Chemical analysis examples
Steady-state model
[74]:
## FIXME: The notebook could use some more inline documentation and explanations
## FIXME: It also uses some random models, use the reference example model instead
/Users/work/miniforge3/envs/prodimo/lib/python3.13/site-packages/IPython/extensions/deduperreload/deduperreload.py:290: DeprecationWarning: ast.Ellipsis is deprecated and will be removed in Python 3.14; use ast.Constant instead
elif not isinstance(ast_elt, (ast.Ellipsis, ast.Pass)):
[75]:
#%%bash
#mkdir chemanaexp
#cd chemanaexp
#wget https://raw.githubusercontent.com/saint-germain/prodimopy_test/master/notebooks/Reactions.out
#wget https://github.com/saint-germain/prodimopy_test/raw/master/notebooks/chemanalysis.out.zip
#wget https://github.com/saint-germain/prodimopy_test/raw/master/notebooks/test_TT_model.zip
#unzip chemanalysis.out.zip
#unzip test_TT_model.zip
[76]:
import prodimopy.read as pread
import prodimopy.plot as pplot
import prodimopy.plot_models as pplotm
pplot.load_style("nb")
INFO: Load prodimopynb mplstyle from package.
[77]:
model=pread.read_prodimo("chemanaexp")
pp=pplot.Plot(None)
READ: Reading File: chemanaexp/ProDiMo.out ...
READ: Reading File: chemanaexp/Species.out ...
READ: Reading File: chemanaexp/FlineEstimates.out ...
READ: Reading File: chemanaexp/Elements.out ...
READ: Reading File: chemanaexp/dust_opac.out ...
WARN: Could not open chemanaexp/dust_sigmaa.out!
READ: Reading File: chemanaexp/StarSpectrum.out ...
READ: Reading File: chemanaexp/line_flux.out ...
READ: Reading File: chemanaexp/SED.out ...
READ: Reading File: chemanaexp/SEDana.out ...
WARN: Could not open chemanaexp/image.out!
INFO: Reading time: 0.42 s
[78]:
# Analyse the chemistry of CO in the model, reads all the required data
# This will create a file chemistry_reactions_CO.txt in the model directory, can be switched off with to_txt=False
chemistry=model.analyse_chemistry('CO',to_txt=True)
#test=pread.analyse_chemistry('CO',model=model,to_txt=True,screenout=False) # same as above, but using the function directly
INFO: Using existing fits file for chemanalysis: chemanalysis.fits
WARN: Try to read an older format ... let's hope it works!
INFO: Loaded 2842 Reactions from chemanaexp/Reactions.out
WARN: Could not load rate coefficients from rate_coeffs_1NZZ.log
INFO: Writing information to: chemanaexp/chemistry_reactions_CO.txt
INFO: Found 209 formation and 43 destruction reactions for species CO.
INFO: Calc time: 0.13 s
[79]:
# plot the total formation rate of CO at everz grid point
fig=pp.plot_cont(model,chemistry.totfrate,'log CO formation rate')
PLOT: plot_cont ...
Main formation and destruction reactions
Here we show ways to visualize the main formation and destruction reactions for the chosen species.
[80]:
# Show the main formation and destruction rates (numbers) on the grid
# by setting level to e.g. 2 the 2nd most important reaction is shown
fig=pp.plot_reaccont(model,chemistry,rtype='d',zlim=[1.e-35,None],level=1,extend="min")
fig=pp.plot_reaccont(model,chemistry,rtype='f',zlim=[1.e-35,None],level=1,extend="min")
[81]:
# This plot shows the main formation and destruction reactions on the 2D grid color-coded
fig=pp.plot_reac_form_dest(chemistry)
INFO: Calculate volumes
WARN: plot_reac_form_dest: more than 10 reactions found, only the first 10 will be plotted, The rest will be in white.
Looking at a particular grid point in detail
Here we show all the relevant reactions for a particular grid point.
[82]:
# now show all the details for a particular grid point
# with lowRatesFrac one can set a threshold down to which the reation should be listed (e.g. don't show unimportant reactions)
chemistry.reac_rates_ix_iz(20,15,lowRatesFrac=1.e-5)
Analysing point x= 16.34573 au z=2.969142 au
Detailed reaction rates for: CO
------------------------------------------------------------------------------------------------------
grid point = 20 15
r,z [au] (cylindrical) = 16.346 2.9691
n<H>,nd [cm^-3] = 3.9e+09 6.9e-05
Tgas,Tdust [K] = 4.6e+01 4.6e+01
AV_rad,AV_ver = 5.3e+01 3.4e-01
CO abundance = 1.380368e-04
------------------------------------------------------------------------------------------------------
Total form. rate [cm^-3 s^-1] = 2.49e-04
207 2594 DT CO# dust -> CO dust 2.49e-04
34 646 DR HCO+ e- -> CO H 5.07e-08
148 1842 NN CH2 O -> CO H H 3.46e-08
147 1841 NN CH2 O -> CO H2 2.08e-08
179 2057 NN O CN -> CO N 6.03e-09
139 1814 NN C O2 -> CO O 4.40e-09
196 2177 PH CO2 PHOTON -> CO O 3.02e-09
183 2070 NN O HCO -> CO OH 2.80e-09
185 2086 NN O OCN -> CO NO 2.70e-09
------------------------------------------------------------------------------------------------------
Total dest. rate [cm^-3 s^-1] = 2.49e-04
43 2593 IC CO dust -> CO# dust 2.49e-04
35 2178 PH CO PHOTON -> O C 7.08e-08
21 1213 IN H3+ CO -> HCO+ H2 3.63e-08
13 1040 IN CO HNSi+ -> SiN HCO+ 9.88e-09
23 1392 IN He+ CO -> O C+ He 9.26e-09
------------------------------------------------------------------------------------------------------
[83]:
# show some other point, but now using physical coordinates (x=10, z=1 au)
# the closest grid point for those coordinates will be shown
chemistry.reac_rates_ix_iz(locau=(10,1),lowRatesFrac=1.e-5)
Analysing point x= 8.917831 au z=1.017758 au
Detailed reaction rates for: CO
------------------------------------------------------------------------------------------------------
grid point = 19 11
r,z [au] (cylindrical) = 8.918 1.0178
n<H>,nd [cm^-3] = 6.8e+10 1.2e-03
Tgas,Tdust [K] = 4.4e+01 4.4e+01
AV_rad,AV_ver = 2.5e+03 4.3e+00
CO abundance = 1.273261e-06
------------------------------------------------------------------------------------------------------
Total form. rate [cm^-3 s^-1] = 7.25e-04
207 2594 DT CO# dust -> CO dust 7.24e-04
34 646 DR HCO+ e- -> CO H 5.41e-07
------------------------------------------------------------------------------------------------------
Total dest. rate [cm^-3 s^-1] = 7.25e-04
43 2593 IC CO dust -> CO# dust 7.24e-04
21 1213 IN H3+ CO -> HCO+ H2 5.12e-07
10 986 IN CH5+ CO -> HCO+ CH4 2.75e-08
23 1392 IN He+ CO -> O C+ He 1.56e-08
14 1041 IN CO HN2+ -> HCO+ N2 1.31e-08
------------------------------------------------------------------------------------------------------
Time-dependent model
Example for using the time-dependent output for the chamanlysis. This is still in an early stage but it is already possible to do some chemistry analyis with time-dependent ProDiMo models (using time_chem_disk). All the figures and analyisis methods for steady-state models can be used for time-dependent models as well. But one always has to specify the time step for which the analysis should be done.
However, the time-dependent models also allow to analyze the chemistry as funtion of time, at least for a particualr grid point. This is useful, because it is not necessarily the case that a dominant reaction in the steady-state was als dominant at all times.
[84]:
# read the time-dependent models
# YOU NEED TO UPDATE THIS PATH TO YOUR MODEL
mdir="../../../../MODELS/TEST_CHEMANA/modNewTD"
models=list()
# Update according to your model, here we have a time-dependent model with 5 time steps
for tdidx in range(5):
m=pread.read_prodimo(mdir,td_fileIdx=tdidx+1)
m.name=f"{m.params["AGE_DISK"][tdidx]:.4g} yr"
models.append(m)
# If the reading of the models was successful the rest of the jupyter notebook should just run ... (as long as you have H2O and H2O# in your chemical network)
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/ProDiMo_0001.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Species.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/FlineEstimates_0001.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Elements.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/dust_opac.out ...
WARN: Could not open ../../../../MODELS/TEST_CHEMANA/modNewTD/dust_sigmaa.out!
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/StarSpectrum.out ...
WARN: Could not open ../../../../MODELS/TEST_CHEMANA/modNewTD/image.out!
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Parameter.out ...
INFO: Reading time: 0.61 s
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/ProDiMo_0002.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Species.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/FlineEstimates_0002.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Elements.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/dust_opac.out ...
WARN: Could not open ../../../../MODELS/TEST_CHEMANA/modNewTD/dust_sigmaa.out!
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/StarSpectrum.out ...
WARN: Could not open ../../../../MODELS/TEST_CHEMANA/modNewTD/image.out!
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Parameter.out ...
INFO: Reading time: 0.49 s
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/ProDiMo_0003.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Species.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/FlineEstimates_0003.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Elements.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/dust_opac.out ...
WARN: Could not open ../../../../MODELS/TEST_CHEMANA/modNewTD/dust_sigmaa.out!
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/StarSpectrum.out ...
WARN: Could not open ../../../../MODELS/TEST_CHEMANA/modNewTD/image.out!
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Parameter.out ...
INFO: Reading time: 0.52 s
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/ProDiMo_0004.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Species.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/FlineEstimates_0004.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Elements.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/dust_opac.out ...
WARN: Could not open ../../../../MODELS/TEST_CHEMANA/modNewTD/dust_sigmaa.out!
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/StarSpectrum.out ...
WARN: Could not open ../../../../MODELS/TEST_CHEMANA/modNewTD/image.out!
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Parameter.out ...
INFO: Reading time: 0.56 s
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/ProDiMo_0005.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Species.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/FlineEstimates_0005.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Elements.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/dust_opac.out ...
WARN: Could not open ../../../../MODELS/TEST_CHEMANA/modNewTD/dust_sigmaa.out!
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/StarSpectrum.out ...
WARN: Could not open ../../../../MODELS/TEST_CHEMANA/modNewTD/image.out!
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNewTD/Parameter.out ...
INFO: Reading time: 0.52 s
[85]:
ppm=pplotm.PlotModels(None)
# the dashed lines in that figure are the ices
fig=ppm.plot_tcdspec(models,"H2O",facGrayBox=None,ice=True,ylim=[1.e11,1.e23],xlog=True)
PLOT: plot_tcdspec ...
INFO: Calculate vertical column densities
INFO: Calculate vertical column densities
INFO: Calculate vertical column densities
INFO: Calculate vertical column densities
INFO: Calculate vertical column densities
[86]:
# now read the chemanalysis output, for all the time-steps at once
chemanas=list()
for model in models:
chemanas.append(model.analyse_chemistry('H2O',to_txt=True))
INFO: Using existing fits file for chemanalysis: chemanalysis_0001.fits
INFO: Loaded 1377 Reactions from ../../../../MODELS/TEST_CHEMANA/modNewTD/Reactions.out
WARN: Could not load rate coefficients from rate_coeffs_1NZZ.log
INFO: Writing information to: ../../../../MODELS/TEST_CHEMANA/modNewTD/chemistry_reactions_H2O_0001.txt
INFO: Found 45 formation and 57 destruction reactions for species H2O.
INFO: Calc time: 0.08 s
INFO: Using existing fits file for chemanalysis: chemanalysis_0002.fits
INFO: Loaded 1377 Reactions from ../../../../MODELS/TEST_CHEMANA/modNewTD/Reactions.out
WARN: Could not load rate coefficients from rate_coeffs_1NZZ.log
INFO: Writing information to: ../../../../MODELS/TEST_CHEMANA/modNewTD/chemistry_reactions_H2O_0002.txt
INFO: Found 45 formation and 57 destruction reactions for species H2O.
INFO: Calc time: 0.07 s
INFO: Using existing fits file for chemanalysis: chemanalysis_0003.fits
INFO: Loaded 1377 Reactions from ../../../../MODELS/TEST_CHEMANA/modNewTD/Reactions.out
WARN: Could not load rate coefficients from rate_coeffs_1NZZ.log
INFO: Writing information to: ../../../../MODELS/TEST_CHEMANA/modNewTD/chemistry_reactions_H2O_0003.txt
INFO: Found 45 formation and 57 destruction reactions for species H2O.
INFO: Calc time: 0.11 s
INFO: Using existing fits file for chemanalysis: chemanalysis_0004.fits
INFO: Loaded 1377 Reactions from ../../../../MODELS/TEST_CHEMANA/modNewTD/Reactions.out
WARN: Could not load rate coefficients from rate_coeffs_1NZZ.log
INFO: Writing information to: ../../../../MODELS/TEST_CHEMANA/modNewTD/chemistry_reactions_H2O_0004.txt
INFO: Found 45 formation and 57 destruction reactions for species H2O.
INFO: Calc time: 0.06 s
INFO: Using existing fits file for chemanalysis: chemanalysis_0005.fits
INFO: Loaded 1377 Reactions from ../../../../MODELS/TEST_CHEMANA/modNewTD/Reactions.out
WARN: Could not load rate coefficients from rate_coeffs_1NZZ.log
INFO: Writing information to: ../../../../MODELS/TEST_CHEMANA/modNewTD/chemistry_reactions_H2O_0005.txt
INFO: Found 45 formation and 57 destruction reactions for species H2O.
INFO: Calc time: 0.06 s
[87]:
# the typical chemanalysis plot for each time-step
import matplotlib.pyplot as plt
pp=pplot.Plot(None)
for model,chemana in zip(models,chemanas):
fig,axes=plt.subplots(1,3,figsize=(11,3))
fig1=pp.plot_cont(model,chemana.totfrate,'H2O formation rate',ax=axes[0])
fig2=pp.plot_reaccont(model,chemana,rtype='f',vmin=-45,ax=axes[1])
fig3=pp.plot_reaccont(model,chemana,rtype='d',vmin=-45,ax=axes[2])
fig.suptitle(model.name)
fig.tight_layout()
PLOT: plot_cont ...
PLOT: plot_cont ...
PLOT: plot_cont ...
PLOT: plot_cont ...
PLOT: plot_cont ...
[88]:
# analyse a grid point at each time step
for chemana in chemanas:
print(" ")
print("YEAR:",chemana.model.name)
chemana.reac_rates_ix_iz(6,10)
print(" ")
YEAR: 1 yr
Analysing point x= 0.3805846 au z=0.04772979 au
Detailed reaction rates for: H2O
------------------------------------------------------------------------------------------------------
grid point = 6 10
r,z [au] (cylindrical) = 0.381 0.0477
n<H>,nd [cm^-3] = 1.3e+12 2.8e-02
Tgas,Tdust [K] = 2.1e+02 2.1e+02
AV_rad,AV_ver = 6.3e+01 6.4e-01
H2O abundance = 1.660914e-07
------------------------------------------------------------------------------------------------------
Total form. rate [cm^-3 s^-1] = 4.09e-01
30 871 NN H2 OH -> H2O H 3.20e-01
42 1259 DT H2O# dust -> H2O dust 8.82e-02
14 366 DR H3O+ e- -> H2O H 5.61e-04
------------------------------------------------------------------------------------------------------
Total dest. rate [cm^-3 s^-1] = 4.09e-01
51 993 PH H2O PHOTON -> OH H 1.69e-01
52 1080 P3 H2O PHOTON -> O H2 1.14e-01
56 1258 IC H2O dust -> H2O# dust 8.82e-02
33 563 IN H2O Si+ -> SiOH+ H 3.74e-02
------------------------------------------------------------------------------------------------------
YEAR: 1000 yr
Analysing point x= 0.3805846 au z=0.04772979 au
Detailed reaction rates for: H2O
------------------------------------------------------------------------------------------------------
grid point = 6 10
r,z [au] (cylindrical) = 0.381 0.0477
n<H>,nd [cm^-3] = 1.3e+12 2.8e-02
Tgas,Tdust [K] = 2.1e+02 2.1e+02
AV_rad,AV_ver = 6.3e+01 6.4e-01
H2O abundance = 1.775422e-07
------------------------------------------------------------------------------------------------------
Total form. rate [cm^-3 s^-1] = 4.15e-01
30 871 NN H2 OH -> H2O H 3.20e-01
42 1259 DT H2O# dust -> H2O dust 9.43e-02
14 366 DR H3O+ e- -> H2O H 5.65e-04
------------------------------------------------------------------------------------------------------
Total dest. rate [cm^-3 s^-1] = 4.15e-01
51 993 PH H2O PHOTON -> OH H 1.65e-01
52 1080 P3 H2O PHOTON -> O H2 1.18e-01
56 1258 IC H2O dust -> H2O# dust 9.43e-02
33 563 IN H2O Si+ -> SiOH+ H 3.72e-02
28 558 IN H2O HCO+ -> CO H3O+ 4.27e-04
------------------------------------------------------------------------------------------------------
YEAR: 1e+04 yr
Analysing point x= 0.3805846 au z=0.04772979 au
Detailed reaction rates for: H2O
------------------------------------------------------------------------------------------------------
grid point = 6 10
r,z [au] (cylindrical) = 0.381 0.0477
n<H>,nd [cm^-3] = 1.3e+12 2.8e-02
Tgas,Tdust [K] = 2.1e+02 2.1e+02
AV_rad,AV_ver = 6.3e+01 6.4e-01
H2O abundance = 1.775422e-07
------------------------------------------------------------------------------------------------------
Total form. rate [cm^-3 s^-1] = 4.15e-01
30 871 NN H2 OH -> H2O H 3.20e-01
42 1259 DT H2O# dust -> H2O dust 9.43e-02
14 366 DR H3O+ e- -> H2O H 5.65e-04
------------------------------------------------------------------------------------------------------
Total dest. rate [cm^-3 s^-1] = 4.15e-01
51 993 PH H2O PHOTON -> OH H 1.65e-01
52 1080 P3 H2O PHOTON -> O H2 1.18e-01
56 1258 IC H2O dust -> H2O# dust 9.43e-02
33 563 IN H2O Si+ -> SiOH+ H 3.72e-02
28 558 IN H2O HCO+ -> CO H3O+ 4.27e-04
------------------------------------------------------------------------------------------------------
YEAR: 1e+05 yr
Analysing point x= 0.3805846 au z=0.04772979 au
Detailed reaction rates for: H2O
------------------------------------------------------------------------------------------------------
grid point = 6 10
r,z [au] (cylindrical) = 0.381 0.0477
n<H>,nd [cm^-3] = 1.3e+12 2.8e-02
Tgas,Tdust [K] = 2.1e+02 2.1e+02
AV_rad,AV_ver = 6.3e+01 6.4e-01
H2O abundance = 1.775422e-07
------------------------------------------------------------------------------------------------------
Total form. rate [cm^-3 s^-1] = 4.15e-01
30 871 NN H2 OH -> H2O H 3.20e-01
42 1259 DT H2O# dust -> H2O dust 9.43e-02
14 366 DR H3O+ e- -> H2O H 5.65e-04
------------------------------------------------------------------------------------------------------
Total dest. rate [cm^-3 s^-1] = 4.15e-01
51 993 PH H2O PHOTON -> OH H 1.65e-01
52 1080 P3 H2O PHOTON -> O H2 1.18e-01
56 1258 IC H2O dust -> H2O# dust 9.43e-02
33 563 IN H2O Si+ -> SiOH+ H 3.72e-02
28 558 IN H2O HCO+ -> CO H3O+ 4.27e-04
------------------------------------------------------------------------------------------------------
YEAR: 1e+06 yr
Analysing point x= 0.3805846 au z=0.04772979 au
Detailed reaction rates for: H2O
------------------------------------------------------------------------------------------------------
grid point = 6 10
r,z [au] (cylindrical) = 0.381 0.0477
n<H>,nd [cm^-3] = 1.3e+12 2.8e-02
Tgas,Tdust [K] = 2.1e+02 2.1e+02
AV_rad,AV_ver = 6.3e+01 6.4e-01
H2O abundance = 1.775422e-07
------------------------------------------------------------------------------------------------------
Total form. rate [cm^-3 s^-1] = 4.15e-01
30 871 NN H2 OH -> H2O H 3.20e-01
42 1259 DT H2O# dust -> H2O dust 9.43e-02
14 366 DR H3O+ e- -> H2O H 5.65e-04
------------------------------------------------------------------------------------------------------
Total dest. rate [cm^-3 s^-1] = 4.15e-01
51 993 PH H2O PHOTON -> OH H 1.65e-01
52 1080 P3 H2O PHOTON -> O H2 1.18e-01
56 1258 IC H2O dust -> H2O# dust 9.43e-02
33 563 IN H2O Si+ -> SiOH+ H 3.72e-02
28 558 IN H2O HCO+ -> CO H3O+ 4.27e-04
------------------------------------------------------------------------------------------------------
[89]:
# now read the chemanalysis output for a different species
chemanasCO=list()
for tdidx,model in enumerate(models):
chemanasCO.append(model.analyse_chemistry('CO'))
# Also load a steady-state model for comparison
modsst=pread.read_prodimo("../../../../MODELS/TEST_CHEMANA/modNew",name="Steady-State")
modsst_chemana=modsst.analyse_chemistry('CO')
modsst_chemana.reac_rates_ix_iz(15,15)
INFO: Using existing fits file for chemanalysis: chemanalysis_0001.fits
INFO: Writing information to: ../../../../MODELS/TEST_CHEMANA/modNewTD/chemistry_reactions_CO_0001.txt
INFO: Found 100 formation and 36 destruction reactions for species CO.
INFO: Calc time: 0.08 s
INFO: Using existing fits file for chemanalysis: chemanalysis_0002.fits
INFO: Writing information to: ../../../../MODELS/TEST_CHEMANA/modNewTD/chemistry_reactions_CO_0002.txt
INFO: Found 100 formation and 36 destruction reactions for species CO.
INFO: Calc time: 0.05 s
INFO: Using existing fits file for chemanalysis: chemanalysis_0003.fits
INFO: Writing information to: ../../../../MODELS/TEST_CHEMANA/modNewTD/chemistry_reactions_CO_0003.txt
INFO: Found 100 formation and 36 destruction reactions for species CO.
INFO: Calc time: 0.05 s
INFO: Using existing fits file for chemanalysis: chemanalysis_0004.fits
INFO: Writing information to: ../../../../MODELS/TEST_CHEMANA/modNewTD/chemistry_reactions_CO_0004.txt
INFO: Found 100 formation and 36 destruction reactions for species CO.
INFO: Calc time: 0.05 s
INFO: Using existing fits file for chemanalysis: chemanalysis_0005.fits
INFO: Writing information to: ../../../../MODELS/TEST_CHEMANA/modNewTD/chemistry_reactions_CO_0005.txt
INFO: Found 100 formation and 36 destruction reactions for species CO.
INFO: Calc time: 0.05 s
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNew/ProDiMo.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNew/Species.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNew/FlineEstimates.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNew/Elements.out ...
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNew/dust_opac.out ...
WARN: Could not open ../../../../MODELS/TEST_CHEMANA/modNew/dust_sigmaa.out!
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNew/StarSpectrum.out ...
WARN: Could not open ../../../../MODELS/TEST_CHEMANA/modNew/image.out!
READ: Reading File: ../../../../MODELS/TEST_CHEMANA/modNew/Parameter.out ...
INFO: Reading time: 0.51 s
INFO: Using existing fits file for chemanalysis: chemanalysis.fits
INFO: Loaded 1377 Reactions from ../../../../MODELS/TEST_CHEMANA/modNew/Reactions.out
WARN: Could not load rate coefficients from rate_coeffs_1NZZ.log
INFO: Writing information to: ../../../../MODELS/TEST_CHEMANA/modNew/chemistry_reactions_CO.txt
INFO: Found 100 formation and 36 destruction reactions for species CO.
INFO: Calc time: 0.07 s
Analysing point x= 6.216286 au z=1.390791 au
Detailed reaction rates for: CO
------------------------------------------------------------------------------------------------------
grid point = 15 15
r,z [au] (cylindrical) = 6.216 1.3908
n<H>,nd [cm^-3] = 5.4e+08 2.1e-06
Tgas,Tdust [K] = 1.9e+02 1.9e+02
AV_rad,AV_ver = 4.6e-03 6.8e-05
CO abundance = 2.656508e-07
------------------------------------------------------------------------------------------------------
Total form. rate [cm^-3 s^-1] = 1.27e-04
11 137 CE H CO+ -> CO H+ 7.71e-05
21 373 DR HCO+ e- -> CO H 3.67e-05
64 814 NN C OH -> CO H 7.94e-06
26 411 IN C+ O2 -> CO O+ 3.56e-06
77 855 NN CH O -> CO H 9.15e-07
63 813 NN C O2 -> CO O 3.43e-07
62 812 NN C NO -> CO N 3.27e-07
86 929 NN O CN -> CO N 2.59e-07
------------------------------------------------------------------------------------------------------
Total dest. rate [cm^-3 s^-1] = 1.27e-04
27 986 PH CO PHOTON -> O C 1.27e-04
19 624 IN He+ CO -> O C+ He 2.54e-07
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[90]:
# Now we plot for a certain grid point the main formation and destriction reactions as function of time.
# The arrow at the right-hand side of the figure shows the results from the steady-state model.
fig=pp.plot_reac_ixiz(15,15,"f",chemanasCO,chemana_steadystate=modsst_chemana)
fig=pp.plot_reac_ixiz(15,15,"d",chemanasCO,chemana_steadystate=modsst_chemana)
[91]:
# main form/dest reaction at the beginning and the end of the time-dependent evolution
fig=pp.plot_reac_form_dest(chemanasCO[0])
fig=pp.plot_reac_form_dest(chemanasCO[-1])
INFO: Calculate volumes
INFO: Calculate volumes
