107 lines
3.9 KiB
Groff
107 lines
3.9 KiB
Groff
LAMMPS (24 Mar 2022)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# Coarse-Grained SPC/E Water
|
|
|
|
variable T equal 300.0
|
|
variable rc equal 9.0
|
|
variable rcD equal 10.0
|
|
|
|
units real
|
|
boundary p p p
|
|
atom_style atomic
|
|
dimension 3
|
|
newton on
|
|
comm_modify vel yes
|
|
|
|
read_data cg_spce.data
|
|
Reading data file ...
|
|
orthogonal box = (0 0 0) to (40.31 40.31 40.31)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
2180 atoms
|
|
read_data CPU = 0.003 seconds
|
|
|
|
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
|
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
|
|
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 ${rc} 385262
|
|
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 9 385262
|
|
|
|
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
|
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
|
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
|
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
|
|
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
|
|
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
|
|
|
|
timestep 1.0
|
|
run_style verlet
|
|
|
|
velocity all create ${T} 68768932
|
|
velocity all create 300 68768932
|
|
|
|
thermo_style custom step time temp press
|
|
thermo 100
|
|
|
|
fix 1 all nve
|
|
|
|
run 1000
|
|
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
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 = 12
|
|
binsize = 6, bins = 7 7 7
|
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
(1) pair table, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
(2) pair dpd/ext/tstat, perpetual, copy from (1)
|
|
attributes: half, newton on
|
|
pair build: copy
|
|
stencil: none
|
|
bin: none
|
|
Per MPI rank memory allocation (min/avg/max) = 5.38 | 5.38 | 5.38 Mbytes
|
|
Step Time Temp Press
|
|
0 0 300 7353.4129
|
|
100 100 303.74025 4964.013
|
|
200 200 298.35396 8007.7802
|
|
300 300 298.28547 6291.5807
|
|
400 400 298.01797 6252.1041
|
|
500 500 299.88984 3489.931
|
|
600 600 302.5718 9092.203
|
|
700 700 305.38722 5909.02
|
|
800 800 294.81401 10282.286
|
|
900 900 292.40724 8338.6878
|
|
1000 1000 293.64788 6951.569
|
|
Loop time of 28.1058 on 1 procs for 1000 steps with 2180 atoms
|
|
|
|
Performance: 3.074 ns/day, 7.807 hours/ns, 35.580 timesteps/s
|
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 27.948 | 27.948 | 27.948 | 0.0 | 99.44
|
|
Neigh | 0.071647 | 0.071647 | 0.071647 | 0.0 | 0.25
|
|
Comm | 0.058215 | 0.058215 | 0.058215 | 0.0 | 0.21
|
|
Output | 0.00026724 | 0.00026724 | 0.00026724 | 0.0 | 0.00
|
|
Modify | 0.014429 | 0.014429 | 0.014429 | 0.0 | 0.05
|
|
Other | | 0.01283 | | | 0.05
|
|
|
|
Nlocal: 2180 ave 2180 max 2180 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 6643 ave 6643 max 6643 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 261826 ave 261826 max 261826 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 261826
|
|
Ave neighs/atom = 120.10367
|
|
Neighbor list builds = 12
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:28
|