GEOS-5 Documentation for Icarus 1.0: Difference between revisions

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__FORCETOC__
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This page lists pages with information on setting up and running GEOS-5 Heracles 5.4.  Earlier and later versions of GEOS-5 may differ in details that, while minor, will require different steps for building and running, so ''caveat utilitor''.  
This page lists pages with information on setting up and running GEOS-5 Icarus 1.0.  Earlier and later versions of GEOS-5 may differ in details that, while minor, will require different steps for building and running, so ''caveat utilitor''.  


'''Back to [[GEOS-5 User's and Developer's Guides]]'''
'''Back to [[GEOS-5 User's and Developer's Guides]]'''
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<pre>
<pre>
==========================================================================
==========================================================================
Nov092016, Takacs,    CVS Tag: Heracles-5_4_p3 (non-zero diff to Heracles-5_4_p2)
10Apr2017, Takacs,    CVS Tag: Icarus-1_0_p1 (non-zero diff to Icarus-1_0)
                       Module: GEOSagcm
                       Module: GEOSagcm
------------------------------------------------------------------------------
------------------------------------------------------------------------------
1) Added emission factors for sea salt and dust at C720 and finer resolutions
1) Implement fix to stop the convective transport of the NI tracers by RAS.
2) A variety of fixes for memory leaks.
  RAS is producing negative constituents which may cause the Radiation to crash when GOCART is not called on the HeartBeat.
3) Update StratChem to tag: Heracles-5_4_p2_JEN_SC
2) Implement essentially zero-diff updates from Pete Colarco for CO.  (Anton's tag: asd-Icarus-UNSTABLE-a0)
4) Updates to QUICKPLOT
  Differences arising from change in order-of-operations.
3) Implement fix for the liquid radii limits as well as integrated Dongmin's ICEFLAG=4 changes for MODIS C6
4) Move to using MPT.


Restart Changes: none
Restart Changes: none
Line 22: Line 24:


==========================================================================
==========================================================================
Oct162016, Takacs,    CVS Tag: Heracles-5_4_p2 (non-zero diff to Heracles-5_4_p1)
28Mar2017, Takacs,    CVS Tag: Icarus-1_0 (non-zero diff to Heracles-5_4_p3)
                       Module: GEOSagcm
                       Module: GEOSagcm
------------------------------------------------------------------------------
------------------------------------------------------------------------------
1) Implement CallBack method between GOCART and 2-Moment Microphysics (zero-diff for single-moment microphysics)
1) Modified Constraints to NOT include QV updates from Chemistry
2) Updates/corrections to GMIChem
2) Modified Constraints to act only where mass in layer has changed
3) Removed moving of Large-Scale Precip/Precip_Flux for Chemistry with the Single-Moment Microphysics.
3) Update Eric Nielson's Chemistry to tag: Heracles-5_4_p3_JEN_GMI-r2 (-r3 for TR directory)
  The 2nd-Momemt Microphysics moves the Large-Scale Precip/Precip_Flux for Chemistry as in Heracles-5_4_p1.
4) Minor modification to GEOS_GcmGridComp.F90 to allow for Regular REPLAY of 4DIAU algorithm
4) 2nd-Moment Microphysics updated to tag: t_H54p1_donifan_0
5) Zero-diff Update to Anton Tag: asd-Heracles-UNSTABLE+multi_dust-a3
5) New format for Native Cube nc4 output (cube faces are now ensemble members)
6) Implement Anton's Tag for GOCART Alarms: asd-Heracles-UNSTABLE+H2O2_HNO3_RECYCLE_ALARMS
6) Grads Utility (dc.gs) has been updated to read both Old and New Native Cube formats.
7) Hardwire SOLAR_DT, IRRAD_DT, GOCART_DT to 3600
8) Implement Icarus Boundary Area to use GMTED TOPO data.
9) Updated and re-tuned GWD and Turbulence for used with Icarus/GMTED TOPO variances.
10) Added NUDGING option for Regular REPLAY.
11) Incorporated EnADAS-5_16_7p1 updates for Chem_Aod.F90 and GOCART_GridComp.F90
12) Updated Tag: mjs100__msuarez of cloudnew.F90 to inhibit SNOW during thunderstorms.
13) Modified AREAMEAN calls to use fast method. This regresses correctly, but needs testing for  
    dry mass conservation.
14) Modified defaults for GWD Parameters: BGSTRESSMAX=2.25 and PGWV=8 for LM=132 case.
15) Modified CAPE diagnostic and Bouyancy calculation in MOIST.
16) Re-introduce code in GOCART to compute GOCART_REFERENCE_TIME based on GOCART_DT and HEARTBEAT.


Restart Changes: none
Restart Changes: YES. ALL RESTARTS require require REGRIDDING (or BOOTSTRAP) to new Topography




==========================================================================
==========================================================================
28Sep2016, Takacs,    CVS Tag: Heracles-5_4_p1 (non-zero diff to Heracles-5_4)
Nov092016, Takacs,    CVS Tag: Heracles-5_4_p3 (non-zero diff to Heracles-5_4_p2)
                       Module: GEOSagcm
                       Module: GEOSagcm
------------------------------------------------------------------------------
------------------------------------------------------------------------------
1) Update to surfacelayer.F90 to fix incorrect approximation when using increased vertical levels (non-zero diff).
1) Added emission factors for sea salt and dust at C720 and finer resolutions
2) Corrected error in Heracles-5_3 and Heracles-5_4 to properly move 3-D Precip Flux for Aerosol Scavenging
2) A variety of fixes for memory leaks.
3) New Physics Tunings for improved NPW Skill
3) Update StratChem to tag: Heracles-5_4_p2_JEN_SC
4) Added updated 132 Levels for set_eta
4) Updates to QUICKPLOT
5) Modified AGCM and MKIAU for:
    a) Zero-diff when replaying to itself
    b) Implement 4D option
6) Updates to StratChem:  Extention from 35 to 52 species now includes all major CFCs, Halons, HCFCs,
                          very short-lived bromocarbons, and two transport tracers.
7) Updates to GMIChem
 
Restart Changes: none
 
 
==========================================================================
08Sep2016, Takacs,    CVS Tag: Heracles-5_4 (non-zero diff to Heracles-5_3)
                      Module: GEOSagcm
------------------------------------------------------------------------------
1) MAJOR update to Single-Moment Microphysics producing improved C360 NWP Skill
2) Change to default fvcore_layout_rc to REMAP using local gmao_cubic on Total Energy
3) Merge with Yuri to provide baseline coupled model tag. (zero-diff to Heracles-5_3)
4) Fix bug for UNDEF treatment within CubeToLatLon.F90 and  MAPL_HorzTransform.F90 (non-zero diff to H53)
5) Updated TURB code for zero-diff rewrite plus added TKE diagnostic
6) Removed unnecesssary RESTART TYPE from AGCM.rc.  Changed logic for CHECKPOINT TYPE.
  a) Use CHECKPOINT_TYPE if it exists
  b) Use Model Default if CHECKPOINT_TYPE does not exist or if CHECKPOINT_TYPE = 'default'
  c) Implement AGCM.rc parameter: DEFAULT_CHECKPOINT_TYPE (pnc4)
 
 
Restart Changes: none
 
 
==========================================================================
30Jun2016, Takacs,    CVS Tag: Heracles-5_3 (pushed,    zero diff)
29Jun2016, Takacs,    CVS Tag: Heracles-5_3 (pushed, non-zero diff)
27Jun2016, Takacs,    CVS Tag: Heracles-5_3 (pushed,    zero diff)
24Jun2016, Takacs,    CVS Tag: Heracles-5_3 (        non-zero diff to Heracles-5_2_p1)
                      Module: GEOSagcm
------------------------------------------------------------------------------
1) Updates to Aerosols (following: AeroChem-Heracles-5_2-b9), including tag: b_AMM_H521MOPS_move2d
  for single moment diagnostic partition of precip, and tag: AMM_H53U_moistforFP for updated 2-Moment
2) Updates to GMI, StratChem, and Tr_GridComp (zero-diff for default case)
3) Updates to QUICKSTAT
 
4) Pushed on 27Jun2016 to correct CLOUDNEW diagnostic and to add MAPL_SKIP to TR_GridComp IMPORT SPEC (Zero-Diff)
5) Pushed on 29Jun2016 to correct REGRESSION for GOCART OPS Sulfates (Non-Zero Diff, minor error)
6) Pushed on 29Jun2016 to correct error in Chem_RegistryMod.F90 in accounting GOCART components
  Note:  Binary GOCART Restarts will be incorrect if using original Heracles-5_3 tag (prior to 29Jun2016)
7) Pushed on 30Jun2016 to update  Chem_BundleMod.F90 (Zero-Diff, new optional arguments)
 
Restart Changes: yes
        Additional Internals to: gocart_internal_rst (Bootstrappable)
        Additional Imports  to: tr_import_rst      (Bootstrappable)
 
 
==========================================================================
08Jun2016, Takacs,    CVS Tag: Heracles-5_2_p1 (non-zero diff to Heracles-5_2)
                      Module: GEOSagcm
------------------------------------------------------------------------------
1) Updates to ADD_INCS, PHYSICS, and AGCM GridComp to perform proper mass-weighted Temperature tendencies.
2) Added option for mass-weighting Analysis Temperature Tendencies (ANA_IS_WEIGHTED, DEFAULT=NO)
3) Updates to QUICKPLOT
 
Restart Changes: none
 
 
==========================================================================
25May2016, Takacs,    CVS Tag: Heracles-5_2 (AKA: Heracles-5_2_BETA_1MOPS, non-zero diff to Heracles-5_1)
                      Module: GEOSagcm
------------------------------------------------------------------------------
1) Updates to 2-Moment Microphysics
2) Revert back to Single-Moment Microphysics of e5131_fp (Ganymed-4_1),but with fixed bug in PRECIP3 argument list
3) Merge LAND with tag: SM-LDASsa_m3-16_0_p2_CatchCatchCN_for_MERRA3
4) Fix to CO2 Emission Files
5) Merge to incorporate Yury's Heracles-4_3_UNSTABLE-CICE_thermo (zero diff when running DataSeaIce)
6) Changed default for BKGAVE in Regular REPLAY to (2/3)xREPLAY_FREQUENCY (Nominally 4 hours)
7) Fixed averaging interval related to BKGAVE in Regular REPLAY (bug caused -3hr endpoint to be omitted in average)
8) Fixed bug in GWD Mid-Layer GeoPotential Height Calculation
9) Updates to QUICKPLOT
10) Updates to MAPL
11) Updates to GMI
12) Changed ROTATE from TRUE to FALSE for Dump_&_Splash WIND INCREMENTS in DyCorGridComp
13) Updates to fvcore_layout.rc (defaults to so-called "2b3b" case based on H52 Forecast Layout Experiments)
14) Updates to sw_core.F90 and tp_core.F90 associated with fvlayout "2b3b"
15) Changed Defaults to Regular REPLAY Grid Transforms within MKIAU Source Code to BiLinary Interpolaton:
            BKG2ANACNSRV: 0 ( Note: Conservative Transformation creates Non-Wavenumber 1 Winds at Poles )
            ANA2BKGCNSRV: 0 ( Note: Conservative Transformation creates Non-Wavenumber 1 Winds at Poles )
16) NOTE: Lat/Lon version of GEOSagcm no-longer regresses.  Last known version which regresses is Heracles-4_3
          Investigation still in progress to determine cause.
 
Restart Changes: none
 
 
==========================================================================
12Jan2016, Takacs,    CVS Tag: Heracles-5_1 (non-zero diff to Heracles-5_0)
                      Module: GEOSagcm
------------------------------------------------------------------------------
1) Updates to CO emissions
2) Updates to GMIchem_GridComp
3) Updates to TR_GridComp
4) Default to Use SST Cool Layer
5) Changed Defaults for SST and Regular REPLAY Grid Transform parameteres within AGCM.rc:
          INTERPOLATE_SST: 0 or 1 ( Defaults are now model decisions based on grid resolution comparisons )
              BKG2ANACNSRV: 0 or 1 ( Defaults are now model decisions based on grid resolution comparisons )
              ANA2BKGCNSRV: 0 or 1 ( Defaults are now model decisions based on grid resolution comparisons )
 
Restart Changes: yes
        Additional Imports to: tr_import_rst (Bootstrappable)
 
 
==========================================================================
07Dec2015, Takacs,    CVS Tag: Heracles-5_0
                      Module: GEOSagcm
------------------------------------------------------------------------------
1) Updates to 2nd-moment microphysics
2) Updates GMIchem_GridComp to tag: Heracles-UNSTABLE_GMI as of 10Nov2015
3) Update  to tag: mat-HU-FixRRTMGLW-v_1 to fix regression issue in RRTMG
4) Updates to QUICKSTAT to compute Confidence
5) Updates to QUICKPLOT
6) Fixed Reverse Order Argument List error for cloudnew.F90 (wrt: VFALLRN & VFALLSN)
7) Implemented RASPARAM.F90 and CLDPARAM.F90 for clarity. (zero-diff)
8) Updated DUST Optical Tables from v14.2 to v15.3
  Note: This change affects ALL Emission Types: OPS, MERRA2, PIESA, etc.
  The only way to get the original MERRA2 emission files is to run with the MERRA2 Tag.
9) Fixed SS_GridComp to maskout emissions over Great Lakes and Capsian Sea.
10) Changed Default Parameters:  SYNCTQ = 1    (ON)
                                PRECIPRAD = 1 (ON)
                                CLDMICRO  = 2MOMENT
11) Changed Single-Moment MicroPhysics behavior. (Note: Default is 2-Moment)


Restart Changes: none
Restart Changes: none
Line 174: Line 61:
</pre>
</pre>


== Running Heracles 5.4 ==
== Running Icarus 1.0 ==


* [[Heracles 5.4 Quick Start]]: This page describes the minimum steps required to build and run GEOS-5 Heracles 5.4 on NCCS discover and NAS pleiades.  You should successfully complete the steps in these instructions before doing anything more complicated.
* [[Icarus 1.0 Quick Start]]: This page describes the minimum steps required to build and run GEOS-5 Icarus 1.0 on NCCS discover and NAS pleiades.  You should successfully complete the steps in these instructions before doing anything more complicated.


* [[Heracles 5.4 User's Guide]]
* [[Icarus 1.0 User's Guide]]


* [[Using the ExtData component]]
* [[Using the ExtData component]]
Line 186: Line 73:
* [[Setting up to create an experiment page on GMAO Intranet]]
* [[Setting up to create an experiment page on GMAO Intranet]]


* [[Using the SatSim Gridded Component in Heracles]]
* [[Using the SatSim Gridded Component in Icarus]]


* [[Heracles Single Column Model]]
* [[Icarus Single Column Model]]


== Heracles 5.4 Documentation ==
== Icarus 1.0 Documentation ==


* [[Media:GEOS5_doc.pdf|GEOS 5 Developer's Guide]] (pdf)
* [[Media:GEOS5_doc.pdf|GEOS 5 Developer's Guide]] (pdf)
* List of Export/Import/Internal states, generated with <code>src/GMAO_Shared/MAPL_Base/mapl_vlist.py</code>
* List of Export/Import/Internal states, generated with <code>src/GMAO_Shared/MAPL_Base/mapl_vlist.py</code>
** [[Heracles 5.4 states sorted by short name | Sorted by short name]]
** [[Icarus 1.0 states sorted by short name | Sorted by short name]]
** [[Heracles 5.4 states sorted by component name | Sorted by component name]]
** [[Icarus 1.0 states sorted by component name | Sorted by component name]]
<!--
<!--
Created by:
Created by:
  $ ./GMAO_Shared/MAPL_Base/mapl_vlist.py --sort comp --format wiki /home/mathomp4/Models/Heracles-5_4_p3/GEOSagcm/src/GEOSgcs_GridComp/ > h54p3_states_sort_by_comp.txt
  $ ./GMAO_Shared/MAPL_Base/mapl_vlist.py --sort comp --format wiki /home/mathomp4/Models/Icarus-1_0_p1/GEOSagcm/src/GEOSgcs_GridComp/ > i10p1_states_sort_by_comp.txt


  $ ./GMAO_Shared/MAPL_Base/mapl_vlist.py --sort short --format wiki /home/mathomp4/Models/Heracles-5_4_p3/GEOSagcm/src/GEOSgcs_GridComp/ > h54p3_states_sort_by_short.txt
  $ ./GMAO_Shared/MAPL_Base/mapl_vlist.py --sort short --format wiki /home/mathomp4/Models/Icarus-1_0_p1/GEOSagcm/src/GEOSgcs_GridComp/ > i10p1_states_sort_by_short.txt
-->
-->


Line 207: Line 94:
* [[GEOS-5 Run-Time Characteristics]]
* [[GEOS-5 Run-Time Characteristics]]


* Hierarchical structure: Below is a (partially folded) view of the Heracles 5.4 hierarchy where each node is a GridComp. Some of the nodes are folded (marked with a circle at the end) for clarity - clicking the composite node reveals the sub-nodes.
* Hierarchical structure: Below is a (partially folded) view of the Icarus 1.0 hierarchy where each node is a GridComp. Some of the nodes are folded (marked with a circle at the end) for clarity - clicking the composite node reveals the sub-nodes.


<!--
<!--
Line 213: Line 100:
GEOSgcs (or agcm or ogcm) and ran:
GEOSgcs (or agcm or ogcm) and ran:


   $ tree -d -I CVS -X | sed -f ~/MindMapFiles/mindmap.sedfile > ~/MindMapFiles/h54p2_tree.mm
   $ tree -d -I CVS -X | sed -f ~/MindMapFiles/mindmap.sedfile > ~/MindMapFiles/i10p1_tree.mm


You'll then need to manually go into the XML file and change the top
You'll then need to manually go into the XML file and change the top
Line 219: Line 106:
-->
-->


<mm>[[h54p3_tree.mm|flash|500px|parameters startCollapsedToLevel=4]]</mm>
<mm>[[i10p1_tree.mm|flash|500px|parameters startCollapsedToLevel=4]]</mm>


----  
----  
'''Back to [[GEOS-5 User's and Developer's Guides]]'''
'''Back to [[GEOS-5 User's and Developer's Guides]]'''

Latest revision as of 11:07, 28 April 2017

This page lists pages with information on setting up and running GEOS-5 Icarus 1.0. Earlier and later versions of GEOS-5 may differ in details that, while minor, will require different steps for building and running, so caveat utilitor.

Back to GEOS-5 User's and Developer's Guides

ChangeLog Entry

In src/Applications/GEOSgcm_App/ChangeLog: 

==========================================================================
10Apr2017, Takacs,    CVS Tag: Icarus-1_0_p1 (non-zero diff to Icarus-1_0)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1) Implement fix to stop the convective transport of the NI tracers by RAS.
   RAS is producing negative constituents which may cause the Radiation to crash when GOCART is not called on the HeartBeat.
2) Implement essentially zero-diff updates from Pete Colarco for CO.  (Anton's tag: asd-Icarus-UNSTABLE-a0)
   Differences arising from change in order-of-operations.
3) Implement fix for the liquid radii limits as well as integrated Dongmin's ICEFLAG=4 changes for MODIS C6
4) Move to using MPT.

Restart Changes: none


==========================================================================
28Mar2017, Takacs,    CVS Tag: Icarus-1_0 (non-zero diff to Heracles-5_4_p3)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1) Modified Constraints to NOT include QV updates from Chemistry
2) Modified Constraints to act only where mass in layer has changed
3) Update Eric Nielson's Chemistry to tag: Heracles-5_4_p3_JEN_GMI-r2 (-r3 for TR directory)
4) Minor modification to GEOS_GcmGridComp.F90 to allow for Regular REPLAY of 4DIAU algorithm
5) Zero-diff Update to Anton Tag: asd-Heracles-UNSTABLE+multi_dust-a3
6) Implement Anton's Tag for GOCART Alarms: asd-Heracles-UNSTABLE+H2O2_HNO3_RECYCLE_ALARMS
7) Hardwire SOLAR_DT, IRRAD_DT, GOCART_DT to 3600
8) Implement Icarus Boundary Area to use GMTED TOPO data.
9) Updated and re-tuned GWD and Turbulence for used with Icarus/GMTED TOPO variances.
10) Added NUDGING option for Regular REPLAY.
11) Incorporated EnADAS-5_16_7p1 updates for Chem_Aod.F90 and GOCART_GridComp.F90
12) Updated Tag: mjs100__msuarez of cloudnew.F90 to inhibit SNOW during thunderstorms.
13) Modified AREAMEAN calls to use fast method. This regresses correctly, but needs testing for 
    dry mass conservation.
14) Modified defaults for GWD Parameters: BGSTRESSMAX=2.25 and PGWV=8 for LM=132 case.
15) Modified CAPE diagnostic and Bouyancy calculation in MOIST.
16) Re-introduce code in GOCART to compute GOCART_REFERENCE_TIME based on GOCART_DT and HEARTBEAT.

Restart Changes: YES. ALL RESTARTS require require REGRIDDING (or BOOTSTRAP) to new Topography


==========================================================================
Nov092016, Takacs,    CVS Tag: Heracles-5_4_p3 (non-zero diff to Heracles-5_4_p2)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1) Added emission factors for sea salt and dust at C720 and finer resolutions
2) A variety of fixes for memory leaks.
3) Update StratChem to tag: Heracles-5_4_p2_JEN_SC
4) Updates to QUICKPLOT

Restart Changes: none

Running Icarus 1.0

  • Icarus 1.0 Quick Start: This page describes the minimum steps required to build and run GEOS-5 Icarus 1.0 on NCCS discover and NAS pleiades. You should successfully complete the steps in these instructions before doing anything more complicated.

Icarus 1.0 Documentation

  • Hierarchical structure: Below is a (partially folded) view of the Icarus 1.0 hierarchy where each node is a GridComp. Some of the nodes are folded (marked with a circle at the end) for clarity - clicking the composite node reveals the sub-nodes.


<mm>flash|500px|parameters startCollapsedToLevel=4</mm>

Back to GEOS-5 User's and Developer's Guides

Retrieved from "https://geos5.org/wiki/index.php?title=GEOS-5_Documentation_for_Icarus_1.0&oldid=3903"