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 2 by 2 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 = 0.00174451 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) = 11.85 | 11.85 | 11.85 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 338 -4.9610706 9.2628112e-06 18.211756 730.90791
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100 338 -15.742442 0.14954269 7.579918 -637.49568
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Loop time of 0.0566185 on 4 procs for 100 steps with 24 atoms
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98.8% CPU use with 4 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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-4.96106135393 -15.5388622715 -15.592899346
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Force two-norm initial, final = 15.474 18.1478
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Force max component initial, final = 5.80042 7.56514
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Final line search alpha, max atom move = 0.00151131 0.0114333
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Iterations, force evaluations = 100 328
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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 | 0.0085177 | 0.016083 | 0.026787 | 5.3 | 28.41
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Bond | 0.00022459 | 0.00031394 | 0.00037575 | 0.0 | 0.55
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Kspace | 0.0049062 | 0.014122 | 0.02044 | 5.0 | 24.94
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.018515 | 0.02086 | 0.023246 | 1.2 | 36.84
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Output | 2.4796e-05 | 2.6047e-05 | 2.9802e-05 | 0.0 | 0.05
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.005213 | | | 9.21
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Nlocal: 6 ave 8 max 3 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Nghost: 1722 ave 1725 max 1720 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Neighs: 1256.75 ave 2101 max 667 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Total # of neighbors = 5027
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Ave neighs/atom = 209.458
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Ave special neighs/atom = 2
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Neighbor list builds = 0
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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) = 11.6 | 11.6 | 11.6 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 518.26667 -15.742442 0 7.4303753 -613.0781
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1000 369.81793 -54.202686 0 -37.667331 294.98823
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Loop time of 0.154891 on 4 procs for 1000 steps with 24 atoms
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Performance: 557.810 ns/day, 0.043 hours/ns, 6456.135 timesteps/s
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98.3% CPU use with 4 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 | 0.0154 | 0.028993 | 0.040525 | 5.5 | 18.72
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Bond | 0.00016999 | 0.0001902 | 0.00023293 | 0.0 | 0.12
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Kspace | 0.019093 | 0.028112 | 0.038976 | 4.3 | 18.15
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Neigh | 0.0020263 | 0.0022184 | 0.002408 | 0.4 | 1.43
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Comm | 0.04947 | 0.053627 | 0.058009 | 1.4 | 34.62
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Output | 2.5749e-05 | 2.7537e-05 | 3.2187e-05 | 0.0 | 0.02
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Modify | 0.035275 | 0.036815 | 0.038425 | 0.7 | 23.77
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Other | | 0.004909 | | | 3.17
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Nlocal: 6 ave 8 max 3 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 1331.5 ave 1369 max 1290 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Neighs: 1259.75 ave 1642 max 428 min
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Histogram: 1 0 0 0 0 0 0 1 0 2
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Total # of neighbors = 5039
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Ave neighs/atom = 209.958
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Ave special neighs/atom = 2
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Neighbor list builds = 27
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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) = 11.6 | 11.6 | 11.6 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 369.81793 295.32434 -54.202686 16.535355 0.23910963 24 0 0 0 0 8 16
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2000 84.544466 -2810.9047 -344.81664 14.364627 0.86677242 87 0.052198354 0.0099581757 0 0 29 58
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3000 75.188527 -3688.256 -425.02228 14.567977 0.98632724 99 0.030546787 0.0049111089 0 0 33 66
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4000 75.019396 -5669.3063 -427.69454 14.535207 0.98632724 99 0.019972039 0.0033375609 0 0 33 66
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5000 90.415371 -2141.7596 -434.65925 17.518218 0.98632724 99 0.014909796 0.002514964 0 0 33 66
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6000 78.212628 -943.75125 -428.80584 15.153904 0.98632724 99 0.01181521 0.0020316119 0 0 33 66
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7000 71.754139 -2028.5122 -435.2139 13.902555 0.98632724 99 0.0099466198 0.0016755471 0 0 33 66
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8000 84.446231 -1969.1657 -428.27313 16.361681 0.98632724 99 0.0084791272 0.0014442102 0 0 33 66
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9000 70.952348 -2476.9812 -446.33824 14.170197 1.0162159 102 0.0077150892 0.0012556189 0 0 34 68
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10000 71.418543 -1875.7083 -443.7214 14.263302 1.0162159 102 0.0068355714 0.0011197957 0 0 34 68
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11000 86.094994 -4508.7581 -444.82687 17.194399 1.0162159 102 0.0061494515 0.0010082475 0 0 34 68
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12000 81.906091 -1547.8105 -442.36719 16.357815 1.0162159 102 0.0055834729 0.00091775114 0 0 34 68
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13000 57.221548 -4607.6222 -448.30939 11.42796 1.0162159 102 0.0051230355 0.00084046326 0 0 34 68
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14000 61.288344 -2518.1779 -445.70636 12.240157 1.0162159 102 0.0047276997 0.00077602396 0 0 34 68
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15000 85.787669 -2407.7111 -443.3834 17.133022 1.0162159 102 0.0043983485 0.00071920715 0 0 34 68
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16000 74.845939 -3288.3403 -445.8247 14.947802 1.0162159 102 0.0042321884 0.00080654918 0 0 34 68
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17000 73.835431 -1926.9566 -445.67476 14.745989 1.0162159 102 0.0039751059 0.00075470749 0 0 34 68
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18000 72.634985 -3997.552 -447.2351 14.506243 1.0162159 102 0.0037395847 0.00071063946 0 0 34 68
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19000 96.776472 -714.44132 -453.65552 19.904587 1.0461046 105 0.0036487876 0.00066993446 0 0 35 70
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20000 75.470786 183.16972 -464.04688 15.522521 1.0461046 105 0.0034630763 0.00063350614 0 0 35 70
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21000 65.658309 -773.41266 -466.27068 13.504331 1.0461046 105 0.003289113 0.00060198052 0 0 35 70
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Loop time of 84.4085 on 4 procs for 20000 steps with 105 atoms
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Performance: 20.472 ns/day, 1.172 hours/ns, 236.943 timesteps/s
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98.8% CPU use with 4 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 | 6.3571 | 9.7574 | 13.984 | 90.7 | 11.56
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Bond | 0.026374 | 0.031321 | 0.035482 | 2.1 | 0.04
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Kspace | 0.57402 | 4.7894 | 8.1754 | 129.0 | 5.67
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Neigh | 0.34952 | 0.34987 | 0.35021 | 0.1 | 0.41
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Comm | 2.4028 | 2.4228 | 2.4372 | 0.9 | 2.87
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Output | 0.0012269 | 0.0012826 | 0.0014355 | 0.2 | 0.00
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Modify | 66.819 | 66.828 | 66.837 | 0.1 | 79.17
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Other | | 0.2281 | | | 0.27
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Nlocal: 26.25 ave 31 max 22 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Nghost: 6049.25 ave 6133 max 5962 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Neighs: 23613 ave 35083 max 14025 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Total # of neighbors = 94452
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Ave neighs/atom = 899.543
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Ave special neighs/atom = 2
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Neighbor list builds = 20428
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Dangerous builds = 0
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Total wall time: 0:01:24
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