146 lines
8.5 KiB
Groff
146 lines
8.5 KiB
Groff
LAMMPS (10 Feb 2021)
|
|
# Charge regulation lammps for simple weak electrolyte
|
|
|
|
units real
|
|
atom_style charge
|
|
neighbor 10.0 bin
|
|
read_data data.chreg-acid-real
|
|
Reading data file ...
|
|
orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
219 atoms
|
|
read_data CPU = 0.002 seconds
|
|
|
|
#real units
|
|
variable sigma equal 7.2 # particle diameter 0.72 nm
|
|
variable temperature equal 298 # temperature 298 K
|
|
variable kb index 0.0019872067 # kB in Kcal/mol/K
|
|
variable epsilon equal ${kb}*${temperature}
|
|
variable epsilon equal 0.0019872067*${temperature}
|
|
variable epsilon equal 0.0019872067*298
|
|
variable tunit equal 2000 # time unit is 2000 fs
|
|
variable timestep equal 0.005*${tunit}
|
|
variable timestep equal 0.005*2000
|
|
|
|
variable cut_long equal 12.5*${sigma}
|
|
variable cut_long equal 12.5*7.2
|
|
variable nevery equal 100
|
|
variable nmc equal 100
|
|
variable pH equal 7.0
|
|
variable pKa equal 6.0
|
|
variable pIm equal 3.0
|
|
variable pIp equal 3.0
|
|
|
|
variable cut_lj equal 2^(1.0/6.0)*${sigma}
|
|
variable cut_lj equal 2^(1.0/6.0)*7.2
|
|
velocity all create ${temperature} 8008 loop geom
|
|
velocity all create 298 8008 loop geom
|
|
|
|
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
|
|
pair_style lj/cut/coul/long 8.08172674782749 ${cut_long}
|
|
pair_style lj/cut/coul/long 8.08172674782749 90
|
|
pair_coeff * * ${epsilon} ${sigma}
|
|
pair_coeff * * 0.5921875966 ${sigma}
|
|
pair_coeff * * 0.5921875966 7.2
|
|
kspace_style pppm 1.0e-3
|
|
dielectric 78
|
|
pair_modify shift yes
|
|
|
|
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
|
fix fnve all nve
|
|
compute dtemp all temp
|
|
compute_modify dtemp dynamic yes
|
|
fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
|
|
fix fT all langevin 298 $(v_temperature) $(v_tunit) 123
|
|
fix fT all langevin 298 298 $(v_tunit) 123
|
|
fix fT all langevin 298 298 2000 123
|
|
fix_modify fT temp dtemp
|
|
|
|
fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
|
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
|
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
|
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
|
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
|
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
|
|
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 seed 2345 tempfixid fT
|
|
thermo 100
|
|
thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
|
timestep ${timestep}
|
|
timestep 10
|
|
run 2000
|
|
PPPM initialization ...
|
|
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
|
|
G vector (1/distance) = 0.019408615
|
|
grid = 8 8 8
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.00012527706
|
|
estimated relative force accuracy = 3.7726815e-07
|
|
using double precision KISS FFT
|
|
3d grid and FFT values/proc = 2197 512
|
|
0 atoms in group FixChargeRegulation:exclusion_group:chareg
|
|
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../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 = 100
|
|
ghost atom cutoff = 100
|
|
binsize = 50, bins = 8 8 8
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/cut/coul/long, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/3d/newton
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 3.708 | 3.708 | 3.708 Mbytes
|
|
Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
|
0 -6.4798431 298 0 0 1 99 0 0 109 10
|
|
100 -6.9219668 306.44177 100 77 15 85 0 0 94 9
|
|
200 -6.8175255 306.64254 200 164 23 77 0 0 87 10
|
|
300 -5.2482381 331.67831 300 248 21 79 0 0 85 6
|
|
400 -7.4531538 285.3495 400 326 17 83 0 0 89 6
|
|
500 -6.9662528 286.2123 500 408 14 86 0 0 95 9
|
|
600 -6.528214 291.41762 600 492 14 86 0 0 95 9
|
|
700 -6.290871 271.50948 700 567 14 86 0 0 96 10
|
|
800 -6.4944741 300.66261 800 650 23 77 0 0 83 6
|
|
900 -8.0414672 305.6179 900 731 25 75 0 0 84 9
|
|
1000 -8.5694583 298.73349 1000 810 25 75 0 0 83 8
|
|
1100 -8.6677368 269.67435 1100 894 22 78 0 0 87 9
|
|
1200 -8.2246183 284.14886 1200 969 22 78 0 0 88 10
|
|
1300 -7.7674621 320.04838 1300 1040 23 77 0 0 85 8
|
|
1400 -9.5186335 303.48091 1400 1124 18 82 0 0 93 11
|
|
1500 -5.8437493 271.40712 1500 1204 25 75 0 0 83 8
|
|
1600 -5.9149181 268.24708 1600 1285 23 77 0 0 90 13
|
|
1700 -6.5047738 303.79732 1700 1369 27 73 0 0 84 11
|
|
1800 -7.3010139 308.98213 1800 1450 22 78 0 0 83 5
|
|
1900 -6.3505397 306.94357 1900 1527 22 78 0 0 86 8
|
|
2000 -5.7144173 287.06184 2000 1605 27 73 0 0 80 7
|
|
Loop time of 1.17189 on 1 procs for 2000 steps with 187 atoms
|
|
|
|
Performance: 1474.535 ns/day, 0.016 hours/ns, 1706.638 timesteps/s
|
|
99.6% CPU use with 1 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.035807 | 0.035807 | 0.035807 | 0.0 | 3.06
|
|
Kspace | 0.37689 | 0.37689 | 0.37689 | 0.0 | 32.16
|
|
Neigh | 0.008694 | 0.008694 | 0.008694 | 0.0 | 0.74
|
|
Comm | 0.004793 | 0.004793 | 0.004793 | 0.0 | 0.41
|
|
Output | 0.000746 | 0.000746 | 0.000746 | 0.0 | 0.06
|
|
Modify | 0.74292 | 0.74292 | 0.74292 | 0.0 | 63.39
|
|
Other | | 0.00205 | | | 0.17
|
|
|
|
Nlocal: 187.000 ave 187 max 187 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 437.000 ave 437 max 437 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 1500.00 ave 1500 max 1500 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 1500
|
|
Ave neighs/atom = 8.0213904
|
|
Neighbor list builds = 2080
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:01
|