#+TITLE: QMCkl source code documentation

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* Introduction

  The ultimate goal of QMCkl is to provide a high-performance
  implementation of the main kernels of QMC. In this particular
  repository, we focus on the definition of the API and the tests,
  and on a /pedagogical/ presentation of the algorithms.  We expect the
  HPC experts to use this repository as a reference for re-writing
  optimized libraries.

  Literate programming is particularly adapted in this context.
  Source files are written in [[https://karl-voit.at/2017/09/23/orgmode-as-markup-only/][org-mode]] format, to provide useful
  comments and LaTex formulas close to the code. There exists multiple
  possibilities to convert org-mode files into different formats such as
  HTML or pdf.
  For a tutorial on literate programming with org-mode, follow
  [[http://www.howardism.org/Technical/Emacs/literate-programming-tutorial.html][this link]].

  The code is extracted from the org files using Emacs as a command-line
  tool in the =Makefile=, and then the produced files are compiled.

** Language used

   Fortran is one of the most common languages used by the community,
   and is simple enough to make the algorithms readable. Hence we
   propose in this pedagogical implementation of QMCkl to use Fortran
   to express the algorithms. For specific internal functions where
   the C language is more natural, C is used.

   As Fortran modules generate compiler-dependent files, the use of
   modules is restricted to the internal use of the library, otherwise
   the compliance with C is violated.

   The external dependencies should be kept as small as possible, so
   external libraries should be used /only/ if their used is strongly
   justified.

** Source code editing

   Any text editor can be used to edit org-mode files. For a better
   user experience Emacs is recommended.
   For users hating Emacs, it is good to know that Emacs can behave
   like Vim when switched into ``Evil'' mode. There also exists
   [[https://www.spacemacs.org][Spacemacs]] which helps the transition for Vim users.

   For users with a preference for Jupyter notebooks, the following
   script can convert jupyter notebooks to org-mode files:

   #+BEGIN_SRC sh tangle: nb_to_org.sh
#!/bin/bash
# $ nb_to_org.sh notebook.ipynb
# produces the org-mode file notebook.org

set -e

nb=$(basename $1 .ipynb)
jupyter nbconvert --to markdown ${nb}.ipynb --output ${nb}.md
pandoc ${nb}.md -o ${nb}.org
rm ${nb}.md
   #+END_SRC

   And pandoc can convert multiple markdown formats into org-mode.

** Writing in Fortran

   The Fortran source files should provide a C interface using
   =iso_c_binding=. The name of the Fortran source files should end
   with =_f.f90= to be properly handled by the Makefile.
   The names of the functions defined in fortran should be the same as
   those exposed in the API suffixed by =_f=.
   Fortran interface files should also be written in a file with a
   =.fh= extension.
   
** Coding style
   # TODO: decide on a coding style

   To improve readability, we maintain a consistent coding style in the library.

   - For C source files, we will use __(decide on a coding style)__                           
   - For Fortran source files, we will use __(decide on a coding style)__

   Coding style can be automatically checked with [[https://clang.llvm.org/docs/ClangFormat.html][clang-format]].

* Design of the library

  The proposed API should allow the library to:
  - deal with memory transfers between CPU and accelerators
  - use different levels of floating-point precision

  We chose a multi-layered design with low-level and high-level
  functions (see below).

** Naming conventions

   Use =qmckl_= as a prefix for all exported functions and variables.
   All exported header files should have a filename with the prefix
   =qmckl_=.

   If the name of the org-mode file is =xxx.org=, the name of the
   produced C files should be =xxx.c= and =xxx.h= and the name of the
   produced Fortran files should be =xxx.f90=
   
   Arrays are in uppercase and scalars are in lowercase.

** Application programming interface

   The application programming interface (API) is designed to be
   compatible with the C programming language (not C++), to ensure
   that the library will be easily usable in any language.
   This implies that only the following data types are allowed in the API:

   - 32-bit and 64-bit floats and arrays (=real= and =double=)
   - 32-bit and 64-bit integers and arrays (=int32_t= and =int64_t=)
   - Pointers should be represented as 64-bit integers (even on
     32-bit architectures)
   - ASCII strings are represented as a pointers to a character arrays
     and terminated by a zero character (C convention).

   # TODO : Link to repositories for bindings
   To facilitate the use in other languages than C, we provide some
   bindings in other languages in other repositories.

** Global state

   Global variables should be avoided in the library, because it is
   possible that one single program needs to use multiple instances of
   the library. To solve this problem we propose to use a pointer to a
   =context= variable, built by the library with the
   =qmckl_context_create= function. The =context= contains the global
   state of the library, and is used as the first argument of many
   QMCkl functions.

   Modifying the state is done by setters and getters, prefixed
   by =qmckl_context_set_= an =qmckl_context_get_=.
   When a context variable is modified by a setter, a copy of the old
   data structure is made and updated, and the pointer to the new data
   structure is returned, such that the old contexts can still be
   accessed.
   It is also possible to modify the state in an impure fashion, using
   the =qmckl_context_update_= functions.
   The context and its old versions can be destroyed with
   =qmckl_context_destroy=.

** Low-level functions

   Low-level functions are very simple functions which are leaves of the
   function call tree (they don't call any other QMCkl function).

   This functions are /pure/, and unaware of the QMCkl =context=. They are
   not allowed to allocate/deallocate memory, and if they need
   temporary memory it should be provided in input.

** High-level functions

   High-level functions are at the top of the function call tree.
   They are able to choose which lower-level function to call
   depending on the required precision, and do the corresponding type
   conversions.
   These functions are also responsible for allocating temporary
   storage, to simplify the use of accelerators.

   The high-level functions should be pure, unless the introduction of
   non-purity is justified. All the side effects should be made in the
   =context= variable.

   # TODO : We need an identifier for impure functions

** Numerical precision

   The number of bits of precision required for a function should be
   given as an input of low-level computational functions. This input will
   be used to define the values of the different thresholds that might
   be used to avoid computing unnecessary noise.
   High-level functions will use the precision specified in the
   =context= variable.

* Algorithms
  
  Reducing the scaling of an algorithm usually implies also reducing
  its arithmetic complexity (number of flops per byte). Therefore,
  for small sizes \(\mathcal{O}(N^3)\) and \(\mathcal{O}(N^2)\) algorithms
  are better adapted than linear scaling algorithms.
  As QMCkl is a general purpose library, multiple algorithms should
  be implemented adapted to different problem sizes.

* Rules for the API
   
  - =stdint= should be used for integers (=int32_t=, =int64_t=)
  - integers used for counting should always be =int64_t=
  - floats should be by default =double=, unless explicitly mentioned 
  - pointers are converted to =int64_t= to increase portability

* Documentation

  - [[./qmckl.org][Main QMCkl header file]]
  - [[./qmckl_memory.org][Memory management]]
  - [[./qmckl_context.org][Context]]
  - [[./qmckl_distance.org][Distance]]
  - [[./qmckl_ao.org][Atomic orbitals]]

* Acknowledgments

  [[https://trex-coe.eu/sites/default/files/inline-images/euflag.jpg]]
  [[https://trex-coe.eu][TREX: Targeting Real Chemical Accuracy at the Exascale]] project has received funding from the European Union’s Horizon 2020 - Research and Innovation program - under grant agreement no. 952165. The content of this document does not represent the opinion of the European Union, and the European Union is not responsible for any use that might be made of such content.