Topics

Calculating ionization fractions and excitation ratios for input cloud composition, density and temperature

Manos Chatz
 

Dear Cloudy community,

I need to import my own cloud structure data (i.e. radius vs composition (5 species), temperature and density) into CLOUDY and then use it to calculate the ionization fractions (HI, HII etc) as well as the hydrogen excitation density ratios (specifically, n2 and n3/n2, where n2 is the number of H atoms in the n=2 state and n3 the number of H atoms in the n=3 state). Is this functionality available? If so, I would really appreciate an example/template on how to make something like this work. Preferably, I would like the output to be in the same grid (radial cells) as my input. For example if I input:

cell #, radius, density, temperature, H, He, C
1 1.0e+14 1.0e-6  5000  0.7 0.28 0.02
2 1.2e+14 0.6e-6  4888  0.7 0.28 0.02
3 1.4e+14 0.3e-6  4550  0.7 0.28 0.02
4 1.6e+14 0.1e-6  4320  0.7 0.28 0.02

I want to receive an output of the form:

cell #, radius, HI, HII, n2, n3
1 1.0e+14  x1,y1,z1,t1
2 1.2e+14  x2,y2,z2,t2
3 1.4e+14  x3,y3,z3,t3
4 1.6e+14  x4,y4,z4,t4

etc.

Is this functionality available or I would have to do that cell by cell? Also, would that work with a zero specified intensity field (since my input data is already "illuminated")? 
I just have this static atmosphere data described above (stratified composition, density, temperature) and would simply like to calculate ionization/excitation states.

I would really appreciate your help.

With kind regards,

Manos Chatzopoulos

Marios Chatzikos
 

Hello Manos,

Cloudy provides a number of commands for importing pre-computed cloud structures.  "dlaw table" (Hazy 1, 8.5.3) can be used to import a density profile, "tlaw table" (11.17.1) for a temperature profile, and "element <name> table" for an elemental abundance profile.

For output, you may use the 'save species densities' command, 16.87.1.  Note, however, that Cloudy l-resolves principal quantum numbers n <= 4, so you'd have to add up nl densities to get the ratios you mentioned.  See 12.4.2 for details.

I hope this helps,

Marios

On 6/17/20 18:47, Manos Chatz via groups.io wrote:
Dear Cloudy community,

I need to import my own cloud structure data (i.e. radius vs composition (5 species), temperature and density) into CLOUDY and then use it to calculate the ionization fractions (HI, HII etc) as well as the hydrogen excitation density ratios (specifically, n2 and n3/n2, where n2 is the number of H atoms in the n=2 state and n3 the number of H atoms in the n=3 state). Is this functionality available? If so, I would really appreciate an example/template on how to make something like this work. Preferably, I would like the output to be in the same grid (radial cells) as my input. For example if I input:

cell #, radius, density, temperature, H, He, C
1 1.0e+14 1.0e-6  5000  0.7 0.28 0.02
2 1.2e+14 0.6e-6  4888  0.7 0.28 0.02
3 1.4e+14 0.3e-6  4550  0.7 0.28 0.02
4 1.6e+14 0.1e-6  4320  0.7 0.28 0.02

I want to receive an output of the form:

cell #, radius, HI, HII, n2, n3
1 1.0e+14  x1,y1,z1,t1
2 1.2e+14  x2,y2,z2,t2
3 1.4e+14  x3,y3,z3,t3
4 1.6e+14  x4,y4,z4,t4

etc.

Is this functionality available or I would have to do that cell by cell? Also, would that work with a zero specified intensity field (since my input data is already "illuminated")? 
I just have this static atmosphere data described above (stratified composition, density, temperature) and would simply like to calculate ionization/excitation states.

I would really appreciate your help.

With kind regards,

Manos Chatzopoulos

Manos Chatz
 

Marios,

I sincerely appreciate your very helpful response; I could not find an option in hazy1/hazy2 for setting a stratified abundance profile. I will do my best to make this work; if there is a template or input file that uses these three input modes it would be a great help for me. In addition to that, I meant to ask; this is a stellar atmosphere profile, so there is really no "incident" radiation field. To make sure the calculation is set up correctly, do I just adopt a constant incident intensity in the inner boundary corresponding to the intensity of the radiation in my stellar model at this radius? Can one avoid including an "incident" radiation field and just use T, rho and abundances to get the excitation/ionization fractions?

Kindly,

Manos

Manos Chatz
 

Marios,

Also, I meant to ask; is there a chapter/reference in hazy1 or hazy2 on the element <name> table functionality so that I can see how to set it up? Or it's formatted the same way as tlaw table and dlaw table? Many thanks! A working template input would be very helpful too (apologies for all the questions!).

Kind regards,

Manos

Marios Chatzikos
 

Hello Manos,

Sorry, I forgot to add a reference to the 'element name table' command: It is 7.7.9 in Hazy 1.

That said, Cloudy is not designed as a stellar atmospheres code, and I'm not certain it'd give you the correct results.  Gary may have more to say on that.

Thanks,

Marios

On 6/18/20 11:21, Manos Chatz via groups.io wrote:
Marios,

Also, I meant to ask; is there a chapter/reference in hazy1 or hazy2 on the element <name> table functionality so that I can see how to set it up? Or it's formatted the same way as tlaw table and dlaw table? Many thanks! A working template input would be very helpful too (apologies for all the questions!).

Kind regards,

Manos

Manos Chatz
 

Dear Marios,

I am making progress (thanks to the suggestions you sent me) but I had one more question with regards to the 'save species densities' command (16.87.1). I have now used that as following (following the instructions) in my input script:

save species densities "dens.pop"
"H"
"H+"
"H[1:3]
"e-"
end

The dens.pop output I get, I assume, lists the densities of these species (neutral and ionized H, plus levels n=1 through n=3 for neutral hydrogen), correct? In your message, you mentioned that I would have to add up nl densities to get the ratios I mentioned (specifically, n2 and n3/n2 for neutral H), but I am not quite sure where these nl densities are printed out. Shouldn't simply taking column 6 (H3) and dividing by column 5 (H2) from that output give me the correct, target n3/n2 ratio? What am I still missing?

Thank you in advance,

Manos

Marios Chatzikos
 

Dear Manos,

Species "H[1:3]" gives you the first 3 levels of hydrogen, as coded in Cloudy, that is, 1s, 2s, and 2p.  If you want to include n=3, you need to extend the upper index to 6, and that'd give you the densities for 3s, 3p, and 3d.  So, to get the densities for n=2 you need to add columns 5 & 6, and for n=3 you need to add columns 7 through 9.

I hope this helps,

-Marios

On 6/23/20 19:20, Manos Chatz via groups.io wrote:
Dear Marios,

I am making progress (thanks to the suggestions you sent me) but I had one more question with regards to the 'save species densities' command (16.87.1). I have now used that as following (following the instructions) in my input script:

save species densities "dens.pop"
"H"
"H+"
"H[1:3]
"e-"
end

The dens.pop output I get, I assume, lists the densities of these species (neutral and ionized H, plus levels n=1 through n=3 for neutral hydrogen), correct? In your message, you mentioned that I would have to add up nl densities to get the ratios I mentioned (specifically, n2 and n3/n2 for neutral H), but I am not quite sure where these nl densities are printed out. Shouldn't simply taking column 6 (H3) and dividing by column 5 (H2) from that output give me the correct, target n3/n2 ratio? What am I still missing?

Thank you in advance,

Manos

Manos Chatz
 

Dear Marios,

As always, I am very grateful for your fast responses and great help. I have made a lot of progress and I think I am almost where I need to be. I just have a couple of (hopefully last) questions related to my input script.in file (appended in the end of this message). First, just to give you a general idea of what I am doing. I am inputing a black body incident radiation field determined by the "blackbody T" command and the "luminosity total" command. This is my "star" in the middle of my cloud. I am setting the inner radius of this cloud (the edge close to the star) to be at logR = 14.951 or ~8.94 x 10^14 cm. My understanding is that the outer radius is determined by default based on the "stop temperature" command (which, by default, is set to 4000 K).

1) Here is my first question: As you can see in my input by looking at the custom density/temperature input (dlaw, tlaw tables), the temperatures for my Cloud are all below 4000 K (logT ranges in 3.56-3.78). When, however, I change the stop temperature to "stop temperature 1000.0" my run crashes (the last line in the script.out is: 

requested radius outside range of dense_tabden

radius was  1.52e+01 min, max= -3.50e+01  1.52e+01

[Stop in tabval at depth_table.cpp:46, something went wrong]


When I comment "stop temperature 1000.0" out and I use the default, the code runs OK but I am curious as if it calculates the ionization/excitation populations correctly all the way to the outer input radius of my data.

2) My second - and very important question is: looking at my input data for the cloud (tlaw table depth and dlaw table depth), you will notice that the cloud data start at logR_inner = 14.956 or R_inner = 9.04 x 10^14 cm and end at logR_outer = 15.17 or R_outer = 1.48 x 10^15 cm. My output file ("species.pop", attached here for your reference), however, has radial data (first column) that range from 0.5 to 1.47316 x 10^15 cm. A big portion of this output is therefore corresponding to "cloud" data within the requested inner cloud radius of 8.94 x 10^14 cm, yet the outer radius is close to the one that is included in the data. My question is, why is that? I am sure I am missing something - how come data for r < r_inner radius of the cloud is computed when I have requested an inner radius with the "radius" command and then I have included tabulated tlaw/dlaw data that are clearly above that inner radius? For the cloud ideally I need output data that range between the requested inner radius (logR = 14.951) and the outer radius of the input dlaw/tlaw data (logR = 15.17). To help you visualize my 1D setup, here is a pseudo-plot of it:

Star (input BB radiation field based on TBB, Luminosity) <---------[NO CLOUD]--------------> R_in (this is where cloud data starts determined by dlaw/tlaw or by the radius chosen via the "radius" command) <--------------[INPUT CLOUD DATA]---------------> R_out (should end at the radius where the input cloud data determined by dlaw/tlaw end, but "stop temperature 1000.0" to allow the code to compute population levels below the default value of 4000 K does not work).

In general, I would be really grateful if you could help me with these two issues but also if you could take a quick look at my script.in input below and let me know if I have done something obviously wrong in my attempt to simulate populations for this setup. I believe I am really close to doing it right, but your expert eye will definitely catch something I am missing.

Many thanks in advance!

Manos


####INPUT SCRIPT.IN USED#####

title CSI levels input file

blackbody 6351.676 K

luminosity total 41.956

radius 14.951

sphere

#stop temperature 1000.0

dlaw table depth

continue -35 11.134

continue 14.956 11.063

continue 14.965 11.001

continue 14.974 10.944

continue 14.981 10.898

continue 14.986 10.889

continue 14.988 10.893

continue 14.99 10.887

continue 14.992 10.887

continue 14.993 10.887

continue 14.994 10.872

continue 14.996 10.863

continue 14.997 10.858

continue 14.998 10.846

continue 15.0 10.831

continue 15.001 10.825

continue 15.003 10.817

continue 15.004 10.799

continue 15.006 10.767

continue 15.009 10.722

continue 15.011 10.631

continue 15.028 10.344

continue 15.044 10.283

continue 15.057 10.254

continue 15.065 10.255

continue 15.074 10.149

continue 15.091 9.855

continue 15.117 9.549

continue 15.152 9.303

continue 15.17 9.064

end of dlaw

tlaw table depth

continue -35 3.803

continue 14.956 3.781

continue 14.965 3.762

continue 14.974 3.749

continue 14.981 3.738

continue 14.986 3.732

continue 14.988 3.727

continue 14.99 3.725

continue 14.992 3.722

continue 14.993 3.72

continue 14.994 3.718

continue 14.996 3.716

continue 14.997 3.713

continue 14.998 3.712

continue 15.0 3.71

continue 15.001 3.709

continue 15.003 3.707

continue 15.004 3.705

continue 15.006 3.703

continue 15.009 3.7

continue 15.011 3.698

continue 15.028 3.69

continue 15.044 3.676

continue 15.057 3.667

continue 15.065 3.661

continue 15.074 3.655

continue 15.091 3.643

continue 15.117 3.629

continue 15.152 3.608

continue 15.17 3.588

end of tlaw

element helium abundance -0.845

element carbon abundance -3.635

element nitrogen abundance -3.305

element oxygen abundance -3.139

save species densities "species.pop"

"H"

"H+"

"H[1:6]"

"e-"

end

save overview "script.ovr"

save continuum "spectrum.dat" units angstroms

Marios Chatzikos
 

Dear Manos,

1) By using the 'stop temperature 1000' command, the code will continue the integration until the temperature drops below 1000, which is impossible in your case.  Look at the .out of the run with that command disabled, and search for "Calculation stopped because" to see why the calculation ended.  I'm sure you'll find it is because the outer bound of your cloud was reached.

2) Depth and radius are two different things.  The radius is measured from the star, while the depth is measured from the edge of the cloud facing the star.  What you're using in your 'dlaw table' etc commands is depth, when I think you need to use the 'radius' keyword (in which case, I'd remove the lines starting with 'continue -35').  In the output of the 'save species command' what you see is the depth from the illuminated face of the cloud, so it's okay if it differs from your input, although do check that its total thickness is what you specified.

I hope this helps.

Marios

On 6/24/20 17:05, Manos Chatz via groups.io wrote:

Dear Marios,

As always, I am very grateful for your fast responses and great help. I have made a lot of progress and I think I am almost where I need to be. I just have a couple of (hopefully last) questions related to my input script.in file (appended in the end of this message). First, just to give you a general idea of what I am doing. I am inputing a black body incident radiation field determined by the "blackbody T" command and the "luminosity total" command. This is my "star" in the middle of my cloud. I am setting the inner radius of this cloud (the edge close to the star) to be at logR = 14.951 or ~8.94 x 10^14 cm. My understanding is that the outer radius is determined by default based on the "stop temperature" command (which, by default, is set to 4000 K).

1) Here is my first question: As you can see in my input by looking at the custom density/temperature input (dlaw, tlaw tables), the temperatures for my Cloud are all below 4000 K (logT ranges in 3.56-3.78). When, however, I change the stop temperature to "stop temperature 1000.0" my run crashes (the last line in the script.out is: 

requested radius outside range of dense_tabden

radius was  1.52e+01 min, max= -3.50e+01  1.52e+01

[Stop in tabval at depth_table.cpp:46, something went wrong]


When I comment "stop temperature 1000.0" out and I use the default, the code runs OK but I am curious as if it calculates the ionization/excitation populations correctly all the way to the outer input radius of my data.

2) My second - and very important question is: looking at my input data for the cloud (tlaw table depth and dlaw table depth), you will notice that the cloud data start at logR_inner = 14.956 or R_inner = 9.04 x 10^14 cm and end at logR_outer = 15.17 or R_outer = 1.48 x 10^15 cm. My output file ("species.pop", attached here for your reference), however, has radial data (first column) that range from 0.5 to 1.47316 x 10^15 cm. A big portion of this output is therefore corresponding to "cloud" data within the requested inner cloud radius of 8.94 x 10^14 cm, yet the outer radius is close to the one that is included in the data. My question is, why is that? I am sure I am missing something - how come data for r < r_inner radius of the cloud is computed when I have requested an inner radius with the "radius" command and then I have included tabulated tlaw/dlaw data that are clearly above that inner radius? For the cloud ideally I need output data that range between the requested inner radius (logR = 14.951) and the outer radius of the input dlaw/tlaw data (logR = 15.17). To help you visualize my 1D setup, here is a pseudo-plot of it:

Star (input BB radiation field based on TBB, Luminosity) <---------[NO CLOUD]--------------> R_in (this is where cloud data starts determined by dlaw/tlaw or by the radius chosen via the "radius" command) <--------------[INPUT CLOUD DATA]---------------> R_out (should end at the radius where the input cloud data determined by dlaw/tlaw end, but "stop temperature 1000.0" to allow the code to compute population levels below the default value of 4000 K does not work).

In general, I would be really grateful if you could help me with these two issues but also if you could take a quick look at my script.in input below and let me know if I have done something obviously wrong in my attempt to simulate populations for this setup. I believe I am really close to doing it right, but your expert eye will definitely catch something I am missing.

Many thanks in advance!

Manos


####INPUT SCRIPT.IN USED#####

title CSI levels input file

blackbody 6351.676 K

luminosity total 41.956

radius 14.951

sphere

#stop temperature 1000.0

dlaw table depth

continue -35 11.134

continue 14.956 11.063

continue 14.965 11.001

continue 14.974 10.944

continue 14.981 10.898

continue 14.986 10.889

continue 14.988 10.893

continue 14.99 10.887

continue 14.992 10.887

continue 14.993 10.887

continue 14.994 10.872

continue 14.996 10.863

continue 14.997 10.858

continue 14.998 10.846

continue 15.0 10.831

continue 15.001 10.825

continue 15.003 10.817

continue 15.004 10.799

continue 15.006 10.767

continue 15.009 10.722

continue 15.011 10.631

continue 15.028 10.344

continue 15.044 10.283

continue 15.057 10.254

continue 15.065 10.255

continue 15.074 10.149

continue 15.091 9.855

continue 15.117 9.549

continue 15.152 9.303

continue 15.17 9.064

end of dlaw

tlaw table depth

continue -35 3.803

continue 14.956 3.781

continue 14.965 3.762

continue 14.974 3.749

continue 14.981 3.738

continue 14.986 3.732

continue 14.988 3.727

continue 14.99 3.725

continue 14.992 3.722

continue 14.993 3.72

continue 14.994 3.718

continue 14.996 3.716

continue 14.997 3.713

continue 14.998 3.712

continue 15.0 3.71

continue 15.001 3.709

continue 15.003 3.707

continue 15.004 3.705

continue 15.006 3.703

continue 15.009 3.7

continue 15.011 3.698

continue 15.028 3.69

continue 15.044 3.676

continue 15.057 3.667

continue 15.065 3.661

continue 15.074 3.655

continue 15.091 3.643

continue 15.117 3.629

continue 15.152 3.608

continue 15.17 3.588

end of tlaw

element helium abundance -0.845

element carbon abundance -3.635

element nitrogen abundance -3.305

element oxygen abundance -3.139

save species densities "species.pop"

"H"

"H+"

"H[1:6]"

"e-"

end

save overview "script.ovr"

save continuum "spectrum.dat" units angstroms

Manos Chatz
 

Hi Marios,

Awesome, now I understand (1) better and it looks like things are working minus one more thing: when I use "dlaw table radius" and "tlaw table radius" instead of "depth", the output radii (1st column) in my species.pop (attached) are all below the inner cloud radius! You can see that that my dlaw/tlaw data range from logR = 14.965 to 15.17 but the radii in species.pop from logR = 3.105 to logR = 14.713. When I use "depth", on the other hand (which I understand is incorrect), I get a "radial" extent equal to the one I mentioned in my previous message. Any ideas why my output is not within the cloud input ranges?

Thanks (Euxristw) again,

Manos


### INPUT SCRIPT.IN USED###

title CSI levels input file

blackbody 6033.88 K

luminosity total 41.886

radius 14.965

sphere

dlaw table radius

continue 14.965 11.001

continue 14.974 10.944

continue 14.981 10.898

continue 14.986 10.889

continue 14.988 10.893

continue 14.99 10.887

continue 14.992 10.887

continue 14.993 10.887

continue 14.994 10.872

continue 14.996 10.863

continue 14.997 10.858

continue 14.998 10.846

continue 15.0 10.831

continue 15.001 10.825

continue 15.003 10.817

continue 15.004 10.799

continue 15.006 10.767

continue 15.009 10.722

continue 15.011 10.631

continue 15.028 10.344

continue 15.044 10.283

continue 15.057 10.254

continue 15.065 10.255

continue 15.074 10.149

continue 15.091 9.855

continue 15.117 9.549

continue 15.152 9.303

continue 15.17 9.064

end of dlaw

tlaw table radius

continue 14.965 3.762

continue 14.974 3.749

continue 14.981 3.738

continue 14.986 3.732

continue 14.988 3.727

continue 14.99 3.725

continue 14.992 3.722

continue 14.993 3.72

continue 14.994 3.718

continue 14.996 3.716

continue 14.997 3.713

continue 14.998 3.712

continue 15.0 3.71

continue 15.001 3.709

continue 15.003 3.707

continue 15.004 3.705

continue 15.006 3.703

continue 15.009 3.7

continue 15.011 3.698

continue 15.028 3.69

continue 15.044 3.676

continue 15.057 3.667

continue 15.065 3.661

continue 15.074 3.655

continue 15.091 3.643

continue 15.117 3.629

continue 15.152 3.608

continue 15.17 3.588

end of tlaw

element helium abundance -0.845

element carbon abundance -3.635

element nitrogen abundance -3.305

element oxygen abundance -3.139

save species densities "species.pop"

"H"

"H+"

"H[1:6]"

"e-"

end

save overview "script.ovr"

save continuum "spectrum.dat" units angstroms

Manos Chatz
 

Marios,

In addition, I forgot to mention, that for that last input, without the temperature stop 1000.0 command, I get: "Calculation Stopped because lowest Te reached". Iteration 1 of 1." Note sure if that's pointing to a hint on the problem I described in my previous e-mail (when using tlaw radius getting radial output outside the input data range).

Manos

Manos Chatz
 

Also, when I remove the "continue -35" lines the cloudy run immediately fails with:

"requested radius outside range of dense_tabden
radius was -3.00e+1 min, max = 1.5e+1 1.52e+01"

I am probably still missing something really simple.

Manos Chatz
 

*meant to say with "dlaw table depth" removing the -35 is a problem. With "dlaw table radius" that is not a problem, but then again, the output gives me radial data outside my input cloud data ranges (for smaller radii that the smallest/inner cloud radius).

Manos

Marios Chatzikos
 

Hi Manos,

What you see in the first column of the populations file is the depth into the cloud, i.e., distance from the illuminated face.  The total depth is 5.16915e+14, which is within 7% of the depth of your cloud, 10^15.17 - 10^14.965.  The temperature drops below 4000, so the calculation ends before the entire cloud structure you specified is processed.

To recover the entire cloud use the commands

stop temperature 1000
stop radius 15.17

The first lets you go past the current ending point, while the latter explicitly stops the calculation at the edge of the cloud -- you will not get the errors you reported yesterday.  The total depth is then within 1% of that specified.

I hope this helps,

Marios

On 6/24/20 18:28, Manos Chatz via groups.io wrote:
Hi Marios,

Awesome, now I understand (1) better and it looks like things are working minus one more thing: when I use "dlaw table radius" and "tlaw table radius" instead of "depth", the output radii (1st column) in my species.pop (attached) are all below the inner cloud radius! You can see that that my dlaw/tlaw data range from logR = 14.965 to 15.17 but the radii in species.pop from logR = 3.105 to logR = 14.713. When I use "depth", on the other hand (which I understand is incorrect), I get a "radial" extent equal to the one I mentioned in my previous message. Any ideas why my output is not within the cloud input ranges?

Thanks (Euxristw) again,

Manos


### INPUT SCRIPT.IN USED###

title CSI levels input file

blackbody 6033.88 K

luminosity total 41.886

radius 14.965

sphere

dlaw table radius

continue 14.965 11.001

continue 14.974 10.944

continue 14.981 10.898

continue 14.986 10.889

continue 14.988 10.893

continue 14.99 10.887

continue 14.992 10.887

continue 14.993 10.887

continue 14.994 10.872

continue 14.996 10.863

continue 14.997 10.858

continue 14.998 10.846

continue 15.0 10.831

continue 15.001 10.825

continue 15.003 10.817

continue 15.004 10.799

continue 15.006 10.767

continue 15.009 10.722

continue 15.011 10.631

continue 15.028 10.344

continue 15.044 10.283

continue 15.057 10.254

continue 15.065 10.255

continue 15.074 10.149

continue 15.091 9.855

continue 15.117 9.549

continue 15.152 9.303

continue 15.17 9.064

end of dlaw

tlaw table radius

continue 14.965 3.762

continue 14.974 3.749

continue 14.981 3.738

continue 14.986 3.732

continue 14.988 3.727

continue 14.99 3.725

continue 14.992 3.722

continue 14.993 3.72

continue 14.994 3.718

continue 14.996 3.716

continue 14.997 3.713

continue 14.998 3.712

continue 15.0 3.71

continue 15.001 3.709

continue 15.003 3.707

continue 15.004 3.705

continue 15.006 3.703

continue 15.009 3.7

continue 15.011 3.698

continue 15.028 3.69

continue 15.044 3.676

continue 15.057 3.667

continue 15.065 3.661

continue 15.074 3.655

continue 15.091 3.643

continue 15.117 3.629

continue 15.152 3.608

continue 15.17 3.588

end of tlaw

element helium abundance -0.845

element carbon abundance -3.635

element nitrogen abundance -3.305

element oxygen abundance -3.139

save species densities "species.pop"

"H"

"H+"

"H[1:6]"

"e-"

end

save overview "script.ovr"

save continuum "spectrum.dat" units angstroms

Manos Chatz
 

Hi Marios,

Again, thank you for your patience with all my questions and help. I am happy to say that I now understand better the output "depth" variable and that helps a lot already. However, even after using your two suggested commands, I still have the same issue with 'stop temperature'. If I do not include it, the simulation runs but the calculation ends because lowest Te is reached. And I get some "scary" warnings under that message about some energies being zero and unphysical. When I do include 'stop temperature 1000.0' the calculation will not complete; I get the "requested radius outside range of dense_tabden" message followed by "Stop in tabval at depth_table.cpp:45, something went wrong". As a matter of fact, no value for the stop temperature command below 3890 K will allow the simulation to complete, and those that complete do so because lowest Te has been reached, and not because "the outer radius of the cloud" has been reached. So this is the only (and hopefully) last issue I have. I have attached my script.in in case you would like to give it a quick go. I am using the latest CLOUDY release (c17.02). 

Many thanks, as always!

Manos

Marios Chatzikos
 

Hi Manos,

Okay, I see.  Here's a thing you can do: Disable the temperature stopping criterion, and stop the integration at a radius that is a little lower than your outer radius:

stop radius 15.169
stop temperature off

This works for me, and gives a thickness within 1% of the specified.

Please let me know if you still have problems.

Marios

On 6/25/20 14:13, Manos Chatz via groups.io wrote:

Hi Marios,

Again, thank you for your patience with all my questions and help. I am happy to say that I now understand better the output "depth" variable and that helps a lot already. However, even after using your two suggested commands, I still have the same issue with 'stop temperature'. If I do not include it, the simulation runs but the calculation ends because lowest Te is reached. And I get some "scary" warnings under that message about some energies being zero and unphysical. When I do include 'stop temperature 1000.0' the calculation will not complete; I get the "requested radius outside range of dense_tabden" message followed by "Stop in tabval at depth_table.cpp:45, something went wrong". As a matter of fact, no value for the stop temperature command below 3890 K will allow the simulation to complete, and those that complete do so because lowest Te has been reached, and not because "the outer radius of the cloud" has been reached. So this is the only (and hopefully) last issue I have. I have attached my script.in in case you would like to give it a quick go. I am using the latest CLOUDY release (c17.02). 

Many thanks, as always!

Manos

Manos Chatz
 

Marios,

This seems to have worked! I appreciate the huge help and patience - especially for a CLOUDY rookie like myself. I look forward to utilizing this great software.

Best,

Manos