Added doc page for compute mliap and updated examples
This commit is contained in:
Aidan Thompson
199
examples/mliap/log.03Jul20.mliap.quadratic.compute.g++.1
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199
examples/mliap/log.03Jul20.mliap.quadratic.compute.g++.1
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@ -0,0 +1,199 @@
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LAMMPS (15 Jun 2020)
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# Demonstrate MLIAP quadratic compute
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# initialize simulation
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variable nsteps index 0
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variable nrep equal 1
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variable a equal 2.0
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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 1
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variable ny equal ${nrep}
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variable ny equal 1
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variable nz equal ${nrep}
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variable nz equal 1
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boundary p p p
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atom_modify map hash
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lattice bcc $a
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lattice bcc 2
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Lattice spacing in x,y,z = 2 2 2
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 1 0 ${ny} 0 ${nz}
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region box block 0 1 0 1 0 ${nz}
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region box block 0 1 0 1 0 1
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create_box 2 box
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Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
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1 by 1 by 1 MPI processor grid
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create_atoms 2 box
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Created 2 atoms
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create_atoms CPU = 0.000 seconds
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mass * 180.88
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displace_atoms all random 0.1 0.1 0.1 123456
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# set up reference potential
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 73
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pair_style zbl ${zblcutinner} ${zblcutouter}
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pair_style zbl 4 ${zblcutouter}
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pair_style zbl 4 4.8
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pair_coeff * * ${zblz} ${zblz}
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pair_coeff * * 73 ${zblz}
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pair_coeff * * 73 73
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# choose SNA parameters
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variable twojmax equal 2
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variable rcutfac equal 1.0
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variable rfac0 equal 0.99363
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variable rmin0 equal 0
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variable radelem1 equal 2.3
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variable radelem2 equal 2.0
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variable wj1 equal 1.0
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variable wj2 equal 0.96
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variable quadratic equal 1
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variable bzero equal 0
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variable switch equal 0
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variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
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1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
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# set up per-atom computes
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compute b all sna/atom ${snap_options}
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compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
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compute vb all snav/atom ${snap_options}
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compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
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compute db all snad/atom ${snap_options}
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compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
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# perform sums over atoms
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group snapgroup1 type 1
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0 atoms in group snapgroup1
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group snapgroup2 type 2
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2 atoms in group snapgroup2
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compute bsum1 snapgroup1 reduce sum c_b[*]
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compute bsum2 snapgroup2 reduce sum c_b[*]
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# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
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# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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compute vbsum all reduce sum c_vb[*]
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# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
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variable db_2_100 equal c_db[2][100]
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# set up compute snap generating global array
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compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21
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SNAP keyword rcutfac 1.0
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SNAP keyword twojmax 2
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SNAP keyword nelems 2
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SNAP keyword elems A
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SNAP keyword radelems 2.3
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SNAP keyword welems 1.0
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SNAP keyword rfac0 0.99363
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SNAP keyword rmin0 0
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SNAP keyword bzeroflag 0
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SNAP keyword switchflag 0
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fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector
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thermo 100
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# test output: 1: total potential energy
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# 2: xy component of stress tensor
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# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
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# 4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
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# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
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#
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# followed by 5 counterparts from compute snap
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thermo_style custom pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
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thermo_modify norm no
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# dump mydump_db all custom 1000 dump_db id c_db[*]
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# dump_modify mydump_db sort id
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# Run MD
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run ${nsteps}
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run 0
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 6.8
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ghost atom cutoff = 6.8
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binsize = 3.4, bins = 1 1 1
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5 neighbor lists, perpetual/occasional/extra = 1 4 0
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(1) pair zbl, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) compute sna/atom, occasional
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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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(3) compute snav/atom, occasional
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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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(4) compute snad/atom, occasional
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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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(5) compute mliap, occasional
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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) = 22.45 | 22.45 | 22.45 Mbytes
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PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
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322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
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Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
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100.0% CPU use with 1 MPI tasks x no 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 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 1e-06 | | |100.00
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Nlocal: 2 ave 2 max 2 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 853 ave 853 max 853 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 330 ave 330 max 330 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 660 ave 660 max 660 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 660
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Ave neighs/atom = 330
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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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200
examples/mliap/log.03Jul20.mliap.quadratic.compute.g++.4
Normal file
200
examples/mliap/log.03Jul20.mliap.quadratic.compute.g++.4
Normal file
@ -0,0 +1,200 @@
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LAMMPS (15 Jun 2020)
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# Demonstrate MLIAP quadratic compute
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# initialize simulation
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variable nsteps index 0
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variable nrep equal 1
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variable a equal 2.0
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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 1
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variable ny equal ${nrep}
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variable ny equal 1
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variable nz equal ${nrep}
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variable nz equal 1
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boundary p p p
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atom_modify map hash
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lattice bcc $a
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lattice bcc 2
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Lattice spacing in x,y,z = 2 2 2
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 1 0 ${ny} 0 ${nz}
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region box block 0 1 0 1 0 ${nz}
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region box block 0 1 0 1 0 1
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create_box 2 box
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Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
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1 by 2 by 2 MPI processor grid
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create_atoms 2 box
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Created 2 atoms
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create_atoms CPU = 0.001 seconds
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mass * 180.88
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displace_atoms all random 0.1 0.1 0.1 123456
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# set up reference potential
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 73
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pair_style zbl ${zblcutinner} ${zblcutouter}
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pair_style zbl 4 ${zblcutouter}
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pair_style zbl 4 4.8
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pair_coeff * * ${zblz} ${zblz}
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pair_coeff * * 73 ${zblz}
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pair_coeff * * 73 73
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# choose SNA parameters
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variable twojmax equal 2
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variable rcutfac equal 1.0
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variable rfac0 equal 0.99363
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variable rmin0 equal 0
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variable radelem1 equal 2.3
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variable radelem2 equal 2.0
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variable wj1 equal 1.0
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variable wj2 equal 0.96
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variable quadratic equal 1
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variable bzero equal 0
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variable switch equal 0
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variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
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1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
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# set up per-atom computes
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compute b all sna/atom ${snap_options}
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compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
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compute vb all snav/atom ${snap_options}
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compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
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compute db all snad/atom ${snap_options}
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compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
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# perform sums over atoms
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group snapgroup1 type 1
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0 atoms in group snapgroup1
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group snapgroup2 type 2
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2 atoms in group snapgroup2
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compute bsum1 snapgroup1 reduce sum c_b[*]
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compute bsum2 snapgroup2 reduce sum c_b[*]
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# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
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# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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compute vbsum all reduce sum c_vb[*]
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# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
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variable db_2_100 equal c_db[2][100]
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# set up compute snap generating global array
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compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21
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SNAP keyword rcutfac 1.0
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SNAP keyword twojmax 2
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SNAP keyword nelems 2
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SNAP keyword elems A
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SNAP keyword radelems 2.3
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SNAP keyword welems 1.0
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SNAP keyword rfac0 0.99363
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SNAP keyword rmin0 0
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SNAP keyword bzeroflag 0
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SNAP keyword switchflag 0
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fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector
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thermo 100
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# test output: 1: total potential energy
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# 2: xy component of stress tensor
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# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
|
||||
# 4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
|
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# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
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#
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# followed by 5 counterparts from compute snap
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thermo_style custom pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
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thermo_modify norm no
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# dump mydump_db all custom 1000 dump_db id c_db[*]
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||||
# dump_modify mydump_db sort id
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# Run MD
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run ${nsteps}
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run 0
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Neighbor list info ...
|
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update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.8
|
||||
ghost atom cutoff = 6.8
|
||||
binsize = 3.4, bins = 1 1 1
|
||||
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||
(1) pair zbl, perpetual
|
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attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
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bin: standard
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(2) compute sna/atom, occasional
|
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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
|
||||
bin: standard
|
||||
(3) compute snav/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(4) compute snad/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(5) compute mliap, occasional
|
||||
attributes: full, newton on
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pair build: full/bin/atomonly
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||||
stencil: full/bin/3d
|
||||
bin: standard
|
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WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
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Per MPI rank memory allocation (min/avg/max) = 22.18 | 22.18 | 22.18 Mbytes
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PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
|
||||
322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
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Loop time of 2e-06 on 4 procs for 0 steps with 2 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2e-06 | | |100.00
|
||||
|
||||
Nlocal: 0.5 ave 1 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 734.5 ave 735 max 734 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 82.5 ave 177 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
FullNghs: 165 ave 330 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 660
|
||||
Ave neighs/atom = 330
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
199
examples/mliap/log.03Jul20.mliap.snap.compute.g++.1
Normal file
199
examples/mliap/log.03Jul20.mliap.snap.compute.g++.1
Normal file
@ -0,0 +1,199 @@
|
||||
LAMMPS (15 Jun 2020)
|
||||
# Demonstrate bispectrum computes
|
||||
|
||||
# initialize simulation
|
||||
|
||||
variable nsteps index 0
|
||||
variable nrep equal 1
|
||||
variable a equal 2.0
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 1
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 1
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 1
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_modify map hash
|
||||
lattice bcc $a
|
||||
lattice bcc 2
|
||||
Lattice spacing in x,y,z = 2 2 2
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 2 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
|
||||
# set up reference potential
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
pair_style zbl ${zblcutinner} ${zblcutouter}
|
||||
pair_style zbl 4 ${zblcutouter}
|
||||
pair_style zbl 4 4.8
|
||||
pair_coeff * * ${zblz} ${zblz}
|
||||
pair_coeff * * 73 ${zblz}
|
||||
pair_coeff * * 73 73
|
||||
|
||||
# choose SNA parameters
|
||||
|
||||
variable twojmax equal 2
|
||||
variable rcutfac equal 1.0
|
||||
variable rfac0 equal 0.99363
|
||||
variable rmin0 equal 0
|
||||
variable radelem1 equal 2.3
|
||||
variable radelem2 equal 2.0
|
||||
variable wj1 equal 1.0
|
||||
variable wj2 equal 0.96
|
||||
variable quadratic equal 0
|
||||
variable bzero equal 0
|
||||
variable switch equal 0
|
||||
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
|
||||
1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
|
||||
# set up per-atom computes
|
||||
|
||||
compute b all sna/atom ${snap_options}
|
||||
compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
compute vb all snav/atom ${snap_options}
|
||||
compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
compute db all snad/atom ${snap_options}
|
||||
compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
|
||||
# perform sums over atoms
|
||||
|
||||
group snapgroup1 type 1
|
||||
0 atoms in group snapgroup1
|
||||
group snapgroup2 type 2
|
||||
2 atoms in group snapgroup2
|
||||
compute bsum1 snapgroup1 reduce sum c_b[*]
|
||||
compute bsum2 snapgroup2 reduce sum c_b[*]
|
||||
# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
|
||||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
variable db_2_25 equal c_db[2][25]
|
||||
|
||||
# set up compute snap generating global array
|
||||
|
||||
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6
|
||||
SNAP keyword rcutfac 1.0
|
||||
SNAP keyword twojmax 2
|
||||
SNAP keyword nelems 2
|
||||
SNAP keyword elems A
|
||||
SNAP keyword radelems 2.3
|
||||
SNAP keyword welems 1.0
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword switchflag 0
|
||||
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
|
||||
|
||||
thermo 100
|
||||
|
||||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(B_{000}^i, all i of type 2)
|
||||
# 4: xz component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
|
||||
# 5: y component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
|
||||
thermo_modify norm no
|
||||
|
||||
# dump mydump_db all custom 1000 dump_db id c_db[*]
|
||||
# dump_modify mydump_db sort id
|
||||
|
||||
# Run MD
|
||||
|
||||
run ${nsteps}
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.8
|
||||
ghost atom cutoff = 6.8
|
||||
binsize = 3.4, bins = 1 1 1
|
||||
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||
(1) pair zbl, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) compute sna/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(3) compute snav/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(4) compute snad/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(5) compute mliap, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.73 | 10.73 | 10.73 Mbytes
|
||||
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
|
||||
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
|
||||
Loop time of 0 on 1 procs for 0 steps with 2 atoms
|
||||
|
||||
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0 | | | 0.00
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 853 ave 853 max 853 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 330 ave 330 max 330 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 660 ave 660 max 660 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 660
|
||||
Ave neighs/atom = 330
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
200
examples/mliap/log.03Jul20.mliap.snap.compute.g++.4
Normal file
200
examples/mliap/log.03Jul20.mliap.snap.compute.g++.4
Normal file
@ -0,0 +1,200 @@
|
||||
LAMMPS (15 Jun 2020)
|
||||
# Demonstrate bispectrum computes
|
||||
|
||||
# initialize simulation
|
||||
|
||||
variable nsteps index 0
|
||||
variable nrep equal 1
|
||||
variable a equal 2.0
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 1
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 1
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 1
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_modify map hash
|
||||
lattice bcc $a
|
||||
lattice bcc 2
|
||||
Lattice spacing in x,y,z = 2 2 2
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 2 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
|
||||
# set up reference potential
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
pair_style zbl ${zblcutinner} ${zblcutouter}
|
||||
pair_style zbl 4 ${zblcutouter}
|
||||
pair_style zbl 4 4.8
|
||||
pair_coeff * * ${zblz} ${zblz}
|
||||
pair_coeff * * 73 ${zblz}
|
||||
pair_coeff * * 73 73
|
||||
|
||||
# choose SNA parameters
|
||||
|
||||
variable twojmax equal 2
|
||||
variable rcutfac equal 1.0
|
||||
variable rfac0 equal 0.99363
|
||||
variable rmin0 equal 0
|
||||
variable radelem1 equal 2.3
|
||||
variable radelem2 equal 2.0
|
||||
variable wj1 equal 1.0
|
||||
variable wj2 equal 0.96
|
||||
variable quadratic equal 0
|
||||
variable bzero equal 0
|
||||
variable switch equal 0
|
||||
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
|
||||
1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
|
||||
# set up per-atom computes
|
||||
|
||||
compute b all sna/atom ${snap_options}
|
||||
compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
compute vb all snav/atom ${snap_options}
|
||||
compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
compute db all snad/atom ${snap_options}
|
||||
compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
|
||||
# perform sums over atoms
|
||||
|
||||
group snapgroup1 type 1
|
||||
0 atoms in group snapgroup1
|
||||
group snapgroup2 type 2
|
||||
2 atoms in group snapgroup2
|
||||
compute bsum1 snapgroup1 reduce sum c_b[*]
|
||||
compute bsum2 snapgroup2 reduce sum c_b[*]
|
||||
# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
|
||||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
variable db_2_25 equal c_db[2][25]
|
||||
|
||||
# set up compute snap generating global array
|
||||
|
||||
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6
|
||||
SNAP keyword rcutfac 1.0
|
||||
SNAP keyword twojmax 2
|
||||
SNAP keyword nelems 2
|
||||
SNAP keyword elems A
|
||||
SNAP keyword radelems 2.3
|
||||
SNAP keyword welems 1.0
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword switchflag 0
|
||||
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
|
||||
|
||||
thermo 100
|
||||
|
||||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(B_{000}^i, all i of type 2)
|
||||
# 4: xz component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
|
||||
# 5: y component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
|
||||
thermo_modify norm no
|
||||
|
||||
# dump mydump_db all custom 1000 dump_db id c_db[*]
|
||||
# dump_modify mydump_db sort id
|
||||
|
||||
# Run MD
|
||||
|
||||
run ${nsteps}
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.8
|
||||
ghost atom cutoff = 6.8
|
||||
binsize = 3.4, bins = 1 1 1
|
||||
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||
(1) pair zbl, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) compute sna/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(3) compute snav/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(4) compute snad/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(5) compute mliap, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.69 | 10.69 | 10.7 Mbytes
|
||||
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
|
||||
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
|
||||
Loop time of 3.25e-06 on 4 procs for 0 steps with 2 atoms
|
||||
|
||||
115.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.25e-06 | | |100.00
|
||||
|
||||
Nlocal: 0.5 ave 1 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 734.5 ave 735 max 734 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 82.5 ave 177 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
FullNghs: 165 ave 330 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 660
|
||||
Ave neighs/atom = 330
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
Reference in New Issue
Block a user