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Update isotope paleo exercise
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sophmaca authored Jul 30, 2024
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"<div class=\"alert alert-info\">\n",
"<strong>Exercise: Run a preindustrial simulation with water isotope tracers</strong><br><br>\n",
"\n",
"Download isotope-enabled CESM1.3 (iCESM1.3) code (the version of CESM used in this tutorial does not include water isotope capabilities). \n",
"Download isotope-enabled CESM1.3 (iCESM1.3; [code available here](https://github.com/NCAR/iCESM1.3_iHESP_hires)) code (the version of CESM used in this tutorial does not include water isotope capabilities). \n",
"\n",
"Create, configure, build and run a fully coupled preindustrial case called ``b.e13.B1850.f19_g17.piControl.001`` following [CESM naming conventions](https://www.cesm.ucar.edu/models/cesm2/naming-conventions) including water isotope tracers. \n",
"\n",
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"<summary> <font face=\"Times New Roman\" color='blue'>Click here for hints</font> </summary>\n",
"<br>\n",
"\n",
"**Where is the code for iCESM1.3 located?**\n",
"\n",
"- https://github.com/NCAR/iCESM1.3_iHESP_hires \n",
"\n",
"**What is the resolution for B1850?**\n",
"\n",
"- Use resolution ``f19_g17`` for fast throughput \n",
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"\n",
"\n",
"**# Set run length**\n",
"\n",
"\n",
"```\n",
"./xmlchange STOP_N=1,STOP_OPTION=nyears\n",
"```\n",
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"<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 (<sup>18</sup>O) to light (<sup>16</sup>O) isotopes are most commonly expressed relative to a standard in delta (δ) notation: \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",
"####δ<sup>18</sup>O = (R<sub>sample</sub> - R<sub>std</sub>)/(R<sub>std</sub>) * 1000‰ \n",
"$$ \\delta^{18}O = \\frac{R_{\\text{sample}} - R_{\\text{std}}}{R_{\\text{std}}} \\times 1000‰ $$\n",
"\n",
"where \n",
"- R<sub>sample</sub> = ratio of <sup>18</sup>O to <sup>16</sup>O in sample \n",
"- R<sub>std</sub> = ratio of <sup>18</sup>O to <sup>16</sup>O in a standard \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 δ<sup>18</sup>O of a sample which is identical to the standard would be 0‰, positive values indicate a greater proportion of <sup>18</sup>O than the standard, and negative values indicate a lower proportion of <sup>18</sup>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 <sup>16</sup>O and <sup>18</sup>O are already adjusted to their naturally occurring global abundances (99.757% and 0.205%, respectively), so we do not include R<sub>std</sub> in the calculation of δ<sup>18</sup>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",
"####δ<sup>18</sup>O = ((PRECRC_H218Or + PRECSC_H218Os + PRECRL_H218OR + PRECSL_H218OS)/ \n",
"####(PRECRC_H216Or + PRECSC_H216Os + PRECRL_H216OR + PRECSL_H216OS) - 1) * 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/$CASENAME.cam.h0.0001-01.nc | less`` to define each isotope variable above \n",
"- Use ``ncdump /glade/derecho/scratch/$USER/$CASENAME/atm/hist/$CASENAME.cam.h0.0001-01.nc | less`` to check the definition of each isotope variable above \n",
"- For example, search for ``PRECRC_H218Or`` using ``/PRECRC_H218Or + <enter>``) \n",
"\n",
"To calculate the δ<sup>18</sup>O of precipitation from the simulation using NCO, \n",
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"ncap2 -s 'd18Op=((PRECRC_H218Or+PRECSC_H218Os+PRECRL_H218OR+PRECSL_H218OS)/(PRECRC_H216Or+PRECSC_H216Os+PRECRL_H216OR+PRECSL_H216OS) - 1)*1000.' -v $CASENAME.cam.h0.0001-12.nc d18Op.$CASENAME.cam.h0.0001-12.nc \n",
"```\n",
"\n",
"**# Use Ncview to visualize precipitation δ<sup>18</sup>O**\n",
"**# Use Ncview to visualize precipitation $\\delta^{18}\\text{O}$**\n",
"\n",
"Earth's orbital configuration influences incoming solar insolation.\n",
"Take a look at the ``d18Op`` variable we calculated for 1 month in the pre-industrial run.\n",
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"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",
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"```\n",
"\n",
"\n",
"**# Questions for reflection:**\n",
"- Do you notice any spatial patterns in precipitation δ<sup>18</sup>O? \n",
"### Questions for reflection:\n",
"- Do you notice any spatial patterns in precipitation $\\delta^{18}\\text{O}$? \n",
"\n",
"</details>\n",
"</div>\n"
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