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