Difference between revisions of "Latest changes"

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{| class="wikitable"
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!colspan="6"|Latest revision: 500
+
!colspan="6"|Latest revision: 1137
 +
 
 +
|-
 +
|01/15/2024
 +
|Fixed some bugs with llcalcs.sh and improved ChemKnow algorithm (new keyword CK_minima)
 +
|-
 +
|11/07/2023
 +
|Fixed some issues with the HL calcs of fragments
 +
|-
 +
|05/12/2022
 +
|Fixed some issues with qcore calcs
 +
|-
 +
|04/26/2022
 +
|Bugfix in utils and improved performace hl calcs
 +
|-
 +
|04/13/2022
 +
|Removed STOP in diag.f. 
 +
|-
 +
|03/17/2022
 +
|Bugfix in final.sh. 
 +
|-
 +
|03/11/2022
 +
|Interface with Gaussian 16. 
 +
|-
 +
|02/03/2022
 +
|Min and Max temperatures for the kinetics set to 100 K and 9999 K, respectively. 
 +
|-
 +
|12/10/2021
 +
|Bugfixes in Python scripts that read inputfile (charge and long mopac inputs were not read correctly). 
 +
|-
 +
|12/01/2021
 +
|Bugfix in LocateTS.py. 
 +
|-
 +
|11/18/2021
 +
|Bugfix in ChemKnow. Improved torsional search
 +
|-
 +
|11/16/2021
 +
|ChemKnow and barrierless search improved. Tutorial updated
 +
|-
 +
|11/10/2021
 +
|Tutorial updated and amk-tools described
 +
|-
 +
|10/17/2021
 +
|update tables with the geometry orientation for normal mode calcls in FINALDIR (low-level one). Tutorial updated
 +
|-
 +
|10/16/2021
 +
|Tutorial updated
 +
|-
 +
|10/02/2021
 +
|Tutorial updated
 +
|-
 +
|09/25/2021
 +
|References updated in tutorial and wiki
 +
|-
 +
|09/17/2021
 +
|tutorial updated and select.sh now exectuted from WRKDIR
 +
|-
 +
|09/06/2021
 +
|Max no. of species in population.pdf set to 20
 +
|-
 +
|07/26/2021
 +
|Bugfixes in FINAL and max no. of TSs in Energy Profile set to 100
 +
|-
 +
|07/24/2021
 +
|Bugfixes in screening
 +
|-
 +
|07/23/2021
 +
|Barrierless process are now included in the search (not in the kinetics)
 +
|-
 +
|06/25/2021
 +
|Screening and rxnetwork build optimized. Adaptive selection of temp in MD optimized.
 +
|-
 +
|06/18/2021
 +
|Bugfix in select_assoc script
 +
|-
 +
|06/17/2021
 +
|Systems with charge can now be modeled with ChemKnow and BXDE
 +
|-
 +
|04/06/2021
 +
|Bugfixes in irc_analysis.sh (mopac2021) and Heuristics (crossed bonds)
 +
|-
 +
|05/28/2021
 +
|New keyword Use_LET for mopac TS optimizations
 +
|-
 +
|05/27/2021
 +
|New keywords (recalc and Hookean) and improved efficiency
 +
|-
 +
|05/14/2021
 +
|ChemKnow improved and calcfc in g09 ts opt calcs
 +
|-
 +
|05/10/2021
 +
|keyword tight_ts and bug in bxde
 +
|-
 +
|05/02/2021
 +
|kinetics module improved and bugs corrected
 +
|-
 +
|04/07/2021
 +
|in tors.sh do not consider rotation about bonds that belong to a ring
 +
|-
 +
|03/16/2021
 +
|mopac calculator updated to ase3.21.1
 +
|-
 +
|03/14/2021
 +
|Bugfixes
 +
|-
 +
|02/15/2021
 +
|2021 release. Revision 1007--> qcore high-level calcs available
 +
|-
 +
|10/20/2020
 +
|linked_paths in python and 1D rotors in rrkm
 +
|-
 +
|10/18/2020
 +
|bug fix in linked_paths.sh
 +
|-
 +
|10/14/2020
 +
|tutorial updated and bug fixes in DVV.py
 +
|-
 +
|10/05/2020
 +
|Density matrix read in freq calc (MOPAC) and new xtb parameters for better convergence
 +
|-
 +
|07/15/2020
 +
|Implemented interface with Entos Qcore
 +
|-
 +
|04/21/2020
 +
|Implemented ExtForce and fixed some bugs
 +
|-
 +
|01/28/2020
 +
|Simplified adjacency matrix from XYZ
 +
|-
 +
|01/21/2020
 +
|2020 version
 
|-
 
|-
 
|12/02/2019
 
|12/02/2019
Line 37: Line 167:
  
 
Return to [[AutoMeKin]]
 
Return to [[AutoMeKin]]
−
 
−
## AutoMeKin
 
−
 
−
AutoMeKin (formerly known as tsscds) is a computer program that has been designed to discover reaction mechanisms and solve the kinetics in an automated fashion. AutoMeKin obtains transition state guess structures from trajectory simulations of the highly vibrationally excited species. From the obtained TS structures, minima and product fragments are determined following the intrinsic reaction coordinate. Finally, having determined the stationary points, the reaction network is constructed and the kinetics is solved. The program is interfaced with MOPAC2016 and Gaussian 09 (G09).
 
−
 
−
A computer program for finding reaction mechanisms and solving the kinetics.
 
−
 
−
## Authors
 
−
 
−
* George L. Barnes
 
−
* David R. Glowacki
 
−
* Sabine Kopec
 
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* Emilio Martinez-Nunez
 
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* Daniel Pelaez-Ruiz
 
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* Aurelio Rodriguez
 
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* Roberto Rodriguez-Fernandez
 
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* Robin J. Shannon
 
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* James J. P. Stewart
 
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* Pablo G. Tahoces
 
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* Saulo A. Vazquez
 
−
 
−
## LICENSE
 

Latest revision as of 08:29, 15 January 2024

Latest revision: 1137
01/15/2024 Fixed some bugs with llcalcs.sh and improved ChemKnow algorithm (new keyword CK_minima)
11/07/2023 Fixed some issues with the HL calcs of fragments
05/12/2022 Fixed some issues with qcore calcs
04/26/2022 Bugfix in utils and improved performace hl calcs
04/13/2022 Removed STOP in diag.f.
03/17/2022 Bugfix in final.sh.
03/11/2022 Interface with Gaussian 16.
02/03/2022 Min and Max temperatures for the kinetics set to 100 K and 9999 K, respectively.
12/10/2021 Bugfixes in Python scripts that read inputfile (charge and long mopac inputs were not read correctly).
12/01/2021 Bugfix in LocateTS.py.
11/18/2021 Bugfix in ChemKnow. Improved torsional search
11/16/2021 ChemKnow and barrierless search improved. Tutorial updated
11/10/2021 Tutorial updated and amk-tools described
10/17/2021 update tables with the geometry orientation for normal mode calcls in FINALDIR (low-level one). Tutorial updated
10/16/2021 Tutorial updated
10/02/2021 Tutorial updated
09/25/2021 References updated in tutorial and wiki
09/17/2021 tutorial updated and select.sh now exectuted from WRKDIR
09/06/2021 Max no. of species in population.pdf set to 20
07/26/2021 Bugfixes in FINAL and max no. of TSs in Energy Profile set to 100
07/24/2021 Bugfixes in screening
07/23/2021 Barrierless process are now included in the search (not in the kinetics)
06/25/2021 Screening and rxnetwork build optimized. Adaptive selection of temp in MD optimized.
06/18/2021 Bugfix in select_assoc script
06/17/2021 Systems with charge can now be modeled with ChemKnow and BXDE
04/06/2021 Bugfixes in irc_analysis.sh (mopac2021) and Heuristics (crossed bonds)
05/28/2021 New keyword Use_LET for mopac TS optimizations
05/27/2021 New keywords (recalc and Hookean) and improved efficiency
05/14/2021 ChemKnow improved and calcfc in g09 ts opt calcs
05/10/2021 keyword tight_ts and bug in bxde
05/02/2021 kinetics module improved and bugs corrected
04/07/2021 in tors.sh do not consider rotation about bonds that belong to a ring
03/16/2021 mopac calculator updated to ase3.21.1
03/14/2021 Bugfixes
02/15/2021 2021 release. Revision 1007--> qcore high-level calcs available
10/20/2020 linked_paths in python and 1D rotors in rrkm
10/18/2020 bug fix in linked_paths.sh
10/14/2020 tutorial updated and bug fixes in DVV.py
10/05/2020 Density matrix read in freq calc (MOPAC) and new xtb parameters for better convergence
07/15/2020 Implemented interface with Entos Qcore
04/21/2020 Implemented ExtForce and fixed some bugs
01/28/2020 Simplified adjacency matrix from XYZ
01/21/2020 2020 version
12/02/2019 Bug in FINAL.sh
11/22/2019 Maximum number of paths set to 50 (in bbfs.f90).
11/16/2019 Check of input structure in amk.sh. Fragmented molecules are no longer valid.
09/16/2019 pdfs are now also generated in FINAL_HL
07/09/2019 if name of working dir is too long, name--->wrkdir
06/30/2019 amk acronym replaces old tsscds acronym
04/18/2019 MIT license
04/17/2019 The label of the starting min in the kmc simulations is in tsdirll/KMC/starting_minimum
04/15/2019 A bug in get_energy_g09_MP2.sh was corrected
04/01/2019 threads=1 has been added to the input files in the examples folder. The use of this keyword is highly recommented to avoid multhreading in MOPAC calculations for much better performance
03/01/2019 A bug in the kmc.f90 source file was corrected

Return to AutoMeKin

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