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<!DOCTYPE html>
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<li><a class="reference internal" href="#">Welcome to MIDAS documentation</a></li>
<li><a class="reference internal" href="#high-level-documentation">High-level documentation</a></li>
<li><a class="reference internal" href="#programs">Programs</a></li>
<li><a class="reference internal" href="#modules-1-high-level-functionality">Modules: 1. High-level functionality</a></li>
<li><a class="reference internal" href="#modules-2-b-and-r-matrices">Modules: 2. B and R matrices</a></li>
<li><a class="reference internal" href="#modules-3-observation-input-output">Modules: 3. Observation input/output</a></li>
<li><a class="reference internal" href="#modules-4-data-object-transformations">Modules: 4. Data object transformations</a></li>
<li><a class="reference internal" href="#modules-5-observation-operators">Modules: 5. Observation operators</a></li>
<li><a class="reference internal" href="#modules-6-high-level-data-objects">Modules: 6. High-level data objects</a></li>
<li><a class="reference internal" href="#modules-7-low-level-data-objects">Modules: 7. Low-level data objects</a></li>
<li><a class="reference internal" href="#modules-8-low-level-utilities-and-constants">Modules: 8. Low-level utilities and constants</a></li>
<li><a class="reference internal" href="#modules-9-global-interfaces">Modules: 9. Global interfaces</a></li>
<li><a class="reference internal" href="#additional-information">Additional information</a></li>
<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
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<section id="welcome-to-midas-documentation">
<h1>Welcome to MIDAS documentation<a class="headerlink" href="#welcome-to-midas-documentation" title="Permalink to this headline">¶</a></h1>
<p>This is the documentation for version v_3.9.1</p>
<p>This is the automatically generated MIDAS documentation. Below you
will find a list of all fortran programs and modules that make up
the MIDAS software. Documentation in the fortran code that appears
in comments immediately following the program or module or subroutine
statement will be included. It can be formatted using <em>reStructuredText</em>.
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<p><a class="reference external" href="https://matplotlib.org/sampledoc/cheatsheet.html">https://matplotlib.org/sampledoc/cheatsheet.html</a></p>
</section>
<section id="high-level-documentation">
<h1>High-level documentation<a class="headerlink" href="#high-level-documentation" title="Permalink to this headline">¶</a></h1>
<ul class="simple">
<li><p>Introduction: <a class="reference internal" href="what_is_midas.html"><span class="doc">what is MIDAS?</span></a></p></li>
<li><p>MIDAS <a class="reference internal" href="midas_design_philosophy.html"><span class="doc">code design philosophy.</span></a></p></li>
<li><p>Overall MIDAS <a class="reference internal" href="overall_midas_design.html"><span class="doc">code design description.</span></a></p></li>
<li><p>Use of <a class="reference internal" href="mpi_in_midas.html"><span class="doc">MPI parallelization in MIDAS.</span></a></p></li>
<li><p>MIDAS <a class="reference external" href="https://gitlab.science.gc.ca/atmospheric-data-assimilation/midas/blob/main/docs/codingStandards.md">coding standards</a></p></li>
</ul>
</section>
<section id="programs">
<h1>Programs<a class="headerlink" href="#programs" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_adjointTest.html">midas_adjointTest</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_analysisErrorOI.html">midas_analysisErrorOI</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_calcStats.html">midas_calcStats</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_diagBmatrix.html">midas_diagBmatrix</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_diagHBHt.html">midas_diagHBHt</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_ensembleH.html">midas_ensembleH</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_ensPostProcess.html">midas_ensPostProcess</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_extractBmatrixFor1Dvar.html">midas_extractBmatrixFor1Dvar</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_genCoeff.html">midas_genCoeff</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_letkf.html">midas_letkf</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_obsImpact.html">midas_obsImpact</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_obsSelection.html">midas_obsSelection</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_oMinusF.html">midas_oMinusF</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_prepcma.html">midas_prepcma</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_pseudoSSTobs.html">midas_pseudoSSTobs</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_randomPert.html">midas_randomPert</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_sstBias.html">midas_sstBias</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_sstTrial.html">midas_sstTrial</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_thinning.html">midas_thinning</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_var1D.html">midas_var1D</a></li>
<li class="toctree-l1"><a class="reference internal" href="programs/midas_var.html">midas_var</a></li>
</ul>
</div>
</section>
<section id="modules-1-high-level-functionality">
<h1>Modules: 1. High-level functionality<a class="headerlink" href="#modules-1-high-level-functionality" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/analysiserroroi_mod.html">analysisErrorOI_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/backgroundcheck_mod.html">backgroundCheck_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/bgckcsr_mod.html">bgckCSR_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/bgckmicrowave_mod.html">bgckMicrowave_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/bgckocean_mod.html">bgckOcean_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/bgckssmis_mod.html">bgckSSMIS_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/biascorrectionconv_mod.html">biasCorrectionConv_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/biascorrectionsat_mod.html">biasCorrectionSat_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/calcstatsglb_mod.html">calcStatsGlb_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/calcstatslam_mod.html">calcStatsLam_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/enkf_mod.html">enkf_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/enspostprocess_mod.html">ensPostProcess_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/fsoi_mod.html">fsoi_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/increment_mod.html">increment_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/innovation_mod.html">innovation_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/menetrierdiag_mod.html">menetrierDiag_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/minimization_mod.html">minimization_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/multiirbgck_mod.html">multiIRbgck_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsspacediag_mod.html">obsSpaceDiag_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsspaceerrorstddev_mod.html">obsSpaceErrorStdDev_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/oceanbackground_mod.html">oceanBackground_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/oceanobservations_mod.html">oceanObservations_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/ominusf_mod.html">oMinusF_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/quasinewton_mod.html">quasiNewton_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/residual_mod.html">residual_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/sstbias_mod.html">sstBias_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/thinning_mod.html">thinning_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/varqc_mod.html">varQC_mod</a></li>
</ul>
</div>
</section>
<section id="modules-2-b-and-r-matrices">
<h1>Modules: 2. B and R matrices<a class="headerlink" href="#modules-2-b-and-r-matrices" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/bmatrix1dvar_mod.html">bMatrix1DVar_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/bmatrixchem_mod.html">bMatrixChem_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/bmatrixdiff_mod.html">bMatrixDiff_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/bmatrixensemble_mod.html">bMatrixEnsemble_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/bmatrixhi_mod.html">bMatrixHI_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/bmatrix_mod.html">bMatrix_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/lambmatrixhi_mod.html">lamBmatrixHI_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/localizationfunction_mod.html">localizationFunction_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/localization_mod.html">localization_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/localizationspectral_mod.html">localizationSpectral_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obserrors_mod.html">obsErrors_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/rmatrix_mod.html">rMatrix_mod</a></li>
</ul>
</div>
</section>
<section id="modules-3-observation-input-output">
<h1>Modules: 3. Observation input/output<a class="headerlink" href="#modules-3-observation-input-output" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/burpfiles_mod.html">burpFiles_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/burpread_mod.html">burpRead_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsdbfiles_mod.html">obsdbFiles_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsdiagfiles_mod.html">obsDiagFiles_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsfiles_mod.html">obsFiles_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsutil_mod.html">obsUtil_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/sqlitefiles_mod.html">sqliteFiles_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/sqliteread_mod.html">sqliteRead_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/sqliteutilities_mod.html">sqliteUtilities_mod</a></li>
</ul>
</div>
</section>
<section id="modules-4-data-object-transformations">
<h1>Modules: 4. Data object transformations<a class="headerlink" href="#modules-4-data-object-transformations" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/advection_mod.html">advection_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/calcheightandpressure_mod.html">calcHeightAndPressure_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/columnvariabletransforms_mod.html">columnVariableTransforms_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/diffusion_mod.html">diffusion_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/globalspectraltransform_mod.html">globalSpectralTransform_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/gridbinning_mod.html">gridBinning_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/gridstatevectorfileio_mod.html">gridStateVectorFileIO_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/gridvariabletransforms_mod.html">gridVariableTransforms_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/humiditylimits_mod.html">humidityLimits_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/interpolation_mod.html">interpolation_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/lamspectraltransform_mod.html">lamSpectralTransform_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obstimeinterp_mod.html">obsTimeInterp_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsvariabletransforms_mod.html">obsVariableTransforms_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/statetocolumn_mod.html">stateToColumn_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/var1d_mod.html">var1D_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/verticalmodes_mod.html">verticalModes_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/windrotation_mod.html">windRotation_mod</a></li>
</ul>
</div>
</section>
<section id="modules-5-observation-operators">
<h1>Modules: 5. Observation operators<a class="headerlink" href="#modules-5-observation-operators" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/costfunction_mod.html">costFunction_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/gps_mod.html">gps_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsfilter_mod.html">obsFilter_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsoperatorschem_mod.html">obsOperatorsChem_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsoperators_mod.html">obsOperators_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/ozoneclim_mod.html">ozoneClim_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/radialvelocity_mod.html">radialVelocity_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/slantprofilelatlon_mod.html">slantProfileLatLon_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/tovslin_mod.html">tovsLin_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/tovsnl_mod.html">tovsNL_mod</a></li>
</ul>
</div>
</section>
<section id="modules-6-high-level-data-objects">
<h1>Modules: 6. High-level data objects<a class="headerlink" href="#modules-6-high-level-data-objects" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/bcovarsetupchem_mod.html">bCovarSetupChem_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/columndata_mod.html">columnData_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/controlvector_mod.html">controlVector_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/ensembleobservations_mod.html">ensembleObservations_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/ensemblestatevector_mod.html">ensembleStateVector_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/gridstatevector_mod.html">gridStateVector_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsspacedata_mod.html">ObsSpaceData_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obssubspacedata_mod.html">obsSubSpaceData_mod</a></li>
</ul>
</div>
</section>
<section id="modules-7-low-level-data-objects">
<h1>Modules: 7. Low-level data objects<a class="headerlink" href="#modules-7-low-level-data-objects" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/filenames_mod.html">fileNames_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/horizontalcoord_mod.html">horizontalCoord_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/indexlistdepot_mod.html">IndexListDepot_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/lamanalysisgridtransforms_mod.html">lamAnalysisGridTransforms_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obscolumnnames_mod.html">ObsColumnNames_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsdatacolumn_mod.html">ObsDataColumn_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/obsfamilylist_mod.html">obsFamilyList_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/oceanmask_mod.html">oceanMask_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/regions_mod.html">regions_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/timecoord_mod.html">timeCoord_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/varnamelist_mod.html">varNameList_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/verticalcoord_mod.html">verticalCoord_mod</a></li>
</ul>
</div>
</section>
<section id="modules-8-low-level-utilities-and-constants">
<h1>Modules: 8. Low-level utilities and constants<a class="headerlink" href="#modules-8-low-level-utilities-and-constants" title="Permalink to this headline">¶</a></h1>
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<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/bufr_mod.html">bufr_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/codeprecision_mod.html">codePrecision_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/codtyp_mod.html">codtyp_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/earthconstants_mod.html">earthConstants_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/getgridposition_mod.html">getGridPosition_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/kdtree2_mod.html">kdTree2_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/kdtree2_precision_mod.html">kdtree2_precision_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/kdtree2_priority_queue_mod.html">kdtree2_priority_queue_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/mathphysconstants_mod.html">mathPhysConstants_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/message_mod.html">message_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/midasmpi_mod.html">midasMpi_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/physicsfunctions_mod.html">physicsFunctions_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/presprofileoperators_mod.html">presProfileOperators_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/ramdisk_mod.html">ramDisk_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/randomnumber_mod.html">randomNumber_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/spectralfilter_mod.html">spectralFilter_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/utilities_mod.html">utilities_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/version_mod.html">version_mod</a></li>
</ul>
</div>
</section>
<section id="modules-9-global-interfaces">
<h1>Modules: 9. Global interfaces<a class="headerlink" href="#modules-9-global-interfaces" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/clibinterfaces_mod.html">clibInterfaces_mod</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/rttovinterfaces_mod.html">rttovInterfaces_mod</a></li>
</ul>
</div>
</section>
<section id="additional-information">
<h1>Additional information<a class="headerlink" href="#additional-information" title="Permalink to this headline">¶</a></h1>
<ul class="simple">
<li><p>Namelists: Information is <a class="reference internal" href="namelists_in_each_program.html"><span class="doc">here on which namelists are used for each program.</span></a></p></li>
<li><p>Namelists: Information is <a class="reference external" href="namelists.html">here on the definition of all namelists.</a></p></li>
<li><p>TMG timing blocks: Information is <a class="reference internal" href="tmg_information.html"><span class="doc">here on the numbering and labelling of all TMG timing blocks.</span></a></p></li>
</ul>
</section>
<section id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
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