[restructured] all main changes to add bond-atom triplets and bond-ce…

…ntered spherical decomposition
metatensor · Oct 24, 2023 · fd77379 · fd77379
1 parent ebff16d
commit fd77379
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Showing 17 changed files with 3,404 additions and 27 deletions.
diff --git a/rascaline/src/calculators/bondatom_neighbor_list.rs b/rascaline/src/calculators/bondatom_neighbor_list.rs
diff --git a/rascaline/src/calculators/descriptors_by_systems.rs b/rascaline/src/calculators/descriptors_by_systems.rs
@@ -131,12 +131,13 @@ pub fn split_tensor_map_by_system(descriptor: &mut TensorMap, n_systems: usize)
                 let mut structure_per_sample = vec![LabelValue::new(-1); block_data.samples.count()];
 
                 let system_start = *system_end;
-                for (sample_i, &[structure, center]) in block_data.samples.iter_fixed_size().enumerate().skip(system_start) {
+                for (sample_i, sample_label) in block_data.samples.iter().enumerate().skip(system_start) {
+                    let structure = sample_label[0];
                     structure_per_sample[sample_i] = structure;
 
                     if structure.usize() == system_i {
                         // this sample is part of to the current system
-                        samples.add(&[structure, center]);
+                        samples.add(sample_label);
                         let new_sample = samples_mapping.len();
                         samples_mapping.insert(sample_i, new_sample);
 

diff --git a/rascaline/src/calculators/mod.rs b/rascaline/src/calculators/mod.rs
@@ -84,6 +84,9 @@ pub use self::sorted_distances::SortedDistances;
 mod neighbor_list;
 pub use self::neighbor_list::NeighborList;
 
+mod bondatom_neighbor_list;
+pub use self::bondatom_neighbor_list::BANeighborList;
+
 mod radial_basis;
 pub use self::radial_basis::{RadialBasis, GtoRadialBasis};
 
@@ -93,6 +96,8 @@ pub(crate) use self::descriptors_by_systems::{array_mut_for_system, split_tensor
 pub mod soap;
 pub use self::soap::{SphericalExpansionByPair, SphericalExpansionParameters};
 pub use self::soap::SphericalExpansion;
+pub use self::soap::{SphericalExpansionForBondType, SphericalExpansionForBondsParameters};
+pub use self::soap::SphericalExpansionForBonds;
 pub use self::soap::{SoapPowerSpectrum, PowerSpectrumParameters};
 pub use self::soap::{SoapRadialSpectrum, RadialSpectrumParameters};
 

diff --git a/rascaline/src/calculators/soap/mod.rs b/rascaline/src/calculators/soap/mod.rs
@@ -12,9 +12,15 @@ pub use self::cutoff::RadialScaling;
 mod spherical_expansion_pair;
 pub use self::spherical_expansion_pair::{SphericalExpansionByPair, SphericalExpansionParameters};
 
+mod spherical_expansion_bondcentered_pair;
+pub use self::spherical_expansion_bondcentered_pair::{SphericalExpansionForBondType, SphericalExpansionForBondsParameters};
+
 mod spherical_expansion;
 pub use self::spherical_expansion::SphericalExpansion;
 
+mod spherical_expansion_bondcentered;
+pub use self::spherical_expansion_bondcentered::SphericalExpansionForBonds;
+
 mod power_spectrum;
 pub use self::power_spectrum::{SoapPowerSpectrum, PowerSpectrumParameters};