294 lines
14 KiB
Groff
294 lines
14 KiB
Groff
LAMMPS (23 Oct 2017)
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using 1 OpenMP thread(s) per MPI task
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# fix gcmc example with fix shake
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# variables available on command line
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variable mu index -8.1
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variable disp index 0.5
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variable temp index 338.0
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variable lbox index 10.0
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variable spacing index 5.0
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# global model settings
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units real
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atom_style full
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boundary p p p
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pair_style lj/cut/coul/long 14
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pair_modify mix arithmetic tail yes
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kspace_style ewald 0.0001
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bond_style harmonic
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angle_style harmonic
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# box, start molecules on simple cubic lattice
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lattice sc ${spacing}
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lattice sc 5.0
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Lattice spacing in x,y,z = 5 5 5
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region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
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region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
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region box block 0 10.0 0 10.0 0 ${lbox} units box
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region box block 0 10.0 0 10.0 0 10.0 units box
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create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
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Created orthogonal box = (0 0 0) to (10 10 10)
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1 by 1 by 1 MPI processor grid
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# we can load multiple molecule templates, but don't have to use them all
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molecule co2mol CO2.txt
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Read molecule co2mol:
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3 atoms with 2 types
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2 bonds with 1 types
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1 angles with 1 types
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0 dihedrals with 0 types
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0 impropers with 0 types
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molecule h2omol H2O.txt
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Read molecule h2omol:
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3 atoms with 2 types
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2 bonds with 1 types
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1 angles with 1 types
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0 dihedrals with 0 types
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0 impropers with 0 types
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create_atoms 0 box mol h2omol 464563 units box
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Created 24 atoms
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Time spent = 0.00201297 secs
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# rigid SPC/E water model
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pair_coeff 1 1 0.15535 3.166
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pair_coeff * 2 0.0000 0.0000
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bond_coeff 1 1000 1.0
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angle_coeff 1 100 109.47
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# masses
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mass 1 15.9994
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mass 2 1.0
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# MD settings
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group h2o type 1 2
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24 atoms in group h2o
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neighbor 2.0 bin
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neigh_modify every 1 delay 1 check yes
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velocity all create ${temp} 54654
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velocity all create 338.0 54654
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timestep 1.0
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minimize 0.0 0.0 100 1000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
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Ewald initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.170448
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estimated absolute RMS force accuracy = 0.0332064
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estimated relative force accuracy = 0.0001
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KSpace vectors: actual max1d max3d = 16 2 62
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kxmax kymax kzmax = 2 2 2
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 16
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ghost atom cutoff = 16
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binsize = 8, bins = 2 2 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long, perpetual
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attributes: half, newton on
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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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Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 338 -4.1890564 9.2628112e-06 18.98377 739.06991
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100 338 -30.182886 0.85607237 -6.1539961 -2535.3207
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Loop time of 0.0507543 on 1 procs for 100 steps with 24 atoms
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99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = max iterations
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Energy initial, next-to-last, final =
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-4.18904713252 -28.9258064504 -29.3268133965
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Force two-norm initial, final = 18.0027 42.4511
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Force max component initial, final = 5.8993 16.0523
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Final line search alpha, max atom move = 0.00353207 0.056698
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Iterations, force evaluations = 100 238
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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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Pair | 0.042597 | 0.042597 | 0.042597 | 0.0 | 83.93
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Bond | 0.00047708 | 0.00047708 | 0.00047708 | 0.0 | 0.94
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Kspace | 0.0031135 | 0.0031135 | 0.0031135 | 0.0 | 6.13
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Neigh | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.90
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Comm | 0.0032997 | 0.0032997 | 0.0032997 | 0.0 | 6.50
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Output | 1.359e-05 | 1.359e-05 | 1.359e-05 | 0.0 | 0.03
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.0007946 | | | 1.57
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Nlocal: 24 ave 24 max 24 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2047 ave 2047 max 2047 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 4936 ave 4936 max 4936 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 4936
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Ave neighs/atom = 205.667
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Ave special neighs/atom = 2
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Neighbor list builds = 2
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Dangerous builds = 0
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reset_timestep 0
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# rigid constraints with thermostat
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fix mynvt all nvt temp ${temp} ${temp} 100
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fix mynvt all nvt temp 338.0 ${temp} 100
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fix mynvt all nvt temp 338.0 338.0 100
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fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
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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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8 = # of frozen angles
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# gcmc
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run 1000
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Ewald initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.170448
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estimated absolute RMS force accuracy = 0.0332064
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estimated relative force accuracy = 0.0001
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KSpace vectors: actual max1d max3d = 16 2 62
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kxmax kymax kzmax = 2 2 2
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Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 518.26667 -30.182886 0 -7.0100684 993.1985
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1000 326.9865 -62.258445 0 -47.638175 -5.3440813
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Loop time of 0.141449 on 1 procs for 1000 steps with 24 atoms
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Performance: 610.819 ns/day, 0.039 hours/ns, 7069.663 timesteps/s
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99.7% CPU use with 1 MPI tasks x 1 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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Pair | 0.10788 | 0.10788 | 0.10788 | 0.0 | 76.27
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Bond | 0.00018954 | 0.00018954 | 0.00018954 | 0.0 | 0.13
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Kspace | 0.011867 | 0.011867 | 0.011867 | 0.0 | 8.39
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Neigh | 0.0045254 | 0.0045254 | 0.0045254 | 0.0 | 3.20
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Comm | 0.011277 | 0.011277 | 0.011277 | 0.0 | 7.97
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Output | 1.5497e-05 | 1.5497e-05 | 1.5497e-05 | 0.0 | 0.01
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Modify | 0.00383 | 0.00383 | 0.00383 | 0.0 | 2.71
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Other | | 0.001868 | | | 1.32
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Nlocal: 24 ave 24 max 24 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1660 ave 1660 max 1660 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5112 ave 5112 max 5112 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5112
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Ave neighs/atom = 213
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Ave special neighs/atom = 2
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Neighbor list builds = 25
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Dangerous builds = 0
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variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
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fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
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# atom counts
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variable oxygen atom "type==1"
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variable hydrogen atom "type==2"
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group oxygen dynamic all var oxygen
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dynamic group oxygen defined
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group hydrogen dynamic all var hydrogen
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dynamic group hydrogen defined
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variable nO equal count(oxygen)
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variable nH equal count(hydrogen)
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# output
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variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
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variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
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variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
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variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
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compute_modify thermo_temp dynamic/dof yes
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thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
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thermo 1000
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# run
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run 20000
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Ewald initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.170448
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estimated absolute RMS force accuracy = 0.0332064
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estimated relative force accuracy = 0.0001
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KSpace vectors: actual max1d max3d = 16 2 62
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kxmax kymax kzmax = 2 2 2
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WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
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0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
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0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
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WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
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Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
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Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
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1000 326.9865 -4.3509713 -62.258445 14.62027 0.23910963 24 0 0 0 0 8 16
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2000 116.99793 -5344.1527 -286.61595 17.088682 0.74721761 75 0.048183096 0.013941446 0 0 25 50
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3000 106.86746 -3920.4926 -361.60598 18.794545 0.89666113 90 0.035637919 0.012768883 0 0 30 60
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4000 75.002668 540.46846 -414.8511 14.531966 0.98632724 99 0.025963651 0.0093451705 0 0 33 66
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5000 79.924788 -2131.1173 -437.21216 15.962121 1.0162159 102 0.019879728 0.0070418993 0 0 34 68
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6000 95.552773 -3647.0233 -438.24276 19.083253 1.0162159 102 0.015753613 0.0056885133 0 0 34 68
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7000 79.501736 -2071.5369 -440.77351 15.877631 1.0162159 102 0.01326216 0.0046915318 0 0 34 68
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8000 62.567091 -3102.9616 -442.21884 12.495541 1.0162159 102 0.011305503 0.0040437885 0 0 34 68
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9000 68.324047 -3812.7866 -440.46835 13.645287 1.0162159 102 0.0099549538 0.0035157329 0 0 34 68
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10000 83.857631 -2158.2659 -444.8183 16.747566 1.0162159 102 0.0088200922 0.0031354281 0 0 34 68
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11000 68.350984 -2084.0789 -440.14081 13.650667 1.0162159 102 0.0081331455 0.0030247424 0 0 34 68
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12000 76.867315 -1585.6723 -443.36199 15.3515 1.0162159 102 0.0073845932 0.0027532534 0 0 34 68
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13000 59.74266 -2211.0211 -446.07791 11.931462 1.0162159 102 0.0067756276 0.0025213898 0 0 34 68
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14000 81.154979 -907.0176 -441.53368 16.207808 1.0162159 102 0.0062527642 0.0023280719 0 0 34 68
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15000 66.814346 -2804.5134 -455.80704 13.7421 1.0461046 105 0.0059590528 0.0021576214 0 0 35 70
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16000 71.42983 -3930.4004 -458.43218 14.691394 1.0461046 105 0.0055547473 0.0020163729 0 0 35 70
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17000 89.624855 -3569.8136 -455.18164 18.433672 1.0461046 105 0.0052173265 0.0018867687 0 0 35 70
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18000 63.519962 -1882.8157 -456.58939 13.064525 1.0461046 105 0.0049082049 0.0017765986 0 0 35 70
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19000 71.872698 -2243.5046 -454.93359 14.782481 1.0461046 105 0.0046439115 0.0016748361 0 0 35 70
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20000 73.660765 -2285.3173 -476.35473 15.589381 1.0759934 108 0.0045124933 0.0015837653 0 0 36 72
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21000 95.675868 987.92089 -475.46736 20.248603 1.0759934 108 0.004285814 0.0015049513 0 0 36 72
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Loop time of 220.662 on 1 procs for 20000 steps with 108 atoms
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Performance: 7.831 ns/day, 3.065 hours/ns, 90.637 timesteps/s
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99.6% CPU use with 1 MPI tasks x 1 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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Pair | 37.459 | 37.459 | 37.459 | 0.0 | 16.98
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Bond | 0.087067 | 0.087067 | 0.087067 | 0.0 | 0.04
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Kspace | 0.90234 | 0.90234 | 0.90234 | 0.0 | 0.41
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Neigh | 1.2299 | 1.2299 | 1.2299 | 0.0 | 0.56
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Comm | 0.95437 | 0.95437 | 0.95437 | 0.0 | 0.43
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Output | 0.0010636 | 0.0010636 | 0.0010636 | 0.0 | 0.00
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Modify | 179.85 | 179.85 | 179.85 | 0.0 | 81.51
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Other | | 0.1754 | | | 0.08
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Nlocal: 108 ave 108 max 108 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 7850 ave 7850 max 7850 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 99828 ave 99828 max 99828 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 99828
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Ave neighs/atom = 924.333
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Ave special neighs/atom = 2
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Neighbor list builds = 20439
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Dangerous builds = 0
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Total wall time: 0:03:40
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