├── .gitignore ├── Cu ├── Cu.snapcoeff ├── Cu.snapparam ├── README.md └── training │ ├── AIMD.json │ ├── Elastic.json │ ├── README.md │ ├── Surface.json │ └── Vacancy.json ├── LICENSE ├── Li3N ├── Li3N.snapcoeff ├── Li3N.snapparam ├── README.md ├── data.li3n └── training │ ├── AIMD.json │ ├── Elastic.json │ └── Lattice.json ├── Mo ├── Mo.snapcoeff ├── Mo.snapparam ├── README.md ├── training │ ├── AIMD_NPT.json │ ├── AIMD_NVT.json │ ├── Elastic.json │ ├── GB.json │ ├── README.md │ ├── Surface.json │ ├── Vacancy.json │ └── weights.png └── usage │ └── elastic_example │ ├── Mo.snap │ ├── Mo.snapcoeff │ ├── Mo.snapparam │ ├── README.md │ ├── displace.mod │ ├── elastic.txt │ ├── in.elastic │ ├── init.mod │ ├── log.lammps │ ├── potential.mod │ └── restart.equil ├── NbMoTaW ├── README.md ├── Ta-W-Nb-Mo.snapcoeff ├── Ta-W-Nb-Mo.snapparam └── training │ ├── MoTa_SS.json │ ├── MoTa_Test.json │ ├── MoW_SS.json │ ├── MoW_Test.json │ ├── Mo_AIMD.json │ ├── Mo_Elastic.json │ ├── Mo_Surface.json │ ├── Mo_Test.json │ ├── Multinary_SQS.json │ ├── Multinary_Test.json │ ├── NbMo_SS.json │ ├── NbMo_Test.json │ ├── NbTa_SS.json │ ├── NbTa_Test.json │ ├── NbW_SS.json │ ├── NbW_Test.json │ ├── Nb_AIMD.json │ ├── Nb_Elastic.json │ ├── Nb_Surface.json │ ├── Nb_Test.json │ ├── README.md │ ├── TaW_SS.json │ ├── TaW_Test.json │ ├── Ta_AIMD.json │ ├── Ta_Elastic.json │ ├── Ta_Surface.json │ ├── Ta_Test.json │ ├── W_AIMD.json │ ├── W_Elastic.json │ ├── W_Surface.json │ └── W_Test.json ├── Ni-Mo ├── Ni_Mo.snapcoeff ├── Ni_Mo.snapparam ├── README.md └── training │ ├── Mo_dopedwith_Ni.json │ ├── Ni3Mo_AIMD.json │ ├── Ni3Mo_Elastic.json │ ├── Ni4Mo_AIMD.json │ ├── Ni4Mo_Elastic.json │ ├── Ni_dopedwith_Mo.json │ └── README.md ├── Ni ├── Ni.snapcoeff ├── Ni.snapparam ├── README.md └── training │ ├── AIMD.json │ ├── Elastic.json │ ├── README.md │ ├── Surface.json │ ├── Surface_test.json │ └── Vacancy.json └── README.md /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | env/ 12 | build/ 13 | develop-eggs/ 14 | dist/ 15 | downloads/ 16 | eggs/ 17 | .eggs/ 18 | lib/ 19 | lib64/ 20 | parts/ 21 | sdist/ 22 | var/ 23 | wheels/ 24 | *.egg-info/ 25 | .installed.cfg 26 | *.egg 27 | 28 | # PyInstaller 29 | # Usually these files are written by a python script from a template 30 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 31 | *.manifest 32 | *.spec 33 | 34 | # Installer logs 35 | pip-log.txt 36 | pip-delete-this-directory.txt 37 | 38 | # Unit test / coverage reports 39 | htmlcov/ 40 | .tox/ 41 | .coverage 42 | .coverage.* 43 | .cache 44 | nosetests.xml 45 | coverage.xml 46 | *.cover 47 | .hypothesis/ 48 | 49 | # Translations 50 | *.mo 51 | *.pot 52 | 53 | # Django stuff: 54 | *.log 55 | local_settings.py 56 | 57 | # Flask stuff: 58 | instance/ 59 | .webassets-cache 60 | 61 | # Scrapy stuff: 62 | .scrapy 63 | 64 | # Sphinx documentation 65 | docs/_build/ 66 | 67 | # PyBuilder 68 | target/ 69 | 70 | # Jupyter Notebook 71 | .ipynb_checkpoints 72 | 73 | # pyenv 74 | .python-version 75 | 76 | # celery beat schedule file 77 | celerybeat-schedule 78 | 79 | # SageMath parsed files 80 | *.sage.py 81 | 82 | # dotenv 83 | .env 84 | 85 | # virtualenv 86 | .venv 87 | venv/ 88 | ENV/ 89 | 90 | # Spyder project settings 91 | .spyderproject 92 | .spyproject 93 | 94 | # Rope project settings 95 | .ropeproject 96 | 97 | # mkdocs documentation 98 | /site 99 | 100 | # mypy 101 | .mypy_cache/ 102 | -------------------------------------------------------------------------------- /Cu/Cu.snapcoeff: -------------------------------------------------------------------------------- 1 | # LAMMPS SNAP coefficients for Cu 2 | # generated by pymacy.potential.snap.SNAPotential 3 | 4 | 1 31 5 | Cu 0.5 1.0 6 | -6.12504445402 7 | 0.0170339591761 8 | 0.018791727619 9 | 0.213133266867 10 | 0.0607119024338 11 | 0.163794802565 12 | -0.0479404407441 13 | 0.0149630865808 14 | 0.0244640634017 15 | 0.103081548545 16 | -0.0729564871532 17 | 0.057008096796 18 | -0.000515616922693 19 | -0.0109511390916 20 | 0.0144624411802 21 | 0.114025473695 22 | -0.00751444068581 23 | -0.00426417155673 24 | 0.047086996016 25 | 0.0126808290667 26 | -0.0011322857993 27 | -0.0116089436873 28 | 0.120609416506 29 | 0.0299664295467 30 | 0.0202376248034 31 | 0.0202344867868 32 | 0.0137888798179 33 | -0.00022212683053 34 | 0.0246304219645 35 | -0.00366294171114 36 | 0.00813829979942 -------------------------------------------------------------------------------- /Cu/Cu.snapparam: -------------------------------------------------------------------------------- 1 | # LAMMPS SNAP parameters for Cu 2 | # generated by pymacy.potential.snap.SNAPotential 3 | 4 | rcutfac 3.7 5 | twojmax 6 6 | rfac0 0.99363 7 | rmin0 0 8 | diagonalstyle 3 9 | bzeroflag 0 -------------------------------------------------------------------------------- /Cu/README.md: -------------------------------------------------------------------------------- 1 | ## SNAP potential for Cu 2 | 3 | This directory contains the SNAP force field parameters for Cu. This potential is fitted from the DFT data, including bulk structures with elastic deformation, surfaces and DFT calculated molecular dynamics trajectories. 4 | 5 | The hyperparameter tuning and fitting procedures are described in detail in our publication [1] and thus are excluded from the repo. 6 | 7 | 8 | ### Reference 9 | [1]: X. Li, C. Hu, C. Chen, Z. Deng, J. Luo, & S.P. Ong (2018). Quantum-Accurate Spectral Neighbor Analysis Potential Models for Ni-Mo Binary Alloys and FCC Metals. arXiv:1806.04777 10 | -------------------------------------------------------------------------------- /Cu/training/README.md: -------------------------------------------------------------------------------- 1 | # Using the training data 2 | 3 | The training data is provided in json files, which can be read by any standard json parser. Each json file contains contains one data group (e.g., AIMD, elastic, surfaces, etc.) used in the training of the SNAP model. 4 | 5 | The data is provided as a list of dicts. Each dict contains one structure with data. The format of the json file is as follows: 6 | 7 | ```json 8 | [ 9 | { 10 | "_id": "a string", 11 | "params": {"Dict of parameters used for DFT calculations, e.g. pseudopotential, energy cutoff, etc."}, 12 | "group": "Cu", 13 | "tags": "Md", 14 | "structure": {"Dict representation of Structure as output by pymatgen"}, 15 | "num_atoms": 108, 16 | "outputs": { 17 | "energy": -619.08666252, 18 | "forces": [], 19 | "stress": [] 20 | } 21 | }, 22 | ... 23 | ] 24 | ``` 25 | 26 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | BSD 3-Clause License 2 | 3 | Copyright (c) 2017, Materials Virtual Lab 4 | All rights reserved. 5 | 6 | Redistribution and use in source and binary forms, with or without 7 | modification, are permitted provided that the following conditions are met: 8 | 9 | * Redistributions of source code must retain the above copyright notice, this 10 | list of conditions and the following disclaimer. 11 | 12 | * Redistributions in binary form must reproduce the above copyright notice, 13 | this list of conditions and the following disclaimer in the documentation 14 | and/or other materials provided with the distribution. 15 | 16 | * Neither the name of the copyright holder nor the names of its 17 | contributors may be used to endorse or promote products derived from 18 | this software without specific prior written permission. 19 | 20 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 21 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 22 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 23 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 24 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 25 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 26 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 27 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 28 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 29 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 30 | -------------------------------------------------------------------------------- /Li3N/Li3N.snapcoeff: -------------------------------------------------------------------------------- 1 | # LAMMPS SNAP coefficients for Li3N 2 | # generated by pymacy.potential.snap.SNAPotential 3 | 4 | 2 31 5 | Li 0.5 0.1 6 | -41.97323930758951 7 | -0.006975291543708552 8 | 1.9434438303637722 9 | 1.9439606652091586 10 | 1.8963721272975047 11 | 0.8184150253310739 12 | -0.11552574562753412 13 | 0.024662060558673055 14 | 0.645913664832655 15 | 0.029473213939390678 16 | -0.8355694040515903 17 | 0.26042157703949004 18 | -0.5318774132868211 19 | 0.2979554491697543 20 | 0.10023866910294173 21 | -0.5692975828766904 22 | -0.6836106218130198 23 | 0.07683922184552483 24 | 0.15747793760306317 25 | 0.24539614677129887 26 | 0.2189952475964869 27 | -0.20326553979631898 28 | -0.23272661308601275 29 | -0.3528380317030206 30 | 0.112930317776087 31 | 0.537951697554698 32 | 0.08228478406496283 33 | -0.1789667225760126 34 | -0.2836764164156765 35 | 0.08901293984293195 36 | 0.044042461635336136 37 | N 0.7 -0.1 38 | 5.070489350565292 39 | 1.456429449741217 40 | -0.7417518951788988 41 | 1.391487252718133 42 | -0.05799391981425649 43 | 4.490489555500009 44 | 1.038809274414984 45 | 2.017342084202995 46 | 0.2977526383647907 47 | 2.234672087302177 48 | 0.8642128029636933 49 | 2.0279416008181443 50 | 0.5344950927985814 51 | 0.29943675723907504 52 | -0.14945337171905423 53 | 0.5412801525545897 54 | 0.1814464847359337 55 | 0.32453496880994626 56 | -0.11236523983947481 57 | 0.14314633605288057 58 | 0.008000929122986318 59 | -0.1912670516117714 60 | -0.16715285409415928 61 | -0.3697173126253156 62 | -0.12303505777195632 63 | 0.5597456490031791 64 | 0.2904966729321746 65 | -0.02909290591797242 66 | -0.18013437424998538 67 | 0.2523311830460235 68 | 0.008318824055866198 -------------------------------------------------------------------------------- /Li3N/Li3N.snapparam: -------------------------------------------------------------------------------- 1 | # LAMMPS SNAP parameters for Li3N 2 | # generated by pymacy.potential.snap.SNAPotential 3 | 4 | rcutfac 4 5 | twojmax 6 6 | rfac0 0.99363 7 | rmin0 0 8 | diagonalstyle 3 9 | bzeroflag 0 -------------------------------------------------------------------------------- /Li3N/README.md: -------------------------------------------------------------------------------- 1 | ## eSNAP for Li3N 2 | 3 | This directory contains the electrostatic SNAP (eSNAP) force field parameters for Li3N. This potential is fitted from the DFT data, including bulk structures with elastic deformation on lattice, and DFT calculated molecular dynamics trajectories. 4 | 5 | 6 | ### Reference 7 | [1]: Z. Deng, C. Chen, X. Li & S.P. Ong (2019). An Electrostatic Spectral Neighbor Analysis Potential (eSNAP) for Lithium Nitride. arXiv:1901.08749 8 | -------------------------------------------------------------------------------- /Li3N/data.li3n: -------------------------------------------------------------------------------- 1 | Generated by pymatgen.io.lammps.data.LammpsData 2 | 3 | 4 atoms 4 | 5 | 2 atom types 6 | 7 | 0.000000 3.650690 xlo xhi 8 | 0.000000 3.161590 ylo yhi 9 | 0.000000 3.888635 zlo zhi 10 | -1.825345 0.000000 0.000000 xy xz yz 11 | 12 | Masses 13 | 14 | 1 6.9410 15 | 2 14.0067 16 | 17 | Atoms 18 | 19 | 1 1 0.239 0.000000 0.000000 1.944317 20 | 2 1 0.239 -0.000000 2.107727 0.000000 21 | 3 1 0.239 1.825345 1.053863 0.000000 22 | 4 2 -0.717 0.000000 0.000000 0.000000 23 | 24 | -------------------------------------------------------------------------------- /Mo/Mo.snapcoeff: -------------------------------------------------------------------------------- 1 | #Generated by Materials Virtual Lab 2 | 1 31 3 | Mo 0.5 1 4 | -17.2757958404 5 | 0.00431015861472 6 | 0.0657685117891 7 | 0.477733335702 8 | 0.0152688837211 9 | 0.77559888196 10 | 0.284846429566 11 | 0.148804982644 12 | 0.0573702179736 13 | 0.19281989434 14 | 0.323441703578 15 | 0.101324335724 16 | 0.0139639846514 17 | -0.0324444749083 18 | 0.0349797952779 19 | 0.0613023441282 20 | 0.0881078513046 21 | 0.118716074611 22 | 0.0069662975532 23 | -0.0174658914685 24 | -0.0178902177779 25 | 0.0195993756659 26 | 0.0719238160707 27 | 0.0344832661036 28 | -0.0358616891662 29 | -0.0292380783172 30 | -0.0334933909866 31 | 0.00595462520243 32 | 0.0754556638328 33 | -0.000972545258845 34 | -0.0100170422751 35 | -------------------------------------------------------------------------------- /Mo/Mo.snapparam: -------------------------------------------------------------------------------- 1 | rcutfac 4.615858 2 | twojmax 6 -------------------------------------------------------------------------------- /Mo/README.md: -------------------------------------------------------------------------------- 1 | ## SNAP potential for Mo 2 | 3 | This directory contains various DFT data for fitting the Mo SNAP potential, including bulk structures with elastic deformation, surfaces, grain boundaries and DFT calculated molecular dynamics trajectories. We also include the test data of molecular dynamics trajectories of vacancy-containing structures. 4 | 5 | The hyperparameter tuning and fitting procedures are described in detail in our publication [1] and thus are excluded from the repo. 6 | 7 | The parameters are fitted with lammps version `17Nov2016`. To reproduce the exact values, the readers are adviced to use the same lammps release. 8 | 9 | ### Reference 10 | [1]: Chen, C., Deng, Z., Tran, R., Tang, H., Chu, I. H., & Ong, S. P. (2017). Accurate force field for molybdenum by machine learning large materials data. Physical Review Materials, 1(4), 043603. 11 | -------------------------------------------------------------------------------- /Mo/training/README.md: -------------------------------------------------------------------------------- 1 | # Using the training data 2 | 3 | The training data is provided in json files, which can be read by any standard json parser. Each json file contains contains one data group (e.g., AIMD-NpT, AIMD-NVT, elastic, surfaces, etc.) used in the training of the SNAP model. 4 | 5 | The data is provided as a list of dicts. Each dict contains one structure with data. The format of the json file is as follows: 6 | 7 | ```json 8 | [ 9 | { 10 | "structure": {"Dict representation of Structure as output by pymatgen"}, 11 | "group": "AIMD-NVT", 12 | "description": "Snapshot 1 of 40 of AIMD NVT simulation at 300 K", 13 | "data": { 14 | "energy_per_atom": -1.24324, 15 | "forces": [], 16 | "virial_stress": [] 17 | }, 18 | "optimized parameters": { 19 | "bispectrum_coefficients": [], 20 | } 21 | }, 22 | ... 23 | ] 24 | ``` 25 | Note that the order for stress is `xx, yy, zz, yz, xz, xy` in this data set as in `SNAP` formulism, and the unit is in `kB`, same as in VASP. The raw stress data taken from VASP has the order `xx, yy, zz, xy, yz, xz` and the calculated stress from LAMMPS takes the order `xx, yy, zz, xy, zx, yz`. Please make sure that the order is correct and matches the SNAP feature order `xx, yy, zz, yz, xz, xy`. 26 | 27 | The `bispectrum coefficient` has been averaged by the number of atoms in the structure and the `stress descriptor` has been converted from a unit of `eV/A^3` to `kB` (times 1602.1766). 28 | 29 | To reproduce these results, please use `LAMMPS 17 Nov 2016`. The cutoff radius is `4.61585753 Angstrom` for Mo, with element weight equals to `1`. 30 | The weights for training data groups are as follows: 31 | 32 | ![weights](weights.png) 33 | 34 | # Data sources 35 | 36 | * Surfaces with Miller indices up to 3. 37 | 38 | ``` 39 | Tran, R.; Xu, Z.; Radhakrishnan, B.; Winston, D.; Sun, W.; Persson, K. A.; Ong, S. P. Surface energies of elemental crystals. Sci. Data 2016, 3, 160080 DOI: 10.1038/sdata.2016.80. 40 | ``` 41 | 42 | * (110) Σ3 twist, (111) Σ3 tilt, (110) Σ11 twist, (100) Σ5 twist and (310) Σ5 tilt grain boundaries 43 | 44 | ``` 45 | Tran, R.; Xu, Z.; Zhou, N.; Radhakrishnan, B.; Luo, J.; Ong, S. P. Computational study of metallic dopant segregation and embrittlement at Molybdenum grain boundaries. Acta Mater. 2016, 117, 91–99 DOI: 10.1016/j.actamat.2016.07.005. 46 | ``` 47 | -------------------------------------------------------------------------------- /Mo/training/weights.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/materialsvirtuallab/snap/5fc2251b45c72dea0c9799d7aad3e3261a077a5b/Mo/training/weights.png -------------------------------------------------------------------------------- /Mo/usage/elastic_example/Mo.snap: -------------------------------------------------------------------------------- 1 | 2 | pair_style snap 3 | pair_coeff * * Mo.snapcoeff Mo Mo.snapparam Mo 4 | -------------------------------------------------------------------------------- /Mo/usage/elastic_example/Mo.snapcoeff: -------------------------------------------------------------------------------- 1 | #Generated by Materials Virtual Lab 2 | 1 31 3 | Mo 0.5 1 4 | -17.2757958404 5 | 0.00431015861472 6 | 0.0657685117891 7 | 0.477733335702 8 | 0.0152688837211 9 | 0.77559888196 10 | 0.284846429566 11 | 0.148804982644 12 | 0.0573702179736 13 | 0.19281989434 14 | 0.323441703578 15 | 0.101324335724 16 | 0.0139639846514 17 | -0.0324444749083 18 | 0.0349797952779 19 | 0.0613023441282 20 | 0.0881078513046 21 | 0.118716074611 22 | 0.0069662975532 23 | -0.0174658914685 24 | -0.0178902177779 25 | 0.0195993756659 26 | 0.0719238160707 27 | 0.0344832661036 28 | -0.0358616891662 29 | -0.0292380783172 30 | -0.0334933909866 31 | 0.00595462520243 32 | 0.0754556638328 33 | -0.000972545258845 34 | -0.0100170422751 35 | -------------------------------------------------------------------------------- /Mo/usage/elastic_example/Mo.snapparam: -------------------------------------------------------------------------------- 1 | rcutfac 4.615858 2 | twojmax 6 -------------------------------------------------------------------------------- /Mo/usage/elastic_example/README.md: -------------------------------------------------------------------------------- 1 | Assuming your lammps executable is lmp_serial, you can calculate the elastic constants with the SNAP potential with the following command. 2 | 3 | ```bash 4 | lmp_serial -in in.elastic 5 | ``` 6 | 7 | Note: Make sure the snap package is installed when installing LAMMPS. -------------------------------------------------------------------------------- /Mo/usage/elastic_example/displace.mod: -------------------------------------------------------------------------------- 1 | # NOTE: This script should not need to be 2 | # modified. See in.elastic for more info. 3 | # 4 | # Find which reference length to use 5 | 6 | if "${dir} == 1" then & 7 | "variable len0 equal ${lx0}" 8 | if "${dir} == 2" then & 9 | "variable len0 equal ${ly0}" 10 | if "${dir} == 3" then & 11 | "variable len0 equal ${lz0}" 12 | if "${dir} == 4" then & 13 | "variable len0 equal ${lz0}" 14 | if "${dir} == 5" then & 15 | "variable len0 equal ${lz0}" 16 | if "${dir} == 6" then & 17 | "variable len0 equal ${ly0}" 18 | 19 | # Reset box and simulation parameters 20 | 21 | clear 22 | box tilt large 23 | read_restart restart.equil 24 | include potential.mod 25 | 26 | # Negative deformation 27 | 28 | variable delta equal -${up}*${len0} 29 | variable deltaxy equal -${up}*xy 30 | variable deltaxz equal -${up}*xz 31 | variable deltayz equal -${up}*yz 32 | if "${dir} == 1" then & 33 | "change_box all x delta 0 ${delta} xy delta ${deltaxy} xz delta ${deltaxz} remap units box" 34 | if "${dir} == 2" then & 35 | "change_box all y delta 0 ${delta} yz delta ${deltayz} remap units box" 36 | if "${dir} == 3" then & 37 | "change_box all z delta 0 ${delta} remap units box" 38 | if "${dir} == 4" then & 39 | "change_box all yz delta ${delta} remap units box" 40 | if "${dir} == 5" then & 41 | "change_box all xz delta ${delta} remap units box" 42 | if "${dir} == 6" then & 43 | "change_box all xy delta ${delta} remap units box" 44 | 45 | # Relax atoms positions 46 | 47 | minimize ${etol} ${ftol} ${maxiter} ${maxeval} 48 | 49 | # Obtain new stress tensor 50 | 51 | variable tmp equal pxx 52 | variable pxx1 equal ${tmp} 53 | variable tmp equal pyy 54 | variable pyy1 equal ${tmp} 55 | variable tmp equal pzz 56 | variable pzz1 equal ${tmp} 57 | variable tmp equal pxy 58 | variable pxy1 equal ${tmp} 59 | variable tmp equal pxz 60 | variable pxz1 equal ${tmp} 61 | variable tmp equal pyz 62 | variable pyz1 equal ${tmp} 63 | 64 | # Compute elastic constant from pressure tensor 65 | 66 | variable C1neg equal ${d1} 67 | variable C2neg equal ${d2} 68 | variable C3neg equal ${d3} 69 | variable C4neg equal ${d4} 70 | variable C5neg equal ${d5} 71 | variable C6neg equal ${d6} 72 | 73 | # Reset box and simulation parameters 74 | 75 | clear 76 | box tilt large 77 | read_restart restart.equil 78 | include potential.mod 79 | 80 | # Positive deformation 81 | 82 | variable delta equal ${up}*${len0} 83 | variable deltaxy equal ${up}*xy 84 | variable deltaxz equal ${up}*xz 85 | variable deltayz equal ${up}*yz 86 | if "${dir} == 1" then & 87 | "change_box all x delta 0 ${delta} xy delta ${deltaxy} xz delta ${deltaxz} remap units box" 88 | if "${dir} == 2" then & 89 | "change_box all y delta 0 ${delta} yz delta ${deltayz} remap units box" 90 | if "${dir} == 3" then & 91 | "change_box all z delta 0 ${delta} remap units box" 92 | if "${dir} == 4" then & 93 | "change_box all yz delta ${delta} remap units box" 94 | if "${dir} == 5" then & 95 | "change_box all xz delta ${delta} remap units box" 96 | if "${dir} == 6" then & 97 | "change_box all xy delta ${delta} remap units box" 98 | 99 | # Relax atoms positions 100 | 101 | minimize ${etol} ${ftol} ${maxiter} ${maxeval} 102 | 103 | # Obtain new stress tensor 104 | 105 | variable tmp equal pe 106 | variable e1 equal ${tmp} 107 | variable tmp equal press 108 | variable p1 equal ${tmp} 109 | variable tmp equal pxx 110 | variable pxx1 equal ${tmp} 111 | variable tmp equal pyy 112 | variable pyy1 equal ${tmp} 113 | variable tmp equal pzz 114 | variable pzz1 equal ${tmp} 115 | variable tmp equal pxy 116 | variable pxy1 equal ${tmp} 117 | variable tmp equal pxz 118 | variable pxz1 equal ${tmp} 119 | variable tmp equal pyz 120 | variable pyz1 equal ${tmp} 121 | 122 | # Compute elastic constant from pressure tensor 123 | 124 | variable C1pos equal ${d1} 125 | variable C2pos equal ${d2} 126 | variable C3pos equal ${d3} 127 | variable C4pos equal ${d4} 128 | variable C5pos equal ${d5} 129 | variable C6pos equal ${d6} 130 | 131 | # Combine positive and negative 132 | 133 | variable C1${dir} equal 0.5*(${C1neg}+${C1pos}) 134 | variable C2${dir} equal 0.5*(${C2neg}+${C2pos}) 135 | variable C3${dir} equal 0.5*(${C3neg}+${C3pos}) 136 | variable C4${dir} equal 0.5*(${C4neg}+${C4pos}) 137 | variable C5${dir} equal 0.5*(${C5neg}+${C5pos}) 138 | variable C6${dir} equal 0.5*(${C6neg}+${C6pos}) 139 | 140 | # Delete dir to make sure it is not reused 141 | 142 | variable dir delete 143 | -------------------------------------------------------------------------------- /Mo/usage/elastic_example/elastic.txt: -------------------------------------------------------------------------------- 1 | 472.74677443108 151.6255440472 106.300142462772 2 | -------------------------------------------------------------------------------- /Mo/usage/elastic_example/in.elastic: -------------------------------------------------------------------------------- 1 | # Compute elastic constant tensor for a crystal 2 | # 3 | # Written by Aidan Thompson (Sandia, athomps@sandia.gov) 4 | # 5 | # This script uses the following three include files. 6 | # 7 | # init.mod (must be modified for different crystal structures) 8 | # Define units, deformation parameters and initial 9 | # configuration of the atoms and simulation cell. 10 | # 11 | # 12 | # potential.mod (must be modified for different pair styles) 13 | # Define pair style and other attributes 14 | # not stored in restart file 15 | # 16 | # 17 | # displace.mod (displace.mod should not need to be modified) 18 | # Perform positive and negative box displacements 19 | # in direction ${dir} and size ${up}. 20 | # It uses the resultant changes 21 | # in stress to compute one 22 | # row of the elastic stiffness tensor 23 | # 24 | # Inputs variables: 25 | # dir = the Voigt deformation component 26 | # (1,2,3,4,5,6) 27 | # Global constants: 28 | # up = the deformation magnitude (strain units) 29 | # cfac = conversion from LAMMPS pressure units to 30 | # output units for elastic constants 31 | # 32 | # 33 | # To run this on a different system, it should only be necessary to 34 | # modify the files init.mod and potential.mod. In order to calculate 35 | # the elastic constants correctly, care must be taken to specify 36 | # the correct units in init.mod (units, cfac and cunits). It is also 37 | # important to verify that the minimization of energy w.r.t atom 38 | # positions in the deformed cell is fully converged. 39 | # One indication of this is that the elastic constants are insensitive 40 | # to the choice of the variable ${up} in init.mod. Another is to check 41 | # the final max and two-norm forces reported in the log file. If you know 42 | # that minimization is not required, you can set maxiter = 0.0 in 43 | # init.mod. 44 | # 45 | 46 | include init.mod 47 | include potential.mod 48 | 49 | # Compute initial state 50 | fix 3 all box/relax aniso 0.0 51 | minimize ${etol} ${ftol} ${maxiter} ${maxeval} 52 | 53 | variable tmp equal pxx 54 | variable pxx0 equal ${tmp} 55 | variable tmp equal pyy 56 | variable pyy0 equal ${tmp} 57 | variable tmp equal pzz 58 | variable pzz0 equal ${tmp} 59 | variable tmp equal pyz 60 | variable pyz0 equal ${tmp} 61 | variable tmp equal pxz 62 | variable pxz0 equal ${tmp} 63 | variable tmp equal pxy 64 | variable pxy0 equal ${tmp} 65 | 66 | variable tmp equal lx 67 | variable lx0 equal ${tmp} 68 | variable tmp equal ly 69 | variable ly0 equal ${tmp} 70 | variable tmp equal lz 71 | variable lz0 equal ${tmp} 72 | 73 | # These formulas define the derivatives w.r.t. strain components 74 | # Constants uses $, variables use v_ 75 | variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac} 76 | variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac} 77 | variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac} 78 | variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac} 79 | variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac} 80 | variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac} 81 | 82 | displace_atoms all random ${atomjiggle} ${atomjiggle} ${atomjiggle} 87287 units box 83 | 84 | # Write restart 85 | unfix 3 86 | write_restart restart.equil 87 | 88 | # uxx Perturbation 89 | 90 | variable dir equal 1 91 | include displace.mod 92 | 93 | # uyy Perturbation 94 | 95 | variable dir equal 2 96 | include displace.mod 97 | 98 | # uzz Perturbation 99 | 100 | variable dir equal 3 101 | include displace.mod 102 | 103 | # uyz Perturbation 104 | 105 | variable dir equal 4 106 | include displace.mod 107 | 108 | # uxz Perturbation 109 | 110 | variable dir equal 5 111 | include displace.mod 112 | 113 | # uxy Perturbation 114 | 115 | variable dir equal 6 116 | include displace.mod 117 | 118 | # Output final values 119 | 120 | variable C11all equal ${C11} 121 | variable C22all equal ${C22} 122 | variable C33all equal ${C33} 123 | 124 | variable C12all equal 0.5*(${C12}+${C21}) 125 | variable C13all equal 0.5*(${C13}+${C31}) 126 | variable C23all equal 0.5*(${C23}+${C32}) 127 | 128 | variable C44all equal ${C44} 129 | variable C55all equal ${C55} 130 | variable C66all equal ${C66} 131 | 132 | variable C14all equal 0.5*(${C14}+${C41}) 133 | variable C15all equal 0.5*(${C15}+${C51}) 134 | variable C16all equal 0.5*(${C16}+${C61}) 135 | 136 | variable C24all equal 0.5*(${C24}+${C42}) 137 | variable C25all equal 0.5*(${C25}+${C52}) 138 | variable C26all equal 0.5*(${C26}+${C62}) 139 | 140 | variable C34all equal 0.5*(${C34}+${C43}) 141 | variable C35all equal 0.5*(${C35}+${C53}) 142 | variable C36all equal 0.5*(${C36}+${C63}) 143 | 144 | variable C45all equal 0.5*(${C45}+${C54}) 145 | variable C46all equal 0.5*(${C46}+${C64}) 146 | variable C56all equal 0.5*(${C56}+${C65}) 147 | 148 | # Average moduli for cubic crystals 149 | 150 | variable C11cubic equal (${C11all}+${C22all}+${C33all})/3.0 151 | variable C12cubic equal (${C12all}+${C13all}+${C23all})/3.0 152 | variable C44cubic equal (${C44all}+${C55all}+${C66all})/3.0 153 | 154 | variable bulkmodulus equal (${C11cubic}+2*${C12cubic})/3.0 155 | variable shearmodulus1 equal ${C44cubic} 156 | variable shearmodulus2 equal (${C11cubic}-${C12cubic})/2.0 157 | variable poissonratio equal 1.0/(1.0+${C11cubic}/${C12cubic}) 158 | 159 | # For Stillinger-Weber silicon, the analytical results 160 | # are known to be (E. R. Cowley, 1988): 161 | # C11 = 151.4 GPa 162 | # C12 = 76.4 GPa 163 | # C44 = 56.4 GPa 164 | print "${C11all} ${C12all} ${C44all}" file elastic.txt 165 | print "=========================================" 166 | print "Components of the Elastic Constant Tensor" 167 | print "=========================================" 168 | 169 | print "Elastic Constant C11all = ${C11all} ${cunits}" 170 | print "Elastic Constant C22all = ${C22all} ${cunits}" 171 | print "Elastic Constant C33all = ${C33all} ${cunits}" 172 | 173 | print "Elastic Constant C12all = ${C12all} ${cunits}" 174 | print "Elastic Constant C13all = ${C13all} ${cunits}" 175 | print "Elastic Constant C23all = ${C23all} ${cunits}" 176 | 177 | print "Elastic Constant C44all = ${C44all} ${cunits}" 178 | print "Elastic Constant C55all = ${C55all} ${cunits}" 179 | print "Elastic Constant C66all = ${C66all} ${cunits}" 180 | 181 | print "Elastic Constant C14all = ${C14all} ${cunits}" 182 | print "Elastic Constant C15all = ${C15all} ${cunits}" 183 | print "Elastic Constant C16all = ${C16all} ${cunits}" 184 | 185 | print "Elastic Constant C24all = ${C24all} ${cunits}" 186 | print "Elastic Constant C25all = ${C25all} ${cunits}" 187 | print "Elastic Constant C26all = ${C26all} ${cunits}" 188 | 189 | print "Elastic Constant C34all = ${C34all} ${cunits}" 190 | print "Elastic Constant C35all = ${C35all} ${cunits}" 191 | print "Elastic Constant C36all = ${C36all} ${cunits}" 192 | 193 | print "Elastic Constant C45all = ${C45all} ${cunits}" 194 | print "Elastic Constant C46all = ${C46all} ${cunits}" 195 | print "Elastic Constant C56all = ${C56all} ${cunits}" 196 | 197 | print "=========================================" 198 | print "Average properties for a cubic crystal" 199 | print "=========================================" 200 | 201 | print "Bulk Modulus = ${bulkmodulus} ${cunits}" 202 | print "Shear Modulus 1 = ${shearmodulus1} ${cunits}" 203 | print "Shear Modulus 2 = ${shearmodulus2} ${cunits}" 204 | print "Poisson Ratio = ${poissonratio}" 205 | -------------------------------------------------------------------------------- /Mo/usage/elastic_example/init.mod: -------------------------------------------------------------------------------- 1 | # NOTE: This script can be modified for different atomic structures, 2 | # units, etc. See in.elastic for more info. 3 | # 4 | 5 | # Define the finite deformation size. Try several values of this 6 | # variable to verify that results do not depend on it. 7 | variable up equal 1.0e-6 8 | 9 | # Define the amount of random jiggle for atoms 10 | # This prevents atoms from staying on saddle points 11 | variable atomjiggle equal 1.0e-5 12 | 13 | # Uncomment one of these blocks, depending on what units 14 | # you are using in LAMMPS and for output 15 | 16 | # metal units, elastic constants in eV/A^3 17 | #units metal 18 | #variable cfac equal 6.2414e-7 19 | #variable cunits string eV/A^3 20 | 21 | # metal units, elastic constants in GPa 22 | units metal 23 | variable cfac equal 1.0e-4 24 | variable cunits string GPa 25 | 26 | # real units, elastic constants in GPa 27 | #units real 28 | #variable cfac equal 1.01325e-4 29 | #variable cunits string GPa 30 | 31 | # Define minimization parameters 32 | variable etol equal 0.0 33 | variable ftol equal 1.0e-10 34 | variable maxiter equal 400 35 | variable maxeval equal 400 36 | variable dmax equal 1.0e-2 37 | 38 | # generate the box and atom positions using a diamond lattice 39 | variable a equal 3.169 40 | 41 | boundary p p p 42 | 43 | lattice bcc $a 44 | region box prism 0 2.0 0 3.0 0 4.0 0.0 0.0 0.0 45 | create_box 1 box 46 | create_atoms 1 box 47 | 48 | # Need to set mass to something, just to satisfy LAMMPS 49 | mass 1 95.94 50 | 51 | -------------------------------------------------------------------------------- /Mo/usage/elastic_example/potential.mod: -------------------------------------------------------------------------------- 1 | # NOTE: This script can be modified for different pair styles 2 | # See in.elastic for more info. 3 | 4 | # Choose potential 5 | include Mo.snap 6 | # Setup neighbor style 7 | neighbor 1.0 nsq 8 | neigh_modify once no every 1 delay 0 check yes 9 | 10 | # Setup minimization style 11 | min_style cg 12 | min_modify dmax ${dmax} line quadratic 13 | 14 | # Setup output 15 | thermo 1 16 | thermo_style custom step temp pe press pxx pyy pzz pxy pxz pyz lx ly lz vol 17 | thermo_modify norm no 18 | -------------------------------------------------------------------------------- /Mo/usage/elastic_example/restart.equil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/materialsvirtuallab/snap/5fc2251b45c72dea0c9799d7aad3e3261a077a5b/Mo/usage/elastic_example/restart.equil -------------------------------------------------------------------------------- /NbMoTaW/README.md: -------------------------------------------------------------------------------- 1 | ## SNAP potential for NbMoTaW Multi-Principal Element Alloy system 2 | 3 | This directory contains the SNAP force field parameters for NbMoTaW Multi-Principal Element Alloy system. This potential is fitted from the DFT data, including, 4 | ``` 5 | - Undistorted ground state structures for Nb, Mo, Ta, W; 6 | - Distorted structures constructed by applying different strains to a bulk supercell; 7 | - Surface structures of elemental structures; 8 | - DFT calculated molecular dynamics trajectories for bulk supercells at different volumes and temperatures; 9 | - Binary solite solution structures; 10 | - Multinary Special Quasi-random Structures and their AIMD trajectories at different temperatures; 11 | ``` 12 | 13 | The hyperparameter tuning and fitting procedures are described in detail in our publication [1] and thus are excluded from the repo. 14 | 15 | 16 | ### Reference 17 | [1]: X. Li, C. Chen, H. Zheng & S.P. Ong (2019). Unravelling Complex Strengthening Mechanisms in the NbMoTaW Multi-Principal Element Alloy with Machine Learning Potentials. submitted. 18 | -------------------------------------------------------------------------------- /NbMoTaW/Ta-W-Nb-Mo.snapcoeff: -------------------------------------------------------------------------------- 1 | # LAMMPS SNAP coefficients for Ta-W-Nb-Mo 2 | # generated by pymacy.potential.snap.SNAPotential 3 | 4 | 4 31 5 | Ta 0.489 0.8 6 | -1.425109684260578 7 | 0.05044506979910916 8 | 0.1449574749052033 9 | 1.0670061695028303 10 | 0.08835574861819201 11 | 1.0091130598473406 12 | 0.0036650093926857696 13 | 0.20964097166522078 14 | 0.027932575440179207 15 | 0.22963708003947503 16 | -0.12847119843372223 17 | 0.00030024745127657515 18 | -0.13468637024590582 19 | -0.007981276930546451 20 | -0.014405098123407893 21 | 0.17846475358239833 22 | -0.0859772211353582 23 | -0.008756843306830419 24 | -0.040877748648188335 25 | 0.07376556334297912 26 | -0.029246356137059636 27 | 0.03598447349482439 28 | -0.0352277596323274 29 | -0.003930723814269409 30 | 0.023065271885315274 31 | -0.06175022826179577 32 | -0.04469023362685083 33 | -0.006488080091133344 34 | 0.06171927791526725 35 | 0.033014192344766255 36 | 0.011402709319943728 37 | Nb 0.511 0.7 38 | -1.4956456721567826 39 | 0.05612130673255633 40 | 0.1502059130083596 41 | 1.1765970981344198 42 | 0.09138677115524516 43 | 1.0893224938097958 44 | 0.07116057752471085 45 | 0.29643896578953877 46 | 0.005917067856183067 47 | 0.22943045948782287 48 | 0.05120162692800945 49 | -0.11410328847254875 50 | -0.03518353952849171 51 | -0.02723043677972764 52 | 0.007082433891911488 53 | 0.10469188998010706 54 | -0.14411573137255962 55 | 0.011938606596523203 56 | -0.12556281025512428 57 | 0.03301632129224241 58 | -0.08909986972846293 59 | 0.017935188428179857 60 | -0.054454727413837424 61 | -0.0433903076638232 62 | 0.025536416668651654 63 | -0.0239815972348659 64 | 0.034221871817031534 65 | -0.008323616081167884 66 | 0.02563216390951105 67 | -0.00042023441146921137 68 | 0.013456804789307497 69 | Mo 0.5 0.5 70 | -5.332775538023719 71 | 0.15674126073329253 72 | 0.015395641264471807 73 | 0.7791458291136816 74 | 0.06757535917316412 75 | 0.6810570537109905 76 | 0.07959640495755643 77 | 0.17892885206043524 78 | -0.09889209577892899 79 | 0.5959585651636085 80 | -0.007871724339218691 81 | -0.12618022623106998 82 | 0.07716807502575751 83 | 0.035708703224163474 84 | 0.020263110501164583 85 | 0.16664544292354017 86 | 0.05964025625144153 87 | 0.03811975065430609 88 | -0.005472739018676759 89 | 0.011923522896261987 90 | -0.1913922461503378 91 | -0.01714921484058099 92 | 0.13973572865725772 93 | 0.15724490604740066 94 | 0.13480633068516545 95 | -0.04995662933129731 96 | -0.09740354664413556 97 | -0.02512020698717432 98 | 0.22885239620797626 99 | -0.013055058833242927 100 | -0.03939990040049368 101 | W 0.489 0.6 102 | 5.7029676093982005 103 | 0.11853512186639753 104 | 0.2567164809376236 105 | 1.0832713883093203 106 | 0.019530402078965114 107 | 0.7464016286516474 108 | 0.013848807116599113 109 | -0.10236298932931918 110 | -0.0642024450789832 111 | 0.2562948462745133 112 | -0.447096465838605 113 | -0.0019873338805882768 114 | -0.20397449941118037 115 | -0.04160992790666708 116 | -0.011681892166092313 117 | 0.0022127135637891133 118 | -0.1570300376751524 119 | -0.10148288310873241 120 | -0.05873051411860312 121 | 0.06069251303373516 122 | -0.237457141471944 123 | 0.021297299380757514 124 | 0.06635798980874233 125 | 0.014581887658784987 126 | -0.06896060186462204 127 | -0.07999004096468468 128 | -0.11227718040417425 129 | -0.013953913002948445 130 | 0.22636172122049372 131 | 0.050407379980334094 132 | 0.049903565483977536 -------------------------------------------------------------------------------- /NbMoTaW/Ta-W-Nb-Mo.snapparam: -------------------------------------------------------------------------------- 1 | # LAMMPS SNAP parameters for Ta-W-Nb-Mo 2 | # generated by pymacy.potential.snap.SNAPotential 3 | 4 | rcutfac 4.6 5 | twojmax 6 6 | rfac0 0.99363 7 | rmin0 0 8 | diagonalstyle 3 9 | quadraticflag 0 10 | bzeroflag 0 -------------------------------------------------------------------------------- /NbMoTaW/training/Mo_Surface.json: -------------------------------------------------------------------------------- 1 | [{"_id": "59c55cc6ffc31da19ce29317", "params": {"pp": {"Mo": "Mo_pv"}, "env": "bulk", "e_cut": 520, "k_prod": "NAN", "bader": false}, "group": "Mo", "tags": "Surface", "structure": {"@module": "pymatgen.core.structure", "sites": [{"abc": [0.0, 0.598601, 0.200068], "xyz": [0.0, 4.240970160603, 5.66976906628], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.0, 0.197315, 0.150478], "xyz": [0.0, 1.397937903945, 4.26442764238], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.0, 0.797763, 0.10099], "xyz": [0.0, 5.651993695689, 2.8619768179], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.0, 0.408264, 0.051061], "xyz": [0.0, 2.892470011992, 1.4470284018100001], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.0, 0.986798, 0.007255], "xyz": [0.0, 6.9912694307939995, 0.20560096855], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.5, 0.497766, 0.123756], "xyz": [1.584218, 3.526574050098, 3.50714727276], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.5, 0.101967, 0.073649], "xyz": [1.584218, 0.722416107501, 2.0871544772900004], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.5, 0.707715, 0.026824], "xyz": [1.584218, 5.014021355145, 0.76017096904], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.5, 0.301538, 0.224304], "xyz": [1.584218, 2.1363373270139996, 6.356598159840001], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.5, 0.899631, 0.174991], "xyz": [1.584218, 6.373708407693, 4.95910669711], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.0, 0.592285, 0.448176], "xyz": [0.0, 4.196222544855, 12.70095378096], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.0, 0.198033, 0.401351], "xyz": [0.0, 1.4030247924989998, 11.37397027271], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.0, 0.802234, 0.351244], "xyz": [0.0, 5.683669849902, 9.95397747724], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.0, 0.400369, 0.300009], "xyz": [0.0, 2.8365354923069996, 8.502018052890001], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.0, 0.998462, 0.250696], "xyz": [0.0, 7.073906572986, 7.10452659016], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.5, 0.502237, 0.37401], "xyz": [1.584218, 3.5582502043110003, 10.599147932100001], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.5, 0.102685, 0.324522], "xyz": [1.584218, 0.727502996055, 9.19669710762], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.5, 0.701399, 0.274932], "xyz": [1.584218, 4.969273739397, 7.791355683720001], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.5, 0.313202, 0.467745], "xyz": [1.584218, 2.218974469206, 13.255523781450002], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.5, 0.891736, 0.423939], "xyz": [1.584218, 6.317773888007999, 12.014096348190002], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}], "lattice": {"beta": 90.0, "c": 28.33921, "a": 3.168436, "gamma": 90.0, "matrix": [[3.168436, 0.0, 0.0], [0.0, 7.084803, 0.0], [0.0, 0.0, 28.33921]], "volume": 636.151356127127, "alpha": 90.0, "b": 7.084803}, "@class": "Structure"}, "num_atoms": 20, "outputs": {"energy": -208.29086882, "forces": [[0.0, -0.01699373, 0.00209772], [0.0, 0.02759536, 0.00741959], [0.0, -0.02621707, -0.04633367], [0.0, 0.03132237, 0.03109207], [0.0, -0.00699514, 0.04706954], [0.0, -0.00326094, 0.01608451], [0.0, 0.00986883, -0.01647521], [0.0, -0.02081216, 0.01419922], [0.0, 0.02270756, -0.00413121], [0.0, -0.00015196, 0.04248754], [0.0, 0.02081216, -0.01419922], [0.0, -0.00986883, 0.01647521], [0.0, 0.00326094, -0.01608451], [0.0, 0.00015196, -0.04248754], [0.0, -0.02270756, 0.00413121], [0.0, 0.02621707, 0.04633367], [0.0, -0.02759536, -0.00741959], [0.0, 0.01699373, -0.00209772], [0.0, 0.00699514, -0.04706954], [0.0, -0.03132237, -0.03109207]], "stress": [-17.2381, -17.43636, -2.2529, -0.23058, 0.0, 0.0]}, "group_id": 286, "add_on": "2017-09-22 11:56:06.673000"}, {"_id": "59c55cc6ffc31da19ce29318", "params": {"pp": {"Mo": "Mo_pv"}, "env": "bulk", "e_cut": 520, "k_prod": "NAN", "bader": false}, "group": "Mo", "tags": "Surface", "structure": {"@module": "pymatgen.core.structure", "sites": [{"abc": [0.299843, 0.281172, 0.2812], "xyz": [0.562117626025, 1.9205686832759998, 7.003559272994], "species": [{"occu": 1, "element": "Mo"}], "label": "Mo"}, {"abc": [0.71838, 0.556782, 0.224121], "xyz": 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0.02270848], [-0.0, -0.0, 0.04887438], [-0.0, 0.0, 0.02052789], [0.0, 0.0, 0.00192345], [0.0, -0.0, -0.02052789], [0.0, 0.0, -0.04887438], [-0.0, -0.0, -0.00192345], [0.0, -0.0, 0.00178901], [-0.0, -0.0, 0.03899736], [-0.0, 0.0, -0.02270848]], "stress": [-16.46445, -16.46445, -1.55009, 0.0, 0.0, 0.0]}, "group_id": 296, "add_on": "2017-09-22 11:56:06.703000"}] -------------------------------------------------------------------------------- /NbMoTaW/training/README.md: -------------------------------------------------------------------------------- 1 | # Using the training and test data 2 | 3 | The training and test data is provided in json files, which can be read by any standard json parser. Each json file contains one data group (e.g., Ta_Surface, NbMo_SS, Multinary_SQS,Mo_Test,NbMo_Test, etc.) used in the training or test of the SNAP model. 4 | 5 | The data is provided as a list of dicts. Each dict contains one structure with data. The format of the json file is as follows: 6 | 7 | ```json 8 | [ 9 | { 10 | "_id": "a string", 11 | "params": {"Dict of parameters used for DFT calculations, e.g. pseudopotential, energy cutoff, etc."}, 12 | "group": "Ni3Mo", 13 | "tags": "Md", 14 | "structure": {"Dict representation of Structure as output by pymatgen"}, 15 | "num_atoms": 108, 16 | "outputs": { 17 | "energy": -619.08666252, 18 | "forces": [], 19 | "stress": [] 20 | } 21 | }, 22 | ... 23 | ] 24 | ``` 25 | 26 | -------------------------------------------------------------------------------- /Ni-Mo/Ni_Mo.snapcoeff: -------------------------------------------------------------------------------- 1 | # LAMMPS SNAP coefficients for Ni_Mo 2 | # generated by pymacy.potential.snap.SNAPotential 3 | 4 | 2 31 5 | Ni 0.575 0.5 6 | -5.74137597148 7 | 0.00261516042413 8 | -0.009699168626 9 | 0.0818951233671 10 | -0.0569299158728 11 | 0.300080068305 12 | 0.0752233805991 13 | 0.147857919016 14 | 0.0221085009743 15 | 0.131302557568 16 | 0.14467283511 17 | 0.0531194735283 18 | -0.0708752194168 19 | -0.0386225752369 20 | 0.0230915952873 21 | 0.0643797269545 22 | -0.00309279910187 23 | 0.055335750844 24 | -0.101194753284 25 | -0.0788356620704 26 | -0.01485153828 27 | 0.0144374653104 28 | -0.00207986530203 29 | 0.0333887815654 30 | -0.0639521013963 31 | -0.0306755928606 32 | 0.000464150398115 33 | 0.00714699762365 34 | 0.0199617506567 35 | -0.0108048397609 36 | 0.00604686131228 37 | Mo 0.575 1.0 38 | -11.1413071988 39 | 0.00192312103792 40 | 0.021374495125 41 | 0.050856734008 42 | 0.0122594678199 43 | 0.337635694818 44 | 0.0659367410297 45 | 0.175561579396 46 | 0.00127883428484 47 | 0.0676248614536 48 | 0.0299955866199 49 | 0.00903307768795 50 | -0.00936459285804 51 | 0.00300577725833 52 | 0.0233490189313 53 | 0.00309233746324 54 | 0.0323573241607 55 | 0.0632850422634 56 | -0.0621491501344 57 | -0.0210252233996 58 | -0.0357231556094 59 | 0.0147004224035 60 | 0.00378753597796 61 | 0.0235912050139 62 | -0.022833337709 63 | -0.0269919600435 64 | 0.00847966833367 65 | 0.00318728648989 66 | 0.0380433712112 67 | -0.000450141523948 68 | -0.00371851801313 -------------------------------------------------------------------------------- /Ni-Mo/Ni_Mo.snapparam: -------------------------------------------------------------------------------- 1 | # LAMMPS SNAP parameters for Ni_Mo 2 | # generated by pymacy.potential.snap.SNAPotential 3 | 4 | rcutfac 4.0 5 | twojmax 6 6 | rfac0 0.99363 7 | rmin0 0 8 | diagonalstyle 3 9 | bzeroflag 0 -------------------------------------------------------------------------------- /Ni-Mo/README.md: -------------------------------------------------------------------------------- 1 | ## SNAP potential for Ni-Mo binary system 2 | 3 | This directory contains the SNAP force field parameters for Ni-Mo binary system. This potential is fitted from the DFT data, including, 4 | ``` 5 | - Undistorted ground state structures for Ni, Mo and the two binary intermetallics Ni3Mo and Ni4Mo; 6 | - Distorted structures constructed by applying different strains to a bulk supercell; 7 | - Surface structures of elemental structures; 8 | - DFT calculated molecular dynamics trajectories for bulk supercells; 9 | - Alloy structures constructed by partial substitution of supercells of the bulk fcc Ni with Mo and the bulk bcc Mo with Ni. 10 | ``` 11 | 12 | The hyperparameter tuning and fitting procedures are described in detail in our publication [1] and thus are excluded from the repo. 13 | 14 | 15 | ### Reference 16 | [1]: X. Li, C. Hu, C. Chen, Z. Deng, J. Luo, & S.P. Ong Phys. Rev. B 98, 094104 (2018). Quantum-Accurate Spectral Neighbor Analysis Potential Models for Ni-Mo Binary Alloys and FCC Metals. 17 | -------------------------------------------------------------------------------- /Ni-Mo/training/README.md: -------------------------------------------------------------------------------- 1 | # Using the training data 2 | 3 | The training data is provided in json files, which can be read by any standard json parser. Each json file contains one data group (e.g., Ni3Mo_AIMD, Ni4Mo_elastic, Ni_dopedwith_Mo, etc.) used in the training of the SNAP model. 4 | 5 | The data is provided as a list of dicts. Each dict contains one structure with data. The format of the json file is as follows: 6 | 7 | ```json 8 | [ 9 | { 10 | "_id": "a string", 11 | "params": {"Dict of parameters used for DFT calculations, e.g. pseudopotential, energy cutoff, etc."}, 12 | "group": "Ni3Mo", 13 | "tags": "Md", 14 | "structure": {"Dict representation of Structure as output by pymatgen"}, 15 | "num_atoms": 108, 16 | "outputs": { 17 | "energy": -619.08666252, 18 | "forces": [], 19 | "stress": [] 20 | } 21 | }, 22 | ... 23 | ] 24 | ``` 25 | 26 | -------------------------------------------------------------------------------- /Ni/Ni.snapcoeff: -------------------------------------------------------------------------------- 1 | # LAMMPS SNAP coefficients for Ni 2 | # generated by pymacy.potential.snap.SNAPotential 3 | 4 | 1 31 5 | Ni 0.5 1.0 6 | -9.91671474359 7 | 0.00781991474169 8 | 0.046585005432 9 | 0.197329374995 10 | 0.0323391405206 11 | 0.317054017673 12 | 0.0861929766181 13 | 0.0744345550377 14 | 0.0249956556105 15 | 0.146882240782 16 | 0.0498114600916 17 | 0.0852648800679 18 | 0.0185269869953 19 | 0.00795087307619 20 | 0.0157902736601 21 | 0.047788117794 22 | 0.0214484359448 23 | 0.0841001653161 24 | 0.0477991214477 25 | -0.00606616418849 26 | 0.0180053698392 27 | 0.000627976855351 28 | 0.045574281612 29 | 0.0255736787933 30 | 0.0237355373884 31 | 0.017684575357 32 | -0.0104123071669 33 | -0.00067224052877 34 | 0.0215960322169 35 | -0.000416651145044 36 | -0.00912068611489 -------------------------------------------------------------------------------- /Ni/Ni.snapparam: -------------------------------------------------------------------------------- 1 | # LAMMPS SNAP parameters for Ni 2 | # generated by pymacy.potential.snap.SNAPotential 3 | 4 | rcutfac 3.9 5 | twojmax 6 6 | rfac0 0.99363 7 | rmin0 0 8 | diagonalstyle 3 9 | bzeroflag 0 -------------------------------------------------------------------------------- /Ni/README.md: -------------------------------------------------------------------------------- 1 | ## SNAP potential for Ni 2 | 3 | This directory contains the SNAP force field parameters for Ni. This potential is fitted from the DFT data, including bulk structures with elastic deformation, surfaces and DFT calculated molecular dynamics trajectories. 4 | 5 | The hyperparameter tuning and fitting procedures are described in detail in our publication [1] and thus are excluded from the repo. 6 | 7 | 8 | ### Reference 9 | [1]: X. Li, C. Hu, C. Chen, Z. Deng, J. Luo, & S.P. Ong (2018). Quantum-Accurate Spectral Neighbor Analysis Potential Models for Ni-Mo Binary Alloys and FCC Metals. arXiv:1806.04777 10 | -------------------------------------------------------------------------------- /Ni/training/README.md: -------------------------------------------------------------------------------- 1 | # Using the training data 2 | 3 | The training data is provided in json files, which can be read by any standard json parser. Each json file contains contains one data group (e.g., AIMD, elastic, surfaces, etc.) used in the training of the SNAP model. 4 | 5 | The data is provided as a list of dicts. Each dict contains one structure with data. The format of the json file is as follows: 6 | 7 | ```json 8 | [ 9 | { 10 | "_id": "a string", 11 | "params": {"Dict of parameters used for DFT calculations, e.g. pseudopotential, energy cutoff, etc."}, 12 | "group": "Ni", 13 | "tags": "Md", 14 | "structure": {"Dict representation of Structure as output by pymatgen"}, 15 | "num_atoms": 108, 16 | "outputs": { 17 | "energy": -619.08666252, 18 | "forces": [], 19 | "stress": [] 20 | } 21 | }, 22 | ... 23 | ] 24 | ``` 25 | 26 | -------------------------------------------------------------------------------- /Ni/training/Surface.json: -------------------------------------------------------------------------------- 1 | [{"_id": "59b4ba43ffc31d171c78afb8", "params": {"pp": {"Ni": "Ni_pv"}, "env": "bulk", "e_cut": 520, "k_prod": 40, "bader": false}, "group": "Ni", "tags": ["Surface"], "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "lattice": {"matrix": [[2.477035, 0.0, 0.121008], [1.235567, 4.112177, 0.120902], [0.0, 0.0, 25.413008]], "a": 2.479988977251512, "b": 4.295490982928727, "c": 25.413008, "alpha": 88.3871251691446, "beta": 87.20321265467301, "gamma": 73.22144109133339, "volume": 258.85706099262137}, "sites": [{"species": [{"element": "Ni", "occu": 1}], "abc": [0.352317, 0.941675, 0.353691], "xyz": [2.03620409482, 3.872334276475, 9.144835778913999], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.937179, 0.851843, 0.2738], "xyz": [3.373934284246, 3.502929192211, 7.174477269218], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.647928, 0.394476, 0.309667], "xyz": [2.0923418613719997, 1.622155134252, 7.995667357112001], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.479207, 0.562653, 0.478934], "xyz": [1.8822079904959998, 2.313728725581, 12.297167327134002], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.062568, 0.47987, 0.394994], "xyz": [0.74789466217, 1.97331037699, 10.103574153236002], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.770972, 0.020916, 0.43714], "xyz": [1.9355677473919999, 0.086010294132, 11.204864883128], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.604099, 0.186797, 0.605006], "xyz": [1.727174575364, 0.768142327069, 15.470707260734002], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.18746, 0.104014, 0.521066], "xyz": [0.5928612470379999, 0.427723978478, 13.277114086836002], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.895694, 0.64575, 0.56286], "xyz": [3.0165327775399997, 2.65543829775, 14.490424288932001], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.729488, 0.814824, 0.7262], "xyz": [2.813736953288, 3.3507005118479998, 18.641714144751997], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.31435, 0.724992, 0.646309], "xyz": [1.674432142714, 2.981295427584, 16.550347635056003], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.018738, 0.27219, 0.690333], "xyz": [0.38272366356, 1.11929345763, 17.578613814948], "label": "Ni"}]}, "num_atoms": 12, "outputs": {"energy": -66.4017178, "forces": [[-0.00068966, -0.00710514, 0.01411742], [0.00035368, -0.00542322, -0.00723987], [0.00061527, -0.00593359, -0.01259465], [0.00184955, -0.00105289, -0.03786031], [0.00083109, 0.0284126, -0.01701234], [-0.0012335, 0.02808465, 0.02524981], [-0.00083109, -0.0284126, 0.01701234], [-0.00184955, 0.00105289, 0.03786031], [0.0012335, -0.02808465, -0.02524981], [-0.00035368, 0.00542322, 0.00723987], [0.00068966, 0.00710514, -0.01411742], [-0.00061527, 0.00593359, 0.01259465]], "stress": [-21.72382435, -17.94860256, -12.70439954, 0.01335585, -0.27346362, -0.44167152]}}, {"_id": "59b4ba43ffc31d171c78afb9", "params": {"pp": {"Ni": "Ni_pv"}, "env": "bulk", "e_cut": 520, "k_prod": 40, "bader": false}, "group": "Ni", "tags": ["Surface"], "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "lattice": {"matrix": [[2.480314, 0.0, 0.0], [0.0, 6.051603, -0.535607], [0.0, 0.0, 22.999866]], "a": 2.480314, "b": 6.075259149045249, "c": 22.999866, "alpha": 95.05787711849808, "beta": 90.0, "gamma": 90.0, "volume": 345.22512847352976}, "sites": [{"species": [{"element": "Ni", "occu": 1}], "abc": [0.0, 0.323947, 0.109041], "xyz": [0.0, 1.960398637041, 2.334420107677], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.0, 0.639803, 0.047045], "xyz": [0.0, 3.8718337542090002, 0.7393457305490001], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.5, 0.980398, 0.0746], "xyz": [1.240157, 5.932979477994, 1.190681972014], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.5, 0.30306, 0.018775], "xyz": [1.240157, 1.83399880518, 0.26950142673], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.0, 0.702958, 0.234374], "xyz": [0.0, 4.2540227416739995, 5.014061368378], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.0, 0.014509, 0.170715], "xyz": [0.0, 0.087802707927, 3.918651002227], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.5, 0.358305, 0.202853], "xyz": [1.240157, 2.168319612915, 4.473681151563], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.5, 0.672363, 0.140326], "xyz": [1.240157, 4.068873947889, 2.8673568669750003], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.0, 0.077684, 0.359665], "xyz": [0.0, 0.470112727452, 8.230638710702001], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.0, 0.39167, 0.297163], "xyz": [0.0, 2.3702313470100003, 6.624927986468], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.5, 0.735509, 0.329301], "xyz": [1.240157, 4.4510084709269995, 7.1799351047030004], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.5, 0.046938, 0.265652], "xyz": [1.240157, 0.284050141614, 6.084820081266], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.0, 0.446935, 0.481209], "xyz": [0.0, 2.704673186805, 10.828361003449], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.0, 0.769643, 0.425372], "xyz": [0.0, 4.657573887729, 9.371272821851], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.5, 0.110188, 0.452939], "xyz": [1.240157, 0.666814031364, 10.358518842058], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.5, 0.426091, 0.39097], "xyz": [1.240157, 2.578533573873, 8.764040287782999], "label": "Ni"}]}, "num_atoms": 16, "outputs": {"energy": -88.24676543, "forces": [[0.0, -0.00227585, -0.00221412], [0.0, 0.01048518, 0.00762845], [0.0, -0.01052716, 0.02185477], [0.0, -0.00238198, 0.00623196], [0.0, -0.00177681, -0.0003005], [0.0, 0.00047052, 0.00488315], [0.0, 0.00019924, 0.01097655], [0.0, -0.00123758, -0.00129409], [0.0, 0.00039605, 0.00427773], [0.0, -0.00049834, -0.01209526], [0.0, -0.00235497, -0.0056905], [0.0, 0.0060006, -0.0053467], [0.0, 0.00226641, -0.00445878], [0.0, 0.00923473, -0.01875176], [0.0, -0.00908288, -0.00600023], [0.0, 0.00108282, 0.00029931]], "stress": [-24.52014717, -19.7482174, -14.93644047, 0.0, 0.68806904, 0.0]}}, {"_id": "59b4ba43ffc31d171c78afba", "params": {"pp": {"Ni": "Ni_pv"}, "env": "bulk", "e_cut": 520, "k_prod": 40, "bader": false}, "group": "Ni", "tags": ["Surface"], "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "lattice": {"matrix": [[3.499603, 0.0, 0.210214], [1.743459, 6.322179, 0.210709], [0.0, 0.0, 29.235547]], "a": 3.505910877846868, "b": 6.561554303318917, "c": 29.235547, "alpha": 88.15976340992366, "beta": 86.56249001201286, "gamma": 74.5049193335209, "volume": 646.8398860917607}, "sites": [{"species": [{"element": "Ni", "occu": 1}], "abc": [0.401196, 0.822977, 0.37463], "xyz": [2.838853382631, 5.203007906883, 11.210258649247], "label": "Ni"}, {"species": [{"element": "Ni", "occu": 1}], "abc": [0.199924, 0.294053, 0.306098], "xyz": 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analysis potential (SNAP) models for 5 | various elements, including the force field models, the corresponding parameters and training data used to develop the models. For SNAP model training and potential generations, please use the maml package [https://github.com/materialsvirtuallab/maml](https://github.com/materialsvirtuallab/maml). 6 | 7 | The structure of the folder organization is as follows 8 | 9 | ``` 10 | - Element/ 11 | - training/ 12 | - usage/ 13 | - elastic_example/ 14 | - element.snapcoeff 15 | - element.snapparam 16 | ``` 17 | where the `training` folder contains the original datasets used for developing the model, `element.snapcoeff` and `element.snapparam` are the force field parameters ready for LAMMPS, and `usage` contains examples for running the simulations with developed potentials. 18 | 19 | Below are the units of training metrics: 20 | 21 | * Energy: `eV` 22 | * Forces: `eV/Angstrom` 23 | * Stress: `-1 * kbar` 24 | 25 | ## LAMMPS installation 26 | The calculations rely on [LAMMPS package](http://lammps.sandia.gov/). During installation, the SNAP package should be installed by the following command in the `src` directory. 27 | > make yes-snap 28 | 29 | You can check if the inclusion is successful by 30 | > make package-status 31 | 32 | We recommand the users to install also the `REPLICA` , `MEAM` and `PYTHON`packages following the same procedure. 33 | 34 | After that, the serial version of lammps can be installed by 35 | > make serial 36 | 37 | Please refer to the [lammps website](http://lammps.sandia.gov/) for the installation of other versions. 38 | 39 | In case the user wants to use the `lammps` package in python (not supported by python 3 for now), lammps should be installed as a shared library by the following command. 40 | > make serial mode=shlib 41 | 42 | Usually, the lammps simulations are run by 43 | > lmp_serial -in foo.in 44 | 45 | assuming the executable is `lmp_serial` and the input file is `foo.in`. 46 | 47 | 48 | ## Potential development 49 | 50 | The JSON data file contains all the necessary information for developping the force field. Specifically, you will need the descriptors and the targets. The targets are the DFT computed energies per atom in the structure, atomic forces and stress components, which are stored under "data" in the json file. The descriptors for energy, force and stress are different, even though they share the same coefficients. For bispectrum coefficients calculated with $$j_{max}$$ = 3, the energy descriptor is the atomic average of bispectrum coefficients having a dimension of (1, 31) where 31 is a number dictated by the bispectrum coefficient order ($$j_{max}$$), the force descriptor is the first derivatives of individual atomic bispectrum coefficients that has a dimension of (n, 31), where n is the number of atoms, and lastly the stress descriptor is a matrix with dimension (6, 31), where 6 corresponds to the unique six components in the stress tensors. 51 | 52 | The model coefficients can be fitted by gathering all data in the training folder and then by a linear model that relates the descriptors to the targets, with the linear fitting weights listed under "optimized params/weights" in the json file. In the previous example, we will need to fit **31** coefficients from the linear model as the SNAP coefficients. 53 | 54 | 55 | ## Running examples 56 | 57 | The examples are under the `usage` folder. 58 | Noting that the current SNAP parameters are compatible with Lammps-2018 version. 59 | For newer version of Lammps, minor changes may need to be adjusted. 60 | 61 | For example, one can run the `Mo/usage/elastic_example` by simply the following command 62 | > lmp_serial -in in.elastic 63 | 64 | The final results should look like the following: 65 | 66 | ``` 67 | ========================================= 68 | Components of the Elastic Constant Tensor 69 | ========================================= 70 | Elastic Constant C11all = 472.830692948326 GPa 71 | Elastic Constant C22all = 472.830692952315 GPa 72 | Elastic Constant C33all = 472.830692945432 GPa 73 | Elastic Constant C12all = 151.92547560401 GPa 74 | Elastic Constant C13all = 151.925475607608 GPa 75 | Elastic Constant C23all = 151.925475607655 GPa 76 | Elastic Constant C44all = 106.589112603853 GPa 77 | Elastic Constant C55all = 106.589112606229 GPa 78 | Elastic Constant C66all = 106.589112606586 GPa 79 | Elastic Constant C14all = -1.64471728492463e-09 GPa 80 | Elastic Constant C15all = -3.16276324848469e-09 GPa 81 | Elastic Constant C16all = 6.3790059985881e-10 GPa 82 | Elastic Constant C24all = -2.92113212529259e-09 GPa 83 | Elastic Constant C25all = 5.7165004803867e-10 GPa 84 | Elastic Constant C26all = 6.09399861920712e-09 GPa 85 | Elastic Constant C34all = -1.85699578515759e-09 GPa 86 | Elastic Constant C35all = -1.13746544837262e-09 GPa 87 | Elastic Constant C36all = 1.70693557054728e-09 GPa 88 | Elastic Constant C45all = -8.163048780782e-11 GPa 89 | Elastic Constant C46all = 3.04624246101865e-09 GPa 90 | Elastic Constant C56all = 1.08037347240268e-09 GPa 91 | ========================================= 92 | Average properties for a cubic crystal 93 | ========================================= 94 | Bulk Modulus = 258.89388138718 GPa 95 | Shear Modulus 1 = 106.589112605556 GPa 96 | Shear Modulus 2 = 160.452608671134 GPa 97 | Poisson Ratio = 0.243175631155087 98 | Total wall time: 0:00:06 99 | ``` 100 | --------------------------------------------------------------------------------