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lammps/examples/gcmc/log.24Mar17.gcmc.lj.g++.4
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LAMMPS (17 Mar 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
# rho ~ 0.5
# p ~ 1.5
# mu_ex ~ 0.0
# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
# variables modifiable using -var command line switch
variable mu index -1.25
variable temp index 2.0
variable disp index 1.0
variable lbox index 5.0
# global model settings
units lj
atom_style atomic
pair_style lj/cut 3.0
pair_modify tail no # turn of to avoid triggering full_energy
# box
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
region box block 0 5.0 0 ${lbox} 0 ${lbox}
region box block 0 5.0 0 5.0 0 ${lbox}
region box block 0 5.0 0 5.0 0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (5 5 5)
1 by 2 by 2 MPI processor grid
# lj parameters
pair_coeff * * 1.0 1.0
mass * 1.0
# gcmc
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
# averaging
variable rho equal density
variable p equal press
variable nugget equal 1.0e-8
variable lambda equal 1.0
variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
variable muex equal -1.25-2.0*ln(density*1+${nugget})
variable muex equal -1.25-2.0*ln(density*1+1e-08)
fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
variable rhoav equal f_ave[1]
variable pav equal f_ave[2]
variable muexav equal f_ave[3]
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
compute_modify thermo_temp dynamic yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
thermo 1000
# run
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.3
ghost atom cutoff = 3.3
binsize = 1.65, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
0 0 0 0 -0 0 0 0 0 0 0 0 0
1000 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866
2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794
3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578
4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078
5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867
6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549
7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793
8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191
9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837
10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238
Loop time of 13.0611 on 4 procs for 10000 steps with 69 atoms
Performance: 330753.007 tau/day, 765.632 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.08888 | 0.09443 | 0.099889 | 1.4 | 0.72
Neigh | 0.27721 | 0.28532 | 0.29177 | 1.1 | 2.18
Comm | 0.27648 | 0.28875 | 0.30268 | 1.9 | 2.21
Output | 0.00029635 | 0.00043058 | 0.00048113 | 0.0 | 0.00
Modify | 12.384 | 12.384 | 12.384 | 0.0 | 94.82
Other | | 0.008055 | | | 0.06
Nlocal: 17.25 ave 23 max 10 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 506.5 ave 519 max 490 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 705.75 ave 998 max 369 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 2823
Ave neighs/atom = 40.913
Neighbor list builds = 10000
Dangerous builds = 0
Total wall time: 0:00:13
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