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lammps/examples/gcmc/log.6Jul17.gcmc.co2.g++.1
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log.6Jul17.gcmc.co2.g++.1
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LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
# mixtures containing alkanes, carbon dioxide and
# nitrogen AIChE J., 47,1676-1682 (2001)].
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
# global model settings
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 10.0 units box
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
molecule co2mol CO2.txt
Read molecule co2mol:
3 atoms with 2 types
2 bonds with 1 types
1 angles with 1 types
0 dihedrals with 0 types
0 impropers with 0 types
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
# rigid CO2 TraPPE model
pair_coeff 1 1 0.053649 2.8
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
# masses
mass 1 12.0107
mass 2 15.9994
# MD settings
group co2 type 1 2
24 atoms in group co2
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
8 rigid bodies with 24 atoms
1.16 = max distance from body owner to body atom
fix_modify myrigidnvt dynamic/dof no
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
thermo 1000
# run
run 20000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.164636
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0
WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
1000 420.43475 1722.4052 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0
2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0
3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0
4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0
5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0
6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0
7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0
8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0
9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0
10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0
11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0
12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0
13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0
14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0
15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0
16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0
17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0
18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0
19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0
20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0
Loop time of 20.153 on 1 procs for 20000 steps with 30 atoms
Performance: 85.744 ns/day, 0.280 hours/ns, 992.408 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5352 | 2.5352 | 2.5352 | 0.0 | 12.58
Bond | 0.026112 | 0.026112 | 0.026112 | 0.0 | 0.13
Kspace | 0.25 | 0.25 | 0.25 | 0.0 | 1.24
Neigh | 0.10364 | 0.10364 | 0.10364 | 0.0 | 0.51
Comm | 0.22907 | 0.22907 | 0.22907 | 0.0 | 1.14
Output | 0.0013065 | 0.0013065 | 0.0013065 | 0.0 | 0.01
Modify | 16.957 | 16.957 | 16.957 | 0.0 | 84.14
Other | | 0.05061 | | | 0.25
Nlocal: 30 ave 30 max 30 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2310 ave 2310 max 2310 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7736 ave 7736 max 7736 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7736
Ave neighs/atom = 257.867
Ave special neighs/atom = 2
Neighbor list builds = 20349
Dangerous builds = 0
Total wall time: 0:00:20
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