<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Juncheng, <div><br></div><div>You will need to change the dimension of the bathy.bin file to match the grid number in X and Y directions. Meanwhile, the dimension of the gridding parameters in data file should also be consistent with what you changed in SIZE.h. </div><div>One of the simple example that comes to my mind is <a href="https://github.com/MITgcm/MITgcm/tree/master/verification/isomip/input">https://github.com/MITgcm/MITgcm/tree/master/verification/isomip/input</a></div><div>If you are familiar with Matlab, the gendata.m in this directory should give you an understanding of the grid generation processes. </div><div>You can also use python to read in the bathy.bin. I think in your case for the baroclinic gyre example, it shall be something like below.</div><div><br></div><div><div>import numpy as np</div><div># Specify the path to your binary file</div><div>file_path = ‘bathy.bin'</div><div><br></div><div># Read the data from the file as REAL*8 (double precision float)</div><div>data = np.fromfile(file_path, dtype='float64’) # or float32</div><div><br></div><div>print(data.shape)</div><div><br></div><div>The dimension in float64 gives 1922, but in float32 it shows 3844 (correct for this case), which is also 62*62, consistent with what is defined in SIZE.h and data. </div><div>You will need to further reformat the 1D array into 2D for the bathy file.</div><div><br></div><div>Cheers,</div><div>Yilang </div><div><div style="font-size: 16px; caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Aptos;"><p class="MsoNormal" style="margin: 0in; font-size: 10pt; font-family: Aptos, sans-serif;"><span style="font-family: "Times New Roman", serif;">__________________________________</span></p></div><div style="font-size: 16px; caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Aptos;"><p class="MsoNormal" style="margin: 0in; font-size: 10pt; font-family: Aptos, sans-serif;"><b><span style="font-size: 11pt; font-family: "Times New Roman", serif; line-height: 1.2;">Yilang Xu</span></b><span style="font-size: 11pt; font-family: "Times New Roman", serif; line-height: 1.2;">, Ph.D. </span></p></div><div style="font-size: 16px; caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Aptos;"><p class="MsoNormal" style="margin: 0in; font-size: 10pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: "Times New Roman", serif; line-height: 1.2;">Postdoctoral Fellow</span></p></div><div style="font-size: 16px; caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Aptos;"><p class="MsoNormal" style="margin: 0in; font-size: 10pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: "Times New Roman", serif; line-height: 1.2;">Department of Earth & Planetary Sciences</span></p></div><div style="font-size: 16px; caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Aptos;"><p class="MsoNormal" style="margin: 0in; font-size: 10pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: "Times New Roman", serif; line-height: 1.2;">Johns Hopkins University</span></p></div><div style="font-size: 16px; caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Aptos;"><p class="MsoNormal" style="margin: 0in; font-size: 10pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: "Times New Roman", serif; color: rgb(0, 112, 192); line-height: 1.2;"><a href="mailto:Yxu243@jhu.edu" title="mailto:Yxu243@jhu.edu" data-outlook-id="260059c8-ba35-49ad-afbf-e44f23ab14d6" style="color: rgb(0, 120, 215);"><span style="color: rgb(0, 112, 192);">yxu243@jhu.edu</span></a></span></p></div></div><div><br><blockquote type="cite"><div>On Oct 15, 2024, at 23:13, Juncheng Zhang <juncheng.zhang@mail.utoronto.ca> wrote:</div><br class="Apple-interchange-newline"><div><meta charset="UTF-8"><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt;">Hi,<o:p></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt;"><o:p> </o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt;">I hope you are doing well.<o:p></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt;"><o:p> </o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt;">I am Juncheng, one of PhD student in University of Toronto, and I am trying to run a tutorial simulation with MITgcm, for example the Baroclinic_ocean_gyre, however, I had several questions:<o:p></o:p></span></div><ul type="disc" style="margin-bottom: 0cm; margin-top: 0cm;"><li class="MsoListParagraph" style="margin: 0cm; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt;">I want to change the grid numbers, I try to change the grid parameters in SIZE.h and data files, when I run the simulation, I had some error which is related to the bathy.bin file due to the changed grids. I am wondering what is a good way to change the grid numbers.<o:p></o:p></span></li><li class="MsoListParagraph" style="margin: 0cm; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt;">I try to open the bathy.bin file in Jupyter Notebook, however, it can not be opened,<o:p></o:p></span></li></ul><div style="margin: 0cm 0cm 0cm 36pt; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt;">Error: bathy.bin is not UTF-8 encoded saving disabled. See console for more details<o:p></o:p></span></div><ul type="disc" style="margin-bottom: 0cm; margin-top: 0cm;"><li class="MsoListParagraph" style="margin: 0cm; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt;">I am also curious about if I want to change the bottom topography, what should I do to modify it.<o:p></o:p></span></li></ul><div style="margin: 0cm; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt;">I hope you can give me some advice to solve the issues.<o:p></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt;"><o:p> </o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt;">Thank you very much, and have a good day!<o:p></o:p></span></div><div><p class="MsoNormal" style="margin: 0cm 0cm 6pt; font-size: 12pt; font-family: Aptos, sans-serif;"><b><span style="font-size: 11pt; font-family: Arial, sans-serif; color: rgb(0, 127, 163);"><o:p> </o:p></span></b></p><p class="MsoNormal" style="margin: 0cm 0cm 6pt; font-size: 12pt; font-family: Aptos, sans-serif;"><b><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(0, 127, 163);">Kind Regards<o:p></o:p></span></b></p><p class="MsoNormal" style="margin: 0cm 0cm 6pt; font-size: 12pt; font-family: Aptos, sans-serif;"><b><span style="font-size: 10.5pt; font-family: Arial, sans-serif; color: rgb(30, 55, 101);">Juncheng Zhang</span></b><span style="font-size: 10pt; font-family: Arial, sans-serif;"><br><span style="color: rgb(0, 127, 163);">PhD Student,<span class="Apple-converted-space"> </span><o:p></o:p></span></span></p><p class="MsoNormal" style="margin: 0cm 0cm 6pt; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(0, 127, 163);">Earth, Atmospheric, and Planetary Physics</span><span style="font-size: 10pt; font-family: Arial, sans-serif;"><br><br><span style="color: rgb(30, 55, 101);">Department of Physics<br>University of Toronto<br>McLennan Physical Laboratories<br>60 St Gorge St<br>Toronto, Ontario, M5S 1A7<br><br></span><a href="mailto:juncheng.zhang@mail.utoronto.ca"><span style="color: rgb(5, 99, 193);">juncheng.zhang@mail.utoronto.ca</span></a><br><br></span><a href="https://www.physics.utoronto.ca/"><b><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(0, 120, 148); text-decoration: none;"><span id="cid:image001.jpg@01DB1F56.BF7D25A0"><image001.jpg></span></span></b></a><span style="font-size: 10pt; font-family: Arial, sans-serif;"><o:p></o:p></span></p></div><div style="margin: 0cm; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; 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text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">MITgcm-support@mitgcm.org</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><a href="http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support</a></div></blockquote></div><br></div></body></html>