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example Ta06A using nn

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Pedro Antonio Santos Flórez
2021-03-03 14:53:56 -03:00
parent b7367e713a
commit 6c0c6ce3b0
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examples/mliap/Ta06A.mliap.nn Normal file
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# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# Definition of SNAP potential Ta_Cand06A
# Assumes 1 LAMMPS atom type
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73
# Specify hybrid with SNAP, ZBL
pair_style hybrid/overlay &
zbl ${zblcutinner} ${zblcutouter} &
mliap model nn Ta06A_nn.mliap.model &
descriptor sna Ta06A.mliap.descriptor
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff * * mliap Ta

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examples/mliap/Ta06A_nn.mliap.model Normal file
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# DATE: 2021-03-03 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# LAMMPS SNAP_nn coefficients for Ta_Cand06A
# nelements nparams
1 31
# NET #ndescriptors #nlayers #activation_func for layer 1 #number of nodes for layer 1, ..., ..., ....,
NET 30 1 linear 1
#scale0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#scale1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#coeff
-2.92477
-0.01137 -0.00775 -0.04907 -0.15047 0.09157 0.05590 0.05785 -0.11615 -0.17122 -0.10583 0.03941 -0.11284 0.03939 -0.07331 -0.06582 -0.09341 -0.10587 -0.15497 0.04820 0.00205 0.00060 -0.04898 -0.05084 -0.03371 -0.01441 -0.01501 -0.00599 -0.06373 0.03965 0.01072

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# Demonstrate MLIAP interface to linear SNAP potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.316
units metal
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable ny equal ${nrep}
variable nz equal ${nrep}
boundary p p p
lattice bcc $a
region box block 0 ${nx} 0 ${ny} 0 ${nz}
create_box 1 box
create_atoms 1 box
mass 1 180.88
# choose potential
include Ta06A.mliap.nn
# Setup output
compute eatom all pe/atom
compute energy all reduce sum c_eatom
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp epair c_energy etotal press v_press
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 4928459 loop geom
fix 1 all nve
run ${nsteps}

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LAMMPS (10 Feb 2021)
# Demonstrate MLIAP interface to linear SNAP potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.316
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 3.316
Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
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 = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000 13.264000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
create_atoms CPU = 0.000 seconds
mass 1 180.88
# choose potential
include Ta06A.mliap.nn
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# Definition of SNAP potential Ta_Cand06A
# Assumes 1 LAMMPS atom type
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73
# Specify hybrid with SNAP, ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model nn Ta06A_nn.mliap.model descriptor sna Ta06A.mliap.descriptor
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model nn Ta06A_nn.mliap.model descriptor sna Ta06A.mliap.descriptor
pair_style hybrid/overlay zbl 4 4.8 mliap model nn Ta06A_nn.mliap.model descriptor sna Ta06A.mliap.descriptor
Reading potential file Ta06A_nn.mliap.model with DATE: 2021-03-03
Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
SNAP keyword rcutfac 4.67637
SNAP keyword twojmax 6
SNAP keyword nelems 1
SNAP keyword elems Ta
SNAP keyword radelems 0.5
SNAP keyword welems 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 73 ${zblz}
pair_coeff 1 1 zbl 73 73
pair_coeff * * mliap Ta
# Setup output
compute eatom all pe/atom
compute energy all reduce sum c_eatom
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp epair c_energy etotal press v_press
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 4928459 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 = 5.8
ghost atom cutoff = 5.8
binsize = 2.9, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair zbl, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 18.15 | 18.15 | 18.15 Mbytes
Step Temp E_pair c_energy TotEng Press v_press
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796
20 284.53666 -11.849587 -11.849587 -11.813095 2289.1527 -2289.1527
30 266.51577 -11.847275 -11.847275 -11.813095 1851.7131 -1851.7131
40 243.05007 -11.844266 -11.844266 -11.813095 1570.684 -1570.684
50 215.51032 -11.840734 -11.840734 -11.813094 1468.1899 -1468.1899
60 185.48331 -11.836883 -11.836883 -11.813094 1524.8757 -1524.8757
70 154.6736 -11.832931 -11.832931 -11.813094 1698.3351 -1698.3351
80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715
90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563
100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526
Loop time of 1.19515 on 1 procs for 100 steps with 128 atoms
Performance: 3.615 ns/day, 6.640 hours/ns, 83.671 timesteps/s
98.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1924 | 1.1924 | 1.1924 | 0.0 | 99.77
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.000961 | 0.000961 | 0.000961 | 0.0 | 0.08
Output | 0.000707 | 0.000707 | 0.000707 | 0.0 | 0.06
Modify | 0.000459 | 0.000459 | 0.000459 | 0.0 | 0.04
Other | | 0.00065 | | | 0.05
Nlocal: 128.000 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 727.000 ave 727 max 727 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3712.00 ave 3712 max 3712 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 7424.00 ave 7424 max 7424 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7424
Ave neighs/atom = 58.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01