size[0]*vertex_idx_size[1];
- std::vector<int> vidx(3*ncells);
- for(int c=0; c<ncells; ++c){
- vidx[3*c+0] = (vertex_idx[c+0*offset] - 1) + nverts_arr[0]*(vertex_blk[c+0*offset] - 1);
- vidx[3*c+1] = (vertex_idx[c+1*offset] - 1) + nverts_arr[0]*(vertex_blk[c+1*offset] - 1);
- vidx[3*c+2] = (vertex_idx[c+2*offset] - 1) + nverts_arr[0]*(vertex_blk[c+2*offset] - 1);
- }
- channel["data/topologies/mesh/elements/connectivity"].set(vidx);
-
- // add all 2d variables
- for(void* it = comin_var_get_descr_list_head();
- it != nullptr;
- it = comin_var_get_descr_list_next(it)){
- t_comin_var_descriptor var_desc;
- comin_var_get_descr_list_var_desc(it, &var_desc);
- int zaxis_id = -1;
- comin_metadata_get_integer(var_desc, "zaxis_id", &zaxis_id);
- if(var_desc.id == jg &&
- zaxis_id == COMIN_ZAXIS_2D){
- // TODO split tracers in separate arrays
- channel["data/fields/" + std::string(var_desc.name) + "/association"] = "element";
- channel["data/fields/" + std::string(var_desc.name) + "/topology"] = "mesh";
- channel["data/fields/" + std::string(var_desc.name) + "/volume_dependend"] = false;
- int ep = EP_ATM_WRITE_OUTPUT_BEFORE;
- void* handle = comin_var_get(1, &ep, var_desc, COMIN_FLAG_READ);
- channel["data/fields/" + std::string(var_desc.name) + "/values"]
- .set_external(comin_var_get_ptr(handle), ncells);
- }
- }
-
- // add some special fields
- channel["data/fields/mpi_rank/association"] = "element";
- channel["data/fields/mpi_rank/topology"] = "mesh";
- channel["data/fields/mpi_rank/volume_dependend"] = false;
- channel["data/fields/mpi_rank/values"]
- .set(std::vector<int>(ncells, comin_parallel_get_host_mpi_rank()));
-
- channel["data/fields/decomp_domain/association"] = "element";
- channel["data/fields/decomp_domain/topology"] = "mesh";
- channel["data/fields/decomp_domain/volume_dependend"] = false;
- int* decomp_domain_ptr = nullptr;
- int arr_size2[2];
- comin_descrdata_get_domain_cells_decomp_domain(jg, &decomp_domain_ptr, arr_size2);
- channel["data/fields/decomp_domain/values"]
- .set_external(decomp_domain_ptr, ncells);
+ auto domain_node = catalyst_adapter_2d_domain(jg);
+ catalyst_exec_params[std::string("catalyst/channels/2d_domain")+std::to_string(jg)] =
+ domain_node;
}
}
--
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