mirror of https://github.com/lammps/lammps.git
142 lines
6.0 KiB
Groff
142 lines
6.0 KiB
Groff
LAMMPS (27 Nov 2018)
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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 2 by 2 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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Neighbor list info ...
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update every 1 steps, delay 10 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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 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 2.4378552 1.9014939 -3.23439 3.6030066 0.544 68 0.073050445 0.070796636 0.11934255 0.52552 1.3006333 0.04152087 62.56
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2000 1.9339159 1.0360287 -3.5001391 2.8594327 0.56 70 0.069588893 0.068587488 0.11319584 0.542 1.4012888 -0.020696665 64.56
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3000 1.8891807 2.2857708 -3.3755633 2.7954769 0.592 74 0.068329031 0.067640916 0.11187803 0.53536 1.3380926 0.0062359288 64.21
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4000 2.0436517 1.7600211 -3.4067452 3.0229014 0.576 72 0.067464211 0.067003868 0.11060324 0.54144 1.4484907 -0.016246603 64.75
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5000 2.1512268 1.0811095 -3.2418366 3.1786785 0.536 67 0.066830654 0.066717982 0.1094094 0.54368 1.4962073 -0.025791643 65.04
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6000 2.128931 1.5444487 -3.1904474 3.1450116 0.528 66 0.067479197 0.067193531 0.1104464 0.53112 1.4247377 0.019908014 63.01
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7000 1.8194311 0.72981963 -3.6601329 2.6912418 0.576 72 0.068131849 0.067910074 0.11182024 0.51968 1.4517098 0.063444774 61.72
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8000 1.947817 0.74570466 -3.0935809 2.8753489 0.504 63 0.068034071 0.067855883 0.11217045 0.53304 1.4924302 0.012298733 63.45
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9000 1.8942389 1.3367401 -2.8925016 2.7962574 0.504 63 0.068117479 0.067943081 0.11236152 0.536 1.4091106 0.0011494886 63.73
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10000 2.2092799 0.95517153 -2.9117781 3.2586879 0.48 60 0.068264792 0.068016591 0.11310789 0.52272 1.4774174 0.051284873 62.04
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Loop time of 26.0069 on 4 procs for 10000 steps with 60 atoms
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Performance: 166109.741 tau/day, 384.513 timesteps/s
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95.9% 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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---------------------------------------------------------------
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Pair | 0.10309 | 0.115 | 0.1225 | 2.2 | 0.44
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Neigh | 0.3907 | 0.40447 | 0.41957 | 1.7 | 1.56
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Comm | 0.44236 | 0.46678 | 0.49472 | 2.8 | 1.79
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Output | 0.0011411 | 0.0062903 | 0.0080109 | 3.7 | 0.02
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Modify | 25 | 25.002 | 25.005 | 0.0 | 96.14
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Other | | 0.01231 | | | 0.05
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Nlocal: 15 ave 16 max 14 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 437 ave 446 max 431 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Neighs: 529 ave 595 max 437 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Total # of neighbors = 2116
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Ave neighs/atom = 35.2667
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Neighbor list builds = 10000
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Dangerous builds = 0
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Total wall time: 0:00:26
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