Debugging the Chemistry with slot_keep

After running a complete ProDiMo model, one can re-run a selected (ix,iz)-point in analysis mode with verbose=2 and chemanalysis=T to better understand what is going on, for example why a certain point is so slow.
We are using the molecular_clouds_models-setup like this

.true.      ! restart
.true.      ! mc_only
.false.     ! time_chem_disk
.true.      ! mc_steady_state
.true.      ! mc_thermal_balance
.true.      ! Xray_mc
.true.      ! slot_keep
17          ! slot_ix
12          ! slot_iz
.true.      ! chemanalysis
2           ! verbose_level

In which case ProDiMo sets up the disk via restart, and then uses the density, temperatures, radiation field, column densities etc. at point (slot_ix,slot_iz), and proceeds with the determination of the chemistry at that point. Using verbose=2 helps to understand what is going on. When it's finished, you can go into the chemical analysis mode where you can check which molecule is produced and destroyed by what processes and rates.

There are these further options:

  • time_chem_disk=T, mc_steady_state=F, mc_thermal_balance=F, molecular_cloud=F

    advance the chemistry from initial concentrations given in Species.in * time_chem_disk=T, mc_steady_state=F, mc_thermal_balance=F, molecular_cloud=T

    advance the chemistry from initial concentrations given in Molecular_cloud.out * time_chem_disk=F, mc_steady_state=T, mc_thermal_balance=F

    solve the chemistry once for given Tgas * time_chem_disk=F, mc_steady_state=T, mc_thermal_balance=T

    solve the chemistry multiple times, until heating==cooling is achieved.

If you set mc_steady_state=T, the initial concentrations are taken from the restart at that point, but if you say time_chem_disk=F it uses the initial concentrations from the grid-point above, from restart, as it would do during an ordinary run of ProDiMo. But by setting mc_steady_state=T, time_chem_disk=T you can solve the chemistry from the initial concentrations stored in the restart at (slot_ix,slot_iz).

If you want to study the time-dependent chemistry, set time steps like this:

104         ! N_age_mc
1.e-20 1.e-18 1.e-16 1.e-15 1.00000e-14 1.66810e-14 2.78256e-14 4.64159e-14 7.74263e-14 1.29155e-13 2.15444e-13 3.59381e-13 5.99485e-13 1.00000e-12 1.66810e-12 2.78256e-12 4.64159e-12 7.74264e-12 1.29155e-11 2.15444e-11 3.59382e-11 5.99484e-11 9.99999e-11 1.66810e-10 2.78256e-10 4.64158e-10 7.74264e-10 1.29155e-09 2.15443e-09 3.59381e-09 5.99485e-09 1.00000e-08 1.66810e-08 2.78256e-08 4.64159e-08 7.74263e-08 1.29155e-07 2.15444e-07 3.59381e-07 5.99484e-07 9.99999e-07 1.66810e-06 2.78256e-06 4.64159e-06 7.74264e-06 1.29155e-05 2.15443e-05 3.59381e-05 5.99484e-05 0.000100000 0.000166810 0.000278256 0.000464158 0.000774263 0.00129155 0.00215443 0.00359381 0.00599483 0.00999999 0.0166810 0.0278256 0.0464159 0.0774262 0.129155 0.215443 0.359381 0.599484 1.00000 1.66810 2.78255 4.64159 7.74263 12.9155 21.5443 35.9381 59.9483 99.9997 166.810 278.256 464.158 774.264 1291.55 2154.43 3593.80 5994.84 9999.98 16681.0 27825.6 46415.8 77426.2 129155. 215443. 359381. 599482. 999999. 1.66810e+06 2.78255e+06 4.64159e+06 7.74262e+06 1.29155e+07 2.15443e+07 3.59381e+07 5.99483e+07 9.99996e+07