diff --git a/binder/environment.yml b/binder/environment.yml index cca497587c95f9106193e800020be7fa94b2c30c..97833690f747b48f98e9bb7f345f40c3f7de40ce 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -11,7 +11,7 @@ dependencies: - pyiron_base =0.2.2 - pyiron_contrib =0.0.8 - pyiron_gpl =0.0.2 -- pyiron-data =0.0.12 +- pyiron-data =0.0.13 - pymatgen =2021.3.4 - nglview =2.7.7 - structdbrest =0.0.1 diff --git a/resources/lammps/potentials/potentials_lammps.csv b/resources/lammps/potentials/potentials_lammps.csv index ed93ee28253d6cb023cae31879fd2bccef1c18e7..8f36194122398f8f4acd1f11c1ca7fe1b09fe3b7 100644 --- a/resources/lammps/potentials/potentials_lammps.csv +++ b/resources/lammps/potentials/potentials_lammps.csv @@ -4,7 +4,6 @@ 0,"['pair_style eam/fs\n', 'pair_coeff * * residual68.2249.eam.fs Cu\n']",['atomicrex/residual68.2249.eam.fs'],ACE,Cu-atomicrex-df1-68-22,['Cu'],{} 0,"['pair_style eam/fs\n', 'pair_coeff * * residual68.2524.eam.fs Cu\n']",['atomicrex/residual68.2524.eam.fs'],ACE,Cu-atomicrex-df1-68-25,['Cu'],{} 0,"['pair_style eam/fs\n', 'pair_coeff * * residual107.251.eam.fs Cu\n']",['atomicrex/residual107.251.eam.fs'],ACE,Cu-atomicrex-df1-107-25,['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'],{} 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/df1/input.nn', 'runner/df1/weights.029.data', 'runner/df1/scaling.data']",RuNNer,Cu-runner-df1,['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/df4/input.nn', 'runner/df4/weights.029.data', 'runner/df4/scaling.data']",RuNNer,Cu-runner-df4,['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/df4-lowerRMSE/input.nn', 'runner/df4-lowerRMSE/weights.029.data', 'runner/df4-lowerRMSE/scaling.data']",RuNNer,Cu-runner-df4-lowerRMSE,['Cu'],{} diff --git a/resources/lammps/potentials/runner/input.nn b/resources/lammps/potentials/runner/input.nn deleted file mode 100644 index 4792cbf805e04e70b463a1749dd422ca36b9bbab..0000000000000000000000000000000000000000 --- a/resources/lammps/potentials/runner/input.nn +++ /dev/null @@ -1,95 +0,0 @@ -### #################################################################################################################### -### 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 diff --git a/resources/lammps/potentials/runner/scaling.data b/resources/lammps/potentials/runner/scaling.data deleted file mode 100644 index fc3779e520a3d6719fd3682760a4022ef86dc7d6..0000000000000000000000000000000000000000 --- a/resources/lammps/potentials/runner/scaling.data +++ /dev/null @@ -1,14 +0,0 @@ - 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 diff --git a/resources/lammps/potentials/runner/weights.029.data b/resources/lammps/potentials/runner/weights.029.data deleted file mode 100644 index e3505a1a2b72b867f9885f58fb9e494952e26609..0000000000000000000000000000000000000000 --- a/resources/lammps/potentials/runner/weights.029.data +++ /dev/null @@ -1,466 +0,0 @@ - 0.0002929493 - -0.6941954269 - 0.9059192336 - -0.8539511180 - 0.6945597416 - 0.4158165063 - 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