132 lines
6.7 KiB
Groff
132 lines
6.7 KiB
Groff
LAMMPS (10 Feb 2021)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# Charge regulation lammps for a polymer chain
|
|
units lj
|
|
atom_style full
|
|
neighbor 3.0 bin
|
|
read_data data.chreg-polymer
|
|
Reading data file ...
|
|
orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
160 atoms
|
|
scanning bonds ...
|
|
1 = max bonds/atom
|
|
reading bonds ...
|
|
79 bonds
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 0 0 0
|
|
special bond factors coul: 0 0 0
|
|
2 = max # of 1-2 neighbors
|
|
2 = max # of 1-3 neighbors
|
|
4 = max # of 1-4 neighbors
|
|
6 = max # of special neighbors
|
|
special bonds CPU = 0.001 seconds
|
|
read_data CPU = 0.009 seconds
|
|
|
|
bond_style harmonic
|
|
bond_coeff 1 100 1.122462 # K R0
|
|
velocity all create 1.0 8008 loop geom
|
|
|
|
pair_style lj/cut/coul/long 1.122462 20
|
|
pair_coeff * * 1.0 1.0 1.122462 # charges
|
|
kspace_style pppm 1.0e-3
|
|
pair_modify shift yes
|
|
dielectric 1.0
|
|
|
|
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
|
fix fnve all nve
|
|
compute dtemp all temp
|
|
compute_modify dtemp dynamic yes
|
|
fix fT all langevin 1.0 1.0 1.0 123
|
|
fix_modify fT temp dtemp
|
|
|
|
fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345
|
|
fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345
|
|
fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345
|
|
|
|
thermo 100
|
|
# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
|
|
thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
|
|
|
|
timestep 0.005
|
|
run 2000
|
|
PPPM initialization ...
|
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
|
G vector (1/distance) = 0.077106934
|
|
grid = 8 8 8
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.00074388331
|
|
estimated relative force accuracy = 0.00074388331
|
|
using double precision FFTW3
|
|
3d grid and FFT values/proc = 2197 512
|
|
0 atoms in group FixChargeRegulation:exclusion_group:chareg1
|
|
0 atoms in group FixChargeRegulation:exclusion_group:chareg2
|
|
0 atoms in group FixChargeRegulation:exclusion_group:chareg3
|
|
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 10 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 23
|
|
ghost atom cutoff = 23
|
|
binsize = 11.5, bins = 9 9 9
|
|
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) = 6.962 | 6.962 | 6.962 Mbytes
|
|
Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
|
|
0 0.50528297 1 0 80 80 0 0 0
|
|
100 0.61185377 0.95892928 13 67 74 7 0 0
|
|
200 0.54355177 1.1282424 19 61 76 15 0 0
|
|
300 0.4519957 1.0764688 20 60 85 26 1 0
|
|
400 0.41479389 0.99212685 24 56 92 36 0 0
|
|
500 0.37382446 0.99776674 28 52 98 46 0 0
|
|
600 0.34785337 1.1115081 28 52 109 57 0 0
|
|
700 0.34637618 1.0332262 28 52 120 68 0 0
|
|
800 0.21020932 1.1264036 29 51 125 74 0 0
|
|
900 0.21246108 1.1168609 30 50 131 81 0 0
|
|
1000 0.20997475 1.1201478 32 48 132 84 0 0
|
|
1100 0.1984165 1.0209092 31 49 144 95 0 0
|
|
1200 0.2061932 0.95880059 35 45 151 106 0 0
|
|
1300 0.17220376 0.980077 36 44 156 112 0 0
|
|
1400 0.15671143 0.93535342 37 43 161 118 0 0
|
|
1500 0.16174665 0.9495928 36 44 168 124 0 0
|
|
1600 0.11062965 0.94072924 40 40 164 124 0 0
|
|
1700 0.13002563 0.95010828 38 42 167 125 0 0
|
|
1800 0.14527814 0.93555342 37 43 172 129 0 0
|
|
1900 0.17627465 0.96682495 32 48 176 128 0 0
|
|
2000 0.16497265 0.95226954 33 47 180 133 0 0
|
|
Loop time of 7.45499 on 1 procs for 2000 steps with 393 atoms
|
|
|
|
Performance: 115895.577 tau/day, 268.277 timesteps/s
|
|
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.45607 | 0.45607 | 0.45607 | 0.0 | 6.12
|
|
Bond | 0.0062385 | 0.0062385 | 0.0062385 | 0.0 | 0.08
|
|
Kspace | 2.3257 | 2.3257 | 2.3257 | 0.0 | 31.20
|
|
Neigh | 0.067103 | 0.067103 | 0.067103 | 0.0 | 0.90
|
|
Comm | 0.02577 | 0.02577 | 0.02577 | 0.0 | 0.35
|
|
Output | 0.00087047 | 0.00087047 | 0.00087047 | 0.0 | 0.01
|
|
Modify | 4.5664 | 4.5664 | 4.5664 | 0.0 | 61.25
|
|
Other | | 0.006848 | | | 0.09
|
|
|
|
Nlocal: 393.000 ave 393 max 393 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 749.000 ave 749 max 749 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 5359.00 ave 5359 max 5359 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 5359
|
|
Ave neighs/atom = 13.636132
|
|
Ave special neighs/atom = 1.1908397
|
|
Neighbor list builds = 1489
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:07
|