- 15 Feb, 2021 2 commits
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Ferland, Gary authored
Maser See merge request !9
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Ferland, Gary authored
This adds a commented-out debug print statement to the routine that calls esc_CRDwing_1side. The report extends over the range of interesting optical depths. The range extends from close to the lower limit of the maser optical depths we can handle due to floating point limits to a high enough value well into the positive tau case. Note that this printout occurs for whatever damping constant the routine is called the first time. The print code exits after doing one loop. It does not test a range of damping constant and would not illustrate the problem being fixed on this branch.. An assert for positive escape probability has been added to esc_CRDwing_1side. That assert would have made it much easier to trace down the original thrown assert. Add tfile to list of ignored files. Improve the usefulness of error print when maser optical depth becomes too small by giving the smallest optical depth considered.
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- 08 Feb, 2021 2 commits
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Ferland, Gary authored
Correct algebra on line 197 to preserve intent of original source.
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Ferland, Gary authored
A sim that used all levels of the new Fe II and Fe III datasets threw an assert at Failed: escgrd_v > 0. It happened in the file ../rt_escprob.cpp at line number 330 It was due to a long-standing bug/oversight. The complete redistribution with wings escape probability did not protect against masers and a negative escape probability resulted. We now use the appropriate routine when the optical depth is negative. The sim follows. This oversight has been present for a long time. It is surprising that it has only now bitten. This is likely because we now have atomic models that are much larger than in the past. --- ```` set save prefix "assert" TURBULENCE= 0.600000 LOG 3.000000 species "Fe+" dataset="Smyth19" species "Fe+" levels=all species "Fe+2" levels=all stop column density 23 stop temperature exceeds 1e7 K print lines sort wavelength print lines column print lines faint 1 iterate print last hden 14 table SED "AGN_Jin12_Eddr_mid.sed" phi(H) 23 normalize to "Inci" 1215 scale factor = 1215 ````
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- 29 Jan, 2021 2 commits
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Chatzikos, Marios authored
Refactor dynamical iteration test into method See merge request !8
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Marios Chatzikos authored
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- 26 Jan, 2021 2 commits
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Ferland, Gary authored
Gargi Shaw docs CR background and PAH interactions See merge request !7
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Marios Chatzikos authored
A plethora of syntaxes exists across the code for testing whether an iteration is to be considered an initial relaxation iteration in dynamical models. For consistency, it is better for the task to be encapsulated in a function, and to call that instead. The only remaining instance of the check that is not replaced by the method call occurs in source/conv_itercheck.cpp, which applies to advective models. The intent there is to guarantee that one iteration is done after the initial ones with dynamical sources, and without declaring convergence prematurely. https://groups.google.com/g/cloudy-dev/c/3jd_sNqfCtE
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- 24 Jan, 2021 1 commit
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Ferland, Gary authored
This updates two parts of Hazy 1 and adds a citation to Shaw & Ferland (2021arXiv210103732S). The discussion reviews how the PAH abundance affects the cosmic ray secondary ionization rate and gives the recommended Galactic background for the case where PAHs are present. Our recommended default CR background rate remains the Indriolo+ value but we give the Cloudy command to change this rate to our recommended value when PAHs are present.
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- 20 Jan, 2021 4 commits
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Ferland, Gary authored
Docs See merge request !6
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Chatzikos, Marios authored
Silence Oracle compiler warning See merge request !5
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Marios Chatzikos authored
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Ferland, Gary authored
Gargi Shaw investigated why we have warnings about duplicate reactions in the development version. These still occur in release versions but have been silenced. Her document was converted to markdown and is posted on the GitLab wiki and is included here to make it easy to find.
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- 19 Jan, 2021 4 commits
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Marios Chatzikos authored
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Marios Chatzikos authored
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Chatzikos, Marios authored
Update monitors of two sims to new timestep logic See merge request !4
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Marios Chatzikos authored
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- 18 Jan, 2021 1 commit
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Marios Chatzikos authored
Incorporate changes to: - Revert adaptive timestep logic - Add 'save dt' command - Prevent FPEs in cooling sims with external radiation fields - Add columns for advective terms to save cool/heat - Force consistency of equilibrium solves in non-eq sims (bugfix) - Ensure consistent policy for equilibrium in non-eq runs
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- 17 Jan, 2021 4 commits
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Ferland, Gary authored
The notation in the description of the U and xi forms of the ionization parameter was slightly inconsistent, which caused problems for one user. These are updated. There is no change in content. The TexShop app on macOS cares a number of helper files to cross-reference the source and compiled text. These have been added to .gitignore
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Marios Chatzikos authored
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Marios Chatzikos authored
Code for deciding whether to include non-equilibrium terms in population solves was repeated across the codebase, allowing for inconsistencies to creep in. Establish and use method to ensure consistent treatment. https://groups.google.com/g/cloudy-dev/c/kFDQe9yq0Ts
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Marios Chatzikos authored
The command 'set dynamics population equilibrium' forced the solves for the populations of neutrals and ions to their steady-state setup, but it did not do so for molecules. Add checks for the command's status in the molecular network matrix setup to keep equilibrium treatment in non-equilibrium runs consistent across the different branches of the code. Reported-by: M. Chatzikos https://groups.google.com/g/cloudy-dev/c/kFDQe9yq0Ts
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- 21 Dec, 2020 3 commits
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Ferland, Gary authored
additional entries for .gitignore See merge request !3
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Ferland, Gary authored
## The documentation By default, we build both documentation and executables in folders below master. The code's documentation is in the docs/latex and we generate PDF copies of the three parts of Hazy and the QuickStart. The default .gitignore does ignore the latex helper files so only the final PDF needs be added. ## The executable We build in the sys_* directories below source. The default .gitignore does ignore the compiler-generated files so only a few implementation-dependent configuration files needed to be added. ## The test suite The tsuite directory has several folders, a large number of models, and an even larger number of files created during the test suite. My workflow involves regularly testing with gcc and llvm and on occasion with the Intel compiler. All three versions of the test suite should be available. I created three symbolic link folders, gtsuite, ltsuite, and itsuite, to hold the test suite for the gcc, llvm, and icc compilers. These three directories are ignored.
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Ferland, Gary authored
## The documentation By default, we build both documentation and executables in folders below master. The code's documentation is in the docs/latex and we generate PDF copies of the three parts of Hazy and the QuickStart. The default .gitignore does ignore the latex helper files so only the final PDF needs be added. ## The executable We build in the sys_* directories below source. The default .gitignore does ignore the compiler-generated files so only a few implementation-dependent configuration files needed to be added. ## The test suite The tsuite directory has several folders, a large number of models, and an even larger number of files created during the test suite. My workflow involves regularly testing with gcc and llvm and on occasion with the Intel compiler. All three versions of the test suite should be available. I created three symbolic link folders, gtsuite, ltsuite, and itsuite, to hold the test suite for the gcc, llvm, and icc compilers. These three directories are ignored.
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- 19 Dec, 2020 1 commit
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Marios Chatzikos authored
Superfluous spaces in the Makefile if-statement caused the script gitversion.sh to not be executed, except from a sys_* directory. Remove.
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- 16 Dec, 2020 5 commits
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Chatzikos, Marios authored
Adjust printed Cloudy version to Git See merge request !1
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Chatzikos, Marios authored
Clean out deprecated versioning variables See merge request !2
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Marios Chatzikos authored
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Marios Chatzikos authored
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Marios Chatzikos authored
Switching to a new workflow has made superfluous variables that tell if the code is in beta-version, or on a release branch. Delete them.
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- 12 Dec, 2020 1 commit
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Marios Chatzikos authored
As part of the switch to git, a new workflow is to be established. The previous practice of releasing every few years would better be replaced by a scheme where we release every few months. We seem to be gravitating toward a model where feature branches are merged onto master, which is merged onto a release branch for periodical releases. The Cloudy version reported in the .out file treats the release branch as any other, which would be opaque to users. The version number stored as a tag to the appropriate git commit is now employed as the Cloudy version in user-facing runs. Reported-by: M. Dehghanian https://groups.google.com/g/cloudy-dev/c/N_tKJTriDDw
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- 07 Dec, 2020 3 commits
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Marios Chatzikos authored
The output of the save cooling/heating commands treats advective heating and cooling terms ambiguously. It excludes them from the total when reporting fractional contributions, but reports them as contributing agents. As a result, advective terms with fractions >>100% are commonly encountered in cooling simulations. Add columns to report these contributions, but exclude them from the list of cooling/heating agents. https://groups.google.com/g/cloudy-dev/c/69NLm1Ru_cs
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Marios Chatzikos authored
Including external radiation fields (e.g., the CMB) in cooling sims may lead to FPEs. The cumulative radiation field intensity involves multiplication by a factor that may be near the maximum value a float can hold. This is not a problem with diffuse radiation. However, when the CMB is included, the product exceeds that limit and an FPE occurs. The adopted bugfix hides in a new class the details of how the integrated flux is accumulated, while preserving how the flux vectors are accessed. The latter is mainly useful for the instantaneous flux. As an added feature, the time-weighted mean flux is also computed. Reported-by: M. Chatzikos https://groups.google.com/g/cloudy-dev/c/GSWoDN_hxqc
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Marios Chatzikos authored
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- 04 Dec, 2020 1 commit
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Marios Chatzikos authored
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- 02 Dec, 2020 4 commits
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Milby, Jonathan S. authored
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Milby, Jonathan S. authored
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Milby, Jonathan S. authored
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Milby, Jonathan S. authored
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