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Mark Mieschbenjaminmenetrierfabiolrdinizshlyaeva
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Feature/doxygen cleanup (#1367)
* ATLAS interfaces test working for ATLAS-based models (#1366) * ATLAS interfaces test working for ATLAS-based models * Fix coding norms * Clean up doxygen landing page * fix for name of l95 simplified tests (#1365) Co-authored-by: Anna Shlyaeva <shlyaeva@gmail.com> * typos * update license * update doxyfile * review comments Co-authored-by: Benjamin Menetrier <30638301+benjaminmenetrier@users.noreply.github.com> Co-authored-by: Fabio L R Diniz <45880035+fabiolrdiniz@users.noreply.github.com> Co-authored-by: Anna Shlyaeva <shlyaeva@gmail.com>
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LICENSE renamed to LICENSE.md

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identification within third-party archives.
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Copyright 2009-2016 European Centre for Medium-Range Weather Forecasts (ECMWF)
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Copyright 2017-2020 University Corporation for Atmospheric Research (UCAR)
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Copyright 2017-2021 University Corporation for Atmospheric Research (UCAR)
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.

‎docs/Doxyfile.in‎

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ALPHABETICAL_INDEX = YES
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# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
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# which the alphabetical index list will be split.
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# Minimum value: 1, maximum value: 20, default value: 5.
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# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
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COLS_IN_ALPHA_INDEX = 5
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# In case all classes in a project start with a common prefix, all classes will
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# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
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# can be used to specify a prefix (or a list of prefixes) that should be ignored

‎docs/mainpage.h‎

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#pragma once
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// This file defines what appears on the Main Page of the documentation
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// generated by doxygen. The file contains no code, and does not appear
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// in any cpp include statement.
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//
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/*!
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* \mainpage Object Oriented Prediction System (OOPS)
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*
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* OOPS is the top level of JEDI that orchestrates the configuration and execution of applications. This is where DA applications are implemented. OOPS also includes the Lorenz 95 and Quasi-geostrophic toy models that can used to run many of the DA applications.
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*/

l95/ewok/README.md renamed to l95/ewok/README

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‎l95/test/CMakeLists.txt‎

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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_DRIPCG.yaml )
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ecbuild_add_test( TARGET test_l95_simplifiedl95_DRPCG
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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_DRPCG.yaml )
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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_DRPFOM.yaml )
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ecbuild_add_test( TARGET simplifiedl95_DRPLanczos
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ecbuild_add_test( TARGET test_l95_simplifiedl95_DRPLanczos
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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_DRPLanczos.yaml )
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ecbuild_add_test( TARGET simplifiedl95_FGMRES
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ecbuild_add_test( TARGET test_l95_simplifiedl95_FGMRES
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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_FGMRES.yaml )
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ecbuild_add_test( TARGET simplifiedl95_GMRESR
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ecbuild_add_test( TARGET test_l95_simplifiedl95_GMRESR
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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_GMRESR.yaml )
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ecbuild_add_test( TARGET simplifiedl95_IPCG
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ecbuild_add_test( TARGET test_l95_simplifiedl95_IPCG
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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_IPCG.yaml )
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ecbuild_add_test( TARGET simplifiedl95_LBGMRESR
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ecbuild_add_test( TARGET test_l95_simplifiedl95_LBGMRESR
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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_LBGMRESR.yaml )
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ecbuild_add_test( TARGET simplifiedl95_MINRES
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ecbuild_add_test( TARGET test_l95_simplifiedl95_MINRES
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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_MINRES.yaml )
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ecbuild_add_test( TARGET simplifiedl95_PCG
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ecbuild_add_test( TARGET test_l95_simplifiedl95_PCG
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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_PCG.yaml )
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ecbuild_add_test( TARGET simplifiedl95_PLanczos
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ecbuild_add_test( TARGET test_l95_simplifiedl95_PLanczos
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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_PLanczos.yaml )
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ecbuild_add_test( TARGET simplifiedl95_RPCG
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ecbuild_add_test( TARGET test_l95_simplifiedl95_RPCG
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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_RPCG.yaml )
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ecbuild_add_test( TARGET simplifiedl95_RPLanczos
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ecbuild_add_test( TARGET test_l95_simplifiedl95_RPLanczos
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COMMAND l95_4dvar.x
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ARGS testinput/simplifiedl95_RPLanczos.yaml )

qg/ewok/README.md renamed to qg/ewok/README

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‎src/test/interface/Increment.h‎

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#include "oops/util/Logger.h"
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#include "test/TestEnvironment.h"
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namespace test {
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// =============================================================================
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typedef oops::Increment<MODEL> Increment_;
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if (Test_::skipAtlas() == 0) {
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// Create random increment and copy it
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// Create random increment
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Increment_ dx1(Test_::resol(), Test_::ctlvars(), Test_::time());
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dx1.random();
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Increment_ dx2(dx1);
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// Create ATLAS fieldset
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std::unique_ptr<atlas::FieldSet> atlasFieldSet(new atlas::FieldSet());
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// Test setAtlas-toAtlas-fromAtlas
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dx1.setAtlas(atlasFieldSet.get());
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dx1.toAtlas(atlasFieldSet.get());
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dx1.zero();
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dx1.fromAtlas(atlasFieldSet.get());
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std::unique_ptr<atlas::FieldSet> atlasFieldSet1(new atlas::FieldSet());
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dx1.setAtlas(atlasFieldSet1.get());
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dx1.toAtlas(atlasFieldSet1.get());
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// Create zero increment
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Increment_ dx2(Test_::resol(), Test_::ctlvars(), Test_::time());
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dx2.zero();
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std::unique_ptr<atlas::FieldSet> atlasFieldSet2(new atlas::FieldSet());
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dx2.setAtlas(atlasFieldSet2.get());
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// Copy ATLAS fieldset content
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for ( atlas::FieldSet::const_iterator field1 = atlasFieldSet1->cbegin();
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field1 != atlasFieldSet1->cend(); ++field1 ) {
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atlas::Field field2 = atlasFieldSet2->field(field1->name());
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if (field1->rank() == 1) {
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auto array1 = atlas::array::make_view<double, 1>(*field1);
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auto array2 = atlas::array::make_view<double, 1>(field2);
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for (int i1 = 0; i1 < array1.shape(0); ++i1) {
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array2(i1) = array1(i1);
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}
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}
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if (field1->rank() == 2) {
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auto array1 = atlas::array::make_view<double, 2>(*field1);
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auto array2 = atlas::array::make_view<double, 2>(field2);
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for (int i1 = 0; i1 < array1.shape(0); ++i1) {
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for (int i2 = 0; i2 < array1.shape(1); ++i2) {
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array2(i1, i2) = array1(i1, i2);
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}
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}
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}
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}
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// Copy back to increment
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dx2.fromAtlas(atlasFieldSet2.get());
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// Check increment difference
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dx2 -= dx1;
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EXPECT(dx2.norm() == 0.0);
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}

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