diff --git a/examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.1 b/examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.1 new file mode 100644 index 0000000000..45e0df251d --- /dev/null +++ b/examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.1 @@ -0,0 +1,155 @@ +LAMMPS (2 Jun 2020) +# Demonstrate SNAP InP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 5.83 +units metal + +# generate the box and atom positions using a FCC 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 diamond $a +lattice diamond 5.83 +Lattice spacing in x,y,z = 5.83 5.83 5.83 +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 2 box +Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 +Created 512 atoms + create_atoms CPU = 0.000 seconds + +mass 1 114.76 +mass 2 30.98 + +# choose potential + +include InP_JCPA2020.snap +# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020) + +# Definition of SNAP+ZBL potential. + +variable zblcutinner equal 4 +variable zblcutouter equal 4.2 +variable zblz1 equal 49 +variable zblz2 equal 15 + +# Specify hybrid with SNAP and ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 4.2 snap +pair_coeff 1 1 zbl ${zblz1} ${zblz1} +pair_coeff 1 1 zbl 49 ${zblz1} +pair_coeff 1 1 zbl 49 49 +pair_coeff 1 2 zbl ${zblz1} ${zblz2} +pair_coeff 1 2 zbl 49 ${zblz2} +pair_coeff 1 2 zbl 49 15 +pair_coeff 2 2 zbl ${zblz2} ${zblz2} +pair_coeff 2 2 zbl 15 ${zblz2} +pair_coeff 2 2 zbl 15 15 +pair_coeff * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In P +Reading potential file InP_JCPA2020.snapcoeff with DATE: 2020-06-01 +SNAP Element = In, Radius 3.81205, Weight 1 +SNAP Element = P, Radius 3.82945, Weight 0.929316 +Reading potential file InP_JCPA2020.snapparam with DATE: 2020-06-01 +SNAP keyword rcutfac 1.0 +SNAP keyword twojmax 6 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0.0 +SNAP keyword bzeroflag 1 +SNAP keyword quadraticflag 0 +SNAP keyword wselfallflag 1 +SNAP keyword alloyflag 1 + +# 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 = 8.6589 + ghost atom cutoff = 8.6589 + binsize = 4.32945, bins = 6 6 6 + 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) = 6.027 | 6.027 | 6.027 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -3.4805794 0 -3.4418771 1353.5968 + 10 286.42264 -3.4788274 0 -3.4418767 1586.4881 + 20 250.14148 -3.4741459 0 -3.4418757 2219.0344 + 30 202.52417 -3.4680017 0 -3.4418745 2982.7272 + 40 157.39113 -3.4621782 0 -3.4418735 3631.0936 + 50 126.7004 -3.4582183 0 -3.441873 4053.7725 + 60 117.00722 -3.4569679 0 -3.441873 4204.9542 + 70 127.65968 -3.4583427 0 -3.4418736 4106.3112 + 80 151.50217 -3.4614195 0 -3.4418745 3840.7205 + 90 177.67607 -3.464797 0 -3.4418754 3527.9794 + 100 195.30359 -3.4670717 0 -3.4418761 3300.3795 +Loop time of 18.1983 on 1 procs for 100 steps with 512 atoms + +Performance: 0.237 ns/day, 101.102 hours/ns, 5.495 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 18.196 | 18.196 | 18.196 | 0.0 | 99.99 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00104 | 0.00104 | 0.00104 | 0.0 | 0.01 +Output | 0.000262 | 0.000262 | 0.000262 | 0.0 | 0.00 +Modify | 0.000576 | 0.000576 | 0.000576 | 0.0 | 0.00 +Other | | 0.000486 | | | 0.00 + +Nlocal: 512 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1959 ave 1959 max 1959 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 31232 ave 31232 max 31232 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 62464 ave 62464 max 62464 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 62464 +Ave neighs/atom = 122 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:18 diff --git a/examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.4 b/examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.4 new file mode 100644 index 0000000000..613ef679f5 --- /dev/null +++ b/examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.4 @@ -0,0 +1,155 @@ +LAMMPS (2 Jun 2020) +# Demonstrate SNAP InP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 5.83 +units metal + +# generate the box and atom positions using a FCC 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 diamond $a +lattice diamond 5.83 +Lattice spacing in x,y,z = 5.83 5.83 5.83 +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 2 box +Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 +Created 512 atoms + create_atoms CPU = 0.001 seconds + +mass 1 114.76 +mass 2 30.98 + +# choose potential + +include InP_JCPA2020.snap +# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020) + +# Definition of SNAP+ZBL potential. + +variable zblcutinner equal 4 +variable zblcutouter equal 4.2 +variable zblz1 equal 49 +variable zblz2 equal 15 + +# Specify hybrid with SNAP and ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 4.2 snap +pair_coeff 1 1 zbl ${zblz1} ${zblz1} +pair_coeff 1 1 zbl 49 ${zblz1} +pair_coeff 1 1 zbl 49 49 +pair_coeff 1 2 zbl ${zblz1} ${zblz2} +pair_coeff 1 2 zbl 49 ${zblz2} +pair_coeff 1 2 zbl 49 15 +pair_coeff 2 2 zbl ${zblz2} ${zblz2} +pair_coeff 2 2 zbl 15 ${zblz2} +pair_coeff 2 2 zbl 15 15 +pair_coeff * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In P +Reading potential file InP_JCPA2020.snapcoeff with DATE: 2020-06-01 +SNAP Element = In, Radius 3.81205, Weight 1 +SNAP Element = P, Radius 3.82945, Weight 0.929316 +Reading potential file InP_JCPA2020.snapparam with DATE: 2020-06-01 +SNAP keyword rcutfac 1.0 +SNAP keyword twojmax 6 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0.0 +SNAP keyword bzeroflag 1 +SNAP keyword quadraticflag 0 +SNAP keyword wselfallflag 1 +SNAP keyword alloyflag 1 + +# 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 = 8.6589 + ghost atom cutoff = 8.6589 + binsize = 4.32945, bins = 6 6 6 + 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) = 4.587 | 4.587 | 4.587 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -3.4805794 0 -3.4418771 1353.5968 + 10 286.58246 -3.478848 0 -3.4418767 1582.995 + 20 250.70996 -3.4742192 0 -3.4418757 2207.7507 + 30 203.58199 -3.4681382 0 -3.4418746 2968.5206 + 40 158.84622 -3.462366 0 -3.4418736 3619.0285 + 50 128.30488 -3.4584254 0 -3.4418731 4047.173 + 60 118.40349 -3.4571481 0 -3.4418731 4203.3421 + 70 128.48973 -3.4584499 0 -3.4418737 4109.0296 + 80 151.54241 -3.4614247 0 -3.4418746 3847.4617 + 90 176.92084 -3.4646996 0 -3.4418755 3548.7811 + 100 193.9555 -3.4668978 0 -3.4418761 3342.8083 +Loop time of 5.73708 on 4 procs for 100 steps with 512 atoms + +Performance: 0.753 ns/day, 31.873 hours/ns, 17.430 timesteps/s +99.3% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.5736 | 5.5812 | 5.591 | 0.3 | 97.28 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.14432 | 0.15366 | 0.16168 | 1.6 | 2.68 +Output | 0.000187 | 0.00024775 | 0.000419 | 0.0 | 0.00 +Modify | 0.000293 | 0.00038075 | 0.000582 | 0.0 | 0.01 +Other | | 0.00161 | | | 0.03 + +Nlocal: 128 ave 128 max 128 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1099 ave 1099 max 1099 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 7808 ave 7808 max 7808 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 15616 ave 15616 max 15616 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 62464 +Ave neighs/atom = 122 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:05