update log files for peptide, peri, pour and python examples
This commit is contained in:
Axel Kohlmeyer
148
examples/python/log.27Nov18.pair_python_long.g++.4
Normal file
148
examples/python/log.27Nov18.pair_python_long.g++.4
Normal file
@ -0,0 +1,148 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style python 12.0
|
||||
pair_coeff * * py_pot.LJCutSPCE OW HW
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
1500 = # of frozen angles
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
# create only lj/cut table for the oxygen atoms from python
|
||||
shell rm -f spce.table
|
||||
WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308)
|
||||
WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308)
|
||||
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
|
||||
# switch to tabulated potential with long-range coulomb as overlay
|
||||
pair_style hybrid/overlay coul/long 12.0 table linear 2000
|
||||
kspace_style pppm 1.0e-6
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff 1 1 table spce.table OW-OW
|
||||
WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:481)
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394674
|
||||
estimated relative force accuracy = 1.18855e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 34263 16000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.5 | 13.5 | 13.5 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -16690.019 0 -16690.019 -1268.9124
|
||||
10 120.58553 -17767.489 0 -16689.521 -4063.8136
|
||||
20 136.11736 -17882.538 0 -16665.724 -5124.6194
|
||||
30 137.00764 -17872.302 0 -16647.529 -5337.1515
|
||||
40 153.38867 -17999.256 0 -16628.046 -5213.5616
|
||||
50 167.70342 -18103.046 0 -16603.87 -4460.6216
|
||||
60 163.07134 -18034.842 0 -16577.074 -3284.9621
|
||||
70 169.59286 -18064.622 0 -16548.556 -2606.3642
|
||||
80 182.92892 -18153.485 0 -16518.202 -2385.4747
|
||||
90 191.2793 -18195.343 0 -16485.411 -2235.3292
|
||||
100 194.68587 -18192.446 0 -16452.061 -1948.3379
|
||||
Loop time of 2.26946 on 4 procs for 100 steps with 4500 atoms
|
||||
|
||||
Performance: 3.807 ns/day, 6.304 hours/ns, 44.063 timesteps/s
|
||||
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.4676 | 1.53 | 1.6054 | 4.5 | 67.42
|
||||
Bond | 9.7752e-05 | 0.00012088 | 0.00013947 | 0.0 | 0.01
|
||||
Kspace | 0.51974 | 0.59375 | 0.65496 | 7.2 | 26.16
|
||||
Neigh | 0.075271 | 0.075279 | 0.075287 | 0.0 | 3.32
|
||||
Comm | 0.028602 | 0.029937 | 0.031052 | 0.5 | 1.32
|
||||
Output | 0.00035477 | 0.00062722 | 0.0014365 | 0.0 | 0.03
|
||||
Modify | 0.03581 | 0.035956 | 0.036059 | 0.1 | 1.58
|
||||
Other | | 0.003819 | | | 0.17
|
||||
|
||||
Nlocal: 1125 ave 1154 max 1092 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Nghost: 12256.2 ave 12296 max 12213 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 650442 ave 678830 max 626373 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2601768
|
||||
Ave neighs/atom = 578.171
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
shell rm spce.table
|
||||
|
||||
Total wall time: 0:00:02
|
||||
Reference in New Issue
Block a user