156 lines
5.7 KiB
Groff
156 lines
5.7 KiB
Groff
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-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 POD potential for InP
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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 5.83
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units metal
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# generate the box and atom positions using a FCC 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 diamond $a
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lattice diamond 5.83
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Lattice spacing in x,y,z = 5.83 5.83 5.83
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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 2 box
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Created orthogonal box = (0 0 0) to (23.32 23.32 23.32)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
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Created 512 atoms
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using lattice units in orthogonal box = (0 0 0) to (23.32 23.32 23.32)
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create_atoms CPU = 0.001 seconds
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mass 1 114.76
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mass 2 30.98
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# POD potential
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pair_style pod
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pair_coeff * * InP_param.pod InP_coefficients.pod In P
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**************** Begin of POD Potentials ****************
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species: In P
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periodic boundary conditions: 1 1 1
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number of environment clusters: 1
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number of principal compoments: 2
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inner cut-off radius: 0.8
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outer cut-off radius: 5
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bessel polynomial degree: 4
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inverse polynomial degree: 8
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one-body potential: 1
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two-body radial basis functions: 6
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three-body radial basis functions: 5
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three-body angular degree: 4
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four-body radial basis functions: 4
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four-body angular degree: 2
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five-body radial basis functions: 0
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five-body angular degree: 0
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six-body radial basis functions: 0
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six-body angular degree: 0
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seven-body radial basis functions: 0
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seven-body angular degree: 0
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number of local descriptors per element for one-body potential: 1
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number of local descriptors per element for two-body potential: 12
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number of local descriptors per element for three-body potential: 75
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number of local descriptors per element for four-body potential: 64
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number of local descriptors per element for five-body potential: 0
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number of local descriptors per element for six-body potential: 0
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number of local descriptors per element for seven-body potential: 0
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number of local descriptors per element for all potentials: 152
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number of global descriptors: 304
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**************** End of POD Potentials ****************
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**************** Begin of Model Coefficients ****************
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total number of coefficients for POD potential: 304
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total number of elements for PCA projection matrix: 0
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total number of elements for PCA centroids: 0
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**************** End of Model Coefficients ****************
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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 4928459 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
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ghost atom cutoff = 6
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binsize = 3, bins = 8 8 8
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair pod, 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) = 3.215 | 3.215 | 3.215 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -4.8392777 0 -4.8005754 1561.0654
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10 291.27079 -4.8381515 0 -4.8005753 1709.509
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20 266.69372 -4.8349805 0 -4.8005749 2126.86
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30 230.86163 -4.8303573 0 -4.8005744 2735.6894
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40 190.64668 -4.8251686 0 -4.8005738 3416.9247
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50 153.9516 -4.8204341 0 -4.8005732 4022.2533
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60 127.93805 -4.8170778 0 -4.8005728 4405.9763
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70 117.12501 -4.8156828 0 -4.8005727 4475.6131
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80 122.09497 -4.8163242 0 -4.800573 4231.7934
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90 139.42686 -4.8185607 0 -4.8005735 3766.8505
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100 162.84813 -4.8215828 0 -4.8005741 3221.8605
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Loop time of 0.818141 on 4 procs for 100 steps with 512 atoms
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Performance: 5.280 ns/day, 4.545 hours/ns, 122.228 timesteps/s, 62.581 katom-step/s
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94.0% 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 | 0.70717 | 0.7255 | 0.75748 | 2.2 | 88.68
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.05765 | 0.088203 | 0.10797 | 6.3 | 10.78
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Output | 0.00030107 | 0.00039215 | 0.00055987 | 0.0 | 0.05
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Modify | 0.00051915 | 0.00059064 | 0.00069306 | 0.0 | 0.07
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Other | | 0.003452 | | | 0.42
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Nlocal: 128 ave 128 max 128 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 783 ave 783 max 783 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: 4352 ave 4352 max 4352 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 17408
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Ave neighs/atom = 34
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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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