GEOS-5 Documentation for Heracles 5.4: Difference between revisions

(5 intermediate revisions by the same user not shown)

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__FORCETOC__

This page lists pages with information on setting up and running GEOS-5 Heracles 5.3. 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 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''.

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

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<pre>

==========================================================================

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

==========================================================================

Oct162016, Takacs, CVS Tag: Heracles-5_4_p2 (non-zero diff to Heracles-5_4_p1)

Module: GEOSagcm

------------------------------------------------------------------------------

1) Implement CallBack method between GOCART and 2-Moment Microphysics (zero-diff for single-moment microphysics)

2) Updates/corrections to GMIChem

3) Removed moving of Large-Scale Precip/Precip_Flux for Chemistry with the Single-Moment Microphysics.

The 2nd-Momemt Microphysics moves the Large-Scale Precip/Precip_Flux for Chemistry as in Heracles-5_4_p1.

4) 2nd-Moment Microphysics updated to tag: t_H54p1_donifan_0

5) New format for Native Cube nc4 output (cube faces are now ensemble members)

6) Grads Utility (dc.gs) has been updated to read both Old and New Native Cube formats.

Restart Changes: none

==========================================================================

28Sep2016, Takacs, CVS Tag: Heracles-5_4_p1 (non-zero diff to Heracles-5_4)

Module: GEOSagcm

------------------------------------------------------------------------------

1) Update to surfacelayer.F90 to fix incorrect approximation when using increased vertical levels (non-zero diff).

2) Corrected error in Heracles-5_3 and Heracles-5_4 to properly move 3-D Precip Flux for Aerosol Scavenging

3) New Physics Tunings for improved NPW Skill

4) Added updated 132 Levels for set_eta

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)

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</pre>

== Running Heracles 5.3 ==

== Running Heracles 5.4 ==

* [[Heracles 5.3 Quick Start]]: This page describes the minimum steps required to build and run GEOS-5 Heracles 5.3 on NCCS discover and NAS pleiades. You should successfully complete the steps in these instructions before doing anything more complicated.

* [[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.

* [[Heracles 5.3 User's Guide]]

* [[Heracles 5.4 User's Guide]]

* [[Using the ExtData component]]

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* [[Heracles Single Column Model]]

== Heracles 5.3 Documentation ==

== Heracles 5.4 Documentation ==

* [[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>

** [[Heracles 5.3 states sorted by short name | Sorted by short name]]

** [[Heracles 5.4 states sorted by short name | Sorted by short name]]

** [[Heracles 5.3 states sorted by component name | Sorted by component name]]

** [[Heracles 5.4 states sorted by component name | Sorted by component name]]

<!--

Created by:

$ ./GMAO_Shared/MAPL_Base/mapl_vlist.py --sort comp --format wiki /home/mathomp4/Models/Heracles-~~5_3~~/GEOSagcm/src/GEOSgcs_GridComp/ > ~~states_sort_by_comp~~.txt

$ ./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 short --format wiki /home/mathomp4/Models/Heracles-~~5_3~~/GEOSagcm/src/GEOSgcs_GridComp/ > ~~states_sort_by_short~~.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

-->

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* [[GEOS-5 Run-Time Characteristics]]

* Hierarchical structure: Below is a (partially folded) view of the Heracles 5.3 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 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.

<!--

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GEOSgcs (or agcm or ogcm) and ran:

$ tree -d -I CVS -X | sed -f ~/MindMapFiles/mindmap.sedfile > ~/MindMapFiles/~~h53_tree~~.mm

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

You'll then need to manually go into the XML file and change the top

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-->

<mm>[[~~h53_tree~~.mm|flash|500px|parameters startCollapsedToLevel=4]]</mm>

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

----

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

@@ Line 1: / Line 1: @@
 __FORCETOC__
-This page lists pages with information on setting up and running GEOS-5 Heracles 5.3.  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 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''.
 '''Back to [[GEOS-5 User's and Developer's Guides]]'''
@@ Line 9: / Line 9: @@
 <pre>
+==========================================================================
+Nov092016, Takacs,    CVS Tag: Heracles-5_4_p3 (non-zero diff to Heracles-5_4_p2)
+                       Module: GEOSagcm
+------------------------------------------------------------------------------
+) Added emission factors for sea salt and dust at C720 and finer resolutions
+) A variety of fixes for memory leaks.
+) Update StratChem to tag: Heracles-5_4_p2_JEN_SC
+) Updates to QUICKPLOT
+Restart Changes: none
+==========================================================================
+Oct162016, Takacs,    CVS Tag: Heracles-5_4_p2 (non-zero diff to Heracles-5_4_p1)
+                       Module: GEOSagcm
+------------------------------------------------------------------------------
+) Implement CallBack method between GOCART and 2-Moment Microphysics (zero-diff for single-moment microphysics)
+) Updates/corrections to GMIChem
+) Removed moving of Large-Scale Precip/Precip_Flux for Chemistry with the Single-Moment Microphysics.
+   The 2nd-Momemt Microphysics moves the Large-Scale Precip/Precip_Flux for Chemistry as in Heracles-5_4_p1.
+) 2nd-Moment Microphysics updated to tag: t_H54p1_donifan_0
+) New format for Native Cube nc4 output (cube faces are now ensemble members)
+) Grads Utility (dc.gs) has been updated to read both Old and New Native Cube formats.
+Restart Changes: none
+==========================================================================
+Sep2016, Takacs,    CVS Tag: Heracles-5_4_p1 (non-zero diff to Heracles-5_4)
+                       Module: GEOSagcm
+------------------------------------------------------------------------------
+) Update to surfacelayer.F90 to fix incorrect approximation when using increased vertical levels (non-zero diff).
+) Corrected error in Heracles-5_3 and Heracles-5_4 to properly move 3-D Precip Flux for Aerosol Scavenging
+) New Physics Tunings for improved NPW Skill
+) Added updated 132 Levels for set_eta
+) Modified AGCM and MKIAU for:
+     a) Zero-diff when replaying to itself
+     b) Implement 4D option
+) Updates to StratChem:  Extention from 35 to 52 species now includes all major CFCs, Halons, HCFCs,
+                          very short-lived bromocarbons, and two transport tracers.
+) Updates to GMIChem
+Restart Changes: none
+==========================================================================
+Sep2016, Takacs,    CVS Tag: Heracles-5_4 (non-zero diff to Heracles-5_3)
+                       Module: GEOSagcm
+------------------------------------------------------------------------------
+) MAJOR update to Single-Moment Microphysics producing improved C360 NWP Skill
+) Change to default fvcore_layout_rc to REMAP using local gmao_cubic on Total Energy
+) Merge with Yuri to provide baseline coupled model tag. (zero-diff to Heracles-5_3)
+) Fix bug for UNDEF treatment within CubeToLatLon.F90 and  MAPL_HorzTransform.F90 (non-zero diff to H53)
+) Updated TURB code for zero-diff rewrite plus added TKE diagnostic
+) 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
 ==========================================================================
 Jun2016, Takacs,    CVS Tag: Heracles-5_3 (pushed,     zero diff)
@@ Line 111: / Line 174: @@
 </pre>
-== Running Heracles 5.3 ==
+== Running Heracles 5.4 ==
-* [[Heracles 5.3 Quick Start]]: This page describes the minimum steps required to build and run GEOS-5 Heracles 5.3 on NCCS discover and NAS pleiades.  You should successfully complete the steps in these instructions before doing anything more complicated.
+* [[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.
-* [[Heracles 5.3 User's Guide]]
+* [[Heracles 5.4 User's Guide]]
 * [[Using the ExtData component]]
@@ Line 127: / Line 190: @@
 * [[Heracles Single Column Model]]
-== Heracles 5.3 Documentation ==
+== Heracles 5.4 Documentation ==
 * [[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>
-** [[Heracles 5.3 states sorted by short name | Sorted by short name]]
+** [[Heracles 5.4 states sorted by short name | Sorted by short name]]
-** [[Heracles 5.3 states sorted by component name | Sorted by component name]]
+** [[Heracles 5.4 states sorted by component name | Sorted by component name]]
 <!--
 Created by:
-  $ ./GMAO_Shared/MAPL_Base/mapl_vlist.py --sort comp --format wiki /home/mathomp4/Models/Heracles-5_3/GEOSagcm/src/GEOSgcs_GridComp/ > states_sort_by_comp.txt
+  $ ./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 short --format wiki /home/mathomp4/Models/Heracles-5_3/GEOSagcm/src/GEOSgcs_GridComp/ > states_sort_by_short.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
 -->
@@ Line 144: / Line 207: @@
 * [[GEOS-5 Run-Time Characteristics]]
-* Hierarchical structure: Below is a (partially folded) view of the Heracles 5.3 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 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.
 <!--
@@ Line 150: / Line 213: @@
 GEOSgcs (or agcm or ogcm) and ran:
-   $ tree -d -I CVS -X | sed -f ~/MindMapFiles/mindmap.sedfile > ~/MindMapFiles/h53_tree.mm
+   $ tree -d -I CVS -X | sed -f ~/MindMapFiles/mindmap.sedfile > ~/MindMapFiles/h54p2_tree.mm
 You'll then need to manually go into the XML file and change the top
@@ Line 156: / Line 219: @@
 -->
-<mm>[[h53_tree.mm|flash|500px|parameters startCollapsedToLevel=4]]</mm>
+<mm>[[h54p3_tree.mm|flash|500px|parameters startCollapsedToLevel=4]]</mm>
 ----
 '''Back to [[GEOS-5 User's and Developer's Guides]]'''