update ML-UF3 examples
This commit is contained in:
Axel Kohlmeyer
@ -25,7 +25,7 @@ mass 1 183.84
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# # ============= set pair style
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pair_style uf3 2 1
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pair_coeff 1 1 W_W
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pair_coeff 1 1 W_W.uf3
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# # ============= Setup output
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@ -25,8 +25,8 @@ mass 1 183.84
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# # ============= set pair style
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pair_style uf3 3 1
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pair_coeff 1 1 W_W
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pair_coeff 3b 1 1 1 W_W_W
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pair_coeff 1 1 W_W.uf3
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pair_coeff 3b 1 1 1 W_W_W.uf3
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# # ============= Setup output
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122
examples/PACKAGES/uf3/log.27Mar24.uf3.2b.g++.1
Normal file
122
examples/PACKAGES/uf3/log.27Mar24.uf3.2b.g++.1
Normal file
@ -0,0 +1,122 @@
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-324-gfda433a7ee-modified)
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using 1 OpenMP thread(s) per MPI task
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# Demonstrate UF3 W potential
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# # ============= Initialize simulation
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variable nsteps index 100
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variable nrep equal 4
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variable a equal 3.187
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable nx equal 4
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variable ny equal ${nrep}
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variable ny equal 4
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variable nz equal ${nrep}
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variable nz equal 4
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boundary p p p
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lattice bcc $a
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lattice bcc 3.187
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Lattice spacing in x,y,z = 3.187 3.187 3.187
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 4 0 ${ny} 0 ${nz}
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region box block 0 4 0 4 0 ${nz}
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region box block 0 4 0 4 0 4
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create_box 1 box
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Created orthogonal box = (0 0 0) to (12.748 12.748 12.748)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 128 atoms
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using lattice units in orthogonal box = (0 0 0) to (12.748 12.748 12.748)
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create_atoms CPU = 0.000 seconds
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mass 1 183.84
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# # ============= set pair style
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pair_style uf3 2 1
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pair_coeff 1 1 W_W.uf3
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UF3: Opening W_W.uf3 file
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UF3: W_W.uf3 file should contain UF3 potential for 1 1
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UF3: File W_W.uf3 contains 2-body UF3 potential
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UF3: File W_W.uf3 contains 2-body UF3 potential with uniform
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knot spacing
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# # ============= Setup output
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thermo 10
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thermo_modify norm yes
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# # ============= Set up NVE run
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timestep 0.5e-3
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neighbor 1.0 bin
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neigh_modify once no every 1 delay 0 check yes
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# # ============= Run MD
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velocity all create 300.0 2367804 loop geom
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fix 1 all nve
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run ${nsteps}
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run 100
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 6.5
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ghost atom cutoff = 6.5
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binsize = 3.25, bins = 4 4 4
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair uf3, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.113 | 3.113 | 3.113 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -4.9097145 0 -4.8712394 -398022.13
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10 297.43433 -4.9093854 0 -4.8712394 -397994.78
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20 289.88359 -4.908417 0 -4.8712393 -397922.72
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30 277.73497 -4.9068589 0 -4.8712393 -397829.84
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40 261.57286 -4.904786 0 -4.8712392 -397731.28
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50 242.14207 -4.902294 0 -4.8712392 -397640.01
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60 220.31079 -4.899494 0 -4.8712391 -397572.33
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70 197.03391 -4.8965087 0 -4.871239 -397551.93
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80 173.31044 -4.893466 0 -4.8712389 -397601.62
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90 150.12364 -4.8904922 0 -4.8712388 -397739.2
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100 128.38807 -4.8877046 0 -4.8712388 -397980.01
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Loop time of 0.0344773 on 1 procs for 100 steps with 128 atoms
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Performance: 125.300 ns/day, 0.192 hours/ns, 2900.463 timesteps/s, 371.259 katom-step/s
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98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.033145 | 0.033145 | 0.033145 | 0.0 | 96.14
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00071163 | 0.00071163 | 0.00071163 | 0.0 | 2.06
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Output | 0.0002018 | 0.0002018 | 0.0002018 | 0.0 | 0.59
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Modify | 0.00017741 | 0.00017741 | 0.00017741 | 0.0 | 0.51
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Other | | 0.0002413 | | | 0.70
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Nlocal: 128 ave 128 max 128 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1113 ave 1113 max 1113 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 8192 ave 8192 max 8192 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 8192
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Ave neighs/atom = 64
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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122
examples/PACKAGES/uf3/log.27Mar24.uf3.2b.g++.4
Normal file
122
examples/PACKAGES/uf3/log.27Mar24.uf3.2b.g++.4
Normal file
@ -0,0 +1,122 @@
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-324-gfda433a7ee-modified)
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using 1 OpenMP thread(s) per MPI task
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# Demonstrate UF3 W potential
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# # ============= Initialize simulation
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variable nsteps index 100
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variable nrep equal 4
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variable a equal 3.187
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable nx equal 4
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variable ny equal ${nrep}
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variable ny equal 4
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variable nz equal ${nrep}
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variable nz equal 4
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boundary p p p
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lattice bcc $a
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lattice bcc 3.187
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Lattice spacing in x,y,z = 3.187 3.187 3.187
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 4 0 ${ny} 0 ${nz}
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region box block 0 4 0 4 0 ${nz}
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region box block 0 4 0 4 0 4
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create_box 1 box
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Created orthogonal box = (0 0 0) to (12.748 12.748 12.748)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 128 atoms
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using lattice units in orthogonal box = (0 0 0) to (12.748 12.748 12.748)
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create_atoms CPU = 0.000 seconds
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mass 1 183.84
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# # ============= set pair style
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pair_style uf3 2 1
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pair_coeff 1 1 W_W.uf3
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UF3: Opening W_W.uf3 file
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UF3: W_W.uf3 file should contain UF3 potential for 1 1
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UF3: File W_W.uf3 contains 2-body UF3 potential
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UF3: File W_W.uf3 contains 2-body UF3 potential with uniform
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knot spacing
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# # ============= Setup output
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thermo 10
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thermo_modify norm yes
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# # ============= Set up NVE run
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timestep 0.5e-3
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neighbor 1.0 bin
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neigh_modify once no every 1 delay 0 check yes
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# # ============= Run MD
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velocity all create 300.0 2367804 loop geom
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fix 1 all nve
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run ${nsteps}
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run 100
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 6.5
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ghost atom cutoff = 6.5
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binsize = 3.25, bins = 4 4 4
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair uf3, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.104 | 3.104 | 3.104 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -4.9097145 0 -4.8712394 -398022.13
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10 297.43433 -4.9093854 0 -4.8712394 -397994.78
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20 289.88359 -4.908417 0 -4.8712393 -397922.72
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30 277.73497 -4.9068589 0 -4.8712393 -397829.84
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40 261.57286 -4.904786 0 -4.8712392 -397731.28
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50 242.14207 -4.902294 0 -4.8712392 -397640.01
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60 220.31079 -4.899494 0 -4.8712391 -397572.33
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70 197.03391 -4.8965087 0 -4.871239 -397551.93
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80 173.31044 -4.893466 0 -4.8712389 -397601.62
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90 150.12364 -4.8904922 0 -4.8712388 -397739.2
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100 128.38807 -4.8877046 0 -4.8712388 -397980.01
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Loop time of 0.0111207 on 4 procs for 100 steps with 128 atoms
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Performance: 388.463 ns/day, 0.062 hours/ns, 8992.202 timesteps/s, 1.151 Matom-step/s
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98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0087312 | 0.008777 | 0.0088396 | 0.0 | 78.92
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0019835 | 0.0020323 | 0.0020742 | 0.1 | 18.27
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Output | 7.6664e-05 | 8.1924e-05 | 9.4556e-05 | 0.0 | 0.74
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Modify | 5.4618e-05 | 5.8768e-05 | 6.2489e-05 | 0.0 | 0.53
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Other | | 0.0001708 | | | 1.54
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Nlocal: 32 ave 32 max 32 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 697 ave 697 max 697 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 2048 ave 2048 max 2048 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 8192
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Ave neighs/atom = 64
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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132
examples/PACKAGES/uf3/log.27Mar24.uf3.3b.g++.1
Normal file
132
examples/PACKAGES/uf3/log.27Mar24.uf3.3b.g++.1
Normal file
@ -0,0 +1,132 @@
|
||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-324-gfda433a7ee-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate UF3 W potential
|
||||
|
||||
# # ============= Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
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variable nrep equal 4
|
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variable a equal 3.187
|
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units metal
|
||||
|
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# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
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variable nx equal 4
|
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variable ny equal ${nrep}
|
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variable ny equal 4
|
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variable nz equal ${nrep}
|
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variable nz equal 4
|
||||
|
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boundary p p p
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||||
|
||||
lattice bcc $a
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lattice bcc 3.187
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Lattice spacing in x,y,z = 3.187 3.187 3.187
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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}
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region box block 0 4 0 4 0 4
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create_box 1 box
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Created orthogonal box = (0 0 0) to (12.748 12.748 12.748)
|
||||
1 by 1 by 1 MPI processor grid
|
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create_atoms 1 box
|
||||
Created 128 atoms
|
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using lattice units in orthogonal box = (0 0 0) to (12.748 12.748 12.748)
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create_atoms CPU = 0.000 seconds
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mass 1 183.84
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# # ============= set pair style
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pair_style uf3 3 1
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pair_coeff 1 1 W_W.uf3
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UF3: Opening W_W.uf3 file
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UF3: W_W.uf3 file should contain UF3 potential for 1 1
|
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UF3: File W_W.uf3 contains 2-body UF3 potential
|
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UF3: File W_W.uf3 contains 2-body UF3 potential with uniform
|
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knot spacing
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pair_coeff 3b 1 1 1 W_W_W.uf3
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UF3: Opening W_W_W.uf3 file
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UF3: W_W_W.uf3 file should contain UF3 potential for 1 1 1
|
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UF3: File W_W_W.uf3 contains 3-body UF3 potential
|
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UF3: File W_W_W.uf3 contains 3-body UF3 potential with uniform
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knot spacing
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UF3: 3b min cutoff W_W_W.uf3 1-1-1_jk=1.5 1-1-1_jk=1.5
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UF3: 3b min cutoff W_W_W.uf3 1-1-1_ik=1.5 1-1-1_ik=1.5
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UF3: 3b min cutoff W_W_W.uf3 1-1-1_ij=1.5 1-1-1_ij=1.5
|
||||
|
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|
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# # ============= 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 2367804 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 = 6.5
|
||||
ghost atom cutoff = 6.5
|
||||
binsize = 3.25, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair uf3, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.214 | 3.214 | 3.214 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -4.3916353 0 -4.3531602 -21224
|
||||
10 292.96093 -4.3907325 0 -4.3531602 -21177.095
|
||||
20 272.60651 -4.3881219 0 -4.35316 -21038.525
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||||
30 241.12074 -4.3840835 0 -4.3531597 -20793.964
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||||
40 201.8718 -4.3790495 0 -4.3531594 -20444.219
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||||
50 159.06853 -4.3735596 0 -4.353159 -19996.634
|
||||
60 117.24817 -4.3681958 0 -4.3531587 -19470.011
|
||||
70 80.716097 -4.3635102 0 -4.3531584 -18905.505
|
||||
80 53.030322 -4.3599593 0 -4.3531582 -18362.596
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||||
90 36.611518 -4.3578535 0 -4.3531581 -17898.612
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||||
100 32.512413 -4.3573279 0 -4.3531581 -17551.048
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Loop time of 0.486699 on 1 procs for 100 steps with 128 atoms
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||||
|
||||
Performance: 8.876 ns/day, 2.704 hours/ns, 205.466 timesteps/s, 26.300 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
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MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.48518 | 0.48518 | 0.48518 | 0.0 | 99.69
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
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||||
Comm | 0.00082659 | 0.00082659 | 0.00082659 | 0.0 | 0.17
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||||
Output | 0.00014676 | 0.00014676 | 0.00014676 | 0.0 | 0.03
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||||
Modify | 0.00025566 | 0.00025566 | 0.00025566 | 0.0 | 0.05
|
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Other | | 0.0002862 | | | 0.06
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|
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Nlocal: 128 ave 128 max 128 min
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||||
Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1113 ave 1113 max 1113 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: 8192 ave 8192 max 8192 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8192
|
||||
Ave neighs/atom = 64
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
132
examples/PACKAGES/uf3/log.27Mar24.uf3.3b.g++.4
Normal file
132
examples/PACKAGES/uf3/log.27Mar24.uf3.3b.g++.4
Normal file
@ -0,0 +1,132 @@
|
||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-324-gfda433a7ee-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate UF3 W potential
|
||||
|
||||
# # ============= Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.187
|
||||
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 3.187
|
||||
Lattice spacing in x,y,z = 3.187 3.187 3.187
|
||||
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 (12.748 12.748 12.748)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (12.748 12.748 12.748)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 183.84
|
||||
|
||||
# # ============= set pair style
|
||||
|
||||
pair_style uf3 3 1
|
||||
pair_coeff 1 1 W_W.uf3
|
||||
|
||||
UF3: Opening W_W.uf3 file
|
||||
UF3: W_W.uf3 file should contain UF3 potential for 1 1
|
||||
UF3: File W_W.uf3 contains 2-body UF3 potential
|
||||
UF3: File W_W.uf3 contains 2-body UF3 potential with uniform
|
||||
knot spacing
|
||||
pair_coeff 3b 1 1 1 W_W_W.uf3
|
||||
|
||||
UF3: Opening W_W_W.uf3 file
|
||||
UF3: W_W_W.uf3 file should contain UF3 potential for 1 1 1
|
||||
UF3: File W_W_W.uf3 contains 3-body UF3 potential
|
||||
UF3: File W_W_W.uf3 contains 3-body UF3 potential with uniform
|
||||
knot spacing
|
||||
UF3: 3b min cutoff W_W_W.uf3 1-1-1_jk=1.5 1-1-1_jk=1.5
|
||||
UF3: 3b min cutoff W_W_W.uf3 1-1-1_ik=1.5 1-1-1_ik=1.5
|
||||
UF3: 3b min cutoff W_W_W.uf3 1-1-1_ij=1.5 1-1-1_ij=1.5
|
||||
|
||||
|
||||
# # ============= 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 2367804 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 = 6.5
|
||||
ghost atom cutoff = 6.5
|
||||
binsize = 3.25, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair uf3, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.205 | 3.205 | 3.205 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -4.3916353 0 -4.3531602 -21224
|
||||
10 292.96093 -4.3907325 0 -4.3531602 -21177.095
|
||||
20 272.60651 -4.3881219 0 -4.35316 -21038.525
|
||||
30 241.12074 -4.3840835 0 -4.3531597 -20793.964
|
||||
40 201.8718 -4.3790495 0 -4.3531594 -20444.219
|
||||
50 159.06853 -4.3735596 0 -4.353159 -19996.634
|
||||
60 117.24817 -4.3681958 0 -4.3531587 -19470.011
|
||||
70 80.716097 -4.3635102 0 -4.3531584 -18905.505
|
||||
80 53.030322 -4.3599593 0 -4.3531582 -18362.596
|
||||
90 36.611518 -4.3578535 0 -4.3531581 -17898.612
|
||||
100 32.512413 -4.3573279 0 -4.3531581 -17551.048
|
||||
Loop time of 0.133856 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 32.273 ns/day, 0.744 hours/ns, 747.069 timesteps/s, 95.625 katom-step/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 | 0.1196 | 0.1221 | 0.12575 | 0.7 | 91.22
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0074076 | 0.011068 | 0.01359 | 2.4 | 8.27
|
||||
Output | 0.00013888 | 0.00015365 | 0.00018854 | 0.0 | 0.11
|
||||
Modify | 0.00010546 | 0.00011783 | 0.00013025 | 0.0 | 0.09
|
||||
Other | | 0.0004172 | | | 0.31
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 697 ave 697 max 697 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: 2048 ave 2048 max 2048 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8192
|
||||
Ave neighs/atom = 64
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
Reference in New Issue
Block a user