145 lines
6.8 KiB
Groff
145 lines
6.8 KiB
Groff
LAMMPS (8 Feb 2023)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
|
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
|
|
|
|
# we recommend setting up a dedicated group for gcmc
|
|
|
|
group gcmcgroup type 1
|
|
0 atoms in group gcmcgroup
|
|
|
|
# gcmc
|
|
|
|
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
|
|
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
|
|
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
|
|
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 1.0
|
|
|
|
# atom count
|
|
|
|
variable type1 atom "type==1"
|
|
group type1 dynamic gcmcgroup var type1
|
|
dynamic group type1 defined
|
|
variable n1 equal count(type1)
|
|
|
|
# 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 v_n1 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]
|
|
variable n1av equal f_ave[4]
|
|
|
|
# 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 v_n1av
|
|
thermo 1000
|
|
|
|
# run
|
|
|
|
run 10000
|
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 0 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
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 0.4492 | 0.4492 | 0.4492 Mbytes
|
|
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
|
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
|
|
1000 2.4378552 1.9014939 -3.23439 3.6030066 0.544 68 0.073050445 0.070796636 0.11934255 0.52552 1.3006333 0.04152087 65.69
|
|
2000 1.9339159 1.0360287 -3.5001391 2.8594327 0.56 70 0.069588893 0.068587488 0.11319584 0.542 1.4012888 -0.020696665 67.75
|
|
3000 1.8891807 2.2857708 -3.3755633 2.7954769 0.592 74 0.068329031 0.067640916 0.11187803 0.53536 1.3380926 0.0062359288 66.92
|
|
4000 2.0436517 1.7600211 -3.4067452 3.0229014 0.576 72 0.067464211 0.067003868 0.11060324 0.54144 1.4484907 -0.016246603 67.68
|
|
5000 2.1512268 1.0811095 -3.2418366 3.1786785 0.536 67 0.066830654 0.066717982 0.1094094 0.54368 1.4962073 -0.025791643 67.96
|
|
6000 2.128931 1.5444487 -3.1904474 3.1450116 0.528 66 0.067479197 0.067193531 0.1104464 0.53112 1.4247377 0.019908014 66.39
|
|
7000 1.8194311 0.72981963 -3.6601329 2.6912418 0.576 72 0.068131849 0.067910074 0.11182024 0.51968 1.4517098 0.063444774 64.96
|
|
8000 1.947817 0.74570466 -3.0935809 2.8753489 0.504 63 0.068034071 0.067855883 0.11217045 0.53304 1.4924302 0.012298733 66.63
|
|
9000 1.8942389 1.3367401 -2.8925016 2.7962574 0.504 63 0.068117479 0.067943081 0.11236152 0.536 1.4091106 0.0011494886 67
|
|
10000 2.2092799 0.95517153 -2.9117781 3.2586879 0.48 60 0.068264792 0.068016591 0.11310789 0.52272 1.4774174 0.051284873 65.34
|
|
Loop time of 14.6475 on 4 procs for 10000 steps with 60 atoms
|
|
|
|
Performance: 294930.892 tau/day, 682.710 timesteps/s, 40.963 katom-step/s
|
|
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.079336 | 0.086188 | 0.093829 | 2.2 | 0.59
|
|
Neigh | 0.25224 | 0.26194 | 0.26946 | 1.4 | 1.79
|
|
Comm | 0.31594 | 0.33181 | 0.34839 | 2.4 | 2.27
|
|
Output | 0.00039633 | 0.00063799 | 0.00071881 | 0.0 | 0.00
|
|
Modify | 13.956 | 13.957 | 13.958 | 0.0 | 95.29
|
|
Other | | 0.01003 | | | 0.07
|
|
|
|
Nlocal: 15 ave 16 max 14 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Nghost: 437 ave 446 max 431 min
|
|
Histogram: 2 0 0 0 0 0 1 0 0 1
|
|
Neighs: 529 ave 595 max 437 min
|
|
Histogram: 1 0 0 0 1 0 0 0 0 2
|
|
|
|
Total # of neighbors = 2116
|
|
Ave neighs/atom = 35.266667
|
|
Neighbor list builds = 10000
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:14
|