forked from lijiext/lammps
133 lines
5.9 KiB
Plaintext
133 lines
5.9 KiB
Plaintext
boundary p p p
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units metal # ev, ps
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atom_style dpd
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atom_modify map array
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fix 4 all rx kinetics.dpdrx none dense lammps_rk4 1
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lattice hcp 6.6520898 origin 0.0833333333333 0.25 0.25 orient z 1 0 0 orient x 0 1 0 orient y 0 0 1
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Lattice spacing in x,y,z = 11.5218 10.8628 6.65209
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region box block 0 6.0 0 6.0 0.0 6.0 units lattice
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create_box 2 box
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Created orthogonal box = (0 0 0) to (69.1305 65.1769 39.9125)
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1 by 1 by 1 MPI processor grid
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region atoms block 0 6.0 0 6.0 0.0 6.0 units lattice
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create_atoms 1 region atoms
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Created 864 atoms
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comm_modify mode single vel yes
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mass * 222.12
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#Set concentrations
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set atom * d_rdx 1.00
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864 settings made for d_rdx
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set atom * d_h2 0.0
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864 settings made for d_h2
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set atom * d_no2 0.0
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864 settings made for d_no2
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set atom * d_n2 0.0
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864 settings made for d_n2
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set atom * d_hcn 0.0
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864 settings made for d_hcn
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set atom * d_no 0.0
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864 settings made for d_no
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set atom * d_h2o 0.0
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864 settings made for d_h2o
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set atom * d_co 0.0
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864 settings made for d_co
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set atom * d_co2 0.0
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864 settings made for d_co2
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#Set the kinetic temperature of the particles
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velocity all create 2065.0 875661 dist gaussian
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#Set the internal temperature of the particles
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set atom * dpd/theta 2065.00
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864 settings made for dpd/theta
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timestep 0.001
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pair_style hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
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pair_coeff * * dpd/fdt/energy 0.0 0.05 10.0 16.00
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pair_coeff * * exp6/rx params.exp6 1fluid 1fluid exponent 1.0 1.0 16.00
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fix 1 all shardlow
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fix 2 all nve
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fix 3 all eos/table/rx linear table.eos 4001 KEYWORD thermo.dpdrx
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compute dpdU all dpd
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compute dpdUatom all dpd/atom
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compute crdx all property/atom d_rdx
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variable totEnergy equal pe+c_dpdU[1]+c_dpdU[2]+c_dpdU[3]
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thermo 1
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thermo_style custom step temp press vol pe ke c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4]
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thermo_modify format float %15.8f flush yes
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dump 2 all custom 1 dump.dpdrx id x y z vx vy vz c_dpdUatom[1] c_dpdUatom[2] c_dpdUatom[3] c_dpdUatom[4] c_crdx
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dump_modify 2 sort id
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run 10
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 18
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ghost atom cutoff = 18
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binsize = 9, bins = 8 8 5
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3 neighbor lists, perpetual/occasional/extra = 3 0 0
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(1) pair dpd/fdt/energy, perpetual
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) pair exp6/rx, perpetual, copy from (1)
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pair build: copy
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stencil: none
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bin: none
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(3) fix shardlow, perpetual, ssa
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pair build: half/bin/newton/ssa
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stencil: half/bin/3d/newton/ssa
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bin: ssa
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Memory usage per processor = 8.39564 Mbytes
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Step Temp Press Volume PotEng KinEng c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4]
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0 2065.00000000 1368.17463335 179834.51777865 0.00000000 230.35385810 0.00000000 7682.84786557 0.00000000 7682.84786557 2065.00000000
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1 2064.93210437 1368.12964881 179834.51777865 0.00000000 230.34628424 0.00000000 7682.85543943 0.00000000 7682.85543943 2065.20275230
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2 2067.82089565 1370.04362990 179834.51777865 -0.00000000 230.66853326 0.00000000 7682.53319042 0.00000000 7682.53319042 2065.32453473
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3 2070.45225169 1371.78704616 179834.51777865 -0.00000000 230.96206499 0.00000000 7682.23965869 0.00000000 7682.23965869 2065.45336917
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4 2075.00241157 1374.80177416 179834.51777865 -0.00000000 231.46964217 0.00000000 7681.73208151 0.00000000 7681.73208151 2065.52973333
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5 2073.96509212 1374.11449370 179834.51777865 -0.00000000 231.35392762 -0.00000000 7681.84779605 0.00000000 7681.84779605 2065.76011517
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6 2074.26516936 1374.31331117 179834.51777865 -0.00000000 231.38740169 -0.00000000 7681.81432198 0.00000000 7681.81432198 2065.95399323
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7 2071.41069700 1372.42206822 179834.51777865 -0.00000000 231.06898100 -0.00000000 7682.13274267 0.00000000 7682.13274267 2066.23407076
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8 2071.35844957 1372.38745146 179834.51777865 -0.00000000 231.06315272 0.00000000 7682.13857095 0.00000000 7682.13857095 2066.43766287
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9 2071.35676496 1372.38633532 179834.51777865 -0.00000000 231.06296480 0.00000000 7682.13875887 0.00000000 7682.13875887 2066.64001166
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10 2066.53172340 1369.18948328 179834.51777865 -0.00000000 230.52472415 0.00000000 7682.67699952 0.00000000 7682.67699952 2066.97516855
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Loop time of 0.611304 on 1 procs for 10 steps with 864 atoms
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Performance: 1.413 ns/day, 16.981 hours/ns, 16.358 timesteps/s
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98.2% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.34177 | 0.34177 | 0.34177 | 0.0 | 55.91
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0013342 | 0.0013342 | 0.0013342 | 0.0 | 0.22
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Output | 0.083583 | 0.083583 | 0.083583 | 0.0 | 13.67
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Modify | 0.18451 | 0.18451 | 0.18451 | 0.0 | 30.18
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Other | | 0.0001087 | | | 0.02
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Nlocal: 864 ave 864 max 864 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2700 ave 2700 max 2700 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 55296 ave 55296 max 55296 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 55296
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Ave neighs/atom = 64
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Neighbor list builds = 0
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:00
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