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WIP: Long tutorial #225

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6480aa8
first steps towards new ACEpotentials kernels : envelopes
May 3, 2024
9ed960a
initial transfer and a bit of cleanup of agnesi transform
May 3, 2024
582af44
first draft of transforms finished
May 3, 2024
7c6886d
draft learnable Rnlrzz basis
May 5, 2024
1b9fa97
simple Rnlrzz constructor
May 6, 2024
cc00109
several steps towards generating an ACE model
May 6, 2024
dec0643
cleanup ace model generation
May 6, 2024
7f31983
draft model evaluation + symmetry tests
May 6, 2024
b9b67d9
r gradient of Rnlzz basis
May 6, 2024
7957bb7
intermediate backup
May 7, 2024
cd83fb9
site energy gradient done and tested
May 7, 2024
982ead4
first working version of grad_params
May 8, 2024
bb83dc9
reverse over reverse done
May 8, 2024
39dc240
benchmark cleanup
May 8, 2024
d811cc7
a first bad basis implementation
May 10, 2024
b9d0afd
jacobians of forces
May 10, 2024
b1fd824
towards splinifying the basis
May 10, 2024
8c2918c
full implementation and test of splines
May 10, 2024
eed5ffd
draft calculator
May 12, 2024
d0f70d6
pullback through EFV
May 13, 2024
e8f8c67
fix force assembly bug
May 13, 2024
c818ea3
simple test to differentiate through loss
May 13, 2024
de58353
improved loss diff test
May 13, 2024
ded8e40
remove JuLIP dependence of new calculators
May 14, 2024
3ed974a
switch params to tensors
May 14, 2024
d23e3d2
cleanup of new tests
May 15, 2024
40fb188
most of the way to include pair potentials
May 15, 2024
3bbf7b6
Merge branch 'main' into newkernels
May 15, 2024
6f7f54c
pair basis done
May 15, 2024
1fa798c
some more test cleanup
May 15, 2024
929ed11
towards a tutorial for the new models
May 15, 2024
de815de
more on the tutorial
May 15, 2024
ce3e292
nonlinear regression example
May 16, 2024
e4e4f87
remove params from models to strictly follow Lux; splinify convenienc…
May 16, 2024
c8b2d5e
update to newkernels tutorial
May 16, 2024
517ef8d
extend basis eval to calculator
May 17, 2024
476e61d
tutorial draft done
May 17, 2024
0dcfe3f
fix Molly example
tjjarvinen May 18, 2024
2dd015f
a little bit of cleanup of the newkernels tutorial
May 18, 2024
9cb610d
E0s
May 19, 2024
8273fea
wrapped A, AA, B into a new tensor struct
May 19, 2024
76546d0
fixed tests
May 20, 2024
d12f524
add missing deps for newkernels example
jameskermode May 20, 2024
a59a8a3
add CondaPkg to gitignore
May 22, 2024
6446761
Merge pull request #195 from ACEsuit/newkernels
cortner May 22, 2024
e73719c
Merge pull request #198 from ACEsuit/doc_update
cortner May 27, 2024
31a273c
allow passing E0
CheukHinHoJerry May 31, 2024
4e7266e
passes r0incuts correctly
CheukHinHoJerry Jun 1, 2024
431f30f
add randz to E0s test
Jun 1, 2024
769d1bf
fixed acemodel display
Jun 1, 2024
a7a1a5a
restrict E0 to be a dictionary with Symbol and Uniful.Quantity
CheukHinHoJerry Jun 2, 2024
e72e839
Merge pull request #200 from ACEsuit/chho/fix_E0
cortner Jun 2, 2024
1ea1240
fix rSH for ACEModel
CheukHinHoJerry Jun 2, 2024
2f165c5
add ybasis tests
CheukHinHoJerry Jun 2, 2024
4df33f6
fix typo
CheukHinHoJerry Jun 2, 2024
f14a8c6
change solid vs spher test
Jun 3, 2024
641a2e9
Merge pull request #203 from ACEsuit/chho/fix_rSH
cortner Jun 3, 2024
8557bca
add get nl
CheukHinHoJerry Jun 3, 2024
a210592
renaming and minimal doc
CheukHinHoJerry Jun 3, 2024
668621f
Merge pull request #205 from ACEsuit/chho/add_getnl
cortner Jun 3, 2024
04311a3
update most tests
Jun 22, 2024
da1db05
fixed tests for new code
Jun 22, 2024
414efe3
many steps towards bumper
Jul 2, 2024
c4aed63
fixing versions, which fixes lots of Lux warnings
Jul 2, 2024
b0618cb
steps towards withalloc in derivatives
Jul 3, 2024
8ceecf2
intermediate
Jul 4, 2024
68d183f
bugfix
Jul 4, 2024
8d3a03a
grad_params and rev2
Jul 4, 2024
771a718
fix basis evaluation
Jul 4, 2024
27aeee7
update splined radials
Jul 4, 2024
b05e355
fix calculators
Jul 4, 2024
4d9b201
all non-sklearn tests pass
Jul 4, 2024
6843bb5
replace GeometryOptimisation in example script
Jul 4, 2024
094abf7
Merge pull request #207 from ACEsuit/co/p4ml
cortner Jul 4, 2024
cfd6a04
fix version bounds
Jul 20, 2024
6708d6a
towards linear ACE2
Jul 20, 2024
24d6f01
linear ACE weights for multi-species
Jul 21, 2024
2f4c84b
allow maxq > maxn
Jul 21, 2024
5d8de53
backup
Jul 24, 2024
f868357
example script for linear fit
Jul 25, 2024
c53d0a2
add rbasis_analysis script
Jul 25, 2024
6242233
fix lux bug in linear.jl
Jul 25, 2024
00ff95b
perfect math of pair and radial
Jul 28, 2024
faaae9b
confirm Ylms span the same space
Jul 28, 2024
8d71f0d
angular coupled basis fcns are inconsistent
Jul 28, 2024
f1ce953
small cleanup
Jul 28, 2024
8241d1a
perfect basis match
Jul 29, 2024
a6d3b1b
regression is closer (no match yet)
Jul 29, 2024
3f8f137
match the full pair+mb basis
Jul 29, 2024
e5bdd73
simplified basis matching test
Jul 29, 2024
4d1a011
closely matching regression results
Jul 29, 2024
4aabf61
cleanup basic linear script
Jul 29, 2024
cd54c51
streamlining and cleanup
Jul 29, 2024
51bf4d9
linear-nonlinear optim example
Jul 29, 2024
62960d9
minor typo fix
CheukHinHoJerry Jul 30, 2024
6570ee2
test for connor bug
cortner Jul 30, 2024
a0a9731
update test and julia bound
Jul 30, 2024
797e4d7
Merge pull request #213 from ACEsuit/co/bug208
cortner Jul 30, 2024
0e5e2ad
stop reexporting ACE1
Jul 31, 2024
ad48bd7
fix non-exports
Jul 31, 2024
d5984a5
Merge pull request #215 from ACEsuit/co/fix#211
cortner Jul 31, 2024
a4e9142
Merge branch 'main' into co/initw
Jul 31, 2024
8a648b0
Merge pull request #209 from ACEsuit/co/initw
cortner Jul 31, 2024
b5952e6
start on ace1 compat
Aug 1, 2024
c3588f9
ace1-compat - match radials
Aug 1, 2024
3ee6e7e
ace1-compat matching pair basis
Aug 2, 2024
58aa8c0
ace1compat - mb matching
Aug 2, 2024
95cfc24
full match
Aug 2, 2024
b49757c
ACE1-compat E0s and sitepot
Aug 2, 2024
e09d558
ace1-compat, allow ace2 to be a superset
Aug 3, 2024
b57de27
cleanup compat tests
Aug 3, 2024
837c8c4
ACE1 style r envelope
Aug 3, 2024
a9fb55e
ACE1 compat - two more tests
Aug 3, 2024
2f1d00c
replace :linear with :onehot
Aug 4, 2024
160effc
ACE1-compat, multispecies example
Aug 4, 2024
662c135
failing 3-species test
Aug 4, 2024
e05fd03
final fix: bring variablecutoffs back
Aug 5, 2024
5b5f046
Merge pull request #216 from ACEsuit/co/ace1
cortner Aug 7, 2024
f6d42d3
get tests to pass
Aug 7, 2024
359f26f
rough sketch of priors
Aug 7, 2024
15d12b8
Update python_ase.md.
wcwitt Aug 9, 2024
7e26c15
smoothness priors compat with ACE1
Aug 21, 2024
4a09741
Merge pull request #219 from ACEsuit/co/priors
cortner Aug 22, 2024
b4a02ad
First attempt at adding the long tutorial.
wcwitt Aug 22, 2024
85323f1
fixing CI and docs
Aug 23, 2024
e0c06b0
Merge pull request #229 from ACEsuit/co/fixci
cortner Aug 23, 2024
61b7333
Merge branch 'main' into wcw/long-tutorial
wcwitt Aug 23, 2024
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5 changes: 2 additions & 3 deletions .github/workflows/CI.yml
Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,8 @@ jobs:
fail-fast: false
matrix:
julia-version:
- '1.9'
- '1'
- 'nightly'
- '1.10'
# - 'nightly'
python-version:
- '3.8'
os:
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3 changes: 2 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,5 @@
scratch
/docs/src/literate_tutorials
.vscode
.ipynb_checkpoints
.ipynb_checkpoints
.CondaPkg
39 changes: 35 additions & 4 deletions Project.toml
Original file line number Diff line number Diff line change
@@ -1,38 +1,69 @@
name = "ACEpotentials"
uuid = "3b96b61c-0fcc-4693-95ed-1ef9f35fcc53"
version = "0.6.6"
version = "0.8.0-dev"

[deps]
ACE1 = "e3f9bc04-086e-409a-ba78-e9769fe067bb"
ACE1x = "5cc4c08c-8782-4a30-af6d-550b302e9707"
ACEbase = "14bae519-eb20-449c-a949-9c58ed33163e"
ACEfit = "ad31a8ef-59f5-4a01-b543-a85c2f73e95c"
ACEmd = "69e0c927-b120-467d-b2b3-5b6842148cf4"
AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
AtomsBuilder = "f5cc8831-eeb7-4288-8d9f-d6c1ddb77004"
AtomsCalculators = "a3e0e189-c65a-42c1-833c-339540406eb1"
Bumper = "8ce10254-0962-460f-a3d8-1f77fea1446e"
ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
ChunkSplitters = "ae650224-84b6-46f8-82ea-d812ca08434e"
EmpiricalPotentials = "38527215-9240-4c91-a638-d4250620c9e2"
EquivariantModels = "73ee3e68-46fd-466f-9c56-451dc0291ebc"
ExtXYZ = "352459e4-ddd7-4360-8937-99dcb397b478"
Folds = "41a02a25-b8f0-4f67-bc48-60067656b558"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
JuLIP = "945c410c-986d-556a-acb1-167a618e0462"
LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Lux = "b2108857-7c20-44ae-9111-449ecde12c47"
LuxCore = "bb33d45b-7691-41d6-9220-0943567d0623"
NamedTupleTools = "d9ec5142-1e00-5aa0-9d6a-321866360f50"
NeighbourLists = "2fcf5ba9-9ed4-57cf-b73f-ff513e316b9c"
OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
Optimisers = "3bd65402-5787-11e9-1adc-39752487f4e2"
OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
Polynomials4ML = "03c4bcba-a943-47e9-bfa1-b1661fc2974f"
PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
RepLieGroups = "f07d36f2-91c4-427a-b67b-965fe5ebe1d2"
ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
SpheriCart = "5caf2b29-02d9-47a3-9434-5931c85ba645"
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
StrideArrays = "d1fa6d79-ef01-42a6-86c9-f7c551f8593b"
UltraFastACE = "8bb720ee-daac-48fb-af73-8a282a9cbbd7"
Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
WithAlloc = "fb1aa66a-603c-4c1d-9bc4-66947c7b08dd"
YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"

[compat]
ACE1 = "0.12"
ACE1 = "0.12.2"
ACE1x = "0.1.8"
ACEfit = "0.1.4"
ACEmd = "0.1.6"
AtomsCalculators = "0.1"
EquivariantModels = "0.0.4"
ExtXYZ = "0.1.14"
Interpolations = "0.15"
JuLIP = "0.13.9, 0.14.2"
PrettyTables = "1.3, 2.0"
Reexport = "1"
UltraFastACE = "0.0.6"
StaticArrays = "1"
YAML = "0.4"
julia = "1.9"
UltraFastACE = "0.0.2"
julia = "~1.10.0"

[extras]
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
Expand Down
1 change: 1 addition & 0 deletions data/README
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
The file length_scales_VASP_auto_length_scales.yaml is taken from https://github.com/libAtoms/universalSOAP/blob/main/calculations/length_scales_VASP_auto_length_scales.yaml
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