Merge pull request #181 from duvivier/main

updating user synatx and toc
NCAR · Jul 24, 2023 · 49f5b2e · 49f5b2e
2 parents e6acad7 + 7ac4848
commit 49f5b2e
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diff --git a/_toc.yml b/_toc.yml
@@ -98,6 +98,7 @@ chapters:
   - file: notebooks/sourcemods/exercises_overview
     sections:
     - file: notebooks/sourcemods/exercises/exercise_add_field
+    - file: notebooks/sourcemods/exercises/exercise_rain_threshold
 
 - file: notebooks/diagnostics/diagnostics
   sections:
@@ -107,17 +108,17 @@ chapters:
     - file: notebooks/diagnostics/cam/advanced_cam
     - file: notebooks/diagnostics/cam/cam_se_native_example
   - file: notebooks/diagnostics/cam-chem_waccm
-  - file: notebooks/diagnostics/cice/cice
-    sections:
-    - file: notebooks/diagnostics/cice/basics_cice
-    - file: notebooks/diagnostics/cice/advanced_cice
   - file: notebooks/diagnostics/clm_ctsm/clm_ctsm
     sections:
     - file: notebooks/diagnostics/clm_ctsm/basics_clm
   - file: notebooks/diagnostics/pop/pop
     sections:
     - file: notebooks/diagnostics/pop/basics_pop
     - file: notebooks/diagnostics/pop/advanced_pop
+  - file: notebooks/diagnostics/cice/cice
+    sections:
+    - file: notebooks/diagnostics/cice/basics_cice
+    - file: notebooks/diagnostics/cice/advanced_cice
   - file: notebooks/diagnostics/additional/additional
     sections:
     - file: notebooks/diagnostics/additional/postprocessing
@@ -140,16 +141,6 @@ chapters:
     - file: notebooks/challenge/cam-chem_waccm/exercise_2
     - file: notebooks/challenge/cam-chem_waccm/exercise_3
     - file: notebooks/challenge/cam-chem_waccm/visualization
-  - file: notebooks/challenge/cice/cice
-    sections:
-    - file: notebooks/challenge/cice/cice_exercise_1
-    - file: notebooks/challenge/cice/cice_exercise_2
-    - file: notebooks/challenge/cice/cice_exercise_3
-  - file: notebooks/challenge/cism/cism
-    sections:
-    - file: notebooks/challenge/cism/cism_exercise_1
-    - file: notebooks/challenge/cism/cism_exercise_2
-    - file: notebooks/challenge/cism/cism_exercise_3
   - file: notebooks/challenge/clm_ctsm/clm_ctsm
     sections:
     - file: notebooks/challenge/clm_ctsm/clm_exercise_1
@@ -161,6 +152,16 @@ chapters:
     - file: notebooks/challenge/pop/pop_exercise_2
     - file: notebooks/challenge/pop/pop_exercise_3
     - file: notebooks/challenge/pop/pop_exercise_4
+  - file: notebooks/challenge/cice/cice
+    sections:
+    - file: notebooks/challenge/cice/cice_exercise_1
+    - file: notebooks/challenge/cice/cice_exercise_2
+    - file: notebooks/challenge/cice/cice_exercise_3
+  - file: notebooks/challenge/cism/cism
+    sections:
+    - file: notebooks/challenge/cism/cism_exercise_1
+    - file: notebooks/challenge/cism/cism_exercise_2
+    - file: notebooks/challenge/cism/cism_exercise_3
   - file: notebooks/challenge/bgc/bgc
     sections:
     - file: notebooks/challenge/bgc/bgc_exercise_1

diff --git a/notebooks/challenge/cam/exercise_1.ipynb b/notebooks/challenge/cam/exercise_1.ipynb
@@ -170,7 +170,7 @@
     "    \n",
     "(1) Check that your archive directory on cheyenne (The path will be different on other machines): \n",
     "```\n",
-    "cd /glade/scratch/$user/archive/$CASENAME/atm/hist\n",
+    "cd /glade/scratch/$USER/archive/$CASENAME/atm/hist\n",
     "ls \n",
     "```\n",
     "\n",
@@ -179,7 +179,7 @@
     "(2) Look at the contents of the ``h1`` files using ``ncdump``.\n",
     "\n",
     "```\n",
-    "cd /glade/scratch/$user/archive/$CASENAME/atm/hist\n",
+    "cd /glade/scratch/$USER/archive/$CASENAME/atm/hist\n",
     "ncdump -h f2000_control.cam.h1.0001-01-01-00000.nc\n",
     "```\n",
     "\n",

diff --git a/notebooks/challenge/cam/exercise_2.ipynb b/notebooks/challenge/cam/exercise_2.ipynb
@@ -175,7 +175,7 @@
     "    \n",
     "(1) Check that your archive directory on cheyenne (The path will be different on other machines): \n",
     "```\n",
-    "cd /glade/scratch/$user/archive/$CASENAME/atm/hist\n",
+    "cd /glade/scratch/$USER/archive/$CASENAME/atm/hist\n",
     "ls \n",
     "```\n",
     "\n",

diff --git a/notebooks/challenge/cam/exercise_3.ipynb b/notebooks/challenge/cam/exercise_3.ipynb
@@ -190,7 +190,7 @@
     "    \n",
     "(1) Check that your archive directory on cheyenne (The path will be different on other machines): \n",
     "```\n",
-    "cd /glade/scratch/$user/archive/$CASENAME/atm/hist\n",
+    "cd /glade/scratch/$USER/archive/$CASENAME/atm/hist\n",
     "ls \n",
     "```\n",
     "\n",

diff --git a/notebooks/challenge/cam/exercise_4.ipynb b/notebooks/challenge/cam/exercise_4.ipynb
@@ -212,7 +212,7 @@
     "    \n",
     "(1) Check that your archive directory on cheyenne (The path will be different on other machines): \n",
     "```\n",
-    "cd /glade/scratch/$user/archive/$CASENAME/atm/hist\n",
+    "cd /glade/scratch/$USER/archive/$CASENAME/atm/hist\n",
     "ls \n",
     "```\n",
     "\n",

diff --git a/notebooks/challenge/cam/exercise_5.ipynb b/notebooks/challenge/cam/exercise_5.ipynb
@@ -215,7 +215,7 @@
     "    \n",
     "(1) Check that your archive directory on cheyenne (The path will be different on other machines): \n",
     "```\n",
-    "cd /glade/scratch/$user/archive/$CASENAME/atm/hist\n",
+    "cd /glade/scratch/$USER/archive/$CASENAME/atm/hist\n",
     "ls \n",
     "```\n",
     "\n",

diff --git a/notebooks/challenge/cam/exercise_6.ipynb b/notebooks/challenge/cam/exercise_6.ipynb
@@ -216,7 +216,7 @@
     "    \n",
     "(1) Check that your archive directory on cheyenne (The path will be different on other machines): \n",
     "```\n",
-    "cd /glade/scratch/$user/archive/$CASENAME/atm/hist\n",
+    "cd /glade/scratch/$USER/archive/$CASENAME/atm/hist\n",
     "ls \n",
     "```\n",
     "\n",

diff --git a/notebooks/challenge/clm_ctsm/clm_exercise_1.ipynb b/notebooks/challenge/clm_ctsm/clm_exercise_1.ipynb
@@ -81,7 +81,7 @@
     "    \n",
     "(1) Check that your archive directory on cheyenne (The path will be different on otehr machines): \n",
     "```\n",
-    "cd /glade/scratch/$user/archive/i.day5.a/lnd/hist\n",
+    "cd /glade/scratch/$USER/archive/i.day5.a/lnd/hist\n",
     "\n",
     "ls \n",
     "```\n",

diff --git a/notebooks/challenge/clm_ctsm/clm_exercise_2.ipynb b/notebooks/challenge/clm_ctsm/clm_exercise_2.ipynb
@@ -117,7 +117,7 @@
     "    \n",
     "(1) Check that your archive directory on cheyenne (The path will be different on other machines): \n",
     "```\n",
-    "cd /glade/scratch/$user/archive/i.day5.b/lnd/hist\n",
+    "cd /glade/scratch/$USER/archive/i.day5.b/lnd/hist\n",
     "\n",
     "ls \n",
     "```\n",
@@ -126,7 +126,7 @@
     "    \n",
     "(2) Compare to control run:\n",
     "```\n",
-    "ncdiff -v TLAI i.day5.b.clm2.XXX.nc /glade/scratch/$user/archive/i.day5.a/lnd/hist/i.day5.a.clm2.XXX.nc i_diff.nc\n",
+    "ncdiff -v TLAI i.day5.b.clm2.XXX.nc /glade/scratch/$USER/archive/i.day5.a/lnd/hist/i.day5.a.clm2.XXX.nc i_diff.nc\n",
     "\n",
     "ncview i_diff.nc\n",
     "```\n",

diff --git a/notebooks/challenge/clm_ctsm/clm_exercise_3.ipynb b/notebooks/challenge/clm_ctsm/clm_exercise_3.ipynb
@@ -126,15 +126,15 @@
     "    \n",
     "(1) Check that your archive directory on cheyenne (The path will be different on otehr machines): \n",
     "```\n",
-    "cd /glade/scratch/$user/archive/i.day5.a_pft/lnd/hist\n",
+    "cd /glade/scratch/$USER/archive/i.day5.a_pft/lnd/hist\n",
     "\n",
     "ls \n",
     "```\n",
     "<br>\n",
     "\n",
     "(2) Compare to control run:\n",
     "```\n",
-    "ncdiff i.day5.a_pft.clm2.XXX.nc /glade/scratch/$user/archive/i.day5.a/lnd/hist/i.day5.a.clm2.XXX.nc i_diff.nc\n",
+    "ncdiff i.day5.a_pft.clm2.XXX.nc /glade/scratch/$USER/archive/i.day5.a/lnd/hist/i.day5.a.clm2.XXX.nc i_diff.nc\n",
     "\n",
     "ncview i_diff.nc\n",
     "```\n",

diff --git a/notebooks/namelist/exercises/exercise_cam_output.ipynb b/notebooks/namelist/exercises/exercise_cam_output.ipynb
@@ -171,7 +171,7 @@
     "    \n",
     "(1) Check that your archive directory on cheyenne (The path will be different on otehr machines): \n",
     "```\n",
-    "cd /glade/scratch/$user/archive/b1850_high_freq/atm/hist\n",
+    "cd /glade/scratch/$USER/archive/b1850_high_freq/atm/hist\n",
     "ls \n",
     "```\n",
     "\n",
@@ -216,7 +216,7 @@
     "```\n",
     "- Check the size of the files\n",
     "```\n",
-    "du –ks –h /glade/scratch/$user/archive/b1850_high_freq/atm/hist/*\n",
+    "du –ks –h /glade/scratch/$USER/archive/b1850_high_freq/atm/hist/*\n",
     "```\n",
     "```\n",
     "234M    b1850_high_freq.cam.h0.0001-01.nc\n",

diff --git a/notebooks/namelist/exercises/exercise_tuning_parameter.ipynb b/notebooks/namelist/exercises/exercise_tuning_parameter.ipynb
@@ -50,7 +50,7 @@
     "- Compare to this run to the first run you did today: `b1850_high_freq`.\n",
     "-  You can use `ncdiff` and `ncview` to look at the difference between the 2 runs. For instance:\n",
     "```\n",
-    "ncdiff /glade/scratch/$user/archive/b1850_dcs/atm/hist/b1850_dcs.cam.h0.0001-01.nc /glade/scratch/$user/archive/b1850_high_freq/atm/hist/b1850_high_freq.cam.h0.0001-01.nc diff.nc\n",
+    "ncdiff /glade/scratch/$USER/archive/b1850_dcs/atm/hist/b1850_dcs.cam.h0.0001-01.nc /glade/scratch/$USER/archive/b1850_high_freq/atm/hist/b1850_high_freq.cam.h0.0001-01.nc diff.nc\n",
     "\n",
     "ncview diff.nc\n",
     "```\n",
@@ -139,8 +139,8 @@
     "\n",
     "- For instance, use `ncdiff` to create a file with the difference between the 2 runs:\n",
     "```\n",
-    "cd /glade/scratch/$user/archive/b1850_dcs \n",
-    "ncdiff /glade/scratch/$user/archive/b1850_dcs/atm/hist/b1850_dcs.cam.h0.0001-01.nc /glade/scratch/$user/archive/b1850_high_freq/atm/hist/b1850_high_freq.cam.h0.0001-01.nc diff.nc\n",
+    "cd /glade/scratch/$USER/archive/b1850_dcs \n",
+    "ncdiff /glade/scratch/$USER/archive/b1850_dcs/atm/hist/b1850_dcs.cam.h0.0001-01.nc /glade/scratch/$USER/archive/b1850_high_freq/atm/hist/b1850_high_freq.cam.h0.0001-01.nc diff.nc\n",
     "```    \n",
     "\n",
     "- Use `ncview` to look at the file you created.\n",

diff --git a/notebooks/sourcemods/exercises/exercise_add_field.ipynb b/notebooks/sourcemods/exercises/exercise_add_field.ipynb
@@ -173,7 +173,7 @@
     "    \n",
     "When the run is completed, check the fields `T750` and `T500` are in the file `h1`:\n",
     "```  \n",
-    "cd /glade/scratch/$user/archive/b1850_T750/atm/hist/ \n",
+    "cd /glade/scratch/$USER/archive/b1850_T750/atm/hist/ \n",
     "ncdump -h b1850_T750.cam.h1.0001-01-01-00000.nc\n",
     "```\n",
     "    \n",
@@ -192,13 +192,13 @@
     "    \n",
     "Create a file with the difference between `T750-T500`:\n",
     "```    \n",
-    "cd /glade/scratch/$user/archive/b1850_T750/atm/hist/ \n",
+    "cd /glade/scratch/$USER/archive/b1850_T750/atm/hist/ \n",
     "ncap2 -s 'T750_minus_T500=T750-T500' b1850_T750.cam.h1.0001-01-01-00000.nc  T750-T500.nc \n",
     "```\n",
     "\n",
     "Look at the difference between `T750-T500` with `ncview`: \n",
     "```\n",
-    "cd /glade/scratch/$user/archive/b1850_T750/atm/hist/ \n",
+    "cd /glade/scratch/$USER/archive/b1850_T750/atm/hist/ \n",
     "ncview T750-T500.nc\n",
     "```\n",
     "  \n",

diff --git a/notebooks/sourcemods/exercises/exercise_rain_threshold.ipynb b/notebooks/sourcemods/exercises/exercise_rain_threshold.ipynb
@@ -130,7 +130,7 @@
     "    \n",
     "When the run is completed, check the fields `T750` and `T500` are in the file `h1`:\n",
     "```  \n",
-    "cd /glade/scratch/$user/archive/b1850_rain_threshold/atm/hist/ \n",
+    "cd /glade/scratch/$USER/archive/b1850_rain_threshold/atm/hist/ \n",
     "ncdump -h bb1850_rain_threshold.cam.h1.0001-01-01-00000.nc\n",
     "```\n",
     "    \n",
@@ -149,13 +149,13 @@
     "    \n",
     "Create a file with the difference between `T750-T500`:\n",
     "```    \n",
-    "cd /glade/scratch/$user/archive/b1850_rain_threshold/atm/hist/ \n",
+    "cd /glade/scratch/$USER/archive/b1850_rain_threshold/atm/hist/ \n",
     "ncap2 -s ‘T750_minus_T500=T750-T500' b1850_T750.cam.h1.0001-01-01-00000.nc  T750-T500.nc \n",
     "```\n",
     "\n",
     "Look at the difference between `T750-T500` with `ncview`: \n",
     "```\n",
-    "cd /glade/scratch/$user/archive/b1850_rain_threshold/atm/hist/ \n",
+    "cd /glade/scratch/$USER/archive/b1850_rain_threshold/atm/hist/ \n",
     "ncview T750-T500.nc\n",
     "```\n",
     "  \n",