Merge pull request #4110 from uf3/ml-uf3
Implementation of pair_style uf3 and uf3/kk
This commit is contained in:
Axel Kohlmeyer
1
examples/PACKAGES/uf3/Nb.uf3
Symbolic link
1
examples/PACKAGES/uf3/Nb.uf3
Symbolic link
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../../../potentials/Nb.uf3
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46
examples/PACKAGES/uf3/in.uf3.Nb
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46
examples/PACKAGES/uf3/in.uf3.Nb
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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 3.3005
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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 ny equal ${nrep}
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variable nz equal ${nrep}
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boundary p p p
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lattice bcc $a
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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create_box 1 box
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create_atoms 1 box
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mass 1 92.906
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# # ============= set pair style
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pair_style uf3 3
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pair_coeff * * Nb.uf3 Nb
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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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118
examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.1
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118
examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.1
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LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-199-g49f20229ad-modified)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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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 3.3005
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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 3.3005
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Lattice spacing in x,y,z = 3.3005 3.3005 3.3005
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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 (13.202 13.202 13.202)
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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 (13.202 13.202 13.202)
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create_atoms CPU = 0.000 seconds
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mass 1 92.906
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# # ============= set pair style
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pair_style uf3 3
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pair_coeff * * Nb.uf3 Nb
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Reading potential file Nb.uf3 with DATE: 2024-04-02
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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 = 9
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ghost atom cutoff = 9
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binsize = 4.5, bins = 3 3 3
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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) = 3.376 | 3.376 | 3.376 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -4.4256832 0 -4.3872081 90756.437
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10 294.36659 -4.4249607 0 -4.3872081 91006.427
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20 277.9021 -4.422849 0 -4.387208 91716.126
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30 251.88303 -4.4195119 0 -4.3872078 92789.12
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40 218.42803 -4.4152211 0 -4.3872076 94118.45
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50 180.40641 -4.4103445 0 -4.3872073 95579.009
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60 141.2326 -4.4053202 0 -4.3872071 97031.816
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70 104.54429 -4.4006146 0 -4.3872068 98332.882
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80 73.787889 -4.3966699 0 -4.3872066 99351.332
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90 51.759956 -4.3938446 0 -4.3872064 99992.934
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100 40.209821 -4.3923633 0 -4.3872064 100211.98
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Loop time of 0.385575 on 1 procs for 100 steps with 128 atoms
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Performance: 11.204 ns/day, 2.142 hours/ns, 259.353 timesteps/s, 33.197 katom-step/s
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99.7% 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 | 0.38403 | 0.38403 | 0.38403 | 0.0 | 99.60
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00090609 | 0.00090609 | 0.00090609 | 0.0 | 0.23
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Output | 0.00017626 | 0.00017626 | 0.00017626 | 0.0 | 0.05
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Modify | 0.00018204 | 0.00018204 | 0.00018204 | 0.0 | 0.05
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Other | | 0.0002795 | | | 0.07
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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: 1601 ave 1601 max 1601 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: 21504 ave 21504 max 21504 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 21504
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Ave neighs/atom = 168
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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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118
examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.4
Normal file
118
examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.4
Normal file
@ -0,0 +1,118 @@
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LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-199-g49f20229ad-modified)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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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 3.3005
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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 3.3005
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Lattice spacing in x,y,z = 3.3005 3.3005 3.3005
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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 (13.202 13.202 13.202)
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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 (13.202 13.202 13.202)
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create_atoms CPU = 0.001 seconds
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mass 1 92.906
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# # ============= set pair style
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pair_style uf3 3
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pair_coeff * * Nb.uf3 Nb
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Reading potential file Nb.uf3 with DATE: 2024-04-02
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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 = 9
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ghost atom cutoff = 9
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binsize = 4.5, bins = 3 3 3
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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) = 3.351 | 3.351 | 3.351 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -4.4256832 0 -4.3872081 90756.437
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10 294.36659 -4.4249607 0 -4.3872081 91006.427
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20 277.9021 -4.422849 0 -4.387208 91716.126
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30 251.88303 -4.4195119 0 -4.3872078 92789.12
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40 218.42803 -4.4152211 0 -4.3872076 94118.45
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50 180.40641 -4.4103445 0 -4.3872073 95579.009
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60 141.2326 -4.4053202 0 -4.3872071 97031.816
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70 104.54429 -4.4006146 0 -4.3872068 98332.882
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80 73.787889 -4.3966699 0 -4.3872066 99351.332
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90 51.759956 -4.3938446 0 -4.3872064 99992.934
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100 40.209821 -4.3923633 0 -4.3872064 100211.98
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Loop time of 0.11881 on 4 procs for 100 steps with 128 atoms
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Performance: 36.361 ns/day, 0.660 hours/ns, 841.679 timesteps/s, 107.735 katom-step/s
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99.3% 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 | 0.10673 | 0.10875 | 0.11236 | 0.7 | 91.53
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0057324 | 0.0093477 | 0.011375 | 2.4 | 7.87
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Output | 0.00016629 | 0.00018236 | 0.00022483 | 0.0 | 0.15
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Modify | 9.4948e-05 | 0.00010621 | 0.00012066 | 0.0 | 0.09
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Other | | 0.0004263 | | | 0.36
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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: 1049 ave 1049 max 1049 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: 5376 ave 5376 max 5376 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 21504
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Ave neighs/atom = 168
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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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