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lammps/examples/gcmc/log.27Nov18.gcmc.co2.g++.1

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LAMMPS (27 Nov 2018)
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 max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00134993 secs
# 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 co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
fix myrigidnvt co2 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
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigidnvt dynamic/dof yes
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic co2 var carbon
dynamic group carbon defined
group oxygen dynamic co2 var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
# 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)
# dynamically update default temperature ndof
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 v_nC v_nO
thermo 1000
# run
run 20000
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/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 (src/MC/fix_gcmc.cpp:487)
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 (src/neighbor.cpp:471)
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 v_nC v_nO
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
1000 267.9799 -73.919548 -3.6735999 5.8578459 0.36539744 15 0.23663972 0.2494423 0 0 5 10
2000 409.06596 -98.033864 -6.7570039 10.974131 0.43847693 18 0.29379544 0.29816284 0 0 6 12
3000 279.3225 -836.47758 -26.434976 15.819539 0.87695385 36 0.23798567 0.24203908 0 0 12 24
4000 333.6181 606.63478 -30.35312 18.894592 0.87695385 36 0.19121778 0.19481508 0 0 12 24
5000 405.98741 -103.97582 -14.180277 16.942399 0.65771539 27 0.15272841 0.15982952 0 0 9 18
6000 283.5835 -240.01076 -6.7198093 7.607777 0.43847693 18 0.1606796 0.16536735 0 0 6 12
7000 142.00717 154.95914 -0.74192319 0.98769159 0.14615898 6 0.19501993 0.20103405 0 0 2 4
8000 376.67702 -118.12474 -10.774631 13.847899 0.5846359 24 0.20133396 0.20468352 0 0 8 16
9000 305.43166 -1095.8633 -10.388279 9.7112935 0.51155641 21 0.19445239 0.19869334 0 0 7 14
10000 244.08225 -179.31274 -12.974988 8.9732748 0.5846359 24 0.19098971 0.19586397 0 0 8 16
11000 305.03389 -568.94714 -21.745425 14.244887 0.73079488 30 0.18517522 0.18978828 0 0 10 20
12000 318.29735 767.76579 -37.184231 21.189508 1.0231128 42 0.17256426 0.17580267 0 0 14 28
13000 411.21707 433.01125 -4.5149215 8.9889065 0.36539744 15 0.16329385 0.16767604 0 0 5 10
14000 304.29535 148.28607 -2.3505844 6.6516754 0.36539744 15 0.17435868 0.17897674 0 0 5 10
15000 338.00555 2384.1424 -21.438264 17.463859 0.80387436 33 0.17237066 0.17634112 0 0 11 22
16000 613.56062 610.93867 -0.057364228 1.2192718 0.073079488 3 0.17128158 0.1758886 0 0 1 2
17000 432.63323 -980.52384 -15.79844 18.054365 0.65771539 27 0.17145651 0.17504846 0 0 9 18
18000 181.74572 -352.81765 -1.8617959 2.1669979 0.21923846 9 0.17292463 0.17654774 0 0 3 6
19000 208.55292 -248.38735 -4.2287767 4.5588154 0.36539744 15 0.18168324 0.18454331 0 0 5 10
20000 304.73317 -649.9896 -16.532405 12.716924 0.65771539 27 0.18085983 0.18345574 0 0 9 18
Loop time of 21.0434 on 1 procs for 20000 steps with 27 atoms
Performance: 82.116 ns/day, 0.292 hours/ns, 950.415 timesteps/s
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2373 | 2.2373 | 2.2373 | 0.0 | 10.63
Bond | 0.022895 | 0.022895 | 0.022895 | 0.0 | 0.11
Kspace | 0.16756 | 0.16756 | 0.16756 | 0.0 | 0.80
Neigh | 0.11436 | 0.11436 | 0.11436 | 0.0 | 0.54
Comm | 0.26988 | 0.26988 | 0.26988 | 0.0 | 1.28
Output | 0.0014684 | 0.0014684 | 0.0014684 | 0.0 | 0.01
Modify | 18.193 | 18.193 | 18.193 | 0.0 | 86.45
Other | | 0.03692 | | | 0.18
Nlocal: 27 ave 27 max 27 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2081 ave 2081 max 2081 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6264 ave 6264 max 6264 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6264
Ave neighs/atom = 232
Ave special neighs/atom = 2
Neighbor list builds = 20177
Dangerous builds = 0
Total wall time: 0:00:21
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