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NNP: Neural Network Potential force environment
Add implementation of Behler-Parrinello HD-NNPs Contributions by F. Brieuc, O. Marsalek, H. Forbert are acknowledged.
This commit is contained in:
Christoph Schran
GitHub
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54 changed files with 23876 additions and 26 deletions
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data/NNP/bulkH2O-jcp2020-cnnp/README.md
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data/NNP/bulkH2O-jcp2020-cnnp/README.md
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# Supplementary data for a paper on committee neural network potentials
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This directory contains NNP models from the following paper:
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Committee neural network potentials control generalization errors
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and enable active learning
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Christoph Schran, Kyrstof Brezina, and Ondrej Marsalek
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J. Chem. Phys. 153, 2020, DOI: [10.1063/5.0016004](
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https://doi.org/10.1063/5.0016004)
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arXiv: [2006.01541](https://arxiv.org/abs/2006.01541)
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## Contents
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* `nnp-1/2/3/4/5/6/7/8`
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All parameters of the C-NNP model from generation 4 of the active learning procedure.
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data/NNP/bulkH2O-jcp2020-cnnp/nnp-1/input.nn
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data/NNP/bulkH2O-jcp2020-cnnp/nnp-1/input.nn
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###############################################################################
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# GENERAL NNP SETTINGS
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###############################################################################
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# These keywords are (almost) always required.
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number_of_elements 2 # Number of elements.
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elements O H # Specification of elements.
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atom_energy O -74.94518524 # free atom reference energy (atomic zora)
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atom_energy H -0.45890771 # free atom reference energy (atomic zora)
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cutoff_type 2 # Cutoff type (optional argument: shift parameter alpha).
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scale_symmetry_functions # Scale all symmetry functions with min/max values.
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#scale_symmetry_functions_sigma # Scale all symmetry functions with sigma.
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scale_min_short 0.0 # Minimum value for scaling.
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scale_max_short 1.0 # Maximum value for scaling.
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center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value.
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global_hidden_layers_short 2 # Number of hidden layers.
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global_nodes_short 20 20 # Number of nodes in each hidden layer.
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global_activation_short t t l # Activation function for each hidden layer and output layer.
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#normalize_nodes # Normalize input of nodes.
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###############################################################################
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# ADDITIONAL SETTINGS FOR DATASET TOOLS
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###############################################################################
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# These keywords are used only by some tools handling data sets:
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# nnp-comp2, nnp-scaling, nnp-dataset, nnp-train.
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#use_short_forces # Use forces. Disable - repeated below.
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random_seed 0 # Random number generator seed.
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###############################################################################
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# ADDITIONAL SETTINGS FOR TRAINING
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###############################################################################
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# These keywords are solely used for training with nnp-train.
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epochs 100 # Number of training epochs.
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updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter).
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parallel_mode 1 # Training parallelization used (0 = Parallel (rank 0 update), 1 = Parallel (all update)).
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jacobian_mode 2 # Jacobian computation mode (0 = Summation to single gradient, 1 = Per-task summed gradient, 2 = Full Jacobian).
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update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element).
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selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold).
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task_batch_size_energy 1 # Number of energy update candidates prepared per task for each update (0 = Entire training set).
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task_batch_size_force 1 # Number of force update candidates prepared per task for each update (0 = Entire training set).
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memorize_symfunc_results # Keep symmetry function results in memory.
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test_fraction 0.1 # Fraction of structures kept for testing.
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use_short_forces # Use forces for training.
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force_weight 2.0 # Weight of force updates relative to energy updates.
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short_energy_fraction 1.0 # Fraction of energy updates per epoch.
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short_force_fraction 0.05 # Fraction of force updates per epoch.
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short_energy_error_threshold 0.8 # RMSE threshold for energy update candidates.
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short_force_error_threshold 1.0 # RMSE threshold for force update candidates.
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rmse_threshold_trials 3 # Maximum number of RMSE threshold trials.
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#use_old_weights_short # Restart fitting with old weight parameters.
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weights_min -1.0 # Minimum value for initial random weights.
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weights_max 1.0 # Maximum value for initial random weights.
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#precondition_weights # Precondition weights with initial energies.
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nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme.
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write_trainpoints 0 # Write energy comparison every this many epochs.
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write_trainforces 0 # Write force comparison every this many epochs.
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write_weights_epoch 1 # Write weights every this many epochs.
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write_neuronstats 0 # Write neuron statistics every this many epochs.
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#write_trainlog # Write training log file.
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############################
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# KALMAN FILTER (STANDARD) #
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############################
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kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory).
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kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001).
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kalman_q0 0.01 # General Kalman filter parameter q0 ("large").
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kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch).
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kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6).
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kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0).
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kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch).
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kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+).
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# Are these only for fading Kalman?
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kalman_lambda_short 0.98000
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kalman_nue_short 0.99870
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###############################################################################
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# SYMMETRY FUNCTIONS
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###############################################################################
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# INFO: symfunction format: reference atom, type, neighbor element 1 (and neighbor element 2), symfunction parameters
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#
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# radial
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#
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# central_atom type neighbor_atom eta rshift funccutoff
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# H H
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symfunction_short H 2 H 0.001 0.0 12.00
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symfunction_short H 2 H 0.01 0.0 12.00
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symfunction_short H 2 H 0.03 0.0 12.00
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symfunction_short H 2 H 0.06 0.0 12.00
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symfunction_short H 2 H 0.15 1.9 12.00
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symfunction_short H 2 H 0.30 1.9 12.00
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symfunction_short H 2 H 0.60 1.9 12.00
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symfunction_short H 2 H 1.50 1.9 12.00
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# H O / O H
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symfunction_short H 2 O 0.001 0.0 12.00
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symfunction_short H 2 O 0.01 0.0 12.00
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symfunction_short H 2 O 0.03 0.0 12.00
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symfunction_short H 2 O 0.06 0.0 12.00
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symfunction_short H 2 O 0.15 0.9 12.00
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symfunction_short H 2 O 0.30 0.9 12.00
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symfunction_short H 2 O 0.60 0.9 12.00
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symfunction_short H 2 O 1.50 0.9 12.00
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symfunction_short O 2 H 0.001 0.0 12.00
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symfunction_short O 2 H 0.01 0.0 12.00
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symfunction_short O 2 H 0.03 0.0 12.00
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symfunction_short O 2 H 0.06 0.0 12.00
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symfunction_short O 2 H 0.15 0.9 12.00
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symfunction_short O 2 H 0.30 0.9 12.00
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symfunction_short O 2 H 0.60 0.9 12.00
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symfunction_short O 2 H 1.50 0.9 12.00
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# O O
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symfunction_short O 2 O 0.001 0.0 12.00
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symfunction_short O 2 O 0.01 0.0 12.00
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symfunction_short O 2 O 0.03 0.0 12.00
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symfunction_short O 2 O 0.06 0.0 12.00
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symfunction_short O 2 O 0.15 4.0 12.00
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symfunction_short O 2 O 0.30 4.0 12.00
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symfunction_short O 2 O 0.60 4.0 12.00
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symfunction_short O 2 O 1.50 4.0 12.00
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#
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# angular
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#
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# central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 O H 0.2 1.0 1.0 12.00000
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symfunction_short O 3 H H 0.07 1.0 1.0 12.00000
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symfunction_short H 3 O H 0.07 1.0 1.0 12.00000
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symfunction_short O 3 H H 0.07 -1.0 1.0 12.00000
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symfunction_short H 3 O H 0.07 -1.0 1.0 12.00000
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symfunction_short O 3 H H 0.03 1.0 1.0 12.00000
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symfunction_short H 3 O H 0.03 1.0 1.0 12.00000
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symfunction_short O 3 H H 0.03 -1.0 1.0 12.00000
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symfunction_short H 3 O H 0.03 -1.0 1.0 12.00000
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symfunction_short O 3 H H 0.01 1.0 4.0 12.00000
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symfunction_short H 3 O H 0.01 1.0 4.0 12.00000
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symfunction_short O 3 H H 0.01 -1.0 4.0 12.00000
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symfunction_short H 3 O H 0.01 -1.0 4.0 12.00000
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symfunction_short O 3 O H 0.03 1.0 1.0 12.00000
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symfunction_short O 3 O H 0.03 -1.0 1.0 12.00000
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symfunction_short O 3 O H 0.001 1.0 4.0 12.00000
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symfunction_short O 3 O H 0.001 -1.0 4.0 12.00000
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symfunction_short H 3 O O 0.03 1.0 1.0 12.00000
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symfunction_short H 3 O O 0.03 -1.0 1.0 12.00000
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symfunction_short H 3 O O 0.001 1.0 4.0 12.00000
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symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000
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symfunction_short O 3 O O 0.03 1.0 1.0 12.00000
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symfunction_short O 3 O O 0.03 -1.0 1.0 12.00000
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symfunction_short O 3 O O 0.001 1.0 4.0 12.00000
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symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000
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data/NNP/bulkH2O-jcp2020-cnnp/nnp-1/scaling.data
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################################################################################
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# Symmetry function scaling data.
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################################################################################
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# Col Name Description
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################################################################################
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# 1 e_index Element index.
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# 2 sf_index Symmetry function index.
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# 3 sf_min Symmetry function minimum.
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# 4 sf_max Symmetry function maximum.
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# 5 sf_mean Symmetry function mean.
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# 6 sf_sigma Symmetry function sigma.
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#########################################################################################################################
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# 1 2 3 4 5 6
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# e_index sf_index sf_min sf_max sf_mean sf_sigma
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#########################################################################################################################
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1 1 2.8655329382224032E-01 3.6364355962665180E+00 2.2119784681576431E+00 3.8982164788327173E-01
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1 2 3.5699082862581144E-01 2.0031124569208267E+00 1.2994521098968692E+00 1.9314919398540351E-01
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1 3 2.4253583906212917E-01 2.6983010627072188E+00 1.6071345237783108E+00 2.8699477114002836E-01
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1 4 3.3542904629093495E-01 1.5372546465126264E+00 9.9744101045215550E-01 1.4138420759837253E-01
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1 5 1.8503709795923420E-01 1.5491787211705357E+00 8.9011559742158242E-01 1.6054085816869779E-01
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1 6 2.8986050983056133E-01 9.5851457739199852E-01 6.4070535049617816E-01 7.7829435282263632E-02
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1 7 1.2998738560021622E-01 8.1181447628465786E-01 4.5034968386667112E-01 7.9668681985812853E-02
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1 8 2.3854599156072026E-01 5.8192272360200603E-01 4.2158764571359919E-01 4.0539426354469568E-02
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1 9 2.2019401469736052E-01 4.9816927636901054E-01 3.6305272944627820E-01 3.1419040668322185E-02
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1 10 1.7723908244726444E-01 1.0169045685317621E+00 5.3120597962909666E-01 9.6163510042362274E-02
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1 11 1.5931165210644979E-01 3.9224005962648778E-01 2.7312983872261626E-01 2.0878706459593787E-02
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1 12 1.0106474384096639E-01 6.8318193294241025E-01 2.9555524220090679E-01 5.2779720067392157E-02
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1 13 7.4340659297091619E-02 3.2028897659649835E-01 1.9454657712167572E-01 2.2645835164129727E-02
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1 14 2.7867297613902112E-02 4.8859027683498957E-01 1.5882253801165483E-01 3.7102407780211344E-02
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1 15 6.0765964821426774E-03 2.6933341009926554E-01 8.7030393842343720E-02 2.3954982883266532E-02
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1 16 8.6176614291566273E-04 3.2616869984647917E-01 5.8437222538056915E-02 3.2524425477896177E-02
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1 17 2.3905486661473520E-08 3.7621880078986758E-02 1.7099399409671343E-02 5.6190834887742307E-03
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1 18 5.7485161297593659E-05 5.6704347475877770E-02 2.0751242479452557E-02 7.2790207725133855E-03
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1 19 3.7937631629716383E-06 4.4789516076805022E-02 1.6338823698108001E-02 5.6967712606260726E-03
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1 20 2.4960312085019903E-02 2.7218197030245517E-01 1.3743696285440943E-01 2.8868015901656875E-02
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1 21 2.2980773998953256E-03 4.9986220828384470E-02 1.6950824167726739E-02 5.4132966616365161E-03
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1 22 2.0814361457387778E-07 1.7422614782322748E-02 5.8877295715452881E-03 2.3169759281881160E-03
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1 23 2.3616425302076981E-02 1.4766564930840750E-01 7.8026009579545141E-02 1.4328402520229913E-02
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1 24 9.3734209417262540E-06 1.2706009724968383E-02 3.8602266983488228E-03 1.5349222936123124E-03
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1 25 6.7292482219397467E-04 1.3437347615997143E-02 3.5879997188162024E-03 1.0083099406231295E-03
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1 26 8.9492218473814448E-03 4.7435519247870893E-02 2.4574480321592800E-02 3.7562620321718062E-03
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1 27 2.9688834832940051E-04 1.0922315444849038E-02 2.4362779164791831E-03 7.5891040984896283E-04
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2 1 7.1532528297088083E-01 4.0098976770174595E+00 2.5989042197937424E+00 3.8240252948889814E-01
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2 2 5.6301628567420527E-02 1.6234842194053070E+00 9.3805754679203801E-01 1.8736449645837872E-01
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2 3 6.5703695712707699E-01 3.0791315022675048E+00 1.9948820209043090E+00 2.7857971836047618E-01
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2 4 3.1024606077905838E-02 1.1551308858105025E+00 6.4059931260962955E-01 1.3511922517043573E-01
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2 5 5.8421509973169194E-01 1.9420240206857451E+00 1.2814107009923557E+00 1.5028032758627546E-01
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2 6 8.7055091560538176E-03 5.7824321471805962E-01 2.9826715576421964E-01 6.8317345917309091E-02
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2 7 4.9061923640751393E-01 1.1928444832852640E+00 8.4317529142720038E-01 7.3313958696524129E-02
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2 8 1.4113901292375167E-03 2.2139468783209257E-01 1.0800688415169929E-01 2.7030088273230075E-02
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2 9 4.9849874092941715E-01 9.8733752198909885E-01 7.2610545889255584E-01 5.0426765272667665E-02
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2 10 6.2957062567264221E-03 9.5794186401597337E-01 4.6455014321576582E-01 1.1560059533210541E-01
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2 11 3.6577588459988464E-01 7.7230200150326977E-01 5.4625967744523274E-01 3.4592870857204361E-02
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2 12 8.7085544804932510E-04 6.5807276191584230E-01 3.0944891033609334E-01 8.5000814741670302E-02
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2 13 1.8948992752075242E-01 5.7888624801215693E-01 3.8909315424335073E-01 3.4526650397124353E-02
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2 14 1.5622199228642329E-05 4.9780490905368319E-01 1.6953376146057866E-01 6.2315791454946173E-02
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2 15 3.3004285384528591E-02 4.0762166080748574E-01 1.7406078768468747E-01 3.4501395384273312E-02
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2 16 1.0729012446445082E-10 2.7047079448224992E-01 4.4653384790197932E-02 3.1107465231072717E-02
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2 17 1.0846205849416071E-05 3.9543401427987353E-02 1.5074459823996014E-02 4.7702333660869338E-03
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2 18 7.4829063908554593E-11 2.5884908058550057E-03 6.5717634939948741E-04 3.2655127951476974E-04
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2 19 3.6205850570885452E-03 4.3221294145342604E-01 1.8756542069538726E-01 5.3162621310716140E-02
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2 20 3.8440097917265245E-07 3.6534575078121363E-02 9.8772821155134766E-03 5.2062500369707458E-03
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2 21 2.6911400517410067E-03 6.4611970894949161E-02 2.9305443392707006E-02 6.1496063694629561E-03
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2 22 1.2827584708500362E-03 1.7529487759454226E-01 6.8509716444031324E-02 2.2077211658804222E-02
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2 23 1.5545977333502778E-02 9.9331349879191635E-02 4.7998454143224914E-02 8.6592611829803771E-03
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2 24 1.5745634781781375E-05 1.9308534172604155E-02 6.0894070240362346E-03 2.3678290544763931E-03
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2 25 8.5856663153437229E-11 1.3944217824039388E-03 2.2274994125481316E-04 1.8366900313163595E-04
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2 26 9.1829498430736033E-03 1.1557634414039414E-01 4.6978379604047091E-02 1.2100545333930842E-02
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2 27 1.7898602665033226E-04 8.1694699794021677E-02 3.2902418055540193E-02 9.9562973177386334E-03
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2 28 7.4320386544780976E-10 3.9418035349310827E-03 6.3479370917995861E-04 5.2607016457668443E-04
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2 29 6.3415719088815280E-03 3.9243185159612948E-02 1.6708820854971284E-02 2.8310386784518786E-03
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2 30 2.8195782382410411E-03 3.2846540596866002E-02 1.1453659185437720E-02 2.6398096406069294E-03
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Normal file
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-2/input.nn
Normal file
|
|
@ -0,0 +1,165 @@
|
|||
###############################################################################
|
||||
# GENERAL NNP SETTINGS
|
||||
###############################################################################
|
||||
# These keywords are (almost) always required.
|
||||
number_of_elements 2 # Number of elements.
|
||||
elements O H # Specification of elements.
|
||||
atom_energy O -74.94518524 # free atom reference energy (atomic zora)
|
||||
atom_energy H -0.45890771 # free atom reference energy (atomic zora)
|
||||
cutoff_type 2 # Cutoff type (optional argument: shift parameter alpha).
|
||||
scale_symmetry_functions # Scale all symmetry functions with min/max values.
|
||||
#scale_symmetry_functions_sigma # Scale all symmetry functions with sigma.
|
||||
scale_min_short 0.0 # Minimum value for scaling.
|
||||
scale_max_short 1.0 # Maximum value for scaling.
|
||||
center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value.
|
||||
global_hidden_layers_short 2 # Number of hidden layers.
|
||||
global_nodes_short 20 20 # Number of nodes in each hidden layer.
|
||||
global_activation_short t t l # Activation function for each hidden layer and output layer.
|
||||
#normalize_nodes # Normalize input of nodes.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR DATASET TOOLS
|
||||
###############################################################################
|
||||
# These keywords are used only by some tools handling data sets:
|
||||
# nnp-comp2, nnp-scaling, nnp-dataset, nnp-train.
|
||||
#use_short_forces # Use forces. Disable - repeated below.
|
||||
random_seed 1 # Random number generator seed.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR TRAINING
|
||||
###############################################################################
|
||||
# These keywords are solely used for training with nnp-train.
|
||||
epochs 100 # Number of training epochs.
|
||||
updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter).
|
||||
parallel_mode 1 # Training parallelization used (0 = Parallel (rank 0 update), 1 = Parallel (all update)).
|
||||
jacobian_mode 2 # Jacobian computation mode (0 = Summation to single gradient, 1 = Per-task summed gradient, 2 = Full Jacobian).
|
||||
update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element).
|
||||
selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold).
|
||||
task_batch_size_energy 1 # Number of energy update candidates prepared per task for each update (0 = Entire training set).
|
||||
task_batch_size_force 1 # Number of force update candidates prepared per task for each update (0 = Entire training set).
|
||||
memorize_symfunc_results # Keep symmetry function results in memory.
|
||||
test_fraction 0.1 # Fraction of structures kept for testing.
|
||||
use_short_forces # Use forces for training.
|
||||
force_weight 2.0 # Weight of force updates relative to energy updates.
|
||||
short_energy_fraction 1.0 # Fraction of energy updates per epoch.
|
||||
short_force_fraction 0.05 # Fraction of force updates per epoch.
|
||||
short_energy_error_threshold 0.8 # RMSE threshold for energy update candidates.
|
||||
short_force_error_threshold 1.0 # RMSE threshold for force update candidates.
|
||||
rmse_threshold_trials 3 # Maximum number of RMSE threshold trials.
|
||||
#use_old_weights_short # Restart fitting with old weight parameters.
|
||||
weights_min -1.0 # Minimum value for initial random weights.
|
||||
weights_max 1.0 # Maximum value for initial random weights.
|
||||
#precondition_weights # Precondition weights with initial energies.
|
||||
nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme.
|
||||
write_trainpoints 0 # Write energy comparison every this many epochs.
|
||||
write_trainforces 0 # Write force comparison every this many epochs.
|
||||
write_weights_epoch 1 # Write weights every this many epochs.
|
||||
write_neuronstats 0 # Write neuron statistics every this many epochs.
|
||||
#write_trainlog # Write training log file.
|
||||
|
||||
############################
|
||||
# KALMAN FILTER (STANDARD) #
|
||||
############################
|
||||
kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory).
|
||||
kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001).
|
||||
kalman_q0 0.01 # General Kalman filter parameter q0 ("large").
|
||||
kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6).
|
||||
kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0).
|
||||
kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+).
|
||||
|
||||
# Are these only for fading Kalman?
|
||||
kalman_lambda_short 0.98000
|
||||
kalman_nue_short 0.99870
|
||||
|
||||
|
||||
|
||||
###############################################################################
|
||||
# SYMMETRY FUNCTIONS
|
||||
###############################################################################
|
||||
|
||||
# INFO: symfunction format: reference atom, type, neighbor element 1 (and neighbor element 2), symfunction parameters
|
||||
|
||||
|
||||
#
|
||||
# radial
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom eta rshift funccutoff
|
||||
|
||||
# H H
|
||||
symfunction_short H 2 H 0.001 0.0 12.00
|
||||
symfunction_short H 2 H 0.01 0.0 12.00
|
||||
symfunction_short H 2 H 0.03 0.0 12.00
|
||||
symfunction_short H 2 H 0.06 0.0 12.00
|
||||
symfunction_short H 2 H 0.15 1.9 12.00
|
||||
symfunction_short H 2 H 0.30 1.9 12.00
|
||||
symfunction_short H 2 H 0.60 1.9 12.00
|
||||
symfunction_short H 2 H 1.50 1.9 12.00
|
||||
|
||||
# H O / O H
|
||||
symfunction_short H 2 O 0.001 0.0 12.00
|
||||
symfunction_short H 2 O 0.01 0.0 12.00
|
||||
symfunction_short H 2 O 0.03 0.0 12.00
|
||||
symfunction_short H 2 O 0.06 0.0 12.00
|
||||
symfunction_short H 2 O 0.15 0.9 12.00
|
||||
symfunction_short H 2 O 0.30 0.9 12.00
|
||||
symfunction_short H 2 O 0.60 0.9 12.00
|
||||
symfunction_short H 2 O 1.50 0.9 12.00
|
||||
symfunction_short O 2 H 0.001 0.0 12.00
|
||||
symfunction_short O 2 H 0.01 0.0 12.00
|
||||
symfunction_short O 2 H 0.03 0.0 12.00
|
||||
symfunction_short O 2 H 0.06 0.0 12.00
|
||||
symfunction_short O 2 H 0.15 0.9 12.00
|
||||
symfunction_short O 2 H 0.30 0.9 12.00
|
||||
symfunction_short O 2 H 0.60 0.9 12.00
|
||||
symfunction_short O 2 H 1.50 0.9 12.00
|
||||
|
||||
# O O
|
||||
symfunction_short O 2 O 0.001 0.0 12.00
|
||||
symfunction_short O 2 O 0.01 0.0 12.00
|
||||
symfunction_short O 2 O 0.03 0.0 12.00
|
||||
symfunction_short O 2 O 0.06 0.0 12.00
|
||||
symfunction_short O 2 O 0.15 4.0 12.00
|
||||
symfunction_short O 2 O 0.30 4.0 12.00
|
||||
symfunction_short O 2 O 0.60 4.0 12.00
|
||||
symfunction_short O 2 O 1.50 4.0 12.00
|
||||
|
||||
#
|
||||
# angular
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
|
||||
|
||||
symfunction_short H 3 O H 0.2 1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.07 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short O 3 H H 0.01 -1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short H 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000
|
||||
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-2/scaling.data
Normal file
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-2/scaling.data
Normal file
|
|
@ -0,0 +1,72 @@
|
|||
################################################################################
|
||||
# Symmetry function scaling data.
|
||||
################################################################################
|
||||
# Col Name Description
|
||||
################################################################################
|
||||
# 1 e_index Element index.
|
||||
# 2 sf_index Symmetry function index.
|
||||
# 3 sf_min Symmetry function minimum.
|
||||
# 4 sf_max Symmetry function maximum.
|
||||
# 5 sf_mean Symmetry function mean.
|
||||
# 6 sf_sigma Symmetry function sigma.
|
||||
#########################################################################################################################
|
||||
# 1 2 3 4 5 6
|
||||
# e_index sf_index sf_min sf_max sf_mean sf_sigma
|
||||
#########################################################################################################################
|
||||
1 1 2.8655329382224032E-01 3.6364355962665180E+00 2.2119784681576440E+00 3.8982164788327173E-01
|
||||
1 2 3.5699082862581144E-01 2.0031124569208267E+00 1.2994521098968697E+00 1.9314919398539723E-01
|
||||
1 3 2.4253583906212917E-01 2.6983010627072188E+00 1.6071345237783108E+00 2.8699477114002342E-01
|
||||
1 4 3.3542904629093495E-01 1.5372546465126264E+00 9.9744101045215572E-01 1.4138420759836895E-01
|
||||
1 5 1.8503709795923420E-01 1.5491787211705357E+00 8.9011559742158053E-01 1.6054085816871039E-01
|
||||
1 6 2.8986050983056133E-01 9.5851457739199852E-01 6.4070535049617849E-01 7.7829435282258760E-02
|
||||
1 7 1.2998738560021622E-01 8.1181447628465786E-01 4.5034968386667079E-01 7.9668681985814283E-02
|
||||
1 8 2.3854599156072026E-01 5.8192272360200603E-01 4.2158764571359891E-01 4.0539426354475487E-02
|
||||
1 9 2.2019401469736052E-01 4.9816927636901054E-01 3.6305272944627803E-01 3.1419040668323392E-02
|
||||
1 10 1.7723908244726444E-01 1.0169045685317621E+00 5.3120597962909566E-01 9.6163510042366215E-02
|
||||
1 11 1.5931165210644979E-01 3.9224005962648778E-01 2.7312983872261587E-01 2.0878706459600438E-02
|
||||
1 12 1.0106474384096639E-01 6.8318193294241025E-01 2.9555524220090662E-01 5.2779720067393711E-02
|
||||
1 13 7.4340659297091619E-02 3.2028897659649835E-01 1.9454657712167572E-01 2.2645835164128471E-02
|
||||
1 14 2.7867297613902112E-02 4.8859027683498957E-01 1.5882253801165500E-01 3.7102407780210490E-02
|
||||
1 15 6.0765964821426774E-03 2.6933341009926554E-01 8.7030393842343706E-02 2.3954982883266532E-02
|
||||
1 16 8.6176614291566273E-04 3.2616869984647917E-01 5.8437222538056915E-02 3.2524425477896114E-02
|
||||
1 17 2.3905486661473520E-08 3.7621880078986758E-02 1.7099399409671322E-02 5.6190834887742793E-03
|
||||
1 18 5.7485161297593659E-05 5.6704347475877770E-02 2.0751242479452550E-02 7.2790207725134228E-03
|
||||
1 19 3.7937631629716383E-06 4.4789516076805022E-02 1.6338823698108018E-02 5.6967712606260336E-03
|
||||
1 20 2.4960312085019903E-02 2.7218197030245517E-01 1.3743696285440926E-01 2.8868015901657586E-02
|
||||
1 21 2.2980773998953256E-03 4.9986220828384470E-02 1.6950824167726763E-02 5.4132966616364199E-03
|
||||
1 22 2.0814361457387778E-07 1.7422614782322748E-02 5.8877295715452924E-03 2.3169759281881212E-03
|
||||
1 23 2.3616425302076981E-02 1.4766564930840750E-01 7.8026009579545155E-02 1.4328402520229969E-02
|
||||
1 24 9.3734209417262540E-06 1.2706009724968383E-02 3.8602266983488289E-03 1.5349222936122914E-03
|
||||
1 25 6.7292482219397467E-04 1.3437347615997143E-02 3.5879997188162033E-03 1.0083099406231308E-03
|
||||
1 26 8.9492218473814448E-03 4.7435519247870893E-02 2.4574480321592814E-02 3.7562620321716618E-03
|
||||
1 27 2.9688834832940051E-04 1.0922315444849038E-02 2.4362779164791822E-03 7.5891040984896326E-04
|
||||
2 1 7.1532528297088083E-01 4.0098976770174595E+00 2.5989042197937433E+00 3.8240252948889386E-01
|
||||
2 2 5.6301628567420527E-02 1.6234842194053070E+00 9.3805754679203734E-01 1.8736449645838005E-01
|
||||
2 3 6.5703695712707699E-01 3.0791315022675048E+00 1.9948820209043110E+00 2.7857971836046458E-01
|
||||
2 4 3.1024606077905838E-02 1.1551308858105025E+00 6.4059931260962955E-01 1.3511922517043537E-01
|
||||
2 5 5.8421509973169194E-01 1.9420240206857451E+00 1.2814107009923548E+00 1.5028032758628354E-01
|
||||
2 6 8.7055091560538176E-03 5.7824321471805962E-01 2.9826715576421992E-01 6.8317345917307606E-02
|
||||
2 7 4.9061923640751393E-01 1.1928444832852640E+00 8.4317529142720082E-01 7.3313958696518619E-02
|
||||
2 8 1.4113901292375167E-03 2.2139468783209257E-01 1.0800688415169923E-01 2.7030088273230429E-02
|
||||
2 9 4.9849874092941715E-01 9.8733752198909885E-01 7.2610545889255551E-01 5.0426765272681688E-02
|
||||
2 10 6.2957062567264221E-03 9.5794186401597337E-01 4.6455014321576632E-01 1.1560059533210344E-01
|
||||
2 11 3.6577588459988464E-01 7.7230200150326977E-01 5.4625967744523196E-01 3.4592870857221875E-02
|
||||
2 12 8.7085544804932510E-04 6.5807276191584230E-01 3.0944891033609345E-01 8.5000814741670302E-02
|
||||
2 13 1.8948992752075242E-01 5.7888624801215693E-01 3.8909315424335078E-01 3.4526650397123625E-02
|
||||
2 14 1.5622199228642329E-05 4.9780490905368319E-01 1.6953376146057880E-01 6.2315791454945715E-02
|
||||
2 15 3.3004285384528591E-02 4.0762166080748574E-01 1.7406078768468741E-01 3.4501395384273402E-02
|
||||
2 16 1.0729012446445082E-10 2.7047079448224992E-01 4.4653384790197967E-02 3.1107465231072679E-02
|
||||
2 17 1.0846205849416071E-05 3.9543401427987353E-02 1.5074459823996007E-02 4.7702333660869702E-03
|
||||
2 18 7.4829063908554593E-11 2.5884908058550057E-03 6.5717634939948828E-04 3.2655127951476811E-04
|
||||
2 19 3.6205850570885452E-03 4.3221294145342604E-01 1.8756542069538726E-01 5.3162621310716023E-02
|
||||
2 20 3.8440097917265245E-07 3.6534575078121363E-02 9.8772821155134697E-03 5.2062500369707615E-03
|
||||
2 21 2.6911400517410067E-03 6.4611970894949161E-02 2.9305443392707037E-02 6.1496063694628442E-03
|
||||
2 22 1.2827584708500362E-03 1.7529487759454226E-01 6.8509716444031282E-02 2.2077211658804313E-02
|
||||
2 23 1.5545977333502778E-02 9.9331349879191635E-02 4.7998454143224949E-02 8.6592611829803094E-03
|
||||
2 24 1.5745634781781375E-05 1.9308534172604155E-02 6.0894070240362363E-03 2.3678290544763879E-03
|
||||
2 25 8.5856663153437229E-11 1.3944217824039388E-03 2.2274994125481316E-04 1.8366900313163595E-04
|
||||
2 26 9.1829498430736033E-03 1.1557634414039414E-01 4.6978379604047077E-02 1.2100545333930924E-02
|
||||
2 27 1.7898602665033226E-04 8.1694699794021677E-02 3.2902418055540193E-02 9.9562973177386438E-03
|
||||
2 28 7.4320386544780976E-10 3.9418035349310827E-03 6.3479370917995850E-04 5.2607016457668486E-04
|
||||
2 29 6.3415719088815280E-03 3.9243185159612948E-02 1.6708820854971287E-02 2.8310386784518439E-03
|
||||
2 30 2.8195782382410411E-03 3.2846540596866002E-02 1.1453659185437727E-02 2.6398096406069294E-03
|
||||
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-2/weights.001.data
Normal file
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-2/weights.001.data
Normal file
File diff suppressed because it is too large
Load diff
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-2/weights.008.data
Normal file
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-2/weights.008.data
Normal file
File diff suppressed because it is too large
Load diff
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-3/input.nn
Normal file
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-3/input.nn
Normal file
|
|
@ -0,0 +1,165 @@
|
|||
###############################################################################
|
||||
# GENERAL NNP SETTINGS
|
||||
###############################################################################
|
||||
# These keywords are (almost) always required.
|
||||
number_of_elements 2 # Number of elements.
|
||||
elements O H # Specification of elements.
|
||||
atom_energy O -74.94518524 # free atom reference energy (atomic zora)
|
||||
atom_energy H -0.45890771 # free atom reference energy (atomic zora)
|
||||
cutoff_type 2 # Cutoff type (optional argument: shift parameter alpha).
|
||||
scale_symmetry_functions # Scale all symmetry functions with min/max values.
|
||||
#scale_symmetry_functions_sigma # Scale all symmetry functions with sigma.
|
||||
scale_min_short 0.0 # Minimum value for scaling.
|
||||
scale_max_short 1.0 # Maximum value for scaling.
|
||||
center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value.
|
||||
global_hidden_layers_short 2 # Number of hidden layers.
|
||||
global_nodes_short 20 20 # Number of nodes in each hidden layer.
|
||||
global_activation_short t t l # Activation function for each hidden layer and output layer.
|
||||
#normalize_nodes # Normalize input of nodes.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR DATASET TOOLS
|
||||
###############################################################################
|
||||
# These keywords are used only by some tools handling data sets:
|
||||
# nnp-comp2, nnp-scaling, nnp-dataset, nnp-train.
|
||||
#use_short_forces # Use forces. Disable - repeated below.
|
||||
random_seed 2 # Random number generator seed.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR TRAINING
|
||||
###############################################################################
|
||||
# These keywords are solely used for training with nnp-train.
|
||||
epochs 100 # Number of training epochs.
|
||||
updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter).
|
||||
parallel_mode 1 # Training parallelization used (0 = Parallel (rank 0 update), 1 = Parallel (all update)).
|
||||
jacobian_mode 2 # Jacobian computation mode (0 = Summation to single gradient, 1 = Per-task summed gradient, 2 = Full Jacobian).
|
||||
update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element).
|
||||
selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold).
|
||||
task_batch_size_energy 1 # Number of energy update candidates prepared per task for each update (0 = Entire training set).
|
||||
task_batch_size_force 1 # Number of force update candidates prepared per task for each update (0 = Entire training set).
|
||||
memorize_symfunc_results # Keep symmetry function results in memory.
|
||||
test_fraction 0.1 # Fraction of structures kept for testing.
|
||||
use_short_forces # Use forces for training.
|
||||
force_weight 2.0 # Weight of force updates relative to energy updates.
|
||||
short_energy_fraction 1.0 # Fraction of energy updates per epoch.
|
||||
short_force_fraction 0.05 # Fraction of force updates per epoch.
|
||||
short_energy_error_threshold 0.8 # RMSE threshold for energy update candidates.
|
||||
short_force_error_threshold 1.0 # RMSE threshold for force update candidates.
|
||||
rmse_threshold_trials 3 # Maximum number of RMSE threshold trials.
|
||||
#use_old_weights_short # Restart fitting with old weight parameters.
|
||||
weights_min -1.0 # Minimum value for initial random weights.
|
||||
weights_max 1.0 # Maximum value for initial random weights.
|
||||
#precondition_weights # Precondition weights with initial energies.
|
||||
nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme.
|
||||
write_trainpoints 0 # Write energy comparison every this many epochs.
|
||||
write_trainforces 0 # Write force comparison every this many epochs.
|
||||
write_weights_epoch 1 # Write weights every this many epochs.
|
||||
write_neuronstats 0 # Write neuron statistics every this many epochs.
|
||||
#write_trainlog # Write training log file.
|
||||
|
||||
############################
|
||||
# KALMAN FILTER (STANDARD) #
|
||||
############################
|
||||
kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory).
|
||||
kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001).
|
||||
kalman_q0 0.01 # General Kalman filter parameter q0 ("large").
|
||||
kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6).
|
||||
kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0).
|
||||
kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+).
|
||||
|
||||
# Are these only for fading Kalman?
|
||||
kalman_lambda_short 0.98000
|
||||
kalman_nue_short 0.99870
|
||||
|
||||
|
||||
|
||||
###############################################################################
|
||||
# SYMMETRY FUNCTIONS
|
||||
###############################################################################
|
||||
|
||||
# INFO: symfunction format: reference atom, type, neighbor element 1 (and neighbor element 2), symfunction parameters
|
||||
|
||||
|
||||
#
|
||||
# radial
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom eta rshift funccutoff
|
||||
|
||||
# H H
|
||||
symfunction_short H 2 H 0.001 0.0 12.00
|
||||
symfunction_short H 2 H 0.01 0.0 12.00
|
||||
symfunction_short H 2 H 0.03 0.0 12.00
|
||||
symfunction_short H 2 H 0.06 0.0 12.00
|
||||
symfunction_short H 2 H 0.15 1.9 12.00
|
||||
symfunction_short H 2 H 0.30 1.9 12.00
|
||||
symfunction_short H 2 H 0.60 1.9 12.00
|
||||
symfunction_short H 2 H 1.50 1.9 12.00
|
||||
|
||||
# H O / O H
|
||||
symfunction_short H 2 O 0.001 0.0 12.00
|
||||
symfunction_short H 2 O 0.01 0.0 12.00
|
||||
symfunction_short H 2 O 0.03 0.0 12.00
|
||||
symfunction_short H 2 O 0.06 0.0 12.00
|
||||
symfunction_short H 2 O 0.15 0.9 12.00
|
||||
symfunction_short H 2 O 0.30 0.9 12.00
|
||||
symfunction_short H 2 O 0.60 0.9 12.00
|
||||
symfunction_short H 2 O 1.50 0.9 12.00
|
||||
symfunction_short O 2 H 0.001 0.0 12.00
|
||||
symfunction_short O 2 H 0.01 0.0 12.00
|
||||
symfunction_short O 2 H 0.03 0.0 12.00
|
||||
symfunction_short O 2 H 0.06 0.0 12.00
|
||||
symfunction_short O 2 H 0.15 0.9 12.00
|
||||
symfunction_short O 2 H 0.30 0.9 12.00
|
||||
symfunction_short O 2 H 0.60 0.9 12.00
|
||||
symfunction_short O 2 H 1.50 0.9 12.00
|
||||
|
||||
# O O
|
||||
symfunction_short O 2 O 0.001 0.0 12.00
|
||||
symfunction_short O 2 O 0.01 0.0 12.00
|
||||
symfunction_short O 2 O 0.03 0.0 12.00
|
||||
symfunction_short O 2 O 0.06 0.0 12.00
|
||||
symfunction_short O 2 O 0.15 4.0 12.00
|
||||
symfunction_short O 2 O 0.30 4.0 12.00
|
||||
symfunction_short O 2 O 0.60 4.0 12.00
|
||||
symfunction_short O 2 O 1.50 4.0 12.00
|
||||
|
||||
#
|
||||
# angular
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
|
||||
|
||||
symfunction_short H 3 O H 0.2 1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.07 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short O 3 H H 0.01 -1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short H 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000
|
||||
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-3/scaling.data
Normal file
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-3/scaling.data
Normal file
|
|
@ -0,0 +1,72 @@
|
|||
################################################################################
|
||||
# Symmetry function scaling data.
|
||||
################################################################################
|
||||
# Col Name Description
|
||||
################################################################################
|
||||
# 1 e_index Element index.
|
||||
# 2 sf_index Symmetry function index.
|
||||
# 3 sf_min Symmetry function minimum.
|
||||
# 4 sf_max Symmetry function maximum.
|
||||
# 5 sf_mean Symmetry function mean.
|
||||
# 6 sf_sigma Symmetry function sigma.
|
||||
#########################################################################################################################
|
||||
# 1 2 3 4 5 6
|
||||
# e_index sf_index sf_min sf_max sf_mean sf_sigma
|
||||
#########################################################################################################################
|
||||
1 1 2.8655329382224032E-01 3.6364355962665180E+00 2.2119784681576449E+00 3.8982164788326240E-01
|
||||
1 2 3.5699082862581144E-01 2.0031124569208267E+00 1.2994521098968692E+00 1.9314919398540142E-01
|
||||
1 3 2.4253583906212917E-01 2.6983010627072188E+00 1.6071345237783119E+00 2.8699477114001992E-01
|
||||
1 4 3.3542904629093495E-01 1.5372546465126264E+00 9.9744101045215283E-01 1.4138420759839751E-01
|
||||
1 5 1.8503709795923420E-01 1.5491787211705357E+00 8.9011559742158031E-01 1.6054085816870911E-01
|
||||
1 6 2.8986050983056133E-01 9.5851457739199852E-01 6.4070535049617972E-01 7.7829435282249032E-02
|
||||
1 7 1.2998738560021622E-01 8.1181447628465786E-01 4.5034968386667051E-01 7.9668681985816017E-02
|
||||
1 8 2.3854599156072026E-01 5.8192272360200603E-01 4.2158764571359936E-01 4.0539426354468014E-02
|
||||
1 9 2.2019401469736052E-01 4.9816927636901054E-01 3.6305272944627826E-01 3.1419040668321782E-02
|
||||
1 10 1.7723908244726444E-01 1.0169045685317621E+00 5.3120597962909666E-01 9.6163510042361747E-02
|
||||
1 11 1.5931165210644979E-01 3.9224005962648778E-01 2.7312983872261604E-01 2.0878706459596507E-02
|
||||
1 12 1.0106474384096639E-01 6.8318193294241025E-01 2.9555524220090673E-01 5.2779720067392989E-02
|
||||
1 13 7.4340659297091619E-02 3.2028897659649835E-01 1.9454657712167572E-01 2.2645835164129727E-02
|
||||
1 14 2.7867297613902112E-02 4.8859027683498957E-01 1.5882253801165511E-01 3.7102407780210109E-02
|
||||
1 15 6.0765964821426774E-03 2.6933341009926554E-01 8.7030393842343706E-02 2.3954982883266761E-02
|
||||
1 16 8.6176614291566273E-04 3.2616869984647917E-01 5.8437222538056957E-02 3.2524425477896191E-02
|
||||
1 17 2.3905486661473520E-08 3.7621880078986758E-02 1.7099399409671336E-02 5.6190834887742697E-03
|
||||
1 18 5.7485161297593659E-05 5.6704347475877770E-02 2.0751242479452564E-02 7.2790207725133924E-03
|
||||
1 19 3.7937631629716383E-06 4.4789516076805022E-02 1.6338823698107997E-02 5.6967712606260899E-03
|
||||
1 20 2.4960312085019903E-02 2.7218197030245517E-01 1.3743696285440929E-01 2.8868015901657697E-02
|
||||
1 21 2.2980773998953256E-03 4.9986220828384470E-02 1.6950824167726752E-02 5.4132966616364294E-03
|
||||
1 22 2.0814361457387778E-07 1.7422614782322748E-02 5.8877295715452924E-03 2.3169759281881082E-03
|
||||
1 23 2.3616425302076981E-02 1.4766564930840750E-01 7.8026009579545266E-02 1.4328402520229419E-02
|
||||
1 24 9.3734209417262540E-06 1.2706009724968383E-02 3.8602266983488258E-03 1.5349222936123044E-03
|
||||
1 25 6.7292482219397467E-04 1.3437347615997143E-02 3.5879997188162024E-03 1.0083099406231325E-03
|
||||
1 26 8.9492218473814448E-03 4.7435519247870893E-02 2.4574480321592790E-02 3.7562620321718982E-03
|
||||
1 27 2.9688834832940051E-04 1.0922315444849038E-02 2.4362779164791831E-03 7.5891040984896077E-04
|
||||
2 1 7.1532528297088083E-01 4.0098976770174595E+00 2.5989042197937406E+00 3.8240252948890341E-01
|
||||
2 2 5.6301628567420527E-02 1.6234842194053070E+00 9.3805754679203801E-01 1.8736449645837763E-01
|
||||
2 3 6.5703695712707699E-01 3.0791315022675048E+00 1.9948820209043110E+00 2.7857971836047041E-01
|
||||
2 4 3.1024606077905838E-02 1.1551308858105025E+00 6.4059931260962955E-01 1.3511922517043537E-01
|
||||
2 5 5.8421509973169194E-01 1.9420240206857451E+00 1.2814107009923552E+00 1.5028032758627749E-01
|
||||
2 6 8.7055091560538176E-03 5.7824321471805962E-01 2.9826715576421953E-01 6.8317345917310188E-02
|
||||
2 7 4.9061923640751393E-01 1.1928444832852640E+00 8.4317529142720093E-01 7.3313958696515871E-02
|
||||
2 8 1.4113901292375167E-03 2.2139468783209257E-01 1.0800688415169928E-01 2.7030088273230311E-02
|
||||
2 9 4.9849874092941715E-01 9.8733752198909885E-01 7.2610545889255573E-01 5.0426765272667665E-02
|
||||
2 10 6.2957062567264221E-03 9.5794186401597337E-01 4.6455014321576615E-01 1.1560059533210508E-01
|
||||
2 11 3.6577588459988464E-01 7.7230200150326977E-01 5.4625967744523274E-01 3.4592870857207282E-02
|
||||
2 12 8.7085544804932510E-04 6.5807276191584230E-01 3.0944891033609356E-01 8.5000814741669858E-02
|
||||
2 13 1.8948992752075242E-01 5.7888624801215693E-01 3.8909315424335084E-01 3.4526650397123625E-02
|
||||
2 14 1.5622199228642329E-05 4.9780490905368319E-01 1.6953376146057847E-01 6.2315791454946631E-02
|
||||
2 15 3.3004285384528591E-02 4.0762166080748574E-01 1.7406078768468747E-01 3.4501395384273041E-02
|
||||
2 16 1.0729012446445082E-10 2.7047079448224992E-01 4.4653384790197932E-02 3.1107465231072710E-02
|
||||
2 17 1.0846205849416071E-05 3.9543401427987353E-02 1.5074459823996002E-02 4.7702333660869702E-03
|
||||
2 18 7.4829063908554593E-11 2.5884908058550057E-03 6.5717634939948741E-04 3.2655127951477001E-04
|
||||
2 19 3.6205850570885452E-03 4.3221294145342604E-01 1.8756542069538715E-01 5.3162621310716439E-02
|
||||
2 20 3.8440097917265245E-07 3.6534575078121363E-02 9.8772821155134853E-03 5.2062500369707294E-03
|
||||
2 21 2.6911400517410067E-03 6.4611970894949161E-02 2.9305443392707013E-02 6.1496063694629404E-03
|
||||
2 22 1.2827584708500362E-03 1.7529487759454226E-01 6.8509716444031268E-02 2.2077211658804528E-02
|
||||
2 23 1.5545977333502778E-02 9.9331349879191635E-02 4.7998454143224949E-02 8.6592611829801498E-03
|
||||
2 24 1.5745634781781375E-05 1.9308534172604155E-02 6.0894070240362346E-03 2.3678290544763918E-03
|
||||
2 25 8.5856663153437229E-11 1.3944217824039388E-03 2.2274994125481327E-04 1.8366900313163587E-04
|
||||
2 26 9.1829498430736033E-03 1.1557634414039414E-01 4.6978379604047056E-02 1.2100545333930957E-02
|
||||
2 27 1.7898602665033226E-04 8.1694699794021677E-02 3.2902418055540186E-02 9.9562973177386334E-03
|
||||
2 28 7.4320386544780976E-10 3.9418035349310827E-03 6.3479370917995839E-04 5.2607016457668454E-04
|
||||
2 29 6.3415719088815280E-03 3.9243185159612948E-02 1.6708820854971277E-02 2.8310386784519311E-03
|
||||
2 30 2.8195782382410411E-03 3.2846540596866002E-02 1.1453659185437731E-02 2.6398096406068873E-03
|
||||
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-3/weights.001.data
Normal file
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-3/weights.001.data
Normal file
File diff suppressed because it is too large
Load diff
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-3/weights.008.data
Normal file
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-3/weights.008.data
Normal file
File diff suppressed because it is too large
Load diff
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-4/input.nn
Normal file
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-4/input.nn
Normal file
|
|
@ -0,0 +1,165 @@
|
|||
###############################################################################
|
||||
# GENERAL NNP SETTINGS
|
||||
###############################################################################
|
||||
# These keywords are (almost) always required.
|
||||
number_of_elements 2 # Number of elements.
|
||||
elements O H # Specification of elements.
|
||||
atom_energy O -74.94518524 # free atom reference energy (atomic zora)
|
||||
atom_energy H -0.45890771 # free atom reference energy (atomic zora)
|
||||
cutoff_type 2 # Cutoff type (optional argument: shift parameter alpha).
|
||||
scale_symmetry_functions # Scale all symmetry functions with min/max values.
|
||||
#scale_symmetry_functions_sigma # Scale all symmetry functions with sigma.
|
||||
scale_min_short 0.0 # Minimum value for scaling.
|
||||
scale_max_short 1.0 # Maximum value for scaling.
|
||||
center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value.
|
||||
global_hidden_layers_short 2 # Number of hidden layers.
|
||||
global_nodes_short 20 20 # Number of nodes in each hidden layer.
|
||||
global_activation_short t t l # Activation function for each hidden layer and output layer.
|
||||
#normalize_nodes # Normalize input of nodes.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR DATASET TOOLS
|
||||
###############################################################################
|
||||
# These keywords are used only by some tools handling data sets:
|
||||
# nnp-comp2, nnp-scaling, nnp-dataset, nnp-train.
|
||||
#use_short_forces # Use forces. Disable - repeated below.
|
||||
random_seed 3 # Random number generator seed.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR TRAINING
|
||||
###############################################################################
|
||||
# These keywords are solely used for training with nnp-train.
|
||||
epochs 100 # Number of training epochs.
|
||||
updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter).
|
||||
parallel_mode 1 # Training parallelization used (0 = Parallel (rank 0 update), 1 = Parallel (all update)).
|
||||
jacobian_mode 2 # Jacobian computation mode (0 = Summation to single gradient, 1 = Per-task summed gradient, 2 = Full Jacobian).
|
||||
update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element).
|
||||
selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold).
|
||||
task_batch_size_energy 1 # Number of energy update candidates prepared per task for each update (0 = Entire training set).
|
||||
task_batch_size_force 1 # Number of force update candidates prepared per task for each update (0 = Entire training set).
|
||||
memorize_symfunc_results # Keep symmetry function results in memory.
|
||||
test_fraction 0.1 # Fraction of structures kept for testing.
|
||||
use_short_forces # Use forces for training.
|
||||
force_weight 2.0 # Weight of force updates relative to energy updates.
|
||||
short_energy_fraction 1.0 # Fraction of energy updates per epoch.
|
||||
short_force_fraction 0.05 # Fraction of force updates per epoch.
|
||||
short_energy_error_threshold 0.8 # RMSE threshold for energy update candidates.
|
||||
short_force_error_threshold 1.0 # RMSE threshold for force update candidates.
|
||||
rmse_threshold_trials 3 # Maximum number of RMSE threshold trials.
|
||||
#use_old_weights_short # Restart fitting with old weight parameters.
|
||||
weights_min -1.0 # Minimum value for initial random weights.
|
||||
weights_max 1.0 # Maximum value for initial random weights.
|
||||
#precondition_weights # Precondition weights with initial energies.
|
||||
nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme.
|
||||
write_trainpoints 0 # Write energy comparison every this many epochs.
|
||||
write_trainforces 0 # Write force comparison every this many epochs.
|
||||
write_weights_epoch 1 # Write weights every this many epochs.
|
||||
write_neuronstats 0 # Write neuron statistics every this many epochs.
|
||||
#write_trainlog # Write training log file.
|
||||
|
||||
############################
|
||||
# KALMAN FILTER (STANDARD) #
|
||||
############################
|
||||
kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory).
|
||||
kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001).
|
||||
kalman_q0 0.01 # General Kalman filter parameter q0 ("large").
|
||||
kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6).
|
||||
kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0).
|
||||
kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+).
|
||||
|
||||
# Are these only for fading Kalman?
|
||||
kalman_lambda_short 0.98000
|
||||
kalman_nue_short 0.99870
|
||||
|
||||
|
||||
|
||||
###############################################################################
|
||||
# SYMMETRY FUNCTIONS
|
||||
###############################################################################
|
||||
|
||||
# INFO: symfunction format: reference atom, type, neighbor element 1 (and neighbor element 2), symfunction parameters
|
||||
|
||||
|
||||
#
|
||||
# radial
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom eta rshift funccutoff
|
||||
|
||||
# H H
|
||||
symfunction_short H 2 H 0.001 0.0 12.00
|
||||
symfunction_short H 2 H 0.01 0.0 12.00
|
||||
symfunction_short H 2 H 0.03 0.0 12.00
|
||||
symfunction_short H 2 H 0.06 0.0 12.00
|
||||
symfunction_short H 2 H 0.15 1.9 12.00
|
||||
symfunction_short H 2 H 0.30 1.9 12.00
|
||||
symfunction_short H 2 H 0.60 1.9 12.00
|
||||
symfunction_short H 2 H 1.50 1.9 12.00
|
||||
|
||||
# H O / O H
|
||||
symfunction_short H 2 O 0.001 0.0 12.00
|
||||
symfunction_short H 2 O 0.01 0.0 12.00
|
||||
symfunction_short H 2 O 0.03 0.0 12.00
|
||||
symfunction_short H 2 O 0.06 0.0 12.00
|
||||
symfunction_short H 2 O 0.15 0.9 12.00
|
||||
symfunction_short H 2 O 0.30 0.9 12.00
|
||||
symfunction_short H 2 O 0.60 0.9 12.00
|
||||
symfunction_short H 2 O 1.50 0.9 12.00
|
||||
symfunction_short O 2 H 0.001 0.0 12.00
|
||||
symfunction_short O 2 H 0.01 0.0 12.00
|
||||
symfunction_short O 2 H 0.03 0.0 12.00
|
||||
symfunction_short O 2 H 0.06 0.0 12.00
|
||||
symfunction_short O 2 H 0.15 0.9 12.00
|
||||
symfunction_short O 2 H 0.30 0.9 12.00
|
||||
symfunction_short O 2 H 0.60 0.9 12.00
|
||||
symfunction_short O 2 H 1.50 0.9 12.00
|
||||
|
||||
# O O
|
||||
symfunction_short O 2 O 0.001 0.0 12.00
|
||||
symfunction_short O 2 O 0.01 0.0 12.00
|
||||
symfunction_short O 2 O 0.03 0.0 12.00
|
||||
symfunction_short O 2 O 0.06 0.0 12.00
|
||||
symfunction_short O 2 O 0.15 4.0 12.00
|
||||
symfunction_short O 2 O 0.30 4.0 12.00
|
||||
symfunction_short O 2 O 0.60 4.0 12.00
|
||||
symfunction_short O 2 O 1.50 4.0 12.00
|
||||
|
||||
#
|
||||
# angular
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
|
||||
|
||||
symfunction_short H 3 O H 0.2 1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.07 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short O 3 H H 0.01 -1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short H 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000
|
||||
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-4/scaling.data
Normal file
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-4/scaling.data
Normal file
|
|
@ -0,0 +1,72 @@
|
|||
################################################################################
|
||||
# Symmetry function scaling data.
|
||||
################################################################################
|
||||
# Col Name Description
|
||||
################################################################################
|
||||
# 1 e_index Element index.
|
||||
# 2 sf_index Symmetry function index.
|
||||
# 3 sf_min Symmetry function minimum.
|
||||
# 4 sf_max Symmetry function maximum.
|
||||
# 5 sf_mean Symmetry function mean.
|
||||
# 6 sf_sigma Symmetry function sigma.
|
||||
#########################################################################################################################
|
||||
# 1 2 3 4 5 6
|
||||
# e_index sf_index sf_min sf_max sf_mean sf_sigma
|
||||
#########################################################################################################################
|
||||
1 1 2.8655329382224032E-01 3.6364355962665180E+00 2.2119784681576462E+00 3.8982164788324997E-01
|
||||
1 2 3.5699082862581144E-01 2.0031124569208267E+00 1.2994521098968697E+00 1.9314919398539934E-01
|
||||
1 3 2.4253583906212917E-01 2.6983010627072188E+00 1.6071345237783119E+00 2.8699477114001926E-01
|
||||
1 4 3.3542904629093495E-01 1.5372546465126264E+00 9.9744101045215405E-01 1.4138420759838252E-01
|
||||
1 5 1.8503709795923420E-01 1.5491787211705357E+00 8.9011559742158164E-01 1.6054085816870095E-01
|
||||
1 6 2.8986050983056133E-01 9.5851457739199852E-01 6.4070535049617849E-01 7.7829435282258122E-02
|
||||
1 7 1.2998738560021622E-01 8.1181447628465786E-01 4.5034968386667074E-01 7.9668681985815226E-02
|
||||
1 8 2.3854599156072026E-01 5.8192272360200603E-01 4.2158764571359902E-01 4.0539426354474550E-02
|
||||
1 9 2.2019401469736052E-01 4.9816927636901054E-01 3.6305272944627814E-01 3.1419040668323794E-02
|
||||
1 10 1.7723908244726444E-01 1.0169045685317621E+00 5.3120597962909599E-01 9.6163510042366729E-02
|
||||
1 11 1.5931165210644979E-01 3.9224005962648778E-01 2.7312983872261626E-01 2.0878706459593787E-02
|
||||
1 12 1.0106474384096639E-01 6.8318193294241025E-01 2.9555524220090662E-01 5.2779720067393711E-02
|
||||
1 13 7.4340659297091619E-02 3.2028897659649835E-01 1.9454657712167567E-01 2.2645835164130282E-02
|
||||
1 14 2.7867297613902112E-02 4.8859027683498957E-01 1.5882253801165494E-01 3.7102407780210747E-02
|
||||
1 15 6.0765964821426774E-03 2.6933341009926554E-01 8.7030393842343762E-02 2.3954982883266366E-02
|
||||
1 16 8.6176614291566273E-04 3.2616869984647917E-01 5.8437222538056929E-02 3.2524425477896142E-02
|
||||
1 17 2.3905486661473520E-08 3.7621880078986758E-02 1.7099399409671336E-02 5.6190834887742923E-03
|
||||
1 18 5.7485161297593659E-05 5.6704347475877770E-02 2.0751242479452540E-02 7.2790207725134705E-03
|
||||
1 19 3.7937631629716383E-06 4.4789516076805022E-02 1.6338823698107987E-02 5.6967712606261290E-03
|
||||
1 20 2.4960312085019903E-02 2.7218197030245517E-01 1.3743696285440926E-01 2.8868015901657586E-02
|
||||
1 21 2.2980773998953256E-03 4.9986220828384470E-02 1.6950824167726749E-02 5.4132966616364615E-03
|
||||
1 22 2.0814361457387778E-07 1.7422614782322748E-02 5.8877295715452933E-03 2.3169759281881064E-03
|
||||
1 23 2.3616425302076981E-02 1.4766564930840750E-01 7.8026009579545183E-02 1.4328402520229913E-02
|
||||
1 24 9.3734209417262540E-06 1.2706009724968383E-02 3.8602266983488250E-03 1.5349222936123044E-03
|
||||
1 25 6.7292482219397467E-04 1.3437347615997143E-02 3.5879997188162020E-03 1.0083099406231317E-03
|
||||
1 26 8.9492218473814448E-03 4.7435519247870893E-02 2.4574480321592811E-02 3.7562620321717013E-03
|
||||
1 27 2.9688834832940051E-04 1.0922315444849038E-02 2.4362779164791813E-03 7.5891040984896988E-04
|
||||
2 1 7.1532528297088083E-01 4.0098976770174595E+00 2.5989042197937411E+00 3.8240252948889703E-01
|
||||
2 2 5.6301628567420527E-02 1.6234842194053070E+00 9.3805754679203779E-01 1.8736449645837899E-01
|
||||
2 3 6.5703695712707699E-01 3.0791315022675048E+00 1.9948820209043090E+00 2.7857971836048490E-01
|
||||
2 4 3.1024606077905838E-02 1.1551308858105025E+00 6.4059931260962932E-01 1.3511922517043592E-01
|
||||
2 5 5.8421509973169194E-01 1.9420240206857451E+00 1.2814107009923559E+00 1.5028032758627077E-01
|
||||
2 6 8.7055091560538176E-03 5.7824321471805962E-01 2.9826715576421947E-01 6.8317345917310562E-02
|
||||
2 7 4.9061923640751393E-01 1.1928444832852640E+00 8.4317529142720071E-01 7.3313958696521381E-02
|
||||
2 8 1.4113901292375167E-03 2.2139468783209257E-01 1.0800688415169940E-01 2.7030088273229783E-02
|
||||
2 9 4.9849874092941715E-01 9.8733752198909885E-01 7.2610545889255584E-01 5.0426765272676678E-02
|
||||
2 10 6.2957062567264221E-03 9.5794186401597337E-01 4.6455014321576604E-01 1.1560059533210486E-01
|
||||
2 11 3.6577588459988464E-01 7.7230200150326977E-01 5.4625967744523274E-01 3.4592870857207282E-02
|
||||
2 12 8.7085544804932510E-04 6.5807276191584230E-01 3.0944891033609356E-01 8.5000814741669997E-02
|
||||
2 13 1.8948992752075242E-01 5.7888624801215693E-01 3.8909315424335095E-01 3.4526650397120703E-02
|
||||
2 14 1.5622199228642329E-05 4.9780490905368319E-01 1.6953376146057855E-01 6.2315791454946423E-02
|
||||
2 15 3.3004285384528591E-02 4.0762166080748574E-01 1.7406078768468741E-01 3.4501395384273312E-02
|
||||
2 16 1.0729012446445082E-10 2.7047079448224992E-01 4.4653384790197946E-02 3.1107465231072686E-02
|
||||
2 17 1.0846205849416071E-05 3.9543401427987353E-02 1.5074459823996002E-02 4.7702333660869858E-03
|
||||
2 18 7.4829063908554593E-11 2.5884908058550057E-03 6.5717634939948730E-04 3.2655127951476990E-04
|
||||
2 19 3.6205850570885452E-03 4.3221294145342604E-01 1.8756542069538706E-01 5.3162621310716675E-02
|
||||
2 20 3.8440097917265245E-07 3.6534575078121363E-02 9.8772821155134784E-03 5.2062500369707511E-03
|
||||
2 21 2.6911400517410067E-03 6.4611970894949161E-02 2.9305443392707020E-02 6.1496063694629326E-03
|
||||
2 22 1.2827584708500362E-03 1.7529487759454226E-01 6.8509716444031241E-02 2.2077211658804455E-02
|
||||
2 23 1.5545977333502778E-02 9.9331349879191635E-02 4.7998454143224963E-02 8.6592611829801724E-03
|
||||
2 24 1.5745634781781375E-05 1.9308534172604155E-02 6.0894070240362346E-03 2.3678290544763892E-03
|
||||
2 25 8.5856663153437229E-11 1.3944217824039388E-03 2.2274994125481327E-04 1.8366900313163576E-04
|
||||
2 26 9.1829498430736033E-03 1.1557634414039414E-01 4.6978379604047091E-02 1.2100545333930811E-02
|
||||
2 27 1.7898602665033226E-04 8.1694699794021677E-02 3.2902418055540172E-02 9.9562973177386733E-03
|
||||
2 28 7.4320386544780976E-10 3.9418035349310827E-03 6.3479370917995828E-04 5.2607016457668530E-04
|
||||
2 29 6.3415719088815280E-03 3.9243185159612948E-02 1.6708820854971287E-02 2.8310386784518526E-03
|
||||
2 30 2.8195782382410411E-03 3.2846540596866002E-02 1.1453659185437722E-02 2.6398096406069342E-03
|
||||
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-4/weights.001.data
Normal file
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-4/weights.001.data
Normal file
File diff suppressed because it is too large
Load diff
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-4/weights.008.data
Normal file
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-4/weights.008.data
Normal file
File diff suppressed because it is too large
Load diff
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-5/input.nn
Normal file
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-5/input.nn
Normal file
|
|
@ -0,0 +1,165 @@
|
|||
###############################################################################
|
||||
# GENERAL NNP SETTINGS
|
||||
###############################################################################
|
||||
# These keywords are (almost) always required.
|
||||
number_of_elements 2 # Number of elements.
|
||||
elements O H # Specification of elements.
|
||||
atom_energy O -74.94518524 # free atom reference energy (atomic zora)
|
||||
atom_energy H -0.45890771 # free atom reference energy (atomic zora)
|
||||
cutoff_type 2 # Cutoff type (optional argument: shift parameter alpha).
|
||||
scale_symmetry_functions # Scale all symmetry functions with min/max values.
|
||||
#scale_symmetry_functions_sigma # Scale all symmetry functions with sigma.
|
||||
scale_min_short 0.0 # Minimum value for scaling.
|
||||
scale_max_short 1.0 # Maximum value for scaling.
|
||||
center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value.
|
||||
global_hidden_layers_short 2 # Number of hidden layers.
|
||||
global_nodes_short 20 20 # Number of nodes in each hidden layer.
|
||||
global_activation_short t t l # Activation function for each hidden layer and output layer.
|
||||
#normalize_nodes # Normalize input of nodes.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR DATASET TOOLS
|
||||
###############################################################################
|
||||
# These keywords are used only by some tools handling data sets:
|
||||
# nnp-comp2, nnp-scaling, nnp-dataset, nnp-train.
|
||||
#use_short_forces # Use forces. Disable - repeated below.
|
||||
random_seed 4 # Random number generator seed.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR TRAINING
|
||||
###############################################################################
|
||||
# These keywords are solely used for training with nnp-train.
|
||||
epochs 100 # Number of training epochs.
|
||||
updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter).
|
||||
parallel_mode 1 # Training parallelization used (0 = Parallel (rank 0 update), 1 = Parallel (all update)).
|
||||
jacobian_mode 2 # Jacobian computation mode (0 = Summation to single gradient, 1 = Per-task summed gradient, 2 = Full Jacobian).
|
||||
update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element).
|
||||
selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold).
|
||||
task_batch_size_energy 1 # Number of energy update candidates prepared per task for each update (0 = Entire training set).
|
||||
task_batch_size_force 1 # Number of force update candidates prepared per task for each update (0 = Entire training set).
|
||||
memorize_symfunc_results # Keep symmetry function results in memory.
|
||||
test_fraction 0.1 # Fraction of structures kept for testing.
|
||||
use_short_forces # Use forces for training.
|
||||
force_weight 2.0 # Weight of force updates relative to energy updates.
|
||||
short_energy_fraction 1.0 # Fraction of energy updates per epoch.
|
||||
short_force_fraction 0.05 # Fraction of force updates per epoch.
|
||||
short_energy_error_threshold 0.8 # RMSE threshold for energy update candidates.
|
||||
short_force_error_threshold 1.0 # RMSE threshold for force update candidates.
|
||||
rmse_threshold_trials 3 # Maximum number of RMSE threshold trials.
|
||||
#use_old_weights_short # Restart fitting with old weight parameters.
|
||||
weights_min -1.0 # Minimum value for initial random weights.
|
||||
weights_max 1.0 # Maximum value for initial random weights.
|
||||
#precondition_weights # Precondition weights with initial energies.
|
||||
nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme.
|
||||
write_trainpoints 0 # Write energy comparison every this many epochs.
|
||||
write_trainforces 0 # Write force comparison every this many epochs.
|
||||
write_weights_epoch 1 # Write weights every this many epochs.
|
||||
write_neuronstats 0 # Write neuron statistics every this many epochs.
|
||||
#write_trainlog # Write training log file.
|
||||
|
||||
############################
|
||||
# KALMAN FILTER (STANDARD) #
|
||||
############################
|
||||
kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory).
|
||||
kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001).
|
||||
kalman_q0 0.01 # General Kalman filter parameter q0 ("large").
|
||||
kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6).
|
||||
kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0).
|
||||
kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+).
|
||||
|
||||
# Are these only for fading Kalman?
|
||||
kalman_lambda_short 0.98000
|
||||
kalman_nue_short 0.99870
|
||||
|
||||
|
||||
|
||||
###############################################################################
|
||||
# SYMMETRY FUNCTIONS
|
||||
###############################################################################
|
||||
|
||||
# INFO: symfunction format: reference atom, type, neighbor element 1 (and neighbor element 2), symfunction parameters
|
||||
|
||||
|
||||
#
|
||||
# radial
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom eta rshift funccutoff
|
||||
|
||||
# H H
|
||||
symfunction_short H 2 H 0.001 0.0 12.00
|
||||
symfunction_short H 2 H 0.01 0.0 12.00
|
||||
symfunction_short H 2 H 0.03 0.0 12.00
|
||||
symfunction_short H 2 H 0.06 0.0 12.00
|
||||
symfunction_short H 2 H 0.15 1.9 12.00
|
||||
symfunction_short H 2 H 0.30 1.9 12.00
|
||||
symfunction_short H 2 H 0.60 1.9 12.00
|
||||
symfunction_short H 2 H 1.50 1.9 12.00
|
||||
|
||||
# H O / O H
|
||||
symfunction_short H 2 O 0.001 0.0 12.00
|
||||
symfunction_short H 2 O 0.01 0.0 12.00
|
||||
symfunction_short H 2 O 0.03 0.0 12.00
|
||||
symfunction_short H 2 O 0.06 0.0 12.00
|
||||
symfunction_short H 2 O 0.15 0.9 12.00
|
||||
symfunction_short H 2 O 0.30 0.9 12.00
|
||||
symfunction_short H 2 O 0.60 0.9 12.00
|
||||
symfunction_short H 2 O 1.50 0.9 12.00
|
||||
symfunction_short O 2 H 0.001 0.0 12.00
|
||||
symfunction_short O 2 H 0.01 0.0 12.00
|
||||
symfunction_short O 2 H 0.03 0.0 12.00
|
||||
symfunction_short O 2 H 0.06 0.0 12.00
|
||||
symfunction_short O 2 H 0.15 0.9 12.00
|
||||
symfunction_short O 2 H 0.30 0.9 12.00
|
||||
symfunction_short O 2 H 0.60 0.9 12.00
|
||||
symfunction_short O 2 H 1.50 0.9 12.00
|
||||
|
||||
# O O
|
||||
symfunction_short O 2 O 0.001 0.0 12.00
|
||||
symfunction_short O 2 O 0.01 0.0 12.00
|
||||
symfunction_short O 2 O 0.03 0.0 12.00
|
||||
symfunction_short O 2 O 0.06 0.0 12.00
|
||||
symfunction_short O 2 O 0.15 4.0 12.00
|
||||
symfunction_short O 2 O 0.30 4.0 12.00
|
||||
symfunction_short O 2 O 0.60 4.0 12.00
|
||||
symfunction_short O 2 O 1.50 4.0 12.00
|
||||
|
||||
#
|
||||
# angular
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
|
||||
|
||||
symfunction_short H 3 O H 0.2 1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.07 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short O 3 H H 0.01 -1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short H 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000
|
||||
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-5/scaling.data
Normal file
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-5/scaling.data
Normal file
|
|
@ -0,0 +1,72 @@
|
|||
################################################################################
|
||||
# Symmetry function scaling data.
|
||||
################################################################################
|
||||
# Col Name Description
|
||||
################################################################################
|
||||
# 1 e_index Element index.
|
||||
# 2 sf_index Symmetry function index.
|
||||
# 3 sf_min Symmetry function minimum.
|
||||
# 4 sf_max Symmetry function maximum.
|
||||
# 5 sf_mean Symmetry function mean.
|
||||
# 6 sf_sigma Symmetry function sigma.
|
||||
#########################################################################################################################
|
||||
# 1 2 3 4 5 6
|
||||
# e_index sf_index sf_min sf_max sf_mean sf_sigma
|
||||
#########################################################################################################################
|
||||
1 1 2.8655329382224032E-01 3.6364355962665180E+00 2.2119784681576444E+00 3.8982164788326135E-01
|
||||
1 2 3.5699082862581144E-01 2.0031124569208267E+00 1.2994521098968683E+00 1.9314919398540875E-01
|
||||
1 3 2.4253583906212917E-01 2.6983010627072188E+00 1.6071345237783112E+00 2.8699477114002486E-01
|
||||
1 4 3.3542904629093495E-01 1.5372546465126264E+00 9.9744101045215361E-01 1.4138420759838610E-01
|
||||
1 5 1.8503709795923420E-01 1.5491787211705357E+00 8.9011559742158097E-01 1.6054085816870473E-01
|
||||
1 6 2.8986050983056133E-01 9.5851457739199852E-01 6.4070535049617849E-01 7.7829435282260065E-02
|
||||
1 7 1.2998738560021622E-01 8.1181447628465786E-01 4.5034968386667046E-01 7.9668681985816184E-02
|
||||
1 8 2.3854599156072026E-01 5.8192272360200603E-01 4.2158764571359925E-01 4.0539426354468631E-02
|
||||
1 9 2.2019401469736052E-01 4.9816927636901054E-01 3.6305272944627814E-01 3.1419040668322989E-02
|
||||
1 10 1.7723908244726444E-01 1.0169045685317621E+00 5.3120597962909655E-01 9.6163510042364370E-02
|
||||
1 11 1.5931165210644979E-01 3.9224005962648778E-01 2.7312983872261637E-01 2.0878706459593183E-02
|
||||
1 12 1.0106474384096639E-01 6.8318193294241025E-01 2.9555524220090662E-01 5.2779720067391796E-02
|
||||
1 13 7.4340659297091619E-02 3.2028897659649835E-01 1.9454657712167561E-01 2.2645835164130979E-02
|
||||
1 14 2.7867297613902112E-02 4.8859027683498957E-01 1.5882253801165500E-01 3.7102407780210275E-02
|
||||
1 15 6.0765964821426774E-03 2.6933341009926554E-01 8.7030393842343623E-02 2.3954982883266990E-02
|
||||
1 16 8.6176614291566273E-04 3.2616869984647917E-01 5.8437222538056957E-02 3.2524425477896149E-02
|
||||
1 17 2.3905486661473520E-08 3.7621880078986758E-02 1.7099399409671350E-02 5.6190834887742082E-03
|
||||
1 18 5.7485161297593659E-05 5.6704347475877770E-02 2.0751242479452547E-02 7.2790207725134974E-03
|
||||
1 19 3.7937631629716383E-06 4.4789516076805022E-02 1.6338823698108001E-02 5.6967712606261246E-03
|
||||
1 20 2.4960312085019903E-02 2.7218197030245517E-01 1.3743696285440932E-01 2.8868015901657423E-02
|
||||
1 21 2.2980773998953256E-03 4.9986220828384470E-02 1.6950824167726756E-02 5.4132966616364520E-03
|
||||
1 22 2.0814361457387778E-07 1.7422614782322748E-02 5.8877295715452881E-03 2.3169759281881212E-03
|
||||
1 23 2.3616425302076981E-02 1.4766564930840750E-01 7.8026009579545183E-02 1.4328402520229665E-02
|
||||
1 24 9.3734209417262540E-06 1.2706009724968383E-02 3.8602266983488289E-03 1.5349222936122963E-03
|
||||
1 25 6.7292482219397467E-04 1.3437347615997143E-02 3.5879997188162024E-03 1.0083099406231202E-03
|
||||
1 26 8.9492218473814448E-03 4.7435519247870893E-02 2.4574480321592818E-02 3.7562620321717013E-03
|
||||
1 27 2.9688834832940051E-04 1.0922315444849038E-02 2.4362779164791822E-03 7.5891040984896532E-04
|
||||
2 1 7.1532528297088083E-01 4.0098976770174595E+00 2.5989042197937384E+00 3.8240252948892556E-01
|
||||
2 2 5.6301628567420527E-02 1.6234842194053070E+00 9.3805754679203801E-01 1.8736449645837763E-01
|
||||
2 3 6.5703695712707699E-01 3.0791315022675048E+00 1.9948820209043097E+00 2.7857971836047618E-01
|
||||
2 4 3.1024606077905838E-02 1.1551308858105025E+00 6.4059931260962943E-01 1.3511922517043592E-01
|
||||
2 5 5.8421509973169194E-01 1.9420240206857451E+00 1.2814107009923554E+00 1.5028032758627749E-01
|
||||
2 6 8.7055091560538176E-03 5.7824321471805962E-01 2.9826715576421947E-01 6.8317345917310188E-02
|
||||
2 7 4.9061923640751393E-01 1.1928444832852640E+00 8.4317529142720071E-01 7.3313958696520687E-02
|
||||
2 8 1.4113901292375167E-03 2.2139468783209257E-01 1.0800688415169926E-01 2.7030088273230279E-02
|
||||
2 9 4.9849874092941715E-01 9.8733752198909885E-01 7.2610545889255607E-01 5.0426765272669670E-02
|
||||
2 10 6.2957062567264221E-03 9.5794186401597337E-01 4.6455014321576626E-01 1.1560059533210355E-01
|
||||
2 11 3.6577588459988464E-01 7.7230200150326977E-01 5.4625967744523185E-01 3.4592870857218225E-02
|
||||
2 12 8.7085544804932510E-04 6.5807276191584230E-01 3.0944891033609356E-01 8.5000814741669858E-02
|
||||
2 13 1.8948992752075242E-01 5.7888624801215693E-01 3.8909315424335084E-01 3.4526650397122896E-02
|
||||
2 14 1.5622199228642329E-05 4.9780490905368319E-01 1.6953376146057872E-01 6.2315791454946021E-02
|
||||
2 15 3.3004285384528591E-02 4.0762166080748574E-01 1.7406078768468741E-01 3.4501395384273680E-02
|
||||
2 16 1.0729012446445082E-10 2.7047079448224992E-01 4.4653384790197946E-02 3.1107465231072658E-02
|
||||
2 17 1.0846205849416071E-05 3.9543401427987353E-02 1.5074459823996007E-02 4.7702333660869494E-03
|
||||
2 18 7.4829063908554593E-11 2.5884908058550057E-03 6.5717634939948719E-04 3.2655127951476974E-04
|
||||
2 19 3.6205850570885452E-03 4.3221294145342604E-01 1.8756542069538712E-01 5.3162621310716675E-02
|
||||
2 20 3.8440097917265245E-07 3.6534575078121363E-02 9.8772821155134732E-03 5.2062500369707606E-03
|
||||
2 21 2.6911400517410067E-03 6.4611970894949161E-02 2.9305443392707024E-02 6.1496063694628997E-03
|
||||
2 22 1.2827584708500362E-03 1.7529487759454226E-01 6.8509716444031296E-02 2.2077211658804295E-02
|
||||
2 23 1.5545977333502778E-02 9.9331349879191635E-02 4.7998454143224942E-02 8.6592611829802175E-03
|
||||
2 24 1.5745634781781375E-05 1.9308534172604155E-02 6.0894070240362337E-03 2.3678290544763931E-03
|
||||
2 25 8.5856663153437229E-11 1.3944217824039388E-03 2.2274994125481311E-04 1.8366900313163587E-04
|
||||
2 26 9.1829498430736033E-03 1.1557634414039414E-01 4.6978379604047091E-02 1.2100545333930811E-02
|
||||
2 27 1.7898602665033226E-04 8.1694699794021677E-02 3.2902418055540207E-02 9.9562973177386039E-03
|
||||
2 28 7.4320386544780976E-10 3.9418035349310827E-03 6.3479370917995839E-04 5.2607016457668432E-04
|
||||
2 29 6.3415719088815280E-03 3.9243185159612948E-02 1.6708820854971287E-02 2.8310386784518265E-03
|
||||
2 30 2.8195782382410411E-03 3.2846540596866002E-02 1.1453659185437722E-02 2.6398096406069433E-03
|
||||
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-5/weights.001.data
Normal file
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-5/weights.001.data
Normal file
File diff suppressed because it is too large
Load diff
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-5/weights.008.data
Normal file
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-5/weights.008.data
Normal file
File diff suppressed because it is too large
Load diff
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-6/input.nn
Normal file
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-6/input.nn
Normal file
|
|
@ -0,0 +1,165 @@
|
|||
###############################################################################
|
||||
# GENERAL NNP SETTINGS
|
||||
###############################################################################
|
||||
# These keywords are (almost) always required.
|
||||
number_of_elements 2 # Number of elements.
|
||||
elements O H # Specification of elements.
|
||||
atom_energy O -74.94518524 # free atom reference energy (atomic zora)
|
||||
atom_energy H -0.45890771 # free atom reference energy (atomic zora)
|
||||
cutoff_type 2 # Cutoff type (optional argument: shift parameter alpha).
|
||||
scale_symmetry_functions # Scale all symmetry functions with min/max values.
|
||||
#scale_symmetry_functions_sigma # Scale all symmetry functions with sigma.
|
||||
scale_min_short 0.0 # Minimum value for scaling.
|
||||
scale_max_short 1.0 # Maximum value for scaling.
|
||||
center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value.
|
||||
global_hidden_layers_short 2 # Number of hidden layers.
|
||||
global_nodes_short 20 20 # Number of nodes in each hidden layer.
|
||||
global_activation_short t t l # Activation function for each hidden layer and output layer.
|
||||
#normalize_nodes # Normalize input of nodes.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR DATASET TOOLS
|
||||
###############################################################################
|
||||
# These keywords are used only by some tools handling data sets:
|
||||
# nnp-comp2, nnp-scaling, nnp-dataset, nnp-train.
|
||||
#use_short_forces # Use forces. Disable - repeated below.
|
||||
random_seed 5 # Random number generator seed.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR TRAINING
|
||||
###############################################################################
|
||||
# These keywords are solely used for training with nnp-train.
|
||||
epochs 100 # Number of training epochs.
|
||||
updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter).
|
||||
parallel_mode 1 # Training parallelization used (0 = Parallel (rank 0 update), 1 = Parallel (all update)).
|
||||
jacobian_mode 2 # Jacobian computation mode (0 = Summation to single gradient, 1 = Per-task summed gradient, 2 = Full Jacobian).
|
||||
update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element).
|
||||
selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold).
|
||||
task_batch_size_energy 1 # Number of energy update candidates prepared per task for each update (0 = Entire training set).
|
||||
task_batch_size_force 1 # Number of force update candidates prepared per task for each update (0 = Entire training set).
|
||||
memorize_symfunc_results # Keep symmetry function results in memory.
|
||||
test_fraction 0.1 # Fraction of structures kept for testing.
|
||||
use_short_forces # Use forces for training.
|
||||
force_weight 2.0 # Weight of force updates relative to energy updates.
|
||||
short_energy_fraction 1.0 # Fraction of energy updates per epoch.
|
||||
short_force_fraction 0.05 # Fraction of force updates per epoch.
|
||||
short_energy_error_threshold 0.8 # RMSE threshold for energy update candidates.
|
||||
short_force_error_threshold 1.0 # RMSE threshold for force update candidates.
|
||||
rmse_threshold_trials 3 # Maximum number of RMSE threshold trials.
|
||||
#use_old_weights_short # Restart fitting with old weight parameters.
|
||||
weights_min -1.0 # Minimum value for initial random weights.
|
||||
weights_max 1.0 # Maximum value for initial random weights.
|
||||
#precondition_weights # Precondition weights with initial energies.
|
||||
nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme.
|
||||
write_trainpoints 0 # Write energy comparison every this many epochs.
|
||||
write_trainforces 0 # Write force comparison every this many epochs.
|
||||
write_weights_epoch 1 # Write weights every this many epochs.
|
||||
write_neuronstats 0 # Write neuron statistics every this many epochs.
|
||||
#write_trainlog # Write training log file.
|
||||
|
||||
############################
|
||||
# KALMAN FILTER (STANDARD) #
|
||||
############################
|
||||
kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory).
|
||||
kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001).
|
||||
kalman_q0 0.01 # General Kalman filter parameter q0 ("large").
|
||||
kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6).
|
||||
kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0).
|
||||
kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+).
|
||||
|
||||
# Are these only for fading Kalman?
|
||||
kalman_lambda_short 0.98000
|
||||
kalman_nue_short 0.99870
|
||||
|
||||
|
||||
|
||||
###############################################################################
|
||||
# SYMMETRY FUNCTIONS
|
||||
###############################################################################
|
||||
|
||||
# INFO: symfunction format: reference atom, type, neighbor element 1 (and neighbor element 2), symfunction parameters
|
||||
|
||||
|
||||
#
|
||||
# radial
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom eta rshift funccutoff
|
||||
|
||||
# H H
|
||||
symfunction_short H 2 H 0.001 0.0 12.00
|
||||
symfunction_short H 2 H 0.01 0.0 12.00
|
||||
symfunction_short H 2 H 0.03 0.0 12.00
|
||||
symfunction_short H 2 H 0.06 0.0 12.00
|
||||
symfunction_short H 2 H 0.15 1.9 12.00
|
||||
symfunction_short H 2 H 0.30 1.9 12.00
|
||||
symfunction_short H 2 H 0.60 1.9 12.00
|
||||
symfunction_short H 2 H 1.50 1.9 12.00
|
||||
|
||||
# H O / O H
|
||||
symfunction_short H 2 O 0.001 0.0 12.00
|
||||
symfunction_short H 2 O 0.01 0.0 12.00
|
||||
symfunction_short H 2 O 0.03 0.0 12.00
|
||||
symfunction_short H 2 O 0.06 0.0 12.00
|
||||
symfunction_short H 2 O 0.15 0.9 12.00
|
||||
symfunction_short H 2 O 0.30 0.9 12.00
|
||||
symfunction_short H 2 O 0.60 0.9 12.00
|
||||
symfunction_short H 2 O 1.50 0.9 12.00
|
||||
symfunction_short O 2 H 0.001 0.0 12.00
|
||||
symfunction_short O 2 H 0.01 0.0 12.00
|
||||
symfunction_short O 2 H 0.03 0.0 12.00
|
||||
symfunction_short O 2 H 0.06 0.0 12.00
|
||||
symfunction_short O 2 H 0.15 0.9 12.00
|
||||
symfunction_short O 2 H 0.30 0.9 12.00
|
||||
symfunction_short O 2 H 0.60 0.9 12.00
|
||||
symfunction_short O 2 H 1.50 0.9 12.00
|
||||
|
||||
# O O
|
||||
symfunction_short O 2 O 0.001 0.0 12.00
|
||||
symfunction_short O 2 O 0.01 0.0 12.00
|
||||
symfunction_short O 2 O 0.03 0.0 12.00
|
||||
symfunction_short O 2 O 0.06 0.0 12.00
|
||||
symfunction_short O 2 O 0.15 4.0 12.00
|
||||
symfunction_short O 2 O 0.30 4.0 12.00
|
||||
symfunction_short O 2 O 0.60 4.0 12.00
|
||||
symfunction_short O 2 O 1.50 4.0 12.00
|
||||
|
||||
#
|
||||
# angular
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
|
||||
|
||||
symfunction_short H 3 O H 0.2 1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.07 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short O 3 H H 0.01 -1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short H 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000
|
||||
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-6/scaling.data
Normal file
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-6/scaling.data
Normal file
|
|
@ -0,0 +1,72 @@
|
|||
################################################################################
|
||||
# Symmetry function scaling data.
|
||||
################################################################################
|
||||
# Col Name Description
|
||||
################################################################################
|
||||
# 1 e_index Element index.
|
||||
# 2 sf_index Symmetry function index.
|
||||
# 3 sf_min Symmetry function minimum.
|
||||
# 4 sf_max Symmetry function maximum.
|
||||
# 5 sf_mean Symmetry function mean.
|
||||
# 6 sf_sigma Symmetry function sigma.
|
||||
#########################################################################################################################
|
||||
# 1 2 3 4 5 6
|
||||
# e_index sf_index sf_min sf_max sf_mean sf_sigma
|
||||
#########################################################################################################################
|
||||
1 1 2.8655329382224032E-01 3.6364355962665180E+00 2.2119784681576471E+00 3.8982164788324480E-01
|
||||
1 2 3.5699082862581144E-01 2.0031124569208267E+00 1.2994521098968692E+00 1.9314919398540248E-01
|
||||
1 3 2.4253583906212917E-01 2.6983010627072188E+00 1.6071345237783112E+00 2.8699477114002486E-01
|
||||
1 4 3.3542904629093495E-01 1.5372546465126264E+00 9.9744101045215361E-01 1.4138420759838821E-01
|
||||
1 5 1.8503709795923420E-01 1.5491787211705357E+00 8.9011559742158108E-01 1.6054085816870503E-01
|
||||
1 6 2.8986050983056133E-01 9.5851457739199852E-01 6.4070535049617905E-01 7.7829435282256818E-02
|
||||
1 7 1.2998738560021622E-01 8.1181447628465786E-01 4.5034968386666990E-01 7.9668681985818710E-02
|
||||
1 8 2.3854599156072026E-01 5.8192272360200603E-01 4.2158764571359886E-01 4.0539426354471435E-02
|
||||
1 9 2.2019401469736052E-01 4.9816927636901054E-01 3.6305272944627787E-01 3.1419040668328617E-02
|
||||
1 10 1.7723908244726444E-01 1.0169045685317621E+00 5.3120597962909644E-01 9.6163510042363842E-02
|
||||
1 11 1.5931165210644979E-01 3.9224005962648778E-01 2.7312983872261626E-01 2.0878706459592580E-02
|
||||
1 12 1.0106474384096639E-01 6.8318193294241025E-01 2.9555524220090690E-01 5.2779720067391560E-02
|
||||
1 13 7.4340659297091619E-02 3.2028897659649835E-01 1.9454657712167570E-01 2.2645835164130143E-02
|
||||
1 14 2.7867297613902112E-02 4.8859027683498957E-01 1.5882253801165480E-01 3.7102407780211254E-02
|
||||
1 15 6.0765964821426774E-03 2.6933341009926554E-01 8.7030393842343678E-02 2.3954982883266630E-02
|
||||
1 16 8.6176614291566273E-04 3.2616869984647917E-01 5.8437222538056971E-02 3.2524425477895975E-02
|
||||
1 17 2.3905486661473520E-08 3.7621880078986758E-02 1.7099399409671336E-02 5.6190834887742394E-03
|
||||
1 18 5.7485161297593659E-05 5.6704347475877770E-02 2.0751242479452554E-02 7.2790207725134878E-03
|
||||
1 19 3.7937631629716383E-06 4.4789516076805022E-02 1.6338823698108015E-02 5.6967712606260336E-03
|
||||
1 20 2.4960312085019903E-02 2.7218197030245517E-01 1.3743696285440926E-01 2.8868015901657586E-02
|
||||
1 21 2.2980773998953256E-03 4.9986220828384470E-02 1.6950824167726756E-02 5.4132966616364337E-03
|
||||
1 22 2.0814361457387778E-07 1.7422614782322748E-02 5.8877295715452889E-03 2.3169759281881051E-03
|
||||
1 23 2.3616425302076981E-02 1.4766564930840750E-01 7.8026009579545183E-02 1.4328402520229721E-02
|
||||
1 24 9.3734209417262540E-06 1.2706009724968383E-02 3.8602266983488276E-03 1.5349222936122972E-03
|
||||
1 25 6.7292482219397467E-04 1.3437347615997143E-02 3.5879997188162072E-03 1.0083099406231111E-03
|
||||
1 26 8.9492218473814448E-03 4.7435519247870893E-02 2.4574480321592818E-02 3.7562620321716488E-03
|
||||
1 27 2.9688834832940051E-04 1.0922315444849038E-02 2.4362779164791831E-03 7.5891040984896532E-04
|
||||
2 1 7.1532528297088083E-01 4.0098976770174595E+00 2.5989042197937402E+00 3.8240252948889814E-01
|
||||
2 2 5.6301628567420527E-02 1.6234842194053070E+00 9.3805754679203801E-01 1.8736449645837763E-01
|
||||
2 3 6.5703695712707699E-01 3.0791315022675048E+00 1.9948820209043094E+00 2.7857971836048201E-01
|
||||
2 4 3.1024606077905838E-02 1.1551308858105025E+00 6.4059931260962955E-01 1.3511922517043518E-01
|
||||
2 5 5.8421509973169194E-01 1.9420240206857451E+00 1.2814107009923545E+00 1.5028032758628354E-01
|
||||
2 6 8.7055091560538176E-03 5.7824321471805962E-01 2.9826715576421958E-01 6.8317345917309730E-02
|
||||
2 7 4.9061923640751393E-01 1.1928444832852640E+00 8.4317529142720049E-01 7.3313958696523449E-02
|
||||
2 8 1.4113901292375167E-03 2.2139468783209257E-01 1.0800688415169922E-01 2.7030088273230602E-02
|
||||
2 9 4.9849874092941715E-01 9.8733752198909885E-01 7.2610545889255640E-01 5.0426765272669670E-02
|
||||
2 10 6.2957062567264221E-03 9.5794186401597337E-01 4.6455014321576571E-01 1.1560059533210595E-01
|
||||
2 11 3.6577588459988464E-01 7.7230200150326977E-01 5.4625967744523252E-01 3.4592870857210925E-02
|
||||
2 12 8.7085544804932510E-04 6.5807276191584230E-01 3.0944891033609345E-01 8.5000814741670302E-02
|
||||
2 13 1.8948992752075242E-01 5.7888624801215693E-01 3.8909315424335084E-01 3.4526650397123625E-02
|
||||
2 14 1.5622199228642329E-05 4.9780490905368319E-01 1.6953376146057861E-01 6.2315791454946375E-02
|
||||
2 15 3.3004285384528591E-02 4.0762166080748574E-01 1.7406078768468755E-01 3.4501395384272583E-02
|
||||
2 16 1.0729012446445082E-10 2.7047079448224992E-01 4.4653384790197932E-02 3.1107465231072703E-02
|
||||
2 17 1.0846205849416071E-05 3.9543401427987353E-02 1.5074459823996002E-02 4.7702333660869702E-03
|
||||
2 18 7.4829063908554593E-11 2.5884908058550057E-03 6.5717634939948741E-04 3.2655127951476974E-04
|
||||
2 19 3.6205850570885452E-03 4.3221294145342604E-01 1.8756542069538723E-01 5.3162621310716321E-02
|
||||
2 20 3.8440097917265245E-07 3.6534575078121363E-02 9.8772821155134784E-03 5.2062500369707320E-03
|
||||
2 21 2.6911400517410067E-03 6.4611970894949161E-02 2.9305443392707013E-02 6.1496063694628919E-03
|
||||
2 22 1.2827584708500362E-03 1.7529487759454226E-01 6.8509716444031324E-02 2.2077211658804261E-02
|
||||
2 23 1.5545977333502778E-02 9.9331349879191635E-02 4.7998454143224914E-02 8.6592611829803771E-03
|
||||
2 24 1.5745634781781375E-05 1.9308534172604155E-02 6.0894070240362372E-03 2.3678290544763853E-03
|
||||
2 25 8.5856663153437229E-11 1.3944217824039388E-03 2.2274994125481308E-04 1.8366900313163600E-04
|
||||
2 26 9.1829498430736033E-03 1.1557634414039414E-01 4.6978379604047091E-02 1.2100545333930811E-02
|
||||
2 27 1.7898602665033226E-04 8.1694699794021677E-02 3.2902418055540193E-02 9.9562973177386629E-03
|
||||
2 28 7.4320386544780976E-10 3.9418035349310827E-03 6.3479370917995882E-04 5.2607016457668454E-04
|
||||
2 29 6.3415719088815280E-03 3.9243185159612948E-02 1.6708820854971294E-02 2.8310386784518439E-03
|
||||
2 30 2.8195782382410411E-03 3.2846540596866002E-02 1.1453659185437729E-02 2.6398096406069107E-03
|
||||
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-6/weights.001.data
Normal file
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-6/weights.001.data
Normal file
File diff suppressed because it is too large
Load diff
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-6/weights.008.data
Normal file
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-6/weights.008.data
Normal file
File diff suppressed because it is too large
Load diff
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-7/input.nn
Normal file
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-7/input.nn
Normal file
|
|
@ -0,0 +1,165 @@
|
|||
###############################################################################
|
||||
# GENERAL NNP SETTINGS
|
||||
###############################################################################
|
||||
# These keywords are (almost) always required.
|
||||
number_of_elements 2 # Number of elements.
|
||||
elements O H # Specification of elements.
|
||||
atom_energy O -74.94518524 # free atom reference energy (atomic zora)
|
||||
atom_energy H -0.45890771 # free atom reference energy (atomic zora)
|
||||
cutoff_type 2 # Cutoff type (optional argument: shift parameter alpha).
|
||||
scale_symmetry_functions # Scale all symmetry functions with min/max values.
|
||||
#scale_symmetry_functions_sigma # Scale all symmetry functions with sigma.
|
||||
scale_min_short 0.0 # Minimum value for scaling.
|
||||
scale_max_short 1.0 # Maximum value for scaling.
|
||||
center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value.
|
||||
global_hidden_layers_short 2 # Number of hidden layers.
|
||||
global_nodes_short 20 20 # Number of nodes in each hidden layer.
|
||||
global_activation_short t t l # Activation function for each hidden layer and output layer.
|
||||
#normalize_nodes # Normalize input of nodes.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR DATASET TOOLS
|
||||
###############################################################################
|
||||
# These keywords are used only by some tools handling data sets:
|
||||
# nnp-comp2, nnp-scaling, nnp-dataset, nnp-train.
|
||||
#use_short_forces # Use forces. Disable - repeated below.
|
||||
random_seed 6 # Random number generator seed.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR TRAINING
|
||||
###############################################################################
|
||||
# These keywords are solely used for training with nnp-train.
|
||||
epochs 100 # Number of training epochs.
|
||||
updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter).
|
||||
parallel_mode 1 # Training parallelization used (0 = Parallel (rank 0 update), 1 = Parallel (all update)).
|
||||
jacobian_mode 2 # Jacobian computation mode (0 = Summation to single gradient, 1 = Per-task summed gradient, 2 = Full Jacobian).
|
||||
update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element).
|
||||
selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold).
|
||||
task_batch_size_energy 1 # Number of energy update candidates prepared per task for each update (0 = Entire training set).
|
||||
task_batch_size_force 1 # Number of force update candidates prepared per task for each update (0 = Entire training set).
|
||||
memorize_symfunc_results # Keep symmetry function results in memory.
|
||||
test_fraction 0.1 # Fraction of structures kept for testing.
|
||||
use_short_forces # Use forces for training.
|
||||
force_weight 2.0 # Weight of force updates relative to energy updates.
|
||||
short_energy_fraction 1.0 # Fraction of energy updates per epoch.
|
||||
short_force_fraction 0.05 # Fraction of force updates per epoch.
|
||||
short_energy_error_threshold 0.8 # RMSE threshold for energy update candidates.
|
||||
short_force_error_threshold 1.0 # RMSE threshold for force update candidates.
|
||||
rmse_threshold_trials 3 # Maximum number of RMSE threshold trials.
|
||||
#use_old_weights_short # Restart fitting with old weight parameters.
|
||||
weights_min -1.0 # Minimum value for initial random weights.
|
||||
weights_max 1.0 # Maximum value for initial random weights.
|
||||
#precondition_weights # Precondition weights with initial energies.
|
||||
nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme.
|
||||
write_trainpoints 0 # Write energy comparison every this many epochs.
|
||||
write_trainforces 0 # Write force comparison every this many epochs.
|
||||
write_weights_epoch 1 # Write weights every this many epochs.
|
||||
write_neuronstats 0 # Write neuron statistics every this many epochs.
|
||||
#write_trainlog # Write training log file.
|
||||
|
||||
############################
|
||||
# KALMAN FILTER (STANDARD) #
|
||||
############################
|
||||
kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory).
|
||||
kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001).
|
||||
kalman_q0 0.01 # General Kalman filter parameter q0 ("large").
|
||||
kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6).
|
||||
kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0).
|
||||
kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+).
|
||||
|
||||
# Are these only for fading Kalman?
|
||||
kalman_lambda_short 0.98000
|
||||
kalman_nue_short 0.99870
|
||||
|
||||
|
||||
|
||||
###############################################################################
|
||||
# SYMMETRY FUNCTIONS
|
||||
###############################################################################
|
||||
|
||||
# INFO: symfunction format: reference atom, type, neighbor element 1 (and neighbor element 2), symfunction parameters
|
||||
|
||||
|
||||
#
|
||||
# radial
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom eta rshift funccutoff
|
||||
|
||||
# H H
|
||||
symfunction_short H 2 H 0.001 0.0 12.00
|
||||
symfunction_short H 2 H 0.01 0.0 12.00
|
||||
symfunction_short H 2 H 0.03 0.0 12.00
|
||||
symfunction_short H 2 H 0.06 0.0 12.00
|
||||
symfunction_short H 2 H 0.15 1.9 12.00
|
||||
symfunction_short H 2 H 0.30 1.9 12.00
|
||||
symfunction_short H 2 H 0.60 1.9 12.00
|
||||
symfunction_short H 2 H 1.50 1.9 12.00
|
||||
|
||||
# H O / O H
|
||||
symfunction_short H 2 O 0.001 0.0 12.00
|
||||
symfunction_short H 2 O 0.01 0.0 12.00
|
||||
symfunction_short H 2 O 0.03 0.0 12.00
|
||||
symfunction_short H 2 O 0.06 0.0 12.00
|
||||
symfunction_short H 2 O 0.15 0.9 12.00
|
||||
symfunction_short H 2 O 0.30 0.9 12.00
|
||||
symfunction_short H 2 O 0.60 0.9 12.00
|
||||
symfunction_short H 2 O 1.50 0.9 12.00
|
||||
symfunction_short O 2 H 0.001 0.0 12.00
|
||||
symfunction_short O 2 H 0.01 0.0 12.00
|
||||
symfunction_short O 2 H 0.03 0.0 12.00
|
||||
symfunction_short O 2 H 0.06 0.0 12.00
|
||||
symfunction_short O 2 H 0.15 0.9 12.00
|
||||
symfunction_short O 2 H 0.30 0.9 12.00
|
||||
symfunction_short O 2 H 0.60 0.9 12.00
|
||||
symfunction_short O 2 H 1.50 0.9 12.00
|
||||
|
||||
# O O
|
||||
symfunction_short O 2 O 0.001 0.0 12.00
|
||||
symfunction_short O 2 O 0.01 0.0 12.00
|
||||
symfunction_short O 2 O 0.03 0.0 12.00
|
||||
symfunction_short O 2 O 0.06 0.0 12.00
|
||||
symfunction_short O 2 O 0.15 4.0 12.00
|
||||
symfunction_short O 2 O 0.30 4.0 12.00
|
||||
symfunction_short O 2 O 0.60 4.0 12.00
|
||||
symfunction_short O 2 O 1.50 4.0 12.00
|
||||
|
||||
#
|
||||
# angular
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
|
||||
|
||||
symfunction_short H 3 O H 0.2 1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.07 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short O 3 H H 0.01 -1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short H 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000
|
||||
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-7/scaling.data
Normal file
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-7/scaling.data
Normal file
|
|
@ -0,0 +1,72 @@
|
|||
################################################################################
|
||||
# Symmetry function scaling data.
|
||||
################################################################################
|
||||
# Col Name Description
|
||||
################################################################################
|
||||
# 1 e_index Element index.
|
||||
# 2 sf_index Symmetry function index.
|
||||
# 3 sf_min Symmetry function minimum.
|
||||
# 4 sf_max Symmetry function maximum.
|
||||
# 5 sf_mean Symmetry function mean.
|
||||
# 6 sf_sigma Symmetry function sigma.
|
||||
#########################################################################################################################
|
||||
# 1 2 3 4 5 6
|
||||
# e_index sf_index sf_min sf_max sf_mean sf_sigma
|
||||
#########################################################################################################################
|
||||
1 1 2.8655329382224032E-01 3.6364355962665180E+00 2.2119784681576466E+00 3.8982164788324686E-01
|
||||
1 2 3.5699082862581144E-01 2.0031124569208267E+00 1.2994521098968672E+00 1.9314919398541502E-01
|
||||
1 3 2.4253583906212917E-01 2.6983010627072188E+00 1.6071345237783126E+00 2.8699477114001432E-01
|
||||
1 4 3.3542904629093495E-01 1.5372546465126264E+00 9.9744101045215450E-01 1.4138420759838038E-01
|
||||
1 5 1.8503709795923420E-01 1.5491787211705357E+00 8.9011559742158164E-01 1.6054085816870253E-01
|
||||
1 6 2.8986050983056133E-01 9.5851457739199852E-01 6.4070535049617894E-01 7.7829435282255846E-02
|
||||
1 7 1.2998738560021622E-01 8.1181447628465786E-01 4.5034968386667051E-01 7.9668681985816336E-02
|
||||
1 8 2.3854599156072026E-01 5.8192272360200603E-01 4.2158764571359925E-01 4.0539426354469256E-02
|
||||
1 9 2.2019401469736052E-01 4.9816927636901054E-01 3.6305272944627826E-01 3.1419040668322989E-02
|
||||
1 10 1.7723908244726444E-01 1.0169045685317621E+00 5.3120597962909599E-01 9.6163510042368838E-02
|
||||
1 11 1.5931165210644979E-01 3.9224005962648778E-01 2.7312983872261587E-01 2.0878706459599532E-02
|
||||
1 12 1.0106474384096639E-01 6.8318193294241025E-01 2.9555524220090690E-01 5.2779720067391199E-02
|
||||
1 13 7.4340659297091619E-02 3.2028897659649835E-01 1.9454657712167578E-01 2.2645835164129168E-02
|
||||
1 14 2.7867297613902112E-02 4.8859027683498957E-01 1.5882253801165483E-01 3.7102407780211254E-02
|
||||
1 15 6.0765964821426774E-03 2.6933341009926554E-01 8.7030393842343651E-02 2.3954982883266990E-02
|
||||
1 16 8.6176614291566273E-04 3.2616869984647917E-01 5.8437222538056943E-02 3.2524425477896149E-02
|
||||
1 17 2.3905486661473520E-08 3.7621880078986758E-02 1.7099399409671343E-02 5.6190834887742307E-03
|
||||
1 18 5.7485161297593659E-05 5.6704347475877770E-02 2.0751242479452554E-02 7.2790207725134401E-03
|
||||
1 19 3.7937631629716383E-06 4.4789516076805022E-02 1.6338823698107977E-02 5.6967712606261593E-03
|
||||
1 20 2.4960312085019903E-02 2.7218197030245517E-01 1.3743696285440926E-01 2.8868015901657530E-02
|
||||
1 21 2.2980773998953256E-03 4.9986220828384470E-02 1.6950824167726739E-02 5.4132966616364979E-03
|
||||
1 22 2.0814361457387778E-07 1.7422614782322748E-02 5.8877295715452872E-03 2.3169759281881199E-03
|
||||
1 23 2.3616425302076981E-02 1.4766564930840750E-01 7.8026009579545183E-02 1.4328402520229612E-02
|
||||
1 24 9.3734209417262540E-06 1.2706009724968383E-02 3.8602266983488284E-03 1.5349222936123003E-03
|
||||
1 25 6.7292482219397467E-04 1.3437347615997143E-02 3.5879997188162089E-03 1.0083099406231041E-03
|
||||
1 26 8.9492218473814448E-03 4.7435519247870893E-02 2.4574480321592797E-02 3.7562620321718062E-03
|
||||
1 27 2.9688834832940051E-04 1.0922315444849038E-02 2.4362779164791813E-03 7.5891040984896988E-04
|
||||
2 1 7.1532528297088083E-01 4.0098976770174595E+00 2.5989042197937415E+00 3.8240252948890446E-01
|
||||
2 2 5.6301628567420527E-02 1.6234842194053070E+00 9.3805754679203701E-01 1.8736449645838249E-01
|
||||
2 3 6.5703695712707699E-01 3.0791315022675048E+00 1.9948820209043101E+00 2.7857971836047041E-01
|
||||
2 4 3.1024606077905838E-02 1.1551308858105025E+00 6.4059931260962977E-01 1.3511922517043443E-01
|
||||
2 5 5.8421509973169194E-01 1.9420240206857451E+00 1.2814107009923568E+00 1.5028032758626403E-01
|
||||
2 6 8.7055091560538176E-03 5.7824321471805962E-01 2.9826715576421947E-01 6.8317345917310285E-02
|
||||
2 7 4.9061923640751393E-01 1.1928444832852640E+00 8.4317529142720071E-01 7.3313958696519993E-02
|
||||
2 8 1.4113901292375167E-03 2.2139468783209257E-01 1.0800688415169930E-01 2.7030088273230106E-02
|
||||
2 9 4.9849874092941715E-01 9.8733752198909885E-01 7.2610545889255584E-01 5.0426765272671668E-02
|
||||
2 10 6.2957062567264221E-03 9.5794186401597337E-01 4.6455014321576582E-01 1.1560059533210584E-01
|
||||
2 11 3.6577588459988464E-01 7.7230200150326977E-01 5.4625967744523218E-01 3.4592870857211661E-02
|
||||
2 12 8.7085544804932510E-04 6.5807276191584230E-01 3.0944891033609356E-01 8.5000814741669789E-02
|
||||
2 13 1.8948992752075242E-01 5.7888624801215693E-01 3.8909315424335067E-01 3.4526650397125457E-02
|
||||
2 14 1.5622199228642329E-05 4.9780490905368319E-01 1.6953376146057852E-01 6.2315791454946423E-02
|
||||
2 15 3.3004285384528591E-02 4.0762166080748574E-01 1.7406078768468752E-01 3.4501395384272764E-02
|
||||
2 16 1.0729012446445082E-10 2.7047079448224992E-01 4.4653384790197932E-02 3.1107465231072693E-02
|
||||
2 17 1.0846205849416071E-05 3.9543401427987353E-02 1.5074459823996005E-02 4.7702333660869598E-03
|
||||
2 18 7.4829063908554593E-11 2.5884908058550057E-03 6.5717634939948730E-04 3.2655127951477001E-04
|
||||
2 19 3.6205850570885452E-03 4.3221294145342604E-01 1.8756542069538715E-01 5.3162621310716439E-02
|
||||
2 20 3.8440097917265245E-07 3.6534575078121363E-02 9.8772821155134853E-03 5.2062500369707198E-03
|
||||
2 21 2.6911400517410067E-03 6.4611970894949161E-02 2.9305443392707024E-02 6.1496063694628364E-03
|
||||
2 22 1.2827584708500362E-03 1.7529487759454226E-01 6.8509716444031268E-02 2.2077211658804420E-02
|
||||
2 23 1.5545977333502778E-02 9.9331349879191635E-02 4.7998454143224942E-02 8.6592611829803094E-03
|
||||
2 24 1.5745634781781375E-05 1.9308534172604155E-02 6.0894070240362390E-03 2.3678290544763840E-03
|
||||
2 25 8.5856663153437229E-11 1.3944217824039388E-03 2.2274994125481335E-04 1.8366900313163573E-04
|
||||
2 26 9.1829498430736033E-03 1.1557634414039414E-01 4.6978379604047084E-02 1.2100545333930826E-02
|
||||
2 27 1.7898602665033226E-04 8.1694699794021677E-02 3.2902418055540186E-02 9.9562973177386733E-03
|
||||
2 28 7.4320386544780976E-10 3.9418035349310827E-03 6.3479370917995839E-04 5.2607016457668465E-04
|
||||
2 29 6.3415719088815280E-03 3.9243185159612948E-02 1.6708820854971284E-02 2.8310386784518964E-03
|
||||
2 30 2.8195782382410411E-03 3.2846540596866002E-02 1.1453659185437731E-02 2.6398096406068969E-03
|
||||
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-7/weights.001.data
Normal file
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-7/weights.001.data
Normal file
File diff suppressed because it is too large
Load diff
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-7/weights.008.data
Normal file
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-7/weights.008.data
Normal file
File diff suppressed because it is too large
Load diff
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/input.nn
Normal file
165
data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/input.nn
Normal file
|
|
@ -0,0 +1,165 @@
|
|||
###############################################################################
|
||||
# GENERAL NNP SETTINGS
|
||||
###############################################################################
|
||||
# These keywords are (almost) always required.
|
||||
number_of_elements 2 # Number of elements.
|
||||
elements O H # Specification of elements.
|
||||
atom_energy O -74.94518524 # free atom reference energy (atomic zora)
|
||||
atom_energy H -0.45890771 # free atom reference energy (atomic zora)
|
||||
cutoff_type 2 # Cutoff type (optional argument: shift parameter alpha).
|
||||
scale_symmetry_functions # Scale all symmetry functions with min/max values.
|
||||
#scale_symmetry_functions_sigma # Scale all symmetry functions with sigma.
|
||||
scale_min_short 0.0 # Minimum value for scaling.
|
||||
scale_max_short 1.0 # Maximum value for scaling.
|
||||
center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value.
|
||||
global_hidden_layers_short 2 # Number of hidden layers.
|
||||
global_nodes_short 20 20 # Number of nodes in each hidden layer.
|
||||
global_activation_short t t l # Activation function for each hidden layer and output layer.
|
||||
#normalize_nodes # Normalize input of nodes.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR DATASET TOOLS
|
||||
###############################################################################
|
||||
# These keywords are used only by some tools handling data sets:
|
||||
# nnp-comp2, nnp-scaling, nnp-dataset, nnp-train.
|
||||
#use_short_forces # Use forces. Disable - repeated below.
|
||||
random_seed 7 # Random number generator seed.
|
||||
|
||||
###############################################################################
|
||||
# ADDITIONAL SETTINGS FOR TRAINING
|
||||
###############################################################################
|
||||
# These keywords are solely used for training with nnp-train.
|
||||
epochs 100 # Number of training epochs.
|
||||
updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter).
|
||||
parallel_mode 1 # Training parallelization used (0 = Parallel (rank 0 update), 1 = Parallel (all update)).
|
||||
jacobian_mode 2 # Jacobian computation mode (0 = Summation to single gradient, 1 = Per-task summed gradient, 2 = Full Jacobian).
|
||||
update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element).
|
||||
selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold).
|
||||
task_batch_size_energy 1 # Number of energy update candidates prepared per task for each update (0 = Entire training set).
|
||||
task_batch_size_force 1 # Number of force update candidates prepared per task for each update (0 = Entire training set).
|
||||
memorize_symfunc_results # Keep symmetry function results in memory.
|
||||
test_fraction 0.1 # Fraction of structures kept for testing.
|
||||
use_short_forces # Use forces for training.
|
||||
force_weight 2.0 # Weight of force updates relative to energy updates.
|
||||
short_energy_fraction 1.0 # Fraction of energy updates per epoch.
|
||||
short_force_fraction 0.05 # Fraction of force updates per epoch.
|
||||
short_energy_error_threshold 0.8 # RMSE threshold for energy update candidates.
|
||||
short_force_error_threshold 1.0 # RMSE threshold for force update candidates.
|
||||
rmse_threshold_trials 3 # Maximum number of RMSE threshold trials.
|
||||
#use_old_weights_short # Restart fitting with old weight parameters.
|
||||
weights_min -1.0 # Minimum value for initial random weights.
|
||||
weights_max 1.0 # Maximum value for initial random weights.
|
||||
#precondition_weights # Precondition weights with initial energies.
|
||||
nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme.
|
||||
write_trainpoints 0 # Write energy comparison every this many epochs.
|
||||
write_trainforces 0 # Write force comparison every this many epochs.
|
||||
write_weights_epoch 1 # Write weights every this many epochs.
|
||||
write_neuronstats 0 # Write neuron statistics every this many epochs.
|
||||
#write_trainlog # Write training log file.
|
||||
|
||||
############################
|
||||
# KALMAN FILTER (STANDARD) #
|
||||
############################
|
||||
kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory).
|
||||
kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001).
|
||||
kalman_q0 0.01 # General Kalman filter parameter q0 ("large").
|
||||
kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6).
|
||||
kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0).
|
||||
kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch).
|
||||
kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+).
|
||||
|
||||
# Are these only for fading Kalman?
|
||||
kalman_lambda_short 0.98000
|
||||
kalman_nue_short 0.99870
|
||||
|
||||
|
||||
|
||||
###############################################################################
|
||||
# SYMMETRY FUNCTIONS
|
||||
###############################################################################
|
||||
|
||||
# INFO: symfunction format: reference atom, type, neighbor element 1 (and neighbor element 2), symfunction parameters
|
||||
|
||||
|
||||
#
|
||||
# radial
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom eta rshift funccutoff
|
||||
|
||||
# H H
|
||||
symfunction_short H 2 H 0.001 0.0 12.00
|
||||
symfunction_short H 2 H 0.01 0.0 12.00
|
||||
symfunction_short H 2 H 0.03 0.0 12.00
|
||||
symfunction_short H 2 H 0.06 0.0 12.00
|
||||
symfunction_short H 2 H 0.15 1.9 12.00
|
||||
symfunction_short H 2 H 0.30 1.9 12.00
|
||||
symfunction_short H 2 H 0.60 1.9 12.00
|
||||
symfunction_short H 2 H 1.50 1.9 12.00
|
||||
|
||||
# H O / O H
|
||||
symfunction_short H 2 O 0.001 0.0 12.00
|
||||
symfunction_short H 2 O 0.01 0.0 12.00
|
||||
symfunction_short H 2 O 0.03 0.0 12.00
|
||||
symfunction_short H 2 O 0.06 0.0 12.00
|
||||
symfunction_short H 2 O 0.15 0.9 12.00
|
||||
symfunction_short H 2 O 0.30 0.9 12.00
|
||||
symfunction_short H 2 O 0.60 0.9 12.00
|
||||
symfunction_short H 2 O 1.50 0.9 12.00
|
||||
symfunction_short O 2 H 0.001 0.0 12.00
|
||||
symfunction_short O 2 H 0.01 0.0 12.00
|
||||
symfunction_short O 2 H 0.03 0.0 12.00
|
||||
symfunction_short O 2 H 0.06 0.0 12.00
|
||||
symfunction_short O 2 H 0.15 0.9 12.00
|
||||
symfunction_short O 2 H 0.30 0.9 12.00
|
||||
symfunction_short O 2 H 0.60 0.9 12.00
|
||||
symfunction_short O 2 H 1.50 0.9 12.00
|
||||
|
||||
# O O
|
||||
symfunction_short O 2 O 0.001 0.0 12.00
|
||||
symfunction_short O 2 O 0.01 0.0 12.00
|
||||
symfunction_short O 2 O 0.03 0.0 12.00
|
||||
symfunction_short O 2 O 0.06 0.0 12.00
|
||||
symfunction_short O 2 O 0.15 4.0 12.00
|
||||
symfunction_short O 2 O 0.30 4.0 12.00
|
||||
symfunction_short O 2 O 0.60 4.0 12.00
|
||||
symfunction_short O 2 O 1.50 4.0 12.00
|
||||
|
||||
#
|
||||
# angular
|
||||
#
|
||||
|
||||
# central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
|
||||
|
||||
symfunction_short H 3 O H 0.2 1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.07 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.07 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 H H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O H 0.03 -1.0 1.0 12.00000
|
||||
|
||||
symfunction_short O 3 H H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 1.0 4.0 12.00000
|
||||
symfunction_short O 3 H H 0.01 -1.0 4.0 12.00000
|
||||
symfunction_short H 3 O H 0.01 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O H 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O H 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short H 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000
|
||||
|
||||
symfunction_short O 3 O O 0.03 1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.03 -1.0 1.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 1.0 4.0 12.00000
|
||||
symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000
|
||||
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/scaling.data
Normal file
72
data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/scaling.data
Normal file
|
|
@ -0,0 +1,72 @@
|
|||
################################################################################
|
||||
# Symmetry function scaling data.
|
||||
################################################################################
|
||||
# Col Name Description
|
||||
################################################################################
|
||||
# 1 e_index Element index.
|
||||
# 2 sf_index Symmetry function index.
|
||||
# 3 sf_min Symmetry function minimum.
|
||||
# 4 sf_max Symmetry function maximum.
|
||||
# 5 sf_mean Symmetry function mean.
|
||||
# 6 sf_sigma Symmetry function sigma.
|
||||
#########################################################################################################################
|
||||
# 1 2 3 4 5 6
|
||||
# e_index sf_index sf_min sf_max sf_mean sf_sigma
|
||||
#########################################################################################################################
|
||||
1 1 2.8655329382224032E-01 3.6364355962665180E+00 2.2119784681576435E+00 3.8982164788326551E-01
|
||||
1 2 3.5699082862581144E-01 2.0031124569208267E+00 1.2994521098968683E+00 1.9314919398540822E-01
|
||||
1 3 2.4253583906212917E-01 2.6983010627072188E+00 1.6071345237783112E+00 2.8699477114002625E-01
|
||||
1 4 3.3542904629093495E-01 1.5372546465126264E+00 9.9744101045215383E-01 1.4138420759838538E-01
|
||||
1 5 1.8503709795923420E-01 1.5491787211705357E+00 8.9011559742158120E-01 1.6054085816870442E-01
|
||||
1 6 2.8986050983056133E-01 9.5851457739199852E-01 6.4070535049617816E-01 7.7829435282261689E-02
|
||||
1 7 1.2998738560021622E-01 8.1181447628465786E-01 4.5034968386667024E-01 7.9668681985817127E-02
|
||||
1 8 2.3854599156072026E-01 5.8192272360200603E-01 4.2158764571359947E-01 4.0539426354468319E-02
|
||||
1 9 2.2019401469736052E-01 4.9816927636901054E-01 3.6305272944627848E-01 3.1419040668316967E-02
|
||||
1 10 1.7723908244726444E-01 1.0169045685317621E+00 5.3120597962909699E-01 9.6163510042361219E-02
|
||||
1 11 1.5931165210644979E-01 3.9224005962648778E-01 2.7312983872261637E-01 2.0878706459594696E-02
|
||||
1 12 1.0106474384096639E-01 6.8318193294241025E-01 2.9555524220090690E-01 5.2779720067391435E-02
|
||||
1 13 7.4340659297091619E-02 3.2028897659649835E-01 1.9454657712167572E-01 2.2645835164130004E-02
|
||||
1 14 2.7867297613902112E-02 4.8859027683498957E-01 1.5882253801165500E-01 3.7102407780210449E-02
|
||||
1 15 6.0765964821426774E-03 2.6933341009926554E-01 8.7030393842343637E-02 2.3954982883267122E-02
|
||||
1 16 8.6176614291566273E-04 3.2616869984647917E-01 5.8437222538056971E-02 3.2524425477896073E-02
|
||||
1 17 2.3905486661473520E-08 3.7621880078986758E-02 1.7099399409671336E-02 5.6190834887742654E-03
|
||||
1 18 5.7485161297593659E-05 5.6704347475877770E-02 2.0751242479452540E-02 7.2790207725134774E-03
|
||||
1 19 3.7937631629716383E-06 4.4789516076805022E-02 1.6338823698107987E-02 5.6967712606261160E-03
|
||||
1 20 2.4960312085019903E-02 2.7218197030245517E-01 1.3743696285440937E-01 2.8868015901657423E-02
|
||||
1 21 2.2980773998953256E-03 4.9986220828384470E-02 1.6950824167726752E-02 5.4132966616364337E-03
|
||||
1 22 2.0814361457387778E-07 1.7422614782322748E-02 5.8877295715452907E-03 2.3169759281881134E-03
|
||||
1 23 2.3616425302076981E-02 1.4766564930840750E-01 7.8026009579545169E-02 1.4328402520229969E-02
|
||||
1 24 9.3734209417262540E-06 1.2706009724968383E-02 3.8602266983488245E-03 1.5349222936123085E-03
|
||||
1 25 6.7292482219397467E-04 1.3437347615997143E-02 3.5879997188162059E-03 1.0083099406231117E-03
|
||||
1 26 8.9492218473814448E-03 4.7435519247870893E-02 2.4574480321592825E-02 3.7562620321716748E-03
|
||||
1 27 2.9688834832940051E-04 1.0922315444849038E-02 2.4362779164791818E-03 7.5891040984896836E-04
|
||||
2 1 7.1532528297088083E-01 4.0098976770174595E+00 2.5989042197937402E+00 3.8240252948891079E-01
|
||||
2 2 5.6301628567420527E-02 1.6234842194053070E+00 9.3805754679203801E-01 1.8736449645837711E-01
|
||||
2 3 6.5703695712707699E-01 3.0791315022675048E+00 1.9948820209043081E+00 2.7857971836048634E-01
|
||||
2 4 3.1024606077905838E-02 1.1551308858105025E+00 6.4059931260962999E-01 1.3511922517043462E-01
|
||||
2 5 5.8421509973169194E-01 1.9420240206857451E+00 1.2814107009923554E+00 1.5028032758627749E-01
|
||||
2 6 8.7055091560538176E-03 5.7824321471805962E-01 2.9826715576421958E-01 6.8317345917309452E-02
|
||||
2 7 4.9061923640751393E-01 1.1928444832852640E+00 8.4317529142720060E-01 7.3313958696522061E-02
|
||||
2 8 1.4113901292375167E-03 2.2139468783209257E-01 1.0800688415169930E-01 2.7030088273230075E-02
|
||||
2 9 4.9849874092941715E-01 9.8733752198909885E-01 7.2610545889255551E-01 5.0426765272679683E-02
|
||||
2 10 6.2957062567264221E-03 9.5794186401597337E-01 4.6455014321576626E-01 1.1560059533210355E-01
|
||||
2 11 3.6577588459988464E-01 7.7230200150326977E-01 5.4625967744523263E-01 3.4592870857206547E-02
|
||||
2 12 8.7085544804932510E-04 6.5807276191584230E-01 3.0944891033609356E-01 8.5000814741669858E-02
|
||||
2 13 1.8948992752075242E-01 5.7888624801215693E-01 3.8909315424335084E-01 3.4526650397123992E-02
|
||||
2 14 1.5622199228642329E-05 4.9780490905368319E-01 1.6953376146057855E-01 6.2315791454946576E-02
|
||||
2 15 3.3004285384528591E-02 4.0762166080748574E-01 1.7406078768468752E-01 3.4501395384273041E-02
|
||||
2 16 1.0729012446445082E-10 2.7047079448224992E-01 4.4653384790197939E-02 3.1107465231072679E-02
|
||||
2 17 1.0846205849416071E-05 3.9543401427987353E-02 1.5074459823996010E-02 4.7702333660869546E-03
|
||||
2 18 7.4829063908554593E-11 2.5884908058550057E-03 6.5717634939948730E-04 3.2655127951477017E-04
|
||||
2 19 3.6205850570885452E-03 4.3221294145342604E-01 1.8756542069538720E-01 5.3162621310716265E-02
|
||||
2 20 3.8440097917265245E-07 3.6534575078121363E-02 9.8772821155134766E-03 5.2062500369707415E-03
|
||||
2 21 2.6911400517410067E-03 6.4611970894949161E-02 2.9305443392707013E-02 6.1496063694629561E-03
|
||||
2 22 1.2827584708500362E-03 1.7529487759454226E-01 6.8509716444031241E-02 2.2077211658804545E-02
|
||||
2 23 1.5545977333502778E-02 9.9331349879191635E-02 4.7998454143224963E-02 8.6592611829801273E-03
|
||||
2 24 1.5745634781781375E-05 1.9308534172604155E-02 6.0894070240362363E-03 2.3678290544763840E-03
|
||||
2 25 8.5856663153437229E-11 1.3944217824039388E-03 2.2274994125481308E-04 1.8366900313163598E-04
|
||||
2 26 9.1829498430736033E-03 1.1557634414039414E-01 4.6978379604047084E-02 1.2100545333930859E-02
|
||||
2 27 1.7898602665033226E-04 8.1694699794021677E-02 3.2902418055540207E-02 9.9562973177386039E-03
|
||||
2 28 7.4320386544780976E-10 3.9418035349310827E-03 6.3479370917995861E-04 5.2607016457668389E-04
|
||||
2 29 6.3415719088815280E-03 3.9243185159612948E-02 1.6708820854971270E-02 2.8310386784519571E-03
|
||||
2 30 2.8195782382410411E-03 3.2846540596866002E-02 1.1453659185437726E-02 2.6398096406069151E-03
|
||||
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/weights.001.data
Normal file
1017
data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/weights.001.data
Normal file
File diff suppressed because it is too large
Load diff
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/weights.008.data
Normal file
1077
data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/weights.008.data
Normal file
File diff suppressed because it is too large
Load diff
Loading…
Add table
Add a link
Reference in a new issue