commit 141b7e99d212888aa6e06f2f4a010c8c76daed4e
parent 4089a3c30c2eb68b0e7771196ebe50aa2b014574
Author: Vincent Forest <vincent.forest@meso-star.com>
Date: Mon, 9 Jan 2023 10:10:08 +0100
Merge branch 'release_0.0.1'
Diffstat:
27 files changed, 123 insertions(+), 58 deletions(-)
diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@ It also depends on the
[Astoria: Thermodynamic Properties](https://gitlab.com/meso-star/atrtp/),
[RSys](https://gitlab.com/vaplv/rsys/),
[Star-UnstructuredVolumetricMesh](https://gitlab.com/meso-star/star-uvm/),
-[Star-TetraHedra](https://gitlab.com/meso-star/star-tetrahedra/) libraries,
+[Star-Mesh](https://gitlab.com/meso-star/star-mesh/) libraries,
and on [OpenMP](https://www.openmp.org) 1.2 the parallelize its computations.
First ensure that CMake is installed on your system. Then install the RCMake
@@ -23,9 +23,22 @@ resulting project can be edited, built, tested and installed as any CMake
project. Refer to the [CMake documentation](https://cmake.org/documentation)
for further informations on CMake.
+## Release notes
+
+### Version 0.0.1
+
+- Relies on the Star-Mesh library rather than the obsolete Star-Tetrahedra
+ library.
+- Fix a possible memory leak.
+- Fix a wrong assertion.
+
+## Copyright
+
+Copyright (C) 2022, 2023 [|Méso|Star](http://www.meso-star.com) (<contact@meso-star.com>)
+Copyright (C) 2020, 2021 Centre National de la Recherche Scientifique (CNRS)
+
## License
-Copyright (C) 2020, 2021 Centre National de la Recherche Scientifique (CNRS).
AtrSTM is free software released under the GPL v3+ license: GNU GPL version 3
or later. You are welcome to redistribute it under certain conditions; refer to
the COPYING file for details.
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
@@ -1,3 +1,4 @@
+# Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
# Copyright (C) 2020, 2021 CNRS
#
# This program is free software: you can redistribute it and/or modify
@@ -28,7 +29,7 @@ find_package(AtrTP 0.0 REQUIRED)
find_package(OpenMP 1.2 REQUIRED)
find_package(RCMake 0.4 REQUIRED)
find_package(RSys 0.12 REQUIRED)
-find_package(StarTetraHedra 0.0 REQUIRED)
+find_package(StarMesh REQUIRED)
find_package(StarUVM 0.0 REQUIRED)
find_package(StarVX 0.2 REQUIRED)
find_package(RSIMD 0.3)
@@ -50,7 +51,7 @@ include_directories(
${AtrRI_INCLUDE_DIR}
${AtrTP_INCLUDE_DIR}
${RSys_INCLUDE_DIR}
- ${StarTetraHedra_INCLUDE_DIR}
+ ${StarMesh_INCLUDE_DIR}
${StarUVM_INCLUDE_DIR}
${StarVX_INCLUDE_DIR})
@@ -59,7 +60,7 @@ include_directories(
################################################################################
set(VERSION_MAJOR 0)
set(VERSION_MINOR 0)
-set(VERSION_PATCH 0)
+set(VERSION_PATCH 1)
set(VERSION ${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH})
set(ATRSTM_FILES_SRC
@@ -106,7 +107,7 @@ add_library(atrstm SHARED
${ATRSTM_FILES_SRC}
${ATRSTM_FILES_INC}
${ATRSTM_FILES_INC_API})
-target_link_libraries(atrstm AtrRI AtrTP RSys StarTetraHedra StarUVM StarVX m)
+target_link_libraries(atrstm AtrRI AtrTP RSys StarMesh StarUVM StarVX m)
# Setup SIMD support on the target
if(USE_SIMD)
diff --git a/src/atrstm.c b/src/atrstm.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm.h b/src/atrstm.h
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_c.h b/src/atrstm_c.h
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_cache.c b/src/atrstm_cache.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_cache.h b/src/atrstm_cache.h
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_dump_svx_octree.c b/src/atrstm_dump_svx_octree.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_log.c b/src/atrstm_log.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_log.h b/src/atrstm_log.h
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_partition.c b/src/atrstm_partition.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -88,6 +89,7 @@ pool_release(struct pool* pool)
LIST_FOR_EACH_SAFE(node, tmp_node, &pool->parts_full) {
struct part* part = CONTAINER_OF(node, struct part, node);
list_del(node);
+ part_release(part);
MEM_RM(pool->allocator, part);
}
ASSERT(is_list_empty(&pool->parts_full));
diff --git a/src/atrstm_partition.h b/src/atrstm_partition.h
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -20,7 +21,7 @@
#include <rsys/list.h>
#include <string.h>
-/* Definition of a partition along the 4 axis */
+/* Definition of a partition along the 3 axis */
#define LOG2_PARTITION_DEFINITION 5
#define PARTITION_DEFINITION BIT(LOG2_PARTITION_DEFINITION) /*32*/
#define PARTITION_NVOXELS \
diff --git a/src/atrstm_radcoefs.c b/src/atrstm_radcoefs.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_radcoefs.h b/src/atrstm_radcoefs.h
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_radcoefs_simd4.c b/src/atrstm_radcoefs_simd4.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_radcoefs_simd4.h b/src/atrstm_radcoefs_simd4.h
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_rdgfa.c b/src/atrstm_rdgfa.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_rdgfa.h b/src/atrstm_rdgfa.h
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_rdgfa_simd4.h b/src/atrstm_rdgfa_simd4.h
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_setup_octrees.c b/src/atrstm_setup_octrees.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -200,8 +201,8 @@ voxelize_partition
ivxl_upp[1] = (uint32_t)ceil((poly_upp[1] - part_low[1]) / vxsz[1]);
ivxl_upp[2] = (uint32_t)ceil((poly_upp[2] - part_low[2]) / vxsz[2]);
ASSERT(ivxl_upp[0] <= PARTITION_DEFINITION);
- ASSERT(ivxl_upp[0] <= PARTITION_DEFINITION);
- ASSERT(ivxl_upp[0] <= PARTITION_DEFINITION);
+ ASSERT(ivxl_upp[1] <= PARTITION_DEFINITION);
+ ASSERT(ivxl_upp[2] <= PARTITION_DEFINITION);
/* Iterate over the partition voxels intersected by the primitive AABB */
FOR_EACH(ivxl[2], ivxl_low[2], ivxl_upp[2]) {
diff --git a/src/atrstm_setup_octrees.h b/src/atrstm_setup_octrees.h
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_setup_uvm.c b/src/atrstm_setup_uvm.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -16,7 +17,7 @@
#include "atrstm_c.h"
#include "atrstm_log.h"
-#include <star/sth.h>
+#include <star/smsh.h>
#include <star/suvm.h>
#include <rsys/clock_time.h>
@@ -24,13 +25,34 @@
/*******************************************************************************
* Helper functions
******************************************************************************/
+static res_T
+check_smsh_desc(struct atrstm* atrstm, const struct smsh_desc* desc)
+{
+ res_T res = RES_OK;
+ ASSERT(atrstm && desc);
+
+ if(desc->dnode != 3 || desc->dcell != 4) {
+ log_err(atrstm,
+ "The mesh of a semi-transparent material must be a 3D tetrahedral mesh "
+ "(dimension of the mesh: %u; dimension of the vertices: %u)\n",
+ desc->dnode, desc->dcell);
+ res = RES_BAD_ARG;
+ goto error;
+ }
+
+exit:
+ return res;
+error:
+ goto exit;
+}
+
static INLINE void
tetrahedron_get_indices(const size_t itetra, size_t ids[4], void* ctx)
{
- const struct sth_desc* sth_desc = ctx;
+ const struct smsh_desc* smsh_desc = ctx;
const uint64_t* indices = NULL;
- ASSERT(ctx && ids && itetra < sth_desc->ntetrahedra);
- indices = sth_desc_get_tetrahedron_indices(sth_desc, itetra);
+ ASSERT(ctx && ids && itetra < smsh_desc->ncells && smsh_desc->dcell == 4);
+ indices = smsh_desc_get_cell(smsh_desc, itetra);
ids[0] = (size_t)indices[0];
ids[1] = (size_t)indices[1];
ids[2] = (size_t)indices[2];
@@ -40,10 +62,10 @@ tetrahedron_get_indices(const size_t itetra, size_t ids[4], void* ctx)
static INLINE void
vertex_get_position(const size_t ivert, double pos[3], void* ctx)
{
- struct sth_desc* sth_desc = ctx;
+ struct smsh_desc* smsh_desc = ctx;
const double* position = NULL;
- ASSERT(ctx && pos && ivert < sth_desc->nvertices);
- position = sth_desc_get_vertex_position(sth_desc, ivert);
+ ASSERT(ctx && pos && ivert < smsh_desc->nnodes && smsh_desc->dnode == 3);
+ position = smsh_desc_get_node(smsh_desc, ivert);
pos[0] = position[0];
pos[1] = position[1];
pos[2] = position[2];
@@ -56,40 +78,46 @@ res_T
setup_unstructured_volumetric_mesh
(struct atrstm* atrstm,
const int precompute_normals,
- const char* sth_filename,
+ const char* smsh_filename,
struct suvm_volume** out_volume)
{
struct suvm_tetrahedral_mesh_args mesh_args = SUVM_TETRAHEDRAL_MESH_ARGS_NULL;
- struct sth_desc sth_desc = STH_DESC_NULL;
- struct sth* sth = NULL;
+ struct smsh_create_args args = SMSH_CREATE_ARGS_DEFAULT;
+ struct smsh_desc smsh_desc = SMSH_DESC_NULL;
+ struct smsh* smsh = NULL;
struct suvm_volume* volume = NULL;
struct time t0, t1;
char buf[128];
res_T res = RES_OK;
- ASSERT(atrstm && sth_filename && out_volume);
+ ASSERT(atrstm && smsh_filename && out_volume);
log_info(atrstm, "Load and structure the volumetric mesh '%s'.\n",
- sth_filename);
+ smsh_filename);
time_current(&t0);
/* Load the volumetric mesh */
- res = sth_create(atrstm->logger, atrstm->allocator, atrstm->verbose, &sth);
+ args.logger = atrstm->logger;
+ args.allocator = atrstm->allocator;
+ args.verbose = atrstm->verbose;
+ res = smsh_create(&args, &smsh);
+ if(res != RES_OK) goto error;
+ res = smsh_load(smsh, smsh_filename);
if(res != RES_OK) goto error;
- res = sth_load(sth, sth_filename);
+ res = smsh_get_desc(smsh, &smsh_desc);
if(res != RES_OK) goto error;
- res = sth_get_desc(sth, &sth_desc);
+ res = check_smsh_desc(atrstm, &smsh_desc);
if(res != RES_OK) goto error;
/* Partition the unstructured volumetric mesh */
- mesh_args.ntetrahedra = sth_desc.ntetrahedra;
- mesh_args.nvertices = sth_desc.nvertices;
+ mesh_args.ntetrahedra = smsh_desc.ncells;
+ mesh_args.nvertices = smsh_desc.nnodes;
mesh_args.get_indices = tetrahedron_get_indices;
mesh_args.get_position = vertex_get_position;
mesh_args.tetrahedron_data = SUVM_DATA_NULL; /* Tetra data are not in SUVM */
mesh_args.vertex_data = SUVM_DATA_NULL; /* Vertex data are not in SUVM */
mesh_args.precompute_normals = precompute_normals;
- mesh_args.context = &sth_desc;
+ mesh_args.context = &smsh_desc;
res = suvm_tetrahedral_mesh_create(atrstm->suvm, &mesh_args, &volume);
if(res != RES_OK) goto error;
@@ -100,7 +128,7 @@ setup_unstructured_volumetric_mesh
exit:
*out_volume = volume;
- if(sth) STH(ref_put(sth));
+ if(smsh) SMSH(ref_put(smsh));
return res;
error:
if(volume) {
@@ -109,4 +137,3 @@ error:
}
goto exit;
}
-
diff --git a/src/atrstm_svx.c b/src/atrstm_svx.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/atrstm_svx.h b/src/atrstm_svx.h
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -23,7 +24,7 @@
*
* For each SVX voxel, the data of the optical property are stored
* linearly as N single precision floating point data, with N computed as
- * bellow:
+ * below:
*
* N = ATRSTM_RADCOEFS_COUNT__ #optical properties per voxel
* * ATRSTM_SVX_OPS_COUNT__ #supported operations on each properties
@@ -34,7 +35,7 @@
* C' according to the operation `enum atrstm_svx_op O' is
* then computed as bellow:
*
- * id = C * NFLOATS_PER_CPNT + P * HTSKY_SVX_OPS_COUNT__ + O;
+ * id = C * NFLOATS_PER_CPNT + P * ATRSTM_SVX_OPS_COUNT__ + O;
* NFLOATS_PER_CPNT = ATRSTM_SVX_OPS_COUNT__ * ATRSTM_RADCOEFS_COUNT__;
*/
diff --git a/src/test_atrstm.c b/src/test_atrstm.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -82,14 +83,13 @@ print_help(const char* cmd)
" along the 3 axis. Its default value is [%u, %u, %u].\n",
SPLIT3(ATRSTM_ARGS_DEFAULT.grid_max_definition));
printf(
-" -v make the program verobse.\n");
+" -v make the program verbose.\n");
printf(
" -w WAVELENGTH shortwave wavelength to use, in nanometer.\n"
" By default it is set to %g nm\n",
ATRSTM_ARGS_DEFAULT.wlen_range[0]);
printf("\n");
printf(
-"Copyright (C) 2020, 2021 CNRS.\n"
"This is free software released under the GNU GPL license, version 3 or\n"
"later. You are free to change or redistribute it under certain\n"
"conditions <http://gnu.org.licenses/gpl.html>\n");
diff --git a/src/test_atrstm_radcoefs.c b/src/test_atrstm_radcoefs.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
diff --git a/src/test_atrstm_radcoefs_simd.c b/src/test_atrstm_radcoefs_simd.c
@@ -1,4 +1,5 @@
-/* Copyright (C) 2020, 2021 CNRS
+/* Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2020, 2021 CNRS
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
