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enhanced stochastic wall example

This commit is contained in:
Steve Plimpton 2020-01-14 13:20:35 -07:00
parent b9c6e0f700
commit ceeae57172
16 changed files with 893 additions and 52 deletions
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1
examples/README
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@ -112,6 +112,7 @@ tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
threebody: regression test input for a variety of manybody potentials
vashishta: models using the Vashishta potential
voronoi: Voronoi tesselation via compute voronoi/atom command
wall: use of reflective walls with different stochastic models
Here is how you might run and visualize one of the sample problems:

50
examples/wall/in.shearflow
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@ -1,50 +0,0 @@
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# Mirror reflection
#fix ywalls all wall/reflect ylo EDGE yhi EDGE
# Diffusive reflection, upper wall velocity = 0.1, lower wall fixed
#fix ywalls all wall/stochastic diffusive 2308 ylo EDGE 300 0 0 0 yhi EDGE 300 0.1 0 0
# Maxwell wall, upper wall velocity = 0.1, lower wall fixed, accommodation coefficient = 0.2 for both walls
#fix ywalls all wall/stochastic maxwell ylo EDGE 300 0 0 0 0.2 yhi EDGE 300 0 0 0.1 0.2
# Diffusive reflection, upper wall velocity = 0.1, lower wall fixed, accommodation coefficients = 0.1, 0.2 and 0.3 along directions x,y,z
fix ywalls all wall/reflect/stochastic 345533 cercignanilampis ylo EDGE 300 0 0 0 0.1 0.2 0.3 yhi EDGE 300 0.1 0 0 0.1 0.2 0.3
# Run
thermo 1000
run 1000000

37
examples/wall/in.wall.ccl Normal file
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@ -0,0 +1,37 @@
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# CCL reflection model
# upper wall velocity = 0.1, lower wall fixed,
# accommodation coefficients = 0.1, 0.2 and 0.3 along directions x,y,z
fix ywalls all wall/reflect/stochastic ccl 345533 &
ylo EDGE 300 0 0 0 0.1 0.2 0.3 yhi EDGE 300 0.1 0 0 0.1 0.2 0.3
# run
thermo 1000
run 10000

36
examples/wall/in.wall.diffusive Normal file
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@ -0,0 +1,36 @@
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# diffusive reflection
# upper wall velocity = 0.1, lower wall fixed
fix ywalls all wall/reflect/stochastic diffusive 2308 &
ylo EDGE 300 0 0 0 yhi EDGE 300 0.1 0 0
# run
thermo 1000
run 10000

37
examples/wall/in.wall.maxwell Normal file
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@ -0,0 +1,37 @@
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# Maxwellian reflection
# upper wall velocity = 0.1, lower wall fixed,
# accommodation coefficient = 0.2 for both walls
fix ywalls all wall/reflect/stochastic maxwell 29839 &
ylo EDGE 300 0 0 0 0.2 yhi EDGE 300 0 0 0.1 0.2
# run
thermo 1000
run 10000

34
examples/wall/in.wall.specular Normal file
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@ -0,0 +1,34 @@
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# specular reflection
fix ywalls all wall/reflect ylo EDGE yhi EDGE
# run
thermo 1000
run 10000

94
examples/wall/log.9Jan20.wall.ccl.g++.1 Normal file
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@ -0,0 +1,94 @@
LAMMPS (09 Jan 2020)
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
Lattice spacing in x,y,z = 10 10 10
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (100 100 100)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 1000 atoms
create_atoms CPU = 0 secs
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# CCL reflection model
# upper wall velocity = 0.1, lower wall fixed,
# accommodation coefficients = 0.1, 0.2 and 0.3 along directions x,y,z
fix ywalls all wall/reflect/stochastic ccl 345533 ylo EDGE 300 0 0 0 0.1 0.2 0.3 yhi EDGE 300 0.1 0 0 0.1 0.2 0.3
# run
thermo 1000
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 20 20 20
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 38.739265 41.378094
1000 306.83507 -0.80022033 0 38.821664 43.50764
2000 315.15424 -1.9016844 0 38.794461 43.585384
3000 312.36801 -1.8819804 0 38.454377 44.018894
4000 311.67545 -1.9198476 0 38.327078 43.113898
5000 310.81453 -1.9015886 0 38.234167 42.677902
6000 312.35612 -1.9639553 0 38.370867 44.057738
7000 312.24146 -2.042721 0 38.277295 42.858047
8000 313.51516 -2.2080206 0 38.276469 42.739369
9000 313.82536 -2.1370876 0 38.387459 42.315362
10000 310.97164 -1.8717207 0 38.284323 44.847594
Loop time of 1.06468 on 1 procs for 10000 steps with 1000 atoms
Performance: 811.511 ns/day, 0.030 hours/ns, 9392.484 timesteps/s
74.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12906 | 0.12906 | 0.12906 | 0.0 | 12.12
Neigh | 0.8392 | 0.8392 | 0.8392 | 0.0 | 78.82
Comm | 0.01259 | 0.01259 | 0.01259 | 0.0 | 1.18
Output | 9.9897e-05 | 9.9897e-05 | 9.9897e-05 | 0.0 | 0.01
Modify | 0.065229 | 0.065229 | 0.065229 | 0.0 | 6.13
Other | | 0.0185 | | | 1.74
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 484 ave 484 max 484 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2362 ave 2362 max 2362 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2362
Ave neighs/atom = 2.362
Neighbor list builds = 97
Dangerous builds = 0
Total wall time: 0:00:01

94
examples/wall/log.9Jan20.wall.ccl.g++.4 Normal file
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@ -0,0 +1,94 @@
LAMMPS (09 Jan 2020)
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
Lattice spacing in x,y,z = 10 10 10
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (100 100 100)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 1000 atoms
create_atoms CPU = 0 secs
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# CCL reflection model
# upper wall velocity = 0.1, lower wall fixed,
# accommodation coefficients = 0.1, 0.2 and 0.3 along directions x,y,z
fix ywalls all wall/reflect/stochastic ccl 345533 ylo EDGE 300 0 0 0 0.1 0.2 0.3 yhi EDGE 300 0.1 0 0 0.1 0.2 0.3
# run
thermo 1000
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 20 20 20
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.085 | 3.09 | 3.096 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 38.739265 41.378094
1000 307.61429 -0.85349762 0 38.869007 42.748162
2000 316.84849 -2.1095683 0 38.805357 42.517397
3000 314.15659 -1.9669177 0 38.6004 43.327219
4000 313.37791 -1.8445245 0 38.622242 44.646022
5000 313.79504 -2.1011994 0 38.419432 42.438395
6000 314.34351 -2.1124765 0 38.478979 44.346967
7000 316.05924 -2.2571113 0 38.555899 43.78324
8000 315.02356 -1.8808116 0 38.798459 45.155529
9000 317.88137 -2.1260496 0 38.922253 44.193922
10000 317.81667 -2.1475718 0 38.892376 43.988987
Loop time of 0.373009 on 4 procs for 10000 steps with 1000 atoms
Performance: 2316.298 ns/day, 0.010 hours/ns, 26809.007 timesteps/s
98.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.043001 | 0.060502 | 0.082004 | 6.7 | 16.22
Neigh | 0.0089996 | 0.0097498 | 0.011001 | 0.8 | 2.61
Comm | 0.151 | 0.17826 | 0.19801 | 4.8 | 47.79
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.066 | 0.076501 | 0.087001 | 2.9 | 20.51
Other | | 0.048 | | | 12.87
Nlocal: 250 ave 286 max 222 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 270.5 ave 300 max 242 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 582.5 ave 742 max 424 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 2330
Ave neighs/atom = 2.33
Neighbor list builds = 88
Dangerous builds = 0
Total wall time: 0:00:00

93
examples/wall/log.9Jan20.wall.diffusive.g++.1 Normal file
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@ -0,0 +1,93 @@
LAMMPS (09 Jan 2020)
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
Lattice spacing in x,y,z = 10 10 10
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (100 100 100)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 1000 atoms
create_atoms CPU = 0 secs
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# diffusive reflection
# upper wall velocity = 0.1, lower wall fixed
fix ywalls all wall/reflect/stochastic diffusive 2308 ylo EDGE 300 0 0 0 yhi EDGE 300 0.1 0 0
# run
thermo 1000
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 20 20 20
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 38.739265 41.378094
1000 312.67753 -0.87571164 0 39.500614 43.641187
2000 320.10672 -1.8866145 0 39.44905 44.817235
3000 317.64782 -1.760419 0 39.257725 46.481585
4000 320.69015 -2.0183637 0 39.392639 44.958979
5000 319.94001 -2.0405034 0 39.273633 42.918123
6000 322.34085 -2.0667328 0 39.557427 45.352614
7000 320.30901 -1.922786 0 39.438999 44.189986
8000 322.25492 -1.9643206 0 39.648742 46.633235
9000 326.28632 -2.0989926 0 40.034649 46.114074
10000 325.68184 -2.1242578 0 39.931326 45.875723
Loop time of 0.915023 on 1 procs for 10000 steps with 1000 atoms
Performance: 944.239 ns/day, 0.025 hours/ns, 10928.689 timesteps/s
50.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.055415 | 0.055415 | 0.055415 | 0.0 | 6.06
Neigh | 0.002049 | 0.002049 | 0.002049 | 0.0 | 0.22
Comm | 0.0018332 | 0.0018332 | 0.0018332 | 0.0 | 0.20
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.85254 | 0.85254 | 0.85254 | 0.0 | 93.17
Other | | 0.003183 | | | 0.35
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 477 ave 477 max 477 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2325 ave 2325 max 2325 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2325
Ave neighs/atom = 2.325
Neighbor list builds = 97
Dangerous builds = 0
Total wall time: 0:00:00

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examples/wall/log.9Jan20.wall.diffusive.g++.4 Normal file
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@ -0,0 +1,93 @@
LAMMPS (09 Jan 2020)
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
Lattice spacing in x,y,z = 10 10 10
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (100 100 100)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 1000 atoms
create_atoms CPU = 0 secs
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# diffusive reflection
# upper wall velocity = 0.1, lower wall fixed
fix ywalls all wall/reflect/stochastic diffusive 2308 ylo EDGE 300 0 0 0 yhi EDGE 300 0.1 0 0
# run
thermo 1000
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 20 20 20
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.085 | 3.09 | 3.096 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 38.739265 41.378094
1000 310.89471 -0.79880791 0 39.347301 43.751589
2000 320.50481 -2.0317993 0 39.35527 43.068073
3000 318.27899 -2.0007056 0 39.098941 44.164018
4000 317.36789 -1.7177074 0 39.264288 46.423062
5000 320.35583 -2.1568752 0 39.210956 43.576324
6000 320.84464 -2.0723583 0 39.358594 45.13774
7000 322.44996 -2.0841776 0 39.554071 45.974409
8000 318.71892 -1.8599126 0 39.296544 45.737848
9000 317.51275 -1.9303928 0 39.07031 45.138145
10000 318.85556 -2.0522739 0 39.121827 44.160918
Loop time of 0.367009 on 4 procs for 10000 steps with 1000 atoms
Performance: 2354.165 ns/day, 0.010 hours/ns, 27247.276 timesteps/s
97.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.054003 | 0.071752 | 0.097001 | 6.1 | 19.55
Neigh | 0.012 | 0.01275 | 0.014 | 0.7 | 3.47
Comm | 0.14101 | 0.17301 | 0.198 | 5.3 | 47.14
Output | 0.007 | 0.007 | 0.007 | 0.0 | 1.91
Modify | 0.045 | 0.060251 | 0.076001 | 5.3 | 16.42
Other | | 0.04225 | | | 11.51
Nlocal: 250 ave 278 max 220 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 270.25 ave 291 max 246 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 578.25 ave 719 max 389 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 2313
Ave neighs/atom = 2.313
Neighbor list builds = 96
Dangerous builds = 0
Total wall time: 0:00:00

94
examples/wall/log.9Jan20.wall.maxwell.g++.1 Normal file
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@ -0,0 +1,94 @@
LAMMPS (09 Jan 2020)
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
Lattice spacing in x,y,z = 10 10 10
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (100 100 100)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 1000 atoms
create_atoms CPU = 0 secs
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# Maxwellian reflection
# upper wall velocity = 0.1, lower wall fixed,
# accommodation coefficient = 0.2 for both walls
fix ywalls all wall/reflect/stochastic maxwell 29839 ylo EDGE 300 0 0 0 0.2 yhi EDGE 300 0 0 0.1 0.2
# run
thermo 1000
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 20 20 20
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 38.739265 41.378094
1000 305.84027 -0.81554574 0 38.677879 43.038024
2000 313.63839 -1.8725314 0 38.627871 43.582384
3000 314.36459 -1.8810929 0 38.713084 44.238028
4000 313.62061 -1.8781065 0 38.62 44.16173
5000 314.62707 -2.0017812 0 38.626291 43.314646
6000 316.56502 -2.0984304 0 38.77989 44.63432
7000 316.76017 -2.1273978 0 38.776123 43.255178
8000 317.92744 -2.2609826 0 38.79327 44.492912
9000 317.48386 -2.1531603 0 38.843812 41.927957
10000 316.18654 -2.0295818 0 38.799865 43.73621
Loop time of 1.15703 on 1 procs for 10000 steps with 1000 atoms
Performance: 746.740 ns/day, 0.032 hours/ns, 8642.825 timesteps/s
24.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0516 | 1.0516 | 1.0516 | 0.0 | 90.89
Neigh | 0.015567 | 0.015567 | 0.015567 | 0.0 | 1.35
Comm | 0.01 | 0.01 | 0.01 | 0.0 | 0.86
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.070344 | 0.070344 | 0.070344 | 0.0 | 6.08
Other | | 0.009534 | | | 0.82
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 475 ave 475 max 475 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2334 ave 2334 max 2334 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2334
Ave neighs/atom = 2.334
Neighbor list builds = 90
Dangerous builds = 0
Total wall time: 0:00:01

94
examples/wall/log.9Jan20.wall.maxwell.g++.4 Normal file
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LAMMPS (09 Jan 2020)
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
Lattice spacing in x,y,z = 10 10 10
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (100 100 100)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 1000 atoms
create_atoms CPU = 0.000599861 secs
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# Maxwellian reflection
# upper wall velocity = 0.1, lower wall fixed,
# accommodation coefficient = 0.2 for both walls
fix ywalls all wall/reflect/stochastic maxwell 29839 ylo EDGE 300 0 0 0 0.2 yhi EDGE 300 0 0 0.1 0.2
# run
thermo 1000
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 20 20 20
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.085 | 3.09 | 3.096 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 38.739265 41.378094
1000 306.84606 -0.81991676 0 38.803387 42.677043
2000 315.55292 -1.9938298 0 38.753798 43.826963
3000 315.05535 -1.9899076 0 38.693469 43.699674
4000 313.78121 -1.8410878 0 38.677757 44.457758
5000 317.0712 -2.1014946 0 38.84219 43.200259
6000 316.56544 -2.0144551 0 38.863921 44.622296
7000 318.00823 -2.0601205 0 39.004564 45.31096
8000 316.36755 -1.8389853 0 39.013836 45.50011
9000 318.31 -2.1029696 0 39.000683 44.238038
10000 317.06931 -2.0706174 0 38.872823 44.009842
Loop time of 0.372642 on 4 procs for 10000 steps with 1000 atoms
Performance: 2318.579 ns/day, 0.010 hours/ns, 26835.401 timesteps/s
94.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.060702 | 0.074426 | 0.103 | 6.3 | 19.97
Neigh | 0.006001 | 0.0081906 | 0.010001 | 1.6 | 2.20
Comm | 0.13 | 0.18175 | 0.21098 | 7.2 | 48.77
Output | 0 | 6.2346e-05 | 0.00024939 | 0.0 | 0.02
Modify | 0.039276 | 0.066821 | 0.090003 | 7.1 | 17.93
Other | | 0.04139 | | | 11.11
Nlocal: 250 ave 278 max 221 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 286.25 ave 308 max 263 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 573.5 ave 724 max 413 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 2294
Ave neighs/atom = 2.294
Neighbor list builds = 99
Dangerous builds = 0
Total wall time: 0:00:00

92
examples/wall/log.9Jan20.wall.specular.g++.1 Normal file
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@ -0,0 +1,92 @@
LAMMPS (09 Jan 2020)
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
Lattice spacing in x,y,z = 10 10 10
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (100 100 100)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 1000 atoms
create_atoms CPU = 0 secs
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# specular reflection
fix ywalls all wall/reflect ylo EDGE yhi EDGE
# run
thermo 1000
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 20 20 20
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 38.739265 41.378094
1000 305.24846 -0.81252388 0 38.604479 42.984882
2000 313.42563 -1.9181413 0 38.554788 43.314782
3000 312.765 -1.8445772 0 38.543044 44.006858
4000 312.70958 -1.8420045 0 38.53846 44.808265
5000 313.4634 -1.9373681 0 38.540438 43.27283
6000 314.19203 -2.0319378 0 38.539957 44.403177
7000 314.51643 -2.0700345 0 38.543751 42.566368
8000 314.67639 -2.0991652 0 38.535275 44.02504
9000 315.17416 -2.1591689 0 38.53955 43.421838
10000 314.20849 -2.0315185 0 38.542502 43.522426
Loop time of 1.08403 on 1 procs for 10000 steps with 1000 atoms
Performance: 797.028 ns/day, 0.030 hours/ns, 9224.862 timesteps/s
56.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.96636 | 0.96636 | 0.96636 | 0.0 | 89.15
Neigh | 0.0087926 | 0.0087926 | 0.0087926 | 0.0 | 0.81
Comm | 0.022686 | 0.022686 | 0.022686 | 0.0 | 2.09
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.071106 | 0.071106 | 0.071106 | 0.0 | 6.56
Other | | 0.01508 | | | 1.39
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 480 ave 480 max 480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2304 ave 2304 max 2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2304
Ave neighs/atom = 2.304
Neighbor list builds = 87
Dangerous builds = 0
Total wall time: 0:00:01

92
examples/wall/log.9Jan20.wall.specular.g++.4 Normal file
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@ -0,0 +1,92 @@
LAMMPS (09 Jan 2020)
units metal
dimension 3
boundary p f p
atom_style atomic
neighbor 2.0 bin
# create geometry
lattice sc 10
Lattice spacing in x,y,z = 10 10 10
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (100 100 100)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 1000 atoms
create_atoms CPU = 0 secs
mass 1 39.95
# LJ potentials
pair_style lj/cut 8.5
pair_coeff * * 0.01 3.4 8.5
# initial velocities
velocity all create 300 482748
fix 1 all nve
# specular reflection
fix ywalls all wall/reflect ylo EDGE yhi EDGE
# run
thermo 1000
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 20 20 20
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.085 | 3.09 | 3.096 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 38.739265 41.378094
1000 305.18674 -0.80847964 0 38.600554 42.877223
2000 313.99246 -1.9948292 0 38.551295 43.475585
3000 313.86673 -1.987971 0 38.541917 43.155182
4000 313.11947 -1.8945644 0 38.53883 44.035201
5000 314.92476 -2.1260059 0 38.540507 42.012978
6000 313.46259 -1.93896 0 38.538742 44.197131
7000 314.97475 -2.1392782 0 38.53369 43.91008
8000 313.88617 -1.9970823 0 38.535317 44.277056
9000 314.1612 -2.0304174 0 38.537496 43.495036
10000 315.4836 -2.2052704 0 38.533406 42.624901
Loop time of 0.337861 on 4 procs for 10000 steps with 1000 atoms
Performance: 2557.262 ns/day, 0.009 hours/ns, 29597.934 timesteps/s
96.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.044001 | 0.059837 | 0.1 | 9.5 | 17.71
Neigh | 0.0062642 | 0.0090668 | 0.015001 | 3.7 | 2.68
Comm | 0.144 | 0.18421 | 0.21583 | 6.2 | 54.52
Output | 0 | 0.0042874 | 0.017 | 11.2 | 1.27
Modify | 0.031019 | 0.037255 | 0.045001 | 2.7 | 11.03
Other | | 0.0432 | | | 12.79
Nlocal: 250 ave 278 max 220 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 277.5 ave 302 max 252 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 568 ave 709 max 391 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 2272
Ave neighs/atom = 2.272
Neighbor list builds = 86
Dangerous builds = 0
Total wall time: 0:00:00

2
src/USER-MISC/fix_wall_reflect_stochastic.cpp
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@ -116,7 +116,7 @@ FixWallReflectStochastic(LAMMPS *lmp, int narg, char **arg) :
// DIFFUSIVE = no accomodation coeffs
// MAXWELL = one for all dimensions
// CLL = one for each dimension
// CCL = one for each dimension
if (rstyle == CCL)
wallaccom[nwall][dir]= force->numeric(FLERR,arg[iarg+dir+6]);

2
src/random_mars.cpp
View File

@ -149,7 +149,7 @@ double RanMars::besselexp(double theta, double alpha, double cp)
{
double first,v1,v2;
if (theta < 0.0 || alpha < 0.0 || alpha < 1.0)
if (theta < 0.0 || alpha < 0.0 || alpha > 1.0)
error->all(FLERR,"Invalid Bessel exponential distribution parameters");
v1 = uniform();