wiki:NextRelease

Version 225 (modified by matt, 4 years ago) (diff)

Add carbon line changes

New in Next Release

This page summarizes all major changes and improvements to Cloudy that will be included in the next release. You may also view the HotFixes and KnownProblems pages, or return to the main RevisionHistory page.

Parallel execution of grids

In a previous release of Cloudy we added support for parallel execution of model grids using MPI. In this release we added support for parallel execution based on the fork() system call. The big advantage of this approach is that no external packages or support libraries are needed. The disadvantage is that this method can only work on a single shared-memory machine. We offer this possibility enabled by default on all UNIX, Mac and Cygwin systems. On those machines, grid runs will run parallel using all available threads unless the user alters this behavior. This can be done using the grid sequential and grid ncpus options described below. We will continue to support MPI-based grid runs. This will be the preferred method for very large grids requiring more threads than a single node can offer.

Grids on Macs. By default this will use all available cores even if hyperthreading is enabled. Tests on a MacBook Pro show that the machine will become unresponsive if all hyperthreads are used. You can still set the number of cores using the grid ncpus option.

For very large MPI-based grid runs, gathering the main output files into a single (enormously large) output file can become a significant burden. We have therefore parallelized this part of the code using MPI I/O. There is also a new option grid separate described below which causes this step to be skipped.

New commands or options

The print iso collapsed command is now enabled by default and disabled with an additional off keyword. This change was motivated by a significant improvement to the treatment of collapsed levels in H-like and He-like isoelectronic sequence models. Note, however, that predictions from collapsed levels are still generally unreliable below the critical density for L-mixing at a particular principal quantum number.

Commas are no longer allowed to be embedded in numbers, they are treated as separators along with most other symbols. Standard exponential format 3.14159e16 can be used instead to make the scale of a number clear. This use of embedded commas has been deprecated for several versions, with warning prints issued.

The save species departure coefficients commands saves departure coefficients for any resolved species.

The save data sources command creates a list of atomic and molecular data sources.

The built-in abundance sets have been exported to external files located in the cloudy/data/abundances directory. These are much easier to add or change since updates no longer require editing the C++ source. There is no change in the abundances type commands which use these files.

The default composition, which will be used if nothing else is specified, is specified by the file cloudy/data/abundances/default.abn. The default composition can be updated by changing this file.

A new abundance "filename" command has been introduced. The chemical composition will be read from filename, which may be located in the current directory or in cloudy/data/abundances.

The abundance "filename" command has a print option to report grain types and abundances used.

The command crash bounds vector has been added to test array bounds violations in standard STL containers like e.g. vector.

When computing very large grids, gathering the main Cloudy output into a single output file can become a significant burden (and the resulting output file can become unmanageably large). To alleviate this problem, we have added the keyword SEPARATE to the grid command. This will cause the gathering of the main output files to be skipped (and the run to finish quicker). They will remain in files with names like: grid000000000_yoursimname.out, etc. If you still want to create the single output file later, this can be done with the command

cat grid*_yoursimname.out >> yoursimname.out

The new option grid sequential forces grids to be run on a single thread. This reverts the code to the behavior of C13 and before.

With the new option grid ncpus <n> you can choose how many threads the grid command will use while executing the grid. The default is to use all available threads.

The atom Lamda, atom Chianti, and atom Stout commands now have similar options to adjust or report which models are in place.

The command print lines off has been introduced, which may be used to omit printing the main line block in the output file. In parallel grids, this command has been found to lead to a great reduction in the size of the output file, and also to modest speed-ups.

By default, line intensities are now corrected for pumping by incident isotropic continuua. The command no lines subtract isotropic may be issued to forego the correction.

The command abundances isotopes may be used to specify isotope fractions for the isotopes of astrophysical interest. By default, the isotope abundances of Asplund+09 are used, with a couple of modifications (see data/abundances/default-iso.abn).

The command element name isotopes may be issued to modify the default isotopic abundances to user-specified values. For instance, the commands to specify isotope fractions for the hydrogen and carbon are now:

element hydrogen isotopes (1, 1) (2, 2e-5)
element carbon isotopes (12, 29) (13, 1)

The commands set 12C13C and set D/H have been removed.

The command element [name] isotopes [on, off] can be used to enable the use of isotopes with molecules. The command set isotopes all has been removed.

The AGN command now has a vary option to change the Big Bump temperature.

The chemistry reaction off command allows individual chemical reactions to be disabled, to study the impact of the reaction on the overall network.

Linear quantities in the save output

We are converting the save command output to report linear quantities. The save output had reported a mix of log and linear quantities. A log option has been added to report quantities in the old style, for backwards compatibility. The following commands now produce linear output:

  • save overview
  • save averages

Grain physics

Support has been added for alpha-SiC grains. The refractive index data were taken from Laor & Draine (1993) ApJ 402, 441 and the enthalpy function from Chekhovskoy (1971) J. Chem. Thermodynamics, 3, 289.

Multiplet sums or line blends in output

These often had been denoted by the label TOTL although there were many exceptions. They now have the label Blnd although we have tried to keep the wavelength the same.

Finding lines in the output

Previous versions had found the first line that came "close" to a specified line, we now go over the entire set of lines and find the "best" match.

As a result the line "H2 2.121m" would find a very faint high-v line rather than the expected 1-0 S(0) transition. We have added a "Blnd 2.121m" that is the sum of these three H2 lines, with intensities given in a typical H2 model

H2 2.12057m -22.528 0.0003
H2 2.12099m -20.696 0.0197
H2 2.12125m -18.991 1.0000

Default wavelength precision changed

The default wavelength precision has been changed from 4 significant figures to 6. The script tsuite/auto/fix_input_scripts_wl.pl is provided to aid with updating wavelengths in older input scripts to the new precision. This Perl script parses the output file for wavelength mismatches, and updates the input script, as well as any ini files and linelists invoked by the input script, to the higher precision wavelengths.

Stellar grids and other SEDs

The built-in SEDs have been exported to external files located in the cloudy/data/SED directory. These are much easier to add or change since updates no longer require editing the C++ source. There is no change in the table name commands which use these SEDs files.

A new table SED "filename" command has been introduced. The SED will be read from filename, which may be located in the current directory or in cloudy/data/SED.

Improved physics and numerical methods

Primordial abundances updated to Steigman arXiv:1208.0032. He/H is now 0.085 to be slightly smaller than photospheric abundances of Asplund+09 ARAA 47, 481.

The value of the Thomson cross section used in the code has been updated from 6.65e-25 cm2 to a more accurate value, approximately 6.6524587e-25 cm2, determined from other fundamental constants which are already stored and consistent with the CODATA recommended value.

Atomic/molecular data updates

HD cooling, when large HD model is not used, now comes from Flower et al. (2000), MNRAS, 314, 753 . Previous versions had used Puy, D., Grenacher, L, & Jetzer, P., 1999, A&A, 345, 723

The version has a major reworking of the atomic database. We have removed our internal database and replace with with a mix of data from Chianti or our own internal database.

All ions of S are now treated with external databases. S 4 through S 14 come from Chianti. S 2 and S 3 use our new Stout format. Collision strengths for IR lines in the ground term of S 3 are from Hudson C.E., Ramsbottom C.A., Scott M.P., 2012, ApJ, 750, 65 and are substantially different. This changes the electron temperature in some H II regions.

Fe III has been added to our Stout database.

All Chianti species have been updated from 7.0 to 7.1

The following Chianti species are now enabled by default:

  • Fe IV, V
  • S IV - XIV
  • Ni II
  • Na III - Na IX
  • Al II, III, V - XI

We are rationalizing our treatment of lines blends. They are now indicated by the label Blnd and a wavelength. The replaces the ad hoc method that had been used before, where the blends were often, but not always, indicated by TOTL.

The following lines have slightly changed wavelength due to improved data or are now listed as blends.

[Sulphur]

Before After
S 21256ABlnd1256A
S 24074ABlnd4074A
S 26720ABlnd6720A
S 21.033mBlnd1.033m
S II4070AS 24068.6A
S II4078AS 24076.35A
S II6716AS 26716.44A
S II6731AS 26730.82A
S II1.029mS 21.02867m
S II1.032mS 21.03205m
S II1.034mS 21.03364m
S II1.037mS 21.03705m
S 31198ABlnd1198A
S 31720ABlnd1720A
S 33722ABlnd3722A
S 36312AS 36312.06A
S 39069AS 39068.62A
S 39532AS 39530.62A
S 318.67mS 318.7078m
S 333.47mS 333.4704m
TOTL1406ABlnd1406A
S 41398AS 41398.04A
S 41405AS 41404.81A
S 41406AS 41406.02A
S 41417AS 41416.89A
S 41424AS 41423.84A
S 410.51mS 410.5076m
TOTL1198ABlnd1199A
S 51188AS 51188.28A
S 51198AS 51199.14A
S 5786.473AS 5786.470A
S 6933.378AS 6933.380A
S 6944.523AS 6944.524A
S 91.252mS 91.25201m
S 93.754mS 93.75414m
S 111.92010mS 111.91960m
S 111.39270mS 111.39238m

[Iron]

BeforeAfter
Fe 31125.79AFe 3Removed
Fe 73586.00AFe 73586.32A
Fe 73759.42AFe 73758.92A
Fe 74698.74AFe 74698.24A
Fe 74893.87AFe 74893.37A
Fe 74942.98AFe 74942.48A
Fe 74989.85AFe 74988.55A
Fe 75159.39AFe 75158.90A
Fe 75276.88AFe 75276.38A
Fe 75721.21AFe 75720.71A
Fe 76087.00AFe 76086.97A
Fe106375AFe106374.53A
Fe117892.30AFe117891.87A
Fe145303AFe145303.01A

[Vanadium]

BeforeAfter
V 71.304mV 71.30376m

[Calcium]

BeforeAfter
Ca 52413ACa 52412.87A
Ca 53998ACa 53997.88A
Ca 55309ACa 55309.11A
Ca 56086ACa 56086.37A
Ca 54.157mCa 54.15739m
Ca 511.48mCa 511.4792m

[Sodium]

BeforeAfter
Na 15891.94ABlnd5892A
Na 37.320mNa 37.31706m
Na 49.039mNa 49.03098m
Na 421.29mNa 421.3162m
Na 614.40mNa 614.3228m
Na 68.611mNa 68.61836m

[Scandium]

BeforeAfter
Sc 52.310mSc 52.31119m

[Aluminium]

BeforeAfter
Al 22660AAl 22660.35A
TOTL2665ABlnd2665A
Al 31855AAl 31854.72A
Al 31863AAl 31862.79A
TOTL1860ABlnd1860A
Al 52.90520mAl 52.90450m
Al 63.660mAl 63.65799m
Al 69.116mAl 69.13828m
Al 83.690mAl 83.69722m
Al 85.848mAl 85.82933m

[Argon]

BeforeAfter
Ar 26.980mAr 26.98337m
Ar 37135AAr 37135.79A
Ar 37751AAr 37751.11A
Ar 39.00mAr 38.98898m
Ar 321.83mAr 321.8253m
Ar 44740AAr 47135.79A
Ar 47331AAr 47751.11A
TOTL2860ABlnd2860A
TOTL4725ABlnd4725A
TOTL7250ABlnd7250A
Ar 57005AAr 57005.83A
Ar 58.000mAr 57.89971m
Ar 513.1mAr 513.0985m
Ar 64.530mAr 64.52800m

[Silicon]

BeforeAfter
Si 21263.32ASi 21264.74A
Si 21307.66ASi 21309.28A
Si 21531ASi 21533.43A
Si 21813.99ASi 21816.93A
Si 234.8140mSi 234.8046m
Si 31207ASi 31206.50A
Si 31883ASi 31882.71A
Si 31892ASi 31892.03A
Si 41394ASi 41393.75A
Si 41403ASi 41402.77A
Si 61.96310mSi 61.96247m
Si 72146.73ASi 72146.64A
Si 72.481mSi 72.48071m
Si 76.492mSi 76.51288m
Si 92.584mSi 92.58394m
Si 93.929mSi 93.92820m
Si101.430mSi101.43008m
totl1397ABlnd1397A
totl1888ABlnd1888A
totl2335ABlnd2335A

[Neon]

BeforeAfter
Ne 212.81mNe 212.8115m
Ne 315.55mNe 315.5503m
Ne 336.0140mNe 336.0132m
Ne 33869ANe 33868.75A
Ne 31814.56ANe 31814.63A
Ne 33342.18ANe 33342.42A
Ne 44720ANe 44724.17A
Ne 514.32mNe 514.3228m
Ne 524.31mNe 524.2065m
Ne 51141ANe 51136.51A
Ne 53426ANe 53426.03A
Ne 67.652mNe 67.64318m
Ne 8770.404ANe 8770.41A
Ne 8780.324ANe 8780.325A
Ne 42424.28Ablnd2424
totl774blnd774
totl895blnd895

[Chlorine]

BeforeAfter
Cl 28579ACl 28578.70A
Cl 33354ACl 33353.17A
Cl 48047ACl 48045.62A
Cl 97334ACl 97335.27A
totl5525blnd5525
totl3350blnd3350
totl8494blnd8494

[Magnesium]

BeforeAfter
Mg 44.485mMg 44.48712m
Mg 55.610mMg 55.60700m
Mg 513.52mMg 513.5464m
Mg 75.503mMg 75.50177m
Mg 79.033mMg 79.00655m
Mg 83.030mMg 83.02765m
Mg10609.793AMg10609.794A
Mg10624.941AMg10624.943A
totl615blnd615
totl2798blnd2798

[Carbon]

BeforeAfter
C  1369.7mC 1370.269m
C  1609.2mC 1609.590m
C  2157.6mC 2157.636m
C  31176C 31175.99
C  41548C 41548.19
C  41551C 41550.78
totl1549blnd1549
totl1909blnd1909
totl2326blnd2326
totl9850blnd9850

Enhancements for time-dependent cases

Other changes


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