include NIST natural broadening

check/check.py

@@ -154,7 +154,7 @@
 print('TestNIST001', file = f)
 os.system('pwd')
 
-er = os.system('python3 ../../nist_ELevels.py -Z 26 -I 0')
+er = os.system('python3 ../../nist_ELevels2.py -Z 26 -I 0')
 er = os.system('python3 ../../nist_partition.py -Z 26 -I 0')
 
 er = filecmp.cmp('NIST2600.pf', '../../data/NIST2600.pf')
@@ -163,7 +163,7 @@
 if(er == False):
 	success = 0
 
-er = os.system('python3 ../../nist_Lines.py -Z 26 -I 0')
+er = os.system('python3 ../../nist_Lines3.py -Z 26 -I 0')
 er = os.system('python3 ../../nist_Lines2.py -Z 26 -I 0')
 er = filecmp.cmp('NIST2600.param', '../../data/NIST2600.param')
 print("error", er)

docs/helios_k/bins.rst

@@ -11,6 +11,8 @@ from small to large, and mapped to a new parameter y, rangin from 0 to 1.
 When the opcity function has empty parts inside or is not ranging to the full
 bin width, then the sorted opacity function is zero (or kmin, if used) on the
 lower part.
+
+
 | Relevant parameters for this example:
 
  - doResampling = 0

docs/helios_k/compilation.rst

@@ -10,46 +10,45 @@ Requirements
 
 - exomol.py and exomol2.py
 
- - bs4
- - requests
- - sys
- - os
- - subprocess
- - numpy
- - argparse
- - math
+  - bs4
+  - requests
+  - sys
+  - os
+  - subprocess
+  - numpy
+  - argparse
+  - math
 
 - Kurucz2.py
 
- - numpy
- - math
- - struct
- - os
- - argparse
+  - numpy
+  - math
+  - struct
+  - os
+  - argparse
 
-- nist_ELevels.py and nist_Lines.py
+- nist_ELevels2.py and nist_Lines3.py
 
- - sys
- - time
- - pyperclip
- - subprocess
- - selenium
- - argparse
+  - sys
+  - argparse
+  - csv
+  - requests
 
 - nist_partition.py
 
- - numpy
- - sys
- - argparse
+  - numpy
+  - sys
+  - argparse
 
 - nist_Lines2.py
 
- - numpy
- - struct
- - math
- - csh
- - pandas
- - argparse
+  - numpy
+  - struct
+  - math
+  - csh
+  - pandas
+  - argparse
+  - re
 
 
 Note, when using a computing cluster, all these libraries can be installed locally in the home directory  with: 

docs/helios_k/cut.rst

@@ -0,0 +1,26 @@
+Cut the line wings
+==================
+
+
+The line wings can be cut by the ``cutMode`` and ``cut`` parameters. Reasons
+for cutting the line wings can either be that the line wings would be 
+overestimated, or just to save computing time. Line wings or cut at the 
+specified distance from their central peak location. Choosing a broader cutting
+lenght can increase the computational time.
+In :numref:`figcut` is shown an example with three different cutting lenghts. 
+
+
+| Relevant parameters for this example:
+
+ - doStoreFullK = 1
+ - cutMode = 0
+ - cut = 25, 100 or 0
+
+
+
+.. figure:: ../plots/p008/plot001.png  
+   :name: figcut
+
+   Three cutting lengths of the line wings. An infinity cuttoff lengths can be set by `cut = 0`.
+
+

docs/helios_k/heliosk.rst

@@ -129,8 +129,8 @@ used parameters are listed here, the order can not be changed.
 
    - 1: Voigt
    - 2: Lorentzian
-   - 3: Gaussia
-   - 4: cross section
+   - 3: Gaussian
+   - 4: Integrated Binned Gaussian
 
 -  doTuning:
 

docs/helios_k/nist.rst

@@ -18,13 +18,12 @@ This step can be done either manually or by using a script.
 
 -  Automatical download:
 
-   -  type ``python3 nist_ELevels.py -Z <z> -I <i>``, where ``<z>``\ is
+   -  type ``python3 nist_ELevels2.py -Z <z> -I <i>``, where ``<z>``\ is
       the atomic number and ``<i>``\ the ionization state , e.g. -Z 3 -I 0
    -  The script will download the data and store it in a file called ``NIST_ELevels<Z><I>.dat``.
-   -  This script will need geckodriver to be installed.
 
-Step 2, Generate partition functions
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Step 2, Generate the partition functions
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Run ``python3 nist_partition.py - -Z <z> -I <i>``. This script will read
 the previously produces file ``NIST_ELevels<Z><I>.dat``, and writes a ``*.pf`` file.
@@ -53,17 +52,16 @@ This step can be done either manually or by using a script.
    -  select ``Show Advanced Settings``
    -  select the Format output to csv
    -  Select ``Wavenumbers (in cm-1)`` (keep ``Observed``, ``Ritz`` and ``Uncertainties`` selected)
-   -  Select ``Wavenumbers (all wavelenghts)``
+   -  Select ``Vacuum (all wavelengths)``
    -  Select ``g``
    -  click ``Retrieve Data``\ and store the data in a file called
       ``NIST_Lines<Z><I>.dat``.
    -  remove all ``?, =, [,],( and )``\ from the file
 
 -  Automatical download:
 
-   -  type ``python3 nist_Lines.py -Z <z> -I <i>``.
+   -  type ``python3 nist_Lines3.py -Z <z> -I <i>``.
    -  The script will download the data and store it in a file called ``NIST_Lines<Z><I>.dat``.
-   -  This script will need geckodriver to be installed .
 
 .. _step-5-create-<-species->.param-file-and-binary-files:
 
@@ -76,6 +74,8 @@ All necessary files can be created with:
 
    python3 nist_Lines2.py -Z <z> -I <i>
 
+This step includes the calculation of the natural broadening coefficients. This can take o moment to complete.
+
 Step 6, data path
 ~~~~~~~~~~~~~~~~~
 

docs/helios_k/profiles.rst

@@ -0,0 +1,85 @@
+Line Profiles
+==============
+
+
+| HELIOS-K supports four different line profiles which can be set by the ``profile`` parameter.
+| The supported profiles are:
+
+- 1: Voigt
+- 2: Lorentz
+
+.. math::
+   :label: eq_fL
+
+   f_L(\nu) = \frac{1}{\pi} \frac{\gamma_L}{(\nu - \nu_0)^2 + \gamma_L^2}
+
+
+- 3: Doppler
+
+.. math::
+   :label: eq_fG
+
+   f_G(\nu) = \frac{ln(2)}{\pi} \frac{1}{\alpha_D} \exp\left(-\frac{ (\nu - \nu_0)^2 ln(2)}{\alpha_D^2} \right)
+
+
+- 4: Binned Gaussian integrated cross section 
+
+
+
+.. math::
+   :label: eq_sigma
+
+   f_{BG} = \frac{1}{\Delta \nu} \int_{\nu - \nu/2}^{\nu + \nu/2} f_G(\nu) d \nu = \frac{1}{2 \Delta \nu} \left[ erf(\chi^+) - erf(\chi^-) \right]
+
+[Yurchenko et al. 2018: (ExoCross : a general program for generating spectra from molecular
+line lists)]
+
+
+
+with the Doppler half-width:
+
+.. math::
+   :label: eq_GD
+
+   \alpha_D = \frac{\nu}{c} \sqrt{\frac{2 ln(2) k_B T}{m}}
+
+
+and the Lorentz half-width for Hitran like data:
+
+.. math::
+   :label: eqGL1
+
+   \gamma_L = \frac{A}{4\pi c} + \left( \frac{T}{T_{ref}}\right)^{-n} \left[ \frac{\alpha_{air} (P-P_{self})}{P_{ref}} + \frac{\alpha_{self} P_{self}}{P_{ref}}\right]
+
+
+or the Lorentz half-width for ExoMol like data:
+
+.. math::
+   :label: eqGL2
+
+   \gamma_L = \frac{A}{4\pi c} + \left( \frac{T_{ref}}{T} \right)^n \cdot \left( \frac{P}{P_{ref}}\right)
+
+
+or the Lorentz half-width for Atomic data:
+
+.. math::
+   :label: eqGL3
+
+   \gamma_L = \frac{\Gamma_{nat}}{4\pi c} + \left( \frac{T_{ref}}{T} \right)^n \cdot \left( \frac{P}{P_{ref}}\right)
+
+
+In :numref:`figprofile` is shown an example with four different line profiles. 
+
+
+| Relevant parameters for this example:
+
+ - doStoreFullK = 1
+ - profile = 1 or 2 or 3 or 4
+
+
+
+.. figure:: ../plots/p009/plot001.png  
+   :name: figprofile
+
+   Example with four different line profiles 
+

docs/helios_k/resampling.rst

@@ -39,7 +39,8 @@ Chebyshev polynomial to resample over these sharp edge would introduce oscillati
 into the resampled opacity functions. In order to avoid these oscillations, we resample
 only the part of the sorted opacity function, which is not 0 or kmin. That leads
 to better results, but when reconstructing the polynomial from the Chebyshev
-coefficients, then the empty parts must be added again. 
+coefficients, then the empty parts must be added again. How this can be done is 
+shown next.
 
 
 .. figure:: ../plots/p005/plot001.png  

docs/index.rst

@@ -51,6 +51,8 @@ OPTIONS
 .. toctree::
   :maxdepth: 1
 
+  helios_k/profiles.rst
+  helios_k/cut.rst
   helios_k/bins.rst
   helios_k/resampling.rst
   helios_k/options.rst

docs/plots/p008/Info_c0.dat

@@ -0,0 +1,72 @@
+Name:GeForce GTX 980, Major:5, Minor:2, Max threads per Block:1024, Max x dim:1024
+, #Multiprocessors:16, Clock Rate:1215500, Memory Clock Rate:3505000, Global Memory:4230807552, Shared memory per block: 49152
+
+Version: 2
+Using device 0
+
+Runtime Version 10000
+Driver Version 10010
+GIT Describe: v1.0-108-g3f9e55a
+Build Date: Di 19. Mai 18:15:05 CEST 2020
+Build Path: /home/sigrimm/kCalc
+Build System: Linux mashu 4.15.0-96-generic #97-Ubuntu SMP Wed Apr 1 03:25:46 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
+Build Compute Capability: SM=52
+
+name = c0
+T = 1500
+P = 1
+cia System = -
+pathToData = ../../../data/
+numin = 0
+numax = 30000
+dnu = 0.1
+Nnu per bin = 60000
+Number of points: 300000
+cutMode = 0
+cut = 100
+doResampling = 0
+nC = 20
+doTransmission = 0
+nTr = 1000
+dTr =  0.05
+doStoreFullK = 1
+pathToK = 
+dostoreK = 2
+nbins = 5
+kmin = 0
+qalphaL = 1
+gammaF = 1
+doMean = 1
+Units = 0
+Replace files = 1
+profile = 1
+doTuning = 1
+def_TOL = 1.43e-17
+def_TOLf = 2.48e-12
+def_nthmax = 1048576
+def_nlmax = 32768
+def_maxlines = 1048576
+def_maxfiles = 500
+def_NmaxSample = 100
+
+Species Name = 01_hit16
+dataBase = 0
+Molecule Number = 1
+default L = 0
+default n = 0
+
+File 0 of 1
+Number of lines: 304225
+Time for input:        0.0770169 seconds
+Time for Lines:        0.00555155 seconds
+Time for K(x):         0.402035 seconds
+
+Time for input total:	 0 seconds
+Time for Lines total:  0 seconds
+Time for K(x) total: 	 0 seconds
+Time for write K(x):   0.250061 seconds
+Time for mean K(x):    0.00183994 seconds
+Time for sort K(x):    0.0025481 seconds
+Time for Resampling:   0.000106208 seconds
+Time for write K(y):   0.140505 seconds
+Time for Transmission: 1.4464e-05 seconds