Split maintResp into soilMaintResp and microbeMaintResp for clarity

[dlebauer]

This is mostly to help avoid the confusion noted in this comment:

sipnet/src/sipnet/sipnet.c

Lines 1131 to 1132 in 1a7481b

	// TBD We seem to be conflating maintResp and rSoil in the non-microbe
	// case, need to dig in. With that said...

I think the issue is that 'maintResp' has two meanings because it operates at two levels of abstraction (with and w/o microbes). w/o microbes, rSoil = maintResp; with microbes, rSoil = maintResp + growthResp

If this is the case, the solution may simply be in naming, i.e. split fluxes.maintRespiration into distinct fluxes: fluxes.microbeMaintRespiration and fluxes.soilMaintRespiration for the different cases.

1. First - this is a tangent, but helps with clarity

de-conflate the base resp from the temp effect

sipnet/src/sipnet/sipnet.c

Lines 1165 to 1166 in 1a7481b

	tempEffect = params.baseMicrobeResp * pow(params.microbeQ10, tsoil / 10);
	fluxes.maintRespiration = envi.microbeC * moistEffect * tempEffect;

(since params.baseMicrobeResp is not part of the temp effect)
should be:

tempEffect = pow(params.microbeQ10, tsoil / 10);
fluxes.maintRespiration = envi.microbeC * params.baseMicrobeResp * moistEffect * tempEffect;

2. Then de-conflate the different modes of maintresp (soil vs microbe), split fluxes.maintRespiration into fluxes.microbeMaintRespiration and fluxes.soilMaintRespiration :

tempEffect = pow(params.microbeQ10, tsoil / 10);
fluxes.microbeMaintRespiration = envi.microbeC * params.baseMicrobeResp * moistEffect * tempEffect;

And

sipnet/src/sipnet/sipnet.c

Lines 1227 to 1234 in 1a7481b

	envi.microbeC += (microbeEff * fluxes.microbeIngestion + fluxes.soilPulse -
	fluxes.maintRespiration) *
	climate->length;
	// rSoil is maintenance resp + growth (microbe) resp
	// :: from [4], eq (5.10) for microbe term
	fluxes.rSoil =
	fluxes.maintRespiration + (1 - microbeEff) * fluxes.microbeIngestion;

becomes

    envi.microbeC += (microbeEff * fluxes.microbeIngestion + fluxes.soilPulse -
                      fluxes.microbeMaintRespiration) *
                     climate->length;

    fluxes.rSoil =
                    fluxes.microbeMaintRespiration + (1 - microbeEff) * fluxes.microbeIngestion;

2.3 Analogously in the soil resp case

sipnet/src/sipnet/sipnet.c

Lines 1169 to 1170 in 1a7481b

	tempEffect = params.baseSoilResp * pow(params.soilRespQ10, tsoil / 10);
	fluxes.maintRespiration = envi.soil * moistEffect * tempEffect;

becomes

    tempEffect = pow(params.soilRespQ10, tsoil / 10);
    fluxes.soilMaintRespiration = envi.soil * params.baseSoilResp * moistEffect * tempEffect;

and finally,

sipnet/src/sipnet/sipnet.c

Line 1239 in 1a7481b

fluxes.rSoil = fluxes.maintRespiration;

Becomes

fluxes.soilMaintRespiration = envi.soil * moistEffect * tempEffect;
// and 
fluxes.rSoil = fluxes.soilMaintRespiration;