Merge pull request #237 from sophmaca/main

Fix some issues in paleo challenge

notebooks/challenge/paleo/exercise_2.ipynb

@@ -57,7 +57,7 @@
     "\n",
     "**What was the orbital configuration 6 ka BP?**\n",
     "\n",
-    "- According to Table 1 of [Otto-Bliesner et al., (2017)](chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://gmd.copernicus.org/articles/10/3979/2017/gmd-10-3979-2017.pdf), Eccentricity = 0.018682, Obliquity (degrees) = 24.105, Perihelion = 0.87 (for simplicity, we don't consider the other forcings here, i.e., CO2) \n",
+    "- According to Table 1 of [Otto-Bliesner et al., (2017)](https://doi.org/10.5194/gmd-10-3979-2017), Eccentricity = 0.018682, Obliquity (degrees) = 24.105, Perihelion = 0.87 (for simplicity, we don't consider the other forcings here, i.e., CO2) \n",
     "\n",
     "**How to modify orbital configuration in CESM world?**\n",
     "\n",
@@ -265,7 +265,7 @@
     "- Changes in Earth's orbit alter the length of months or seasons over time, this is referred to as the 'paleo calendar effect' \n",
     "- This means that the modern fixed-length definition of months do not apply when the Earth traversed different portions of its orbit \n",
     "- Tools exist to adjust monthly CESM output to account for the 'paleo calendar effect' \n",
-    "- See [Bartlein & Shafer et al. (2019)](chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://gmd.copernicus.org/articles/12/3889/2019/gmd-12-3889-2019.pdf) for more information \n",
+    "- See [PaleoCalAdjust tool](https://github.com/CESM-Development/paleoToolkit/tree/master/PaleoCalAdjust) from [Bartlein & Shafer et al. (2019)](https://doi.org/10.5194/gmd-12-3889-2019) for more information \n",
     "- For simplicity, we assume in this exercise that the definition of months is the same for the pre-industrial and mid-Holocene \n",
     "\n",
     "Now, let's take a look at the differences between the two cases more clearly using NCO. \n",
@@ -282,7 +282,7 @@
     "**# Questions for reflection:**\n",
     "- Which orbital parameters are different at the middle Holocene (6 ka BP)? \n",
     "- How does the orbital parameter impact the top-of-atmosphere shortwave radiation (solar insolation) during summertime in the Northern Hemisphere? \n",
-    "- Do the results look correct? You can compare your results with Figure 3b of [Otto-Bliesner et al., (2017)](chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://gmd.copernicus.org/articles/10/3979/2017/gmd-10-3979-2017.pdf) \n",
+    "- Do the results look correct? You can compare your results with Figure 3b of [Otto-Bliesner et al., (2017)](https://doi.org/10.5194/gmd-10-3979-2017) \n",
     "- What other aspects of climate are different between the mid-Holocene and pre-industrial runs?",
     "\n",
     "</details>\n",

notebooks/challenge/paleo/exercise_3.ipynb

@@ -182,7 +182,6 @@
     "\n",
     "\n",
     "After submitting the job, use ``qstat -u $USER`` to check the status of your job. \n",
-    "It may take ~16 minutes to finish the one-year simulation. \n",
     "\n",
     "**# Check your solution**\n",
     "\n",
@@ -216,13 +215,13 @@
     "<summary> <font face=\"Times New Roman\" color='blue'>Click here to visualize results</font> </summary>\n",
     "<br>\n",
     "\n",
-    "### Option 1 \n",
+    "**--------------- Option 1 ---------------** \n",
     "\n",
     "**# Use NCO to calculate the oxygen isotopic composition of precipitation**\n",
     "\n",
     "The ratio of heavy ($^{18}\\text{O}$) to light ($^{16}\\text{O}$)) isotopes are most commonly expressed relative to a standard in delta (δ) notation: \n",
     "\n",
-    "$$ \\delta^{18}O = \\frac{R_{\\text{sample}} - R_{\\text{std}}}{R_{\\text{std}}} \\times 1000‰ $$\n",
+    "$$ \\delta^{18}\\text{O} = \\frac{R_{\\text{sample}} - R_{\\text{std}}}{R_{\\text{std}}} \\times 1000‰ $$\n",
     "\n",
     "where \n",
     "- $R_{\\text{sample}}$ = ratio of $^{18}\\text{O}$ to $^{16}\\text{O}$ in sample \n",
@@ -233,7 +232,7 @@
     "In isotope-enabled CESM, the relative abundances of $^{16}\\text{O}$ and $^{18}\\text{O}$ are already adjusted to their naturally occurring global abundances (99.757% and 0.205%, respectively), so we do not include $R_{\\text{std}}$ in the calculation of $\\delta^{18}\\text{O}$. Rather, isotope variables in CESM are expressed in delta (δ) notation as: \n",
     "\n",
     "\n",
-    "$$ \\delta^{18}O = (\\frac{\\text{PRECRC\\_H218Or} + \\text{PRECSC\\_H218Os} + \\text{PRECRL\\_H218OR} + \\text{PRECSL\\_H218OS}}{\\text{PRECRC\\_H216Or} + \\text{PRECSC\\_H216Os} + \\text{PRECRL\\_H216OR} + \\text{PRECSL\\_H216OS}} - 1) \\times 1000‰  $$\n",
+    "$$ \\delta^{18}O = (\\frac{\\text{PRECRC_H218Or} + \\text{PRECSC_H218Os} + \\text{PRECRL_H218OR} + \\text{PRECSL_H218OS}}{\\text{PRECRC_H216Or} + \\text{PRECSC_H216Os} + \\text{PRECRL_H216OR} + \\text{PRECSL_H216OS}} - 1) \\times 1000‰  $$\n",
     "\n",
     "\n",
     "- Use ``ncdump /glade/derecho/scratch/$USER/$CASENAME/atm/hist/$CASENAME.cam.h0.0001-01.nc | less`` to check the definition of each isotope variable above \n",
@@ -254,7 +253,7 @@
     "ncview d18Op.$CASENAME.cam.h0.0001-12.nc \n",
     "```\n",
     "\n",
-    "### Option 2 \n",
+    "**--------------- Option 2 ---------------** \n",
     "\n",
     "**# Use Python to calculate and plot the oxygen isotopic composition of precipitation**\n",
     "\n",
@@ -320,7 +319,7 @@
     "```\n",
     "\n",
     "\n",
-    "### Questions for reflection:\n",
+    "**--------------- Questions for reflection ---------------** \n",
     "- Do you notice any spatial patterns in precipitation $\\delta^{18}\\text{O}$? \n",
     "\n",
     "</details>\n",