fix(model.py): fix model header after interpolation

The header now starts with "KURUCZ" and the next line include stellar parameters. When no
interpolation is needed the output is correct.

pymoog/internal.py

@@ -128,4 +128,4 @@ def combine_linelist()
     vald.sort_values('wavelength', inplace=True)
     vald.reset_index(drop=True, inplace=True)
 
-    line_data.save_linelist(vald, 'files/linelist/vald')
+    line_data.save_linelist(vald, 'files/linelist/vald')

pymoog/line_data.py

@@ -149,10 +149,8 @@ def save_linelist(linelist_all, sub_ll_name, wav_start=None, wav_end=None, type=
     with open(sub_ll_name, 'w') as file:
         file.write('VALD linelist\n')
         for i in range(len(sub_linelist)):
-            if np.isnan(sub_linelist.iloc[i].values[-1]):
-                file.write('{:10.4f}{:10.5f}{:10.4f}{:10.3f}{:10.3f}\n'.format(*sub_linelist.iloc[i].values[:-1]))
-            else:
-                file.write('{:10.4f}{:10.5f}{:10.4f}{:10.3f}{:10.3f}{:10.3f}\n'.format(*sub_linelist.iloc[i].values))
+            line = '{:10.4f}{:10.5f}{:10.4f}{:10.3f}{:10.3f}{:10.3f}{:10.3f}\n'.format(*sub_linelist.iloc[i].values).replace('nan', '   ')
+            file.write(line)
 
 def read_linelist(linelist_path, loggf_cut=None):
     '''
@@ -166,14 +164,13 @@ def read_linelist(linelist_path, loggf_cut=None):
         Cut on loggf (only save for the lines with loggf > loggf_cut)
     '''
     linelist = pd.read_fwf(linelist_path,
-            colspecs=[(0,11), (11,21), (21,31), (31,41), (41,51), (51,61)],
-            names=['wavelength', 'id', 'EP', 'loggf', 'C6', 'D0'],
+            colspecs=[(0,11), (11,21), (21,31), (31,41), (41,51), (51,61), (61,71)],
+            names=['wavelength', 'id', 'EP', 'loggf', 'C6', 'D0', 'EW'],
             skiprows=1)
-    # MOOG seems will crash if there is line with EP larger than 50eV, so they are removed.
+    # MOOG seems to crash if there is line with EP larger than 50eV, so they are removed.
     linelist = linelist[(linelist['EP'] <= 50)]
     if loggf_cut != None:
         linelist = linelist[(linelist['loggf'] >= loggf_cut)]
-        print('fsdfadsf')
         linelist.reset_index(drop=True, inplace=True)
     return linelist
 
@@ -212,8 +209,7 @@ def vald2moog_format(init_linelist_name, out_linelist_name, head=None, loggf_cut
 
     # subprocess.run(['sed', "s/'//g", init_linelist_name, '>', 'temp'])
     # subprocess.run(['mv', "temp", init_linelist_name])    
-    vald_init = pd.read_csv(init_linelist_name,skiprows=2, skipfooter=footer_index, usecols=range(9), engine = 'python' ,
-                                names=['element', 'wavelength', 'EP', 'loggf', 'rad_damp', 'Stark_damp', 'Walls_damp', 'Lande_factor', 'Comment'])
+    vald_init = pd.read_csv(init_linelist_name,skiprows=2, skipfooter=footer_index, usecols=range(9), engine = 'python', names=['element', 'wavelength', 'EP', 'loggf', 'rad_damp', 'Stark_damp', 'Walls_damp', 'Lande_factor', 'Comment'])
 
     if head != None:
         vald_init = vald_init[:head]

pymoog/model.py

@@ -95,7 +95,7 @@ def save_interpo_model(teff, logg, m_h, abun, model_line, pradk, to_path):
     else:
         pass
 
-    content = ['Kurucz model: ' + 'TEFF   {:.0f}  GRAVITY {:.5f} LTE\n'.format(teff, logg)]
+    content = ['Kurucz model: ' + 'TEFF   {:.1f}  GRAVITY {:.5f} LTE\n'.format(teff, logg)]
     content = content + ['TITLE SDSC GRID  [{:+.1f}]   VTURB 2.0 KM/S    L/H 1.25\n'.format(m_h)]    
     content = content + [' OPACITY IFOP 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0\n']
     content = content + [' CONVECTION ON   1.25 TURBULENCE OFF  0.00  0.00  0.00  0.00\n']
@@ -223,20 +223,20 @@ def KURUCZ_convert(model_path=None, vmicro=2.0, abun_change=None, converted_mode
     # Convert the model files into MOOG format.
 
     # Read and save the first two lines (except 'TITLE ') into header.
-    header = ['Kurucz model: ' + model_file.readline()]
-    header = header + [model_file.readline()]
-    try:
-        m_h = re.findall(r'\[(.*)\]', header[1])[0]
-    except IndexError:
-        m_h = 0
-        print(header)
+    header = model_file.readline() + model_file.readline()
+    teff, logg, m_h, vmicro_model, l_h = [float(s) for s in re.findall(r'[-+]?[0-9]*\.?[0-9]+', header)]
+    # try:
+    #     m_h = re.findall(r'\[(.*)\]', header[1])[0]
+    # except IndexError:
+    #     m_h = 0
+    #     print(header)
 
     # Read the abundance change as well as model lines.
     temp = model_file.readline() + model_file.readline() + model_file.readline()
 
     abun_list = ''
     temp = model_file.readline()
-    while temp[:17] == ' ABUNDANCE CHANGE':
+    while 'ABUNDANCE CHANGE' in temp[:17]:
         abun_list = abun_list + temp[17:]
         temp = model_file.readline()
     abun = np.array(abun_list.split(), dtype='f').reshape(int(len(abun_list.split())/2), 2)
@@ -272,8 +272,8 @@ def KURUCZ_convert(model_path=None, vmicro=2.0, abun_change=None, converted_mode
     c_model_file = open(c_model_path, 'w')
 
     # Header part
-    c_model_file.writelines(header[0])
-    c_model_file.writelines(header[1])
+    c_model_file.writelines('KURUCZ\n')
+    c_model_file.writelines('TEFF = {:.1f}, LOGG = {:.1f}, M/H = {:.1f}, VTURB = {:.1f}, L/H = {:.2f}\n'.format(teff, logg, m_h, vmicro_model, l_h))
 
     # Model part
     c_model_file.writelines('ntau=       ' + str(model_linen) + '\n')

pymoog/synth.py

@@ -69,7 +69,7 @@ def prepare_file(self, model_file=None, line_list=None, loggf_cut=None):
 
         if line_list == None:
             # Linelist file is not specified, will use built-in VALD linelist according to wavelength specification.
-            vald = line_data.read_linelist(MOOG_file_path + '/linelist/vald', loggf_cut=loggf_cut)
+            vald = line_data.read_linelist(MOOG_file_path + 'linelist/ges/ges_hfs_iso', loggf_cut=loggf_cut)
             line_data.save_linelist(vald, MOOG_run_path + 'line.list', wav_start=self.start_wav, wav_end=self.end_wav)
             self.line_list = 'line.list'
         else:

pymoog/temp

@@ -0,0 +1,9 @@
+Kurucz model: EFF   4500.  GRAVITY 3.00000 LTE 
+ITLE SDSC GRID  [-2.0]   VTURB 2.0 KM/S    L/H 1.25                            
+ntau=       3
+ ABUNDANCE CHANGE 9 -7.48 10 -3.95 11
+ ABUNDANCE CHANGE 15 -6.59 16 -4.83 17
+ ABUNDANCE CHANGE 21 -8.94 22 -7.05 23
+    2.0E00
+NATOMS      0   -2.0
+NMOL        0