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