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Merge pull request #638 from billsacks/water_tracers
Add water tracers ### Description of changes Core changes needed to add water tracers in CESM, for the sake of water isotopes and other purposes. Major pieces of this include: - XML and config variables for defining water tracers - Addition of all necessary water tracers in esmFldsExchange_cesm_mod and fd_cesm.yaml. These use an ungridded dimension for water tracers. - Calls to a routine to check that test tracers maintain their initial ratios. This ensures that tracers are being treated the same as their bulk counterparts (in terms of mapping, merging, etc.). - Addition of water tracer fields in med_test_comps, so this tracer infrastructure can be verified in an X compset test - Various other changes to some of the med_test_comps to better exercise CMEPS functionality, especially for the lnd -> glc mapping; also added some fields from GLC and to ROF in med_test_comps: Fgrg_rofi and Fgrg_rofl Some pieces are not yet implemented: - Including water tracers in the custom lnd->rof mapping - Including water tracers/isotopes in atm-ocn flux calculations - Including water tracers in the budget tables (med_diag_mod) Depends on ESCOMP/CESM_share#82 ### Specific notes Contributors other than yourself, if any: CMEPS Issues Fixed (include github issue #): - Resolves #583 (though this turned out to be much more extensive than simply reviewing and updating what had been in place before) - Resolves #601 Are changes expected to change answers? (specify if bfb, different at roundoff, more substantial) Changes answers for X compsets (due to some changed counter logic and maybe other things); should be bit-for-bit for all other compsets Any User Interface Changes (namelist or namelist defaults changes)? Adds xml and config variables controlling water tracers ### Testing performed In the context of cesm3_0_alpha08o, with this branch along with ESCOMP/CESM_share#82, ran CESM prealpha tests on derecho and izumi, and aux_glc tests on derecho, all with baseline comparisons. All failures also failed in the baseline except for `SMS_D_Ln9_P1536x1.ne0CONUSne30x8_ne0CONUSne30x8_mt12.FHIST.derecho_intel.cam-outfrq9s` (which seemed to fail due to ESCOMP/CTSM#3772, which is a sporadic issue), and all baseline comparisons passed. (Note: full testing was done before final commits addressing review points; only minimal additional testing was done after those final commits.)
2 parents a0343bc + 9e59f75 commit d92fcf6

40 files changed

Lines changed: 2350 additions & 775 deletions

‎cesm/driver/esm.F90‎

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@@ -401,6 +401,7 @@ subroutine InitAttributes(driver, rc)
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use shr_wv_sat_mod , only : shr_wv_sat_make_tables, ShrWVSatTableSpec
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use shr_wv_sat_mod , only : shr_wv_sat_get_scheme_idx, shr_wv_sat_valid_idx
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use glc_elevclass_mod, only : glc_elevclass_init
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use shr_wtracers_mod , only : shr_wtracers_init
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!use shr_scam_mod , only : shr_scam_checkSurface
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! input/output variables
@@ -544,6 +545,13 @@ subroutine InitAttributes(driver, rc)
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call shr_wv_sat_make_tables(liquid_spec, ice_spec, mixed_spec)
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end if
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548+
!----------------------------------------------------------
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! Initialize water tracer info
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!----------------------------------------------------------
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call shr_wtracers_init(driver, maintask, rc)
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if (chkerr(rc,__LINE__,u_FILE_u)) return
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547555
end subroutine InitAttributes
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!================================================================================

‎cesm/share_wrappers/wtracers_mod.F90‎

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@@ -4,15 +4,30 @@ module wtracers_mod
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! This module wraps shr_wtracers_mod from the CESM_share repository to avoid direct
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! dependencies on this share code from CMEPS.
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!
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! It is acceptable for CESM-specific CMEPS code (e.g., in the cesm directory) to call
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! directly into shr_wtracers_mod, but CMEPS code shared between CESM and other modeling
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! systems (e.g., UFS) should go through this module.
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!
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! See also the version of wtracers_mod in the ufs directory for when we do not have
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! access to the CESM_share library.
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!-----------------------------------------------------------------------------
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11-
use shr_wtracers_mod, only : wtracers_is_wtracer_field => shr_wtracers_is_wtracer_field
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use shr_wtracers_mod, only : wtracers_present => shr_wtracers_present
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use shr_wtracers_mod, only : wtracers_get_num_tracers => shr_wtracers_get_num_tracers
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use shr_wtracers_mod, only : wtracers_is_wtracer_field => shr_wtracers_is_wtracer_field
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use shr_wtracers_mod, only : wtracers_get_bulk_fieldname => shr_wtracers_get_bulk_fieldname
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use shr_wtracers_mod, only : wtracers_check_tracer_ratios => shr_wtracers_check_tracer_ratios
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use shr_wtracers_mod, only : WTRACERS_SUFFIX
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implicit none
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private
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16-
public :: wtracers_is_wtracer_field ! return true if the given field name is a water tracer field
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public :: wtracers_present ! return true if there are water tracers in this simulation
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public :: wtracers_get_num_tracers ! get number of water tracers in this simulation
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public :: wtracers_is_wtracer_field ! return true if the given field name is a water tracer field
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public :: wtracers_get_bulk_fieldname ! return the name of the equivalent bulk field corresponding to a water tracer field
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public :: wtracers_check_tracer_ratios ! check tracer ratios against expectations
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public :: WTRACERS_SUFFIX ! suffix for water tracer field names
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end module wtracers_mod

‎cime_config/buildnml‎

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@@ -305,6 +305,11 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
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nmlgen.set_value("esp_cpl_dt", value=esp_time)
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# End if pause is active
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# --------------------------------
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# Overwrite: set water tracers
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# --------------------------------
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_add_water_tracers(case.get_value("WATER_TRACERS"), nmlgen)
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# --------------------------------
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# Specify input data list file
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# --------------------------------
@@ -553,6 +558,44 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
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nmlgen.write_output_file(drv_flds_in)
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###############################################################################
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def _add_water_tracers(water_tracers_xml, nmlgen):
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###############################################################################
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if not water_tracers_xml.strip():
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water_tracers = []
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else:
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water_tracers = water_tracers_xml.split(":")
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tracer_names = []
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tracer_species = []
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tracer_initial_ratios = []
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for tracer in water_tracers:
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# Each item in the list consists of a name and then, optionally, a '%' followed by
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# the isotope species for this tracer. For standard water tracers (i.e., tracers
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# of bulk water), the list item will only contain the name (without a '%').
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expect(
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tracer.count("%") <= 1,
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f"Invalid WATER_TRACERS element, '{tracer}': Each element of WATER_TRACERS must contain at most 1 '%' separator",
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)
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parts = tracer.split("%")
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tracer_names.append(parts[0])
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if len(parts) > 1:
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tracer_species.append(parts[1])
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# We could check the validity of the species name here (confirming that it's
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# one of the handled species), but that would lead to this allowed list being
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# replicated in multiple places (here as well as in the Fortran), which would
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# make it more difficult to add new species later. So we're deferring this
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# check to runtime.
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else:
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tracer_species.append("-")
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tracer_initial_ratios.append("1.0")
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nmlgen.add_default("water_tracer_names", ":".join(tracer_names))
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nmlgen.add_default("water_tracer_species", ":".join(tracer_species))
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nmlgen.add_default("water_tracer_initial_ratios", ":".join(tracer_initial_ratios))
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###############################################################################
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def _create_runseq(case, coupling_times, valid_comps):
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###############################################################################

‎cime_config/config_component_cesm.xml‎

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@@ -501,7 +501,7 @@
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</entry>
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<!-- ===================================================================== -->
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<!-- averaged history frequencies -->
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<!-- controls over various other options -->
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<!-- ===================================================================== -->
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<entry id="BUDGETS">
@@ -581,5 +581,30 @@
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<desc>Freezing point calculation for salt water.</desc>
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</entry>
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<entry id="WATER_TRACERS">
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<type>char</type>
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<default_value></default_value>
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<group>run_coupling</group>
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<file>env_run.xml</file>
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<desc>
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Colon-delimited list of water tracers enabled in this run.
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Each item in the list consists of a name and then, optionally, a '%' followed by the
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isotope species for this tracer. For standard water tracers (i.e., tracers of bulk
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water), the list item will only contain the name (without a '%'). The name can be
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anything; if an isotope species is specified, it must match one of the implemented
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water isotopes: H218O, H217O or HDO. By convention, a tracer that is the full
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quantity of a given isotope will have a name that is identical to the species (e.g.,
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H218O:H218O).
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For example, this list could be:
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MyRegularTracer:HDO%HDO:H218O%H218O:SomeOtherTracer:MyHdoTracer%HDO:YetAnotherTracer
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This specifies three standard (bulk water) tracers (MyRegularTracer, SomeOtherTracer
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and YetAnotherTracer), two isotopes (HDO and H218O), and a tracer that is a subset
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of HDO (MyHdoTracer). (Note that the ordering in the list is not important.)
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</desc>
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</entry>
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</entry_id>

‎cime_config/namelist_definition_drv.xml‎

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@@ -853,7 +853,6 @@
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</desc>
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<values>
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<value>on</value>
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<value COMP_LND="xlnd">off</value>
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</values>
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</entry>
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<entry id="remove_negative_runoff_lnd">
@@ -2537,18 +2536,6 @@
25372536
</values>
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</entry>
25392538

2540-
<entry id="flds_wiso" modify_via_xml="FLDS_WISO">
2541-
<type>logical</type>
2542-
<category>flds</category>
2543-
<group>ALLCOMP_attributes</group>
2544-
<desc>
2545-
Pass water isotopes between components
2546-
</desc>
2547-
<values>
2548-
<value>.false.</value>
2549-
</values>
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</entry>
2551-
25522539
<entry id="flds_r2l_stream_channel_depths">
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<type>logical</type>
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<category>flds</category>
@@ -2599,6 +2586,66 @@
25992586
</values>
26002587
</entry>
26012588

2589+
<entry id="water_tracer_names" modify_via_xml="WATER_TRACERS" skip_default_entry="true">
2590+
<type>char</type>
2591+
<category>water_tracers</category>
2592+
<group>ALLCOMP_attributes</group>
2593+
<desc>
2594+
Colon-delimited list of names of water tracers in this run.
2595+
</desc>
2596+
<values>
2597+
<value></value>
2598+
</values>
2599+
</entry>
2600+
2601+
<entry id="water_tracer_species" modify_via_xml="WATER_TRACERS" skip_default_entry="true">
2602+
<type>char</type>
2603+
<category>water_tracers</category>
2604+
<group>ALLCOMP_attributes</group>
2605+
<desc>
2606+
Colon-delimited list of species of water tracers in this run.
2607+
2608+
Each element in the list corresponds to an element in water_tracer_names. A value of
2609+
'-' for a given element indicates a standard water tracer (i.e., a tracer of bulk
2610+
water).
2611+
</desc>
2612+
<values>
2613+
<value></value>
2614+
</values>
2615+
</entry>
2616+
2617+
<entry id="water_tracer_initial_ratios" skip_default_entry="true">
2618+
<type>char</type>
2619+
<category>water_tracers</category>
2620+
<group>ALLCOMP_attributes</group>
2621+
<desc>
2622+
Colon-delimited list of initial water tracer ratios (as a fraction of total water).
2623+
2624+
Each element in the list corresponds to an element in water_tracer_names.
2625+
2626+
For water isotopes, this ratio is typically set to 1 for numerical reasons; the
2627+
actual isotopic ratios can then be determined via reference to standard global
2628+
ratios.
2629+
</desc>
2630+
<values>
2631+
<value></value>
2632+
</values>
2633+
</entry>
2634+
2635+
<entry id="water_tracers_do_checks">
2636+
<type>logical</type>
2637+
<category>water_tracers</category>
2638+
<group>ALLCOMP_attributes</group>
2639+
<desc>
2640+
Check consistency between water tracer fields and their corresponding bulk fields.
2641+
2642+
This should only be used with artificial tracers that maintain a fixed ratio.
2643+
</desc>
2644+
<values>
2645+
<value>.false.</value>
2646+
</values>
2647+
</entry>
2648+
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<!-- =========================== -->
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<!-- CLOCK Attributes -->
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<!-- =========================== -->

‎cime_config/testdefs/testlist_drv.xml‎

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@@ -247,6 +247,17 @@
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</options>
248248
</test>
249249

250+
<test compset="X" grid="f19_g17" name="SMS_D_Ld2" testmods="drv/water_tracers--drv/glc_avg_frequently">
251+
<machines>
252+
<machine name="derecho" compiler="intel" category="aux_cmeps"/>
253+
<machine name="derecho" compiler="intel" category="prealpha"/>
254+
</machines>
255+
<options>
256+
<option name="wallclock"> 00:20:00 </option>
257+
<option name="comment">Test handling of water tracers in CMEPS; includes glc_avg_frequently testmod to exercise the lnd-to-glc mapping.</option>
258+
</options>
259+
</test>
260+
250261
<!-- ======================================= -->
251262
<!-- TG compsets -->
252263
<!-- ======================================= -->

‎cime_config/testdefs/testmods_dirs/drv/glc_avg_frequently/README‎

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This testmod turns on more frequent averaging of the fields sent to glc so that the
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mapping of these fields can be tested in a run shorter than a year.

‎cime_config/testdefs/testmods_dirs/drv/glc_avg_frequently/shell_commands‎

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./xmlchange GLC_AVG_PERIOD=glc_coupling_period

‎cime_config/testdefs/testmods_dirs/drv/water_tracers/README‎

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This testmod turns on multiple water tracers along with checks to ensure that they
2+
maintain their correct ratio over time. (These checks will only pass if the water tracers
3+
used in the test do not invoke any physics that would cause a change in their ratios.)

‎cime_config/testdefs/testmods_dirs/drv/water_tracers/shell_commands‎

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./xmlchange WATER_TRACERS=tracer1:tracer2

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