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Repository: CompPhysVienna/n2p2
Branch: master
Commit: 29b9c9f10b1a
Files: 733
Total size: 43.0 MB
Directory structure:
gitextract_tn4psl0z/
├── .github/
│ ├── ISSUE_TEMPLATE/
│ │ ├── bug_report.md
│ │ ├── feature_request.md
│ │ └── question.md
│ └── workflows/
│ └── n2p2-ci.yaml
├── .gitignore
├── AUTHORS.rst
├── CHANGELOG.rst
├── LICENSE
├── README.md
├── bin/
│ └── .gitignore
├── doc/
│ ├── .gitignore
│ └── doxygen/
│ └── .gitignore
├── examples/
│ ├── coarse-graining/
│ │ ├── README.md
│ │ ├── step-0_cg-data-set/
│ │ │ ├── input.data
│ │ │ ├── makefile
│ │ │ └── nnp-cgdata.cpp
│ │ ├── step-1_scaling-data/
│ │ │ ├── input.data
│ │ │ └── input.nn
│ │ ├── step-2_atomic-env/
│ │ │ └── scaling.data
│ │ └── step-3_cluster-analysis/
│ │ ├── analyze-descriptors.ipynb
│ │ └── atomic-env.dGdx
│ ├── configuration-sets/
│ │ ├── input.data.Anisole
│ │ ├── input.data.Cu2S_PBE
│ │ ├── input.data.DMABN
│ │ ├── input.data.Ethylbenzene
│ │ ├── input.data.H2O_RPBE-D3
│ │ └── input.data.LJ
│ ├── configuration-single/
│ │ ├── input.data.Anisole
│ │ ├── input.data.Cu2S_144_low-chalcocite
│ │ ├── input.data.DMABN
│ │ ├── input.data.Ethylbenzene
│ │ └── input.data.H2O_1080_liquid
│ ├── input.nn.recommended
│ ├── interface-LAMMPS/
│ │ ├── AlAuMgO_4G/
│ │ │ ├── AlAuMgO.data
│ │ │ ├── AlAuMgO.data-n2p2
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── hardness.008.data
│ │ │ │ ├── hardness.012.data
│ │ │ │ ├── hardness.013.data
│ │ │ │ ├── hardness.079.data
│ │ │ │ ├── input.nn
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.008.data
│ │ │ │ ├── weights.012.data
│ │ │ │ ├── weights.013.data
│ │ │ │ ├── weights.079.data
│ │ │ │ ├── weightse.008.data
│ │ │ │ ├── weightse.012.data
│ │ │ │ ├── weightse.013.data
│ │ │ │ └── weightse.079.data
│ │ │ ├── input.data
│ │ │ ├── input.data.q
│ │ │ ├── md-external.lmp
│ │ │ ├── md.lmp
│ │ │ └── nnp-predict/
│ │ │ ├── hardness.008.data
│ │ │ ├── hardness.012.data
│ │ │ ├── hardness.013.data
│ │ │ ├── hardness.079.data
│ │ │ ├── input.data
│ │ │ ├── input.data-2
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.008.data
│ │ │ ├── weights.012.data
│ │ │ ├── weights.013.data
│ │ │ ├── weights.079.data
│ │ │ ├── weightse.008.data
│ │ │ ├── weightse.012.data
│ │ │ ├── weightse.013.data
│ │ │ └── weightse.079.data
│ │ ├── Cu2S_PBE/
│ │ │ ├── cu2s_144_low-chalcocite_Evans-1979_PBE.data
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── input.nn
│ │ │ │ ├── nnp-train.log.0000
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.016.data
│ │ │ │ └── weights.029.data
│ │ │ └── md.lmp
│ │ ├── Cu2S_PBE_external/
│ │ │ ├── cu2s_144_low-chalcocite_Evans-1979_PBE.data
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── input.nn
│ │ │ │ ├── nnp-train.log.0000
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.016.data
│ │ │ │ └── weights.029.data
│ │ │ └── md.lmp
│ │ ├── H2O_4G/
│ │ │ ├── correct-input-data/
│ │ │ │ ├── input.data-h2o-192
│ │ │ │ ├── input.data-h2o-36
│ │ │ │ ├── input.data-h2o-768
│ │ │ │ ├── water.data-h2o-192
│ │ │ │ ├── water.data-h2o-36
│ │ │ │ └── water.data-h2o-768
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── hardness.001.data
│ │ │ │ ├── hardness.008.data
│ │ │ │ ├── input.nn
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ ├── weights.008.data
│ │ │ │ ├── weightse.001.data
│ │ │ │ └── weightse.008.data
│ │ │ ├── md.lmp
│ │ │ ├── nnp-predict/
│ │ │ │ ├── hardness.001.data
│ │ │ │ ├── hardness.008.data
│ │ │ │ ├── input.data
│ │ │ │ ├── input.nn
│ │ │ │ ├── other-input-data/
│ │ │ │ │ ├── input.data-1np
│ │ │ │ │ ├── input.data-1p
│ │ │ │ │ ├── input.data-36-angs
│ │ │ │ │ ├── input.data-36p
│ │ │ │ │ ├── input.data-36s
│ │ │ │ │ ├── input.data-angs-p
│ │ │ │ │ ├── input.data-h2o-192-neg
│ │ │ │ │ ├── input.data-h2o-36-neg
│ │ │ │ │ └── input.data-h2o-768-neg
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ ├── weights.008.data
│ │ │ │ ├── weightse.001.data
│ │ │ │ └── weightse.008.data
│ │ │ ├── water.data
│ │ │ └── water.data.q
│ │ ├── H2O_RPBE-D3/
│ │ │ ├── h2o_8640_liquid_NpT_RPBE-D3.data
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── input.nn
│ │ │ │ ├── nnp-train.log.0000
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ └── weights.008.data
│ │ │ └── md.lmp
│ │ ├── H2O_RPBE-D3_128mol/
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── input.nn
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ └── weights.008.data
│ │ │ ├── iceIh_128.data
│ │ │ └── md.lmp
│ │ ├── H2O_RPBE-D3_128mol_develop/
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── hardness.001.data
│ │ │ │ ├── hardness.008.data
│ │ │ │ ├── input.nn
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ ├── weights.008.data
│ │ │ │ ├── weightse.001.data
│ │ │ │ └── weightse.008.data
│ │ │ ├── iceIh_128.data
│ │ │ └── md.lmp
│ │ ├── H2O_RPBE-D3_128mol_external/
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── input.nn
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ └── weights.008.data
│ │ │ ├── iceIh_128.data
│ │ │ └── md.lmp
│ │ ├── H2O_RPBE-D3_external/
│ │ │ ├── h2o_8640_liquid_NpT_RPBE-D3.data
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── input.nn
│ │ │ │ ├── nnp-train.log.0000
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ └── weights.008.data
│ │ │ └── md.lmp
│ │ └── TO_BE_CHECKED/
│ │ ├── carbon-chain/
│ │ │ ├── lammps-nnp/
│ │ │ │ ├── carbon-chain.data
│ │ │ │ ├── log.lammps
│ │ │ │ ├── md-external.lmp
│ │ │ │ ├── md.lmp
│ │ │ │ └── nnp-data/
│ │ │ │ ├── hardness.001.data
│ │ │ │ ├── hardness.006.data
│ │ │ │ ├── input.nn
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ ├── weights.006.data
│ │ │ │ ├── weightse.001.data
│ │ │ │ └── weightse.006.data
│ │ │ └── nnp-predict/
│ │ │ ├── hardness.001.data
│ │ │ ├── hardness.006.data
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ ├── weights.006.data
│ │ │ ├── weightse.001.data
│ │ │ └── weightse.006.data
│ │ └── carbon-chain2/
│ │ ├── lammps-nnp/
│ │ │ ├── carbon-chain.data
│ │ │ ├── carbon-chain.data-eg
│ │ │ ├── carbon-chain.data-mod
│ │ │ ├── carbon-chain.data-n2p2
│ │ │ ├── carbon-chain.data-org
│ │ │ ├── carbon-chain.data-q0
│ │ │ ├── carbon-chain.data-sameq
│ │ │ ├── carbond-chain.data
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── debug.out
│ │ │ │ ├── energy.out
│ │ │ │ ├── external.out
│ │ │ │ ├── hardness.001.data
│ │ │ │ ├── hardness.006.data
│ │ │ │ ├── input.data
│ │ │ │ ├── input.data-org
│ │ │ │ ├── input.nn
│ │ │ │ ├── nnatoms.out
│ │ │ │ ├── nnforces.out
│ │ │ │ ├── nnp-predict.log
│ │ │ │ ├── output.data
│ │ │ │ ├── scaling.data
│ │ │ │ ├── structure.out
│ │ │ │ ├── weights.001.data
│ │ │ │ ├── weights.006.data
│ │ │ │ ├── weightse.001.data
│ │ │ │ └── weightse.006.data
│ │ │ ├── md-external.lmp
│ │ │ └── md.lmp
│ │ └── nnp-predict/
│ │ ├── energy.out
│ │ ├── hardness.001.data
│ │ ├── hardness.006.data
│ │ ├── input.data
│ │ ├── input.nn
│ │ ├── nnatoms.out
│ │ ├── nnforces.out
│ │ ├── nnp-predict.log
│ │ ├── output.data
│ │ ├── scaling.data
│ │ ├── weights.001.data
│ │ ├── weights.006.data
│ │ ├── weightse.001.data
│ │ └── weightse.006.data
│ ├── nnp-atomenv/
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ └── scaling.data
│ │ └── H2O_RPBE-D3/
│ │ ├── input.data
│ │ ├── input.nn
│ │ └── scaling.data
│ ├── nnp-checkdw/
│ │ ├── H2O_RPBE-D3/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.008.data
│ │ └── LJ/
│ │ ├── input.data
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ └── weights.010.data
│ ├── nnp-checkf/
│ │ ├── H2O_RPBE-D3/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.008.data
│ │ └── LJ/
│ │ ├── input.data
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ └── weights.010.data
│ ├── nnp-comp2/
│ │ └── Cu2S_PBE/
│ │ ├── input.data
│ │ ├── nnp-data-1/
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.016.data
│ │ │ └── weights.029.data
│ │ └── nnp-data-2/
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ ├── weights.016.data
│ │ └── weights.029.data
│ ├── nnp-convert/
│ │ └── Cu2S_PBE/
│ │ └── input.data
│ ├── nnp-dataset/
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.016.data
│ │ │ └── weights.029.data
│ │ └── H2O_RPBE-D3/
│ │ ├── input.data
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ ├── weights.001.data
│ │ └── weights.008.data
│ ├── nnp-dist/
│ │ ├── Cu2S_PBE/
│ │ │ └── input.data
│ │ └── H2O_RPBE-D3/
│ │ └── input.data
│ ├── nnp-norm/
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ └── input.nn
│ │ └── H2O_RPBE-D3/
│ │ ├── input.data
│ │ └── input.nn
│ ├── nnp-norm2/
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ └── scaling.data
│ │ └── H2O_RPBE-D3/
│ │ ├── input.data
│ │ ├── input.nn
│ │ └── scaling.data
│ ├── nnp-predict/
│ │ ├── AlAuMgO_4G/
│ │ │ ├── hardness.008.data
│ │ │ ├── hardness.012.data
│ │ │ ├── hardness.013.data
│ │ │ ├── hardness.079.data
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.008.data
│ │ │ ├── weights.012.data
│ │ │ ├── weights.013.data
│ │ │ ├── weights.079.data
│ │ │ ├── weightse.008.data
│ │ │ ├── weightse.012.data
│ │ │ ├── weightse.013.data
│ │ │ └── weightse.079.data
│ │ ├── Anisole_SCAN/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ ├── weights.006.data
│ │ │ └── weights.008.data
│ │ ├── Carbon_chain_4G/
│ │ │ ├── hardness.001.data
│ │ │ ├── hardness.006.data
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ ├── weights.006.data
│ │ │ ├── weightse.001.data
│ │ │ └── weightse.006.data
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.016.data
│ │ │ └── weights.029.data
│ │ ├── DMABN_SCAN/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ ├── weights.006.data
│ │ │ └── weights.007.data
│ │ ├── Ethylbenzene_SCAN/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.006.data
│ │ ├── H2O_RPBE-D3/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.008.data
│ │ └── H2O_RPBE-D3_4G/
│ │ ├── hardness.001.data
│ │ ├── hardness.008.data
│ │ ├── input.data
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ ├── weights.001.data
│ │ ├── weights.008.data
│ │ ├── weightse.001.data
│ │ └── weightse.008.data
│ ├── nnp-prune/
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── sensitivity.016.out
│ │ │ └── sensitivity.029.out
│ │ └── H2O_RPBE-D3/
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ ├── sensitivity.001.out
│ │ └── sensitivity.008.out
│ ├── nnp-scaling/
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ └── input.nn
│ │ ├── H2O_RPBE-D3/
│ │ │ ├── input.data
│ │ │ └── input.nn
│ │ └── LJ/
│ │ ├── input.data
│ │ └── input.nn
│ ├── nnp-select/
│ │ └── H2O_RPBE-D3/
│ │ └── input.data
│ ├── nnp-symfunc/
│ │ └── H2O_RPBE-D3/
│ │ └── input.nn
│ ├── nnp-train/
│ │ ├── AlAuMgO_4G/
│ │ │ ├── hardness.008.data
│ │ │ ├── hardness.012.data
│ │ │ ├── hardness.013.data
│ │ │ ├── hardness.079.data
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weightse.008.data
│ │ │ ├── weightse.012.data
│ │ │ ├── weightse.013.data
│ │ │ └── weightse.079.data
│ │ ├── Carbon_chain_4G/
│ │ │ ├── hardness.001.data
│ │ │ ├── hardness.006.data
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weightse.001.data
│ │ │ └── weightse.006.data
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ └── scaling.data
│ │ ├── H2O_RPBE-D3/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ └── scaling.data
│ │ ├── H2O_RPBE-D3_4G/
│ │ │ ├── hardness.001.data
│ │ │ ├── hardness.008.data
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weightse.001.data
│ │ │ └── weightse.008.data
│ │ ├── H2O_RPBE-D3_norm-force/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ └── scaling.data
│ │ ├── LJ/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ └── scaling.data
│ │ └── QM9/
│ │ ├── input.data
│ │ ├── input.nn
│ │ └── input.nn.wacsf
│ ├── potentials/
│ │ ├── Anisole_SCAN/
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ ├── weights.006.data
│ │ │ └── weights.008.data
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.nn
│ │ │ ├── nnp-train.log.0000
│ │ │ ├── scaling.data
│ │ │ ├── weights.016.data
│ │ │ └── weights.029.data
│ │ ├── DMABN_SCAN/
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ ├── weights.006.data
│ │ │ └── weights.007.data
│ │ ├── Ethylbenzene_SCAN/
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.006.data
│ │ ├── H2O_BLYP/
│ │ │ ├── input.nn
│ │ │ ├── nnp-train.log.0000
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.008.data
│ │ ├── H2O_BLYP-D3/
│ │ │ ├── input.nn
│ │ │ ├── nnp-train.log.0000
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.008.data
│ │ ├── H2O_RPBE/
│ │ │ ├── input.nn
│ │ │ ├── nnp-train.log.0000
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.008.data
│ │ └── H2O_RPBE-D3/
│ │ ├── input.nn
│ │ ├── nnp-train.log.0000
│ │ ├── scaling.data
│ │ ├── weights.001.data
│ │ └── weights.008.data
│ └── pynnp/
│ ├── prediction/
│ │ ├── example-simple.py
│ │ ├── example-verbose.py
│ │ ├── input.data
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ ├── weights.001.data
│ │ └── weights.008.data
│ └── symfunc-only/
│ ├── example.ipynb
│ ├── example.py
│ ├── input.data.1
│ ├── input.data.2
│ ├── input.nn
│ └── scaling.data
├── include/
│ └── .gitignore
├── lib/
│ └── .gitignore
├── src/
│ ├── application/
│ │ ├── makefile
│ │ ├── nnp-atomenv.cpp
│ │ ├── nnp-checkdw.cpp
│ │ ├── nnp-checkf.cpp
│ │ ├── nnp-comp2.cpp
│ │ ├── nnp-convert.cpp
│ │ ├── nnp-cutoff.cpp
│ │ ├── nnp-dataset.cpp
│ │ ├── nnp-dist.cpp
│ │ ├── nnp-norm.cpp
│ │ ├── nnp-norm2.cpp
│ │ ├── nnp-predict.cpp
│ │ ├── nnp-prune.cpp
│ │ ├── nnp-scaling.cpp
│ │ ├── nnp-select.cpp
│ │ ├── nnp-symfunc.cpp
│ │ └── nnp-train.cpp
│ ├── doc/
│ │ ├── doxygen/
│ │ │ ├── Doxyfile
│ │ │ ├── README.md
│ │ │ └── makefile
│ │ └── sphinx/
│ │ ├── Makefile
│ │ └── source/
│ │ ├── about/
│ │ │ ├── authors.rst
│ │ │ ├── changelog.rst
│ │ │ ├── how_to_cite.rst
│ │ │ └── license.rst
│ │ ├── api/
│ │ │ ├── cutoff_functions.rst
│ │ │ ├── memory_layout.rst
│ │ │ ├── neural_network.rst
│ │ │ ├── symmetry_function_scaling.rst
│ │ │ └── symmetry_function_types.rst
│ │ ├── conf.py
│ │ ├── helper.rst
│ │ ├── index.rst
│ │ ├── interfaces/
│ │ │ ├── if_cabanamd.rst
│ │ │ └── if_lammps.rst
│ │ ├── misc/
│ │ │ ├── cabanamd_build_example.rst
│ │ │ └── cg_descriptor_analysis.rst
│ │ ├── old/
│ │ │ └── pair_nnp.rst
│ │ ├── tools/
│ │ │ ├── libnnp.rst
│ │ │ ├── nnp-atomenv.rst
│ │ │ ├── nnp-checkf.rst
│ │ │ ├── nnp-convert.rst
│ │ │ ├── nnp-norm.rst
│ │ │ ├── nnp-predict.rst
│ │ │ ├── nnp-prune.rst
│ │ │ ├── nnp-scaling.rst
│ │ │ ├── nnp-select.rst
│ │ │ └── nnp-train.rst
│ │ └── topics/
│ │ ├── build.rst
│ │ ├── cfg_file.rst
│ │ ├── descriptors.rst
│ │ ├── keywords.rst
│ │ ├── training.rst
│ │ └── units.rst
│ ├── interface/
│ │ ├── LAMMPS/
│ │ │ └── src/
│ │ │ └── ML-HDNNP/
│ │ │ ├── Install.sh
│ │ │ ├── README
│ │ │ ├── fix_hdnnp.cpp
│ │ │ ├── fix_hdnnp.h
│ │ │ ├── kspace_hdnnp.cpp
│ │ │ ├── kspace_hdnnp.h
│ │ │ ├── pair_hdnnp.cpp
│ │ │ ├── pair_hdnnp.h
│ │ │ ├── pair_hdnnp_4g.cpp
│ │ │ ├── pair_hdnnp_4g.h
│ │ │ ├── pair_hdnnp_develop.cpp
│ │ │ ├── pair_hdnnp_develop.h
│ │ │ ├── pair_hdnnp_external.cpp
│ │ │ └── pair_hdnnp_external.h
│ │ └── makefile
│ ├── libnnp/
│ │ ├── Atom.cpp
│ │ ├── Atom.h
│ │ ├── CompactFunction.cpp
│ │ ├── CompactFunction.h
│ │ ├── CoreFunction.cpp
│ │ ├── CoreFunction.h
│ │ ├── CutoffFunction.cpp
│ │ ├── CutoffFunction.h
│ │ ├── Element.cpp
│ │ ├── Element.h
│ │ ├── ElementMap.cpp
│ │ ├── ElementMap.h
│ │ ├── ErfcBuf.cpp
│ │ ├── ErfcBuf.h
│ │ ├── EwaldSetup.cpp
│ │ ├── EwaldSetup.h
│ │ ├── EwaldTruncJackson.cpp
│ │ ├── EwaldTruncJackson.h
│ │ ├── EwaldTruncKolafaFixR.cpp
│ │ ├── EwaldTruncKolafaFixR.h
│ │ ├── EwaldTruncKolafaOptEta.cpp
│ │ ├── EwaldTruncKolafaOptEta.h
│ │ ├── IEwaldTrunc.h
│ │ ├── ISettings.h
│ │ ├── Key.h
│ │ ├── Kspace.cpp
│ │ ├── Kspace.h
│ │ ├── Log.cpp
│ │ ├── Log.h
│ │ ├── Mode.cpp
│ │ ├── Mode.h
│ │ ├── NeuralNetwork.cpp
│ │ ├── NeuralNetwork.h
│ │ ├── Prediction.cpp
│ │ ├── Prediction.h
│ │ ├── ScreeningFunction.cpp
│ │ ├── ScreeningFunction.h
│ │ ├── Settings.cpp
│ │ ├── Settings.h
│ │ ├── SetupAnalysis.cpp
│ │ ├── SetupAnalysis.h
│ │ ├── Stopwatch.cpp
│ │ ├── Stopwatch.h
│ │ ├── Structure.cpp
│ │ ├── Structure.h
│ │ ├── SymFnc.cpp
│ │ ├── SymFnc.h
│ │ ├── SymFncBaseComp.cpp
│ │ ├── SymFncBaseComp.h
│ │ ├── SymFncBaseCompAng.cpp
│ │ ├── SymFncBaseCompAng.h
│ │ ├── SymFncBaseCompAngWeighted.cpp
│ │ ├── SymFncBaseCompAngWeighted.h
│ │ ├── SymFncBaseCutoff.cpp
│ │ ├── SymFncBaseCutoff.h
│ │ ├── SymFncBaseExpAng.cpp
│ │ ├── SymFncBaseExpAng.h
│ │ ├── SymFncCompAngn.cpp
│ │ ├── SymFncCompAngn.h
│ │ ├── SymFncCompAngnWeighted.cpp
│ │ ├── SymFncCompAngnWeighted.h
│ │ ├── SymFncCompAngw.cpp
│ │ ├── SymFncCompAngw.h
│ │ ├── SymFncCompAngwWeighted.cpp
│ │ ├── SymFncCompAngwWeighted.h
│ │ ├── SymFncCompRad.cpp
│ │ ├── SymFncCompRad.h
│ │ ├── SymFncCompRadWeighted.cpp
│ │ ├── SymFncCompRadWeighted.h
│ │ ├── SymFncExpAngn.cpp
│ │ ├── SymFncExpAngn.h
│ │ ├── SymFncExpAngnWeighted.cpp
│ │ ├── SymFncExpAngnWeighted.h
│ │ ├── SymFncExpAngw.cpp
│ │ ├── SymFncExpAngw.h
│ │ ├── SymFncExpRad.cpp
│ │ ├── SymFncExpRad.h
│ │ ├── SymFncExpRadWeighted.cpp
│ │ ├── SymFncExpRadWeighted.h
│ │ ├── SymFncStatistics.cpp
│ │ ├── SymFncStatistics.h
│ │ ├── SymGrp.cpp
│ │ ├── SymGrp.h
│ │ ├── SymGrpBaseComp.cpp
│ │ ├── SymGrpBaseComp.h
│ │ ├── SymGrpBaseCompAng.cpp
│ │ ├── SymGrpBaseCompAng.h
│ │ ├── SymGrpBaseCompAngWeighted.cpp
│ │ ├── SymGrpBaseCompAngWeighted.h
│ │ ├── SymGrpBaseCutoff.cpp
│ │ ├── SymGrpBaseCutoff.h
│ │ ├── SymGrpBaseExpAng.cpp
│ │ ├── SymGrpBaseExpAng.h
│ │ ├── SymGrpCompAngn.cpp
│ │ ├── SymGrpCompAngn.h
│ │ ├── SymGrpCompAngnWeighted.cpp
│ │ ├── SymGrpCompAngnWeighted.h
│ │ ├── SymGrpCompAngw.cpp
│ │ ├── SymGrpCompAngw.h
│ │ ├── SymGrpCompAngwWeighted.cpp
│ │ ├── SymGrpCompAngwWeighted.h
│ │ ├── SymGrpCompRad.cpp
│ │ ├── SymGrpCompRad.h
│ │ ├── SymGrpCompRadWeighted.cpp
│ │ ├── SymGrpCompRadWeighted.h
│ │ ├── SymGrpExpAngn.cpp
│ │ ├── SymGrpExpAngn.h
│ │ ├── SymGrpExpAngnWeighted.cpp
│ │ ├── SymGrpExpAngnWeighted.h
│ │ ├── SymGrpExpAngw.cpp
│ │ ├── SymGrpExpAngw.h
│ │ ├── SymGrpExpRad.cpp
│ │ ├── SymGrpExpRad.h
│ │ ├── SymGrpExpRadWeighted.cpp
│ │ ├── SymGrpExpRadWeighted.h
│ │ ├── Vec3D.h
│ │ ├── makefile
│ │ ├── mpi-extra.h
│ │ ├── utility.cpp
│ │ ├── utility.h
│ │ └── version.h
│ ├── libnnpif/
│ │ ├── CabanaMD/
│ │ │ ├── ElementCabana.h
│ │ │ ├── ElementCabana_impl.h
│ │ │ ├── ModeCabana.h
│ │ │ ├── ModeCabana_impl.h
│ │ │ └── typesCabana.h
│ │ ├── LAMMPS/
│ │ │ ├── InterfaceLammps.cpp
│ │ │ ├── InterfaceLammps.h
│ │ │ └── Makefile.lammps
│ │ └── makefile
│ ├── libnnptrain/
│ │ ├── Dataset.cpp
│ │ ├── Dataset.h
│ │ ├── GradientDescent.cpp
│ │ ├── GradientDescent.h
│ │ ├── KalmanFilter.cpp
│ │ ├── KalmanFilter.h
│ │ ├── Training.cpp
│ │ ├── Training.h
│ │ ├── Updater.cpp
│ │ ├── Updater.h
│ │ └── makefile
│ ├── makefile
│ ├── makefile.gnu
│ ├── makefile.intel
│ ├── makefile.llvm
│ └── pynnp/
│ ├── Atom.pyx
│ ├── CutoffFunction.pyx
│ ├── ElementMap.pyx
│ ├── Log.pyx
│ ├── Mode.pyx
│ ├── Prediction.pyx
│ ├── Settings.pyx
│ ├── Structure.pyx
│ ├── Vec3D.pyx
│ ├── makefile
│ ├── pynnp.pyx
│ ├── pynnp_dec.pxd
│ ├── setup-test.py
│ └── setup.py
├── test/
│ ├── cpp/
│ │ ├── BoostDataContainer.h
│ │ ├── Example.h
│ │ ├── ExamplePrediction.h
│ │ ├── ExampleScreeningFunction.h
│ │ ├── Example_lammps_hdnnp.h
│ │ ├── Example_nnp.h
│ │ ├── Example_nnp_atomenv.h
│ │ ├── Example_nnp_checkdw.h
│ │ ├── Example_nnp_checkf.h
│ │ ├── Example_nnp_convert.h
│ │ ├── Example_nnp_dataset.h
│ │ ├── Example_nnp_dist.h
│ │ ├── Example_nnp_norm.h
│ │ ├── Example_nnp_predict.h
│ │ ├── Example_nnp_prune.h
│ │ ├── Example_nnp_scaling.h
│ │ ├── Example_nnp_select.h
│ │ ├── Example_nnp_symfunc.h
│ │ ├── Example_nnp_train.h
│ │ ├── fileHelpers.h
│ │ ├── fixtures.h
│ │ ├── makefile
│ │ ├── nnp_test.h
│ │ ├── test_CutoffFunction.cpp
│ │ ├── test_Prediction.cpp
│ │ ├── test_ScreeningFunction.cpp
│ │ ├── test_Settings.cpp
│ │ ├── test_SymmetryFunctionGroups.cpp
│ │ ├── test_SymmetryFunctions.cpp
│ │ ├── test_lammps_hdnnp.cpp
│ │ ├── test_nnp-atomenv.cpp
│ │ ├── test_nnp-checkdw.cpp
│ │ ├── test_nnp-checkf.cpp
│ │ ├── test_nnp-convert.cpp
│ │ ├── test_nnp-dataset.cpp
│ │ ├── test_nnp-dist.cpp
│ │ ├── test_nnp-norm.cpp
│ │ ├── test_nnp-predict.cpp
│ │ ├── test_nnp-prune.cpp
│ │ ├── test_nnp-scaling.cpp
│ │ ├── test_nnp-select.cpp
│ │ ├── test_nnp-symfunc.cpp
│ │ └── test_nnp-train.cpp
│ ├── makefile
│ └── python/
│ ├── .coveragerc
│ ├── makefile
│ ├── setups/
│ │ └── Settings/
│ │ └── input.nn
│ ├── test_Atom.py
│ ├── test_CutoffFunction.py
│ ├── test_ElementMap.py
│ ├── test_Log.py
│ ├── test_Neighbor.py
│ ├── test_Settings.py
│ └── test_Vec3D.py
└── tools/
├── converter/
│ └── convert-VASP_OUTCAR.py
├── misc/
│ ├── convert_nnp.py
│ ├── generate-acsf-angular_narrow.py
│ ├── generate-acsf-angular_wide.py
│ ├── generate-acsf-radial.py
│ └── nnp-archive.sh
└── plot/
├── plot-symfunc-histograms.ipynb
└── plot-symfunc-shape-rdf.ipynb
================================================
FILE CONTENTS
================================================
================================================
FILE: .github/ISSUE_TEMPLATE/bug_report.md
================================================
---
name: Bug report
about: Create a report to help us improve
---
**Describe the bug**
A clear and concise description of what the bug is.
**To Reproduce**
Steps to reproduce the behavior:
1. Which git commit version is used?
2. What are the compilation options (compiler, flags)?
3. Which application is affected?
4. What are the actual settings (please provide a minimal example if possible)?
5. Please provide the error message or describe the crash behavior.
**Expected behavior**
A clear and concise description of what you expected to happen.
**Additional context**
Add any other context about the problem here.
================================================
FILE: .github/ISSUE_TEMPLATE/feature_request.md
================================================
---
name: Feature request
about: Suggest an idea for this project
---
**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
**Describe the solution you'd like**
A clear and concise description of what you want to happen.
**Describe alternatives you've considered**
A clear and concise description of any alternative solutions or features you've considered.
**Reference**
If you'd like some specific method to be implemented, please point to a useful reference.
================================================
FILE: .github/ISSUE_TEMPLATE/question.md
================================================
---
name: Question
about: Ask a general question about the project
---
**The question**
Ask what you want to know about the code.. e.g. "Can I do [...] with this software?" or "Is [...] supported?"
**What did you already try?**
Have you already installed the project and tried something out?
**Background**
What system are you working on?
================================================
FILE: .github/workflows/n2p2-ci.yaml
================================================
name: n2p2-ci
on:
push:
pull_request:
branches:
- master
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Install required system packages
run: |
# Docs
# API docs with doxygen (built via makefile, needs cmake),
# generating graphs with doxygen requires dot.
sudo apt install cmake graphviz
# Build
# MPI
sudo apt install openmpi-bin libopenmpi-dev
# BLAS
sudo apt install libblas3 libblas-dev
# OpenBLAS
sudo apt install libopenblas0 libopenblas-dev
# Eigen library
sudo apt install libeigen3-dev
# GSL library
sudo apt install libgsl-dev libgslcblas0
# Tests
# Boost Test for C++ testing
sudo apt install libboost-test-dev libboost-filesystem-dev
# Coverage for C++
sudo apt install lcov
- name: Install required Python packages
run: |
# Docs
pip install sphinx
pip install sphinx_rtd_theme
pip install breathe
# pynnp
pip install cython==3.0.11
# python tests
pip install pytest #==7.1.3
pip install pytest-cov #==4.0.0
pip install coverage #==7.6.1
- name: Build n2p2 libraries and applications
run: make MODE=test -j4
working-directory: ./src
- name: Build documentation
run: |
# Pre-build doxygen only on 4 cores (-j hangs on Github Actions).
cd doc/doxygen/
make CORES=4 doxygen
cd ../..
# Now build the rest of the documentation.
make doc
# Prevent GitHub Jekyll to interfere with Sphinx theme.
touch ../doc/sphinx/html/.nojekyll
working-directory: ./src
- name: Build LAMMPS with n2p2 support
run: make MODE=test lammps-hdnnp
working-directory: ./src
- name: Run C++ tests and coverage
run: |
make cpp
cd cpp
make coverage
rm *.gcda *.gcno
working-directory: ./test
- name: Build pynnp
run: make pynnp MODE=test
working-directory: ./src
- name: Run python tests
run: make python
working-directory: ./test
- name: Upload C++ coverage to Codecov
uses: codecov/codecov-action@v2
with:
files: test/cpp/tests.info
flags: cpp
verbose: true
- name: Upload Python coverage to Codecov
uses: codecov/codecov-action@v2
with:
directory: test/python
flags: python
verbose: true
- name: Deploy Github pages
if: ${{ github.ref == 'refs/heads/master' }}
uses: JamesIves/github-pages-deploy-action@v4.3.3
with:
branch: gh-pages
folder: doc/sphinx/html
================================================
FILE: .gitignore
================================================
*.o
compile_commands.json
.clangd
.idea/
src/interface/stable_29Sep2021.tar.gz
================================================
FILE: AUTHORS.rst
================================================
Authors
=======
This software was originally created by `Andreas Singraber
<andreas.singraber@gmx.at>`_ during his PhD programme at the University of
Vienna. Code development started in 2015 and the first release to the public
was in 2018.
Contributions are much appreciated and will be recorded here:
* CabanaMD interface (`libnnpif/CabanaMD`): Saaketh Desai and Sam Reeve
* Polynomial symmetry functions (`libnnp/Sym(Fnc/Grp)(Base)Comp...`): Martin P.
Bircher and Andreas Singraber
* 4G-HDNNP training/prediction implementation in n2p2: Philipp Misof
* 4G-HDNNP prediction implementation in LAMMPS+n2p2: Emir Kocer
================================================
FILE: CHANGELOG.rst
================================================
Changelog
=========
All notable changes to this project will be documented in this file.
Version 3.0.0 - 2024-1?-??
--------------------------
New features
^^^^^^^^^^^^
* 4G-HDNNPs training/prediction in n2p2 (Philipp Misof).
* 4G-HDNNPs prediction in LAMMPS+n2p2 (Emir Kocer).
Version 2.3.0 - 2024-11-23
--------------------------
New features
^^^^^^^^^^^^
* Allow manual definition of train/test set (add ``set=train/test`` after ``begin`` in
input.data).
* Additional symmetry function log output, extra column ``spread``.
* Structure ``remap()`` function is now available in pynnp.
Maintenance
^^^^^^^^^^^
* Fixed CI: Cython updated to version 3.0+, added ``__rmul__`` to ``Vec3D`` in
pynnp.
Important changes
^^^^^^^^^^^^^^^^^
* Synchronized LAMMPS developer build with LAMMPS-distributed source: Finally
switched to pair style ``hdnnp`` everywhere.
Documentation
^^^^^^^^^^^^^
* Removed old ``nnp`` pair style description page.
* Updated LAMMPS interface build instructions page.
* Added train/test set split documentation.
Version 2.2.0 - 2022-05-23
--------------------------
New features
^^^^^^^^^^^^
* Normalization procedure on-the-fly via nnp-train, keyword ``normalize_data_set``.
* New normalization scheme based on force predictions.
* New keyword ``force_energy_ratio`` for nnp-train.
* Additional neighbor statistics output from nnp-scaling.
* New tool nnp-checkdw (for testing purposes).
Important changes
^^^^^^^^^^^^^^^^^
* New CI via Github Actions.
* Use self-compiled doxygen for API docs, use version 1.9.4.
Bugfixes
^^^^^^^^
* Fixed missing atomic energy offsets for LAMMPS interface.
* Fixed NaNs from nnp-dist when running mixed data sets.
* Fixed bugs in pynnp examples.
Version 2.1.4 - 2021-05-11
--------------------------
New features
^^^^^^^^^^^^
* Changed build behavior for LAMMPS interface to conform with PR (lammps/lammps#2626)
Version 2.1.3 - 2021-04-26
--------------------------
Bugfixes
^^^^^^^^
* Fixed bug in nnp-scaling which could cause segfaults (MPI only).
Version 2.1.2 - 2021-04-12
--------------------------
New features
^^^^^^^^^^^^
* New tool to check numeric vs. analytic forces
Bugfixes
^^^^^^^^
* Fixed critical bug for large cutoff values (large compared to lattice vectors)
Version 2.1.1 - 2021-01-15
--------------------------
New features
^^^^^^^^^^^^
* Now compatible with latest LAMMPS stable release 29Oct2020
* Improved EW warnings in LAMMPS
* Citation header in screen output
* Restructured training to prepare for multi-network HDNNPs (e.g. 4G-HDNNP)
* New training "properties" can be added more easily now
Bugfixes
^^^^^^^^
* Fixed bugs in makefiles
* Fixed bug when creating scaling data
Version 2.1.0 - 2020-12-21
--------------------------
New features
^^^^^^^^^^^^
* Polynomial symmetry functions (Martin P. Bircher and Andreas Singraber)
* Better symmetry function cache mechanism
Important changes
^^^^^^^^^^^^^^^^^
* Documentation updates (API docs in Sphinx via Breathe)
Version 2.0.3 - 2020-11-30
--------------------------
New features
^^^^^^^^^^^^
* Tool nnp-scaling puts out rejected configurations into a separate file.
Version 2.0.2 - 2020-11-25
--------------------------
Bugfixes
^^^^^^^^
* Bugfix in CabanaMD interface: SF group initialization
Version 2.0.1 - 2020-10-05
--------------------------
Bugfixes
^^^^^^^^
* Fix bug in makefile which sometimes causes a failed build due to parallel execution
Version 2.0.0 - 2020-10-05
--------------------------
New features
^^^^^^^^^^^^
* Training library (Multi-stream Kalman filter training).
* Tools for HDNNP data set handling, etc.
* Python interface (basic functionality).
* Sphinx documentation (+ Doxygen API reference).
* CabanaMD interface (by Saaketh Desai and Sam Reeve)
Important changes
^^^^^^^^^^^^^^^^^
* License change from MPL 2.0 to GPL v3 or later.
Version 1.0.0 - 2018-08-13
--------------------------
New features
^^^^^^^^^^^^
* Core library (NN, symmetry functions, ...).
* LAMMPS interface.
* Documentation (in parts) via doxygen.
================================================
FILE: LICENSE
================================================
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
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The licenses for most software and other practical works are designed
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================================================
FILE: README.md
================================================
n2p2 - A neural network potential package
=========================================
[](https://doi.org/10.5281/zenodo.1344446)
[](https://GitHub.com/CompPhysVienna/n2p2/releases/)
[](https://app.travis-ci.com/CompPhysVienna/n2p2)
[](https://codecov.io/gh/CompPhysVienna/n2p2)
[](https://www.gnu.org/licenses/gpl-3.0)
This repository provides ready-to-use software for high-dimensional neural
network potentials in computational physics and chemistry.
# [Documentation](http://compphysvienna.github.io/n2p2)
This package uses automatic documentation generation via
[Sphinx](http://www.sphinx-doc.org),
[Breathe](https://breathe.readthedocs.io/en/latest/#) and
[doxygen](http://www.doxygen.nl/). An online version of the documentation which
is automatically updated with the master branch of the repository can be found
[__here__](http://compphysvienna.github.io/n2p2).
# Authors
See [AUTHORS.rst](https://github.com/CompPhysVienna/n2p2/blob/master/AUTHORS.rst) for a list of contributions.
# License
This software is licensed under the [GNU General Public License version 3 or any later version (GPL-3.0-or-later)](https://www.gnu.org/licenses/gpl.txt).
================================================
FILE: bin/.gitignore
================================================
================================================
FILE: doc/.gitignore
================================================
================================================
FILE: doc/doxygen/.gitignore
================================================
================================================
FILE: examples/coarse-graining/README.md
================================================
Descriptor analysis/Coarse-graining
===================================
Please have a look at the online documentation:
https://compphysvienna.github.io/n2p2/misc/cg_descriptor_analysis.html
================================================
FILE: examples/coarse-graining/step-0_cg-data-set/input.data
================================================
begin
comment
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gitextract_tn4psl0z/
├── .github/
│ ├── ISSUE_TEMPLATE/
│ │ ├── bug_report.md
│ │ ├── feature_request.md
│ │ └── question.md
│ └── workflows/
│ └── n2p2-ci.yaml
├── .gitignore
├── AUTHORS.rst
├── CHANGELOG.rst
├── LICENSE
├── README.md
├── bin/
│ └── .gitignore
├── doc/
│ ├── .gitignore
│ └── doxygen/
│ └── .gitignore
├── examples/
│ ├── coarse-graining/
│ │ ├── README.md
│ │ ├── step-0_cg-data-set/
│ │ │ ├── input.data
│ │ │ ├── makefile
│ │ │ └── nnp-cgdata.cpp
│ │ ├── step-1_scaling-data/
│ │ │ ├── input.data
│ │ │ └── input.nn
│ │ ├── step-2_atomic-env/
│ │ │ └── scaling.data
│ │ └── step-3_cluster-analysis/
│ │ ├── analyze-descriptors.ipynb
│ │ └── atomic-env.dGdx
│ ├── configuration-sets/
│ │ ├── input.data.Anisole
│ │ ├── input.data.Cu2S_PBE
│ │ ├── input.data.DMABN
│ │ ├── input.data.Ethylbenzene
│ │ ├── input.data.H2O_RPBE-D3
│ │ └── input.data.LJ
│ ├── configuration-single/
│ │ ├── input.data.Anisole
│ │ ├── input.data.Cu2S_144_low-chalcocite
│ │ ├── input.data.DMABN
│ │ ├── input.data.Ethylbenzene
│ │ └── input.data.H2O_1080_liquid
│ ├── input.nn.recommended
│ ├── interface-LAMMPS/
│ │ ├── AlAuMgO_4G/
│ │ │ ├── AlAuMgO.data
│ │ │ ├── AlAuMgO.data-n2p2
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── hardness.008.data
│ │ │ │ ├── hardness.012.data
│ │ │ │ ├── hardness.013.data
│ │ │ │ ├── hardness.079.data
│ │ │ │ ├── input.nn
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.008.data
│ │ │ │ ├── weights.012.data
│ │ │ │ ├── weights.013.data
│ │ │ │ ├── weights.079.data
│ │ │ │ ├── weightse.008.data
│ │ │ │ ├── weightse.012.data
│ │ │ │ ├── weightse.013.data
│ │ │ │ └── weightse.079.data
│ │ │ ├── input.data
│ │ │ ├── input.data.q
│ │ │ ├── md-external.lmp
│ │ │ ├── md.lmp
│ │ │ └── nnp-predict/
│ │ │ ├── hardness.008.data
│ │ │ ├── hardness.012.data
│ │ │ ├── hardness.013.data
│ │ │ ├── hardness.079.data
│ │ │ ├── input.data
│ │ │ ├── input.data-2
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.008.data
│ │ │ ├── weights.012.data
│ │ │ ├── weights.013.data
│ │ │ ├── weights.079.data
│ │ │ ├── weightse.008.data
│ │ │ ├── weightse.012.data
│ │ │ ├── weightse.013.data
│ │ │ └── weightse.079.data
│ │ ├── Cu2S_PBE/
│ │ │ ├── cu2s_144_low-chalcocite_Evans-1979_PBE.data
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── input.nn
│ │ │ │ ├── nnp-train.log.0000
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.016.data
│ │ │ │ └── weights.029.data
│ │ │ └── md.lmp
│ │ ├── Cu2S_PBE_external/
│ │ │ ├── cu2s_144_low-chalcocite_Evans-1979_PBE.data
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── input.nn
│ │ │ │ ├── nnp-train.log.0000
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.016.data
│ │ │ │ └── weights.029.data
│ │ │ └── md.lmp
│ │ ├── H2O_4G/
│ │ │ ├── correct-input-data/
│ │ │ │ ├── input.data-h2o-192
│ │ │ │ ├── input.data-h2o-36
│ │ │ │ ├── input.data-h2o-768
│ │ │ │ ├── water.data-h2o-192
│ │ │ │ ├── water.data-h2o-36
│ │ │ │ └── water.data-h2o-768
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── hardness.001.data
│ │ │ │ ├── hardness.008.data
│ │ │ │ ├── input.nn
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ ├── weights.008.data
│ │ │ │ ├── weightse.001.data
│ │ │ │ └── weightse.008.data
│ │ │ ├── md.lmp
│ │ │ ├── nnp-predict/
│ │ │ │ ├── hardness.001.data
│ │ │ │ ├── hardness.008.data
│ │ │ │ ├── input.data
│ │ │ │ ├── input.nn
│ │ │ │ ├── other-input-data/
│ │ │ │ │ ├── input.data-1np
│ │ │ │ │ ├── input.data-1p
│ │ │ │ │ ├── input.data-36-angs
│ │ │ │ │ ├── input.data-36p
│ │ │ │ │ ├── input.data-36s
│ │ │ │ │ ├── input.data-angs-p
│ │ │ │ │ ├── input.data-h2o-192-neg
│ │ │ │ │ ├── input.data-h2o-36-neg
│ │ │ │ │ └── input.data-h2o-768-neg
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ ├── weights.008.data
│ │ │ │ ├── weightse.001.data
│ │ │ │ └── weightse.008.data
│ │ │ ├── water.data
│ │ │ └── water.data.q
│ │ ├── H2O_RPBE-D3/
│ │ │ ├── h2o_8640_liquid_NpT_RPBE-D3.data
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── input.nn
│ │ │ │ ├── nnp-train.log.0000
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ └── weights.008.data
│ │ │ └── md.lmp
│ │ ├── H2O_RPBE-D3_128mol/
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── input.nn
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ └── weights.008.data
│ │ │ ├── iceIh_128.data
│ │ │ └── md.lmp
│ │ ├── H2O_RPBE-D3_128mol_develop/
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── hardness.001.data
│ │ │ │ ├── hardness.008.data
│ │ │ │ ├── input.nn
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ ├── weights.008.data
│ │ │ │ ├── weightse.001.data
│ │ │ │ └── weightse.008.data
│ │ │ ├── iceIh_128.data
│ │ │ └── md.lmp
│ │ ├── H2O_RPBE-D3_128mol_external/
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── input.nn
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ └── weights.008.data
│ │ │ ├── iceIh_128.data
│ │ │ └── md.lmp
│ │ ├── H2O_RPBE-D3_external/
│ │ │ ├── h2o_8640_liquid_NpT_RPBE-D3.data
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── input.nn
│ │ │ │ ├── nnp-train.log.0000
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ └── weights.008.data
│ │ │ └── md.lmp
│ │ └── TO_BE_CHECKED/
│ │ ├── carbon-chain/
│ │ │ ├── lammps-nnp/
│ │ │ │ ├── carbon-chain.data
│ │ │ │ ├── log.lammps
│ │ │ │ ├── md-external.lmp
│ │ │ │ ├── md.lmp
│ │ │ │ └── nnp-data/
│ │ │ │ ├── hardness.001.data
│ │ │ │ ├── hardness.006.data
│ │ │ │ ├── input.nn
│ │ │ │ ├── scaling.data
│ │ │ │ ├── weights.001.data
│ │ │ │ ├── weights.006.data
│ │ │ │ ├── weightse.001.data
│ │ │ │ └── weightse.006.data
│ │ │ └── nnp-predict/
│ │ │ ├── hardness.001.data
│ │ │ ├── hardness.006.data
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ ├── weights.006.data
│ │ │ ├── weightse.001.data
│ │ │ └── weightse.006.data
│ │ └── carbon-chain2/
│ │ ├── lammps-nnp/
│ │ │ ├── carbon-chain.data
│ │ │ ├── carbon-chain.data-eg
│ │ │ ├── carbon-chain.data-mod
│ │ │ ├── carbon-chain.data-n2p2
│ │ │ ├── carbon-chain.data-org
│ │ │ ├── carbon-chain.data-q0
│ │ │ ├── carbon-chain.data-sameq
│ │ │ ├── carbond-chain.data
│ │ │ ├── hdnnp-data/
│ │ │ │ ├── debug.out
│ │ │ │ ├── energy.out
│ │ │ │ ├── external.out
│ │ │ │ ├── hardness.001.data
│ │ │ │ ├── hardness.006.data
│ │ │ │ ├── input.data
│ │ │ │ ├── input.data-org
│ │ │ │ ├── input.nn
│ │ │ │ ├── nnatoms.out
│ │ │ │ ├── nnforces.out
│ │ │ │ ├── nnp-predict.log
│ │ │ │ ├── output.data
│ │ │ │ ├── scaling.data
│ │ │ │ ├── structure.out
│ │ │ │ ├── weights.001.data
│ │ │ │ ├── weights.006.data
│ │ │ │ ├── weightse.001.data
│ │ │ │ └── weightse.006.data
│ │ │ ├── md-external.lmp
│ │ │ └── md.lmp
│ │ └── nnp-predict/
│ │ ├── energy.out
│ │ ├── hardness.001.data
│ │ ├── hardness.006.data
│ │ ├── input.data
│ │ ├── input.nn
│ │ ├── nnatoms.out
│ │ ├── nnforces.out
│ │ ├── nnp-predict.log
│ │ ├── output.data
│ │ ├── scaling.data
│ │ ├── weights.001.data
│ │ ├── weights.006.data
│ │ ├── weightse.001.data
│ │ └── weightse.006.data
│ ├── nnp-atomenv/
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ └── scaling.data
│ │ └── H2O_RPBE-D3/
│ │ ├── input.data
│ │ ├── input.nn
│ │ └── scaling.data
│ ├── nnp-checkdw/
│ │ ├── H2O_RPBE-D3/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.008.data
│ │ └── LJ/
│ │ ├── input.data
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ └── weights.010.data
│ ├── nnp-checkf/
│ │ ├── H2O_RPBE-D3/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.008.data
│ │ └── LJ/
│ │ ├── input.data
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ └── weights.010.data
│ ├── nnp-comp2/
│ │ └── Cu2S_PBE/
│ │ ├── input.data
│ │ ├── nnp-data-1/
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.016.data
│ │ │ └── weights.029.data
│ │ └── nnp-data-2/
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ ├── weights.016.data
│ │ └── weights.029.data
│ ├── nnp-convert/
│ │ └── Cu2S_PBE/
│ │ └── input.data
│ ├── nnp-dataset/
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.016.data
│ │ │ └── weights.029.data
│ │ └── H2O_RPBE-D3/
│ │ ├── input.data
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ ├── weights.001.data
│ │ └── weights.008.data
│ ├── nnp-dist/
│ │ ├── Cu2S_PBE/
│ │ │ └── input.data
│ │ └── H2O_RPBE-D3/
│ │ └── input.data
│ ├── nnp-norm/
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ └── input.nn
│ │ └── H2O_RPBE-D3/
│ │ ├── input.data
│ │ └── input.nn
│ ├── nnp-norm2/
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ └── scaling.data
│ │ └── H2O_RPBE-D3/
│ │ ├── input.data
│ │ ├── input.nn
│ │ └── scaling.data
│ ├── nnp-predict/
│ │ ├── AlAuMgO_4G/
│ │ │ ├── hardness.008.data
│ │ │ ├── hardness.012.data
│ │ │ ├── hardness.013.data
│ │ │ ├── hardness.079.data
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.008.data
│ │ │ ├── weights.012.data
│ │ │ ├── weights.013.data
│ │ │ ├── weights.079.data
│ │ │ ├── weightse.008.data
│ │ │ ├── weightse.012.data
│ │ │ ├── weightse.013.data
│ │ │ └── weightse.079.data
│ │ ├── Anisole_SCAN/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ ├── weights.006.data
│ │ │ └── weights.008.data
│ │ ├── Carbon_chain_4G/
│ │ │ ├── hardness.001.data
│ │ │ ├── hardness.006.data
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ ├── weights.006.data
│ │ │ ├── weightse.001.data
│ │ │ └── weightse.006.data
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.016.data
│ │ │ └── weights.029.data
│ │ ├── DMABN_SCAN/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ ├── weights.006.data
│ │ │ └── weights.007.data
│ │ ├── Ethylbenzene_SCAN/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.006.data
│ │ ├── H2O_RPBE-D3/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.008.data
│ │ └── H2O_RPBE-D3_4G/
│ │ ├── hardness.001.data
│ │ ├── hardness.008.data
│ │ ├── input.data
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ ├── weights.001.data
│ │ ├── weights.008.data
│ │ ├── weightse.001.data
│ │ └── weightse.008.data
│ ├── nnp-prune/
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── sensitivity.016.out
│ │ │ └── sensitivity.029.out
│ │ └── H2O_RPBE-D3/
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ ├── sensitivity.001.out
│ │ └── sensitivity.008.out
│ ├── nnp-scaling/
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ └── input.nn
│ │ ├── H2O_RPBE-D3/
│ │ │ ├── input.data
│ │ │ └── input.nn
│ │ └── LJ/
│ │ ├── input.data
│ │ └── input.nn
│ ├── nnp-select/
│ │ └── H2O_RPBE-D3/
│ │ └── input.data
│ ├── nnp-symfunc/
│ │ └── H2O_RPBE-D3/
│ │ └── input.nn
│ ├── nnp-train/
│ │ ├── AlAuMgO_4G/
│ │ │ ├── hardness.008.data
│ │ │ ├── hardness.012.data
│ │ │ ├── hardness.013.data
│ │ │ ├── hardness.079.data
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weightse.008.data
│ │ │ ├── weightse.012.data
│ │ │ ├── weightse.013.data
│ │ │ └── weightse.079.data
│ │ ├── Carbon_chain_4G/
│ │ │ ├── hardness.001.data
│ │ │ ├── hardness.006.data
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weightse.001.data
│ │ │ └── weightse.006.data
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ └── scaling.data
│ │ ├── H2O_RPBE-D3/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ └── scaling.data
│ │ ├── H2O_RPBE-D3_4G/
│ │ │ ├── hardness.001.data
│ │ │ ├── hardness.008.data
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weightse.001.data
│ │ │ └── weightse.008.data
│ │ ├── H2O_RPBE-D3_norm-force/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ └── scaling.data
│ │ ├── LJ/
│ │ │ ├── input.data
│ │ │ ├── input.nn
│ │ │ └── scaling.data
│ │ └── QM9/
│ │ ├── input.data
│ │ ├── input.nn
│ │ └── input.nn.wacsf
│ ├── potentials/
│ │ ├── Anisole_SCAN/
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ ├── weights.006.data
│ │ │ └── weights.008.data
│ │ ├── Cu2S_PBE/
│ │ │ ├── input.nn
│ │ │ ├── nnp-train.log.0000
│ │ │ ├── scaling.data
│ │ │ ├── weights.016.data
│ │ │ └── weights.029.data
│ │ ├── DMABN_SCAN/
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ ├── weights.006.data
│ │ │ └── weights.007.data
│ │ ├── Ethylbenzene_SCAN/
│ │ │ ├── input.nn
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.006.data
│ │ ├── H2O_BLYP/
│ │ │ ├── input.nn
│ │ │ ├── nnp-train.log.0000
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.008.data
│ │ ├── H2O_BLYP-D3/
│ │ │ ├── input.nn
│ │ │ ├── nnp-train.log.0000
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.008.data
│ │ ├── H2O_RPBE/
│ │ │ ├── input.nn
│ │ │ ├── nnp-train.log.0000
│ │ │ ├── scaling.data
│ │ │ ├── weights.001.data
│ │ │ └── weights.008.data
│ │ └── H2O_RPBE-D3/
│ │ ├── input.nn
│ │ ├── nnp-train.log.0000
│ │ ├── scaling.data
│ │ ├── weights.001.data
│ │ └── weights.008.data
│ └── pynnp/
│ ├── prediction/
│ │ ├── example-simple.py
│ │ ├── example-verbose.py
│ │ ├── input.data
│ │ ├── input.nn
│ │ ├── scaling.data
│ │ ├── weights.001.data
│ │ └── weights.008.data
│ └── symfunc-only/
│ ├── example.ipynb
│ ├── example.py
│ ├── input.data.1
│ ├── input.data.2
│ ├── input.nn
│ └── scaling.data
├── include/
│ └── .gitignore
├── lib/
│ └── .gitignore
├── src/
│ ├── application/
│ │ ├── makefile
│ │ ├── nnp-atomenv.cpp
│ │ ├── nnp-checkdw.cpp
│ │ ├── nnp-checkf.cpp
│ │ ├── nnp-comp2.cpp
│ │ ├── nnp-convert.cpp
│ │ ├── nnp-cutoff.cpp
│ │ ├── nnp-dataset.cpp
│ │ ├── nnp-dist.cpp
│ │ ├── nnp-norm.cpp
│ │ ├── nnp-norm2.cpp
│ │ ├── nnp-predict.cpp
│ │ ├── nnp-prune.cpp
│ │ ├── nnp-scaling.cpp
│ │ ├── nnp-select.cpp
│ │ ├── nnp-symfunc.cpp
│ │ └── nnp-train.cpp
│ ├── doc/
│ │ ├── doxygen/
│ │ │ ├── Doxyfile
│ │ │ ├── README.md
│ │ │ └── makefile
│ │ └── sphinx/
│ │ ├── Makefile
│ │ └── source/
│ │ ├── about/
│ │ │ ├── authors.rst
│ │ │ ├── changelog.rst
│ │ │ ├── how_to_cite.rst
│ │ │ └── license.rst
│ │ ├── api/
│ │ │ ├── cutoff_functions.rst
│ │ │ ├── memory_layout.rst
│ │ │ ├── neural_network.rst
│ │ │ ├── symmetry_function_scaling.rst
│ │ │ └── symmetry_function_types.rst
│ │ ├── conf.py
│ │ ├── helper.rst
│ │ ├── index.rst
│ │ ├── interfaces/
│ │ │ ├── if_cabanamd.rst
│ │ │ └── if_lammps.rst
│ │ ├── misc/
│ │ │ ├── cabanamd_build_example.rst
│ │ │ └── cg_descriptor_analysis.rst
│ │ ├── old/
│ │ │ └── pair_nnp.rst
│ │ ├── tools/
│ │ │ ├── libnnp.rst
│ │ │ ├── nnp-atomenv.rst
│ │ │ ├── nnp-checkf.rst
│ │ │ ├── nnp-convert.rst
│ │ │ ├── nnp-norm.rst
│ │ │ ├── nnp-predict.rst
│ │ │ ├── nnp-prune.rst
│ │ │ ├── nnp-scaling.rst
│ │ │ ├── nnp-select.rst
│ │ │ └── nnp-train.rst
│ │ └── topics/
│ │ ├── build.rst
│ │ ├── cfg_file.rst
│ │ ├── descriptors.rst
│ │ ├── keywords.rst
│ │ ├── training.rst
│ │ └── units.rst
│ ├── interface/
│ │ ├── LAMMPS/
│ │ │ └── src/
│ │ │ └── ML-HDNNP/
│ │ │ ├── Install.sh
│ │ │ ├── README
│ │ │ ├── fix_hdnnp.cpp
│ │ │ ├── fix_hdnnp.h
│ │ │ ├── kspace_hdnnp.cpp
│ │ │ ├── kspace_hdnnp.h
│ │ │ ├── pair_hdnnp.cpp
│ │ │ ├── pair_hdnnp.h
│ │ │ ├── pair_hdnnp_4g.cpp
│ │ │ ├── pair_hdnnp_4g.h
│ │ │ ├── pair_hdnnp_develop.cpp
│ │ │ ├── pair_hdnnp_develop.h
│ │ │ ├── pair_hdnnp_external.cpp
│ │ │ └── pair_hdnnp_external.h
│ │ └── makefile
│ ├── libnnp/
│ │ ├── Atom.cpp
│ │ ├── Atom.h
│ │ ├── CompactFunction.cpp
│ │ ├── CompactFunction.h
│ │ ├── CoreFunction.cpp
│ │ ├── CoreFunction.h
│ │ ├── CutoffFunction.cpp
│ │ ├── CutoffFunction.h
│ │ ├── Element.cpp
│ │ ├── Element.h
│ │ ├── ElementMap.cpp
│ │ ├── ElementMap.h
│ │ ├── ErfcBuf.cpp
│ │ ├── ErfcBuf.h
│ │ ├── EwaldSetup.cpp
│ │ ├── EwaldSetup.h
│ │ ├── EwaldTruncJackson.cpp
│ │ ├── EwaldTruncJackson.h
│ │ ├── EwaldTruncKolafaFixR.cpp
│ │ ├── EwaldTruncKolafaFixR.h
│ │ ├── EwaldTruncKolafaOptEta.cpp
│ │ ├── EwaldTruncKolafaOptEta.h
│ │ ├── IEwaldTrunc.h
│ │ ├── ISettings.h
│ │ ├── Key.h
│ │ ├── Kspace.cpp
│ │ ├── Kspace.h
│ │ ├── Log.cpp
│ │ ├── Log.h
│ │ ├── Mode.cpp
│ │ ├── Mode.h
│ │ ├── NeuralNetwork.cpp
│ │ ├── NeuralNetwork.h
│ │ ├── Prediction.cpp
│ │ ├── Prediction.h
│ │ ├── ScreeningFunction.cpp
│ │ ├── ScreeningFunction.h
│ │ ├── Settings.cpp
│ │ ├── Settings.h
│ │ ├── SetupAnalysis.cpp
│ │ ├── SetupAnalysis.h
│ │ ├── Stopwatch.cpp
│ │ ├── Stopwatch.h
│ │ ├── Structure.cpp
│ │ ├── Structure.h
│ │ ├── SymFnc.cpp
│ │ ├── SymFnc.h
│ │ ├── SymFncBaseComp.cpp
│ │ ├── SymFncBaseComp.h
│ │ ├── SymFncBaseCompAng.cpp
│ │ ├── SymFncBaseCompAng.h
│ │ ├── SymFncBaseCompAngWeighted.cpp
│ │ ├── SymFncBaseCompAngWeighted.h
│ │ ├── SymFncBaseCutoff.cpp
│ │ ├── SymFncBaseCutoff.h
│ │ ├── SymFncBaseExpAng.cpp
│ │ ├── SymFncBaseExpAng.h
│ │ ├── SymFncCompAngn.cpp
│ │ ├── SymFncCompAngn.h
│ │ ├── SymFncCompAngnWeighted.cpp
│ │ ├── SymFncCompAngnWeighted.h
│ │ ├── SymFncCompAngw.cpp
│ │ ├── SymFncCompAngw.h
│ │ ├── SymFncCompAngwWeighted.cpp
│ │ ├── SymFncCompAngwWeighted.h
│ │ ├── SymFncCompRad.cpp
│ │ ├── SymFncCompRad.h
│ │ ├── SymFncCompRadWeighted.cpp
│ │ ├── SymFncCompRadWeighted.h
│ │ ├── SymFncExpAngn.cpp
│ │ ├── SymFncExpAngn.h
│ │ ├── SymFncExpAngnWeighted.cpp
│ │ ├── SymFncExpAngnWeighted.h
│ │ ├── SymFncExpAngw.cpp
│ │ ├── SymFncExpAngw.h
│ │ ├── SymFncExpRad.cpp
│ │ ├── SymFncExpRad.h
│ │ ├── SymFncExpRadWeighted.cpp
│ │ ├── SymFncExpRadWeighted.h
│ │ ├── SymFncStatistics.cpp
│ │ ├── SymFncStatistics.h
│ │ ├── SymGrp.cpp
│ │ ├── SymGrp.h
│ │ ├── SymGrpBaseComp.cpp
│ │ ├── SymGrpBaseComp.h
│ │ ├── SymGrpBaseCompAng.cpp
│ │ ├── SymGrpBaseCompAng.h
│ │ ├── SymGrpBaseCompAngWeighted.cpp
│ │ ├── SymGrpBaseCompAngWeighted.h
│ │ ├── SymGrpBaseCutoff.cpp
│ │ ├── SymGrpBaseCutoff.h
│ │ ├── SymGrpBaseExpAng.cpp
│ │ ├── SymGrpBaseExpAng.h
│ │ ├── SymGrpCompAngn.cpp
│ │ ├── SymGrpCompAngn.h
│ │ ├── SymGrpCompAngnWeighted.cpp
│ │ ├── SymGrpCompAngnWeighted.h
│ │ ├── SymGrpCompAngw.cpp
│ │ ├── SymGrpCompAngw.h
│ │ ├── SymGrpCompAngwWeighted.cpp
│ │ ├── SymGrpCompAngwWeighted.h
│ │ ├── SymGrpCompRad.cpp
│ │ ├── SymGrpCompRad.h
│ │ ├── SymGrpCompRadWeighted.cpp
│ │ ├── SymGrpCompRadWeighted.h
│ │ ├── SymGrpExpAngn.cpp
│ │ ├── SymGrpExpAngn.h
│ │ ├── SymGrpExpAngnWeighted.cpp
│ │ ├── SymGrpExpAngnWeighted.h
│ │ ├── SymGrpExpAngw.cpp
│ │ ├── SymGrpExpAngw.h
│ │ ├── SymGrpExpRad.cpp
│ │ ├── SymGrpExpRad.h
│ │ ├── SymGrpExpRadWeighted.cpp
│ │ ├── SymGrpExpRadWeighted.h
│ │ ├── Vec3D.h
│ │ ├── makefile
│ │ ├── mpi-extra.h
│ │ ├── utility.cpp
│ │ ├── utility.h
│ │ └── version.h
│ ├── libnnpif/
│ │ ├── CabanaMD/
│ │ │ ├── ElementCabana.h
│ │ │ ├── ElementCabana_impl.h
│ │ │ ├── ModeCabana.h
│ │ │ ├── ModeCabana_impl.h
│ │ │ └── typesCabana.h
│ │ ├── LAMMPS/
│ │ │ ├── InterfaceLammps.cpp
│ │ │ ├── InterfaceLammps.h
│ │ │ └── Makefile.lammps
│ │ └── makefile
│ ├── libnnptrain/
│ │ ├── Dataset.cpp
│ │ ├── Dataset.h
│ │ ├── GradientDescent.cpp
│ │ ├── GradientDescent.h
│ │ ├── KalmanFilter.cpp
│ │ ├── KalmanFilter.h
│ │ ├── Training.cpp
│ │ ├── Training.h
│ │ ├── Updater.cpp
│ │ ├── Updater.h
│ │ └── makefile
│ ├── makefile
│ ├── makefile.gnu
│ ├── makefile.intel
│ ├── makefile.llvm
│ └── pynnp/
│ ├── Atom.pyx
│ ├── CutoffFunction.pyx
│ ├── ElementMap.pyx
│ ├── Log.pyx
│ ├── Mode.pyx
│ ├── Prediction.pyx
│ ├── Settings.pyx
│ ├── Structure.pyx
│ ├── Vec3D.pyx
│ ├── makefile
│ ├── pynnp.pyx
│ ├── pynnp_dec.pxd
│ ├── setup-test.py
│ └── setup.py
├── test/
│ ├── cpp/
│ │ ├── BoostDataContainer.h
│ │ ├── Example.h
│ │ ├── ExamplePrediction.h
│ │ ├── ExampleScreeningFunction.h
│ │ ├── Example_lammps_hdnnp.h
│ │ ├── Example_nnp.h
│ │ ├── Example_nnp_atomenv.h
│ │ ├── Example_nnp_checkdw.h
│ │ ├── Example_nnp_checkf.h
│ │ ├── Example_nnp_convert.h
│ │ ├── Example_nnp_dataset.h
│ │ ├── Example_nnp_dist.h
│ │ ├── Example_nnp_norm.h
│ │ ├── Example_nnp_predict.h
│ │ ├── Example_nnp_prune.h
│ │ ├── Example_nnp_scaling.h
│ │ ├── Example_nnp_select.h
│ │ ├── Example_nnp_symfunc.h
│ │ ├── Example_nnp_train.h
│ │ ├── fileHelpers.h
│ │ ├── fixtures.h
│ │ ├── makefile
│ │ ├── nnp_test.h
│ │ ├── test_CutoffFunction.cpp
│ │ ├── test_Prediction.cpp
│ │ ├── test_ScreeningFunction.cpp
│ │ ├── test_Settings.cpp
│ │ ├── test_SymmetryFunctionGroups.cpp
│ │ ├── test_SymmetryFunctions.cpp
│ │ ├── test_lammps_hdnnp.cpp
│ │ ├── test_nnp-atomenv.cpp
│ │ ├── test_nnp-checkdw.cpp
│ │ ├── test_nnp-checkf.cpp
│ │ ├── test_nnp-convert.cpp
│ │ ├── test_nnp-dataset.cpp
│ │ ├── test_nnp-dist.cpp
│ │ ├── test_nnp-norm.cpp
│ │ ├── test_nnp-predict.cpp
│ │ ├── test_nnp-prune.cpp
│ │ ├── test_nnp-scaling.cpp
│ │ ├── test_nnp-select.cpp
│ │ ├── test_nnp-symfunc.cpp
│ │ └── test_nnp-train.cpp
│ ├── makefile
│ └── python/
│ ├── .coveragerc
│ ├── makefile
│ ├── setups/
│ │ └── Settings/
│ │ └── input.nn
│ ├── test_Atom.py
│ ├── test_CutoffFunction.py
│ ├── test_ElementMap.py
│ ├── test_Log.py
│ ├── test_Neighbor.py
│ ├── test_Settings.py
│ └── test_Vec3D.py
└── tools/
├── converter/
│ └── convert-VASP_OUTCAR.py
├── misc/
│ ├── convert_nnp.py
│ ├── generate-acsf-angular_narrow.py
│ ├── generate-acsf-angular_wide.py
│ ├── generate-acsf-radial.py
│ └── nnp-archive.sh
└── plot/
├── plot-symfunc-histograms.ipynb
└── plot-symfunc-shape-rdf.ipynb
SYMBOL INDEX (555 symbols across 166 files)
FILE: examples/coarse-graining/step-0_cg-data-set/nnp-cgdata.cpp
function main (line 41) | int main(int argc, char* argv[])
FILE: src/application/nnp-atomenv.cpp
function main (line 30) | int main(int argc, char* argv[])
FILE: src/application/nnp-checkdw.cpp
function main (line 33) | int main(int argc, char* argv[])
FILE: src/application/nnp-checkf.cpp
function main (line 33) | int main(int argc, char* argv[])
FILE: src/application/nnp-comp2.cpp
function main (line 31) | int main(int argc, char* argv[])
FILE: src/application/nnp-convert.cpp
function main (line 34) | int main(int argc, char* argv[])
FILE: src/application/nnp-cutoff.cpp
function runTest (line 42) | void runTest(bool write)
function runTest (line 76) | void runTest(CutoffFunction::CutoffType cutoffType)
function main (line 119) | int main()
FILE: src/application/nnp-dataset.cpp
function main (line 33) | int main(int argc, char* argv[])
FILE: src/application/nnp-dist.cpp
function main (line 35) | int main(int argc, char* argv[])
FILE: src/application/nnp-norm.cpp
function main (line 30) | int main(int argc, char* argv[])
FILE: src/application/nnp-norm2.cpp
function main (line 30) | int main(int argc, char* argv[])
FILE: src/application/nnp-predict.cpp
function main (line 30) | int main(int argc, char* argv[])
FILE: src/application/nnp-prune.cpp
function main (line 27) | int main(int argc, char* argv[])
FILE: src/application/nnp-scaling.cpp
function main (line 30) | int main(int argc, char* argv[])
FILE: src/application/nnp-select.cpp
function main (line 28) | int main(int argc, char* argv[])
FILE: src/application/nnp-symfunc.cpp
function main (line 26) | int main(int argc, char* argv[])
FILE: src/application/nnp-train.cpp
function main (line 28) | int main(int argc, char* argv[])
FILE: src/interface/LAMMPS/src/ML-HDNNP/fix_hdnnp.h
function namespace (line 27) | namespace LAMMPS_NS {
FILE: src/interface/LAMMPS/src/ML-HDNNP/kspace_hdnnp.h
type FFT_SCALAR (line 38) | typedef float FFT_SCALAR;
type FFT_SCALAR (line 43) | typedef double FFT_SCALAR;
function namespace (line 51) | namespace LAMMPS_NS {
FILE: src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp.h
function namespace (line 32) | namespace nnp {
function namespace (line 36) | namespace LAMMPS_NS {
FILE: src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_4g.h
function namespace (line 35) | namespace LAMMPS_NS {
FILE: src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_develop.h
function namespace (line 28) | namespace LAMMPS_NS {
FILE: src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_external.h
function namespace (line 30) | namespace LAMMPS_NS {
FILE: src/libnnp/Atom.cpp
function Vec3D (line 371) | Vec3D Atom::calculateSelfForceShort() const
function Vec3D (line 381) | Vec3D Atom::calculatePairForceShort(Neighbor const& neighbor,
function Vec3D (line 403) | Vec3D Atom::calculateDChidr(size_t const atomIndexOfR,
function string (line 461) | string Atom::getChargeLine() const
FILE: src/libnnp/Atom.h
function namespace (line 28) | namespace nnp
FILE: src/libnnp/CompactFunction.h
function class (line 27) | class CompactFunction
FILE: src/libnnp/CoreFunction.h
function class (line 28) | class CoreFunction
FILE: src/libnnp/CutoffFunction.h
function class (line 25) | class CutoffFunction
FILE: src/libnnp/Element.h
type Atom (line 34) | struct Atom
function class (line 38) | class Element
FILE: src/libnnp/ElementMap.cpp
function string (line 56) | string ElementMap::getElementsString() const
function string (line 76) | string ElementMap::symbol(size_t const index) const
function string (line 106) | string ElementMap::symbolFromAtomicNumber(size_t atomicNumber)
FILE: src/libnnp/ElementMap.h
function namespace (line 25) | namespace nnp
FILE: src/libnnp/ErfcBuf.h
function namespace (line 12) | namespace nnp
FILE: src/libnnp/EwaldSetup.h
function EWALDTruncMethod (line 29) | enum class EWALDTruncMethod {
FILE: src/libnnp/EwaldTruncJackson.cpp
type nnp (line 9) | namespace nnp
FILE: src/libnnp/EwaldTruncJackson.h
function namespace (line 9) | namespace nnp
FILE: src/libnnp/EwaldTruncKolafaFixR.cpp
type nnp (line 10) | namespace nnp
FILE: src/libnnp/EwaldTruncKolafaFixR.h
function namespace (line 11) | namespace nnp
FILE: src/libnnp/EwaldTruncKolafaOptEta.cpp
type nnp (line 11) | namespace nnp
FILE: src/libnnp/EwaldTruncKolafaOptEta.h
function namespace (line 10) | namespace nnp
FILE: src/libnnp/IEwaldTrunc.h
function namespace (line 10) | namespace nnp
FILE: src/libnnp/ISettings.h
function namespace (line 10) | namespace nnp
FILE: src/libnnp/Key.h
function namespace (line 12) | namespace nnp
FILE: src/libnnp/Kspace.h
function KSPACESolver (line 26) | enum class KSPACESolver {
FILE: src/libnnp/Log.cpp
function Log (line 28) | Log& Log::operator<<(string const& entry)
function Log (line 34) | Log& Log::operator<<(vector<string> const& entries)
FILE: src/libnnp/Log.h
function namespace (line 25) | namespace nnp
FILE: src/libnnp/Mode.cpp
function string (line 2214) | string Mode::settingsGetValue(std::string const& keyword) const
FILE: src/libnnp/Mode.h
type class (line 90) | enum class
FILE: src/libnnp/NeuralNetwork.h
function namespace (line 24) | namespace nnp
FILE: src/libnnp/Prediction.h
function namespace (line 24) | namespace nnp
FILE: src/libnnp/ScreeningFunction.h
function class (line 26) | class ScreeningFunction
FILE: src/libnnp/Settings.cpp
function createKnownKeywordsMap (line 27) | map<string, shared_ptr<settings::Key>> const createKnownKeywordsMap()
function string (line 182) | string Settings::operator[](string const& keyword) const
function string (line 222) | string Settings::keywordCheck(string const& keyword) const
function string (line 252) | string Settings::getValue(Key const& key) const
function string (line 257) | string Settings::getValue(string const& keyword) const
FILE: src/libnnp/Settings.h
function namespace (line 30) | namespace nnp
FILE: src/libnnp/SetupAnalysis.h
function namespace (line 23) | namespace nnp
FILE: src/libnnp/Stopwatch.h
function namespace (line 34) | namespace nnp
FILE: src/libnnp/Structure.cpp
function Vec3D (line 566) | Vec3D Structure::applyMinimumImageConvention(Vec3D const& dr)
function VectorXd (line 1184) | VectorXd const Structure::calculateForceLambdaTotal() const
function VectorXd (line 1197) | VectorXd const Structure::calculateForceLambdaElec() const
function string (line 1412) | string Structure::getEnergyLine() const
FILE: src/libnnp/Structure.h
function namespace (line 34) | namespace nnp
FILE: src/libnnp/SymFnc.cpp
function string (line 225) | string SymFnc::scalingLine() const
function string (line 285) | string SymFnc::getPrintFormat() const
FILE: src/libnnp/SymFnc.h
type Atom (line 31) | struct Atom
function class (line 39) | class SymFnc
FILE: src/libnnp/SymFncBaseComp.h
function namespace (line 27) | namespace nnp
FILE: src/libnnp/SymFncBaseCompAng.cpp
function string (line 127) | string SymFncBaseCompAng::getSettingsLine() const
function string (line 144) | string SymFncBaseCompAng::parameterLine() const
FILE: src/libnnp/SymFncBaseCompAng.h
function class (line 30) | class SymFncBaseCompAng : public SymFncBaseComp
FILE: src/libnnp/SymFncBaseCompAngWeighted.cpp
function string (line 114) | string SymFncBaseCompAngWeighted::getSettingsLine() const
function string (line 129) | string SymFncBaseCompAngWeighted::parameterLine() const
FILE: src/libnnp/SymFncBaseCompAngWeighted.h
function class (line 30) | class SymFncBaseCompAngWeighted : public SymFncBaseComp
FILE: src/libnnp/SymFncBaseCutoff.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymFncBaseExpAng.cpp
function string (line 108) | string SymFncBaseExpAng::getSettingsLine() const
function string (line 125) | string SymFncBaseExpAng::parameterLine() const
FILE: src/libnnp/SymFncBaseExpAng.h
function namespace (line 25) | namespace nnp
FILE: src/libnnp/SymFncCompAngn.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymFncCompAngnWeighted.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymFncCompAngw.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymFncCompAngwWeighted.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymFncCompRad.cpp
function string (line 112) | string SymFncCompRad::getSettingsLine() const
function string (line 185) | string SymFncCompRad::parameterLine() const
FILE: src/libnnp/SymFncCompRad.h
type Atom (line 29) | struct Atom
function class (line 55) | class SymFncCompRad : public SymFncBaseComp
FILE: src/libnnp/SymFncCompRadWeighted.cpp
function string (line 108) | string SymFncCompRadWeighted::getSettingsLine() const
function string (line 171) | string SymFncCompRadWeighted::parameterLine() const
FILE: src/libnnp/SymFncCompRadWeighted.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymFncExpAngn.h
function namespace (line 25) | namespace nnp
FILE: src/libnnp/SymFncExpAngnWeighted.cpp
function string (line 132) | string SymFncExpAngnWeighted::getSettingsLine() const
function string (line 290) | string SymFncExpAngnWeighted::parameterLine() const
FILE: src/libnnp/SymFncExpAngnWeighted.h
function namespace (line 25) | namespace nnp
FILE: src/libnnp/SymFncExpAngw.h
function namespace (line 25) | namespace nnp
FILE: src/libnnp/SymFncExpRad.cpp
function string (line 111) | string SymFncExpRad::getSettingsLine() const
function string (line 186) | string SymFncExpRad::parameterLine() const
FILE: src/libnnp/SymFncExpRad.h
function namespace (line 25) | namespace nnp
FILE: src/libnnp/SymFncExpRadWeighted.cpp
function string (line 107) | string SymFncExpRadWeighted::getSettingsLine() const
function string (line 172) | string SymFncExpRadWeighted::parameterLine() const
FILE: src/libnnp/SymFncExpRadWeighted.h
type Atom (line 28) | struct Atom
function class (line 48) | class SymFncExpRadWeighted : public SymFncBaseCutoff
FILE: src/libnnp/SymFncStatistics.h
function namespace (line 25) | namespace nnp
FILE: src/libnnp/SymGrp.cpp
function string (line 97) | string SymGrp::getPrintFormatCommon() const
function string (line 130) | string SymGrp::getPrintFormatMember() const
FILE: src/libnnp/SymGrp.h
type Atom (line 29) | struct Atom
function class (line 32) | class SymGrp
FILE: src/libnnp/SymGrpBaseComp.h
function namespace (line 27) | namespace nnp
FILE: src/libnnp/SymGrpBaseCompAng.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymGrpBaseCompAngWeighted.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymGrpBaseCutoff.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymGrpBaseExpAng.h
function namespace (line 25) | namespace nnp
FILE: src/libnnp/SymGrpCompAngn.h
function namespace (line 27) | namespace nnp
FILE: src/libnnp/SymGrpCompAngnWeighted.h
function namespace (line 27) | namespace nnp
FILE: src/libnnp/SymGrpCompAngw.h
function namespace (line 27) | namespace nnp
FILE: src/libnnp/SymGrpCompAngwWeighted.h
function namespace (line 27) | namespace nnp
FILE: src/libnnp/SymGrpCompRad.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymGrpCompRadWeighted.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymGrpExpAngn.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymGrpExpAngnWeighted.h
function namespace (line 25) | namespace nnp
FILE: src/libnnp/SymGrpExpAngw.h
function namespace (line 26) | namespace nnp
FILE: src/libnnp/SymGrpExpRad.h
function namespace (line 25) | namespace nnp
FILE: src/libnnp/SymGrpExpRadWeighted.h
function namespace (line 25) | namespace nnp
FILE: src/libnnp/Vec3D.h
function namespace (line 25) | namespace nnp
function Vec3D (line 205) | inline Vec3D& Vec3D::operator+=(Vec3D const& rhs)
function Vec3D (line 214) | inline Vec3D& Vec3D::operator-=(Vec3D const& rhs)
function Vec3D (line 223) | inline Vec3D& Vec3D::operator*=(double const a)
function Vec3D (line 232) | inline Vec3D& Vec3D::operator*=(Vec3D const (& A) [3])
function Vec3D (line 246) | inline Vec3D& Vec3D::operator/=(double const a)
function const (line 271) | inline double const& Vec3D::operator[](std::size_t const index) const
function rhs (line 281) | inline bool Vec3D::operator==(Vec3D const& rhs) const
function rhs (line 289) | inline bool Vec3D::operator!=(Vec3D const& rhs) const
function norm (line 294) | inline double Vec3D::norm() const
function l1norm (line 304) | inline double Vec3D::l1norm() const
function Vec3D (line 319) | inline Vec3D Vec3D::cross(Vec3D const& v) const
function a (line 346) | double const a)
FILE: src/libnnp/utility.cpp
type nnp (line 30) | namespace nnp
function split (line 33) | vector<string> split(string const& input, char delimiter)
function string (line 47) | string trim(string const& line, string const& whitespace)
function string (line 60) | string reduce(string const& line,
function string (line 79) | string pad(string const& input, size_t num, char fill, bool right)
function string (line 90) | string strpr(const char* format, ...)
function string (line 104) | string cap(string word)
function createFileHeader (line 111) | vector<string> createFileHeader(vector<string> const& title,
function appendLinesToFile (line 225) | void appendLinesToFile(ofstream& file, vector<string> const lines)
function appendLinesToFile (line 236) | void appendLinesToFile(FILE* const& file, vector<string> const lines)
function readColumnsFromFile (line 247) | map<size_t, vector<double>> readColumnsFromFile(string fileName,
function pow_int (line 292) | double pow_int(double x, int n)
FILE: src/libnnp/utility.h
function namespace (line 30) | namespace nnp
FILE: src/libnnpif/CabanaMD/ElementCabana.h
function namespace (line 31) | namespace nnp
function setScalingType (line 285) | void
function unscale (line 340) | double ElementCabana::unscale( int attype, double value, int k,
FILE: src/libnnpif/CabanaMD/ElementCabana_impl.h
function namespace (line 28) | namespace nnp
function setupSymmetryFunctionGroups (line 308) | void ElementCabana::setupSymmetryFunctionGroups( t_SF SF,
FILE: src/libnnpif/CabanaMD/ModeCabana.h
function namespace (line 36) | namespace nnp
FILE: src/libnnpif/CabanaMD/ModeCabana_impl.h
function namespace (line 29) | namespace nnp
function calc_radial_symm_op (line 625) | auto calc_radial_symm_op = KOKKOS_LAMBDA( const int i, const int j )
function calc_angular_symm_op (line 676) | auto calc_angular_symm_op =
function scale_symm_op (line 797) | auto scale_symm_op = KOKKOS_LAMBDA( const int i )
function calculateAtomicNeuralNetworks (line 836) | void ModeCabana<t_device>::calculateAtomicNeuralNetworks(
function calc_radial_force_op (line 951) | auto calc_radial_force_op = KOKKOS_LAMBDA( const int i, const int j )
function calc_angular_force_op (line 1023) | auto calc_angular_force_op =
FILE: src/libnnpif/CabanaMD/typesCabana.h
type ScalingType (line 26) | enum ScalingType {
FILE: src/libnnpif/LAMMPS/InterfaceLammps.h
function namespace (line 28) | namespace nnp
FILE: src/libnnptrain/Dataset.h
function namespace (line 30) | namespace nnp
FILE: src/libnnptrain/GradientDescent.cpp
function string (line 144) | string GradientDescent::status(size_t epoch) const
FILE: src/libnnptrain/GradientDescent.h
function namespace (line 25) | namespace nnp
FILE: src/libnnptrain/KalmanFilter.cpp
function string (line 243) | string KalmanFilter::status(size_t epoch) const
FILE: src/libnnptrain/KalmanFilter.h
function namespace (line 27) | namespace nnp
FILE: src/libnnptrain/Training.h
function namespace (line 31) | namespace nnp
FILE: src/libnnptrain/Updater.h
function namespace (line 27) | namespace nnp
FILE: test/cpp/BoostDataContainer.h
function setup (line 13) | void setup()
FILE: test/cpp/Example.h
type Example (line 7) | struct Example
FILE: test/cpp/ExamplePrediction.h
function Example (line 9) | struct ExamplePrediction : public Example
function setup (line 30) | void BoostDataContainer<ExamplePrediction>::setup()
FILE: test/cpp/ExampleScreeningFunction.h
function Example (line 15) | struct ExampleScreeningFunction : public Example
function setup (line 44) | void BoostDataContainer<ExampleScreeningFunction>::setup()
FILE: test/cpp/Example_lammps_hdnnp.h
function Example (line 7) | struct Example_lammps_hdnnp : public Example
function setup (line 35) | void BoostDataContainer<Example_lammps_hdnnp>::setup()
FILE: test/cpp/Example_nnp.h
function Example (line 6) | struct Example_nnp : public Example
FILE: test/cpp/Example_nnp_atomenv.h
function Example_nnp (line 10) | struct Example_nnp_atomenv : public Example_nnp
function setup (line 23) | void BoostDataContainer<Example_nnp_atomenv>::setup()
FILE: test/cpp/Example_nnp_checkdw.h
function Example_nnp (line 7) | struct Example_nnp_checkdw : public Example_nnp
function setup (line 14) | void BoostDataContainer<Example_nnp_checkdw>::setup()
FILE: test/cpp/Example_nnp_checkf.h
function Example_nnp (line 7) | struct Example_nnp_checkf : public Example_nnp
function setup (line 14) | void BoostDataContainer<Example_nnp_checkf>::setup()
FILE: test/cpp/Example_nnp_convert.h
function Example_nnp (line 8) | struct Example_nnp_convert : public Example_nnp
function setup (line 17) | void BoostDataContainer<Example_nnp_convert>::setup()
FILE: test/cpp/Example_nnp_dataset.h
function Example_nnp (line 7) | struct Example_nnp_dataset : public Example_nnp
function setup (line 14) | void BoostDataContainer<Example_nnp_dataset>::setup()
FILE: test/cpp/Example_nnp_dist.h
function Example_nnp (line 8) | struct Example_nnp_dist : public Example_nnp
function setup (line 17) | void BoostDataContainer<Example_nnp_dist>::setup()
FILE: test/cpp/Example_nnp_norm.h
function Example_nnp (line 8) | struct Example_nnp_norm : public Example_nnp
function setup (line 17) | void BoostDataContainer<Example_nnp_norm>::setup()
FILE: test/cpp/Example_nnp_predict.h
function Example_nnp (line 8) | struct Example_nnp_predict : public Example_nnp
function setup (line 18) | void BoostDataContainer<Example_nnp_predict>::setup()
FILE: test/cpp/Example_nnp_prune.h
function Example_nnp (line 8) | struct Example_nnp_prune : public Example_nnp
function setup (line 17) | void BoostDataContainer<Example_nnp_prune>::setup()
FILE: test/cpp/Example_nnp_scaling.h
function Example_nnp (line 7) | struct Example_nnp_scaling : public Example_nnp
function setup (line 14) | void BoostDataContainer<Example_nnp_scaling>::setup()
FILE: test/cpp/Example_nnp_select.h
function Example_nnp (line 8) | struct Example_nnp_select : public Example_nnp
function setup (line 17) | void BoostDataContainer<Example_nnp_select>::setup()
FILE: test/cpp/Example_nnp_symfunc.h
function Example_nnp (line 8) | struct Example_nnp_symfunc : public Example_nnp
function setup (line 17) | void BoostDataContainer<Example_nnp_symfunc>::setup()
FILE: test/cpp/Example_nnp_train.h
function Example_nnp (line 9) | struct Example_nnp_train : public Example_nnp
function setup (line 24) | void BoostDataContainer<Example_nnp_train>::setup()
FILE: test/cpp/fileHelpers.h
function copy_directory_recursively (line 10) | bool copy_directory_recursively(bfs::path const& src, bfs::path const& d...
function else (line 65) | struct FixtureRepairDir
FILE: test/cpp/fixtures.h
function FixtureThreeAtomsMono (line 11) | struct FixtureThreeAtomsMono
function FixtureThreeAtomsDual (line 53) | struct FixtureThreeAtomsDual
type FixtureFourAtomsMixed (line 97) | struct FixtureFourAtomsMixed
FILE: test/cpp/test_CutoffFunction.cpp
function BOOST_AUTO_TEST_CASE (line 53) | BOOST_AUTO_TEST_CASE(CheckCutoffTypeNumbers_CorrectNumbering)
function BOOST_AUTO_TEST_CASE (line 66) | BOOST_AUTO_TEST_CASE(CheckUnknownCutoffType_ThrowsError)
function BOOST_AUTO_TEST_CASE (line 76) | BOOST_AUTO_TEST_CASE(CheckDefaultInitialization_AllZeroOutput)
function BOOST_AUTO_TEST_CASE (line 85) | BOOST_AUTO_TEST_CASE(CheckInvalidCutoffParameter_ThrowsError)
function BOOST_DATA_TEST_CASE (line 136) | BOOST_DATA_TEST_CASE(CalculateFunctionsOutOfCutoff_ZeroResult,
function BOOST_DATA_TEST_CASE (line 147) | BOOST_DATA_TEST_CASE(CalculateDerivativesOutOfCutoff_ZeroResult,
function BOOST_DATA_TEST_CASE (line 158) | BOOST_DATA_TEST_CASE(CalculateFunctionsAndDerivativesOutOfCutoff_ZeroRes...
function BOOST_DATA_TEST_CASE (line 173) | BOOST_DATA_TEST_CASE(CalculateFunctionsInsideInnerCutoff_OneResult,
function BOOST_DATA_TEST_CASE (line 196) | BOOST_DATA_TEST_CASE(CalculateDerivativesInsideInnerCutoff_ZeroResult,
function BOOST_DATA_TEST_CASE (line 219) | BOOST_DATA_TEST_CASE(
FILE: test/cpp/test_ScreeningFunction.cpp
function BOOST_AUTO_TEST_CASE (line 28) | BOOST_AUTO_TEST_CASE(CheckUnknownCoreFunctionType_ThrowsError)
function BOOST_AUTO_TEST_CASE (line 36) | BOOST_AUTO_TEST_CASE(CheckDefaultInitialization_AllZeroOutput)
function BOOST_AUTO_TEST_CASE (line 44) | BOOST_AUTO_TEST_CASE(CheckInvalidCutoffParameter_ThrowsError)
FILE: test/cpp/test_Settings.cpp
function BOOST_FIXTURE_TEST_CASE (line 21) | BOOST_FIXTURE_TEST_CASE(ReadRecommendedSettings_NoCriticalErrors,
function BOOST_FIXTURE_TEST_CASE (line 43) | BOOST_FIXTURE_TEST_CASE(UnknownKeyword_NoCriticalErrors,
function BOOST_FIXTURE_TEST_CASE (line 74) | BOOST_FIXTURE_TEST_CASE(DuplicatedKeyword_CriticalError,
function BOOST_FIXTURE_TEST_CASE (line 102) | BOOST_FIXTURE_TEST_CASE(DuplicatedAlternativeKeyword_CriticalError,
function BOOST_FIXTURE_TEST_CASE (line 130) | BOOST_FIXTURE_TEST_CASE(UseAlternativeKeyword_CorrectValue,
FILE: test/cpp/test_SymmetryFunctionGroups.cpp
function SymFnc (line 52) | SymFnc* setupSymmetryFunction(ElementMap em,
function SymGrp (line 100) | SymGrp* setupSymmetryFunctionGroup(ElementMap em, SymFnc const& sf)
function recalculateSymmetryFunctionGroup (line 127) | void recalculateSymmetryFunctionGroup(Structure& s,
function compareAnalyticNumericDerivGroup (line 139) | void compareAnalyticNumericDerivGroup(Structure& s,
function checkAbsoluteValueGroup (line 203) | void checkAbsoluteValueGroup(Structure& s,
FILE: test/cpp/test_SymmetryFunctions.cpp
function SymFnc (line 41) | SymFnc* setupSymmetryFunction(ElementMap em,
function recalculateSymmetryFunction (line 89) | void recalculateSymmetryFunction(Structure& s,
function compareAnalyticNumericDeriv (line 101) | void compareAnalyticNumericDeriv(Structure& s,
function checkAbsoluteValue (line 162) | void checkAbsoluteValue(Structure& s,
FILE: test/cpp/test_lammps_hdnnp.cpp
function nnpToolTestBody (line 21) | void nnpToolTestBody(Example_lammps_hdnnp const example)
FILE: test/cpp/test_nnp-atomenv.cpp
function nnpToolTestBody (line 19) | void nnpToolTestBody(Example_nnp_atomenv const example)
FILE: test/cpp/test_nnp-checkdw.cpp
function nnpToolTestBody (line 16) | void nnpToolTestBody(Example_nnp_checkdw const /*example*/)
FILE: test/cpp/test_nnp-checkf.cpp
function nnpToolTestBody (line 16) | void nnpToolTestBody(Example_nnp_checkf const /*example*/)
FILE: test/cpp/test_nnp-convert.cpp
function nnpToolTestBody (line 16) | void nnpToolTestBody(Example_nnp_convert const example)
FILE: test/cpp/test_nnp-dataset.cpp
function nnpToolTestBody (line 16) | void nnpToolTestBody(Example_nnp_dataset const /*example*/)
FILE: test/cpp/test_nnp-dist.cpp
function nnpToolTestBody (line 16) | void nnpToolTestBody(Example_nnp_dist const example)
FILE: test/cpp/test_nnp-norm.cpp
function nnpToolTestBody (line 16) | void nnpToolTestBody(Example_nnp_norm const example)
FILE: test/cpp/test_nnp-predict.cpp
function nnpToolTestBody (line 19) | void nnpToolTestBody(Example_nnp_predict const example)
FILE: test/cpp/test_nnp-prune.cpp
function nnpToolTestBody (line 16) | void nnpToolTestBody(Example_nnp_prune const example)
FILE: test/cpp/test_nnp-scaling.cpp
function nnpToolTestBody (line 16) | void nnpToolTestBody(Example_nnp_scaling const /*example*/)
FILE: test/cpp/test_nnp-select.cpp
function nnpToolTestBody (line 16) | void nnpToolTestBody(Example_nnp_select const example)
FILE: test/cpp/test_nnp-symfunc.cpp
function nnpToolTestBody (line 16) | void nnpToolTestBody(Example_nnp_symfunc const example)
FILE: test/cpp/test_nnp-train.cpp
function nnpToolTestBody (line 18) | void nnpToolTestBody(Example_nnp_train const example)
FILE: test/python/test_Atom.py
function a1 (line 10) | def a1():
function v1 (line 18) | def v1():
class Test___cinit__ (line 24) | class Test___cinit__:
method test_skeleton_initialization (line 25) | def test_skeleton_initialization(self):
method test_empty_initialization (line 28) | def test_empty_initialization(self):
class Test_hasNeighborList (line 35) | class Test_hasNeighborList:
method test_correct_type (line 36) | def test_correct_type(self, a1):
method test_set_and_get (line 38) | def test_set_and_get(self, a1):
class Test_hasSymmetryFunctions (line 43) | class Test_hasSymmetryFunctions:
method test_correct_type (line 44) | def test_correct_type(self, a1):
method test_set_and_get (line 47) | def test_set_and_get(self, a1):
class Test_hasSymmetryFunctionDerivatives (line 53) | class Test_hasSymmetryFunctionDerivatives:
method test_correct_type (line 54) | def test_correct_type(self, a1):
method test_set_and_get (line 57) | def test_set_and_get(self, a1):
class Test_index (line 63) | class Test_index:
method test_correct_type (line 64) | def test_correct_type(self, a1):
method test_set_and_get (line 66) | def test_set_and_get(self, a1):
class Test_indexStructure (line 72) | class Test_indexStructure:
method test_correct_type (line 73) | def test_correct_type(self, a1):
method test_set_and_get (line 75) | def test_set_and_get(self, a1):
class Test_tag (line 81) | class Test_tag:
method test_correct_type (line 82) | def test_correct_type(self, a1):
method test_set_and_get (line 84) | def test_set_and_get(self, a1):
class Test_element (line 90) | class Test_element:
method test_correct_type (line 91) | def test_correct_type(self, a1):
method test_set_and_get (line 93) | def test_set_and_get(self, a1):
class Test_numNeighbors (line 99) | class Test_numNeighbors:
method test_correct_type (line 100) | def test_correct_type(self, a1):
method test_set_and_get (line 102) | def test_set_and_get(self, a1):
class Test_numNeighborsUnique (line 108) | class Test_numNeighborsUnique:
method test_correct_type (line 109) | def test_correct_type(self, a1):
method test_set_and_get (line 111) | def test_set_and_get(self, a1):
class Test_numSymmetryFunctions (line 117) | class Test_numSymmetryFunctions:
method test_correct_type (line 118) | def test_correct_type(self, a1):
method test_set_and_get (line 121) | def test_set_and_get(self, a1):
class Test_energy (line 128) | class Test_energy:
method test_correct_type (line 129) | def test_correct_type(self, a1):
method test_set_and_get (line 131) | def test_set_and_get(self, a1):
class Test_charge (line 137) | class Test_charge:
method test_correct_type (line 138) | def test_correct_type(self, a1):
method test_set_and_get (line 140) | def test_set_and_get(self, a1):
class Test_r (line 146) | class Test_r:
method test_correct_type (line 147) | def test_correct_type(self, a1):
method test_set_and_get (line 149) | def test_set_and_get(self, a1, v1):
class Test_f (line 156) | class Test_f:
method test_correct_type (line 157) | def test_correct_type(self, a1):
method test_set_and_get (line 159) | def test_set_and_get(self, a1, v1):
class Test_fRef (line 166) | class Test_fRef:
method test_correct_type (line 167) | def test_correct_type(self, a1):
method test_set_and_get (line 169) | def test_set_and_get(self, a1, v1):
class Test_neighborsUnique (line 176) | class Test_neighborsUnique:
method test_correct_type (line 177) | def test_correct_type(self, a1):
class Test_numNeighborsPerElement (line 181) | class Test_numNeighborsPerElement:
method test_correct_type (line 182) | def test_correct_type(self, a1):
class Test_G (line 187) | class Test_G:
method test_correct_type (line 188) | def test_correct_type(self, a1):
class Test_dEdG (line 193) | class Test_dEdG:
method test_correct_type (line 194) | def test_correct_type(self, a1):
class Test_dGdr (line 205) | class Test_dGdr:
method test_correct_type (line 206) | def test_correct_type(self, a1):
class Test_neighbors (line 211) | class Test_neighbors:
method test_correct_type (line 212) | def test_correct_type(self, a1):
class Test_info (line 217) | class Test_info():
method test_return_list (line 218) | def test_return_list(self, a1):
FILE: test/python/test_CutoffFunction.py
function c1 (line 39) | def c1():
class Test___cinit__ (line 45) | class Test___cinit__:
method test_skeleton_initialization (line 46) | def test_skeleton_initialization(self):
method test_empty_initialization (line 50) | def test_empty_initialization(self):
class Test_setCutoffType (line 55) | class Test_setCutoffType:
method test_set_correct_type (line 57) | def test_set_correct_type(self, c1, cf_type):
method test_set_unknown_type (line 59) | def test_set_unknown_type(self, c1):
class Test_setCutoffRadius (line 63) | class Test_setCutoffRadius:
method test_set_float_value (line 64) | def test_set_float_value(self, c1):
method test_set_wrong_argument (line 66) | def test_set_wrong_argument(self, c1):
class Test_setCutoffParameter (line 70) | class Test_setCutoffParameter:
method test_set_float_value (line 71) | def test_set_float_value(self, c1):
method test_set_wrong_float_value (line 73) | def test_set_wrong_float_value(self, c1):
method test_set_wrong_argument (line 80) | def test_set_wrong_argument(self, c1):
class Test_f (line 84) | class Test_f:
method test_boundaries (line 86) | def test_boundaries(self, c1, cf_type):
method test_nonzero_radius (line 98) | def test_nonzero_radius(self, c1, cf_type, cf_value):
method test_nonfloat_argument (line 102) | def test_nonfloat_argument(self, c1):
class Test_df (line 106) | class Test_df:
method test_boundaries (line 108) | def test_boundaries(self, c1, cf_type):
method test_nonzero_radius (line 118) | def test_nonzero_radius(self, c1, cf_type, cf_dvalue):
method test_nonfloat_argument (line 122) | def test_nonfloat_argument(self, c1):
class Test_fdf (line 126) | class Test_fdf:
method test_boundaries (line 128) | def test_boundaries(self, c1, cf_type):
method test_nonzero_radius (line 153) | def test_nonzero_radius(self, c1, cf_type, cf_value, cf_dvalue):
method test_nonfloat_argument (line 160) | def test_nonfloat_argument(self, c1):
FILE: test/python/test_ElementMap.py
function em1 (line 5) | def em1():
class Test___cinit__ (line 13) | class Test___cinit__:
method test_skeleton_initialization (line 14) | def test_skeleton_initialization(self):
method test_empty_initialization (line 18) | def test_empty_initialization(self):
class Test_registerElements (line 23) | class Test_registerElements:
method test_nonstring_argument (line 24) | def test_nonstring_argument(self):
method test_correct_elements_registered (line 28) | def test_correct_elements_registered(self):
class Test___getitem__ (line 36) | class Test___getitem__:
method test_correct_element_index (line 37) | def test_correct_element_index(self, em1):
method test_correct_element_symbol (line 40) | def test_correct_element_symbol(self, em1):
method test_out_of_bounds_index (line 43) | def test_out_of_bounds_index(self, em1):
method test_unknown_symbol (line 46) | def test_unknown_symbol(self, em1):
method test_wrong_argument_type (line 49) | def test_wrong_argument_type(self, em1):
class Test_size (line 53) | class Test_size:
method test_correct_empty_size_returned (line 54) | def test_correct_empty_size_returned(self):
method test_correct_size_returned (line 57) | def test_correct_size_returned(self, em1):
class Test_index (line 60) | class Test_index:
method test_correct_element_index (line 61) | def test_correct_element_index(self, em1):
method test_wrong_argument_type (line 64) | def test_wrong_argument_type(self, em1):
class Test_symbol (line 68) | class Test_symbol:
method test_correct_element_index (line 69) | def test_correct_element_index(self, em1):
method test_wrong_argument_type (line 72) | def test_wrong_argument_type(self, em1):
class Test_deregisterElements (line 76) | class Test_deregisterElements:
method test_empty_map (line 77) | def test_empty_map(self, em1):
class Test_symbolFromAtomicNumber (line 81) | class Test_symbolFromAtomicNumber:
method test_some_elements (line 82) | def test_some_elements(self, em1):
class Test_info (line 92) | class Test_info():
method test_return_list (line 93) | def test_return_list(self, em1):
FILE: test/python/test_Log.py
function l1 (line 7) | def l1():
class Test___cinit__ (line 11) | class Test___cinit__:
method test_skeleton_initialization (line 12) | def test_skeleton_initialization(self):
method test_empty_initialization (line 16) | def test_empty_initialization(self):
class Test_addLogEntry (line 21) | class Test_addLogEntry:
method test_add_string_entry (line 22) | def test_add_string_entry(self):
method test_add_nonstring_entry (line 25) | def test_add_nonstring_entry(self):
class Test_getLog (line 30) | class Test_getLog:
method test_read_two_entries (line 31) | def test_read_two_entries(self):
class Test_writeToStdout (line 39) | class Test_writeToStdout:
method test_correct_type (line 40) | def test_correct_type(self, l1):
method test_set_and_get (line 42) | def test_set_and_get(self, l1):
FILE: test/python/test_Neighbor.py
function n1 (line 9) | def n1():
function n2 (line 19) | def n2():
class Test___cinit__ (line 28) | class Test___cinit__:
method test_skeleton_initialization (line 29) | def test_skeleton_initialization(self):
method test_empty_initialization (line 33) | def test_empty_initialization(self):
class Test_index (line 39) | class Test_index:
method test_correct_type (line 40) | def test_correct_type(self, n1):
method test_set_and_get (line 42) | def test_set_and_get(self, n1):
class Test_tag (line 48) | class Test_tag:
method test_correct_type (line 49) | def test_correct_type(self, n1):
method test_set_and_get (line 51) | def test_set_and_get(self, n1):
class Test_element (line 57) | class Test_element:
method test_correct_type (line 58) | def test_correct_type(self, n1):
method test_set_and_get (line 60) | def test_set_and_get(self, n1):
class Test_d (line 66) | class Test_d:
method test_correct_type (line 67) | def test_correct_type(self, n1):
method test_set_and_get (line 69) | def test_set_and_get(self, n1):
class Test_dr (line 75) | class Test_dr:
method test_correct_type (line 76) | def test_correct_type(self, n1):
method test_set_and_get (line 78) | def test_set_and_get(self, n1):
class Test_dGdr (line 86) | class Test_dGdr:
method test_correct_type (line 87) | def test_correct_type(self, n1):
class Test___eq__ (line 91) | class Test___eq__:
method test_not_equal (line 92) | def test_not_equal(self, n1, n2):
method test_element_different (line 94) | def test_element_different(self, n1, n2):
method test_distance_different (line 97) | def test_distance_different(self, n1, n2):
method test_equal (line 100) | def test_equal(self, n1, n2):
class Test___ne__ (line 105) | class Test___ne__:
method test_equal (line 106) | def test_equal(self, n1, n2):
method test_element_different (line 108) | def test_element_different(self, n1, n2):
method test_distance_different (line 111) | def test_distance_different(self, n1, n2):
method test_equal (line 114) | def test_equal(self, n1, n2):
class Test___le__ (line 151) | class Test___le__:
method test_less_than (line 152) | def test_less_than(self, n1, n2):
method test_greater_than (line 154) | def test_greater_than(self, n1, n2):
method test_equal_distance (line 156) | def test_equal_distance(self, n1, n2):
method test_equal_element (line 159) | def test_equal_element(self, n1, n2):
method test_equal (line 162) | def test_equal(self, n1, n2):
class Test___ge__ (line 167) | class Test___ge__:
method test_less_than (line 168) | def test_less_than(self, n1, n2):
method test_greater_than (line 170) | def test_greater_than(self, n1, n2):
method test_equal_distance (line 172) | def test_equal_distance(self, n1, n2):
method test_equal_element (line 175) | def test_equal_element(self, n1, n2):
method test_equal (line 178) | def test_equal(self, n1, n2):
FILE: test/python/test_Settings.py
function prepare_dir (line 6) | def prepare_dir(request):
function s1 (line 22) | def s1():
class Test___cinit__ (line 27) | class Test___cinit__:
method test_skeleton_initialization (line 28) | def test_skeleton_initialization(self):
method test_empty_initialization (line 32) | def test_empty_initialization(self):
class Test_loadFile (line 38) | class Test_loadFile:
method test_file_read (line 39) | def test_file_read(self, prepare_dir):
class Test___getitem__ (line 46) | class Test___getitem__:
method test_existing_key (line 47) | def test_existing_key(self, prepare_dir, s1):
method test_nonexisting_key (line 52) | def test_nonexisting_key(self, prepare_dir, s1):
method test_nonstring_key (line 55) | def test_nonstring_key(self, prepare_dir, s1):
class Test_keywordExists (line 60) | class Test_keywordExists:
method test_existing_key (line 61) | def test_existing_key(self, prepare_dir, s1):
method test_nonexisting_key (line 64) | def test_nonexisting_key(self, prepare_dir, s1):
method test_nonstring_key (line 67) | def test_nonstring_key(self, prepare_dir, s1):
class Test_getValue (line 72) | class Test_getValue:
method test_existing_key (line 73) | def test_existing_key(self, prepare_dir, s1):
method test_nonexisting_key (line 78) | def test_nonexisting_key(self, prepare_dir, s1):
method test_nonstring_key (line 81) | def test_nonstring_key(self, prepare_dir, s1):
class Test_info (line 86) | class Test_info():
method test_return_list (line 87) | def test_return_list(self, prepare_dir, s1):
class Test_getSettingsLines (line 94) | class Test_getSettingsLines():
method test_return_list (line 95) | def test_return_list(self, prepare_dir, s1):
FILE: test/python/test_Vec3D.py
function v1 (line 7) | def v1():
function v2 (line 14) | def v2():
class Test___cinit__ (line 20) | class Test___cinit__:
method test_skeleton_initialization (line 21) | def test_skeleton_initialization(self):
method test_empty_initialization (line 24) | def test_empty_initialization(self):
method test_float_initialization (line 29) | def test_float_initialization(self):
method test_Vec3D_initialization (line 39) | def test_Vec3D_initialization(self):
class Test___getitem__ (line 46) | class Test___getitem__():
method test_no_integer_index (line 47) | def test_no_integer_index(self, v1):
method test_negative_index (line 50) | def test_negative_index(self, v1):
method test_large_index (line 53) | def test_large_index(self, v1):
method test_components (line 56) | def test_components(self, v1):
class Test___setitem__ (line 61) | class Test___setitem__():
method test_no_integer_index (line 62) | def test_no_integer_index(self, v1):
method test_negative_index (line 65) | def test_negative_index(self, v1):
method test_large_index (line 68) | def test_large_index(self, v1):
method test_wrong_type (line 71) | def test_wrong_type(self, v1):
method test_components (line 74) | def test_components(self, v1):
class Test___str__ (line 82) | class Test___str__():
method test_return_string (line 83) | def test_return_string(self, v1):
method test_string_content (line 85) | def test_string_content(self, v1):
class Test___iadd__ (line 91) | class Test___iadd__():
method test_wrong_type (line 92) | def test_wrong_type(self, v1):
method test_correct_addition (line 95) | def test_correct_addition(self, v1, v2):
method test_added_Vec3D_unchanged (line 100) | def test_added_Vec3D_unchanged(self, v1, v2):
class Test___isub__ (line 106) | class Test___isub__():
method test_wrong_type (line 107) | def test_wrong_type(self, v1):
method test_correct_subtraction (line 110) | def test_correct_subtraction(self, v1, v2):
method test_subtracted_Vec3D_unchanged (line 115) | def test_subtracted_Vec3D_unchanged(self, v1, v2):
class Test___imul__ (line 121) | class Test___imul__():
method test_wrong_type (line 122) | def test_wrong_type(self, v1):
method test_correct_float_multiplication (line 125) | def test_correct_float_multiplication(self, v1):
class Test___itruediv__ (line 131) | class Test___itruediv__():
method test_wrong_type (line 132) | def test_wrong_type(self, v1):
method test_correct_float_division (line 135) | def test_correct_float_division(self, v1):
class Test___mul__ (line 141) | class Test___mul__():
method test_wrong_type (line 142) | def test_wrong_type(self, v1):
method test_scalar_product (line 147) | def test_scalar_product(self, v1, v2):
method test_right_float_multiplication (line 152) | def test_right_float_multiplication(self, v1):
method test_left_float_multiplication (line 158) | def test_left_float_multiplication(self, v1):
class Test___eq__ (line 165) | class Test___eq__():
method test_wrong_type (line 166) | def test_wrong_type(self, v1):
method test_equal_components (line 169) | def test_equal_components(self, v1):
class Test___ne__ (line 176) | class Test___ne__():
method test_wrong_type (line 177) | def test_wrong_type(self, v1):
method test_one_different_component (line 180) | def test_one_different_component(self, v1):
class Test_norm (line 194) | class Test_norm():
method test_correct_result (line 195) | def test_correct_result(self, v1):
class Test_norm2 (line 201) | class Test_norm2():
method test_correct_result (line 202) | def test_correct_result(self, v1):
class Test_normalize (line 207) | class Test_normalize():
method test_correct_result (line 208) | def test_correct_result(self, v1):
class Test_cross (line 212) | class Test_cross():
method test_wrong_type (line 213) | def test_wrong_type(self, v1):
method test_correct_return_type (line 216) | def test_correct_return_type(self, v1, v2):
method test_correct_result (line 219) | def test_correct_result(self, v1, v2):
class Test___add__ (line 225) | class Test___add__():
method test_wrong_type (line 226) | def test_wrong_type(self, v1):
method test_correct_return_type (line 231) | def test_correct_return_type(self, v1, v2):
method test_new_object_returned (line 234) | def test_new_object_returned(self, v1, v2):
method test_correct_result (line 238) | def test_correct_result(self, v1, v2):
class Test___sub__ (line 244) | class Test___sub__():
method test_wrong_type (line 245) | def test_wrong_type(self, v1):
method test_correct_return_type (line 250) | def test_correct_return_type(self, v1, v2):
method test_new_object_returned (line 253) | def test_new_object_returned(self, v1, v2):
method test_correct_result (line 257) | def test_correct_result(self, v1, v2):
class Test___neg__ (line 263) | class Test___neg__():
method test_correct_return_type (line 264) | def test_correct_return_type(self, v1):
method test_new_object_returned (line 266) | def test_new_object_returned(self, v1):
method test_correct_result (line 268) | def test_correct_result(self, v1):
class Test___truediv__ (line 274) | class Test___truediv__():
method test_wrong_type (line 275) | def test_wrong_type(self, v1, v2):
method test_correct_return_type (line 282) | def test_correct_return_type(self, v1):
method test_new_object_returned (line 285) | def test_new_object_returned(self, v1):
method test_correct_result (line 288) | def test_correct_result(self, v1):
class Test_r (line 294) | class Test_r():
method test_getter_correct_type (line 295) | def test_getter_correct_type(self, v1):
method test_getter_correct_size (line 297) | def test_getter_correct_size(self, v1):
method test_getter_correct_content (line 299) | def test_getter_correct_content(self, v1):
method test_setter_wrong_size (line 301) | def test_setter_wrong_size(self, v1):
method test_setter_wrong_type (line 304) | def test_setter_wrong_type(self, v1):
method test_setter_wrong_list_size (line 307) | def test_setter_wrong_list_size(self, v1):
method test_setter_correct_assignment (line 310) | def test_setter_correct_assignment(self, v1, v2):
method test_setter_correct_assignment_to_Vec3D (line 313) | def test_setter_correct_assignment_to_Vec3D(self, v1, v2):
method test_setter_index_assignment_not_possible (line 317) | def test_setter_index_assignment_not_possible(self, v1, v2):
FILE: tools/converter/convert-VASP_OUTCAR.py
function print_usage (line 28) | def print_usage():
FILE: tools/misc/convert_nnp.py
class ScalingData (line 51) | class ScalingData:
method __init__ (line 52) | def __init__(self, line):
method __eq__ (line 62) | def __eq__(self, other):
function split_columns (line 74) | def split_columns(line, delimiter=' '):
function read_scaling_data (line 87) | def read_scaling_data(file_name):
function convert_scaling_data (line 99) | def convert_scaling_data(old_file, new_file, data: Dict[int, List[Scalin...
function convert_input_nn (line 116) | def convert_input_nn(old_file, new_file):
function convert_weights_file (line 149) | def convert_weights_file(old_file, new_file, order):
function main (line 199) | def main():
Copy disabled (too large)
Download .json
Condensed preview — 733 files, each showing path, character count, and a content snippet. Download the .json file for the full structured content (45,740K chars).
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"path": ".github/ISSUE_TEMPLATE/bug_report.md",
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"preview": "---\nname: Question\nabout: Ask a general question about the project\n\n---\n\n**The question**\nAsk what you want to know abou"
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"preview": "*.o\ncompile_commands.json\n.clangd\n.idea/\nsrc/interface/stable_29Sep2021.tar.gz\n"
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"preview": "Authors\n=======\n\nThis software was originally created by `Andreas Singraber\n<andreas.singraber@gmx.at>`_ during his PhD "
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"chars": 4057,
"preview": "Changelog\n=========\n\nAll notable changes to this project will be documented in this file.\n\nVersion 3.0.0 - 2024-1?-??\n--"
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"preview": " GNU GENERAL PUBLIC LICENSE\n Version 3, 29 June 2007\n\n Copyright (C) 2007 Free "
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"preview": "n2p2 - A neural network potential package\n=========================================\n\n[![DOI](https://zenodo.org/badge/DO"
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"preview": "Descriptor analysis/Coarse-graining\n===================================\n\nPlease have a look at the online documentation:"
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"preview": "begin\ncomment \nlattice 4.3300044700000001E+01 0.0000000000000000E+00 0.0000000000000000E+00\nlattice 0.0000000000"
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"preview": "#!/bin/make -f\n\n###############################################################################\n# PROJECT PATHS\n########"
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"path": "examples/coarse-graining/step-0_cg-data-set/nnp-cgdata.cpp",
"chars": 5972,
"preview": "// n2p2 - A neural network potential package\n// Copyright (C) 2018 Andreas Singraber (University of Vienna)\n//\n// This p"
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"preview": "{\n \"cells\": [\n {\n \"cell_type\": \"markdown\",\n \"metadata\": {},\n \"source\": [\n \"This notebook requires some package"
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"chars": 828300,
"preview": "begin\ncomment frame number 26\nlattice 26.9097 0.0000 0.0000\nlattice 0.0000 26.9097 0.0000\nlattic"
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"path": "examples/interface-LAMMPS/AlAuMgO_4G/input.data",
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"chars": 13129,
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"path": "examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/weightse.008.data",
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"path": "examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/weightse.012.data",
"chars": 19684,
"preview": " -0.0391205871\n 0.0670690098\n 0.0643653699\n 0.1420071877\n 0.0476605813\n 0.0793169996\n "
},
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"path": "examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/weightse.013.data",
"chars": 10849,
"preview": " -0.0797436466\n 0.0752912334\n -0.0489901026\n 0.0089452996\n -0.0214947398\n 0.0074417583\n -"
},
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"path": "examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/weightse.079.data",
"chars": 12844,
"preview": " 0.2745880954\n 0.0480606327\n -0.4245035214\n 0.2005294056\n -0.0849154137\n 0.1674717077\n "
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE/cu2s_144_low-chalcocite_Evans-1979_PBE.data",
"chars": 11867,
"preview": "Generated by sg2cfg\n\n144 atoms\n2 atom types\n\n 0.0000000000000000E+00 1.5246000000000000E+01 xlo xhi\n 0.0000000000000"
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE/hdnnp-data/input.nn",
"chars": 20740,
"preview": "###############################################################################\n# HDNNP for copper sulfide Cu2S\n########"
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE/hdnnp-data/nnp-train.log.0000",
"chars": 58383,
"preview": "\n*** SETUP: MPI ****************************************************************\n\nNumber of processors: 16\nProcess 1 of "
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE/hdnnp-data/scaling.data",
"chars": 17868,
"preview": "################################################################################\n# Symmetry function scaling data.\n#####"
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE/hdnnp-data/weights.016.data",
"chars": 152939,
"preview": "################################################################################\n# Neural network connection values (wei"
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE/hdnnp-data/weights.029.data",
"chars": 143789,
"preview": "################################################################################\n# Neural network connection values (wei"
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE/md.lmp",
"chars": 1926,
"preview": "###############################################################################\n# MD simulation for HDNNP copper sulfide"
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE_external/cu2s_144_low-chalcocite_Evans-1979_PBE.data",
"chars": 11867,
"preview": "Generated by sg2cfg\n\n144 atoms\n2 atom types\n\n 0.0000000000000000E+00 1.5246000000000000E+01 xlo xhi\n 0.0000000000000"
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE_external/hdnnp-data/input.nn",
"chars": 20740,
"preview": "###############################################################################\n# HDNNP for copper sulfide Cu2S\n########"
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE_external/hdnnp-data/nnp-train.log.0000",
"chars": 58383,
"preview": "\n*** SETUP: MPI ****************************************************************\n\nNumber of processors: 16\nProcess 1 of "
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE_external/hdnnp-data/scaling.data",
"chars": 17868,
"preview": "################################################################################\n# Symmetry function scaling data.\n#####"
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE_external/hdnnp-data/weights.016.data",
"chars": 152939,
"preview": "################################################################################\n# Neural network connection values (wei"
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE_external/hdnnp-data/weights.029.data",
"chars": 143789,
"preview": "################################################################################\n# Neural network connection values (wei"
},
{
"path": "examples/interface-LAMMPS/Cu2S_PBE_external/md.lmp",
"chars": 1886,
"preview": "###############################################################################\n# MD simulation for NN copper sulfide\n##"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/correct-input-data/input.data-h2o-192",
"chars": 40343,
"preview": "begin\ncomment Values for ['energy', 'charge', 'force of atom'] were set to default values\nlattice 2.3488727120000000E+"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/correct-input-data/input.data-h2o-36",
"chars": 7895,
"preview": "begin\ncomment Values for ['energy', 'charge', 'force of atom'] were set to default values\nlattice 1.3443888628000000E+"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/correct-input-data/input.data-h2o-768",
"chars": 160151,
"preview": "begin\ncomment Values for ['energy', 'charge', 'force of atom'] were set to default values\nlattice 3.7285997399999999E+"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/correct-input-data/water.data-h2o-192",
"chars": 16925,
"preview": "Generated by RuNNerUC, original comment lines: 12.4297\n\n192 atoms\n2 atom types\n\n0.0 1.2429699051257149E+01 xlo xhi\n0.0 1"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/correct-input-data/water.data-h2o-36",
"chars": 3351,
"preview": "Generated by RuNNerUC, original comment lines: 7.1142\n\n36 atoms\n2 atom types\n\n0.0 7.1141994570823028E+00 xlo xhi\n0.0 7.1"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/correct-input-data/water.data-h2o-768",
"chars": 65491,
"preview": "LAMMPS data file via BUILD_WATER.f\n\n768 atoms\n2 atom types\n\n0.0 1.9730900024520210E+01 xlo xhi\n0.0 1.9730900024520210E+0"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/hdnnp-data/hardness.001.data",
"chars": 19,
"preview": " 12.5140142151\n"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/hdnnp-data/hardness.008.data",
"chars": 19,
"preview": " 9.0176209746\n"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/hdnnp-data/input.nn",
"chars": 7569,
"preview": "## #############################################################\n### This is the input file for RuNNer \n### ############"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/hdnnp-data/scaling.data",
"chars": 3486,
"preview": " 1 1 0.332976205 0.801624245 0.529022897\n 1 2 0.302337347 0.559557103 0."
},
{
"path": "examples/interface-LAMMPS/H2O_4G/hdnnp-data/weights.001.data",
"chars": 13129,
"preview": " -1.0108086508\n -0.4063663554\n 0.0997905118\n 0.1496758881\n -0.3728702687\n -0.6242685691\n -"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/hdnnp-data/weights.008.data",
"chars": 12844,
"preview": " 0.2222784853\n 0.5463480993\n 0.4833330714\n 0.4496531686\n -0.3571127566\n 0.9591269481\n "
},
{
"path": "examples/interface-LAMMPS/H2O_4G/hdnnp-data/weightse.001.data",
"chars": 12844,
"preview": " -0.9204217177\n -0.3890858779\n 0.1521122945\n 0.2613280526\n -0.3567201299\n -0.6461570957\n -"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/hdnnp-data/weightse.008.data",
"chars": 12559,
"preview": " 0.7059554103\n 0.3270412537\n -0.6963072690\n 0.4828653898\n 0.6190307873\n -0.3971467595\n -"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/md.lmp",
"chars": 2257,
"preview": "###############################################################################\n# MD simulation for carbon chain\n#######"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/hardness.001.data",
"chars": 19,
"preview": " 12.5140142151\n"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/hardness.008.data",
"chars": 19,
"preview": " 9.0176209746\n"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/input.data",
"chars": 7895,
"preview": "begin\ncomment Values for ['energy', 'charge', 'force of atom'] were set to default values\nlattice 1.3443888628000000E+"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/input.nn",
"chars": 7569,
"preview": "## #############################################################\n### This is the input file for RuNNer \n### ############"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-1np",
"chars": 556,
"preview": "begin\ncomment 7.1142\ncomment Values for ['energy', 'charge', 'force of atom'] were set to default values\nlattice 50.0\t0."
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-1p",
"chars": 652,
"preview": "begin\ncomment 7.1142\ncomment Values for ['energy', 'charge', 'force of atom'] were set to default values\ncomment lattice"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-36-angs",
"chars": 2336,
"preview": "begin\natom 0.544077 -3.475781 -2.618007 O 0.0 0.0 0.0 0.0 0.0\natom 1.081703 -3.556415 -1.778688 H 0.0 0."
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-36p",
"chars": 4357,
"preview": "begin\ncomment 7.1142\ncomment Values for ['energy', 'charge', 'force of atom'] were set to default values\nlattice 13.4438"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-36s",
"chars": 4381,
"preview": "begin\ncomment 7.1142\ncomment Values for ['energy', 'charge', 'force of atom'] were set to default values\ncomment lattice"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-angs-p",
"chars": 2423,
"preview": "begin\nlattice 7.1142 0.0000 0.0000\nlattice 0.0000 7.1142 0.0000\nlattice 0.0000 0.0000 7.1142\natom 0.544077 -3.475781"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-h2o-192-neg",
"chars": 21920,
"preview": "begin\ncomment 12.4297\ncomment Values for ['energy', 'charge', 'force of atom'] were set to default values\nlattice 23.488"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-h2o-36-neg",
"chars": 4357,
"preview": "begin\ncomment 7.1142\ncomment Values for ['energy', 'charge', 'force of atom'] were set to default values\nlattice 13.4438"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-h2o-768-neg",
"chars": 96311,
"preview": "begin\ncomment 19.7309\ncomment Values for ['energy', 'charge', 'force of atom'] were set to default values\nlattice 3.7285"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/scaling.data",
"chars": 3486,
"preview": " 1 1 0.332976205 0.801624245 0.529022897\n 1 2 0.302337347 0.559557103 0."
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/weights.001.data",
"chars": 13129,
"preview": " -1.0108086508\n -0.4063663554\n 0.0997905118\n 0.1496758881\n -0.3728702687\n -0.6242685691\n -"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/weights.008.data",
"chars": 12844,
"preview": " 0.2222784853\n 0.5463480993\n 0.4833330714\n 0.4496531686\n -0.3571127566\n 0.9591269481\n "
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/weightse.001.data",
"chars": 12844,
"preview": " -0.9204217177\n -0.3890858779\n 0.1521122945\n 0.2613280526\n -0.3567201299\n -0.6461570957\n -"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/nnp-predict/weightse.008.data",
"chars": 12559,
"preview": " 0.7059554103\n 0.3270412537\n -0.6963072690\n 0.4828653898\n 0.6190307873\n -0.3971467595\n -"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/water.data",
"chars": 3351,
"preview": "Generated by RuNNerUC, original comment lines: 7.1142\n\n36 atoms\n2 atom types\n\n0.0 7.1141994570823028E+00 xlo xhi\n0.0 7.1"
},
{
"path": "examples/interface-LAMMPS/H2O_4G/water.data.q",
"chars": 4071,
"preview": "Generated by RuNNerUC, original comment lines: 7.1142\n\n36 atoms\n2 atom types\n\n0.0 7.1141994570823028E+00 xlo xhi\n0.0 7.1"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3/h2o_8640_liquid_NpT_RPBE-D3.data",
"chars": 1369060,
"preview": "LAMMPS data file via write_data, version 11 Aug 2017, timestep = 4000000\n\n8640 atoms\n2 atom types\n\n-3.2819324253026849e-"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3/hdnnp-data/input.nn",
"chars": 9969,
"preview": "###############################################################################\n# HDNNP for water H2O\n##################"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3/hdnnp-data/nnp-train.log.0000",
"chars": 36210,
"preview": "\n*** SETUP: MPI ****************************************************************\n\nNumber of processors: 16\nProcess 1 of "
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3/hdnnp-data/scaling.data",
"chars": 7986,
"preview": "################################################################################\n# Symmetry function scaling data.\n#####"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3/hdnnp-data/weights.001.data",
"chars": 84314,
"preview": "################################################################################\n# Neural network connection values (wei"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3/hdnnp-data/weights.008.data",
"chars": 88889,
"preview": "################################################################################\n# Neural network connection values (wei"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3/md.lmp",
"chars": 1892,
"preview": "###############################################################################\n# MD simulation for HDNNP water\n########"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol/hdnnp-data/input.nn",
"chars": 28883,
"preview": "## #############################################################\n### This is the input file for RuNNer (version 0_44 and"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol/hdnnp-data/scaling.data",
"chars": 3746,
"preview": " 1 1 1.088201664 9.616641912 2.270109565\n 1 2 0.732744389 5.002855932 1."
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol/hdnnp-data/weights.001.data",
"chars": 75068,
"preview": " -0.7927042964 a 1 0 1 1 1\n -0.1198851087 a 2 0 1 1 2\n 0.05"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol/hdnnp-data/weights.008.data",
"chars": 79193,
"preview": " -0.5597848858 a 1 0 1 1 1\n -0.0789699327 a 2 0 1 1 2\n -0.04"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol/iceIh_128.data",
"chars": 31466,
"preview": "Generated by ./convert_pgxyzinfo_lammpsdata.sh from iceIh_Cmc21.xyz, comment: \n\n384 atoms\n\n2 atom types\n\n 0.00000000000"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol/md.lmp",
"chars": 1730,
"preview": "###############################################################################\n# MD simulation for NN water\n###########"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_develop/hdnnp-data/hardness.001.data",
"chars": 8,
"preview": "13.0342\n"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_develop/hdnnp-data/hardness.008.data",
"chars": 8,
"preview": "12.5756\n"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_develop/hdnnp-data/input.nn",
"chars": 10307,
"preview": "###############################################################################\n# DATA SET NORMALIZATION\n###############"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_develop/hdnnp-data/scaling.data",
"chars": 7498,
"preview": "################################################################################\n# Symmetry function scaling data.\n#####"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_develop/hdnnp-data/weights.001.data",
"chars": 42769,
"preview": "################################################################################\n# Neural network connection values (wei"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_develop/hdnnp-data/weights.008.data",
"chars": 41854,
"preview": "################################################################################\n# Neural network connection values (wei"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_develop/hdnnp-data/weightse.001.data",
"chars": 41854,
"preview": "################################################################################\n# Neural network connection values (wei"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_develop/hdnnp-data/weightse.008.data",
"chars": 40939,
"preview": "################################################################################\n# Neural network connection values (wei"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_develop/iceIh_128.data",
"chars": 31465,
"preview": "Generated by ./convert_pgxyzinfo_lammpsdata.sh from iceIh_Cmc21.xyz, comment:\n\n384 atoms\n\n2 atom types\n\n 0.000000000000"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_develop/md.lmp",
"chars": 1967,
"preview": "###############################################################################\n# MD simulation for NN water\n###########"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_external/hdnnp-data/input.nn",
"chars": 28883,
"preview": "## #############################################################\n### This is the input file for RuNNer (version 0_44 and"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_external/hdnnp-data/scaling.data",
"chars": 3746,
"preview": " 1 1 1.088201664 9.616641912 2.270109565\n 1 2 0.732744389 5.002855932 1."
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_external/hdnnp-data/weights.001.data",
"chars": 75068,
"preview": " -0.7927042964 a 1 0 1 1 1\n -0.1198851087 a 2 0 1 1 2\n 0.05"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_external/hdnnp-data/weights.008.data",
"chars": 79193,
"preview": " -0.5597848858 a 1 0 1 1 1\n -0.0789699327 a 2 0 1 1 2\n -0.04"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_external/iceIh_128.data",
"chars": 31466,
"preview": "Generated by ./convert_pgxyzinfo_lammpsdata.sh from iceIh_Cmc21.xyz, comment: \n\n384 atoms\n\n2 atom types\n\n 0.00000000000"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_128mol_external/md.lmp",
"chars": 1842,
"preview": "###############################################################################\n# MD simulation for NN water\n###########"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_external/h2o_8640_liquid_NpT_RPBE-D3.data",
"chars": 1369060,
"preview": "LAMMPS data file via write_data, version 11 Aug 2017, timestep = 4000000\n\n8640 atoms\n2 atom types\n\n-3.2819324253026849e-"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_external/hdnnp-data/input.nn",
"chars": 9969,
"preview": "###############################################################################\n# HDNNP for water H2O\n##################"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_external/hdnnp-data/nnp-train.log.0000",
"chars": 36210,
"preview": "\n*** SETUP: MPI ****************************************************************\n\nNumber of processors: 16\nProcess 1 of "
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_external/hdnnp-data/scaling.data",
"chars": 7986,
"preview": "################################################################################\n# Symmetry function scaling data.\n#####"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_external/hdnnp-data/weights.001.data",
"chars": 84314,
"preview": "################################################################################\n# Neural network connection values (wei"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_external/hdnnp-data/weights.008.data",
"chars": 88889,
"preview": "################################################################################\n# Neural network connection values (wei"
},
{
"path": "examples/interface-LAMMPS/H2O_RPBE-D3_external/md.lmp",
"chars": 1715,
"preview": "###############################################################################\n# MD simulation for NN water\n###########"
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/carbon-chain.data",
"chars": 795,
"preview": "Carbon chain, first structure from input.data\n\n12 atoms\n\n2 atom types\n\n -12.94 12.67 xlo xhi\n -0.36 1.20 ylo yhi\n "
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/log.lammps",
"chars": 48147,
"preview": "LAMMPS (29 Oct 2020)\n###############################################################################\n# MD simulation for"
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/md-external.lmp",
"chars": 1802,
"preview": "###############################################################################\n# MD simulation for carbon chain\n#######"
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/md.lmp",
"chars": 1723,
"preview": "###############################################################################\n# MD simulation for carbon chain\n#######"
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/hardness.001.data",
"chars": 19,
"preview": " 0.0088953312\n"
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/hardness.006.data",
"chars": 19,
"preview": " 0.0661189426\n"
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/input.nn",
"chars": 11812,
"preview": "## #############################################################\n### This is the input file for RuNNer \n### ############"
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/scaling.data",
"chars": 3941,
"preview": " 1 1 0.000000000 0.168474325 0.051436597\n 1 2 0.304058579 0.417104776 0."
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/weights.001.data",
"chars": 7239,
"preview": " -1.4888017024\n -1.0017511436\n -1.1705029344\n 0.6414103790\n 0.2140403300\n -0.1026432602\n -"
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/weights.006.data",
"chars": 9519,
"preview": " 0.4988126195\n 0.2333500107\n -0.6270625769\n -0.5561242588\n -1.7136514762\n -0.8495140302\n "
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/weightse.001.data",
"chars": 11989,
"preview": " -0.7239126988\n 0.2887945015\n 0.6150030559\n -0.0745244807\n 0.1922931645\n 0.5450717030\n "
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/weightse.006.data",
"chars": 15409,
"preview": " -0.4585604868\n -0.7675412208\n 0.2621257041\n 0.2779028370\n 1.1979669560\n -0.2910217745\n "
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/hardness.001.data",
"chars": 19,
"preview": " 0.0088953312\n"
},
{
"path": "examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/hardness.006.data",
"chars": 19,
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]
// ... and 533 more files (download for full content)
About this extraction
This page contains the full source code of the CompPhysVienna/n2p2 GitHub repository, extracted and formatted as plain text for AI agents and large language models (LLMs). The extraction includes 733 files (43.0 MB), approximately 11.3M tokens, and a symbol index with 555 extracted functions, classes, methods, constants, and types. Use this with OpenClaw, Claude, ChatGPT, Cursor, Windsurf, or any other AI tool that accepts text input. You can copy the full output to your clipboard or download it as a .txt file.
Extracted by GitExtract — free GitHub repo to text converter for AI. Built by Nikandr Surkov.