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lammps/examples/gcmc/log.24Mar17.gcmc.co2.g++.4

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LAMMPS (17 Mar 2017)
# 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 2 by 2 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 100 100 100 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 100 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 100 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:439)
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) = 15.4 | 15.4 | 15.4 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0
WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
1000 760.80877 -39.270882 -3.5239626 12.851016 0.29231795 12 0.24161633 0.22984103 0.71087092 0.85283311
2000 308.0739 -255.061 -20.411926 14.386853 0.73079488 30 0.26075352 0.24898725 0.73128383 0.88590474
3000 432.34358 -1361.3278 -12.644057 15.894387 0.5846359 24 0.21121583 0.21051229 0.70036003 0.86735027
4000 631.524 -63.488785 -3.6517158 13.804656 0.36539744 15 0.22486443 0.22886173 0.72358173 0.87172606
5000 730.61244 -1029.284 -6.2144028 19.600352 0.43847693 18 0.23017182 0.22740779 0.72281887 0.87820845
6000 752.43412 503.4547 -3.7053679 16.447663 0.36539744 15 0.22943971 0.226183 0.71450085 0.87447436
7000 660.68448 828.51735 -10.592278 21.006666 0.51155641 21 0.24702096 0.24218506 0.71815602 0.8740222
8000 331.58822 -621.22187 -5.3705759 7.2482776 0.36539744 15 0.23211903 0.22906813 0.70281376 0.86269411
9000 413.91538 869.51669 -11.28701 15.216905 0.5846359 24 0.23246466 0.22923961 0.70832684 0.86244176
10000 242.20861 -808.23311 -5.4533937 5.2945044 0.36539744 15 0.22024676 0.22031775 0.70785097 0.85712561
11000 348.20046 -372.16895 -3.4663358 7.6114092 0.36539744 15 0.2252033 0.22688969 0.71513402 0.86123263
12000 251.99682 303.30092 -18.58289 11.768089 0.73079488 30 0.20916844 0.21068047 0.694787 0.84635875
13000 306.83592 -1582.0137 -20.810287 14.329041 0.73079488 30 0.19494837 0.196527 0.67554784 0.83056119
14000 476.57411 268.94927 -14.185859 19.888076 0.65771539 27 0.19779631 0.20016859 0.67957528 0.83375167
15000 267.03534 730.71183 -9.3348616 9.8171066 0.5846359 24 0.19468305 0.19814971 0.68032974 0.83810439
16000 639.83235 2190.3244 -9.6666503 26.701062 0.65771539 27 0.19520687 0.19848997 0.68514387 0.84100361
17000 2237.1203 -222.59057 -0.18248834 4.4456205 0.073079488 3 0.20412446 0.20757814 0.69175318 0.8434939
18000 754.44841 205.54694 -10.501943 27.736031 0.5846359 24 0.2129422 0.21508015 0.69665031 0.84758331
19000 1610.1148 1293.6003 -0.20849836 3.1996309 0.073079488 3 0.22061668 0.22356929 0.69949369 0.84851405
20000 231.61458 -39.696514 -4.6452226 5.0629266 0.36539744 15 0.21984893 0.22246517 0.69914635 0.85058457
Loop time of 21.1019 on 4 procs for 20000 steps with 15 atoms
Performance: 81.888 ns/day, 0.293 hours/ns, 947.781 timesteps/s
98.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.31897 | 0.41973 | 0.49748 | 10.1 | 1.99
Bond | 0.014808 | 0.015063 | 0.015289 | 0.2 | 0.07
Kspace | 0.3813 | 0.46228 | 0.56585 | 9.8 | 2.19
Neigh | 0.049173 | 0.050043 | 0.050868 | 0.3 | 0.24
Comm | 0.9755 | 0.99686 | 1.0205 | 1.9 | 4.72
Output | 0.0014546 | 0.0015051 | 0.0016098 | 0.2 | 0.01
Modify | 19.043 | 19.062 | 19.085 | 0.4 | 90.33
Other | | 0.09438 | | | 0.45
Nlocal: 3.75 ave 6 max 3 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 876.5 ave 937 max 818 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 490.5 ave 647 max 363 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 1962
Ave neighs/atom = 130.8
Ave special neighs/atom = 2
Neighbor list builds = 40070
Dangerous builds = 115
Total wall time: 0:00:21
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