diff --git a/examples/README b/examples/README index a0f27e2c05..996176c548 100644 --- a/examples/README +++ b/examples/README @@ -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: diff --git a/examples/wall/in.shearflow b/examples/wall/in.shearflow deleted file mode 100644 index 6e5629cc6e..0000000000 --- a/examples/wall/in.shearflow +++ /dev/null @@ -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 diff --git a/examples/wall/in.wall.ccl b/examples/wall/in.wall.ccl new file mode 100644 index 0000000000..ba4fb7b827 --- /dev/null +++ b/examples/wall/in.wall.ccl @@ -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 diff --git a/examples/wall/in.wall.diffusive b/examples/wall/in.wall.diffusive new file mode 100644 index 0000000000..34ccadacac --- /dev/null +++ b/examples/wall/in.wall.diffusive @@ -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 diff --git a/examples/wall/in.wall.maxwell b/examples/wall/in.wall.maxwell new file mode 100644 index 0000000000..42d7c98cbe --- /dev/null +++ b/examples/wall/in.wall.maxwell @@ -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 diff --git a/examples/wall/in.wall.specular b/examples/wall/in.wall.specular new file mode 100644 index 0000000000..7fae47e56a --- /dev/null +++ b/examples/wall/in.wall.specular @@ -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 diff --git a/examples/wall/log.9Jan20.wall.ccl.g++.1 b/examples/wall/log.9Jan20.wall.ccl.g++.1 new file mode 100644 index 0000000000..b76b59969a --- /dev/null +++ b/examples/wall/log.9Jan20.wall.ccl.g++.1 @@ -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 diff --git a/examples/wall/log.9Jan20.wall.ccl.g++.4 b/examples/wall/log.9Jan20.wall.ccl.g++.4 new file mode 100644 index 0000000000..109a308651 --- /dev/null +++ b/examples/wall/log.9Jan20.wall.ccl.g++.4 @@ -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 diff --git a/examples/wall/log.9Jan20.wall.diffusive.g++.1 b/examples/wall/log.9Jan20.wall.diffusive.g++.1 new file mode 100644 index 0000000000..ca51670777 --- /dev/null +++ b/examples/wall/log.9Jan20.wall.diffusive.g++.1 @@ -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 diff --git a/examples/wall/log.9Jan20.wall.diffusive.g++.4 b/examples/wall/log.9Jan20.wall.diffusive.g++.4 new file mode 100644 index 0000000000..76d953b749 --- /dev/null +++ b/examples/wall/log.9Jan20.wall.diffusive.g++.4 @@ -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 diff --git a/examples/wall/log.9Jan20.wall.maxwell.g++.1 b/examples/wall/log.9Jan20.wall.maxwell.g++.1 new file mode 100644 index 0000000000..9467e2645e --- /dev/null +++ b/examples/wall/log.9Jan20.wall.maxwell.g++.1 @@ -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 diff --git a/examples/wall/log.9Jan20.wall.maxwell.g++.4 b/examples/wall/log.9Jan20.wall.maxwell.g++.4 new file mode 100644 index 0000000000..31f81e0182 --- /dev/null +++ b/examples/wall/log.9Jan20.wall.maxwell.g++.4 @@ -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 = 0.000599861 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 diff --git a/examples/wall/log.9Jan20.wall.specular.g++.1 b/examples/wall/log.9Jan20.wall.specular.g++.1 new file mode 100644 index 0000000000..3d85cb02e7 --- /dev/null +++ b/examples/wall/log.9Jan20.wall.specular.g++.1 @@ -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 diff --git a/examples/wall/log.9Jan20.wall.specular.g++.4 b/examples/wall/log.9Jan20.wall.specular.g++.4 new file mode 100644 index 0000000000..9c957f80ed --- /dev/null +++ b/examples/wall/log.9Jan20.wall.specular.g++.4 @@ -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 diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.cpp b/src/USER-MISC/fix_wall_reflect_stochastic.cpp index 6221395f1d..dc58580d80 100644 --- a/src/USER-MISC/fix_wall_reflect_stochastic.cpp +++ b/src/USER-MISC/fix_wall_reflect_stochastic.cpp @@ -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]); diff --git a/src/random_mars.cpp b/src/random_mars.cpp index 396cc7e9f1..a832b3640f 100644 --- a/src/random_mars.cpp +++ b/src/random_mars.cpp @@ -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();