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Last modified: Fri Aug 5 09:56:39 2005.
PROJECT
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME
CH_SS
PURPOSE:
to calculate CHIANTI line intensities and continua, to create a
synthetic spectrum.
CALLING SEQUENCE:
IDL> ch_ss
PROCEDURE:
This routine calculates a synthetic spectrum by merging line
intensities and continua.
The widget is organised into four Sections:
SECTION 1:
-The Calculation of the CHIANTI line intensities.
This can be done in two ways:
1-Restore a save file with the CHIANTI line intensities already
calculated.
2-Calculate CHIANTI line intensities with a call to CH_SYNTHETIC.
In this case, A series of parameters must be set:
- Minimum and maximum wavelengths in Angstroms
- The model used for the calculation. Three are the options:
1) a constant density (cm^-3)
2) a constant pressure (cm^-3 K)
3) a general (Te,Ne) model. In this case, a file will be read.
This file should have two columns, one with the Te (K)
values, and one with the Ne (cm^-3) values.
- The ionization fraction file to be used. "*.ioneq" files
can be selected from either the CHIANTI database, the
working directory or selected via a widget.
- All ions ? If set to yes (default), then all the ions present in the
database will be included.
If set to no, then it is possible to select a list of ions
with a widget
- All lines ? If set to no (default), only the lines for which there are
observed energy levels are included
If set to yes, also the lines that do not have
corresponding observed energy levels are included. In this
case, the wavelengths are calculated from the theoretical
energy levels, and might not be very accurate.
- Isothermal ? If set to no (default), a DEM file must be selected.
"*.dem" files (i.e. files with a .dem extension)
can be selected from either the CHIANTI database, the
working directory or selected via a widget.
If set to yes, then the user is requested to enter one
or more temperatures (as logarithmic values - Log T )
and correspondent column emission measures EM
logarithmic values.
NOTE: if more than one value is entered, then the
sequence must be separated by commas (e.g.: 6.0,
6.5, 7.), and both Log T and Log EM must have the
same number of values
- Photoexcitation ?
If set to yes, you have to define:
Trad: The blackbody radiation field temperature
R/Ro: Distance from the centre of the star in stellar
radius units
Units: Photons or Ergs'
Protons: If set to Yes, the proton data are used to calculate the level population
Once all the parameters have been defined, the user should click on the
"Calculate intensities" button to start the calculation (which calls
CH_SYNTHETIC).
Once the calculation is finished, an IDL structure is loaded into
memory. It is then possible to save it for later use by clicking on the
"SAVE" button.
The RESTORE button is to restore previously saved files into an IDL
structure in memory.
Once the IDL structure with the line intensities is in the memory, it is
then possible to calculate and plot a spectrum (SECTION 2).
SECTION 2:
This section controls the parameters that are needed to fold the
line intensities and the continua into a synthetic
spectrum. These parameters are used by MAKE_CHIANTI_SPEC.
Before this is done, a set of line intensities MUST be in the
program memory. This is done either by calculating the
intensities or by restoring a save file with
previously calculated values (SECTION 1).
Setting the parameters:
-Minimum and maximum wavelengths in Angstroms
-spectrum bin size in Angstroms. Disallowed if an Effective area
file is used.
-instrumental FWHM: Setting this to a non-zero value broadens
each of the spectral lines with a Gaussian of
the specified FWHM (in Angstroms) so
mimicking the effects of instrumental
broadening.
-continuum: Add continua to the binned spectrum:
free-free, free-bound and two-photon.
Please note that the continuum calculation takes some
time and you may want to define a minimum abundance
value to speed the calculations.
- All lines ? If set to no (default), only the lines for which there are
observed energy levels are included.
If set to yes, the "unobserved lines" will be added, but
only if they are present in the structure.
-elemental abundances
"*.abund" files (i.e. files with a .abund
extension) can be selected either from the CHIANTI database,
the working directory, or via a widget.
-select a minimum abundance value
If set not null, only the lines of those elements
which have an abundance greater than the value set are
selected. Also, the continuum is calculated only for
those elements which have an abundance greater than
the value set. This can significantly speed up the
calculations. By default, the minimum value in the
selected abundance file is used. To have an idea of
what minimum abundance should be set, the abundances
of Allen (1973) give:
abundance (H) = 1.
abundance (He) = 0.085
abundance (C) = 3.3e-4
abundance (O) = 6.6e-4
abundance (Si) = 3.3e-5
abundance (Fe) = 3.9e-5
Eff. Area: Yes/No
If you want to fold the spectrum with an effective area.
If set to Yes, you are requested to choose an input ascii file
with two columns, the wavelength and the effective area values
(cm^2).
The wavelenghts in the file (that might not be linear) are used
to create the spectrum, that is multiplied with the effective
area values.
Note that this option only works well if a sufficient number
of bins is given. The line intensities contributing to each
bin are summed, and subsequently convolved with a gaussian
of full-width-half-maximum FWHM, if FWHM is not set = 0.
Please note that the convolution might not work if a small
number of bins is defined.
Also note that to have the correct output units (counts s-1
bin-1) the appropiately scaled DEM (or EM) values must be provided.
After this, by clicking on the "Calculate and plot" button the
program calculates and plots the synthetic spectrum.
Once the spectrum is displayed, it is then possible to
view the details of the lines by clicking with the mouse in the
plot window, and to perform various operations by clicking on
the buttons in SECTION 3
SECTION 3:
This Section allows the user to select a few parameters for the
plotting, and to create different types of OUTPUT.
Labels ? : Setting this to yes plots a vertical line for each
spectral line in the spectrum, and also writes a label
above the strongest lines indicating the ion from
which the line arises.
Min.: Only lines which have an intensity greater than the
value set here will be listed and, if requested,
labelled and selected for inclusion in the various
outputs. Setting the value=0. will result in all
lines being listed and written in the outputs.
X,Y, XOOM, UNZOOM: It si possible to select a region of the
spectrum, by zooming with the use of the mouse
or by setting the X,Y ranges.
NOTE that only the line details and portion of
the spectrum shown will be output.
LINEAR/LOG To plot the spectrum in linear or log scale
Create PS file: A postscript file is created.
Hardcopy: the postscript file "idl.ps" is created and sent to the
default printer.
Save Line details (latex): The details of the lines shown in the
plot will be saved in a latex file.
Save Line details (ascii): The details of the lines shown in the
plot will be saved in an ascii file.
Save Spectrum (ascii): The X,Y values of the plot are saved in
an ascii file.
Save Spectrum (IDL/FITS): The details of all the lines and the arrays
of the X,Y values of the plot are saved into
an IDL or FITS file. The IDL structure
has the following tags:
.LAMBDA: The array of wavelength X values
.SPECTRUM: The array of spectrum Y values
.UNITS The units of LAMBDA, SPECTRUM
.INSTR_FWHM The Instrumental FWHM
.BIN_SIZE Width of the Bins (fixed) in angstroms
.ABUND_NAME The CHIANTI abundance file name
.ABUND The abundance values
.MIN_ABUND The minimum abundance value used
.ABUND_REF The references
.CONTINUUM The values of the continuum (if
calculated)
.EFFAREA The array of effective area
values (optional)
.FILE_EFFAREA The name of the effective area file used (optional).
.IONEQ_NAME The ion balance file used (full path).
.IONEQ_LOGT The Log10 T values associated.
.IONEQ_REF The references.
.DEM_NAME The differential emission measure file eventually used
(full path).
.DEM The Log10 DEM values
.DEM_LOGT The Log10 T values associated.
.DEM_REF The references.
.MODEL_NAME A string indicating the model used
(e.g. constant density or constant pressure).
.MODEL_NE the Ne value.
.MODEL_PE the Pe value.
.WVL_UNITS The wavelength units.
.WVL_LIMITS The wavelength limits specified by the user.
.INT_UNITS The intensity units
.LOGT_ISOTHERMAL
The Log10(T) values used.
.LOGEM_ISOTHERMAL
The Log10(EM) values used.
.TIME The date and time when the structure was created.
.VERSION The version number of the CHIANTI database used.
.ADD_PROTONS
A flag (0/1) to indicate whether proton data were used (1)
or not (0) to calculate the level population.
.PHOTOEXCITATION
A flag (0/1) to indicate if photoexcitation was included (1)
or not (0).
.RADTEMP
The blackbody radiation field temperature used (if
photoexcitation was included).
.RPHOT
Distance from the centre of the star in stellar radius units
(if photoexcitation was included).
THEN, FOR EACH LINE USED TO CALCULATE THE
SPECTRUM:
.LINES A structure containing information about the lines.
Its size is the number of lines in the spectrum. The
tags are:
.peak The peak intensity value
.iz The atomic number of the elements (e.g., 26=Fe)
.ion The ionisation stage (e.g., 13=XIII)
.snote The identification of the ion (e.g., 'Fe XXIV d')
.ident The identification of the transition, configuration
and terms in text form.
.ident_latex
The identification of the transition, configuration
and terms in latex form.
.lvl1 The lower level of the transition (see .elvlc
file for ion)
.lvl2 The upper level for transition.
.tmax The temperature of maximum emission of the line
(i.e., the temperature at which the product of
the emissivity and the ion fraction has its
maximum). Rounded to nearest 0.1, and zero in case
the isothermal approximation is used.
.fwhm
.wvl Wavelength of the transition, in Angstroms.
.flag A flag, =-1 if the line has only theoretical energy
levels. Otherwise flag=0.
.int Intensity of line (with the abundance factor multiplied)
Save Spectrum (FITS): The entire information contained in the
IDL structure is stored in a FITS file.
SECTION 4:
Here, text information messages are printed.
INPUTS
None.
OPTIONAL INPUTS:
The font
OUTPUTS:
Many.
KEYWORD PARAMETERS:
FONT the font to be used. Can be useful to customize the appearance of
the widget.
CALLS:
CH_SYNTHETIC, CH_LINE_LIST, CH_DRAWBOX, MAKE_CHIANTI_SPEC, CH_XMENU_SEL,
plus many other CHIANTI and SolarSoft routines.
PROGRAMMING NOTES
Within CH_SS, there are several other routines which are:
OPLOT_LINES This overplots lines and a label on the displayed
spectrum.
SYN_CURSOR When the mouse is clicked when on the spectrum window,
this routine prints out the list of nearby lines and
their IDs in the text window.
CALC_SYN_SPECTRUM
Calculates line intensities with a call to CH_SYNTHETIC
PLOT_SYN_SPECTRUM This calls make_chianti_spec to produce the
intensity vs. wavelength plot.
SYN_MAIN_EVENT This handles the widget operations
SYN_WID This creates the widgets.
COMMON BLOCKS:
many
RESTRICTIONS:
SIDE EFFECTS:
EXAMPLE:
IDL> ch_ss
CATEGORY:
spectral synthesis.
WRITTEN :
Ver.1, 7-Nov-01, Giulio Del Zanna (GDZ) and Peter Young (PRY)
MODIFICATION HISTORY:
V.2, 7-Nov-01, GDZ . Fixed a small bug (now the spectrum plot is always
plotted within the widget), and modified the option to add continua.
Changed the suggested names of the outputs.
Corrected a bug when creating an IDL save file with the spectrum, when
no line details are present.
V.3 28-Jan-02 GDZ
fixed a bug in the density text widget, added a few buttons
and options, including the effective area.
Added noprot, rphot, radtemp keywords to the call to ch_synthetic
V 4, 18-Apr-2002, GDZ
Added photoexcitation, changed IDL save files to FITS files,
V.5, 21-May-2002, GDZ
fixed a few small bugs: checking min_abund before calculating the
spectrum; checking the ioneq file when
restoring the structure; changed the status of
all lines; chnaged the font system.
generalized directory concatenation to work for
Unix, Windows and VMS.
V.6, 15-July-2002, GDZ - New major revision.
Changed the chianti top directory (for Effective areas).
Changed Linear/Log button.
Rearranged the sizes of the buttons and added a special cursor to
highlight the area where details of the lines will be given. Works
only in linear scale.
Added quite a lot of new checks to avoid crashes and
fixed the problem with the zoom/unzoom/change units.
V.7, 2-Aug-02, GDZ
Modified the output labels on the plot, inside and on the axis.
Also modified a few minor things like the appearance of the Log T,EM
values.
Fixed a bug when creating the latex output.
Now it restores at the end previous colors and settings.
V.8, 8-Aug-02, GDZ
Changed the CHIANTI system variables. Fixed.
Also fixed a problem with the element ab. file.
V.9, 13-Aug-02, GDZ
Restored the correct use of ch_line_int, now only the lines in the
plot window are listed, and the ALL keyword is in use.
Now the correct xrange is loaded into COMMON when line int. are
restored. Now it checks if all ions were in the structure, when
restoring the line intensities, and flags the widget button accordingly.
Added a device,decomposed=0. to remove problems with colors.
Corrected the use of the DEM, IONEQ and ABUND pulldown menus,
avoiding conflicts between files in the working and CHIANTI
directory having the same name.
Added printing of references for ancillary files, and a check on the
element abundances vs. the elements present in the structure.
V.10, 7-Nov-03 GDZ
Modified format e8.2 to e9.2 for Windows compatibility.
Replaced f9.4 with f11.4 format for the wavelengths.
Some minor modifications to the widget.
Added extended details in the ascii output spectrum.
Added more explanations in the HELP buttons.
V.11, 22-Jul-2005 GDZ
-Added keV option and a few more extra checks.
V.12, 2-Aug-2005 GDZ
put RETAIN=2 in the main plotting window.
TO DO LIST:
Control the range of Angstroms when clicking
kev
Allow plots in intensities instead of intensities A-1
VERSION : V.12, 2-Aug-2005
(See /home/gdz/ss/chianti/www/v5.0/idl/ch_ss.pro)
need to add a fwhm tag to tran.lines in order for this to work (need to divide intensity of line by FWHM) to get peak of line NEED TO ADD A CHECK ON THE X-RANGE ?
(See /home/gdz/ss/chianti/www/v5.0/idl/ch_ss.pro)
PROJECT
CHIANTI http://wwwsolar.nrl.navy.mil/chianti.html
CHIANTI is an atomic database package for the calculation of
continuum and emission line spectra from astrophysical plasmas. It is a
collaborative project involving the Naval Research Laboratory
(Washington DC, USA), the Arcetri Observatory (Firenze, Italy), and the
Cambridge University (United Kingdom).
NAME
dens_plotter
PURPOSE:
A widget-based routine to allow the analysis of density sensitive
ratios. **** See RATIO_PLOTTER for details. *****
CALLING SEQUENCE:
IDL> dens_plotter, name,$
EM, PATH=PATH, NOPROT=NOPROT, $
IONEQ_FILE=IONEQ_FILE, ABUND_FILE=ABUND_FILE
INPUTS:
The ion name (e.g. 'si_3' for Si III)
OPTIONAL INPUTS : none
OUTPUTS:
OPTIONAL OUTPUTS:
EM: Save the displayed emissivities to structure EM.
**** See RATIO_PLOTTER for details. *****
KEYWORDS:
PATH: Data in the CHIANTI format that is not in the CHIANTI
database can be read by specifying the directory in which
it lies through PATH.
ABUND_FILE The name of a CHIANTI abundance file. This is used for
calculating the proton to electron ratio. Default is
!abund_file.
IONEQ_FILE The name of a CHIANTI ion balance file. This is used for
calculating the proton to electron ratio and evaluating
the T_max of the ion. Default is !ioneq_file.
NOPROT If set, then the default setting will be NOT to use
proton rates. This can be changed within the routine.
CALLS: CONVERTNAME RATIO_PLOTTER
COMMON BLOCKS: none
RESTRICTIONS:
SIDE EFFECTS:
CATEGORY:
spectral synthesis.
EXAMPLE:
IDL> dens_plotter, 'si_9'
WRITTEN :
Ver.1, 18-Apr-2002, Giulio Del Zanna (GDZ) written as a wrapper
routine to call RATIO_PLOTTER.
MODIFIED: V.2, 2-Aug-2005, GDZ
Now the routine handles the dielectronic case
VERSION : 2, 2-Aug-2005
(See /home/gdz/ss/chianti/www/v5.0/idl/extra/dens_plotter.pro)
PROJECT: CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME:
READ_IONEQ
PURPOSE:
to read files containing the ionization equilibrium values
CATEGORY:
science.
CALLING SEQUENCE:
READ_IONEQ, File, T, Ioneq, Ref
INPUTS:
File: for example, !xuvtop+'/ioneq/arnaud_rothenflug.ioneq'
OPTIONAL INPUTS:
None:
OUTPUTS:
T: array of log10 temperatures
Ioneq: 3-d array (T,element,ion)
of the fractional abundance of the ion in
ionization equilibrium.
Ref: reference in the scientific literature
EXAMPLE:
> read_ioneq,!xuvtop+'/ioneq/arnaud_rothenflug.ioneq'
> help,t,ioneq
> T FLOAT = Array(41)
> IONEQ FLOAT = Array(41, 28, 29)
> print, minmax(t)
> 4.00000 8.00000
> print,t(20)
> 6.0000
> print,ioneq(20,25,9)
> 0.269 = fractional abundance of Fe X in
ionization equilibrium
MODIFICATION HISTORY:
Written by: Ken Dere (KPD)
March 1996: Version 2.0
March 1999: KPD to read both number of temperature and number
of elements
25-Oct-2000 V. 4, Giulio Del Zanna (GDZ).
Corrected to interpret the '-1' as a reference only
if within the first 3 columns
V. 5, 21-May-2002, Giulio Del Zanna (GDZ)
generalized directory concatenation to work for
Unix, Windows and VMS.
v.6, 25-Oct-2004, Peter Young
modified format statement so that it will read any number of
temperatures.
V 7, 25-May-2005, GDZ
corrected routine header.
VERSION : 7, 25-May-2005
(See /home/gdz/ss/chianti/www/v5.0/idl/low_level/read_ioneq.pro)