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Make sure that supercell_matrices of single-atom-displaced and rattled supercells are the same per default #258

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merged 33 commits into from
Nov 20, 2024
Merged

Make sure that supercell_matrices of single-atom-displaced and rattled supercells are the same per default #258

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3022c3b
increase M3GNET RMSE tolereance because of fluctuations
QuantumChemist Nov 14, 2024
a01c5a6
prettify GAP parameters representation and remove GAP related things …
QuantumChemist Nov 14, 2024
f3d35a0
rearrange file entires to make it look better, added user-defined for…
QuantumChemist Nov 15, 2024
1b7e6c0
fix unit test
QuantumChemist Nov 15, 2024
3754c8c
fix unit test
QuantumChemist Nov 15, 2024
d76dc84
small format fix
QuantumChemist Nov 15, 2024
4dc423e
fix unit test
QuantumChemist Nov 15, 2024
c02bfc3
removed a comment
QuantumChemist Nov 15, 2024
1b95862
decrease default max_length for rattled supercells
QuantumChemist Nov 15, 2024
8d0c3a8
Merge branch 'autoatml:main' into main
QuantumChemist Nov 18, 2024
0337f46
reducing max_length default a bit
QuantumChemist Nov 18, 2024
e51db69
Merge branch 'main' of github.com:QuantumChemist/autoplex
QuantumChemist Nov 18, 2024
eacd697
added missing doctsring
QuantumChemist Nov 19, 2024
c89312c
set max_length to 20
QuantumChemist Nov 19, 2024
a508a53
set max_length to 20
QuantumChemist Nov 19, 2024
b8ae70c
add fallback to single-atom-dsipl- supercells
QuantumChemist Nov 19, 2024
10ac1e5
minor changes in file format
QuantumChemist Nov 19, 2024
bc5ca78
supercell_matrix is only determined once by reduce_supercell_size_job
QuantumChemist Nov 19, 2024
cb4c995
filter out supercell_matrix key to prevent problems with mismacthing …
QuantumChemist Nov 19, 2024
9f02c13
filter out supercell_matrix mpid key as mpids are not used here
QuantumChemist Nov 19, 2024
d60d9fc
adjust job number and remove print
QuantumChemist Nov 19, 2024
75f2668
adjust defaults
QuantumChemist Nov 19, 2024
6da2b0f
fix unit tests
QuantumChemist Nov 20, 2024
14a9eb5
fix unit tests
QuantumChemist Nov 20, 2024
776384d
putting the phonon GAP defaults to SI settings
QuantumChemist Nov 20, 2024
6b3ceb2
fix unit test
QuantumChemist Nov 20, 2024
125eec1
fix unit test
QuantumChemist Nov 20, 2024
a0f3d83
fix unit test
QuantumChemist Nov 20, 2024
f35ef28
added user info about supercell settings
QuantumChemist Nov 20, 2024
bbae8f5
Merge branch 'autoatml:main' into main
QuantumChemist Nov 20, 2024
bc7dec9
addressing Yb's comments
QuantumChemist Nov 20, 2024
5b35adf
adjust unit test
QuantumChemist Nov 20, 2024
a84458d
fix unit test
QuantumChemist Nov 20, 2024
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13 changes: 7 additions & 6 deletions src/autoplex/fitting/common/mlip-phonon-defaults.json
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Expand Up @@ -2,15 +2,16 @@
"GAP": {
"general": {
"at_file": "train.extxyz",
"default_sigma": "{0.0001 0.05 0.05 0}",
"default_sigma": "{0.0001 0.1 0.05 0}",
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For accurate phonon calculations, achieving high precision in force evaluations is crucial. While I understand that specific settings have been made for each structure, I believe a default force sigma of 0.05 would be more appropriate.

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As before, from the Si JCP2020 paper settings.

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I still recommend to use 0.05. 0.1 still seems too large. For most phonon calculations, when I don't use single-atom rattling, I prefer not to enable the automatic sigma setting. In this case, I can use the default value of 0.05 for fitting.

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Ok, then I will change this back! :)

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thank you

"energy_parameter_name": "REF_energy",
"force_parameter_name": "REF_forces",
"virial_parameter_name": "REF_virial",
"sparse_jitter": 1.0e-8,
"do_copy_at_file": "F",
"openmp_chunk_size": 10000,
"gp_file": "gap_file.xml",
"two_body": true,
"e0_offset": 2.0,
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Why do we force e0_offset to equal 2 instead of using the default value of 0? This setting is not common in GAP fitting.

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Because I put the Si settings from the JCP2020 paper. But I can also set it to 0 if you think that this is better.

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Yes, please set it to 0. The program will automatically calculate this value, or the user can customize it. A value of 2 might be a specific setting for Si.

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Ok!

"two_body": false,
"three_body": false,
"soap": true
},
Expand Down Expand Up @@ -40,15 +41,15 @@
},
"soap": {
"add_species": "T",
"l_max": 10,
"n_max": 12,
"l_max": 12,
"n_max": 10,
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I would increase n_max before increasing l_max. Or we can stick to n_max=l_max=10.

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@QuantumChemist QuantumChemist Nov 20, 2024 •
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Here, I also use Si settings from JCP2020 paper. But I can doublecheck that I didn't mix it up.

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image

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The default values here, including those mentioned earlier, are intended to be applicable to most systems. Increasing l_max would greatly impact computational efficiency.

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Ok, then I'll change it back too.

"atom_sigma": 0.5,
"zeta": 4,
"cutoff": 5.0,
"cutoff_transition_width": 0.5,
"cutoff_transition_width": 1.0,
"central_weight": 1.0,
"n_sparse": 6000,
"delta": 0.50,
"delta": 1.00,
"f0": 0.0,
"covariance_type": "dot_product",
"sparse_method": "cur_points"
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