Pre-fates integration preparations #1519

rgknox · 2017-05-10T21:52:10Z

This changeset introduces more code preparation to enable the forthcoming FATES
integration. Attention in this PR was applied to the interface with biogeochemical
coupling, specifically FATES handles above-ground bgc, and only needs below
ground. The above and below-ground components were split. Finer-grain
identification of what processes can be turned off with FATES needs to be applied,
however the current implementation safe-guards existing modules and full bgc
implementation. Other aspects covered in this PR are the preparations for dynamic
plant water storage, and the need to differentiate soil to root water flux from
transpiration flux, as well as the tracking on the ALM side of plant stored water.

[BFB]

…ommit placed on laying out the BGC pathway and call-sequence in the fates case.

…-relevant carbon fluxes to turn-off for first pass, re-instated some summary carbon flux variables, that while irrelevant are still allocated. Updated code to reflect different number of decomp cascade pools for fates (which does not have a cwd pool on the bgc side because fates handles cwd decomposition.

…al stored internal plant water. This is necessary for the integration of plant hydraulic modules which have dynamic storage capacity, and will thus affect the water balance checks.

…tgautam.

…deCN changes (which are similar to what was requested in CNDecompCascadeBGC.

bishtgautam · 2017-05-10T21:59:40Z

Made the following changes to the first comment message:

Removed:
This is a re-submission of PR pre-fates integration preparations #1470 (reason: corrected branch naming
convention, PR was approved)
~~tested acme_land_developer on edison, b4b with known exceptions~~
Added: [BFB]
Limited the characters in a single line to be approx less than 80 by
splitting the text over multiple lines.

bishtgautam · 2017-05-10T22:00:15Z

This PR replaces #1470

This changeset introduces more code preparation to enable the forthcoming FATES integration. Attention in this PR was applied to the interface with biogeochemical coupling, specifically FATES handles above-ground bgc, and only needs below ground. The above and below-ground components were split. Finer-grain identification of what processes can be turned off with FATES needs to be applied, however the current implementation safe-guards existing modules and full bgc implementation. Other aspects covered in this PR are the preparations for dynamic plant water storage, and the need to differentiate soil to root water flux from transpiration flux, as well as the tracking on the ALM side of plant stored water. [BFB]

…branch-for-to-acme-12-06-2017-pr * commit '530c337666de1af28698c74b9e58e8baf93a6bbf': fix issue in scripts_regression_tests Add ability to customize CaseStatus success message for a phase. Fix bug in compare namelists add test for xmlquery DOCN_MODE Fix memory leak of newtimers in merge_thread_data in splitting comp vars make sure comp isnt subset of name Update ChangeLog nthrds > 1 should set build_threaded flag Update ChangeLog Update ChangeLog fix pylint issue fix gptl threaded build, batch change for cheyenne correct path for includes used in build Check for unicode in expect() update ACME to E3SM and changes related to Issue #1519 and PR #2062 Do not use normalization when mapping glc2ocn Add comments about not needing to add fields to x2o_fluxes and x2i_fluxes Point to new glc2ocn mapping files Allow different glc2ocn mappings for liq and ice

…1963) Fixes: * DOCN_MODE fix for xmlchange * compare_namelist bug in rare code path * Fix memleak in gptl * Fix setting of build_threaded * Fix unicode problems with expect Feature list: * Add job-id info for CaseStatus entry for job submit * Allow different glc2ocn mappings for liq and ice [BFB] * jgfouca/branch-for-to-acme-12-06-2017-pr: This is no longer needed fix issue in scripts_regression_tests Add ability to customize CaseStatus success message for a phase. Fix bug in compare namelists add test for xmlquery DOCN_MODE Fix memory leak of newtimers in merge_thread_data in splitting comp vars make sure comp isnt subset of name Update ChangeLog nthrds > 1 should set build_threaded flag Update ChangeLog Update ChangeLog fix pylint issue fix gptl threaded build, batch change for cheyenne correct path for includes used in build Check for unicode in expect() update ACME to E3SM and changes related to Issue #1519 and PR #2062 Do not use normalization when mapping glc2ocn Add comments about not needing to add fields to x2o_fluxes and x2i_fluxes Point to new glc2ocn mapping files Allow different glc2ocn mappings for liq and ice

#1963) Fixes: * DOCN_MODE fix for xmlchange * compare_namelist bug in rare code path * Fix memleak in gptl * Fix setting of build_threaded * Fix unicode problems with expect Feature list: * Add job-id info for CaseStatus entry for job submit * Allow different glc2ocn mappings for liq and ice [BFB] * jgfouca/branch-for-to-acme-12-06-2017-pr: (21 commits) Ignore buildlib python bytecode files This is no longer needed fix issue in scripts_regression_tests Add ability to customize CaseStatus success message for a phase. Fix bug in compare namelists add test for xmlquery DOCN_MODE Fix memory leak of newtimers in merge_thread_data in splitting comp vars make sure comp isnt subset of name Update ChangeLog nthrds > 1 should set build_threaded flag Update ChangeLog Update ChangeLog fix pylint issue fix gptl threaded build, batch change for cheyenne correct path for includes used in build Check for unicode in expect() update ACME to E3SM and changes related to Issue #1519 and PR #2062 Do not use normalization when mapping glc2ocn Add comments about not needing to add fields to x2o_fluxes and x2i_fluxes Point to new glc2ocn mapping files ...