Functional conversion script

build/fix_mechanism_fac.py

@@ -10,7 +10,6 @@
 # -----------------------------------------------------------------------------
 
 # -------------------------------------------------------------------- #
-
 # This script corrects the content of a chemical mechanism file in
 # FACSIMILE format (.fac ) by removing incorrect newline characters.
 #
@@ -134,6 +133,8 @@ def fix_fac_full_contents(input_file):
     # Reattach the header lines, and unwrap the list of lists in interim_contents.
     fixed_file = contents[:end_of_header_index] \
         + [item for sublist in interim_contents for item in sublist]
+
+    # Return the corrected mechanism file
     return fixed_file
 
 # ------------------------------------------------------------ #

build/kpp_conversion.py

@@ -0,0 +1,160 @@
+# -----------------------------------------------------------------------------
+#
+# Copyright (c) 2017 Sam Cox, Roberto Sommariva
+#
+# This file is part of the AtChem2 software package.
+#
+# This file is covered by the MIT license which can be found in the file
+# LICENSE.md at the top level of the AtChem2 distribution.
+#
+# -----------------------------------------------------------------------------
+
+# -------------------------------------------------------------------- #
+# This script
+#
+# ARGUMENT:
+#   1.
+# -------------------------------------------------------------------- #
+from __future__ import print_function
+import sys
+import re
+
+
+# =========================== FUNCTIONS =========================== #
+
+
+def extract_section(input_lines, start_marker, end_marker):
+    """
+    Extracts lines between start_marker and end_marker from input_lines.
+    """
+    nlines = len(input_lines)
+
+    start_i = 0
+    for i in range(start_i, nlines):
+        if start_marker in input_lines[i]:
+            start_i = i + 1
+            break
+
+    end_i = nlines
+    if end_marker:
+        for i in range (start_i, nlines):
+            if end_marker in input_lines[i]:
+                end_i = i + 1
+                break
+
+    section_lines = input_lines[start_i:end_i]
+    return section_lines
+
+# ------------------------------------------------------------ #
+
+def convert_rates(section_lines):
+    """
+    Converts the format of section_lines and returns the converted lines.
+    """
+    simplelist = ['KRO2NO','KRO2HO2','KAPHO2','KAPNO','KRO2NO3','KNO3AL','KDEC',
+                  'KROPRIM','KROSEC','KCH3O2','K298CH3O2','K14ISOM1']
+    mechlist1 = []
+    mechlist2 =[]
+    for reac in section_lines: #kk = kk.replace('**', '@')
+        xx = re.split(r'=', reac)
+        if xx[0].strip() in simplelist:
+            mechlist1.append(reac)
+        else:
+            mechlist2.append(reac)
+    return mechlist1, mechlist2
+
+# ------------------------------------------------------------ #
+
+def convert_ro2(section_lines):
+    """
+    Converts the format of section_lines and returns the converted lines.
+    """
+    mechlist = []
+    for line in section_lines:
+        cleaned_line = re.sub(r'C\(ind_([A-Z0-9_]+)\s*\)', r'\1', line)
+        cleaned_line = re.sub(r'\s*&', r'', cleaned_line.strip())
+        mechlist.append(cleaned_line)
+    return mechlist
+
+# ------------------------------------------------------------ #
+
+def convert_reactions(section_lines):
+    """
+    Converts the format of section_lines and returns the converted lines.
+    """
+    mechlist = []
+    for reac in section_lines:
+        if re.match(r'{\d+\.}', reac):
+            xx = re.split(r'[}:;]', reac)
+            kk = re.sub(r'J\((\d+)\)', r'J<\1>', xx[2])
+            kk = kk.replace('**', '@')
+            yy = '%' + kk + ':' + xx[1] + ';\n'
+            mechlist.append(yy)
+    return mechlist
+
+# ------------------------------------------------------------ #
+
+def kpp_to_facsimile(input_file):
+    """
+    workhorse function
+    """
+
+    with open(input_file, 'r') as file_open:
+        contents = file_open.readlines()
+
+    start_ro2 = 'RO2 = & '
+    end_ro2 = ') \n'
+    ro2_lines = extract_section(contents, start_ro2, end_ro2)
+    converted_ro2 = convert_ro2(ro2_lines)
+
+    start_rates = end_ro2
+    end_rates = '#ENDINLINE'
+    rates_lines = extract_section(contents, start_rates, end_rates)[:-2]
+    converted_rate1, converted_rate2 = convert_rates(rates_lines)
+
+    start_reactions = '#EQUATIONS'
+    end_reactions = ''
+    reactions_lines = extract_section(contents, start_reactions, end_reactions)
+    converted_reactions = convert_reactions(reactions_lines)
+
+    #
+    return converted_rate1, converted_rate2, converted_ro2, converted_reactions
+
+# ------------------------------------------------------------ #
+
+def write_fac_file(input_file):
+    """
+    wrapper
+    """
+    print('Running write_fac_file on ' + str(input_file))
+    contents1, contents2, contents3, contents4 = kpp_to_facsimile(input_file)
+    output_file = input_file.split('.')[0] + '.fac1'
+    with open(output_file, 'w') as file_open:
+        file_open.write('\n* Generic Rate Coefficients ;\n')
+        file_open.writelines(contents1)
+        file_open.write('\n* Complex reactions ;\n')
+        file_open.writelines(contents2)
+        file_open.write('\n* Peroxy radicals. ;\n')
+        file_open.write('RO2 = ')
+        file_open.writelines(contents3)
+        file_open.write(';\n')
+        file_open.write('\n* Reaction definitions. ;\n')
+        file_open.writelines(contents4)
+
+
+# =========================== MAIN =========================== #
+
+
+def main():
+    # Pass argument from command line - name of the .kpp file to be converted
+    if len(sys.argv) > 1:
+        #aa = kpp_to_facsimile(sys.argv[1])
+        write_fac_file(sys.argv[1])
+    else:
+        print('******************************************')
+        print('Please pass a filename as script argument.')
+        print('******************************************')
+
+# Call the main function if executed as script
+if __name__ == '__main__':
+    main()

build/mech_converter.py

@@ -35,7 +35,7 @@
 import sys
 import re
 import fix_mechanism_fac
-import convert_kpp
+import kpp_conversion
 
 reservedSpeciesList = ['N2', 'O2', 'M', 'RH', 'H2O', 'BLHEIGHT', 'DEC', 'JFAC',
                        'DILUTE', 'ROOF', 'ASA', 'RO2']
@@ -174,9 +174,9 @@ def convert_to_fortran(input_file, mech_dir, mcm_vers):
     print(input_directory)
 
     # Check if the chemical mechanism file is in KPP format, in which case convert it
-    # to FACSIMILE format (see documentation of `convert_kpp.py` for more info)
+    # to FACSIMILE format (see documentation of `kpp_conversion.py` for more info)
     if input_filename.split('.')[1] == 'kpp':
-        #input_fac = convert_kpp.kpp2fac(input_filename)
+        #input_fac = kpp_conversion.kpp_to_facsimile(input_filename)
         sys.exit('KPP format is not supported yet')
     else:
         input_fac = input_filename

mcm/mechanism_skel.fac

@@ -1,11 +1,11 @@
 * Generic Rate Coefficients ;
+...
 
 * Complex reactions ;
+...
 
 * Peroxy radicals. ;
-
-RO2 =  ;
+RO2 = ... ;
 
 * Reaction definitions. ;
-
 % k : A + B = C ;

mcm/mechanism_skel.kpp

@@ -0,0 +1,9 @@
+#INLINE F90_RCONST
+RO2 = & 
+ C(ind_...) 
+...
+CALL mcm_constants(time, temp, M, N2, O2, RO2, H2O)
+#ENDINLINE
+
+#EQUATIONS
+{1.} A + B = C : k ;