forked from lijiext/lammps
291 lines
13 KiB
Groff
291 lines
13 KiB
Groff
LAMMPS (27 Nov 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 = 0.00128841 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 (src/min.cpp:168)
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Ewald initialization ...
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using 12-bit tables for long-range coulomb (src/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 -36.122455 0.67828405 -12.271354 573.22675
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Loop time of 0.0461962 on 1 procs for 100 steps with 24 atoms
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98.3% 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 -34.586018764 -35.4441713339
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Force two-norm initial, final = 18.0027 42.115
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Force max component initial, final = 5.8993 15.4907
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Final line search alpha, max atom move = 0.00127226 0.0197082
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Iterations, force evaluations = 100 239
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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 | 0.038526 | 0.038526 | 0.038526 | 0.0 | 83.40
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Bond | 0.00031209 | 0.00031209 | 0.00031209 | 0.0 | 0.68
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Kspace | 0.0019636 | 0.0019636 | 0.0019636 | 0.0 | 4.25
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Neigh | 0.00055456 | 0.00055456 | 0.00055456 | 0.0 | 1.20
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Comm | 0.0040288 | 0.0040288 | 0.0040288 | 0.0 | 8.72
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Output | 1.5259e-05 | 1.5259e-05 | 1.5259e-05 | 0.0 | 0.03
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.0007958 | | | 1.72
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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: 2011 ave 2011 max 2011 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 4921 ave 4921 max 4921 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 4921
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Ave neighs/atom = 205.042
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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 (src/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 -36.122455 0 -12.949638 703.43827
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1000 260.39219 -55.141232 0 -43.498537 -1698.672
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Loop time of 0.140376 on 1 procs for 1000 steps with 24 atoms
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Performance: 615.489 ns/day, 0.039 hours/ns, 7123.720 timesteps/s
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99.1% 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 | 0.10434 | 0.10434 | 0.10434 | 0.0 | 74.33
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Bond | 0.00013041 | 0.00013041 | 0.00013041 | 0.0 | 0.09
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Kspace | 0.008199 | 0.008199 | 0.008199 | 0.0 | 5.84
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Neigh | 0.0061581 | 0.0061581 | 0.0061581 | 0.0 | 4.39
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Comm | 0.015352 | 0.015352 | 0.015352 | 0.0 | 10.94
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Output | 1.4305e-05 | 1.4305e-05 | 1.4305e-05 | 0.0 | 0.01
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Modify | 0.004544 | 0.004544 | 0.004544 | 0.0 | 3.24
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Other | | 0.001639 | | | 1.17
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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: 1776 ave 1776 max 1776 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5073 ave 5073 max 5073 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5073
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Ave neighs/atom = 211.375
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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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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 (src/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 (src/MC/fix_gcmc.cpp:487)
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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 (src/neighbor.cpp:471)
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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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0 260.39219 -1699.3643 -55.141232 11.642695 0.23910963 24 0 0 0 0 8 16
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1000 340.44409 -2560.1501 -280.70157 53.784356 0.80699501 81 0.054205983 0.015933081 0 0 27 54
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2000 302.57602 592.41718 -310.37771 53.213377 0.89666113 90 0.030546787 0.0078577743 0 0 30 60
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3000 270.18045 -817.18659 -346.75773 50.737466 0.95643854 96 0.021969243 0.0060076096 0 0 32 64
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4000 334.17192 1153.3017 -335.25519 62.75449 0.95643854 96 0.016400775 0.0045269353 0 0 32 64
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5000 360.36872 -647.99689 -336.2928 67.674015 0.95643854 96 0.012996731 0.0036569014 0 0 32 64
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6000 282.37822 -986.51765 -341.91848 53.028098 0.95643854 96 0.010941282 0.0030159847 0 0 32 64
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7000 363.01448 2952.0391 -358.72963 70.335018 0.98632724 99 0.0098923151 0.0028884203 0 0 33 66
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8000 331.70391 323.34886 -382.04165 68.223498 1.0461046 105 0.0092083323 0.0025112378 0 0 35 70
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9000 337.2032 -3637.5257 -390.66472 69.35457 1.0461046 105 0.0081585853 0.0022395915 0 0 35 70
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10000 373.67063 3081.3271 -380.5107 76.855041 1.0461046 105 0.0073396679 0.0020164949 0 0 35 70
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11000 336.64665 5535.9451 -405.21548 71.247059 1.0759934 108 0.0068442571 0.0018355023 0 0 36 72
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12000 306.51164 1448.1757 -410.3655 64.869362 1.0759934 108 0.0062798499 0.0016809265 0 0 36 72
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13000 319.03497 177.44405 -406.17113 67.519768 1.0759934 108 0.0057952448 0.0015520479 0 0 36 72
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14000 309.89701 -1022.6798 -384.20239 65.585833 1.0759934 108 0.005391524 0.0014384143 0 0 36 72
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15000 398.91559 2058.9251 -404.32604 84.425503 1.0759934 108 0.0050257238 0.0013442486 0 0 36 72
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16000 318.98778 873.46142 -392.13338 67.50978 1.0759934 108 0.0047204383 0.0012578458 0 0 36 72
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17000 333.16025 2347.0215 -387.73943 70.509206 1.0759934 108 0.0044407568 0.0011843991 0 0 36 72
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18000 353.23789 -2305.787 -382.1633 74.758389 1.0759934 108 0.0042016342 0.0011165574 0 0 36 72
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19000 322.70939 5619.9631 -381.81328 68.297412 1.0759934 108 0.0039877848 0.0010558436 0 0 36 72
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20000 371.07261 3916.1113 -389.76357 78.532884 1.0759934 108 0.0037874635 0.0010033009 0 0 36 72
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Loop time of 242.59 on 1 procs for 20000 steps with 108 atoms
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Performance: 7.123 ns/day, 3.369 hours/ns, 82.444 timesteps/s
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99.8% 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 | 38.279 | 38.279 | 38.279 | 0.0 | 15.78
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Bond | 0.055672 | 0.055672 | 0.055672 | 0.0 | 0.02
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Kspace | 0.60623 | 0.60623 | 0.60623 | 0.0 | 0.25
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Neigh | 4.4189 | 4.4189 | 4.4189 | 0.0 | 1.82
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Comm | 1.2719 | 1.2719 | 1.2719 | 0.0 | 0.52
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Output | 0.00096583 | 0.00096583 | 0.00096583 | 0.0 | 0.00
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Modify | 197.85 | 197.85 | 197.85 | 0.0 | 81.56
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Other | | 0.1098 | | | 0.05
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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: 8000 ave 8000 max 8000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 100006 ave 100006 max 100006 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 100006
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Ave neighs/atom = 925.981
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Ave special neighs/atom = 2
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Neighbor list builds = 20903
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Dangerous builds = 0
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Total wall time: 0:04:02
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