diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 new file mode 100644 index 0000000000..c5e0f6abab --- /dev/null +++ b/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 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 diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 new file mode 100644 index 0000000000..c25f1f5530 --- /dev/null +++ b/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 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 diff --git a/examples/snap/log.5Oct16.snap.Ta06A.g++.1 b/examples/snap/log.20Apr18.snap.Ta06A.g++.1 similarity index 71% rename from examples/snap/log.5Oct16.snap.Ta06A.g++.1 rename to examples/snap/log.20Apr18.snap.Ta06A.g++.1 index 647ffac8b4..d2296852a0 100644 --- a/examples/snap/log.5Oct16.snap.Ta06A.g++.1 +++ b/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 snap zbl 4 ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 4.8 - +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 ${zblcutouter} snap +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 -Memory usage per processor = 2.92823 Mbytes + binsize = 2.9, bins = 5 5 5 + 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 -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.706 ns/day, 14.070 hours/ns, 39.484 timesteps/s +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 -Output | 0.00010014 | 0.00010014 | 0.00010014 | 0.0 | 0.00 -Modify | 0.00024533 | 0.00024533 | 0.00024533 | 0.0 | 0.01 -Other | | 0.0002978 | | | 0.01 +Comm | 0.00051379 | 0.00051379 | 0.00051379 | 0.0 | 0.02 +Output | 0.00023317 | 0.00023317 | 0.00023317 | 0.0 | 0.01 +Modify | 0.00023675 | 0.00023675 | 0.00023675 | 0.0 | 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 diff --git a/examples/snap/log.5Oct16.snap.Ta06A.g++.4 b/examples/snap/log.20Apr18.snap.Ta06A.g++.4 similarity index 71% rename from examples/snap/log.5Oct16.snap.Ta06A.g++.4 rename to examples/snap/log.20Apr18.snap.Ta06A.g++.4 index 19d64c557c..4d26481d5d 100644 --- a/examples/snap/log.5Oct16.snap.Ta06A.g++.4 +++ b/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 snap zbl 4 ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 4.8 - +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 ${zblcutouter} snap +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 -Memory usage per processor = 2.91109 Mbytes + binsize = 2.9, bins = 5 5 5 + 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 -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3.172 ns/day, 7.567 hours/ns, 73.416 timesteps/s +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 -Output | 0.00024009 | 0.00026137 | 0.00027895 | 0.1 | 0.03 -Modify | 8.2493e-05 | 9.352e-05 | 0.00010061 | 0.1 | 0.01 -Other | | 0.0008071 | | | 0.09 +Comm | 0.0096083 | 0.050652 | 0.072999 | 10.9 | 3.72 +Output | 0.00031447 | 0.00060236 | 0.0014303 | 0.0 | 0.04 +Modify | 0.00014234 | 0.00016212 | 0.00018811 | 0.0 | 0.01 +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 diff --git a/examples/snap/log.21Feb17.snap.W.2940.g++.1 b/examples/snap/log.20Apr18.snap.W.2940.g++.1 similarity index 79% rename from examples/snap/log.21Feb17.snap.W.2940.g++.1 rename to examples/snap/log.20Apr18.snap.W.2940.g++.1 index 8c74380b8b..19b2bfb40d 100644 --- a/examples/snap/log.21Feb17.snap.W.2940.g++.1 +++ b/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 -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +include W_2940_2017_2.snap +# 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 -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.445 ns/day, 53.874 hours/ns, 10.312 timesteps/s +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 -Output | 0.00013232 | 0.00013232 | 0.00013232 | 0.0 | 0.00 -Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.00 -Other | | 0.0002718 | | | 0.00 +Comm | 0.00044036 | 0.00044036 | 0.00044036 | 0.0 | 0.00 +Output | 0.00024843 | 0.00024843 | 0.00024843 | 0.0 | 0.00 +Modify | 0.00023937 | 0.00023937 | 0.00023937 | 0.0 | 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 diff --git a/examples/snap/log.21Feb17.snap.W.2940.g++.4 b/examples/snap/log.20Apr18.snap.W.2940.g++.4 similarity index 79% rename from examples/snap/log.21Feb17.snap.W.2940.g++.4 rename to examples/snap/log.20Apr18.snap.W.2940.g++.4 index 97ed5cc8d1..dfa63fc6ea 100644 --- a/examples/snap/log.21Feb17.snap.W.2940.g++.4 +++ b/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 -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +include W_2940_2017_2.snap +# 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 -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.838 ns/day, 28.645 hours/ns, 19.394 timesteps/s +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 -Output | 0.00021601 | 0.00024045 | 0.00027442 | 0.0 | 0.01 -Modify | 9.6798e-05 | 0.00011188 | 0.00011802 | 0.0 | 0.00 -Other | | 0.000698 | | | 0.02 +Comm | 0.060802 | 0.07661 | 0.10305 | 6.1 | 1.49 +Output | 0.00040722 | 0.00078458 | 0.0018959 | 0.0 | 0.02 +Modify | 0.0002389 | 0.00024962 | 0.00027442 | 0.0 | 0.00 +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 diff --git a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 similarity index 83% rename from examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 rename to examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 index 846eef269c..3f40936308 100644 --- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 +++ b/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 -# 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 +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. "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 -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.485 ns/day, 49.456 hours/ns, 11.233 timesteps/s +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 -Neigh | 0.00041604 | 0.00041604 | 0.00041604 | 0.0 | 0.00 -Comm | 0.00046253 | 0.00046253 | 0.00046253 | 0.0 | 0.00 -Output | 0.0001657 | 0.0001657 | 0.0001657 | 0.0 | 0.00 -Modify | 0.0002265 | 0.0002265 | 0.0002265 | 0.0 | 0.00 -Other | | 0.0003119 | | | 0.00 +Pair | 8.9002 | 8.9002 | 8.9002 | 0.0 | 99.98 +Neigh | 0.00043058 | 0.00043058 | 0.00043058 | 0.0 | 0.00 +Comm | 0.00045776 | 0.00045776 | 0.00045776 | 0.0 | 0.01 +Output | 0.00025344 | 0.00025344 | 0.00025344 | 0.0 | 0.00 +Modify | 0.00022483 | 0.00022483 | 0.00022483 | 0.0 | 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 diff --git a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 similarity index 84% rename from examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 rename to examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 index 9bcbd288aa..4ec85a63d0 100644 --- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 +++ b/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 -# 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 +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. "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 -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.896 ns/day, 26.783 hours/ns, 20.742 timesteps/s +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 -Output | 0.00023842 | 0.00025076 | 0.0002861 | 0.0 | 0.01 -Modify | 9.2506e-05 | 9.9301e-05 | 0.00010395 | 0.0 | 0.00 -Other | | 0.0006654 | | | 0.02 +Comm | 0.057389 | 0.14453 | 0.33421 | 29.4 | 3.00 +Output | 0.00038719 | 0.00073916 | 0.0017841 | 0.0 | 0.02 +Modify | 0.00018716 | 0.00022203 | 0.00026417 | 0.0 | 0.00 +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