precommit: Wrap Markdown lines after 100 characters

README.md

@@ -1,18 +1,16 @@
 # CP2K
 
-CP2K is a quantum chemistry and solid state physics software package that can
-perform atomistic simulations of solid state, liquid, molecular, periodic,
-material, crystal, and biological systems. CP2K provides a general framework for
-different modeling methods such as DFT using the mixed Gaussian and plane waves
-approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2,
-RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, ...), and classical force
-fields (AMBER, CHARMM, ...). CP2K can do simulations of molecular dynamics,
-metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level
-spectroscopy, energy minimization, and transition state optimization using NEB
-or dimer method.
-
-CP2K is written in Fortran 2008 and can be run efficiently in parallel using
-a combination of multi-threading, MPI, and CUDA.
+CP2K is a quantum chemistry and solid state physics software package that can perform atomistic
+simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.
+CP2K provides a general framework for different modeling methods such as DFT using the mixed
+Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA,
+MP2, RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, ...), and classical force fields (AMBER,
+CHARMM, ...). CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest
+dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state
+optimization using NEB or dimer method.
+
+CP2K is written in Fortran 2008 and can be run efficiently in parallel using a combination of
+multi-threading, MPI, and CUDA.
 
 ## Downloading CP2K source code
 
@@ -30,27 +28,28 @@ To clone a release version v*x.y*:
 git clone -b support/vx.y --recursive https://github.com/cp2k/cp2k.git cp2k
 ```
 
-For more information on downloading CP2K, see [Downloading CP2K](https://www.cp2k.org/download).
-For help on git, see [Git Tips & Tricks](https://github.com/cp2k/cp2k/wiki/Git-Tips-&-Tricks).
+For more information on downloading CP2K, see [Downloading CP2K](https://www.cp2k.org/download). For
+help on git, see [Git Tips & Tricks](https://github.com/cp2k/cp2k/wiki/Git-Tips-&-Tricks).
 
 ## Install CP2K
 
-The easiest way to build CP2K with all of its dependencies is as a [Docker container](./tools/docker/README.md).
+The easiest way to build CP2K with all of its dependencies is as a
+[Docker container](./tools/docker/README.md).
 
 For building CP2K from scratch see the [installation instructions](./INSTALL.md).
 
 ## Links
 
-- [CP2K.org](https://www.cp2k.org)
-  for showcases of scientific work, tutorials, exercises, presentation slides, etc.
-- [The manual](https://manual.cp2k.org/)
-  with descriptions of all the keywords for the CP2K input file
-- [The dashboard](https://dashboard.cp2k.org)
-  to get an overview of the currently tested architectures
-- [The Google group](https://groups.google.com/group/cp2k) to get help if you
-  could not find an answer in one of the previous links
-- [Acknowledgements](https://www.cp2k.org/funding) for list of institutions and
-  grants that help to fund the development of CP2K
+- [CP2K.org](https://www.cp2k.org) for showcases of scientific work, tutorials, exercises,
+  presentation slides, etc.
+- [The manual](https://manual.cp2k.org/) with descriptions of all the keywords for the CP2K input
+  file
+- [The dashboard](https://dashboard.cp2k.org) to get an overview of the currently tested
+  architectures
+- [The Google group](https://groups.google.com/group/cp2k) to get help if you could not find an
+  answer in one of the previous links
+- [Acknowledgements](https://www.cp2k.org/funding) for list of institutions and grants that help to
+  fund the development of CP2K
 
 ## Directory organization
 

README_cmake.md

@@ -1,15 +1,13 @@
 # Build CP2K with CMake
 
-This document regroups information about the CP2K CMake system. CMake is used to
-detect CP2K dependencies and configure the compilation process. Dependencies
-should be installed independently either with a distribution package manager,
-easybuild, or spack to name a few.
-
-It is easier to build and install all manually built dependencies in a single
-directory ideally where CP2K will also be installed. CMake will have less
-difficulties to find the `FindPACKAGE.cmake` files and dependent libraries. CMake
-will also use environment variables such as `ORNL_FFTW3_ROOT`, etc. Usually a
-standard prefix is used in HPC environments. If known just add it in the
+This document regroups information about the CP2K CMake system. CMake is used to detect CP2K
+dependencies and configure the compilation process. Dependencies should be installed independently
+either with a distribution package manager, easybuild, or spack to name a few.
+
+It is easier to build and install all manually built dependencies in a single directory ideally
+where CP2K will also be installed. CMake will have less difficulties to find the `FindPACKAGE.cmake`
+files and dependent libraries. CMake will also use environment variables such as `ORNL_FFTW3_ROOT`,
+etc. Usually a standard prefix is used in HPC environments. If known just add it in the
 `cmake/cp2k_utils.cmake` file.
 
 The CMake build system requires a minimum set of dependencies:
@@ -22,20 +20,19 @@ The CMake build system requires a minimum set of dependencies:
 - fftw3
 - CMake
 
-Major vendors implementations of BLAS, LAPACK, and scalapack are supported. The
-build system was tested with MKL, cray libsci, OpenBLAS, flexiblas, blis or
-ATLAS.
+Major vendors implementations of BLAS, LAPACK, and scalapack are supported. The build system was
+tested with MKL, cray libsci, OpenBLAS, flexiblas, blis or ATLAS.
 
-All optional dependencies are turned off by default. DBCSR is the only dependency that
-can be built at the same time than CP2K. It is OFF by default. We assume that mpi, blas,
-lapack, and scalapack are installed. To compile `CP2K and `DBCSR\` open a terminal and write
+All optional dependencies are turned off by default. DBCSR is the only dependency that can be built
+at the same time than CP2K. It is OFF by default. We assume that mpi, blas, lapack, and scalapack
+are installed. To compile `CP2K and `DBCSR\` open a terminal and write
 
 ```shell
 cmake -DCMAKE_INSTALL_PREFIX=/pyprefix -DCP2K_BUILD_DBCSR=ON ..
 ```
 
-This command will build cp2k and dbcsr dependencies in cpu only mode. Openmp is turned
-on by default for dbcsr (see dedicated session in this README).
+This command will build cp2k and dbcsr dependencies in cpu only mode. Openmp is turned on by default
+for dbcsr (see dedicated session in this README).
 
 If MKL is present on your system then add this
 
@@ -57,8 +54,8 @@ CP2K can be compiled on CRAY systems with the following command line
 make -j
 ```
 
-MKL (or openblas, etc) can be combined with CUDA or HIP after adding the
-additional flags enabling GPU support to the one of the previous cmake commands.
+MKL (or openblas, etc) can be combined with CUDA or HIP after adding the additional flags enabling
+GPU support to the one of the previous cmake commands.
 
 To get CUDA support (V100 gpus) write this command
 
@@ -80,26 +77,24 @@ cmake -DCMAKE_INSTALL_PREFIX=/pyprefix \
 make -j
 ```
 
-The option `CP2K_ENABLE_REGTESTS=ON` will configure the build system such that
-the regtests are ran as usuall. `CMake` will create the binaries in the
-`exe/cmake-build-{cpu,cuda,hip}` directory located in the cp2k root
-directory. Users will have to set the environment variabble `CP2K_DATA_DIR`
+The option `CP2K_ENABLE_REGTESTS=ON` will configure the build system such that the regtests are ran
+as usuall. `CMake` will create the binaries in the `exe/cmake-build-{cpu,cuda,hip}` directory
+located in the cp2k root directory. Users will have to set the environment variabble `CP2K_DATA_DIR`
 accordingly.
 
 For additional options please read the section below.
 
 ## Use of spack to build cp2k
 
-The \[spack\]{https://github.com/spack/spack.git} tool can build CP2K and all its
-dependencies with relative ease. We assume that you have spack available on your
-system. Enter the command
+The \[spack\]{https://github.com/spack/spack.git} tool can build CP2K and all its dependencies with
+relative ease. We assume that you have spack available on your system. Enter the command
 
 ```shell
 spack install cp2k@master build_system=cmake ^openblas
 ```
 
-To build cp2k master with MPI, openblas, scalapack, fftw and openmp. CP2K with
-CUDA support is compiled with
+To build cp2k master with MPI, openblas, scalapack, fftw and openmp. CP2K with CUDA support is
+compiled with
 
 ```shell
 spack install cp2k@master build_system=cmake +cuda cuda_arch=70 ^openblas ^dbcsr+cuda cuda_arch=70
@@ -136,8 +131,8 @@ build_system=cmake \
 
 The CP2K cmake build system also supports the following dependencies :
 
-- `CP2K_USE_SIRIUS = OFF`: add [SIRIUS](https://github.com/electronic-structure/SIRIUS)
-  support to CP2K
+- `CP2K_USE_SIRIUS = OFF`: add [SIRIUS](https://github.com/electronic-structure/SIRIUS) support to
+  CP2K
 
 - `CP2K_USE_FFTW3 = ON`: add support of [fftw3](https://www.fftw.org)
 
@@ -148,82 +143,73 @@ The CP2K cmake build system also supports the following dependencies :
 
 - `CP2K_USE_SUPERLU = OFF`: detection should work but needs improvement
 
-- `CP2K_USE_COSMA = OFF` : add [cosma](https://github.com/eth-cscs/COSMA) drop-in
-  replacement for sclapack pdgemnm
+- `CP2K_USE_COSMA = OFF` : add [cosma](https://github.com/eth-cscs/COSMA) drop-in replacement for
+  sclapack pdgemnm
 
-- `CP2K_USE_LIBINT2 = OFF`: add [libint2](https://github.com/evaleev/libint) support
-  (detection works ok, module files may not be found at compilation time though)
+- `CP2K_USE_LIBINT2 = OFF`: add [libint2](https://github.com/evaleev/libint) support (detection
+  works ok, module files may not be found at compilation time though)
 
-- `CP2K_USE_VORI = OFF`: detection is fine compilation might fail at linking time
-  (investigating why)
+- `CP2K_USE_VORI = OFF`: detection is fine compilation might fail at linking time (investigating
+  why)
 
 - `CP2K_USE_QUIP = OFF` :
 
 - `CP2K_USE_SPGLIB = OFF`: everything alright
 
-- `CP2K_USE_LIBXC = OFF`: Use `pkg-config` by default (ideally
-  the library should be built with CMake, if so we can get rid of the
-  `FindLibXC.cmake`). If you installed LIBXC in a non-standard location,
-  modify the `PKG_CONFIG_PATH` variable accordingly.
+- `CP2K_USE_LIBXC = OFF`: Use `pkg-config` by default (ideally the library should be built with
+  CMake, if so we can get rid of the `FindLibXC.cmake`). If you installed LIBXC in a non-standard
+  location, modify the `PKG_CONFIG_PATH` variable accordingly.
 
-- `CP2K_USE_SPLA = OFF`: enable spla off-loading capabilities (use CMake modules
-  to detect it)
+- `CP2K_USE_SPLA = OFF`: enable spla off-loading capabilities (use CMake modules to detect it)
 
 - `CP2K_USE_METIS = OFF`:
 
-- `CP2K_USE_LIBXSMM = OFF`: use [libxsmm](https://libxsmm.readthedocs.io/en/latest/)
-  library for small matrices operations. Detection based on `pkg-config`. If you
-  installed libxsmm in a non-standard location, modify the `PKG_CONFIG_PATH` variable
-  accordingly.
+- `CP2K_USE_LIBXSMM = OFF`: use [libxsmm](https://libxsmm.readthedocs.io/en/latest/) library for
+  small matrices operations. Detection based on `pkg-config`. If you installed libxsmm in a
+  non-standard location, modify the `PKG_CONFIG_PATH` variable accordingly.
 
 - `CP2K_USE_ACCEL = NONE, CUDA, HIP`: enable GPU support
 
-- `CP2K_BLAS_VENDOR = auto`: CMake will search for the most common blas / lapack
-  implementations. If possible indicate which implementation you are using. Supported
-  values are: `auto` (default), `MKL`, `SCI`, `OpenBLAS`, `FlexiBLAS`, `Armpl`.
+- `CP2K_BLAS_VENDOR = auto`: CMake will search for the most common blas / lapack implementations. If
+  possible indicate which implementation you are using. Supported values are: `auto` (default),
+  `MKL`, `SCI`, `OpenBLAS`, `FlexiBLAS`, `Armpl`.
 
-- `CP2K_SCALAPACK_VENDOR = MKL, SCI, GENERIC`: similar to the previous option but for
-  scalapack
+- `CP2K_SCALAPACK_VENDOR = MKL, SCI, GENERIC`: similar to the previous option but for scalapack
 
-- `CP2K_BLAS_THREADING = sequential, openmp, etc...`: leave the default value (or
-  use it at your own peril)
+- `CP2K_BLAS_THREADING = sequential, openmp, etc...`: leave the default value (or use it at your own
+  peril)
 
-- `CP2K_BLAS_INTERFACE = 32 bits, 64 bits`: size of the integers for the matrices
-  and vectors sizes. Default: 32 bits
+- `CP2K_BLAS_INTERFACE = 32 bits, 64 bits`: size of the integers for the matrices and vectors sizes.
+  Default: 32 bits
 
-- `CP2K_DEV_OPTIONS = OFF`: enable developer options. The main purpose is for
-  debugging
+- `CP2K_DEV_OPTIONS = OFF`: enable developer options. The main purpose is for debugging
 
   - `CP2K_USE_GRID_GPU = ON`: turn on of gpu support for collocate integrate
   - `CP2K_USE_PW_GPU = ON`: turn on or off gpu fft support
   - `CP2K_USE_DBM_GPU = ON`: turn on or off dbm gpu support
-  - `CP2K_CHECK_CONSISTENCY = OFF` : Compare the list of compiled files to the
-    files found in the tree. This function is only relevant to developers and should
-    be left to its default value. It has no incidence on the binaries generated by
-    the build.
-
-ROCM 5.0.x is known to have a bug in the CMake configuration files. It is
-possible to go around this but at the expense of time. The build system was not
-tested with ROCM 5.1.x but this version shows performance regression and should
-be avoided. The Jiting capabilities of ROCM 5.2.x do not work properly which
-affects DBCSR. It is highly recommended to update ROCM to the latest version to
-avoid all these issues. CP2K can be built with ROCM 5.2.x but GPU support in
-DBCSR should be turned off otherwise a crash is expected. ROCM 5.3.x and
-later seems to work fine.
+  - `CP2K_CHECK_CONSISTENCY = OFF` : Compare the list of compiled files to the files found in the
+    tree. This function is only relevant to developers and should be left to its default value. It
+    has no incidence on the binaries generated by the build.
+
+ROCM 5.0.x is known to have a bug in the CMake configuration files. It is possible to go around this
+but at the expense of time. The build system was not tested with ROCM 5.1.x but this version shows
+performance regression and should be avoided. The Jiting capabilities of ROCM 5.2.x do not work
+properly which affects DBCSR. It is highly recommended to update ROCM to the latest version to avoid
+all these issues. CP2K can be built with ROCM 5.2.x but GPU support in DBCSR should be turned off
+otherwise a crash is expected. ROCM 5.3.x and later seems to work fine.
 
 ## Threading with blas and lapack
 
 CP2K expect by default a single threaded version of blas and lapack. The option
-`-DCP2K_BLAS_THREADING` can change this behavior. Be careful when tweaking this
-specific option as many implementations of blas / lapack are either threaded or
-(exclusive) sequential but not both. I think the only exception to this is MKL.
-Also note that CP2K dependencies will most likely have the same issue (COSMA
-with cray-libsci for instance).
+`-DCP2K_BLAS_THREADING` can change this behavior. Be careful when tweaking this specific option as
+many implementations of blas / lapack are either threaded or (exclusive) sequential but not both. I
+think the only exception to this is MKL. Also note that CP2K dependencies will most likely have the
+same issue (COSMA with cray-libsci for instance).
 
 ## Typical examples of CMake use
 
-The following list gives several examples of CMake command lines. Just add
-`-DCP2K_USE_SIRIUS=ON` to add support of SIRIUS in CP2K
+The following list gives several examples of CMake command lines. Just add `-DCP2K_USE_SIRIUS=ON` to
+add support of SIRIUS in CP2K
 
 ```shell
 cmake -DCP2K_INSTALL_PREFIX=/myprefix -DCP2K_USE_SIRIUS=ON ..
@@ -251,8 +237,7 @@ MPICC=cc MPICXX=CC cmake -DCP2K_INSTALL_PREFIX=/myprefix
 
 ## CUDA / HIP
 
-Let us consider the case where OpenBLAS and netlib scalapack are installed
-(openmpi or mpich)
+Let us consider the case where OpenBLAS and netlib scalapack are installed (openmpi or mpich)
 
 ```shell
 cmake -DCP2K_INSTALL_PREFIX=/myprefix -DCP2K_BLAS_VENDOR=OpenBLAS
@@ -268,30 +253,29 @@ cmake -DCP2K_INSTALL_PREFIX=/myprefix -DCP2K_BLAS_VENDOR=OpenBLAS
 
 ## Troubleshooting
 
-This build system is relatevily stable and was tested on Cray, IBM, and redhat
-like distributions. However it is not perfect and problems will show up, that's
-why the two build systems will be available. We encourage the user to test the
-build system just reporting the output of `cmake ..` is already beneficial.
+This build system is relatevily stable and was tested on Cray, IBM, and redhat like distributions.
+However it is not perfect and problems will show up, that's why the two build systems will be
+available. We encourage the user to test the build system just reporting the output of `cmake ..` is
+already beneficial.
 
-The best way to report these problems is to open an issue including the CMake
-command line, error message, and operating systems.
+The best way to report these problems is to open an issue including the CMake command line, error
+message, and operating systems.
 
 What is known to fail sometimes
 
-- Nvidia HPC SDK: The location of the cuda maths libraries has changed
-  recently. While CUDA support will be detected, the CUDA maths libraries may not.
+- Nvidia HPC SDK: The location of the cuda maths libraries has changed recently. While CUDA support
+  will be detected, the CUDA maths libraries may not.
 
-- HIP : CMake support of ROCM is still under development and is known to fail
-  from time to time. Update to ROCM 5.3.x or above to solve the issue.
+- HIP : CMake support of ROCM is still under development and is known to fail from time to time.
+  Update to ROCM 5.3.x or above to solve the issue.
 
-- BLAS / LAPACK / SCALAPACK : use the options `CP2K_BLAS_VENDOR` and
-  `CP2K_SCALPACK_VENDOR` if you know that `MKL` or `SCI` (cray libsci) are
-  present. `-DCP2k_BLAS_VENDOR=OpenBLAS` will also help CMake to find OpenBLAS if
-  it is used. Detecting the scalapack library might also fail if the user
+- BLAS / LAPACK / SCALAPACK : use the options `CP2K_BLAS_VENDOR` and `CP2K_SCALPACK_VENDOR` if you
+  know that `MKL` or `SCI` (cray libsci) are present. `-DCP2k_BLAS_VENDOR=OpenBLAS` will also help
+  CMake to find OpenBLAS if it is used. Detecting the scalapack library might also fail if the user
   environment is not properly set up.
 
-- BLAS / LAPACK / SCALAPACK: It is possible to set up BLAS / LAPACK / SCALAPACK
-  libraries manually with the command
+- BLAS / LAPACK / SCALAPACK: It is possible to set up BLAS / LAPACK / SCALAPACK libraries manually
+  with the command
 
 ```shell
 cmake -DCP2K_BLAS_LINK_LIBRARIES=libmyblas.so -DCP2K_BLAS_VENDOR=CUSTOM