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lammps/examples/USER/atc/molecule/water.screen
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LAMMPS (30 Aug 2013)
Scanning data file ...
2 = max bonds/atom
1 = max angles/atom
Reading data file ...
orthogonal box = (-15 -15 -15) to (15 15 15)
1 by 2 by 2 MPI processor grid
2709 atoms
2709 velocities
1806 bonds
903 angles
Finding 1-2 1-3 1-4 neighbors ...
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
Lattice spacing in x,y,z = 0.05 0.05 0.05
2709 atoms in group water
1806 atoms in group hyd
903 atoms in group oxy
Finding 1-2 1-3 1-4 neighbors ...
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
ATC: constructing electrostatic species coupling with parameter file water.mat
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
ATC: 1 materials defined from water.mat
ATC: creating fem_efield extrinsic model
ATC: 1 materials defined from water.mat
ATC: created uniform mesh with 8 nodes, 1 unique nodes, and 1 elements
Finding SHAKE clusters ...
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
903 = # of frozen angles
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationHyd
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationOxy
species_concentration : species_concentrationHyd
species_concentration : species_concentrationOxy
PPPM initialization ...
G vector (1/distance) = 0.297171
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.00115732
estimated relative force accuracy = 8.03715e-05
using double precision FFTs
3d grid and FFT values/proc = 6400 1620
Setting up run ...
ATC: WARNING: material: [water] cannot find mass_density
ATC: WARNING: physics model: [species], material: [water] does not provide all interfaces for <mass_density> physics and will be treated as null
ATC: WARNING: all initial conditions for mass_density have not been defined and the undefined are assumed zero
ATC: WARNING: all initial conditions for charge_density have not been defined and the undefined are assumed zero
ATC: WARNING: all initial conditions for species_concentration have not been defined and the undefined are assumed zero
ATC: WARNING: material: [water] cannot find mass_density
ATC: WARNING: physics model: [species electrostatic], material: [water] does not provide all interfaces for <mass_density> physics and will be treated as null
Memory usage per processor = 110.158 Mbytes
Step Temp E_pair E_mol TotEng Press
0 295.5587 -442.89515 0 -373.937 -131998.23
100 290.87863 -434.43358 0 -366.56736 -44230.026
200 291.92834 -434.76926 0 -366.65812 -44008.69
300 300.25145 -435.04826 0 -364.99523 -44050.489
400 295.94333 -436.37626 0 -367.32837 -44134.004
500 291.82014 -433.60004 0 -365.51415 -43960.556
600 297.07921 -434.96259 0 -365.64968 -44403.145
700 290.21983 -434.02012 0 -366.30761 -44175.149
800 291.85669 -434.29732 0 -366.2029 -44436.275
900 301.54816 -436.20597 0 -365.85039 -44253.686
1000 295.98791 -434.24829 0 -365.19 -43743.988
Loop time of 59.4778 on 4 procs for 1000 steps with 2709 atoms
Pair time (%) = 50.9628 (85.6837)
Bond time (%) = 0.00689393 (0.0115908)
Kspce time (%) = 4.90648 (8.24926)
Neigh time (%) = 1.00524 (1.69011)
Comm time (%) = 0.578538 (0.972696)
Outpt time (%) = 0.019442 (0.0326879)
Other time (%) = 1.99843 (3.35996)
FFT time (% of Kspce) = 0.683713 (13.9349)
FFT Gflps 3d (1d only) = 1.47928 3.47903
Nlocal: 677.25 ave 699 max 659 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 11513.2 ave 11625 max 11415 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 820083 ave 844320 max 799220 min
Histogram: 1 0 1 0 0 1 0 0 0 1
FullNghs: 963001 ave 994085 max 936561 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 3852004
Ave neighs/atom = 1421.93
Ave special neighs/atom = 2
Neighbor list builds = 15
Dangerous builds = 0
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