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mlip-arena

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cyrusyc commited on Jul 5

Commit

d9ed521

•

1 Parent(s): f6fdc0c

add mlip diatomic curves

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Files changed (11) hide show

README.md +1 -1
mlip_arena/models/registry.yaml +10 -1
mlip_arena/tasks/diatomics/chgnet/homonuclear-diatomics.json +1 -0
mlip_arena/tasks/diatomics/gpaw/ClCl_AFM/traj.extxyz +44 -0
mlip_arena/tasks/diatomics/gpaw/MgMg_AFM/traj.extxyz +0 -28
mlip_arena/tasks/diatomics/gpaw/SS_AFM/traj.extxyz +40 -0
mlip_arena/tasks/diatomics/gpaw/SiSi_AFM/traj.extxyz +44 -0
mlip_arena/tasks/diatomics/mace-mp/homonuclear-diatomics.json +1 -0
app.py → serve/app.py +10 -8
serve/tasks/homonuclear-diatomics.py +99 -45
serve/tools/ptable.py +92 -0

README.md CHANGED Viewed

@@ -3,7 +3,7 @@ title: MLIP Arena
 emoji: ⚛
 sdk: streamlit
 sdk_version: 1.36.0 # The latest supported version
-app_file: app.py
 ---
 # mlip-arena

 emoji: ⚛
 sdk: streamlit
 sdk_version: 1.36.0 # The latest supported version
+app_file: serve/app.py
 ---
 # mlip-arena

mlip_arena/models/registry.yaml CHANGED Viewed

@@ -10,4 +10,13 @@ MACE_MP_Medium:
     - alexandria
     - qmof
   gpu-tasks:

     - alexandria
     - qmof
   gpu-tasks:
+    - diatomics
+CHGNet:
+  module: chgnet
+  username: cyrusyc
+  datetime: 2024-03-25T14:30:00
+  datasets:
+    - atomind/mptrj
+  cpu-tasks:
+    - diatomics

mlip_arena/tasks/diatomics/chgnet/homonuclear-diatomics.json ADDED Viewed

	@@ -0,0 +1 @@

+ 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mlip_arena/tasks/diatomics/gpaw/ClCl_AFM/traj.extxyz CHANGED Viewed

@@ -42,3 +42,47 @@ Cl       7.51628571       5.64200000       5.64200000      -5.00000000      -0.4
 Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-0.6362307456758872 free_energy=-0.6362307456758872 dipole="-6.23444412816076e-13 4.224599845528633e-08 9.766026461949354e-08" magmom=-7.0067028017747165e-15 pbc="T T T"
 Cl       3.87290476       5.64200000       5.64200000       5.00000000       0.41212465
 Cl       7.41109524       5.64200000       5.64200000      -5.00000000      -0.41212465

 Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-0.6362307456758872 free_energy=-0.6362307456758872 dipole="-6.23444412816076e-13 4.224599845528633e-08 9.766026461949354e-08" magmom=-7.0067028017747165e-15 pbc="T T T"
 Cl       3.87290476       5.64200000       5.64200000       5.00000000       0.41212465
 Cl       7.41109524       5.64200000       5.64200000      -5.00000000      -0.41212465
+2
+Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-0.8214194441479813 free_energy=-0.8214194441479813 dipole="3.031008398392218e-15 3.62639251524717e-08 4.853343314726535e-08" magmom=-9.59680372038913e-16 pbc="T T T"
+Cl       3.97809524       5.64200000       5.64200000       5.00000000       0.36824720       0.50594916       0.00000009       0.00000032
+Cl       7.30590476       5.64200000       5.64200000      -5.00000000      -0.36824720      -0.50594916       0.00000009       0.00000032
+2
+Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-0.9744416063810685 free_energy=-0.9744416063810685 dipole="-1.0811936539188394e-15 4.02433059462361e-08 3.6996328393298045e-08" magmom=1.902850737514897e-15 pbc="T T T"
+Cl       4.08328571       5.64200000       5.64200000       5.00000000       0.32032644       0.98640219       0.00000000       0.00000117
+Cl       7.20071429       5.64200000       5.64200000      -5.00000000      -0.32032644      -0.98640219       0.00000000       0.00000117
+2
+Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-1.2775831370374562 free_energy=-1.2775831370374562 dipole="1.0675304429229721e-12 2.893539756435728e-08 6.278255714709154e-09" magmom=-4.415183980536728e-15 pbc="T T T"
+Cl       4.18847619       5.64200000       5.64200000       5.00000000       0.18936843       2.02970072       0.00000061       0.00000048
+Cl       7.09552381       5.64200000       5.64200000      -5.00000000      -0.18936843      -2.02970072       0.00000057      -0.00000119
+2
+Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-1.8057105218266352 free_energy=-1.8057105218266352 dipole="-3.4608418034857716e-11 1.152462814085366e-08 2.0075345434954526e-08" magmom=-5.3189152213278416e-15 pbc="T T T"
+Cl       4.29366667       5.64200000       5.64200000       5.00000000      -0.00050656       2.81726869      -0.00000016       0.00000008
+Cl       6.99033333       5.64200000       5.64200000      -5.00000000       0.00050656      -2.81726869      -0.00000017      -0.00000051
+2
+Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-2.427495082323482 free_energy=-2.427495082323482 dipole="-1.0495821921180604e-11 2.578891299581512e-08 4.920262866209571e-08" magmom=6.148806719500548e-16 pbc="T T T"
+Cl       4.39885714       5.64200000       5.64200000       5.00000000      -0.00000078       3.08800480       0.00000020       0.00000033
+Cl       6.88514286       5.64200000       5.64200000      -5.00000000       0.00000078      -3.08800480       0.00000020       0.00000040
+2
+Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-3.052013389867105 free_energy=-3.052013389867105 dipole="-3.428500183860969e-14 2.0336666886586886e-08 4.418968059606245e-08" magmom=1.0258199308851289e-14 pbc="T T T"
+Cl       4.50404762       5.64200000       5.64200000       5.00000000       0.00000003       2.73735610      -0.00000002      -0.00000016
+Cl       6.77995238       5.64200000       5.64200000      -5.00000000      -0.00000003      -2.73735610      -0.00000002      -0.00000016
+2
+Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-3.4764220153807246 free_energy=-3.4764220153807246 dipole="1.508837559325854e-15 1.3225649213312095e-08 2.885772677479711e-08" magmom=7.844884745995615e-15 pbc="T T T"
+Cl       4.60923810       5.64200000       5.64200000       5.00000000       0.00000000       0.95062936       0.00000003       0.00000012
+Cl       6.67476190       5.64200000       5.64200000      -5.00000000      -0.00000000      -0.95062936       0.00000003       0.00000012
+2
+Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-3.223949531641405 free_energy=-3.223949531641405 dipole="-3.217189467511924e-15 1.7808263039149192e-08 3.43383904853661e-08" magmom=5.365221205814371e-16 pbc="T T T"
+Cl       4.71442857       5.64200000       5.64200000       5.00000000       0.00000000      -4.16695098       0.00000021       0.00000044
+Cl       6.56957143       5.64200000       5.64200000      -5.00000000      -0.00000000       4.16695098       0.00000021       0.00000044
+2
+Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-1.1700250836228716 free_energy=-1.1700250836228716 dipole="3.449011404357495e-15 2.0746956339343378e-08 4.084945998710388e-08" magmom=-5.1685190641446925e-15 pbc="T T T"
+Cl       4.81961905       5.64200000       5.64200000       5.00000000      -0.00000000     -17.37941950      -0.00000003      -0.00000007
+Cl       6.46438095       5.64200000       5.64200000      -5.00000000       0.00000000      17.37941950      -0.00000003      -0.00000007
+2
+Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=5.45971214912991 free_energy=5.45971214912991 dipole="1.3722143897742859e-15 1.823162783844328e-08 3.776677923261878e-08" magmom=-3.1652456091193807e-15 pbc="T T T"
+Cl       4.92480952       5.64200000       5.64200000       5.00000000       0.00000000     -50.81606443      -0.00000039      -0.00000065
+Cl       6.35919048       5.64200000       5.64200000      -5.00000000      -0.00000000      50.81606443      -0.00000039      -0.00000065
+2
+Lattice="11.284 0.0 0.0 0.0 11.285 0.0 0.0 0.0 11.286000000000001" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=23.83541143475322 free_energy=23.83541143475322 dipole="-1.6827525271393086e-14 2.511662752649596e-09 5.042134828448459e-09" magmom=6.230988124242401e-15 pbc="T T T"
+Cl       5.03000000       5.64200000       5.64200000       5.00000000      -0.00000000    -137.43831052      -0.00000001       0.00000018
+Cl       6.25400000       5.64200000       5.64200000      -5.00000000       0.00000000     137.43831052      -0.00000001       0.00000018

mlip_arena/tasks/diatomics/gpaw/MgMg_AFM/traj.extxyz DELETED Viewed

@@ -1,28 +0,0 @@
-2
-Lattice="15.562 0.0 0.0 0.0 15.562999999999999 0.0 0.0 0.0 15.564" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-0.23607773829833478 free_energy=-0.23607773829833478 dipole="-0.0008663671284904556 0.005625720881675098 0.004713154323759408" magmom=-3.383048371242272e-15 pbc="T T T"
-Mg       3.89050000       7.78100000       7.78100000       2.00000000      -0.00000391
-Mg      11.67150000       7.78100000       7.78100000      -2.00000000       0.00000394
-2
-Lattice="15.562 0.0 0.0 0.0 15.562999999999999 0.0 0.0 0.0 15.564" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-0.2361635561769566 free_energy=-0.2361635561769566 dipole="4.166314783156733e-08 1.3147325756581941e-06 0.00010462807712492037" magmom=-7.232801577136727e-15 pbc="T T T"
-Mg       3.99548276       7.78100000       7.78100000      -2.00000000      -0.00000029
-Mg      11.56651724       7.78100000       7.78100000       2.00000000       0.00000029
-2
-Lattice="15.562 0.0 0.0 0.0 15.562999999999999 0.0 0.0 0.0 15.564" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-0.23638343568667458 free_energy=-0.23638343568667458 dipole="5.994061559535258e-08 2.9847530385328577e-06 3.201547219484154e-05" magmom=9.362002680121302e-14 pbc="T T T"
-Mg       4.10046552       7.78100000       7.78100000      -2.00000000      -0.00000056
-Mg      11.46153448       7.78100000       7.78100000       2.00000000       0.00000056
-2
-Lattice="15.562 0.0 0.0 0.0 15.562999999999999 0.0 0.0 0.0 15.564" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-0.23676092479276822 free_energy=-0.23676092479276822 dipole="-6.605824149770908e-07 -2.903899710505136e-06 -2.3628098424942243e-05" magmom=3.9130486647129224e-13 pbc="T T T"
-Mg       4.20544828       7.78100000       7.78100000      -2.00000000      -0.00000072
-Mg      11.35655172       7.78100000       7.78100000       2.00000000       0.00000074
-2
-Lattice="15.562 0.0 0.0 0.0 15.562999999999999 0.0 0.0 0.0 15.564" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-0.2373175929965371 free_energy=-0.2373175929965371 dipole="2.3147035249859067e-06 -1.725753672446766e-07 6.468482941674519e-07" magmom=-9.930560185261779e-12 pbc="T T T"
-Mg       4.31043103       7.78100000       7.78100000      -2.00000000      -0.00000118
-Mg      11.25156897       7.78100000       7.78100000       2.00000000       0.00000124
-2
-Lattice="15.562 0.0 0.0 0.0 15.562999999999999 0.0 0.0 0.0 15.564" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-0.23808565497613038 free_energy=-0.23808565497613038 dipole="9.389956331350595e-07 2.395179430657185e-07 4.115907298995057e-07" magmom=-2.882232132864536e-10 pbc="T T T"
-Mg       4.41541379       7.78100000       7.78100000      -2.00000000      -0.00000043
-Mg      11.14658621       7.78100000       7.78100000       2.00000000       0.00000044
-2
-Lattice="15.562 0.0 0.0 0.0 15.562999999999999 0.0 0.0 0.0 15.564" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-0.23911376540392726 free_energy=-0.23911376540392726 dipole="3.103603705470817e-05 1.4874452521265978e-08 1.5647314747441154e-07" magmom=-1.6613975213138008e-13 pbc="T T T"
-Mg       4.52039655       7.78100000       7.78100000      -2.00000000       0.00000005
-Mg      11.04160345       7.78100000       7.78100000       2.00000000      -0.00000003

mlip_arena/tasks/diatomics/gpaw/SS_AFM/traj.extxyz CHANGED Viewed

@@ -46,3 +46,43 @@ S        7.69350000       5.85900000       5.85900000      -4.00000000      -0.9
 Lattice="11.718 0.0 0.0 0.0 11.719 0.0 0.0 0.0 11.72" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-1.9524021673265366 free_energy=-1.9524021673265366 dipole="8.648728149746012e-08 3.7151671782460395e-06 1.1011625089236083e-05" magmom=-8.507052887892137e-15 pbc="T T T"
 S        4.13400000       5.85900000       5.85900000       4.00000000       0.97588439
 S        7.58400000       5.85900000       5.85900000      -4.00000000      -0.97588437

 Lattice="11.718 0.0 0.0 0.0 11.719 0.0 0.0 0.0 11.72" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-1.9524021673265366 free_energy=-1.9524021673265366 dipole="8.648728149746012e-08 3.7151671782460395e-06 1.1011625089236083e-05" magmom=-8.507052887892137e-15 pbc="T T T"
 S        4.13400000       5.85900000       5.85900000       4.00000000       0.97588439
 S        7.58400000       5.85900000       5.85900000      -4.00000000      -0.97588437
+2
+Lattice="11.718 0.0 0.0 0.0 11.719 0.0 0.0 0.0 11.72" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-2.4754979021056105 free_energy=-2.4754979021056105 dipole="-9.068529462346077e-11 -4.404073258102355e-09 -8.663119545562142e-09" magmom=2.7463903207804998e-15 pbc="T T T"
+S        4.24350000       5.85900000       5.85900000       4.00000000       0.86739354       1.03324085       0.00000004      -0.00000002
+S        7.47450000       5.85900000       5.85900000      -4.00000000      -0.86739354      -1.03324086       0.00000004      -0.00000002
+2
+Lattice="11.718 0.0 0.0 0.0 11.719 0.0 0.0 0.0 11.72" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-2.7767417251109054 free_energy=-2.7767417251109054 dipole="-5.867801409732914e-10 -1.3130890982217635e-09 6.827248541061529e-10" magmom=4.7371232682523474e-15 pbc="T T T"
+S        4.35300000       5.85900000       5.85900000       4.00000000       0.76304927       1.75834541      -0.00000005      -0.00000004
+S        7.36500000       5.85900000       5.85900000      -4.00000000      -0.76304927      -1.75834481      -0.00000005      -0.00000004
+2
+Lattice="11.718 0.0 0.0 0.0 11.719 0.0 0.0 0.0 11.72" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-3.258351890958282 free_energy=-3.258351890958282 dipole="-8.25529736066669e-07 2.9594622483356695e-09 2.178906719515088e-09" magmom=2.203723015310609e-12 pbc="T T T"
+S        4.46250000       5.85900000       5.85900000       4.00000000       0.62060871       2.59017909       0.00000001       0.00000002
+S        7.25550000       5.85900000       5.85900000      -4.00000000      -0.62060892      -2.59020032       0.00000001       0.00000002
+2
+Lattice="11.718 0.0 0.0 0.0 11.719 0.0 0.0 0.0 11.72" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-4.3988946520648735 free_energy=-4.3988946520648735 dipole="-0.001622641443223675 7.840535958111968e-11 3.171243313295675e-09" magmom=3.040904184817457e-14 pbc="T T T"
+S        4.57200000       5.85900000       5.85900000       4.00000000       0.00615030       4.43907180      -0.00000008      -0.00000004
+S        7.14600000       5.85900000       5.85900000      -4.00000000      -0.00622389      -4.41929551      -0.00000004      -0.00000003
+2
+Lattice="11.718 0.0 0.0 0.0 11.719 0.0 0.0 0.0 11.72" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-5.3996322156935985 free_energy=-5.3996322156935985 dipole="-0.0004705846630342035 2.6428249065571766e-09 2.0131954590530433e-09" magmom=-5.852425428574635e-09 pbc="T T T"
+S        4.68150000       5.85900000       5.85900000       4.00000000       0.00028130       4.62371800       0.00000001      -0.00000001
+S        7.03650000       5.85900000       5.85900000      -4.00000000      -0.00028276      -4.62707329       0.00000001      -0.00000001
+2
+Lattice="11.718 0.0 0.0 0.0 11.719 0.0 0.0 0.0 11.72" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-6.355011487963147 free_energy=-6.355011487963147 dipole="-0.0002565400339933681 1.701061399478038e-09 3.756612054832852e-09" magmom=5.5137122623194315e-12 pbc="T T T"
+S        4.79100000       5.85900000       5.85900000       4.00000000       0.00000530       3.80003676      -0.00000000       0.00000003
+S        6.92700000       5.85900000       5.85900000      -4.00000000      -0.00000525      -3.79437305      -0.00000000       0.00000003
+2
+Lattice="11.718 0.0 0.0 0.0 11.719 0.0 0.0 0.0 11.72" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-6.864989485271182 free_energy=-6.864989485271182 dipole="-2.4295054339974333e-07 4.829326582293934e-09 3.512739215409518e-09" magmom=1.396992497174256e-13 pbc="T T T"
+S        4.90050000       5.85900000       5.85900000       4.00000000       0.00000001       0.14266223      -0.00000002       0.00000003
+S        6.81750000       5.85900000       5.85900000      -4.00000000      -0.00000002      -0.14244610      -0.00000002       0.00000003
+2
+Lattice="11.718 0.0 0.0 0.0 11.719 0.0 0.0 0.0 11.72" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-5.910986335781827 free_energy=-5.910986335781827 dipole="-5.050899102418916e-08 1.3059356960041258e-09 1.0905790050203337e-09" magmom=-1.1747464789937136e-13 pbc="T T T"
+S        5.01000000       5.85900000       5.85900000       4.00000000      -0.00000000     -10.63466386       0.00000001       0.00000002
+S        6.70800000       5.85900000       5.85900000      -4.00000000      -0.00000000      10.63466681       0.00000001       0.00000002
+2
+Lattice="11.718 0.0 0.0 0.0 11.719 0.0 0.0 0.0 11.72" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-0.9079304777624212 free_energy=-0.9079304777624212 dipole="-5.034922852075231e-09 -8.112889099915873e-11 9.953151544433073e-10" magmom=-7.532204103831928e-14 pbc="T T T"
+S        5.11950000       5.85900000       5.85900000       4.00000000       0.00000000     -39.61907637      -0.00000002       0.00000010
+S        6.59850000       5.85900000       5.85900000      -4.00000000       0.00000000      39.61907637      -0.00000002       0.00000010
+2
+Lattice="11.718 0.0 0.0 0.0 11.719 0.0 0.0 0.0 11.72" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=14.648212060240844 free_energy=14.648212060240844 dipole="8.991280081992044e-08 -3.1987904484984434e-09 -1.7801637360774048e-09" magmom=1.0225729821146675e-14 pbc="T T T"
+S        5.22900000       5.85900000       5.85900000       4.00000000       0.00000000    -113.59576350      -0.00000000       0.00000001
+S        6.48900000       5.85900000       5.85900000      -4.00000000       0.00000001     113.59575924      -0.00000000       0.00000001

mlip_arena/tasks/diatomics/gpaw/SiSi_AFM/traj.extxyz CHANGED Viewed

@@ -62,3 +62,47 @@ Si       8.71430769       6.78900000       6.78900000      -2.00000000      -0.4
 Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-2.29727654834893 free_energy=-2.29727654834893 dipole="-4.987523004589227e-07 -2.6959496732403502e-06 3.4038488756166403e-07" magmom=6.119018896352277e-10 pbc="T T T"
 Si       4.96863462       6.78900000       6.78900000       2.00000000       0.40921037
 Si       8.60936538       6.78900000       6.78900000      -2.00000000      -0.40920434

 Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1 energy=-2.29727654834893 free_energy=-2.29727654834893 dipole="-4.987523004589227e-07 -2.6959496732403502e-06 3.4038488756166403e-07" magmom=6.119018896352277e-10 pbc="T T T"
 Si       4.96863462       6.78900000       6.78900000       2.00000000       0.40921037
 Si       8.60936538       6.78900000       6.78900000      -2.00000000      -0.40920434
+2
+Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-2.5532493443448385 free_energy=-2.5532493443448385 dipole="7.352819717213404e-07 -7.062323292453009e-09 -6.301025008880651e-09" magmom=-4.9589881320518486e-15 pbc="T T T"
+Si       5.07357692       6.78900000       6.78900000       2.00000000       0.35118372       1.35621663       0.00000004       0.00000004
+Si       8.50442308       6.78900000       6.78900000      -2.00000000      -0.35118407      -1.35622652       0.00000004       0.00000004
+2
+Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-3.188423219416578 free_energy=-3.188423219416578 dipole="-0.00040787073584288067 1.1289027987331761e-06 -4.1191330374468776e-07" magmom=2.757386756668508e-14 pbc="T T T"
+Si       5.17851923       6.78900000       6.78900000       2.00000000       0.02066497       2.26566770      -0.00001833      -0.00000254
+Si       8.39948077       6.78900000       6.78900000      -2.00000000      -0.02072537      -2.26373507       0.00002194      -0.00001311
+2
+Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-3.683917327329515 free_energy=-3.683917327329515 dipole="-0.00010729599428164871 6.079730339053743e-08 -8.067142876407431e-08" magmom=-1.315858111579632e-08 pbc="T T T"
+Si       5.28346154       6.78900000       6.78900000       2.00000000      -0.00160632       2.43573053      -0.00000436       0.00000021
+Si       8.29453846       6.78900000       6.78900000      -2.00000000       0.00161219      -2.43752268       0.00000558      -0.00000180
+2
+Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-4.197843597964851 free_energy=-4.197843597964851 dipole="0.00017131138366368795 -1.0613950218331658e-08 -1.5175115513324666e-08" magmom=-1.5961398450537137e-09 pbc="T T T"
+Si       5.38840385       6.78900000       6.78900000       2.00000000       0.00002089       2.41743018      -0.00000127       0.00000015
+Si       8.18959615       6.78900000       6.78900000      -2.00000000      -0.00002123      -2.41783947       0.00000124      -0.00000018
+2
+Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-4.6740222596332295 free_energy=-4.6740222596332295 dipole="-2.6692989092788546e-05 1.2487156145607518e-09 -7.09709453081909e-09" magmom=1.117780919509961e-09 pbc="T T T"
+Si       5.49334615       6.78900000       6.78900000       2.00000000      -0.00000087       2.02293019      -0.00000006      -0.00000001
+Si       8.08465385       6.78900000       6.78900000      -2.00000000       0.00000092      -2.02297999       0.00000007      -0.00000002
+2
+Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-4.996413821947155 free_energy=-4.996413821947155 dipole="1.0936788322896686e-06 -4.867689005956423e-09 -2.7750338709558942e-09" magmom=4.576907028376879e-11 pbc="T T T"
+Si       5.59828846       6.78900000       6.78900000       2.00000000      -0.00000000       0.86194442      -0.00000000       0.00000004
+Si       7.97971154       6.78900000       6.78900000      -2.00000000       0.00000000      -0.86194491       0.00000001       0.00000003
+2
+Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-4.931602182881434 free_energy=-4.931602182881434 dipole="3.7174961826305685e-08 3.621057283674936e-08 3.5829876284998824e-08" magmom=-3.495473263730297e-13 pbc="T T T"
+Si       5.70323077       6.78900000       6.78900000       2.00000000       0.00000003      -1.83409458       0.00000017       0.00000025
+Si       7.87476923       6.78900000       6.78900000      -2.00000000      -0.00000002       1.83409467       0.00000017       0.00000025
+2
+Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-4.573854449836713 free_energy=-4.573854449836713 dipole="-1.2460613949634714e-07 -0.016267332341179754 -0.00848808973042689" magmom=-4.4104910695841326e-14 pbc="T T T"
+Si       5.80817308       6.78900000       6.78900000       2.00000000       0.01405424      -4.29228874       0.00192538       0.00339464
+Si       7.76982692       6.78900000       6.78900000      -2.00000000       0.01405424       4.29228861       0.00192528       0.00339462
+2
+Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=-2.876166265900186 free_energy=-2.876166265900186 dipole="2.2797855185657538e-10 -0.0002978691035081787 -0.00014992392723568344" magmom=-4.6571019963537285e-06 pbc="T T T"
+Si       5.91311538       6.78900000       6.78900000       2.00000000      -0.00012983     -12.93090397      -0.00020118      -0.00007331
+Si       7.66488462       6.78900000       6.78900000      -2.00000000      -0.00012983      12.93090396      -0.00020118      -0.00007331
+2
+Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=1.4624058641173112 free_energy=1.4624058641173112 dipole="-3.872246998051089e-11 4.580942933692496e-07 2.1507861904836858e-07" magmom=9.142577920530893e-09 pbc="T T T"
+Si       6.01805769       6.78900000       6.78900000       2.00000000      -0.00000031     -30.96276185      -0.00000044      -0.00000011
+Si       7.55994231       6.78900000       6.78900000      -2.00000000      -0.00000031      30.96276185      -0.00000044      -0.00000011
+2
+Lattice="13.578 0.0 0.0 0.0 13.578999999999999 0.0 0.0 0.0 13.58" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:magmoms:R:1:forces:R:3 energy=11.41097421595209 free_energy=11.41097421595209 dipole="1.7453736480191038e-13 1.7129078057442776e-08 7.220828334726962e-09" magmom=-2.009967008321909e-11 pbc="T T T"
+Si       6.12300000       6.78900000       6.78900000       2.00000000      -0.00000000     -67.35607511      -0.00000019      -0.00000008
+Si       7.45500000       6.78900000       6.78900000      -2.00000000      -0.00000000      67.35607511      -0.00000019      -0.00000008

mlip_arena/tasks/diatomics/mace-mp/homonuclear-diatomics.json ADDED Viewed

	@@ -0,0 +1 @@

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app.py → serve/app.py RENAMED Viewed

@@ -25,25 +25,27 @@ st.set_page_config(
 # logout_page = st.Page(logout, title="Log out", icon=":material/logout:")
 dashboard = st.Page(
-    "serve/reports/dashboard.py", title="Dashboard", icon=":material/dashboard:", default=True
 )
-bugs = st.Page("serve/reports/bugs.py", title="Bug reports", icon=":material/bug_report:")
 alerts = st.Page(
-    "serve/reports/alerts.py", title="System alerts", icon=":material/notification_important:"
 )
-search = st.Page("serve/tools/search.py", title="Search", icon=":material/search:")
-history = st.Page("serve/tools/history.py", title="History", icon=":material/history:")
-diatomics = st.Page("serve/tasks/homonuclear-diatomics.py", title="Homonuclear diatomics", icon="")
 # if st.session_state.logged_in:
 pg = st.navigation(
     {
         # "Account": [logout_page],
-        "Reports": [dashboard, bugs, alerts],
-        "Tools": [search, history],
         "Tasks": [diatomics],
     }
 )
 # else:

 # logout_page = st.Page(logout, title="Log out", icon=":material/logout:")
 dashboard = st.Page(
+    "reports/dashboard.py", title="Dashboard", icon=":material/dashboard:"
 )
+bugs = st.Page("reports/bugs.py", title="Bug reports", icon=":material/bug_report:")
 alerts = st.Page(
+    "reports/alerts.py", title="System alerts", icon=":material/notification_important:"
 )
+search = st.Page("tools/search.py", title="Search", icon=":material/search:")
+history = st.Page("tools/history.py", title="History", icon=":material/history:")
+ptable = st.Page("tools/ptable.py", title="Periodic table", icon=":material/gradient:")
+diatomics = st.Page("tasks/homonuclear-diatomics.py", title="Homonuclear diatomics", icon="", default=True)
 # if st.session_state.logged_in:
 pg = st.navigation(
     {
         # "Account": [logout_page],
+        # "Reports": [dashboard, bugs, alerts],
+        # "Tools": [search, history, ptable],
         "Tasks": [diatomics],
+        "Tools": [ptable],
     }
 )
 # else:

serve/tasks/homonuclear-diatomics.py CHANGED Viewed

@@ -1,73 +1,127 @@
 from pathlib import Path
 import numpy as np
-import numpy.linalg as LA
-import plotly.express as px
 import streamlit as st
 from ase.data import chemical_symbols
-from ase.io import read
 from scipy.interpolate import CubicSpline
-st.markdown("# Homonuclear diatomics")
-DATA_DIR = Path("mlip_arena/tasks/diatomics")
-for i, symbol in enumerate(chemical_symbols[1:10]):
-    if i % 3 == 0:
-        cols = st.columns(3)
-    fpath = DATA_DIR / "gpaw" / f"{symbol+symbol}_AFM" / "traj.extxyz"
-    if not fpath.exists():
-        continue
-    trj = read(fpath, index=":")
-    rs, es, s2s = [], [], []
-    for atoms in trj:
-        rs.append(LA.norm(atoms.positions[1] - atoms.positions[0]))
-        es.append(atoms.get_potential_energy())
-        s2s.append(np.power(atoms.get_magnetic_moments(), 2).mean())
-    rs = np.array(rs)
-    ind = np.argsort(rs)
-    es = np.array(es)
-    s2s = np.array(s2s)
-    rs = rs[ind]
-    es = es[ind]
-    s2s = s2s[ind]
-    es = es - es[-1]
-    xs = np.linspace(rs.min()*0.99, rs.max()*1.01, int(5e2))
-    cs = CubicSpline(rs, es)
-    ys = cs(xs)
-    cs = CubicSpline(rs, s2s)
-    s2s = cs(xs)
-    ylo = min(ys.min()*1.5, -1)
-    fig = px.scatter(
-        x=xs, y=ys,
-        render_mode="webgl",
-        color=s2s,
-        range_color=[0, s2s.max()],
-        width=500,
-        range_y=[ylo, 1.2*(abs(ylo))],
-        # title=f"{atoms.get_chemical_formula()}",
-        labels={"x": "Bond length (Å)", "y": "Energy", "color": "Magnetic moment"},
     )
-    cols[i % 3].title(f"{symbol+symbol}")
-    cols[i % 3].plotly_chart(fig, use_container_width=False)
-# st.latex(r"\frac{d^2E}{dr^2} = \frac{d^2E}{dr^2}")
-# st.components.v1.html(fig.to_html(include_mathjax='cdn'),height=500)

 from pathlib import Path
 import numpy as np
+import pandas as pd
+import plotly.colors as pcolors
+import plotly.graph_objects as go
 import streamlit as st
 from ase.data import chemical_symbols
+from plotly.subplots import make_subplots
 from scipy.interpolate import CubicSpline
+color_sequence = pcolors.qualitative.Plotly
+st.markdown("# Homonuclear diatomics")
+# button to toggle plots
+container = st.container(border=True)
+energy_plot = container.checkbox("Show energy curves", value=True)
+force_plot = container.checkbox("Show force curves", value=False)
+ncols = 2
+DATA_DIR = Path("mlip_arena/tasks/diatomics")
+mlips = ["MACE-MP", "CHGNet"]
+dfs = [pd.read_json(DATA_DIR / mlip.lower() /  "homonuclear-diatomics.json") for mlip in mlips]
+df = pd.concat(dfs, ignore_index=True)
+df.drop_duplicates(inplace=True, subset=["name", "method"])
+for i, symbol in enumerate(chemical_symbols[1:]):
+    if i % ncols == 0:
+        cols = st.columns(ncols)
+    rows = df[df["name"] == symbol + symbol]
+    if rows.empty:
+        continue
+    # fig = go.Figure()
+    fig = make_subplots(specs=[[{"secondary_y": True}]])
+    ylo = float("inf")
+    for j, method in enumerate(rows["method"].unique()):
+        row = rows[rows["method"] == method].iloc[0]
+        rs = np.array(row["R"])
+        es = np.array(row["E"])
+        fs = np.array(row["F"])
+        rs = np.array(rs)
+        ind = np.argsort(rs)
+        es = np.array(es)
+        fs = np.array(fs)
+        rs = rs[ind]
+        es = es[ind]
+        es = es - es[-1]
+        fs = fs[ind]
+        xs = np.linspace(rs.min()*0.99, rs.max()*1.01, int(5e2))
+        if energy_plot:
+            cs = CubicSpline(rs, es)
+            ys = cs(xs)
+            ylo = min(ylo, ys.min()*1.2, -1)
+            fig.add_trace(
+                go.Scatter(
+                    x=xs, y=ys,
+                    mode="lines",
+                    line=dict(
+                        color=color_sequence[j % len(color_sequence)],
+                        width=2,
+                    ),
+                    name=method,
+                ),
+                secondary_y=False,
+            )
+        if force_plot:
+            cs = CubicSpline(rs, fs)
+            ys = cs(xs)
+            fig.add_trace(
+                go.Scatter(
+                    x=xs, y=ys,
+                    mode="lines",
+                    line=dict(
+                        color=color_sequence[j % len(color_sequence)],
+                        width=1,
+                        dash="dot",
+                    ),
+                    name=method,
+                    showlegend=False if energy_plot else True,
+                ),
+                secondary_y=True,
+            )
+    fig.update_layout(
+        showlegend=True,
+        title_text=f"{symbol}-{symbol}",
+        title_x=0.5,
+        # yaxis_range=[ylo, 2*(abs(ylo))],
     )
+    # Set x-axis title
+    fig.update_xaxes(title_text="Bond length (Å)")
+    # Set y-axes titles
+    if energy_plot:
+        fig.update_yaxes(title_text="Energy [eV]", secondary_y=False)
+    if force_plot:
+        fig.update_yaxes(title_text="Force [eV/Å]", secondary_y=True)
+    # cols[i % ncols].title(f"{row['name']}")
+    cols[i % ncols].plotly_chart(fig, use_container_width=True, height=250)

serve/tools/ptable.py ADDED Viewed

	@@ -0,0 +1,92 @@

+import streamlit as st
+from ase.data import chemical_symbols
+from pymatgen.core import Element
+elements = [Element.from_Z(z) for z in range(1, 119)]
+# Define the number of rows and columns in the periodic table
+rows = 9  # There are 7 rows in the conventional periodic table
+columns = 18
+# Define a function to display the periodic table
+def display_periodic_table():
+    # elements = [
+    #     (element, element) for element in chemical_symbols[1:]
+    # ]
+    # cols = st.columns(18, gap='small', vertical_alignment='bottom')  # Create 18 columns for the periodic table layout
+    row = 0
+    for element in elements:
+        symbol = element.symbol
+        atomic_number = element.Z
+        group = element.group
+        if element.row > row:
+            cols = st.columns(columns, gap='small', vertical_alignment='bottom')
+        row = element.row
+        if element.block == 'f':
+            continue
+        with cols[group - 1]:
+            if st.button(symbol, use_container_width=True):
+                st.session_state.selected_element = symbol
+                st.session_state.selected_name = symbol
+                st.rerun()
+                # st.experimental_rerun()
+    for element in elements:
+        symbol = element.symbol
+        atomic_number = element.Z
+        group = element.group
+        if element.row > row:
+            cols = st.columns(columns, gap='small', vertical_alignment='bottom')
+        row = element.row
+        if element.block == 'f':
+            noble = Element.from_row_and_group(row-1, 18)
+            row += 2
+            group += atomic_number - noble.Z - 2
+        else:
+            continue
+        with cols[group - 1]:
+            if st.button(symbol, use_container_width=True):
+                st.session_state.selected_element = symbol
+                st.session_state.selected_name = symbol
+                st.rerun()
+                # st.experimental_rerun()
+    # for idx, (symbol, name) in enumerate(elements):
+    #     with cols[idx % 18]:  # Place each element in the correct column
+    #         if st.button(symbol, use_container_width=True):
+    #             st.session_state.selected_element = symbol
+    #             st.session_state.selected_name = name
+    #             st.experimental_rerun()
+# Define a function to display the details of an element
+def display_element_details():
+    symbol = st.session_state.selected_element
+    name = st.session_state.selected_name
+    st.write(f"### {name} ({symbol})")
+    st.write(f"Details about {name} ({symbol}) will be displayed here.")
+    if st.button("Back to Periodic Table"):
+        st.session_state.selected_element = None
+        st.session_state.selected_name = None
+        st.experimental_rerun()
+st.title("Periodic Table")
+# st.balloons()
+if 'selected_element' not in st.session_state:
+    st.session_state.selected_element = None
+if st.session_state.selected_element:
+    display_element_details()
+else:
+    display_periodic_table()