145 lines
6.8 KiB
Groff
145 lines
6.8 KiB
Groff
LAMMPS (8 Feb 2023)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# GCMC for LJ simple fluid, no dynamics
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# T = 2.0
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# rho ~ 0.5
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# p ~ 1.5
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# mu_ex ~ 0.0
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# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
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# variables modifiable using -var command line switch
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variable mu index -1.25
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variable temp index 2.0
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variable disp index 1.0
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variable lbox index 5.0
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# global model settings
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units lj
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atom_style atomic
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pair_style lj/cut 3.0
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pair_modify tail no # turn of to avoid triggering full_energy
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# box
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region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
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region box block 0 5.0 0 ${lbox} 0 ${lbox}
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region box block 0 5.0 0 5.0 0 ${lbox}
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region box block 0 5.0 0 5.0 0 5.0
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create_box 1 box
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Created orthogonal box = (0 0 0) to (5 5 5)
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1 by 1 by 1 MPI processor grid
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# lj parameters
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pair_coeff * * 1.0 1.0
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mass * 1.0
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# we recommend setting up a dedicated group for gcmc
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group gcmcgroup type 1
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0 atoms in group gcmcgroup
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# gcmc
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fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
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fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
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fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
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fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 1.0
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# atom count
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variable type1 atom "type==1"
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group type1 dynamic gcmcgroup var type1
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dynamic group type1 defined
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variable n1 equal count(type1)
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# averaging
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variable rho equal density
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variable p equal press
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variable nugget equal 1.0e-8
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variable lambda equal 1.0
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variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
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variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
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variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
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variable muex equal -1.25-2.0*ln(density*1+${nugget})
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variable muex equal -1.25-2.0*ln(density*1+1e-08)
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fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
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variable rhoav equal f_ave[1]
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variable pav equal f_ave[2]
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variable muexav equal f_ave[3]
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variable n1av equal f_ave[4]
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# output
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variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
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variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08)
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variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
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variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
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variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
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variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
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compute_modify thermo_temp dynamic yes
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thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
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thermo 1000
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# run
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run 10000
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WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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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 = 3.3
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ghost atom cutoff = 3.3
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binsize = 1.65, bins = 4 4 4
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 0.4341 | 0.4341 | 0.4341 Mbytes
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Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
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0 0 0 0 -0 0 0 0 0 0 0 0 0 0
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1000 2.0603874 2.9024736 -3.2576986 3.0482443 0.584 73 0.069266074 0.066959582 0.11158434 0.53624 1.3978532 0.0014407586 67.03
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2000 2.1586837 1.5581387 -2.8420766 3.1857993 0.496 62 0.068487803 0.067570935 0.1126652 0.53128 1.3713694 0.020274019 66.41
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3000 2.4664064 0.65471138 -3.3428236 3.6435549 0.528 66 0.068182273 0.067547792 0.11226502 0.53472 1.3892234 0.0070204504 66.84
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4000 1.8880496 1.4802782 -2.7846019 2.785647 0.488 61 0.068250075 0.067843541 0.11299989 0.52744 1.299496 0.033918563 65.93
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5000 2.0578649 1.3204331 -3.5571862 3.0433213 0.568 71 0.067858571 0.067732262 0.11271981 0.5364 1.4237505 0.00065741209 67.05
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6000 2.3627973 0.97064566 -3.1107668 3.4879388 0.504 63 0.067846204 0.06757018 0.11272207 0.5332 1.3945131 0.014216594 66.65
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7000 1.6629817 0.98138972 -2.7780297 2.4514644 0.464 58 0.067451389 0.067269791 0.11263692 0.53688 1.4207486 -0.0012887793 67.11
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8000 2.2135488 2.0878792 -3.0471089 3.2707661 0.536 67 0.067926473 0.067738312 0.1135594 0.52736 1.4348314 0.034380623 65.92
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9000 1.8904287 0.52639383 -3.3548657 2.7920177 0.52 65 0.06818197 0.068003094 0.11356319 0.53072 1.4528143 0.021683615 66.34
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10000 2.2353281 0.73275312 -3.2197702 3.3006016 0.512 64 0.068465059 0.068208485 0.11414748 0.52712 1.4143492 0.03497858 65.89
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Loop time of 12.3703 on 1 procs for 10000 steps with 64 atoms
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Performance: 349224.803 tau/day, 808.391 timesteps/s, 51.737 katom-step/s
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99.5% 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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---------------------------------------------------------------
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Pair | 0.28 | 0.28 | 0.28 | 0.0 | 2.26
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Neigh | 0.76133 | 0.76133 | 0.76133 | 0.0 | 6.15
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Comm | 0.073181 | 0.073181 | 0.073181 | 0.0 | 0.59
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Output | 0.00031081 | 0.00031081 | 0.00031081 | 0.0 | 0.00
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Modify | 11.24 | 11.24 | 11.24 | 0.0 | 90.87
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Other | | 0.01498 | | | 0.12
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Nlocal: 64 ave 64 max 64 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 714 ave 714 max 714 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2423 ave 2423 max 2423 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2423
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Ave neighs/atom = 37.859375
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Neighbor list builds = 10000
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Dangerous builds = 0
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Total wall time: 0:00:12
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