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Add a first version of the 5D geometry in (tor1,tor2,tor3,vpar,mu)
This version is a temporary step that will quickly be moved to a 4D geometry (tor1,tor2,vpar,mu) because we realized the strategy to create directly a 5D geometry with only one point in tor3 direction is not a good idea. The interest of merging this temporary branch is due to the fact that it contains, - a first example of HDF5 file reading (initialized from external python scripts developed in [gysela_io project](https://gitlab.maisondelasimulation.fr/gysela-developpers/gysela_io) - a first coupling with collision operator developed within [koliop library](https://gitlab.com/cines/code.gysela/libkoliop) - Adastra configuration See merge request gysela-developpers/gyselalibxx!405 -------------------------------------------- Co-authored-by: Etienne Malaboeuf <[email protected]>
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| /build*/ | ||
| *.pyc |
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| #!/bin/bash | ||
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| [[ -z ${1+x} ]] && echo -e "Gyselalibxx preparation shortcut script:\n ./prepare.gyselalibxx.sh <toolchain/machine [mi250.cce.adastra.spack|...]> <do prepare [default: TRUE|FALSE]> <force a fresh build [default: TRUE|FALSE]> <extra CMake flags>" && exit 1 | ||
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| PREPARE_ROOT_DIRECTORY="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" &>/dev/null && pwd -P)" | ||
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| set -eu | ||
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| PREPARE_TOOLCHAIN_NAME="${1}" | ||
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| if [[ ! -z ${2+x} ]]; then | ||
| PREPARE_DONT_SKIP="${2}" | ||
| else | ||
| PREPARE_DONT_SKIP="TRUE" | ||
| fi | ||
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| if [[ ! -z ${3+x} ]]; then | ||
| PREPARE_FORCE_FRESH_BUILD="${3}" | ||
| else | ||
| PREPARE_FORCE_FRESH_BUILD="TRUE" | ||
| fi | ||
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| # A toolchain script should NOT expect we source/execute them from the toolchain | ||
| # directory. | ||
| PREPARE_TOOLCHAIN_PATH="${PREPARE_ROOT_DIRECTORY}/toolchains/${PREPARE_TOOLCHAIN_NAME}" | ||
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| if [[ "${PREPARE_DONT_SKIP}" != "TRUE" ]]; then | ||
| echo "[PREPARE] Skipping the environment preparation (presumably already prepared)." | ||
| else | ||
| # Anything that does not match "TRUE" disable the feature. | ||
| echo "[PREPARE] Preparing the environment. Preparation log in 'log.prepare.${PREPARE_TOOLCHAIN_NAME}'." | ||
| # Maybe a noop. | ||
| "${PREPARE_TOOLCHAIN_PATH}/prepare.sh" >"log.prepare.${PREPARE_TOOLCHAIN_NAME}" 2>&1 || (echo "The environment preparation failed! Check the log." && exit 1) | ||
| fi | ||
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| PREPARE_BUILD_NAME="build.${PREPARE_TOOLCHAIN_NAME}" | ||
| PREPARE_BUILD_DIRECTORY="${PREPARE_ROOT_DIRECTORY}/${PREPARE_BUILD_NAME}" | ||
| PREPARE_TOOLCHAIN_FILE="${PREPARE_TOOLCHAIN_PATH}/toolchain.cmake" | ||
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| if [[ "${PREPARE_FORCE_FRESH_BUILD}" != "TRUE" ]]; then | ||
| echo "[PREPARE] Keeping the old build directory." | ||
| else | ||
| # Anything that does not machine "TRUE" disable the feature. | ||
| echo "[PREPARE] Removing old build directory..." | ||
| rm -rf -- "${PREPARE_BUILD_DIRECTORY}" | ||
| fi | ||
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| PREPARE_BUILD_GENERATOR="Unix Makefiles" | ||
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| if which ninja >/dev/null 2>&1; then | ||
| PREPARE_BUILD_GENERATOR="Ninja" | ||
| fi | ||
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| echo "[PREPARE] Using build system: '${PREPARE_BUILD_GENERATOR}'." | ||
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| source -- "${PREPARE_TOOLCHAIN_PATH}/environment.sh" | ||
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| PREPARE_BUILD_CMAKE_FLAG="${@:4}" | ||
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| cmake \ | ||
| -B "${PREPARE_BUILD_DIRECTORY}" \ | ||
| -S . \ | ||
| -G "${PREPARE_BUILD_GENERATOR}" \ | ||
| -DCMAKE_TOOLCHAIN_FILE="${PREPARE_TOOLCHAIN_FILE}" \ | ||
| "${PREPARE_BUILD_CMAKE_FLAG}" | ||
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| echo "Building in '${PREPARE_BUILD_NAME}'. Build log in 'log.build.${PREPARE_TOOLCHAIN_NAME}'." | ||
| cmake --build "${PREPARE_BUILD_DIRECTORY}" >"log.build.${PREPARE_TOOLCHAIN_NAME}" 2>&1 || (echo "The build failed! Check the log." && exit 1) | ||
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| echo "The build completed. You can use the binaries in the following directory:" | ||
| echo " \"${PREPARE_BUILD_DIRECTORY}\"" | ||
| echo "Do not forget to source the environment file like so:" | ||
| echo " $ source -- \"${PREPARE_TOOLCHAIN_PATH}/environment.sh\"" |
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| # SPDX-License-Identifier: MIT | ||
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| add_subdirectory(testcollisions) |
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| # SPDX-License-Identifier: MIT | ||
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| add_executable(testcollisions testcollisions.cpp) | ||
| target_compile_features(testcollisions PUBLIC cxx_std_17) | ||
| target_link_libraries(testcollisions | ||
| PUBLIC | ||
| DDC::DDC | ||
| DDC::PDI_Wrapper | ||
| gslx::speciesinfo | ||
| gslx::geometry5D | ||
| gslx::paraconfpp | ||
| gslx::quadrature | ||
| gslx::collisions_rhs_5D | ||
| PDI::pdi | ||
| paraconf::paraconf | ||
| ) | ||
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| install(TARGETS testcollisions) | ||
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| // SPDX-License-Identifier: MIT | ||
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| constexpr char const* const PDI_CFG = R"PDI_CFG( | ||
| metadata: | ||
| read_restart_filename_size: size_t | ||
| read_restart_filename: {type: array, subtype: char, size: "$read_restart_filename_size"} | ||
| write_restart_filename_size: size_t | ||
| write_restart_filename: {type: array, subtype: char, size: "$write_restart_filename_size"} | ||
| iter_start : int | ||
| iter_saved : int | ||
| time_saved : double | ||
| grid_tor1_extents: { type: array, subtype: size_t, size: 1 } | ||
| grid_tor2_extents: { type: array, subtype: size_t, size: 1 } | ||
| grid_tor3_extents: { type: array, subtype: size_t, size: 1 } | ||
| grid_vpar_extents: { type: array, subtype: size_t, size: 1 } | ||
| grid_mu_extents: { type: array, subtype: size_t, size: 1 } | ||
| species_extents: { type: array, subtype: size_t, size: 1 } | ||
| masses_extents: { type: array, subtype: size_t, size: 1 } | ||
| charges_extents: { type: array, subtype: size_t, size: 1 } | ||
| data: | ||
| grid_tor1: | ||
| type: array | ||
| subtype: double | ||
| size: [ '$grid_tor1_extents[0]' ] | ||
| grid_tor2: | ||
| type: array | ||
| subtype: double | ||
| size: [ '$grid_tor2_extents[0]' ] | ||
| grid_tor3: | ||
| type: array | ||
| subtype: double | ||
| size: [ '$grid_tor3_extents[0]' ] | ||
| grid_vpar: | ||
| type: array | ||
| subtype: double | ||
| size: [ '$grid_vpar_extents[0]' ] | ||
| grid_mu: | ||
| type: array | ||
| subtype: double | ||
| size: [ '$grid_mu_extents[0]' ] | ||
| species: | ||
| type: array | ||
| subtype: int | ||
| size: [ '$species_extents[0]' ] | ||
| masses: | ||
| type: array | ||
| subtype: double | ||
| size: [ '$masses_extents[0]' ] | ||
| charges: | ||
| type: array | ||
| subtype: double | ||
| size: [ '$charges_extents[0]' ] | ||
| densityTorCS: | ||
| type: array | ||
| subtype: double | ||
| size: [ '$species_extents[0]', '$grid_tor2_extents[0]', '$grid_tor1_extents[0]' ] | ||
| temperatureTorCS: | ||
| type: array | ||
| subtype: double | ||
| size: [ '$species_extents[0]', '$grid_tor2_extents[0]', '$grid_tor1_extents[0]' ] | ||
| UparTorCS: | ||
| type: array | ||
| subtype: double | ||
| size: [ '$species_extents[0]', '$grid_tor2_extents[0]', '$grid_tor1_extents[0]' ] | ||
| fdistribu: | ||
| type: array | ||
| subtype: double | ||
| size: [ '$species_extents[0]', '$grid_tor3_extents[0]', '$grid_tor2_extents[0]', '$grid_tor1_extents[0]', '$grid_vpar_extents[0]', '$grid_mu_extents[0]' ] | ||
| plugins: | ||
| decl_hdf5: | ||
| - file: '${read_restart_filename}' | ||
| on_event: [read_grid_extents] | ||
| read: | ||
| grid_tor1_extents: {size_of: grid_tor1} | ||
| grid_tor2_extents: {size_of: grid_tor2} | ||
| grid_tor3_extents: {size_of: grid_tor3} | ||
| grid_vpar_extents: {size_of: grid_vpar} | ||
| grid_mu_extents: {size_of: grid_mu} | ||
| species_extents: {size_of: species} | ||
| masses_extents: {size_of: masses} | ||
| charges_extents: {size_of: charges} | ||
| - file: '${read_restart_filename}' | ||
| on_event: [read_grid] | ||
| read: | ||
| grid_tor1: ~ | ||
| grid_tor2: ~ | ||
| grid_tor3: ~ | ||
| grid_vpar: ~ | ||
| grid_mu: ~ | ||
| species: ~ | ||
| masses: ~ | ||
| charges: ~ | ||
| - file: '${read_restart_filename}' | ||
| on_event: [read_profiles] | ||
| read: | ||
| - densityTorCS | ||
| - temperatureTorCS | ||
| - UparTorCS | ||
| - file: '${read_restart_filename}' | ||
| on_event: [read_fdistribu] | ||
| read: | ||
| - time_saved | ||
| - fdistribu | ||
| - file: '${write_restart_filename}' | ||
| on_event: [write_restart] | ||
| collision_policy: skip_and_warn | ||
| write: | ||
| - iter_saved | ||
| - time_saved | ||
| - grid_tor1 | ||
| - grid_tor2 | ||
| - grid_tor3 | ||
| - grid_vpar | ||
| - grid_mu | ||
| - species | ||
| - masses | ||
| - charges | ||
| - densityTorCS | ||
| - temperatureTorCS | ||
| - UparTorCS | ||
| - fdistribu | ||
| trace: ~ | ||
| )PDI_CFG"; |
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