1) If you define any NCAP_AFC (i.e. a flow-based availability factor), your capacity will be flow-based. To have the capacity instead represent the amount of storable energy, you should not define it to be flow-based. And, when the capacity is the amount of storable energy, of course the Var_Fin, Var_Fout and Var_Act are usually all larger than the capacity (unless you would have only a one storage cycle in a year/season). For example, many batteries are typically charged/discharged on a daily basis, and not only once per year or season. For a DAYNITE storage, the input/output flows thus obviously become usually much larger than the capacity, as described in the documentation. For example, if the summer season is 92 days long, and the DAYNITE cycle under it is a representative summer day, assume that a certain storage is fully charged and discharged once each day. Then the input/output flows within the summer would be 92 times as high as the capacity.
2) I am not able to confirm you findings. If I put NCAP_AFC=1 (and STG_EFF=1, PRC_CAPACT=1), I am getting capacity equal to Var_Fout as you said, but if I define NCAP_AFC=0.33, I am getting capacity equal to Var_Fout/0.33. Thus, I am not seeing the capacity unit changing from PJ to GW, as you claimed. Please provide a reproducible test case demonstrating the issue.
3) You are not saying which table you are using (e.g ~TFM_INS, ~FI_T), but looking at 2), it looks like you are already able to define NCAP_AFC. There is no difference in defining it for the input or output commodity (unless they are the same, but you said you have them different). Thus, I don't quite understand the question, and perhaps it would indeed be better to post it on the VEDA Forum. Anyway, I just made a quick test with a ~TFM_INS, and specifying the commodity for NCAP_AFC worked equally well both in the Cset_CN and the Other_Indexes column.
4) The PCG of a storage process should include the charged and discharged commodities. So, if you have com1 as a charged commodity and com2 as a discharged commodity, you should thus define them both in the PCG. If they are both of type NRG, usually defining PCG=NRG would be the best choice.
5) Yes, if STG_EFF=1 and STG_LOSS=0 and PRC_ACTFLO©=1, Var_Act (T1)+Var_FIn(T1)−Var_FOut(T1) = Var_Act(T2), in consecutive time slices T1 and T2, as you can see from the equation formulation presented in the documentation.
2) I am not able to confirm you findings. If I put NCAP_AFC=1 (and STG_EFF=1, PRC_CAPACT=1), I am getting capacity equal to Var_Fout as you said, but if I define NCAP_AFC=0.33, I am getting capacity equal to Var_Fout/0.33. Thus, I am not seeing the capacity unit changing from PJ to GW, as you claimed. Please provide a reproducible test case demonstrating the issue.
3) You are not saying which table you are using (e.g ~TFM_INS, ~FI_T), but looking at 2), it looks like you are already able to define NCAP_AFC. There is no difference in defining it for the input or output commodity (unless they are the same, but you said you have them different). Thus, I don't quite understand the question, and perhaps it would indeed be better to post it on the VEDA Forum. Anyway, I just made a quick test with a ~TFM_INS, and specifying the commodity for NCAP_AFC worked equally well both in the Cset_CN and the Other_Indexes column.
4) The PCG of a storage process should include the charged and discharged commodities. So, if you have com1 as a charged commodity and com2 as a discharged commodity, you should thus define them both in the PCG. If they are both of type NRG, usually defining PCG=NRG would be the best choice.
5) Yes, if STG_EFF=1 and STG_LOSS=0 and PRC_ACTFLO©=1, Var_Act (T1)+Var_FIn(T1)−Var_FOut(T1) = Var_Act(T2), in consecutive time slices T1 and T2, as you can see from the equation formulation presented in the documentation.