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create.log
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128 lines (120 loc) · 5.11 KB
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using 8 OpenMP thread(s) per MPI task
using multi-threaded neighbor list subroutines
Lattice spacing in x,y,z = 4.04 4.04 4.04
Created orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
1 by 1 by 1 MPI processor grid
Created 432 atoms
using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
create_atoms CPU = 0.006 seconds
Read molecule template h2omol:
# LAMMPS Input File (License CC BY 4.0)
1 molecules
0 fragments
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
Created 1944 atoms
using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
create_atoms CPU = 0.002 seconds
Created 15 atoms
using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
create_atoms CPU = 0.005 seconds
Created 15 atoms
using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
create_atoms CPU = 0.004 seconds
Setting atom values ...
15 settings made for charge
Setting atom values ...
15 settings made for charge
1944 atoms in group H2O
15 atoms in group Na
15 atoms in group Cl
30 atoms in group ions
1974 atoms in group fluid
432 atoms in group wall
1191 atoms in group top
1215 atoms in group bot
216 atoms in group walltop
216 atoms in group wallbot
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:141)
Deleted 726 atoms, new total = 1680
Deleted 484 bonds, new total = 812
Deleted 242 angles, new total = 406
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.25237451
grid = 18 18 60
stencil order = 5
estimated absolute RMS force accuracy = 0.0034985124
estimated relative force accuracy = 1.0535666e-05
using double precision KISS FFT
3d grid and FFT values/proc = 39375 19440
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (src/comm.cpp:730)
WARNING: Increasing communication cutoff to 15.1118 for TIP4P pair style (src/KSPACE/pair_lj_cut_tip4p_long.cpp:497)
Generated 9 of 10 mixed pair_coeff terms from geometric mixing rule
Last active /omp style is kspace_style pppm/tip4p/omp
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14.3092
ghost atom cutoff = 15.1118
binsize = 7.1546, bins = 4 4 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/tip4p/long/omp, perpetual
attributes: half, newton on, omp
pair build: half/bin/newton/omp
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 19.16 | 19.16 | 19.16 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 501411.03 0 501411.03 6165751.9
Loop time of 3.207e-06 on 8 procs for 0 steps with 1680 atoms
155.9% CPU use with 1 MPI tasks x 8 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Kspace | 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 | | 3.207e-06 | | |100.00
Nlocal: 1680 ave 1680 max 1680 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6827 ave 6827 max 6827 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 829213 ave 829213 max 829213 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 829213
Ave neighs/atom = 493.57917
Ave special neighs/atom = 1.45
Neighbor list builds = 0
Dangerous builds = 0
System init for write_data ...
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.25237451
grid = 18 18 60
stencil order = 5
estimated absolute RMS force accuracy = 0.0034985124
estimated relative force accuracy = 1.0535666e-05
using double precision KISS FFT
3d grid and FFT values/proc = 39375 19440
Generated 9 of 10 mixed pair_coeff terms from geometric mixing rule
Last active /omp style is kspace_style pppm/tip4p/omp