Combine stage yamls into one

Refs NOAA-EMC#2475

parm/stage/stage.yaml.j2

@@ -0,0 +1,98 @@
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
+
+{% if MODE == "cycled" %}
+analysis:
+    mkdir:
+        - "{{ COM_ATMOS_ANALYSIS }}"
+    copy:
+        # TODO: Add abias_int?
+        {% for ftype in ["abias", "abias_air", "abias_pc", "radstat"] %}
+        - ["{{ ICSDIR }}/{{ COM_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ RUN }}.t{{ cycle_HH }}z.{{ ftype }}", "{{ COM_ATMOS_ANALYSIS }}"]
+        {% endfor %}
+{% endif %}
+
+{% if EXP_WARM_START == True %}
+atmosphere_warm:
+    mkdir:
+        - "{{ COM_ATMOS_RESTART_PREV }}"
+    copy:
+        {% for ftype in ["coupler.res", "fv_core.res.nc"] %}
+        - ["{{ ICSDIR }}/{{ COM_ATMOS_RESTART_PREV | relpath(ROTDIR) }}/{{ DTG_PREFIX }}.{{ ftype }}", "{{ COM_ATMOS_RESTART_PREV }}"]
+        {% 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 + 1) %}
+        - ["{{ ICSDIR }}/{{ COM_ATMOS_RESTART_PREV | relpath(ROTDIR) }}/{{ DTG_PREFIX }}.{{ ftype }}.tile{{ ntile }}.nc", "{{ COM_ATMOS_RESTART_PREV }}"]
+            {% endfor %} # ntile
+        {% endfor %} # ftype
+{% else %}
+atmosphere_cold:
+    mkdir:
+        - "{{ COM_ATMOS_INPUT }}"
+    copy:
+        - ["{{ ICSDIR }}/{{ COM_ATMOS_INPUT | relpath(ROTDIR) }}/gfs_ctrl.nc", "{{ COM_ATMOS_INPUT }}"]
+        {% for ftype in ["gfs_data", "sfc_data"] %}
+            {% for ntile in range(1, ntiles + 1) %}
+        - ["{{ ICSDIR }}/{{ COM_ATMOS_INPUT | relpath(ROTDIR) }}/{{ ftype }}.tile{{ ntile }}.nc", "{{ COM_ATMOS_INPUT }}"]
+            {% endfor %} # ntile
+        {% endfor %} # ftype
+{% endif %}
+
+{% if DO_NEST %}
+atmosphere_nest:
+    {% set ntile = 7 %}
+    mkdir:
+        - "{{ COM_ATMOS_RESTART_PREV }}"
+    copy:
+        {% if EXP_WARM_START == True %}
+            {% for ftype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        - ["{{ ICSDIR }}/{{ COM_ATMOS_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.{{ ftype }}.tile{{ ntile }}.nc", "{{ COM_ATMOS_RESTART_PREV }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.{{ ftype }}.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
+            {% endfor %} # ftype
+        {% else %}
+            {% for ftype in ["gfs_data", "sfc_data"] %}
+        - ["{{ COM_ATMOS_INPUT }}/{{ ftype }}.tile{{ ntile }}.nc", "{{ COM_ATMOS_INPUT }}/{{ ftype }}.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
+            {% endfor %} # ftype
+        {% endif %} # cold-start
+{% endif %}
+
+{% if DO_WAVE %}
+wave:
+    mkdir:
+        - "{{ COM_WAVE_RESTART_PREV }}"
+    copy:
+        - ["{{ ICSDIR }}/{{ COM_WAVE_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.restart.{{ waveGRD }}", "{{ COM_WAVE_RESTART_PREV }}"]
+{% endif %}
+
+{% if DO_OCN %}
+ocean:
+    mkdir:
+        - "{{ COM_OCEAN_RESTART_PREV }}"
+    copy:
+        #-------------------------
+        # Ocean initial conditions
+        #-------------------------
+        - ["{{ ICSDIR }}/{{ COM_OCEAN_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.MOM.res.nc", "{{ COM_OCEAN_RESTART_PREV }}"]
+        #------------------------------------
+        # Resolution based initial conditions
+        #------------------------------------
+        {% if OCNRES == "025" %}
+            {% for nn in range(1, 3) %}
+        - ["{{ ICSDIR }}/{{ COM_OCEAN_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.MOM.res_{{ nn }}.nc", "{{ COM_OCEAN_RESTART_PREV }}"]
+            {% endfor %}
+        {% endif %}
+        #-------------------------
+        # Ocean Perturbation Files
+        #-------------------------
+        {% if MEMDIR and REPLAY_ICS == "YES" %}
+        - ["{{ ICSDIR }}/{{ COM_OCEAN_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.mom6_increment.nc", "{{ COM_OCEAN_RESTART_PREV }}"]
+        {% endif %}
+{% endif %}
+
+{% if DO_ICE %}
+ice:
+    mkdir:
+        - "{{ COM_ICE_RESTART_PREV }}"
+    copy:
+        - ["{{ ICSDIR }}/{{ COM_ICE_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.cice_model.res.nc", "{{ COM_ICE_RESTART_PREV }}"]
+{% endif %}