193 lines
9.7 KiB
Groff
193 lines
9.7 KiB
Groff
LAMMPS (23 Oct 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
|
|
Time spent = 0.00196958 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 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
|
|
|
|
# atom counts
|
|
|
|
variable carbon atom "type==1"
|
|
variable oxygen atom "type==2"
|
|
group carbon dynamic all var carbon
|
|
dynamic group carbon defined
|
|
group oxygen dynamic all 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)
|
|
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 ...
|
|
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 v_nC v_nO
|
|
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
|
|
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 8 16
|
|
2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0 10 20
|
|
3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0 7 14
|
|
4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0 9 18
|
|
5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0 9 18
|
|
6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0 10 20
|
|
7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0 12 24
|
|
8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0 8 16
|
|
9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0 1 2
|
|
10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0 13 26
|
|
11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0 11 22
|
|
12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0 0 0
|
|
13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0 2 4
|
|
14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0 5 10
|
|
15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0 9 18
|
|
16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0 12 24
|
|
17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0 10 20
|
|
18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0 3 6
|
|
19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0 8 16
|
|
20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0 10 20
|
|
Loop time of 20.6928 on 1 procs for 20000 steps with 30 atoms
|
|
|
|
Performance: 83.507 ns/day, 0.287 hours/ns, 966.519 timesteps/s
|
|
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 2.5462 | 2.5462 | 2.5462 | 0.0 | 12.30
|
|
Bond | 0.029783 | 0.029783 | 0.029783 | 0.0 | 0.14
|
|
Kspace | 0.26167 | 0.26167 | 0.26167 | 0.0 | 1.26
|
|
Neigh | 0.10705 | 0.10705 | 0.10705 | 0.0 | 0.52
|
|
Comm | 0.23409 | 0.23409 | 0.23409 | 0.0 | 1.13
|
|
Output | 0.0013416 | 0.0013416 | 0.0013416 | 0.0 | 0.01
|
|
Modify | 17.458 | 17.458 | 17.458 | 0.0 | 84.37
|
|
Other | | 0.05433 | | | 0.26
|
|
|
|
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
|