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Merge branch 'ml-dft-sandia-master'
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‎ml-dft-sandia/README.md‎

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# ML-DFT-SANDIA
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3-
The Sandia code goes here.
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This is the original code used in [1].

‎ml-dft-sandia/descriptors/bispectrum.grid/README‎

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This example shows how to generate the SNAP bispectrum on a grid.
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Usage:
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python3.7 ./bgrid.py > bgrid.out
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Requirements:
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Python 3.6 or 3.7
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LAMMPS, with compute sna/grid, from here:
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https://github.com/athomps/lammps/tree/compute-grid
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Before running, you will need to do the following:
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1. Compile the LAMMPS shared library with the SNAP package installed
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2. Make the shared library visible e.g.
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ln -s $LAMMPS/src/liblammps.so .
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(for other ways see https://lammps.sandia.gov/doc/Python_shlib.html)
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3. Make the LAMMPS lammps.py visible e.g.
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ln -s $LAMMPS/python/lammps.py .
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(for better ways see https://lammps.sandia.gov/doc/Python_install.html)
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The files that are produced are as follows:
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bgrid.out: Screen output from LAMMPS and bgrid.py
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log.lammps: LAMMPS log file
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b.dump: per-atom bispectrum components
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bgrid.dat: grid bispectrum components as LAMMPS array
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bgrid_np.dat: grid bispectrum components as Numpy array
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pgrid_np.dat: grid power spectrum components as Numpy array
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bgridnorm_np.dat: normalized bispectrum
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pgridnorm_np.dat: normalized power spectrum
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You can compare these to the corresponding files
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with names containing a timestamp e.g. b.25Oct2019.dump

‎ml-dft-sandia/descriptors/bispectrum.grid/b.16Mar2020.dump‎

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ITEM: TIMESTEP
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0
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ITEM: NUMBER OF ATOMS
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2
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ITEM: BOX BOUNDS pp pp pp
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0.0000000000000000e+00 3.3159999999999998e+00
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0.0000000000000000e+00 3.3159999999999998e+00
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0.0000000000000000e+00 3.3159999999999998e+00
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ITEM: ATOMS id x y z c_b[1] c_b[2] c_b[3] c_b[4] c_b[5]
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1 0 0 0 108.173 3.21778 0.712238 7.06634 1.04273
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2 1.658 1.658 1.658 108.173 3.21778 0.712238 7.06634 1.04273

‎ml-dft-sandia/descriptors/bispectrum.grid/b.25Oct2019.dump‎

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ITEM: TIMESTEP
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0
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ITEM: NUMBER OF ATOMS
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2
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ITEM: BOX BOUNDS pp pp pp
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0.0000000000000000e+00 3.3159999999999998e+00
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0.0000000000000000e+00 3.3159999999999998e+00
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0.0000000000000000e+00 3.3159999999999998e+00
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ITEM: ATOMS id c_b[1] c_b[2] c_b[3] c_b[4] c_b[5]
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1 3375 846.026 36.811 8.51924 0.247118
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2 3375 846.026 36.811 8.51924 0.247118

‎ml-dft-sandia/descriptors/bispectrum.grid/bgrid.16Mar2020.dat‎

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x, y, z = 0 0 0
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108.173 3.21778 0.712238 7.06634 1.04273
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x, y, z = 1.658 0 0
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174.4 5.59324 1.35171 13.8088 2.13628
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x, y, z = 0 0.829 0
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183.116 3.64679 1.14854 30.7642 7.26691
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x, y, z = 1.658 0.829 0
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168.973 6.62458 1.46561 11.0631 1.61839
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x, y, z = 0 1.658 0
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174.4 5.59324 1.35171 13.8088 2.13628
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x, y, z = 1.658 1.658 0
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174.4 5.59324 1.35171 13.8088 2.13628
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x, y, z = 0 2.487 0
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183.116 3.64679 1.14854 30.7642 7.26691
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x, y, z = 1.658 2.487 0
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168.973 6.62458 1.46561 11.0631 1.61839
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x, y, z = 0 0 0.4145
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189.401 2.43052 0.962196 44.4583 12.4353
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x, y, z = 1.658 0 0.4145
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172.181 6.01397 1.39915 12.5923 1.90608
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x, y, z = 0 0.829 0.4145
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180.705 4.08676 1.22596 27.1833 6.05503
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x, y, z = 1.658 0.829 0.4145
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170.986 6.15471 1.45038 13.3359 2.10603
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x, y, z = 0 1.658 0.4145
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172.181 6.01397 1.39915 12.5923 1.90608
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x, y, z = 1.658 1.658 0.4145
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175.99 5.14283 1.33312 18.0104 3.26169
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x, y, z = 0 2.487 0.4145
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180.705 4.08676 1.22596 27.1833 6.05503
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x, y, z = 1.658 2.487 0.4145
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170.986 6.15471 1.45038 13.3359 2.10603
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x, y, z = 0 0 0.829
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183.116 3.64679 1.14854 30.7642 7.26691
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x, y, z = 1.658 0 0.829
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168.973 6.62458 1.46561 11.0631 1.61839
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x, y, z = 0 0.829 0.829
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175.638 5.11301 1.3681 19.6169 3.72319
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x, y, z = 1.658 0.829 0.829
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175.638 5.11301 1.3681 19.6169 3.72319
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x, y, z = 0 1.658 0.829
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168.973 6.62458 1.46561 11.0631 1.61839
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x, y, z = 1.658 1.658 0.829
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183.116 3.64679 1.14854 30.7642 7.26691
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x, y, z = 0 2.487 0.829
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175.638 5.11301 1.3681 19.6169 3.72319
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x, y, z = 1.658 2.487 0.829
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175.638 5.11301 1.3681 19.6169 3.72319
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x, y, z = 0 0 1.2435
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175.99 5.14283 1.33312 18.0104 3.26169
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x, y, z = 1.658 0 1.2435
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172.181 6.01397 1.39915 12.5923 1.90608
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x, y, z = 0 0.829 1.2435
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170.986 6.15471 1.45038 13.3359 2.10603
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x, y, z = 1.658 0.829 1.2435
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180.705 4.08676 1.22596 27.1833 6.05503
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x, y, z = 0 1.658 1.2435
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172.181 6.01397 1.39915 12.5923 1.90608
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x, y, z = 1.658 1.658 1.2435
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189.401 2.43052 0.962196 44.4583 12.4353
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x, y, z = 0 2.487 1.2435
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170.986 6.15471 1.45038 13.3359 2.10603
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x, y, z = 1.658 2.487 1.2435
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180.705 4.08676 1.22596 27.1833 6.05503
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x, y, z = 0 0 1.658
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174.4 5.59324 1.35171 13.8088 2.13628
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x, y, z = 1.658 0 1.658
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174.4 5.59324 1.35171 13.8088 2.13628
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x, y, z = 0 0.829 1.658
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168.973 6.62458 1.46561 11.0631 1.61839
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x, y, z = 1.658 0.829 1.658
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183.116 3.64679 1.14854 30.7642 7.26691
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x, y, z = 0 1.658 1.658
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174.4 5.59324 1.35171 13.8088 2.13628
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x, y, z = 1.658 1.658 1.658
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108.173 3.21778 0.712238 7.06634 1.04273
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x, y, z = 0 2.487 1.658
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168.973 6.62458 1.46561 11.0631 1.61839
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x, y, z = 1.658 2.487 1.658
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183.116 3.64679 1.14854 30.7642 7.26691
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x, y, z = 0 0 2.0725
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175.99 5.14283 1.33312 18.0104 3.26169
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x, y, z = 1.658 0 2.0725
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172.181 6.01397 1.39915 12.5923 1.90608
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x, y, z = 0 0.829 2.0725
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170.986 6.15471 1.45038 13.3359 2.10603
87+
x, y, z = 1.658 0.829 2.0725
88+
180.705 4.08676 1.22596 27.1833 6.05503
89+
x, y, z = 0 1.658 2.0725
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172.181 6.01397 1.39915 12.5923 1.90608
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x, y, z = 1.658 1.658 2.0725
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189.401 2.43052 0.962196 44.4583 12.4353
93+
x, y, z = 0 2.487 2.0725
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170.986 6.15471 1.45038 13.3359 2.10603
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x, y, z = 1.658 2.487 2.0725
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180.705 4.08676 1.22596 27.1833 6.05503
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x, y, z = 0 0 2.487
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183.116 3.64679 1.14854 30.7642 7.26691
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x, y, z = 1.658 0 2.487
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168.973 6.62458 1.46561 11.0631 1.61839
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x, y, z = 0 0.829 2.487
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175.638 5.11301 1.3681 19.6169 3.72319
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x, y, z = 1.658 0.829 2.487
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175.638 5.11301 1.3681 19.6169 3.72319
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x, y, z = 0 1.658 2.487
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168.973 6.62458 1.46561 11.0631 1.61839
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x, y, z = 1.658 1.658 2.487
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183.116 3.64679 1.14854 30.7642 7.26691
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x, y, z = 0 2.487 2.487
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175.638 5.11301 1.3681 19.6169 3.72319
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x, y, z = 1.658 2.487 2.487
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175.638 5.11301 1.3681 19.6169 3.72319
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x, y, z = 0 0 2.9015
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189.401 2.43052 0.962196 44.4583 12.4353
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x, y, z = 1.658 0 2.9015
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172.181 6.01397 1.39915 12.5923 1.90608
117+
x, y, z = 0 0.829 2.9015
118+
180.705 4.08676 1.22596 27.1833 6.05503
119+
x, y, z = 1.658 0.829 2.9015
120+
170.986 6.15471 1.45038 13.3359 2.10603
121+
x, y, z = 0 1.658 2.9015
122+
172.181 6.01397 1.39915 12.5923 1.90608
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x, y, z = 1.658 1.658 2.9015
124+
175.99 5.14283 1.33312 18.0104 3.26169
125+
x, y, z = 0 2.487 2.9015
126+
180.705 4.08676 1.22596 27.1833 6.05503
127+
x, y, z = 1.658 2.487 2.9015
128+
170.986 6.15471 1.45038 13.3359 2.10603

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