ADM1 Documentation Update #1116
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MarcusHolly
added
documentation
Codecov ReportPatch coverage has no change and project coverage change:
Additional details and impacted files@@ Coverage Diff @@
## main #1116 +/- ##
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+ Coverage 94.74% 94.92% +0.18%
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Files 331 331
Lines 32501 32501
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+ Hits 30792 30852 +60
+ Misses 1709 1649 -60 ☔ View full report in Codecov by Sentry. |
adam-a-a
reviewed
Aug 25, 2023
| @@ -139,13 +139,14 @@ Kinetic Parameters | |||
| "First-order decay rate for X_pro, k_dec_X_pro", ":math:`k_{dec,X_{pro}}`", "k_dec_X_pro", 0.02, ":math:`\text{d}^{-1}`" | |||
| "First-order decay rate for X_ac, k_dec_X_ac", ":math:`k_{dec,X_{ac}}`", "k_dec_X_ac", 0.02, ":math:`\text{d}^{-1}`" | |||
| "First-order decay rate for X_h2, k_dec_X_h2", ":math:`k_{dec,X_{h2}}`", "k_dec_X_h2", 0.02, ":math:`\text{d}^{-1}`" | |||
| "Water dissociation constant, KW", ":math:`KW`", "KW", 2.08e-14, ":math:`(\text{kmol/}\text{m}^3)^2`" | |||
| "Water dissociation constant, pKW", ":math:`pKW`", "pKW", 14, ":math:`\text{dimensionless}`" | |||
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Suggested change
| "Water dissociation constant, pKW", ":math:`pKW`", "pKW", 14, ":math:`\text{dimensionless}`" | |
| "Water dissociation constant, pKW", ":math:`pK_W`", "pKW", 14, ":math:`\text{dimensionless}`" |
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I was debating whether we should explicitly describe in terms of "negative logarithm of ..." but I see below in constraints that that gets spelled out, so perhaps this is good enough.
adam-a-a
reviewed
Aug 25, 2023
Comment on lines
209
to
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| "Mass concentration of valerate, va-", ":math:`C_{va,ref} = C_{va} (1 + \frac{S_{H}}{K_a_va})`" | ||
| "Mass concentration of butyrate, bu-", ":math:`C_{bu,ref} = C_{bu} (1 + \frac{S_{H}}{K_a_bu})`" | ||
| "Mass concentration of propionate, pro-", ":math:`C_{pro,ref} = C_{pro} (1 + \frac{S_{H}}{K_a_pro})`" | ||
| "Mass concentration of acetate, ac-", ":math:`C_{ac,ref} = C_{ac} (1 + \frac{S_{H}}{K_a_ac})`" | ||
| "Molar concentration of bicarbonate, HCO3", ":math:`pK_a_co2 = log(M_{co2}) - log(M_{hco3}) + pH`" | ||
| "Molar concentration of ammonia, NH3", ":math:`pK_a_IN = log(M_{nh4}) - log(M_{nh3}) + pH`" |
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I think you need curly braces for any math expressions that have more than one underscore. This is what is currently showing in readthedocs:
adam-a-a
reviewed
Aug 25, 2023
| "Mass concentration of acetate, ac-", ":math:`C_{ac} = \frac{K_{a,ac} * C_{ac,ref}}{K_{a,ac} + S_{H}}`" | ||
| "Molar concentration of bicarbonate, HCO3", ":math:`M_{hco3} = \frac{K_{a,co2} * \frac{C_{S_{IC},ref}}{12}}{K_{a,co2} + S_{H}}`" | ||
| "Molar concentration of ammonia, NH3", ":math:`M_{nh3} = \frac{K_{a,IN} * \frac{C_{S_{IN},ref}}{14}}{K_{a,IN} + S_{H}}`" | ||
| "Water dissociation constant constraint", ":math:`log(10^{-pKW}) = log(1e-14) + (\frac{55900}{R} * (\frac{1}{T_{ref}} - \frac{1}{T}))`" |
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Suggested change
| "Water dissociation constant constraint", ":math:`log(10^{-pKW}) = log(1e-14) + (\frac{55900}{R} * (\frac{1}{T_{ref}} - \frac{1}{T}))`" | |
| "Water dissociation constant constraint", ":math:`log(10^{-pKW}) = log(10^{-14}) + (\frac{55900}{R} * (\frac{1}{T_{ref}} - \frac{1}{T}))`" |
adam-a-a
reviewed
Aug 25, 2023
| "Mass concentration of acetate, ac-", ":math:`C_{ac} = \frac{K_{a,ac} * C_{ac,ref}}{K_{a,ac} + S_{H}}`" | ||
| "Molar concentration of bicarbonate, HCO3", ":math:`M_{hco3} = \frac{K_{a,co2} * \frac{C_{S_{IC},ref}}{12}}{K_{a,co2} + S_{H}}`" | ||
| "Molar concentration of ammonia, NH3", ":math:`M_{nh3} = \frac{K_{a,IN} * \frac{C_{S_{IN},ref}}{14}}{K_{a,IN} + S_{H}}`" | ||
| "Water dissociation constant constraint", ":math:`log(10^{-pKW}) = log(1e-14) + (\frac{55900}{R} * (\frac{1}{T_{ref}} - \frac{1}{T}))`" |
There was a problem hiding this comment.
Suggested change
| "Water dissociation constant constraint", ":math:`log(10^{-pKW}) = log(1e-14) + (\frac{55900}{R} * (\frac{1}{T_{ref}} - \frac{1}{T}))`" | |
| "Water dissociation constant constraint", ":math:`log(10^{-pKW}) = log(10^{-14}) + (\frac{55900}{R} * (\frac{1}{T_{ref}} - \frac{1}{T}))`" |
adam-a-a
reviewed
Aug 25, 2023
Comment on lines
281
to
286
| "Mass concentration of valerate, va-", ":math:`C_{va,ref} = C_{va} (1 + \frac{S_{H}}{K_a_va})`" | ||
| "Mass concentration of butyrate, bu-", ":math:`C_{bu,ref} = C_{bu} (1 + \frac{S_{H}}{K_a_bu})`" | ||
| "Mass concentration of propionate, pro-", ":math:`C_{pro,ref} = C_{pro} (1 + \frac{S_{H}}{K_a_pro})`" | ||
| "Mass concentration of acetate, ac-", ":math:`C_{ac,ref} = C_{ac} (1 + \frac{S_{H}}{K_a_ac})`" | ||
| "Molar concentration of bicarbonate, HCO3", ":math:`pK_a_co2 = log(M_{co2}) - log(M_{hco3}) + pH`" | ||
| "Molar concentration of ammonia, NH3", ":math:`pK_a_IN = log(M_{nh4}) - log(M_{nh3}) + pH`" |
There was a problem hiding this comment.
Check these again for the issue with more than one underscore in certain math expressions, requiring curly braces for properly displaying in readthedocs (see previous comment)
adam-a-a
requested changes
Aug 25, 2023
adam-a-a
approved these changes
Aug 29, 2023
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Summary/Motivation:
Updates ADM1 and Modified ADM1 documentation based on changes made in #1038
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