From abfc4465b090fb7ac4313f9f0f6a8af41220dbdf Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Wed, 3 Mar 2021 11:38:05 -0700 Subject: [PATCH] Rearranged nn file locations and names --- examples/mliap/Cu.nn.mliap.model | 1 + examples/mliap/Cu.snap.mliap.descriptor | 1 + examples/mliap/Ta06A.mliap.nn | 19 +-- examples/mliap/Ta06A.nn.mliap.model | 1 + examples/mliap/in.mliap.snap.nn.Cu | 6 +- ....mliap.nn.Ta06A => in.mliap.snap.nn.Ta06A} | 0 ..._nn => log.03Mar21.mliap.snap.nn.Cu.g++.1} | 31 ++-- .../mliap/log.03Mar21.mliap.snap.nn.Cu.g++.4 | 134 +++++++++++++++ ... => log.03Mar21.mliap.snap.nn.Ta06A.g++.1} | 27 +-- .../log.03Mar21.mliap.snap.nn.Ta06A.g++.4 | 157 ++++++++++++++++++ examples/mliap/log.snap.Ta06A.ref | 154 ----------------- .../Cu.nn.mliap.model | 0 .../Cu.snap.mliap.descriptor | 0 potentials/Ta06A.mliap.nn | 18 ++ .../mliap => potentials}/Ta06A.mliap.pytorch | 0 .../Ta06A.nn.mliap.model | 0 16 files changed, 344 insertions(+), 205 deletions(-) create mode 120000 examples/mliap/Cu.nn.mliap.model create mode 120000 examples/mliap/Cu.snap.mliap.descriptor mode change 100644 => 120000 examples/mliap/Ta06A.mliap.nn create mode 120000 examples/mliap/Ta06A.nn.mliap.model rename examples/mliap/{in.mliap.nn.Ta06A => in.mliap.snap.nn.Ta06A} (100%) rename examples/mliap/{log.Cu_nn => log.03Mar21.mliap.snap.nn.Cu.g++.1} (82%) create mode 100644 examples/mliap/log.03Mar21.mliap.snap.nn.Cu.g++.4 rename examples/mliap/{log.03Mar21.mliap.nn_Ta06A => log.03Mar21.mliap.snap.nn.Ta06A.g++.1} (85%) create mode 100644 examples/mliap/log.03Mar21.mliap.snap.nn.Ta06A.g++.4 delete mode 100644 examples/mliap/log.snap.Ta06A.ref rename examples/mliap/Cu_nn.mliap.model => potentials/Cu.nn.mliap.model (100%) rename examples/mliap/Cu_snap.mliap.descriptor => potentials/Cu.snap.mliap.descriptor (100%) create mode 100644 potentials/Ta06A.mliap.nn rename {examples/mliap => potentials}/Ta06A.mliap.pytorch (100%) rename examples/mliap/Ta06A_nn.mliap.model => potentials/Ta06A.nn.mliap.model (100%) diff --git a/examples/mliap/Cu.nn.mliap.model b/examples/mliap/Cu.nn.mliap.model new file mode 120000 index 0000000000..5905004548 --- /dev/null +++ b/examples/mliap/Cu.nn.mliap.model @@ -0,0 +1 @@ +../../potentials/Cu.nn.mliap.model \ No newline at end of file diff --git a/examples/mliap/Cu.snap.mliap.descriptor b/examples/mliap/Cu.snap.mliap.descriptor new file mode 120000 index 0000000000..6cc612ec54 --- /dev/null +++ b/examples/mliap/Cu.snap.mliap.descriptor @@ -0,0 +1 @@ +../../potentials/Cu.snap.mliap.descriptor \ No newline at end of file diff --git a/examples/mliap/Ta06A.mliap.nn b/examples/mliap/Ta06A.mliap.nn deleted file mode 100644 index 01246354c5..0000000000 --- a/examples/mliap/Ta06A.mliap.nn +++ /dev/null @@ -1,18 +0,0 @@ -# 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_coeff 1 1 zbl ${zblz} ${zblz} -pair_coeff * * mliap Ta - diff --git a/examples/mliap/Ta06A.mliap.nn b/examples/mliap/Ta06A.mliap.nn new file mode 120000 index 0000000000..4aab212e4f --- /dev/null +++ b/examples/mliap/Ta06A.mliap.nn @@ -0,0 +1 @@ +../../potentials/Ta06A.mliap.nn \ No newline at end of file diff --git a/examples/mliap/Ta06A.nn.mliap.model b/examples/mliap/Ta06A.nn.mliap.model new file mode 120000 index 0000000000..a67f930cf8 --- /dev/null +++ b/examples/mliap/Ta06A.nn.mliap.model @@ -0,0 +1 @@ +../../potentials/Ta06A.nn.mliap.model \ No newline at end of file diff --git a/examples/mliap/in.mliap.snap.nn.Cu b/examples/mliap/in.mliap.snap.nn.Cu index bc6648ff46..7ac7d4b56e 100644 --- a/examples/mliap/in.mliap.snap.nn.Cu +++ b/examples/mliap/in.mliap.snap.nn.Cu @@ -1,4 +1,3 @@ - # Demonstrate MLIAP interface to SNAP nn Cu potential # Initialize simulation @@ -8,7 +7,6 @@ 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} @@ -26,8 +24,8 @@ mass 1 63.546 # choose potential -pair_style mliap model nn Cu_nn.mliap.model descriptor sna Cu_snap.mliap.descriptor -pair_coeff * * Cu Cu +pair_style mliap model nn Cu.nn.mliap.model descriptor sna Cu.snap.mliap.descriptor +pair_coeff * * Cu # Setup output diff --git a/examples/mliap/in.mliap.nn.Ta06A b/examples/mliap/in.mliap.snap.nn.Ta06A similarity index 100% rename from examples/mliap/in.mliap.nn.Ta06A rename to examples/mliap/in.mliap.snap.nn.Ta06A diff --git a/examples/mliap/log.Cu_nn b/examples/mliap/log.03Mar21.mliap.snap.nn.Cu.g++.1 similarity index 82% rename from examples/mliap/log.Cu_nn rename to examples/mliap/log.03Mar21.mliap.snap.nn.Cu.g++.1 index 69aacd817f..678de992f7 100644 --- a/examples/mliap/log.Cu_nn +++ b/examples/mliap/log.03Mar21.mliap.snap.nn.Cu.g++.1 @@ -1,5 +1,5 @@ LAMMPS (10 Feb 2021) - + using 1 OpenMP thread(s) per MPI task # Demonstrate MLIAP interface to SNAP nn Cu potential # Initialize simulation @@ -9,8 +9,7 @@ variable nrep equal 4 variable a equal 3.621262 units metal - -# generate the box and atom positions using a BCC lattice +# generate the box and atom positions using a FCC lattice variable nx equal ${nrep} variable nx equal 4 @@ -39,9 +38,9 @@ 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 +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 @@ -52,7 +51,7 @@ SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword bzeroflag 0 SNAP keyword switchflag 1 -pair_coeff * * Cu Cu +pair_coeff * * Cu # Setup output @@ -104,20 +103,20 @@ Step Temp E_pair c_energy TotEng Press v_press 80 75.426905 -4.0642423 -4.0642423 -4.0545307 7766.2217 -7766.2217 90 58.150738 -4.0620015 -4.0620015 -4.0545143 8668.0598 -8668.0598 100 52.301012 -4.0612408 -4.0612408 -4.0545067 9049.3141 -9049.3141 -Loop time of 4.41003 on 1 procs for 100 steps with 256 atoms +Loop time of 12.8453 on 1 procs for 100 steps with 256 atoms -Performance: 0.980 ns/day, 24.500 hours/ns, 22.676 timesteps/s -98.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.336 ns/day, 71.363 hours/ns, 7.785 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.4064 | 4.4064 | 4.4064 | 0.0 | 99.92 +Pair | 12.842 | 12.842 | 12.842 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.001466 | 0.001466 | 0.001466 | 0.0 | 0.03 -Output | 0.000872 | 0.000872 | 0.000872 | 0.0 | 0.02 -Modify | 0.000699 | 0.000699 | 0.000699 | 0.0 | 0.02 -Other | | 0.000632 | | | 0.01 +Comm | 0.0014137 | 0.0014137 | 0.0014137 | 0.0 | 0.01 +Output | 0.00090703 | 0.00090703 | 0.00090703 | 0.0 | 0.01 +Modify | 0.0007583 | 0.0007583 | 0.0007583 | 0.0 | 0.01 +Other | | 0.0003434 | | | 0.00 Nlocal: 256.000 ave 256 max 256 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -132,4 +131,4 @@ Total # of neighbors = 19968 Ave neighs/atom = 78.000000 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:04 +Total wall time: 0:00:13 diff --git a/examples/mliap/log.03Mar21.mliap.snap.nn.Cu.g++.4 b/examples/mliap/log.03Mar21.mliap.snap.nn.Cu.g++.4 new file mode 100644 index 0000000000..cc4e98a249 --- /dev/null +++ b/examples/mliap/log.03Mar21.mliap.snap.nn.Cu.g++.4 @@ -0,0 +1,134 @@ +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task +# 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 + 10 294.19698 -4.0927997 -4.0927997 -4.0549203 -2653.7504 2653.7504 + 20 277.15991 -4.0905816 -4.0905816 -4.0548958 -1875.7718 1875.7718 + 30 250.30462 -4.0870777 -4.0870777 -4.0548496 -618.45378 618.45378 + 40 215.94455 -4.0825861 -4.0825861 -4.0547821 1014.6151 -1014.6151 + 50 177.29307 -4.0775299 -4.0775299 -4.0547025 2846.7675 -2846.7675 + 60 138.26899 -4.072429 -4.072429 -4.0546261 4698.9654 -4698.9654 + 70 103.04321 -4.0678341 -4.0678341 -4.0545667 6401.8077 -6401.8077 + 80 75.426905 -4.0642423 -4.0642423 -4.0545307 7766.2217 -7766.2217 + 90 58.150738 -4.0620015 -4.0620015 -4.0545143 8668.0598 -8668.0598 + 100 52.301012 -4.0612408 -4.0612408 -4.0545067 9049.3141 -9049.3141 +Loop time of 3.39121 on 4 procs for 100 steps with 256 atoms + +Performance: 1.274 ns/day, 18.840 hours/ns, 29.488 timesteps/s +100.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.3037 | 3.3421 | 3.3808 | 2.0 | 98.55 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0084965 | 0.047256 | 0.085777 | 17.1 | 1.39 +Output | 0.00091401 | 0.00094114 | 0.00099209 | 0.0 | 0.03 +Modify | 0.00022695 | 0.00024041 | 0.00026185 | 0.0 | 0.01 +Other | | 0.0006503 | | | 0.02 + +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: 0:00:03 diff --git a/examples/mliap/log.03Mar21.mliap.nn_Ta06A b/examples/mliap/log.03Mar21.mliap.snap.nn.Ta06A.g++.1 similarity index 85% rename from examples/mliap/log.03Mar21.mliap.nn_Ta06A rename to examples/mliap/log.03Mar21.mliap.snap.nn.Ta06A.g++.1 index 966f644684..58dd94a5f0 100644 --- a/examples/mliap/log.03Mar21.mliap.nn_Ta06A +++ b/examples/mliap/log.03Mar21.mliap.snap.nn.Ta06A.g++.1 @@ -1,4 +1,5 @@ LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task # Demonstrate MLIAP interface to linear SNAP potential # Initialize simulation @@ -49,10 +50,10 @@ 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 +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 @@ -124,20 +125,20 @@ Step Temp E_pair c_energy TotEng Press v_press 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 1.19515 on 1 procs for 100 steps with 128 atoms +Loop time of 2.93897 on 1 procs for 100 steps with 128 atoms -Performance: 3.615 ns/day, 6.640 hours/ns, 83.671 timesteps/s -98.5% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.470 ns/day, 16.328 hours/ns, 34.026 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.1924 | 1.1924 | 1.1924 | 0.0 | 99.77 +Pair | 2.9368 | 2.9368 | 2.9368 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.000961 | 0.000961 | 0.000961 | 0.0 | 0.08 -Output | 0.000707 | 0.000707 | 0.000707 | 0.0 | 0.06 -Modify | 0.000459 | 0.000459 | 0.000459 | 0.0 | 0.04 -Other | | 0.00065 | | | 0.05 +Comm | 0.00074209 | 0.00074209 | 0.00074209 | 0.0 | 0.03 +Output | 0.00078955 | 0.00078955 | 0.00078955 | 0.0 | 0.03 +Modify | 0.00039202 | 0.00039202 | 0.00039202 | 0.0 | 0.01 +Other | | 0.0002685 | | | 0.01 Nlocal: 128.000 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -153,4 +154,4 @@ Ave neighs/atom = 58.000000 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:02 diff --git a/examples/mliap/log.03Mar21.mliap.snap.nn.Ta06A.g++.4 b/examples/mliap/log.03Mar21.mliap.snap.nn.Ta06A.g++.4 new file mode 100644 index 0000000000..31ca171200 --- /dev/null +++ b/examples/mliap/log.03Mar21.mliap.snap.nn.Ta06A.g++.4 @@ -0,0 +1,157 @@ +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task +# 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 = 0.000 seconds + +mass 1 180.88 + +# choose potential + +include Ta06A.mliap.nn +# 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 0.806392 on 4 procs for 100 steps with 128 atoms + +Performance: 5.357 ns/day, 4.480 hours/ns, 124.009 timesteps/s +100.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.75456 | 0.77908 | 0.7935 | 1.7 | 96.61 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0116 | 0.026033 | 0.050547 | 9.2 | 3.23 +Output | 0.00071782 | 0.00075547 | 0.0008103 | 0.0 | 0.09 +Modify | 0.00011633 | 0.00012274 | 0.0001295 | 0.0 | 0.02 +Other | | 0.0004031 | | | 0.05 + +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.snap.Ta06A.ref b/examples/mliap/log.snap.Ta06A.ref deleted file mode 100644 index 8c89ac1957..0000000000 --- a/examples/mliap/log.snap.Ta06A.ref +++ /dev/null @@ -1,154 +0,0 @@ -LAMMPS (19 Mar 2020) -# Demonstrate SNAP Ta 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 = 3.316 3.316 3.316 -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 (13.264 13.264 13.264) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 128 atoms - create_atoms CPU = 0.000254 secs - -mass 1 180.88 - -# choose potential - -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 -# 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} 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 -pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta -Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05 -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 rfac0 0.99363 -SNAP keyword rmin0 0 -SNAP keyword bzeroflag 0 -SNAP keyword quadraticflag 0 - - -# 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 -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 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) = 6.591 | 6.591 | 6.591 Mbytes -Step Temp E_pair c_energy TotEng Press v_press - 0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661 - 10 295.96579 -11.851053 -11.851053 -11.813095 2696.1559 -2696.1559 - 20 284.32535 -11.84956 -11.84956 -11.813095 2301.3713 -2301.3713 - 30 266.04602 -11.847215 -11.847215 -11.813095 1832.1745 -1832.1745 - 40 242.2862 -11.844168 -11.844168 -11.813095 1492.6765 -1492.6765 - 50 214.48968 -11.840603 -11.840603 -11.813094 1312.8908 -1312.8908 - 60 184.32523 -11.836734 -11.836734 -11.813094 1284.582 -1284.582 - 70 153.58055 -11.832791 -11.832791 -11.813094 1374.4457 -1374.4457 - 80 124.04276 -11.829003 -11.829003 -11.813094 1537.703 -1537.703 - 90 97.37622 -11.825582 -11.825582 -11.813094 1734.9662 -1734.9662 - 100 75.007873 -11.822714 -11.822714 -11.813094 1930.8005 -1930.8005 -Loop time of 0.995328 on 1 procs for 100 steps with 128 atoms - -Performance: 4.340 ns/day, 5.530 hours/ns, 100.469 timesteps/s -99.5% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.99426 | 0.99426 | 0.99426 | 0.0 | 99.89 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.000305 | 0.000305 | 0.000305 | 0.0 | 0.03 -Output | 0.000413 | 0.000413 | 0.000413 | 0.0 | 0.04 -Modify | 0.000159 | 0.000159 | 0.000159 | 0.0 | 0.02 -Other | | 0.000191 | | | 0.02 - -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: 3712 ave 3712 max 3712 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: 0:00:01 diff --git a/examples/mliap/Cu_nn.mliap.model b/potentials/Cu.nn.mliap.model similarity index 100% rename from examples/mliap/Cu_nn.mliap.model rename to potentials/Cu.nn.mliap.model diff --git a/examples/mliap/Cu_snap.mliap.descriptor b/potentials/Cu.snap.mliap.descriptor similarity index 100% rename from examples/mliap/Cu_snap.mliap.descriptor rename to potentials/Cu.snap.mliap.descriptor diff --git a/potentials/Ta06A.mliap.nn b/potentials/Ta06A.mliap.nn new file mode 100644 index 0000000000..01246354c5 --- /dev/null +++ b/potentials/Ta06A.mliap.nn @@ -0,0 +1,18 @@ +# 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_coeff 1 1 zbl ${zblz} ${zblz} +pair_coeff * * mliap Ta + diff --git a/examples/mliap/Ta06A.mliap.pytorch b/potentials/Ta06A.mliap.pytorch similarity index 100% rename from examples/mliap/Ta06A.mliap.pytorch rename to potentials/Ta06A.mliap.pytorch diff --git a/examples/mliap/Ta06A_nn.mliap.model b/potentials/Ta06A.nn.mliap.model similarity index 100% rename from examples/mliap/Ta06A_nn.mliap.model rename to potentials/Ta06A.nn.mliap.model