1LAMMPS (15 Jun 2020)
2# Demonstrate MLIAP interface to ChemSNAP potential
3
4# Initialize simulation
5
6variable nsteps index 100
7variable nrep equal 4
8variable a equal 5.83
9units           metal
10
11# generate the box and atom positions using a FCC lattice
12
13variable nx equal ${nrep}
14variable nx equal 4
15variable ny equal ${nrep}
16variable ny equal 4
17variable nz equal ${nrep}
18variable nz equal 4
19
20boundary        p p p
21
22lattice         diamond $a
23lattice         diamond 5.83
24Lattice spacing in x,y,z = 5.83 5.83 5.83
25region          box block 0 ${nx} 0 ${ny} 0 ${nz}
26region          box block 0 4 0 ${ny} 0 ${nz}
27region          box block 0 4 0 4 0 ${nz}
28region          box block 0 4 0 4 0 4
29create_box      2 box
30Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32)
31  1 by 2 by 2 MPI processor grid
32create_atoms    1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
33Created 512 atoms
34  create_atoms CPU = 0.000 seconds
35
36mass 1 114.76
37mass 2 30.98
38
39# choose potential
40
41include InP_JCPA2020.mliap
42# DATE: 2020-06-01 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)
43
44# Definition of SNAP+ZBL potential.
45
46variable zblcutinner index 4
47variable zblcutouter index 4.2
48variable zblz1 index 49
49variable zblz2 index 15
50
51# Specify hybrid with SNAP and ZBL
52
53pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
54pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
55pair_style hybrid/overlay zbl 4 4.2 mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
56Reading potential file InP_JCPA2020.mliap.model with DATE: 2020-06-01
57Reading potential file InP_JCPA2020.mliap.descriptor with DATE: 2020-06-01
58SNAP keyword rcutfac 1.0
59SNAP keyword twojmax 6
60SNAP keyword nelems 2
61SNAP keyword elems In
62SNAP keyword radelems 3.81205
63SNAP keyword welems 1
64SNAP keyword rfac0 0.99363
65SNAP keyword rmin0 0.0
66SNAP keyword bzeroflag 1
67SNAP keyword wselfallflag 1
68SNAP keyword chemflag 1
69SNAP keyword bnormflag 1
70pair_coeff 1 1 zbl ${zblz1} ${zblz1}
71pair_coeff 1 1 zbl 49 ${zblz1}
72pair_coeff 1 1 zbl 49 49
73pair_coeff 1 2 zbl ${zblz1} ${zblz2}
74pair_coeff 1 2 zbl 49 ${zblz2}
75pair_coeff 1 2 zbl 49 15
76pair_coeff 2 2 zbl ${zblz2} ${zblz2}
77pair_coeff 2 2 zbl 15 ${zblz2}
78pair_coeff 2 2 zbl 15 15
79pair_coeff * * mliap   In P
80
81
82# Setup output
83
84thermo          10
85thermo_modify norm yes
86
87# Set up NVE run
88
89timestep 0.5e-3
90neighbor 1.0 bin
91neigh_modify once no every 1 delay 0 check yes
92
93# Run MD
94
95velocity all create 300.0 4928459 loop geom
96fix 1 all nve
97run             ${nsteps}
98run             100
99Neighbor list info ...
100  update every 1 steps, delay 0 steps, check yes
101  max neighbors/atom: 2000, page size: 100000
102  master list distance cutoff = 8.6589
103  ghost atom cutoff = 8.6589
104  binsize = 4.32945, bins = 6 6 6
105  2 neighbor lists, perpetual/occasional/extra = 2 0 0
106  (1) pair zbl, perpetual, half/full from (2)
107      attributes: half, newton on
108      pair build: halffull/newton
109      stencil: none
110      bin: none
111  (2) pair mliap, perpetual
112      attributes: full, newton on
113      pair build: full/bin/atomonly
114      stencil: full/bin/3d
115      bin: standard
116Per MPI rank memory allocation (min/avg/max) = 4.591 | 4.591 | 4.591 Mbytes
117Step Temp E_pair E_mol TotEng Press
118       0          300   -3.4805794            0   -3.4418771    1353.5968
119      10    285.84677   -3.4787531            0   -3.4418766    1611.7131
120      20    248.14649   -3.4738884            0   -3.4418756    2312.0308
121      30    198.94136   -3.4675394            0   -3.4418744    3168.1543
122      40    152.74831   -3.4615791            0   -3.4418734    3903.5749
123      50     121.9796   -3.4576091            0   -3.4418728    4387.1254
124      60    113.27555   -3.4564863            0   -3.4418729    4556.3003
125      70    125.68089   -3.4580873            0   -3.4418735    4431.2083
126      80    151.47475   -3.4614159            0   -3.4418745    4107.2369
127      90    179.18708   -3.4649919            0   -3.4418754    3739.5881
128     100    197.50662   -3.4673559            0    -3.441876    3492.7778
129Loop time of 5.01913 on 4 procs for 100 steps with 512 atoms
130
131Performance: 0.861 ns/day, 27.884 hours/ns, 19.924 timesteps/s
13299.7% CPU use with 4 MPI tasks x no OpenMP threads
133
134MPI task timing breakdown:
135Section |  min time  |  avg time  |  max time  |%varavg| %total
136---------------------------------------------------------------
137Pair    | 4.9328     | 4.9409     | 4.952      |   0.3 | 98.44
138Neigh   | 0          | 0          | 0          |   0.0 |  0.00
139Comm    | 0.065669   | 0.076754   | 0.084728   |   2.5 |  1.53
140Output  | 0.000173   | 0.00028775 | 0.000617   |   0.0 |  0.01
141Modify  | 0.000256   | 0.00026675 | 0.000281   |   0.0 |  0.01
142Other   |            | 0.0009633  |            |       |  0.02
143
144Nlocal:    128 ave 128 max 128 min
145Histogram: 4 0 0 0 0 0 0 0 0 0
146Nghost:    1099 ave 1099 max 1099 min
147Histogram: 4 0 0 0 0 0 0 0 0 0
148Neighs:    7808 ave 7808 max 7808 min
149Histogram: 4 0 0 0 0 0 0 0 0 0
150FullNghs:  15616 ave 15616 max 15616 min
151Histogram: 4 0 0 0 0 0 0 0 0 0
152
153Total # of neighbors = 62464
154Ave neighs/atom = 122
155Neighbor list builds = 0
156Dangerous builds = 0
157
158Total wall time: 0:00:05
159