soap_turbo is copyright (c) 2019-2023, Miguel A. Caro
soap_turbo is published and distributed under the Academic Software License v1.0 (ASL)
soap_turbo is distributed in the hope that it will be useful for non-commercial academic research, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ASL for more details. You should have received a copy of the ASL along with this program (e.g., in a LICENSE.md file); if not, you can write to the original licensor, Miguel Caro ([email protected]). The ASL is also published at http://github.com/gabor1/ASL
When using this software, please cite the following reference:
Miguel A. Caro. Optimizing many-body atomic descriptors for enhanced computational performance of machine learning based interatomic potentials. Phys. Rev. B 100, 024112 (2019).
soap_turbo comprises a series of libraries to be used in combination with QUIP/GAP and TurboGAP.
soap_turbo is closely related to the original soap descriptor implemented in GAP but there are several details in which they differ, both regarding how the atomic density field is represented and how the expansion is carried out. Briefly, soap_turbo in principle allows very detailed fine-tuning of the atomic representation through many hyperparameters (about twice as many as in soap) and most of these hyperparameters can be specified, unlike in soap, individually for each species. In practice, one can usually "translate" a soap definition to the soap_turbo quasi-equivalent definition. The table below gives a rough equivalence between soap and soap_turbo descriptor strings, useful for users of gap_fit and quippy who want to migrate their descriptors from soap to soap_turbo. A general note for gap_fit usage is that, while for soap descriptors arrays are provided within single brackets, {a b c}, because of the way that soap_turbo strings are parsed they need to be provided within double brackets, {{a b c}}. In quippy single brackets are enough.
| soap | soap_turbo | Default | Info | Example |
|---|---|---|---|---|
| n_max (integer scalar) | alpha_max (integer array) | No default - required | One per species. Should not be > 12 because of numerial instabilities. A maximum of 8 is a safe bet. | alpha_max={{8 8 8}} |
| l_max (integer scalar) | l_max (integer array) | No default - required | l_max=8 | |
| atom_sigma (real scalar) | atom_sigma_r (real array) atom_sigma_t (real array) |
No default - required | One per species. "r" for radial and "t" for angular. | atom_sigma_r={{0.5 0.5 0.5}} atom_sigma_t={{0.5 0.5 0.5}} |
| n/a | atom_sigma_r_scaling (real array) atom_sigma_t_scaling (real array) |
No default - required | One per species. "r" for radial and "t" for angular. | atom_sigma_r_scaling={{0. 0. 0.}} atom_sigma_t_scaling={{0. 0. 0.}} |
| n/a | radial_enhancement (integer) | 0 | Can be 0, 1 or 2. | radial_enhancement=1 |
| n/a | amplitude_scaling (real array) | No default - required | Any real, one per species. > 0 and not too large (e.g., not greater than 2-3) makes most sense. | amplitude_scaling={{1. 1. 1.}} |
| central_weight (real) | central_weight (real array) | No default - required | Any real, one per species. > 0 and not too large (e.g., not greater than 2-3) makes most sense. | central_weight={{1. 1. 1.}} |
| n/a | basis (string) | "poly3" | Can be "poly3" (default) or "poly3gauss" | basis="poly3gauss" |
| n/a | compress_mode (string) | "None" | Not required but recommended. Detailed documentation coming up. | compress_mode="trivial" |
| cutoff (real) | rcut_hard (real) | No default - required | rcut_hard=5.0 | |
| transition_width (real) | rcut_soft (real) | No default - required | IMPORTANT: rcut_soft is the rcut_hard - transision_width equivalent. | rcut_soft=4.5 |
| n_scpecies (integer) | n_species (integer) | 1 | n_species=3 | |
| species_Z (integer array) | species_Z (integer array) | No default - required | species_Z={{1 6 8}} | |
| n/a | central_index (integer) | 1 | Position in species_Z array occupied by the central atom species of the SOAP environment. I.e., each soap_turbo definition only sees central species of this type. | central_index=2 |
| add_species (logical) | add_species (logical) | No default - required setting it to F (add add_species=F to your string!) | IMPORTANT: for soap_turbo there is currently no recipe to build the descriptor for all species automatically. It must be explicitly set to false. | add_species=F |
The poly3 and poly3gauss bases use a numerical orthonormalization procedure that becomes unstable for too
large number of basis functions (see paper(s) linked above for more details). For poly3 one can safely use
up to 7 basis functions (alpha_max = {7}), whereas for poly3gauss one can use an extra basis function
(alpha_max = {8} is safe to use). The code will print a warning if you go slightly above these values, and
an error if you try to use too many basis functions. Below is a figure showing the matrix elements in the
orthornomality matrix, where O_{ij} gives the overlap integral between basis functions i and j. This number
should be 1 if i=j and 0 otherwise. Results for poly3 are on the two columns on the left, and for poly3gauss
on the two columns on the right. Note the color bar gives the log10 of the matrix elements. For the
recommended alpha_max maxima, O_{ij} stays below 10^{-5} for i != j. The procedure becomes increasingly
unstable above that and catastrophically so at alpha_max = 12, 13 for poly3 and poly3gauss, respectively.
