diff --git a/TIRAMISU/add_and_write_mechanism.py b/TIRAMISU/add_and_write_mechanism.py
new file mode 100644
index 0000000000000000000000000000000000000000..ce4f8175aaf70ad8909c15699bfa3b1ce4a7c151
--- /dev/null
+++ b/TIRAMISU/add_and_write_mechanism.py
@@ -0,0 +1,702 @@
+import copy
+import re
+import os
+
+def recursive_addition(to_add_mech, model1_translated, model2, warning, depth=1e10) :
+ warn_to_check=set()
+ new_species=[]
+ skip=0
+ for species in to_add_mech :
+ if species not in model1_translated.reactions[1] :
+ print(f'ERROR : {species} not in model1')
+ print(species, to_add_mech)
+ print(model1_translated.reactions[1])
+ return('')
+ if species in model2.spe :
+
+ while True and skip !=1 :
+ conti=input(f'I think the mech {species} is already in model2. Do you want to continue (y/y_all/n)?')
+ if conti == 'y' or conti == 'Y':
+ break
+ if conti == 'y_all' :
+ skip = 1
+ break
+ elif conti == 'n' or conti == 'N' :
+ return('ERROR : already in model2')
+ new_species.append([species, model1_translated.spe_model[species]])
+ new_reactions=[]
+
+ n_species=[x for x,y in new_species]
+ count_depth=0
+ last_reactions=[]
+ while (n_species != [] and count_depth < depth) :
+ print(n_species)
+ last2_reactions = copy.deepcopy(last_reactions)
+ last_reactions=[]
+ count_depth+=1
+ tmp_n_species=copy.deepcopy(n_species)
+ n_species = []
+ if tmp_n_species != [] :
+ for n_spe in tmp_n_species :
+ count=0
+ for reaction in model1_translated.reactions[2] :
+
+ if n_spe in reaction.species[0] or n_spe in reaction.species[1] :
+
+ if reaction in model2.reactions[2] :
+ print(reaction.species, "Error ?")
+
+ else :
+
+ if reaction not in new_reactions :
+ new_reactions.append(reaction)
+ else :
+
+ len1=len([0 for x in new_reactions[new_reactions.index(reaction)].supinfo if x.strip().startswith('dup')])
+ len2=len([0 for x in reaction.supinfo if x.strip().startswith('dup')])
+ if len1 == 0 and len2 != 0 :
+ print(f'\nERROR LUMPING : {new_reactions[new_reactions.index(reaction)].__dict__} {reaction.__dict__}\n')
+ new_reactions.remove(reaction)
+ new_reactions.append(reaction)
+ last_reactions.append(reaction)
+ elif len1 != 0 and len2 != 0 :
+ xor=[rea.speed for rea in new_reactions if rea==reaction]
+ # print(f'Faux xor : {xor}')
+ if reaction.speed not in xor :
+ new_reactions.append(reaction)
+ last_reactions.append(reaction)
+ # print(f'Xor : {xor}')
+ # print(f'{" + ".join(reaction.species[0])} = {" + ".join(reaction.species[1]):30} {reaction.third_body.upper() if reaction.third_body!=0 else ""}')
+ for side in reaction.species :
+ for species in side :
+
+ if species == "hv" :
+ print(f'REGARDE ! UN PHOTON ! {reaction.species}')
+ if species != "hv" and species not in [x for x,y in new_species] \
+ and species not in model2.spe :
+ if species in warning :
+ print(f'WARNING : {species} ENCOUNTERED IN REACTION AND NOT TRADUCTED (!CHECK)')
+ warn_to_check.add(species)
+
+ n_species.append(species)
+ new_species.append([species, model1_translated.spe_model[species]])
+
+ count+=1
+ else :
+ break
+ # list_to_check=[]
+ # for reaction in last_reactions :
+ # for species in [*reaction.species[0],reaction.species[1]]
+
+
+ # print(count)
+ for ind_spe, species in enumerate([x for x,y in new_species].copy()) :
+ if species in model2.reactions[1] :
+ print('Already there ....', species)
+ del new_species[ind_spe]
+ for reaction in new_reactions :
+ len1=len([0 for x in reaction.supinfo if x.strip().startswith('dup')])
+ if len1 != 0 :
+ len2=len([0 for x in new_reactions if x==reaction])
+ if len2 == 1 :
+ print(f'\nA reaction have been duplicated :\n{reaction.__dict__}\n')
+ new_reactions.append(reaction)
+ elif len2 < 1 :
+ print('FATAL ERROR')
+
+
+ print(f'DEPTH = {count_depth}')
+ print(f'\nNumber of species that can cause issue : {len(warn_to_check)}\n {warn_to_check}')
+ return(new_reactions, new_species)
+
+def mechanism_writing(outp, md1, md2, model1_translated, model2, to_add, custom='') :
+
+ """ MECH """
+
+ with open(outp+'.mech', 'w') as out :
+
+ """ INTRODUCTION """
+
+ out.write(custom)
+
+ """ ELEMENTS """
+
+ out.write('elements\n'.upper())
+ elements=set(model1_translated.reactions[0]+model2.reactions[0])
+ for element in elements :
+ out.write(f'{element}\n'.upper())
+
+ """ SPECIES 2 """
+
+ out.write(f'end\n{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" SPECIES":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\nspecies\n'.upper())
+ for species in model2.reactions[1] :
+ out.write(f'{species}\n'.upper())
+
+ """ SPECIES 1 """
+
+ out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" SPECIES":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+ if to_add != '' :
+ for species in to_add[1] :
+ out.write(f'{species}\n'.upper())
+
+ """ REACTIONS 2 """
+
+ out.write(f'end\n{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" REACTIONS":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\nreactions\n'.upper())
+ for reaction in model2.reactions[2] :
+ if reaction.is_rev == True :
+ equal= '='
+ elif reaction.is_rev == False :
+ equal= '=>'
+ else :
+ print(f'ERROR, NO REV {reaction.__dict__}')
+
+ if reaction.third_body != 0 :
+ tb=f"+{reaction.third_body}"
+ if reaction.supinfo != [] :
+ low_check=["low/" for x in reaction.supinfo if 'low/' in x or 'low /' in x]
+ tcheb_check=["tcheb/" for x in reaction.supinfo if 'tcheb/' in x or 'tcheb /' in x]
+ if len(low_check) >= 1 or len(tcheb_check) >= 1 :
+ tb=f"(+{reaction.third_body})"
+ else :
+ tb=''
+
+ reactant=[]
+ product=[]
+ # print(reaction.speed[1])
+ for s, c in zip(reaction.species[0], reaction.coef[0]) :
+ if c == 1 :
+ c=''
+ elif int(c) == c :
+ c=int(c)
+ reactant.append(str(c) + str (s))
+
+ for s, c in zip(reaction.species[1], reaction.coef[1]) :
+ if c == 1 :
+ c=''
+ elif int(c) == c :
+ c=int(c)
+ product.append(str(c) + str (s))
+
+ final_reaction=f'{"+".join(reactant)}{tb if tb!= "" else ""}{equal}{"+".join(product)}{tb if tb!= "" else ""}'
+ # to_write=f'{final_reaction:48} {reaction.speed[0]}{reaction.speed[1]:<+7.3f}{reaction.speed[2]:+11.3e}'
+ to_write='{:<48}{:>+12.3e}{:>+9.3f}{:>+11.1f}'.format\
+ (final_reaction, reaction.speed[0], reaction.speed[1], reaction.speed[2])
+ if len(to_write)>80 :
+ print(f'Reaction from base model too big ! :\n{to_write}')
+ to_write=re.sub(r"\s+", " ", to_write)
+ print(to_write)
+ out.write((to_write+'\n').upper())
+ # print(to_write,len(to_write))
+ for sup in reaction.supinfo :
+ out.write(('\t'+sup+'\n').upper())
+
+ """ REACTIONS 1 """
+
+ out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" REACTIONS":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+ if to_add != '' :
+
+ for reaction in to_add[0] :
+
+ if reaction.is_rev == True :
+ equal= '='
+ elif reaction.is_rev == False :
+ equal= '=>'
+ else :
+ print(f'ERROR, NO REV {reaction.__dict__}')
+
+ if reaction.third_body != 0 :
+ tb=f"+{reaction.third_body}"
+ if reaction.supinfo != [] :
+ low_check=["low/" for x in reaction.supinfo if 'low/' in x or 'low /' in x]
+ tcheb_check=["tcheb/" for x in reaction.supinfo if 'tcheb/' in x or 'tcheb /' in x]
+ if len(low_check) >= 1 or len(tcheb_check) >= 1 :
+ tb=f"(+{reaction.third_body})"
+ else :
+ tb=''
+
+ reactant=[]
+ product=[]
+ # print(reaction.speed[1])
+ for s, c in zip(reaction.species[0], reaction.coef[0]) :
+ if c == 1 :
+ c=''
+ elif int(c) == c :
+ c=int(c)
+ reactant.append(str(c) + str (s))
+
+ for s, c in zip(reaction.species[1], reaction.coef[1]) :
+ if c == 1 :
+ c=''
+ elif int(c) == c :
+ c=int(c)
+ product.append(str(c) + str (s))
+
+ final_reaction=f'{"+".join(reactant)}{tb if tb!= "" else ""}{equal}{"+".join(product)}{tb if tb!= "" else ""}'
+ to_write='{:<48}{:>+12.3e}{:>+9.3f}{:>+11.1f}'.format\
+ (final_reaction, reaction.speed[0], reaction.speed[1], reaction.speed[2])
+ # to_write=f'{final_reaction:48} {reaction.speed[0]:<+12.3e}{reaction.speed[1]:<+7.3f}{reaction.speed[2]:+11.3e}'
+ if len(to_write)>80 :
+ print(f'Reaction from added model too big !\n{to_write}')
+ to_write=re.sub(r"\s+", " ", to_write)
+ print(to_write)
+
+ out.write((to_write+'\n').upper())
+ # print(to_write,len(to_write))
+ for sup in reaction.supinfo :
+ out.write(('\t'+sup+'\n').upper())
+ out.write('end'.upper())
+
+ """ THERMO """
+
+ with open(outp+'.therm', 'w') as out :
+
+ """ INTRODUCTION """
+
+ out.write(custom)
+
+ """ START """
+
+ out.write(f'thermo\n{300:>10.3f}{1000:>10.3f}{5000:>10.3f}\n'.upper())
+
+ out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" THERMO":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+
+ for species in model2.reactions[1] :
+ name=model2.therm[species]
+ ato_comp=name.atomic_composition
+ string=''
+ for ato in ato_comp :
+ string+=ato+' '*(5-len(str(ato_comp[ato]))-len(ato))+str(ato_comp[ato])
+#
+ temp=name.temp_list
+
+ out.write(f'{name.species:<16}{" "*8}{string:<20}G{temp[0]:>10.2f}{temp[2]:>10.2f}{temp[1]:>8.2f}{" "*6}1\n'.upper())
+ for idx,item in enumerate(name.nasa_list) :
+ if idx in [4,9,13] :
+
+ if idx == 4 :
+ strsup=' 2'
+ if idx == 9 :
+ strsup=' 3'
+ if idx == 13 :
+ strsup=' '*15+' 4'
+
+ out.write(f'{item:>+15.8e}{strsup}\n'.upper())
+ else :
+ out.write(f'{item:>+15.8e}'.upper())
+
+ out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" THERMO":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+ if to_add != '' :
+ for species in to_add[1] :
+ name=model1_translated.therm[species]
+ ato_comp=name.atomic_composition
+ string=''
+ for ato in ato_comp :
+ string+=ato+' '*(5-len(str(ato_comp[ato]))-len(ato))+str(ato_comp[ato])
+ #
+ temp=name.temp_list
+
+ out.write(f'{name.species:<16}{" "*8}{string:<20}G{temp[0]:>10.2f}{temp[2]:>10.2f}{temp[1]:>8.2f}{" "*6}1\n'.upper())
+ for idx,item in enumerate(name.nasa_list) :
+ if idx in [4,9,13] :
+
+ if idx == 4 :
+ strsup=' 2'
+ if idx == 9 :
+ strsup=' 3'
+ if idx == 13 :
+ strsup=' '*15+' 4'
+
+ out.write(f'{item:>+15.8e}{strsup}\n'.upper())
+ else :
+ out.write(f'{item:>+15.8e}'.upper())
+
+ out.write('end'.upper())
+
+ """ TRANSPORT """
+
+ with open(outp+'.trans', 'w') as out :
+
+ """ INTRODUCTION """
+
+ out.write(custom)
+
+ """ START """
+
+ out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" TRANSPORT":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+
+ for species in model2.reactions[1] :
+
+ trans=model2.trans[species]
+ out.write(f'{trans.species:<20}{trans.geo:>10.0f}{trans.lj_p:>10.3f}{trans.lj_cd:>10.3f}{trans.dp:>10.3f}{trans.p:>10.3f}{trans.rr:>10.3f}\n'.upper())
+
+ out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" THERMO":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+ if to_add !='' and model1_translated.path_trans != '':
+ for species in to_add[1] :
+
+ trans=model1_translated.trans[species]
+ out.write(f'{trans.species:<20}{trans.geo:>10.0f}{trans.lj_p:>10.3f}{trans.lj_cd:>10.3f}{trans.dp:>10.3f}{trans.p:>10.3f}{trans.rr:>10.3f}\n'.upper())
+ else :
+ if model1_translated.path_trans == '' :
+ out.write('NOT COMPLETE\nNOT COMPLETE\n')
+ out.write('end'.upper())
+
+def merging(outp, md_core, md_to_translate, max_len_name, model_core, model_to_translate_translated, order, custom='',flag_extraction=False, to_add=[]) :
+ #(out+f'_{order}', md_translate, md_core, max_len_name, model_to_translate_translated, model_core, order, custom=introduction, flag_extraction=flag_extraction, to_add=to_add)
+
+
+ def write_species(out, model1, model2, md1, md2, flag_extraction=False, to_add=[]) :
+ out.write(f'end\nspecies\n'.upper())#'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" SPECIES":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\nspecies\n'.upper())
+ spe_list=[]
+ for species in model1.spe :
+ if species not in spe_list :
+ spe_list.append(species)
+ out.write((f'{species:<80}'+f'\t! *:_:* {model1.spe_model[species]} *:_:* \n').upper())
+ if flag_extraction == True :
+ # out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" SPECIES":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+ for species in to_add[1] :
+ if species[0] not in spe_list :
+ spe_list.append(species)
+ if species[0] not in model1.spe :
+ out.write((f'{species[0]:<80}'+f'\t! *:_:* {species[1]} *:_:* \n').upper())
+ elif model2 != '' :
+ # out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" SPECIES":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+ for species in model2.spe :
+ if species not in spe_list :
+ spe_list.append(species)
+ out.write((f'{species:<80}'+f'\t! *:_:* {model2.spe_model[species]} *:_:* \n').upper())
+
+
+ def write_reactions(out, model1, model2, md1, md2, max_len_name, flag_extraction=False, to_add=[]) :
+ out.write(f'end\nreactions\n'.upper())#{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" REACTIONS":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\nreactions\n'.upper())
+ rea_list=[]
+ for reaction in model1.rea :
+ if reaction not in rea_list :
+ rea_list.append(reaction)
+ out.write(reaction.print_reaction(path='return', pr=False, max_len_name=max_len_name))
+ if flag_extraction == True :
+ # out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" REACTIONS":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+
+ for reaction in to_add[0] :
+ if reaction not in rea_list :
+ rea_list.append(reaction)
+ out.write(reaction.print_reaction(path='return', pr=False, max_len_name=max_len_name))
+ elif model2 !='' :
+ # out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" REACTIONS":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+ for reaction in model2.rea :
+ if reaction not in rea_list :
+ rea_list.append(reaction)
+ out.write(reaction.print_reaction(path='return', pr=False, max_len_name=max_len_name))
+ out.write('end'.upper())
+
+
+ def write_therm(out, model1, model2, md1, md2, flag_extraction=False, to_add=[]) :
+ out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" THERMO":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+ spe_list=[]
+ # print(f'model1 : {model1.path_mech}')
+ for species in model1.spe :
+ if species not in spe_list :
+ # print(species)
+ spe_list.append(species)
+ name=model1.therm[species]
+ ato_comp=name.atomic_composition
+ string=''
+ for ato in ato_comp :
+ string+=ato+' '*(5-len(str(ato_comp[ato]))-len(ato))+str(ato_comp[ato])
+
+ temp=name.temp_list
+
+ out.write(f'{name.species:<16}{" "*8}{string:<20}G{temp[0]:>10.2f}{temp[2]:>10.2f}{temp[1]:>8.2f}{" "*6}1\n'.upper())
+
+ for idx,item in enumerate(name.nasa_list) :
+ if idx in [4,9,13] :
+
+ if idx == 4 :
+ strsup=' 2'
+ if idx == 9 :
+ strsup=' 3'
+ if idx == 13 :
+ strsup=' '*15+' 4'
+
+ out.write(f'{item:>+15.8e}{strsup}\n'.upper())
+ else :
+ out.write(f'{item:>+15.8e}'.upper())
+
+ if flag_extraction == True :
+ out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" THERMO":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+ for species in to_add[1] :
+ if species[0] not in spe_list :
+ spe_list.append(species[0])
+ name=model2.therm[species[0]]
+ ato_comp=name.atomic_composition
+ string=''
+ for ato in ato_comp :
+ string+=ato+' '*(5-len(str(ato_comp[ato]))-len(ato))+str(ato_comp[ato])
+
+ temp=name.temp_list
+
+ out.write(f'{name.species:<16}{" "*8}{string:<20}G{temp[0]:>10.2f}{temp[2]:>10.2f}{temp[1]:>8.2f}{" "*6}1\n'.upper())
+
+ for idx,item in enumerate(name.nasa_list) :
+ if idx in [4,9,13] :
+
+ if idx == 4 :
+ strsup=' 2'
+ if idx == 9 :
+ strsup=' 3'
+ if idx == 13 :
+ strsup=' '*15+' 4'
+
+ out.write(f'{item:>+15.8e}{strsup}\n'.upper())
+ else :
+ out.write(f'{item:>+15.8e}'.upper())
+ elif model2 !='' :
+ out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" THERMO":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+ for species in model2.spe :
+ if species not in spe_list :
+ spe_list.append(species)
+ name=model2.therm[species]
+ ato_comp=name.atomic_composition
+ string=''
+ for ato in ato_comp :
+ string+=ato+' '*(5-len(str(ato_comp[ato]))-len(ato))+str(ato_comp[ato])
+
+ temp=name.temp_list
+
+ out.write(f'{name.species:<16}{" "*8}{string:<20}G{temp[0]:>10.2f}{temp[2]:>10.2f}{temp[1]:>8.2f}{" "*6}1\n'.upper())
+
+ for idx,item in enumerate(name.nasa_list) :
+ if idx in [4,9,13] :
+
+ if idx == 4 :
+ strsup=' 2'
+ if idx == 9 :
+ strsup=' 3'
+ if idx == 13 :
+ strsup=' '*15+' 4'
+
+ out.write(f'{item:>+15.8e}{strsup}\n'.upper())
+ else :
+ out.write(f'{item:>+15.8e}'.upper())
+
+ out.write('end'.upper())
+
+
+
+ def write_trans(out, model1, model2, md1, md2, flag_extraction=False, to_add=[]) :
+ spe_list=[]
+ out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" TRANSPORT":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+
+ for species in model1.spe :
+ if species not in spe_list :
+ spe_list.append(species)
+ trans=model1.trans[species]
+ out.write(f'{trans.species:<20}{trans.geo:>10.0f}{trans.lj_p:>10.3f}{trans.lj_cd:>10.3f}{trans.dp:>10.3f}{trans.p:>10.3f}{trans.rr:>10.3f}\n'.upper())
+ if flag_extraction == True :
+ out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" TRANSPORT":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+ for species in to_add[1] :
+ if species[0] not in spe_list :
+ spe_list.append(species[0])
+ out.write(f'{trans.species:<20}{trans.geo:>10.0f}{trans.lj_p:>10.3f}{trans.lj_cd:>10.3f}{trans.dp:>10.3f}{trans.p:>10.3f}{trans.rr:>10.3f}\n'.upper())
+ elif model2 !='' :
+ out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" TRANSPORT":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
+ for species in model2.spe :
+ if species not in spe_list :
+ spe_list.append(species)
+ trans=model2.trans[species]
+ out.write(f'{trans.species:<20}{trans.geo:>10.0f}{trans.lj_p:>10.3f}{trans.lj_cd:>10.3f}{trans.dp:>10.3f}{trans.p:>10.3f}{trans.rr:>10.3f}\n'.upper())
+ out.write('end'.upper())
+
+ """ MECH """
+
+ with open(outp+'.mech', 'w') as out :
+
+ """ INTRODUCTION """
+
+ out.write(custom)
+
+ """ ELEMENTS """
+
+ out.write('elements\n'.upper())
+ elements=set(model_core.elem+model_to_translate_translated.elem if model_to_translate_translated != '' else model_core.elem)
+
+ for element in elements :
+ out.write(f'{element}\n'.upper())
+
+ """ SPECIES """
+ if 'k' in order :
+
+ write_species(out, model_core, model_to_translate_translated, md_core, md_to_translate, flag_extraction, to_add)
+ write_reactions(out, model_core, model_to_translate_translated, md_core, md_to_translate, max_len_name, flag_extraction, to_add)
+
+ else :
+
+ write_species(out, model_to_translate_translated, model_core, md_to_translate, md_core, flag_extraction, to_add)
+ write_reactions(out, model_to_translate_translated, model_core, md_to_translate, md_core, max_len_name, flag_extraction, to_add)
+
+ """ THERMO """
+
+ with open(outp+'.therm', 'w') as out :
+
+ """ INTRODUCTION """
+
+ out.write(custom)
+ out.write('!'+order+'\n')
+
+ """ START """
+
+ out.write(f'thermo\n{300:>10.3f}{1000:>10.3f}{5000:>10.3f}\n'.upper())
+
+ if 't' in order :
+
+ write_therm(out, model_core, model_to_translate_translated, md_core, md_to_translate, flag_extraction, to_add)
+
+ else :
+ write_therm(out, model_to_translate_translated, model_core, md_to_translate, md_core, flag_extraction, to_add)
+
+ """ TRANSPORT """
+ if (model_core.path_trans != '' and model_to_translate_translated == '') or (model_core.path_trans != '' and model_to_translate_translated.path_trans != '') :
+ with open(outp+'.trans', 'w') as out :
+
+ """ INTRODUCTION """
+
+ out.write(custom)
+ out.write('!'+order+'\n')
+
+ """ START """
+
+ if 't' in order :
+ write_trans(out, model_core, model_to_translate_translated, md_core, md_to_translate, flag_extraction, to_add)
+
+def writing_modified_mechanism(outp, new_md_name, true_model, list_species=[], list_reactions=[], dict_translation={}, verbose=True) :
+
+ model=copy.deepcopy(true_model)
+ # for species in list_species :
+
+ # print(f'nb reaction {len(write[1])}')
+ if list_species != [] :
+ rea_removed=[]
+ spe_removed=[]
+ for spe in copy.deepcopy(model.reactions[1]) :
+ if spe in list_species :
+ # print([spe])
+ spe_removed.append(model.reactions[1].pop(model.reactions[1].index(spe)))
+ model.therm.pop(spe)
+ model.trans.pop(spe)
+
+ for rea in copy.deepcopy(model.reactions[2]) :
+ testing=[x for x in [*rea.species[0],*rea.species[1]] if x in list_species]
+ if len(testing)>0 :
+ # print(testing)
+ for index,r in enumerate(model.reactions[2]) :
+ if r.eq_rea(rea) :
+ # print('a ',index)
+ break
+ # print('b ',index)
+ rea_removed.append(copy.deepcopy(model.reactions[2][index]))
+ del model.reactions[2][index]
+
+ with open(outp+new_md_name+'_spe&rea_removed.txt', 'w') as s_r :
+ for spe in spe_removed :
+ s_r.write(f'{spe}\n')
+
+ for rea in rea_removed :
+ if verbose == True :
+ rea.print_reaction(outp+new_md_name+'_spe&rea_removed.txt')
+
+ print('nb rea removed because of spe :', len(rea_removed))
+ print('nb spe removed :',len(spe_removed))
+
+ if list_reactions != [] :
+ rea_force_removed=[]
+ for rea in list_reactions :
+ for index,r in enumerate(copy.deepcopy(model.reactions[2])) :
+ if r.eq_rea(rea) :
+ rea_force_removed.append(copy.deepcopy(model.reactions[2][index]))
+ del model.reactions[2][index]
+ break
+
+ with open(outp+new_md_name+'_spe&rea_force_removed.txt', 'w') as cl :
+ pass
+ for rea in rea_force_removed :
+ rea.print_reaction(outp+new_md_name+'_spe&rea_force_removed.txt', pr=False)
+ print('nb rea force removed :', len(rea_force_removed))
+
+ if dict_translation != {} :
+ for spe in copy.deepcopy(model.reactions[1]) :
+ # print(spe)
+ if spe in dict_translation :
+ print('1 :'+spe)
+ tmp=model.reactions[1].index(spe)
+ model.reactions[1][tmp] = dict_translation[spe]
+ print('2 :'+model.reactions[1][tmp])
+
+ # for spe in dict_translate :
+ for index,rea in enumerate(copy.deepcopy(model.reactions[2])) :
+ for index2, side in enumerate(rea.species) :
+ for index3, spe in enumerate(side) :
+ if spe in dict_translation :
+ print(f'before : {model.reactions[2][index].species}')
+ model.reactions[2][index].species[index2][index3] = dict_translation[spe]
+ print(f'after : {model.reactions[2][index].species}')
+
+
+ spe_removed=[]
+ spe_set=set()
+
+ for rea in copy.deepcopy(model.reactions[2]) :
+ for spe in [*rea.species[0], *rea.species[1]] :
+ spe_set.add(spe)
+
+ for spe in copy.deepcopy(model.reactions[1]) :
+ if spe not in spe_set and spe not in ['he', 'ar', 'ne']:
+ print('No reaction for',spe)
+ spe_removed.append(model.reactions[1].pop(model.reactions[1].index(spe)))
+ model.therm.pop(spe)
+ model.trans.pop(spe)
+
+ with open(outp+new_md_name+'_norea_spe_removed.txt', 'w') as nr_s :
+ for spe in spe_removed :
+ nr_s.write(f'{spe}\n')
+
+ merging(outp+new_md_name, 'model', '', max(list(set([len(x.from_model) if x.from_model != '' else len(x.model) for x in model.rea]))),
+ model, '', 'kt', custom='' ,flag_extraction=False, to_add=[])
+
+
+# def full_merging(output, prefix_to_del, spe_to_del, model_to_translate) :
+# rea_to_del=[]
+
+# for species in (copy.deepcopy(model_to_translate.spe)) :
+# for pref in prefix_to_del :
+# # print(pref, species)
+# if pref in species :
+# # print(pref, species)
+# spe_to_del.append(model_to_translate.spe[model_to_translate.spe.index(species)])
+# # print(len(model1.reactions[1]))
+
+# print('Is spe_to_del well written ?',len(spe_to_del), len(set(spe_to_del)))
+# print('Length therm start :',len(model_to_translate.therm))
+# print('Length trans start :',len(model_to_translate.trans))
+# for species in spe_to_del :
+# if species in copy.deepcopy(model_to_translate.therm) :
+# del model_to_translate.therm[species]
+
+# for species in spe_to_del :
+# if species in copy.deepcopy(model_to_translate.trans) :
+# del model_to_translate.trans[species]
+
+# print('Length therm end :',len(model_to_translate.therm))
+# print('Length trans end :',len(model_to_translate.trans))
+
+# with open(f'{output}removed_by_prefix.txt','w') as rm :
+# for spe in spe_to_del :
+# rm.write(f'{spe}\n')
+
+# for species in spe_to_del :
+# for reaction in copy.deepcopy(model_to_translate.rea) :
+# if species in [*reaction.species[0],*reaction.species[1]] :
+# rea_to_del.append(reaction.identifier)
+
+# model_to_translate.spe=[x for x in model_to_translate.spe if x not in spe_to_del]
+# batch_rea=[x for x in model_to_translate.rea if x.identifier not in rea_to_del]
+# model_to_translate.rea=batch_rea
+# return model_to_translate
\ No newline at end of file