diff --git a/examples/mliap/in.mliap.so3.Ni_Mo b/examples/mliap/in.mliap.so3.Ni_Mo index 901600e156..34c900a972 100644 --- a/examples/mliap/in.mliap.so3.Ni_Mo +++ b/examples/mliap/in.mliap.so3.Ni_Mo @@ -23,7 +23,3 @@ velocity all create 300.0 4928459 loop geom fix 1 all nve run 3 -variable emin equal $e -variable EperAtom equal (${emin}/${N}) - -print "Total energy (eV/atom) = ${EperAtom} " diff --git a/examples/mliap/log.14Jun21.mliap.nn.Cu.g++.1 b/examples/mliap/log.14Jun21.mliap.nn.Cu.g++.1 new file mode 100644 index 0000000000..7e23163086 --- /dev/null +++ b/examples/mliap/log.14Jun21.mliap.nn.Cu.g++.1 @@ -0,0 +1,133 @@ +LAMMPS (27 May 2021) +# Demonstrate MLIAP interface to SNAP nn Cu potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.621262 +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 fcc $a +lattice fcc 3.621262 +Lattice spacing in x,y,z = 3.6212620 3.6212620 3.6212620 +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 = (0.0000000 0.0000000 0.0000000) to (14.485048 14.485048 14.485048) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 63.546 + +# choose potential + +pair_style mliap model nn Cu.nn.mliap.model descriptor sna Cu.snap.mliap.descriptor +Reading potential file Cu.nn.mliap.model with DATE: 2021-03-03 +Reading potential file Cu.snap.mliap.descriptor with DATE: 2021-03-03 +SNAP keyword rcutfac 5.0 +SNAP keyword twojmax 6 +SNAP keyword nelems 1 +SNAP keyword elems Cu +SNAP keyword radelems 0.5 +SNAP keyword welems 1.0 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0 +SNAP keyword bzeroflag 0 +SNAP keyword switchflag 1 +pair_coeff * * Cu + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +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 loop geom +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 = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 31.17 | 31.17 | 31.17 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 300 -4.0935581 -4.0935581 -4.0549315 -2916.7505 2916.7505 + 10 294.11049 -4.0927998 -4.0927998 -4.0549315 -2654.7826 2654.7826 + 20 276.89115 -4.0905826 -4.0905826 -4.0549314 -1879.2872 1879.2872 + 30 249.71134 -4.0870829 -4.0870829 -4.0549312 -627.47006 627.47006 + 40 214.92415 -4.0826036 -4.0826036 -4.054931 995.44801 -995.44801 + 50 175.86879 -4.0775747 -4.0775747 -4.0549307 2811.6019 -2811.6019 + 60 136.62706 -4.0725218 -4.0725218 -4.0549303 4640.4144 -4640.4144 + 70 101.48566 -4.0679968 -4.0679968 -4.05493 6313.5871 -6313.5871 + 80 74.248664 -4.0644897 -4.0644897 -4.0549298 7644.1364 -7644.1364 + 90 57.500423 -4.0623332 -4.0623332 -4.0549297 8514.2222 -8514.2222 + 100 52.104609 -4.0616385 -4.0616385 -4.0549298 8870.8923 -8870.8923 +Loop time of 4.77867 on 1 procs for 100 steps with 256 atoms + +Performance: 0.904 ns/day, 26.548 hours/ns, 20.926 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.7771 | 4.7771 | 4.7771 | 0.0 | 99.97 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00052619 | 0.00052619 | 0.00052619 | 0.0 | 0.01 +Output | 0.00054073 | 0.00054073 | 0.00054073 | 0.0 | 0.01 +Modify | 0.00021744 | 0.00021744 | 0.00021744 | 0.0 | 0.00 +Other | | 0.0002317 | | | 0.00 + +Nlocal: 256.000 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1431.00 ave 1431 max 1431 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 19968.0 ave 19968 max 19968 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19968 +Ave neighs/atom = 78.000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/mliap/log.14Jun21.mliap.nn.Cu.g++.4 b/examples/mliap/log.14Jun21.mliap.nn.Cu.g++.4 new file mode 100644 index 0000000000..6738ce3f75 --- /dev/null +++ b/examples/mliap/log.14Jun21.mliap.nn.Cu.g++.4 @@ -0,0 +1,133 @@ +LAMMPS (27 May 2021) +# Demonstrate MLIAP interface to SNAP nn Cu potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.621262 +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 fcc $a +lattice fcc 3.621262 +Lattice spacing in x,y,z = 3.6212620 3.6212620 3.6212620 +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 = (0.0000000 0.0000000 0.0000000) to (14.485048 14.485048 14.485048) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 63.546 + +# choose potential + +pair_style mliap model nn Cu.nn.mliap.model descriptor sna Cu.snap.mliap.descriptor +Reading potential file Cu.nn.mliap.model with DATE: 2021-03-03 +Reading potential file Cu.snap.mliap.descriptor with DATE: 2021-03-03 +SNAP keyword rcutfac 5.0 +SNAP keyword twojmax 6 +SNAP keyword nelems 1 +SNAP keyword elems Cu +SNAP keyword radelems 0.5 +SNAP keyword welems 1.0 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0 +SNAP keyword bzeroflag 0 +SNAP keyword switchflag 1 +pair_coeff * * Cu + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +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 loop geom +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 = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 30.85 | 30.85 | 30.85 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 300 -4.0935581 -4.0935581 -4.0549315 -2916.7505 2916.7505 + 10 294.11049 -4.0927998 -4.0927998 -4.0549315 -2654.7826 2654.7826 + 20 276.89115 -4.0905826 -4.0905826 -4.0549314 -1879.2872 1879.2872 + 30 249.71134 -4.0870829 -4.0870829 -4.0549312 -627.47006 627.47006 + 40 214.92415 -4.0826036 -4.0826036 -4.054931 995.44801 -995.44801 + 50 175.86879 -4.0775747 -4.0775747 -4.0549307 2811.6019 -2811.6019 + 60 136.62706 -4.0725218 -4.0725218 -4.0549303 4640.4144 -4640.4144 + 70 101.48566 -4.0679968 -4.0679968 -4.05493 6313.5871 -6313.5871 + 80 74.248664 -4.0644897 -4.0644897 -4.0549298 7644.1364 -7644.1364 + 90 57.500423 -4.0623332 -4.0623332 -4.0549297 8514.2222 -8514.2222 + 100 52.104609 -4.0616385 -4.0616385 -4.0549298 8870.8923 -8870.8923 +Loop time of 1.25021 on 4 procs for 100 steps with 256 atoms + +Performance: 3.455 ns/day, 6.946 hours/ns, 79.987 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2256 | 1.2347 | 1.2415 | 0.5 | 98.76 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0074687 | 0.014311 | 0.023481 | 4.8 | 1.14 +Output | 0.00060678 | 0.00062859 | 0.00066781 | 0.0 | 0.05 +Modify | 8.7976e-05 | 9.7811e-05 | 0.00010943 | 0.0 | 0.01 +Other | | 0.0004484 | | | 0.04 + +Nlocal: 64.0000 ave 64 max 64 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 843.000 ave 843 max 843 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 4992.00 ave 4992 max 4992 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19968 +Ave neighs/atom = 78.000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.1 b/examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.1 new file mode 100644 index 0000000000..088e00fced --- /dev/null +++ b/examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.1 @@ -0,0 +1,156 @@ +LAMMPS (27 May 2021) +# Demonstrate MLIAP interface to linear SNAP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +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 3.316 +Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000 +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 = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000 13.264000) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + +# choose potential + +include Ta06A.nn.mliap +# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) + +# Definition of SNAP potential Ta_Cand06A +# Assumes 1 LAMMPS atom type + +variable zblcutinner equal 4 +variable zblcutouter equal 4.8 +variable zblz equal 73 + +# Specify hybrid with SNAP, ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor +pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor +pair_style hybrid/overlay zbl 4 4.8 mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor +Reading potential file Ta06A.nn.mliap.model with DATE: 2021-03-03 +Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05 +SNAP keyword rcutfac 4.67637 +SNAP keyword twojmax 6 +SNAP keyword nelems 1 +SNAP keyword elems Ta +SNAP keyword radelems 0.5 +SNAP keyword welems 1 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0 +SNAP keyword bzeroflag 0 +pair_coeff 1 1 zbl ${zblz} ${zblz} +pair_coeff 1 1 zbl 73 ${zblz} +pair_coeff 1 1 zbl 73 73 +pair_coeff * * mliap Ta + + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +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 loop geom +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 = 5.8 + ghost atom cutoff = 5.8 + 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 mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 18.15 | 18.15 | 18.15 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661 + 10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796 + 20 284.53666 -11.849587 -11.849587 -11.813095 2289.1527 -2289.1527 + 30 266.51577 -11.847275 -11.847275 -11.813095 1851.7131 -1851.7131 + 40 243.05007 -11.844266 -11.844266 -11.813095 1570.684 -1570.684 + 50 215.51032 -11.840734 -11.840734 -11.813094 1468.1899 -1468.1899 + 60 185.48331 -11.836883 -11.836883 -11.813094 1524.8757 -1524.8757 + 70 154.6736 -11.832931 -11.832931 -11.813094 1698.3351 -1698.3351 + 80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715 + 90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563 + 100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526 +Loop time of 1.46158 on 1 procs for 100 steps with 128 atoms + +Performance: 2.956 ns/day, 8.120 hours/ns, 68.419 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.4607 | 1.4607 | 1.4607 | 0.0 | 99.94 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00028086 | 0.00028086 | 0.00028086 | 0.0 | 0.02 +Output | 0.00035334 | 0.00035334 | 0.00035334 | 0.0 | 0.02 +Modify | 0.00011992 | 0.00011992 | 0.00011992 | 0.0 | 0.01 +Other | | 0.0001502 | | | 0.01 + +Nlocal: 128.000 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 727.000 ave 727 max 727 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3712.00 ave 3712 max 3712 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7424.00 ave 7424 max 7424 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58.000000 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.4 b/examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.4 new file mode 100644 index 0000000000..eb03f14da5 --- /dev/null +++ b/examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.4 @@ -0,0 +1,156 @@ +LAMMPS (27 May 2021) +# Demonstrate MLIAP interface to linear SNAP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +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 3.316 +Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000 +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 = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000 13.264000) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + create_atoms CPU = 0.001 seconds + +mass 1 180.88 + +# choose potential + +include Ta06A.nn.mliap +# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) + +# Definition of SNAP potential Ta_Cand06A +# Assumes 1 LAMMPS atom type + +variable zblcutinner equal 4 +variable zblcutouter equal 4.8 +variable zblz equal 73 + +# Specify hybrid with SNAP, ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor +pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor +pair_style hybrid/overlay zbl 4 4.8 mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor +Reading potential file Ta06A.nn.mliap.model with DATE: 2021-03-03 +Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05 +SNAP keyword rcutfac 4.67637 +SNAP keyword twojmax 6 +SNAP keyword nelems 1 +SNAP keyword elems Ta +SNAP keyword radelems 0.5 +SNAP keyword welems 1 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0 +SNAP keyword bzeroflag 0 +pair_coeff 1 1 zbl ${zblz} ${zblz} +pair_coeff 1 1 zbl 73 ${zblz} +pair_coeff 1 1 zbl 73 73 +pair_coeff * * mliap Ta + + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +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 loop geom +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 = 5.8 + ghost atom cutoff = 5.8 + 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 mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 18.06 | 18.06 | 18.06 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661 + 10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796 + 20 284.53666 -11.849587 -11.849587 -11.813095 2289.1527 -2289.1527 + 30 266.51577 -11.847275 -11.847275 -11.813095 1851.7131 -1851.7131 + 40 243.05007 -11.844266 -11.844266 -11.813095 1570.684 -1570.684 + 50 215.51032 -11.840734 -11.840734 -11.813094 1468.1899 -1468.1899 + 60 185.48331 -11.836883 -11.836883 -11.813094 1524.8757 -1524.8757 + 70 154.6736 -11.832931 -11.832931 -11.813094 1698.3351 -1698.3351 + 80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715 + 90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563 + 100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526 +Loop time of 0.466162 on 4 procs for 100 steps with 128 atoms + +Performance: 9.267 ns/day, 2.590 hours/ns, 214.518 timesteps/s +99.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.36478 | 0.41101 | 0.45575 | 6.9 | 88.17 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0095217 | 0.054209 | 0.10046 | 19.0 | 11.63 +Output | 0.00042248 | 0.00045168 | 0.00051188 | 0.0 | 0.10 +Modify | 5.4359e-05 | 6.0737e-05 | 6.5088e-05 | 0.0 | 0.01 +Other | | 0.0004352 | | | 0.09 + +Nlocal: 32.0000 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 431.000 ave 431 max 431 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 928.000 ave 928 max 928 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1856.00 ave 1856 max 1856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58.000000 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/mliap/log.14Jun21.mliap.so3.Ni_Mo.g++.1 b/examples/mliap/log.14Jun21.mliap.so3.Ni_Mo.g++.1 new file mode 100644 index 0000000000..057732ec8c --- /dev/null +++ b/examples/mliap/log.14Jun21.mliap.so3.Ni_Mo.g++.1 @@ -0,0 +1,88 @@ +LAMMPS (27 May 2021) +# ---------- Initialize Simulation --------------------- +clear +units metal +dimension 3 +boundary p p p +atom_style atomic +read_data Ni_Mo.data +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.7209005 5.7209005 3.5556620) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + read_data CPU = 0.000 seconds + +#change_box all x scale 0.9 y scale 0.9 z scale 0.9 + +pair_style mliap model linear Ni_Mo.mliap.model descriptor so3 Ni_Mo.mliap.descriptor +Reading potential file Ni_Mo.mliap.descriptor with DATE: 2014-09-05 +SO3 keyword rcutfac 4.1 +SO3 keyword nmax 3 +SO3 keyword lmax 2 +SO3 keyword alpha 2.0 +SO3 keyword nelems 2 +SO3 keyword elems Mo +SO3 keyword radelems 0.5 +SO3 keyword welems 42 +pair_coeff * * Mo Ni + +variable e equal pe +variable N equal count(all) + +thermo_style custom pe pxx pyy pzz pxy pxz pyz +thermo 1 + +# dump 1 all custom 1 dump.myforce.* id type fx fy fz + +velocity all create 300.0 4928459 loop geom +fix 1 all nve + +run 3 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.1 + ghost atom cutoff = 6.1 + binsize = 3.05, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 17.22 | 17.22 | 17.22 Mbytes +PotEng Pxx Pyy Pzz Pxy Pxz Pyz + -60.509577 -38.702887 -342.91582 1831.0743 -819.59439 427.87407 446.40498 + -60.509344 -29.050171 -342.67124 1839.4215 -832.92479 439.72661 448.55829 + -60.509056 -9.4119072 -335.83361 1856.2802 -846.04664 451.4663 450.35456 + -60.508714 20.205972 -322.43019 1881.6 -858.97774 463.10122 451.79916 +Loop time of 0.00634885 on 1 procs for 3 steps with 10 atoms + +Performance: 40.826 ns/day, 0.588 hours/ns, 472.527 timesteps/s +78.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0063019 | 0.0063019 | 0.0063019 | 0.0 | 99.26 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 | 0.0 | 0.12 +Output | 3.4094e-05 | 3.4094e-05 | 3.4094e-05 | 0.0 | 0.54 +Modify | 2.1458e-06 | 2.1458e-06 | 2.1458e-06 | 0.0 | 0.03 +Other | | 3.099e-06 | | | 0.05 + +Nlocal: 10.0000 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 423.000 ave 423 max 423 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 780.000 ave 780 max 780 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 780 +Ave neighs/atom = 78.000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/mliap/log.14Jun21.mliap.so3.Ni_Mo.g++.4 b/examples/mliap/log.14Jun21.mliap.so3.Ni_Mo.g++.4 new file mode 100644 index 0000000000..a7da331482 --- /dev/null +++ b/examples/mliap/log.14Jun21.mliap.so3.Ni_Mo.g++.4 @@ -0,0 +1,88 @@ +LAMMPS (27 May 2021) +# ---------- Initialize Simulation --------------------- +clear +units metal +dimension 3 +boundary p p p +atom_style atomic +read_data Ni_Mo.data +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.7209005 5.7209005 3.5556620) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 10 atoms + read_data CPU = 0.000 seconds + +#change_box all x scale 0.9 y scale 0.9 z scale 0.9 + +pair_style mliap model linear Ni_Mo.mliap.model descriptor so3 Ni_Mo.mliap.descriptor +Reading potential file Ni_Mo.mliap.descriptor with DATE: 2014-09-05 +SO3 keyword rcutfac 4.1 +SO3 keyword nmax 3 +SO3 keyword lmax 2 +SO3 keyword alpha 2.0 +SO3 keyword nelems 2 +SO3 keyword elems Mo +SO3 keyword radelems 0.5 +SO3 keyword welems 42 +pair_coeff * * Mo Ni + +variable e equal pe +variable N equal count(all) + +thermo_style custom pe pxx pyy pzz pxy pxz pyz +thermo 1 + +# dump 1 all custom 1 dump.myforce.* id type fx fy fz + +velocity all create 300.0 4928459 loop geom +fix 1 all nve + +run 3 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.1 + ghost atom cutoff = 6.1 + binsize = 3.05, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 17.23 | 17.23 | 17.23 Mbytes +PotEng Pxx Pyy Pzz Pxy Pxz Pyz + -60.509577 -38.702887 -342.91582 1831.0743 -819.59439 427.87407 446.40498 + -60.509344 -29.050171 -342.67124 1839.4215 -832.92479 439.72661 448.55829 + -60.509056 -9.4119072 -335.83361 1856.2802 -846.04664 451.4663 450.35456 + -60.508714 20.205972 -322.43019 1881.6 -858.97774 463.10122 451.79916 +Loop time of 0.00191921 on 4 procs for 3 steps with 10 atoms + +Performance: 135.056 ns/day, 0.178 hours/ns, 1563.143 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0012183 | 0.0015162 | 0.0018141 | 0.8 | 79.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 5.3883e-05 | 0.00035822 | 0.00065947 | 0.0 | 18.67 +Output | 3.4094e-05 | 3.8326e-05 | 4.6492e-05 | 0.0 | 2.00 +Modify | 9.5367e-07 | 1.1325e-06 | 1.4305e-06 | 0.0 | 0.06 +Other | | 5.305e-06 | | | 0.28 + +Nlocal: 2.50000 ave 3 max 2 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 303.500 ave 304 max 303 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 195.000 ave 234 max 156 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 780 +Ave neighs/atom = 78.000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/mliap/log.14Jun21.mliap.so3.nn.Si.g++.1 b/examples/mliap/log.14Jun21.mliap.so3.nn.Si.g++.1 new file mode 100644 index 0000000000..0b67712e7e --- /dev/null +++ b/examples/mliap/log.14Jun21.mliap.so3.nn.Si.g++.1 @@ -0,0 +1,124 @@ +LAMMPS (27 May 2021) +# Run NPT MD simulation for Si at 500 K. +variable nsteps index 100 #0 + +# NOTE: These are not intended to represent real materials + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +#read_data Si.data +lattice diamond 5.43 +Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000 +region box block 0 2 0 2 0 2 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.860000 10.860000 10.860000) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 64 atoms + create_atoms CPU = 0.000 seconds +mass 1 29.0 + +# temperature +variable t equal 500. + + +# Potential +#pair_style mliap model nn Si-snap/NN_weights.txt descriptor sna Si-snap/DescriptorParam.txt +pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor +SO3 keyword rcutfac 5.0 +SO3 keyword nmax 3 +SO3 keyword lmax 4 +SO3 keyword alpha 2.0 +SO3 keyword nelems 1 +SO3 keyword elems Si +SO3 keyword radelems 0.5 +SO3 keyword welems 14 +pair_coeff * * Si Si + +# Set-up output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +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 $t 5287287 loop geom +velocity all create 500 5287287 loop geom +fix 1 all npt temp ${t} ${t} 0.2 iso 0.0 0.0 2 +fix 1 all npt temp 500 ${t} 0.2 iso 0.0 0.0 2 +fix 1 all npt temp 500 500 0.2 iso 0.0 0.0 2 +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 = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 298.3 | 298.3 | 298.3 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 500 -3.8376374 -3.8376374 -3.7740172 -7295.2456 7295.2456 + 10 489.81 -3.8363423 -3.8363423 -3.7740187 -6964.5624 6964.5624 + 20 460.24523 -3.8325828 -3.8325828 -3.774021 -6014.7165 6014.7165 + 30 414.4367 -3.826752 -3.826752 -3.7740189 -4572.0641 4572.0641 + 40 358.34511 -3.8196022 -3.8196022 -3.7740062 -2849.9177 2849.9177 + 50 300.80447 -3.8122536 -3.8122536 -3.7739791 -1128.7008 1128.7008 + 60 251.6276 -3.8059543 -3.8059543 -3.7739371 306.20639 -306.20639 + 70 218.02888 -3.8016236 -3.8016236 -3.7738815 1253.4391 -1253.4391 + 80 201.70095 -3.7994767 -3.7994767 -3.7738122 1661.6675 -1661.6675 + 90 198.91416 -3.7990366 -3.7990366 -3.7737266 1628.78 -1628.78 + 100 203.36197 -3.799497 -3.799497 -3.7736212 1338.0458 -1338.0458 +Loop time of 3.39264 on 1 procs for 100 steps with 64 atoms + +Performance: 1.273 ns/day, 18.848 hours/ns, 29.476 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.391 | 3.391 | 3.391 | 0.0 | 99.95 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00029302 | 0.00029302 | 0.00029302 | 0.0 | 0.01 +Output | 0.00039387 | 0.00039387 | 0.00039387 | 0.0 | 0.01 +Modify | 0.00074792 | 0.00074792 | 0.00074792 | 0.0 | 0.02 +Other | | 0.0002153 | | | 0.01 + +Nlocal: 64.0000 ave 64 max 64 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 557.000 ave 557 max 557 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 2944.00 ave 2944 max 2944 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2944 +Ave neighs/atom = 46.000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/mliap/log.14Jun21.mliap.so3.nn.Si.g++.4 b/examples/mliap/log.14Jun21.mliap.so3.nn.Si.g++.4 new file mode 100644 index 0000000000..7cde39a04e --- /dev/null +++ b/examples/mliap/log.14Jun21.mliap.so3.nn.Si.g++.4 @@ -0,0 +1,124 @@ +LAMMPS (27 May 2021) +# Run NPT MD simulation for Si at 500 K. +variable nsteps index 100 #0 + +# NOTE: These are not intended to represent real materials + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +#read_data Si.data +lattice diamond 5.43 +Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000 +region box block 0 2 0 2 0 2 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.860000 10.860000 10.860000) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 64 atoms + create_atoms CPU = 0.000 seconds +mass 1 29.0 + +# temperature +variable t equal 500. + + +# Potential +#pair_style mliap model nn Si-snap/NN_weights.txt descriptor sna Si-snap/DescriptorParam.txt +pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor +SO3 keyword rcutfac 5.0 +SO3 keyword nmax 3 +SO3 keyword lmax 4 +SO3 keyword alpha 2.0 +SO3 keyword nelems 1 +SO3 keyword elems Si +SO3 keyword radelems 0.5 +SO3 keyword welems 14 +pair_coeff * * Si Si + +# Set-up output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +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 $t 5287287 loop geom +velocity all create 500 5287287 loop geom +fix 1 all npt temp ${t} ${t} 0.2 iso 0.0 0.0 2 +fix 1 all npt temp 500 ${t} 0.2 iso 0.0 0.0 2 +fix 1 all npt temp 500 500 0.2 iso 0.0 0.0 2 +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 = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 298.2 | 298.2 | 298.2 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 500 -3.8376374 -3.8376374 -3.7740172 -7295.2456 7295.2456 + 10 489.81 -3.8363423 -3.8363423 -3.7740187 -6964.5624 6964.5624 + 20 460.24523 -3.8325828 -3.8325828 -3.774021 -6014.7165 6014.7165 + 30 414.4367 -3.826752 -3.826752 -3.7740189 -4572.0641 4572.0641 + 40 358.34511 -3.8196022 -3.8196022 -3.7740062 -2849.9177 2849.9177 + 50 300.80447 -3.8122536 -3.8122536 -3.7739791 -1128.7008 1128.7008 + 60 251.6276 -3.8059543 -3.8059543 -3.7739371 306.20639 -306.20639 + 70 218.02888 -3.8016236 -3.8016236 -3.7738815 1253.4391 -1253.4391 + 80 201.70095 -3.7994767 -3.7994767 -3.7738122 1661.6675 -1661.6675 + 90 198.91416 -3.7990366 -3.7990366 -3.7737266 1628.78 -1628.78 + 100 203.36197 -3.799497 -3.799497 -3.7736212 1338.0458 -1338.0458 +Loop time of 1.06231 on 4 procs for 100 steps with 64 atoms + +Performance: 4.067 ns/day, 5.902 hours/ns, 94.135 timesteps/s +95.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.97395 | 1.0072 | 1.048 | 2.7 | 94.81 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.012069 | 0.052803 | 0.086037 | 12.0 | 4.97 +Output | 0.00052595 | 0.0005523 | 0.00062776 | 0.0 | 0.05 +Modify | 0.0014014 | 0.001442 | 0.0014772 | 0.1 | 0.14 +Other | | 0.0003045 | | | 0.03 + +Nlocal: 16.0000 ave 16 max 16 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 349.000 ave 349 max 349 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 736.000 ave 736 max 736 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2944 +Ave neighs/atom = 46.000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01