update log files for SNAP package examples to reflect current state of keywords.

examples/snap/log.20Apr18.snap.Mo_Chen.g++.1

@@ -0,0 +1,127 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.160
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary	p p p
+
+lattice         bcc $a
+lattice         bcc 3.16
+Lattice spacing in x,y,z = 3.16 3.16 3.16
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 4 0 ${ny} 0 ${nz}
+region		box block 0 4 0 4 0 ${nz}
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0 0 0) to (12.64 12.64 12.64)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 128 atoms
+  Time spent = 0.000223637 secs
+
+mass 1 183.84
+
+# choose potential
+
+include Mo_Chen_PRM2017.snap
+
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+# Definition of SNAP potential.
+pair_style snap
+pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
+Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
+SNAP Element = Mo, Radius 0.5, Weight 1 
+Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
+SNAP keyword rcutfac 4.615858 
+SNAP keyword twojmax 6 
+
+
+# Setup output
+
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.61586
+  ghost atom cutoff = 5.61586
+  binsize = 2.80793, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair snap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.507 | 3.507 | 3.507 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -22.405975            0     -22.3675    2575.7657 
+      10    294.77555   -22.405305            0     -22.3675    2756.6894 
+      20    279.53011    -22.40335            0     -22.3675    3285.8272 
+      30    255.52174    -22.40027            0     -22.3675    4122.8933 
+      40     224.7299   -22.396321            0   -22.367499    5204.3499 
+      50    189.67529   -22.391825            0   -22.367499    6449.1308 
+      60    153.18862   -22.387145            0   -22.367499     7765.911 
+      70    118.14998   -22.382652            0   -22.367499    9061.1616 
+      80    87.224916   -22.378685            0   -22.367499     10247.68 
+      90    62.623892    -22.37553            0   -22.367498    11250.067 
+     100      45.9103   -22.373386            0   -22.367498    12011.726 
+Loop time of 3.3917 on 1 procs for 100 steps with 128 atoms
+
+Performance: 1.274 ns/day, 18.843 hours/ns, 29.484 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.3906     | 3.3906     | 3.3906     |   0.0 | 99.97
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00039721 | 0.00039721 | 0.00039721 |   0.0 |  0.01
+Output  | 0.00023007 | 0.00023007 | 0.00023007 |   0.0 |  0.01
+Modify  | 0.00021887 | 0.00021887 | 0.00021887 |   0.0 |  0.01
+Other   |            | 0.0002868  |            |       |  0.01
+
+Nlocal:    128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    727 ave 727 max 727 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  7424 ave 7424 max 7424 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:03

examples/snap/log.20Apr18.snap.Mo_Chen.g++.4

@@ -0,0 +1,127 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.160
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary	p p p
+
+lattice         bcc $a
+lattice         bcc 3.16
+Lattice spacing in x,y,z = 3.16 3.16 3.16
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 4 0 ${ny} 0 ${nz}
+region		box block 0 4 0 4 0 ${nz}
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0 0 0) to (12.64 12.64 12.64)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 128 atoms
+  Time spent = 0.000277281 secs
+
+mass 1 183.84
+
+# choose potential
+
+include Mo_Chen_PRM2017.snap
+
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+# Definition of SNAP potential.
+pair_style snap
+pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
+Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
+SNAP Element = Mo, Radius 0.5, Weight 1 
+Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
+SNAP keyword rcutfac 4.615858 
+SNAP keyword twojmax 6 
+
+
+# Setup output
+
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.61586
+  ghost atom cutoff = 5.61586
+  binsize = 2.80793, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair snap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.486 | 3.486 | 3.486 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -22.405975            0     -22.3675    2575.7657 
+      10    294.63153   -22.405286            0     -22.3675    2753.4662 
+      20    278.98535    -22.40328            0     -22.3675     3272.416 
+      30    254.38916   -22.400125            0     -22.3675    4091.8933 
+      40    222.91191   -22.396088            0   -22.367499    5148.5505 
+      50    187.16984   -22.391504            0   -22.367499    6362.2454 
+      60    150.08253   -22.386747            0   -22.367499    7643.2732 
+      70    114.60307   -22.382197            0   -22.367499    8900.2448 
+      80    83.449257   -22.378201            0   -22.367499    10047.619 
+      90    58.862643   -22.375048            0   -22.367498    11012.233 
+     100     42.41931   -22.372939            0   -22.367498    11740.641 
+Loop time of 1.91636 on 4 procs for 100 steps with 128 atoms
+
+Performance: 2.254 ns/day, 10.646 hours/ns, 52.182 timesteps/s
+97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.8147     | 1.8411     | 1.8875     |   2.1 | 96.07
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.022276   | 0.069629   | 0.095057   |  10.7 |  3.63
+Output  | 0.00032496 | 0.00065821 | 0.0016179  |   0.0 |  0.03
+Modify  | 0.00019503 | 0.00020915 | 0.00023341 |   0.0 |  0.01
+Other   |            | 0.00481    |            |       |  0.25
+
+Nlocal:    32 ave 32 max 32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    431 ave 431 max 431 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1856 ave 1856 max 1856 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:01

examples/snap/log.20Apr18.snap.Ta06A.g++.1

@@ -1,4 +1,6 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
 # Demonstrate SNAP Ta potential
 
 # Initialize simulation
@@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
   1 by 1 by 1 MPI processor grid
 create_atoms	1 box
 Created 128 atoms
+  Time spent = 0.000328064 secs
 
 mass 1 180.88
 
 # choose potential
 
-include Ta06A_pot.snap
+include Ta06A.snap
 # DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
 
 # Definition of SNAP potential Ta_Cand06A
@@ -48,10 +51,9 @@ variable zblz equal 73
 
 # Specify hybrid with SNAP, ZBL
 
-pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter}
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
-pair_style hybrid/overlay snap zbl 4 ${zblcutouter}
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
-pair_style hybrid/overlay snap zbl 4 4.8
+pair_style hybrid/overlay zbl 4 4.8 snap
-
 pair_coeff 1 1 zbl ${zblz} ${zblz}
 pair_coeff 1 1 zbl 73 ${zblz}
 pair_coeff 1 1 zbl 73 73
@@ -61,10 +63,11 @@ SNAP Element = Ta, Radius 0.5, Weight 1
 Reading potential file Ta06A.snapparam with DATE: 2014-09-05
 SNAP keyword rcutfac 4.67637 
 SNAP keyword twojmax 6 
-SNAP keyword gamma 1 
 SNAP keyword rfac0 0.99363 
 SNAP keyword rmin0 0 
 SNAP keyword diagonalstyle 3 
+SNAP keyword bzeroflag 0 
+SNAP keyword quadraticflag 0 
 
 
 # Setup output
@@ -85,13 +88,23 @@ fix 1 all nve
 run             ${nsteps}
 run             100
 Neighbor list info ...
-  2 neighbor list requests
   update every 1 steps, delay 0 steps, check yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 5.8
   ghost atom cutoff = 5.8
-  binsize = 2.9 -> bins = 5 5 5
+  binsize = 2.9, bins = 5 5 5
-Memory usage per processor = 2.92823 Mbytes
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair snap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.138 | 4.138 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300    -11.85157            0   -11.813095    2717.1661 
       10    295.96579   -11.851053            0   -11.813095    2696.1559 
@@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press
       80    124.04276   -11.829003            0   -11.813094     1537.703 
       90     97.37622   -11.825582            0   -11.813094    1734.9662 
      100    75.007873   -11.822714            0   -11.813094    1930.8005 
-Loop time of 3.43062 on 1 procs for 100 steps with 128 atoms
+Loop time of 2.53266 on 1 procs for 100 steps with 128 atoms
 
-Performance: 1.259 ns/day, 19.059 hours/ns, 29.149 timesteps/s
+Performance: 1.706 ns/day, 14.070 hours/ns, 39.484 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 3.4295     | 3.4295     | 3.4295     |   0.0 | 99.97
+Pair    | 2.5313     | 2.5313     | 2.5313     |   0.0 | 99.95
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00043988 | 0.00043988 | 0.00043988 |   0.0 |  0.01
+Comm    | 0.00051379 | 0.00051379 | 0.00051379 |   0.0 |  0.02
-Output  | 0.00010014 | 0.00010014 | 0.00010014 |   0.0 |  0.00
+Output  | 0.00023317 | 0.00023317 | 0.00023317 |   0.0 |  0.01
-Modify  | 0.00024533 | 0.00024533 | 0.00024533 |   0.0 |  0.01
+Modify  | 0.00023675 | 0.00023675 | 0.00023675 |   0.0 |  0.01
-Other   |            | 0.0002978  |            |       |  0.01
+Other   |            | 0.0003583  |            |       |  0.01
 
 Nlocal:    128 ave 128 max 128 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -133,4 +146,4 @@ Ave neighs/atom = 58
 Neighbor list builds = 0
 Dangerous builds = 0
 
-Total wall time: 0:00:03
+Total wall time: 0:00:02

examples/snap/log.20Apr18.snap.Ta06A.g++.4

@@ -1,4 +1,6 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
 # Demonstrate SNAP Ta potential
 
 # Initialize simulation
@@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
   1 by 2 by 2 MPI processor grid
 create_atoms	1 box
 Created 128 atoms
+  Time spent = 0.000288486 secs
 
 mass 1 180.88
 
 # choose potential
 
-include Ta06A_pot.snap
+include Ta06A.snap
 # DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
 
 # Definition of SNAP potential Ta_Cand06A
@@ -48,10 +51,9 @@ variable zblz equal 73
 
 # Specify hybrid with SNAP, ZBL
 
-pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter}
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
-pair_style hybrid/overlay snap zbl 4 ${zblcutouter}
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
-pair_style hybrid/overlay snap zbl 4 4.8
+pair_style hybrid/overlay zbl 4 4.8 snap
-
 pair_coeff 1 1 zbl ${zblz} ${zblz}
 pair_coeff 1 1 zbl 73 ${zblz}
 pair_coeff 1 1 zbl 73 73
@@ -61,10 +63,11 @@ SNAP Element = Ta, Radius 0.5, Weight 1
 Reading potential file Ta06A.snapparam with DATE: 2014-09-05
 SNAP keyword rcutfac 4.67637 
 SNAP keyword twojmax 6 
-SNAP keyword gamma 1 
 SNAP keyword rfac0 0.99363 
 SNAP keyword rmin0 0 
 SNAP keyword diagonalstyle 3 
+SNAP keyword bzeroflag 0 
+SNAP keyword quadraticflag 0 
 
 
 # Setup output
@@ -85,13 +88,23 @@ fix 1 all nve
 run             ${nsteps}
 run             100
 Neighbor list info ...
-  2 neighbor list requests
   update every 1 steps, delay 0 steps, check yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 5.8
   ghost atom cutoff = 5.8
-  binsize = 2.9 -> bins = 5 5 5
+  binsize = 2.9, bins = 5 5 5
-Memory usage per processor = 2.91109 Mbytes
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair snap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.118 | 4.118 | 4.118 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300    -11.85157            0   -11.813095    2717.1661 
       10     295.8664    -11.85104            0   -11.813095     2702.935 
@@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press
       80    121.80051   -11.828715            0   -11.813094    1627.6911 
       90    95.262635   -11.825311            0   -11.813094    1812.9327 
      100    73.194645   -11.822481            0   -11.813094    1995.2199 
-Loop time of 0.89193 on 4 procs for 100 steps with 128 atoms
+Loop time of 1.3621 on 4 procs for 100 steps with 128 atoms
 
-Performance: 4.843 ns/day, 4.955 hours/ns, 112.116 timesteps/s
+Performance: 3.172 ns/day, 7.567 hours/ns, 73.416 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.84444    | 0.86772    | 0.88108    |   1.6 | 97.29
+Pair    | 1.2867     | 1.309      | 1.35       |   2.1 | 96.10
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.009577   | 0.023049   | 0.046417   |   9.8 |  2.58
+Comm    | 0.0096083  | 0.050652   | 0.072999   |  10.9 |  3.72
-Output  | 0.00024009 | 0.00026137 | 0.00027895 |   0.1 |  0.03
+Output  | 0.00031447 | 0.00060236 | 0.0014303  |   0.0 |  0.04
-Modify  | 8.2493e-05 | 9.352e-05  | 0.00010061 |   0.1 |  0.01
+Modify  | 0.00014234 | 0.00016212 | 0.00018811 |   0.0 |  0.01
-Other   |            | 0.0008071  |            |       |  0.09
+Other   |            | 0.001728   |            |       |  0.13
 
 Nlocal:    32 ave 32 max 32 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -133,4 +146,4 @@ Ave neighs/atom = 58
 Neighbor list builds = 0
 Dangerous builds = 0
 
-Total wall time: 0:00:00
+Total wall time: 0:00:01

examples/snap/log.20Apr18.snap.W.2940.g++.1

@@ -1,4 +1,6 @@
-LAMMPS (13 Feb 2017)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
 # Demonstrate SNAP Ta potential
 
 # Initialize simulation
@@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
   1 by 1 by 1 MPI processor grid
 create_atoms	1 box
 Created 128 atoms
+  Time spent = 0.000190258 secs
 
 mass 1 183.84
 
 # choose potential
 
-include W_2940_2017_2.pot.snap
+include W_2940_2017_2.snap
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 #
 # Definition of SNAP+ZBL potential.
 variable zblcutinner equal 4
 variable zblcutouter equal 4.8
 variable zblz equal 74
 
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
 
 pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
 pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
@@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1
 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
 SNAP keyword rcutfac 4.73442 
 SNAP keyword twojmax 8 
-SNAP keyword gamma 1 
 SNAP keyword rfac0 0.99363 
 SNAP keyword rmin0 0 
 SNAP keyword diagonalstyle 3 
+SNAP keyword bzeroflag 0 
+SNAP keyword quadraticflag 0 
 
 #Nomenclature on the snap files are Element_DakotaID_Year_Month
 
@@ -99,7 +103,7 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Memory usage per processor = 5.14696 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 5.15 | 5.15 | 5.15 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300   -11.028325            0    -10.98985     3010.497 
       10    293.40666   -11.027479            0   -10.989849    3246.0559 
@@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press
       80    58.605244   -10.997364            0   -10.989848    11289.914 
       90    39.754503   -10.994946            0   -10.989848    11824.945 
      100    32.524085   -10.994019            0   -10.989848    11932.118 
-Loop time of 11.8271 on 1 procs for 100 steps with 128 atoms
+Loop time of 9.69738 on 1 procs for 100 steps with 128 atoms
 
-Performance: 0.365 ns/day, 65.706 hours/ns, 8.455 timesteps/s
+Performance: 0.445 ns/day, 53.874 hours/ns, 10.312 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 11.826     | 11.826     | 11.826     |   0.0 | 99.99
+Pair    | 9.6961     | 9.6961     | 9.6961     |   0.0 | 99.99
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00044084 | 0.00044084 | 0.00044084 |   0.0 |  0.00
+Comm    | 0.00044036 | 0.00044036 | 0.00044036 |   0.0 |  0.00
-Output  | 0.00013232 | 0.00013232 | 0.00013232 |   0.0 |  0.00
+Output  | 0.00024843 | 0.00024843 | 0.00024843 |   0.0 |  0.00
-Modify  | 0.00021887 | 0.00021887 | 0.00021887 |   0.0 |  0.00
+Modify  | 0.00023937 | 0.00023937 | 0.00023937 |   0.0 |  0.00
-Other   |            | 0.0002718  |            |       |  0.00
+Other   |            | 0.0003347  |            |       |  0.00
 
 Nlocal:    128 ave 128 max 128 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -141,4 +145,4 @@ Ave neighs/atom = 58
 Neighbor list builds = 0
 Dangerous builds = 0
 
-Total wall time: 0:00:11
+Total wall time: 0:00:09

examples/snap/log.20Apr18.snap.W.2940.g++.4

@@ -1,4 +1,6 @@
-LAMMPS (13 Feb 2017)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
 # Demonstrate SNAP Ta potential
 
 # Initialize simulation
@@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
   1 by 2 by 2 MPI processor grid
 create_atoms	1 box
 Created 128 atoms
+  Time spent = 0.000309944 secs
 
 mass 1 183.84
 
 # choose potential
 
-include W_2940_2017_2.pot.snap
+include W_2940_2017_2.snap
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 #
 # Definition of SNAP+ZBL potential.
 variable zblcutinner equal 4
 variable zblcutouter equal 4.8
 variable zblz equal 74
 
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
 
 pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
 pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
@@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1
 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
 SNAP keyword rcutfac 4.73442 
 SNAP keyword twojmax 8 
-SNAP keyword gamma 1 
 SNAP keyword rfac0 0.99363 
 SNAP keyword rmin0 0 
 SNAP keyword diagonalstyle 3 
+SNAP keyword bzeroflag 0 
+SNAP keyword quadraticflag 0 
 
 #Nomenclature on the snap files are Element_DakotaID_Year_Month
 
@@ -99,7 +103,7 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Memory usage per processor = 5.12833 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 5.13 | 5.13 | 5.13 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300   -11.028325            0    -10.98985     3010.497 
       10    293.22504   -11.027456            0   -10.989849     3258.275 
@@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press
       80    56.127265   -10.997046            0   -10.989848    11551.687 
       90    38.025013   -10.994724            0   -10.989847    12069.936 
      100    31.768127   -10.993922            0   -10.989847    12145.648 
-Loop time of 3.03545 on 4 procs for 100 steps with 128 atoms
+Loop time of 5.15615 on 4 procs for 100 steps with 128 atoms
 
-Performance: 1.423 ns/day, 16.864 hours/ns, 32.944 timesteps/s
+Performance: 0.838 ns/day, 28.645 hours/ns, 19.394 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.9594     | 2.9866     | 3.0319     |   1.6 | 98.39
+Pair    | 5.0497     | 5.0762     | 5.092      |   0.8 | 98.45
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.0024238  | 0.047825   | 0.075032   |  12.5 |  1.58
+Comm    | 0.060802   | 0.07661    | 0.10305    |   6.1 |  1.49
-Output  | 0.00021601 | 0.00024045 | 0.00027442 |   0.0 |  0.01
+Output  | 0.00040722 | 0.00078458 | 0.0018959  |   0.0 |  0.02
-Modify  | 9.6798e-05 | 0.00011188 | 0.00011802 |   0.0 |  0.00
+Modify  | 0.0002389  | 0.00024962 | 0.00027442 |   0.0 |  0.00
-Other   |            | 0.000698   |            |       |  0.02
+Other   |            | 0.002315   |            |       |  0.04
 
 Nlocal:    32 ave 32 max 32 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -141,4 +145,4 @@ Ave neighs/atom = 58
 Neighbor list builds = 0
 Dangerous builds = 0
 
-Total wall time: 0:00:03
+Total wall time: 0:00:05

examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1

@@ -1,4 +1,6 @@
-LAMMPS (13 Feb 2017)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
 # Demonstrate SNAP Ta potential
 
 # Initialize simulation
@@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
   1 by 1 by 1 MPI processor grid
 create_atoms	1 box
 Created 128 atoms
+  Time spent = 0.000431538 secs
 mass 1 183.84
 mass 2 4.0026
 
@@ -42,15 +45,15 @@ group	helium	type 2
 5 atoms in group helium
 # choose potential
 
-include W.SNAP_HePair.pot
+include W_2940_2017_2_He_JW2013.snap
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 #
 # Definition of SNAP+ZBL+Tabulated potential.
 variable zblcutinner equal 4
 variable zblcutouter equal 4.8
 variable zblz equal 74
 
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
 
 pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
 pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
@@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1
 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
 SNAP keyword rcutfac 4.73442 
 SNAP keyword twojmax 8 
-SNAP keyword gamma 1 
 SNAP keyword rfac0 0.99363 
 SNAP keyword rmin0 0 
 SNAP keyword diagonalstyle 3 
+SNAP keyword bzeroflag 0 
+SNAP keyword quadraticflag 0 
 pair_coeff      2 2 table 1 He_He_JW2013.table HeHe
 Reading potential file He_He_JW2013.table with DATE: 2017-02-20
 WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:476)
+  Should only be flagged at inflection points (../pair_table.cpp:481)
 pair_coeff      1 2 table 2 W_He_JW2013.table WHe
 Reading potential file W_He_JW2013.table with DATE: 2017-02-20
 WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:476)
+  Should only be flagged at inflection points (../pair_table.cpp:481)
 #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
 #This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
 
@@ -134,7 +138,7 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Memory usage per processor = 7.6729 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.676 | 7.676 | 7.676 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300   -10.438105            0    -10.39963   -5445.2808 
       10    290.48923   -10.436885            0   -10.399629   -5646.4813 
@@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press
       80    85.903126   -10.410645            0   -10.399628    857.74986 
       90    65.223651   -10.407993            0   -10.399628    1494.2746 
      100    59.833542   -10.407302            0   -10.399628    1938.9164 
-Loop time of 11.0736 on 1 procs for 100 steps with 128 atoms
+Loop time of 8.902 on 1 procs for 100 steps with 128 atoms
 
-Performance: 0.390 ns/day, 61.520 hours/ns, 9.030 timesteps/s
+Performance: 0.485 ns/day, 49.456 hours/ns, 11.233 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 11.072     | 11.072     | 11.072     |   0.0 | 99.99
+Pair    | 8.9002     | 8.9002     | 8.9002     |   0.0 | 99.98
-Neigh   | 0.00041604 | 0.00041604 | 0.00041604 |   0.0 |  0.00
+Neigh   | 0.00043058 | 0.00043058 | 0.00043058 |   0.0 |  0.00
-Comm    | 0.00046253 | 0.00046253 | 0.00046253 |   0.0 |  0.00
+Comm    | 0.00045776 | 0.00045776 | 0.00045776 |   0.0 |  0.01
-Output  | 0.0001657  | 0.0001657  | 0.0001657  |   0.0 |  0.00
+Output  | 0.00025344 | 0.00025344 | 0.00025344 |   0.0 |  0.00
-Modify  | 0.0002265  | 0.0002265  | 0.0002265  |   0.0 |  0.00
+Modify  | 0.00022483 | 0.00022483 | 0.00022483 |   0.0 |  0.00
-Other   |            | 0.0003119  |            |       |  0.00
+Other   |            | 0.0003953  |            |       |  0.00
 
 Nlocal:    128 ave 128 max 128 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156
 Neighbor list builds = 1
 Dangerous builds = 0
 
-Total wall time: 0:00:11
+Total wall time: 0:00:09

examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4

@@ -1,4 +1,6 @@
-LAMMPS (13 Feb 2017)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
 # Demonstrate SNAP Ta potential
 
 # Initialize simulation
@@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
   1 by 2 by 2 MPI processor grid
 create_atoms	1 box
 Created 128 atoms
+  Time spent = 0.000274658 secs
 mass 1 183.84
 mass 2 4.0026
 
@@ -42,15 +45,15 @@ group	helium	type 2
 5 atoms in group helium
 # choose potential
 
-include W.SNAP_HePair.pot
+include W_2940_2017_2_He_JW2013.snap
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 #
 # Definition of SNAP+ZBL+Tabulated potential.
 variable zblcutinner equal 4
 variable zblcutouter equal 4.8
 variable zblz equal 74
 
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
 
 pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
 pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
@@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1
 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
 SNAP keyword rcutfac 4.73442 
 SNAP keyword twojmax 8 
-SNAP keyword gamma 1 
 SNAP keyword rfac0 0.99363 
 SNAP keyword rmin0 0 
 SNAP keyword diagonalstyle 3 
+SNAP keyword bzeroflag 0 
+SNAP keyword quadraticflag 0 
 pair_coeff      2 2 table 1 He_He_JW2013.table HeHe
 Reading potential file He_He_JW2013.table with DATE: 2017-02-20
 WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:476)
+  Should only be flagged at inflection points (../pair_table.cpp:481)
 pair_coeff      1 2 table 2 W_He_JW2013.table WHe
 Reading potential file W_He_JW2013.table with DATE: 2017-02-20
 WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:476)
+  Should only be flagged at inflection points (../pair_table.cpp:481)
 #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
 #This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
 
@@ -134,7 +138,7 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Memory usage per processor = 7.65426 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.656 | 7.656 | 7.656 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300   -10.438105            0    -10.39963   -5445.2808 
       10    292.13979   -10.437097            0    -10.39963   -5516.3963 
@@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press
       80    79.985938   -10.409886            0   -10.399628    2392.1106 
       90    62.568933   -10.407652            0   -10.399628    3141.7027 
      100    56.697933   -10.406899            0   -10.399628    3583.9538 
-Loop time of 2.8757 on 4 procs for 100 steps with 128 atoms
+Loop time of 4.82103 on 4 procs for 100 steps with 128 atoms
 
-Performance: 1.502 ns/day, 15.976 hours/ns, 34.774 timesteps/s
+Performance: 0.896 ns/day, 26.783 hours/ns, 20.742 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.7363     | 2.8122     | 2.8636     |   2.9 | 97.79
+Pair    | 4.4837     | 4.6734     | 4.7605     |   5.2 | 96.94
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.011014   | 0.062439   | 0.13842    |  19.3 |  2.17
+Comm    | 0.057389   | 0.14453    | 0.33421    |  29.4 |  3.00
-Output  | 0.00023842 | 0.00025076 | 0.0002861  |   0.0 |  0.01
+Output  | 0.00038719 | 0.00073916 | 0.0017841  |   0.0 |  0.02
-Modify  | 9.2506e-05 | 9.9301e-05 | 0.00010395 |   0.0 |  0.00
+Modify  | 0.00018716 | 0.00022203 | 0.00026417 |   0.0 |  0.00
-Other   |            | 0.0006654  |            |       |  0.02
+Other   |            | 0.002119   |            |       |  0.04
 
 Nlocal:    32 ave 32 max 32 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156
 Neighbor list builds = 0
 Dangerous builds = 0
 
-Total wall time: 0:00:02
+Total wall time: 0:00:04