Fix typo in readme. Fix upper-case conversion in phys.chem_safe()

Author: nichollsh

make/Mk_cmd

@@ -1,6 +1,6 @@
 # Generated automatically
 # System: Linux atmlxint6.atm.ox.ac.uk 5.4.0-193-generic #213-Ubuntu SMP Fri Aug 2 19:14:16 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux 
-# Date: Wed 30 Oct 20:07:01 GMT 2024 
+# Date: Thu 31 Oct 13:48:05 GMT 2024 
 
 FORTCOMP        = /usr/bin/gfortran -Ofast -march=native -fPIC  -c 
 LINK            = /usr/bin/gfortran -Ofast -march=native -fPIC  

spectraltools/README.md

@@ -5,9 +5,9 @@ This subdirectory is not part of the original SOCRATES repository. It is distrib
 ### Overview
 
 Computing k-coefficients from a line-list is very expensive because there can be a large number of transitions for a single molecule. To speed this up, it is useful to split the process into two steps:
-1. Calculating cross-sections from a line-list (at line resolution).    
-2. Calculating k-coefficients from the cross-sections (at a lower resolution).     
-  
+1. Calculating cross-sections from a line-list (at line resolution).
+2. Calculating k-coefficients from the cross-sections (at a lower resolution).
+
 Step 1 is by far the slowest, so it is helpful to use pre-computed opacities. These tools aim to generalise the creation of SpectralFiles from pre-computed opacity tables by converting them into a common netCDF format. These netCDF files can then be read by SOCRATES when generating SpectralFiles with the required properties.
 
 **You will need to download the source cross-sections yourself**. For a given database (`db`) and absorber (`ab`), the files should be placed in the directory `data/db/ab/`. All output files will be written to `output/`, which **you will also need to create yourself** or create a symbolic link called `output` which points to another extant location. The tools are primarily targeted at parsing cross-sections from DACE, with other databases partially supported for comparison purposes. It is recommended that you download cross-sections using the `Tinterpolate_dace.py` tool, and then generate spectral files using `Tmake_spectralfile.py`.
@@ -16,10 +16,10 @@ These tools all operate by storing the spectral absorption cross-section (versus
 
 ### Content
 
-| Tool                     | Description   |   
+| Tool                     | Description   |
 |--------------------------|---------------|
 | `Tmake_spectralfile.py`  | Generate a spectral file for the specified absorbers and wavenumber/pressure/temperature range |
-| `Tconvert_dace.py`       | Convert DACE binary files into the netCDF format for the specified absorber   | 
+| `Tconvert_dace.py`       | Convert DACE binary files into the netCDF format for the specified absorber   |
 | `Tdownload_cia.py`       | Download CIA databases from the HITRAN website into `data/cia/` |
 | `Tplot_absorption.py`    | Plot absorption cross-section versus wavenumber  |
 | `Tcalc_checksum.py`      | Calculate the BLAKE2b checksum of a file in order to verify its integrity  |
@@ -32,15 +32,15 @@ These tools all operate by storing the spectral absorption cross-section (versus
 * SOCRATES
    - Must have been compiled
    - Executables have been added to your `PATH` variable using `. ./set_rad_env`
-* Python (version >= 3.11) and the following libraries 
+* Python (version >= 3.11) and the following libraries
    - numpy
    - netcdf4
    - glob
    - shutil
    - requests
    - hashlib
    - matplotlib
-   - dace_query
+   - dace-query
    - h5py
 
 ### Online sources

spectraltools/Tmake_spectralfile.py

@@ -1,7 +1,7 @@
-#!/usr/bin/env python3 
+#!/usr/bin/env python3
 # Python wizard for interactive file conversion
 
-# Import local files 
+# Import local files
 import src.utils as utils
 import src.spectral as spectral
 import src.dace as dace
@@ -38,7 +38,7 @@ def main():
 
 
 
-   
+
     # ------------ EXECUTION -------------
     # Check volatile names
     for i in range(len(vols)):
@@ -53,7 +53,7 @@ def main():
         formula_path = os.path.join(utils.dirs[source], v.strip()+"/")
         if not os.path.exists(formula_path):
             raise Exception("Could not find folder '%s'" % formula_path)
-        
+
 
     # ===========
     # Remove content of output folder under this alias (optionally including netCDFs)
@@ -71,7 +71,7 @@ def main():
     print("Parameters")
     print("    source: %s"%source)
     print("    alias:  %s"%alias)
-    print("    vols:   %s"%utils.get_arr_as_str(vols))  
+    print("    vols:   %s"%utils.get_arr_as_str(vols))
     print("    nvols:  %d"%len(vols))
     print("    nband:  %d"%nband)
     print("    numin, numax, dnu : %.1f, %g, %.2f cm-1"%(numin, numax, dnu))
@@ -104,7 +104,7 @@ def main():
         dat_numax = max(dat_numax, vol_numax)
         print("        numin, numax = %.1f, %.1f cm-1"%(vol_numin, vol_numax))
 
-        #     get tmin, tmax 
+        #     get tmin, tmax
         _,at,_ = dace.list_all_ptf(formula_path)
         dat_tmin = min(dat_tmin, np.amin(at))
         dat_tmax = max(dat_tmax, np.amax(at))
@@ -133,7 +133,7 @@ def main():
 
 
     # ===========
-    # Determine bands 
+    # Determine bands
     band_edges = spectral.best_bands(nu_arr, method, nband)
 
 
@@ -154,7 +154,7 @@ def main():
         nc_paths[v] = ncp
         if os.path.exists(ncp) and preNC:
             print("WARNING: Using pre-existing netCDF file for %s lbl absorption. Any configuration mismatch here will lead to issues."%v)
-            continue 
+            continue
 
         # Get numin, numax for this volatile
         formula_path = os.path.join(utils.dirs[source], v+"/")
@@ -167,7 +167,7 @@ def main():
         # This is for performance reasons, but is also critical for ensuring that the volatiles all use the same p,t points
         files = []
         print("Using pt->f map from %s for %s"%(vols[-1],v))
-        for f in arr_f: 
+        for f in arr_f:
             # Try simply substituting volatile name and wavenumber range
             ftry = list(str(f).replace(vols[-1], v))
             ftry[-26:-21] = str_numin[:]
@@ -176,16 +176,16 @@ def main():
 
             if os.path.exists(ftry):
                 files.append(ftry)
-                continue 
+                continue
 
-            # Try also substituting "out"<->"itp" 
+            # Try also substituting "out"<->"itp"
             if "Itp" in ftry:
                 ftry = ftry.replace("Itp", "Out")
             else:
                 ftry = ftry.replace("Out", "Itp")
             if os.path.exists(ftry):
                 files.append(ftry)
-                continue 
+                continue
 
             raise Exception("Could not find bin file for '%s' corresponding to '%s'"%(v,f))
 
@@ -203,14 +203,14 @@ def main():
 
 
     # ===========
-    # Calculate k-coefficients from netCDF 
+    # Calculate k-coefficients from netCDF
     for i,f1 in enumerate(vols):
         spectral.calc_kcoeff_lbl(alias, f1, nc_paths[f1])
-        for f2 in vols[i:]: 
+        for f2 in vols[i:]:
             spectral.calc_kcoeff_cia(alias, f1, f2, dnu_last)
 
 
-    # =========== 
+    # ===========
     # Calculate water droplet properties
     if drops and ("H2O" in vols):
         spectral.calc_waterdroplets(alias)
@@ -221,8 +221,8 @@ def main():
     spectral.assemble(alias, vols)
 
     # ------------------------------------
-    return 
-    
+    return
+
 
 if __name__ == "__main__":
     utils.checkenv()

spectraltools/src/phys.py

@@ -1,10 +1,10 @@
-# Physical constants 
+# Physical constants
 
 # Universal gas constant [J K-1 mol-1]
-R_gas = 8.31446261815324 
+R_gas = 8.31446261815324
 
 # Stefan-boltzmann constant [W m−2 K−4]
-sigma = 5.670367e-8 
+sigma = 5.670367e-8
 
 # Avogadro's constant [mol-1]
 N_av = 6.02214076e+23
@@ -30,9 +30,9 @@ def iso_to_formula(iso:str):
         for c in str(a):  # for each char
             if amu: # skip AMU
                 if c.isdigit():
-                    continue 
+                    continue
                 else:
-                    amu=False 
+                    amu=False
             f += c
     return f
 
@@ -115,77 +115,76 @@ def iso_to_formula(iso:str):
     "Magnesium oxide"       :"MgO",
 }
 
-# Get chemical's safe name 
+# Get chemical's safe name
 def chemsafe(name:str):
-    up = name.upper()
 
     # name provided
-    if up in chem_dict.keys():
-        return chem_dict[up]
-    
+    if name in chem_dict.keys():
+        return chem_dict[name]
+
     # form provided
-    if up in chem_dict.values():
-        return up
-    
+    if name in chem_dict.values():
+        return name
+
     # nope
     return None
 
 # Formulae's MMW in g/mol (taken from src/radiance_core/gas_list_pcf.f90 -- see references therein)
 form_mmw = {
-    "H2O":        18.0153, 
-    "CO2":        44.0100, 
-    "O3":         47.9982, 
-    "N2O":        44.0128, 
-    "CO":         28.0106, 
-    "CH4":        16.0430, 
-    "O2":         31.9988, 
-    "NO":         30.0061, 
-    "SO2":        64.0628, 
-    "NO2":        46.0055, 
-    "NH3":        17.0306, 
-    "HNO3":       63.0129, 
-    "N2":         28.0134, 
-    "CFC11":      137.3686, 
-    "CFC12":      120.9140, 
-    "CFC113":     187.3765, 
-    "HCFC22":     86.46892, 
-    "HFC125":     120.02227, 
-    "HFC134a":    102.03184, 
-    "CFC114":     170.921, 
-    "TiO ":       63.866, 
-    "VO":         66.9409, 
-    "H2":         2.01588, 
-    "He":         4.002602, 
-    "OCS":        60.075, 
-    "Na":         22.98976928, 
-    "K":          39.0983, 
-    "FeH":        56.853, 
-    "CrH":        53.004, 
-    "Li":         6.941, 
-    "Rb":         85.4678, 
-    "Cs":         132.9054519, 
-    "PH3":        33.99758, 
-    "C2H2":       26.0373, 
-    "HCN":        27.0253, 
-    "H2S":        34.081, 
-    "Ar":         39.948, 
-    "O":          15.9994, 
-    "N":          14.00674, 
-    "NO3":        63.0128, 
-    "N2O5":       108.0104, 
-    "HONO":       47.0134, 
-    "HO2NO2":     79.0122, 
-    "H2O2":       34.0147, 
-    "C2H6":       30.0690, 
-    "CH3 ":       15.0345, 
-    "H2CO ":      30.0260, 
-    "HO2":        33.0067, 
-    "HDO":        19.0214, 
-    "HCl":        36.461, 
-    "HF":         20.00689, 
-    "cis-OSSO":   96.129, 
-    "trans-OSSO": 96.129, 
-    "OSO-S":      96.129, 
+    "H2O":        18.0153,
+    "CO2":        44.0100,
+    "O3":         47.9982,
+    "N2O":        44.0128,
+    "CO":         28.0106,
+    "CH4":        16.0430,
+    "O2":         31.9988,
+    "NO":         30.0061,
+    "SO2":        64.0628,
+    "NO2":        46.0055,
+    "NH3":        17.0306,
+    "HNO3":       63.0129,
+    "N2":         28.0134,
+    "CFC11":      137.3686,
+    "CFC12":      120.9140,
+    "CFC113":     187.3765,
+    "HCFC22":     86.46892,
+    "HFC125":     120.02227,
+    "HFC134a":    102.03184,
+    "CFC114":     170.921,
+    "TiO ":       63.866,
+    "VO":         66.9409,
+    "H2":         2.01588,
+    "He":         4.002602,
+    "OCS":        60.075,
+    "Na":         22.98976928,
+    "K":          39.0983,
+    "FeH":        56.853,
+    "CrH":        53.004,
+    "Li":         6.941,
+    "Rb":         85.4678,
+    "Cs":         132.9054519,
+    "PH3":        33.99758,
+    "C2H2":       26.0373,
+    "HCN":        27.0253,
+    "H2S":        34.081,
+    "Ar":         39.948,
+    "O":          15.9994,
+    "N":          14.00674,
+    "NO3":        63.0128,
+    "N2O5":       108.0104,
+    "HONO":       47.0134,
+    "HO2NO2":     79.0122,
+    "H2O2":       34.0147,
+    "C2H6":       30.0690,
+    "CH3 ":       15.0345,
+    "H2CO ":      30.0260,
+    "HO2":        33.0067,
+    "HDO":        19.0214,
+    "HCl":        36.461,
+    "HF":         20.00689,
+    "cis-OSSO":   96.129,
+    "trans-OSSO": 96.129,
+    "OSO-S":      96.129,
 
 }