add vald database

exoclime · Jun 18, 2020 · 086932a · 086932a
1 parent c040833
commit 086932a
Show file tree

Hide file tree

Showing 46 changed files with 1,132 additions and 21 deletions.
diff --git a/ISO.h b/ISO.h
@@ -159,6 +159,10 @@ int Init(Molecule &m, Param &param, char (*qFilename)[160]){
 			//NIST
 			sprintf(m.dataFilename[i], "%s%s.", param.path, m.mName);
 		}
+		if(param.dataBase == 32){
+			//VALD
+			sprintf(m.dataFilename[i], "%s%s.", param.path, m.mName);
+		}
 
 	}
 	fgets(sp, 4, pFile);

diff --git a/Kurucz3.py b/Kurucz3.py
@@ -354,7 +354,6 @@ def processLineList(i, j, Download, printA):
 
 			if(element == els):
 				A = 8.0 * math.pi * wn * wn * (10.0**loggf) / gUP * math.pi * e * e / (me * c)
-				gamma = 2.223e13 / (wl * wl)
 
 				sameLabel = 0
 				if(LabelL == LabelLOld and LabelU == LabelUOld and gUP == gUPOld and gLow == gLowOld and ELow == ELowOld and EUP == EUPOld):

diff --git a/Kurucz4.py b/Kurucz4.py
@@ -209,6 +209,8 @@ def processLineList(i, j, printA):
 		#print(A[i], GammaRad, GammaR[i], wn[i])	
 		if(printA == 1):
 			print(i, wn[i], A[i], ELow[i], ELowAverage[i], gUP[i], GammaRad, GammaR[i], Z, mass, file = Afile)	
+		if(i % 10000 == 0):
+			print("reached line %d from %d" % (i, len(wn)))
 
 		G = GammaR[i]
 		if(G == 1.0):

diff --git a/docs/helios_k/atoms.rst b/docs/helios_k/atoms.rst
@@ -6,37 +6,73 @@ Kurucz database. We use T = 3000 K and P = 1 bar.
 
 
 
-.. figure:: ../plots/atomic/plot00.png  
+.. figure:: ../plots/atomic/plotB00.png  
    :name: atomic00
 
-.. figure:: ../plots/atomic/plot01.png  
+.. figure:: ../plots/atomic/plotB01.png  
    :name: atomic01
 
-.. figure:: ../plots/atomic/plot02.png  
+.. figure:: ../plots/atomic/plotB02.png  
    :name: atomic02
 
-.. figure:: ../plots/atomic/plot03.png  
+.. figure:: ../plots/atomic/plotB03.png  
    :name: atomic03
 
-.. figure:: ../plots/atomic/plot04.png  
+.. figure:: ../plots/atomic/plotB04.png  
    :name: atomic04
 
-.. figure:: ../plots/atomic/plot05.png  
+.. figure:: ../plots/atomic/plotB05.png  
    :name: atomic05
 
-.. figure:: ../plots/atomic/plot06.png  
+.. figure:: ../plots/atomic/plotB06.png  
    :name: atomic06
 
-.. figure:: ../plots/atomic/plot07.png  
+.. figure:: ../plots/atomic/plotB07.png  
    :name: atomic07
 
-.. figure:: ../plots/atomic/plot08.png  
+.. figure:: ../plots/atomic/plotB08.png  
    :name: atomic08
 
-.. figure:: ../plots/atomic/plot09.png  
+.. figure:: ../plots/atomic/plotB09.png  
    :name: atomic09
 
-.. figure:: ../plots/atomic/plot10.png  
+.. figure:: ../plots/atomic/plotB10.png  
    :name: atomic10
+
+.. figure:: ../plots/atomic/plotB11.png  
+   :name: atomic11
+
+.. figure:: ../plots/atomic/plotB12.png  
+   :name: atomic12
+
+.. figure:: ../plots/atomic/plotB13.png  
+   :name: atomic13
+
+.. figure:: ../plots/atomic/plotB14.png  
+   :name: atomic14
+
+.. figure:: ../plots/atomic/plotB15.png  
+   :name: atomic15
+
+.. figure:: ../plots/atomic/plotB16.png  
+   :name: atomic16
+
+.. figure:: ../plots/atomic/plotB17.png  
+   :name: atomic17
+
+.. figure:: ../plots/atomic/plotB18.png  
+   :name: atomic18
+
+.. figure:: ../plots/atomic/plotB19.png  
+   :name: atomic19
+
+.. figure:: ../plots/atomic/plotB20.png  
+   :name: atomic20
 
+.. figure:: ../plots/atomic/plotB21.png  
+   :name: atomic21
+
+.. figure:: ../plots/atomic/plotB22.png  
+   :name: atomic22
+
 
diff --git a/docs/helios_k/compilation.rst b/docs/helios_k/compilation.rst
@@ -49,7 +49,28 @@ Requirements
   - pandas
   - argparse
   - re
-
+
+- vald_request.py
+
+  - selenium
+  - argparse
+
+- vald_download.py
+
+  - numpy
+  - math
+  - struct
+  - os
+  - argparse 
+
+- vald.py
+
+  - numpy
+  - math
+  - struct
+  - os
+  - argparse
+
 
 Note, when using a computing cluster, all these libraries can be installed locally in the home directory  with: 
 

diff --git a/docs/helios_k/vald.rst b/docs/helios_k/vald.rst
@@ -0,0 +1,157 @@
+VALD3 Database
+--------------
+
+Step 1, Request the files
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The download of the line lists can either be done manually through
+the website, or in a more automated way, by using navigation scripts. 
+
+Before the VALD data can be acessed, one has to register on the VALD website.
+
+Attention, there is a limit of 100000 transition lines per query. Some species have more lines
+than that. Is this case, the wavenumber ranges have to be split into two parts. This is
+especially the case for Fe and Cr.
+
+
+Method A, manual request
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+- Vist ``http://vald.astro.uu.se/``
+- Register with email address
+- Choose Mirror Server
+- Click ``Extract Element``
+- Click ``Unit selections`` and select:
+
+  -  Energy level units: cm-1
+  -  Give wavelenths in medium: vacuum
+  -  Wavelength units: cm-1
+  -  Van der Waals syntax: Default
+  -  Isotopic scaling: Off
+  -  click ``Save settings``
+
+- click again ``Extract Element``
+- check the units, they must be ``Energy unit: 1/cm - Medium: vacuum - Wavelength unit: 1/cm - VdW syntax: default``
+- Enter Starting wavenumber, e.g. 0.001
+- Enter Ending wavenumber : e.g. 1000000
+- Enter Element: e.g Fe 1, (ionizaion number = 1 means neutral)
+- Extraction format : Long format
+- Retrieve data via : FTP
+- Select ``Include HFS splitting``
+- Enter a comment in ``Optional comment for request``, for example the element and ionization number.
+- Click ``Submit request``
+
+
+
+Method B, using scripts
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Also this mehod requires to first visit the web interface manually and to
+choose the correct units, the same way as Method A.
+After that, the vald_request.py script can navigate the webiste and fill in the necessary webforms. 
+For this, a geckodriver needs to be installed. 
+
+Then type:
+
+::
+
+   python3 vald_request.py -Z <z> -I <i> -u <email address>
+
+where ``<z>``\ is the atomic number and ``<i>``\ the ionization state (i = 0 is neutral)
+The email address must be the same as the user account from the VALD website.
+
+
+Step 2, download the files
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+After a few minutes you will get an email from VALD with a link to download the data file.
+
+
+Method A, manual download
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Download the file and unpack it. Rename the file to ``VALD<Z><I>.dat``.
+E.g VALD2600.dat for Z = 26, I = 0 (I = 0 means neutral atoms).
+
+
+Method B, using scripts
+^^^^^^^^^^^^^^^^^^^^^^^
+
+The requested files are stored temporarely on the VALD webiste with a name similar to
+``SimonGrimm.4199418``, where the first part is the user name, and the second part is the 
+job number. The vald_download.py script can download all requested files, scan which element
+they contain and rename them according to the element number. 
+
+::
+
+   python3 vald_download.py -jobstart <start> -jobend <end> -jobname <name>
+
+The name is the user name from the VALD webiste, e.g SimonGrimm.
+The jobstart is the first jobnumber (check email from VALD) .e.g 4199418.
+The jobend is the last jobnumber (check email from VALD) .e.g 4199420.
+
+The files are renamed as ``VALD<Z><I>.dat``.
+
+
+Step 3, partition function files
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Partition functions are not available in the VALD database.
+Therefore we use the partition functions calculated from the NIST database.
+
+
+Step 4, calculate natural broadening coefficients and create the binary files and ``< species >.param`` files
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+For many species, the vald database provides broadening coefficients,
+but not for all. The missing coefficients are calculated in this step.
+That can take a while to complete.
+
+::
+
+   python3 vald.py -Z <z> -I <i>
+
+
+This step creates the ``< species >.param`` and the `*.bin` files. 
+
+
+Step 5, data path
+~~~~~~~~~~~~~~~~~
+
+Include the path of the directory, which contains the obtained binary
+files, the ``*.pf`` partition function files and the ``*.param`` file to
+the HELIOS-K ``param.dat`` file under ``pathToData``.
+
+
+
+References
+~~~~~~~~~~
+
+Vald provides reference files for each species. We rename these ``*.bib``
+the same way as the data files. When using data from VALD, all these references
+must be cited in publications.
+
+
+We list here also the citation conditions from VALD:
+
+::
+
+	A short note on using VALD data :
+
+	The VALD data and services are provided free of charge on the following conditions:
+
+	    1. If VALD has been used in your research work, you agree to include the acknowledge
+	       below as well as citations to the following papers where appropriate:
+
+	    "This work has made use of the VALD database, operated at Uppsala University, the
+	     Institute of Astronomy RAS in Moscow, and the University of Vienna."
+
+		Ryabchikova T., Piskunov, N., Kurucz, R.L., et al., Physics Scripta, vol 90, issue 5, article id. 054005 (2015), (VALD-3)
+		Kupka F., Ryabchikova T.A., Piskunov N.E., Stempels H.C., Weiss W.W., 2000, Baltic Astronomy, vol. 9, 590-594 (2000), (VALD-2)
+		Kupka F., Piskunov N.E., Ryabchikova T.A., Stempels H.C., Weiss W.W., A&AS 138, 119-133 (1999), (VALD-2)
+		Ryabchikova T.A. Piskunov N.E., Stempels H.C., Kupka F., Weiss W.W. Proc. of the 6th International Colloquium on Atomic Spectra and Oscillator Strengths, Victoria BC, Canada, 1998, Physica Scripta T83, 162-173 (1999), (VALD-2)
+		Piskunov N.E., Kupka F., Ryabchikova T.A., Weiss W.W., Jeffery C.S., A&AS 112, 525 (1995) (VALD-1) 
+
+	    2. You also agree to reference to original source(s) of the line data that are important for your research.
+	       A complete list of references is available from the bibliography section of the VALD manual. A short list
+	       of references is compiled and sent to you with every reply from VALD. 
+
diff --git a/docs/index.rst b/docs/index.rst
@@ -35,6 +35,7 @@ Databases
   helios_k/hitemp.rst
   helios_k/kurucz.rst
   helios_k/nist.rst
+  helios_k/vald.rst
 
 Running HELIOS-K
 ~~~~~~~~~~~~~~~~

diff --git a/docs/plots/atomic/plot00.png b/docs/plots/atomic/plot00.png
diff --git a/docs/plots/atomic/plot01.png b/docs/plots/atomic/plot01.png
diff --git a/docs/plots/atomic/plot02.png b/docs/plots/atomic/plot02.png
diff --git a/docs/plots/atomic/plot03.png b/docs/plots/atomic/plot03.png
diff --git a/docs/plots/atomic/plot04.png b/docs/plots/atomic/plot04.png
diff --git a/docs/plots/atomic/plot05.png b/docs/plots/atomic/plot05.png
diff --git a/docs/plots/atomic/plot06.png b/docs/plots/atomic/plot06.png
diff --git a/docs/plots/atomic/plot07.png b/docs/plots/atomic/plot07.png
diff --git a/docs/plots/atomic/plot08.png b/docs/plots/atomic/plot08.png
diff --git a/docs/plots/atomic/plot09.png b/docs/plots/atomic/plot09.png
diff --git a/docs/plots/atomic/plot10.png b/docs/plots/atomic/plot10.png
diff --git a/docs/plots/atomic/plotB00.png b/docs/plots/atomic/plotB00.png
diff --git a/docs/plots/atomic/plotB01.png b/docs/plots/atomic/plotB01.png
diff --git a/docs/plots/atomic/plotB02.png b/docs/plots/atomic/plotB02.png
diff --git a/docs/plots/atomic/plotB03.png b/docs/plots/atomic/plotB03.png
diff --git a/docs/plots/atomic/plotB04.png b/docs/plots/atomic/plotB04.png
diff --git a/docs/plots/atomic/plotB05.png b/docs/plots/atomic/plotB05.png
diff --git a/docs/plots/atomic/plotB06.png b/docs/plots/atomic/plotB06.png
diff --git a/docs/plots/atomic/plotB07.png b/docs/plots/atomic/plotB07.png
diff --git a/docs/plots/atomic/plotB08.png b/docs/plots/atomic/plotB08.png
diff --git a/docs/plots/atomic/plotB09.png b/docs/plots/atomic/plotB09.png
diff --git a/docs/plots/atomic/plotB10.png b/docs/plots/atomic/plotB10.png
diff --git a/docs/plots/atomic/plotB11.png b/docs/plots/atomic/plotB11.png
diff --git a/docs/plots/atomic/plotB12.png b/docs/plots/atomic/plotB12.png
diff --git a/docs/plots/atomic/plotB13.png b/docs/plots/atomic/plotB13.png
diff --git a/docs/plots/atomic/plotB14.png b/docs/plots/atomic/plotB14.png
diff --git a/docs/plots/atomic/plotB15.png b/docs/plots/atomic/plotB15.png
diff --git a/docs/plots/atomic/plotB16.png b/docs/plots/atomic/plotB16.png
diff --git a/docs/plots/atomic/plotB17.png b/docs/plots/atomic/plotB17.png
diff --git a/docs/plots/atomic/plotB18.png b/docs/plots/atomic/plotB18.png
diff --git a/docs/plots/atomic/plotB19.png b/docs/plots/atomic/plotB19.png
diff --git a/docs/plots/atomic/plotB20.png b/docs/plots/atomic/plotB20.png
diff --git a/docs/plots/atomic/plotB21.png b/docs/plots/atomic/plotB21.png
diff --git a/docs/plots/atomic/plotB22.png b/docs/plots/atomic/plotB22.png