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Add periodic hamiltonian learning example #75

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Add periodic hamiltonian learning example #75

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679762d
Add periodic hamiltonian learning example
ppegolo Sep 9, 2024
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Linting
ppegolo Sep 9, 2024
806494a
Update environment
ppegolo Sep 9, 2024
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Add dependency
ppegolo Sep 9, 2024
45c96a4
Update ml-models.rst
ppegolo Sep 9, 2024
464774f
Fix format
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Update hamiltonian example
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Update example
ppegolo Sep 17, 2024
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Update environment.yml
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Try installing pyscf with conda
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Fix typos
ppegolo Sep 26, 2024
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Restructured the data folder, misc cleanups
ceriottm Sep 27, 2024
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Add figure
ppegolo Oct 1, 2024
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Update example
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Carbon is gray - proofreading and small tweaks
ceriottm Oct 6, 2024
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1 change: 1 addition & 0 deletions docs/src/software/cp2k.sec
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Expand Up @@ -7,3 +7,4 @@ material, crystal, and biological systems. Learn more about it on its `homepage
<https://cp2k.org>`_.

- examples/batch-cp2k/reference-trajectory
- examples/periodic-hamiltonian/periodic-hamiltonian
1 change: 1 addition & 0 deletions docs/src/software/rascaline.sec
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Expand Up @@ -14,3 +14,4 @@ version from the `github repository <https://github.com/Luthaf/rascaline>`_
- examples/lode-linear/lode-linear
- examples/roy-gch/roy-gch
- examples/sample-selection/sample-selection
- examples/periodic-hamiltonian/periodic-hamiltonian
1 change: 1 addition & 0 deletions docs/src/topics/ml-models.sec
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Expand Up @@ -8,3 +8,4 @@ data.
- examples/dos-align/dos-align
- examples/lode-linear/lode-linear
- examples/sample-selection/sample-selection
- examples/periodic-hamiltonian/periodic-hamiltonian
3 changes: 3 additions & 0 deletions examples/periodic-hamiltonian/README.rst
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Periodic Hamiltonian Learning
=============================

28 changes: 28 additions & 0 deletions examples/periodic-hamiltonian/data/BASIS_STO3G
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#----------------------------------------------------------------------
# Basis Set Exchange
# Version v0.9.1
# https://www.basissetexchange.org
#----------------------------------------------------------------------
# Basis set: STO-3G
# Description: STO-3G Minimal Basis (3 functions/AO)
# Role: orbital
# Version: 1 (Data from Gaussian09)
#----------------------------------------------------------------------


# Carbon STO-3G (6s,3p) -> [2s,1p]
C STO-3G
2
1 0 0 3 1
0.7161683735E+02 0.1543289673E+00
0.1304509632E+02 0.5353281423E+00
0.3530512160E+01 0.4446345422E+00
1 0 1 3 1 1
0.2941249355E+01 -0.9996722919E-01 0.1559162750E+00
0.6834830964E+00 0.3995128261E+00 0.6076837186E+00
0.2222899159E+00 0.7001154689E+00 0.3919573931E+00



140 changes: 140 additions & 0 deletions examples/periodic-hamiltonian/data/C2.xyz
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2
Lattice="2.321189 0.0 0.0 -1.155982 1.986034 0.0 -0.37381 -0.001243 106.457295" Properties=species:S:1:pos:R:3 pbc="T T F"
C -0.08351854 -0.00307582 1.62727708
C -0.05879422 1.33906047 1.60493484
2
Lattice="2.292099 0.0 0.0 -1.223659 2.063605 0.0 0.021344 0.646819 106.294756" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.01526967 0.15893965 1.58664361
C -0.01481984 1.55278985 1.56429722
2
Lattice="2.236061 0.0 0.0 -1.153526 1.997966 0.0 0.0 0.0 106.227097" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00000000 0.00000000 1.55677425
C -0.02366480 1.33197800 1.55677425
2
Lattice="2.297961 0.0 0.0 -1.14898 1.990093 0.0 0.0 0.0 106.227097" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00000000 0.00000000 1.55677425
C -0.00000082 1.32672933 1.55677425
2
Lattice="2.395273 0.0 0.0 -1.14898 1.990093 0.0 0.0 0.0 105.967224" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00993388 -0.00276424 1.50476084
C 0.06402213 1.34207693 1.48241956
2
Lattice="2.297961 0.0 0.0 -1.14898 1.990093 0.0 0.263751 0.152277 106.318023" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.07587250 0.03530473 1.59245770
C 0.09752113 1.38014676 1.57011717
2
Lattice="2.297961 0.0 0.0 -1.176539 2.037827 0.0 0.0 0.0 106.227097" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00000000 0.00000000 1.55677425
C -0.01837349 1.35855201 1.55677425
2
Lattice="2.312702 0.0 0.0 -1.119515 2.006816 0.0 0.0 0.0 106.409587" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00071308 -0.00008429 1.60239675
C 0.02384542 1.33796229 1.60239675
2
Lattice="2.336932 0.0 0.0 -0.998849 2.069523 0.0 0.0 0.0 105.947627" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00993437 -0.00276488 1.49986068
C 0.14466347 1.39503027 1.47751545
2
Lattice="2.3713 0.0 0.0 -1.220678 2.114278 0.0 0.0 0.412583 106.473131" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00000000 0.10314575 1.61828275
C -0.02335320 1.51266512 1.61828275
2
Lattice="2.3713 0.0 0.0 -1.165341 2.018432 0.0 0.453069 0.261579 106.225241" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.11375064 0.06618396 1.55631025
C 0.12632202 1.41022755 1.55631025
2
Lattice="2.3713 0.0 0.0 -1.330946 1.962561 0.0 -0.083921 0.133479 106.405776" Properties=species:S:1:pos:R:3 pbc="T T F"
C -0.02294377 0.03441187 1.60144400
C -0.11587959 1.34070228 1.60144400
2
Lattice="2.311962 0.0 0.0 -1.18565 2.053606 0.0 0.0 0.0 106.425834" Properties=species:S:1:pos:R:3 pbc="T T F"
C -0.00059072 -0.00111922 1.60645850
C -0.01918978 1.37019057 1.60645850
2
Lattice="2.480636 0.0 0.0 -1.208047 2.092399 0.0 0.0 0.279671 106.419745" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00993567 0.06715103 1.61789130
C 0.05309740 1.48019981 1.59554416
2
Lattice="2.3713 0.0 0.0 -1.18565 2.053606 0.0 -0.231464 -0.133636 106.351346" Properties=species:S:1:pos:R:3 pbc="T T F"
C -0.04793269 -0.03617456 1.60078689
C -0.02628320 1.35101137 1.57844921
2
Lattice="2.415222 0.0 0.0 -1.18565 2.053606 0.0 0.0 -0.479047 106.307035" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00000000 -0.11976175 1.57675875
C 0.01463947 1.24930960 1.57675875
2
Lattice="2.3713 0.0 0.0 -1.189577 2.051334 0.0 -0.246145 0.454992 106.404978" Properties=species:S:1:pos:R:3 pbc="T T F"
C -0.06163595 0.11380544 1.60124450
C -0.06405573 1.48124725 1.60124450
2
Lattice="2.398523 0.0 0.0 -1.180965 2.045492 0.0 0.0 -0.128692 106.730214" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00993495 -0.03493873 1.69550916
C 0.04378159 1.34683791 1.67316485
2
Lattice="2.444639 0.0 0.0 -1.253686 2.171449 0.0 0.0 0.373074 106.614058" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00993418 0.09050295 1.66646483
C 0.01067295 1.55624976 1.64412254
2
Lattice="2.444639 0.0 0.0 -1.389228 1.992181 0.0 0.0 0.0 106.624571" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00993444 -0.00276515 1.66909379
C -0.07968886 1.34346909 1.64675573
2
Lattice="2.451565 0.0 0.0 -1.222319 2.11712 0.0 0.0 0.454355 106.608972" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00993389 0.11082302 1.66519659
C 0.03389293 1.54034988 1.64285165
2
Lattice="2.54493 0.0 0.0 -1.108732 2.178576 0.0 0.0179 0.345442 106.728616" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.01440967 0.08359422 1.69510659
C 0.14521338 1.55409287 1.67276758
2
Lattice="2.343757 0.0 0.0 -1.064869 2.103133 0.0 -0.220008 -0.603298 106.555214" Properties=species:S:1:pos:R:3 pbc="T T F"
C -0.05300592 -0.15247546 1.63880350
C 0.01434045 1.25291583 1.63880350
2
Lattice="2.444639 0.0 0.0 -1.242413 2.151923 0.0 0.0 0.0 106.624571" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00000000 0.00000000 1.65614275
C -0.01339690 1.43461605 1.65614275
2
Lattice="2.41426 0.0 0.0 -1.35096 2.037442 0.0 -0.548096 0.112718 106.496947" Properties=species:S:1:pos:R:3 pbc="T T F"
C -0.14037392 0.02936122 1.62423675
C -0.22956066 1.38529109 1.62423675
2
Lattice="2.444639 0.0 0.0 -1.351634 2.0373 0.0 0.0 0.0 106.624571" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00993326 -0.00276462 1.66909379
C -0.05462749 1.37354970 1.64675573
2
Lattice="2.517979 0.0 0.0 -1.236616 2.141882 0.0 0.283452 0.163651 106.77526" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.07181119 0.04237566 1.69381500
C 0.08483174 1.46737189 1.69381500
2
Lattice="2.517979 0.0 0.0 -1.389247 2.10005 0.0 0.0 0.0 106.823308" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00000000 0.00000000 1.70582700
C -0.08683964 1.40003403 1.70582700
2
Lattice="2.527906 0.0 0.0 -1.287031 2.229204 0.0 0.0 0.0 106.823308" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00000000 0.00000000 1.70582700
C -0.01538660 1.48613674 1.70582700
2
Lattice="2.517979 0.0 0.0 -1.258989 2.180634 0.0 0.0 -0.228791 106.819472" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00000000 -0.05719775 1.70486800
C -0.00000093 1.39655898 1.70486800
2
Lattice="2.517979 0.0 0.0 -1.297692 2.259268 0.0 -0.090565 -0.121788 106.82162" Properties=species:S:1:pos:R:3 pbc="T T F"
C -0.02264125 -0.03044700 1.70540500
C -0.04844419 1.47573242 1.70540500
2
Lattice="2.505494 0.0 0.0 -1.301622 2.155457 0.0 0.229407 0.81562 106.7705" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.05735175 0.20390500 1.69262500
C 0.02476715 1.64087705 1.69262500
2
Lattice="2.517979 0.0 0.0 -1.41732 2.081206 0.0 -0.545915 -0.130377 106.800185" Properties=species:S:1:pos:R:3 pbc="T T F"
C -0.14216919 -0.02958483 1.70004625
C -0.23634329 1.35186769 1.70004625
2
Lattice="2.460394 0.0 0.0 -1.26336 2.044166 0.0 -0.139209 -0.407369 106.809714" Properties=species:S:1:pos:R:3 pbc="T T F"
C -0.03480225 -0.10184225 1.70242850
C -0.05691216 1.26093576 1.70242850
2
Lattice="2.517979 0.0 0.0 -1.317654 2.282245 0.0 0.0 0.0 106.55201" Properties=species:S:1:pos:R:3 pbc="T T F"
C 0.00993403 -0.00276608 1.65095582
C -0.00752587 1.53684553 1.62861347
109 changes: 109 additions & 0 deletions examples/periodic-hamiltonian/data/reftraj_hamiltonian.cp2k
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&GLOBAL
PROJECT //PROJECT//
RUN_TYPE MD
PRINT_LEVEL MEDIUM
FFTW_PLAN_TYPE MEASURE
&END GLOBAL

&MOTION
&PRINT
&CELL
&EACH
MD 1
&END EACH
&END CELL
&FORCES
&EACH
MD 1
&END EACH
&END FORCES
&END PRINT
&MD
ENSEMBLE REFTRAJ
&REFTRAJ ! Loads an external trajectory file and performs analysis on the loaded snapshots.
EVAL ENERGY_FORCES
CELL_FILE_NAME reftraj.cell
TRAJ_FILE_NAME reftraj.xyz
FIRST_SNAPSHOT 1
VARIABLE_VOLUME TRUE
LAST_SNAPSHOT //LAST_SNAPSHOT//
&END REFTRAJ
&END MD
&END MOTION

&FORCE_EVAL
METHOD Quickstep
&DFT
&MGRID
NGRIDS 5
CUTOFF 200
REL_CUTOFF 70
&END MGRID
UKS F
BASIS_SET_FILE_NAME ../BASIS_STO3G
POTENTIAL_FILE_NAME ../POTENTIAL

&QS
METHOD GAPW
EXTRAPOLATION USE_GUESS
EPS_DEFAULT 1.0E-12
&END QS
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-8
MAX_SCF 300
ADDED_MOS -1
&DIAGONALIZATION
ALGORITHM STANDARD
&END DIAGONALIZATION
&SMEAR ON
METHOD FERMI_DIRAC
ELECTRONIC_TEMPERATURE [K] 300
&END SMEAR

&MIXING
METHOD BROYDEN_MIXING
ALPHA 0.4
BETA 0.5
NBROYDEN 8
&END MIXING

&END SCF
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC
&KPOINTS
SCHEME MONKHORST-PACK 15 15 1
WAVEFUNCTIONS COMPLEX
&END KPOINTS
&PRINT
&KS_CSR_WRITE
REAL_SPACE
FILENAME ./FOCK/
&END KS_CSR_WRITE
&S_CSR_WRITE
REAL_SPACE
FILENAME ./OVER/
&END S_CSR_WRITE
&END PRINT
&END DFT

&SUBSYS
&CELL
A //CELL_A//
B //CELL_B//
C //CELL_C//
PERIODIC XYZ
&END CELL
&TOPOLOGY
COORD_FILE_NAME init.xyz
COORD_FILE_FORMAT XYZ
&END TOPOLOGY
&KIND C
ELEMENT C
BASIS_SET ORB STO-3G
POTENTIAL ALL
&END KIND
&END SUBSYS
&END FORCE_EVAL
26 changes: 26 additions & 0 deletions examples/periodic-hamiltonian/environment.yml
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channels:
- conda-forge
dependencies:
- python>=3.11
- pip
- graphviz
- pyscf=2.3.0
- rust>=1.65
- pip:
- pyscfad @ git+https://github.com/fishjojo/pyscfad.git@ml#egg=pyscfad
- ase==3.22.1
- seekpath
- requests
- metatensor
- metatensor-core
- metatensor-learn
- metatensor-operations
- metatensor-torch
- --extra-index-url https://download.pytorch.org/whl/cpu
- rascaline-torch @ git+https://github.com/luthaf/rascaline#subdirectory=python/rascaline-torch
- lightning
- xitorch
- keras_core
- tensorboard
- torchviz
- mlelec @ git+https://github.com/curiosity54/mlelec.git@tutorial_periodic#egg=mlelec
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