rnatm

Load and structure data describing an atmosphere
git clone git://git.meso-star.fr/rnatm.git
Log | Files | Refs | README | LICENSE
commit 6157111187462de60c56d375f846540e6b022037
parent 01d9b2bc03acc75ff351ed791d925456fc5f30ff
Author: Vincent Forest <vincent.forest@meso-star.com>
Date:   Wed,  1 Oct 2025 15:49:45 +0200

Merge branch 'release_0.2'

Diffstat:

M.gitignore | 3+--


MMakefile | 170+++++++++++++++++++++++++++++++++++++++----------------------------------------


MREADME.md | 26++++++++++++++++++--------


Mconfig.mk | 66++++++++++--------------------------------------------------------


Adoc/rnatm.1 | 304+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


Adoc/rngt.5 | 94+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


Adoc/rnpfi.5 | 93+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


Dmake.sh | 46----------------------------------------------


Drngt.5 | 94-------------------------------------------------------------------------------


Drnpfi.5 | 93-------------------------------------------------------------------------------


Msrc/rnatm.c | 16++++++++--------


Msrc/rnatm.h | 16++++++++--------


Msrc/rnatm_c.h | 16++++++++--------


Msrc/rnatm_log.c | 16++++++++--------


Msrc/rnatm_log.h | 16++++++++--------


Asrc/rnatm_main.c | 424+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


Msrc/rnatm_mesh.c | 16++++++++--------


Msrc/rnatm_octree.c | 16++++++++--------


Msrc/rnatm_octrees_storage.c | 16++++++++--------


Msrc/rnatm_octrees_storage.h | 16++++++++--------


Msrc/rnatm_properties.c | 16++++++++--------


Msrc/rnatm_radcoef.c | 16++++++++--------


Msrc/rnatm_voxel.h | 16++++++++--------


Msrc/rnatm_voxel_partition.c | 16++++++++--------


Msrc/rnatm_voxel_partition.h | 16++++++++--------


Msrc/rnatm_write_vtk.c | 16++++++++--------


Dsrc/test_rnatm.c | 485-------------------------------------------------------------------------------


27 files changed, 1148 insertions(+), 990 deletions(-)

diff --git a/.gitignore b/.gitignore
@@ -4,8 +4,7 @@
 *.[aod]
 *.so
 *~
-test*
-!test*.[ch]
+rnatm
 .config
 .test
 tags
diff --git a/Makefile b/Makefile
@@ -1,11 +1,11 @@
-# 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
+# Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+# Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+# Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+# Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+# Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+# Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+# Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+# Copyright (C) 2022, 2023, 2025 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
@@ -29,6 +29,9 @@ LIBNAME_STATIC = librnatm.a
 LIBNAME_SHARED = librnatm.so
 LIBNAME = $(LIBNAME_$(LIB_TYPE))
 
+default: library
+all: default util
+
 ################################################################################
 # Library building
 ################################################################################
@@ -45,7 +48,10 @@ SRC =\
 OBJ = $(SRC:.c=.o)
 DEP = $(SRC:.c=.d)
 
-build_library: .config $(DEP)
+CFLAGS_LIB = $(CFLAGS_SO) $(INCS) -DRNATM_SHARED_BUILD
+LDFLAGS_LIB = $(LDFLAGS_SO) $(LIBS)
+
+library: .config $(DEP)
 	@$(MAKE) -fMakefile $$(for i in $(DEP); do echo -f $${i}; done) \
 	$$(if [ -n "$(LIBNAME)" ]; then \
 	     echo "$(LIBNAME)"; \
@@ -56,7 +62,7 @@ build_library: .config $(DEP)
 $(DEP) $(OBJ): config.mk
 
 $(LIBNAME_SHARED): $(OBJ)
-	$(CC) $(CFLAGS_SO) $(DPDC_CFLAGS) -o $@ $(OBJ) $(LDFLAGS_SO) $(DPDC_LIBS)
+	$(CC) $(CFLAGS_LIB) -o $@ $(OBJ) $(LDFLAGS_LIB)
 
 $(LIBNAME_STATIC): librnatm.o
 	$(AR) -rc $@ $?
@@ -67,37 +73,53 @@ librnatm.o: $(OBJ)
 	$(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" > $@
+	$(PKG_CONFIG) --atleast-version $(RNSF_VERSION) rnsf
+	$(PKG_CONFIG) --atleast-version $(RNSL_VERSION) rnsl
+	$(PKG_CONFIG) --atleast-version $(RSYS_VERSION) rsys
+	$(PKG_CONFIG) --atleast-version $(SARS_VERSION) sars
+	$(PKG_CONFIG) --atleast-version $(SBUF_VERSION) sbuf
+	$(PKG_CONFIG) --atleast-version $(SCK_VERSION) sck
+	$(PKG_CONFIG) --atleast-version $(SMSH_VERSION) smsh
+	$(PKG_CONFIG) --atleast-version $(SSF_VERSION) ssf
+	$(PKG_CONFIG) --atleast-version $(SUVM_VERSION) suvm
+	$(PKG_CONFIG) --atleast-version $(SVX_VERSION) svx
+	echo "config done" > $@
 
 .SUFFIXES: .c .d .o
 .c.d:
-	@$(CC) $(CFLAGS_SO) $(DPDC_CFLAGS) -MM -MT "$(@:.d=.o) $@" $< -MF $@
+	@$(CC) $(CFLAGS_LIB) -MM -MT "$(@:.d=.o) $@" $< -MF $@
 
 .c.o:
-	$(CC) $(CFLAGS_SO) $(DPDC_CFLAGS) -DRNATM_SHARED_BUILD -c $< -o $@
+	$(CC) $(CFLAGS_LIB) -c $< -o $@
+
+################################################################################
+# Tests
+################################################################################
+UTIL_SRC = src/rnatm_main.c
+UTIL_OBJ = $(UTIL_SRC:.c=.o)
+UTIL_DEP = $(UTIL_SRC:.c=.d)
+
+PKG_CONFIG_LOCAL = PKG_CONFIG_PATH="./:$${PKG_CONFIG_PATH}" $(PKG_CONFIG)
+INCS_UTIL = $$($(PKG_CONFIG_LOCAL) $(PCFLAGS) --cflags rnatm-local rsys)
+LIBS_UTIL = $$($(PKG_CONFIG_LOCAL) $(PCFLAGS) --libs rnatm-local rsys)
+
+CFLAGS_UTIL = $(CFLAGS_EXE) $(INCS_UTIL)
+LDFLAGS_UTIL = $(LDFLAGS_EXE) $(LIBS_UTIL)
+
+util: library $(UTIL_DEP)
+	@$(MAKE) -fMakefile -f src/rnatm_main.d rnatm
+
+$(UTIL_DEP): config.mk rnatm-local.pc
+	@$(CC) $(CFLAGS_UTIL) -MM -MT "$(@:.d=.o) $@" $(@:.d=.c) -MF $@
+
+$(UTIL_OBJ): config.mk rnatm-local.pc
+	$(CC) $(CFLAGS_UTIL) -c $(@:.o=.c) -o $@
+
+rnatm: src/rnatm_main.o config.mk rnatm-local.pc $(LIBNAME)
+	$(CC) $(CFLAGS_UTIL) -o $@ src/rnatm_main.o $(LDFLAGS_UTIL)
 
 ################################################################################
-# Installation
+# Miscellaneous
 ################################################################################
 pkg:
 	sed -e 's#@PREFIX@#$(PREFIX)#g'\
@@ -131,63 +153,39 @@ rnatm-local.pc: rnatm.pc.in
 	    -e 's#@SVX_VERSION@#$(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
+install: library util pkg
+	install() { mode="$$1"; prefix="$$2"; shift 2; \
+	  mkdir -p "$${prefix}"; \
+	  cp "$$@" "$${prefix}"; \
+	  chmod "$${mode}" "$${prefix}/$${@##*/}"; \
+	}; \
+	install 755 "$(DESTDIR)$(BINPREFIX)" rnatm; \
+	install 755 "$(DESTDIR)$(LIBPREFIX)" $(LIBNAME); \
+	install 644 "$(DESTDIR)$(LIBPREFIX)/pkgconfig" rnatm.pc; \
+	install 644 "$(DESTDIR)$(INCPREFIX)/rad-net" src/rnatm.h; \
+	install 644 "$(DESTDIR)$(MANPREFIX)/man1" doc/rnatm.1; \
+	install 644 "$(DESTDIR)$(MANPREFIX)/man5" doc/rngt.5; \
+	install 644 "$(DESTDIR)$(MANPREFIX)/man5" doc/rnpfi.5; \
+	install 644 "$(DESTDIR)$(PREFIX)/share/doc/rnatm" COPYING; \
+	install 644 "$(DESTDIR)$(PREFIX)/share/doc/rnatm" README.md
 
 uninstall:
-	rm -f "$(DESTDIR)$(PREFIX)/lib/$(LIBNAME)"
-	rm -f "$(DESTDIR)$(PREFIX)/lib/pkgconfig/rnatm.pc"
+	rm -f "$(DESTDIR)$(BINPREFIX)/rnatm"
+	rm -f "$(DESTDIR)$(LIBPREFIX)/$(LIBNAME)"
+	rm -f "$(DESTDIR)$(LIBPREFIX)/pkgconfig/rnatm.pc"
+	rm -f "$(DESTDIR)$(INCPREFIX)/rad-net/rnatm.h"
+	rm -f "$(DESTDIR)$(MANPREFIX)/man1/rnatm.1"
+	rm -f "$(DESTDIR)$(MANPREFIX)/man5/rngt.5"
+	rm -f "$(DESTDIR)$(MANPREFIX)/man5/rnpfi.5"
 	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)
+clean:
+	rm -f $(DEP) $(OBJ) $(LIBNAME)
+	rm -f $(UTIL_DEP) $(UTIL_OBJ) rnatm
 	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 = $$($(PKG_CONFIG_LOCAL) $(PCFLAGS) --libs rnatm-local.pc)
-
-build_tests: build_library src/test_rnatm.d
-	@$(MAKE) -fMakefile -f src/test_rnatm.d test_rnatm
-
-clean_test:
-	rm -f test_rnatm src/test_rnatm.o
-
-$(TEST_DEP): config.mk rnatm-local.pc
-	@$(CC) $(CFLAGS_EXE) $(RNATM_CFLAGS) $(RSYS_CFLAGS) \
-	-MM -MT "$(@:.d=.o) $@" $(@:.d=.c) -MF $@
-
-src/test_rnatm.o: config.mk rnatm-local.pc
-	$(CC) $(CFLAGS_EXE) $(RNATM_CFLAGS) $(RSYS_CFLAGS) -c $(@:.o=.c) -o $@
-
-test_rnatm: src/test_rnatm.o config.mk rnatm-local.pc $(LIBNAME)
-	$(CC) $(CFLAGS_EXE) $(RNATM_CFLAGS) $(RSYS_CFLAGS) -o $@ src/$@.o \
-	$(LDFLAGS_EXE) $(RNATM_LIBS) $(RSYS_LIBS)
+	mandoc -Tlint -Wall doc/rnatm.1 || [ $$? -le 1 ]
+	mandoc -Tlint -Wall doc/rngt.5 || [ $$? -le 1 ]
+	mandoc -Tlint -Wall doc/rnpfi.5 || [ $$? -le 1 ]
diff --git a/README.md b/README.md
@@ -26,6 +26,16 @@ Edit config.mk as needed, then run:
 
 ## Release notes
 
+### Version 0.2
+
+- Add the rnatm tool to facilitate verification of input data and the
+  library.
+  This is actually the `test_rnatm` test, which has become an external
+  tool to offer users a quick way to verify their system data.
+- Improves the building system.
+  Simplify it by doing everything in one place (the Makefile).
+  Add macros to control installation subdirectories
+
 ###  Version 0.1
 
 - Fix voxelization deadlock.
@@ -60,14 +70,14 @@ identical:
 
 ## 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 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
+Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique  
+Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace  
+Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris  
+Copyright (C) 2022, 2023, 2025 [|Méso|Star>](https://www.meso-star.com) (contact@meso-star.com)  
+Copyright (C) 2022, 2023, 2025 Observatoire de Paris  
+Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne  
+Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin  
+Copyright (C) 2022, 2023, 2025 Université Paul Sabatier
 
 ## License
 
diff --git a/config.mk b/config.mk
@@ -1,5 +1,10 @@
-VERSION = 0.1.0
+VERSION = 0.2.0
+
 PREFIX = /usr/local
+BINPREFIX = $(PREFIX)/bin
+LIBPREFIX = $(PREFIX)/lib
+INCPREFIX = $(PREFIX)/include
+MANPREFIX = $(PREFIX)/share/man
 
 LIB_TYPE = SHARED
 #LIB_TYPE = STATIC
@@ -25,71 +30,20 @@ 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
+INCS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags\
+  rnsf rnsl rsys sars sbuf sck smsh ssf suvm svx) -fopenmp
+LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs\
+  rnsf rnsl rsys sars sbuf sck smsh ssf suvm svx) -fopenmp -lm
 
 ################################################################################
 # Compilation options
diff --git a/doc/rnatm.1 b/doc/rnatm.1
@@ -0,0 +1,304 @@
+.\" Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+.\" Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+.\" Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+.\" Copyright (C) 2022, 2023, 2025 |Méso|Star>(contact@meso-star.com)
+.\" Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+.\" Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+.\" Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+.\" Copyright (C) 2022, 2023, 2025 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 October 1, 2025
+.Dt RNATM 1
+.Os
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh NAME
+.Nm rnatm
+.Nd check atmospheric data and structures built to manage them
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh SYNOPSIS
+.Nm
+.Op Fl hNv
+.Op Fl a Ar aerosol_opt Ns Op : Ns Ar aerosol_opt No ...
+.Op Fl c
+.Op Fl d Ar octrees
+.Op Fl i Ar storage
+.Op Fl n Ar name
+.Op Fl o Ar storage
+.Op Fl s Ar nu0 , Ns Ar nu1
+.Op Fl T Ar optical_thickness
+.Op Fl t Ar thread_count
+.Op Fl V Ar definition
+.Fl g Ar gas_opt Ns Op : Ns Ar gas_opt No ...
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh DESCRIPTION
+.Nm
+helps to check and diagnose errors in input data as submitted to the RaD-net
+atmospheric library.
+It also makes it easy to check the internal workings of the library, such as the
+construction of structures used to accelerate ray tracing in the heterogeneous
+semi-transparent environment described by the input data.
+.Pp
+In addition to regular verification of the input data format, additional tests
+can be performed
+.Pq option Fl c
+to further validate the data, at the cost of longer execution time.
+For example, enabling this option allows to verify the validity of aerosol
+phase function indices with respect to the mesh to which they are associated and
+the list of loaded phase functions.
+.Pp
+The options are as follows:
+.Bl -tag -width Ds
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl a Ar aerosol
+Define an aerosol.
+Use this option once per aerosol, and duplicate it as many times as
+necessary.
+.Pp
+The aerosol options are as follows:
+.Bl -tag -width Ds
+.It Cm mesh= Ns Ar volume_mesh
+Aerosol tetrahedral mesh saved in
+.Xr smsh 5
+format.
+.It Cm name= Ns Ar string
+Name assigned to the aerosol.
+.It Cm radprop= Ns Ar radiative_properties
+Radiatve properties of the aerosol saved in
+.Xr sars 5
+format.
+Radiative properties are defined per volumetric mesh node.
+This file and the tetrahedral mesh
+.Pq option Cm mesh
+must therefore be consistent with each other, i.e. the nodes must be
+listed in the same order.
+.It Cm phasefn= Ns Ar phase_functions_list
+List in
+.Xr rnsl 5
+format of phase functions to be loaded.
+Each phase function is saved in
+.Xr rnsf 5
+format.
+The correspondence between these phase functions and the nodes of the
+volumetric mesh is defined in another file
+.Pq option Cm phaseids .
+.It Cm phaseids= Ns Ar per_node_phase_function
+Path to the
+.Xr rnpfi 5
+file that stores the index of the phase function to be used per
+volumetric mesh node.
+The list of phase function is defined in another file
+.Pq option Cm phasefn .
+Note that this file and the tetrahedral mesh
+.Pq option Cm mesh
+must be consistent with each other, i.e. the nodes must be
+listed in the same order.
+.El
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl c
+Thorough data validation.
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl d Ar octrees
+Write the builded acceleration structures (i.e., the octrees) to file according
+to the VTK file format.
+They are written to standard ouput if the file is a dash
+.Pq - .
+To split the resulting file
+into
+.Ar n
+VTK files, each storing an octree, one can use the csplit command.
+For example with
+.Ar n
+= 4:
+.Bd -literal -offset Ds
+csplit -f octree -k file %^#\ vtk% /^#\ vtk/ {2};
+.Ed
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl g Ar gas_opt Ns Op : Ns Ar gas_opt No ...
+Gas mixture.
+.Pp
+The gas options are as follows:
+.Bl -tag -width Ds
+.It Cm mesh= Ns Ar volumetric_mesh
+Gas tetrahedral mesh saved in
+.Xr smsh 5
+format.
+.It Cm ck= Ns Ar correlated_k
+Correlated K fof the gas saved in
+.Xr sck 5
+format.
+The correlated K are defined per volumetric mesh node.
+This file and the tetrahedral mesh
+.Pq option Cm mesh
+must therefore be consistent with each other, i.e. the nodes must be
+listed in the same order.
+.It Cm temp= Ns Ar temperature
+Gas temperatures saved in
+.Xr rngt 5
+format.
+The temperature is defined per volumetric mesh node.
+This file and the tetrahedral mesh
+.Pq option Cm mesh
+must therefore be consistent with each other, i.e. the nodes must be
+listed in the same order.
+.El
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl h
+Display short help and exit.
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl i Ar storage
+Acceleration structures are not built from scratch, but loaded from the
+.Ar storage
+file.
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl N
+Precalculate tetrahedron normals.
+This speeds up execution performance for applications that search for the
+tetrahedron to which a position belongs.
+In return, the memory space used to store normals increases the memory
+footprint.
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl n Ar name
+Atmosphere name.
+Default is
+.Dq atmosphere .
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl o Ar storage
+Offload acceleration structures to the
+.Ar storage
+file.
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl s Ar nu0 , Ns Ar nu1
+Spectral range to consider
+.Pq in nanometers .
+Default is visible spectrum, i.e., [380, 780] nm.
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl T Ar optical_thickness
+Optical thickness criteria for the construction of acceleration structures.
+Default is 1.
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl t Ar thread_count
+Advice on the number of threads to use to build acceleration structures.
+Default assumes as many threads as processor cores.
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl V Ar definition
+Advice on the definition of the acceleration structures along the 3 axis.
+Default is 512.
+.\""""""""""""""""""""""""""""""""""""""
+.It Fl v
+Make
+.Nm
+Verbose.
+.El
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh EXIT STATUS
+.Ex -std
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh EXAMPLES
+A
+.Nm
+command line can be lengthy due to the options required to describe the
+atmopshere.
+For editing purposes, the following command line spans multiple lines using the
+backslash character
+.Pq \e .
+While there's nothing original about this practice, we'd like to
+emphasize the importance of spaces or their absence before the backslash
+character, particularly for options defining aerosols
+.Pq option Fl a :
+their argument must be a single character string with no spaces other
+than those that may be required for file names.
+.Bd -literal -offset Ds
+rnatm -v -c \\
+      -g mesh=gas.smsh:ck=gas.sck:temp=gas.rngt \\
+      -a name=clouds\\
+:mesh=clouds_tetrahedra.smsh\\
+:radprop=clouds_properties.sars\\
+:phasefn=clouds_phase_functions.rnsf\\
+:phaseids=clouds_phase_function_ids.rnpfi \\
+      -a name=haze\\
+:mesh=haze_tetrahedra.smsh\\
+:radprop=haze_properties.sars\\
+:phasefn=haze_phase_functions.rnsf\\
+:phaseids=haze_phase_function_ids.rnpfi \\
+      -N \\
+      -T 10 \\
+      -V 1024
+      -o storage.bin
+.Ed
+.Pp
+The above command line runs
+.Nm
+in a verbose way
+.Pq option Fl v
+for a thorough verification of the input data
+.Pq option Fl c .
+The gas of the planetary atmosphere
+.Pq option Fl g
+is described by the tetrahedral mesh recorded in the
+.Pa gas.smsh
+file, while its spectral data and temperature are given by the files
+.Pa gas.sck
+and
+.Pa gas.rngt ,
+respectively.
+.Pp
+Two aerosols complete the planetary atmosphere
+.Pq option Fl a :
+one for
+.Ar clouds
+and one for
+.Ar haze .
+Their respective meshes are stored in the
+.Pa clouds_tetrahedra.smsh No and Pa haze_tetrahedra.smsh
+files while their radiative properties are given by the
+.Pa clouds_properties.sars No and Pa haze_properties.sars
+files.
+Finally, their phase functions are described by a set of 2 files: the
+.Pa clouds_phase_functions.rnsf No and Pa haze_phase_functions.rnsf
+files which list the aerosol phase functions,
+and the
+.Pa clouds_phase_function_ids.rnpfi No and Pa haze_phase_function_ids.rnpfi
+files which reference them by volumetric mesh node.
+.Pp
+The normals of the tetrahedral meshes of the gas and aerosols are
+precalculated
+once and for all
+.Pq option Fl N .
+The definition of acceleration structures
+cannot exceed
+.Ar 1024^3
+.Pq option Fl V
+and its voxels can be merged until their optical thickness
+is greater than
+.Ar 10
+.Pq option Fl T .
+These structures are finally stored in
+.Pa storage.bin
+.Pq option Fl o .
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh SEE ALSO
+.Xr htrdr-planets 1 ,
+.Xr rnpfi 5 ,
+.Xr rnsf 5 ,
+.Xr rnsl 5 ,
+.Xr sars 5 ,
+.Xr sck 5 ,
+.Xr smsh 5
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh HISTORY
+.Nm
+has been developed as part of
+.Ql ANR-21-CE49-0020
+RaD-net project.
diff --git a/doc/rngt.5 b/doc/rngt.5
@@ -0,0 +1,94 @@
+.\" Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+.\" Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+.\" Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+.\" Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+.\" Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+.\" Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+.\" Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+.\" Copyright (C) 2022, 2023, 2025 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/doc/rnpfi.5 b/doc/rnpfi.5
@@ -0,0 +1,93 @@
+.\" Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+.\" Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+.\" Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+.\" Copyright (C) 2022, 2023, 2025 |Méso|Star>(contact@meso-star.com)
+.\" Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+.\" Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+.\" Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+.\" Copyright (C) 2022, 2023, 2025 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/make.sh b/make.sh
@@ -1,46 +0,0 @@
-#!/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/rngt.5 b/rngt.5
@@ -1,94 +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/>.
-.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
@@ -1,93 +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/>.
-.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.c b/src/rnatm.c
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm.h b/src/rnatm.h
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_c.h b/src/rnatm_c.h
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_log.c b/src/rnatm_log.c
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_log.h b/src/rnatm_log.h
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_main.c b/src/rnatm_main.c
@@ -0,0 +1,424 @@
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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/>. */
+
+#define _POSIX_C_SOURCE 200809L /* strdup, strtok_r */
+
+#include "rnatm.h"
+
+#include <rsys/cstr.h>
+#include <rsys/mem_allocator.h>
+#include <rsys/rsys.h>
+#include <rsys/stretchy_array.h>
+
+#include <getopt.h>
+#include <string.h>
+
+struct args {
+  struct rnatm_create_args rnatm;
+  const char* vtk_filename;
+  int check;
+  int quit;
+};
+#define ARGS_DEFAULT__ { RNATM_CREATE_ARGS_DEFAULT__, NULL, 0, 0 }
+static const struct args ARGS_DEFAULT = ARGS_DEFAULT__;
+
+/*******************************************************************************
+ * Helper functions
+ ******************************************************************************/
+static void
+usage(FILE* stream)
+{
+  ASSERT(stream);
+  fprintf(stream,
+"usage: rnatm [-hNv] [-a aerosol_opt[:aerosol_opt ...]] [-c] [-d octrees]\n"
+"              [-i storage] [-n name] [-o storage] [-s nu0,nu1]\n"
+"              [-T optical_thickness] [-t thread_count] [-V definition]\n"
+"              -g gas_opt[:gas_opt ...]\n");
+}
+
+static res_T
+parse_gas_parameters(const char* str, void* ptr)
+{
+  enum { MESH, CK, TEMP } iparam;
+  char buf[BUFSIZ];
+  struct args* args = ptr;
+  char* key;
+  char* val;
+  char* tk_ctx;
+  res_T res = RES_OK;
+  ASSERT(args && str);
+
+  if(strlen(str) >= sizeof(buf) -1/*NULL char*/) {
+    fprintf(stderr, "Could not duplicate the gas parameter `%s'\n", str);
+    res = RES_MEM_ERR;
+    goto error;
+  }
+  strncpy(buf, str, sizeof(buf));
+
+  key = strtok_r(buf, "=", &tk_ctx);
+  val = strtok_r(NULL, "", &tk_ctx);
+
+       if(!strcmp(key, "mesh")) iparam = MESH;
+  else if(!strcmp(key, "ck")) iparam = CK;
+  else if(!strcmp(key, "temp")) iparam = TEMP;
+  else {
+    fprintf(stderr, "Invalid gas parameter `%s'\n", key);
+    res = RES_BAD_ARG;
+    goto error;
+  }
+
+  if(!val) {
+    fprintf(stderr, "Invalid null value for gas parameter `%s'\n", key);
+    res = RES_BAD_ARG;
+    goto error;
+  }
+
+  switch(iparam) {
+    case MESH:
+      args->rnatm.gas.smsh_filename = strdup(val);
+      if(!args->rnatm.gas.smsh_filename) res = RES_MEM_ERR;
+      break;
+    case CK:
+      args->rnatm.gas.sck_filename = strdup(val);
+      if(!args->rnatm.gas.sck_filename) res = RES_MEM_ERR;
+      break;
+    case TEMP:
+      args->rnatm.gas.temperatures_filename = strdup(val);
+      if(!args->rnatm.gas.temperatures_filename) res = RES_MEM_ERR;
+      break;
+    default: FATAL("Unreachable code\n"); break;
+  }
+  if(res != RES_OK) {
+    fprintf(stderr, "Unable to parse the gas parameter `%s' -- %s\n",
+      str, res_to_cstr(res));
+    goto error;
+  }
+
+exit:
+  return res;
+error:
+  goto exit;
+}
+
+static res_T
+parse_aerosol_parameters(const char* str, void* ptr)
+{
+  enum { MESH, NAME, RADPROP, PHASEFN, PHASEIDS } iparam;
+  struct rnatm_aerosol_args* aerosol = NULL;
+  char buf[BUFSIZ];
+  struct args* args = ptr;
+  char* key;
+  char* val;
+  char* tk_ctx;
+  res_T res = RES_OK;
+  ASSERT(args && str);
+
+  if(strlen(str) >= sizeof(buf) -1/*NULL char*/) {
+    fprintf(stderr, "Could not duplicate the aerosol parameter `%s'\n", str);
+    res = RES_MEM_ERR;
+    goto error;
+  }
+  strncpy(buf, str, sizeof(buf));
+
+  key = strtok_r(buf, "=", &tk_ctx);
+  val = strtok_r(NULL, "", &tk_ctx);
+
+       if(!strcmp(key, "mesh")) iparam = MESH;
+  else if(!strcmp(key, "name")) iparam = NAME;
+  else if(!strcmp(key, "radprop")) iparam = RADPROP;
+  else if(!strcmp(key, "phasefn")) iparam = PHASEFN;
+  else if(!strcmp(key, "phaseids")) iparam = PHASEIDS;
+  else {
+    fprintf(stderr, "Invalid aerosol parameter `%s'\n", key);
+    res = RES_BAD_ARG;
+    goto error;
+  }
+
+  if(!val) {
+    fprintf(stderr, "Invalid null value for aerosol parameter `%s'\n", key);
+    res = RES_BAD_ARG;
+    goto error;
+  }
+
+  ASSERT(args->rnatm.naerosols);
+  aerosol = args->rnatm.aerosols + (args->rnatm.naerosols - 1);
+
+  switch(iparam) {
+    case MESH:
+      aerosol->smsh_filename = strdup(val);
+      if(!aerosol->smsh_filename) res = RES_MEM_ERR;
+      break;
+    case NAME:
+      aerosol->name = strdup(val);
+      if(!aerosol->name) res = RES_MEM_ERR;
+      break;
+    case RADPROP:
+      aerosol->sars_filename = strdup(val);
+      if(!aerosol->sars_filename) res = RES_MEM_ERR;
+      break;
+    case PHASEFN:
+      aerosol->phase_fn_lst_filename = strdup(val);
+      if(!aerosol->phase_fn_lst_filename) res = RES_MEM_ERR;
+      break;
+    case PHASEIDS:
+      aerosol->phase_fn_ids_filename = strdup(val);
+      if(!aerosol->phase_fn_ids_filename) res = RES_MEM_ERR;
+      break;
+    default: FATAL("Unreachable code\n"); break;
+  }
+  if(res != RES_OK) {
+    fprintf(stderr, "Unable to parse the aerosol parameter `%s' -- %s\n",
+      str, res_to_cstr(res));
+    goto error;
+  }
+
+exit:
+  return res;
+error:
+  goto exit;
+}
+
+static res_T
+parse_spectral_range(struct args* args, char* str)
+{
+  size_t len = 0;
+  res_T res = RES_OK;
+  ASSERT(args && str);
+
+  res = cstr_to_list_double(str, ',', args->rnatm.spectral_range, &len, 2);
+  if(res == RES_OK && len != 2) res = RES_BAD_ARG;
+  if(res != RES_OK) goto error;
+
+  if(args->rnatm.spectral_range[0] < 0
+  || args->rnatm.spectral_range[1] < 0
+  || args->rnatm.spectral_range[0] > args->rnatm.spectral_range[1])
+    goto error;
+
+exit:
+  return res;
+error:
+  goto exit;
+}
+
+static void
+args_release(struct args* args)
+{
+  size_t i;
+  ASSERT(args);
+  if(args->rnatm.gas.smsh_filename) free(args->rnatm.gas.smsh_filename);
+  if(args->rnatm.gas.sck_filename) free(args->rnatm.gas.sck_filename);
+  if(args->rnatm.gas.temperatures_filename)
+    free(args->rnatm.gas.temperatures_filename);
+  if(args->rnatm.octrees_storage) CHK(fclose(args->rnatm.octrees_storage) == 0);
+
+  FOR_EACH(i, 0, args->rnatm.naerosols) {
+    struct rnatm_aerosol_args* aerosol = args->rnatm.aerosols + i;
+    if(aerosol->name) free(aerosol->name);
+    if(aerosol->smsh_filename) free(aerosol->smsh_filename);
+    if(aerosol->sars_filename) free(aerosol->sars_filename);
+    if(aerosol->phase_fn_ids_filename) free(aerosol->phase_fn_ids_filename);
+    if(aerosol->phase_fn_lst_filename) free(aerosol->phase_fn_lst_filename);
+  }
+  sa_release(args->rnatm.aerosols);
+  *args = ARGS_DEFAULT;
+}
+
+static res_T
+args_init(struct args* args, int argc, char** argv)
+{
+  const char* storage_filename = NULL;
+  size_t i = 0;
+  res_T res = RES_OK;
+  int opt;
+  ASSERT(args && argc && argv);
+
+  *args = ARGS_DEFAULT;
+
+  while((opt = getopt(argc, argv, "a:cd:g:hi:Nn:o:s:T:t:V:v")) != -1) {
+    switch(opt) {
+      case 'a':
+        (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);
+        break;
+      case 'c': args->check = 1; break;
+      case 'd': args->vtk_filename = optarg; break;
+      case 'g':
+        res = cstr_parse_list(optarg, ':', parse_gas_parameters, args);
+        break;
+      case 'h':
+        usage(stdout);
+        args_release(args);
+        args->quit = 1;
+        goto exit;
+      case 'N': args->rnatm.precompute_normals = 1; break;
+      case 'n': args->rnatm.name = optarg; break;
+      case 'o':
+        args->rnatm.load_octrees_from_storage = 0;
+        storage_filename = optarg;
+        break;
+      case 'i':
+        args->rnatm.load_octrees_from_storage = 1;
+        storage_filename = optarg;
+        break;
+      case 's':
+        res = parse_spectral_range(args, optarg);
+        break;
+      case 'T':
+        res = cstr_to_double(optarg, &args->rnatm.optical_thickness);
+        if(res != RES_OK && args->rnatm.optical_thickness<=0) res = RES_BAD_ARG;
+        break;
+      case 't':
+        res = cstr_to_uint(optarg, &args->rnatm.nthreads);
+        if(res == RES_OK && !args->rnatm.nthreads) res = RES_BAD_ARG;
+        break;
+      case 'V':
+        res = cstr_to_uint(optarg, &args->rnatm.grid_definition_hint);
+        if(res == RES_OK && !args->rnatm.grid_definition_hint) res = RES_BAD_ARG;
+        break;
+      case 'v': args->rnatm.verbose = 1; break;
+      default: res = RES_BAD_ARG; break;
+    }
+    if(res != RES_OK) {
+      if(optarg) {
+        fprintf(stderr, "%s: invalid option args `%s' -- `%c'\n",
+          argv[0], optarg, opt);
+      }
+      goto error;
+    }
+  }
+
+  if(storage_filename) {
+    const char* mode = args->rnatm.load_octrees_from_storage ? "r" : "w+";
+    args->rnatm.octrees_storage = fopen(storage_filename, mode);
+    if(!args->rnatm.octrees_storage) {
+      fprintf(stderr, "Unable to open octree storage file %s\n",
+        storage_filename);
+      res = RES_IO_ERR;
+      goto error;
+    }
+  }
+
+  /* Check the required options */
+  if(!args->rnatm.gas.smsh_filename
+  || !args->rnatm.gas.sck_filename
+  || !args->rnatm.gas.temperatures_filename) {
+    fprintf(stderr, "Incomplete gas definition -- option `-g'\n");
+    res = RES_BAD_ARG;
+    goto error;
+  }
+
+  FOR_EACH(i, 0, args->rnatm.naerosols) {
+    struct rnatm_aerosol_args* aerosol = args->rnatm.aerosols + i;
+
+    if(!aerosol->smsh_filename
+    || !aerosol->sars_filename
+    || !aerosol->phase_fn_ids_filename
+    || !aerosol->phase_fn_lst_filename) {
+      fprintf(stderr, "Incomplete %lu^th aerosol definition -- option `-a'\n",
+        (unsigned long)i);
+      res = RES_BAD_ARG;
+      goto error;
+    }
+  }
+
+exit:
+  return res;
+error:
+  usage(stderr);
+  args_release(args);
+  goto exit;
+}
+
+static res_T
+write_vtk_octrees(struct rnatm* atm, const char* filename)
+{
+  size_t octrees_range[2];
+  FILE* fp = NULL;
+  res_T res = RES_OK;
+  ASSERT(atm && filename);
+
+  if(!strcmp(filename, "-")) {
+    fp = stdout;
+  } else {
+    fp = fopen(filename, "w");
+    if(!fp) {
+      fprintf(stderr, "Could not open `%s' -- %s\n", filename, strerror(errno));
+      res = RES_IO_ERR;
+      goto error;
+    }
+  }
+
+  octrees_range[0] = 0;
+  octrees_range[1] = rnatm_get_spectral_items_count(atm) - 1;
+
+  res = rnatm_write_vtk_octrees(atm, octrees_range, fp);
+  if(res != RES_OK) goto error;
+
+exit:
+  if(fp != stdout) CHK(fclose(fp) == 0);
+  return res;
+error:
+  goto exit;
+}
+
+/*******************************************************************************
+ * Main function
+ ******************************************************************************/
+int
+main(int argc, char** argv)
+{
+  struct args  args = ARGS_DEFAULT;
+  struct rnatm* atm = NULL;
+  res_T res = RES_OK;
+  int err = 0;
+
+  res = args_init(&args, argc, argv);
+  if(res != RES_OK) goto error;
+
+  res = rnatm_create(&args.rnatm, &atm);
+  if(res != RES_OK) goto error;
+
+  if(args.check) {
+    res = rnatm_validate(atm);
+    if(res != RES_OK) goto error;
+  }
+
+  if(args.vtk_filename) {
+    res = write_vtk_octrees(atm, args.vtk_filename);
+    if(res != RES_OK) goto error;
+  }
+
+exit:
+  args_release(&args);
+  if(atm) RNATM(ref_put(atm));
+  if(mem_allocated_size() != 0) {
+    fprintf(stderr, "Memory leaks: %lu bytes\n",
+      (unsigned long)mem_allocated_size());
+    err = -1;
+  }
+  return err;
+error:
+  err = -1;
+  goto exit;
+}
diff --git a/src/rnatm_mesh.c b/src/rnatm_mesh.c
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_octree.c b/src/rnatm_octree.c
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_octrees_storage.c b/src/rnatm_octrees_storage.c
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_octrees_storage.h b/src/rnatm_octrees_storage.h
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_properties.c b/src/rnatm_properties.c
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_radcoef.c b/src/rnatm_radcoef.c
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_voxel.h b/src/rnatm_voxel.h
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_voxel_partition.c b/src/rnatm_voxel_partition.c
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_voxel_partition.h b/src/rnatm_voxel_partition.h
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/rnatm_write_vtk.c b/src/rnatm_write_vtk.c
@@ -1,11 +1,11 @@
-/* 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
+/* Copyright (C) 2022, 2023, 2025 Centre National de la Recherche Scientifique
+ * Copyright (C) 2022, 2023, 2025 Institut Pierre-Simon Laplace
+ * Copyright (C) 2022, 2023, 2025 Institut de Physique du Globe de Paris
+ * Copyright (C) 2022, 2023, 2025 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022, 2023, 2025 Observatoire de Paris
+ * Copyright (C) 2022, 2023, 2025 Université de Reims Champagne-Ardenne
+ * Copyright (C) 2022, 2023, 2025 Université de Versaille Saint-Quentin
+ * Copyright (C) 2022, 2023, 2025 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
diff --git a/src/test_rnatm.c b/src/test_rnatm.c
@@ -1,485 +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/>. */
-
-#define _POSIX_C_SOURCE 200809L /* strdup, strtok_r */
-
-#include "rnatm.h"
-
-#include <rsys/cstr.h>
-#include <rsys/mem_allocator.h>
-#include <rsys/rsys.h>
-#include <rsys/stretchy_array.h>
-
-#include <getopt.h>
-#include <string.h>
-
-struct args {
-  struct rnatm_create_args rnatm;
-  const char* vtk_filename;
-  int check;
-  int quit;
-};
-#define ARGS_DEFAULT__ { RNATM_CREATE_ARGS_DEFAULT__, NULL, 0, 0 }
-static const struct args ARGS_DEFAULT = ARGS_DEFAULT__;
-
-/*******************************************************************************
- * Helper functions
- ******************************************************************************/
-static void
-print_help(const char* cmd)
-{
-  ASSERT(cmd);
-  printf(
-"Usage: %s -g gas\n"
-"Test the Rad-Net ATMosphere library\n\n",
-    cmd);
-  printf(
-"  -a aerosol     atmospheric aerosol. Use this option as many times as\n"
-"                 there are aerosols to declare. An aerosol is defined\n"
-"                 by the following parameters, each parameter is\n"
-"                 separated from the previous one by a colon (:)\n\n");
-  printf(
-"                   mesh=path       aerosol mesh (smsh(5))\n"
-"                   name=string     aerosol name\n"
-"                   radprop=path    radiative properties (sars(5))\n"
-"                   phasefn=path    list of phase functions (rnsl(5))\n"
-"                   phaseids=path   phase function id by node (rnpfi(5))\n\n");
-  printf(
-"  -c             check data\n");
-  printf(
-"  -d file        write the builded octrees to file according to the VTK\n"
-"                 file format. The octrees are written to standard ouput\n"
-"                 if the file is a dash (-). To split the resulting file\n"
-"                 into n VTK files, each storing an octree, one can use\n"
-"                 the csplit command. For example with n = 4:\n\n");
-  printf(
-"                   csplit -f octree -k file %%^#\\ vtk%% /^#\\ vtk/ {2}\n\n");
-  printf(
-"  -g gas         atmospheric gas mixture. This mixture is defined by\n"
-"                 the following parameters, each parameter is separated\n"
-"                 from the previous one by a colon (:)\n\n");
-  printf(
-"                   mesh=path       gas mesh (smsh(5))\n"
-"                   ck=path         correlated-K of the mixture (sck(5))\n"
-"                   temp=path       temperatures (rngt(5))\n\n");
-  printf(
-"  -h             display this help and exit\n");
-  printf(
-"  -i file        octrees are loaded from file\n");
-  printf(
-"  -N             precompute_normals the tetrahedra normals\n");
-  printf(
-"  -n             atmosphere name. Default is `%s'\n",
-    ARGS_DEFAULT.rnatm.name);
-  printf(
-"  -o file        offload octrees to file\n");
-  printf(
-"  -s nu0,nu1     spectral range to consider (in nm).\n"
-"                 Default is visible spectrum, i.e [%g, %g] nm\n",
-    ARGS_DEFAULT.rnatm.spectral_range[0],
-    ARGS_DEFAULT.rnatm.spectral_range[1]);
-  printf(
-"  -T threshold   optical thickness criteria for octree building.\n"
-"                 Default is %g\n",
-    ARGS_DEFAULT.rnatm.optical_thickness);
-  printf(
-"  -t nthreads    hint on the number of threads. Default assumes\n"
-"                 as many threads as CPU cores\n");
-  printf(
-"  -V definition  advice on the definiton of the acceleration\n"
-"                 structure along the 3 axes. Default is %u\n",
-    ARGS_DEFAULT.rnatm.grid_definition_hint);
-  printf(
-"  -v             make the program verbose\n");
-  printf("\n");
-  printf(
-"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");
-}
-
-static res_T
-parse_gas_parameters(const char* str, void* ptr)
-{
-  enum { MESH, CK, TEMP } iparam;
-  char buf[BUFSIZ];
-  struct args* args = ptr;
-  char* key;
-  char* val;
-  char* tk_ctx;
-  res_T res = RES_OK;
-  ASSERT(args && str);
-
-  if(strlen(str) >= sizeof(buf) -1/*NULL char*/) {
-    fprintf(stderr, "Could not duplicate the gas parameter `%s'\n", str);
-    res = RES_MEM_ERR;
-    goto error;
-  }
-  strncpy(buf, str, sizeof(buf));
-
-  key = strtok_r(buf, "=", &tk_ctx);
-  val = strtok_r(NULL, "", &tk_ctx);
-
-       if(!strcmp(key, "mesh")) iparam = MESH;
-  else if(!strcmp(key, "ck")) iparam = CK;
-  else if(!strcmp(key, "temp")) iparam = TEMP;
-  else {
-    fprintf(stderr, "Invalid gas parameter `%s'\n", key);
-    res = RES_BAD_ARG;
-    goto error;
-  }
-
-  if(!val) {
-    fprintf(stderr, "Invalid null value for gas parameter `%s'\n", key);
-    res = RES_BAD_ARG;
-    goto error;
-  }
-
-  switch(iparam) {
-    case MESH:
-      args->rnatm.gas.smsh_filename = strdup(val);
-      if(!args->rnatm.gas.smsh_filename) res = RES_MEM_ERR;
-      break;
-    case CK:
-      args->rnatm.gas.sck_filename = strdup(val);
-      if(!args->rnatm.gas.sck_filename) res = RES_MEM_ERR;
-      break;
-    case TEMP:
-      args->rnatm.gas.temperatures_filename = strdup(val);
-      if(!args->rnatm.gas.temperatures_filename) res = RES_MEM_ERR;
-      break;
-    default: FATAL("Unreachable code\n"); break;
-  }
-  if(res != RES_OK) {
-    fprintf(stderr, "Unable to parse the gas parameter `%s' -- %s\n",
-      str, res_to_cstr(res));
-    goto error;
-  }
-
-exit:
-  return res;
-error:
-  goto exit;
-}
-
-static res_T
-parse_aerosol_parameters(const char* str, void* ptr)
-{
-  enum { MESH, NAME, RADPROP, PHASEFN, PHASEIDS } iparam;
-  struct rnatm_aerosol_args* aerosol = NULL;
-  char buf[BUFSIZ];
-  struct args* args = ptr;
-  char* key;
-  char* val;
-  char* tk_ctx;
-  res_T res = RES_OK;
-  ASSERT(args && str);
-
-  if(strlen(str) >= sizeof(buf) -1/*NULL char*/) {
-    fprintf(stderr, "Could not duplicate the aerosol parameter `%s'\n", str);
-    res = RES_MEM_ERR;
-    goto error;
-  }
-  strncpy(buf, str, sizeof(buf));
-
-  key = strtok_r(buf, "=", &tk_ctx);
-  val = strtok_r(NULL, "", &tk_ctx);
-
-       if(!strcmp(key, "mesh")) iparam = MESH;
-  else if(!strcmp(key, "name")) iparam = NAME;
-  else if(!strcmp(key, "radprop")) iparam = RADPROP;
-  else if(!strcmp(key, "phasefn")) iparam = PHASEFN;
-  else if(!strcmp(key, "phaseids")) iparam = PHASEIDS;
-  else {
-    fprintf(stderr, "Invalid aerosol parameter `%s'\n", key);
-    res = RES_BAD_ARG;
-    goto error;
-  }
-
-  if(!val) {
-    fprintf(stderr, "Invalid null value for aerosol parameter `%s'\n", key);
-    res = RES_BAD_ARG;
-    goto error;
-  }
-
-  ASSERT(args->rnatm.naerosols);
-  aerosol = args->rnatm.aerosols + (args->rnatm.naerosols - 1);
-
-  switch(iparam) {
-    case MESH:
-      aerosol->smsh_filename = strdup(val);
-      if(!aerosol->smsh_filename) res = RES_MEM_ERR;
-      break;
-    case NAME:
-      aerosol->name = strdup(val);
-      if(!aerosol->name) res = RES_MEM_ERR;
-      break;
-    case RADPROP:
-      aerosol->sars_filename = strdup(val);
-      if(!aerosol->sars_filename) res = RES_MEM_ERR;
-      break;
-    case PHASEFN:
-      aerosol->phase_fn_lst_filename = strdup(val);
-      if(!aerosol->phase_fn_lst_filename) res = RES_MEM_ERR;
-      break;
-    case PHASEIDS:
-      aerosol->phase_fn_ids_filename = strdup(val);
-      if(!aerosol->phase_fn_ids_filename) res = RES_MEM_ERR;
-      break;
-    default: FATAL("Unreachable code\n"); break;
-  }
-  if(res != RES_OK) {
-    fprintf(stderr, "Unable to parse the aerosol parameter `%s' -- %s\n",
-      str, res_to_cstr(res));
-    goto error;
-  }
-
-exit:
-  return res;
-error:
-  goto exit;
-}
-
-static res_T
-parse_spectral_range(struct args* args, char* str)
-{
-  size_t len = 0;
-  res_T res = RES_OK;
-  ASSERT(args && str);
-
-  res = cstr_to_list_double(str, ',', args->rnatm.spectral_range, &len, 2);
-  if(res == RES_OK && len != 2) res = RES_BAD_ARG;
-  if(res != RES_OK) goto error;
-
-  if(args->rnatm.spectral_range[0] < 0
-  || args->rnatm.spectral_range[1] < 0
-  || args->rnatm.spectral_range[0] > args->rnatm.spectral_range[1])
-    goto error;
-
-exit:
-  return res;
-error:
-  goto exit;
-}
-
-static void
-args_release(struct args* args)
-{
-  size_t i;
-  ASSERT(args);
-  if(args->rnatm.gas.smsh_filename) free(args->rnatm.gas.smsh_filename);
-  if(args->rnatm.gas.sck_filename) free(args->rnatm.gas.sck_filename);
-  if(args->rnatm.gas.temperatures_filename)
-    free(args->rnatm.gas.temperatures_filename);
-  if(args->rnatm.octrees_storage) CHK(fclose(args->rnatm.octrees_storage) == 0);
-
-  FOR_EACH(i, 0, args->rnatm.naerosols) {
-    struct rnatm_aerosol_args* aerosol = args->rnatm.aerosols + i;
-    if(aerosol->name) free(aerosol->name);
-    if(aerosol->smsh_filename) free(aerosol->smsh_filename);
-    if(aerosol->sars_filename) free(aerosol->sars_filename);
-    if(aerosol->phase_fn_ids_filename) free(aerosol->phase_fn_ids_filename);
-    if(aerosol->phase_fn_lst_filename) free(aerosol->phase_fn_lst_filename);
-  }
-  sa_release(args->rnatm.aerosols);
-  *args = ARGS_DEFAULT;
-}
-
-static res_T
-args_init(struct args* args, int argc, char** argv)
-{
-  const char* storage_filename = NULL;
-  size_t i = 0;
-  res_T res = RES_OK;
-  int opt;
-  ASSERT(args && argc && argv);
-
-  *args = ARGS_DEFAULT;
-
-  while((opt = getopt(argc, argv, "a:cd:g:hi:Nn:o:s:T:t:V:v")) != -1) {
-    switch(opt) {
-      case 'a':
-        (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);
-        break;
-      case 'c': args->check = 1; break;
-      case 'd': args->vtk_filename = optarg; break;
-      case 'g':
-        res = cstr_parse_list(optarg, ':', parse_gas_parameters, args);
-        break;
-      case 'h':
-        print_help(argv[0]);
-        args_release(args);
-        args->quit = 1;
-        goto exit;
-      case 'N': args->rnatm.precompute_normals = 1; break;
-      case 'n': args->rnatm.name = optarg; break;
-      case 'o':
-        args->rnatm.load_octrees_from_storage = 0;
-        storage_filename = optarg;
-        break;
-      case 'i':
-        args->rnatm.load_octrees_from_storage = 1;
-        storage_filename = optarg;
-        break;
-      case 's':
-        res = parse_spectral_range(args, optarg);
-        break;
-      case 'T':
-        res = cstr_to_double(optarg, &args->rnatm.optical_thickness);
-        if(res != RES_OK && args->rnatm.optical_thickness<=0) res = RES_BAD_ARG;
-        break;
-      case 't':
-        res = cstr_to_uint(optarg, &args->rnatm.nthreads);
-        if(res == RES_OK && !args->rnatm.nthreads) res = RES_BAD_ARG;
-        break;
-      case 'V':
-        res = cstr_to_uint(optarg, &args->rnatm.grid_definition_hint);
-        if(res == RES_OK && !args->rnatm.grid_definition_hint) res = RES_BAD_ARG;
-        break;
-      case 'v': args->rnatm.verbose = 1; break;
-      default: res = RES_BAD_ARG; break;
-    }
-    if(res != RES_OK) {
-      if(optarg) {
-        fprintf(stderr, "%s: invalid option args `%s' -- `%c'\n",
-          argv[0], optarg, opt);
-      }
-      goto error;
-    }
-  }
-
-  if(storage_filename) {
-    const char* mode = args->rnatm.load_octrees_from_storage ? "r" : "w+";
-    args->rnatm.octrees_storage = fopen(storage_filename, mode);
-    if(!args->rnatm.octrees_storage) {
-      fprintf(stderr, "Unable to open octree storage file %s\n",
-        storage_filename);
-      res = RES_IO_ERR;
-      goto error;
-    }
-  }
-
-  /* Check the required options */
-  if(!args->rnatm.gas.smsh_filename
-  || !args->rnatm.gas.sck_filename
-  || !args->rnatm.gas.temperatures_filename) {
-    fprintf(stderr, "Incomplete gas definition -- option `-g'\n");
-    res = RES_BAD_ARG;
-    goto error;
-  }
-
-  FOR_EACH(i, 0, args->rnatm.naerosols) {
-    struct rnatm_aerosol_args* aerosol = args->rnatm.aerosols + i;
-
-    if(!aerosol->smsh_filename
-    || !aerosol->sars_filename
-    || !aerosol->phase_fn_ids_filename
-    || !aerosol->phase_fn_lst_filename) {
-      fprintf(stderr, "Incomplete %lu^th aerosol definition -- option `-a'\n",
-        (unsigned long)i);
-      res = RES_BAD_ARG;
-      goto error;
-    }
-  }
-
-exit:
-  return res;
-error:
-  args_release(args);
-  goto exit;
-}
-
-static res_T
-write_vtk_octrees(struct rnatm* atm, const char* filename)
-{
-  size_t octrees_range[2];
-  FILE* fp = NULL;
-  res_T res = RES_OK;
-  ASSERT(atm && filename);
-
-  if(!strcmp(filename, "-")) {
-    fp = stdout;
-  } else {
-    fp = fopen(filename, "w");
-    if(!fp) {
-      fprintf(stderr, "Could not open `%s' -- %s\n", filename, strerror(errno));
-      res = RES_IO_ERR;
-      goto error;
-    }
-  }
-
-  octrees_range[0] = 0;
-  octrees_range[1] = rnatm_get_spectral_items_count(atm) - 1;
-
-  res = rnatm_write_vtk_octrees(atm, octrees_range, fp);
-  if(res != RES_OK) goto error;
-
-exit:
-  if(fp != stdout) CHK(fclose(fp) == 0);
-  return res;
-error:
-  goto exit;
-}
-
-/*******************************************************************************
- * Main function
- ******************************************************************************/
-int
-main(int argc, char** argv)
-{
-  struct args  args = ARGS_DEFAULT;
-  struct rnatm* atm = NULL;
-  res_T res = RES_OK;
-  int err = 0;
-
-  res = args_init(&args, argc, argv);
-  if(res != RES_OK) goto error;
-
-  res = rnatm_create(&args.rnatm, &atm);
-  if(res != RES_OK) goto error;
-
-  if(args.check) {
-    res = rnatm_validate(atm);
-    if(res != RES_OK) goto error;
-  }
-
-  if(args.vtk_filename) {
-    res = write_vtk_octrees(atm, args.vtk_filename);
-    if(res != RES_OK) goto error;
-  }
-
-exit:
-  args_release(&args);
-  if(atm) RNATM(ref_put(atm));
-  if(mem_allocated_size() != 0) {
-    fprintf(stderr, "Memory leaks: %lu bytes\n",
-      (unsigned long)mem_allocated_size());
-    err = -1;
-  }
-  return err;
-error:
-  err = -1;
-  goto exit;
-}