Cloudy & Associates

  1. 15 Feb, 2021 2 commits
    • Ferland, Gary's avatar
      Merge branch 'maser' into 'master' · 4fe48fb5
      Ferland, Gary authored
      Maser
      
      See merge request !9
      4fe48fb5
    • Ferland, Gary's avatar
      Add debug print for special maser escape probability · c9e18a78
      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.
      c9e18a78
  2. 08 Feb, 2021 2 commits
    • Ferland, Gary's avatar
      BUGFIX to f3bc9247 · 5a84fee3
      Ferland, Gary authored
      Correct algebra on line 197 to preserve intent
      of original source.
      5a84fee3
    • Ferland, Gary's avatar
      BUGFIX - CRD with damping wings did not do masers · f3bc9247
      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
      ````
      f3bc9247
  3. 29 Jan, 2021 2 commits
  4. 26 Jan, 2021 2 commits
    • Ferland, Gary's avatar
      Merge branch 'docs' into 'master' · 3d178da0
      Ferland, Gary authored
      Gargi Shaw docs CR background and PAH interactions
      
      See merge request !7
      3d178da0
    • Marios Chatzikos's avatar
      Refactor dynamical iteration test into method · 204d69cb
      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
      204d69cb
  5. 24 Jan, 2021 1 commit
    • Ferland, Gary's avatar
      Gargi Shaw docs CR background and PAH interactions · 7cc0d453
      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.
      7cc0d453
  6. 20 Jan, 2021 4 commits
  7. 19 Jan, 2021 4 commits
  8. 18 Jan, 2021 1 commit
    • Marios Chatzikos's avatar
      Merge newdyna back onto master · 4e0bf1e8
      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
      4e0bf1e8
  9. 17 Jan, 2021 4 commits
  10. 21 Dec, 2020 3 commits
    • Ferland, Gary's avatar
      Merge branch 'gholding' into 'master' · 8b9a59c7
      Ferland, Gary authored
      additional entries for .gitignore
      
      See merge request !3
      8b9a59c7
    • Ferland, Gary's avatar
      additional entries for .gitignore · e68dbf67
      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.
      e68dbf67
    • Ferland, Gary's avatar
      # additional entries for .gitignore · 239c18fd
      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.
      239c18fd
  11. 19 Dec, 2020 1 commit
    • Marios Chatzikos's avatar
      Fix bug with setting REVISION · 67b5f87b
      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.
      67b5f87b
  12. 16 Dec, 2020 5 commits
  13. 12 Dec, 2020 1 commit
    • Marios Chatzikos's avatar
      Enable use of git tags in printed Cloudy versions · 940d8478
      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
      940d8478
  14. 07 Dec, 2020 3 commits
  15. 04 Dec, 2020 1 commit
  16. 02 Dec, 2020 4 commits