commit 01d9b2bc03acc75ff351ed791d925456fc5f30ff
parent 00a6a570df5a6e9bd235c17ae4bda0dd17f30051
Author: Vincent Forest <vincent.forest@meso-star.com>
Date: Tue, 31 Oct 2023 12:56:05 +0100
Merge branch 'release_0.1'
Diffstat:
19 files changed, 674 insertions(+), 375 deletions(-)
diff --git a/.gitignore b/.gitignore
@@ -1,12 +1,12 @@
.gitignore
-CMakeCache.txt
-CMakeFiles
-Makefile
-tmp
[Bb]uild*
*.sw[po]
-*.[ao]
-*.orig
+*.[aod]
+*.so
*~
+test*
+!test*.[ch]
+.config
+.test
tags
-
+*.pc
diff --git a/Makefile b/Makefile
@@ -0,0 +1,193 @@
+# Copyright (C) 2022, 2023 Centre National de la Recherche Scientifique
+# Copyright (C) 2022, 2023 Institut Pierre-Simon Laplace
+# Copyright (C) 2022, 2023 Institut de Physique du Globe de Paris
+# Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+# Copyright (C) 2022, 2023 Observatoire de Paris
+# Copyright (C) 2022, 2023 Université de Reims Champagne-Ardenne
+# Copyright (C) 2022, 2023 Université de Versaille Saint-Quentin
+# Copyright (C) 2022, 2023 Université Paul Sabatier
+#
+# 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
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+.POSIX:
+.SUFFIXES: # Clean up default inference rules
+
+include config.mk
+
+LIBNAME_STATIC = librnatm.a
+LIBNAME_SHARED = librnatm.so
+LIBNAME = $(LIBNAME_$(LIB_TYPE))
+
+################################################################################
+# Library building
+################################################################################
+SRC =\
+ src/rnatm.c\
+ src/rnatm_log.c\
+ src/rnatm_mesh.c\
+ src/rnatm_octree.c\
+ src/rnatm_octrees_storage.c\
+ src/rnatm_properties.c\
+ src/rnatm_radcoef.c\
+ src/rnatm_voxel_partition.c\
+ src/rnatm_write_vtk.c
+OBJ = $(SRC:.c=.o)
+DEP = $(SRC:.c=.d)
+
+build_library: .config $(DEP)
+ @$(MAKE) -fMakefile $$(for i in $(DEP); do echo -f $${i}; done) \
+ $$(if [ -n "$(LIBNAME)" ]; then \
+ echo "$(LIBNAME)"; \
+ else \
+ echo "$(LIBNAME_SHARED)"; \
+ fi)
+
+$(DEP) $(OBJ): config.mk
+
+$(LIBNAME_SHARED): $(OBJ)
+ $(CC) $(CFLAGS_SO) $(DPDC_CFLAGS) -o $@ $(OBJ) $(LDFLAGS_SO) $(DPDC_LIBS)
+
+$(LIBNAME_STATIC): librnatm.o
+ $(AR) -rc $@ $?
+ $(RANLIB) $@
+
+librnatm.o: $(OBJ)
+ $(LD) -r $(OBJ) -o $@
+ $(OBJCOPY) $(OCPFLAGS) $@
+
+.config: config.mk
+ @if ! $(PKG_CONFIG) --atleast-version $(RNSF_VERSION) rnsf; then \
+ echo "rnsf $(RNSF_VERSION) not found" >&2; exit 1; fi
+ @if ! $(PKG_CONFIG) --atleast-version $(RNSL_VERSION) rnsl; then \
+ echo "rnsl $(RNSL_VERSION) not found" >&2; exit 1; fi
+ @if ! $(PKG_CONFIG) --atleast-version $(RSYS_VERSION) rsys; then \
+ echo "rsys $(RSYS_VERSION) not found" >&2; exit 1; fi
+ @if ! $(PKG_CONFIG) --atleast-version $(SARS_VERSION) sars; then \
+ echo "sars $(SARS_VERSION) not found" >&2; exit 1; fi
+ @if ! $(PKG_CONFIG) --atleast-version $(SBUF_VERSION) sbuf; then \
+ echo "sbuf $(SBUF_VERSION) not found" >&2; exit 1; fi
+ @if ! $(PKG_CONFIG) --atleast-version $(SCK_VERSION) sck; then \
+ echo "sck $(SCK_VERSION) not found" >&2; exit 1; fi
+ @if ! $(PKG_CONFIG) --atleast-version $(SMSH_VERSION) smsh; then \
+ echo "smsh $(SMSH_VERSION) not found" >&2; exit 1; fi
+ @if ! $(PKG_CONFIG) --atleast-version $(SSF_VERSION) ssf; then \
+ echo "ssf $(SSF_VERSION) not found" >&2; exit 1; fi
+ @if ! $(PKG_CONFIG) --atleast-version $(SUVM_VERSION) suvm; then \
+ echo "suvm $(SUVM_VERSION) not found" >&2; exit 1; fi
+ @if ! $(PKG_CONFIG) --atleast-version $(SVX_VERSION) svx; then \
+ echo "svx $(SVX_VERSION) not found" >&2; exit 1; fi
+ @echo "config done" > $@
+
+.SUFFIXES: .c .d .o
+.c.d:
+ @$(CC) $(CFLAGS_SO) $(DPDC_CFLAGS) -MM -MT "$(@:.d=.o) $@" $< -MF $@
+
+.c.o:
+ $(CC) $(CFLAGS_SO) $(DPDC_CFLAGS) -DRNATM_SHARED_BUILD -c $< -o $@
+
+################################################################################
+# Installation
+################################################################################
+pkg:
+ sed -e 's#@PREFIX@#$(PREFIX)#g'\
+ -e 's#@VERSION@#$(VERSION)#g'\
+ -e 's#@RNSF_VERSION@#$(RNSF_VERSION)#g'\
+ -e 's#@RNSL_VERSION@#$(RNSL_VERSION)#g'\
+ -e 's#@RSYS_VERSION@#$(RSYS_VERSION)#g'\
+ -e 's#@SARS_VERSION@#$(SARS_VERSION)#g'\
+ -e 's#@SBUF_VERSION@#$(SBUF_VERSION)#g'\
+ -e 's#@SCK_VERSION@#$(SCK_VERSION)#g'\
+ -e 's#@SMSH_VERSION@#$(SMSH_VERSION)#g'\
+ -e 's#@SSF_VERSION@#$(SSF_VERSION)#g'\
+ -e 's#@SUVM_VERSION@#$(SUVM_VERSION)#g'\
+ -e 's#@SVX_VERSION@#$(SVX_VERSION)#g'\
+ rnatm.pc.in > rnatm.pc
+
+rnatm-local.pc: rnatm.pc.in
+ sed -e '1d'\
+ -e 's#^includedir=.*#includedir=./src/#'\
+ -e 's#^libdir=.*#libdir=./#'\
+ -e 's#@VERSION@#$(VERSION)#g'\
+ -e 's#@RNSF_VERSION@#$(RNSF_VERSION)#g'\
+ -e 's#@RNSL_VERSION@#$(RNSL_VERSION)#g'\
+ -e 's#@RSYS_VERSION@#$(RSYS_VERSION)#g'\
+ -e 's#@SARS_VERSION@#$(SARS_VERSION)#g'\
+ -e 's#@SBUF_VERSION@#$(SBUF_VERSION)#g'\
+ -e 's#@SCK_VERSION@#$(SCK_VERSION)#g'\
+ -e 's#@SMSH_VERSION@#$(SMSH_VERSION)#g'\
+ -e 's#@SSF_VERSION@#$(SSF_VERSION)#g'\
+ -e 's#@SUVM_VERSION@#$(SUVM_VERSION)#g'\
+ -e 's#@SVX_VERSION@#$(SVX_VERSION)#g'\
+ rnatm.pc.in > $@
+
+install: build_library pkg
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/lib" $(LIBNAME)
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/lib/pkgconfig" rnatm.pc
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/include/rad-net" src/rnatm.h
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/share/doc/rnatm" COPYING README.md
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/share/man/man5" rngt.5 rnpfi.5
+
+uninstall:
+ rm -f "$(DESTDIR)$(PREFIX)/lib/$(LIBNAME)"
+ rm -f "$(DESTDIR)$(PREFIX)/lib/pkgconfig/rnatm.pc"
+ rm -f "$(DESTDIR)$(PREFIX)/share/doc/rnatm/COPYING"
+ rm -f "$(DESTDIR)$(PREFIX)/share/doc/rnatm/README.md"
+ rm -f "$(DESTDIR)$(PREFIX)/include/rad-net/rnatm.h"
+ rm -f "$(DESTDIR)$(PREFIX)/share/man/man5/rngt.5"
+ rm -f "$(DESTDIR)$(PREFIX)/share/man/man5/rnpfi.5"
+
+################################################################################
+# Miscellaneous targets
+################################################################################
+all: build_library build_tests
+
+clean: clean_test
+ rm -f $(OBJ) $(LIBNAME)
+ rm -f .config librnatm.o rnatm.pc rnatm-local.pc
+
+distclean: clean
+ rm -f $(DEP) src/test_rnatm.d
+
+lint:
+ shellcheck -o all make.sh
+ mandoc -Tlint -Wall rngt.5 || [ $$? -le 1 ]
+ mandoc -Tlint -Wall rnpfi.5 || [ $$? -le 1 ]
+
+################################################################################
+# Tests
+################################################################################
+TEST_SRC = src/test_rnatm.c
+TEST_OBJ = $(TEST_SRC:.c=.o)
+TEST_DEP = $(TEST_SRC:.c=.d)
+
+PKG_CONFIG_LOCAL = PKG_CONFIG_PATH="./:$${PKG_CONFIG_PATH}" $(PKG_CONFIG)
+RNATM_CFLAGS = $$($(PKG_CONFIG_LOCAL) $(PCFLAGS) --cflags rnatm-local.pc)
+RNATM_LIBS = $$($(PKG_CONFIG_LOCAL) $(PCFLAGS) --libs rnatm-local.pc)
+
+build_tests: build_library src/test_rnatm.d
+ @$(MAKE) -fMakefile -f src/test_rnatm.d test_rnatm
+
+clean_test:
+ rm -f test_rnatm src/test_rnatm.o
+
+$(TEST_DEP): config.mk rnatm-local.pc
+ @$(CC) $(CFLAGS_EXE) $(RNATM_CFLAGS) $(RSYS_CFLAGS) \
+ -MM -MT "$(@:.d=.o) $@" $(@:.d=.c) -MF $@
+
+src/test_rnatm.o: config.mk rnatm-local.pc
+ $(CC) $(CFLAGS_EXE) $(RNATM_CFLAGS) $(RSYS_CFLAGS) -c $(@:.o=.c) -o $@
+
+test_rnatm: src/test_rnatm.o config.mk rnatm-local.pc $(LIBNAME)
+ $(CC) $(CFLAGS_EXE) $(RNATM_CFLAGS) $(RSYS_CFLAGS) -o $@ src/$@.o \
+ $(LDFLAGS_EXE) $(RNATM_LIBS) $(RSYS_LIBS)
diff --git a/README.md b/README.md
@@ -1,65 +1,69 @@
# Rad-Net ATMosphere
-This C library loads and manages data from atmosphere. The gas volumetric mesh
-is described by a [Star-Mesh](https://gitlab.com/meso-star/star-mesh) file
-while its radiative properties are stored in a
-[Star-CorrelatedK](https://gitlab.com/meso-star/star-ck) file. Its temperature
-is recorded per node in a
-[Star-Buffer](https://gitla.com/meso-star/star-buffer) file. Aerosol volumetric
-meshes are also Star-Mesh geometries and their radiative properties are stored
-in [Star-Aerosol](https://gitlab.com/meso-star/star-aerosol) files. The
-properties of the phase functions are finally listed in files following the
-[Rad-Net Scattering Function](https://gitlab.com/meso-star/rnsf) file format.
-
-## How to build
-
-This library is compatible with 64-bits POSIX systems. It relies the
-[CMake](http://www.cmake.org) and the
-[RCMake](https://gitlab.com/vaplv/rcmake/) packages to build. It also depends
-on the [Rad-Net Scattering Function](https://gitlab.com/meso-star/rnsf),
-[RNSL](https://gitlab.com/meso-star/rnsl),
-[RSys](https://gitlab.com/vaplv/rsys/),
-[Star-Aerosol](https://gitlab.com/meso-star/star-aerosol),
-[Star-Buffer](https://gitlab.com/meso-star/star-buffer),
-[Star-CorrelatedK](https://gitlab.com/meso-star/star-ck),
-[Star-Mesh](https://gitlab.com/meso-star/star-mesh),
-[Star-ScatteringFunctions](https://gitlab.com/meso-star/star-sf),
-[Star-UnstructuredVolumetricMesh](https://gitlab.com/meso-star/star-uvm),
-[Star-VoXel](https://gitlab.com/meso-star/star-vx)
-libraries, and on [OpenMP](https://www.openmp.org) 1.2 to parallelize its
-computations. It optionally depends on [scdoc](https://sr.ht/~sircmpwn/scdoc/)
-which, if available, is used to generate the man pages.
-
-First ensure that CMake is installed on your system. Then install the RCMake
-package as well as the aforementioned prerequisites. Finally generate the
-project from the `cmake/CMakeLists.txt` file by appending to the
-`CMAKE_PREFIX_PATH` variable the install directories of its dependencies. The
-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.
+This C library loads and manages data describing an atmosphere.
+
+## Requirements
+
+- C compiler with OpenMP support
+- POSIX make
+- pkg-config
+- [Rad-Net Scattering Functions](https://gitlab.com/meso-star/rnsf)
+- [Rad-Net String List](https://gitlab.com/meso-star/rnsl)
+- [RSys](https://gitlab.com/vaplv/rsys)
+- [Star AeRoSol](https://gitlab.com/meso-star/star-aerosol)
+- [Star Buffer](https://gitlab.com/meso-star/star-buffer)
+- [Star CorrelatedK](https://gitlab.com/meso-star/star-ck)
+- [Star Mesh](https://gitlab.com/meso-star/star-mesh)
+- [Star Scattering Functions](https://gitlab.com/meso-star/star-sf)
+- [Star Unstructured Volumetric Mesh](https://gitlab.com/meso-star/star-uvm)
+- [Star VoXel](https://gitlab.com/meso-star/star-vx)
+
+## Installation
+
+Edit config.mk as needed, then run:
+
+ make clean install
## Release notes
+### Version 0.1
+
+- Fix voxelization deadlock.
+- Fix of a bug when calculating the octree definition: the definition
+ should be equal to 0, which would result in an error.
+- Fix the calculation of radiative coefficients. They were erroneous
+ when the gas band overlapped several aerosol bands: the aerosol
+ average was wrongly reduced to the integration domain.
+- Write the man pages directly in mdoc's roff macros, instead of using
+ the scdoc markup language as a source for man pages.
+- Replace CMake by Makefile as build system.
+- Update compiler and linker flags to increase the security and
+ robustness of generated binaries.
+- Provide a pkg-config file to link the library as an external
+ dependency.
+
### Version 0.0.1
-Fix several bugs when volumetric meshes of the components are not identical:
+Fix several bugs when volumetric meshes of the components are not
+identical:
- Fix the `rnatm_sample_component` function. The cumulative was
- calculated assuming that all components are either present or absent at the
- queried position. Thus, the accumulation was only correct when the volumetric
- meshes were the same for all components.
-- Fix the calculation of the minimum radiative coefficient of a voxel in the
- octree. It was simply miscalculated and its value might not be the minimum.
-- Fix the accumulation of radiative coefficients in the voxels of the octree.
- When the volumetric meshes were not the same for all components, some voxels
- could be "emptied" during the accumulation.
+ calculated assuming that all components are either present or absent
+ at the queried position. Thus, the accumulation was only correct when
+ the volumetric meshes were the same for all components.
+- Fix the calculation of the minimum radiative coefficient of a voxel in
+ the octree. It was simply miscalculated and its value might not be the
+ minimum.
+- Fix the accumulation of radiative coefficients in the voxels of the
+ octree. When the volumetric meshes were not the same for all
+ components, some voxels could be "emptied" during the accumulation.
-## Copyright notice
+## Copyrights
Copyright (C) 2022, 2023 Centre National de la Recherche Scientifique
Copyright (C) 2022, 2023 Institut Pierre-Simon Laplace
Copyright (C) 2022, 2023 Institut de Physique du Globe de Paris
-Copyright (C) 2022, 2023 [|Méso|Star>](https://www.meso-star.com) (<contact@meso-star.com>)
+Copyright (C) 2022, 2023 [|Méso|Star>](https://www.meso-star.com) (contact@meso-star.com)
Copyright (C) 2022, 2023 Observatoire de Paris
Copyright (C) 2022, 2023 Université de Reims Champagne-Ardenne
Copyright (C) 2022, 2023 Université de Versaille Saint-Quentin
@@ -67,6 +71,6 @@ Copyright (C) 2022, 2023 Université Paul Sabatier
## License
-Rad-Net Atmosphere 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.
+Rad-Net Atmosphere 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
@@ -1,161 +0,0 @@
-# Copyright (C) 2022, 2023 Centre National de la Recherche Scientifique
-# Copyright (C) 2022, 2023 Institut Pierre-Simon Laplace
-# Copyright (C) 2022, 2023 Institut de Physique du Globe de Paris
-# Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
-# Copyright (C) 2022, 2023 Observatoire de Paris
-# Copyright (C) 2022, 2023 Université de Reims Champagne-Ardenne
-# Copyright (C) 2022, 2023 Université de Versaille Saint-Quentin
-# Copyright (C) 2022, 2023 Université Paul Sabatier
-#
-# 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
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-cmake_minimum_required(VERSION 3.1)
-project(rnatm C)
-enable_testing()
-
-set(RNATM_SOURCE_DIR ${PROJECT_SOURCE_DIR}/../src)
-option(NO_TEST "Do not build tests" OFF)
-
-################################################################################
-# Check dependencies
-################################################################################
-find_package(OpenMP 1.2 REQUIRED)
-find_package(RCMake 0.4 REQUIRED)
-find_package(RNSL REQUIRED)
-find_package(RNSF REQUIRED)
-find_package(RSys 0.12.1 REQUIRED)
-find_package(StarAerosol REQUIRED)
-find_package(StarBuffer REQUIRED)
-find_package(StarCK REQUIRED)
-find_package(StarMesh REQUIRED)
-find_package(StarSF 0.8 REQUIRED)
-find_package(StarUVM 0.0 REQUIRED)
-find_package(StarVX 0.2 REQUIRED)
-
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${RCMAKE_SOURCE_DIR})
-include(rcmake)
-include(rcmake_runtime)
-
-include_directories(
- ${RNSL_INCLUDE_DIR}
- ${RNSF_INCLUDE_DIR}
- ${RSys_INCLUDE_DIR}
- ${StarAerosol_INCLUDE_DIR}
- ${StarBuffer_INCLUDE_DIR}
- ${StarCK_INCLUDE_DIR}
- ${StarMesh_INCLUDE_DIR}
- ${StarSF_INCLUDE_DIR}
- ${StarUVM_INCLUDE_DIR}
- ${StarVX_INCLUDE_DIR})
-
-################################################################################
-# Configure and define targets
-################################################################################
-set(VERSION_MAJOR 0)
-set(VERSION_MINOR 0)
-set(VERSION_PATCH 1)
-set(VERSION ${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH})
-
-set(RNATM_FILES_SRC
- rnatm.c
- rnatm_log.c
- rnatm_mesh.c
- rnatm_octree.c
- rnatm_octrees_storage.c
- rnatm_properties.c
- rnatm_radcoef.c
- rnatm_voxel_partition.c
- rnatm_write_vtk.c)
-set(RNATM_FILES_INC
- rnatm_c.h
- rnatm_log.h
- rnatm_octrees_storage.h
- rnatm_voxel.h
- rnatm_voxel_partition.h)
-set(RNATM_FILES_INC_API rnatm.h)
-set(RNATM_FILES_DOC COPYING README.md)
-
-# Prepend each file in the `RNATM_FILES_<SRC|INC>' list by `RNATM_SOURCE_DIR'
-rcmake_prepend_path(RNATM_FILES_SRC ${RNATM_SOURCE_DIR})
-rcmake_prepend_path(RNATM_FILES_INC ${RNATM_SOURCE_DIR})
-rcmake_prepend_path(RNATM_FILES_INC_API ${RNATM_SOURCE_DIR})
-rcmake_prepend_path(RNATM_FILES_DOC ${PROJECT_SOURCE_DIR}/../)
-
-add_library(rnatm SHARED ${RNATM_FILES_SRC} ${RNATM_FILES_INC} ${RNATM_FILES_INC_API})
-target_link_libraries(rnatm RNSL RNSF RSys StarAerosol StarBuffer StarCK StarMesh
- StarSF StarUVM StarVX m)
-
-set_target_properties(rnatm PROPERTIES
- COMPILE_FLAGS "${OpenMP_C_FLAGS}"
- LINK_FLAGS "${OpenMP_C_FLAGS}"
- DEFINE_SYMBOL RNATM_SHARED_BUILD
- VERSION ${VERSION}
- SOVERSION ${VERSION_MAJOR})
-
-rcmake_setup_devel(rnatm RNATM ${VERSION} rad-net/rnatm_version.h)
-
-################################################################################
-# Add tests
-################################################################################
-if(NOT NO_TEST)
- function(build_test _name)
- add_executable(${_name}
- ${RNATM_SOURCE_DIR}/${_name}.c)
- target_link_libraries(${_name} rnatm RSys)
- endfunction()
-
- function(new_test _name)
- build_test(${_name})
- add_test(${_name} ${_name})
- endfunction()
-
- build_test(test_rnatm)
-
-endif()
-
-################################################################################
-# Man page
-###############################################################################
-find_program(SCDOC NAMES scdoc)
-if(NOT SCDOC)
- message(WARNING
- "The `scdoc' program is missing. "
- "The Rad Net ATMopshere man page cannot be generated.")
-else()
- set(_man_names rngt.5 rnpfi.5)
-
- foreach(_man IN LISTS _man_names)
- set(_src ${PROJECT_SOURCE_DIR}/../doc/${_man}.scd)
- add_custom_command(
- OUTPUT ${_man}
- COMMAND ${SCDOC} < ${_src} > ${_man}
- DEPENDS ${_src}
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMENT "Buid ROFF man page ${_man}"
- VERBATIM)
- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${_man} DESTINATION share/man/man5)
- endforeach()
- add_custom_target(man-roff ALL DEPENDS ${_man_names})
-endif()
-
-
-################################################################################
-# Define output & install directories
-################################################################################
-install(TARGETS rnatm
- ARCHIVE DESTINATION bin
- LIBRARY DESTINATION lib
- RUNTIME DESTINATION bin)
-install(FILES ${RNATM_FILES_INC_API} DESTINATION include/rad-net)
-install(FILES ${RNATM_FILES_DOC} DESTINATION share/doc/rnatm)
diff --git a/config.mk b/config.mk
@@ -0,0 +1,141 @@
+VERSION = 0.1.0
+PREFIX = /usr/local
+
+LIB_TYPE = SHARED
+#LIB_TYPE = STATIC
+
+BUILD_TYPE = RELEASE
+#BUILD_TYPE = DEBUG
+
+################################################################################
+# Tools
+################################################################################
+AR = ar
+CC = cc
+LD = ld
+OBJCOPY = objcopy
+PKG_CONFIG = pkg-config
+RANLIB = ranlib
+
+################################################################################
+# Dependencies
+################################################################################
+PCFLAGS_SHARED =
+PCFLAGS_STATIC = --static
+PCFLAGS = $(PCFLAGS_$(LIB_TYPE))
+
+RNSF_VERSION = 0.1
+RNSF_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags rnsf)
+RNSF_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs rnsf)
+
+RNSL_VERSION = 0.1
+RNSL_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags rnsl)
+RNSL_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs rnsl)
+
+RSYS_VERSION = 0.14
+RSYS_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags rsys)
+RSYS_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs rsys)
+
+SARS_VERSION = 0.1
+SARS_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags sars)
+SARS_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs sars)
+
+SBUF_VERSION = 0.1
+SBUF_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags sbuf)
+SBUF_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs sbuf)
+
+SCK_VERSION = 0.1
+SCK_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags sck)
+SCK_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs sck)
+
+SMSH_VERSION = 0.1
+SMSH_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags smsh)
+SMSH_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs smsh)
+
+SSF_VERSION = 0.9
+SSF_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags ssf)
+SSF_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs ssf)
+
+SUVM_VERSION = 0.3
+SUVM_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags suvm)
+SUVM_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs suvm)
+
+SVX_VERSION = 0.3
+SVX_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags svx)
+SVX_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs svx)
+
+DPDC_CFLAGS =\
+ $(RNSF_CFLAGS)\
+ $(RNSL_CFLAGS)\
+ $(RSYS_CFLAGS)\
+ $(SARS_CFLAGS)\
+ $(SBUF_CFLAGS)\
+ $(SCK_CFLAGS)\
+ $(SMSH_CFLAGS)\
+ $(SSF_CFLAGS)\
+ $(SUVM_CFLAGS)\
+ $(SVX_CFLAGS)\
+ -fopenmp
+
+DPDC_LIBS =\
+ $(RNSF_LIBS)\
+ $(RNSL_LIBS)\
+ $(RSYS_LIBS)\
+ $(SARS_LIBS)\
+ $(SBUF_LIBS)\
+ $(SCK_LIBS)\
+ $(SMSH_LIBS)\
+ $(SSF_LIBS)\
+ $(SUVM_LIBS)\
+ $(SVX_LIBS)\
+ -fopenmp\
+ -lm
+
+################################################################################
+# Compilation options
+################################################################################
+WFLAGS =\
+ -Wall\
+ -Wcast-align\
+ -Wconversion\
+ -Wextra\
+ -Wmissing-declarations\
+ -Wmissing-prototypes\
+ -Wshadow
+
+# Increase the security and robustness of generated binaries
+CFLAGS_HARDENED =\
+ -D_FORTIFY_SOURCES=2\
+ -fcf-protection=full\
+ -fstack-clash-protection\
+ -fstack-protector-strong
+
+CFLAGS_COMMON =\
+ -std=c89\
+ -pedantic\
+ -fvisibility=hidden\
+ -fstrict-aliasing\
+ $(CFLAGS_HARDENED)\
+ $(WFLAGS)
+
+CFLAGS_DEBUG = -g $(CFLAGS_COMMON)
+CFLAGS_RELEASE = -O2 -DNDEBUG $(CFLAGS_COMMON)
+CFLAGS = $(CFLAGS_$(BUILD_TYPE))
+
+CFLAGS_SO = $(CFLAGS) -fPIC
+CFLAGS_EXE = $(CFLAGS) -fPIE
+
+################################################################################
+# Linker options
+################################################################################
+LDFLAGS_HARDENED = -Wl,-z,relro,-z,now
+LDFLAGS_DEBUG = $(LDFLAGS_HARDENED)
+LDFLAGS_RELEASE = -s $(LDFLAGS_HARDENED)
+LDFLAGS = $(LDFLAGS_$(BUILD_TYPE))
+
+LDFLAGS_SO = $(LDFLAGS) -shared -Wl,--no-undefined
+LDFLAGS_EXE = $(LDFLAGS) -pie
+
+OCPFLAGS_DEBUG = --localize-hidden
+OCPFLAGS_RELEASE = --localize-hidden --strip-unneeded
+OCPFLAGS = $(OCPFLAGS_$(BUILD_TYPE))
diff --git a/doc/rngt.5.scd b/doc/rngt.5.scd
@@ -1,71 +0,0 @@
-rngt(5)
-
-; Copyright (C) 2022, 2023 Centre National de la Recherche Scientifique
-; Copyright (C) 2022, 2023 Institut Pierre-Simon Laplace
-; Copyright (C) 2022, 2023 Institut de Physique du Globe de Paris
-; Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
-; Copyright (C) 2022, 2023 Observatoire de Paris
-; Copyright (C) 2022, 2023 Université de Reims Champagne-Ardenne
-; Copyright (C) 2022, 2023 Université de Versaille Saint-Quentin
-; Copyright (C) 2022, 2023 Université Paul Sabatier
-;
-; 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
-; the Free Software Foundation, either version 3 of the License, or
-; (at your option) any later version.
-;
-; This program is distributed in the hope that it will be useful,
-; but WITHOUT ANY WARRANTY; without even the implied warranty of
-; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-; GNU General Public License for more details.
-;
-; You should have received a copy of the GNU General Public License
-; along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# NAME
-
-rngt - Rad-Net Gas Temperatures
-
-# DESCRIPTION
-
-*rngt* is a binary file format for storing gas temperatures. The temperatures
-are discretized according to the mesh of the gas. The mesh to which the
-temperatures are attached is _not_ described there but must be defined in a
-separate file, for example in an *smsh*(5) file. The number of temperatures and
-their order must therefore correspond to the data of the mesh to which they are
-attached, i.e. to the nodes|cells listed in the corresponding mesh.
-
-*rngt* file is actually a Star-Buffer file (see *sbuf*(5)). It starts with a
-header of 4 64-bit integers describing the layout of the data. The first integer
-is a power of two (usually 4096) that defines the size of the memory page in
-bytes to which the list of temperatures aligns (_pagesize_). The second integer
-is the _size_ of the array, i.e. the number of temperatures defined in the list.
-Finally, the 2 remaining integers store the memory size (4 bytes) and the memory
-alignment (4 bytes) of a temperature.
-
-Padding bytes follow the file header to align the listed temperatures to
-_pagesize_.
-
-The end of the file is eventually padded with dummy bytes to ensure that the
-overall file size is a multiple of _pagesize_.
-
-# BINARY FILE FORMAT
-
-Data are encoded with respect to the little endian bytes ordering, i.e. least
-significant bytes are stored first.
-
-```
-<rngt> ::= <pagesize> <size> 4 4
- <padding>
- <temperatures>
- <padding>
-
-<pagesize> ::= UINT64
-<size> ::= UINT64 # Number of temperatures stored
-<temperatures> ::= FLOAT ... # In K
-<padding> ::= [ BYTE ... ] # Ensure alignement
-```
-
-# SEE ALSO
-
-*sbuf*(5), *smsh*(5)
diff --git a/doc/rnpfi.5.scd b/doc/rnpfi.5.scd
@@ -1,71 +0,0 @@
-rnpfi(5)
-
-; Copyright (C) 2022, 2023 Centre National de la Recherche Scientifique
-; Copyright (C) 2022, 2023 Institut Pierre-Simon Laplace
-; Copyright (C) 2022, 2023 Institut de Physique du Globe de Paris
-; Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
-; Copyright (C) 2022, 2023 Observatoire de Paris
-; Copyright (C) 2022, 2023 Université de Reims Champagne-Ardenne
-; Copyright (C) 2022, 2023 Université de Versaille Saint-Quentin
-; Copyright (C) 2022, 2023 Université Paul Sabatier
-;
-; 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
-; the Free Software Foundation, either version 3 of the License, or
-; (at your option) any later version.
-;
-; This program is distributed in the hope that it will be useful,
-; but WITHOUT ANY WARRANTY; without even the implied warranty of
-; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-; GNU General Public License for more details.
-;
-; You should have received a copy of the GNU General Public License
-; along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# NAME
-
-rnpfi - Rad-Net Phase Function Indices
-
-# DESCRIPTION
-
-*rnpfi* is a binary file format for storing a list of indices referring to phase
-functions. The indices are attached to a volumetric mesh which is _not_
-described there but must be defined in a separate file, for example in an
-*smsh*(5) file. The number of indices and their order must therefore correspond
-to the data of the mesh to which they are attached, i.e. to the nodes|cells
-listed in the corresponding mesh.
-
-*rnpfi* file is actually a Star-Buffer file (see *sbuf*(5)). It starts with a
-header of 4 64-bit integers describing the layout of the data. The first integer
-is a power of two (usually 4096) that defines the size of the memory page in
-bytes to which the list of indices aligns (_pagesize_). The second integer is
-the _size_ of the array, i.e. the number of indices defined in the list.
-Finally, the 2 remaining integers store the memory size (4 bytes) and the memory
-alignment (4 bytes) of an index.
-
-Padding bytes follow the file header to align the listed indices to
-_pagesize_.
-
-The end of the file is eventually padded with dummy bytes to ensure that the
-overall file size is a multiple of _pagesize_.
-
-# BINARY FILE FORMAT
-
-Data are encoded with respect to the little endian bytes ordering, i.e. least
-significant bytes are stored first.
-
-```
-<rngt> ::= <pagesize> <size> 4 4
- <padding>
- <indices>
- <padding>
-
-<pagesize> ::= UINT64
-<size> ::= UINT64 # Number of indices stored
-<indices> ::= UINT32 ...
-<padding> ::= [ BYTE ... ] # Ensure alignement
-```
-
-# SEE ALSO
-
-*sbuf*(5), *smsh*(5)
diff --git a/make.sh b/make.sh
@@ -0,0 +1,46 @@
+#!/bin/sh
+
+# Copyright (C) 2022, 2023 Centre National de la Recherche Scientifique
+# Copyright (C) 2022, 2023 Institut Pierre-Simon Laplace
+# Copyright (C) 2022, 2023 Institut de Physique du Globe de Paris
+# Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+# Copyright (C) 2022, 2023 Observatoire de Paris
+# Copyright (C) 2022, 2023 Université de Reims Champagne-Ardenne
+# Copyright (C) 2022, 2023 Université de Versaille Saint-Quentin
+# Copyright (C) 2022, 2023 Université Paul Sabatier
+#
+# 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
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+set -e
+
+install()
+{
+ prefix=$1
+ shift 1
+
+ mkdir -p "${prefix}"
+
+ for i in "$@"; do
+ dst="${prefix}/${i##*/}"
+
+ if cmp -s "${i}" "${dst}"; then
+ printf "Up to date %s\n" "${dst}"
+ else
+ printf "Installing %s\n" "${dst}"
+ cp "${i}" "${prefix}"
+ fi
+ done
+}
+
+"$@"
diff --git a/rnatm.pc.in b/rnatm.pc.in
@@ -0,0 +1,19 @@
+prefix=@PREFIX@
+includedir=${prefix}/include
+libdir=${prefix}/lib
+
+Requires: rsys >= @RSYS_VERSION@, suvm >= @SUVM_VERSION@, svx >= @SVX_VERSION@
+Requires.private:\
+ rnsl >= @RNSL_VERSION@,\
+ rnsf >= @RNSF_VERSION@,\
+ sars >= @SARS_VERSION@,\
+ sbuf >= @SBUF_VERSION@,\
+ sck >= @SCK_VERSION@,\
+ smsh >= @SMSH_VERSION@,\
+ ssf >= @SSF_VERSION@
+Name: rnatm
+Description: Rad-Net ATMopshere
+Version: @VERSION@
+Libs: -L${libdir} -lrnatm
+Libs.private: -fopenmp -lm
+CFlags: -I${includedir}
diff --git a/rngt.5 b/rngt.5
@@ -0,0 +1,94 @@
+.\" Copyright (C) 2022, 2023 Centre National de la Recherche Scientifique
+.\" Copyright (C) 2022, 2023 Institut Pierre-Simon Laplace
+.\" Copyright (C) 2022, 2023 Institut de Physique du Globe de Paris
+.\" Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+.\" Copyright (C) 2022, 2023 Observatoire de Paris
+.\" Copyright (C) 2022, 2023 Université de Reims Champagne-Ardenne
+.\" Copyright (C) 2022, 2023 Université de Versaille Saint-Quentin
+.\" Copyright (C) 2022, 2023 Université Paul Sabatier
+.\"
+.\" 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
+.\" the Free Software Foundation, either version 3 of the License, or
+.\" (at your option) any later version.
+.\"
+.\" This program is distributed in the hope that it will be useful,
+.\" but WITHOUT ANY WARRANTY; without even the implied warranty of
+.\" MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+.\" GNU General Public License for more details.
+.\"
+.\" You should have received a copy of the GNU General Public License
+.\" along with this program. If not, see <http://www.gnu.org/licenses/>.
+.Dd September 26, 2023
+.Dt RNGT 5
+.Os
+.Sh NAME
+.Nm rngt
+.Nd Rad-Net Gas Temperatures
+.Sh DESCRIPTION
+.Nm
+is a binary file format for storing gas temperatures.
+The temperatures are discretized according to the mesh of the gas.
+The mesh to which the temperatures are attached is
+.Em not
+described there but must be defined in a separate file, for example in an
+.Xr smsh 5
+file.
+The number of temperatures and their order must therefore correspond to
+the data of the mesh to which they are attached, i.e. to the nodes or
+cells listed in the corresponding mesh.
+.Pp
+A
+.Nm
+file is actually a Star-Buffer file
+.Pq see Xr sbuf 5 .
+It starts with a header of 4 integers.
+The first integer is a power of two
+.Pq usually 4096
+that defines the size of the memory page in bytes
+.Pq Va pagesize
+on which the list of temperatures are aligned.
+By aligning data to pagesize, and depending on system requirements,
+memory mapping can be used to automatically load/unload pages on demand
+.Pq see Xr mmap 2 .
+The second integer is the
+.Va size
+of the array, i.e. the number of temperatures stored in the list.
+The two remaining integers store the memory size
+.Pq 4 bytes
+and the memory alignment
+.Pq 4 bytes
+of a temperature.
+.Pp
+Padding bytes follow the file header to align the listed temperatures to
+.Va pagesize .
+.Pp
+Padding bytes are finally added at the end of the file to align its
+overall size with the size of a page.
+.Pp
+Data are encoded with respect to the little endian bytes ordering,
+i.e. least significant bytes are stored first.
+.Pp
+The file format is as follows:
+.Bl -column (temperature) (::=) ()
+.It Ao Va rngt Ac Ta ::= Ta Ao Va pagesize Ac Ao Va size Ac Li 4 4
+.It Ta Ta Aq Va padding
+.It Ta Ta Aq Va temperatures
+.It Ta Ta Aq Va padding
+.It Ao Va pagesize Ac Ta ::= Ta Vt uint64_t
+.It Ao Va size Ac Ta ::= Ta Vt uint64_t
+# Number of temperatures stored
+.It Ao Va temperatures Ac Ta ::= Ta Vt float ...
+# In K
+.It Ao Va padding Ac Ta ::= Ta Op Vt int8_t ...
+.El
+.Sh SEE ALSO
+.Xr mmap 2 ,
+.Xr sbuf 5 ,
+.Xr smsh 5
+.Sh HISTORY
+The
+.Nm
+format was first developed for the
+.Xr htrdr-planeto 1
+program.
diff --git a/rnpfi.5 b/rnpfi.5
@@ -0,0 +1,93 @@
+.\" Copyright (C) 2022, 2023 Centre National de la Recherche Scientifique
+.\" Copyright (C) 2022, 2023 Institut Pierre-Simon Laplace
+.\" Copyright (C) 2022, 2023 Institut de Physique du Globe de Paris
+.\" Copyright (C) 2022, 2023 |Méso|Star>(contact@meso-star.com)
+.\" Copyright (C) 2022, 2023 Observatoire de Paris
+.\" Copyright (C) 2022, 2023 Université de Reims Champagne-Ardenne
+.\" Copyright (C) 2022, 2023 Université de Versaille Saint-Quentin
+.\" Copyright (C) 2022, 2023 Université Paul Sabatier
+.\"
+.\" 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
+.\" the Free Software Foundation, either version 3 of the License, or
+.\" (at your option) any later version.
+.\"
+.\" This program is distributed in the hope that it will be useful,
+.\" but WITHOUT ANY WARRANTY; without even the implied warranty of
+.\" MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+.\" GNU General Public License for more details.
+.\"
+.\" You should have received a copy of the GNU General Public License
+.\" along with this program. If not, see <http://www.gnu.org/licenses/>.
+.Dd September 26, 2023
+.Dt RNPFI 5
+.Os
+.Sh NAME
+.Nm rnpfi
+.Nd Rad-Net Phase Function Indices
+.Sh DESCRIPTION
+.Nm
+is a binary file format for storing a list of indices referring to
+phase functions.
+The indices are attached to a volumetric mesh which is
+.Em not
+described there but must be defined in a separate file, for example in an
+.Xr smsh 5
+file.
+The number of indices and their order must therefore correspond to the
+data of the mesh to which they are attached, i.e. to the nodes or cells
+listed in the corresponding mesh.
+.Pp
+A
+.Nm
+file is actually a Star-Buffer file
+.Pq see Xr sbuf 5 .
+It starts with a header of 4 integers.
+The first integer is a power of two
+.Pq usually 4096
+that defines the size of the memory page in bytes
+.Pq Va pagesize
+on which the list of indices are aligned.
+By aligning data to pagesize, and depending on system requirements,
+memory mapping can be used to automatically load/unload pages on demand
+.Pq see Xr mmap 2 .
+The second integer is the
+.Va size
+of the array, i.e. the number of indices stored in the list.
+The two remaining integers store the memory size
+.Pq 4 bytes
+and the memory alignment
+.Pq 4 bytes
+of an index.
+.Pp
+Padding bytes follow the file header to align the listed indices to
+.Va pagesize .
+.Pp
+Padding bytes are finally added at the end of the file to align its
+overall size with the size of a page.
+.Pp
+Data are encoded with respect to the little endian bytes ordering,
+i.e. least significant bytes are stored first.
+.Pp
+The file format is as follows:
+.Bl -column (pagesize) (::=) ()
+.It Ao Va rnpfi Ac Ta ::= Ta Ao Va pagesize Ac Ao Va size Ac Li 4 4
+.It Ta Ta Aq Va padding
+.It Ta Ta Aq Va indices
+.It Ta Ta Aq Va padding
+.It Ao Va pagesize Ac Ta ::= Ta Vt uint64_t
+.It Ao Va size Ac Ta ::= Ta Vt uint64_t
+# Number of indices stored
+.It Ao Va indices Ac Ta ::= Ta Vt uint32_t ...
+.It Ao Va padding Ac Ta ::= Ta Op Vt int8_t ...
+.El
+.Sh SEE ALSO
+.Xr mmap 2 ,
+.Xr sbuf 5 ,
+.Xr smsh 5
+.Sh HISTORY
+The
+.Nm
+format was first developed for the
+.Xr htrdr-planeto 1
+program.
diff --git a/src/rnatm.h b/src/rnatm.h
@@ -23,7 +23,6 @@
#ifndef RNATM_H
#define RNATM_H
-#include <star/s3d.h>
#include <star/suvm.h>
#include <star/svx.h>
diff --git a/src/rnatm_c.h b/src/rnatm_c.h
@@ -215,7 +215,7 @@ accel_struct_copy_and_release
#define DARRAY_DATA struct accel_struct
#define DARRAY_FUNCTOR_INIT accel_struct_init
#define DARRAY_FUNCTOR_RELEASE accel_struct_release
-#define DARRAY_FUNCTOR_COPY accel_struct_copy_and_release
+#define DARRAY_FUNCTOR_COPY accel_struct_copy
#define DARRAY_FUNCTOR_COPY_AND_RELEASE accel_struct_copy_and_release
#include <rsys/dynamic_array.h>
diff --git a/src/rnatm_mesh.c b/src/rnatm_mesh.c
@@ -90,13 +90,16 @@ setup_uvm
size_t* nvertices)
{
struct suvm_tetrahedral_mesh_args mesh_args = SUVM_TETRAHEDRAL_MESH_ARGS_NULL;
+ struct smsh_load_args smsh_load_args = SMSH_LOAD_ARGS_NULL;
struct smsh_desc smsh_desc = SMSH_DESC_NULL;
struct suvm_volume* volume = NULL;
res_T res = RES_OK;
ASSERT(atm && args && filename && suvm && smsh && out_volume);
/* Load and retrieve the Star-Mesh data */
- res = smsh_load(smsh, filename);
+ smsh_load_args.path = filename;
+ smsh_load_args.memory_mapping = 0;
+ res = smsh_load(smsh, &smsh_load_args);
if(res != RES_OK) goto error;
res = smsh_get_desc(smsh, &smsh_desc);
if(res != RES_OK) goto error;
diff --git a/src/rnatm_octree.c b/src/rnatm_octree.c
@@ -280,7 +280,7 @@ static FINLINE unsigned
round_pow2(const unsigned val)
{
const unsigned next_pow2 = (unsigned)round_up_pow2(val);
- if(next_pow2 - val <= next_pow2/4) {
+ if(val == 0 || next_pow2 - val <= next_pow2/4) {
return next_pow2;
} else {
return next_pow2/2;
@@ -1365,7 +1365,7 @@ create_octrees(struct rnatm* atm, const struct rnatm_create_args* args)
const res_T res_local = voxelize_atmosphere(atm, pool, &sync);
if(res_local != RES_OK) {
log_err(atm, "error when voxelizing the atmosphere -- %s\n",
- res_to_cstr((res_T)res));
+ res_to_cstr((res_T)res_local));
pool_invalidate(pool);
ATOMIC_SET(&res, res_local);
}
@@ -1375,7 +1375,8 @@ create_octrees(struct rnatm* atm, const struct rnatm_create_args* args)
{
const res_T res_local = build_octrees(atm, args, pool, &sync);
if(res_local != RES_OK) {
- log_err(atm, "error building octrees -- %s\n", res_to_cstr((res_T)res));
+ log_err(atm, "error building octrees -- %s\n",
+ res_to_cstr((res_T)res_local));
pool_invalidate(pool);
ATOMIC_SET(&res, res_local);
}
diff --git a/src/rnatm_properties.c b/src/rnatm_properties.c
@@ -610,6 +610,7 @@ setup_gas_properties(struct rnatm* atm, const struct rnatm_gas_args* gas_args)
{
char buf[128];
struct time t0, t1;
+ struct sck_load_args sck_load_args = SCK_LOAD_ARGS_NULL;
struct sck_band band_low = SCK_BAND_NULL;
struct sck_band band_upp = SCK_BAND_NULL;
struct sck_create_args sck_args = SCK_CREATE_ARGS_DEFAULT;
@@ -651,7 +652,9 @@ setup_gas_properties(struct rnatm* atm, const struct rnatm_gas_args* gas_args)
if(res != RES_OK) goto error;
/* Load correlated-K */
- res = sck_load(atm->gas.ck, gas_args->sck_filename);
+ sck_load_args.path = gas_args->sck_filename;
+ sck_load_args.memory_mapping = 1;
+ res = sck_load(atm->gas.ck, &sck_load_args);
if(res != RES_OK) goto error;
res = check_gas_ck_desc(atm, gas_args);
if(res != RES_OK) goto error;
@@ -689,6 +692,7 @@ setup_aerosol_properties
size_t ibands[2];
struct time t0, t1;
struct sars_create_args sars_args = SARS_CREATE_ARGS_DEFAULT;
+ struct sars_load_args sars_load_args = SARS_LOAD_ARGS_NULL;
struct sbuf_create_args sbuf_args = SBUF_CREATE_ARGS_DEFAULT;
struct sbuf_desc sbuf_desc = SBUF_DESC_NULL;
@@ -707,7 +711,9 @@ setup_aerosol_properties
if(res != RES_OK) goto error;
/* Load the aerosol radiative properties */
- res = sars_load(aerosol->sars, aerosol_args->sars_filename);
+ sars_load_args.path = aerosol_args->sars_filename;
+ sars_load_args.memory_mapping = 1;
+ res = sars_load(aerosol->sars, &sars_load_args);
if(res != RES_OK) goto error;
res = check_aerosol_sars_desc(atm, aerosol, aerosol_args);
if(res != RES_OK) goto error;
diff --git a/src/rnatm_radcoef.c b/src/rnatm_radcoef.c
@@ -164,10 +164,6 @@ tetra_get_radcoef_aerosol
lambda_min = MMAX(gas_band.lower, ars_band.lower);
lambda_max = MMIN(gas_band.upper, ars_band.upper); /* exclusive */
lambda_max = nextafter(lambda_max, 0); /* inclusive */
-
- /* Shrink lambda_<min|max> to the spectral range */
- lambda_min = MMAX(lambda_min, atm->spectral_range[0]);
- lambda_max = MMIN(lambda_max, atm->spectral_range[1]);
lambda_len = (float)(lambda_max - lambda_min);
ASSERT(lambda_len > 0);
diff --git a/src/rnatm_voxel_partition.c b/src/rnatm_voxel_partition.c
@@ -122,6 +122,7 @@ partition_init
partition->id = SIZE_MAX;
partition->tile = NULL;
partition->pool = pool;
+ partition->ref = 0;
}
static void
@@ -251,11 +252,17 @@ partition_free(struct partition* partition)
pool = partition->pool;
- if(ATOMIC_DECR(&partition->ref) != 0)
+ /* The partition reference counter can be zero before being decremented: it is
+ * initialized to the voxel width once the partition has been commited. So, if
+ * the partition is released before any commit (for example, when it doesn't
+ * overlap the atmosphere grid), it can be negative after it has been
+ * decremented */
+ if(ATOMIC_DECR(&partition->ref) > 0)
return; /* The partition is still referenced */
mutex_lock(pool->mutex);
list_move_tail(&partition->node, &pool->parts_free); /* Free the partition */
+ partition->ref = 0; /* Reset to 0 rather than letting a negative value */
if(partition->tile) { /* Free the reserved tile */
list_move_tail(&partition->tile->node, &pool->tiles_free);
partition->tile = NULL;
diff --git a/src/test_rnatm.c b/src/test_rnatm.c
@@ -318,7 +318,7 @@ args_init(struct args* args, int argc, char** argv)
while((opt = getopt(argc, argv, "a:cd:g:hi:Nn:o:s:T:t:V:v")) != -1) {
switch(opt) {
case 'a':
- sa_add(args->rnatm.aerosols, 1);
+ (void)sa_add(args->rnatm.aerosols, 1);
args->rnatm.aerosols[args->rnatm.naerosols] = RNATM_AEROSOL_ARGS_NULL;
args->rnatm.naerosols += 1;
res = cstr_parse_list(optarg, ':', parse_aerosol_parameters, args);
