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Uncertainty Quantification with PET-MAD (#163)
--------- Co-authored-by: Michele Ceriotti <michele.ceriotti@gmail.com>
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‎examples/pet-finetuning/pet-ft-nc.py‎

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:Authors: Michele Ceriotti `@ceriottm <https://github.com/ceriottm/>`_,
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Sofiia Chorna `@sofiia-chorna <https://github.com/sofiia-chorna>`_
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This example demonstrates a "conservative fine-tuning strategy", to train a model
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using a (faster) direct, non-conservative force prediction, and then fine-tune it
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This example demonstrates a "conservative fine-tuning" (or equivalently,
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"non-conservative pre-training") strategy, to train a model using a (faster)
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direct, non-conservative force prediction, and then fine-tune it
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in back-propagation force mode to achieve an accurate conservative model.
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As discussed in `this paper <https://openreview.net/pdf?id=OEl3L8osas>`_, while

‎examples/pet-mad-uq/.gitignore‎

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models
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data
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RESTART
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\#*
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*.out
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*.xyz
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*.committee_pot_0*
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*.txt

‎examples/pet-mad-uq/README.rst‎

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Uncertainty Quantification with PET-MAD
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=======================================
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Three examples of using PET-MAD's uncertainty quantification.

‎examples/pet-mad-uq/data/Al_mp-134_conventional_standard.cif‎

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# generated using pymatgen
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data_Al
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_symmetry_space_group_name_H-M 'P 1'
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_cell_length_a 4.03893000
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_cell_length_b 4.03893000
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_cell_length_c 4.03893000
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_cell_angle_alpha 90.00000000
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_cell_angle_beta 90.00000000
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_cell_angle_gamma 90.00000000
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_symmetry_Int_Tables_number 1
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_chemical_formula_structural Al
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_chemical_formula_sum Al4
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_cell_volume 65.88688554
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_cell_formula_units_Z 4
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loop_
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_symmetry_equiv_pos_site_id
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_symmetry_equiv_pos_as_xyz
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1 'x, y, z'
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loop_
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_atom_site_type_symbol
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_atom_site_label
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_atom_site_symmetry_multiplicity
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_atom_site_fract_x
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_atom_site_fract_y
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_atom_site_fract_z
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_atom_site_occupancy
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Al Al0 1 0.00000000 0.00000000 0.00000000 1
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Al Al1 1 0.00000000 0.50000000 0.50000000 1
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Al Al2 1 0.50000000 0.00000000 0.50000000 1
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Al Al3 1 0.50000000 0.50000000 0.00000000 1

‎examples/pet-mad-uq/data/h2o-32.xml‎

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<simulation verbosity='medium'>
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<output prefix='h2o-32'>
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<properties filename='out' stride='10'> [ time{picosecond}, temperature{kelvin}, kinetic_md ] </properties>
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<trajectory filename='pos' format='xyz' stride='10' cell_units='angstrom'> positions{angstrom} </trajectory>
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<trajectory filename="committee_pot" stride="10" extra_type="committee_pot"> extras </trajectory>
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</output>
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<prng>
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<seed>23658</seed>
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</prng>
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<ffdirect name='nocons' pbc="true">
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<pes>metatomic</pes>
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<parameters>{template:data/h2o-32.xyz,model:models/pet-mad-latest-llpr.pt,device:cpu,non_conservative:True,energy_ensemble:True,check_consistency:False}</parameters>
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</ffdirect>
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<system>
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<initialize nbeads='1'>
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<file mode='xyz' units="angstrom"> data/h2o-32.xyz </file>
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<velocities mode='thermal' units='kelvin'> 300 </velocities>
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</initialize>
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<forces>
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<force forcefield='nocons'/>
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</forces>
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<ensemble>
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<temperature units='kelvin'>300</temperature>
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</ensemble>
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<motion mode='dynamics'>
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<fixcom>True</fixcom>
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<dynamics mode='nvt'>
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<timestep units='femtosecond'>0.5</timestep>
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<thermostat mode='langevin'>
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<tau units='femtosecond'>50</tau>
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</thermostat>
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</dynamics>
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</motion>
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</system>
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</simulation>

‎examples/pet-mad-uq/data/h2o-32.xyz‎

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# CELL(abcABC): 9.865916 9.865916 9.865916 90.00000 90.00000 90.00000 Step: 5120 Bead: 0 positions{angstrom} cell{angstrom}
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O -7.79487e-01 -3.74296e+00 -2.10136e+00
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H 5.94789e-02 -3.45848e+00 -2.44656e+00
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O -3.80733e-01 7.29146e-01 -1.96576e+00
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H -6.26380e-01 1.36288e+00 -2.59311e+00
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H 1.75026e-01 2.02345e-01 -2.41688e+00
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O 1.86355e+00 6.47914e+00 2.66457e+00
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H 1.03340e+00 6.20999e+00 2.28387e+00
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H 1.58120e+00 7.08220e+00 3.41410e+00
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O 3.61225e-01 4.75076e+00 -4.73767e+00
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H 1.23941e+00 4.75186e+00 -5.19157e+00
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H 7.92374e-02 5.66798e+00 -4.66720e+00
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O -5.38119e+00 4.59176e+00 -3.91941e+00
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H -4.54514e+00 5.02244e+00 -3.82532e+00
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H -5.59575e+00 4.41493e+00 -3.04569e+00
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O -3.09479e+00 3.44980e+00 2.44433e+00
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H -3.35523e+00 3.17247e+00 1.55847e+00
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H -2.82121e+00 2.61449e+00 2.76831e+00
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O -1.14063e+00 2.18066e+00 -3.99268e+00
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H -7.23886e-01 1.74974e+00 -4.77728e+00
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H -6.29454e-01 3.02135e+00 -3.88583e+00
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O 4.34294e+00 -3.18496e+00 8.75093e+00
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H 5.03181e+00 -2.77143e+00 8.19620e+00
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H 4.07596e+00 -2.46677e+00 9.32790e+00
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O -2.97534e+00 -4.11053e+00 6.47614e+00
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H -3.37064e+00 -3.28376e+00 6.45630e+00
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H -2.80466e+00 -4.35438e+00 5.56913e+00
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O -5.82368e-01 -4.49175e+00 1.92936e+00
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H -9.12238e-01 -3.82049e+00 1.24878e+00
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H -1.30166e+00 -4.58382e+00 2.58472e+00
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O 2.84708e+00 4.19635e+00 3.62698e+00
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H 3.73225e+00 4.21823e+00 3.92288e+00
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H 2.47076e+00 5.04517e+00 3.23021e+00
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O 7.28153e+00 -8.79752e-02 -3.48091e-01
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H 7.80694e+00 3.59272e-01 -1.01379e+00
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H 7.05289e+00 7.06265e-01 1.54069e-01
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O 1.34813e+00 2.02128e+00 2.58333e+00
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H 1.89970e+00 2.79706e+00 2.76635e+00
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H 1.15962e+00 2.07153e+00 1.67332e+00
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O -1.09090e+00 4.19322e+00 -4.20171e-01
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H -1.12173e+00 4.46828e+00 5.00373e-01
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H -1.08775e+00 4.97520e+00 -9.19116e-01
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O 4.05783e+00 1.60275e+00 5.43977e+00
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H 3.77971e+00 8.54369e-01 4.88435e+00
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H 3.60978e+00 2.35374e+00 5.13026e+00
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O 2.43776e+00 -4.99482e-02 -2.62072e+00
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H 2.86338e+00 7.11211e-01 -2.93717e+00
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H 2.97253e+00 -9.94903e-02 -1.85240e+00
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O 4.19163e+00 -2.28337e+00 2.65931e+00
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H 3.49022e+00 -2.92189e+00 2.61029e+00
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H 3.73537e+00 -1.55872e+00 3.12926e+00
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H -1.72968e+00 -3.08233e+00 -6.27425e-01
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H -2.10385e+00 -1.76017e+00 9.73129e-02
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O 1.92287e+00 4.27244e+00 -1.67407e+00
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H 1.42634e+00 4.25473e+00 -2.51279e+00
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H 1.78700e+00 3.41107e+00 -1.26398e+00
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O 6.28409e+00 -1.73525e+00 -2.82764e+00
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H 6.32088e+00 -1.00193e+00 -3.42952e+00
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H 6.46909e+00 -1.41869e+00 -1.98218e+00
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O 3.96284e+00 -7.23149e-01 2.62377e-01
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H 3.95229e+00 -1.25779e+00 1.05422e+00
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H 4.87913e+00 -4.01939e-01 1.95048e-01
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O 9.24235e-01 2.23061e+00 -8.61337e-02
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H 5.46549e-01 1.54775e+00 -6.38430e-01
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H 2.12575e-01 2.87202e+00 -1.31574e-01
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O 1.64438e+00 -2.72311e+00 -2.77752e+00
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H 2.38185e+00 -3.30116e+00 -2.65724e+00
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H 1.95524e+00 -1.77900e+00 -2.71436e+00
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O 1.01467e+00 8.09645e+00 4.79515e+00
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H 1.40914e+00 7.93303e+00 5.67457e+00
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H 3.79807e-01 8.78199e+00 4.90422e+00
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O 6.63510e+00 6.93406e-01 -4.01819e+00
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H 5.82622e+00 1.14584e+00 -4.34895e+00
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H 7.22563e+00 1.38179e+00 -3.64324e+00
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O 2.73534e+00 -3.36928e-01 3.71781e+00
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H 2.02189e+00 -8.16433e-01 4.17998e+00
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H 2.32360e+00 4.36506e-01 3.23950e+00
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O -3.08085e-01 2.74165e-01 4.50852e+00
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H -1.24172e+00 4.29215e-01 4.35617e+00
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H 1.60646e-02 5.09220e-01 3.66907e+00
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O 4.35545e+00 4.27341e+00 -5.80197e-01
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H 4.55787e+00 5.20015e+00 -3.80796e-01
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H 3.45005e+00 4.26144e+00 -8.93148e-01
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O 7.26921e+00 8.39629e-01 3.52705e+00
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H 7.01019e+00 8.49805e-01 4.43944e+00
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H 7.12670e+00 -1.23490e-01 3.43914e+00

‎examples/pet-mad-uq/environment.yml‎

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channels:
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- conda-forge
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dependencies:
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- python=3.12
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- pip
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- tqdm
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- matplotlib
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- pandas
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- pip:
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- ase
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- ipi>=3.1.5.1,<4
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- git+https://github.com/metatensor/metatrain.git
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- git+https://github.com/metatensor/metatomic.git
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