diff --git a/Exemple/.gitkeep b/Example/.gitkeep
similarity index 100%
rename from Exemple/.gitkeep
rename to Example/.gitkeep
diff --git a/Exemple/AA.mech b/Example/AA.mech
similarity index 100%
rename from Exemple/AA.mech
rename to Example/AA.mech
diff --git a/Exemple/AA.therm b/Example/AA.therm
similarity index 100%
rename from Exemple/AA.therm
rename to Example/AA.therm
diff --git a/Exemple/AA.trans b/Example/AA.trans
similarity index 100%
rename from Exemple/AA.trans
rename to Example/AA.trans
diff --git a/Exemple/LLNL.mech b/Example/LLNL.mech
similarity index 100%
rename from Exemple/LLNL.mech
rename to Example/LLNL.mech
diff --git a/Exemple/LLNL.therm b/Example/LLNL.therm
similarity index 100%
rename from Exemple/LLNL.therm
rename to Example/LLNL.therm
diff --git a/Exemple/LLNL.trans b/Example/LLNL.trans
similarity index 100%
rename from Exemple/LLNL.trans
rename to Example/LLNL.trans
diff --git a/Exemple/Results extraction merging/.gitkeep b/Example/Results extraction merging/.gitkeep
similarity index 100%
rename from Exemple/Results extraction merging/.gitkeep
rename to Example/Results extraction merging/.gitkeep
diff --git a/Exemple/Results extraction merging/AA.pick b/Example/Results extraction merging/AA.pick
similarity index 100%
rename from Exemple/Results extraction merging/AA.pick
rename to Example/Results extraction merging/AA.pick
diff --git a/Exemple/Results extraction merging/LLNL.pick b/Example/Results extraction merging/LLNL.pick
similarity index 100%
rename from Exemple/Results extraction merging/LLNL.pick
rename to Example/Results extraction merging/LLNL.pick
diff --git a/Exemple/Results extraction merging/all_comparisons.log b/Example/Results extraction merging/all_comparisons.log
similarity index 100%
rename from Exemple/Results extraction merging/all_comparisons.log
rename to Example/Results extraction merging/all_comparisons.log
diff --git a/Exemple/Results extraction merging/new_model_TIRAMISU_kt.mech b/Example/Results extraction merging/new_model_TIRAMISU_kt.mech
similarity index 100%
rename from Exemple/Results extraction merging/new_model_TIRAMISU_kt.mech
rename to Example/Results extraction merging/new_model_TIRAMISU_kt.mech
diff --git a/Exemple/Results extraction merging/new_model_TIRAMISU_kt.therm b/Example/Results extraction merging/new_model_TIRAMISU_kt.therm
similarity index 100%
rename from Exemple/Results extraction merging/new_model_TIRAMISU_kt.therm
rename to Example/Results extraction merging/new_model_TIRAMISU_kt.therm
diff --git a/Exemple/Results extraction merging/new_model_TIRAMISU_kt.trans b/Example/Results extraction merging/new_model_TIRAMISU_kt.trans
similarity index 100%
rename from Exemple/Results extraction merging/new_model_TIRAMISU_kt.trans
rename to Example/Results extraction merging/new_model_TIRAMISU_kt.trans
diff --git a/Exemple/Results extraction merging/similar_therm_model1.txt b/Example/Results extraction merging/similar_therm_model1.txt
similarity index 100%
rename from Exemple/Results extraction merging/similar_therm_model1.txt
rename to Example/Results extraction merging/similar_therm_model1.txt
diff --git a/Exemple/Results extraction merging/similar_therm_model2.txt b/Example/Results extraction merging/similar_therm_model2.txt
similarity index 100%
rename from Exemple/Results extraction merging/similar_therm_model2.txt
rename to Example/Results extraction merging/similar_therm_model2.txt
diff --git a/Exemple/Results extraction merging/similar_therm_model_core.txt b/Example/Results extraction merging/similar_therm_model_core.txt
similarity index 100%
rename from Exemple/Results extraction merging/similar_therm_model_core.txt
rename to Example/Results extraction merging/similar_therm_model_core.txt
diff --git a/Exemple/Results extraction merging/similar_therm_model_to_translate.txt b/Example/Results extraction merging/similar_therm_model_to_translate.txt
similarity index 100%
rename from Exemple/Results extraction merging/similar_therm_model_to_translate.txt
rename to Example/Results extraction merging/similar_therm_model_to_translate.txt
diff --git a/Exemple/Results extraction merging/tmp_species_traduction.inp b/Example/Results extraction merging/tmp_species_traduction.inp
similarity index 100%
rename from Exemple/Results extraction merging/tmp_species_traduction.inp
rename to Example/Results extraction merging/tmp_species_traduction.inp
diff --git a/Exemple/Results extraction merging/tmp_species_traduction.tmp b/Example/Results extraction merging/tmp_species_traduction.tmp
similarity index 100%
rename from Exemple/Results extraction merging/tmp_species_traduction.tmp
rename to Example/Results extraction merging/tmp_species_traduction.tmp
diff --git a/Exemple/Results full merging/AA.pick b/Example/Results full merging/AA.pick
similarity index 100%
rename from Exemple/Results full merging/AA.pick
rename to Example/Results full merging/AA.pick
diff --git a/Exemple/Results full merging/LLNL.pick b/Example/Results full merging/LLNL.pick
similarity index 100%
rename from Exemple/Results full merging/LLNL.pick
rename to Example/Results full merging/LLNL.pick
diff --git a/Exemple/Results full merging/all_comparisons.log b/Example/Results full merging/all_comparisons.log
similarity index 100%
rename from Exemple/Results full merging/all_comparisons.log
rename to Example/Results full merging/all_comparisons.log
diff --git a/Exemple/Results full merging/new_model_TIRAMISU_kt.mech b/Example/Results full merging/new_model_TIRAMISU_kt.mech
similarity index 100%
rename from Exemple/Results full merging/new_model_TIRAMISU_kt.mech
rename to Example/Results full merging/new_model_TIRAMISU_kt.mech
diff --git a/Exemple/Results full merging/new_model_TIRAMISU_kt.therm b/Example/Results full merging/new_model_TIRAMISU_kt.therm
similarity index 100%
rename from Exemple/Results full merging/new_model_TIRAMISU_kt.therm
rename to Example/Results full merging/new_model_TIRAMISU_kt.therm
diff --git a/Exemple/Results full merging/new_model_TIRAMISU_kt.trans b/Example/Results full merging/new_model_TIRAMISU_kt.trans
similarity index 100%
rename from Exemple/Results full merging/new_model_TIRAMISU_kt.trans
rename to Example/Results full merging/new_model_TIRAMISU_kt.trans
diff --git a/Exemple/Results full merging/new_model_TIRAMISU_n.mech b/Example/Results full merging/new_model_TIRAMISU_n.mech
similarity index 100%
rename from Exemple/Results full merging/new_model_TIRAMISU_n.mech
rename to Example/Results full merging/new_model_TIRAMISU_n.mech
diff --git a/Exemple/Results full merging/new_model_TIRAMISU_n.therm b/Example/Results full merging/new_model_TIRAMISU_n.therm
similarity index 100%
rename from Exemple/Results full merging/new_model_TIRAMISU_n.therm
rename to Example/Results full merging/new_model_TIRAMISU_n.therm
diff --git a/Exemple/Results full merging/new_model_TIRAMISU_n.trans b/Example/Results full merging/new_model_TIRAMISU_n.trans
similarity index 100%
rename from Exemple/Results full merging/new_model_TIRAMISU_n.trans
rename to Example/Results full merging/new_model_TIRAMISU_n.trans
diff --git a/Exemple/Results full merging/similar_therm_model1.txt b/Example/Results full merging/similar_therm_model1.txt
similarity index 100%
rename from Exemple/Results full merging/similar_therm_model1.txt
rename to Example/Results full merging/similar_therm_model1.txt
diff --git a/Exemple/Results full merging/similar_therm_model2.txt b/Example/Results full merging/similar_therm_model2.txt
similarity index 100%
rename from Exemple/Results full merging/similar_therm_model2.txt
rename to Example/Results full merging/similar_therm_model2.txt
diff --git a/Exemple/Results full merging/similar_therm_model_core.txt b/Example/Results full merging/similar_therm_model_core.txt
similarity index 100%
rename from Exemple/Results full merging/similar_therm_model_core.txt
rename to Example/Results full merging/similar_therm_model_core.txt
diff --git a/Exemple/Results full merging/similar_therm_model_to_translate.txt b/Example/Results full merging/similar_therm_model_to_translate.txt
similarity index 100%
rename from Exemple/Results full merging/similar_therm_model_to_translate.txt
rename to Example/Results full merging/similar_therm_model_to_translate.txt
diff --git a/Exemple/Results full merging/tmp_species_traduction.inp b/Example/Results full merging/tmp_species_traduction.inp
similarity index 100%
rename from Exemple/Results full merging/tmp_species_traduction.inp
rename to Example/Results full merging/tmp_species_traduction.inp
diff --git a/Exemple/Results full merging/tmp_species_traduction.tmp b/Example/Results full merging/tmp_species_traduction.tmp
similarity index 100%
rename from Exemple/Results full merging/tmp_species_traduction.tmp
rename to Example/Results full merging/tmp_species_traduction.tmp
diff --git a/Exemple/extraction_merging.txt b/Example/extraction_merging.txt
similarity index 61%
rename from Exemple/extraction_merging.txt
rename to Example/extraction_merging.txt
index a3f54668776913c1507a2321393d49a32f557bf1..b0e3a242da276942a09bc6022825b52e0533f5d7 100644
--- a/Exemple/extraction_merging.txt
+++ b/Example/extraction_merging.txt
@@ -1,7 +1,7 @@
! You can comment with '!'
!
-C:/Users/fages1/Nextcloud/Code_these/TIRAMISU/Exemple/LLNL
-C:/Users/fages1/Nextcloud/Code_these/TIRAMISU/Exemple/AA
+C:/Users/fages1/Nextcloud/Code_these/TIRAMISU/Exemple/ LLNL.mech LLNL.therm LLNL.trans
+C:/Users/fages1/Nextcloud/Code_these/TIRAMISU/Exemple/ AA.mech AA.therm AA.trans
C:/Users/fages1/Nextcloud/Code_these/TIRAMISU/Exemple/
n=10000
introduction=test @
diff --git a/Exemple/full_merging.txt b/Example/full_merging.txt
similarity index 56%
rename from Exemple/full_merging.txt
rename to Example/full_merging.txt
index 3e4e122b6ced276715290161197377174892df65..081641cd369198e0f94f2bf684fe0a8600a46f5f 100644
--- a/Exemple/full_merging.txt
+++ b/Example/full_merging.txt
@@ -1,7 +1,7 @@
! You can comment with '!'
!
-C:/Users/fages1/Nextcloud/Code_these/TIRAMISU/Exemple/LLNL
-C:/Users/fages1/Nextcloud/Code_these/TIRAMISU/Exemple/AA
+C:/Users/fages1/Nextcloud/Code_these/TIRAMISU/Exemple/ LLNL.mech LLNL.therm LLNL.trans
+C:/Users/fages1/Nextcloud/Code_these/TIRAMISU/Exemple/ AA.mech AA.therm AA.trans
C:/Users/fages1/Nextcloud/Code_these/TIRAMISU/Exemple/
n=10000
translation=True
diff --git a/README.md b/README.md
index 3f4e89fbcfefa649b3db68de54bc31de7c59ed90..d39aa6a29c917c1b21e2f294c50c146e6ade8dab 100644
--- a/README.md
+++ b/README.md
@@ -1,93 +1,93 @@
# LRGP - TIRAMISU
+## Name
+TIRAMISU (Thermodynamical Interpretation of Reactions and Automated Merging for Inter-Scheme Union)
+## Description
+The TIRAMISU automatic fusion code allows to efficiently merge large kinetic mechanisms by translating automaticaly species and extracting sub-mechanisms. Allow a complete merging between two mechanism or a sub-mechanism extraction.
-## Getting started
-
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
-
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
-
-## Add your files
-
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-
-```
-cd existing_repo
-git remote add origin https://gitlab.univ-lorraine.fr/fages1/lrgp-tiramisu.git
-git branch -M main
-git push -uf origin main
-```
+## Dependencies
+Python 3.11.8
+library: os, sys, pickle, time, datetime, copy, re, numpy, matplotlib, itertools, collections
-## Integrate with your tools
+## Explanation
+To use it, download the TIRAMISU folder. Two example, one of a full merging and the other of a sub-mechanism extraction, are available in the EXAMPLE folder. The two code to use are Main_exe_1.py and Main_exe_2.py (in this order). You can either execute the code from a terminal by calling "python Main_exe_x.py input.txt" (with x=1 or 2) or by using an IDE and commenting line 10 & 11 and uncommenting line 12 & 13 (then replace "0.txt" in line 12 by your input file).
+INPUT FILE :
+ The input file is the same for the first and second part of the code (Main_exe_1.py and Main_exe_2.py).
+ "!" is used to comment line.
-- [ ] [Set up project integrations](https://gitlab.univ-lorraine.fr/fages1/lrgp-tiramisu/-/settings/integrations)
+ The first 3 lines should be the 3 necessary path (in the same order as below):
+ - The path to the first mechanism and each mech file. Example: C:/Users/mech1/ mech1.mech mech1.therm mech1.trans
+ If the NASA polynomial are in the mech file, put two time the mech file. Example: C:/Users/mech1/ LLNL.mech mech1.mech mech1.trans
+ If there is no transport, put only the mech and therm file. Example: C:/Users/mech1/ mech1.mech mech1.therm
-## Collaborate with your team
+ - The path to the second mechanism and each mech file. Example: C:/Users/mech2/ mech2.mech mech2.therm mech2.trans
+ If the NASA polynomials are in the mech file, put two time the mech file. Example: C:/Users/mech2/ mech2.mech mech2.mech mech2.trans
+ If there is no transport, put only the mech and therm file. Example: C:/Users/mech1/ mech2.mech mech2.therm
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
+ - The path to the output. C:/Users/output/
-## Test and Deploy
+ The mech1 is by default the core mechanism and mech2 the mechanism to translate.
+ The other lines can be in any order.
-Use the built-in continuous integration in GitLab.
+ "task" is an optional keyword that controls whethe a full merging or a sub-mechanism extraction is wanted. Default is full merging. Example: task=full or task=extraction
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
+ "depth" is an optional keyword for extraction task. It controls the maximum number of loop the extraction step does. Default is no maximum (1e10). Example: depth=3
-***
+ "mech_to_extract" is a MANDATORY keyword for the extraction task. It controls wich species sub-mechanism to extract. Example: mech_to_extract=ic8h18, nc7h16
-# Editing this README
+ "translation" is an optional boolean used to enable or disable the translation step. It is only useful if there is already a tmp_species_traduction.tmp or .inp file generated previously.
+ If the two mechanisms have the same translation, it is also possible to disable the translation and create an empty tmp_species_traduction.inp. Example: translation=True
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
+ "n" is an optional keyword that controls the maximum number of permutations that are allowed in method 2. If the number of possible permutations in an isomer group is greater than n, then only method 1 will be used. Example: n=10000
-## Suggestions for a good README
+ "introduction" is an optional keyword used to customize the first lines of the merged mechanism. Example: introduction=test!?!
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
+ "string_to_del" is an optional keyword used to remove species containing a specific string. Example: string_to_del=bb, pb, c6h5c3, c6h5c4, cyc
-## Name
-Choose a self-explaining name for your project.
+ "list_to_del" is an optional keyword used to remove specific species. Example: list_to_del=a1c2hac, a1c2h3ac, a2-x, a2o
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
+ "order" is an optional keyword used to control which mechanism as priority on which part of the mechanism. Possible input are "kt", "k", "t", "n".
+ k = model_core main for kinetic data and model_to_translate main for thermo data.
+ t = model_to_translate main for kinetic data and core_mechanism main for thermo data.
+ kt = model_core main for kinetic and themo data.
+ n = model_to_translate main for kinetic and thermo data.
+ Default order task is kt. You can also specify a list of order to generate multiple mechanism in the form "order=order1, order2, order3, ..."
+ ORDER FOR EXTRACTION_MERGING IS ALWAYS SET TO "kt" !!!
+ Example: order=k
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
+HOW TO USE :
+Once the input created, use "python Main_exe_1.py input". A tmp_species_traduction.tmp file will be created. This file contains all the temporary translation done by the code and also which translation needs to be done manually.
+This file is separated by isomer group. Each isomer group start with its composition (example: c1 o1 h1).
+The next line contains all translation possible contained in mech1.
+Then, each isomer for mech2 is presented, associated with its translation or a possibility of translations.
+Each line starting with !CHECK needs to be looked carefully. Choose the right translation and remove the !CHECK or the species will be treated as if there is no translation.
+If you want to remove a translation, you can comment the line with "!" or change the species with a None.
+Everything after a "!" on a line will be treated as a comment.
+Explanation of a !CHECK line :
+!CHECK species_to_translate = [species1, species2, species3] ![value1, value2, value3]
+First list [species1, species2, species3]
+ species1: This is the species name given by the first translation method.
+ species2: This is the species name corresponding to the best arrangement found by the second translation method.
+ species3: This is the species name corresponding to the second-best arrangement found by the second translation method.
+An arrangement here refers to the match found between all the species to be translated (in the isomer group) and all the species used for translation (in the isomer group). The best arrangement is the one with the minimum mean normalized mean absolute difference (mean NMAD).
+Second list [value1, value2, value3]
+ value1: This is the direct NMAD between the species_to_translate and species1, given by the first method.
+ value2: This is the mean NMAD for the best arrangement of the whole isomer group, given by the second method.
+ value3: This is the mean NMAD for the second-best arrangement of the whole isomer group, given by the second method.
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
+Once you are satisfied with the translation, copy the file and change the ".tmp" to ".inp". Now you can use "python Main_exe_2.py input".
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
+EXAMPLE :
+Two example are available in this project. They contain the two mechanisms and the input for the two tasks possible (extraction_merging.txt and full_merging.txt).
+The results obtained with these two examples are also available so you can compare.
+The base tmp_species_traduction.tmp and the modified tmp_species_traduction.inp are also available.
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-## License
-For open source projects, say how it is licensed.
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
diff --git a/TIRAMISU/Main_exe_1.py b/TIRAMISU/Main_exe_1.py
index 59c59827b41fe43fe391e14d7b4a5c48f6aab0c1..cd958d8aaf9927e0fc9c682f71bbd42858e1a7ed 100644
--- a/TIRAMISU/Main_exe_1.py
+++ b/TIRAMISU/Main_exe_1.py
@@ -12,10 +12,29 @@ with open(sys.argv[1], 'r') as file_input :
# with open("0.txt", 'r') as file_input :
# file = file_input.readlines()
file=[x for x in file if x.strip()[0] != '!']
-core_path=file[0].strip()
-translate_path=file[1].strip()
-name_core=os.path.basename(core_path)
-name_translate=os.path.basename(translate_path)
+file=[x for x in file if x.strip() != '']
+c_path=[x.strip() for x in file[0].split()]
+c_path=[c_path[0]+x if x!=c_path[0] else x for x in c_path]
+if len(c_path)==4 :
+ core_path, path_mech_core, path_therm_core, path_trans_core=c_path[0], c_path[1], c_path[2], c_path[3]
+elif len(c_path) == 3 :
+ core_path, path_mech_core, path_therm_core=c_path[0], c_path[1], c_path[2]
+ path_trans_core=''
+else :
+ raise Exception(f'Error in core path mechanism (mech1).\nThe first line should contain the path to the mechanism and the name of the mech file, the therm file and if there is one, the transport file.\n{file[0]}')
+t_path=[x.strip() for x in file[1].split()]
+t_path=[t_path[0]+x if x!=t_path[0] else x for x in t_path]
+if len(t_path)==4 :
+ translate_path, path_mech_to_translate, path_therm_to_translate, path_trans_to_translate=t_path[0], t_path[1], t_path[2], t_path[3]
+elif len(t_path) == 3 :
+ translate_path, path_mech_to_translate, path_therm_to_translate=t_path[0], t_path[1], t_path[2]
+ path_trans_to_translate=''
+else :
+ raise Exception(f'Error in translate path mechanism (mech2).\nThe second line should contain the path to the mechanism and the name of the mech file, the therm file and if there is one, the transport file.\n{file[1]}')
+
+name_core=os.path.basename(path_mech_core).split('.')[0]
+name_translate=os.path.basename(path_mech_to_translate).split('.')[0]
+
output=file[2].strip()
n=10000
n_find=False
@@ -41,15 +60,6 @@ if translation_find is False :
print('No boolean for translation (translation=True or False). Default is translation=True.')
print(f'\ntranslation={do_translation}')
-
-path_mech_core=f'{core_path}.mech'
-path_therm_core=f'{core_path}.therm'
-path_trans_core=f'{core_path}.trans'
-
-path_mech_to_translate=f'{translate_path}.mech'
-path_therm_to_translate=f'{translate_path}.therm'
-path_trans_to_translate=f'{translate_path}.trans'
-
time_start = time.time()
model_to_translate=rm.Model(path_mech_to_translate, path_therm_to_translate, output, path_trans_to_translate,verbose=False)
diff --git a/TIRAMISU/Main_exe_2.py b/TIRAMISU/Main_exe_2.py
index e21e353dd0a5f774347bf8512385044d42118c72..be2c8c246b9d80ffce35543689b68f50342398cd 100644
--- a/TIRAMISU/Main_exe_2.py
+++ b/TIRAMISU/Main_exe_2.py
@@ -18,11 +18,30 @@ with open(sys.argv[1], 'r') as file_input :
# with open("0.txt", 'r') as file_input :
# file = file_input.readlines()
file=[x for x in file if x.strip()[0] != '!']
+file=[x for x in file if x.strip() != '']
+c_path=[x.strip() for x in file[0].split()]
+c_path=[c_path[0]+x if x!=c_path[0] else x for x in c_path]
+if len(c_path)==4 :
+ core_path, path_mech_core, path_therm_core, path_trans_core=c_path[0], c_path[1], c_path[2], c_path[3]
+elif len(c_path) == 3 :
+ core_path, path_mech_core, path_therm_core=c_path[0], c_path[1], c_path[2]
+ path_trans_core=''
+else :
+ raise Exception(f'Error in core path mechanism (mech1).\nThe first line should contain the path to the mechanism and the name of the mech file, the therm file and if there is one, the transport file.\n{file[0]}')
+t_path=[x.strip() for x in file[1].split()]
+t_path=[t_path[0]+x if x!=t_path[0] else x for x in t_path]
+if len(t_path)==4 :
+ translate_path, path_mech_to_translate, path_therm_to_translate, path_trans_to_translate=t_path[0], t_path[1], t_path[2], t_path[3]
+elif len(t_path) == 3 :
+ translate_path, path_mech_to_translate, path_therm_to_translate=t_path[0], t_path[1], t_path[2]
+ path_trans_to_translate=''
+else :
+ raise Exception(f'Error in translate path mechanism (mech2).\nThe second line should contain the path to the mechanism and the name of the mech file, the therm file and if there is one, the transport file.\n{file[1]}')
+
n=10000
-core_path=file[0].strip()
-translate_path=file[1].strip()
-name_core=os.path.basename(core_path)
-name_translate=os.path.basename(translate_path)
+
+name_core=os.path.basename(path_mech_core).split('.')[0]
+name_translate=os.path.basename(path_mech_to_translate).split('.')[0]
output=file[2].strip()
intro='!'
task='full'
@@ -67,7 +86,7 @@ for line in file :
elif "n=" in line[:2].strip() :
n=int(line.strip()[2:])
elif "task=" in line.strip()[:5] :
- task_request=True
+ task_requested=True
if 'full' in line.strip()[5:].casefold() :
task='full'
elif 'extraction' in line.strip()[5:].casefold() :
@@ -92,15 +111,15 @@ for line in file :
if order_requested is False :
print('No mechanism designed as main ("kt", "k", "t", "n").\nk = model_core main for kinetic data and model_to_translate main for thermo data.\n'+\
't = model_to_translate main for kinetic data and core_mechanism main for thermo data.\n'+\
- 'kt = model_core main for kinetic and themo data.\nn = modle_to_translate main for kinetic and thermo data.\n'+\
+ 'kt = model_core main for kinetic and themo data.\nn = model_to_translate main for kinetic and thermo data.\n'+\
'Default order task is order=kt. You can also specify a list of order to generate multiple mechanism in the form "order=order1, order2, order3, ...".\n'+\
'\nORDER FOR EXTRACTION_MERGING IS ALWAYS SET TO "kt" !!!')
if task_requested is False :
print('No merging task requested ("extraction" or "full"). Default merging task is task=full.\n')
if string_to_del==[] :
- print('No string to remove. You can specify to delete species containing a specific string with "string_to_del=chr1, chr2, chr3, ...".\n')
+ print('No string to remove. You can specify to remove species containing a specific string with "string_to_del=chr1, chr2, chr3, ...".\n')
if list_to_del==[] :
- print('No species to remove. You can specify to delete specific species "list_to_del=species1, species2, species3, ...".\n')
+ print('No species to remove. You can specify to remove specific species "list_to_del=species1, species2, species3, ...".\n')
# =============================================================================
# ############################### EXTRACTION #################################
diff --git a/TIRAMISU/make_translation.py b/TIRAMISU/make_translation.py
index 2c968012677c7b0af7b154f487eeab193972e85a..8df92f09ba71b540d4e33d40af0048871867030e 100644
--- a/TIRAMISU/make_translation.py
+++ b/TIRAMISU/make_translation.py
@@ -435,7 +435,7 @@ def models_translation(model1, model2, output, n, max_permut):
result.write(f'{first_part:<50}{" ":10}!{translation[0][3]} {translation[2]:.1f}\n{sec_part}')
else :
if translation[0][1] != translation[0][2] :
- first_part=f'{iso} = {translation[0][1]}'
+ first_part=f'!CHECK {iso} = {translation[0][1]}'
result.write(f'{first_part:<50}{" ":10}!Should be ok but look : {translation[0][0:3]} {translation[0][3]} {translation[2]:.1f}\n')
else :
first_part=f'{iso} = {translation[0][1]}'
@@ -561,19 +561,20 @@ def translate(model1, translation):
translated.therm[translation[species]]=translated.therm.pop(species)
translated.therm[translation[species]].species=translation[species]
- for ind,species in enumerate(translated.trans.copy()) :
- if species in translation :
- if translation[species] in translation :
- print(f'Trans exception, translation already in mechanism : {species} {translation[species]}')
- translated.trans[translation[species]]=model1_copy.trans[species]
- translated.trans[translation[species]].species=translation[species]
- else :
- translated.trans[translation[species]]=translated.trans.pop(species)
- translated.trans[translation[species]].species=translation[species]
- for ind,reaction in enumerate(translated.reactions[2].copy()) :
- for ind2,side in enumerate(reaction.species) :
- for ind3,spe in enumerate(side) :
- if spe in translation :
- translated.reactions[2][ind].species[ind2][ind3] = translation[spe]
+ if model1.path_trans != '' :
+ for ind,species in enumerate(translated.trans.copy()) :
+ if species in translation :
+ if translation[species] in translation :
+ print(f'Trans exception, translation already in mechanism : {species} {translation[species]}')
+ translated.trans[translation[species]]=model1_copy.trans[species]
+ translated.trans[translation[species]].species=translation[species]
+ else :
+ translated.trans[translation[species]]=translated.trans.pop(species)
+ translated.trans[translation[species]].species=translation[species]
+ for ind,reaction in enumerate(translated.reactions[2].copy()) :
+ for ind2,side in enumerate(reaction.species) :
+ for ind3,spe in enumerate(side) :
+ if spe in translation :
+ translated.reactions[2][ind].species[ind2][ind3] = translation[spe]
return(translated)
\ No newline at end of file