From 3d5a47928b356c86c0845c6fb0781599c05ea21f Mon Sep 17 00:00:00 2001 From: Joe Zuntz Date: Thu, 28 Nov 2024 09:34:24 +0000 Subject: [PATCH 01/15] update to class 3.2.5 --- boltzmann/class/class_v3.2.0/doc/README | 12 - .../class/class_v3.2.0/doc/input/chap2.md | 138 - .../class/class_v3.2.0/doc/input/chap3.md | 536 -- .../class/class_v3.2.0/doc/input/doxyconf | 2575 ------ .../class/class_v3.2.0/doc/input/doxygen.sty | 577 -- .../class/class_v3.2.0/doc/input/intro.md | 211 - .../class_v3.2.0/doc/input/latex/class.aux | 19 - .../class_v3.2.0/doc/input/latex/class.log | 336 - .../class_v3.2.0/doc/input/latex/class.pdf | Bin 191829 -> 0 bytes .../doc/input/latex/class.synctex.gz | Bin 80218 -> 0 bytes .../class_v3.2.0/doc/input/latex/class.tex | 605 -- .../class/class_v3.2.0/doc/input/make1.sh | 14 - .../class/class_v3.2.0/doc/input/make2.sh | 12 - boltzmann/class/class_v3.2.0/doc/input/mod.md | 40 - .../external/HyRec2020/output_xe.dat | 8000 ----------------- 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You can find it here: - https://github.com/lesgourg/class_public/raw/master/doc/manual/CLASS_MANUAL.pdf - -* the files in doc/input/ are auxiliary files for generating it - -* if you wish to update this manual yourself using doxygen, look at instructions in section 6 of CLASS_MANUAL.pdf - -* there is also an html version that you can access from the CLASS webpages. The html version used to be distributed together with CLASS, but we removed it because the html directory was too big. If you do wish to get the html source files on your own computer, you just need to recompile the manual with "cd doc/input/; ./make1.sh" (assuming that you have doxygen installed). \ No newline at end of file diff --git a/boltzmann/class/class_v3.2.0/doc/input/chap2.md b/boltzmann/class/class_v3.2.0/doc/input/chap2.md deleted file mode 100644 index 887b3f29..00000000 --- a/boltzmann/class/class_v3.2.0/doc/input/chap2.md +++ /dev/null @@ -1,138 +0,0 @@ -Where to find information and documentation on CLASS? -====================================================== - -Author: Julien Lesgourgues - - -* __For what the code can actually compute__: all possible input parameters, all coded cosmological models, all functionalities, all observables, etc.: read the file `explanatory.ini` in the main `CLASS` directory: it is THE reference file where we keep track of all possible input and the definition of all input parameters. For that reason we recommend to leave it always unchanged and to work with copies of it, or with short input files written from scratch. - - -* __For the structure, style, and concrete aspects of the code__: this documentation, especially the `CLASS overview` chapter (the extensive automatically-generated part of this documentation is more for advanced users); plus the slides of our `CLASS` lectures, for instance those from New York 2019 available at - - `https://lesgourg.github.io/class-tour-NewYork.html` - - An updated overview of available `CLASS` lecture slides is always available at - - `http://lesgourg.github.io/courses.html` - - in the section `Courses on numerical tools`. - - -* __For the python wrapper of `CLASS`__: at the moment, the best are the "Usage I" and "Usage II" slides of the New York 2019 course, - - `https://lesgourg.github.io/class-tour-NewYork.html` - -* __For the physics and equations used in the code__: mainly, the following papers: - - *Cosmological perturbation theory in the synchronous and conformal Newtonian gauges* - - C. P. Ma and E. Bertschinger. - - http://arxiv.org/abs/astro-ph/9506072 - - 10.1086/176550 - - Astrophys. J. __455__, 7 (1995) - - - *The Cosmic Linear Anisotropy Solving System (CLASS) II: Approximation schemes* - - D. Blas, J. Lesgourgues and T. Tram. - - http://arxiv.org/abs/1104.2933 [astro-ph.CO] - - 10.1088/1475-7516/2011/07/034 - - JCAP __1107__, 034 (2011) - - - *The Cosmic Linear Anisotropy Solving System (CLASS) IV: efficient implementation of non-cold relics* - - J. Lesgourgues and T. Tram. - - http://arxiv.org/abs/1104.2935 [astro-ph.CO] - - 10.1088/1475-7516/2011/09/032 - - JCAP __1109__, 032 (2011) - - - *Optimal polarisation equations in FLRW universes* - - T. Tram and J. Lesgourgues. - - http://arxiv.org/abs/1305.3261 [astro-ph.CO] - - 10.1088/1475-7516/2013/10/002 - - JCAP __1310__, 002 (2013) - - - *Fast and accurate CMB computations in non-flat FLRW universes* - - J. Lesgourgues and T. Tram. - - http://arxiv.org/abs/1312.2697 [astro-ph.CO] - - 10.1088/1475-7516/2014/09/032 - - JCAP __1409__, no. 09, 032 (2014) - - - *The CLASSgal code for Relativistic Cosmological Large Scale Structure* - - E. Di Dio, F. Montanari, J. Lesgourgues and R. Durrer. - - http://arxiv.org/abs/1307.1459 [astro-ph.CO] - - 10.1088/1475-7516/2013/11/044 - - JCAP __1311__, 044 (2013) - - - *The synergy between CMB spectral distortions and anisotropies* - - M. Lucca, N. Schöneberg, D. C. Hooper, J. Lesgourgues, J. Chluba. - - http://arxiv.org/abs/1910.04619 [astro-ph.CO] - - JCAP 02 (2020) 026 - - - *Optimal Boltzmann hierarchies with nonvanishing spatial curvature* - - C. Pitrou, T. S. Pereira, J. Lesgourgues, - - http://arxiv.org/abs/2005.12119 [astro-ph.CO] - - Phys.Rev.D 102 (2020) 2, 023511 - - Plus also some latex notes on specific sectors: - - - *Equations for perturbed recombination* - - (can be turned on optionally by the user since v2.1.0) - - L. Voruz. - - http://lesgourg.github.io/class_public/perturbed_recombination.pdf - - - *PPF formalism in Newtonian and synchronous gauge* - - (used by default for the fluid perturbations since v2.6.0) - - T. Tram. - - http://lesgourg.github.io/class_public/PPF_formalism.pdf - - Interactions between idm and idr are modelled by the ETHOS formalism of Cyr-Racine et al. [1512.05344]. This was introduced in Class v2.9 with a parametrisation described in - - - *Constraining Dark Matter-Dark Radiation interactions with CMB, BAO, and Lyman-alpha* - - M. Archidiacono, D. C. Hooper, R. Murgia, S. Bohr, J. Lesgourgues, M. Viel - - http://arxiv.org/abs/1907.01496 [astro-ph.CO] - - JCAP 10 (2019) 055 - - In Class v3.2, this sector has been generalised to multi-interacting dark matter with three interaction channels (dark radiation, baryons, photons) and a parametrisation described in - - - *Cosmological constraints on multi-interacting dark matter* - - N. Becker, D. C. Hooper,F. Kahlhoefer, J. Lesgourgues, N. Schöneberg - - http://arxiv.org/abs/2010.04074 [astro-ph.CO] - - JCAP 02 (2021) 019 diff --git a/boltzmann/class/class_v3.2.0/doc/input/chap3.md b/boltzmann/class/class_v3.2.0/doc/input/chap3.md deleted file mode 100644 index 884b25a1..00000000 --- a/boltzmann/class/class_v3.2.0/doc/input/chap3.md +++ /dev/null @@ -1,536 +0,0 @@ -CLASS overview (architecture, input/output, general principles) -=============================================================== - -Author: Julien Lesgourgues - - -# Overall architecture of `class` # - -## Files and directories ## - -After downloading `CLASS`, one can see the following files in the root directory contains: - -- some example of input files, the most important being `explanatory.ini`. a reference input file containing all possible flags, options and physical input parameters. While this documentation explains the structure and use of the code, `explanatory.ini` can be seen as the _physical_ documentation of `CLASS`. We also provide a few other input files ending with `.ini` (a concise input file `default.ini` with the most used parameters, and two files corresponding to the best-fit baseline models of respectively Planck 2015 and 2018), and a few precision input files (ending with `.pre`) - -- the `Makefile`, with which you can compile the code by typing `make clean; make -j;` this will create the executable `class` and some binary files in the directory `build/`. The `Makefile` contains other compilation options that you can view inside the file. - -- `CPU.py` is a python script designed for plotting the `CLASS` output; for documentation type `python CPU.py --help` - -- `plot_CLASS_output.m` is the counterpart of `CPU.py` for MatLab - -- there are other input files for various applications: an example of a non-cold dark matter distribution functions (`psd_FD_single.dat`), and examples of evolution and selection functions for galaxy number count observables (`myevolution.dat, myselection.dat`). - -Other files are split between the following directories: - -- `source/` contains the C files for each main `CLASS` module, i.e. each -block containing some part of the physical equations and logic of -the Boltzmann code. - -- `tools/` contains purely numerical algorithms, applicable in any -context: integrators, simple manipulation of arrays (derivation, -integration, interpolation), Bessel function calculation, quadrature algorithms, parser, etc. - -- `main/` contains the main module `class.c` with the main - routine `class(...)`, to be used in interactive runs (but not - necessarily when the code is interfaced with other ones). - -- `test/` contains alternative main routines which can be used to run only some part of the code, to test its accuracy, to illustrate how -it can be interfaced with other codes, etc. - -- `include/` contains all the include files with a `.h` suffix. - -- `output/` is where the output files will be written by default (this can be changed to another directory by adjusting the input parameter `root = <...>`) - -- `python/` contains the python wrapper of `CLASS`, called classy (see `python/README`) - -- `cpp/` contains the C++ wrapper of `CLASS`, called ClassEngine (see `cpp/README`) - -- `doc/` contains the automatic documentation (manual and input files required to build it) - -- `external/` contains auxiliary or external algorithms used by `CLASS`, in particular: - -- `external/hyrec/` contains the recombination code HyRec (Lee and Ali-Haimoud 2020) that solves the recombinaiton equations by default. - -- `external/RecfastCLASS/` contains an modified version of the recombinaiton code RECFAST v1.5. It can be used as an alternative to solve the recombinaiton equations (with `recombination=recfast'). - -- `external/heating/` contains additional peices of code and interpolation tables for the calculation of energy injection (relevant for CMB anisotropies and spectral distorsions). - -- `external/distortions/` contains interpolation tables relevant for the calculation of CMB spectral distortions with J.Chluba's Green function method. - -- `external/bbn/` contains interpolation tables produced by BBN codes, in order to predict e.g. \f$ Y_\mathrm{He}(\omega_b, \Delta N_\mathrm{eff})\f$. - -- `external/external_Pk/` contains examples of external codes that can be used to generate the primordial spectrum and be interfaced with `CLASS`, when one of the many options already built inside the code are not sufficient. - -- `external/RealSpaceInterface` contains a software that uses `CLASS` to plot the eockution of linear perturabtions in reals space, with a graphical interface (credits M. Beutelspacher and G. Samaras). - -## The ten-module backbone ## - -### Ten tasks ### - -The purpose of `class` consists in computing some background quantities, thermodynamical quantities, perturbation transfer functions, and finally 2-point statistics (power spectra) for a given set of cosmological parameters. This task can be decomposed in few steps or modules: - -1. set input parameter values. - -2. compute the evolution of cosmological background quantities. - -3. compute the evolution of thermodynamical quantities (ionization fractions, etc.) - -4. compute the evolution of source functions \f$S(k,\tau)\f$ (by integrating over all perturbations). - -5. compute the primordial spectra. - -6. compute the linear and non-linear 2-point statistics in Fourier space (i.e. the power spectra \f$P(k)\f$). - -7. compute the transfer functions in harmonic space \f$\Delta_l(k)\f$. - -8. compute the linear and non-linear 2-point statistics in harmonic space (harmonic power spectra \f$C_l\f$'s). - -9. compute the lensed CMB spectra (using second-order perturbation theory). - -10. compute the CMB spectral distortions. - -(11. The results can optionally be written in files when `CLASS` is used interactively. The python wrapper does not go through this step.) - -### Ten structures ### - -In `class`, each of these steps is associated with a structure: - -1. `struct precision` for input precision parameters (input physical parameters are dispatched among the other structures listed below) -2. `struct background` for cosmological background, -3. `struct thermodynamics` for thermodynamics, -4. `struct perturbations` for source functions, -5. `struct primordial` for primordial spectra, -6. `struct fourier` for Fourier spectra, -7. `struct transfer` for transfer functions, -8. `struct harmonic` for harmonic spectra, -9. `struct lensing` for lensed CMB spectra, -10. `struct distortions` for CMB spectral distortions, - -(11. `struct output` for auxiliary variable describing the output format.) - -A given structure contains "everything concerning one step that the -subsequent steps need to know" (for instance, `struct perturbations` contains everything about source -functions that the transfer module needs to know). In particular, each -structure contains one array of tabulated values (for `struct background`, background -quantities as a function of time, for `struct thermodynamics`, thermodynamical quantities as a -function of redshift, for `struct perturbations`, sources \f$S(k, \tau)\f$, etc.). It -also contains information about the size of this array and the value -of the index of each physical quantity, so that the table can be -easily read and interpolated. Finally, it contains any derived -quantity that other modules might need to know. Hence, the -communication from one module A to another module B -consists in passing a pointer to the structure filled by A, and nothing else. - -All "precision parameters" are grouped in the single structure -`struct precision`. The code contains _no other arbitrary -numerical coefficient_. - -### Ten modules ### - -Each structure is defined and filled in one of the following modules -(and precisely in the order below): - -1. `input.c` -2. `background.c` -3. `thermodynamics.c` -4. `perturbations.c ` -5. `primordial.c` -6. `fourier.c` -7. `transfer.c` -8. `harmonic.c` -9. `lensing.c` -10. `distortions.c` - -(11. `output.c`) - -Each of these modules contains at least three functions: - -- `module_init(...)` - -- `module_free(...)` - -- `module_something_at_somevalue` - -where _module_ is one of `input, background, thermodynamics, perturb, primordial, nonlinear, transfer, spectra, lensing, distortions, output`. - - -The first function allocates and fills each structure. This can be -done provided that the previous structures in the hierarchy have been -already allocated and filled. In summary, calling one of `module_init(...)` amounts in solving entirely one of the steps 1 to 10. - -The second function deallocates the fields of each structure. This -can be done optionally at the end of the code (or, when the code is embedded -in a sampler, this __must__ be done -between each execution of `class`, and especially before calling `module_init(...)` again with different input parameters). - -The third function is able to interpolate the pre-computed tables. For -instance, `background_init()` fills a table of background -quantities for discrete values of conformal time \f$\tau\f$, but -`background_at_tau(tau, * values)` will return these values for any -arbitrary \f$\tau\f$. - -Note that functions of the type `module_something_at_somevalue` are the only ones which are -called from another module, while functions of the type `module_init(...)` and `module_free(...)` are the only -one called by the main executable. All other functions are for -internal use in each module. - -When writing a C code, the ordering of the functions in the *.c file is in principle arbitrary. However, for the sake of clarity, we always respected the following order in each `CLASS` module: - -1. all functions that may be called by other modules, i.e. "external functions", usually named like `module_something_at_somevalue(...)` -2. then, `module_init(...)` -3. then, `module_free()` -4. then, all functions used only internally by the module - - -## The `main()` function(s) ## - -### The `main.c` file ### - -The main executable of `class` is the function `main()` located in the file `main/main.c`. -This function consist only in the -following lines -(not including comments and error-management lines explained later): - - main() { - struct precision pr; - - struct background ba; - - struct thermodynamics th; - - struct perturbations pt; - - struct primordial pm; - - struct fourier fo; - - struct transfer tr; - - struct harmonic hr; - - struct lensing le; - - struct distortions sd; - - struct output op; - - - input_init(argc, argv,&pr,&ba,&th,&pt,&tr,&pm,&hr,&fo,&le,&sd,&op,errmsg); - - background_init(&pr,&ba); - - thermodynamics_init(&pr,&ba,&th); - - perturbations_init(&pr,&ba,&th,&pt); - - primordial_init(&pr,&pt,&pm); - - fourier_init(&pr,&ba,&th,&pt,&pm,&fo); - - transfer_init(&pr,&ba,&th,&pt,&fo,&tr); - - harmonic_init(&pr,&ba,&pt,&pm,&fo,&tr,&hr); - - lensing_init(&pr,&pt,&hr,&fo,&le); - - distortions_init(&pr,&ba,&th,&pt,&pm,&sd); - - output_init(&ba,&th,&pt,&pm,&tr,&hr,&fo,&le,&op) - - - /****** done ******/ - - - distortions_free(&sd); - - lensing_free(&le); - - harmonic_free(&hr); - - transfer_free(&tr); - - fourier_free(&fo); - - primordial_free(&pm); - - perturbations_free(&pt); - - thermodynamics_free(&th); - - background_free(&ba); - - -We can come back on the role of each argument. The arguments above are all pointers to the 10 structures of the code, excepted `argc, argv` which contains the input files passed by the user, and `errmsg` which contains the output error message of the input module (error management will be described below). - -`input_init_from_arguments` needs all structures, because it will set the precision parameters inside the `precision` structure, and the physical parameters in some fields of the respective other structures. For instance, an input parameter relevant for the primordial spectrum calculation (like the tilt \f$n_s\f$) will be stored in the `primordial` structure. Hence, in ` input_init_from_arguments`, all structures can be seen as output arguments. - -Other `module_init()` functions typically need all previous structures, which contain the result of the previous modules, plus its own structures, which contain some relevant input parameters before the function is called, as well as all the result form the module when the function has been executed. Hence all passed structures can be seen as input argument, excepted the last one which is both input and output. An example is `perturbations_init(&pr,&ba,&th,&pt)`. - -Each function `module_init()` does not need __all__ previous structures, it happens that a module does not depend on a __all__ previous one. For instance, the primordial module does not need information on the background and thermodynamics evolution in order to compute the primordial spectra, so the dependency is reduced: `primordial_init(&pr,&pt,&pm)`. - -Each function `module_init()` only deallocates arrays defined in the structure of their own module, so they need only their own structure as argument. (This is possible because all structures are self-contained, in the sense that when the structure contains an allocated array, it also contains the size of this array). The first and last module, `input` and `output`, have no `input_free()` or `output_free()` functions, because the structures `precision` and `output` do not contain arrays that would need to be de-allocated after the execution of the module. - -### The `test_<...>.c` files ### - -For a given purpose, somebody could only be interested in the -intermediate steps (only background quantities, only the -thermodynamics, only the perturbations and sources, etc.) It is -then straightforward to truncate the full hierarchy of modules 1, ... 10 at some -arbitrary order. We provide several "reduced executables" achieving precisely this. -They are located in `test/test_module_.c` (like, for instance, `test/test_perturbations.c`) and they can -be complied using the Makefile, which contains the appropriate commands and definitions (for instance, you can type `make test_perturbations`). - -The `test/` directory contains other useful example of alternative main functions, like for instance -`test_loops.c` which shows how to call `CLASS` within a loop over different parameter values. -There is also a version `test/test_loops_omp.c` using a double level of openMP parallelisation: one for running several `CLASS` instances in parallel, one for running each `CLASS` instance on several cores. The comments in these files are self-explanatory. - -# Input/output # - -## Input ## - -There are two types of input: - -- "precision parameters" (controlling the precision of the output and the execution time), - -- "input parameters" (cosmological parameters, flags telling to the code what it should compute, ...) - -The code can be executed with a maximum of two input files, e.g. - - ./class explanatory.ini cl_permille.pre - - -The file with a `.ini` extension is the cosmological parameter -input file, and the one with a `.pre` extension is the precision -file. Both files are optional: all parameters are set to default -values corresponding to the "most usual choices", and are eventually -replaced by the parameters passed in the two input files. For -instance, if one is happy with default accuracy settings, it is enough -to run with - - ./class explanatory.ini - -Input files do not -necessarily contain a line for each parameter, since many of them can -be left to default value. The example file `explanatory.ini` is -very long and somewhat indigestible, since it contains all possible -parameters, together with lengthy explanations. We recommend to keep -this file unchanged for reference, and to copy it in e.g. `test.ini`. -In the latter file, the user can erase all sections in -which he/she is absolutely not interested (e.g., all the part on -isocurvature modes, or on tensors, or on non-cold species, -etc.). Another option is to create an input file from scratch, copying -just the relevant lines from `explanatory.ini`. For the simplest -applications, the user will just need a few lines for basic -cosmological parameters, one line for the `output` entry (where -one can specifying which power spectra must be computed), and one line -for the `root` entry (specifying the prefix of all output files). - -The syntax of the input files is explained at the beginning of -`explanatory.ini`. Typically, lines in those files look like: - - - parameter1 = value1 - - free comments - - parameter2 = value2 # further comments - - # commented_parameter = commented_value - -and parameters can be entered in arbitrary order. This is rather -intuitive. The user should just be careful not to put an "=" -sign not preceded by a "#" sign inside a comment: the code -would then think that one is trying to pass some unidentified input -parameter. - -The syntax for the cosmological and precision parameters is the same. -It is clearer to split these parameters in the two files `.ini` -and `.pre`, but there is no strict rule about which parameter goes -into which file: in principle, precision parameters could be passed in -the `.ini`, and vice-versa. The only important thing is not to pass -the same parameter twice: the code would then complain and not run. - -The `CLASS` input files are also user-friendly in the sense that many -different cosmological parameter bases can be used. This is made -possible by the fact that the code does not only read parameters, it -"interprets them" with the level of logic which has been coded in -the `input.c` module. For instance, the Hubble parameter, the photon -density, the baryon density and the ultra-relativistic neutrino density can be -entered as: - - h = 0.7 - - T_cmb = 2.726 # Kelvin units - - omega_b = 0.02 - - N_eff = 3.04 - - -(in arbitrary order), or as - - - H0 = 70 - - omega_g = 2.5e-5 # g is the label for photons - - Omega_b = 0.04 - - omega_ur = 1.7e-5 # ur is the label for ultra-relativistic species - - -or any combination of the two. The code knows that for the photon -density, one should pass one (but not more than one) parameter out of -`T_cmb`, `omega_g`, `Omega_g` (where small omega's refer to -\f$\omega_i \equiv \Omega_i h^2\f$). It searches for one of these values, -and if needed, it converts it into one of the other two parameters, -using also other input parameters. For instance, `omega_g` will -be converted into `Omega_g` even if \f$h\f$ is written later in the -file than `omega_g`: the order makes no difference. Lots of -alternatives have been defined. If the code finds that not enough -parameters have been passed for making consistent deductions, it will -complete the missing information with in-built default values. On the -contrary, if it finds that there is too much information and no unique -solution, it will complain and return an error. - -In summary, the input syntax has been defined in such way that the -user does not need to think too much, and can pass his preferred set -of parameters in a nearly informal way. - -Let us mention a two useful parameters defined at the end of `explanatory.ini`, that we recommend setting to `yes` in order to run the code in a safe way: - -`write parameters = [yes or no]` (_default_: `no`) - -When set to yes, all input/precision parameters which have been read -are written in a file `parameters.ini`, to keep track all the details of this execution; this file can also be re-used as a new input file. Also, with this option, all parameters that have been passed and that the code did not read (because the syntax was wrong, or because the parameter was not relevant in the context of the run) are written in a file `unused_parameters`. When you have doubts about your input or your results, you can check what is in there. - -`write warnings = [yes or no]` (_default_: `no`) - -When set to yes, the parameters that have been passed and that the code did not read -(because the syntax was wrong, or because the parameter was not relevant in the context of the run) are written -in the standard output as `[Warning:]....` - -There is also a list of "verbose" parameters at the end of `explanatory.ini`. They can be used to control -the level of information passed to the standard output (0 means silent; 1 means normal, e.g. information on age of the universe, etc.; 2 is useful for instance when you want to check on how many cores the run is parallelised; 3 and more are intended for debugging). - -`CLASS` comes with a list of precision parameter files ending by `.pre`. Honestly we have not been updating all these files recently, and we need to do a bit of cleaning there. However you can trust `cl_ref.pre`. We have derived this file by studying both the convergence of the CMB output with respect to all `CLASS` precision parameters, and the agreement with `CAMB`. We consider that this file generates good reference CMB spectra, accurate up to the hundredth of per cent level, as explained in the CLASS IV paper and re-checked since then. You can try it with e.g. - - ./class explanatory.ini cl_ref.pre - -but the run will be extremely long. This is an occasion to run a many-core machine with a lot of RAM. It may work also on your laptop, but in half an hour or so. - -If you want a reference matter power spectrum P(k), also accurate up to the hundredth of percent level, we recommend using the file `pk_ref.pre`, identical to `cl_ref.pre` excepted that the truncation of the neutrino hierarchy has been pushed to `l_max_ur=150`. - -In order to increase moderately the precision to a tenth of percent, without prohibitive computing time, we recommend using `cl_permille.pre`. - -## Output ## - -The input file may contain a line - - root = - -where `` is a path of your choice, e.g. `output/test_`. -Then all output files will start like this, e.g. `output/test_cl.dat`, `output/test_cl_lensed.dat`, etc. -Of course the number of output files depends on your settings in the input file. There can be input files for CMB, LSS, background, thermodynamics, transfer functions, primordial spectra, etc. All this is documented in `explanatory.ini`. - -If you do not pass explicitly a `root = `, the code will name the output in its own way, by concatenating `output/`, the name of the input parameter file, and the first available integer number, e.g. - - output/explanatory03_cl.dat, etc. - - -# General principles # - -## Error management ## - -Error management is based on the fact that all functions are defined -as integers returning either `_SUCCESS_` or `_FAILURE_`. Before returning `_FAILURE_`, they write an -error message in the structure of the module to which they belong. The -calling function will read this message, append it to its own error -message, and return a `_FAILURE_`; and so on and so forth, until -the main routine is reached. This error management allows the user to -see the whole nested structure of error messages when an error has -been met. The structure associated to each module contains a field -for writing error messages, called `structure_i.error_message`, where `structure_i` could be one of `background`, `thermo`, `perturbs`, etc. So, when a function from a module \f$i\f$ -is called within module \f$j\f$ and returns an error, the goal is to write -in `structure_j.error_message` a local error message, and to -append to it the error message in `structure_i.error_message`. These steps are implemented in a macro `class_call()`, used for calling whatever function: - - - class_call(module_i_function(...,structure_i), - structure_i.error_message, - structure_j.error_message); - - -So, the first argument of `call_call()` is the function we want -to call; the second argument is the location of the error message -returned by this function; and the third one is the location of the -error message which should be returned to the higher level. -Usually, in the bulk of the code, we use pointer to structures rather than structure themselves; then the syntax is - - class_call(module_i_function(...,pi), - pi->error_message, - pj->error_message);` - -where in this generic example, `pi` and `pj` are assumed to be pointers towards the structures -`structure_i` and `structure_j`. - -The user will find in `include/common.h` a list of additional macros, all -starting by `class_...()`, which are all based on this logic. For -instance, the macro `class_test()` offers a generic way to return -an error in a standard format if a condition is not fulfilled. A -typical error message from `CLASS` looks like: - - -`Error in module_j_function1` - -`module_j_function1 (L:340) : error in module_i_function2(...)` - -`module_i_function2 (L:275) : error in module_k_function3(...)` - -`...` - -`=> module_x_functionN (L:735) : your choice of input parameter blabla=30 -is not consistent with the constraint blabla<1` - - -where the `L`'s refer to line numbers in each file. These error -messages are very informative, and are built almost entirely -automatically by the macros. For instance, in the above example, it -was only necessary to write inside the function `module_x_functionN()` a test like: - - - class_test(blabla >= 1, - px->error_message, - "your choice of input parameter blabla=%e - is not consistent with the constraint blabla<%e", - blabla,blablamax); - - -All the rest was added step by step by the various `class_call()` macros. - - -## Dynamical allocation of indices ## - -On might be tempted to decide that in a given array, matrix or vector, a given quantity is associated with an explicit index value. However, when modifying the code, extra entries will be needed and will mess up the initial scheme; the user will need to study which index is associated to which quantity, and possibly make an error. All this can be avoided by using systematically a dynamical index allocation. This means that all indices remain under a symbolic form, and in each, run the code attributes automatically a value to each index. The user never needs to know this value. - -Dynamical indexing is implemented in a very generic way in CLASS, the same rules apply everywhere. They are explained in these lecture slides: - -`https://www.dropbox.com/sh/ma5muh76sggwk8k/AABl_DDUBEzAjjdywMjeTya2a?dl=0` - -in the folder `CLASS_Lecture_slides/lecture5_index_and_error.pdf`. - -## No hard coding ## - -Any feature or equation which could be true in one cosmology and not in another one should not be written explicitly in the code, and should not be taken as granted in several other places. Discretization and integration steps are usually defined automatically by the code for each cosmology, instead of being set to something which might be optimal for minimal models, and not sufficient for other ones. You will find many example of this in the code. As a consequence, in the list of precision parameter, you rarely find actual stepsize. You find rather parameters representing the ratio between a stepsize and a physical quantity computed for each cosmology. - -## Modifying the code ## - -Implementing a new idea completly from scratch would be rather intimidating, even for the main developpers of `CLASS`. Fortunately, we never have to work from scratch. Usually we want to code a new species, a new observable, a new approximation scheme, etc. The trick is to think of another species, observable, approximation scheme, etc., looking as close as possible to the new one. - -Then, playing with the `grep` command and the `search` command of your editor, search for all occurences of this nearest-as-possible other feature. This is usually easy thanks to our naming scheme. For each species, observable, approximation scheme, etc., we usually use the same sequence of few letters everywhere (fo instance, `fld` for the fluid usually representing Dark Energy). Grep for `fld` and you'll get all the lines related to the fluid. There is another way: we use everywhere some conditional jumps related to a given feature. For instance, the lines related to the fluid are always in between `if (pba->has_fld == _TRUE_) { ... }` and the lines related to the cosmic shear observables are always in between `if (ppt->has_lensing_potential == _TRUE_) { ... }`. Locating these flags and conditional jumps shows you all the parts related to a given feature/ingredient. - -Once you have localised your nearest-as-possible other feature, you can copy/paste these lines and adapt them to the case of your new feature! You are then sure that you didn't miss any step, even the smallest technical steps (definition of indices, etc.) - -# Units # - -Internally, the code uses almost everywhere units of Mpc to some power, excepted in the inflation module, where many quantities are in natural units (wrt the true Planck mass). diff --git a/boltzmann/class/class_v3.2.0/doc/input/doxyconf b/boltzmann/class/class_v3.2.0/doc/input/doxyconf deleted file mode 100644 index 1ad9b48e..00000000 --- a/boltzmann/class/class_v3.2.0/doc/input/doxyconf +++ /dev/null @@ -1,2575 +0,0 @@ -# Doxyfile 1.9.1 - -# This file describes the settings to be used by the documentation system -# doxygen (www.doxygen.org) for a project. -# -# All text after a double hash (##) is considered a comment and is placed in -# front of the TAG it is preceding. -# -# All text after a single hash (#) is considered a comment and will be ignored. -# The format is: -# TAG = value [value, ...] -# For lists, items can also be appended using: -# TAG += value [value, ...] -# Values that contain spaces should be placed between quotes (\" \"). - -#--------------------------------------------------------------------------- -# Project related configuration options -#--------------------------------------------------------------------------- - -# This tag specifies the encoding used for all characters in the configuration -# file that follow. The default is UTF-8 which is also the encoding used for all -# text before the first occurrence of this tag. Doxygen uses libiconv (or the -# iconv built into libc) for the transcoding. See -# https://www.gnu.org/software/libiconv/ for the list of possible encodings. -# The default value is: UTF-8. - -DOXYFILE_ENCODING = UTF-8 - -# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by -# double-quotes, unless you are using Doxywizard) that should identify the -# project for which the documentation is generated. This name is used in the -# title of most generated pages and in a few other places. -# The default value is: My Project. - -PROJECT_NAME = "CLASS MANUAL" - -# The PROJECT_NUMBER tag can be used to enter a project or revision number. This -# could be handy for archiving the generated documentation or if some version -# control system is used. - -PROJECT_NUMBER = - -# Using the PROJECT_BRIEF tag one can provide an optional one line description -# for a project that appears at the top of each page and should give viewer a -# quick idea about the purpose of the project. Keep the description short. - -PROJECT_BRIEF = - -# With the PROJECT_LOGO tag one can specify a logo or an icon that is included -# in the documentation. The maximum height of the logo should not exceed 55 -# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy -# the logo to the output directory. - -PROJECT_LOGO = - -# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path -# into which the generated documentation will be written. If a relative path is -# entered, it will be relative to the location where doxygen was started. If -# left blank the current directory will be used. - -OUTPUT_DIRECTORY = ../manual - -# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- -# directories (in 2 levels) under the output directory of each output format and -# will distribute the generated files over these directories. Enabling this -# option can be useful when feeding doxygen a huge amount of source files, where -# putting all generated files in the same directory would otherwise causes -# performance problems for the file system. -# The default value is: NO. - -CREATE_SUBDIRS = NO - -# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII -# characters to appear in the names of generated files. If set to NO, non-ASCII -# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode -# U+3044. -# The default value is: NO. - -ALLOW_UNICODE_NAMES = YES - -# The OUTPUT_LANGUAGE tag is used to specify the language in which all -# documentation generated by doxygen is written. Doxygen will use this -# information to generate all constant output in the proper language. -# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, -# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), -# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, -# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), -# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, -# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, -# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, -# Ukrainian and Vietnamese. -# The default value is: English. - -OUTPUT_LANGUAGE = English - -# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all -# documentation generated by doxygen is written. Doxygen will use this -# information to generate all generated output in the proper direction. -# Possible values are: None, LTR, RTL and Context. -# The default value is: None. - -OUTPUT_TEXT_DIRECTION = None - -# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member -# descriptions after the members that are listed in the file and class -# documentation (similar to Javadoc). Set to NO to disable this. -# The default value is: YES. - -BRIEF_MEMBER_DESC = YES - -# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief -# description of a member or function before the detailed description -# -# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the -# brief descriptions will be completely suppressed. -# The default value is: YES. - -REPEAT_BRIEF = NO - -# This tag implements a quasi-intelligent brief description abbreviator that is -# used to form the text in various listings. Each string in this list, if found -# as the leading text of the brief description, will be stripped from the text -# and the result, after processing the whole list, is used as the annotated -# text. Otherwise, the brief description is used as-is. If left blank, the -# following values are used ($name is automatically replaced with the name of -# the entity):The $name class, The $name widget, The $name file, is, provides, -# specifies, contains, represents, a, an and the. - -ABBREVIATE_BRIEF = - -# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then -# doxygen will generate a detailed section even if there is only a brief -# description. -# The default value is: NO. - -ALWAYS_DETAILED_SEC = NO - -# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all -# inherited members of a class in the documentation of that class as if those -# members were ordinary class members. Constructors, destructors and assignment -# operators of the base classes will not be shown. -# The default value is: NO. - -INLINE_INHERITED_MEMB = NO - -# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path -# before files name in the file list and in the header files. If set to NO the -# shortest path that makes the file name unique will be used -# The default value is: YES. - -FULL_PATH_NAMES = NO - -# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. -# Stripping is only done if one of the specified strings matches the left-hand -# part of the path. The tag can be used to show relative paths in the file list. -# If left blank the directory from which doxygen is run is used as the path to -# strip. -# -# Note that you can specify absolute paths here, but also relative paths, which -# will be relative from the directory where doxygen is started. -# This tag requires that the tag FULL_PATH_NAMES is set to YES. - -STRIP_FROM_PATH = - -# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the -# path mentioned in the documentation of a class, which tells the reader which -# header file to include in order to use a class. If left blank only the name of -# the header file containing the class definition is used. Otherwise one should -# specify the list of include paths that are normally passed to the compiler -# using the -I flag. - -STRIP_FROM_INC_PATH = - -# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but -# less readable) file names. This can be useful is your file systems doesn't -# support long names like on DOS, Mac, or CD-ROM. -# The default value is: NO. - -SHORT_NAMES = NO - -# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the -# first line (until the first dot) of a Javadoc-style comment as the brief -# description. If set to NO, the Javadoc-style will behave just like regular Qt- -# style comments (thus requiring an explicit @brief command for a brief -# description.) -# The default value is: NO. - -JAVADOC_AUTOBRIEF = NO - -# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line -# such as -# /*************** -# as being the beginning of a Javadoc-style comment "banner". If set to NO, the -# Javadoc-style will behave just like regular comments and it will not be -# interpreted by doxygen. -# The default value is: NO. - -JAVADOC_BANNER = NO - -# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first -# line (until the first dot) of a Qt-style comment as the brief description. If -# set to NO, the Qt-style will behave just like regular Qt-style comments (thus -# requiring an explicit \brief command for a brief description.) -# The default value is: NO. - -QT_AUTOBRIEF = NO - -# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a -# multi-line C++ special comment block (i.e. a block of //! or /// comments) as -# a brief description. This used to be the default behavior. The new default is -# to treat a multi-line C++ comment block as a detailed description. Set this -# tag to YES if you prefer the old behavior instead. -# -# Note that setting this tag to YES also means that rational rose comments are -# not recognized any more. -# The default value is: NO. - -MULTILINE_CPP_IS_BRIEF = NO - -# By default Python docstrings are displayed as preformatted text and doxygen's -# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the -# doxygen's special commands can be used and the contents of the docstring -# documentation blocks is shown as doxygen documentation. -# The default value is: YES. - -PYTHON_DOCSTRING = YES - -# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the -# documentation from any documented member that it re-implements. -# The default value is: YES. - -INHERIT_DOCS = YES - -# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new -# page for each member. If set to NO, the documentation of a member will be part -# of the file/class/namespace that contains it. -# The default value is: NO. - -SEPARATE_MEMBER_PAGES = NO - -# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen -# uses this value to replace tabs by spaces in code fragments. -# Minimum value: 1, maximum value: 16, default value: 4. - -TAB_SIZE = 4 - -# This tag can be used to specify a number of aliases that act as commands in -# the documentation. An alias has the form: -# name=value -# For example adding -# "sideeffect=@par Side Effects:\n" -# will allow you to put the command \sideeffect (or @sideeffect) in the -# documentation, which will result in a user-defined paragraph with heading -# "Side Effects:". You can put \n's in the value part of an alias to insert -# newlines (in the resulting output). You can put ^^ in the value part of an -# alias to insert a newline as if a physical newline was in the original file. -# When you need a literal { or } or , in the value part of an alias you have to -# escape them by means of a backslash (\), this can lead to conflicts with the -# commands \{ and \} for these it is advised to use the version @{ and @} or use -# a double escape (\\{ and \\}) - -ALIASES = - -# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources -# only. Doxygen will then generate output that is more tailored for C. For -# instance, some of the names that are used will be different. The list of all -# members will be omitted, etc. -# The default value is: NO. - -OPTIMIZE_OUTPUT_FOR_C = YES - -# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or -# Python sources only. Doxygen will then generate output that is more tailored -# for that language. For instance, namespaces will be presented as packages, -# qualified scopes will look different, etc. -# The default value is: NO. - -OPTIMIZE_OUTPUT_JAVA = NO - -# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran -# sources. Doxygen will then generate output that is tailored for Fortran. -# The default value is: NO. - -OPTIMIZE_FOR_FORTRAN = NO - -# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL -# sources. Doxygen will then generate output that is tailored for VHDL. -# The default value is: NO. - -OPTIMIZE_OUTPUT_VHDL = NO - -# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice -# sources only. Doxygen will then generate output that is more tailored for that -# language. For instance, namespaces will be presented as modules, types will be -# separated into more groups, etc. -# The default value is: NO. - -OPTIMIZE_OUTPUT_SLICE = NO - -# Doxygen selects the parser to use depending on the extension of the files it -# parses. With this tag you can assign which parser to use for a given -# extension. Doxygen has a built-in mapping, but you can override or extend it -# using this tag. The format is ext=language, where ext is a file extension, and -# language is one of the parsers supported by doxygen: IDL, Java, JavaScript, -# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, VHDL, -# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran: -# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser -# tries to guess whether the code is fixed or free formatted code, this is the -# default for Fortran type files). For instance to make doxygen treat .inc files -# as Fortran files (default is PHP), and .f files as C (default is Fortran), -# use: inc=Fortran f=C. -# -# Note: For files without extension you can use no_extension as a placeholder. -# -# Note that for custom extensions you also need to set FILE_PATTERNS otherwise -# the files are not read by doxygen. When specifying no_extension you should add -# * to the FILE_PATTERNS. -# -# Note see also the list of default file extension mappings. - -EXTENSION_MAPPING = - -# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments -# according to the Markdown format, which allows for more readable -# documentation. See https://daringfireball.net/projects/markdown/ for details. -# The output of markdown processing is further processed by doxygen, so you can -# mix doxygen, HTML, and XML commands with Markdown formatting. 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Such a link can -# be prevented in individual cases by putting a % sign in front of the word or -# globally by setting AUTOLINK_SUPPORT to NO. -# The default value is: YES. - -AUTOLINK_SUPPORT = YES - -# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want -# to include (a tag file for) the STL sources as input, then you should set this -# tag to YES in order to let doxygen match functions declarations and -# definitions whose arguments contain STL classes (e.g. func(std::string); -# versus func(std::string) {}). This also make the inheritance and collaboration -# diagrams that involve STL classes more complete and accurate. -# The default value is: NO. - -BUILTIN_STL_SUPPORT = YES - -# If you use Microsoft's C++/CLI language, you should set this option to YES to -# enable parsing support. -# The default value is: NO. - -CPP_CLI_SUPPORT = NO - -# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: -# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen -# will parse them like normal C++ but will assume all classes use public instead -# of private inheritance when no explicit protection keyword is present. -# The default value is: NO. - -SIP_SUPPORT = NO - -# For Microsoft's IDL there are propget and propput attributes to indicate -# getter and setter methods for a property. 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Alternatively, this can be done per class using the -# \nosubgrouping command. -# The default value is: YES. - -SUBGROUPING = YES - -# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions -# are shown inside the group in which they are included (e.g. using \ingroup) -# instead of on a separate page (for HTML and Man pages) or section (for LaTeX -# and RTF). -# -# Note that this feature does not work in combination with -# SEPARATE_MEMBER_PAGES. -# The default value is: NO. - -INLINE_GROUPED_CLASSES = NO - -# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions -# with only public data fields or simple typedef fields will be shown inline in -# the documentation of the scope in which they are defined (i.e. file, -# namespace, or group documentation), provided this scope is documented. If set -# to NO, structs, classes, and unions are shown on a separate page (for HTML and -# Man pages) or section (for LaTeX and RTF). -# The default value is: NO. - -INLINE_SIMPLE_STRUCTS = YES - -# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or -# enum is documented as struct, union, or enum with the name of the typedef. So -# typedef struct TypeS {} TypeT, will appear in the documentation as a struct -# with name TypeT. When disabled the typedef will appear as a member of a file, -# namespace, or class. And the struct will be named TypeS. This can typically be -# useful for C code in case the coding convention dictates that all compound -# types are typedef'ed and only the typedef is referenced, never the tag name. -# The default value is: NO. - -TYPEDEF_HIDES_STRUCT = YES - -# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This -# cache is used to resolve symbols given their name and scope. Since this can be -# an expensive process and often the same symbol appears multiple times in the -# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small -# doxygen will become slower. If the cache is too large, memory is wasted. The -# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range -# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 -# symbols. At the end of a run doxygen will report the cache usage and suggest -# the optimal cache size from a speed point of view. -# Minimum value: 0, maximum value: 9, default value: 0. - -LOOKUP_CACHE_SIZE = 0 - -# The NUM_PROC_THREADS specifies the number threads doxygen is allowed to use -# during processing. When set to 0 doxygen will based this on the number of -# cores available in the system. You can set it explicitly to a value larger -# than 0 to get more control over the balance between CPU load and processing -# speed. At this moment only the input processing can be done using multiple -# threads. Since this is still an experimental feature the default is set to 1, -# which efficively disables parallel processing. Please report any issues you -# encounter. Generating dot graphs in parallel is controlled by the -# DOT_NUM_THREADS setting. -# Minimum value: 0, maximum value: 32, default value: 1. - -NUM_PROC_THREADS = 1 - -#--------------------------------------------------------------------------- -# Build related configuration options -#--------------------------------------------------------------------------- - -# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in -# documentation are documented, even if no documentation was available. Private -# class members and static file members will be hidden unless the -# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. -# Note: This will also disable the warnings about undocumented members that are -# normally produced when WARNINGS is set to YES. -# The default value is: NO. - -EXTRACT_ALL = NO - -# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will -# be included in the documentation. -# The default value is: NO. - -EXTRACT_PRIVATE = NO - -# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual -# methods of a class will be included in the documentation. -# The default value is: NO. - -EXTRACT_PRIV_VIRTUAL = NO - -# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal -# scope will be included in the documentation. -# The default value is: NO. - -EXTRACT_PACKAGE = NO - -# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be -# included in the documentation. -# The default value is: NO. - -EXTRACT_STATIC = NO - -# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined -# locally in source files will be included in the documentation. 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This option -# has no effect if EXTRACT_ALL is enabled. -# The default value is: NO. - -HIDE_UNDOC_CLASSES = YES - -# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend -# declarations. If set to NO, these declarations will be included in the -# documentation. -# The default value is: NO. - -HIDE_FRIEND_COMPOUNDS = NO - -# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any -# documentation blocks found inside the body of a function. If set to NO, these -# blocks will be appended to the function's detailed documentation block. -# The default value is: NO. - -HIDE_IN_BODY_DOCS = NO - -# The INTERNAL_DOCS tag determines if documentation that is typed after a -# \internal command is included. If the tag is set to NO then the documentation -# will be excluded. Set it to YES to include the internal documentation. -# The default value is: NO. - -INTERNAL_DOCS = NO - -# With the correct setting of option CASE_SENSE_NAMES doxygen will better be -# able to match the capabilities of the underlying filesystem. In case the -# filesystem is case sensitive (i.e. it supports files in the same directory -# whose names only differ in casing), the option must be set to YES to properly -# deal with such files in case they appear in the input. For filesystems that -# are not case sensitive the option should be be set to NO to properly deal with -# output files written for symbols that only differ in casing, such as for two -# classes, one named CLASS and the other named Class, and to also support -# references to files without having to specify the exact matching casing. 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If set to -# YES the compound reference will be hidden. -# The default value is: NO. - -HIDE_COMPOUND_REFERENCE= NO - -# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of -# the files that are included by a file in the documentation of that file. -# The default value is: YES. - -SHOW_INCLUDE_FILES = YES - -# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each -# grouped member an include statement to the documentation, telling the reader -# which file to include in order to use the member. -# The default value is: NO. - -SHOW_GROUPED_MEMB_INC = NO - -# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include -# files with double quotes in the documentation rather than with sharp brackets. -# The default value is: NO. - -FORCE_LOCAL_INCLUDES = NO - -# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the -# documentation for inline members. -# The default value is: YES. - -INLINE_INFO = YES - -# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the -# (detailed) documentation of file and class members alphabetically by member -# name. If set to NO, the members will appear in declaration order. -# The default value is: YES. - -SORT_MEMBER_DOCS = NO - -# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief -# descriptions of file, namespace and class members alphabetically by member -# name. If set to NO, the members will appear in declaration order. Note that -# this will also influence the order of the classes in the class list. -# The default value is: NO. - -SORT_BRIEF_DOCS = NO - -# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the -# (brief and detailed) documentation of class members so that constructors and -# destructors are listed first. If set to NO the constructors will appear in the -# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. -# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief -# member documentation. -# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting -# detailed member documentation. -# The default value is: NO. - -SORT_MEMBERS_CTORS_1ST = NO - -# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy -# of group names into alphabetical order. If set to NO the group names will -# appear in their defined order. -# The default value is: NO. - -SORT_GROUP_NAMES = NO - -# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by -# fully-qualified names, including namespaces. If set to NO, the class list will -# be sorted only by class name, not including the namespace part. -# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. -# Note: This option applies only to the class list, not to the alphabetical -# list. -# The default value is: NO. - -SORT_BY_SCOPE_NAME = NO - -# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper -# type resolution of all parameters of a function it will reject a match between -# the prototype and the implementation of a member function even if there is -# only one candidate or it is obvious which candidate to choose by doing a -# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still -# accept a match between prototype and implementation in such cases. -# The default value is: NO. - -STRICT_PROTO_MATCHING = NO - -# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo -# list. This list is created by putting \todo commands in the documentation. -# The default value is: YES. - -GENERATE_TODOLIST = NO - -# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test -# list. This list is created by putting \test commands in the documentation. -# The default value is: YES. - -GENERATE_TESTLIST = NO - -# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug -# list. This list is created by putting \bug commands in the documentation. -# The default value is: YES. - -GENERATE_BUGLIST = YES - -# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) -# the deprecated list. This list is created by putting \deprecated commands in -# the documentation. -# The default value is: YES. - -GENERATE_DEPRECATEDLIST= YES - -# The ENABLED_SECTIONS tag can be used to enable conditional documentation -# sections, marked by \if ... \endif and \cond -# ... \endcond blocks. - -ENABLED_SECTIONS = - -# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the -# initial value of a variable or macro / define can have for it to appear in the -# documentation. If the initializer consists of more lines than specified here -# it will be hidden. Use a value of 0 to hide initializers completely. The -# appearance of the value of individual variables and macros / defines can be -# controlled using \showinitializer or \hideinitializer command in the -# documentation regardless of this setting. -# Minimum value: 0, maximum value: 10000, default value: 30. - -MAX_INITIALIZER_LINES = 30 - -# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at -# the bottom of the documentation of classes and structs. If set to YES, the -# list will mention the files that were used to generate the documentation. -# The default value is: YES. - -SHOW_USED_FILES = YES - -# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This -# will remove the Files entry from the Quick Index and from the Folder Tree View -# (if specified). -# The default value is: YES. - -SHOW_FILES = YES - -# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces -# page. This will remove the Namespaces entry from the Quick Index and from the -# Folder Tree View (if specified). -# The default value is: YES. - -SHOW_NAMESPACES = YES - -# The FILE_VERSION_FILTER tag can be used to specify a program or script that -# doxygen should invoke to get the current version for each file (typically from -# the version control system). Doxygen will invoke the program by executing (via -# popen()) the command command input-file, where command is the value of the -# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided -# by doxygen. Whatever the program writes to standard output is used as the file -# version. For an example see the documentation. - -FILE_VERSION_FILTER = - -# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed -# by doxygen. The layout file controls the global structure of the generated -# output files in an output format independent way. To create the layout file -# that represents doxygen's defaults, run doxygen with the -l option. You can -# optionally specify a file name after the option, if omitted DoxygenLayout.xml -# will be used as the name of the layout file. -# -# Note that if you run doxygen from a directory containing a file called -# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE -# tag is left empty. - -LAYOUT_FILE = - -# The CITE_BIB_FILES tag can be used to specify one or more bib files containing -# the reference definitions. This must be a list of .bib files. The .bib -# extension is automatically appended if omitted. This requires the bibtex tool -# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info. -# For LaTeX the style of the bibliography can be controlled using -# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the -# search path. See also \cite for info how to create references. - -CITE_BIB_FILES = - -#--------------------------------------------------------------------------- -# Configuration options related to warning and progress messages -#--------------------------------------------------------------------------- - -# The QUIET tag can be used to turn on/off the messages that are generated to -# standard output by doxygen. If QUIET is set to YES this implies that the -# messages are off. -# The default value is: NO. - -QUIET = YES - -# The WARNINGS tag can be used to turn on/off the warning messages that are -# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES -# this implies that the warnings are on. -# -# Tip: Turn warnings on while writing the documentation. -# The default value is: YES. - -WARNINGS = NO - -# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate -# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag -# will automatically be disabled. -# The default value is: YES. - -WARN_IF_UNDOCUMENTED = NO - -# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for -# potential errors in the documentation, such as not documenting some parameters -# in a documented function, or documenting parameters that don't exist or using -# markup commands wrongly. -# The default value is: YES. - -WARN_IF_DOC_ERROR = YES - -# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that -# are documented, but have no documentation for their parameters or return -# value. If set to NO, doxygen will only warn about wrong or incomplete -# parameter documentation, but not about the absence of documentation. If -# EXTRACT_ALL is set to YES then this flag will automatically be disabled. -# The default value is: NO. - -WARN_NO_PARAMDOC = YES - -# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when -# a warning is encountered. If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS -# then doxygen will continue running as if WARN_AS_ERROR tag is set to NO, but -# at the end of the doxygen process doxygen will return with a non-zero status. -# Possible values are: NO, YES and FAIL_ON_WARNINGS. -# The default value is: NO. - -WARN_AS_ERROR = NO - -# The WARN_FORMAT tag determines the format of the warning messages that doxygen -# can produce. The string should contain the $file, $line, and $text tags, which -# will be replaced by the file and line number from which the warning originated -# and the warning text. Optionally the format may contain $version, which will -# be replaced by the version of the file (if it could be obtained via -# FILE_VERSION_FILTER) -# The default value is: $file:$line: $text. - -WARN_FORMAT = "$file:$line: $text" - -# The WARN_LOGFILE tag can be used to specify a file to which warning and error -# messages should be written. If left blank the output is written to standard -# error (stderr). - -WARN_LOGFILE = - -#--------------------------------------------------------------------------- -# Configuration options related to the input files -#--------------------------------------------------------------------------- - -# The INPUT tag is used to specify the files and/or directories that contain -# documented source files. You may enter file names like myfile.cpp or -# directories like /usr/src/myproject. Separate the files or directories with -# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING -# Note: If this tag is empty the current directory is searched. - -INPUT = ../../README.md \ - ../input/chap2.md \ - ../input/chap3.md \ - ../../include \ - ../../source \ - ../../main \ - ../../external/external_Pk \ - ../../external/RecfastCLASS \ - ../../external/heating \ - ../input/mod.md - -# This tag can be used to specify the character encoding of the source files -# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses -# libiconv (or the iconv built into libc) for the transcoding. See the libiconv -# documentation (see: -# https://www.gnu.org/software/libiconv/) for the list of possible encodings. -# The default value is: UTF-8. - -INPUT_ENCODING = UTF-8 - -# If the value of the INPUT tag contains directories, you can use the -# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and -# *.h) to filter out the source-files in the directories. -# -# Note that for custom extensions or not directly supported extensions you also -# need to set EXTENSION_MAPPING for the extension otherwise the files are not -# read by doxygen. -# -# Note the list of default checked file patterns might differ from the list of -# default file extension mappings. -# -# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp, -# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, -# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, -# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment), -# *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd, *.vhdl, -# *.ucf, *.qsf and *.ice. - -FILE_PATTERNS = - -# The RECURSIVE tag can be used to specify whether or not subdirectories should -# be searched for input files as well. -# The default value is: NO. - -RECURSIVE = YES - -# The EXCLUDE tag can be used to specify files and/or directories that should be -# excluded from the INPUT source files. This way you can easily exclude a -# subdirectory from a directory tree whose root is specified with the INPUT tag. -# -# Note that relative paths are relative to the directory from which doxygen is -# run. - -EXCLUDE = ../../include/growTable.h - -# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or -# directories that are symbolic links (a Unix file system feature) are excluded -# from the input. -# The default value is: NO. - -EXCLUDE_SYMLINKS = NO - -# If the value of the INPUT tag contains directories, you can use the -# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude -# certain files from those directories. -# -# Note that the wildcards are matched against the file with absolute path, so to -# exclude all test directories for example use the pattern */test/* - -EXCLUDE_PATTERNS = - -# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names -# (namespaces, classes, functions, etc.) that should be excluded from the -# output. The symbol name can be a fully qualified name, a word, or if the -# wildcard * is used, a substring. Examples: ANamespace, AClass, -# AClass::ANamespace, ANamespace::*Test -# -# Note that the wildcards are matched against the file with absolute path, so to -# exclude all test directories use the pattern */test/* - -EXCLUDE_SYMBOLS = __ALLOCATE_PRECISION_PARAMETER__ - -# The EXAMPLE_PATH tag can be used to specify one or more files or directories -# that contain example code fragments that are included (see the \include -# command). - -EXAMPLE_PATH = - -# If the value of the EXAMPLE_PATH tag contains directories, you can use the -# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and -# *.h) to filter out the source-files in the directories. If left blank all -# files are included. - -EXAMPLE_PATTERNS = - -# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be -# searched for input files to be used with the \include or \dontinclude commands -# irrespective of the value of the RECURSIVE tag. -# The default value is: NO. - -EXAMPLE_RECURSIVE = NO - -# The IMAGE_PATH tag can be used to specify one or more files or directories -# that contain images that are to be included in the documentation (see the -# \image command). - -IMAGE_PATH = - -# The INPUT_FILTER tag can be used to specify a program that doxygen should -# invoke to filter for each input file. Doxygen will invoke the filter program -# by executing (via popen()) the command: -# -# -# -# where is the value of the INPUT_FILTER tag, and is the -# name of an input file. Doxygen will then use the output that the filter -# program writes to standard output. If FILTER_PATTERNS is specified, this tag -# will be ignored. -# -# Note that the filter must not add or remove lines; it is applied before the -# code is scanned, but not when the output code is generated. If lines are added -# or removed, the anchors will not be placed correctly. -# -# Note that for custom extensions or not directly supported extensions you also -# need to set EXTENSION_MAPPING for the extension otherwise the files are not -# properly processed by doxygen. - -INPUT_FILTER = - -# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern -# basis. Doxygen will compare the file name with each pattern and apply the -# filter if there is a match. The filters are a list of the form: pattern=filter -# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how -# filters are used. If the FILTER_PATTERNS tag is empty or if none of the -# patterns match the file name, INPUT_FILTER is applied. -# -# Note that for custom extensions or not directly supported extensions you also -# need to set EXTENSION_MAPPING for the extension otherwise the files are not -# properly processed by doxygen. - -FILTER_PATTERNS = - -# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using -# INPUT_FILTER) will also be used to filter the input files that are used for -# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). -# The default value is: NO. - -FILTER_SOURCE_FILES = NO - -# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file -# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and -# it is also possible to disable source filtering for a specific pattern using -# *.ext= (so without naming a filter). -# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. - -FILTER_SOURCE_PATTERNS = - -# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that -# is part of the input, its contents will be placed on the main page -# (index.html). This can be useful if you have a project on for instance GitHub -# and want to reuse the introduction page also for the doxygen output. - -USE_MDFILE_AS_MAINPAGE = - -#--------------------------------------------------------------------------- -# Configuration options related to source browsing -#--------------------------------------------------------------------------- - -# If the SOURCE_BROWSER tag is set to YES then a list of source files will be -# generated. Documented entities will be cross-referenced with these sources. -# -# Note: To get rid of all source code in the generated output, make sure that -# also VERBATIM_HEADERS is set to NO. -# The default value is: NO. - -SOURCE_BROWSER = NO - -# Setting the INLINE_SOURCES tag to YES will include the body of functions, -# classes and enums directly into the documentation. -# The default value is: NO. - -INLINE_SOURCES = NO - -# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any -# special comment blocks from generated source code fragments. Normal C, C++ and -# Fortran comments will always remain visible. -# The default value is: YES. - -STRIP_CODE_COMMENTS = YES - -# If the REFERENCED_BY_RELATION tag is set to YES then for each documented -# entity all documented functions referencing it will be listed. -# The default value is: NO. - -REFERENCED_BY_RELATION = NO - -# If the REFERENCES_RELATION tag is set to YES then for each documented function -# all documented entities called/used by that function will be listed. -# The default value is: NO. - -REFERENCES_RELATION = NO - -# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set -# to YES then the hyperlinks from functions in REFERENCES_RELATION and -# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will -# link to the documentation. -# The default value is: YES. - -REFERENCES_LINK_SOURCE = YES - -# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the -# source code will show a tooltip with additional information such as prototype, -# brief description and links to the definition and documentation. Since this -# will make the HTML file larger and loading of large files a bit slower, you -# can opt to disable this feature. -# The default value is: YES. -# This tag requires that the tag SOURCE_BROWSER is set to YES. - -SOURCE_TOOLTIPS = YES - -# If the USE_HTAGS tag is set to YES then the references to source code will -# point to the HTML generated by the htags(1) tool instead of doxygen built-in -# source browser. The htags tool is part of GNU's global source tagging system -# (see https://www.gnu.org/software/global/global.html). You will need version -# 4.8.6 or higher. -# -# To use it do the following: -# - Install the latest version of global -# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file -# - Make sure the INPUT points to the root of the source tree -# - Run doxygen as normal -# -# Doxygen will invoke htags (and that will in turn invoke gtags), so these -# tools must be available from the command line (i.e. in the search path). -# -# The result: instead of the source browser generated by doxygen, the links to -# source code will now point to the output of htags. -# The default value is: NO. -# This tag requires that the tag SOURCE_BROWSER is set to YES. - -USE_HTAGS = NO - -# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a -# verbatim copy of the header file for each class for which an include is -# specified. Set to NO to disable this. -# See also: Section \class. -# The default value is: YES. - -VERBATIM_HEADERS = YES - -#--------------------------------------------------------------------------- -# Configuration options related to the alphabetical class index -#--------------------------------------------------------------------------- - -# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all -# compounds will be generated. Enable this if the project contains a lot of -# classes, structs, unions or interfaces. -# The default value is: YES. - -ALPHABETICAL_INDEX = NO - -# In case all classes in a project start with a common prefix, all classes will -# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag -# can be used to specify a prefix (or a list of prefixes) that should be ignored -# while generating the index headers. -# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. - -IGNORE_PREFIX = - -#--------------------------------------------------------------------------- -# Configuration options related to the HTML output -#--------------------------------------------------------------------------- - -# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output -# The default value is: YES. - -GENERATE_HTML = YES - -# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a -# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of -# it. -# The default directory is: html. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_OUTPUT = html - -# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each -# generated HTML page (for example: .htm, .php, .asp). -# The default value is: .html. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_FILE_EXTENSION = .html - -# The HTML_HEADER tag can be used to specify a user-defined HTML header file for -# each generated HTML page. If the tag is left blank doxygen will generate a -# standard header. -# -# To get valid HTML the header file that includes any scripts and style sheets -# that doxygen needs, which is dependent on the configuration options used (e.g. -# the setting GENERATE_TREEVIEW). It is highly recommended to start with a -# default header using -# doxygen -w html new_header.html new_footer.html new_stylesheet.css -# YourConfigFile -# and then modify the file new_header.html. See also section "Doxygen usage" -# for information on how to generate the default header that doxygen normally -# uses. -# Note: The header is subject to change so you typically have to regenerate the -# default header when upgrading to a newer version of doxygen. For a description -# of the possible markers and block names see the documentation. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_HEADER = - -# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each -# generated HTML page. If the tag is left blank doxygen will generate a standard -# footer. See HTML_HEADER for more information on how to generate a default -# footer and what special commands can be used inside the footer. See also -# section "Doxygen usage" for information on how to generate the default footer -# that doxygen normally uses. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_FOOTER = - -# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style -# sheet that is used by each HTML page. It can be used to fine-tune the look of -# the HTML output. If left blank doxygen will generate a default style sheet. -# See also section "Doxygen usage" for information on how to generate the style -# sheet that doxygen normally uses. -# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as -# it is more robust and this tag (HTML_STYLESHEET) will in the future become -# obsolete. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_STYLESHEET = - -# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined -# cascading style sheets that are included after the standard style sheets -# created by doxygen. Using this option one can overrule certain style aspects. -# This is preferred over using HTML_STYLESHEET since it does not replace the -# standard style sheet and is therefore more robust against future updates. -# Doxygen will copy the style sheet files to the output directory. -# Note: The order of the extra style sheet files is of importance (e.g. the last -# style sheet in the list overrules the setting of the previous ones in the -# list). For an example see the documentation. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_EXTRA_STYLESHEET = - -# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or -# other source files which should be copied to the HTML output directory. Note -# that these files will be copied to the base HTML output directory. Use the -# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these -# files. In the HTML_STYLESHEET file, use the file name only. Also note that the -# files will be copied as-is; there are no commands or markers available. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_EXTRA_FILES = - -# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen -# will adjust the colors in the style sheet and background images according to -# this color. Hue is specified as an angle on a colorwheel, see -# https://en.wikipedia.org/wiki/Hue for more information. For instance the value -# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 -# purple, and 360 is red again. -# Minimum value: 0, maximum value: 359, default value: 220. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_COLORSTYLE_HUE = 220 - -# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors -# in the HTML output. For a value of 0 the output will use grayscales only. A -# value of 255 will produce the most vivid colors. -# Minimum value: 0, maximum value: 255, default value: 100. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_COLORSTYLE_SAT = 220 - -# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the -# luminance component of the colors in the HTML output. Values below 100 -# gradually make the output lighter, whereas values above 100 make the output -# darker. The value divided by 100 is the actual gamma applied, so 80 represents -# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not -# change the gamma. -# Minimum value: 40, maximum value: 240, default value: 80. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_COLORSTYLE_GAMMA = 80 - -# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML -# page will contain the date and time when the page was generated. Setting this -# to YES can help to show when doxygen was last run and thus if the -# documentation is up to date. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_TIMESTAMP = YES - -# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML -# documentation will contain a main index with vertical navigation menus that -# are dynamically created via JavaScript. If disabled, the navigation index will -# consists of multiple levels of tabs that are statically embedded in every HTML -# page. Disable this option to support browsers that do not have JavaScript, -# like the Qt help browser. -# The default value is: YES. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_DYNAMIC_MENUS = YES - -# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML -# documentation will contain sections that can be hidden and shown after the -# page has loaded. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_DYNAMIC_SECTIONS = YES - -# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries -# shown in the various tree structured indices initially; the user can expand -# and collapse entries dynamically later on. Doxygen will expand the tree to -# such a level that at most the specified number of entries are visible (unless -# a fully collapsed tree already exceeds this amount). So setting the number of -# entries 1 will produce a full collapsed tree by default. 0 is a special value -# representing an infinite number of entries and will result in a full expanded -# tree by default. -# Minimum value: 0, maximum value: 9999, default value: 100. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_INDEX_NUM_ENTRIES = 100 - -# If the GENERATE_DOCSET tag is set to YES, additional index files will be -# generated that can be used as input for Apple's Xcode 3 integrated development -# environment (see: -# https://developer.apple.com/xcode/), introduced with OSX 10.5 (Leopard). To -# create a documentation set, doxygen will generate a Makefile in the HTML -# output directory. Running make will produce the docset in that directory and -# running make install will install the docset in -# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at -# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy -# genXcode/_index.html for more information. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -GENERATE_DOCSET = NO - -# This tag determines the name of the docset feed. A documentation feed provides -# an umbrella under which multiple documentation sets from a single provider -# (such as a company or product suite) can be grouped. -# The default value is: Doxygen generated docs. -# This tag requires that the tag GENERATE_DOCSET is set to YES. - -DOCSET_FEEDNAME = "Doxygen generated docs" - -# This tag specifies a string that should uniquely identify the documentation -# set bundle. This should be a reverse domain-name style string, e.g. -# com.mycompany.MyDocSet. Doxygen will append .docset to the name. -# The default value is: org.doxygen.Project. -# This tag requires that the tag GENERATE_DOCSET is set to YES. - -DOCSET_BUNDLE_ID = org.doxygen.Project - -# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify -# the documentation publisher. This should be a reverse domain-name style -# string, e.g. com.mycompany.MyDocSet.documentation. -# The default value is: org.doxygen.Publisher. -# This tag requires that the tag GENERATE_DOCSET is set to YES. - -DOCSET_PUBLISHER_ID = org.doxygen.Publisher - -# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. -# The default value is: Publisher. -# This tag requires that the tag GENERATE_DOCSET is set to YES. - -DOCSET_PUBLISHER_NAME = Publisher - -# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three -# additional HTML index files: index.hhp, index.hhc, and index.hhk. The -# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop -# (see: -# https://www.microsoft.com/en-us/download/details.aspx?id=21138) on Windows. -# -# The HTML Help Workshop contains a compiler that can convert all HTML output -# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML -# files are now used as the Windows 98 help format, and will replace the old -# Windows help format (.hlp) on all Windows platforms in the future. Compressed -# HTML files also contain an index, a table of contents, and you can search for -# words in the documentation. The HTML workshop also contains a viewer for -# compressed HTML files. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -GENERATE_HTMLHELP = NO - -# The CHM_FILE tag can be used to specify the file name of the resulting .chm -# file. You can add a path in front of the file if the result should not be -# written to the html output directory. -# This tag requires that the tag GENERATE_HTMLHELP is set to YES. - -CHM_FILE = - -# The HHC_LOCATION tag can be used to specify the location (absolute path -# including file name) of the HTML help compiler (hhc.exe). If non-empty, -# doxygen will try to run the HTML help compiler on the generated index.hhp. -# The file has to be specified with full path. -# This tag requires that the tag GENERATE_HTMLHELP is set to YES. - -HHC_LOCATION = - -# The GENERATE_CHI flag controls if a separate .chi index file is generated -# (YES) or that it should be included in the main .chm file (NO). -# The default value is: NO. -# This tag requires that the tag GENERATE_HTMLHELP is set to YES. - -GENERATE_CHI = NO - -# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) -# and project file content. -# This tag requires that the tag GENERATE_HTMLHELP is set to YES. - -CHM_INDEX_ENCODING = - -# The BINARY_TOC flag controls whether a binary table of contents is generated -# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it -# enables the Previous and Next buttons. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTMLHELP is set to YES. - -BINARY_TOC = NO - -# The TOC_EXPAND flag can be set to YES to add extra items for group members to -# the table of contents of the HTML help documentation and to the tree view. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTMLHELP is set to YES. - -TOC_EXPAND = NO - -# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and -# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that -# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help -# (.qch) of the generated HTML documentation. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -GENERATE_QHP = NO - -# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify -# the file name of the resulting .qch file. The path specified is relative to -# the HTML output folder. -# This tag requires that the tag GENERATE_QHP is set to YES. - -QCH_FILE = - -# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help -# Project output. For more information please see Qt Help Project / Namespace -# (see: -# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace). -# The default value is: org.doxygen.Project. -# This tag requires that the tag GENERATE_QHP is set to YES. - -QHP_NAMESPACE = org.doxygen.Project - -# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt -# Help Project output. For more information please see Qt Help Project / Virtual -# Folders (see: -# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-folders). -# The default value is: doc. -# This tag requires that the tag GENERATE_QHP is set to YES. - -QHP_VIRTUAL_FOLDER = doc - -# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom -# filter to add. For more information please see Qt Help Project / Custom -# Filters (see: -# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters). -# This tag requires that the tag GENERATE_QHP is set to YES. - -QHP_CUST_FILTER_NAME = - -# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the -# custom filter to add. For more information please see Qt Help Project / Custom -# Filters (see: -# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters). -# This tag requires that the tag GENERATE_QHP is set to YES. - -QHP_CUST_FILTER_ATTRS = - -# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this -# project's filter section matches. Qt Help Project / Filter Attributes (see: -# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes). -# This tag requires that the tag GENERATE_QHP is set to YES. - -QHP_SECT_FILTER_ATTRS = - -# The QHG_LOCATION tag can be used to specify the location (absolute path -# including file name) of Qt's qhelpgenerator. If non-empty doxygen will try to -# run qhelpgenerator on the generated .qhp file. -# This tag requires that the tag GENERATE_QHP is set to YES. - -QHG_LOCATION = - -# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be -# generated, together with the HTML files, they form an Eclipse help plugin. To -# install this plugin and make it available under the help contents menu in -# Eclipse, the contents of the directory containing the HTML and XML files needs -# to be copied into the plugins directory of eclipse. The name of the directory -# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. -# After copying Eclipse needs to be restarted before the help appears. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -GENERATE_ECLIPSEHELP = NO - -# A unique identifier for the Eclipse help plugin. When installing the plugin -# the directory name containing the HTML and XML files should also have this -# name. Each documentation set should have its own identifier. -# The default value is: org.doxygen.Project. -# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. - -ECLIPSE_DOC_ID = org.doxygen.Project - -# If you want full control over the layout of the generated HTML pages it might -# be necessary to disable the index and replace it with your own. The -# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top -# of each HTML page. A value of NO enables the index and the value YES disables -# it. Since the tabs in the index contain the same information as the navigation -# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -DISABLE_INDEX = NO - -# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index -# structure should be generated to display hierarchical information. If the tag -# value is set to YES, a side panel will be generated containing a tree-like -# index structure (just like the one that is generated for HTML Help). For this -# to work a browser that supports JavaScript, DHTML, CSS and frames is required -# (i.e. any modern browser). Windows users are probably better off using the -# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can -# further fine-tune the look of the index. As an example, the default style -# sheet generated by doxygen has an example that shows how to put an image at -# the root of the tree instead of the PROJECT_NAME. Since the tree basically has -# the same information as the tab index, you could consider setting -# DISABLE_INDEX to YES when enabling this option. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -GENERATE_TREEVIEW = YES - -# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that -# doxygen will group on one line in the generated HTML documentation. -# -# Note that a value of 0 will completely suppress the enum values from appearing -# in the overview section. -# Minimum value: 0, maximum value: 20, default value: 4. -# This tag requires that the tag GENERATE_HTML is set to YES. - -ENUM_VALUES_PER_LINE = 4 - -# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used -# to set the initial width (in pixels) of the frame in which the tree is shown. -# Minimum value: 0, maximum value: 1500, default value: 250. -# This tag requires that the tag GENERATE_HTML is set to YES. - -TREEVIEW_WIDTH = 250 - -# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to -# external symbols imported via tag files in a separate window. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -EXT_LINKS_IN_WINDOW = NO - -# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg -# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see -# https://inkscape.org) to generate formulas as SVG images instead of PNGs for -# the HTML output. These images will generally look nicer at scaled resolutions. -# Possible values are: png (the default) and svg (looks nicer but requires the -# pdf2svg or inkscape tool). -# The default value is: png. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_FORMULA_FORMAT = png - -# Use this tag to change the font size of LaTeX formulas included as images in -# the HTML documentation. When you change the font size after a successful -# doxygen run you need to manually remove any form_*.png images from the HTML -# output directory to force them to be regenerated. -# Minimum value: 8, maximum value: 50, default value: 10. -# This tag requires that the tag GENERATE_HTML is set to YES. - -FORMULA_FONTSIZE = 10 - -# Use the FORMULA_TRANSPARENT tag to determine whether or not the images -# generated for formulas are transparent PNGs. Transparent PNGs are not -# supported properly for IE 6.0, but are supported on all modern browsers. -# -# Note that when changing this option you need to delete any form_*.png files in -# the HTML output directory before the changes have effect. -# The default value is: YES. -# This tag requires that the tag GENERATE_HTML is set to YES. - -FORMULA_TRANSPARENT = YES - -# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands -# to create new LaTeX commands to be used in formulas as building blocks. See -# the section "Including formulas" for details. - -FORMULA_MACROFILE = - -# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see -# https://www.mathjax.org) which uses client side JavaScript for the rendering -# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX -# installed or if you want to formulas look prettier in the HTML output. When -# enabled you may also need to install MathJax separately and configure the path -# to it using the MATHJAX_RELPATH option. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -USE_MATHJAX = NO - -# When MathJax is enabled you can set the default output format to be used for -# the MathJax output. See the MathJax site (see: -# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details. -# Possible values are: HTML-CSS (which is slower, but has the best -# compatibility), NativeMML (i.e. MathML) and SVG. -# The default value is: HTML-CSS. -# This tag requires that the tag USE_MATHJAX is set to YES. - -MATHJAX_FORMAT = HTML-CSS - -# When MathJax is enabled you need to specify the location relative to the HTML -# output directory using the MATHJAX_RELPATH option. The destination directory -# should contain the MathJax.js script. For instance, if the mathjax directory -# is located at the same level as the HTML output directory, then -# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax -# Content Delivery Network so you can quickly see the result without installing -# MathJax. However, it is strongly recommended to install a local copy of -# MathJax from https://www.mathjax.org before deployment. -# The default value is: https://cdn.jsdelivr.net/npm/mathjax@2. -# This tag requires that the tag USE_MATHJAX is set to YES. - -MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest - -# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax -# extension names that should be enabled during MathJax rendering. For example -# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols -# This tag requires that the tag USE_MATHJAX is set to YES. - -MATHJAX_EXTENSIONS = - -# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces -# of code that will be used on startup of the MathJax code. See the MathJax site -# (see: -# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details. For an -# example see the documentation. -# This tag requires that the tag USE_MATHJAX is set to YES. - -MATHJAX_CODEFILE = - -# When the SEARCHENGINE tag is enabled doxygen will generate a search box for -# the HTML output. The underlying search engine uses javascript and DHTML and -# should work on any modern browser. Note that when using HTML help -# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) -# there is already a search function so this one should typically be disabled. -# For large projects the javascript based search engine can be slow, then -# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to -# search using the keyboard; to jump to the search box use + S -# (what the is depends on the OS and browser, but it is typically -# , /