Committee-NNP

examples/interface-LAMMPS/H2O_RPBE-D3/md.lmp

@@ -29,6 +29,8 @@ mass 1 ${mass_H}
 mass 2 ${mass_O}
 timestep ${dt}
 thermo 1
+thermo_modify format float %14.6f
+dump 4a all custom 5 dump.myforce.* id type fx fy fz
 
 ###############################################################################
 # NN

examples/interface-LAMMPS/H2O_RPBE-D3/nnp-data/input.nn

@@ -1,11 +1,3 @@
-###############################################################################
-# HDNNP for water H2O
-###############################################################################
-# Length unit     : Bohr
-# Energy unit     : Ha
-# Reference method: RPBE-D3
-###############################################################################
-
 ###############################################################################
 # DATA SET NORMALIZATION
 ###############################################################################
@@ -42,7 +34,7 @@ parallel_mode                   4              # Training parallelization used (
 update_strategy                 0              # Update strategy (0 = Combined, 1 = Per-element).
 selection_mode                  2              # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold).
 memorize_symfunc_results                       # Keep symmetry function results in memory.
-random_seed 2
+random_seed 7
 test_fraction                   0.1            # Fraction of structures kept for testing.
 use_short_forces                               # Use forces for training.
 force_weight                    10.0           # Weight of force updates relative to energy updates.

examples/interface-LAMMPS/H2O_RPBE-D3_Committee/md.lmp

@@ -0,0 +1,50 @@
+###############################################################################
+# MD simulation for NN water
+###############################################################################
+
+###############################################################################
+# VARIABLES
+###############################################################################
+clear
+# Configuration files
+variable cfgFile         string "h2o_8640_liquid_NpT_RPBE-D3.data"
+# Timesteps
+variable numSteps        equal  100
+variable dt              equal  0.0005
+# NN
+variable nnpCutoff       equal  6.36
+variable nnpDir          string "nnp-data"
+# Masses
+variable mass_H          equal  1.00794
+variable mass_O          equal  15.9994
+
+###############################################################################
+# GENERAL SETUP
+###############################################################################
+units metal
+boundary p p p
+atom_style atomic
+read_data ${cfgFile}
+mass 1 ${mass_H}
+mass 2 ${mass_O}
+timestep ${dt}
+thermo 1
+thermo_modify format float %14.6f
+dump 4a all custom 1 dump.myforce.* id type fx fy fz
+
+###############################################################################
+# NN
+###############################################################################
+pair_style nnp dir ${nnpDir} showew no showewsum 10 resetew no maxew 100 calcd 1 wricde 1.6 maxcde 3.0 wricdf 0.04 maxcdf 0.10 cflength 1.8897261328 cfenergy 0.0367493254 emap "1:H,2:O"
+pair_coeff * * ${nnpCutoff}
+
+###############################################################################
+# INTEGRATOR
+###############################################################################
+fix INT all nve
+dump 1 all atom 1 traj.dump
+
+###############################################################################
+# SIMULATION
+###############################################################################
+run ${numSteps}

examples/interface-LAMMPS/H2O_RPBE-D3_Committee/nnp-data/input.nn

@@ -0,0 +1,169 @@
+###############################################################################
+# DATA SET NORMALIZATION
+###############################################################################
+# This section was automatically added by nnp-norm.
+mean_energy  -2.5521343547039809E+01
+conv_energy   2.4265748255366972E+02
+conv_length   5.8038448995319847E+00
+###############################################################################
+
+###############################################################################
+# GENERAL NNP SETTINGS
+###############################################################################
+number_of_elements              2              # Number of elements.
+elements                        H O            # Specification of elements.
+#atom_energy                     H -0.45890771  # Free atom reference energy (H).
+#atom_energy                     O -74.94518524 # Free atom reference energy (O).
+cutoff_type                     2              # Cutoff type.
+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              25 25          # 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.
+committee_mode                  prediction     # Enables Committee-HDNNP, possible modes = prediction, validation.
+committee_data                  nnp-data 8     # Committee data directory prefix and committee size.
+
+###############################################################################
+# ADDITIONAL SETTINGS FOR TRAINING
+###############################################################################
+epochs                          25             # Number of training epochs.
+updater_type                    1              # Weight update method (0 = Gradient Descent, 1 = Kalman filter).
+parallel_mode                   4              # Training parallelization used (0 = Serial, 1 = Multi-stream, 2 = MS with PMO).
+update_strategy                 0              # Update strategy (0 = Combined, 1 = Per-element).
+selection_mode                  2              # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold).
+memorize_symfunc_results                       # Keep symmetry function results in memory.
+random_seed 7
+test_fraction                   0.1            # Fraction of structures kept for testing.
+use_short_forces                               # Use forces for training.
+force_weight                    10.0           # Weight of force updates relative to energy updates.
+short_energy_fraction           1.000          # Fraction of energy updates per epoch.
+short_force_fraction            0.041          # Fraction of force updates per epoch.
+short_energy_error_threshold    1.00           # RMSE threshold for energy update candidates.
+short_force_error_threshold     1.00           # RMSE threshold for force update candidates.
+rmse_threshold_trials           3              # Maximum number of RMSE threshold trials.
+#repeated_energy_update                         # After force update perform energy update for corresponding structure.
+#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               25             # Write energy comparison.
+write_trainforces               25             # Write force comparison.
+write_weights_epoch                            # Write weights.
+write_neuronstats               5 10           # Write neuron statistics.
+write_trainlog                                 # Write training log file.
+####################
+# GRADIENT DESCENT #
+####################
+gradient_type                   0              # Gradient descent type (0 = Fixed step size).
+gradient_eta                    1.0E-4         # Gradient descent parameter eta (fixed step size).
+############################
+# 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+).
+#################################
+# KALMAN FILTER (FADING MEMORY) #
+#################################
+#kalman_type                     1              # Kalman filter type (0 = Standard, 1 = Fading memory).
+#kalman_epsilon                  1.0E-1         # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001).
+#kalman_q0                       0.00           # 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                     0.0E-6         # General Kalman filter parameter qmin (typ. 1.0E-6).
+#kalman_lambda_short             0.96000        # Fading memory Kalman filter parameter lambda (forgetting factor 0.95-0.99).
+#kalman_nue_short                0.99950        # Fading memory Kalman filter parameter nu (0.99-0.9995).
+
+###############################################################################
+# SYMMETRY FUNCTIONS
+###############################################################################
+
+# Radial symmetry function (type 2):
+#symfunction_short <element-central> 2 <element-neighbor> <eta> <rshift> <rcutoff>
+
+# Narrow Angular symmetry function (type 3):
+#symfunction_short <element-central> 3 <element-neighbor1> <element-neighbor2> <eta> <lambda> <zeta> <rcutoff>
+
+# Wide Angular symmetry function (type 9):
+#symfunction_short <element-central> 9 <element-neighbor1> <element-neighbor2> <eta> <lambda> <zeta> <rcutoff>
+
+# radial 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
+
+# radial 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
+
+# radial 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
+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