From 21d240076ad458d6383c2cf427873748267a6d9b Mon Sep 17 00:00:00 2001 From: Sophia Macarewich <33048895+sophmaca@users.noreply.github.com> Date: Tue, 30 Jul 2024 09:20:10 -0700 Subject: [PATCH 1/6] Update exercise_2.ipynb --- notebooks/challenge/paleo/exercise_2.ipynb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/notebooks/challenge/paleo/exercise_2.ipynb b/notebooks/challenge/paleo/exercise_2.ipynb index 5d72aaf24..1c217ee07 100644 --- a/notebooks/challenge/paleo/exercise_2.ipynb +++ b/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", "\n", From 8045f6185ceb29fa0747ba446d98b61a0a2def74 Mon Sep 17 00:00:00 2001 From: Sophia Macarewich <33048895+sophmaca@users.noreply.github.com> Date: Tue, 30 Jul 2024 09:25:55 -0700 Subject: [PATCH 2/6] Update exercise_3.ipynb --- notebooks/challenge/paleo/exercise_3.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/notebooks/challenge/paleo/exercise_3.ipynb b/notebooks/challenge/paleo/exercise_3.ipynb index 2bbeccb83..191e7ae96 100644 --- a/notebooks/challenge/paleo/exercise_3.ipynb +++ b/notebooks/challenge/paleo/exercise_3.ipynb @@ -228,9 +228,9 @@ "- $R_{\\text{sample}}$ = ratio of $^{18}\\text{O}$ to $^{16}\\text{O}$ in sample \n", "- $R_{\\text{std}}$ = ratio of $^{18}\\text{O}$ to $^{16}\\text{O}$ in a standard \n", "\n", - "Thus, the $\\delta^{18}\\text{O}$ of a sample which is identical to the standard would be 0‰, positive values indicate a greater proportion of $^{18}\\text{O}$ than the standard, and negative values indicate a lower proportion of $^{18}\\text{O}$ . \n", + "Thus, the $\\delta^{18}O$ of a sample which is identical to the standard would be 0‰, positive values indicate a greater proportion of $^{18}\\text{O}$ than the standard, and negative values indicate a lower proportion of $^{18}\\text{O}$ . \n", "\n", - "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", + "In isotope-enabled CESM, the relative abundances of $^{16}O$ and $^{18}O$ 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 $\\delta^{18}O$. 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", From 806af26569051ee51519c040dac7bc1ede64fe6e Mon Sep 17 00:00:00 2001 From: Sophia Macarewich <33048895+sophmaca@users.noreply.github.com> Date: Tue, 30 Jul 2024 09:28:41 -0700 Subject: [PATCH 3/6] Update exercise_3.ipynb --- notebooks/challenge/paleo/exercise_3.ipynb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/notebooks/challenge/paleo/exercise_3.ipynb b/notebooks/challenge/paleo/exercise_3.ipynb index 191e7ae96..53be63169 100644 --- a/notebooks/challenge/paleo/exercise_3.ipynb +++ b/notebooks/challenge/paleo/exercise_3.ipynb @@ -216,21 +216,21 @@ " Click here to visualize results \n", "
\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", "- $R_{\\text{std}}$ = ratio of $^{18}\\text{O}$ to $^{16}\\text{O}$ in a standard \n", "\n", - "Thus, the $\\delta^{18}O$ of a sample which is identical to the standard would be 0‰, positive values indicate a greater proportion of $^{18}\\text{O}$ than the standard, and negative values indicate a lower proportion of $^{18}\\text{O}$ . \n", + "Thus, the $\\delta^{18}\\text{O}$ of a sample which is identical to the standard would be 0‰, positive values indicate a greater proportion of $^{18}\\text{O}$ than the standard, and negative values indicate a lower proportion of $^{18}\\text{O}$ . \n", "\n", - "In isotope-enabled CESM, the relative abundances of $^{16}O$ and $^{18}O$ 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 $\\delta^{18}O$. Rather, isotope variables in CESM are expressed in delta (δ) notation as: \n", + "In isotope-enabled CESM, the relative abundances of $^{16}O$ 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", @@ -254,7 +254,7 @@ "ncview d18Op.$CASENAME.cam.h0.0001-12.nc \n", "```\n", "\n", - "### Option 2 \n", + "**---------- Option 1 ----------** \n", "\n", "**# Use Python to calculate and plot the oxygen isotopic composition of precipitation**\n", "\n", From 6530e4a87070325d36423ec4830a0e848aeb95e0 Mon Sep 17 00:00:00 2001 From: Sophia Macarewich <33048895+sophmaca@users.noreply.github.com> Date: Tue, 30 Jul 2024 09:31:04 -0700 Subject: [PATCH 4/6] Update exercise_3.ipynb --- notebooks/challenge/paleo/exercise_3.ipynb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/notebooks/challenge/paleo/exercise_3.ipynb b/notebooks/challenge/paleo/exercise_3.ipynb index 53be63169..b042738ae 100644 --- a/notebooks/challenge/paleo/exercise_3.ipynb +++ b/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", @@ -216,7 +215,7 @@ " Click here to visualize results \n", "
\n", "\n", - "**---------- Option 1 ----------** \n", + "**--------------- Option 1 ---------------** \n", "\n", "**# Use NCO to calculate the oxygen isotopic composition of precipitation**\n", "\n", @@ -230,7 +229,7 @@ "\n", "Thus, the $\\delta^{18}\\text{O}$ of a sample which is identical to the standard would be 0‰, positive values indicate a greater proportion of $^{18}\\text{O}$ than the standard, and negative values indicate a lower proportion of $^{18}\\text{O}$ . \n", "\n", - "In isotope-enabled CESM, the relative abundances of $^{16}O$ 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", + "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", @@ -254,7 +253,7 @@ "ncview d18Op.$CASENAME.cam.h0.0001-12.nc \n", "```\n", "\n", - "**---------- Option 1 ----------** \n", + "**--------------- Option 2 ---------------** \n", "\n", "**# Use Python to calculate and plot the oxygen isotopic composition of precipitation**\n", "\n", From 0315444b05c2bef2b656f3c425cd53e3ad524978 Mon Sep 17 00:00:00 2001 From: Sophia Macarewich <33048895+sophmaca@users.noreply.github.com> Date: Tue, 30 Jul 2024 09:31:58 -0700 Subject: [PATCH 5/6] Update exercise_3.ipynb --- notebooks/challenge/paleo/exercise_3.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/notebooks/challenge/paleo/exercise_3.ipynb b/notebooks/challenge/paleo/exercise_3.ipynb index b042738ae..bc26f5689 100644 --- a/notebooks/challenge/paleo/exercise_3.ipynb +++ b/notebooks/challenge/paleo/exercise_3.ipynb @@ -319,7 +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", "\n", From 0d223fb601c1f1c744167ffa108eb45018579c85 Mon Sep 17 00:00:00 2001 From: Sophia Macarewich <33048895+sophmaca@users.noreply.github.com> Date: Tue, 30 Jul 2024 09:33:58 -0700 Subject: [PATCH 6/6] Update exercise_3.ipynb --- notebooks/challenge/paleo/exercise_3.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/notebooks/challenge/paleo/exercise_3.ipynb b/notebooks/challenge/paleo/exercise_3.ipynb index bc26f5689..32f29b485 100644 --- a/notebooks/challenge/paleo/exercise_3.ipynb +++ b/notebooks/challenge/paleo/exercise_3.ipynb @@ -232,7 +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",