added sub-Lorentzian profiles

chiPH89__CO2-CO2.dat

@@ -0,0 +1,11 @@
+sigma1 3.0
+sigma2 30.0
+sigma3 120.0
+
+B	alpha 	beta 	epsilon
+B1	0.0888	-0.160	0.00410
+B2	0.0	0.0526	0.00152
+B3	0.0232	0.0	0.0
+
+range in cm^-1
+2100 2500

chiPH89__CO2-N2.dat

@@ -0,0 +1,12 @@
+sigma1 3.0
+sigma2 10.0
+sigma3 70.0
+
+B	alpha 	beta 	epsilon
+B1	0.416	-0.354	0.00386
+B2	0.00167	0.0421	0.00248
+B3	0.0200	0.0	0.0
+
+range in cm^-1
+2100 2500
+

define.h

@@ -30,7 +30,7 @@
 #endif
 
 
-#define VERSION 2.03
+#define VERSION 2.04
 
 
 #define def_T0 296.0 		//Reference Temperature in K
@@ -158,8 +158,13 @@ struct Param{
 	double gammaF;
 	int doTuning;
 	int removePlinth;
+	char subLorentzianFilename[160];
+	int useSubLorentzian;
 };
 
+//Sub-Lorentzian coefficients
+float sLchi_h[17];
+
 struct Line{
 	double *nu_h, *nu_d;		//Wavenumber
 	double *S_h, *S_d;		//Intensity

docs/helios_k/heliosk.rst

@@ -132,6 +132,15 @@ used parameters are listed here, the order can not be changed.
    - 3: Gaussian
    - 4: Integrated Binned Gaussian
 
+-  subLorentzianfile: A '-' ignores this option, otherwise this option
+   specifies a file name which contains the chi factor parameters for
+   sub-Lorentzian CO2 profiles.
+
+-  removePlinth:
+
+  - 0:  nothing is done here
+  - 1:  the plinth (base) is removed from cutted line profiles 
+
 -  doTuning:
 
    - 0: nothing is done here

docs/helios_k/plinth.rst

@@ -4,10 +4,21 @@ Removing the Plinth
 When using cutted line wing profiles in combination with a continuum and
 far wing background cross section, it can be necessary to remove the plinth
 of each transition line, since this can be already included in the backround. 
-See for example:
-Ptashnik, Igor & McPheat, Robert & Shine, Keith & Smith, Kevin & Williams, Robert. (2012). Water vapour foreign-continuum absorption in near-infrared windows from laboratory measurements. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences. 370. 2557-77. 10.1098/rsta.2011.0218. 
 
-Removing the plinth from the opacities can be done with the `removePlinth` option
+|See for example:
+|Ptashnik, Igor & McPheat, Robert & Shine, Keith & Smith, Kevin & Williams, Robert. (2012). Water vapour foreign-continuum absorption in near-infrared windows from laboratory measurements. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences. 370. 2557-77. 10.1098/rsta.2011.0218. 
+|or
+|S.A. Clough, F.X. Kneizys, R.W. Davies,
+Line shape and the water vapor continuum,
+Atmospheric Research,
+Volume 23, Issues 3–4,
+1989,
+Pages 229-241,
+ISSN 0169-8095,
+https://doi.org/10.1016/0169-8095(89)90020-3.
+
+
+| Removing the plinth from the opacities can be done with the `removePlinth` option
 in the `param.dat` file. The hight of the plinth is defines as the value of the
 line profile at the cutting length. And example is shown in :numref:`fiplinth`.
 

docs/helios_k/subLorentzian.rst

@@ -0,0 +1,67 @@
+CO2 sub-Lorentzian line wings
+=============================
+
+
+HELIOS-K supports sub-Lorentzian profiles according to the :math:`\chi` factors 
+from Perrin and Hartmann 1998. The :math:`\chi` factors are specified in the files
+``chiPH89__CO2-CO2.dat`` and ``chiPH89__CO2-N2.dat``. In these files, the affected 
+wavenumber range can be set. The ``param.dat`` file contains the option
+``subLorentzianfile``, where the file name of the used :math:`\chi` factors file
+can be set. If a filename is set there, the sub-Lorentzian line wings are enabled.
+
+
+In principle, the :math:`\chi` factors can be applied also to other molecules than
+CO2, but this is not recommended to do.
+
+
+
+M.Y.Perrin and J.M.Hartmann, 1988 (TEMPERATURE-DEPENDENT MEASUREMENTS AND MODELING OF ABSORPTION BY CO2-N2 MIXTURES
+IN THE FAR LINE-WINGS OF THE 4.3 # m CO2 BAND).
+
+
+
+In :numref:`figSubLorentzian` is shown an example of the sub-Lorentzian profile for CO2.
+
+
+| Relevant parameters for full Voigt:
+
+ - doStoreFullK = 1
+ - cutMode = 0
+ - cut = 25.0
+ - profile = 1
+ - subLorentzianfile = -
+
+| Relevant parameters for sub-Lorentzian Voigt profile in specific wavenumber band:
+
+ - doStoreFullK = 1
+ - cutMode = 0
+ - cut = 25.0
+ - profile = 1
+ - subLorentzianfile = chiPH89__CO2-CO2.dat
+
+ - in chiPH89__CO2-CO2.dat:
+    - range in cm^-1
+    - 2100 2500
+
+| Relevant parameters for sub-Lorentzian Voigt profile in the full wavenumber range:
+
+ - doStoreFullK = 1
+ - cutMode = 0
+ - cut = 25.0
+ - profile = 1
+ - subLorentzianfile = chiPH89__CO2-CO2.dat
+
+ - in chiPH89__CO2-CO2.dat:
+    - range in cm^-1
+    - 0 10000
+
+
+
+
+.. figure:: ../../plots/SubLorentzian/plot001.png
+   :name: figSubLorentzian
+
+   CO2 sub-Lorentzian wings with :math:`\chi` factors for Perrin and Hartmann 1998. Top panel,:
+   :math:`\chi` factors applied to the band 2100-2600 cm^-1. Bottom panel: :math:`\chi`  factors
+   applied to the full wavenumber range. CO2, Hitran 2016, T = 250 K, P = 2 atm.
+

docs/index.rst

@@ -53,6 +53,7 @@ OPTIONS
   :maxdepth: 1
 
   helios_k/profiles.rst
+  helios_k/subLorentzian.rst
   helios_k/cut.rst
   helios_k/plinth.rst
   helios_k/bins.rst

exomol2.py

@@ -42,11 +42,16 @@ def transitionRanges(url):
 	if(len(transList) > 1):
 		#check range of files
 		for x in transList:
-			x0 = float(x.split('-')[0])
-			x1 = float(x.split('-')[1])
-			dg = len(x.split('-')[0])
-			#print(x1-x0)
-			rangesList.append(x1-x0)
+			#print(x)
+			try:
+				x0 = float(x.split('-')[0])
+				x1 = float(x.split('-')[1])
+				dg = len(x.split('-')[0])
+				#print(x1-x0)
+				rangesList.append(x1-x0)
+			except:
+				print("error", url, x)
+				return(0, 0, 0)
 
 		s = rangesList[0]
 		for r in rangesList:
@@ -99,8 +104,10 @@ def main():
 			url2 = url1 + el1 + "/"
 			page2 = requests.get(url2).text
 			soup2 = BeautifulSoup(page2, "html.parser")
+			#print(soup2)
 
 			List2 = soup2.find_all('a', attrs={"class" : "list-group-item link-list-group-item "})
+			List2 += soup2.find_all('a', attrs={"class" : "list-group-item link-list-group-item"})
 			List2 += soup2.find_all('a', attrs={"class" : "list-group-item link-list-group-item recommended"})
 
 			#Line list

heliosk.cu

@@ -325,6 +325,7 @@ return 0;
 	param.pathK[0] = 0;
 	param.nSpecies = 1;
 	param.useSpeciesFile = 0;
+	param.useSubLorentzian = 0;
 
 	param.T = 0.0;
 	param.P = 0.0;
@@ -405,6 +406,8 @@ return 0;
 		return 0;
 	}
 
+	subLorentzianConstantCopy(param.useSubLorentzian);
+
 	//If the bin file is used, store the boundaries of the bins
 	double *binBoundaries_h, *binBoundaries_d;
 	binBoundaries_h = (double*)malloc((param.nbins + 1) * sizeof(double));
@@ -465,6 +468,11 @@ printf("%g %g %g %g\n", param.numax, param.numin, param.dnu, (param.numax - para
 			return 0;
 		}
 	}
+	if(param.useSubLorentzian == 1){
+		subLorentzianB(param.T);
+		param.useIndividualX = 1;
+		//this is needed because of the nu/nu0 factor
+	}
 
 
 	//If the output edges file is used store the edges
@@ -498,6 +506,7 @@ printf("%g %g %g %g\n", param.numax, param.numin, param.dnu, (param.numax - para
 		if(er == 0) return 0;
 	}
 
+
 	double time[9];
 	double timeT[3];
 	for(int i = 0; i < 9; ++i){
@@ -542,6 +551,9 @@ printf("%g %g %g %g\n", param.numax, param.numin, param.dnu, (param.numax - para
 			fprintf(infofile, "Species in file: %s\n", param.SpeciesFilename);
 			fprintf(infofile, "Number of Species: %d\n", param.nSpecies);
 		}
+		if(param.useSubLorentzian > 0){
+			fprintf(infofile, "sub-Lorentzian file: %s\n", param.SpeciesFilename);
+		}
 		fprintf(infofile, "cia System = %s\n", param.ciaSystem);
 		fprintf(infofile, "pathToData = %s\n", param.path);
 		fprintf(infofile, "numin = %g\n", param.numin);

host.h

@@ -293,6 +293,11 @@ __host__ int read_parameters(Param &param, char *paramFilename, int argc, char*a
 			fscanf (paramFile, "%d", &param.removePlinth);
 			fgets(sp, 3, paramFile);
 		}
+		//read subLorentzianFile
+		else if(strcmp(sp, "subLorentzianfile =") == 0){
+			fscanf (paramFile, "%s", param.subLorentzianFilename);
+			fgets(sp, 3, paramFile);
+		}
 		else{
 			printf("Undefined line in param.dat file: line %d\n", j);
 			return 0;
@@ -486,6 +491,37 @@ __host__ int read_parameters(Param &param, char *paramFilename, int argc, char*a
 		}		
 		fclose(Speciesfile);	
 	}
+	if(strcmp(param.subLorentzianFilename, "-") != 0){
+		printf("Use sub-Lorentzian file %s\n", param.subLorentzianFilename);
+		param.useSubLorentzian = 1;
+		FILE *sLfile;
+		sLfile = fopen(param.subLorentzianFilename, "r");
+		if(sLfile == NULL){
+			printf("Error: sub-Lorentzian file not found: %s\n", param.subLorentzianFilename);
+			return 0;
+		}
+
+		char b[160];
+		int er;
+		//Read Perrin and Hartmann 1989 coefficients
+		er = fscanf(sLfile, "%s %f", b, &sLchi_h[0]);	//sigma1
+		er = fscanf(sLfile, "%s %f", b, &sLchi_h[1]);	//sigma2
+		er = fscanf(sLfile, "%s %f", b, &sLchi_h[2]);	//sigma3
+
+		er = fscanf(sLfile, "%s %s %s %s", b, b, b, b);	//B alpha beta epsilon
+		er = fscanf(sLfile, "%s %f %f %f", b, &sLchi_h[3], &sLchi_h[4], &sLchi_h[5]);	//B1
+		er = fscanf(sLfile, "%s %f %f %f", b, &sLchi_h[6], &sLchi_h[7], &sLchi_h[8]);	//B2
+		er = fscanf(sLfile, "%s %f %f %f", b, &sLchi_h[9], &sLchi_h[10], &sLchi_h[11]);	//B3
+		//read range
+		er = fscanf(sLfile, "%s %s %s", b, b, b);	//range
+		er = fscanf(sLfile, "%f %f", &sLchi_h[12], &sLchi_h[13]);	//B3
+
+		if(er <= 0){
+			printf("Error in sub-Lorentzian file read %s\n", param.subLorentzianFilename);
+			return 0;
+		}
+		fclose(sLfile);
+	}
 	if(strcmp(param.ciaSystem, "-") != 0){
 		param.useCia = 1;
 	}

param.dat

@@ -30,5 +30,6 @@ doMean = 0
 Units = 0
 ReplaceFiles = 1
 profile = 1
+subLorentzianfile = -
 removePlinth = 0
 doTuning = 1

plots/SubLorentzian/Info_i.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: 2.04
+Using device 0
+
+Runtime Version 10000
+Driver Version 10020
+GIT Describe: v1.0-124-gdc31722
+Build Date: Di 11. Aug 12:37:57 CEST 2020
+Build Path: /home/sigrimm/kCalc
+Build System: Linux mashu 4.15.0-112-generic #113-Ubuntu SMP Thu Jul 9 23:41:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
+Build Compute Capability: SM=52
+
+name = i
+T = 250
+P = 2
+cia System = -
+pathToData = ../storage/EXOMOL/
+numin = 0
+numax = 2500
+dnu = 0.1
+Nnu per bin = 25000
+Number of points: 25000
+cutMode = 0
+cut = 100
+doResampling = 0
+nC = 20
+doTransmission = 0
+nTr = 1000
+dTr =  0.05
+doStoreFullK = 1
+pathToK = 
+dostoreK = 0
+nbins = 1
+kmin = 0
+qalphaL = 1
+gammaF = 1
+doMean = 0
+Units = 0
+Replace files = 1
+profile = 1
+doTuning = 0
+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 = 02_hit16
+dataBase = 0
+Molecule Number = 2
+default L = 0
+default n = 0
+
+File 0 of 1
+Number of lines: 559874
+Time for input:        0.15566 seconds
+Time for Lines:        0.00931168 seconds
+Time for K(x):         0.0584077 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):   0.0216046 seconds
+Time for mean K(x):    2.3584e-05 seconds
+Time for sort K(x):    0.000690624 seconds
+Time for Resampling:   1.5584e-05 seconds
+Time for write K(y):   3.968e-06 seconds
+Time for Transmission: 9.344e-06 seconds