darwin3 |
|
|
|
|||
Warning, /doc/phys_pkgs/darwin_growth.rst is written in an unsupported language. File is not indexed.
view on githubraw file Latest commit faa67d17 on 2022-01-31 17:00:48 UTCa4f2018aab Oliv*0001 .. include:: ../defs.hrst 0002 0003 .. _Growth: 0004 0005 Growth 0006 ^^^^^^ 0007 0008 Without :varlink:`DARWIN_ALLOW_GEIDER`, the carbon-specific growth rate is 0009 0010 .. math:: 0011 0012 P^{\mathrm{C}}_j = P_{{\mathrm{C}},j}^{\max} \gamma^{\op{nut}}_j 0013 \gamma^{\op{light}}_j f^{{{\text{phy}}}}_j(T) \gamma_{\op{pCO2}} 0014 0015 where 0016 0017 .. math:: 0018 0019 \gamma^{\op{light}}_j = (1 - \mathrm{e}^{-k^{\op{sat}}_{\op{PAR}j} I}) \cdot 0020 \mathrm{e}^{-k^{\op{inh}}_{\op{PAR}j} I} \cdot n^{\op{light}}_j 0021 0022 and :math:`n^{\op{light}}_j` normalizes the maximum of 0023 :math:`\gamma^{\op{light}}_j` with respect to :math:`I` to unity. For 0024 :math:`\gamma^{\op{nut}}_j`, see :numref:`Uptake`, for 0025 :math:`f^{\op{phy}}_j(T)`, see :numref:`Temperature`. 0026 :math:`\gamma_{\op{pCO2}}` is currently set to 1 in the code. 0027 0028 .. 0029 n^{\op{light}}_j = \frac{k^{\op{sat}}_{\op{PAR}j}+k^{\op{inh}}_{\op{PAR}j}} 0030 {k^{\op{sat}}_{\op{PAR}j}} 0031 \left( \frac{k^{\op{inh}}_{\op{PAR}j}}{k^{\op{sat}}_{\op{PAR}j} 0032 + k^{\op{inh}}_{\op{PAR}j}} 0033 \right)^{-k^{\op{inh}}_{\op{PAR}j}/k^{\op{sat}}_{\op{PAR}j}} 0034 0035 0036 With :varlink:`DARWIN_ALLOW_GEIDER`, 0037 0038 .. math:: 0039 0040 P^{\mathrm{C}}_j = P^{{\mathrm{C}}{\op{m}}}_j \left( 0041 1 - \exp\left\{ -\frac{\gamma^{\op{QFe}}_j 0042 \langle\alpha I\rangle_j 0043 \op{Chl\text{:}C}_j }{ P^{{\mathrm{C}}{\op{m}}}_j } 0044 \right\} 0045 \right) \gamma^{{{\text{inhib}}}}_j 0046 \qquad\text{if } I_{\op{tot}}>I_{\min} 0047 0048 where 0049 0050 .. math:: 0051 0052 \langle\alpha I\rangle_j = \sum_{l=1}^{\op{nlam}} \alpha^{\op{Chl}}_{j,l} I_l 0053 \quad\text{and}\quad 0054 I_{\op{tot}} = \sum_{l=1}^{\op{nlam}} I_l 0055 0056 and :math:`I_l` is photosynthetically active radiation. The Chlorophyll 0057 a-specific initial slope of the photosynthesis-light curve is computed from the 0058 maximum quantum yield of carbon fixation and the coefficient of absorption by faa67d1773 Oliv*0059 photosynthetically active pigments (see :numref:`Spectral`), a4f2018aab Oliv*0060 0061 .. math:: 0062 0063 \alpha^{\op{Chl}}_{j,l} = \Phi_{\op{m}j} a^{\op{chl}}_{\op{ps}j,l} 0064 \;. 0065 0066 Without the radtrans package, spectral PAR, :math:`I_l`, is replaced by total 0067 PAR and the spectral absorption coefficient by an average one, 0068 :varlink:`aphy_chl_ave`. The maximum growth rate is 0069 0070 .. math:: 0071 0072 P^{{\mathrm{C}}{\op{m}}}_j = P_{{\mathrm{C}},j}^{\max} \gamma^{\op{nut}}_j 0073 f^{{{\text{phy}}}}_j(T) \gamma_{\op{pCO2}} 0074 \;. 0075 0076 The iron limitation term, :math:`\gamma^{\op{QFe}}_j`, is discussed in 0077 :numref:`Uptake`. 0078 0079 With :varlink:`DARWIN_ALLOW_CHLQUOTA`, :math:`\op{Chl\text{:}C}_j` is computed 0080 from plankton Chlorophyll and carbon tracers. Without, 0081 0082 .. math:: 0083 0084 \op{Chl\text{:}C}_j = \op{Chl\text{:}C}_j^{\op{acclim}} 0085 faa67d1773 Oliv*0086 where 0087 a4f2018aab Oliv*0088 .. math:: faa67d1773 Oliv*0089 :label: chl2cacclim a4f2018aab Oliv*0090 0091 \op{Chl\text{:}C}_j^{\op{acclim}} = \left[ 0092 \frac{\op{Chl\text{:}C}^{\max}_j} 0093 {1 + \op{Chl\text{:}C}^{\max}_j\langle\alpha I\rangle_j 0094 /(2P^{{\mathrm{C}}{\op{m}}}_j)} 0095 \right]_{\op{Chl\text{:}C}^{\min}_j}^{\op{Chl\text{:}C}^{\max}_j} 0096 0097 If :math:`P^{{\mathrm{C}}{\op{m}}}_j=0`, we set 0098 :math:`\op{Chl\text{:}C}_j^{\op{acclim}}=\op{Chl\text{:}C}^{\min}_j`. With the 0099 readtrans package, 0100 0101 .. math:: 0102 0103 \op{Chl\text{:}C}^{\min}_j = \frac{\op{Chl\text{:}C}^{\max}_j} 0104 { 1 + 2000 \op{Chl\text{:}C}^{\max}_j \overline\alpha_j 0105 /(2 P^{\max}_{\op{C},j}) } 0106 \;, 0107 0108 otherwise zero. Here, 0109 0110 .. math:: 0111 0112 \overline{\alpha}_j = \sum_l \Delta\lambda_l \alpha^{\op{Chl}}_{j,l} \Big/ 0113 \sum_l \Delta\lambda_l 0114 \;. 0115 0116 Photo inhibition is parameterized as 0117 0118 .. math:: 0119 0120 \gamma^{{{\text{inhib}}}}_j = \begin{cases} 0121 c^{\op{inhib}}_j \cdot \op{EkoverE} & \text{if } \op{EkoverE} \le 1 \\ 0122 1 & \text{otherwise} 0123 \end{cases} 0124 0125 where 0126 0127 .. math:: 0128 0129 \op{EkoverE} = \frac{P^{{\mathrm{C}}{\op{m}}}_j/(\op{Chl\text{:}C}_j\cdot\overline{\alpha}_j)} 0130 {\langle\alpha I\rangle_j/\overline{\alpha}_j} 0131 \;. 0132 0133 :numref:`tab_phys_pkgs_darwin_growth` summarized the parameters relevant for 0134 growth. 0135 0136 .. csv-table:: Growth parameters 0137 :delim: & 0138 :widths: auto 0139 :class: longtable 0140 :header: Trait, Param, Symbol, Default, Units, Description 0141 :name: tab_phys_pkgs_darwin_growth 0142** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 144.
0143 :varlink:`ksatPAR` & :varlink:`a_ksatPAR` & :math:`k^{\op{sat}}_{\op{PAR}}` & 0.012 & m\ :sup:`2` s μEin\ :sup:`-1` & saturation coefficient for PAR** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 145.
0144 :varlink:`kinhPAR` & :varlink:`a_kinhPAR` & :math:`k^{\op{inh}}_{\op{PAR}}` & 0.006 & m\ :sup:`2` s μEin\ :sup:`-1` & inhibition coefficient for PAR faa67d1773 Oliv*0145 :varlink:`PCmax` & :varlink:`a <a_PCmax>`,\ :varlink:`b_PCmax` & :math:`P^{\op{max}}_{\op{C}j}` & (1/day) V\ :sup:`--0.15` & 1/s & maximum carbon-specific growth rate a4f2018aab Oliv*** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 147.
0146 & :varlink:`PARmin` & :math:`I_{\min}` & 0.1 & μEin/m\ :sup:`2`/s & minimum light for photosynthesis** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 148.
0147 :varlink:`mQyield` & :varlink:`a_mQyield` & :math:`\Phi_j` & 0.000075 & mmol C (μEin)\ :sup:`-1` & maximum quantum yield 0148 :varlink:`chl2cmax` & :varlink:`a_chl2cmax` & :math:`\op{Chl\text{:}C}^{\op{max}}_j` & 0.3 & mg Chl (mmol C)\ :sup:`-1` & maximum Chlorophyll-carbon ratio 0149 :varlink:`inhibGeider` & :varlink:`a_inhibGeider` & :math:`c^{\op{inhib}}_j` & 0.0 & & photo-inhibition coefficient for Geider growth 0150 :varlink:`aphy_chl_ps` & :varlink:`aphy_chl_ps_type` & :math:`a^{\op{chl}}_{\op{ps}j,l}` & read in & m\ :sup:`2` (mg Chl)\ :sup:`-1` & absorption by PS active pigments 0151 0152 :varlink:`aphy_chl_ps` is assigned from :varlink:`aphy_chl_ps_type` via 0153 :varlink:`grp_aptype`. The type-specific spectra are read in from 0154 :varlink:`darwin_phytoAbsorbFile` and optionally scaled allometrically, see 0155 :ref:`allomSpectra`. 0156
| [ Source navigation ] | [ Diff markup ] | [ Identifier search ] | [ general search ] |
|
This page was automatically generated from https://github.com/darwinproject/darwin3 by the 2.3.7-MITgcm-0.1 LXR engine. The LXR team |
|