Cloudy & Associates

Commit bf87c4d6 authored by Robin Williams's avatar Robin Williams
Browse files

Merge branch 'master' into ca1_cmesh

parents 57ac275b 916e8e7a
......@@ -217,4 +217,5 @@
**************
#Reference:
#ADF04 2018-01-09 lilike_lgy10#mg9.dat
#https://ui.adsabs.harvard.edu/abs/2011A%26A...528A..69L
# Levels 2-8 from NIST 2018-01-09
......@@ -187,10 +187,6 @@
"list" : "default",
"ref" : {
"coll" : [
{
"bibcode" : "1985ADNDT..33..195B",
"name" : "Berrington, K. A., Burke, P. G., Dufton, P. L., Kingston, A. E. 1985, At. Data Nucl. Data Tables, 33, 195"
},
{
"bibcode" : "2014A%26A...566A.104F"
}
......@@ -204,9 +200,6 @@
}
],
"trans" : [
{
"name" : "NIST 2013-10-20"
},
{
"bibcode" : "2014A%26A...566A.104F"
}
......@@ -284,12 +277,12 @@
"coll" : [],
"energy" : [
{
"name" : "NIST 2014-09-16"
"name" : "NIST 2017-10-05"
}
],
"trans" : [
{
"name" : "NIST 2014-09-16"
"name" : "NIST 2017-10-05"
}
]
}
......@@ -313,9 +306,6 @@
}
],
"trans" : [
{
"name" : "NIST 2014-09-16"
},
{
"bibcode" : "2017JPhB...50f5203F"
}
......@@ -487,9 +477,6 @@
}
],
"trans" : [
{
"name" : "NIST 2014-09-16"
},
{
"bibcode" : "2014A%26A...566A.104F"
}
......@@ -615,9 +602,6 @@
}
],
"trans" : [
{
"name" : "NIST 2014-09-16"
},
{
"bibcode" : "2014A%26A...566A.104F"
}
......@@ -671,8 +655,10 @@
"name" : "Griffin,D.C., Mitnik,D.M. & Badnell, N. R.,2001,JPhB,34,4401"
},
{
"bibcode" : "1989ApJ...342..306H",
"name" : "Hollenbach, D. & McKee, C. F. 1989, ApJ, 342, 306"
"bibcode" : "2019ApJ...881....3W"
},
{
"bibcode" : "2017MNRAS.469.1225W"
}
],
"energy" : [
......@@ -970,12 +956,12 @@
],
"energy" : [
{
"name" : "NIST 2013-10-01"
"name" : "NIST 2017-10-09"
}
],
"trans" : [
{
"name" : "NIST 2013-10-01"
"name" : "NIST 2017-10-09"
}
]
}
......@@ -1147,7 +1133,7 @@
"name" : "NIST 2018-01-09"
},
{
"bibcode" : "2011A&A...528A..69L"
"bibcode" : "2011A%26A...528A..69L"
}
],
"trans" : [
......@@ -1165,12 +1151,12 @@
"coll" : [],
"energy" : [
{
"name" : "NIST 2013-10-01"
"name" : "NIST 2017-10-09"
}
],
"trans" : [
{
"name" : "NIST 2013-10-01"
"name" : "NIST 2017-10-09"
}
]
}
......@@ -1657,8 +1643,7 @@
"ref" : {
"coll" : [
{
"bibcode" : "1970RSPSA.318..531K",
"name" : "Krueger, T.K., and Czyzak, S.J. 1970, Proc Roy Soc London A, 318, 531"
"bibcode" : "2004ApJS..150..465T"
}
],
"energy" : [
......@@ -2916,12 +2901,12 @@
"coll" : [],
"energy" : [
{
"name" : "NIST 2014-09-16"
"name" : "NIST 2017-10-05"
}
],
"trans" : [
{
"name" : "NIST 2014-09-16"
"name" : "NIST 2017-10-05"
}
]
}
......@@ -4500,6 +4485,23 @@
]
}
},
"mn_2" : {
"element" : "mn",
"ion" : "2",
"list" : "default",
"ref" : {
"energy" : [
{
"name" : "NIST 2014-09-16"
}
],
"trans" : [
{
"name" : "NIST 2014-09-16"
}
]
}
},
"mn_5" : {
"element" : "mn",
"ion" : "5",
......@@ -5008,9 +5010,6 @@
}
],
"trans" : [
{
"name" : "NIST 2014-09-16"
},
{
"bibcode" : "2014A%26A...565A..77D"
}
......@@ -5130,15 +5129,19 @@
"ion" : "17",
"list" : "all",
"ref" : {
"coll" : [],
"coll" : [
{
"name" : "ADAS 2021-07-22"
}
],
"energy" : [
{
"name" : "NIST 2014-09-16"
"name" : "ADAS 2021-07-22"
}
],
"trans" : [
{
"name" : "NIST 2014-09-16"
"name" : "ADAS 2021-07-22"
}
]
}
......@@ -5785,9 +5788,6 @@
}
],
"trans" : [
{
"name" : "NIST 2014-09-16"
},
{
"bibcode" : "2014A%26A...566A.123D"
}
......
The ARTICLE stuff below is /all/ latex will pick up -- that's the way
Bibtex files work.
The format is described in the Lamport's book, or (from 2 mins on
Google...)
http://www.bibtex.org/
http://www.hep.manchester.ac.uk/u/jenny/jcwdocs/latex/bibtexbasics.html
It it's a kind of basic text-only database with records
doctype{name,
field = value,
nextfield = othervalue
}
-- there are special rules with {} to ensure things get capitalized
properly. The best way to add stuff in the right format is probably
to find a similar entry, copy it and edit...
The NASA ADS database automatically provides bibtex-format data, but
being automatically generated, it sometimes needs some tidying. The
ADS reference codes are obscure, so entries have been added with only
a cross-reference which act as human-friendly aliases to the main
entries.
The \bibitem stuff is now just comments to show where the data came from,
in case the references were messed up by ADS, it gets ignored.
% The ARTICLE stuff below is /all/ latex will pick up -- that's the way
% Bibtex files work.
%
% The format is described in the Lamport's book, or (from 2 mins on
% Google...)
%
% http://www.bibtex.org/
% http://www.hep.manchester.ac.uk/u/jenny/jcwdocs/latex/bibtexbasics.html
%
% It it's a kind of basic text-only database with records
%
% doctype{name,
% field = value,
% nextfield = othervalue
% }
%
% -- there are special rules with {} to ensure things get capitalized
% properly. The best way to add stuff in the right format is probably
% to find a similar entry, copy it and edit...
%
% The NASA ADS database automatically provides bibtex-format data, but
% being automatically generated, it sometimes needs some tidying. The
% ADS reference codes are obscure, so entries have been added with only
% a cross-reference which act as human-friendly aliases to the main
% entries.
%
% The \bibitem stuff is now just comments to show where the data came from,
% in case the references were messed up by ADS, it gets ignored.
 
 
@ARTICLE{2009ApJ...700.1299J,
......@@ -1063,8 +1063,8 @@ archivePrefix = "arXiv",
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
 
CloudyReview should also point to the current review. The specific paper should also
have a unique name that does not change.
% CloudyReview should also point to the current review.
% The specific paper should also have a unique name that does not change.
 
 
@ARTICLE{C17,
......@@ -4368,14 +4368,14 @@ booktitle = {Research supported by SERC.~Bristol, England and Boston, MA, Adam H
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
 
\bibitem[Drake(1993)]{Drake1993}
Drake, G., 1993, Chapt 3 in \emph{Long Range Casimir Forces, theory and
recent experiments on atomic systems}, edited by Levin \& Mihca, Plenum
Press
\bibitem[Drake(1996)]{Drake1996}
Drake, G. W. F. 1996, in \emph{Atomic, Molecular, and Optical Physics
Handbook}, ed. G. W. F. Drake (Woodbury: AIP), 154
% \bibitem[Drake(1993)]{Drake1993}
% Drake, G., 1993, Chapt 3 in \emph{Long Range Casimir Forces, theory and
% recent experiments on atomic systems}, edited by Levin \& Mihca, Plenum
% Press
%
% \bibitem[Drake(1996)]{Drake1996}
% Drake, G. W. F. 1996, in \emph{Atomic, Molecular, and Optical Physics
% Handbook}, ed. G. W. F. Drake (Woodbury: AIP), 154
 
@ARTICLE{Drake1980,
crossref = "1980ApJS...42..351D"
......@@ -5702,9 +5702,19 @@ publisher = {Berlin: Springer},
year = {1998}
}
 
\bibitem[Fuhr, Martin \& Wiese(1988)]{Fuhr1988}
Fuhr, J. R., Martin, G. A., \& Wiese, W. L. 1988, J. Phys. Chem. Ref. Data,
17, Suppl. 4
@ARTICLE{FuhrMartinWiese1988,
crossref = "1988JPCRD..17S....F"
}
@ARTICLE{1988JPCRD..17S....F,
author = {{Fuhr}, J.~R. and {Martin}, G.~A. and {Wiese}, W.~L.},
title = "{Atomic transition probabilities. Iron through Nickel}",
journal = {Journal of Physical and Chemical Reference Data},
year = 1988,
month = jan,
volume = {17},
adsurl = {https://ui.adsabs.harvard.edu/abs/1988JPCRD..17S....F},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
 
@ARTICLE{Gaetz1983,
crossref = "1983ApJS...52..155G"
......@@ -6584,10 +6594,6 @@ archivePrefix = "arXiv",
Volume = 46,
Year = 2008}
 
\bibitem[Hilborn(1982)]{Hilborn1982}
%ADS: 1982AmJPh..50..982H
Hilborn, Robert C., 1982, American Journal of Physics, 50, 982-986,
erratum, 51 471
@ARTICLE{Hilborn1982,
crossref = "1982AmJPh..50..982H"
}
......@@ -6605,6 +6611,24 @@ erratum, 51 471
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
 
@ARTICLE{Hilborn1982-erratum,
crossref = "1983AmJPh..51..471H"
}
@ARTICLE{1983AmJPh..51..471H,
author = {{Hilborn}, Robert C.},
title = "{Erratum: ``Einstein coefficients, cross sections, f values, dipole moments, and all that'' [Am. J. Phys. 50, 982 (1982)]}",
journal = {American Journal of Physics},
keywords = {32.80.-t, 32.70.Cs, 33.80.-b, 99.10.+g, Photon interactions with atoms, Oscillator strengths lifetimes transition moments, Photon interactions with molecules},
year = 1983,
month = may,
volume = {51},
number = {5},
pages = {471-471},
doi = {10.1119/1.13515},
adsurl = {https://ui.adsabs.harvard.edu/abs/1983AmJPh..51..471H},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@ARTICLE{Hjellming1966,
crossref = "1966ApJ...143..420H"
}
......@@ -8234,9 +8258,6 @@ archivePrefix = "arXiv",
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
 
\bibitem[MacAlpine(1971)]{MacAlpine1971}
%ADS: 1971ApJ...175...11M
MacAlpine, G. M. 1971, ApJ, 175, 11
@ARTICLE{MacAlpine1971,
crossref = "1972ApJ...175...11M"
}
......@@ -17635,3 +17656,21 @@ archivePrefix = "arXiv",
doi = {10.1098/rsta.1904.0024},
}
 
@article{Tayal2004,
crossref = "2004ApJS..150..465T"
}
@ARTICLE{2004ApJS..150..465T,
author = {{Tayal}, S.~S.},
title = "{Electron Impact Excitation Collision Strengths and Rates for P II}",
journal = {\apjs},
keywords = {Atomic Data, Methods: Laboratory},
year = 2004,
month = feb,
volume = {150},
number = {2},
pages = {465-477},
doi = {10.1086/380784},
adsurl = {https://ui.adsabs.harvard.edu/abs/2004ApJS..150..465T},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
......@@ -448,6 +448,7 @@ appear, then only the intrinsic or the emergent, respectively,
block of lines will be inhibited.
\subsection{Print line optical depths [\_off, faint]}
\label{sec:PrintLineOptDep}
Mean line optical depths are not printed by default\footnote{Line center optical
depths were printed through version C10. Mean line optical depths
......@@ -1438,18 +1439,27 @@ The fine continuum is designed to account for line transfer.
It shows a normalized attenuated incident continuum and
does not include continuous
emission or absorption from the cloud.
This multi-grid approach is needed to combine
precision and speed. This command reports the line transmission coefficient,
$I_{transmitted}/I_{incident}$, for the fine continuum.
This multi-grid approach is needed to combine precision and speed.
This command reports the energy (see below) of the fine continuum bin in the
first column, and the continuum transmission coefficient,
$I_{transmitted}/I_{incident}$, for the fine continuum in the second column.
What follows is a list of absorption lines centered on that energy bin.
Each line is identified by its spectral label (species and wavelength), and is
followed by its mean optical depth.
The latter is the same as the last entry reported by
\cdCommand{print line optical depths}, see Section \ref{sec:PrintLineOptDep}.
All lines centered on that bin are reported, sorted from most-to-least opaque.
The resulting output will be huge if the entire fine continuum is saved.
The command accepts a \cdCommand{range} option to limit the size of the output file.
{\it Users are advised to make use of the {\rm\cdCommand{range}} option
to limit the size of the output file.}
If the keyword \cdCommand{range} appears then
the lower and upper limits to the range
of the fine continuum must be entered.
The command also accepts
a \cdCommand{units} option,
described on \pageref{output_units}, to change the units used
described on page \pageref{output_units}, to change the units used
in the specified energy range, and in resulting output.
The optional third numerical parameter gives the number
......@@ -1458,6 +1468,8 @@ reducing the size of the output file. The default is to average over 10
cells. If the number of cells to be combined is specified then it must
be the third number on the command line, following the limits
of the range.
Note that in a given energy range, the same number of features is reported,
irrespective of the number of cells merged.
The resolving power of the fine continuum is adjusted when the calculation begins so
that lines of the heavy elements can be resolved.
......
This diff is collapsed.
# Doxygen Style
## Setup
The setup of the Doxygen output is contained in file `Doxygen`.
To change the preset options, run
```
$ doxywizard Doxyfile
```
where `doxywizard` is a GUI program that, at least on Ubuntu, is a standalone
program and needs to be installed in addition to `doxygen`.
The Expert tab has many options.
The Doxygen setup file ignores most of these options, and creates only HTML
output in a new subdirectory `html`, created in this directory.
To run `doxygen`, one can use the `Run` tab on `doxywizard`, or run the command
```
$ cd doxygen
$ doxygen Doxyfile
```
that is, run it from this directory.
## Source Code Markup
Within the codebase, doxygen markup is fully contained in the headers.
All doxygen special comment blocks are using the markup for
[C-like languages](https://www.doxygen.nl/manual/docblocks.html#specialblock).
Some basic rules:
- Special comment blocks are indicated by ``/**``.
- All comment blocks are immediately before what they describe, with the
exception of some struct members, where the comment immediately follows ("/**<" syntax).
- Commands are indicated with the with the syntax `\command`.
- Within special comment blocks, the \, @, &, $, #, <, >, % characters must be
escaped using a preceeding '\'.
- LaTeX formulas can be entered using the `\f$` sentinel, e.g.,
```
\f$ - same as in line $ - opposite is another \f$
```
The following commands are in use:
- `\file <filename> (description)` - description for a file, will appear in
the output above any descriptions of items contained in the file.
- `\verbatim` - Doxygen outputs text enclosed in verbatim/endverbatim tags
exactly (ie, preserving whitespace and newlines)
- `\endverbatim`
- `\param [in|out|in,out] <parameter name> (description)` - describe a
parameter of a function. Parameter name is the name of the variable and
does not include type. The '[in|out|in,out]' is optional.
- `\post (description)` - describe the post conditions for a function
- `\return (description)` - describe what the function returns (in output
"Returns "+description is printed)
- `\author` Joe Blow
The ideal declaration should look like the following:
```
/**
routine_name This is the long description of what routine_name does, appears after
the function name
\brief this is routine brief description - only 1 line long
\param iz a description of what parameter 1 is for
\param [in] in a description of what parameter 2 is for
\param [out] *out description
\author Joe Blow
\return explain the return value
*/
double routine_name(long int iz,
long int in ,
double *out );
```
The full description of these commands and all others is under the
[Special Commands](https://www.doxygen.nl/manual/commands.html) section of the
online reference.
to change options in setup file (Doxyfile) do
doxywizard Doxyfile
mode - optimize for C output
expert tab has many options
to run doxygen and create output do
doxygen Doxyfile
in this directory
check whether INPUT parameter in Doxyfile is set to source_hot or source - this changes
source is the archived version and source_hot is the local development version
to generate the ouput doxygen also needs graphviz, another open source app. graphviz needs
to be on the path for doxygen to find it.
Doxyfile is set up to create only html output. other options are possible. The html will be
in the html directory below this main directory.
Within the codebase, doxygen markup is fully contained in the headers. All doxygen special comment blocks are using the "C style" markup. Special comment blocks are indicated by /**. Commands are indicated with the with the syntax \command. All comment blocks are immediately before what they describe, with the exception of some struct members, where the comment immediately follows ("/**<" syntax). Within special commente blocks, the \, @, &, $, #, <, >, % characters must be escaped using a preceeding \
The following commands are in use:
\file <filename> (description) - description for a file, will appear in the output above any descriptions of items contained in the file.
\verbatim - Doxygen outputs text enclosed in verbatim/endverbatim tags exactly (ie, preserving whitespace and newlines)
\endverbatim
\param [in|out|in,out] <parameter name> (description) - describe a parameter of a function. Parameter name is the name of the variable and does not include type. [in|out|in,out] is optional.
\post (description) - describe the post conditions for a function
\return (description) - describe what the function returns (in output "Returns "+description is printed)
\author Joe Blow
latex in line
\f$ - same as in line $ - opposite is another \f$
The ideal declaration should look like the following:
=======================================================
/**
routine_name This is the long description of what routine_name does, appears after
the function name
\brief this is routine brief description - only 1 line long
\param iz a description of what parameter 1 is for
\param [in] in a description of what parameter 2 is for
\param [out] *out description
\author Joe Blow
\return explain the return value
*/
double routine_name(long int iz,
long int in ,
double *out );
=======================================================
The manual for doxygen can be found: http://www.stack.nl/~dimitri/doxygen/download.html#latestman
The full description of these commands and all others are under "Special Commands" in the "Reference Manual" section.
# Readme for Doxygen
This directory contains the file needed to create Doxygen documentation for the
Cloudy source. You must have `doxygen`, `latex`, and `graphviz` installed for
this to work.
To create the Doxygen documentation run the commands
```
$ cd doxygen
$ doxygen Doxyfile
```
(i.e., run `doxygen` from this directory).
The documentation will be stored in the `html` directory that is created.
Open the `html/index.html` file to view the documentation.
## Requirements
### Doxygen
Doxygen is a source code documentation system that is widely used in open
source projects.
You will need a copy of the `doxygen` executable on your system to create the
documentation.
It is available [on its website](https://www.doxygen.nl), along with its
[manual](https://www.doxygen.nl/manual/index.html).
The full description of its commands is under the
[Special Commands](https://www.doxygen.nl/manual/commands.html) section.
### Graphviz
Doxygen must be able to find the `graphviz`.
This is used to create equations from embedded LaTex.
You may download `graphviz` from [its website](http://www.graphviz.org).
If you receive the error message
```
> sh: dot: command not found
> Problems running dot. Check your installation!
```
this means that `doxygen` cannot find `graphviz`.
## Files
This directory includes the setup file `Doxyfile` that is needed to run
`doxygen`.
It was created with the gui that is lauchned with the command
```
doxywizard Doxyfile
```
this is used to set the parameters for the generated output.
The document file `doxygen_setup_style.txt` in this directory contains some
notes on how Cloudy uses `doxygen`.
## Questions