Cloudy & Associates

Commit ebd1ad4e authored by Chatzikos, Marios's avatar Chatzikos, Marios
Browse files

Merge branch 'prep-release' into 'master'

Update scripts and source for release preparation

See merge request !36
parents 20030830 5d498826
......@@ -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}
}
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
If you run into problems, visit the
[Cloudy forum](https://cloudyastrophysics.groups.io), where you can search
among previous questions for help, or post a new question.
Good luck,<br>
Gary Ferland<br>
[https://www.nublado.org](https://www.nublado.org)
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.
Create the documentation with the command
doxygen Doxyfile
Open the index.html file in the html directory to view the documentation.
======================================================================
Doxygen is a source code documentation system that is widely used in open source projects. It is available on the web at http://www.stack.nl/~dimitri/doxygen/ You will need a copy of the doxygen executable on your system to create the documentation.
graphviz
Doxygen must be able to find the graphviz. This is used to create equations from embedded LaTex. Download graphviz from 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.
This directory includes the setup file "Doxyfile" that is needed to run doxygen. The Cloudy download does not include the output documentation it generates. To create documentation run doxygen with the command
doxygen Doxyfile
in this directory. Doxgyen will create a new html directory below this one. The index.html file in the html directory is the top of the documentation.
The manual for doxygen can be found at http://www.stack.nl/~dimitri/doxygen/download.html#latestman
The full description of its commands is under "Special Commands" in the "Reference Manual" section.
The document file doxygen_setup_style.txt in this directory contains some notes on how Cloudy uses doxygen.
==============================================
the file Doxyfile was created with the gui that is lauchned with the command
doxywizard Doxyfile
this is used to set the parameters for the generated output.
Good luck,
Gary Ferland
http://www.nublado.org
......@@ -3,6 +3,12 @@
# TeX tables relevant to atomic data.
#