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This commit is contained in:
Axel Kohlmeyer 2022-06-17 13:04:25 -04:00
parent ec411df9ec
commit dac99e462f
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GPG Key ID: D9B44E93BF0C375A
4 changed files with 81 additions and 113 deletions
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46
examples/snap/log.15Jun22.grid.snap.g++.1
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@ -1,4 +1,5 @@
LAMMPS (28 Jul 2021)
LAMMPS (2 Jun 2022)
using 1 OpenMP thread(s) per MPI task
# Demonstrate calculation of SNAP bispectrum descriptors on a grid
# CORRECTNESS: The two atom positions coincide with two of
@ -27,17 +28,17 @@ boundary p p p
lattice custom $a a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
lattice custom 3.316 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
Lattice spacing in x,y,z = 3.316 3.316 3.316
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 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (3.3160000 3.3160000 3.3160000)
Created orthogonal box = (0 0 0) to (3.316 3.316 3.316)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 2 atoms
using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (3.3160000 3.3160000 3.3160000)
using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316)
create_atoms CPU = 0.000 seconds
mass 1 180.88
@ -105,14 +106,15 @@ dump 2 all custom 1000 dump.batom id x y z c_b[*]
# run
run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.67637
ghost atom cutoff = 6.67637
binsize = 3.338185, bins = 1 1 1
4 neighbor lists, perpetual/occasional/extra = 1 3 0
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
@ -123,22 +125,12 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute sna/grid, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(4) compute sna/grid/local, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.384 | 8.384 | 8.384 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 0
Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
Per MPI rank memory allocation (min/avg/max) = 7.127 | 7.127 | 7.127 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 9.1551336e-16
Loop time of 1.43e-06 on 1 procs for 0 steps with 2 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
139.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -148,19 +140,19 @@ 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 | | 1e-06 | | |100.00
Other | | 1.43e-06 | | |100.00
Nlocal: 2.00000 ave 2 max 2 min
Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 339.000 ave 339 max 339 min
Nghost: 339 ave 339 max 339 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 64.0000 ave 64 max 64 min
Neighs: 64 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 128.000 ave 128 max 128 min
FullNghs: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 128
Ave neighs/atom = 64.000000
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0

48
examples/snap/log.15Jun22.grid.snap.g++.4
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@ -1,4 +1,5 @@
LAMMPS (28 Jul 2021)
LAMMPS (2 Jun 2022)
using 1 OpenMP thread(s) per MPI task
# Demonstrate calculation of SNAP bispectrum descriptors on a grid
# CORRECTNESS: The two atom positions coincide with two of
@ -27,17 +28,17 @@ boundary p p p
lattice custom $a a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
lattice custom 3.316 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
Lattice spacing in x,y,z = 3.316 3.316 3.316
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 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (3.3160000 3.3160000 3.3160000)
Created orthogonal box = (0 0 0) to (3.316 3.316 3.316)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 2 atoms
using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (3.3160000 3.3160000 3.3160000)
using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316)
create_atoms CPU = 0.001 seconds
mass 1 180.88
@ -105,14 +106,15 @@ dump 2 all custom 1000 dump.batom id x y z c_b[*]
# run
run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.67637
ghost atom cutoff = 6.67637
binsize = 3.338185, bins = 1 1 1
4 neighbor lists, perpetual/occasional/extra = 1 3 0
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
@ -123,23 +125,13 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute sna/grid, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(4) compute sna/grid/local, 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 (src/domain.cpp:964)
Per MPI rank memory allocation (min/avg/max) = 7.381 | 7.889 | 8.397 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 0
Loop time of 1.5e-06 on 4 procs for 0 steps with 2 atoms
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
Per MPI rank memory allocation (min/avg/max) = 6.123 | 6.631 | 7.139 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 1.6316879e-15
Loop time of 2.57125e-06 on 4 procs for 0 steps with 2 atoms
83.3% CPU use with 4 MPI tasks x no OpenMP threads
107.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -149,19 +141,19 @@ 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 | | 1.5e-06 | | |100.00
Other | | 2.571e-06 | | |100.00
Nlocal: 0.500000 ave 1 max 0 min
Nlocal: 0.5 ave 1 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 274.500 ave 275 max 274 min
Nghost: 274.5 ave 275 max 274 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 16.0000 ave 40 max 0 min
Neighs: 16 ave 40 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
FullNghs: 32.0000 ave 64 max 0 min
FullNghs: 32 ave 64 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 128
Ave neighs/atom = 64.000000
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0

50
examples/snap/log.15Jun22.grid.tri.g++.1
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@ -1,4 +1,5 @@
LAMMPS (28 Jul 2021)
LAMMPS (2 Jun 2022)
using 1 OpenMP thread(s) per MPI task
# Demonstrate calculation of SNAP bispectrum
# descriptors on a grid for triclinic cell
@ -51,7 +52,7 @@ boundary p p p
lattice custom $a a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1
lattice custom 3.316 a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1
Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
Lattice spacing in x,y,z = 3.316 3.316 3.316
box tilt large
region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
@ -62,13 +63,13 @@ region box prism 0 3 0 2 0 1 2 ${nz} ${nz}
region box prism 0 3 0 2 0 1 2 1 ${nz}
region box prism 0 3 0 2 0 1 2 1 1
create_box 1 box
Created triclinic box = (0.0000000 0.0000000 0.0000000) to (9.9480000 6.6320000 3.3160000) with tilt (6.6320000 3.3160000 3.3160000)
WARNING: Triclinic box skew is large (src/domain.cpp:219)
Created triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316)
WARNING: Triclinic box skew is large (src/domain.cpp:224)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 12 atoms
using lattice units in triclinic box = (0.0000000 0.0000000 0.0000000) to (9.9480000 6.6320000 3.3160000) with tilt (6.6320000 3.3160000 3.3160000)
create_atoms CPU = 0.001 seconds
using lattice units in triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316)
create_atoms CPU = 0.000 seconds
mass 1 180.88
@ -138,14 +139,15 @@ dump 2 all custom 1000 dump.batom.tri id x y z c_b[*]
# run
run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.67637
ghost atom cutoff = 6.67637
binsize = 3.338185, bins = 6 3 1
4 neighbor lists, perpetual/occasional/extra = 1 3 0
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
@ -156,22 +158,12 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute sna/grid, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(4) compute sna/grid/local, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.435 | 8.435 | 8.435 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 7.2262471e-14
Loop time of 1e-06 on 1 procs for 0 steps with 12 atoms
Per MPI rank memory allocation (min/avg/max) = 7.183 | 7.183 | 7.183 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 7.2262471e-14
Loop time of 1.414e-06 on 1 procs for 0 steps with 12 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
70.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -181,19 +173,19 @@ 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 | | 1e-06 | | |100.00
Other | | 1.414e-06 | | |100.00
Nlocal: 12.0000 ave 12 max 12 min
Nlocal: 12 ave 12 max 12 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 604.000 ave 604 max 604 min
Nghost: 604 ave 604 max 604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 384.000 ave 384 max 384 min
Neighs: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 768.000 ave 768 max 768 min
FullNghs: 768 ave 768 max 768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 768
Ave neighs/atom = 64.000000
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0

50
examples/snap/log.15Jun22.grid.tri.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (28 Jul 2021)
LAMMPS (2 Jun 2022)
using 1 OpenMP thread(s) per MPI task
# Demonstrate calculation of SNAP bispectrum
# descriptors on a grid for triclinic cell
@ -51,7 +52,7 @@ boundary p p p
lattice custom $a a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1
lattice custom 3.316 a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1
Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
Lattice spacing in x,y,z = 3.316 3.316 3.316
box tilt large
region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
@ -62,13 +63,13 @@ region box prism 0 3 0 2 0 1 2 ${nz} ${nz}
region box prism 0 3 0 2 0 1 2 1 ${nz}
region box prism 0 3 0 2 0 1 2 1 1
create_box 1 box
Created triclinic box = (0.0000000 0.0000000 0.0000000) to (9.9480000 6.6320000 3.3160000) with tilt (6.6320000 3.3160000 3.3160000)
WARNING: Triclinic box skew is large (src/domain.cpp:219)
Created triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316)
WARNING: Triclinic box skew is large (src/domain.cpp:224)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 12 atoms
using lattice units in triclinic box = (0.0000000 0.0000000 0.0000000) to (9.9480000 6.6320000 3.3160000) with tilt (6.6320000 3.3160000 3.3160000)
create_atoms CPU = 0.001 seconds
using lattice units in triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316)
create_atoms CPU = 0.000 seconds
mass 1 180.88
@ -138,14 +139,15 @@ dump 2 all custom 1000 dump.batom.tri id x y z c_b[*]
# run
run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.67637
ghost atom cutoff = 6.67637
binsize = 3.338185, bins = 6 3 1
4 neighbor lists, perpetual/occasional/extra = 1 3 0
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
@ -156,22 +158,12 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute sna/grid, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(4) compute sna/grid/local, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.405 | 8.405 | 8.405 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 2.1052124e-14
Loop time of 1.25e-06 on 4 procs for 0 steps with 12 atoms
Per MPI rank memory allocation (min/avg/max) = 7.15 | 7.15 | 7.15 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 1.9367585e-14
Loop time of 2.65825e-06 on 4 procs for 0 steps with 12 atoms
140.0% CPU use with 4 MPI tasks x no OpenMP threads
84.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -181,19 +173,19 @@ 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 | | 1.25e-06 | | |100.00
Other | | 2.658e-06 | | |100.00
Nlocal: 3.00000 ave 4 max 2 min
Nlocal: 3 ave 4 max 2 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 459.000 ave 460 max 458 min
Nghost: 459 ave 460 max 458 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 96.0000 ave 128 max 64 min
Neighs: 96 ave 128 max 64 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 192.000 ave 256 max 128 min
FullNghs: 192 ave 256 max 128 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 768
Ave neighs/atom = 64.000000
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0