Merge branch 'ml-dft-sandia-master'

ml-dft-sandia/README.md

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

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

@@ -0,0 +1,38 @@
+This example shows how to generate the SNAP bispectrum on a grid.
+
+Usage:
+
+python3.7 ./bgrid.py > bgrid.out
+
+Requirements:
+
+Python 3.6 or 3.7
+LAMMPS, with compute sna/grid, from here:
+https://github.com/athomps/lammps/tree/compute-grid
+
+Before running, you will need to do the following:
+
+1. Compile the LAMMPS shared library with the SNAP package installed
+2. Make the shared library visible e.g.
+
+ln -s $LAMMPS/src/liblammps.so .
+(for other ways see https://lammps.sandia.gov/doc/Python_shlib.html)
+
+3. Make the LAMMPS lammps.py visible e.g. 
+
+ln -s $LAMMPS/python/lammps.py .
+(for better ways see https://lammps.sandia.gov/doc/Python_install.html)
+
+The files that are produced are as follows:
+
+bgrid.out: Screen output from LAMMPS and bgrid.py
+log.lammps: LAMMPS log file
+b.dump: per-atom bispectrum components
+bgrid.dat: grid bispectrum components as LAMMPS array
+bgrid_np.dat: grid bispectrum components as Numpy array
+pgrid_np.dat: grid power spectrum components as Numpy array
+bgridnorm_np.dat: normalized bispectrum 
+pgridnorm_np.dat: normalized power spectrum
+
+You can compare these to the corresponding files
+with names containing a timestamp e.g. b.25Oct2019.dump

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

@@ -0,0 +1,11 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+2
+ITEM: BOX BOUNDS pp pp pp
+0.0000000000000000e+00 3.3159999999999998e+00
+0.0000000000000000e+00 3.3159999999999998e+00
+0.0000000000000000e+00 3.3159999999999998e+00
+ITEM: ATOMS id x y z c_b[1] c_b[2] c_b[3] c_b[4] c_b[5] 
+1 0 0 0 108.173 3.21778 0.712238 7.06634 1.04273 
+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

@@ -0,0 +1,11 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+2
+ITEM: BOX BOUNDS pp pp pp
+0.0000000000000000e+00 3.3159999999999998e+00
+0.0000000000000000e+00 3.3159999999999998e+00
+0.0000000000000000e+00 3.3159999999999998e+00
+ITEM: ATOMS id c_b[1] c_b[2] c_b[3] c_b[4] c_b[5] 
+1 3375 846.026 36.811 8.51924 0.247118 
+2 3375 846.026 36.811 8.51924 0.247118 

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

@@ -0,0 +1,128 @@
+x, y, z = 0 0 0
+108.173 3.21778 0.712238 7.06634 1.04273 
+x, y, z = 1.658 0 0
+174.4 5.59324 1.35171 13.8088 2.13628 
+x, y, z = 0 0.829 0
+183.116 3.64679 1.14854 30.7642 7.26691 
+x, y, z = 1.658 0.829 0
+168.973 6.62458 1.46561 11.0631 1.61839 
+x, y, z = 0 1.658 0
+174.4 5.59324 1.35171 13.8088 2.13628 
+x, y, z = 1.658 1.658 0
+174.4 5.59324 1.35171 13.8088 2.13628 
+x, y, z = 0 2.487 0
+183.116 3.64679 1.14854 30.7642 7.26691 
+x, y, z = 1.658 2.487 0
+168.973 6.62458 1.46561 11.0631 1.61839 
+x, y, z = 0 0 0.4145
+189.401 2.43052 0.962196 44.4583 12.4353 
+x, y, z = 1.658 0 0.4145
+172.181 6.01397 1.39915 12.5923 1.90608 
+x, y, z = 0 0.829 0.4145
+180.705 4.08676 1.22596 27.1833 6.05503 
+x, y, z = 1.658 0.829 0.4145
+170.986 6.15471 1.45038 13.3359 2.10603 
+x, y, z = 0 1.658 0.4145
+172.181 6.01397 1.39915 12.5923 1.90608 
+x, y, z = 1.658 1.658 0.4145
+175.99 5.14283 1.33312 18.0104 3.26169 
+x, y, z = 0 2.487 0.4145
+180.705 4.08676 1.22596 27.1833 6.05503 
+x, y, z = 1.658 2.487 0.4145
+170.986 6.15471 1.45038 13.3359 2.10603 
+x, y, z = 0 0 0.829
+183.116 3.64679 1.14854 30.7642 7.26691 
+x, y, z = 1.658 0 0.829
+168.973 6.62458 1.46561 11.0631 1.61839 
+x, y, z = 0 0.829 0.829
+175.638 5.11301 1.3681 19.6169 3.72319 
+x, y, z = 1.658 0.829 0.829
+175.638 5.11301 1.3681 19.6169 3.72319 
+x, y, z = 0 1.658 0.829
+168.973 6.62458 1.46561 11.0631 1.61839 
+x, y, z = 1.658 1.658 0.829
+183.116 3.64679 1.14854 30.7642 7.26691 
+x, y, z = 0 2.487 0.829
+175.638 5.11301 1.3681 19.6169 3.72319 
+x, y, z = 1.658 2.487 0.829
+175.638 5.11301 1.3681 19.6169 3.72319 
+x, y, z = 0 0 1.2435
+175.99 5.14283 1.33312 18.0104 3.26169 
+x, y, z = 1.658 0 1.2435
+172.181 6.01397 1.39915 12.5923 1.90608 
+x, y, z = 0 0.829 1.2435
+170.986 6.15471 1.45038 13.3359 2.10603 
+x, y, z = 1.658 0.829 1.2435
+180.705 4.08676 1.22596 27.1833 6.05503 
+x, y, z = 0 1.658 1.2435
+172.181 6.01397 1.39915 12.5923 1.90608 
+x, y, z = 1.658 1.658 1.2435
+189.401 2.43052 0.962196 44.4583 12.4353 
+x, y, z = 0 2.487 1.2435
+170.986 6.15471 1.45038 13.3359 2.10603 
+x, y, z = 1.658 2.487 1.2435
+180.705 4.08676 1.22596 27.1833 6.05503 
+x, y, z = 0 0 1.658
+174.4 5.59324 1.35171 13.8088 2.13628 
+x, y, z = 1.658 0 1.658
+174.4 5.59324 1.35171 13.8088 2.13628 
+x, y, z = 0 0.829 1.658
+168.973 6.62458 1.46561 11.0631 1.61839 
+x, y, z = 1.658 0.829 1.658
+183.116 3.64679 1.14854 30.7642 7.26691 
+x, y, z = 0 1.658 1.658
+174.4 5.59324 1.35171 13.8088 2.13628 
+x, y, z = 1.658 1.658 1.658
+108.173 3.21778 0.712238 7.06634 1.04273 
+x, y, z = 0 2.487 1.658
+168.973 6.62458 1.46561 11.0631 1.61839 
+x, y, z = 1.658 2.487 1.658
+183.116 3.64679 1.14854 30.7642 7.26691 
+x, y, z = 0 0 2.0725
+175.99 5.14283 1.33312 18.0104 3.26169 
+x, y, z = 1.658 0 2.0725
+172.181 6.01397 1.39915 12.5923 1.90608 
+x, y, z = 0 0.829 2.0725
+170.986 6.15471 1.45038 13.3359 2.10603 
+x, y, z = 1.658 0.829 2.0725
+180.705 4.08676 1.22596 27.1833 6.05503 
+x, y, z = 0 1.658 2.0725
+172.181 6.01397 1.39915 12.5923 1.90608 
+x, y, z = 1.658 1.658 2.0725
+189.401 2.43052 0.962196 44.4583 12.4353 
+x, y, z = 0 2.487 2.0725
+170.986 6.15471 1.45038 13.3359 2.10603 
+x, y, z = 1.658 2.487 2.0725
+180.705 4.08676 1.22596 27.1833 6.05503 
+x, y, z = 0 0 2.487
+183.116 3.64679 1.14854 30.7642 7.26691 
+x, y, z = 1.658 0 2.487
+168.973 6.62458 1.46561 11.0631 1.61839 
+x, y, z = 0 0.829 2.487
+175.638 5.11301 1.3681 19.6169 3.72319 
+x, y, z = 1.658 0.829 2.487
+175.638 5.11301 1.3681 19.6169 3.72319 
+x, y, z = 0 1.658 2.487
+168.973 6.62458 1.46561 11.0631 1.61839 
+x, y, z = 1.658 1.658 2.487
+183.116 3.64679 1.14854 30.7642 7.26691 
+x, y, z = 0 2.487 2.487
+175.638 5.11301 1.3681 19.6169 3.72319 
+x, y, z = 1.658 2.487 2.487
+175.638 5.11301 1.3681 19.6169 3.72319 
+x, y, z = 0 0 2.9015
+189.401 2.43052 0.962196 44.4583 12.4353 
+x, y, z = 1.658 0 2.9015
+172.181 6.01397 1.39915 12.5923 1.90608 
+x, y, z = 0 0.829 2.9015
+180.705 4.08676 1.22596 27.1833 6.05503 
+x, y, z = 1.658 0.829 2.9015
+170.986 6.15471 1.45038 13.3359 2.10603 
+x, y, z = 0 1.658 2.9015
+172.181 6.01397 1.39915 12.5923 1.90608 
+x, y, z = 1.658 1.658 2.9015
+175.99 5.14283 1.33312 18.0104 3.26169 
+x, y, z = 0 2.487 2.9015
+180.705 4.08676 1.22596 27.1833 6.05503 
+x, y, z = 1.658 2.487 2.9015
+170.986 6.15471 1.45038 13.3359 2.10603