update ML-UF3 example
This commit is contained in:
Axel Kohlmeyer
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examples/PACKAGES/uf3/Nb.uf3
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examples/PACKAGES/uf3/Nb.uf3
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../../../potentials/Nb.uf3
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This directory contains a variety of tests for the ML-UF3 package. These include:
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in.uf3.3b.W # UF3 2-body and 3-body potential
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in.uf3.2b.W # UF3 2-body potential
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#UF3 POT
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2B 0 3 uk
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5.5 22
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0.001 0.001 0.001 0.001 0.36759999999999998 0.73419999999999996 1.1007999999999998 1.4673999999999998 1.8339999999999999 2.2005999999999997 2.5671999999999997 2.9337999999999997 3.3003999999999998 3.6669999999999998 4.0335999999999999 4.4001999999999999 4.7667999999999999 5.1334 5.5 5.5 5.5 5.5
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18
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85.256465889606673 85.256465889606673 60.118514370108457 39.372994322346095 23.019905746319598 11.095292589050336 2.5770289203919474 -0.21591409154943711 -0.41582603147952274 -0.29361205978352245 -0.23467230507950282 -0.13083777191249607 -0.031024404500506326 -0.059144784016542738 -0.037145211195670137 0 0 0
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#
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#UF3 POT
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3B 0 3 uk
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7.0 3.5 3.5 19 13 13
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1.5 1.5 1.5 1.5 1.9583333333333333 2.4166666666666665 2.875 3.333333333333333 3.7916666666666665 4.25 4.708333333333333 5.1666666666666661 5.625 6.083333333333333 6.5416666666666661 7 7 7 7
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1.5 1.5 1.5 1.5 1.8333333333333333 2.1666666666666665 2.5 2.833333333333333 3.1666666666666665 3.5 3.5 3.5 3.5
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9 9 15
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|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
#
|
|
||||||
@ -1,47 +0,0 @@
|
|||||||
# Demonstrate UF3 W potential
|
|
||||||
|
|
||||||
# # ============= Initialize simulation
|
|
||||||
|
|
||||||
variable nsteps index 100
|
|
||||||
variable nrep equal 4
|
|
||||||
variable a equal 3.187
|
|
||||||
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 1 183.84
|
|
||||||
|
|
||||||
# # ============= set pair style
|
|
||||||
|
|
||||||
pair_style uf3 3
|
|
||||||
pair_coeff 1 1 W_W.uf3
|
|
||||||
pair_coeff 3b 1 1 1 W_W_W.uf3
|
|
||||||
|
|
||||||
|
|
||||||
# # ============= 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 2367804 loop geom
|
|
||||||
fix 1 all nve
|
|
||||||
run ${nsteps}
|
|
||||||
@ -4,7 +4,7 @@
|
|||||||
|
|
||||||
variable nsteps index 100
|
variable nsteps index 100
|
||||||
variable nrep equal 4
|
variable nrep equal 4
|
||||||
variable a equal 3.187
|
variable a equal 3.3005
|
||||||
units metal
|
units metal
|
||||||
|
|
||||||
# generate the box and atom positions using a BCC lattice
|
# generate the box and atom positions using a BCC lattice
|
||||||
@ -20,12 +20,12 @@ region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
|||||||
create_box 1 box
|
create_box 1 box
|
||||||
create_atoms 1 box
|
create_atoms 1 box
|
||||||
|
|
||||||
mass 1 183.84
|
mass 1 92.906
|
||||||
|
|
||||||
# # ============= set pair style
|
# # ============= set pair style
|
||||||
|
|
||||||
pair_style uf3 2
|
pair_style uf3 3
|
||||||
pair_coeff 1 1 W_W.uf3
|
pair_coeff * * Nb.uf3 Nb
|
||||||
|
|
||||||
|
|
||||||
# # ============= Setup output
|
# # ============= Setup output
|
||||||
118
examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.1
Normal file
118
examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.1
Normal file
@ -0,0 +1,118 @@
|
|||||||
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-199-g49f20229ad-modified)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Demonstrate UF3 W potential
|
||||||
|
|
||||||
|
# # ============= Initialize simulation
|
||||||
|
|
||||||
|
variable nsteps index 100
|
||||||
|
variable nrep equal 4
|
||||||
|
variable a equal 3.3005
|
||||||
|
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 3.3005
|
||||||
|
Lattice spacing in x,y,z = 3.3005 3.3005 3.3005
|
||||||
|
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 0 0) to (13.202 13.202 13.202)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 128 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (13.202 13.202 13.202)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass 1 92.906
|
||||||
|
|
||||||
|
# # ============= set pair style
|
||||||
|
|
||||||
|
pair_style uf3 3
|
||||||
|
pair_coeff * * Nb.uf3 Nb
|
||||||
|
Reading potential file Nb.uf3 with DATE: 2024-04-02
|
||||||
|
|
||||||
|
|
||||||
|
# # ============= 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 2367804 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 = 9
|
||||||
|
ghost atom cutoff = 9
|
||||||
|
binsize = 4.5, bins = 3 3 3
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair uf3, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.376 | 3.376 | 3.376 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 300 -4.4256832 0 -4.3872081 90756.437
|
||||||
|
10 294.36659 -4.4249607 0 -4.3872081 91006.427
|
||||||
|
20 277.9021 -4.422849 0 -4.387208 91716.126
|
||||||
|
30 251.88303 -4.4195119 0 -4.3872078 92789.12
|
||||||
|
40 218.42803 -4.4152211 0 -4.3872076 94118.45
|
||||||
|
50 180.40641 -4.4103445 0 -4.3872073 95579.009
|
||||||
|
60 141.2326 -4.4053202 0 -4.3872071 97031.816
|
||||||
|
70 104.54429 -4.4006146 0 -4.3872068 98332.882
|
||||||
|
80 73.787889 -4.3966699 0 -4.3872066 99351.332
|
||||||
|
90 51.759956 -4.3938446 0 -4.3872064 99992.934
|
||||||
|
100 40.209821 -4.3923633 0 -4.3872064 100211.98
|
||||||
|
Loop time of 0.385575 on 1 procs for 100 steps with 128 atoms
|
||||||
|
|
||||||
|
Performance: 11.204 ns/day, 2.142 hours/ns, 259.353 timesteps/s, 33.197 katom-step/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.38403 | 0.38403 | 0.38403 | 0.0 | 99.60
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.00090609 | 0.00090609 | 0.00090609 | 0.0 | 0.23
|
||||||
|
Output | 0.00017626 | 0.00017626 | 0.00017626 | 0.0 | 0.05
|
||||||
|
Modify | 0.00018204 | 0.00018204 | 0.00018204 | 0.0 | 0.05
|
||||||
|
Other | | 0.0002795 | | | 0.07
|
||||||
|
|
||||||
|
Nlocal: 128 ave 128 max 128 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1601 ave 1601 max 1601 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 21504 ave 21504 max 21504 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 21504
|
||||||
|
Ave neighs/atom = 168
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
118
examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.4
Normal file
118
examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.4
Normal file
@ -0,0 +1,118 @@
|
|||||||
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-199-g49f20229ad-modified)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Demonstrate UF3 W potential
|
||||||
|
|
||||||
|
# # ============= Initialize simulation
|
||||||
|
|
||||||
|
variable nsteps index 100
|
||||||
|
variable nrep equal 4
|
||||||
|
variable a equal 3.3005
|
||||||
|
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 3.3005
|
||||||
|
Lattice spacing in x,y,z = 3.3005 3.3005 3.3005
|
||||||
|
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 0 0) to (13.202 13.202 13.202)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 128 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (13.202 13.202 13.202)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
mass 1 92.906
|
||||||
|
|
||||||
|
# # ============= set pair style
|
||||||
|
|
||||||
|
pair_style uf3 3
|
||||||
|
pair_coeff * * Nb.uf3 Nb
|
||||||
|
Reading potential file Nb.uf3 with DATE: 2024-04-02
|
||||||
|
|
||||||
|
|
||||||
|
# # ============= 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 2367804 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 = 9
|
||||||
|
ghost atom cutoff = 9
|
||||||
|
binsize = 4.5, bins = 3 3 3
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair uf3, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.351 | 3.351 | 3.351 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 300 -4.4256832 0 -4.3872081 90756.437
|
||||||
|
10 294.36659 -4.4249607 0 -4.3872081 91006.427
|
||||||
|
20 277.9021 -4.422849 0 -4.387208 91716.126
|
||||||
|
30 251.88303 -4.4195119 0 -4.3872078 92789.12
|
||||||
|
40 218.42803 -4.4152211 0 -4.3872076 94118.45
|
||||||
|
50 180.40641 -4.4103445 0 -4.3872073 95579.009
|
||||||
|
60 141.2326 -4.4053202 0 -4.3872071 97031.816
|
||||||
|
70 104.54429 -4.4006146 0 -4.3872068 98332.882
|
||||||
|
80 73.787889 -4.3966699 0 -4.3872066 99351.332
|
||||||
|
90 51.759956 -4.3938446 0 -4.3872064 99992.934
|
||||||
|
100 40.209821 -4.3923633 0 -4.3872064 100211.98
|
||||||
|
Loop time of 0.11881 on 4 procs for 100 steps with 128 atoms
|
||||||
|
|
||||||
|
Performance: 36.361 ns/day, 0.660 hours/ns, 841.679 timesteps/s, 107.735 katom-step/s
|
||||||
|
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.10673 | 0.10875 | 0.11236 | 0.7 | 91.53
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0057324 | 0.0093477 | 0.011375 | 2.4 | 7.87
|
||||||
|
Output | 0.00016629 | 0.00018236 | 0.00022483 | 0.0 | 0.15
|
||||||
|
Modify | 9.4948e-05 | 0.00010621 | 0.00012066 | 0.0 | 0.09
|
||||||
|
Other | | 0.0004263 | | | 0.36
|
||||||
|
|
||||||
|
Nlocal: 32 ave 32 max 32 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1049 ave 1049 max 1049 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 5376 ave 5376 max 5376 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 21504
|
||||||
|
Ave neighs/atom = 168
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
@ -1,117 +0,0 @@
|
|||||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-337-g6bdf981942-modified)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Demonstrate UF3 W potential
|
|
||||||
|
|
||||||
# # ============= Initialize simulation
|
|
||||||
|
|
||||||
variable nsteps index 100
|
|
||||||
variable nrep equal 4
|
|
||||||
variable a equal 3.187
|
|
||||||
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 3.187
|
|
||||||
Lattice spacing in x,y,z = 3.187 3.187 3.187
|
|
||||||
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 0 0) to (12.748 12.748 12.748)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
create_atoms 1 box
|
|
||||||
Created 128 atoms
|
|
||||||
using lattice units in orthogonal box = (0 0 0) to (12.748 12.748 12.748)
|
|
||||||
create_atoms CPU = 0.000 seconds
|
|
||||||
|
|
||||||
mass 1 183.84
|
|
||||||
|
|
||||||
# # ============= set pair style
|
|
||||||
|
|
||||||
pair_style uf3 2
|
|
||||||
pair_coeff 1 1 W_W.uf3
|
|
||||||
|
|
||||||
|
|
||||||
# # ============= 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 2367804 loop geom
|
|
||||||
fix 1 all nve
|
|
||||||
run ${nsteps}
|
|
||||||
run 100
|
|
||||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 6.5
|
|
||||||
ghost atom cutoff = 6.5
|
|
||||||
binsize = 3.25, bins = 4 4 4
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair uf3, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.113 | 3.113 | 3.113 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 300 -4.9097145 0 -4.8712394 -398022.13
|
|
||||||
10 297.43433 -4.9093854 0 -4.8712394 -397994.78
|
|
||||||
20 289.88359 -4.908417 0 -4.8712393 -397922.72
|
|
||||||
30 277.73497 -4.9068589 0 -4.8712393 -397829.84
|
|
||||||
40 261.57286 -4.904786 0 -4.8712392 -397731.28
|
|
||||||
50 242.14207 -4.902294 0 -4.8712392 -397640.01
|
|
||||||
60 220.31079 -4.899494 0 -4.8712391 -397572.33
|
|
||||||
70 197.03391 -4.8965087 0 -4.871239 -397551.93
|
|
||||||
80 173.31044 -4.893466 0 -4.8712389 -397601.62
|
|
||||||
90 150.12364 -4.8904922 0 -4.8712388 -397739.2
|
|
||||||
100 128.38807 -4.8877046 0 -4.8712388 -397980.01
|
|
||||||
Loop time of 0.0333361 on 1 procs for 100 steps with 128 atoms
|
|
||||||
|
|
||||||
Performance: 129.589 ns/day, 0.185 hours/ns, 2999.749 timesteps/s, 383.968 katom-step/s
|
|
||||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.032205 | 0.032205 | 0.032205 | 0.0 | 96.61
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.00067389 | 0.00067389 | 0.00067389 | 0.0 | 2.02
|
|
||||||
Output | 9.6021e-05 | 9.6021e-05 | 9.6021e-05 | 0.0 | 0.29
|
|
||||||
Modify | 0.00019596 | 0.00019596 | 0.00019596 | 0.0 | 0.59
|
|
||||||
Other | | 0.0001652 | | | 0.50
|
|
||||||
|
|
||||||
Nlocal: 128 ave 128 max 128 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 1113 ave 1113 max 1113 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 8192 ave 8192 max 8192 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 8192
|
|
||||||
Ave neighs/atom = 64
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,117 +0,0 @@
|
|||||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-337-g6bdf981942-modified)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Demonstrate UF3 W potential
|
|
||||||
|
|
||||||
# # ============= Initialize simulation
|
|
||||||
|
|
||||||
variable nsteps index 100
|
|
||||||
variable nrep equal 4
|
|
||||||
variable a equal 3.187
|
|
||||||
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 3.187
|
|
||||||
Lattice spacing in x,y,z = 3.187 3.187 3.187
|
|
||||||
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 0 0) to (12.748 12.748 12.748)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
create_atoms 1 box
|
|
||||||
Created 128 atoms
|
|
||||||
using lattice units in orthogonal box = (0 0 0) to (12.748 12.748 12.748)
|
|
||||||
create_atoms CPU = 0.000 seconds
|
|
||||||
|
|
||||||
mass 1 183.84
|
|
||||||
|
|
||||||
# # ============= set pair style
|
|
||||||
|
|
||||||
pair_style uf3 2
|
|
||||||
pair_coeff 1 1 W_W.uf3
|
|
||||||
|
|
||||||
|
|
||||||
# # ============= 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 2367804 loop geom
|
|
||||||
fix 1 all nve
|
|
||||||
run ${nsteps}
|
|
||||||
run 100
|
|
||||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 6.5
|
|
||||||
ghost atom cutoff = 6.5
|
|
||||||
binsize = 3.25, bins = 4 4 4
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair uf3, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.104 | 3.104 | 3.104 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 300 -4.9097145 0 -4.8712394 -398022.13
|
|
||||||
10 297.43433 -4.9093854 0 -4.8712394 -397994.78
|
|
||||||
20 289.88359 -4.908417 0 -4.8712393 -397922.72
|
|
||||||
30 277.73497 -4.9068589 0 -4.8712393 -397829.84
|
|
||||||
40 261.57286 -4.904786 0 -4.8712392 -397731.28
|
|
||||||
50 242.14207 -4.902294 0 -4.8712392 -397640.01
|
|
||||||
60 220.31079 -4.899494 0 -4.8712391 -397572.33
|
|
||||||
70 197.03391 -4.8965087 0 -4.871239 -397551.93
|
|
||||||
80 173.31044 -4.893466 0 -4.8712389 -397601.62
|
|
||||||
90 150.12364 -4.8904922 0 -4.8712388 -397739.2
|
|
||||||
100 128.38807 -4.8877046 0 -4.8712388 -397980.01
|
|
||||||
Loop time of 0.0147453 on 4 procs for 100 steps with 128 atoms
|
|
||||||
|
|
||||||
Performance: 292.975 ns/day, 0.082 hours/ns, 6781.825 timesteps/s, 868.074 katom-step/s
|
|
||||||
96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0086489 | 0.010103 | 0.0115 | 1.4 | 68.52
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.0027662 | 0.0041052 | 0.0055079 | 2.1 | 27.84
|
|
||||||
Output | 0.00012555 | 0.0001367 | 0.00015958 | 0.0 | 0.93
|
|
||||||
Modify | 6.4367e-05 | 7.9187e-05 | 9.3374e-05 | 0.0 | 0.54
|
|
||||||
Other | | 0.000321 | | | 2.18
|
|
||||||
|
|
||||||
Nlocal: 32 ave 32 max 32 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 697 ave 697 max 697 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 2048 ave 2048 max 2048 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 8192
|
|
||||||
Ave neighs/atom = 64
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,117 +0,0 @@
|
|||||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-337-g6bdf981942-modified)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Demonstrate UF3 W potential
|
|
||||||
|
|
||||||
# # ============= Initialize simulation
|
|
||||||
|
|
||||||
variable nsteps index 100
|
|
||||||
variable nrep equal 4
|
|
||||||
variable a equal 3.187
|
|
||||||
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 3.187
|
|
||||||
Lattice spacing in x,y,z = 3.187 3.187 3.187
|
|
||||||
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 0 0) to (12.748 12.748 12.748)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
create_atoms 1 box
|
|
||||||
Created 128 atoms
|
|
||||||
using lattice units in orthogonal box = (0 0 0) to (12.748 12.748 12.748)
|
|
||||||
create_atoms CPU = 0.000 seconds
|
|
||||||
|
|
||||||
mass 1 183.84
|
|
||||||
|
|
||||||
# # ============= set pair style
|
|
||||||
|
|
||||||
pair_style uf3 3
|
|
||||||
pair_coeff 1 1 W_W.uf3
|
|
||||||
pair_coeff 3b 1 1 1 W_W_W.uf3
|
|
||||||
|
|
||||||
|
|
||||||
# # ============= 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 2367804 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 = 6.5
|
|
||||||
ghost atom cutoff = 6.5
|
|
||||||
binsize = 3.25, bins = 4 4 4
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair uf3, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.214 | 3.214 | 3.214 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 300 -4.3916353 0 -4.3531602 -21224
|
|
||||||
10 292.96093 -4.3907325 0 -4.3531602 -21177.095
|
|
||||||
20 272.60651 -4.3881219 0 -4.35316 -21038.525
|
|
||||||
30 241.12074 -4.3840835 0 -4.3531597 -20793.964
|
|
||||||
40 201.8718 -4.3790495 0 -4.3531594 -20444.219
|
|
||||||
50 159.06853 -4.3735596 0 -4.353159 -19996.634
|
|
||||||
60 117.24817 -4.3681958 0 -4.3531587 -19470.011
|
|
||||||
70 80.716097 -4.3635102 0 -4.3531584 -18905.505
|
|
||||||
80 53.030322 -4.3599593 0 -4.3531582 -18362.596
|
|
||||||
90 36.611518 -4.3578535 0 -4.3531581 -17898.612
|
|
||||||
100 32.512413 -4.3573279 0 -4.3531581 -17551.048
|
|
||||||
Loop time of 0.48771 on 1 procs for 100 steps with 128 atoms
|
|
||||||
|
|
||||||
Performance: 8.858 ns/day, 2.709 hours/ns, 205.040 timesteps/s, 26.245 katom-step/s
|
|
||||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.48625 | 0.48625 | 0.48625 | 0.0 | 99.70
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.00078 | 0.00078 | 0.00078 | 0.0 | 0.16
|
|
||||||
Output | 0.0001819 | 0.0001819 | 0.0001819 | 0.0 | 0.04
|
|
||||||
Modify | 0.00020794 | 0.00020794 | 0.00020794 | 0.0 | 0.04
|
|
||||||
Other | | 0.0002902 | | | 0.06
|
|
||||||
|
|
||||||
Nlocal: 128 ave 128 max 128 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 1113 ave 1113 max 1113 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 8192 ave 8192 max 8192 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 8192
|
|
||||||
Ave neighs/atom = 64
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,117 +0,0 @@
|
|||||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-337-g6bdf981942-modified)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Demonstrate UF3 W potential
|
|
||||||
|
|
||||||
# # ============= Initialize simulation
|
|
||||||
|
|
||||||
variable nsteps index 100
|
|
||||||
variable nrep equal 4
|
|
||||||
variable a equal 3.187
|
|
||||||
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 3.187
|
|
||||||
Lattice spacing in x,y,z = 3.187 3.187 3.187
|
|
||||||
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 0 0) to (12.748 12.748 12.748)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
create_atoms 1 box
|
|
||||||
Created 128 atoms
|
|
||||||
using lattice units in orthogonal box = (0 0 0) to (12.748 12.748 12.748)
|
|
||||||
create_atoms CPU = 0.000 seconds
|
|
||||||
|
|
||||||
mass 1 183.84
|
|
||||||
|
|
||||||
# # ============= set pair style
|
|
||||||
|
|
||||||
pair_style uf3 3
|
|
||||||
pair_coeff 1 1 W_W.uf3
|
|
||||||
pair_coeff 3b 1 1 1 W_W_W.uf3
|
|
||||||
|
|
||||||
|
|
||||||
# # ============= 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 2367804 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 = 6.5
|
|
||||||
ghost atom cutoff = 6.5
|
|
||||||
binsize = 3.25, bins = 4 4 4
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair uf3, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.205 | 3.205 | 3.205 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 300 -4.3916353 0 -4.3531602 -21224
|
|
||||||
10 292.96093 -4.3907325 0 -4.3531602 -21177.095
|
|
||||||
20 272.60651 -4.3881219 0 -4.35316 -21038.525
|
|
||||||
30 241.12074 -4.3840835 0 -4.3531597 -20793.964
|
|
||||||
40 201.8718 -4.3790495 0 -4.3531594 -20444.219
|
|
||||||
50 159.06853 -4.3735596 0 -4.353159 -19996.634
|
|
||||||
60 117.24817 -4.3681958 0 -4.3531587 -19470.011
|
|
||||||
70 80.716097 -4.3635102 0 -4.3531584 -18905.505
|
|
||||||
80 53.030322 -4.3599593 0 -4.3531582 -18362.596
|
|
||||||
90 36.611518 -4.3578535 0 -4.3531581 -17898.612
|
|
||||||
100 32.512413 -4.3573279 0 -4.3531581 -17551.048
|
|
||||||
Loop time of 0.2463 on 4 procs for 100 steps with 128 atoms
|
|
||||||
|
|
||||||
Performance: 17.540 ns/day, 1.368 hours/ns, 406.010 timesteps/s, 51.969 katom-step/s
|
|
||||||
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.12087 | 0.18077 | 0.24119 | 13.8 | 73.39
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.0041617 | 0.064599 | 0.12453 | 23.1 | 26.23
|
|
||||||
Output | 0.00029596 | 0.00031702 | 0.00036352 | 0.0 | 0.13
|
|
||||||
Modify | 0.00012969 | 0.00013491 | 0.00014544 | 0.0 | 0.05
|
|
||||||
Other | | 0.00048 | | | 0.19
|
|
||||||
|
|
||||||
Nlocal: 32 ave 32 max 32 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 697 ave 697 max 697 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 2048 ave 2048 max 2048 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 8192
|
|
||||||
Ave neighs/atom = 64
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
Reference in New Issue
Block a user