From b7afe412dc939876b0165eaa7325c8bed9e0e56c Mon Sep 17 00:00:00 2001 From: jtclemm Date: Wed, 7 Jun 2023 13:08:46 -0600 Subject: [PATCH] Updating SDPD examples --- .../2d-diffusion-in-shear-flow/in.lammps | 6 +- ...g.24Oct18.2d-diffusion-in-shear-flow.g++.1 | 247 ----------------- ...g.24Oct18.2d-diffusion-in-shear-flow.g++.4 | 247 ----------------- ...g.28Mar23.2d-diffusion-in-shear-flow.g++.1 | 253 ++++++++++++++++++ ...g.28Mar23.2d-diffusion-in-shear-flow.g++.4 | 253 ++++++++++++++++++ .../dpd-smooth/2d-diffusion/in.lammps | 6 +- .../log.24Oct18.2d-diffusion.g++.1 | 226 ---------------- .../log.24Oct18.2d-diffusion.g++.4 | 226 ---------------- .../log.28Mar23.2d-diffusion.g++.1 | 230 ++++++++++++++++ .../log.28Mar23.2d-diffusion.g++.4 | 230 ++++++++++++++++ .../equipartition-verification/in.lammps | 6 +- ....g++.1 => log.28Mar23.equipartition.g++.1} | 91 ++++--- ....g++.4 => log.28Mar23.equipartition.g++.4} | 91 ++++--- 13 files changed, 1069 insertions(+), 1043 deletions(-) delete mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1 delete mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4 create mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.1 create mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.4 delete mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.1 delete mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.4 create mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.1 create mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.4 rename examples/PACKAGES/dpd-smooth/equipartition-verification/{log.24Oct18.equipartition.g++.1 => log.28Mar23.equipartition.g++.1} (58%) rename examples/PACKAGES/dpd-smooth/equipartition-verification/{log.24Oct18.equipartition.g++.4 => log.28Mar23.equipartition.g++.4} (58%) diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/in.lammps b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/in.lammps index 138f7b5338..dd50a5e69f 100644 --- a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/in.lammps +++ b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/in.lammps @@ -1,6 +1,6 @@ dimension 2 units micro -atom_style meso +atom_style sph variable R equal 0.5 # radius of sphere micrometers variable a equal $R/5 # lattice spacing micrometers @@ -37,12 +37,12 @@ group upper_wall type 3 group lower_wall type 4 mass * ${mass} -set group all meso/rho ${rho_0} +set group all sph/rho ${rho_0} pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed pair_coeff * * ${rho_0} ${c_0} ${h} -fix 1 fluid meso +fix 1 fluid sph fix 2 sphere rigid/meso single fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1 b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1 deleted file mode 100644 index cd01601292..0000000000 --- a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1 +++ /dev/null @@ -1,247 +0,0 @@ -LAMMPS (24 Oct 2018) -dimension 2 -units micro -atom_style meso - -variable R equal 0.5 # radius of sphere micrometers -variable a equal $R/5 # lattice spacing micrometers -variable a equal 0.5/5 -variable Lf equal $R*3 -variable Lf equal 0.5*3 -variable Lb equal $R*4 -variable Lb equal 0.5*4 -variable wall_velocity equal 0.01 # micrometers/microsecond -variable T equal 300. -variable rho_0 equal 1. # density picograms/micrometer^3 -variable c_0 equal 100. # speed of sound micrometers/microsecond -variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) -variable h equal $a*4.5 # kernel function cutoff micrometers -variable h equal 0.1*4.5 -variable mass equal $a*$a*$a*${rho_0} -variable mass equal 0.1*$a*$a*${rho_0} -variable mass equal 0.1*0.1*$a*${rho_0} -variable mass equal 0.1*0.1*0.1*${rho_0} -variable mass equal 0.1*0.1*0.1*1 -variable dt equal 1e-3 # timestep microseconds -variable skin equal 0.2*$h -variable skin equal 0.2*0.45 - -region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box -region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box -region box block -2 2 -${Lb} ${Lb} 0 ${a} units box -region box block -2 2 -2 ${Lb} 0 ${a} units box -region box block -2 2 -2 2 0 ${a} units box -region box block -2 2 -2 2 0 0.1 units box -create_box 4 box -Created orthogonal box = (-2 -2 0) to (2 2 0.1) - 1 by 1 by 1 MPI processor grid -lattice sq $a -lattice sq 0.1 -Lattice spacing in x,y,z = 0.1 0.1 0.1 - -create_atoms 1 box -Created 1600 atoms - Time spent = 0.00169706 secs - -region sphere sphere 0 0 0 $R units box -region sphere sphere 0 0 0 0.5 units box -set region sphere type 2 - 81 settings made for type - -region upper_wall block INF INF +${Lf} INF INF INF units box -region upper_wall block INF INF +1.5 INF INF INF units box -set region upper_wall type 3 - 200 settings made for type - -region lower_wall block INF INF INF -${Lf} INF INF units box -region lower_wall block INF INF INF -1.5 INF INF units box -set region lower_wall type 4 - 240 settings made for type - -group fluid type 1 -1079 atoms in group fluid -group sphere type 2 -81 atoms in group sphere -group upper_wall type 3 -200 atoms in group upper_wall -group lower_wall type 4 -240 atoms in group lower_wall - -mass * ${mass} -mass * 0.001 -set group all meso/rho ${rho_0} -set group all meso/rho 1 - 1600 settings made for meso/rho - -pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed -pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 -pair_style sdpd/taitwater/isothermal 300 1 76787 -pair_coeff * * ${rho_0} ${c_0} ${h} -pair_coeff * * 1 ${c_0} ${h} -pair_coeff * * 1 100 ${h} -pair_coeff * * 1 100 0.45 - -fix 1 fluid meso -fix 2 sphere rigid/meso single -1 rigid bodies with 81 atoms -fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box -fix 3 upper_wall meso/move linear +0.01 0 0 units box -fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box -fix 4 lower_wall meso/move linear -0.01 0 0 units box - -fix 2d all enforce2d - -neighbor ${skin} bin -neighbor 0.09 bin -neigh_modify delay 0 every 1 check yes -timestep ${dt} -timestep 0.001 - -dump dump_id all atom 100 dump.lammpstrj - -thermo 100 -thermo_style custom step time nbuild ndanger - -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 0.54 - ghost atom cutoff = 0.54 - binsize = 0.27, bins = 15 15 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair sdpd/taitwater/isothermal, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.937 | 6.937 | 6.937 Mbytes -Step Time Nbuild Ndanger - 0 0 0 0 - 100 0.1 0 0 - 200 0.2 0 0 - 300 0.3 0 0 - 400 0.4 0 0 - 500 0.5 1 0 - 600 0.6 1 0 - 700 0.7 2 0 - 800 0.8 2 0 - 900 0.9 2 0 - 1000 1 3 0 - 1100 1.1 3 0 - 1200 1.2 3 0 - 1300 1.3 4 0 - 1400 1.4 4 0 - 1500 1.5 4 0 - 1600 1.6 5 0 - 1700 1.7 5 0 - 1800 1.8 5 0 - 1900 1.9 6 0 - 2000 2 6 0 - 2100 2.1 6 0 - 2200 2.2 7 0 - 2300 2.3 7 0 - 2400 2.4 7 0 - 2500 2.5 8 0 - 2600 2.6 8 0 - 2700 2.7 8 0 - 2800 2.8 9 0 - 2900 2.9 9 0 - 3000 3 9 0 - 3100 3.1 10 0 - 3200 3.2 10 0 - 3300 3.3 10 0 - 3400 3.4 11 0 - 3500 3.5 11 0 - 3600 3.6 11 0 - 3700 3.7 12 0 - 3800 3.8 12 0 - 3900 3.9 12 0 - 4000 4 13 0 - 4100 4.1 13 0 - 4200 4.2 14 0 - 4300 4.3 14 0 - 4400 4.4 14 0 - 4500 4.5 15 0 - 4600 4.6 15 0 - 4700 4.7 15 0 - 4800 4.8 16 0 - 4900 4.9 16 0 - 5000 5 16 0 - 5100 5.1 17 0 - 5200 5.2 17 0 - 5300 5.3 17 0 - 5400 5.4 17 0 - 5500 5.5 18 0 - 5600 5.6 18 0 - 5700 5.7 19 0 - 5800 5.8 19 0 - 5900 5.9 19 0 - 6000 6 20 0 - 6100 6.1 20 0 - 6200 6.2 21 0 - 6300 6.3 21 0 - 6400 6.4 21 0 - 6500 6.5 22 0 - 6600 6.6 22 0 - 6700 6.7 22 0 - 6800 6.8 23 0 - 6900 6.9 23 0 - 7000 7 23 0 - 7100 7.1 24 0 - 7200 7.2 24 0 - 7300 7.3 25 0 - 7400 7.4 25 0 - 7500 7.5 25 0 - 7600 7.6 26 0 - 7700 7.7 26 0 - 7800 7.8 26 0 - 7900 7.9 27 0 - 8000 8 27 0 - 8100 8.1 27 0 - 8200 8.2 28 0 - 8300 8.3 28 0 - 8400 8.4 28 0 - 8500 8.5 29 0 - 8600 8.6 29 0 - 8700 8.7 30 0 - 8800 8.8 30 0 - 8900 8.9 30 0 - 9000 9 31 0 - 9100 9.1 31 0 - 9200 9.2 31 0 - 9300 9.3 32 0 - 9400 9.4 32 0 - 9500 9.5 32 0 - 9600 9.6 33 0 - 9700 9.7 33 0 - 9800 9.8 33 0 - 9900 9.9 34 0 - 10000 10 34 0 -Loop time of 144.208 on 1 procs for 10000 steps with 1600 atoms - -Performance: 5991348.580 ns/day, 0.000 hours/ns, 69.344 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 143.08 | 143.08 | 143.08 | 0.0 | 99.22 -Neigh | 0.033195 | 0.033195 | 0.033195 | 0.0 | 0.02 -Comm | 0.24139 | 0.24139 | 0.24139 | 0.0 | 0.17 -Output | 0.11687 | 0.11687 | 0.11687 | 0.0 | 0.08 -Modify | 0.61566 | 0.61566 | 0.61566 | 0.0 | 0.43 -Other | | 0.117 | | | 0.08 - -Nlocal: 1600 ave 1600 max 1600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 993 ave 993 max 993 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 73236 ave 73236 max 73236 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 73236 -Ave neighs/atom = 45.7725 -Neighbor list builds = 34 -Dangerous builds = 0 -Total wall time: 0:02:24 diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4 b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4 deleted file mode 100644 index 77823e00fc..0000000000 --- a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4 +++ /dev/null @@ -1,247 +0,0 @@ -LAMMPS (24 Oct 2018) -dimension 2 -units micro -atom_style meso - -variable R equal 0.5 # radius of sphere micrometers -variable a equal $R/5 # lattice spacing micrometers -variable a equal 0.5/5 -variable Lf equal $R*3 -variable Lf equal 0.5*3 -variable Lb equal $R*4 -variable Lb equal 0.5*4 -variable wall_velocity equal 0.01 # micrometers/microsecond -variable T equal 300. -variable rho_0 equal 1. # density picograms/micrometer^3 -variable c_0 equal 100. # speed of sound micrometers/microsecond -variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) -variable h equal $a*4.5 # kernel function cutoff micrometers -variable h equal 0.1*4.5 -variable mass equal $a*$a*$a*${rho_0} -variable mass equal 0.1*$a*$a*${rho_0} -variable mass equal 0.1*0.1*$a*${rho_0} -variable mass equal 0.1*0.1*0.1*${rho_0} -variable mass equal 0.1*0.1*0.1*1 -variable dt equal 1e-3 # timestep microseconds -variable skin equal 0.2*$h -variable skin equal 0.2*0.45 - -region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box -region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box -region box block -2 2 -${Lb} ${Lb} 0 ${a} units box -region box block -2 2 -2 ${Lb} 0 ${a} units box -region box block -2 2 -2 2 0 ${a} units box -region box block -2 2 -2 2 0 0.1 units box -create_box 4 box -Created orthogonal box = (-2 -2 0) to (2 2 0.1) - 2 by 2 by 1 MPI processor grid -lattice sq $a -lattice sq 0.1 -Lattice spacing in x,y,z = 0.1 0.1 0.1 - -create_atoms 1 box -Created 1600 atoms - Time spent = 0.000589566 secs - -region sphere sphere 0 0 0 $R units box -region sphere sphere 0 0 0 0.5 units box -set region sphere type 2 - 81 settings made for type - -region upper_wall block INF INF +${Lf} INF INF INF units box -region upper_wall block INF INF +1.5 INF INF INF units box -set region upper_wall type 3 - 200 settings made for type - -region lower_wall block INF INF INF -${Lf} INF INF units box -region lower_wall block INF INF INF -1.5 INF INF units box -set region lower_wall type 4 - 240 settings made for type - -group fluid type 1 -1079 atoms in group fluid -group sphere type 2 -81 atoms in group sphere -group upper_wall type 3 -200 atoms in group upper_wall -group lower_wall type 4 -240 atoms in group lower_wall - -mass * ${mass} -mass * 0.001 -set group all meso/rho ${rho_0} -set group all meso/rho 1 - 1600 settings made for meso/rho - -pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed -pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 -pair_style sdpd/taitwater/isothermal 300 1 76787 -pair_coeff * * ${rho_0} ${c_0} ${h} -pair_coeff * * 1 ${c_0} ${h} -pair_coeff * * 1 100 ${h} -pair_coeff * * 1 100 0.45 - -fix 1 fluid meso -fix 2 sphere rigid/meso single -1 rigid bodies with 81 atoms -fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box -fix 3 upper_wall meso/move linear +0.01 0 0 units box -fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box -fix 4 lower_wall meso/move linear -0.01 0 0 units box - -fix 2d all enforce2d - -neighbor ${skin} bin -neighbor 0.09 bin -neigh_modify delay 0 every 1 check yes -timestep ${dt} -timestep 0.001 - -dump dump_id all atom 100 dump.lammpstrj - -thermo 100 -thermo_style custom step time nbuild ndanger - -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 0.54 - ghost atom cutoff = 0.54 - binsize = 0.27, bins = 15 15 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair sdpd/taitwater/isothermal, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.854 | 6.854 | 6.854 Mbytes -Step Time Nbuild Ndanger - 0 0 0 0 - 100 0.1 0 0 - 200 0.2 0 0 - 300 0.3 0 0 - 400 0.4 1 0 - 500 0.5 1 0 - 600 0.6 1 0 - 700 0.7 2 0 - 800 0.8 2 0 - 900 0.9 2 0 - 1000 1 3 0 - 1100 1.1 3 0 - 1200 1.2 4 0 - 1300 1.3 4 0 - 1400 1.4 4 0 - 1500 1.5 4 0 - 1600 1.6 5 0 - 1700 1.7 5 0 - 1800 1.8 5 0 - 1900 1.9 6 0 - 2000 2 6 0 - 2100 2.1 6 0 - 2200 2.2 6 0 - 2300 2.3 7 0 - 2400 2.4 7 0 - 2500 2.5 7 0 - 2600 2.6 8 0 - 2700 2.7 8 0 - 2800 2.8 8 0 - 2900 2.9 9 0 - 3000 3 9 0 - 3100 3.1 9 0 - 3200 3.2 10 0 - 3300 3.3 10 0 - 3400 3.4 10 0 - 3500 3.5 11 0 - 3600 3.6 11 0 - 3700 3.7 11 0 - 3800 3.8 12 0 - 3900 3.9 12 0 - 4000 4 12 0 - 4100 4.1 13 0 - 4200 4.2 13 0 - 4300 4.3 13 0 - 4400 4.4 14 0 - 4500 4.5 14 0 - 4600 4.6 15 0 - 4700 4.7 15 0 - 4800 4.8 15 0 - 4900 4.9 16 0 - 5000 5 16 0 - 5100 5.1 17 0 - 5200 5.2 17 0 - 5300 5.3 17 0 - 5400 5.4 17 0 - 5500 5.5 18 0 - 5600 5.6 18 0 - 5700 5.7 18 0 - 5800 5.8 19 0 - 5900 5.9 19 0 - 6000 6 20 0 - 6100 6.1 20 0 - 6200 6.2 20 0 - 6300 6.3 21 0 - 6400 6.4 21 0 - 6500 6.5 21 0 - 6600 6.6 22 0 - 6700 6.7 22 0 - 6800 6.8 22 0 - 6900 6.9 23 0 - 7000 7 23 0 - 7100 7.1 23 0 - 7200 7.2 24 0 - 7300 7.3 24 0 - 7400 7.4 25 0 - 7500 7.5 25 0 - 7600 7.6 25 0 - 7700 7.7 25 0 - 7800 7.8 26 0 - 7900 7.9 26 0 - 8000 8 26 0 - 8100 8.1 27 0 - 8200 8.2 27 0 - 8300 8.3 27 0 - 8400 8.4 28 0 - 8500 8.5 28 0 - 8600 8.6 28 0 - 8700 8.7 29 0 - 8800 8.8 29 0 - 8900 8.9 29 0 - 9000 9 30 0 - 9100 9.1 30 0 - 9200 9.2 31 0 - 9300 9.3 31 0 - 9400 9.4 31 0 - 9500 9.5 32 0 - 9600 9.6 32 0 - 9700 9.7 32 0 - 9800 9.8 32 0 - 9900 9.9 33 0 - 10000 10 33 0 -Loop time of 63.2372 on 4 procs for 10000 steps with 1600 atoms - -Performance: 13662841.706 ns/day, 0.000 hours/ns, 158.135 timesteps/s -94.3% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 51.576 | 53.662 | 55.484 | 23.9 | 84.86 -Neigh | 0.011519 | 0.012395 | 0.013405 | 0.7 | 0.02 -Comm | 6.8389 | 8.5423 | 10.517 | 56.1 | 13.51 -Output | 0.12342 | 0.12513 | 0.1302 | 0.8 | 0.20 -Modify | 0.58708 | 0.69128 | 0.78806 | 11.3 | 1.09 -Other | | 0.2038 | | | 0.32 - -Nlocal: 400 ave 411 max 388 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Nghost: 552.25 ave 567 max 539 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 18298.8 ave 18781 max 17829 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 73195 -Ave neighs/atom = 45.7469 -Neighbor list builds = 33 -Dangerous builds = 0 -Total wall time: 0:01:03 diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.1 b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.1 new file mode 100644 index 0000000000..c4c11205e1 --- /dev/null +++ b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.1 @@ -0,0 +1,253 @@ +LAMMPS (28 Mar 2023 - Development) +dimension 2 +units micro +atom_style sph + +variable R equal 0.5 # radius of sphere micrometers +variable a equal $R/5 # lattice spacing micrometers +variable a equal 0.5/5 +variable Lf equal $R*3 +variable Lf equal 0.5*3 +variable Lb equal $R*4 +variable Lb equal 0.5*4 +variable wall_velocity equal 0.01 # micrometers/microsecond +variable T equal 300. +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 100. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.5 # kernel function cutoff micrometers +variable h equal 0.1*4.5 +variable mass equal $a*$a*$a*${rho_0} +variable mass equal 0.1*$a*$a*${rho_0} +variable mass equal 0.1*0.1*$a*${rho_0} +variable mass equal 0.1*0.1*0.1*${rho_0} +variable mass equal 0.1*0.1*0.1*1 +variable dt equal 1e-3 # timestep microseconds +variable skin equal 0.2*$h +variable skin equal 0.2*0.45 + +region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box +region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box +region box block -2 2 -${Lb} ${Lb} 0 ${a} units box +region box block -2 2 -2 ${Lb} 0 ${a} units box +region box block -2 2 -2 2 0 ${a} units box +region box block -2 2 -2 2 0 0.1 units box +create_box 4 box +Created orthogonal box = (-2 -2 0) to (2 2 0.1) + 1 by 1 by 1 MPI processor grid +lattice sq $a +lattice sq 0.1 +Lattice spacing in x,y,z = 0.1 0.1 0.1 + +create_atoms 1 box +Created 1600 atoms + using lattice units in orthogonal box = (-2 -2 0) to (2 2 0.1) + create_atoms CPU = 0.001 seconds + +region sphere sphere 0 0 0 $R units box +region sphere sphere 0 0 0 0.5 units box +set region sphere type 2 +Setting atom values ... + 81 settings made for type + +region upper_wall block INF INF +${Lf} INF INF INF units box +region upper_wall block INF INF +1.5 INF INF INF units box +set region upper_wall type 3 +Setting atom values ... + 200 settings made for type + +region lower_wall block INF INF INF -${Lf} INF INF units box +region lower_wall block INF INF INF -1.5 INF INF units box +set region lower_wall type 4 +Setting atom values ... + 240 settings made for type + +group fluid type 1 +1079 atoms in group fluid +group sphere type 2 +81 atoms in group sphere +group upper_wall type 3 +200 atoms in group upper_wall +group lower_wall type 4 +240 atoms in group lower_wall + +mass * ${mass} +mass * 0.001 +set group all sph/rho ${rho_0} +set group all sph/rho 1 +Setting atom values ... + 1600 settings made for sph/rho + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 +pair_style sdpd/taitwater/isothermal 300 1 76787 +pair_coeff * * ${rho_0} ${c_0} ${h} +pair_coeff * * 1 ${c_0} ${h} +pair_coeff * * 1 100 ${h} +pair_coeff * * 1 100 0.45 + +fix 1 fluid sph +fix 2 sphere rigid/meso single + 1 rigid bodies with 81 atoms +fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box +fix 3 upper_wall meso/move linear +0.01 0 0 units box +fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box +fix 4 lower_wall meso/move linear -0.01 0 0 units box + +fix 2d all enforce2d + +neighbor ${skin} bin +neighbor 0.09 bin +neigh_modify delay 0 every 1 check yes +timestep ${dt} +timestep 0.001 + +dump dump_id all atom 100 dump.lammpstrj + +thermo 100 +thermo_style custom step time nbuild ndanger + +run 10000 +Generated 0 of 6 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 = 0.54 + ghost atom cutoff = 0.54 + binsize = 0.27, bins = 15 15 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sdpd/taitwater/isothermal, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.313 | 7.313 | 7.313 Mbytes + Step Time Nbuild Ndanger + 0 0 0 0 + 100 0.1 0 0 + 200 0.2 0 0 + 300 0.3 0 0 + 400 0.4 0 0 + 500 0.5 1 0 + 600 0.6 1 0 + 700 0.7 2 0 + 800 0.8 2 0 + 900 0.9 2 0 + 1000 1 3 0 + 1100 1.1 3 0 + 1200 1.2 3 0 + 1300 1.3 4 0 + 1400 1.4 4 0 + 1500 1.5 4 0 + 1600 1.6 5 0 + 1700 1.7 5 0 + 1800 1.8 5 0 + 1900 1.9 6 0 + 2000 2 6 0 + 2100 2.1 6 0 + 2200 2.2 7 0 + 2300 2.3 7 0 + 2400 2.4 7 0 + 2500 2.5 8 0 + 2600 2.6 8 0 + 2700 2.7 8 0 + 2800 2.8 9 0 + 2900 2.9 9 0 + 3000 3 9 0 + 3100 3.1 10 0 + 3200 3.2 10 0 + 3300 3.3 10 0 + 3400 3.4 11 0 + 3500 3.5 11 0 + 3600 3.6 11 0 + 3700 3.7 12 0 + 3800 3.8 12 0 + 3900 3.9 12 0 + 4000 4 13 0 + 4100 4.1 13 0 + 4200 4.2 14 0 + 4300 4.3 14 0 + 4400 4.4 14 0 + 4500 4.5 15 0 + 4600 4.6 15 0 + 4700 4.7 15 0 + 4800 4.8 16 0 + 4900 4.9 16 0 + 5000 5 16 0 + 5100 5.1 17 0 + 5200 5.2 17 0 + 5300 5.3 17 0 + 5400 5.4 17 0 + 5500 5.5 18 0 + 5600 5.6 18 0 + 5700 5.7 19 0 + 5800 5.8 19 0 + 5900 5.9 19 0 + 6000 6 20 0 + 6100 6.1 20 0 + 6200 6.2 21 0 + 6300 6.3 21 0 + 6400 6.4 21 0 + 6500 6.5 22 0 + 6600 6.6 22 0 + 6700 6.7 22 0 + 6800 6.8 23 0 + 6900 6.9 23 0 + 7000 7 23 0 + 7100 7.1 24 0 + 7200 7.2 24 0 + 7300 7.3 25 0 + 7400 7.4 25 0 + 7500 7.5 25 0 + 7600 7.6 26 0 + 7700 7.7 26 0 + 7800 7.8 26 0 + 7900 7.9 27 0 + 8000 8 27 0 + 8100 8.1 27 0 + 8200 8.2 28 0 + 8300 8.3 28 0 + 8400 8.4 28 0 + 8500 8.5 29 0 + 8600 8.6 29 0 + 8700 8.7 30 0 + 8800 8.8 30 0 + 8900 8.9 30 0 + 9000 9 31 0 + 9100 9.1 31 0 + 9200 9.2 31 0 + 9300 9.3 32 0 + 9400 9.4 32 0 + 9500 9.5 32 0 + 9600 9.6 33 0 + 9700 9.7 33 0 + 9800 9.8 33 0 + 9900 9.9 34 0 + 10000 10 34 0 +Loop time of 131.724 on 1 procs for 10000 steps with 1600 atoms + +Performance: 6559168.339 ns/day, 0.000 hours/ns, 75.916 timesteps/s, 121.466 katom-step/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 130.89 | 130.89 | 130.89 | 0.0 | 99.37 +Neigh | 0.02884 | 0.02884 | 0.02884 | 0.0 | 0.02 +Comm | 0.17863 | 0.17863 | 0.17863 | 0.0 | 0.14 +Output | 0.095497 | 0.095497 | 0.095497 | 0.0 | 0.07 +Modify | 0.42063 | 0.42063 | 0.42063 | 0.0 | 0.32 +Other | | 0.1069 | | | 0.08 + +Nlocal: 1600 ave 1600 max 1600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 993 ave 993 max 993 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 73236 ave 73236 max 73236 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 73236 +Ave neighs/atom = 45.7725 +Neighbor list builds = 34 +Dangerous builds = 0 +Total wall time: 0:02:11 diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.4 b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.4 new file mode 100644 index 0000000000..6cb58bc233 --- /dev/null +++ b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.4 @@ -0,0 +1,253 @@ +LAMMPS (28 Mar 2023 - Development) +dimension 2 +units micro +atom_style sph + +variable R equal 0.5 # radius of sphere micrometers +variable a equal $R/5 # lattice spacing micrometers +variable a equal 0.5/5 +variable Lf equal $R*3 +variable Lf equal 0.5*3 +variable Lb equal $R*4 +variable Lb equal 0.5*4 +variable wall_velocity equal 0.01 # micrometers/microsecond +variable T equal 300. +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 100. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.5 # kernel function cutoff micrometers +variable h equal 0.1*4.5 +variable mass equal $a*$a*$a*${rho_0} +variable mass equal 0.1*$a*$a*${rho_0} +variable mass equal 0.1*0.1*$a*${rho_0} +variable mass equal 0.1*0.1*0.1*${rho_0} +variable mass equal 0.1*0.1*0.1*1 +variable dt equal 1e-3 # timestep microseconds +variable skin equal 0.2*$h +variable skin equal 0.2*0.45 + +region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box +region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box +region box block -2 2 -${Lb} ${Lb} 0 ${a} units box +region box block -2 2 -2 ${Lb} 0 ${a} units box +region box block -2 2 -2 2 0 ${a} units box +region box block -2 2 -2 2 0 0.1 units box +create_box 4 box +Created orthogonal box = (-2 -2 0) to (2 2 0.1) + 2 by 2 by 1 MPI processor grid +lattice sq $a +lattice sq 0.1 +Lattice spacing in x,y,z = 0.1 0.1 0.1 + +create_atoms 1 box +Created 1600 atoms + using lattice units in orthogonal box = (-2 -2 0) to (2 2 0.1) + create_atoms CPU = 0.001 seconds + +region sphere sphere 0 0 0 $R units box +region sphere sphere 0 0 0 0.5 units box +set region sphere type 2 +Setting atom values ... + 81 settings made for type + +region upper_wall block INF INF +${Lf} INF INF INF units box +region upper_wall block INF INF +1.5 INF INF INF units box +set region upper_wall type 3 +Setting atom values ... + 200 settings made for type + +region lower_wall block INF INF INF -${Lf} INF INF units box +region lower_wall block INF INF INF -1.5 INF INF units box +set region lower_wall type 4 +Setting atom values ... + 240 settings made for type + +group fluid type 1 +1079 atoms in group fluid +group sphere type 2 +81 atoms in group sphere +group upper_wall type 3 +200 atoms in group upper_wall +group lower_wall type 4 +240 atoms in group lower_wall + +mass * ${mass} +mass * 0.001 +set group all sph/rho ${rho_0} +set group all sph/rho 1 +Setting atom values ... + 1600 settings made for sph/rho + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 +pair_style sdpd/taitwater/isothermal 300 1 76787 +pair_coeff * * ${rho_0} ${c_0} ${h} +pair_coeff * * 1 ${c_0} ${h} +pair_coeff * * 1 100 ${h} +pair_coeff * * 1 100 0.45 + +fix 1 fluid sph +fix 2 sphere rigid/meso single + 1 rigid bodies with 81 atoms +fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box +fix 3 upper_wall meso/move linear +0.01 0 0 units box +fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box +fix 4 lower_wall meso/move linear -0.01 0 0 units box + +fix 2d all enforce2d + +neighbor ${skin} bin +neighbor 0.09 bin +neigh_modify delay 0 every 1 check yes +timestep ${dt} +timestep 0.001 + +dump dump_id all atom 100 dump.lammpstrj + +thermo 100 +thermo_style custom step time nbuild ndanger + +run 10000 +Generated 0 of 6 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 = 0.54 + ghost atom cutoff = 0.54 + binsize = 0.27, bins = 15 15 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sdpd/taitwater/isothermal, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.23 | 7.23 | 7.23 Mbytes + Step Time Nbuild Ndanger + 0 0 0 0 + 100 0.1 0 0 + 200 0.2 0 0 + 300 0.3 0 0 + 400 0.4 1 0 + 500 0.5 1 0 + 600 0.6 1 0 + 700 0.7 2 0 + 800 0.8 2 0 + 900 0.9 2 0 + 1000 1 3 0 + 1100 1.1 3 0 + 1200 1.2 3 0 + 1300 1.3 4 0 + 1400 1.4 4 0 + 1500 1.5 4 0 + 1600 1.6 5 0 + 1700 1.7 5 0 + 1800 1.8 5 0 + 1900 1.9 6 0 + 2000 2 6 0 + 2100 2.1 6 0 + 2200 2.2 7 0 + 2300 2.3 7 0 + 2400 2.4 7 0 + 2500 2.5 8 0 + 2600 2.6 8 0 + 2700 2.7 8 0 + 2800 2.8 9 0 + 2900 2.9 9 0 + 3000 3 9 0 + 3100 3.1 10 0 + 3200 3.2 10 0 + 3300 3.3 10 0 + 3400 3.4 11 0 + 3500 3.5 11 0 + 3600 3.6 11 0 + 3700 3.7 12 0 + 3800 3.8 12 0 + 3900 3.9 12 0 + 4000 4 13 0 + 4100 4.1 13 0 + 4200 4.2 13 0 + 4300 4.3 14 0 + 4400 4.4 14 0 + 4500 4.5 14 0 + 4600 4.6 14 0 + 4700 4.7 15 0 + 4800 4.8 15 0 + 4900 4.9 16 0 + 5000 5 16 0 + 5100 5.1 16 0 + 5200 5.2 17 0 + 5300 5.3 17 0 + 5400 5.4 17 0 + 5500 5.5 18 0 + 5600 5.6 18 0 + 5700 5.7 18 0 + 5800 5.8 19 0 + 5900 5.9 19 0 + 6000 6 20 0 + 6100 6.1 20 0 + 6200 6.2 20 0 + 6300 6.3 21 0 + 6400 6.4 21 0 + 6500 6.5 21 0 + 6600 6.6 22 0 + 6700 6.7 22 0 + 6800 6.8 22 0 + 6900 6.9 23 0 + 7000 7 23 0 + 7100 7.1 23 0 + 7200 7.2 24 0 + 7300 7.3 24 0 + 7400 7.4 24 0 + 7500 7.5 25 0 + 7600 7.6 25 0 + 7700 7.7 25 0 + 7800 7.8 25 0 + 7900 7.9 26 0 + 8000 8 26 0 + 8100 8.1 26 0 + 8200 8.2 27 0 + 8300 8.3 27 0 + 8400 8.4 28 0 + 8500 8.5 28 0 + 8600 8.6 28 0 + 8700 8.7 29 0 + 8800 8.8 29 0 + 8900 8.9 29 0 + 9000 9 30 0 + 9100 9.1 30 0 + 9200 9.2 30 0 + 9300 9.3 31 0 + 9400 9.4 31 0 + 9500 9.5 31 0 + 9600 9.6 32 0 + 9700 9.7 32 0 + 9800 9.8 32 0 + 9900 9.9 32 0 + 10000 10 33 0 +Loop time of 24.8261 on 4 procs for 10000 steps with 1600 atoms + +Performance: 34802055.618 ns/day, 0.000 hours/ns, 402.802 timesteps/s, 644.483 katom-step/s +99.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 21.84 | 22.879 | 23.944 | 21.4 | 92.16 +Neigh | 0.007446 | 0.0079435 | 0.0084435 | 0.6 | 0.03 +Comm | 0.5271 | 1.5894 | 2.6259 | 80.9 | 6.40 +Output | 0.034799 | 0.035302 | 0.036437 | 0.4 | 0.14 +Modify | 0.20079 | 0.21033 | 0.2202 | 1.7 | 0.85 +Other | | 0.1041 | | | 0.42 + +Nlocal: 400 ave 414 max 390 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Nghost: 555.5 ave 564 max 543 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Neighs: 18299.2 ave 18820 max 17906 min +Histogram: 1 1 0 0 0 0 1 0 0 1 + +Total # of neighbors = 73197 +Ave neighs/atom = 45.748125 +Neighbor list builds = 33 +Dangerous builds = 0 +Total wall time: 0:00:24 diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion/in.lammps b/examples/PACKAGES/dpd-smooth/2d-diffusion/in.lammps index 6ef36a0cf6..2e0e821480 100644 --- a/examples/PACKAGES/dpd-smooth/2d-diffusion/in.lammps +++ b/examples/PACKAGES/dpd-smooth/2d-diffusion/in.lammps @@ -1,6 +1,6 @@ dimension 2 units micro -atom_style meso +atom_style sph variable R equal 0.5 # radius of sphere micrometers variable a equal $R/5 # lattice spacing micrometers @@ -27,12 +27,12 @@ group fluid type 1 group sphere type 2 mass * ${mass} -set group all meso/rho ${rho_0} +set group all sph/rho ${rho_0} pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed pair_coeff * * ${rho_0} ${c_0} ${h} -fix 1 fluid meso +fix 1 fluid sph fix 2 sphere rigid/meso single fix 2d all enforce2d diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.1 b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.1 deleted file mode 100644 index d44c0fd6f4..0000000000 --- a/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.1 +++ /dev/null @@ -1,226 +0,0 @@ -LAMMPS (24 Oct 2018) -dimension 2 -units micro -atom_style meso - -variable R equal 0.5 # radius of sphere micrometers -variable a equal $R/5 # lattice spacing micrometers -variable a equal 0.5/5 -variable L equal $R*3 -variable L equal 0.5*3 -variable T equal 300. -variable rho_0 equal 1. # density picograms/micrometer^3 -variable c_0 equal 100. # speed of sound micrometers/microsecond -variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) -variable h equal $a*4.5 # kernel function cutoff micrometers -variable h equal 0.1*4.5 -variable mass equal $a*$a*$a*${rho_0} -variable mass equal 0.1*$a*$a*${rho_0} -variable mass equal 0.1*0.1*$a*${rho_0} -variable mass equal 0.1*0.1*0.1*${rho_0} -variable mass equal 0.1*0.1*0.1*1 -variable dt equal 1e-3 # timestep microseconds -variable skin equal 0.2*$h -variable skin equal 0.2*0.45 - -region box block -$L $L -$L $L 0 $a units box -region box block -1.5 $L -$L $L 0 $a units box -region box block -1.5 1.5 -$L $L 0 $a units box -region box block -1.5 1.5 -1.5 $L 0 $a units box -region box block -1.5 1.5 -1.5 1.5 0 $a units box -region box block -1.5 1.5 -1.5 1.5 0 0.1 units box -create_box 2 box -Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1) - 1 by 1 by 1 MPI processor grid -lattice sq $a -lattice sq 0.1 -Lattice spacing in x,y,z = 0.1 0.1 0.1 - -create_atoms 1 box -Created 900 atoms - Time spent = 0.0015769 secs - -region sphere sphere 0 0 0 $R units box -region sphere sphere 0 0 0 0.5 units box -set region sphere type 2 - 81 settings made for type - -group fluid type 1 -819 atoms in group fluid -group sphere type 2 -81 atoms in group sphere - -mass * ${mass} -mass * 0.001 -set group all meso/rho ${rho_0} -set group all meso/rho 1 - 900 settings made for meso/rho - -pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed -pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 -pair_style sdpd/taitwater/isothermal 300 1 76787 -pair_coeff * * ${rho_0} ${c_0} ${h} -pair_coeff * * 1 ${c_0} ${h} -pair_coeff * * 1 100 ${h} -pair_coeff * * 1 100 0.45 - -fix 1 fluid meso -fix 2 sphere rigid/meso single -1 rigid bodies with 81 atoms - -fix 2d all enforce2d - -neighbor ${skin} bin -neighbor 0.09 bin -neigh_modify delay 0 every 1 check yes -timestep ${dt} -timestep 0.001 - -dump dump_id all atom 100 dump.lammpstrj - -thermo 100 -thermo_style custom step time nbuild ndanger - -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 0.54 - ghost atom cutoff = 0.54 - binsize = 0.27, bins = 12 12 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair sdpd/taitwater/isothermal, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.137 | 6.137 | 6.137 Mbytes -Step Time Nbuild Ndanger - 0 0 0 0 - 100 0.1 0 0 - 200 0.2 0 0 - 300 0.3 0 0 - 400 0.4 1 0 - 500 0.5 1 0 - 600 0.6 1 0 - 700 0.7 2 0 - 800 0.8 2 0 - 900 0.9 2 0 - 1000 1 3 0 - 1100 1.1 3 0 - 1200 1.2 3 0 - 1300 1.3 4 0 - 1400 1.4 4 0 - 1500 1.5 4 0 - 1600 1.6 5 0 - 1700 1.7 5 0 - 1800 1.8 6 0 - 1900 1.9 6 0 - 2000 2 6 0 - 2100 2.1 7 0 - 2200 2.2 7 0 - 2300 2.3 7 0 - 2400 2.4 7 0 - 2500 2.5 8 0 - 2600 2.6 8 0 - 2700 2.7 8 0 - 2800 2.8 9 0 - 2900 2.9 9 0 - 3000 3 10 0 - 3100 3.1 10 0 - 3200 3.2 10 0 - 3300 3.3 11 0 - 3400 3.4 11 0 - 3500 3.5 11 0 - 3600 3.6 12 0 - 3700 3.7 12 0 - 3800 3.8 12 0 - 3900 3.9 13 0 - 4000 4 13 0 - 4100 4.1 13 0 - 4200 4.2 14 0 - 4300 4.3 14 0 - 4400 4.4 14 0 - 4500 4.5 15 0 - 4600 4.6 15 0 - 4700 4.7 15 0 - 4800 4.8 16 0 - 4900 4.9 16 0 - 5000 5 17 0 - 5100 5.1 17 0 - 5200 5.2 17 0 - 5300 5.3 17 0 - 5400 5.4 18 0 - 5500 5.5 18 0 - 5600 5.6 18 0 - 5700 5.7 19 0 - 5800 5.8 19 0 - 5900 5.9 19 0 - 6000 6 19 0 - 6100 6.1 20 0 - 6200 6.2 20 0 - 6300 6.3 20 0 - 6400 6.4 21 0 - 6500 6.5 21 0 - 6600 6.6 21 0 - 6700 6.7 21 0 - 6800 6.8 22 0 - 6900 6.9 22 0 - 7000 7 22 0 - 7100 7.1 23 0 - 7200 7.2 23 0 - 7300 7.3 23 0 - 7400 7.4 24 0 - 7500 7.5 24 0 - 7600 7.6 24 0 - 7700 7.7 25 0 - 7800 7.8 25 0 - 7900 7.9 26 0 - 8000 8 26 0 - 8100 8.1 26 0 - 8200 8.2 26 0 - 8300 8.3 27 0 - 8400 8.4 27 0 - 8500 8.5 27 0 - 8600 8.6 28 0 - 8700 8.7 28 0 - 8800 8.8 28 0 - 8900 8.9 29 0 - 9000 9 29 0 - 9100 9.1 29 0 - 9200 9.2 30 0 - 9300 9.3 30 0 - 9400 9.4 30 0 - 9500 9.5 30 0 - 9600 9.6 31 0 - 9700 9.7 31 0 - 9800 9.8 32 0 - 9900 9.9 32 0 - 10000 10 32 0 -Loop time of 80.9456 on 1 procs for 10000 steps with 900 atoms - -Performance: 10673829.855 ns/day, 0.000 hours/ns, 123.540 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 80.306 | 80.306 | 80.306 | 0.0 | 99.21 -Neigh | 0.017418 | 0.017418 | 0.017418 | 0.0 | 0.02 -Comm | 0.16939 | 0.16939 | 0.16939 | 0.0 | 0.21 -Output | 0.070281 | 0.070281 | 0.070281 | 0.0 | 0.09 -Modify | 0.3154 | 0.3154 | 0.3154 | 0.0 | 0.39 -Other | | 0.067 | | | 0.08 - -Nlocal: 900 ave 900 max 900 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 762 ave 762 max 762 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 40697 ave 40697 max 40697 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 40697 -Ave neighs/atom = 45.2189 -Neighbor list builds = 32 -Dangerous builds = 0 -Total wall time: 0:01:20 diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.4 b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.4 deleted file mode 100644 index f904b78ab4..0000000000 --- a/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.4 +++ /dev/null @@ -1,226 +0,0 @@ -LAMMPS (24 Oct 2018) -dimension 2 -units micro -atom_style meso - -variable R equal 0.5 # radius of sphere micrometers -variable a equal $R/5 # lattice spacing micrometers -variable a equal 0.5/5 -variable L equal $R*3 -variable L equal 0.5*3 -variable T equal 300. -variable rho_0 equal 1. # density picograms/micrometer^3 -variable c_0 equal 100. # speed of sound micrometers/microsecond -variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) -variable h equal $a*4.5 # kernel function cutoff micrometers -variable h equal 0.1*4.5 -variable mass equal $a*$a*$a*${rho_0} -variable mass equal 0.1*$a*$a*${rho_0} -variable mass equal 0.1*0.1*$a*${rho_0} -variable mass equal 0.1*0.1*0.1*${rho_0} -variable mass equal 0.1*0.1*0.1*1 -variable dt equal 1e-3 # timestep microseconds -variable skin equal 0.2*$h -variable skin equal 0.2*0.45 - -region box block -$L $L -$L $L 0 $a units box -region box block -1.5 $L -$L $L 0 $a units box -region box block -1.5 1.5 -$L $L 0 $a units box -region box block -1.5 1.5 -1.5 $L 0 $a units box -region box block -1.5 1.5 -1.5 1.5 0 $a units box -region box block -1.5 1.5 -1.5 1.5 0 0.1 units box -create_box 2 box -Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1) - 2 by 2 by 1 MPI processor grid -lattice sq $a -lattice sq 0.1 -Lattice spacing in x,y,z = 0.1 0.1 0.1 - -create_atoms 1 box -Created 900 atoms - Time spent = 0.0010246 secs - -region sphere sphere 0 0 0 $R units box -region sphere sphere 0 0 0 0.5 units box -set region sphere type 2 - 81 settings made for type - -group fluid type 1 -819 atoms in group fluid -group sphere type 2 -81 atoms in group sphere - -mass * ${mass} -mass * 0.001 -set group all meso/rho ${rho_0} -set group all meso/rho 1 - 900 settings made for meso/rho - -pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed -pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 -pair_style sdpd/taitwater/isothermal 300 1 76787 -pair_coeff * * ${rho_0} ${c_0} ${h} -pair_coeff * * 1 ${c_0} ${h} -pair_coeff * * 1 100 ${h} -pair_coeff * * 1 100 0.45 - -fix 1 fluid meso -fix 2 sphere rigid/meso single -1 rigid bodies with 81 atoms - -fix 2d all enforce2d - -neighbor ${skin} bin -neighbor 0.09 bin -neigh_modify delay 0 every 1 check yes -timestep ${dt} -timestep 0.001 - -dump dump_id all atom 100 dump.lammpstrj - -thermo 100 -thermo_style custom step time nbuild ndanger - -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 0.54 - ghost atom cutoff = 0.54 - binsize = 0.27, bins = 12 12 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair sdpd/taitwater/isothermal, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.087 | 6.087 | 6.087 Mbytes -Step Time Nbuild Ndanger - 0 0 0 0 - 100 0.1 0 0 - 200 0.2 0 0 - 300 0.3 0 0 - 400 0.4 1 0 - 500 0.5 1 0 - 600 0.6 1 0 - 700 0.7 2 0 - 800 0.8 2 0 - 900 0.9 2 0 - 1000 1 3 0 - 1100 1.1 3 0 - 1200 1.2 3 0 - 1300 1.3 4 0 - 1400 1.4 4 0 - 1500 1.5 5 0 - 1600 1.6 5 0 - 1700 1.7 5 0 - 1800 1.8 6 0 - 1900 1.9 6 0 - 2000 2 6 0 - 2100 2.1 7 0 - 2200 2.2 7 0 - 2300 2.3 7 0 - 2400 2.4 8 0 - 2500 2.5 8 0 - 2600 2.6 8 0 - 2700 2.7 9 0 - 2800 2.8 9 0 - 2900 2.9 9 0 - 3000 3 9 0 - 3100 3.1 10 0 - 3200 3.2 10 0 - 3300 3.3 10 0 - 3400 3.4 11 0 - 3500 3.5 11 0 - 3600 3.6 11 0 - 3700 3.7 12 0 - 3800 3.8 12 0 - 3900 3.9 12 0 - 4000 4 13 0 - 4100 4.1 13 0 - 4200 4.2 13 0 - 4300 4.3 14 0 - 4400 4.4 14 0 - 4500 4.5 15 0 - 4600 4.6 15 0 - 4700 4.7 15 0 - 4800 4.8 16 0 - 4900 4.9 16 0 - 5000 5 16 0 - 5100 5.1 16 0 - 5200 5.2 17 0 - 5300 5.3 17 0 - 5400 5.4 18 0 - 5500 5.5 18 0 - 5600 5.6 19 0 - 5700 5.7 19 0 - 5800 5.8 19 0 - 5900 5.9 20 0 - 6000 6 20 0 - 6100 6.1 20 0 - 6200 6.2 21 0 - 6300 6.3 21 0 - 6400 6.4 21 0 - 6500 6.5 22 0 - 6600 6.6 22 0 - 6700 6.7 22 0 - 6800 6.8 23 0 - 6900 6.9 23 0 - 7000 7 23 0 - 7100 7.1 24 0 - 7200 7.2 24 0 - 7300 7.3 24 0 - 7400 7.4 25 0 - 7500 7.5 25 0 - 7600 7.6 25 0 - 7700 7.7 26 0 - 7800 7.8 26 0 - 7900 7.9 26 0 - 8000 8 27 0 - 8100 8.1 27 0 - 8200 8.2 27 0 - 8300 8.3 28 0 - 8400 8.4 28 0 - 8500 8.5 28 0 - 8600 8.6 28 0 - 8700 8.7 29 0 - 8800 8.8 29 0 - 8900 8.9 29 0 - 9000 9 30 0 - 9100 9.1 30 0 - 9200 9.2 31 0 - 9300 9.3 31 0 - 9400 9.4 31 0 - 9500 9.5 31 0 - 9600 9.6 32 0 - 9700 9.7 32 0 - 9800 9.8 32 0 - 9900 9.9 33 0 - 10000 10 33 0 -Loop time of 69.01 on 4 procs for 10000 steps with 900 atoms - -Performance: 12519931.275 ns/day, 0.000 hours/ns, 144.907 timesteps/s -48.7% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 56.528 | 57.936 | 58.729 | 11.0 | 83.95 -Neigh | 0.013157 | 0.013382 | 0.013551 | 0.1 | 0.02 -Comm | 8.9594 | 9.7555 | 11.113 | 26.7 | 14.14 -Output | 0.14644 | 0.15009 | 0.15809 | 1.2 | 0.22 -Modify | 0.72913 | 0.91574 | 1.0524 | 12.4 | 1.33 -Other | | 0.2389 | | | 0.35 - -Nlocal: 225 ave 229 max 223 min -Histogram: 1 2 0 0 0 0 0 0 0 1 -Nghost: 442 ave 444 max 439 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -Neighs: 10188.8 ave 10437 max 9932 min -Histogram: 1 0 0 1 0 0 0 1 0 1 - -Total # of neighbors = 40755 -Ave neighs/atom = 45.2833 -Neighbor list builds = 33 -Dangerous builds = 0 -Total wall time: 0:01:09 diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.1 b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.1 new file mode 100644 index 0000000000..30bf43dcf6 --- /dev/null +++ b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.1 @@ -0,0 +1,230 @@ +LAMMPS (28 Mar 2023 - Development) +dimension 2 +units micro +atom_style sph + +variable R equal 0.5 # radius of sphere micrometers +variable a equal $R/5 # lattice spacing micrometers +variable a equal 0.5/5 +variable L equal $R*3 +variable L equal 0.5*3 +variable T equal 300. +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 100. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.5 # kernel function cutoff micrometers +variable h equal 0.1*4.5 +variable mass equal $a*$a*$a*${rho_0} +variable mass equal 0.1*$a*$a*${rho_0} +variable mass equal 0.1*0.1*$a*${rho_0} +variable mass equal 0.1*0.1*0.1*${rho_0} +variable mass equal 0.1*0.1*0.1*1 +variable dt equal 1e-3 # timestep microseconds +variable skin equal 0.2*$h +variable skin equal 0.2*0.45 + +region box block -$L $L -$L $L 0 $a units box +region box block -1.5 $L -$L $L 0 $a units box +region box block -1.5 1.5 -$L $L 0 $a units box +region box block -1.5 1.5 -1.5 $L 0 $a units box +region box block -1.5 1.5 -1.5 1.5 0 $a units box +region box block -1.5 1.5 -1.5 1.5 0 0.1 units box +create_box 2 box +Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1) + 1 by 1 by 1 MPI processor grid +lattice sq $a +lattice sq 0.1 +Lattice spacing in x,y,z = 0.1 0.1 0.1 + +create_atoms 1 box +Created 900 atoms + using lattice units in orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1) + create_atoms CPU = 0.001 seconds + +region sphere sphere 0 0 0 $R units box +region sphere sphere 0 0 0 0.5 units box +set region sphere type 2 +Setting atom values ... + 81 settings made for type + +group fluid type 1 +819 atoms in group fluid +group sphere type 2 +81 atoms in group sphere + +mass * ${mass} +mass * 0.001 +set group all sph/rho ${rho_0} +set group all sph/rho 1 +Setting atom values ... + 900 settings made for sph/rho + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 +pair_style sdpd/taitwater/isothermal 300 1 76787 +pair_coeff * * ${rho_0} ${c_0} ${h} +pair_coeff * * 1 ${c_0} ${h} +pair_coeff * * 1 100 ${h} +pair_coeff * * 1 100 0.45 + +fix 1 fluid sph +fix 2 sphere rigid/meso single + 1 rigid bodies with 81 atoms + +fix 2d all enforce2d + +neighbor ${skin} bin +neighbor 0.09 bin +neigh_modify delay 0 every 1 check yes +timestep ${dt} +timestep 0.001 + +dump dump_id all atom 100 dump.lammpstrj + +thermo 100 +thermo_style custom step time nbuild ndanger + +run 10000 +Generated 0 of 1 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 = 0.54 + ghost atom cutoff = 0.54 + binsize = 0.27, bins = 12 12 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sdpd/taitwater/isothermal, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.512 | 6.512 | 6.512 Mbytes + Step Time Nbuild Ndanger + 0 0 0 0 + 100 0.1 0 0 + 200 0.2 0 0 + 300 0.3 0 0 + 400 0.4 1 0 + 500 0.5 1 0 + 600 0.6 1 0 + 700 0.7 2 0 + 800 0.8 2 0 + 900 0.9 2 0 + 1000 1 3 0 + 1100 1.1 3 0 + 1200 1.2 3 0 + 1300 1.3 4 0 + 1400 1.4 4 0 + 1500 1.5 4 0 + 1600 1.6 5 0 + 1700 1.7 5 0 + 1800 1.8 6 0 + 1900 1.9 6 0 + 2000 2 6 0 + 2100 2.1 7 0 + 2200 2.2 7 0 + 2300 2.3 7 0 + 2400 2.4 7 0 + 2500 2.5 8 0 + 2600 2.6 8 0 + 2700 2.7 8 0 + 2800 2.8 9 0 + 2900 2.9 9 0 + 3000 3 10 0 + 3100 3.1 10 0 + 3200 3.2 10 0 + 3300 3.3 11 0 + 3400 3.4 11 0 + 3500 3.5 11 0 + 3600 3.6 12 0 + 3700 3.7 12 0 + 3800 3.8 12 0 + 3900 3.9 13 0 + 4000 4 13 0 + 4100 4.1 13 0 + 4200 4.2 14 0 + 4300 4.3 14 0 + 4400 4.4 14 0 + 4500 4.5 15 0 + 4600 4.6 15 0 + 4700 4.7 15 0 + 4800 4.8 16 0 + 4900 4.9 16 0 + 5000 5 17 0 + 5100 5.1 17 0 + 5200 5.2 17 0 + 5300 5.3 17 0 + 5400 5.4 18 0 + 5500 5.5 18 0 + 5600 5.6 18 0 + 5700 5.7 19 0 + 5800 5.8 19 0 + 5900 5.9 19 0 + 6000 6 19 0 + 6100 6.1 20 0 + 6200 6.2 20 0 + 6300 6.3 20 0 + 6400 6.4 21 0 + 6500 6.5 21 0 + 6600 6.6 21 0 + 6700 6.7 21 0 + 6800 6.8 22 0 + 6900 6.9 22 0 + 7000 7 22 0 + 7100 7.1 23 0 + 7200 7.2 23 0 + 7300 7.3 23 0 + 7400 7.4 24 0 + 7500 7.5 24 0 + 7600 7.6 24 0 + 7700 7.7 25 0 + 7800 7.8 25 0 + 7900 7.9 26 0 + 8000 8 26 0 + 8100 8.1 26 0 + 8200 8.2 26 0 + 8300 8.3 27 0 + 8400 8.4 27 0 + 8500 8.5 27 0 + 8600 8.6 28 0 + 8700 8.7 28 0 + 8800 8.8 28 0 + 8900 8.9 29 0 + 9000 9 29 0 + 9100 9.1 29 0 + 9200 9.2 30 0 + 9300 9.3 30 0 + 9400 9.4 30 0 + 9500 9.5 30 0 + 9600 9.6 31 0 + 9700 9.7 31 0 + 9800 9.8 32 0 + 9900 9.9 32 0 + 10000 10 32 0 +Loop time of 78.0094 on 1 procs for 10000 steps with 900 atoms + +Performance: 11075589.479 ns/day, 0.000 hours/ns, 128.190 timesteps/s, 115.371 katom-step/s +99.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 77.441 | 77.441 | 77.441 | 0.0 | 99.27 +Neigh | 0.016471 | 0.016471 | 0.016471 | 0.0 | 0.02 +Comm | 0.14821 | 0.14821 | 0.14821 | 0.0 | 0.19 +Output | 0.062415 | 0.062415 | 0.062415 | 0.0 | 0.08 +Modify | 0.25323 | 0.25323 | 0.25323 | 0.0 | 0.32 +Other | | 0.0877 | | | 0.11 + +Nlocal: 900 ave 900 max 900 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 762 ave 762 max 762 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 40697 ave 40697 max 40697 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 40697 +Ave neighs/atom = 45.218889 +Neighbor list builds = 32 +Dangerous builds = 0 +Total wall time: 0:01:18 diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.4 b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.4 new file mode 100644 index 0000000000..03f5ed01bb --- /dev/null +++ b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.4 @@ -0,0 +1,230 @@ +LAMMPS (28 Mar 2023 - Development) +dimension 2 +units micro +atom_style sph + +variable R equal 0.5 # radius of sphere micrometers +variable a equal $R/5 # lattice spacing micrometers +variable a equal 0.5/5 +variable L equal $R*3 +variable L equal 0.5*3 +variable T equal 300. +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 100. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.5 # kernel function cutoff micrometers +variable h equal 0.1*4.5 +variable mass equal $a*$a*$a*${rho_0} +variable mass equal 0.1*$a*$a*${rho_0} +variable mass equal 0.1*0.1*$a*${rho_0} +variable mass equal 0.1*0.1*0.1*${rho_0} +variable mass equal 0.1*0.1*0.1*1 +variable dt equal 1e-3 # timestep microseconds +variable skin equal 0.2*$h +variable skin equal 0.2*0.45 + +region box block -$L $L -$L $L 0 $a units box +region box block -1.5 $L -$L $L 0 $a units box +region box block -1.5 1.5 -$L $L 0 $a units box +region box block -1.5 1.5 -1.5 $L 0 $a units box +region box block -1.5 1.5 -1.5 1.5 0 $a units box +region box block -1.5 1.5 -1.5 1.5 0 0.1 units box +create_box 2 box +Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1) + 2 by 2 by 1 MPI processor grid +lattice sq $a +lattice sq 0.1 +Lattice spacing in x,y,z = 0.1 0.1 0.1 + +create_atoms 1 box +Created 900 atoms + using lattice units in orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1) + create_atoms CPU = 0.001 seconds + +region sphere sphere 0 0 0 $R units box +region sphere sphere 0 0 0 0.5 units box +set region sphere type 2 +Setting atom values ... + 81 settings made for type + +group fluid type 1 +819 atoms in group fluid +group sphere type 2 +81 atoms in group sphere + +mass * ${mass} +mass * 0.001 +set group all sph/rho ${rho_0} +set group all sph/rho 1 +Setting atom values ... + 900 settings made for sph/rho + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 +pair_style sdpd/taitwater/isothermal 300 1 76787 +pair_coeff * * ${rho_0} ${c_0} ${h} +pair_coeff * * 1 ${c_0} ${h} +pair_coeff * * 1 100 ${h} +pair_coeff * * 1 100 0.45 + +fix 1 fluid sph +fix 2 sphere rigid/meso single + 1 rigid bodies with 81 atoms + +fix 2d all enforce2d + +neighbor ${skin} bin +neighbor 0.09 bin +neigh_modify delay 0 every 1 check yes +timestep ${dt} +timestep 0.001 + +dump dump_id all atom 100 dump.lammpstrj + +thermo 100 +thermo_style custom step time nbuild ndanger + +run 10000 +Generated 0 of 1 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 = 0.54 + ghost atom cutoff = 0.54 + binsize = 0.27, bins = 12 12 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sdpd/taitwater/isothermal, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.463 | 6.463 | 6.463 Mbytes + Step Time Nbuild Ndanger + 0 0 0 0 + 100 0.1 0 0 + 200 0.2 0 0 + 300 0.3 0 0 + 400 0.4 1 0 + 500 0.5 1 0 + 600 0.6 1 0 + 700 0.7 2 0 + 800 0.8 2 0 + 900 0.9 2 0 + 1000 1 3 0 + 1100 1.1 3 0 + 1200 1.2 3 0 + 1300 1.3 4 0 + 1400 1.4 4 0 + 1500 1.5 4 0 + 1600 1.6 5 0 + 1700 1.7 5 0 + 1800 1.8 5 0 + 1900 1.9 6 0 + 2000 2 6 0 + 2100 2.1 6 0 + 2200 2.2 7 0 + 2300 2.3 7 0 + 2400 2.4 7 0 + 2500 2.5 8 0 + 2600 2.6 8 0 + 2700 2.7 8 0 + 2800 2.8 9 0 + 2900 2.9 9 0 + 3000 3 9 0 + 3100 3.1 10 0 + 3200 3.2 10 0 + 3300 3.3 11 0 + 3400 3.4 11 0 + 3500 3.5 11 0 + 3600 3.6 12 0 + 3700 3.7 12 0 + 3800 3.8 12 0 + 3900 3.9 12 0 + 4000 4 13 0 + 4100 4.1 13 0 + 4200 4.2 14 0 + 4300 4.3 14 0 + 4400 4.4 14 0 + 4500 4.5 15 0 + 4600 4.6 15 0 + 4700 4.7 15 0 + 4800 4.8 16 0 + 4900 4.9 16 0 + 5000 5 16 0 + 5100 5.1 17 0 + 5200 5.2 17 0 + 5300 5.3 17 0 + 5400 5.4 17 0 + 5500 5.5 18 0 + 5600 5.6 18 0 + 5700 5.7 18 0 + 5800 5.8 19 0 + 5900 5.9 19 0 + 6000 6 19 0 + 6100 6.1 20 0 + 6200 6.2 20 0 + 6300 6.3 20 0 + 6400 6.4 21 0 + 6500 6.5 21 0 + 6600 6.6 21 0 + 6700 6.7 22 0 + 6800 6.8 22 0 + 6900 6.9 22 0 + 7000 7 23 0 + 7100 7.1 23 0 + 7200 7.2 23 0 + 7300 7.3 24 0 + 7400 7.4 24 0 + 7500 7.5 24 0 + 7600 7.6 25 0 + 7700 7.7 25 0 + 7800 7.8 26 0 + 7900 7.9 26 0 + 8000 8 26 0 + 8100 8.1 26 0 + 8200 8.2 27 0 + 8300 8.3 27 0 + 8400 8.4 28 0 + 8500 8.5 28 0 + 8600 8.6 28 0 + 8700 8.7 29 0 + 8800 8.8 29 0 + 8900 8.9 29 0 + 9000 9 30 0 + 9100 9.1 30 0 + 9200 9.2 30 0 + 9300 9.3 30 0 + 9400 9.4 31 0 + 9500 9.5 31 0 + 9600 9.6 31 0 + 9700 9.7 32 0 + 9800 9.8 32 0 + 9900 9.9 32 0 + 10000 10 33 0 +Loop time of 13.5306 on 4 procs for 10000 steps with 900 atoms + +Performance: 63855371.888 ns/day, 0.000 hours/ns, 739.067 timesteps/s, 665.160 katom-step/s +98.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.327 | 12.56 | 12.738 | 4.3 | 92.83 +Neigh | 0.0043391 | 0.0044297 | 0.0045381 | 0.1 | 0.03 +Comm | 0.53746 | 0.71463 | 0.94685 | 18.1 | 5.28 +Output | 0.021884 | 0.02228 | 0.023428 | 0.4 | 0.16 +Modify | 0.14457 | 0.14548 | 0.14643 | 0.2 | 1.08 +Other | | 0.08351 | | | 0.62 + +Nlocal: 225 ave 228 max 222 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 438.25 ave 442 max 434 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 10152.2 ave 10328 max 9853 min +Histogram: 1 0 0 0 0 0 0 1 1 1 + +Total # of neighbors = 40609 +Ave neighs/atom = 45.121111 +Neighbor list builds = 33 +Dangerous builds = 0 +Total wall time: 0:00:13 diff --git a/examples/PACKAGES/dpd-smooth/equipartition-verification/in.lammps b/examples/PACKAGES/dpd-smooth/equipartition-verification/in.lammps index 0d06723f59..59359d4b38 100644 --- a/examples/PACKAGES/dpd-smooth/equipartition-verification/in.lammps +++ b/examples/PACKAGES/dpd-smooth/equipartition-verification/in.lammps @@ -1,6 +1,6 @@ dimension 3 units micro -atom_style meso +atom_style sph variable a equal 0.1 # lattice spacing micrometers variable L equal $a*10 @@ -21,7 +21,7 @@ lattice sc $a create_atoms 1 box mass * ${mass} -set group all meso/rho ${rho_0} +set group all sph/rho ${rho_0} pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed pair_coeff * * ${rho_0} ${c_0} ${h} @@ -34,7 +34,7 @@ variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T -fix 1 all meso +fix 1 all sph neighbor ${skin} bin timestep ${dt} diff --git a/examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.1 b/examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.1 similarity index 58% rename from examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.1 rename to examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.1 index 06ffd699bc..2fa4771a74 100644 --- a/examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.1 +++ b/examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.1 @@ -1,7 +1,7 @@ -LAMMPS (24 Oct 2018) +LAMMPS (28 Mar 2023 - Development) dimension 3 units micro -atom_style meso +atom_style sph variable a equal 0.1 # lattice spacing micrometers variable L equal $a*10 @@ -38,13 +38,15 @@ Lattice spacing in x,y,z = 0.1 0.1 0.1 create_atoms 1 box Created 8000 atoms - Time spent = 0.00285411 secs + using lattice units in orthogonal box = (-1 -1 -1) to (1 1 1) + create_atoms CPU = 0.002 seconds mass * ${mass} mass * 0.001 -set group all meso/rho ${rho_0} -set group all meso/rho 1 - 8000 settings made for meso/rho +set group all sph/rho ${rho_0} +set group all sph/rho 1 +Setting atom values ... + 8000 settings made for sph/rho pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 @@ -71,7 +73,7 @@ variable vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300 -fix 1 all meso +fix 1 all sph neighbor ${skin} bin neighbor 0.04 bin @@ -82,8 +84,9 @@ thermo 10 thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check run 200 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 0.44 ghost atom cutoff = 0.44 @@ -92,55 +95,55 @@ Neighbor list info ... (1) pair sdpd/taitwater/isothermal, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton + stencil: half/bin/3d bin: standard -Per MPI rank memory allocation (min/avg/max) = 13.54 | 13.54 | 13.54 Mbytes -Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check - 0 0 0 0 0 - 10 0.005 0.70973271 0.71495693 0.71910087 - 20 0.01 0.90418096 0.88845437 0.89659567 - 30 0.015 0.9590736 0.97880338 0.9619016 - 40 0.02 0.98533774 0.96057682 0.95600448 - 50 0.025 0.96433662 0.96650071 0.95509683 - 60 0.03 0.96598029 0.96373656 0.96734888 - 70 0.035 0.95433045 0.98004764 0.96255924 - 80 0.04 0.97872906 0.95987289 0.96623598 - 90 0.045 0.99913888 0.99255731 0.95616142 - 100 0.05 0.98872675 0.97141018 0.95338841 - 110 0.055 0.97794592 0.97389258 0.98473719 - 120 0.06 0.98389266 0.96716284 0.95504862 - 130 0.065 0.98572886 0.96680923 0.95599065 - 140 0.07 0.97602684 0.97580081 0.9886878 - 150 0.075 0.99172003 0.95027467 0.96028033 - 160 0.08 0.96793247 0.94590928 0.95644301 - 170 0.085 0.94167619 0.98048861 0.93439426 - 180 0.09 0.97277934 0.97383622 0.96900866 - 190 0.095 0.96647288 1.0027643 0.96230782 - 200 0.1 0.94864291 0.95902585 0.96398175 -Loop time of 60.1095 on 1 procs for 200 steps with 8000 atoms +Per MPI rank memory allocation (min/avg/max) = 14.29 | 14.29 | 14.29 Mbytes + Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check + 0 0 0 0 0 + 10 0.005 0.70973271 0.71495693 0.71910087 + 20 0.01 0.90418096 0.88845437 0.89659567 + 30 0.015 0.9590736 0.97880338 0.9619016 + 40 0.02 0.98533774 0.96057682 0.95600448 + 50 0.025 0.96433662 0.96650071 0.95509683 + 60 0.03 0.96598029 0.96373656 0.96734888 + 70 0.035 0.95433045 0.98004764 0.96255924 + 80 0.04 0.97872906 0.95987289 0.96623598 + 90 0.045 0.99913888 0.99255731 0.95616142 + 100 0.05 0.98872675 0.97141018 0.95338841 + 110 0.055 0.97794592 0.97389258 0.98473719 + 120 0.06 0.98389266 0.96716284 0.95504862 + 130 0.065 0.98572886 0.96680923 0.95599065 + 140 0.07 0.97602684 0.97580081 0.9886878 + 150 0.075 0.99172003 0.95027467 0.96028033 + 160 0.08 0.96793247 0.94590928 0.95644301 + 170 0.085 0.94167619 0.98048861 0.93439426 + 180 0.09 0.97277934 0.97383622 0.96900866 + 190 0.095 0.96647288 1.0027643 0.96230782 + 200 0.1 0.94864291 0.95902585 0.96398175 +Loop time of 55.7542 on 1 procs for 200 steps with 8000 atoms -Performance: 143737.595 ns/day, 0.000 hours/ns, 3.327 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 154965.922 ns/day, 0.000 hours/ns, 3.587 timesteps/s, 28.697 katom-step/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 59.92 | 59.92 | 59.92 | 0.0 | 99.68 +Pair | 55.642 | 55.642 | 55.642 | 0.0 | 99.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.11154 | 0.11154 | 0.11154 | 0.0 | 0.19 -Output | 0.0063498 | 0.0063498 | 0.0063498 | 0.0 | 0.01 -Modify | 0.043546 | 0.043546 | 0.043546 | 0.0 | 0.07 -Other | | 0.02811 | | | 0.05 +Comm | 0.060977 | 0.060977 | 0.060977 | 0.0 | 0.11 +Output | 0.0066393 | 0.0066393 | 0.0066393 | 0.0 | 0.01 +Modify | 0.028354 | 0.028354 | 0.028354 | 0.0 | 0.05 +Other | | 0.01623 | | | 0.03 -Nlocal: 8000 ave 8000 max 8000 min +Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 16389 ave 16389 max 16389 min +Nghost: 16389 ave 16389 max 16389 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.456e+06 ave 1.456e+06 max 1.456e+06 min +Neighs: 1.456e+06 ave 1.456e+06 max 1.456e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1456000 Ave neighs/atom = 182 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:01:00 +Total wall time: 0:00:56 diff --git a/examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.4 b/examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.4 similarity index 58% rename from examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.4 rename to examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.4 index 88509f0fd1..e4f11d305e 100644 --- a/examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.4 +++ b/examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.4 @@ -1,7 +1,7 @@ -LAMMPS (24 Oct 2018) +LAMMPS (28 Mar 2023 - Development) dimension 3 units micro -atom_style meso +atom_style sph variable a equal 0.1 # lattice spacing micrometers variable L equal $a*10 @@ -38,13 +38,15 @@ Lattice spacing in x,y,z = 0.1 0.1 0.1 create_atoms 1 box Created 8000 atoms - Time spent = 0.00252754 secs + using lattice units in orthogonal box = (-1 -1 -1) to (1 1 1) + create_atoms CPU = 0.001 seconds mass * ${mass} mass * 0.001 -set group all meso/rho ${rho_0} -set group all meso/rho 1 - 8000 settings made for meso/rho +set group all sph/rho ${rho_0} +set group all sph/rho 1 +Setting atom values ... + 8000 settings made for sph/rho pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 @@ -71,7 +73,7 @@ variable vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300 -fix 1 all meso +fix 1 all sph neighbor ${skin} bin neighbor 0.04 bin @@ -82,8 +84,9 @@ thermo 10 thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check run 200 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 0.44 ghost atom cutoff = 0.44 @@ -92,55 +95,55 @@ Neighbor list info ... (1) pair sdpd/taitwater/isothermal, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton + stencil: half/bin/3d bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.795 | 5.795 | 5.795 Mbytes -Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check - 0 0 0 0 0 - 10 0.005 0.71224819 0.71470372 0.7008956 - 20 0.01 0.90627589 0.90683966 0.90116506 - 30 0.015 0.938505 0.95884272 0.93337542 - 40 0.02 0.94394649 0.93668038 0.96468004 - 50 0.025 0.97152309 0.97546161 0.95107762 - 60 0.03 0.94710871 0.95678322 0.97285504 - 70 0.035 0.96253148 0.95838642 0.95450883 - 80 0.04 0.97581495 0.95278681 0.95099478 - 90 0.045 0.96251614 0.9740684 0.96081505 - 100 0.05 0.94191275 0.97137523 0.94084858 - 110 0.055 0.953406 0.95739684 0.98574522 - 120 0.06 0.99001614 0.99608287 0.9839996 - 130 0.065 0.96575225 0.94309655 0.92847798 - 140 0.07 0.97642687 0.97458638 0.94696406 - 150 0.075 0.99316381 0.96876814 0.95440106 - 160 0.08 0.94589744 0.95264791 0.95495169 - 170 0.085 0.97599092 0.95336014 0.97687718 - 180 0.09 0.97214242 0.9726305 0.9726035 - 190 0.095 0.97577583 0.96523645 0.9756968 - 200 0.1 0.96386053 0.97268854 0.94582436 -Loop time of 32.5247 on 4 procs for 200 steps with 8000 atoms +Per MPI rank memory allocation (min/avg/max) = 6.172 | 6.172 | 6.172 Mbytes + Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check + 0 0 0 0 0 + 10 0.005 0.71224819 0.71470372 0.7008956 + 20 0.01 0.90627589 0.90683966 0.90116506 + 30 0.015 0.938505 0.95884272 0.93337542 + 40 0.02 0.94394649 0.93668038 0.96468004 + 50 0.025 0.97152309 0.97546161 0.95107762 + 60 0.03 0.94710871 0.95678322 0.97285504 + 70 0.035 0.96253148 0.95838642 0.95450883 + 80 0.04 0.97581495 0.95278681 0.95099478 + 90 0.045 0.96251614 0.9740684 0.96081505 + 100 0.05 0.94191275 0.97137523 0.94084858 + 110 0.055 0.953406 0.95739684 0.98574522 + 120 0.06 0.99001614 0.99608287 0.9839996 + 130 0.065 0.96575225 0.94309655 0.92847798 + 140 0.07 0.97642687 0.97458638 0.94696406 + 150 0.075 0.99316381 0.96876814 0.95440106 + 160 0.08 0.94589744 0.95264791 0.95495169 + 170 0.085 0.97599092 0.95336014 0.97687718 + 180 0.09 0.97214242 0.9726305 0.9726035 + 190 0.095 0.97577583 0.96523645 0.9756968 + 200 0.1 0.96386053 0.97268854 0.94582436 +Loop time of 9.59181 on 4 procs for 200 steps with 8000 atoms -Performance: 265644.515 ns/day, 0.000 hours/ns, 6.149 timesteps/s -73.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 900768.333 ns/day, 0.000 hours/ns, 20.851 timesteps/s, 166.809 katom-step/s +98.1% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 27.385 | 28.409 | 28.761 | 11.1 | 87.34 +Pair | 8.9729 | 9.2147 | 9.4383 | 5.5 | 96.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 3.582 | 3.9343 | 4.9531 | 29.7 | 12.10 -Output | 0.022267 | 0.026073 | 0.033141 | 2.7 | 0.08 -Modify | 0.031714 | 0.033134 | 0.034367 | 0.6 | 0.10 -Other | | 0.1226 | | | 0.38 +Comm | 0.13739 | 0.36068 | 0.60216 | 27.6 | 3.76 +Output | 0.0022724 | 0.002394 | 0.0026506 | 0.3 | 0.02 +Modify | 0.0068559 | 0.0069926 | 0.0070974 | 0.1 | 0.07 +Other | | 0.007004 | | | 0.07 -Nlocal: 2000 ave 2000 max 2000 min +Nlocal: 2000 ave 2000 max 2000 min Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 8469 ave 8469 max 8469 min +Nghost: 8469 ave 8469 max 8469 min Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 364000 ave 376628 max 351184 min +Neighs: 364000 ave 376628 max 351184 min Histogram: 1 0 1 0 0 0 0 1 0 1 Total # of neighbors = 1456000 Ave neighs/atom = 182 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:32 +Total wall time: 0:00:09