- 04 Jun, 2022 1 commit
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Chatzikos, Marios authored
Report absorption features on output of 'save fine continuum' command See merge request !37
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- 03 Jun, 2022 4 commits
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Chatzikos, Marios authored
Previously, the header produced by the command used the words 'Species' and 'Opt Dep Spec'. The former is outdated, given that we now report the spectral line label (including wavelength), and the latter is not clear to the user, given that we refer to the single-line optical depth as Specific only in the source. Here, the former is replaced with 'SpecLine' and the latter with 'Single Line Opt Depth'.
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Chatzikos, Marios authored
The previous implementation of the code block in LineStackCreate() that quantifies line overlap used an arbitrary value of 20 as the maximum number of lines that could overlap in a bin. During review, Gary questioned the choice. This ad hoc value was picked as a high enough limit to carry out the task, given that currently up to 14 lines overlap in a bin. The previous implementation was also inefficient in that it went over rfield.fine_lstack map several times to produce the report. Here, the overlap across rfield.fine_lstack is established ahead of time, and each fine continuum index in the map is visited only once for the report. The ad hoc value of 20 is removed.
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Chatzikos, Marios authored
A (disabled) block of code was added at the end of LineStackCreate() that worked its way through the map of fine continuum bins and line stack indices to quantify the amount of overlap present. The block did not carry a comment. During review, it was deemed necessary to explain its intent. This is done here. Also, on the output of bins with overlap greater than 10 lines, the line stack index is now reported to show that the repeating species labels are indeed genuine.
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Chatzikos, Marios authored
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- 02 Jun, 2022 3 commits
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Chatzikos, Marios authored
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Chatzikos, Marios authored
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Chatzikos, Marios authored
The previous implementation reported the line center optical depth. Here, we report the mean optical depth to keep the output the same as the specific optical depths reported on the main output with the command 'print line optical depths'.
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- 28 May, 2022 2 commits
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Chatzikos, Marios authored
Update scripts and source for release preparation See merge request !36
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Chatzikos, Marios authored
The previous implementation reported only a feature's species in spectral notation, e.g., 'Fe17'. This is useful if cells are not merged and the energy is reported in wavelength units (say, Angstrom), because the exact wavelength is reported in the first column. Merging cells eliminates the wavelength information, and if the number of cells merged together is high, the output can be confusing. Report the entire spectral label, including the wavelength, to eliminate ambiguity in the output.
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- 27 May, 2022 3 commits
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Chatzikos, Marios authored
The previous implementation reported only the most opaque line per bin. Merging cells may eliminate important lines from the output. All lines contributing opacity to a cell are now reported, if their optical depth exceeds a limit.
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Chatzikos, Marios authored
The previous implementation of 'save fine continuum' accumulated the first bin separately from any requested others (9 more, by default). That forced code duplication relating to identifying the most opaque line in the bin. Restructure the code to treat all bins at once; eliminate duplication.
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Chatzikos, Marios authored
Anna Ogorzalek posted a query on the Cloudy group about identifying absorption features in the output of the 'save xspec mtable' command. A partial answer would be to identify features due to the lines alone. The present adds two columns to the output of 'save fine continuum'. The first identifies the species whose line is centered at that bin, and the second reports the optical depth due that line alone (i.e., not the total including any neighboring lines).
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- 19 May, 2022 1 commit
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Ferland, Gary authored
Protection against division by zero cooling. See merge request !35
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- 27 Apr, 2022 1 commit
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Ferland, Gary authored
The demotes cautions that parts of the SED are zero to notes. The following wc on auto shows that we have a large number of these. They are benign - they occur if we use a blackbody that does go to zero far out in the Wien tail. They are a minor note about the SED rather than something deserving of raising a caution. the number of cautions in tsuite/auto went from Alien20:auto:wc ~gary/cloudy/cautions.txt 5267 72721 544951 /home/gary/cloudy/cautions.txt to Alien20:auto:wc cautions2.txt 3846 64015 460146 cautions2.txt
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- 15 Apr, 2022 1 commit
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Chatzikos, Marios authored
The command in question was 'save chemisty rates'.
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- 14 Apr, 2022 17 commits
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Chatzikos, Marios authored
Missing references lead to undefined number of rows when generating the TeX table. Add guards against that possibility.
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Chatzikos, Marios authored
Ease use of the script by making sure it is not repeatedly asking for the ADS token. Store after first call, use stored in subsequent.
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Chatzikos, Marios authored
There was a bug in the previous implementation, which amounts to issuing ADS BibTex queries in non-interactive mode. Shut them down.
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Chatzikos, Marios authored
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Chatzikos, Marios authored
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Chatzikos, Marios authored
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Chatzikos, Marios authored
The previous ADS BibTeX service (cgi-bin/nph-bib_query) no longer exists. As a result, storing which of the three databases (AST, PHY, and PRE) is the origin of the BibTeX data has become obsolete. Remove all instances of use of the databases, and relevant data fields. Instead, the new API requires users to supply a token in order to query the server from the command-line. Update to current method. Use of the new API requires that an ADS token be used. Users need supply one only in interactive runs.
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Chatzikos, Marios authored
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Chatzikos, Marios authored
This occurs when computing the number of lines in the TeX table.
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Chatzikos, Marios authored
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Chatzikos, Marios authored
The previous implementation reported a file as empty based on the presence of a 'Reference' line. Some files that contain the line but are not followed by any references, were not reported as empty. This is now fixed.
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Chatzikos, Marios authored
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Chatzikos, Marios authored
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Chatzikos, Marios authored
With the previous implementation, the data structure that is written out as a JSON file is pruned of no longer existing references only in interactive mode. Now it is always done. Fixed.
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Chatzikos, Marios authored
With the previous implementation NIST references were processed only in interactive mode. This prevented updating dates on NIST refs. These are now updated, if needed, based on any available dates.
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Chatzikos, Marios authored
Some Stout files miss the 'Reference' line, and yet others contain data on that line. The previous implementation did not handle them correctly.
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Chatzikos, Marios authored
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- 13 Apr, 2022 3 commits
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Chatzikos, Marios authored
Perl module Text::BibTeX already defines them. Previous code caused warnings such as: 'warning: overriding existing definition of macro "dec"' to be issued. This is no longer the case.
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Chatzikos, Marios authored
The file contains several non-BibTeX entries as plain text, which cause warnings to be emitted. Replace some \bibitem entries with their formal BibTeX record from ADS. Comment the rest out with '%'.
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Chatzikos, Marios authored
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- 12 Apr, 2022 3 commits
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Chatzikos, Marios authored
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Ferland, Gary authored
These protect against division by zero. Problems were exposed by the lab sim posted in gtests / bugs / Mancini. The sim does get now much farther along but aborts when the line stack becomes misaligned. The sim is a lab plasma, so it is far from our home base, but we should be able to compute it. It is non-equilibrium. It is unclear why the cooling is zero - perhaps the total is net heating. The changes seem safe since they are have never been needed and will have no effect in most cases.
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Chatzikos, Marios authored
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- 11 Apr, 2022 1 commit
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Chatzikos, Marios authored
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