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lammps/examples/gcmc/log.6Jul17.gcmc.lj.g++.1
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LAMMPS (6 Jul 2017)
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 1 by 1 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) = 0.433 | 0.433 | 0.433 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 2.4038954 2.1735585 -2.7041368 3.5476844 0.496 62 0.064790036 0.06313096 0.1081294 0.54304 1.4513524 -0.025479219
2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004
3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537
4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657
5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777
6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359
7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399
8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766
9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544
10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094
Loop time of 20.6892 on 1 procs for 10000 steps with 60 atoms
Performance: 208804.611 tau/day, 483.344 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.47227 | 0.47227 | 0.47227 | 0.0 | 2.28
Neigh | 1.1729 | 1.1729 | 1.1729 | 0.0 | 5.67
Comm | 0.17133 | 0.17133 | 0.17133 | 0.0 | 0.83
Output | 0.00028253 | 0.00028253 | 0.00028253 | 0.0 | 0.00
Modify | 18.852 | 18.852 | 18.852 | 0.0 | 91.12
Other | | 0.02063 | | | 0.10
Nlocal: 60 ave 60 max 60 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 663 ave 663 max 663 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2133 ave 2133 max 2133 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2133
Ave neighs/atom = 35.55
Neighbor list builds = 10000
Dangerous builds = 0
Total wall time: 0:00:20
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