137 lines
5.9 KiB
Groff
137 lines
5.9 KiB
Groff
LAMMPS (23 Oct 2017)
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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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# gcmc
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fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
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fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
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fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
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fix mygcmc all 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 all 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 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866 63.44
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2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794 62.19
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3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578 63.23
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4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078 62.57
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5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867 62.56
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6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549 63.76
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7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793 62.2
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8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191 62.03
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9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837 64.36
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10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238 63.24
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Loop time of 23.8213 on 4 procs for 10000 steps with 69 atoms
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Performance: 181350.388 tau/day, 419.793 timesteps/s
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97.6% 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 | 0.10935 | 0.11844 | 0.12741 | 2.1 | 0.50
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Neigh | 0.33 | 0.33945 | 0.35091 | 1.6 | 1.42
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Comm | 0.49249 | 0.51745 | 0.53856 | 2.7 | 2.17
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Output | 0.00053334 | 0.0007208 | 0.0007906 | 0.0 | 0.00
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Modify | 22.82 | 22.822 | 22.825 | 0.0 | 95.81
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Other | | 0.02289 | | | 0.10
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Nlocal: 17.25 ave 23 max 10 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Nghost: 506.5 ave 519 max 490 min
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Histogram: 1 0 1 0 0 0 0 0 0 2
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Neighs: 705.75 ave 998 max 369 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Total # of neighbors = 2823
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Ave neighs/atom = 40.913
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Neighbor list builds = 10000
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Dangerous builds = 0
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Total wall time: 0:00:23
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