forked from lijiext/lammps
130 lines
5.6 KiB
Groff
130 lines
5.6 KiB
Groff
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 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 13.05 on 1 procs for 10000 steps with 60 atoms
|
|
|
|
Performance: 331035.016 tau/day, 766.285 timesteps/s
|
|
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.37239 | 0.37239 | 0.37239 | 0.0 | 2.85
|
|
Neigh | 0.94764 | 0.94764 | 0.94764 | 0.0 | 7.26
|
|
Comm | 0.092473 | 0.092473 | 0.092473 | 0.0 | 0.71
|
|
Output | 0.00023365 | 0.00023365 | 0.00023365 | 0.0 | 0.00
|
|
Modify | 11.627 | 11.627 | 11.627 | 0.0 | 89.09
|
|
Other | | 0.01054 | | | 0.08
|
|
|
|
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: 0:00:13
|