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lammps/examples/USER/atc/molecule/polarize.screen
rjones 5302074b3f ATC version 2.0, date: Sep1 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10709 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2013-09-01 08:07:54 +00:00

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LAMMPS (30 Aug 2013)
log log.polarize
variable nstepsequil equal 1000000
variable nsteps equal 100
variable temp equal 300.0
variable tdamp equal 0.100
variable x_dim equal 50
variable y_dim equal 50
variable z_fluid equal 37.7919
variable efieldz equal -0.0723725329978652551934
variable x_max equal ${x_dim}/2
variable x_max equal 50/2
variable y_max equal ${y_dim}/2
variable y_max equal 50/2
variable fluid_half_thickness equal ${z_fluid}/2
variable fluid_half_thickness equal 37.791899999999998272/2
variable buffer equal 2.45
variable zhiwall equal ${fluid_half_thickness}+${buffer}
variable zhiwall equal 18.895949999999999136+${buffer}
variable zhiwall equal 18.895949999999999136+2.4500000000000001776
variable zlowall equal -${fluid_half_thickness}-${buffer}
variable zlowall equal -18.895949999999999136-${buffer}
variable zlowall equal -18.895949999999999136-2.4500000000000001776
variable zmaxatc equal ${fluid_half_thickness}+10
variable zmaxatc equal 18.895949999999999136+10
variable zmaxsub equal ${zmaxatc}-0.1
variable zmaxsub equal 28.895949999999999136-0.1
variable zmaxsup equal ${zmaxatc}+0.1
variable zmaxsup equal 28.895949999999999136+0.1
variable cellatc equal 5
units metal
atom_style full
dimension 3
newton off
neighbor 2 bin
neigh_modify every 1 delay 1 check no
boundary p p f
kspace_style pppm 1e-5
kspace_modify slab 3.0
pair_style lj/cut/coul/long 13.0 13.0
bond_style harmonic
angle_style harmonic
read_data waterequil.init
Scanning data file ...
2 = max bonds/atom
1 = max angles/atom
Reading data file ...
orthogonal box = (-25 -25 -21.8959) to (25 25 21.8959)
2 by 2 by 1 MPI processor grid
9474 atoms
9474 velocities
6316 bonds
3158 angles
Finding 1-2 1-3 1-4 neighbors ...
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
#velocity all create 0.0 482748 dist uniform
lattice sc 0.05
Lattice spacing in x,y,z = 0.05 0.05 0.05
#region ATC block EDGE EDGE EDGE EDGE -${zmaxatc} ${zmaxatc} units box
#variable nelemelec equal round(2*${zmaxatc}/0.05)
region ATC block EDGE EDGE EDGE EDGE EDGE EDGE units box
# region ATC block EDGE EDGE EDGE EDGE 0.0 0.05 units box
#region ATC block -${fem_atc} ${fem_atc} -${fem_atc} ${fem_atc} -${fem_atc} ${fem_atc} units box
variable nelem equal 2
# variable nelem equal 1
group water type 1 2
9474 atoms in group water
group hyd type 1
6316 atoms in group hyd
group oxy type 2
3158 atoms in group oxy
timestep 0.0005
dielectric 1.0
pair_coeff 1 * 0.0 0.0
pair_coeff 2 2 0.006596 3.1507
bond_coeff 1 19.513855 0.957200
angle_coeff 1 2.385027 104.519997
special_bonds amber
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
#fix 2 all nvt temp ${temp} ${temp} ${tdamp}
fix lowall oxy wall/lj1043 zlo ${zlowall} 0.1351 3.1507 11.0275 units box
fix lowall oxy wall/lj1043 zlo -21.345949999999998425 0.1351 3.1507 11.0275 units box
fix hiwall oxy wall/lj1043 zhi ${zhiwall} 0.1351 3.1507 11.0275 units box
fix hiwall oxy wall/lj1043 zhi 21.345949999999998425 0.1351 3.1507 11.0275 units box
fix efield all efield 0. 0. v_efieldz
# assign SHAKE fixes
fix 1 all shake 0.00001 500 5000 b 1 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
3158 = # of frozen angles
thermo 100
thermo_style custom step temp ke pe etotal f_efield f_lowall f_hiwall
variable dumpfreq equal 1
#dump 1 all atom 500 waterequil.dump
#dump_modify 1 image yes scale no flush yes
#run ${nstepsequil}
#write_restart waterequil.restart
#unfix 2
fix 3 all nve
fix AtC all atc hardy
ATC: constructing kernel field estimate
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
fix_modify AtC mesh create 1 1 ${nelem} ATC p p f
fix_modify AtC mesh create 1 1 2 ATC p p f
ATC: created uniform mesh with 12 nodes, 3 unique nodes, and 2 elements
#fix_modify AtC_half mesh create 1 1 ${nelem} ATC p p f
fix_modify AtC kernel cell 25 25 ${cellatc}
fix_modify AtC kernel cell 25 25 5
fix_modify AtC atom_element_map eulerian ${dumpfreq}
fix_modify AtC atom_element_map eulerian 1
fix_modify AtC fields none
fix_modify AtC fields add dipole_moment mass_density
fix_modify AtC add_molecule small Water water
fix_modify AtC output polarizeFE ${dumpfreq} text vector_components
fix_modify AtC output polarizeFE 1 text vector_components
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
run ${nsteps}
run 100
PPPM initialization ...
G vector (1/distance) = 0.229056
grid = 30 30 64
stencil order = 5
estimated absolute RMS force accuracy = 0.000159261
estimated relative force accuracy = 1.10601e-05
using double precision FFTs
3d grid and FFT values/proc = 31944 14400
Setting up run ...
SHAKE stats (type/ave/delta) on step 0
1 0.9572 3.63187e-08
1 104.52 3.67915e-06
ATC: computing kernel matrix molecule ...done
Memory usage per processor = 50.0731 Mbytes
Step Temp KinEng PotEng TotEng efield lowall hiwall
0 295.19689 240.96267 -1265.6426 -1024.6799 0 -25.236036 -26.079483
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
ATC: computing kernel matrix molecule ...done
100 296.18885 241.77239 -1266.3101 -1024.5377 0 -25.105524 -26.164269
Loop time of 39.4264 on 4 procs for 100 steps with 9474 atoms
Pair time (%) = 15.485 (39.2757)
Bond time (%) = 0.00152647 (0.00387171)
Kspce time (%) = 2.45746 (6.23305)
Neigh time (%) = 19.0463 (48.3087)
Comm time (%) = 0.193679 (0.491242)
Outpt time (%) = 0.000291049 (0.00073821)
Other time (%) = 2.24208 (5.68676)
FFT time (% of Kspce) = 0.656798 (26.7267)
FFT Gflps 3d (1d only) = 1.92257 5.45241
Nlocal: 2368.5 ave 2387 max 2357 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Nghost: 9049.75 ave 9086 max 9029 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Neighs: 1.94028e+06 ave 1.95668e+06 max 1.92845e+06 min
Histogram: 1 0 1 1 0 0 0 0 0 1
FullNghs: 2.74796e+06 ave 2.77359e+06 max 2.72966e+06 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 10991852
Ave neighs/atom = 1160.21
Ave special neighs/atom = 2
Neighbor list builds = 100
Dangerous builds = 0
#fix AtCH hyd atc field
#fix_modify AtCH mesh create 1 1 ${nelemelec} ATC p p f
#fix_modify AtCH atom_element_map eulerian ${dumpfreq}
#fix_modify AtCH fields add number_density
#fix_modify AtCH output FEH ${dumpfreq} text binary
#fix AtCO oxy atc field
#fix_modify AtCO mesh create 1 1 ${nelemelec} ATC p p f
#fix_modify AtCO atom_element_map eulerian ${dumpfreq}
#fix_modify AtCO fields add number_density
#fix_modify AtCO output FEO ${dumpfreq} text binary
#run ${nsteps}
#write_restart waterendpolarize.restart
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