forked from lijiext/lammps
138 lines
4.3 KiB
Groff
138 lines
4.3 KiB
Groff
LAMMPS (27 Nov 2018)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# Test volume definitions for 2d and finite systems
|
|
|
|
variable rcut equal 10.0
|
|
variable rskin equal 2.0
|
|
variable rcomm equal 20.0
|
|
variable len equal 4.0
|
|
variable lenz equal 10.0
|
|
|
|
dimension 2
|
|
units metal
|
|
boundary p p p
|
|
|
|
#lattice sq 1.0 origin 0.5 0.5 0.0
|
|
lattice hex 1.0 origin 0.5 0.5 0.0
|
|
Lattice spacing in x,y,z = 1 1.73205 1
|
|
|
|
atom_style atomic
|
|
|
|
region box block 0 ${len} 0 ${len} 0.0 ${lenz}
|
|
region box block 0 4 0 ${len} 0.0 ${lenz}
|
|
region box block 0 4 0 4 0.0 ${lenz}
|
|
region box block 0 4 0 4 0.0 10
|
|
region atoms block 0 ${len} 0 ${len} 0.0 0.0
|
|
region atoms block 0 4 0 ${len} 0.0 0.0
|
|
region atoms block 0 4 0 4 0.0 0.0
|
|
create_box 1 box
|
|
Created orthogonal box = (0 0 0) to (4 6.9282 10)
|
|
1 by 1 by 1 MPI processor grid
|
|
create_atoms 1 region atoms
|
|
Created 32 atoms
|
|
Time spent = 0.000315905 secs
|
|
|
|
mass 1 1.0
|
|
|
|
pair_style lj/cut ${rcut}
|
|
pair_style lj/cut 10
|
|
pair_coeff 1 1 0.0 1.0
|
|
|
|
neighbor ${rskin} nsq
|
|
neighbor 2 nsq
|
|
|
|
# set the minimum communication cut-off
|
|
comm_modify cutoff ${rcomm}
|
|
comm_modify cutoff 20
|
|
|
|
compute v1 all voronoi/atom neighbors yes
|
|
compute volvor all reduce sum c_v1[1]
|
|
variable volsys equal lz*lx*ly
|
|
variable err equal c_volvor-v_volsys
|
|
thermo_style custom c_volvor v_volsys vol v_err
|
|
thermo 1
|
|
|
|
#
|
|
# TEST 1: Volume check for 2d bulk system
|
|
#
|
|
|
|
run 0
|
|
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 10 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 12
|
|
ghost atom cutoff = 20
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/cut, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/nsq/newton
|
|
stencil: none
|
|
bin: none
|
|
Per MPI rank memory allocation (min/avg/max) = 3.007 | 3.007 | 3.007 Mbytes
|
|
c_volvor v_volsys Volume v_err
|
|
277.12813 277.12813 27.712813 5.6843419e-14
|
|
Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms
|
|
|
|
209.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
|
Other | | 9.537e-07 | | |100.00
|
|
|
|
Nlocal: 32 ave 32 max 32 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 2415 ave 2415 max 2415 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 8256 ave 8256 max 8256 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 8256
|
|
Ave neighs/atom = 258
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
|
|
#
|
|
# TEST 2: Volume check for 2d finite system
|
|
# add margins in x and y directions
|
|
#
|
|
|
|
change_box all boundary f f p
|
|
run 0
|
|
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
|
Per MPI rank memory allocation (min/avg/max) = 7.688 | 7.688 | 7.688 Mbytes
|
|
c_volvor v_volsys Volume v_err
|
|
277.12813 277.12813 27.712813 3.4106051e-13
|
|
Loop time of 4.76837e-07 on 1 procs for 0 steps with 32 atoms
|
|
|
|
209.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
|
Other | | 4.768e-07 | | |100.00
|
|
|
|
Nlocal: 32 ave 32 max 32 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 0 ave 0 max 0 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 496 ave 496 max 496 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 496
|
|
Ave neighs/atom = 15.5
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:00
|