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Commit 9a2c4b12 authored by Jan Janssen's avatar Jan Janssen
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add best potentials

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.ci_support/build_notebooks.sh
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#!/bin/bash
# pyiron config
python .ci_support/pyironconfig.py
# install
bash binder/postBuild
......
.ci_support/pyironconfig.py 0 → 100644
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import os
def main():
current_path = os.path.abspath(os.path.curdir)
top_level_path = current_path.replace('\\', '/')
resource_path = os.path.join(current_path, "resources").replace('\\', '/')
pyiron_config = os.path.expanduser('~/.pyiron').replace('\\', '/')
if not os.path.exists(pyiron_config):
with open(pyiron_config, 'w') as f:
f.writelines(['[DEFAULT]\n',
'TOP_LEVEL_DIRS = ' + top_level_path + '\n',
'RESOURCE_PATHS = ' + resource_path + '\n'])
else:
print('config exists')
if __name__ == '__main__':
main()
resources/lammps/potentials/ace/df3_cut75_large_body_order.ace 0 → 100644
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resources/lammps/potentials/ace/df3_cut75_large_body_order.yaml 0 → 100644
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resources/lammps/potentials/potentials_lammps.csv 0 → 100644
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,Config,Filename,Model,Name,Species,Citations
0,"['pair_style pace\n', 'pair_coeff * * df3_cut75_large_body_order.ace Cu\n']",['ace/df3_cut75_large_body_order.ace'],ACE,Cu-ace,['Cu'],{}
0,"['pair_style nnp dir ""."" showew no showewsum 0 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254 emap ""1:Cu""\n', 'pair_coeff * * 12\n']","['runner/input.nn', 'runner/weights.029.data', 'runner/scaling.data']",RuNNer,Cu-runner,['Cu'],{}
resources/lammps/potentials/runner/input.nn 0 → 100644
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### ####################################################################################################################
### This is the input file for the RuNNer tutorial (POTENTIALS WORKSHOP 2021-03-10)
### This input file is intended for release version 1.2
### RuNNer is hosted at www.gitlab.com. The most recent version can only be found in this repository.
### For access please contact Prof. Jörg Behler, joerg.behler@uni-goettingen.de
###
### ####################################################################################################################
### General remarks:
### - commands can be switched off by using the # character at the BEGINNING of the line
### - the input file can be structured by blank lines and comment lines
### - the order of the keywords is arbitrary
### - if keywords are missing, default values will be used and written to runner.out
### - if mandatory keywords or keyword options are missing, RuNNer will stop with an error message
###
########################################################################################################################
########################################################################################################################
### The following keywords just represent a subset of the keywords offered by RuNNer
########################################################################################################################
########################################################################################################################
########################################################################################################################
### general keywords
########################################################################################################################
nn_type_short 1 # 1=Behler-Parrinello
runner_mode 3 # 1=calculate symmetry functions, 2=fitting mode, 3=predicition mode
number_of_elements 1 # number of elements
elements Cu # specification of elements
random_seed 10 # integer seed for random number generator
random_number_type 6 # 6 recommended
########################################################################################################################
### NN structure of the short-range NN
########################################################################################################################
use_short_nn # use NN for short range interactions
global_hidden_layers_short 2 # number of hidden layers
global_nodes_short 15 15 # number of nodes in hidden layers
global_activation_short t t l # activation functions (t = hyperbolic tangent, l = linear)
########################################################################################################################
### symmetry function generation ( mode 1):
########################################################################################################################
test_fraction 0.10000 # threshold for splitting between fitting and test set
########################################################################################################################
### symmetry function definitions (all modes):
########################################################################################################################
cutoff_type 1
symfunction_short Cu 2 Cu 0.000000 0.000000 12.000000
symfunction_short Cu 2 Cu 0.006000 0.000000 12.000000
symfunction_short Cu 2 Cu 0.016000 0.000000 12.000000
symfunction_short Cu 2 Cu 0.040000 0.000000 12.000000
symfunction_short Cu 2 Cu 0.109000 0.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 1.000000 1.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 1.000000 2.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 1.000000 4.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 1.000000 16.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 -1.000000 1.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 -1.000000 2.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 -1.000000 4.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 -1.000000 16.000000 12.000000
########################################################################################################################
### fitting (mode 2):general inputs for short range AND electrostatic part:
########################################################################################################################
epochs 20 # number of epochs
fitting_unit eV # unit for error output in mode 2 (eV or Ha)
precondition_weights # optional precondition initial weights
########################################################################################################################
### fitting options ( mode 2): short range part only:
########################################################################################################################
short_energy_error_threshold 0.10000 # threshold of adaptive Kalman filter short E
short_force_error_threshold 1.00000 # threshold of adaptive Kalman filter short F
kalman_lambda_short 0.98000 # Kalman parameter short E/F, do not change
kalman_nue_short 0.99870 # Kalman parameter short E/F, do not change
use_short_forces # use forces for fitting
repeated_energy_update # optional: repeat energy update for each force update
mix_all_points # do not change
scale_symmetry_functions # optional
center_symmetry_functions # optional
short_force_fraction 0.01 #
force_update_scaling -1.0 #
########################################################################################################################
### output options for mode 2 (fitting):
########################################################################################################################
write_trainpoints # write trainpoints.out and testpoints.out files
write_trainforces # write trainforces.out and testforces.out files
########################################################################################################################
### output options for mode 3 (prediction):
########################################################################################################################
calculate_forces # calculate forces
calculate_stress # calculate stress tensor
resources/lammps/potentials/runner/scaling.data 0 → 100644
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1 1 14.256833324 19.604083786 16.584187995
1 2 10.772870436 14.917517522 12.575789477
1 3 7.067719199 9.940850811 8.325756144
1 4 3.063546892 4.514143322 3.699677080
1 5 0.443438674 0.840539370 0.611310762
1 6 11.372207256 23.338043099 16.099109800
1 7 30.908289966 62.610854904 43.470717798
1 8 4.747847116 10.201151151 6.890568480
1 9 24.299123692 49.473962957 34.262176478
1 10 1.690730707 3.912715044 2.559298728
1 11 16.549052901 34.322241783 23.555567314
1 12 0.252821214 0.820637834 0.460356083
1 13 4.065311900 9.687837138 6.245172716
-0.1359667057 -0.1284178204
resources/lammps/potentials/runner/weights.029.data 0 → 100644
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