147 lines
6.2 KiB
Groff
147 lines
6.2 KiB
Groff
LAMMPS (24 Oct 2018)
|
|
dimension 3
|
|
units micro
|
|
atom_style meso
|
|
|
|
variable a equal 0.1 # lattice spacing micrometers
|
|
variable L equal $a*10
|
|
variable L equal 0.1*10
|
|
variable T equal 300.
|
|
variable kB equal 1.3806504e-8 # picogram-micrometer^2/(microsecond^2-Kelvin)
|
|
variable rho_0 equal 1. # density picograms/micrometer^3
|
|
variable c_0 equal 10. # speed of sound micrometers/microsecond
|
|
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
|
variable h equal $a*4.0 # kernel function cutoff micrometers
|
|
variable h equal 0.1*4.0
|
|
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 5e-4 # timestep microseconds
|
|
variable skin equal 0.1*$h
|
|
variable skin equal 0.1*0.4
|
|
|
|
region box block -$L $L -$L $L -$L $L units box
|
|
region box block -1 $L -$L $L -$L $L units box
|
|
region box block -1 1 -$L $L -$L $L units box
|
|
region box block -1 1 -1 $L -$L $L units box
|
|
region box block -1 1 -1 1 -$L $L units box
|
|
region box block -1 1 -1 1 -1 $L units box
|
|
region box block -1 1 -1 1 -1 1 units box
|
|
create_box 1 box
|
|
Created orthogonal box = (-1 -1 -1) to (1 1 1)
|
|
1 by 1 by 1 MPI processor grid
|
|
lattice sc $a
|
|
lattice sc 0.1
|
|
Lattice spacing in x,y,z = 0.1 0.1 0.1
|
|
|
|
create_atoms 1 box
|
|
Created 8000 atoms
|
|
Time spent = 0.00285411 secs
|
|
|
|
mass * ${mass}
|
|
mass * 0.001
|
|
set group all meso/rho ${rho_0}
|
|
set group all meso/rho 1
|
|
8000 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 10 ${h}
|
|
pair_coeff * * 1 10 0.4
|
|
|
|
variable vx_sq atom vx*vx
|
|
variable vy_sq atom vy*vy
|
|
variable vz_sq atom vz*vz
|
|
compute v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq
|
|
variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
|
|
variable vx_sq_check equal c_v_sq[1]*0.001/${kB}/$T
|
|
variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/$T
|
|
variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/300
|
|
variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
|
|
variable vy_sq_check equal c_v_sq[2]*0.001/${kB}/$T
|
|
variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/$T
|
|
variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/300
|
|
variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
|
|
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
|
|
|
|
neighbor ${skin} bin
|
|
neighbor 0.04 bin
|
|
timestep ${dt}
|
|
timestep 0.0005
|
|
|
|
thermo 10
|
|
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
|
|
|
run 200
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 10 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 0.44
|
|
ghost atom cutoff = 0.44
|
|
binsize = 0.22, bins = 10 10 10
|
|
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/3d/newton
|
|
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
|
|
|
|
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
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 59.92 | 59.92 | 59.92 | 0.0 | 99.68
|
|
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
|
|
|
|
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
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
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
|