ART nouveau code is distributed through gitlab. To have access to the code, please contact me and send me your gitlab username. I will give you access to the repository.
Details
The activation-relaxation technique (ART) is an open-ended search method for finding local transition states (G. T. Barkema and N. Mousseau, Event-based relaxation of continuous disordered systems} Phys. Rev. Lett.77, 4358 (1996).). While the original version used an inverted force for converging to saddle point, ART nouveau directly computes the direction of lowest curvature using the Lanczos algorithm, a very efficient iterative method that offers the fastest and most stable way to follow a local eigendirection (R. Malek and N. Mousseau, Dynamics of Lennard-Jones clusters: A characterization of the activation-relaxation technique, Phys. Rev. E 62, 7723-7728 (2000).).
It is interfaced with LAMMPS to give access to a large number of forcefields.
Over the years, we have continued to bring improvements to the method (see, for example Refs. Eduardo Machado-Charry, Laurent Karim Béland, Damien Caliste, Luigi Genovese, Normand Mousseau and Pascal Pochet, Optimized energy landscape exploration using the ab initio based ART-nouveau} J. Chem Phys. 135, 034102 (2011) and M.-C. Marinica, F. Willaime and Normand Mousseau, Energy landscape of small clusters of self-interstitial dumbbells in iron, Phys. Rev. B 83, 094119 (2011).). Besides myself, the latest version incorporates contributions from a number of people, including :
- Gerard Barkema
- Laurent Karim Béland
- Éric Cancès
- Fadwa El-Mellouhi
- Antoine Jay
- Sami Mahmoud
- Mihai-Cosmin Marinica
- Eduardo Machado-Charry
- Mickaël Trochet
License and distribution
The ART nouveau software is freely distributed under GNU General License.
It can be modified and used for any purpose as long as reference is given to the appropriate references :
- G. T. Barkema and N. Mousseau, Event-based relaxation of continuous disordered systems, Phys. Rev. Lett. 77, 4358 (1996).
- R. Malek and N. Mousseau, {Dynamics of Lennard-Jones clusters: A characterization of the activation-relaxation technique}, Phys. Rev. E {{62}}, 7723-7728 (2000).
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Eduardo Machado-Charry, Laurent Karim Béland, Damien Caliste, Luigi Genovese, Normand Mousseau and Pascal Pochet, Optimized energy landscape exploration using the ab initio based ART-nouveau, J. Chem Phys. 135, 034102 (2011).
ART nouveau linked to the LAMMPS library
It is now possible to use the force library from LAMMPS, a powerful MD code developed at Sandia National Labs. This version is based on version 3.0 but adds access to a large number of forcefields, extending considerably the systems that can be studied out of the box with the code.
Compiling is a bit more delicate, but you get much more flexibility.
You will find all necessary information with the package to compile ART nouveau with LAMMPS. However, to set up the LAMMPS parameters, you will have to look at the documentation prepared by the LAMMPS team.
- Implements a number of modifications to facilitate compiling, to accelerate converge and to use local forces, very useful for large systems (April 22, 2020).
- Corrects a few problems between LAMMPS and ARTn, allows for triclinic boxes and introduces a new compilation procedure inspired by LAMMPS (February 15 2017)
- Brings back the possibility to use more than 1 species with SW potential (including a repulsive potential to simulate a GaAs network) and corrects a few bugs. (December 10th, 2015)
- Version correcting a few problems for compiling and adds an example with Lennard-Jones from LAMMPS (November 29th, 2015)
- ART nouveau coupled to the LAMMPS Library (October 2015):
ART nouveau for empirical potential
This version of ART nouveau incorporates the most recent developments. The difference between this version and that for ab initio codes is mostly in the data management : when running with empirical potentials, one does not have to store configurations at every step and handle a restart at any point.
This version is therefore slightly lighter and more readable than the one in the next section. To use, mostly, for learning the method.
Selected work
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Sanscartier, E., Saint-Denis, F., Bolduc, K.-É., & Mousseau, N. (2023). Evaluating approaches for on-the-fly machine learning interatomic potentials for activated mechanisms sampling with the activation-relaxation technique nouveau.
The Journal of Chemical Physics,
158(24), 244110.
https://doi.org/10.1063/5.0143211 Download Download
De Lile, J. R., & Mousseau, N. (2023). Diffusion of oxygen vacancies formed at the anatase (101) surface: An activation-relaxation technique study.
Physical Review Materials,
7(3), 034602.
https://doi.org/10.1103/PhysRevMaterials.7.034602 Download
Lévesque, C., Roorda, S., Schiettekatte, F., & Mousseau, N. (2022). Internal mechanical dissipation mechanisms in amorphous silicon.
Physical Review Materials,
6(12), 123604.
https://doi.org/10.1103/PhysRevMaterials.6.123604 Download Download
Lapointe, C., Swinburne, T. D., Proville, L., Becquart, C. S., Mousseau, N., & Marinica, M.-C. (2022). Machine learning surrogate models for strain-dependent vibrational properties and migration rates of point defects.
Physical Review Materials,
6(11), 113803.
https://doi.org/10.1103/PhysRevMaterials.6.113803 Download
Sauvé-Lacoursière, A., Gelin, S., Adjanor, G., Domain, C., & Mousseau, N. (2022). Unexpected role of prefactors in defects diffusion: the case of vacancies in the 55Fe-28Ni-17Cr concentrated solid-solution alloys.
Acta Materialia,
237, 118153.
https://doi.org/10.1016/j.actamat.2022.118153 Download
Jay, A., Gunde, M., Salles, N., Poberžnik, M., Martin-Samos, L., Richard, N., Gironcoli, S. de, Mousseau, N., & Hémeryck, A. (2022). Activation–Relaxation Technique: An efficient way to find minima and saddle points of potential energy surfaces.
Computational Materials Science,
209, 111363.
https://doi.org/10.1016/j.commatsci.2022.111363 Download
Moitzi, F., Şopu, D., Holec, D., Perera, D., Mousseau, N., & Eckert, J. (2020). Chemical bonding effects on the brittle-to-ductile transition in metallic glasses.
Acta Materialia,
188, 273–281.
https://doi.org/10.1016/j.actamat.2020.02.002 Download
Gelin, S., Champagne-Ruel, A., & Mousseau, N. (2020). Enthalpy-entropy compensation of atomic diffusion originates from softening of low frequency phonons.
Nature Communications,
11(1), 3977.
https://doi.org/10.1038/s41467-020-17812-2 Download
Şopu, D., Moitzi, F., Mousseau, N., & Eckert, J. (2020). An atomic-level perspective of shear band formation and interaction in monolithic metallic glasses.
Applied Materials Today,
21, 100828.
https://doi.org/10.1016/j.apmt.2020.100828 Download
Jay, A., Huet, C., Salles, N., Gunde, M., Martin-Samos, L., Richard, N., Landa, G., Goiffon, V., de Gironcoli, S., Hemeryck, A., & Mousseau, N. (2020). Finding reaction pathways and transition states: r-ARTn and d-ARTn as an efficient and versatile alternative to string approaches.
Journal of Chemical Theory and Computation,
16(10), 6726–6734.
https://doi.org/10.1021/acs.jctc.0c00541 Download
Tian, L., Li, L., Ding, J., & Mousseau, N. (2019). ART_data_analyzer: Automating parallelized computations to study the evolution of materials.
SoftwareX,
9, 238–243.
https://doi.org/10.1016/j.softx.2019.03.002 Download
Salles, N., Richard, N., Mousseau, N., & Hemeryck, A. (2017). Strain-driven diffusion process during silicon oxidation investigated by coupling density functional theory and activation relaxation technique.
The Journal of Chemical Physics,
147(5), 054701.
https://doi.org/10.1063/1.4996206 Download Download
Ganster, P., Béland, L. K., & Mousseau, N. (2012). First stages of silicon oxidation with the activation relaxation technique.
Physical Review B,
86(7), 075408.
https://doi.org/10.1103/PhysRevB.86.075408 Download
St-Pierre, J.-F., & Mousseau, N. (2012). Large loop conformation sampling using the activation relaxation technique, ART-nouveau method.
Proteins: Structure, Function, and Bioinformatics,
80(7), 1883–1894.
https://doi.org/10.1002/prot.24085 Download
Mousseau, N., Béland, L. K., Brommer, P., Joly, J.-F., El-Mellouhi, F., Machado-Charry, E., Marinica, M.-C., & Pochet, P. (2012). The Activation-Relaxation Technique: ART Nouveau and Kinetic ART.
Journal of Atomic, Molecular, and Optical Physics,
2012, 925278.
https://doi.org/10.1155/2012/925278 Download
Machado-Charry, E., Béland, L. K., Caliste, D., Genovese, L., Deutsch, T., Mousseau, N., & Pochet, P. (2011). Optimized energy landscape exploration using the ab initio based activation-relaxation technique.
The Journal of Chemical Physics,
135(3), 034102.
https://doi.org/10.1063/1.3609924 Download
Marinica, M.-C., Willaime, F., & Mousseau, N. (2011). Energy landscape of small clusters of self-interstitial dumbbells in iron.
Physical Review B,
83(9), 094119.
https://doi.org/10.1103/PhysRevB.83.094119 Download
Kallel, H., Mousseau, N., & Schiettekatte, F. (2010). Evolution of the Potential-Energy Surface of Amorphous Silicon.
Physical Review Letters,
105(4), 045503.
https://doi.org/10.1103/PhysRevLett.105.045503 Download
Dong, X., Chen, W., Mousseau, N., & Derreumaux, P. (2008). Energy landscapes of the monomer and dimer of the Alzheimer’s peptide Aβ(1–28).
The Journal of Chemical Physics,
128(12), 125108.
https://doi.org/10.1063/1.2890033 Download
El-Mellouhi, F., & Mousseau, N. (2007). Ab initio characterization of arsenic vacancy diffusion pathways in GaAs with SIEST-A-RT.
Applied Physics A,
86(3), 309–312.
https://doi.org/10.1007/s00339-006-3761-3 Download
Wei, G., Mousseau, N., & Derreumaux, P. (2007). Computational Simulations of the Early Steps of Protein Aggregation.
Prion,
1(1), 3–8.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633700/ Download
El-Mellouhi, F., & Mousseau, N. (2006). Charge-dependent migration pathways for the Ga vacancy in GaAs.
Physical Review B,
74(20), 205207.
https://doi.org/10.1103/PhysRevB.74.205207 Download
Yun, M.-R., Lavery, R., Mousseau, N., Zakrzewska, K., & Derreumaux, P. (2006). ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes.
Proteins: Structure, Function, and Bioinformatics,
63(4), 967–975.
https://doi.org/10.1002/prot.20938 Download Download
Mousseau, N., & Derreumaux, P. (2005). Exploring the Early Steps of Amyloid Peptide Aggregation by Computers.
Accounts of Chemical Research,
38(11), 885–891.
https://doi.org/10.1021/ar050045a Download
Wei, G., Mousseau, N., & Derreumaux, P. (2004). Exploring the early steps of aggregation of amyloid-forming peptide KFFE.
Journal of Physics: Condensed Matter,
16(44), S5047.
https://doi.org/10.1088/0953-8984/16/44/002 Download
Wei, G., Mousseau, N., & Derreumaux, P. (2004). Complex folding pathways in a simple β-hairpin.
Proteins: Structure, Function, and Bioinformatics,
56(3), 464–474.
https://doi.org/10.1002/prot.20127 Download
Barkema, G. T., Mousseau, N., Vink, Richard L. C., & Biswas, Partha. (2001). Basic mechanisms of structural relaxation and diffusion in amorphous silicon. In Joyce, James B., Cohen, J. David, Hanna, Jun-ichi, Collins, Robert W., & Stutzman, Martin (Eds.),
Amorphous and Heterogeneous Silicon-Based Films-2001 (Vol. 661, p. A28.1). Proceedings of the Materials Research Society.
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Loirat, Y., Brebec, G., Limoge, Y., Mousseau, N., & Bocquet, J. L. (2001). Diffusion in Lennard-Jones glasses: Simulation studies of the activation parameters for collective mechanisms (Y. Limoge & J. L. Bocquet, Eds.; Vols. 194–1). Scitec Publications Ltd.
Mousseau, N., Barkema, G. T., & Leeuw, S. W. de. (2000). Elementary mechanisms governing the dynamics of silica.
The Journal of Chemical Physics,
112(2), 960–964.
https://doi.org/10.1063/1.480621 Download
Barkema, G. T., & Mousseau, N. (1999). Exploring structural mechanisms in disordered materials using the activation-relaxation technique.
Computer Physics Communications,
121–122, 206–209.
https://doi.org/10.1016/S0010-4655(99)00314-8 Download
Mousseau, N., & Barkema, G. T. (1999). Exploring High‐Dimensional Energy Landscapes.
Computing in Science & Engineering,
1(2), 74–82.
https://doi.org/10.1109/5992.753050
Barkema, G. T., & Mousseau, N. (1996). Event-Based Relaxation of Continuous Disordered Systems.
Physical Review Letters,
77(21), 4358–4361.
https://doi.org/10.1103/PhysRevLett.77.4358 Download