forked from lijiext/lammps
291 lines
13 KiB
Groff
291 lines
13 KiB
Groff
LAMMPS (30 Mar 2018)
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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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molecule h2omol H2O.txt
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Read molecule h2omol:
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3 atoms with max type 2
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2 bonds with max type 1
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1 angles with max type 1
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0 dihedrals with max type 0
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0 impropers with max type 0
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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 = 0.00204968 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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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 0.0512006 on 1 procs for 100 steps with 24 atoms
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99.5% 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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---------------------------------------------------------------
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Pair | 0.04303 | 0.04303 | 0.04303 | 0.0 | 84.04
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Bond | 0.00047088 | 0.00047088 | 0.00047088 | 0.0 | 0.92
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Kspace | 0.0029728 | 0.0029728 | 0.0029728 | 0.0 | 5.81
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Neigh | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.90
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Comm | 0.003406 | 0.003406 | 0.003406 | 0.0 | 6.65
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Output | 2.265e-05 | 2.265e-05 | 2.265e-05 | 0.0 | 0.04
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.0008392 | | | 1.64
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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 h2o nvt temp ${temp} ${temp} 100
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fix mynvt h2o nvt temp 338.0 ${temp} 100
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fix mynvt h2o nvt temp 338.0 338.0 100
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fix wshake h2o 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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# important to make temperature dofs dynamic
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compute_modify thermo_temp dynamic/dof yes
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compute_modify mynvt_temp dynamic/dof yes
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run 1000
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Ewald initialization ...
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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 -62.258443 0 -47.638173 -5.3439918
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Loop time of 0.139436 on 1 procs for 1000 steps with 24 atoms
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Performance: 619.641 ns/day, 0.039 hours/ns, 7171.773 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 | 0.10588 | 0.10588 | 0.10588 | 0.0 | 75.94
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Bond | 0.00015759 | 0.00015759 | 0.00015759 | 0.0 | 0.11
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Kspace | 0.011144 | 0.011144 | 0.011144 | 0.0 | 7.99
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Neigh | 0.00459 | 0.00459 | 0.00459 | 0.0 | 3.29
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Comm | 0.011396 | 0.011396 | 0.011396 | 0.0 | 8.17
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Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.01
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Modify | 0.0043328 | 0.0043328 | 0.0043328 | 0.0 | 3.11
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Other | | 0.001914 | | | 1.37
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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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reset_timestep 0
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# gcmc
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variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
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fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
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fix mygcmc h2o 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 h2o 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 h2o 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 h2o 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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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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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:485)
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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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0 326.9865 -4.3508819 -62.258443 14.62027 0.23910963 24 0 0 0 0 8 16
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1000 354.423 -3760.1354 -235.34169 51.766914 0.74721761 75 0.046175467 0.011949811 0 0 25 50
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2000 335.19661 -3018.659 -270.44089 52.955344 0.80699501 81 0.026473882 0.0068755525 0 0 27 54
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3000 333.47175 2657.2052 -336.48359 64.611037 0.98632724 99 0.022634978 0.0060076096 0 0 33 66
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4000 321.48504 2055.4786 -345.06113 62.288579 0.98632724 99 0.016897769 0.0045269353 0 0 33 66
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5000 333.45735 1918.5375 -368.5463 66.596193 1.0162159 102 0.013784412 0.0036569014 0 0 34 68
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6000 301.90666 -698.74074 -371.32122 60.295069 1.0162159 102 0.01160439 0.0030159847 0 0 34 68
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7000 336.42505 1537.9483 -378.51731 69.194524 1.0461046 105 0.010174953 0.0025995783 0 0 35 70
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8000 338.95331 -1032.1084 -390.7067 69.714524 1.0461046 105 0.0089594585 0.002260114 0 0 35 70
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9000 311.44605 -1494.7788 -383.9272 64.056945 1.0461046 105 0.007938083 0.0020156323 0 0 35 70
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10000 330.70877 2082.4597 -366.57249 68.018822 1.0461046 105 0.0071412985 0.0018148454 0 0 35 70
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11000 286.34718 2238.3752 -370.91119 60.601806 1.0759934 108 0.0066641451 0.0016519521 0 0 36 72
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12000 371.02522 3048.7157 -398.51333 78.522854 1.0759934 108 0.0061145907 0.0015128339 0 0 36 72
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13000 392.87611 4486.1134 -387.07077 83.147323 1.0759934 108 0.0056427384 0.0013968431 0 0 36 72
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14000 332.80747 3586.2698 -406.12151 70.434545 1.0759934 108 0.0052496417 0.0012945729 0 0 36 72
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15000 325.61844 4198.3864 -387.5733 68.913077 1.0759934 108 0.0048934679 0.0012098238 0 0 36 72
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16000 254.10285 1560.976 -409.98615 55.292559 1.1058821 111 0.0047204383 0.0011320612 0 0 37 74
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17000 367.46414 2750.8283 -412.22037 79.959878 1.1058821 111 0.0044407568 0.0010659592 0 0 37 74
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18000 407.74215 2308.5027 -408.73046 88.724338 1.1058821 111 0.0042016342 0.0010049017 0 0 37 74
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19000 341.53799 5777.9814 -407.00637 74.31837 1.1058821 111 0.0039877848 0.00095025921 0 0 37 74
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20000 395.75303 3159.4677 -403.82798 86.115516 1.1058821 111 0.0037874635 0.00090297077 0 0 37 74
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Loop time of 231.351 on 1 procs for 20000 steps with 111 atoms
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Performance: 7.469 ns/day, 3.213 hours/ns, 86.449 timesteps/s
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99.4% 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 | 39.09 | 39.09 | 39.09 | 0.0 | 16.90
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Bond | 0.092728 | 0.092728 | 0.092728 | 0.0 | 0.04
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Kspace | 0.87751 | 0.87751 | 0.87751 | 0.0 | 0.38
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Neigh | 3.9658 | 3.9658 | 3.9658 | 0.0 | 1.71
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Comm | 1.0608 | 1.0608 | 1.0608 | 0.0 | 0.46
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Output | 0.00096035 | 0.00096035 | 0.00096035 | 0.0 | 0.00
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Modify | 186.07 | 186.07 | 186.07 | 0.0 | 80.43
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Other | | 0.1892 | | | 0.08
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Nlocal: 111 ave 111 max 111 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 8070 ave 8070 max 8070 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 105469 ave 105469 max 105469 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 105469
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Ave neighs/atom = 950.171
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Ave special neighs/atom = 2
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Neighbor list builds = 20910
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Dangerous builds = 0
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Total wall time: 0:03:51
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