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Added W-Be example to example/snap folder

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Mary Alice Cusentino
2019-09-18 14:34:20 -06:00
parent 572235e66a
commit e847777e43
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examples/snap/WBe_Wood_PRB2019.snap Symbolic link
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../../potentials/WBe_Wood_PRB2019.snap

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examples/snap/WBe_Wood_PRB2019.snapcoeff Symbolic link
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../../potentials/WBe_Wood_PRB2019.snapcoeff

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examples/snap/WBe_Wood_PRB2019.snapparam Symbolic link
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../../potentials/WBe_Wood_PRB2019.snapparam

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examples/snap/in.snap.WBe.PRB2019 Normal file
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# Demonstrate SNAP W-Be potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.1803
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 2 box
create_atoms 1 box
mass 1 183.84
mass 2 9.012182
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
group tungsten type 1
group beryllium type 2
# choose potential
include WBe_Wood_PRB2019.snap
# Setup output
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
fix 1 all nve
run ${nsteps}

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examples/snap/log.18Sep19.snap.WBeSNAP.g++.1 Normal file
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LAMMPS (7 Aug 2019)
# Demonstrate SNAP W-Be potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.1803
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 3.1803
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
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 2 box
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
create_atoms CPU = 0.000234842 secs
mass 1 183.84
mass 2 9.012182
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
5 settings made for type/fraction
group tungsten type 1
123 atoms in group tungsten
group beryllium type 2
5 atoms in group beryllium
# choose potential
include WBe_Wood_PRB2019.snap
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz1 equal 74
variable zblz2 equal 4
# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 4.8 snap
pair_coeff 1 1 zbl ${zblz1} ${zblz1}
pair_coeff 1 1 zbl 74 ${zblz1}
pair_coeff 1 1 zbl 74 74
pair_coeff 1 2 zbl ${zblz1} ${zblz2}
pair_coeff 1 2 zbl 74 ${zblz2}
pair_coeff 1 2 zbl 74 4
pair_coeff 2 2 zbl ${zblz2} ${zblz2}
pair_coeff 2 2 zbl 4 ${zblz2}
pair_coeff 2 2 zbl 4 4
pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be
SNAP Element = W, Radius 0.5, Weight 1
SNAP Element = Be, Radius 0.417932, Weight 0.959049
SNAP keyword rcutfac 4.8123
SNAP keyword twojmax 8
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 1
SNAP keyword quadraticflag 0
# Setup output
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
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 = 5.8123
ghost atom cutoff = 5.8123
binsize = 2.90615, 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 snap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.268 | 4.268 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -8.5980876 0 -8.5596125 -35284.855
10 299.29029 -8.5979965 0 -8.5596125 -35299.259
20 288.99334 -8.5966759 0 -8.5596124 -35004.093
30 269.91027 -8.5942284 0 -8.5596123 -34447.077
40 243.57361 -8.5908505 0 -8.5596121 -33687.105
50 212.21385 -8.5868284 0 -8.5596119 -32821.864
60 178.77144 -8.5825391 0 -8.5596116 -31971.17
70 146.71854 -8.578428 0 -8.5596113 -31245.51
80 119.50956 -8.5749383 0 -8.5596111 -30724.137
90 99.872785 -8.5724197 0 -8.559611 -30440.244
100 89.604584 -8.5711027 0 -8.5596109 -30392.805
Loop time of 3.16831 on 1 procs for 100 steps with 128 atoms
Performance: 1.364 ns/day, 17.602 hours/ns, 31.563 timesteps/s
199.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.1672 | 3.1672 | 3.1672 | 0.0 | 99.97
Neigh | 0.00030208 | 0.00030208 | 0.00030208 | 0.0 | 0.01
Comm | 0.00029612 | 0.00029612 | 0.00029612 | 0.0 | 0.01
Output | 0.00019813 | 0.00019813 | 0.00019813 | 0.0 | 0.01
Modify | 0.00014448 | 0.00014448 | 0.00014448 | 0.0 | 0.00
Other | | 0.0001433 | | | 0.00
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 727 ave 727 max 727 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3710 ave 3710 max 3710 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 7420 ave 7420 max 7420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7420
Ave neighs/atom = 57.9688
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:03

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examples/snap/log.18Sep19.snap.WBeSNAP.g++.4 Normal file
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LAMMPS (7 Aug 2019)
# Demonstrate SNAP W-Be potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.1803
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 3.1803
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
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 2 box
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
create_atoms CPU = 0.000317097 secs
mass 1 183.84
mass 2 9.012182
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
5 settings made for type/fraction
group tungsten type 1
123 atoms in group tungsten
group beryllium type 2
5 atoms in group beryllium
# choose potential
include WBe_Wood_PRB2019.snap
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz1 equal 74
variable zblz2 equal 4
# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 4.8 snap
pair_coeff 1 1 zbl ${zblz1} ${zblz1}
pair_coeff 1 1 zbl 74 ${zblz1}
pair_coeff 1 1 zbl 74 74
pair_coeff 1 2 zbl ${zblz1} ${zblz2}
pair_coeff 1 2 zbl 74 ${zblz2}
pair_coeff 1 2 zbl 74 4
pair_coeff 2 2 zbl ${zblz2} ${zblz2}
pair_coeff 2 2 zbl 4 ${zblz2}
pair_coeff 2 2 zbl 4 4
pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be
SNAP Element = W, Radius 0.5, Weight 1
SNAP Element = Be, Radius 0.417932, Weight 0.959049
SNAP keyword rcutfac 4.8123
SNAP keyword twojmax 8
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 1
SNAP keyword quadraticflag 0
# Setup output
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
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 = 5.8123
ghost atom cutoff = 5.8123
binsize = 2.90615, 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 snap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.167 | 4.167 | 4.167 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -8.5980876 0 -8.5596125 -35284.855
10 296.24946 -8.5976065 0 -8.5596124 -35140.29
20 282.27904 -8.5958147 0 -8.5596123 -34710.3
30 259.54978 -8.5928995 0 -8.5596121 -34060.43
40 230.41412 -8.5891626 0 -8.5596119 -33258.275
50 197.85135 -8.5849861 0 -8.5596116 -32389.527
60 165.21732 -8.5808005 0 -8.5596113 -31550.426
70 135.94024 -8.5770455 0 -8.5596111 -30839.006
80 113.06617 -8.5741117 0 -8.5596109 -30339.177
90 98.542347 -8.572249 0 -8.5596109 -30094.29
100 92.524343 -8.5714774 0 -8.5596111 -30091.988
Loop time of 0.813674 on 4 procs for 100 steps with 128 atoms
Performance: 5.309 ns/day, 4.520 hours/ns, 122.899 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.79079 | 0.79788 | 0.80888 | 0.8 | 98.06
Neigh | 7.1049e-05 | 8.0049e-05 | 9.2983e-05 | 0.0 | 0.01
Comm | 0.0041246 | 0.01515 | 0.022235 | 5.5 | 1.86
Output | 0.000144 | 0.00017095 | 0.00024796 | 0.0 | 0.02
Modify | 4.4823e-05 | 5.8889e-05 | 7.2718e-05 | 0.0 | 0.01
Other | | 0.000338 | | | 0.04
Nlocal: 32 ave 37 max 28 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 431 ave 435 max 426 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 927 ave 1071 max 821 min
Histogram: 1 0 1 0 1 0 0 0 0 1
FullNghs: 1854 ave 2144 max 1624 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 7416
Ave neighs/atom = 57.9375
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00