Lecture 2
Contents
1. the same number of each as for a model The underlying datafile has a two dimensional storage as a function of temperature and density 6 Oct 2009 IPP Garching 5 The program recovers the output temperature density pairs you used when last executing the program Pressing the Default Te or Default Ne buttons insert a default set of temperatures or densities equal to the input values A choice of particular density or particular temperature respectively from the input sets is allowed on a pop up window 6 The Temperature amp Density Values are editable Click on the Edit Table button if you wish to change the values A drop down window the ADAS Table Editor window appears as shown below 7 ADASS501 has a more sophisticated graphical method for Te Ne pair selection Activate the Value Selection by Display button The detailed operation of the widget is described in Chap1 00 of this user manual Output options The third window is called the output options window and has the appearance shown below 1 As in the previous window the full pathway to the file being analysed is shown for information Also the Browse comments button 1s available 2 Graphical display is activated by the Graphical Output button This will cause a graph to be displayed following completion of this window When graphical display is active an arbitrary title may be entered which appears on the top line of the displayed graph 3 By default graph scali2. doc bulletin doc manual doc datastatus doc usernotes doc adas and atomic calculations course doc adopted_laboratory_wavelengths The principal Unix IDL ADAS manual is comprehensive organised in chapters and sub chapters connected to the ADAS series and named as adas doc manual chap lt i gt lt nn gt pdf where lt i gt denotes chapter and lt nn gt denotes the sub chapter number It is unfortunately a bit out of date now There are major appendices in particular appendix B contains full descriptors and current states of the ADAS data formats Bulletins are currently issued about once per year and are named according to date of issue They contain information of bug fixes new data and descriptions of newly added codes There are a number of shorter special manuals which describe particular types of activity within ADAS such as charge exchange spectroscopy or influx spectroscopy These are also a bit out of date now They include flx manual influx spectroscopy bms manual beam emission spectroscopy cxs manual charge exchange spectroscopy ionl manual basic ionisation balance studies ion2 manual advanced ionisation balance studies opac manual opacity studies spec manual spectral analysis cds manual atomic modelling for solar analysis The content of the Datastatus documents named as adas doc datastatus adf lt nn gt pdf where lt nn gt is an ADAS data format number are now present in appendix B of the ma
3. of the top level fortran adaslib subdirectory according to sub routine character Also note the xxdata subdirectory which contains important sub routines for getting data from the ADAS database int your own FORTRAN programs The idl subdirectory structure is similar but note some extras in the top level idl adaslib sub directory There are subdirectories for graphical user interface procedures and read_adf and write_adf procedures which you will find useful Source IDL code is open but FORTRAN code is restricted FORTRAN shared object module libraries are available to user codes ADAS EU Course 8 16 Oct 2009 IPP Garching ADAS data The subdirectory home adas adas contains the central ADAS data archive In also includes sub directories pass of passing files and defaults of defaults files for use by the user adas in testing the distribution The latter two file categories are also required in each individual ADAS user s file space The primary data themselves are stored in sub directories according to ADAS data format number e g adf04 There are currently 56 data formats whose layout and organization is precisely specified These are listed below Itis recommended that each user sets up a personal data space as home lt uid gt adas which parallels the central ADAS structure ADAS codes are designed to go automatically to the correct ADAS data format either in the central or user space driver data sets for ADAS204 calc
4. 00E 04 2 000E 04 4 99858E 01 1 500E 01 5 000E 04 5 000E 04 9 995E 01 2 000E 01 1 000E 05 1 000E 05 1 999E 02 da 3 000E 07 2 000E 05 2 000E 05 4 998E102 re PTET PETER et 10 SO00ELOT 5 000E 05 5 000E 05 9 995E 02 da Default _ Delete Remove Insert _ Copy _ Paste _ Row sskip Column skip _ Scrollup Scroll down Temperature Units ADAS EU Course 8 16 Oct 2009 IPP Garching ADAS EU Course The set of round and square buttons below the table are designed to help in some editing tasks You must be careful to remember the sequence of operations since it is different from that on personal computers Activate the appropriate button position the mouse text cursor or drag over required digits press the return key on the keyboard to complete the sequence The Default round button is the reset to normal editing mode The Delete button allows deletion of the value in a box leaving an empty box the Remove button allows deletion of a value with the column then being pushed up the nsert button creates a new empty box pushing the column down These buttons stay active until you click Default The Copy and Paste round buttons operate for the next immediate action only Square buttons have a continuing effect until an alternative is pressed The Row_skip button causes a jump to the next editable box in a row when the return key on the keyboard is pressed Column_skip c
5. 05 4 920e 13 l 100 fatal 2 070 e 03 4 920a 13 ELECTRON TEMPERATURE ev lt eee a a a 4 1428 03 4 920a 13 ATIONS PER PHI e 3 3 4 5 6 7 IONI DOI Adjust Hetain ADAS EU Course 8 16 Oct 2009 IPP Garching 2 Activate the Adjust button to pop up the Graph Adjust window It s operation is described in Chap1 00 of this user manual 3 Activate the Retain button to pop up the Multiplot window This widget permits superposition of graphs from multiple passes through ADASSOI1 and hence graph comparison The detailed operation of the widget is described in Chap1 00 of this user manual Table Editor A necessary operation in interactive ADAS is entry of user values into a table Since this is common to many ADAS programs a special window has been developed to assist in this task A typical appearance of the Table Editor window is shown below 1 The values in italic font are your input data Click in any of these boxes to edit the number within it The workstation cut paste and copy keys operate Press the return key on the keyboard to record any change This is the normal editing mode ray E 5 T l b e E d i to F Temperatures E Electron lon Neutral Input Hydrogen Value 1 2 000600 S 000E 02 S 000E 02 9 995E 01 3 006400 1 000E 03 1 000E 03 1 999E 00 6 000E 00 2 O00E 03 2 000E 03 4 998E 00 7 000E 00 5 000E 03 5 000E 03 9 995E 00 L000E 01 1 000E 04 1 000E 04 1 999E 01 da 1 39006E 01 2 0
6. Lecture 1b Computational overview of ADAS The ADAS suite comprises mainly IDL and FORTRAN code and runs under UNIX Tested systems include Solaris DEC HP AIX and Linux Pre requisites for an installation of ADAS are 5 0Gb disk space F77 and C compilers IDL fully licensed ADAS will not run in IDL demo mode a PDF viewer such as Acrobat reader Installation is carried out and managed by the ADAS manager Dr Allan Whiteford ADAS is usually installed in the home directory of an account with user name adas The ADAS distribution has the directory structure shown below home adas home adas doc home adas notes home adas setup home adas run ay home adas fortran home adas idl home adas C home adas matlab home adas perl home adas wrapper home adas offline_adas home adas bin home adas lib home adas adas documents adas setup and run code and scripts in various languages binaries and object module libraries the database The interactive ADAS suite comprises in the region of 85 programs They are arranged in 8 series reflecting distinct regions of atomic physics purpose The menu selection for series 5 is shown below ADAS EU Course 8 16 Oct 2009 IPP Garching ADAS SYSTEM MENL 5 General ADAS Interrogation Routines _JADAS501 SXB File Graph and Fit ITonizations per Photon JADAS 502 SZD File Graph and Fit Ionization Rate Coefficients _JADASSOF PEC F
7. appropriate data subdirectories Click the Central Data button to insert the default central ADAS pathway to the correct data type Note that each type of data is stored according to its ADAS data format adf number Click the User Data button to insert the pathway to your own data Note that your data must be held in a similar file structure to central ADAS but with your identifier replacing the first adas to use this facility 2 The Data root can be edited directly Click the Edit Path Name button first to permit editing ADAS EU Course 8 16 Oct 2009 IPP Garching 3 Available sub directories are shown in the large file display window Scroll bars appear if the number of entries exceed the file display window size 4 Click on a name to select it The selected name appears in the smaller selection window above the file display window Then its sub directories in turn are displayed in the file display window Ultimately the individual datafiles are presented for selection Datafiles all have the termination dat 5 Once a data file is selected the set of buttons at the bottom of the main window become active ADAS 501 INPUT Input Dataset Data Root Yatsfhoallfufadasf adasfadf iif isxbh9 64 c sxb9 b4e_pjr e3 dat sxbobte_pjricd sxb9bte_pjrtel dat sxb9b e_pjrte dat sxb9 bte_pjrte dat sxb9b e_pjrte4d dat sxb9bte_pyrteS5 dat sxb9b e_pjutcoO dat sxb9 bte_pjutel dat sxh9 btc_pjute dat sxb9 bt
8. aults for each ADAS program are stored The defaults file for an ADAS series code remembers the user entries at the last run of the code adas pass directory for storing output files from ADAS codes called passing files There a number of important entries in the cshrc file Values at Strathclyde are setenv ADASUSER home lt uid gt adas source packages rsiv idl bin idl_setup sets up default IDL path source packages adas idl_adas adas_setup amends IDL PATH for ADAS defines ADASCENT path to central ADAS archive defines ADASFORT path to FORTRAN executable Working with interactive ADAS widgets A number of IDL screens are common to many of the separate ADAS codes in the interactive series These include the file selection screen on input the table editor screen used for entry of user values for parameters graphical input of user data pairs screens for graphical output graph display adjustment and graph retention Code ADAS501 uses these screens and is suitable for practice The following sub sections summarize the main features and how to work with these screens Programs of series 5 make use of data from archived ADAS datasets and initiate an interactive dialogue with the user in three parts namely input file selection entry of user data and disposition of output Start ADASS5O1 from the interactive ADAS menus File selection The first window has the appearance shown below 1 Data root shows the full pathway to the
9. auses jumping to next box in a column Scroll up moves the whole window down Note that the window only shows ten values in a column but the whole table may be longer that this Preferred Temperature units for working with may be chosen Changing units causes the Inputs from the file to change to the new units It does not change any Output values already typed in It merely interprets Output values in the selected units Press the Done button to record the changes and return to the screen from which Table Editor was initiated The Cancel button prevents the new values being substituted on return 8 16 Oct 2009 IPP Garching
10. ec_pjuted dat sxb9b e_pjutec4d dat sxb9b e_pjute5 dat sxb9bt e vsrtel dat sxbobtec vsrte Data File 6 Clicking on the Browse Comments button displays any information stored with the selected datafile It is important to use this facility to find out what is broadly available in the dataset The possibility of browsing the comments appears in the subsequent main window also 7 Clicking the Done button moves you forward to the next window Clicking the Cancel button takes you back to the previous window Processing options The next window is called the processing options screen and has the appearance shown below 1 An arbitrary title may be given for the case being processed For information the full pathway to the dataset being analysed is also shown The button Browse comments again allows display of the information field section at the foot of the selected dataset if it exists ADAS EU Course 8 16 Oct 2009 IPP Garching 2 The output data extracted from the datafile in the case of ADAS501 an emissivity coefficient may be fitted with a polynomial This is as a function of temperature Clicking the Fit polynomial button activates this The accuracy of the fitting required may be specified in the editable box The value in the box is editable only if the Fit Polynomial button is active ADASSO1 PROCESSING OPTIONS Data File Mame fafs cell ufadas adas adfl3 sxhb9 btc sxb9 btc_pjrted dat Browse Co
11. ile Graph and Fit Photon Emissivities _j ADASSO4 PZD File Graph and Fit Radiated Powers J ADASSOS QTR File Graph and Fit Thermal Charge Exch Coefft _ ADAS5SO6 GFT File Graph and Fit G TE Function _J ADASSOT GCF File Graph and Fit General Contribution Function _ ADASSO8 GTH File Graph and Fit G TE NE Function _J ADASSOI SCH File Graph and Fit Charge Exchange Cross sections Exit The IDL FORTRAN C and MATLAB codes and associated sub routines gt 1000 are organized hierarchically according to series and maintained under CVS adaslib subdirectories contain subroutines common to codes at their hierarchical level Series 1 code subroutines names commence with the letter a followed by the numerical hexadecimal value of the particular code The structure is Shown below in the FORTRAN case fortran adas1xx fortran adas2xx fortran adas2xx adas201 fortran adas2xx adas201 adass201 for fortran adas2xx adas202 fortran adas2xx adas201 b1data for fortran adas3xx fortran adas2xx adas203 fortran adas2xx adas201 b1ispf for fortran adas4xx fortran adas5xx fortran adas6xx fortran adas2xx adaslib fortran adas7xx fortran adas8xx fortran adaslib atomic fortran adaslib fortran adaslib maths fortran adaslib system fortran adaslib utility fortran adaslib xxdata Note the sub directories
12. in user manual There may be additional files such as data reviews conducted by ADAS participants A substantial number of ADAS tutorials have been presented at laboratories in Europe and the USA The tutorials are named as_ adas doc lt lab gt lt yr gt tut lt section gt pdf where lt lab gt is a mnemonic for a laboratory and lt yr gt is a two digit year number They are divided into sections in which a sub area is Summarised with viewgraphs followed by simple learning exercises with ADAS Some of these older tutorial files are postscript ADAS EU Course 8 16 Oct 2009 IPP Garching Initial ADAS user set up There are a number of steps which a user must take in order to prepare his her environment for ADAS properly A directory called adas must be created in the user s home directory as home lt uid gt adas A setup script should then be executed from the newly created directory The appropriate setup script for a user s site can be found in the central ADAS file space The steps at Strathclyde are cd adas adas_strathclyde csh The setup script a creates sub directories with in the user s adas directory space b adds entries to the user s cshrc or profile files to set up the user s environment for IDL and ADAS c sets the user s ADASUSER environment variable which is the pathway to the newly created user s adas directory Important directories are adas defaults directory where the user def
13. mments Polynomial Fitting Fit Polynomial value D Selec INDEX Wavelength Ion t data Block Processing Metastable Source Code Index i l4 1549 1 A Istc3 ADASZO8 1 we Ge Po 307 8 A Iste3 ADAS20S 243 7 A Iste3 ADASZO8 222 0 A ls c3 ADASZO8 930 3 A Istec3 ADASZO8 LI fa pi et jt Es Temperature amp Density Values Temperature Density INDEX Output Input Output Input 9 650E 01 6 890E 01 4 920E 13 1 640E 05 1 380 00 9 650E 01 4 920E 13 1 640E 06 2 070E 00 1 380 00 4 920E 13 1 640E 07 2 760E 00 2 070E 00 4 920E 13 1 6405 098 i Temperature Inits eV Density Units cm 3 Edit Table Default Te Default He Value Selection by displw Edit the processing options data and press Done to proceed Cancel Done 3 ADAS EU Course 8 1 Spectrum lines for which emissivity coefficients are available in the data set are displayed in the line list display window This is a scrollable window using the scroll bar to the right of the window Click anywhere on the row for a line to select it The selected line appears in the selection window just above the line list display window Your settings of electron temperature electron density pairs outputs are shown in the temperature density display window The temperature and density values at which the emissivity coefficients are stored in the datafile inputs are also shown for information Note that you must give temperature density pairs ie
14. ng is adjusted to match the required outputs Press the Explicit Scaling button to allow explicit minima and maxima for the graph axes to be inserted Activating this button makes the minimum and maximum boxes editable 4045501 QUTPUT OFTIGNS Data File Name fafs f cell uf adas fadas adf13 sxb9 bte sxb9bte_pjritecd dat Browse Comments w Graphical Output Select Device Graph Title demonstration Post Ser ipt Post Seript HP PCL HP GL _ Explicit Scaling Hnr EE EEEF I a Yona De I Yaa T Enable Hard Copy epiace 4 TA Eiig Hoppe Text Output _ Append _ Replace Default File Hame File Hame paper txt Output written to file E Return to Input File Selection cancel Done ADAS EU Course 8 16 Oct 2009 IPP Garching 4 Hard copy is activated by the Enable Hard Copy button The File name box then becomes editable If the output graphic file already exits and the Replace button has not been activated a pop up window issues a warning 5 A choice of output graph plotting devices is given in the Device list window Clicking on the required device selects it It appears in the selection window above the Device list window 6 The Text Output button activates writing to a text output file The file name may be entered in the editable File name box when Text Output is on The default file name paper txt may be set by pressing the button Default file name A pop up wind
15. ow issues a warning if the file already exists and the Replace button has not been activated 7 The graph is displayed in a following Graphical Output window described below Graphical output The final graph display window has some additional controls 1 Printing of the currently displayed graph is activated by the Print button ep aDASSOTGRAPHICALOUTPUT O O Z OZ O O T IONISATIONS PER PHOTON VS ELECTRON TEMPERATURE DEMONSTRATION eV ADAS o AS RELEASE ADA 98 YL5 5 GRAN ADAS501 V1 14_DATE 09 07 02 TIME 15 00 FILE afs e ac xb96 Fo_pjr e3 dat BLK 14 C 3 WAVELENGTH 1549 1 A MET 1 MINIMAX y ADENT LOWER 6 UPPER 0 51 KEY CROSSES INPUT DATA FULL LINE SPLINE FIT DASH LINE MINIMAX 1 000 EMITTING ION INFORMATION a ELEMENT SYMBOL NUCLEAR CHARGE CHARGE STATE WAVELENGTH angstrome SPECIFIC ION FILE SOURCE PROCESSING CODE METASTABLE INDEX oN ELECTRON TEMPERATURE DENSITY RELATIONSHIP OTS INDEX TEMPERATURE eV DENSITY cm 3 1 9 550a 01 4 920a 13 1 380e 00 4 920e 13 2 07de 00 4 920e 13 2 760e 00 4 920e 13 4 140e 00 4 920e 13 6 890e 00 4 920e 13 9 550a 00 4 920e 13 1 3B0e 01 4 920e 13 2 07de 01 4 920e 13 Z 76D 01 4 920e 15 4 14De D1 4 920a 13 6 89De 01 4 920e4 15 9 B5De D1 4 920a 13 1 38De D2 4 920e 4135 2 07Deat D2 4 920a 13 Z 76De D2 4 920e 13 4 14Det D2 4 920a 13 6 89De D2 4 920e4 15 amp BS5Dea D2 4 920a 13 0 001 20 1 38De
16. ulation driver data sets for ADAS701 calculations driver data sets for ADAS702 post processing driver data sets for ADAS708 post processing ADAS EU Course 8 16 Oct 2009 IPP Garching BBGP driver datasets for dielectronic recombination adf48 direct resolved radiative recombination coefficients padfSO e a E e adf52 promotion rules ionisation Further layers of sub directories are assigned as necessary for different species etc The sub directory and final data set naming is designed to give some indication of content The final data sets themselves are all ascii and have the extension dat The figure below shows the layout adas adas adas adas adf01 adas adas adf02 adas adas adf03 adas adas adf04 adas adas adf56 adas adas arch101 adas adas arch102 adas adas scripts405 adas adas scripts406 adas adas pass adas adas defaults For central ADAS sub directories arch 01 scripts405 contain only samples Such data is normally personal to a user ADAS EU Course 8 16 Oct 2009 IPP Garching ADAS documentation ADAS documentation is now most easily accessed via the web pages from www adas ac uk and on through OPEN ADAS The documentation is also present on every ADAS sites in PDF format so is available for viewing electronically and for printing It is placed in the adas doc directory under several headings A schematic is shown below adas doc
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