... | ... | @@ -12,17 +12,17 @@ Improved accuracy of H-like n=2 levels and resulting Ka lines. |
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Ability to select atomic data sets and add three new Fe II data collections.
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Added optional *_ISM-HD20.abn ISM abundances file which adopts Table 2 of [ 2020arXiv200900018H](https://ui.adsabs.harvard.edu/abs/2020arXiv200900018H/abstract)*_ for the elements they list.
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Added optional *ISM-HD20.abn ISM abundances file which adopts Table 2 of [ 2020arXiv200900018H](https://ui.adsabs.harvard.edu/abs/2020arXiv200900018H/abstract)* for the elements they list.
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The *_H,,2,, cosmic ray rates have been updated*_ as described in [2020RNAAS...4...78S](https://ui.adsabs.harvard.edu/abs/2020RNAAS...4...78S/abstract).
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The *H,,2,, cosmic ray rates have been updated* as described in [2020RNAAS...4...78S](https://ui.adsabs.harvard.edu/abs/2020RNAAS...4...78S/abstract).
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This resulted in factors of >= 2 changes intensities of some H,,2,, lines in certain models in the test suite.
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The *_save overview output now includes the 912A optical depth*_ to the illuminated face. Thanks to Vianney LeBouteiller for suggesting this on the user group.
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The *save overview output now includes the 912A optical depth* to the illuminated face. Thanks to Vianney LeBouteiller for suggesting this on the user group.
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Fix potential *_buffer overrun*_ for long species labels.
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Fix potential *buffer overrun* for long species labels.
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The following *_LineList files had an incorrect wavelength for C III 977*_, so the entry picked up a faint recombination line rather than the resonance line.
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The following *LineList files had an incorrect wavelength for C III 977*, so the entry picked up a faint recombination line rather than the resonance line.
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```
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data/LineList_BLR.dat
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data/LineList_BLR_Fe2.dat
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... | ... | @@ -30,9 +30,9 @@ data/LineList_HII.dat |
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data/LineList_NLR.dat
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```
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Allow populations of *_highly charged ions to become slightly negative*_ when most of the species is atomic. The solution converges to valid state.
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Allow populations of *highly charged ions to become slightly negative* when most of the species is atomic. The solution converges to valid state.
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Limit the number of levels in our baseline model of *_Na I to, at most the lowest, 142 levels*_ to avoid linear algebra problems.
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Limit the number of levels in our baseline model of *Na I to, at most the lowest, 142 levels* to avoid linear algebra problems.
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|
-------------
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... | ... | @@ -41,50 +41,51 @@ Limit the number of levels in our baseline model of *_Na I to, at most the lowes |
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Released 2020 Jan 24 at revision r13651
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The *_transition rates for forbidden lines of within the lowest three terms S II*_ have been updated to Irima and Froese Fischer Phys. Scr. 71, 172–184 (2005). C17 had used rates from Kisielius+ ApJ 780, 76 but these were not optimized for forbidden lines. This returns the [S II] density diagnostics to their classical values. Thanks to Christophe Morisset for pointing this out.
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The *transition rates for forbidden lines of within the lowest three terms S II* have been updated to Irima and Froese Fischer Phys. Scr. 71, 172–184 (2005). C17 had used rates from Kisielius+ ApJ 780, 76 but these were not optimized for forbidden lines. This returns the [S II] density diagnostics to their classical values. Thanks to Christophe Morisset for pointing this out.
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The *_collision strengths involving He I 2 ^3^P*_ had been at their LS values. These are now split for fine structure. Thanks to Giulio Del Zanna for reporting this.
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The *collision strengths involving He I 2 ^3^P* had been at their LS values. These are now split for fine structure. Thanks to Giulio Del Zanna for reporting this.
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A *_bug in the grain code has been fixed*_ that could lead to a failed assert when using the *set continuum resolution 0.1* command. See [wiki:HotFixes_17] for details.
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A *bug in the grain code has been fixed* that could lead to a failed assert when using the *set continuum resolution 0.1* command. See [wiki:HotFixes_17] for details.
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The code will *_no longer print warnings about exceeding the grain sublimation temperature*_ when the *function sublimation* keyword has been used on the grain command.
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The code will *no longer print warnings about exceeding the grain sublimation temperature* when the *function sublimation* keyword has been used on the grain command.
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A *_bug causing the optimize column density and optimize temperature commands to read the element names incorrectly*_ has been fixed.
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A *bug causing the optimize column density and optimize temperature commands to read the element names incorrectly* has been fixed.
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The *_transition probabilities and collision strengths for P II have been updated*_. This adds important missing lines, such as the 3P-1D forbidden lines at 1.14682m and 1.18828m. This update will substantially change the predictions for the P II spectrum.
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The *transition probabilities and collision strengths for P II have been updated*. This adds important missing lines, such as the 3P-1D forbidden lines at 1.14682m and 1.18828m. This update will substantially change the predictions for the P II spectrum.
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A *_bug causing the LINEAR keyword on the PRINT LINE COLUMN command not to work*_ has been fixed.
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A *bug causing the LINEAR keyword on the PRINT LINE COLUMN command not to work* has been fixed.
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A *_bug prohibiting the use of monotonically increasing wavelengths in a TABLE SED file*_ has been fixed.
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A *bug prohibiting the use of monotonically increasing wavelengths in a TABLE SED file* has been fixed.
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A *_bug in the metals command has been fixed*_ where the *_metals deplete*_ command would reset the multiplication factor set by the regular *_metals*_ command, thus making the results dependent on the order of these two commands.
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A *bug in the metals command has been fixed* where the *metals deplete* command would reset the multiplication factor set by the regular *metals* command, thus making the results dependent on the order of these two commands.
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The blend Inwd 1035 (for O VI) contained the wrong components. This has now been fixed.
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The *_save transmitted continuum command now also works in luminosity mode*_ and the keyword *_last*_ is now implicitly assumed to avoid useless output. The format of the *_save transmitted continuum*_ output has changed, so output from previous versions will no longer be accepted. See the discussion of the *_table read*_ command in Hazy 1 for further information on how spherical dilution is handled when the *_scale*_ keyword is used.
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The *save transmitted continuum command now also works in luminosity mode* and the keyword *last* is now implicitly assumed to avoid useless output. The format of the *save transmitted continuum* output has changed, so output from previous versions will no longer be accepted. See the discussion of the *table read* command in Hazy 1 for further information on how spherical dilution is handled when the *scale* keyword is used.
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A bug has been fixed that could lead to a failed sanity check when running with a very high resolution frequency mesh. As a result the photoionization thresholds now have a slightly different energy, but the wavelengths of the radiative recombination continuum entries on the line stack remain unchanged.
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A bug has been fixed where *_two Blnd lines were missing components*_. The components that have been added are shown in boldface below.
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| Blnd 1657 | **C 1 1656.27** |
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A bug has been fixed where *two Blnd lines were missing components*. The components that have been added are shown in boldface below.
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| Blnd 1657 | C 1 1656.27 |
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|-----------|------------------|
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| | **C 1 1656.93** |
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| | C 1 1656.93 |
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| | C 1 1657.01 |
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| | **C 1 1657.38** |
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| | **C 1 1657.91** |
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| | **C 1 1658.12** |
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| | C 1 1657.38 |
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| | C 1 1657.91 |
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| | C 1 1658.12 |
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| Blnd 6580 | C 2 6578.05 |
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| | **C 2 6582.88** |
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| | C 2 6582.88 |
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The *_NGC 5548 SED has been revised*_ to use data used in [Mehdipour+ A&A 575, A22 (2015)](https://ui.adsabs.harvard.edu/#abs/2015A%26A...575A..22M/abstract). This new SED was used in [2018arXiv181211578D](https://ui.adsabs.harvard.edu/#abs/2018arXiv181211578D/abstract).
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The *NGC 5548 SED has been revised* to use data used in [Mehdipour+ A&A 575, A22 (2015)](https://ui.adsabs.harvard.edu/#abs/2015A%26A...575A..22M/abstract). This new SED was used in [2018arXiv181211578D](https://ui.adsabs.harvard.edu/#abs/2018arXiv181211578D/abstract).
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A bug has been fixed where *_transmitted continua generated in a grid could not be read*_ by the code. The *_save transmitted continuum*_ command now ignores the *_units*_ keyword (using different units never worked when reading the file) and it now implicitly saves to separate files in a grid (since Cloudy cannot read a concatenated file).
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A bug has been fixed where *transmitted continua generated in a grid could not be read* by the code. The *save transmitted continuum* command now ignores the *units* keyword (using different units never worked when reading the file) and it now implicitly saves to separate files in a grid (since Cloudy cannot read a concatenated file).
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A bug has been fixed where the *_AGN*_ command would read the initial value for the temperature incorrectly in an optimizer run.
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A bug has been fixed where the *AGN* command would read the initial value for the temperature incorrectly in an optimizer run.
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A bug leading to *_temperature convergence failures when using the big H2 model*_ in conditions where fluorescence is significant and the molecules are cold, has been fixed.
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A bug leading to *temperature convergence failures when using the big H2 model* in conditions where fluorescence is significant and the molecules are cold, has been fixed.
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|
*_Predictions for Fe Ka*_ have been improved to include one and two-electron emission in addition to inner shell fluorescence. The total Ka is now a bit stronger as a result. The line labels, wavelengths, and description are now
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|
*Predictions for Fe Ka* have been improved to include one and two-electron emission in addition to inner shell fluorescence. The total Ka is now a bit stronger as a result. The line labels, wavelengths, and description are now
|
|
|
```
|
|
|
167592 FeKa 1.78000A # total intensity of Fe K-alpha line, grain, cold, hot, 1 and 2 electron
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|
167593 FeK1 1.78177A # H-like one-electron Ka
|
... | ... | @@ -94,7 +95,7 @@ A bug leading to *_temperature convergence failures when using the big H2 model* |
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|
167597 FeKG 1.75000A # grain production of cold iron
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|
|
```
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|
*_Recombination coefficient for [O III] 4363*_ updated to a mix of Pequignot and Liu suggested by Christophe Morisset. These run about two times smaller than the previous Burgess and Seaton values.
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*Recombination coefficient for [O III] 4363* updated to a mix of Pequignot and Liu suggested by Christophe Morisset. These run about two times smaller than the previous Burgess and Seaton values.
|
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|
|
|
-------------
|
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|
... | ... | @@ -103,23 +104,23 @@ A bug leading to *_temperature convergence failures when using the big H2 model* |
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|
Released 2018 April 18 at revision r12085
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|
We now consistently report *_mean line optical depth*_s in the `print line optical depth` and `save line optical depth` commands.
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|
We now consistently report *mean line optical depth*s in the `print line optical depth` and `save line optical depth` commands.
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|
A *_bug in the save continuum output for the case of a spherical cloud computed in the intensity case*_ has been fixed. The bug resulted in an incorrect geometric factor being applied to the transmitted components of the predicted continuum. In c17.00 the transmitted components would have been a factor (!Rout/Rin)^2^ too low as a result of this bug.
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|
A *bug in the save continuum output for the case of a spherical cloud computed in the intensity case* has been fixed. The bug resulted in an incorrect geometric factor being applied to the transmitted components of the predicted continuum. In c17.00 the transmitted components would have been a factor (!Rout/Rin)^2^ too low as a result of this bug.
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|
A bug causing *_the reflected components of the SAVE CONTINUUM output to have the wrong normalization*_ has been fixed. This would affect spherical models with an open geometry in the luminosity case. See [wiki:HotFixes_17] for details. In c17.00 the reflected components would have been a factor (!Rout/Rin)^2^ too high as a result of this bug.
|
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|
A bug causing *the reflected components of the SAVE CONTINUUM output to have the wrong normalization* has been fixed. This would affect spherical models with an open geometry in the luminosity case. See [wiki:HotFixes_17] for details. In c17.00 the reflected components would have been a factor (!Rout/Rin)^2^ too high as a result of this bug.
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|
*_A bug on the _n_-changing collisional effective rates has been fixed*_. The bug was treating collapsed level transitions as resolved and produced much higher values that they should have. Moreover, collisional rates based on Vriens and Smeets PRA **22** (1980) 940 formulas now use Johnson **174** (1972) 227 transition probabilities to ensure total reproducibility of V&S (1980) results.
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|
*A bug on the _n_-changing collisional effective rates has been fixed*. The bug was treating collapsed level transitions as resolved and produced much higher values that they should have. Moreover, collisional rates based on Vriens and Smeets PRA **22** (1980) 940 formulas now use Johnson **174** (1972) 227 transition probabilities to ensure total reproducibility of V&S (1980) results.
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|
A bug causing *_the SAVE XSPEC command to produce faulty FITS files*_ has been fixed. Several other bugs in this command were also fixed, such as the covering factor being omitted in each of the reflected components of the spectrum.
|
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|
A bug causing *the SAVE XSPEC command to produce faulty FITS files* has been fixed. Several other bugs in this command were also fixed, such as the covering factor being omitted in each of the reflected components of the spectrum.
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|
|
A new option to normalize the spectra in the SAVE XSPEC FITS files has been added. See Hazy 1 for details.
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|
Support for the [Khaire & Srianand (2019)](http://adsabs.harvard.edu/abs/2019MNRAS.484.4174K) extragalactic background calculations has been added. For this a new command *_table ks18*_ has been created (support was added in 2018, before the paper was accepted). See Hazy 1 for further details.
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|
Support for the [Khaire & Srianand (2019)](http://adsabs.harvard.edu/abs/2019MNRAS.484.4174K) extragalactic background calculations has been added. For this a new command *table ks18* has been created (support was added in 2018, before the paper was accepted). See Hazy 1 for further details.
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|
The SED produced by the *_table SED NGC5548*_ command has been extrapolated into the radio and gamma-ray using asymptotic slopes. This is to make the SED more physical and similar to those used in AGN STORM models.
|
|
|
The SED produced by the *table SED NGC5548* command has been extrapolated into the radio and gamma-ray using asymptotic slopes. This is to make the SED more physical and similar to those used in AGN STORM models.
|
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|
|
|
A bug potentially causing *_part of the SED from a stellar atmosphere grid to be omitted*_ has been fixed. Investigation of the standard grids supported by Cloudy (i.e. those covered by the *_compile stars*_ command) shows the effect of this bug is benign. The situation for other grids is not clear and could potentially be more serious (e.g. SEDs taken from the PoWR grids). It is recommended to recompile the binary stellar atmosphere files, otherwise the fix will not have any effect (unless you work directly on the ascii files of course).
|
|
|
A bug potentially causing *part of the SED from a stellar atmosphere grid to be omitted* has been fixed. Investigation of the standard grids supported by Cloudy (i.e. those covered by the *compile stars* command) shows the effect of this bug is benign. The situation for other grids is not clear and could potentially be more serious (e.g. SEDs taken from the PoWR grids). It is recommended to recompile the binary stellar atmosphere files, otherwise the fix will not have any effect (unless you work directly on the ascii files of course).
|
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|
|
A bug has been fixed that could cause line labels to be parsed incorrectly under certain circumstances (see [wiki:KnownProblems_17]). The solution is to make the parser stricter, resulting in the following user-visible changes:
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|
|
* The species label must start in column 1, regardless of whether it is quoted or not.
|
... | ... | @@ -203,45 +204,45 @@ Created from trunk 2016 Dec 21 at revision r11425 |
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|
|
## Caveats
|
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|
|
The atomic emission models have been moved to external databases with far more lines now being predicted. In many cases *_line wavelengths have changed*_.
|
|
|
Most line *_blends are now reported with the label Blnd*_.
|
|
|
The atomic emission models have been moved to external databases with far more lines now being predicted. In many cases *line wavelengths have changed*.
|
|
|
Most line *blends are now reported with the label Blnd*.
|
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|
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|
|
We started to convert the *_save command output to report linear quantities*_. See below for further details.
|
|
|
We started to convert the *save command output to report linear quantities*. See below for further details.
|
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|
|
*_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. Using commas embedded in numbers was deprecated since C10.
|
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|
*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. Using commas embedded in numbers was deprecated since C10.
|
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|
|
|
|
The *_set line precision command is renamed to print line precision*_.
|
|
|
The *set line precision command is renamed to print line precision*.
|
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|
|
|
The commands *_set 12C13C*_ and *_set D/H*_ have been removed. Please use the command *_element <name> isotopes*_ instead. The command *_set isotopes all*_ has also been removed.
|
|
|
The commands *set 12C13C* and *set D/H* have been removed. Please use the command *element <name> isotopes* instead. The command *set isotopes all* has also been removed.
|
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|
|
*_Using the header file path.h to set the search path for Cloudy is now deprecated*_ and will be removed in a future release. The search path will be automatically set when compiling the code with _make_. The search path can be modified using the environment variable CLOUDY_DATA_PATH as described in the EditPath page.
|
|
|
*Using the header file path.h to set the search path for Cloudy is now deprecated* and will be removed in a future release. The search path will be automatically set when compiling the code with make. The search path can be modified using the environment variable CLOUDY_DATA_PATH as described in the EditPath page.
|
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|
|
|
|
The *_save column densities*_ command is now an option to the more flexible and general *_save species*_ command, the original command has been removed.
|
|
|
The *save column densities* command is now an option to the more flexible and general *save species* command, the original command has been removed.
|
|
|
|
|
|
When using Cloudy as a subroutine, *_you should open output files using a call to open_data()*_ rather than fopen(). The latter will result in a compilation error. An example would be:
|
|
|
When using Cloudy as a subroutine, *you should open output files using a call to open_data()* rather than fopen(). The latter will result in a compilation error. An example would be:
|
|
|
```
|
|
|
FILE* io = open_data("sample.out", "w");
|
|
|
```
|
|
|
With this routine there is no need to check for a NULL pointer on return as open_data() will have done that already.
|
|
|
|
|
|
We have fixed problems with the frequency mesh generation and improved the overall resolution of the standard mesh. As a result *_compiled stellar atmosphere grids and user-defined grain opacity files need to be recompiled*_ to match the new frequency mesh if you want to continue using them. See below for further details.
|
|
|
We have fixed problems with the frequency mesh generation and improved the overall resolution of the standard mesh. As a result *compiled stellar atmosphere grids and user-defined grain opacity files need to be recompiled* to match the new frequency mesh if you want to continue using them. See below for further details.
|
|
|
|
|
|
The compiler options have been changed in such a way that *_Cloudy is now optimized for the specific hardware it is being compiled on*_. This was done to take full advantage of AVX vectorizing instructions on supporting hardware. This reduces the portability of the executable as it may no longer run on other hardware that doesn't support the same instruction set. In that case you will need to recompile the code.
|
|
|
The compiler options have been changed in such a way that *Cloudy is now optimized for the specific hardware it is being compiled on*. This was done to take full advantage of AVX vectorizing instructions on supporting hardware. This reduces the portability of the executable as it may no longer run on other hardware that doesn't support the same instruction set. In that case you will need to recompile the code.
|
|
|
|
|
|
We *_stopped testing on 32-bit platforms.*_ We believe that only very few 32-bit systems are still in use today. In the unlikely case you have such a system, you can still try to use Cloudy (though switching to a 64-bit system is preferred). Chances are the code will still compile correctly, but the grid_h2coronal test case in the auto test suite will certainly fail due to single-process memory limitations on 32-bit systems (see also below).
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|
|
We *stopped testing on 32-bit platforms.* We believe that only very few 32-bit systems are still in use today. In the unlikely case you have such a system, you can still try to use Cloudy (though switching to a 64-bit system is preferred). Chances are the code will still compile correctly, but the grid_h2coronal test case in the auto test suite will certainly fail due to single-process memory limitations on 32-bit systems (see also below).
|
|
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|
|
The *_grid_h2coronal test case in the auto test suite may fail on systems with a limited amount of memory*_ (4 GiB or less) due to memory exhaustion. This is true both on 32-bit and 64-bit systems (though on 32-bit systems the failure is guaranteed). This particular sim needs a large amount of memory because all model atoms are set to the maximum size. You can skip this sim when running the test suite by creating a file called _tsuite/auto/skip.dat_ that contains only the text _grid_h2coronal.in_ before starting the test suite.
|
|
|
The *grid_h2coronal test case in the auto test suite may fail on systems with a limited amount of memory* (4 GiB or less) due to memory exhaustion. This is true both on 32-bit and 64-bit systems (though on 32-bit systems the failure is guaranteed). This particular sim needs a large amount of memory because all model atoms are set to the maximum size. You can skip this sim when running the test suite by creating a file called _tsuite/auto/skip.dat_ that contains only the text _grid_h2coronal.in_ before starting the test suite.
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|
|
|
|
|
## 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.
|
|
|
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.
|
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|
|
*_Grids on Macs*_. By default this will use all available physical cores even if hyperthreading is enabled.
|
|
|
*Grids on Macs*. By default this will use all available physical cores even if hyperthreading is enabled.
|
|
|
Tests on a MacBook Pro show that the machine will become unresponsive if all hyperthreads are used, so this is not done by default.
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|
|
You can still set the number of cores using the *_grid ncpus*_ option.
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|
|
You can still set the number of cores using the *grid ncpus* option.
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|
|
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.
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|
|
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.
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|
## The code is faster!
|
... | ... | @@ -251,11 +252,11 @@ There is a significant performance improvement, approaching a factor of two comp |
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|
## New commands or options
|
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The *_monitor departure coeffcients*_ command now accepts levels as part of the input species., e.g., *_monitor departure coefficients "C+4![3]"*_.
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The *monitor departure coeffcients* command now accepts levels as part of the input species., e.g., *monitor departure coefficients "C+4![3]"*.
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The *_table HM12 command has been added*_ implementing the Haardt & Madau (2012) grid of background continua. The command works the same way as the *_table HM05*_ command, except that the keyword *_quasar*_ is not supported (since data files for the quasar-only case do not exist). This command uses the stellar grid infrastructure under the hood to do the interpolation. The *_table HM05*_ command has also been moved over to use this infrastructure, but this should be transparent to the user.
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The *table HM12 command has been added* implementing the Haardt & Madau (2012) grid of background continua. The command works the same way as the *table HM05* command, except that the keyword *quasar* is not supported (since data files for the quasar-only case do not exist). This command uses the stellar grid infrastructure under the hood to do the interpolation. The *table HM05* command has also been moved over to use this infrastructure, but this should be transparent to the user.
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The *_table star "somegrid.ascii" <par1> <par2> ...*_ and *_table star list "somegrid.ascii"*_ commands can now work directly on ascii files without the need to compile them first. They continue to work on binary files as well.
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The *table star "somegrid.ascii" <par1> <par2> ...* and *table star list "somegrid.ascii"* commands can now work directly on ascii files without the need to compile them first. They continue to work on binary files as well.
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The command *set UTA off* may be used to disable all UTA emission lines.
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The command *set UTA Gu06* is now *obsolete*; the Behar & Netzer data have been *removed*.
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... | ... | @@ -293,46 +294,46 @@ commands provides this functionality when the |
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The command *set atomic data H2 collisions* is now an option to the command *database H2*.
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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.
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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.
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*_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.
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*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.
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The *_save species departure coefficients*_ commands saves *_departure coefficients for any resolved species*_.
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The *save species departure coefficients* commands saves *departure coefficients for any resolved species*.
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The *_save data sources command*_ creates a *_list of atomic and molecular data sources*_.
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The *save data sources command* creates a *list of atomic and molecular data sources*.
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The *_save fine opacities and save fine optical depths*_ have an *_all option*_ to report all points, even zeros.
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The *save fine opacities and save fine optical depths* have an *all option* to report all points, even zeros.
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The *_built-in abundance sets have been exported to external files*_
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The *built-in abundance sets have been exported to external files*
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located in the `cloudy/data/abundances` directory.
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These are much easier to add or change since updates no longer require editing the C++ source.
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There is no change in the *_abundances type*_ commands which use these files.
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There is no change in the *abundances type* commands which use these files.
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The *_default composition*_, which will be used if nothing else is specified, is *_specified by the file*_
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The *default composition*, which will be used if nothing else is specified, is *specified by the file*
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`cloudy/data/abundances/default.abn`.
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The default composition can be updated by changing this file.
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A new *_abundance "filename"*_ command has been introduced.
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A new *abundance "filename"* command has been introduced.
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The chemical composition will be read from `filename`,
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which may be located in the current directory or in `cloudy/data/abundances`.
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The *_abundance "filename" command has a print option*_ to report grain types and abundances used.
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The *abundance "filename" command has a print option* to report grain types and abundances used.
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The command *_crash bounds vector*_ has been added to test array bounds violations in standard STL containers like e.g. vector.
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The command *crash bounds vector* has been added to test array bounds violations in standard STL containers like e.g. vector.
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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
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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
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```
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cat grid*_yoursimname.out >> yoursimname.out
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```
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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.
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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.
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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.
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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.
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The *_database Lamda, database Chianti, and database Stout commands now have similar options*_ to adjust or report which models are in place.
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The *database Lamda, database Chianti, and database Stout commands now have similar options* to adjust or report which models are in place.
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The *_species "name"*_ command allows individual species to be adjusted: at the moment, molecular species can be fully disabled, and the number of levels included for species modelled using Chianti, Lamda or Stout data can be set.
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The *species "name"* command allows individual species to be adjusted: at the moment, molecular species can be fully disabled, and the number of levels included for species modelled using Chianti, Lamda or Stout data can be set.
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The commands
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```
|
... | ... | @@ -351,53 +352,53 @@ proper luminosities in the luminosity case__'. The set save luminosity old will |
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cause the old style to be used.
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By default, line intensities are now corrected for pumping by incident isotropic continuua.
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The command *_no lines subtract isotropic*_ may be issued to forego the correction.
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The command *no lines subtract isotropic* may be issued to forego the correction.
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The command *_abundances isotopes*_ may be used to specify isotope fractions for the
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The command *abundances isotopes* may be used to specify isotope fractions for the
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isotopes of astrophysical interest. By default, the isotope abundances of
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[Asplund+09](http://adsabs.harvard.edu/abs/2009ARA%26A..47..481A) are used, with a couple of
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modifications (see data/abundances/default-iso.abn).
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The command *_element <name> isotopes*_ may be issued to modify the default isotopic
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The command *element <name> isotopes* may be issued to modify the default isotopic
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abundances to user-specified values.
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For instance, the commands to specify isotope fractions for the hydrogen and carbon are now:
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```
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element hydrogen isotopes (1, 1) (2, 2e-5)
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|
element carbon isotopes (12, 29) (13, 1)
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|
```
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The commands *_set 12C13C*_ and *_set D/H*_ have been removed.
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The commands *set 12C13C* and *set D/H* have been removed.
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By default we report line wavelengths in air for wavelengths longward of 2000A.
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The *_print line vacuum command will use vacuum wavelengths throughout*_.
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The *print line vacuum command will use vacuum wavelengths throughout*.
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The *_set line precision command is renamed to print line precision*_.
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The *set line precision command is renamed to print line precision*.
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The command *_element <name> isotopes [on, off]*_ can be used to enable the use of
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isotopes with molecules. The command *_set isotopes all*_ has been removed.
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The command *element <name> isotopes [on, off]* can be used to enable the use of
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isotopes with molecules. The command *set isotopes all* has been removed.
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The *_AGN command now has a vary option*_ to change the Big Bump temperature.
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The *AGN command now has a vary option* to change the Big Bump temperature.
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The *_chemistry reaction off*_ command allows individual chemical reactions to be disabled, to study the impact of the reaction on the overall network.
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The *chemistry reaction off* command allows individual chemical reactions to be disabled, to study the impact of the reaction on the overall network.
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The *_print voigt*_ command has been merged into the *_drive voigt*_ command, the user can now specify the filename used to save the results (or give no
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The *print voigt* command has been merged into the *drive voigt* command, the user can now specify the filename used to save the results (or give no
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name for in-line output).
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The *_drive gaunt check*_ command has been added. This exercises the routine for generating the Gaunt free-free factors and checks if it produces any discontinuities.
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The *drive gaunt check* command has been added. This exercises the routine for generating the Gaunt free-free factors and checks if it produces any discontinuities.
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The *_compile gaunt factors*_ command has been removed. This functionality has now been taken over by an external program. The *_trace gaunt*_ option has also been removed as the output it produced wasn't very helpful.
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The *compile gaunt factors* command has been removed. This functionality has now been taken over by an external program. The *trace gaunt* option has also been removed as the output it produced wasn't very helpful.
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The *_stop column density "species" command*_ will allow the column density or any species, atom, ion, or molecule, to be specified.
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The *stop column density "species" command* will allow the column density or any species, atom, ion, or molecule, to be specified.
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The *_tlaw*_ command now has a *_table*_ option, similar in function to the existing *_dlaw table*_ command.
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The *tlaw* command now has a *table* option, similar in function to the existing *dlaw table* command.
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The *_table read*_ command now has a *_scale*_ option allowing the intensity of the continuum to be set by re-scaling the output from the previous calculation.
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The *table read* command now has a *scale* option allowing the intensity of the continuum to be set by re-scaling the output from the previous calculation.
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The *_drive pointers*_ command has been removed.
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|
The *drive pointers* command has been removed.
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|
## Linear quantities in the save output
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|
We are converting the *_save command output to report linear quantities*_. The save output had
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|
We are converting the *save command output to report linear quantities*. The save output had
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|
|
reported a mix of log and linear quantities.
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|
|
A log option has been added to report quantities in the old style, for backwards compatibility.
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|
The following commands now produce linear output:
|
... | ... | @@ -426,9 +427,9 @@ invoke Cloudy as a function to solve (subgrid) micro-physics. |
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The default H,,2,, grain formation rate has been updated to the formalism quoted by Rollig+ 2013, A&A, 549, A85, which includes the Eley-Rideal process.
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|
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.
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|
|
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.
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*_The AC1 and BE1 amorphous carbon refractive index files have been updated.*_ An incorrect beta=2 extrapolation of the laboratory data has been removed. The opacity will now have an expected slope close to beta=1 towards long wavelengths.
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|
*The AC1 and BE1 amorphous carbon refractive index files have been updated.* An incorrect beta=2 extrapolation of the laboratory data has been removed. The opacity will now have an expected slope close to beta=1 towards long wavelengths.
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|
|
|
|
```
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|
... | ... | @@ -453,7 +454,7 @@ As a result the line "H2 2.121m" would find a very faint high-v line rather than |
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|
## Default wavelength precision changed
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|
The default wavelength precision has been changed from 4 significant figures to 6.
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|
The script *_tsuite/auto/fix_input_scripts_wl.pl*_ is provided to aid with
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|
The script *tsuite/auto/fix_input_scripts_wl.pl* is provided to aid with
|
|
|
updating wavelengths in older input scripts to the new precision.
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|
|
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
|
... | ... | @@ -463,29 +464,29 @@ script, to the higher precision wavelengths. |
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|
## Stellar grids and other SEDs
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|
The *_built-in SEDs have been exported to external files*_ located in the `cloudy/data/SED` directory.
|
|
|
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.
|
|
|
There is no change in the *table name* commands which use these SEDs files.
|
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|
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|
|
A new *_table SED "filename"*_ command has been introduced.
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|
|
A new *table SED "filename"* command has been introduced.
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|
|
The SED will be read from `filename`, which may be located in the current directory or in `cloudy/data/SED`.
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## Improved physics and numerical methods
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|
*_The [Lique 2015](http://adsabs.harvard.edu/abs/2015MNRAS.453..810L) H,,2,, collision data are available*_ but not enabled by default at this time.
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|
*The [Lique 2015](http://adsabs.harvard.edu/abs/2015MNRAS.453..810L) H,,2,, collision data are available* but not enabled by default at this time.
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|
|
*_O III collision strengths updated to [ Storey](http://adsabs.harvard.edu/abs/2014MNRAS.441.3028S)+14*_
|
|
|
*O III collision strengths updated to [ Storey](http://adsabs.harvard.edu/abs/2014MNRAS.441.3028S)+14*
|
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|
|
*_The method for generating the frequency mesh has been rewritten from scratch*_. This should solve the long-standing problem where generating a frequency mesh with non-standard parameters would lead to obscure failed asserts while running the code. Since this change invalidates all existing compiled stellar atmosphere and grain opacity files on its own, we decided to combine it with a lowering of the lower frequency limit to 10 MHz (this is the lowest frequency LOFAR can observe). We also increased the standard resolving power to 300 and extended the range where this resolving power is used to 900 Ryd so that all atomic lines are included in that range. As a result, the number of frequency cells has risen from 5277 to 8228 in the standard setup.
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|
*The method for generating the frequency mesh has been rewritten from scratch*. This should solve the long-standing problem where generating a frequency mesh with non-standard parameters would lead to obscure failed asserts while running the code. Since this change invalidates all existing compiled stellar atmosphere and grain opacity files on its own, we decided to combine it with a lowering of the lower frequency limit to 10 MHz (this is the lowest frequency LOFAR can observe). We also increased the standard resolving power to 300 and extended the range where this resolving power is used to 900 Ryd so that all atomic lines are included in that range. As a result, the number of frequency cells has risen from 5277 to 8228 in the standard setup.
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|
|
Primordial abundances updated:
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|
|
He/H updated to Planck concordance, (2014, A&A, 571, A16 http://adsabs.harvard.edu/abs/2014A%26A...571A..16P) .
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|
|
Other light elements updated to Steigman arXiv:1208.0032.
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|
|
The value of the *_Thomson cross section*_ used in the code has been updated from 6.65e-25 cm^2^ to a more accurate value, approximately 6.6524587e-25 cm^2^, determined from other fundamental constants which are already stored and consistent with the CODATA recommended value.
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|
The value of the *Thomson cross section* used in the code has been updated from 6.65e-25 cm^2^ to a more accurate value, approximately 6.6524587e-25 cm^2^, determined from other fundamental constants which are already stored and consistent with the CODATA recommended value.
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The *_fundamental constants have been updated to the CODATA 2014 values.*_
|
|
|
The *fundamental constants have been updated to the CODATA 2014 values.*
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|
## "Species" and the atomic/molecular databases
|
... | ... | @@ -493,22 +494,22 @@ The *_fundamental constants have been updated to the CODATA 2014 values.*_ |
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|
This version has a major reworking of the atomic database. We have removed our internal database and replace with with a mix of
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|
data from Stout (our own internal database) or Chianti.
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*_Chianti has been updated*_ to version 7.1.4.
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|
|
*Chianti has been updated* to version 7.1.4.
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|
The *_atom xxx commands*_ have been *_renamed species xxx*_, although the atom command will be accepted.
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|
The *atom xxx commands* have been *renamed species xxx*, although the atom command will be accepted.
|
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|
*_The Gaunt free-free factors have been updated.*_ The old data used to have discontinuities, and also weren't terribly accurate in some places. [The new data](https://data.nublado.org/gauntff/) are calculated using *_relativistic theory*_ and have a relative accuracy of 0.3% or better everywhere after interpolation (not including errors due to approximations in the theory).
|
|
|
*The Gaunt free-free factors have been updated.* The old data used to have discontinuities, and also weren't terribly accurate in some places. [The new data](https://data.nublado.org/gauntff/) are calculated using *relativistic theory* and have a relative accuracy of 0.3% or better everywhere after interpolation (not including errors due to approximations in the theory).
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|
*_The treatment of electron-electron brems radiation has been updated*_ using the expressions given in Nozawa et al., 2009, A&A 499, 661 and Itoh et al., 2002, Il Nuovo Cimento, 117B, 359. This gives improved expressions for the e-e brems cooling, and also adds the e-e brems diffuse emission and opacity in the model.
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|
|
*The treatment of electron-electron brems radiation has been updated* using the expressions given in Nozawa et al., 2009, A&A 499, 661 and Itoh et al., 2002, Il Nuovo Cimento, 117B, 359. This gives improved expressions for the e-e brems cooling, and also adds the e-e brems diffuse emission and opacity in the model.
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|
The *_rate coefficient for S^2+^ - S^+^ dielectronic recombination has been updated to Badnell+2015*_ and is larger, resulting in stronger [S II] and weaker [S III] emission.
|
|
|
The *rate coefficient for S^2+^ - S^+^ dielectronic recombination has been updated to Badnell+2015* and is larger, resulting in stronger [S II] and weaker [S III] emission.
|
|
|
|
|
|
*_HD cooling 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
|
|
|
*HD cooling 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
|
|
|
|
|
|
*_H2 cooling now comes from Glover & Abel*_ 2008, MNRAS, 388,1627, instead of the older fits by Lepp & Shull 1983, ApJ, 270, 578. For more accurate results, use of the detailed H2 model is still recommended (enabled with the command *_database H2*_).
|
|
|
*H2 cooling now comes from Glover & Abel* 2008, MNRAS, 388,1627, instead of the older fits by Lepp & Shull 1983, ApJ, 270, 578. For more accurate results, use of the detailed H2 model is still recommended (enabled with the command *database H2*).
|
|
|
|
|
|
The *_species print*_ command will *_summarize all species, the number of levels used, and the original database.*_
|
|
|
The *_species Stout print, species Chianti print, and species Lamda print*_, commands will *_summarize the species and number of levels*_ used from each database.
|
|
|
The *species print* command will *summarize all species, the number of levels used, and the original database.*
|
|
|
The *species Stout print, species Chianti print, and species Lamda print*, commands will *summarize the species and number of levels* used from each 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.,
|
... | ... | @@ -793,9 +794,9 @@ The following lines have slightly changed wavelength due to improved data or are |
|
|
|totl|4363|blnd|4363|
|
|
|
|TOTL|7325|blnd|7325|
|
|
|
|
|
|
*_Co II*_ collision strengths and transition probabilities have been updated using [http://adsabs.harvard.edu/abs/2016MNRAS.456.1974S]
|
|
|
*Co II* collision strengths and transition probabilities have been updated using [http://adsabs.harvard.edu/abs/2016MNRAS.456.1974S]
|
|
|
|
|
|
*_Co III*_ collision strengths and transition probabilities have been updated using [http://adsabs.harvard.edu/abs/2016MNRAS.459.2558S]
|
|
|
*Co III* collision strengths and transition probabilities have been updated using [http://adsabs.harvard.edu/abs/2016MNRAS.459.2558S]
|
|
|
|
|
|
|
|
|
## Enhancements for time-dependent cases
|
... | ... | @@ -812,3 +813,4 @@ Return to the [StepByStep](StepByStep) instructions or go [home](home) |
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|
------
|
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|