AME9.3enterpriseThuFeb26162626GMT2009node00402node00403node00404node00405node00406node00407node00408node00409node00410node00411node00412node00413node00414node00415node00416node00417node00418truec3 photosynthesisNet rate of photosynthesis is the minimum of the rates calculated under rubisco limitation and RuBP regeneration limitation. <fileref name="edited photosynthesis.f95" line="81" > Value returned from model. </fileref>trueNet rate of leaf photosynthesis (micromol CO2 m-2 leaf s_1)al_net rate leaf photosynthesistruefn3if (sqrt_error_flag == 1) then av_rub_limited_photosyn else min(av_rub_limited_photosyn, aj_RuBP_regen_limited_photosyn)1av_rub_limited_photosyneqsqrt_error_flag1minav_rub_limited_photosynaj_RuBP_regen_limited_photosyn<fileref name="edited photosynthesis.f95" line="1" > Value passed to model. </fileref>trueExperimental atmospheric CO2 partial pressure (Pa)ca_atmos co2truefn436136<fileref name="edited photosynthesis.f95" line="1" > Value passed to model. </fileref>trueLeaf temperature (oC)tc_leaf temptruefn620120<fileref name="edited photosynthesis.f95" line="33" />trueCO2 compensation point of photosynthesis in the absence of mitochondrial respiration (Pa)gammastar_co2 comp point without mit resptruefn73.69 + 0.188 * (tc_leaf_temp - 25) + 0.0036 * ((tc_leaf_temp -25)^2)13.690.188tc_leaf_temp250.0036tc_leaf_temp252<fileref name="edited photosynthesis.f95" line="40" />trueIntercellular CO2 partial pressure (Pa)ci_intercell co2truefn120.7 * ca_atmos_co210.7ca_atmos_co2<fileref name="edited photosynthesis.f95" line="1" > Value passed to model. </fileref>truePhotosynthetic rubisco capacity per unit leaf area at 25oC (micomol CO2 m-2 s-1)vlmax25_photosyn rub captruefn1319119<fileref name="edited photosynthesis.f95" line="13" />trueUniversal gas constant (J mol-1 k-1)r_gas consttruefn148.31418.314border1node00001node00002node00003node00101node00102node00419node00420node00421node00422node00423node00424node00425node00426node00427node00428node00429node00430node00431node00432node00433node00434node00435node00436node00437node00438node00439node00440node00441node00442node00443node00444node00445node00446node00447node00448node00449node00450node00451node00452node00453node00454node00455node00456node00457node00458node00459node00460truewhitecalc rate of photosynthesis limited by RuBP (ribulose bis-phosphate) regeneration<fileref name="edited photosynthesis.f95" fromline="68" toline="70" />trueFlag that indicates that a term to be square rooted is negativesqrt error flagtruefn1if (rho <= 0) then 1 else 0int1leqrho00border1Enables the user to see how many times an error occured during a simulation without having to view the "sqrt error flag" at each integration step. <fileref name="edited photosynthesis.f95" fromline="68" toline="70" />trueNumber of times error occured during simulationnum errorstruefn101prev(1) + sqrt_error_flagintprev1sqrt_error_flag<fileref name="edited photosynthesis.f95" line="74" />trueRate of photosynthesis limited by RuBP (ribulose bis-phosphate) regeneration (micromol CO2 m-2 leaf s_1)aj_RuBP regen limited photosyntruefn2num = jl_electron_transport * (ci_intercell_co2 - gammastar_co2_comp_point_without_mit_resp), denom = 4 * (ci_intercell_co2 + 2 * gammastar_co2_comp_point_without_mit_resp), num / denom1wherenumjl_electron_transportci_intercell_co2gammastar_co2_comp_point_without_mit_respdenom4ci_intercell_co22gammastar_co2_comp_point_without_mit_respnumdenom<fileref name="edited photosynthesis.f95" line="1" > Value passed to model. </fileref>trueTotal absorbed PAR (photosynthetically active radiation ) per unit leaf area (micromol m-2 s-1)il_total absorbed partruefn81201120<fileref name="edited photosynthesis.f95" line="36" />trueSpectral correction factor. PAR absorbed by other tissue than the chloroplast lamella.fspec_spectral correctiontruefn90.1510.15<fileref name="edited photosynthesis.f95" line="38" />truePhotosynthetically active radiation (PAR) effectively absorbed by PSII (photosystem II) (micromol m-2 s-1)ile_par absorbed psiitruefn10il_total_absorbed_par * (1 - fspec_spectral_correction) / 21il_total_absorbed_par1fspec_spectral_correction2<fileref name="edited photosynthesis.f95" line="45" />truePotential rate of electron transport per unit leaf area at 25oC (micromol m-2 s-1)jm25_pot elec transport 25octruefn242.1 * vlmax25_photosyn_rub_cap12.1vlmax25_photosyn_rub_cap<fileref name="edited photosynthesis.f95" line="52" />trueActivation energy for jm25 (kJ mol-1)eajm_act energy jm25truefn2537000137000<fileref name="edited photosynthesis.f95" line="47" />trueCurvature parameter of Jm (J mol-1)h_curvature param of jmtruefn262200001220000<fileref name="edited photosynthesis.f95" line="50" />trueElectron transport temperature response parameter (J K-1 mol-1)s_elec trans temp resptruefn277101710<fileref name="edited photosynthesis.f95" line="58" />truePotential rate of electron transport per unit leaf area (micromol m-2 s-1)jm_pot elec transporttruefn28jm25_pot_elec_transport_25oc * term1 * term2 / term31jm25_pot_elec_transport_25octerm1term2term3<fileref name="edited photosynthesis.f95" line="61" />trueCurvature of leaf response of electron transport to irradiance (dimensionless)thetal_curve respon elec to irradtruefn290.710.7<fileref name="edited photosynthesis.f95" line="66" />trueIntermediate calc used in quadratic formula for finding jlaatruefn30thetal_curve_respon_elec_to_irrad1thetal_curve_respon_elec_to_irrad<fileref name="edited photosynthesis.f95" line="64" />trueIntermediate calc used in quadratic formula for finding jlbbtruefn31-1 * (ile_par_absorbed_psii + jm_pot_elec_transport)11ile_par_absorbed_psiijm_pot_elec_transport<fileref name="edited photosynthesis.f95" line="65" />trueIntermediate calc used in quadratic formula for finding jlcctruefn32ile_par_absorbed_psii * jm_pot_elec_transport1ile_par_absorbed_psiijm_pot_elec_transport<fileref name="edited photosynthesis.f95" line="67" />trueIntermediate calc used in quadratic formula for finding jl (it is the term in the square root)rhotruefn33bb^2 - 4 * aa * cc1bb24aaccjl is obtained through the resolution of the equation: thetal * j^2 - (ile + jm) * j + ile * jm = 0 The solution is found using the standard quadratic formula. If the term in the square root of the formula (stored in variable "rho") is negative then there is no physically meaningful solution. Under these conditions "sqrt error flag" is set to 1 which sets "jl_electron transport" and aj_RuBP regen limited photosyn" to zero. The error flag also causes "al_net rate leaf photosynthesis" to be set to "av_rub limited photosyn". <fileref name="edited photosynthesis.f95" fromline="62" toline="71" > The Fortran program did not trap the square root error but relied on the generation of "not a number (NaN)" which caused the same effects as the flag system used in the Simile version. The Fortran just printed an error message to the screen. Also note that the message was printed when "rho <= 0" , the Simile version therefore also traps the 0. </fileref>trueElectron transportjl_electron transporttruejl_0if (sqrt_error_flag == 1) then 0 else (-1 * bb - sqrt(rho)) / (2 * aa)10eqsqrt_error_flag11bbsqrtrho2aa<fileref name="edited photosynthesis.f95" line="55" />trueIntermediate calc for jmterm1truefn35num = eajm_act_energy_jm25 * (tc_leaf_temp - 25), denom = 298 * r_gas_const * (tc_leaf_temp + 273), exp(num / denom)1wherenumeajm_act_energy_jm25tc_leaf_temp25denom298r_gas_consttc_leaf_temp273expnumdenom<fileref name="edited photosynthesis.f95" line="56" />trueIntermediate calc for jmterm2truefn36num = s_elec_trans_temp_resp * 298 - h_curvature_param_of_jm, denom = r_gas_const * 298, 1 + exp(num / denom)1wherenums_elec_trans_temp_resp298h_curvature_param_of_jmdenomr_gas_const2981expnumdenom<fileref name="edited photosynthesis.f95" line="57" />trueIntermediate calc for jmterm3truefn37num = s_elec_trans_temp_resp * (273 + tc_leaf_temp) - h_curvature_param_of_jm, denom = r_gas_const * (273 + tc_leaf_temp), 1 + exp(num / denom)1wherenums_elec_trans_temp_resp273tc_leaf_temph_curvature_param_of_jmdenomr_gas_const273tc_leaf_temp1expnumdenomborder1border2border3border4border5border6node00461node00462node00463node00464node00465node00466node00467node00468node00469node00470node00471node00472node00473node00474node00475node00476node00477node00478node00479node00480node00481node00482node00483node00484node00485node00486node00487node00488truewhitecalc rate of photosynthesis limited by rubisco<fileref name="edited photosynthesis.f95" line="42" />trueRubisco-limited photosynthesis (micromol CO2 m-2 leaf s_1)av_rub limited photosyntruefn1num = ci_intercell_co2 - gammastar_co2_comp_point_without_mit_resp, denom = ci_intercell_co2 + kprim_effective_mm_rub, vlmax_leaf_temp_photosyn_rub_cap * (num / denom)1wherenumci_intercell_co2gammastar_co2_comp_point_without_mit_respdenomci_intercell_co2kprim_effective_mm_rubvlmax_leaf_temp_photosyn_rub_capnumdenom<fileref name="edited photosynthesis.f95" line="27" />trueEffective Michaelis-Menten constant of Rubisco (Pa)kprim_effective mm rubtruefn51kc_leaf_temp_mm_rub_co21o2_partial_pressureko_leaf_temp_mm_rub_o2<fileref name="edited photosynthesis.f95" line="15" />trueOxygen partial pressure (Pa)o2_partial pressuretruefn1520500120500<fileref name="edited photosynthesis.f95" line="20" />trueMichaelis-Menten constant of Rubisco for CO2 at leaf temperature (Pa)kc_leaf temp mm rub co2truefn16num=eakc_act_energy_kc25*(tc_leaf_temp-25),denom=298*r_gas_const*(tc_leaf_temp+273),kc25_mic_ment_rub_co2*exp(num/denom)1wherenumeakc_act_energy_kc25tc_leaf_temp25denom298r_gas_consttc_leaf_temp273kc25_mic_ment_rub_co2expnumdenom<fileref name="edited photosynthesis.f95" line="17" />trueMichaelis-Menten constant of Rubisco for CO2 at 25oC (Pa)kc25_mic ment rub co2truefn1740.4140.4<fileref name="edited photosynthesis.f95" line="19" />trueActivation energy for kc25 (kJ mol-1)eakc_act energy kc25truefn1859400159400<fileref name="edited photosynthesis.f95" line="25" />trueMichaelis-Menten constant of Rubisco for O2 at leaf temperature (Pa)ko_leaf temp mm rub o2truefn19num=eako_act_energy_ko25*(tc_leaf_temp-25),denom=298*r_gas_const*(tc_leaf_temp+273),ko25_mic_ment_rub_o2*exp(num/denom)1wherenumeako_act_energy_ko25tc_leaf_temp25denom298r_gas_consttc_leaf_temp273ko25_mic_ment_rub_o2expnumdenom<fileref name="edited photosynthesis.f95" line="22" />trueMichaelis-Menten constant of Rubisco for O2 at 25oC (Pa)ko25_mic ment rub o2truefn2024800124800<fileref name="edited photosynthesis.f95" line="24" />trueActivation energy for ko25 (kJ mol-1)eako_act energy ko25truefn2136000136000<fileref name="edited photosynthesis.f95" line="30" />truePhotosynthetic rubisco capacity per unit leaf area at leaf temperature (micomol CO2 m-2 s-1)vlmax_leaf temp photosyn rub captruefn22num = eavlmax_act_energy_vlmax25 * (tc_leaf_temp - 25), denom = 298 * r_gas_const * (tc_leaf_temp + 273), vlmax25_photosyn_rub_cap * exp(num / denom)1wherenumeavlmax_act_energy_vlmax25tc_leaf_temp25denom298r_gas_consttc_leaf_temp273vlmax25_photosyn_rub_capexpnumdenom<fileref name="edited photosynthesis.f95" line="29" />trueActivation energy for vlmax25 (kJ mol-1)eavlmax_act energy vlmax25truefn2364800164800border7border8border9border10border11border12i3i4i6i7truei201nonein_hierarchytc_leaf_temp1i12truei204nonein_hierarchyca_atmos_co21i13i14truei304nonein_hierarchysqrt_error_flaginttruei102truei209nonein_hierarchyvlmax25_photosyn_rub_cap1truei213nonein_hierarchytc_leaf_temp1truei214nonein_hierarchyr_gas_const1truei405nonein_hierarchyci_intercell_co21truei406nonein_hierarchygammastar_co2_comp_point_without_mit_resp1truei408nonein_hierarchyaj_RuBP_regen_limited_photosyn1i1truei505i101truei503nonein_hierarchysqrt_error_flaginti2i8i9i10truei202nonein_hierarchyil_total_absorbed_par1truei203nonein_hierarchyfspec_spectral_correction1i24i25i26i27i28truei222nonein_hierarchyjm25_pot_elec_transport_25oc1i29i30truei305nonein_hierarchythetal_curve_respon_elec_to_irrad1i31truei301nonein_hierarchyile_par_absorbed_psii1truei302nonein_hierarchyjm_pot_elec_transport1i32truei303nonein_hierarchyile_par_absorbed_psii1truei304nonein_hierarchyjm_pot_elec_transport1truei102nonein_hierarchyrho1i33truei306nonein_hierarchybb1truei307nonein_hierarchyaa1truei308nonein_hierarchycc1truei404nonein_hierarchyjl_electron_transport1truei103nonein_hierarchysqrt_error_flaginti34truei401nonein_hierarchyrho1truei402nonein_hierarchybb1truei403nonein_hierarchyaa1truei223nonein_hierarchyterm11i35truei210nonein_hierarchyeajm_act_energy_jm251truei224nonein_hierarchyterm21i36truei215nonein_hierarchys_elec_trans_temp_resp1truei216nonein_hierarchyh_curvature_param_of_jm1truei225nonein_hierarchyterm31i37truei218nonein_hierarchys_elec_trans_temp_resp1truei220nonein_hierarchyh_curvature_param_of_jm1truei408nonein_hierarchyaj_RuBP_regen_limited_photosyn1truei405nonein_hierarchyci_intercell_co21truei406nonein_hierarchygammastar_co2_comp_point_without_mit_resp1truei209nonein_hierarchyvlmax25_photosyn_rub_cap1truei217nonein_hierarchyr_gas_const1truei221nonein_hierarchyr_gas_const1truei214nonein_hierarchyr_gas_const1truei219nonein_hierarchytc_leaf_temp1truei213nonein_hierarchytc_leaf_temp1truei206nonein_hierarchyci_intercell_co21truei207nonein_hierarchygammastar_co2_comp_point_without_mit_resp1truei407nonein_hierarchyav_rub_limited_photosyn1truei103nonein_hierarchytc_leaf_temp1truei104nonein_hierarchyr_gas_const1truei112nonein_hierarchyvlmax25_photosyn_rub_cap1i1truei208nonein_hierarchykprim_effective_mm_rub1i5truei111nonein_hierarchyo2_partial_pressure1i15truei109nonein_hierarchykc_leaf_temp_mm_rub_co21i16truei101nonein_hierarchykc25_mic_ment_rub_co21i17truei102nonein_hierarchyeakc_act_energy_kc251i18truei110nonein_hierarchyko_leaf_temp_mm_rub_o21i19truei105nonein_hierarchyko25_mic_ment_rub_o21i20truei106nonein_hierarchyeako_act_energy_ko251i21truei205nonein_hierarchyvlmax_leaf_temp_photosyn_rub_cap1i22truei113nonein_hierarchyeavlmax_act_energy_vlmax251i23truei407nonein_hierarchyav_rub_limited_photosyn1truei206nonein_hierarchyci_intercell_co21truei207nonein_hierarchygammastar_co2_comp_point_without_mit_resp1truei104nonein_hierarchyr_gas_const1truei108nonein_hierarchyr_gas_const1truei114nonein_hierarchyr_gas_const1truei103nonein_hierarchytc_leaf_temp1truei107nonein_hierarchytc_leaf_temp1truei115nonein_hierarchytc_leaf_temp1truei112nonein_hierarchyvlmax25_photosyn_rub_cap1