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<details open>
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<details close>
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<summary>
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<h2> 1 Where do I ask questions? </h2>
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</summary>
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<br>
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At the code's [user group](https://cloudyastrophysics.groups.io/).
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We were one of the early adopters of Yahoo groups and moved to this
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[user group](https://cloudyastrophysics.groups.io/) when
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... | ... | @@ -11,13 +12,15 @@ If you encounter an old link to the Cloudy |
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[Yahoo! discussion board](http://tech.groups.yahoo.com/group/cloudy_simulations/)
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you should search for its
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content on the new group.
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</details>
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<details open>
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<details close>
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<summary>
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<h2> 2 How should the code be referenced in publications? </h2>
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</summary>
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<br>
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Cloudy is a research project that involves the creative efforts of many people. It should be cited as follows: "Calculations were performed with version yy.vr of Cloudy, last described by Ferland et al. (xxxx)." The citation should be the most recent review paper:
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For Cloudy versions up to and including C10.vr:
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... | ... | @@ -36,10 +39,15 @@ The citation should explicitly mention the version "yy.vr" of the code since som |
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A more complete version of the citation can be generated by running the code with the command `print citation`.
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This will include the full bibtex reference.
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</details>
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## 3 I added up all the energy in the emission line printout, or in the save continuuum output, and it is less than the energy in the incident spectrum. What happened to the missing energy?
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<details close>
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<summary>
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<h2> 3 I added up all the energy in the emission line printout, or in the save continuuum output, and it is less than the energy in the incident spectrum. What happened to the missing energy? </h2>
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</summary>
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<br>
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Chapter 3 of AGN3 (Osterbrock & Ferland 2006) goes over heating and cooling in a photoionized nebula.
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Much of the incident photon energy goes into ionizing or dissociating a species and the rest is shared
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... | ... | @@ -64,8 +72,14 @@ included in models of intermediate ionization heavy elements is relatively small |
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So, the recombination lines produced by levels higher than our model atoms are included in the energy equation but are not included in the emitted spectrum.
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</details>
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## 4 My code/analytical results do not get the Cloudy results. What is different?
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<details close>
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<summary>
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<h2> 4 My code/analytical results do not get the Cloudy results. What is different? </h2>
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</summary>
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<br>
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The book *_Astrophysics of Gaseous Nebulae*_ (Second edition, described [here](http://www.uscibooks.com/ost2.htm)) goes into most of the underlying physics. The output options given below will isolate which processes are important.
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... | ... | @@ -75,39 +89,72 @@ The *_save heating*_ and *_save cooling*_ commands will list heating and cooling |
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These provide enough information to fully understand the ionization and temperature of the gas.
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</details>
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## 5 How can I drive a C++ program like Cloudy from Fortran?
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<details close>
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<summary>
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<h2> 5 How can I drive a C++ program like Cloudy from Fortran? </h2>
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</summary>
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<br>
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It is possible to drive the current version of Cloudy, which is a C++ code, from existing Fortran programs without too much effort. A good approach is to use the cfortran.h header file described [here](http://www-zeus.desy.de/~burow/cfortran/).
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</details>
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## 6 Is it really necessary to read all of Hazy to find out which commands changed between versions Cxx and Cyy??
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<details close>
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<summary>
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<h2> 6 Is it really necessary to read all of Hazy to find out which commands changed between versions Cxx and Cyy?? </h2>
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</summary>
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<br>
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No. There is a list of changes between Cxx and Cyy are listed in the RevisionHistory page.
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</details>
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## 7 Many of the commands shown in Hazy have an underscore before or after a keyword. Why?
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<details close>
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<summary>
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<h2> 7 Many of the commands shown in Hazy have an underscore before or after a keyword. Why? </h2>
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</summary>
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<br>
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The underscore indicates a required space. The underscore should not be included.
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This is discussed in the chapter _Introduction to Commands_ in Part 1 of Hazy.
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</details>
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## 8 What are all the _assert_ commands in the test cases (Versions C08 and before)?
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## 8 What are all the _monitor_ commands in the test cases (Versions C10 and later)?
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<details close>
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<summary>
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<h2> 8 What are all the _assert_ commands in the test cases (Versions C08 and before)?
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<br> What are all the _monitor_ commands in the test cases (Versions C10 and later)? </h2>
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</summary>
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<br>
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All of the test cases that are part of the distribution include many _assert_ commands. These have nothing to do with the simulation or the astrophysics. Instead, they provide a way for the code to validate itself automatically. _Assert_ commands are described in Part I of Hazy and tell the code what answer it predicted in the past. If it does not obtain this answer it will print a comment. Here in Lexington the entire test suite is recomputed every night, and the _assert_ commands provide a way to discover whether any changes have affected predictions. The _assert_ commands can be safely removed or ignored. In fact the test suite includes a Perl script,
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`tests_remove_asserts.pl`, which will remove them automatically.
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The _assert_ command was renamed to _monitor_ in version C10 to avoid confusion over the C++ assert macro.
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</details>
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## 9 What is the name of the code?
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<details close>
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<summary>
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<h2> 9 What is the name of the code? </h2>
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</summary>
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<br>
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It's Cloudy, not CLOUDY. The tradition of capitalizing names of programs goes back to FORTRAN 77 and its predecessors. The ANSI/ISO standard required that source code be in capital letters. Modern languages allow mixed case. It's Cloudy.
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</details>
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## 10 Line intensities in the output from the save continuum command
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<details close>
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<summary>
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<h2> 10 Line intensities in the output from the save continuum command </h2>
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</summary>
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<br>
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All lines are included in the save output, but there are several tricky points. The basic problem is that the code knows what the intensity or luminosity of the line is, but it does not know over what frequency or wavelength range that energy is spread.
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... | ... | @@ -115,15 +162,27 @@ The line to continuum contrast is a linear function of the assumed line width. |
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All lines include contributions from continuum pumping. This component may or may not be a net contributor to the observed line, depending on whether the continuum source is in the beam. The pumped part of the line is not included in the save continuum output for this reason. Direct continuum excitation will generally be very important for clouds that are optically thin in the lines. The pumped contribution can be printed out separately.
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</details>
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## 11 Where are the emission lines identified?
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<details close>
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<summary>
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<h2> 11 Where are the emission lines identified? </h2>
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</summary>
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<br>
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See the Chapter _The Emission Lines_ in Part 3 of Hazy.
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You can produce a file with all the line labels and wavelengths with the _save line labels_ command. This output is produced by the _func_lines.in_ test case in the auto directory of the test suite.
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</details>
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## 12 What are the spectral features in the *_save continuum*_ output?
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<details close>
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<summary>
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<h2> 12 What are the spectral features in the *_save continuum*_ output? </h2>
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</summary>
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<br>
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Both lines and continua are present in the *_save continuum*_ output.
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The description of the command in Hazy 1 explains the various columns.
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... | ... | @@ -139,8 +198,14 @@ The _print line cell xx_ command can be used to print the label for all lines th |
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within a particular cell.
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You can look at the main output file to see which line is the strongest contributor.
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</details>
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## 13 A low-density cloud with solar (or higher) abundances seemed to crash or stop unexpectedly. What happened?
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<details close>
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<summary>
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<h2> 13 A low-density cloud with solar (or higher) abundances seemed to crash or stop unexpectedly. What happened? </h2>
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</summary>
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<br>
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The first thing to do in any calculation is to understand why the code stopped. In most cases it stops because the kinetic temperature falls below 4000K. This limit can be reset with the _stop temperature_ command. For classical nebulae the gas grows this cool only in neutral regions beyond the H^+^ - H^0^ ionization front, so the effect is to stop the calculation near this ionization front.
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... | ... | @@ -148,10 +213,15 @@ If the gas has solar or higher abundances, and the density is 1,000 cm^-3^ or lo |
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This is not a problem, and it should occur in real nebulae. It is not understood why pure recombination line H II regions are not observed. Cloudy stopped because the gas was too cool. To compute the full ionization structure you should lower the lowest electron temperature with the stop temperature command, say to something like *_stop temperature 100*_. But be aware that thermal instabilities can occur around 1000K where the cooling curve has a maximum due to fine structure cooling.
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</details>
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## 14 The output from a `punch` command is not really described in Hazy (C08 and before)
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## 14 The output from a `save` command is not really described in Hazy (C10 and later)
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<details close>
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<summary>
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<h2> 14 The output from a `punch` command is not really described in Hazy (C08 and before)
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<br> 14 The output from a `save` command is not really described in Hazy (C10 and later) </h2>
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</summary>
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<br>
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Many of the `save` commands are there for debugging and their output changes to suit circumstances.
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The documentation in Hazy is vague for these cases to minimize the workload and maximize accuracy.
|
... | ... | @@ -189,8 +259,14 @@ The code looks like |
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This process will reveal anything ambiguous about the `save` commands.
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</details>
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## 15 Predicted intensities of hydrogen and helium lines in version c08 and before
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<details close>
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<summary>
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<h2> 15 Predicted intensities of hydrogen and helium lines in version c08 and before </h2>
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</summary>
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<br>
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Hydrogen line intensities can be predicted with great precision when Case B applies.
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Ferguson and Ferland (1997) describe Cloudy’s hydrogen atom.
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... | ... | @@ -227,23 +303,44 @@ The code includes a model of the He^0^ atom that is applied all along the helium |
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The model can have an arbitrarily large number of levels.
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The predictions become more exact as the number of levels is increased but the calculations become slower.
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</details>
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## 16 What are the difference between the intrinsic and emergent line intensities in the main output?
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<details close>
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<summary>
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<h2> 16 What are the difference between the intrinsic and emergent line intensities in the main output? </h2>
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</summary>
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<br>
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See Hazy 1, Chapter _Grains_, section _Line intensities with grains_,
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and Hazy 2, Chapter _Observed Quantities_,
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section _Line intensities in a dusty cloud_.
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</details>
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## 17 A simulation with a power-law density law extends to a very large radius and small density, and there may be convergence problems
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<details close>
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<summary>
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<h2> 17 A simulation with a power-law density law extends to a very large radius and small density, and there may be convergence problems </h2>
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</summary>
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<br>
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See Hazy 1, Chapter "Density laws", section "Clouds extending to infinity"
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</details>
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<details close>
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<summary>
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<h2> 18 I want to save some quantity X as a function of depth, but there is no save command to do this. Is it OK to stop the simulation at various depths and combine the information? </h2>
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</summary>
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<br>
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## 18 I want to save some quantity X as a function of depth, but there is no save command to do this. Is it OK to stop the simulation at various depths and combine the information?
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In general, no. Stopping the sim at various depths will _not_ do the right thing. Stopping the model early will change the optical depth to the outer edge of the sim, which will affect physical conditions further in because the escape probability of the radiation is different. In short, stopping early will usually affect quantity X and you will often get the wrong answer that way. This is frequently asked in connection with saving the continuum. Note that there is a keyword EVERY to save the output of the SAVE CONTINUUM command in every zone. Otherwise, the best course of action is to post your problem to the discussion board (see point 1 above).
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</details>
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-----
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Go [home](home)
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... | ... | |