Refactor stage yamls

Refs NOAA-EMC#2475

parm/stage/fv3_cold.yaml.j2

@@ -1,16 +1,11 @@
-# # First 1/2 cycle also needs a atmos increment if doing warm start
-#   if inputs.start in ['warm']:
-#       for ftype in ['atmi003.nc', 'atminc.nc', 'atmi009.nc']:
-# if inputs.nens > 0:
-#for ftype in ['ratmi003.nc', 'ratminc.nc', 'ratmi009.nc']
 {% set cycle_YMDH = current_cycle | to_YMDH %}
 fv3_cold:
     mkdir:
         - "{{ COM_ATMOS_INPUT }}"
     copy:
-        - ["{{ BASE_CPLIC }}/{{ CPL_ATMIC }}/{{ cycle_YMDH }}/atmos/gfs_ctrl.nc", "{{ COM_ATMOS_INPUT }}/gfs_ctrl.nc"]
+        - ["{{ BASE_CPLIC }}/{{ CPL_ATMIC }}/{{ cycle_YMDH }}/{{ MEMDIR }}/atmos/gfs_ctrl.nc", "{{ COM_ATMOS_INPUT }}/gfs_ctrl.nc"]
         {% for ftype in ["gfs_data", "sfc_data"] %}
         {% for ntile in range(1, ntiles + 1) %}
-        - ["{{ BASE_CPLIC }}/{{ CPL_ATMIC }}/{{ cycle_YMDH }}/atmos/{{ ftype }}.tile{{ ntile }}.nc", "{{ COM_ATMOS_INPUT }}/{{ ftype }}.tile{{ ntile }}.nc"]
+        - ["{{ BASE_CPLIC }}/{{ CPL_ATMIC }}/{{ cycle_YMDH }}/{{ MEMDIR }}/atmos/{{ ftype }}.tile{{ ntile }}.nc", "{{ COM_ATMOS_INPUT }}/{{ ftype }}.tile{{ ntile }}.nc"]
         {% endfor %} # ntile
         {% endfor %} # ftype

parm/stage/fv3_nest.yaml.j2

@@ -11,11 +11,14 @@
 #       tgt="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
 # if (( ntiles > 6 )); then
 #       ${NLN} "${COM_ATMOS_INPUT}/${ftype}.tile7.nc" "${COM_ATMOS_INPUT}/${ftype}.nest02.tile7.nc"
-fv3:
-    name: "FV3"
-    target: "{{ COM_ATMOS_RESTART_PREV }}"
-    {% set ntile = 7 %}
-    required:
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
+{% set ntile = 7 %}
+fv3_nest:
+    mkdir:
+        - "{{ COM_ATMOS_RESTART_PREV }}"
+    copy:
         #---------------
         # WARM START
         #---------------

parm/stage/fv3_warm.yaml.j2

@@ -1,19 +1,16 @@
-# # First 1/2 cycle also needs a atmos increment if doing warm start
-#   if inputs.start in ['warm']:
-#       for ftype in ['atmi003.nc', 'atminc.nc', 'atmi009.nc']:
-# if inputs.nens > 0:
-#for ftype in ['ratmi003.nc', 'ratminc.nc', 'ratmi009.nc']
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
 fv3_warm:
-    name: "FV3_WARM"
-    target: "{{ COM_ATMOS_RESTART_PREV }}"
-    required:
-#TODO: Set MEMDIR as empty if not set?
-        {% set head = "{{ BASE_CPLIC }}/{{ CPL_ATMIC }}/{{ cycle_YMD }}{{ cycle_HH }}/{{ MEMDIR }}/atmos/{{ cycle_YMD }}.{{ cycle_HH }}0000." %}
+    mkdir:
+        - "{{ COM_ATMOS_RESTART_PREV }}"
+    copy:
+        {% set head = "{{ BASE_CPLIC }}/{{ CPL_ATMIC }}/{{ cycle_YMDH }}/{{ MEMDIR }}/atmos/{{ cycle_YMD }}.{{ cycle_HH }}0000." %}
         {% for ftype in ["coupler.res", "fv_core.res.nc"] %}
-        - "{{ head }}{{ ftype }}"
+        - ["{{ head }}{{ ftype }}", "{{ COM_ATMOS_RESTART_PREV }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.{{ ftype }}"]
         {% endfor %}
         {% for ftype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data sfc_data"] %}
         {% for ntile in range(1, ntiles) %}
-        - "{{ head }}{{ ftype }}.tile{{ ntile }}.nc"
+        - ["{{ head }}{{ ftype }}.tile{{ ntile }}.nc", "{{ COM_ATMOS_RESTART_PREV }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.{{ ftype }}.tile{{ ntile }}.nc"]
         {% endfor %} # ntile
         {% endfor %} # ftype

parm/stage/ice.yaml.j2

@@ -1,5 +1,8 @@
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
 ice:
-    name: "ICE"
-    target: "{{ COM_ICE_RESTART_PREV }}"
-    required:
-        - "{{ BASE_CPLIC }}/{{ CPL_ICEIC }}/{{ cycle_YMD }}{{ cycle_HH }}/{{ MEMDIR }}/ice/{{ cycle_YMD }}.{{ cycle_HH }}0000.cice_model.res.nc"
+    mkdir:
+        - "{{ COM_ICE_RESTART_PREV }}"
+    copy:
+        - ["{{ BASE_CPLIC }}/{{ CPL_ICEIC }}/{{ cycle_YMDH }}/{{ MEMDIR }}/ice/{{ cycle_YMD }}.{{ cycle_HH }}0000.cice_model.res.nc", "{{ COM_ICE_RESTART_PREV }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.cice_model.res.nc"]

parm/stage/master_forecast_only.yaml.j2

@@ -1,6 +1,3 @@
-{% set cycle_HH = current_cycle | strftime("%H") %}
-{% set cycle_YMD = current_cycle | to_YMD %}
-{% set cycle_YMDH = current_cycle | to_YMDH %}
 datasets:
 
 {% if EXP_WARM_START %}
@@ -20,26 +17,20 @@ datasets:
 {% endif %}
 
 {% if DO_WAVE %}
-{% if EXP_WARM_START %}
 {% filter indent(width=4) %}
 {% include "wave.yaml.j2" %}
 {% endfilter %}
 {% endif %}
-{% endif %}
 
 {% if DO_OCN %}
-{% if EXP_WARM_START %}
 {% filter indent(width=4) %}
 {% include "ocean.yaml.j2" %}
 #TODO:#{% include "mediator.yaml.j2" %}
 {% endfilter %}
 {% endif %}
-{% endif %}
 
 {% if DO_ICE %}
-{% if EXP_WARM_START %}
 {% filter indent(width=4) %}
 {% include "ice.yaml.j2" %}
 {% endfilter %}
 {% endif %}
-{% endif %}

parm/stage/mediator.yaml.j2

@@ -1,5 +1,8 @@
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
 mediator:
-    name: "MEDIATOR"
-    target: "{{ COM_MED_RESTART_PREV }}"
-    required:
-        - "{{ BASE_CPLIC }}/{{ CPL_MEDIC }}/{{ cycle_YMD }}{{ cycle_HH }}/{{ MEMDIR }}/med/{{ cycle_YMD }}.{{ cycle_HH }}0000.ufs.cpld.cpl.r.nc"
+    mkdir:
+        - "{{ COM_MED_RESTART_PREV }}"
+    copy:
+        - ["{{ BASE_CPLIC }}/{{ CPL_MEDIC }}/{{ cycle_YMDH }}/{{ MEMDIR }}/med/{{ cycle_YMD }}.{{ cycle_HH }}0000.ufs.cpld.cpl.r.nc", "{{ COM_MED_RESTART_PREV }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.ufs.cpld.cpl.r.nc"]

parm/stage/ocean.yaml.j2

@@ -1,24 +1,26 @@
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
 ocean:
-    name: "OCEAN"
-    target: "{{ COM_OCEAN_RESTART_PREV }}"
-    required:
-        {% set head = "{{ BASE_CPLIC }}/{{ CPL_OCNIC }}/{{ cycle_YMD }}{{ cycle_HH }}/{{ MEMDIR }}/ocean" %}
+    mkdir:
+        - "{{ COM_OCEAN_RESTART_PREV }}"
+    copy:
+        {% set head = "{{ BASE_CPLIC }}/{{ CPL_OCNIC }}/{{ cycle_YMDH }}/{{ MEMDIR }}/ocean" %}
         #-------------------------
         # Ocean initial conditions
         #-------------------------
-        - "{{ head }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.MOM.res.nc"
+        - ["{{ head }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.MOM.res.nc", "{{ COM_OCEAN_RESTART_PREV }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.MOM.res.nc"]
         #------------------------------------
         # Resolution based initial conditions
         #------------------------------------
         #NOTE: {% if OCNRES == 500 or OCNRES == 100 %} # Nothing more to do for these resolutions
         {% if OCNRES == 025 %}
         {% for nn in $(seq 1 3) %}
-        - "{{ head }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.MOM.res_{{ nn }}.nc"
+        - ["{{ head }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.MOM.res_{{ nn }}.nc", "{{ COM_OCEAN_RESTART_PREV }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.MOM.res_{{ nn }}.nc"]
         {% endfor %}
         {% endif %}
-    optional:
         #-------------------------
         # Ocean Perturbation Files
         #-------------------------
         {% if MEMDIR > 0 and USE_OCN_PERTURB_FILES %}
-        - "{{ head }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.mom6_increment.nc"
+        - ["{{ head }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.mom6_increment.nc", "{{ COM_OCEAN_RESTART_PREV }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.mom6_increment.nc"]

parm/stage/wave.yaml.j2

@@ -1,9 +1,10 @@
-#TODO: these should be placed in $RUN.$gPDY/$gcyc)
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
 wave:
-    #TODO: check if BASE_CPLIC/CPL_WAVIC exists?
-    name: "WAVE"
-    target: "{{ COM_WAVE_RESTART }}"
-    required:
+    mkdir:
+        - "{{ COM_WAVE_RESTART }}"
+    copy:
         {% for grdID in waveGRD %}
-        - "{{ BASE_CPLIC }}/{{ CPL_WAVIC }}/{{ cycle_YMD }}{{ cycle_HH }}/{{ MEMDIR }}/wave/{{ cycle_YMD }}.{{ cycle_HH }}0000.restart.{{ grdID }}"
+        - ["{{ BASE_CPLIC }}/{{ CPL_WAVIC }}/{{ cycle_YMDH }}/{{ MEMDIR }}/wave/{{ cycle_YMD }}.{{ cycle_HH }}0000.restart.{{ grdID }}", "{{ COM_WAVE_RESTART }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.restart.{{ grdID }}"]
         {% endfor %}