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add some additional NNP and helium related data/inputs
This commit is contained in:
Harald Forbert
hforbert
parent
c9ed8e0e9c
commit
93bc24a11a
15 changed files with 7081 additions and 3 deletions
13
data/NNP/protH2OHelium-interaction-nnp/readme.md
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data/NNP/protH2OHelium-interaction-nnp/readme.md
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#### Neural Network IP for Helium and Protonated Water (H<sub>3</sub>O<sup>+</sup>-He)
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This is an updated version of the originally developed NNP to use CCSD(T\*)-F12a/AVTZ-cp
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calculations.
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Original publication of the methodology: "High-dimensional neural network potentials for solvation:
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The case of protonated water clusters in helium" Reference:
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[J. Chem. Phys. 148 (10), 102310 (2018)](https://doi.org/10.1063/1.4996819). Preprint available on
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[arxiv](https://arxiv.org/abs/2103.13123).
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Publication of the updated version: "Properties of hydrogen bonding at ultra-low temperatures in
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superfluid quantum solvents.", C. Schran, PhD thesis, Ruhr-Universitaet Bochum, 2019.
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(https://doi.org/10.13154/294-9852)
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304
data/NNP/protH2Ocluster-jctc2020-nnp/input.nn
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data/NNP/protH2Ocluster-jctc2020-nnp/input.nn
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## #############################################################
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### This is the input file for RuNNer (version 0_44 and upwards)
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### #############################################################
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### General remarks:
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### - commands can be switched off by using the # character at the BEGINNING of the line
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### - the input file can be structured by blank lines and comment lines
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### - the order of the keywords is arbitrary
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### - if keywords are missing, default values will be used and written to runner.out
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### - if mandatory keywords or keyword options are missing, RuNNer will stop with an error message
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element_decoupled_kalman
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########################################################################################################################
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### general keywords
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########################################################################################################################
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nn_type_short 1 # 1=Behler-Parrinello, 2=Pair NN
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runner_mode 2 # 1=calculate symmetry functions, 2=fitting mode, 3=predicition mode (mode)
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number_of_elements 2 # number of elements (nelem) MODE1+2+3+4
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elements O H # specification of elements (element) MODE1+2+3+4
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random_seed 22 # seed for initial random weight parameters and train/test splitting (iseed) MODE1+2
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random_number_type 1 # 1=ran0, 2=ran1, 3=ran2, 4=ran3
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remove_atom_energies # remove atomic energies before fitting (lremoveatomenergies) MODE1+2+3+4
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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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#energy_threshold 100.0d0 # energythreshold for fitting data in Ha per atom (fitethres) MODE1
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#bond_threshold 0.4d0 # threshold for the shortest bond in structure (rmin) MODE1+2+3
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########################################################################################################################
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### NN structure of the short-range NN
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########################################################################################################################
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use_short_nn # use NN for short range interactions (lshort)
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global_hidden_layers_short 2 # number of hidden layers (num_layersshort-1)
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global_nodes_short 30 30 # number of nodes in hidden layers (nodes_short)
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global_activation_short t t l # activation functions (actfunc_short)
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########################################################################################################################
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### symmetry function generation ( mode 1):
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########################################################################################################################
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#use_atom_energies # use atomic energies for fitting (not implemented) (luseatomenergies) MODE1+2+3+4
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use_atom_charges # use atomic charges for fitting(set always true!) (luseatomcharges) MODE1+2+3+4
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test_fraction 0.1 # threshold for splitting between fitting and test set (splitthres) MODE1
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#CAUTION: don't forget use_short_forces below (if you want to generate the training files for the forces)
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########################################################################################################################
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### symmetry function definitions (all modes):
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########################################################################################################################
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# INFO: not yet implemented in this file
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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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# GLOBAL SYMMETRY FUNCTIONS FOR SHORT RANGE NN
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# SAMPLE TYPE 1: global_symfunction_short 1 2.0 ! type funccutoff
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# SAMPLE TYPE 2: global_symfunction_short 2 7.14214 0.0 11.338 ! type eta rshift funccutoff
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# SAMPLE TYPE 3: global_symfunction_short 3 0.03571 -1.0 16.0 7.55891 ! type eta lambda zeta funccutoff
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# SAMPLE TYPE 4: global_symfunction_short 4 7.14214 11.338 ! type eta funccutoff
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# SAMPLE TYPE 5: global_symfunction_short O 5 1.000 ! central_atom type eta ! CARTESIAN COORDINATES
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# SAMPLE TYPE 6: global_symfunction_short O 6 11.338 ! central_atom type funccutoff ! BOND LENGTH
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#
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# ELEMENT-SPECIFIC SYMMETRY FUNCTIONS FOR SHORT RANGE NN
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# SAMPLE TYPE 1: element_symfunction_short O 1 2.0 ! central_atom type funccutoff
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# SAMPLE TYPE 2: element_symfunction_short O 2 7.14214 0.0 11.338 ! central_atom type eta rshift funccutoff
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# SAMPLE TYPE 3: element_symfunction_short O 3 0.03571 -1.0 16.0 7.55891 ! central_atom type eta lambda zeta funccutoff
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# SAMPLE TYPE 4: element_symfunction_short O 4 7.14214 11.338 ! central_atom type eta funccutoff
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# SAMPLE TYPE 5: element_symfunction_short O 5 1.000 ! central_atom type eta ! CARTESIAN COORDINATES
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# SAMPLE TYPE 6: element_symfunction_short O 6 11.338 ! central_atom type funccutoff ! BOND LENGTH
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#
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# CUSTOMIZED SYMMETRY FUNCTIONS FOR SHORT RANGE NN
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# SAMPLE TYPE 1: symfunction_short O 1 O 2.0 ! central_atom type neighbor_atom funccutoff
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# SAMPLE TYPE 2: symfunction_short O 2 O 7.14214 0.0 11.338 ! central_atom type neighbor_atom eta rshift funccutoff
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# SAMPLE TYPE 3: symfunction_short O 3 Zn Zn 0.03571 -1.0 16.0 7.55891 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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# SAMPLE TYPE 4: symfunction_short O 4 O 7.14214 11.338 ! central_atom type neighbor_atom eta funccutoff
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# SAMPLE TYPE 5: symfunction_short O 5 1.000 ! central_atom type eta ! CARTESIAN COORDIATES
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# SAMPLE TYPE 6: symfunction_short O 6 O 11.338 ! central_atom type neighbor_atom funccutoff ! BOND LENGTH
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cutoff_type 1
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symfunction_short H 2 O 0.00100 0.0 4.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.01000 0.0 4.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.03000 0.0 4.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.06000 0.0 4.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.15000 0.0 4.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.15000 1.5 4.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.30000 1.5 4.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.60000 1.5 4.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.00100 0.0 6.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.01000 0.0 6.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.03000 0.0 6.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.06000 0.0 6.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.15000 0.0 6.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.15000 1.5 6.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.30000 1.5 6.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.00100 0.0 12.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.00100 0.0 12.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.01000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.01000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.03000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.03000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.06000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.06000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.15000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.15000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.15000 1.5 12.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.15000 1.5 12.000 ! eta rshift funccutoff
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symfunction_short H 2 H 0.30000 1.5 12.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.30000 1.5 12.000 ! eta rshift funccutoff
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symfunction_short H 2 O 0.60000 1.5 12.000 ! eta rshift funccutoff
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symfunction_short H 3 H O 0.010 -1.0 1.0 6.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.010 1.0 1.0 6.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.010 -1.0 2.0 6.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.010 1.0 2.0 6.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.010 1.0 3.0 6.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.010 -1.0 1.0 8.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.010 1.0 1.0 8.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.010 -1.0 2.0 8.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.010 1.0 2.0 8.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.010 1.0 3.0 8.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 O O 0.001 1.0 4.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.010 -1.0 4.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.010 1.0 4.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.030 -1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 O O 0.030 -1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.030 1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 O O 0.030 1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.070 -1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.070 1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short H 3 H O 0.200 1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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# O:
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symfunction_short O 2 H 0.00100 0.0 4.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.01000 0.0 4.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.03000 0.0 4.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.06000 0.0 4.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.15000 0.0 4.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.15000 1.5 4.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.30000 1.5 4.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.60000 1.5 4.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.00100 0.0 12.000 ! eta rshift funccutoff
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symfunction_short O 2 O 0.00100 0.0 12.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.01000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short O 2 O 0.01000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.03000 1.5 12.000 ! eta rshift funccutoff
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symfunction_short O 2 O 0.03000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short O 2 O 0.06000 1.5 12.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.06000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short O 2 O 0.06000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short O 2 O 0.09000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short O 2 O 0.15000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.15000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.30000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short O 2 H 0.60000 0.0 12.000 ! eta rshift funccutoff
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symfunction_short O 3 H H 0.010 -1.0 1.0 6.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.010 1.0 1.0 6.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.010 -1.0 2.0 6.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.010 1.0 2.0 6.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.010 -1.0 3.0 6.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.010 -1.0 1.0 8.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.010 1.0 1.0 8.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.010 -1.0 2.0 8.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.010 1.0 2.0 8.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.010 -1.0 3.0 8.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H O 0.001 -1.0 4.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H O 0.001 1.0 4.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 O O 0.001 1.0 4.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.010 -1.0 4.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.010 1.0 4.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.030 -1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H O 0.030 -1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 O O 0.030 -1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.030 1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H O 0.030 1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 O O 0.030 1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.070 -1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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symfunction_short O 3 H H 0.070 1.0 1.0 12.00000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff
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#
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# SYMMETRY FUNCTIONS FOR ELECTROSTATIC NN HAVE THE SAME FORMAT, BUT REPLACE "short" by "electrostatic"
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########################################################################################################################
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### fitting (mode 2):general inputs for short range AND electrostatic part:
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########################################################################################################################
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epochs 80 # number of epochs (nepochs) MODE2
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points_in_memory 2000 # max number of structures in memory (nblock) MODE2
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mix_all_points # training with random order of points (lrandomtrain) MODE2
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scale_symmetry_functions # scale symmetry functions (lscalesym) MODE2+3+4
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center_symmetry_functions # remove center of mass of structure function values (lcentersym) MODE2+3+4
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#fix_weights # fix some weights (lfixweights) MODE2
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#growth_mode 11 6 # growth mode (lgrowth,ngrowth,growthstep) MODE2
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#use_damping 0.00001d0 # use weight decay (ldampw,dampw) MODE2
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#pdate_single_element 8 # do weight update just for one element (lupdatebyelement,elemupdate) MODE2
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fitting_unit eV # unit for error output in mode 2 (eV or Ha)
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#joint_energy_force_update # for each atom do one update for energy and averaged forces together (not yet working well)
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########################################################################################################################
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### fitting options ( mode 2): short range part only:
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########################################################################################################################
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print_mad
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optmode_short_energy 1 # optimization mode short range energies(optmodee, 1=Kalman filter, 2=conjugate gradient, 3=steepest descent)
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optmode_short_force 1 # optimization mode short range forces (optmodef, 1=Kalman filter, 2=conjugate gradient, 3=steepest descent)
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short_energy_error_threshold 0.8 # threshold of adaptive Kalman filter short E (kalmanthreshold) MODE2
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short_force_error_threshold 1.0 # threshold of adaptive Kalman filter short F (kalmanthresholdf) MODE2
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kalman_lambda_short 0.98000 # Kalman parameter short E/F (kalmanlambda) MODE2
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kalman_nue_short 0.99870 # Kalman parameter short E/F (kalmannue) MODE2
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#steepest_descent_step_energy_short 0.01d0 # step size for steepest descent energy (steepeststepe) MODE2
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#steepest_descent_step_force_short 0.01d0 # step size for steepest descent force (steepeststepf) MODE2
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#use_old_weights_short # restart fitting with old weight parameters for short (luseoldweightsshort) MODE2
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#update_worst_short_energies 0.1d0 # percentage of the worst energies used for update (worste) MODE2
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#update_worst_short_forces 0.1d0 # percentage of the worst forces used for update (worstf) MODE2
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#force_update_scaling -1.0d0 # scaling factor for the force update (negative value means automatic scaling) (scalefactorf) MODE2
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#short_energy_group 1 # group energies for update (nenergygroup) MODE2
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#short_energy_fraction 1.00 # percentage of energies used for fitting 100%=1.0 (energyrnd) MODE2
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#short_force_group 1 # group forces for update (nforcegroup) MODE2
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#short_force_fraction 0.05 # percentage of forces used for fitting 100%=1.0 (forcernd) MODE2
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#use_short_forces # use forces for fitting (luseforces) MODE2
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#weight_constraint H all fixed # "all" switch
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#weight_constraint O interlayer 1 2 free # "interlayer" layer1 layer2 switch
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#weight_constraint Zn bias 1 2 free # "bias layer" node switch
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#weight_constraint Zn weight 1 3 2 3 free # "weight" layer1 node1 layer2 node2 switch
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#weight_constraint Zn node 1 1 free # "node" layer node switch
|
||||
weights_min -1.0 # minimum value for initial random short range weights
|
||||
weights_max 1.0 # maximum value for initial random short range weights
|
||||
precondition_weights # precondition initial weights (lprecond)
|
||||
#normalize_nodes # normalize input of nodes
|
||||
repeated_energy_update # calculate error of
|
||||
nguyen_widrow_weights_short # initialize short
|
||||
|
||||
|
||||
########################################################################################################################
|
||||
### fitting ( mode 2): electrostatic part only:
|
||||
########################################################################################################################
|
||||
#optmode_charge 1 # optimization mode atomic charges (optmodeq, 1=Kalman filter, 2=conjugate gradient, 3=steepest descent)
|
||||
#charge_error_threshold 1.0 # threshold of adaptive Kalman filter charge (kalmanthresholde) MODE2
|
||||
#kalman_lambda_charge 0.98000 # Kalman parameter charge (kalmanlambdae) MODE2
|
||||
#kalman_nue_charge 0.99870 # Kalman parameter charge (kalmannuee) MODE2
|
||||
#steepest_descent_step_charge 0.01d0 # step size for steepest descent charge (steepeststepq) MODE2
|
||||
#use_old_weights_charge # restart fitting with old weight parameters for charge(luseoldweightscharge) MODE2
|
||||
#update_worst_charges 0.1d0 # percentage of the worst charges used for update (worstq) MODE2
|
||||
#charge_group 20 # group charges for update (nchargegroup) MODE2
|
||||
#charge_fraction 1.00 # percentage of charges used for fitting 100%=1.0 (chargernd) MODE2
|
||||
#weighte_constraint O all fixed # "all" switch
|
||||
#weighte_constraint O interlayer 1 2 free # "interlayer" layer1 layer2 switch
|
||||
#weighte_constraint Zn bias 1 2 free # "bias layer" node switch
|
||||
#weighte_constraint Zn weight 1 3 2 3 free # "weight" layer1 node1 layer2 node2 switch
|
||||
#weighte_constraint Zn node 2 1 free # "node" layer node switch
|
||||
#precondition_weights # precondition initial weights (lprecond)
|
||||
#nguyen_widrow_weights_ewald # initialize short
|
||||
#weightse_min -1.0 # minimum value for initial random charge weights
|
||||
#weightse_max 1.0 # maximum value for initial random charge weights
|
||||
|
||||
########################################################################################################################
|
||||
### options for charge constraint in mode 2 (not tested! not parallel!)
|
||||
########################################################################################################################
|
||||
#use_charge_constraint # use total charge constraint (lchargeconstraint) MODE2
|
||||
#total_charge_error_threshold 0.0000001 # threshold of adaptive Kalman filter charge constraint(kalmanthresholdc) MODE2
|
||||
#kalman_lambda_charge_constraint 0.98000 # Kalman parameter charge constraint (kalmanlambdac) MODE2
|
||||
#kalman_nue_charge_constraint 0.99870 # Kalman parameter charge constraint (kalmannuec) MODE2
|
||||
|
||||
########################################################################################################################
|
||||
### output options for mode 2 (fitting):
|
||||
########################################################################################################################
|
||||
#write_weights_epoch 1 # write set of weight parameters every ith epoch (iwriteweight) MODE2
|
||||
#write_temporary_weights # write temporary weights each data block (lwritetmpweights) MODE2
|
||||
#write_trainpoints # write trainpoints.out and testpoints.out files (lwritetrainpoints) MODE2
|
||||
#write_traincharges # write traincharges.out and testcharges.out files (lwritetraincharges) MODE2
|
||||
#write_trainforces # write trainforces.out and testforces.out files (lwritetrainforces) MODE2
|
||||
|
||||
########################################################################################################################
|
||||
### output options for mode 3 (prediction):
|
||||
########################################################################################################################
|
||||
calculate_forces # calculate forces (ldoforces) MODE3
|
||||
#calculate_stress # calculate stress (ldostress)(not fully implemented) MODE3
|
||||
#write_pdb # write predicted structure in pdb format (lwritepdb) MODE3
|
||||
#write_xyz # write predicted structure in xyz format (lwritexyz) MODE3
|
||||
#write_pov # write predicted structure in pov format (lwritepov) MODE3
|
||||
#write_pwscf # write predicted structure in pwscf format (lwritepw) MODE3
|
||||
|
||||
########################################################################################################################
|
||||
### output options for debug.out file
|
||||
########################################################################################################################
|
||||
#print_all_short_weights
|
||||
#print_all_electrostatic_weights
|
||||
|
||||
########################################################################################################################
|
||||
### options for mode 4 (not yet working)
|
||||
########################################################################################################################
|
||||
#symfunction_check_threshold 0.001d0 # threshold for symmetry function check (symthres) MODE4
|
||||
#charge_check_threshold 0.0002d0 # threshold for atomic charge check (chargethres) MODE4
|
||||
#force_check_threshold 0.0003d0 # threshold for atomic force check (forcethres) MODE4
|
||||
#energy_check_threshold 0.0004d0 # threshold for atomic energy check (energythres)(not yet implemented) MODE4
|
||||
5
data/NNP/protH2Ocluster-jctc2020-nnp/readme.md
Normal file
5
data/NNP/protH2Ocluster-jctc2020-nnp/readme.md
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
#### A Neural Network PES for Protonated Water Cluster (H<sub>2</sub>O, H<sub>3</sub>O<sup>+</sup>, H<sub>5</sub>O<sub>2</sub><sup>+</sup>, H<sub>7</sub>O<sub>3</sub><sup>+</sup>, H<sub>9</sub>O<sub>4</sub><sup>+</sup>)
|
||||
|
||||
Reference:
|
||||
[J. Chem. Theo. Comput. 16 88-99 (2020)](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00805) -
|
||||
Preprint available on [arxiv](https://arxiv.org/abs/1908.08734).
|
||||
98
data/NNP/protH2Ocluster-jctc2020-nnp/scaling.data
Normal file
98
data/NNP/protH2Ocluster-jctc2020-nnp/scaling.data
Normal file
|
|
@ -0,0 +1,98 @@
|
|||
1 1 0.165866306 1.150251278 0.596258580
|
||||
1 2 0.153557832 1.117121138 0.576151625
|
||||
1 3 0.129377333 1.046884305 0.534099497
|
||||
1 4 0.100054708 0.949743512 0.477212046
|
||||
1 5 0.046278101 0.709253284 0.342606118
|
||||
1 6 0.123261629 1.137980874 0.576333141
|
||||
1 7 0.090819048 1.122213144 0.556886439
|
||||
1 8 0.049303191 1.091394050 0.523892578
|
||||
1 9 0.237444578 2.231342694 0.927071145
|
||||
1 10 0.205030225 2.056354519 0.839559591
|
||||
1 11 0.147966614 1.724095491 0.676015706
|
||||
1 12 0.090715711 1.339980859 0.492654192
|
||||
1 13 0.020904454 0.674654564 0.200282009
|
||||
1 14 0.091811226 1.615739187 0.581957504
|
||||
1 15 0.034925820 1.254779643 0.384809986
|
||||
1 16 0.751433278 5.981202053 2.941799272
|
||||
1 17 0.866855577 3.527665557 1.839341041
|
||||
1 18 0.655964897 5.212588917 2.391783325
|
||||
1 19 0.808725291 3.318433461 1.595858867
|
||||
1 20 0.485006608 3.844183495 1.636759612
|
||||
1 21 0.693123352 2.897164460 1.256359093
|
||||
1 22 0.308353043 2.448769562 1.047554995
|
||||
1 23 0.541873300 2.364074731 0.984905817
|
||||
1 24 0.066848987 1.064338339 0.372634018
|
||||
1 25 0.238344311 1.287189548 0.628012203
|
||||
1 26 0.313718706 2.773703678 1.152109163
|
||||
1 27 0.639670343 2.954118854 1.132760729
|
||||
1 28 0.108662427 1.969479056 0.705507231
|
||||
1 29 0.467086800 2.460981749 1.031731943
|
||||
1 30 0.253524242 1.787085849 0.936409559
|
||||
1 31 0.001604317 0.488283013 0.085071113
|
||||
1 32 0.152752128 1.892027291 0.789749004
|
||||
1 33 0.000007644 0.228082000 0.011503735
|
||||
1 34 0.137125573 1.708147539 0.716181627
|
||||
1 35 0.123097616 1.618411278 0.650668981
|
||||
1 36 0.004782681 2.045360990 0.265908405
|
||||
1 37 0.482050526 5.378313230 1.738291957
|
||||
1 38 0.000029793 1.165464167 0.104040644
|
||||
1 39 0.398656831 4.498416406 1.576424196
|
||||
1 40 0.312949092 4.024125448 1.439974415
|
||||
1 41 0.000000000 1.638977784 0.277336855
|
||||
1 42 0.000000000 2.345366024 0.418105282
|
||||
1 43 0.000000002 2.411407835 0.355802422
|
||||
1 44 0.291716290 7.076306974 3.044028766
|
||||
1 45 0.005110613 2.911861916 0.364993787
|
||||
1 46 0.000000000 1.737800060 0.124517952
|
||||
1 47 0.559743272 6.287422066 2.055158900
|
||||
1 48 0.000000000 1.015661692 0.109207393
|
||||
1 49 0.002417389 0.540743798 0.102010577
|
||||
1 50 0.174404163 1.944323477 0.811707172
|
||||
1 51 0.005005377 0.323217524 0.081737304
|
||||
2 1 0.657274824 2.035556327 1.387251737
|
||||
2 2 0.624101027 1.990896131 1.340471012
|
||||
2 3 0.556439880 1.899792923 1.242632777
|
||||
2 4 0.468851968 1.770966345 1.110278766
|
||||
2 5 0.282152111 1.434986601 0.797105398
|
||||
2 6 0.583874553 2.036121388 1.340893327
|
||||
2 7 0.517651379 2.034158158 1.295648745
|
||||
2 8 0.411264390 2.030246850 1.218885418
|
||||
2 9 1.816106690 6.423665448 4.279400147
|
||||
2 10 0.000000000 2.189541276 1.033133655
|
||||
2 11 1.732440032 5.578661499 3.712915940
|
||||
2 12 0.000000000 1.886951428 0.795224774
|
||||
2 13 0.000000000 1.356753513 0.466887254
|
||||
2 14 1.791632237 5.344368008 3.536483686
|
||||
2 15 1.333358805 3.319570974 2.291476135
|
||||
2 16 0.000000000 0.828594178 0.224874979
|
||||
2 17 0.000000000 1.500470197 0.470830607
|
||||
2 18 0.000000000 0.507075315 0.112303320
|
||||
2 19 0.747962094 2.131986148 1.461129531
|
||||
2 20 0.000000000 0.191093591 0.029261491
|
||||
2 21 0.312388927 1.426100462 0.817025816
|
||||
2 22 0.058038559 0.709369295 0.280292723
|
||||
2 23 0.122039701 1.730637203 0.670932369
|
||||
2 24 0.009773230 1.214363043 0.346743324
|
||||
2 25 0.044741762 1.262354388 0.453445211
|
||||
2 26 0.000246995 0.691187474 0.129256166
|
||||
2 27 0.010857802 0.943006651 0.311434796
|
||||
2 28 0.270028501 3.357922699 1.405435122
|
||||
2 29 0.019403340 2.831690039 0.926045318
|
||||
2 30 0.065567757 2.241016565 0.960026987
|
||||
2 31 0.000490372 1.841475028 0.480637183
|
||||
2 32 0.015911795 1.533406115 0.671402062
|
||||
2 33 0.000000000 2.357307473 0.519029987
|
||||
2 34 0.000000000 0.389055598 0.018429503
|
||||
2 35 0.000000000 8.530817821 3.314077670
|
||||
2 36 0.000000000 0.828396152 0.126674366
|
||||
2 37 0.005022603 2.426018991 1.048668182
|
||||
2 38 0.000000487 3.848184040 1.363272649
|
||||
2 39 0.277493995 3.784158320 1.611777182
|
||||
2 40 0.000000000 1.397576616 0.217060308
|
||||
2 41 0.000000000 0.138455586 0.004478793
|
||||
2 42 0.020733761 3.520744462 1.203579386
|
||||
2 43 0.000000000 3.596744231 0.870507742
|
||||
2 44 0.000000000 0.379638470 0.012041681
|
||||
2 45 0.121234911 1.712147007 0.676217801
|
||||
2 46 0.009807347 1.313200307 0.386707395
|
||||
-0.1693317533 -0.0480493525
|
||||
2521
data/NNP/protH2Ocluster-jctc2020-nnp/weights.001.data
Normal file
2521
data/NNP/protH2Ocluster-jctc2020-nnp/weights.001.data
Normal file
File diff suppressed because it is too large
Load diff
2371
data/NNP/protH2Ocluster-jctc2020-nnp/weights.008.data
Normal file
2371
data/NNP/protH2Ocluster-jctc2020-nnp/weights.008.data
Normal file
File diff suppressed because it is too large
Load diff
|
|
@ -31,10 +31,10 @@
|
|||
SAMPLING_METHOD WORM
|
||||
SOLUTE_INTERACTION NNP
|
||||
&NNP
|
||||
NNP_INPUT_FILE_NAME ./input.nn
|
||||
SCALE_FILE_NAME ./scaling.data
|
||||
NNP_INPUT_FILE_NAME NNP/protH2OHelium-interaction-nnp/input.nn
|
||||
SCALE_FILE_NAME NNP/protH2OHelium-interaction-nnp/scaling.data
|
||||
&MODEL
|
||||
WEIGHTS ./weights
|
||||
WEIGHTS NNP/protH2OHelium-interaction-nnp/weights
|
||||
&END MODEL
|
||||
&SR_CUTOFF
|
||||
ELEMENT H
|
||||
|
|
|
|||
95
tests/Pimd/untested_inputs/bulk32_1.6k.inp
Normal file
95
tests/Pimd/untested_inputs/bulk32_1.6k.inp
Normal file
|
|
@ -0,0 +1,95 @@
|
|||
&GLOBAL
|
||||
PRINT_LEVEL low
|
||||
PROJECT_NAME he32_only_worm_p50
|
||||
RUN_TYPE PINT
|
||||
&END GLOBAL
|
||||
|
||||
&MOTION
|
||||
&PINT
|
||||
# NUM_STEPS 400000
|
||||
NUM_STEPS 1000
|
||||
&HELIUM
|
||||
CELL_SHAPE OCTAHEDRON
|
||||
DENSITY 0.0218457
|
||||
HELIUM_ONLY
|
||||
NATOMS 32
|
||||
NBEADS 50
|
||||
N_OUTER 10000
|
||||
PERIODIC T
|
||||
POTENTIAL_FILE_NAME helium_aziz95_80k.potx
|
||||
PRESAMPLE T
|
||||
SAMPLING_METHOD WORM
|
||||
&PRINT
|
||||
&MOMENT_OF_INERTIA OFF
|
||||
&END MOMENT_OF_INERTIA
|
||||
&PROJECTED_AREA_2_AVG OFF
|
||||
&END PROJECTED_AREA_2_AVG
|
||||
&RDF ON
|
||||
&EACH
|
||||
PINT 1000
|
||||
&END EACH
|
||||
&END RDF
|
||||
&WINDING_NUMBER ON
|
||||
&EACH
|
||||
PINT 1
|
||||
&END EACH
|
||||
&END WINDING_NUMBER
|
||||
&END PRINT
|
||||
&RDF T
|
||||
HE_HE T
|
||||
MAXR 15.0
|
||||
NBIN 300
|
||||
SOLUTE_HE F
|
||||
&END RDF
|
||||
&END HELIUM
|
||||
&END PINT
|
||||
&PRINT
|
||||
&RESTART
|
||||
&EACH
|
||||
PINT 1000
|
||||
&END EACH
|
||||
&END RESTART
|
||||
&RESTART_HISTORY OFF
|
||||
&END RESTART_HISTORY
|
||||
&END PRINT
|
||||
&END MOTION
|
||||
|
||||
#dummy force_eval
|
||||
#will be ignore due to MOTION&PINT&HELIUM&HELIUM_ONLY
|
||||
#but some valid force_eval is needed.
|
||||
&FORCE_EVAL
|
||||
METHOD FIST
|
||||
&MM
|
||||
&FORCEFIELD
|
||||
&CHARGE
|
||||
ATOM Ar
|
||||
CHARGE 0.0
|
||||
&END CHARGE
|
||||
&NONBONDED
|
||||
&LENNARD-JONES
|
||||
ATOMS Ar Ar
|
||||
EPSILON 119.8
|
||||
RCUT 8.4
|
||||
SIGMA 3.405
|
||||
&END LENNARD-JONES
|
||||
&END NONBONDED
|
||||
&END FORCEFIELD
|
||||
&POISSON
|
||||
&EWALD
|
||||
EWALD_TYPE none
|
||||
&END EWALD
|
||||
&END POISSON
|
||||
&END MM
|
||||
&SUBSYS
|
||||
&CELL
|
||||
ABC 8.0 8.0 8.0
|
||||
PERIODIC NONE
|
||||
&END CELL
|
||||
&COORD
|
||||
Ar 0.0 0.0 0.0
|
||||
Ar 4.0 4.0 4.0
|
||||
&END COORD
|
||||
&TOPOLOGY
|
||||
&END TOPOLOGY
|
||||
&END SUBSYS
|
||||
&END FORCE_EVAL
|
||||
193
tests/Pimd/untested_inputs/droplet.inp
Normal file
193
tests/Pimd/untested_inputs/droplet.inp
Normal file
|
|
@ -0,0 +1,193 @@
|
|||
&GLOBAL
|
||||
PRINT_LEVEL SILENT
|
||||
PROJECT_NAME "droplet_h3o+_8He_1K"
|
||||
RUN_TYPE PINT
|
||||
&END GLOBAL
|
||||
|
||||
&MOTION
|
||||
&PINT
|
||||
DT 0.1
|
||||
HARM_INT EXACT
|
||||
NRESPA 1
|
||||
# NUM_STEPS 1000000
|
||||
NUM_STEPS 1000
|
||||
P 160
|
||||
PROPAGATOR RPMD
|
||||
TEMP 1.0000000000000000E+000
|
||||
TRANSFORMATION NORMAL
|
||||
&HELIUM T
|
||||
CELL_SHAPE OCTAHEDRON
|
||||
CELL_SIZE 1.9115700000000000E+001
|
||||
DROPLET_RADIUS 15.0
|
||||
GET_FORCES LAST
|
||||
NATOMS 8 # 8 helium atoms
|
||||
NBEADS 80
|
||||
NUM_ENV 1
|
||||
N_OUTER 1000
|
||||
PERIODIC F
|
||||
POTENTIAL_FILE_NAME ./helium_aziz95_80k.potx
|
||||
PRESAMPLE T
|
||||
RNG_SEED 92404581
|
||||
SAMPLING_METHOD WORM
|
||||
SOLUTE_INTERACTION NNP
|
||||
&NNP
|
||||
NNP_INPUT_FILE_NAME NNP/protH2OHelium-interaction-nnp/input.nn
|
||||
SCALE_FILE_NAME NNP/protH2OHelium-interaction-nnp/scaling.data
|
||||
&MODEL
|
||||
WEIGHTS NNP/protH2OHelium-interaction-nnp/weights
|
||||
&END MODEL
|
||||
&SR_CUTOFF
|
||||
ELEMENT "H"
|
||||
RADIUS 1.25
|
||||
&END SR_CUTOFF
|
||||
&SR_CUTOFF
|
||||
ELEMENT "He"
|
||||
RADIUS 0.0000000000000000E+000
|
||||
&END SR_CUTOFF
|
||||
&SR_CUTOFF
|
||||
ELEMENT "O"
|
||||
RADIUS 2.05
|
||||
&END SR_CUTOFF
|
||||
&END NNP
|
||||
&PRINT
|
||||
&COORDINATES ON
|
||||
&EACH
|
||||
PINT 100
|
||||
&END EACH
|
||||
&END COORDINATES
|
||||
&ENERGY SILENT
|
||||
&EACH
|
||||
PINT 100
|
||||
&END EACH
|
||||
&END ENERGY
|
||||
&MOMENT_OF_INERTIA ON
|
||||
&EACH
|
||||
PINT 1
|
||||
&END EACH
|
||||
&END MOMENT_OF_INERTIA
|
||||
&MOMENT_OF_INERTIA_AVG ON
|
||||
&EACH
|
||||
PINT 100
|
||||
&END EACH
|
||||
&END MOMENT_OF_INERTIA_AVG
|
||||
&PERM ON
|
||||
&EACH
|
||||
PINT 100
|
||||
&END EACH
|
||||
&END PERM
|
||||
&PLENGTH OFF
|
||||
&END PLENGTH
|
||||
&PROJECTED_AREA ON
|
||||
&EACH
|
||||
PINT 1
|
||||
&END EACH
|
||||
&END PROJECTED_AREA
|
||||
&PROJECTED_AREA_2_AVG ON
|
||||
&EACH
|
||||
PINT 100
|
||||
&END EACH
|
||||
&END PROJECTED_AREA_2_AVG
|
||||
&RDF ON
|
||||
&EACH
|
||||
PINT 100
|
||||
&END EACH
|
||||
&END RDF
|
||||
&WINDING_NUMBER OFF
|
||||
&END WINDING_NUMBER
|
||||
&WINDING_NUMBER_2_AVG OFF
|
||||
&END WINDING_NUMBER_2_AVG
|
||||
&END PRINT
|
||||
&RDF T
|
||||
HE_HE T
|
||||
MAXR 30.0
|
||||
NBIN 1000
|
||||
SOLUTE_HE T
|
||||
&END RDF
|
||||
&WORM
|
||||
ALLOW_OPEN T
|
||||
CENTROID_DRMAX 0.25
|
||||
MAX_OPEN_CYCLES 100
|
||||
OPEN_CLOSE_SCALE 5.0000000000000000E+001
|
||||
SHOW_STATISTICS T
|
||||
STAGING_L 6
|
||||
&END WORM
|
||||
&END HELIUM
|
||||
&INIT
|
||||
CENTROID_SPEED F
|
||||
RANDOMIZE_POS F
|
||||
THERMOSTAT_SEED 40
|
||||
&END INIT
|
||||
&PILE
|
||||
LAMBDA 0.5
|
||||
TAU 200
|
||||
&END PILE
|
||||
&PRINT
|
||||
&ACTION OFF
|
||||
&END ACTION
|
||||
&CENTROID_GYR OFF
|
||||
&END CENTROID_GYR
|
||||
&CENTROID_POS SILENT
|
||||
&EACH
|
||||
PINT 100
|
||||
&END EACH
|
||||
&END CENTROID_POS
|
||||
&CENTROID_VEL SILENT
|
||||
&EACH
|
||||
PINT 100
|
||||
&END EACH
|
||||
&END CENTROID_VEL
|
||||
&ENERGY SILENT
|
||||
&EACH
|
||||
PINT 100
|
||||
&END EACH
|
||||
&END ENERGY
|
||||
&END PRINT
|
||||
&END PINT
|
||||
&PRINT
|
||||
&RESTART SILENT
|
||||
BACKUP_COPIES 1
|
||||
&EACH
|
||||
PINT 1000
|
||||
&END EACH
|
||||
&END RESTART
|
||||
&RESTART_HISTORY OFF
|
||||
&END RESTART_HISTORY
|
||||
&TRAJECTORY OFF
|
||||
&END TRAJECTORY
|
||||
&VELOCITIES OFF
|
||||
&END VELOCITIES
|
||||
&END PRINT
|
||||
&END MOTION
|
||||
|
||||
&FORCE_EVAL
|
||||
METHOD NNP
|
||||
&NNP
|
||||
# Reference: [J. Chem. Theo. Comput. 16 88-99 (2020)](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00805)
|
||||
NNP_INPUT_FILE_NAME NNP/protH2Ocluster-jctc2020-nnp/input.nn
|
||||
SCALE_FILE_NAME NNP/protH2Ocluster-jctc2020-nnp/scaling.data
|
||||
&MODEL
|
||||
WEIGHTS NNP/protH2Ocluster-jctc2020-nnp/weights
|
||||
&END MODEL
|
||||
&END NNP
|
||||
&SUBSYS
|
||||
&CELL
|
||||
ABC 8.5000000000000053E+000 8.5000000000000053E+000 8.5000000000000053E+000
|
||||
PERIODIC NONE
|
||||
&END CELL
|
||||
&COORD
|
||||
O 0.0000000000 0.0000000000 0.0000000000
|
||||
H 1.0503793728 0.0000000000 0.0000000000
|
||||
H -0.4976819981 0.7788636207 0.0000000000
|
||||
H -0.5579356431 -0.5112027017 -0.4870267348
|
||||
&END COORD
|
||||
&TOPOLOGY
|
||||
NUMBER_OF_ATOMS 4
|
||||
&END TOPOLOGY
|
||||
&VELOCITY
|
||||
0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000
|
||||
0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000
|
||||
0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000
|
||||
0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000
|
||||
&END VELOCITY
|
||||
&END SUBSYS
|
||||
&END FORCE_EVAL
|
||||
1478
tests/Pimd/untested_inputs/helium_aziz95_80k.potx
Normal file
1478
tests/Pimd/untested_inputs/helium_aziz95_80k.potx
Normal file
File diff suppressed because it is too large
Load diff
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