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create new reference log files

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Axel Kohlmeyer
2021-02-11 08:00:59 -05:00
parent c583ad6dc4
commit 7f8e8c635c
5 changed files with 512 additions and 181 deletions
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LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
# Charge regulation lammps for simple weak electrolyte
units lj
atom_style charge
neighbor 3.0 bin
read_data data.chreg-acid
Reading data file ...
orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
219 atoms
read_data CPU = 0.003 seconds
variable cut_long equal 12.5
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)
variable lunit_nm equal 0.72 # in the units of nm
velocity all create 1.0 8008 loop geom
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
pair_style lj/cut/coul/long 1.12246204830937 ${cut_long}
pair_style lj/cut/coul/long 1.12246204830937 12.5
pair_coeff * * 1.0 1.0
kspace_style ewald 1.0e-3
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 1.0 1.0 1.0 123
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 ${lunit_nm} 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 ${lunit_nm} 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 ${lunit_nm} 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 ${lunit_nm} 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 ${lunit_nm} 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 0.72 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 0.72 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 0.72 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 0.005
run 2000
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.14221027
estimated absolute RMS force accuracy = 0.0010128126
estimated relative force accuracy = 0.0010128126
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
0 atoms in group FixChargeRegulation:exclusion_group:chareg
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 = 15.5
ghost atom cutoff = 15.5
binsize = 7.75, bins = 7 7 7
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) = 11.91 | 11.91 | 11.91 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 -0.049662059 1 0 0 1 99 0 0 109 10
100 -0.053672881 0.99159291 100 71 16 84 0 0 92 8
200 -0.053383027 0.90935145 200 156 26 74 0 0 85 11
300 -0.040471335 0.97937429 300 240 21 79 0 0 87 8
400 -0.036188123 1.0837424 400 319 14 86 0 0 92 6
500 -0.057294925 1.0507526 500 407 10 90 0 0 98 8
600 -0.056009748 1.0669354 600 487 15 85 0 0 92 7
700 -0.069686562 0.99202496 700 567 14 86 0 0 96 10
800 -0.054695624 1.0592933 800 647 25 75 0 0 82 7
900 -0.058693653 0.97870458 900 728 27 73 0 0 83 10
1000 -0.062352957 1.0008923 1000 805 24 76 0 0 84 8
1100 -0.065011926 0.91691048 1100 886 22 78 0 0 87 9
1200 -0.080463686 0.98879304 1200 963 23 77 0 0 88 11
1300 -0.062146141 1.0566033 1300 1047 21 79 0 0 88 9
1400 -0.046980246 1.0847512 1400 1129 17 83 0 0 94 11
1500 -0.042935292 1.0075805 1500 1203 24 76 0 0 86 10
1600 -0.056075891 0.94173489 1600 1277 23 77 0 0 90 13
1700 -0.042279161 1.1126317 1700 1355 28 72 0 0 82 10
1800 -0.036842528 1.0255327 1800 1436 24 76 0 0 83 7
1900 -0.038816022 0.93883373 1900 1511 23 77 0 0 86 9
2000 -0.047008287 0.98904085 2000 1592 26 74 0 0 81 7
Loop time of 11.6365 on 1 procs for 2000 steps with 188 atoms
Performance: 74249.079 tau/day, 171.873 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24337 | 0.24337 | 0.24337 | 0.0 | 2.09
Kspace | 4.6009 | 4.6009 | 4.6009 | 0.0 | 39.54
Neigh | 0.023451 | 0.023451 | 0.023451 | 0.0 | 0.20
Comm | 0.027729 | 0.027729 | 0.027729 | 0.0 | 0.24
Output | 0.0007813 | 0.0007813 | 0.0007813 | 0.0 | 0.01
Modify | 6.7345 | 6.7345 | 6.7345 | 0.0 | 57.87
Other | | 0.005713 | | | 0.05
Nlocal: 188.000 ave 188 max 188 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 597.000 ave 597 max 597 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2196.00 ave 2196 max 2196 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2196
Ave neighs/atom = 11.680851
Neighbor list builds = 2059
Dangerous builds = 0
Total wall time: 0:00:11

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LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
# Charge regulation lammps for simple weak electrolyte
units lj
atom_style charge
neighbor 3.0 bin
read_data data.chreg-acid
Reading data file ...
orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
219 atoms
read_data CPU = 0.003 seconds
variable cut_long equal 12.5
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)
variable lunit_nm equal 0.72 # in the units of nm
velocity all create 1.0 8008 loop geom
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
pair_style lj/cut/coul/long 1.12246204830937 ${cut_long}
pair_style lj/cut/coul/long 1.12246204830937 12.5
pair_coeff * * 1.0 1.0
kspace_style ewald 1.0e-3
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 1.0 1.0 1.0 123
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 ${lunit_nm} 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 ${lunit_nm} 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 ${lunit_nm} 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 ${lunit_nm} 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 ${lunit_nm} 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 0.72 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 0.72 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 0.72 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 0.005
run 2000
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.14221027
estimated absolute RMS force accuracy = 0.0010128126
estimated relative force accuracy = 0.0010128126
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
0 atoms in group FixChargeRegulation:exclusion_group:chareg
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 = 15.5
ghost atom cutoff = 15.5
binsize = 7.75, bins = 7 7 7
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) = 11.89 | 11.89 | 11.89 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 -0.049662059 1 0 0 1 99 0 0 109 10
100 -0.06196414 1.0156327 100 72 15 85 0 0 93 8
200 -0.053901683 0.95128403 200 160 24 76 0 0 87 11
300 -0.043852423 0.98035058 300 246 22 78 0 0 85 7
400 -0.048370798 1.0909844 400 324 16 84 0 0 91 7
500 -0.042546472 1.026849 500 410 13 87 0 0 95 8
600 -0.06133022 0.97805065 600 494 14 86 0 0 93 7
700 -0.053815853 1.0641005 700 572 17 83 0 0 91 8
800 -0.059974814 1.0192348 800 650 23 77 0 0 83 6
900 -0.051808132 1.0773288 900 728 25 75 0 0 85 10
1000 -0.050390995 1.0236954 1000 804 28 72 0 0 81 9
1100 -0.069766444 1.030965 1100 890 25 75 0 0 85 10
1200 -0.074580231 1.0490058 1200 963 21 79 0 0 88 9
1300 -0.060169443 0.93456607 1300 1043 22 78 0 0 86 8
1400 -0.05120764 1.0374062 1400 1127 19 81 0 0 92 11
1500 -0.027644416 0.99804782 1500 1204 24 76 0 0 85 9
1600 -0.038599195 0.99015524 1600 1283 22 78 0 0 90 12
1700 -0.050222686 1.1444379 1700 1365 27 73 0 0 84 11
1800 -0.049338003 1.1188048 1800 1449 22 78 0 0 84 6
1900 -0.04533154 0.99894341 1900 1527 22 78 0 0 86 8
2000 -0.058837311 0.95302017 2000 1608 26 74 0 0 81 7
Loop time of 3.98119 on 4 procs for 2000 steps with 188 atoms
Performance: 217020.495 tau/day, 502.362 timesteps/s
96.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.050626 | 0.061127 | 0.071318 | 3.4 | 1.54
Kspace | 1.1987 | 1.2504 | 1.288 | 3.1 | 31.41
Neigh | 0.0056982 | 0.0063858 | 0.0069821 | 0.7 | 0.16
Comm | 0.068302 | 0.11638 | 0.17922 | 12.8 | 2.92
Output | 0.00055408 | 0.00092399 | 0.0020106 | 0.0 | 0.02
Modify | 2.5399 | 2.5406 | 2.5417 | 0.0 | 63.81
Other | | 0.005394 | | | 0.14
Nlocal: 47.0000 ave 55 max 42 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 328.250 ave 335 max 317 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 547.000 ave 659 max 466 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 2188
Ave neighs/atom = 11.638298
Neighbor list builds = 2057
Dangerous builds = 0
Total wall time: 0:00:04

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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

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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 2 by 2 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 = 0.016 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 = 1053 128
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) = 6.878 | 6.935 | 6.992 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 0.60223729 0.89547569 13 67 75 8 0 0
200 0.65253636 0.87662399 18 62 78 16 0 0
300 0.51550501 1.0542131 22 58 84 27 1 0
400 0.43566766 0.94557633 26 54 90 36 0 0
500 0.36269507 1.0386276 31 49 94 45 0 0
600 0.32430641 0.99903033 27 53 111 58 0 0
700 0.30255299 0.91225991 28 52 121 69 0 0
800 0.27189951 0.9747089 28 52 127 75 0 0
900 0.25495247 1.0747821 28 52 135 83 0 0
1000 0.25950416 0.95256449 32 48 134 86 0 0
1100 0.22561248 1.0102255 32 48 147 99 0 0
1200 0.1734754 0.99475154 33 47 157 110 0 0
1300 0.20081084 0.99873599 36 44 160 116 0 0
1400 0.14240417 0.99442152 36 44 164 121 1 0
1500 0.15314186 0.94559876 39 41 167 126 0 0
1600 0.13574107 1.0484195 43 37 164 127 0 0
1700 0.14477789 1.0105172 42 38 166 128 0 0
1800 0.13493107 1.0349667 41 39 171 132 0 0
1900 0.14849779 0.9994329 33 47 178 131 0 0
2000 0.14485171 0.99739608 34 46 183 137 0 0
Loop time of 3.18871 on 4 procs for 2000 steps with 400 atoms
Performance: 270955.695 tau/day, 627.212 timesteps/s
94.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.086456 | 0.11738 | 0.18562 | 11.8 | 3.68
Bond | 0.00099182 | 0.0018544 | 0.0030079 | 1.8 | 0.06
Kspace | 0.77406 | 0.79354 | 0.80895 | 1.5 | 24.89
Neigh | 0.017894 | 0.017948 | 0.018002 | 0.0 | 0.56
Comm | 0.029044 | 0.07885 | 0.11432 | 11.3 | 2.47
Output | 0.00054932 | 0.0009656 | 0.0021319 | 0.0 | 0.03
Modify | 2.1676 | 2.1706 | 2.1733 | 0.2 | 68.07
Other | | 0.007591 | | | 0.24
Nlocal: 100.000 ave 110 max 89 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 415.000 ave 418 max 411 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 1360.75 ave 1872 max 1018 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 5443
Ave neighs/atom = 13.607500
Ave special neighs/atom = 1.1700000
Neighbor list builds = 1492
Dangerous builds = 0
Total wall time: 0:00:03

181
examples/USER/misc/charge_regulation/log_polymer.lammps
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LAMMPS (24 Dec 2020)
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 = 0.000 seconds
read_data CPU = 0.004 seconds
PPPM initialization ...
using 12-bit tables for long-range coulomb (../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 KISS FFT
3d grid and FFT values/proc = 2197 512
0 atoms in group Fix_CR:exclusion_group:chareg1
0 atoms in group Fix_CR:exclusion_group:chareg2
0 atoms in group Fix_CR:exclusion_group:chareg3
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 = 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
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
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 0.49903297 1 0 80 80 0 0 0
100 0.63380666 0.87307225 8 72 77 6 1 0
200 0.5865464 1.0048645 16 64 81 16 0 1
300 0.55802913 1.0499142 19 61 91 29 0 1
400 0.44734087 1.0838048 24 56 98 41 0 1
500 0.47010775 1.005226 23 57 106 48 0 1
600 0.3452105 0.97814306 28 52 109 56 0 1
700 0.29208955 0.99766419 32 48 115 67 0 0
800 0.27821915 1.0091641 31 49 128 80 1 0
900 0.28943788 0.93619239 26 54 145 91 0 0
1000 0.22963142 1.0162138 27 53 150 97 0 0
1100 0.24238916 0.99146577 31 49 149 100 0 0
1200 0.17029095 1.0406453 38 42 144 102 0 0
1300 0.15830969 0.94661447 34 46 155 109 0 0
1400 0.16698712 1.0116563 35 45 159 114 0 0
1500 0.15432936 0.95600941 36 44 162 118 0 0
1600 0.16973501 0.98326602 31 49 171 122 0 0
1700 0.19725116 0.9915273 33 47 175 128 0 0
1800 0.15278999 1.0304873 29 51 193 142 0 0
1900 0.17418479 0.99490216 30 50 194 144 0 0
2000 0.14238391 0.9638301 32 48 189 141 0 0
2100 0.13054378 0.97164976 32 48 192 144 0 0
2200 0.092083069 1.0112059 40 40 191 151 0 0
2300 0.085175091 1.0070667 39 41 200 159 0 0
2400 0.083367076 0.9934796 35 45 208 163 0 0
2500 0.11494744 0.97650855 31 49 220 172 1 0
2600 0.10796032 0.97047046 34 46 221 175 0 0
2700 0.11080141 0.93570013 36 44 223 179 0 0
2800 0.096699277 0.97702627 35 45 223 178 0 0
2900 0.079403783 1.0870961 32 48 229 181 0 0
3000 0.08288836 1.0642515 35 45 231 186 0 0
3100 0.094000833 1.0241111 38 42 229 187 0 0
3200 0.10011052 1.043594 34 46 235 189 0 0
3300 0.096782103 0.99549134 34 46 234 188 0 0
3400 0.057703946 1.00292 34 46 236 190 0 0
3500 0.074345642 0.95064523 36 44 234 190 0 0
3600 0.085872341 0.9759514 35 45 238 192 0 1
3700 0.086427565 0.99843063 35 45 240 194 0 1
3800 0.076091357 0.98516844 32 48 252 203 0 1
3900 0.047187813 1.0063336 37 43 247 204 0 0
4000 0.068269223 1.0390369 35 45 248 203 0 0
4100 0.074209582 0.99912762 36 44 249 205 0 0
4200 0.087016078 1.050265 36 44 246 202 0 0
4300 0.081325479 1.0417103 35 45 245 200 0 0
4400 0.047345973 0.96517298 39 41 243 202 0 0
4500 0.041856955 0.94569673 38 42 245 203 0 0
4600 0.049588267 0.99046371 42 38 249 211 0 0
4700 0.043079897 1.0098538 43 37 245 208 0 0
4800 0.049122913 1.0229995 41 39 247 208 0 0
4900 0.059151797 1.0236679 36 44 249 205 0 0
5000 0.053806841 1.0308397 42 38 243 205 0 0
5100 0.053623833 1.0638841 39 41 246 205 0 0
5200 0.086215806 1.0027613 37 43 243 200 0 0
5300 0.031422797 1.0338154 38 42 245 203 0 0
5400 0.051341116 0.92205149 34 46 246 200 0 0
5500 0.039292708 0.97530704 32 48 251 203 0 0
5600 0.035215415 1.023123 33 47 246 199 0 0
5700 0.054553598 0.95833063 30 50 253 203 0 0
5800 0.035699456 1.0721613 37 43 248 205 0 0
5900 0.062426908 1.0612245 38 42 252 210 0 0
6000 0.056362902 1.0002968 36 44 248 204 0 0
6100 0.061550208 0.97270904 38 42 245 203 0 0
6200 0.051825485 0.98187623 36 44 253 209 0 0
6300 0.052137885 0.98906723 36 44 253 210 1 0
6400 0.068218075 1.0511584 36 44 256 212 0 0
6500 0.080167413 0.97270144 36 44 252 208 0 0
6600 0.052169204 1.0160108 41 39 249 210 0 0
6700 0.057313326 0.98033894 38 42 251 209 0 0
6800 0.073008094 0.96239565 35 45 256 211 0 0
6900 0.060159599 1.0063892 37 43 264 221 0 0
7000 0.061738744 1.0031443 39 41 259 218 0 0
7100 0.043263424 1.0425248 44 36 255 219 0 0
7200 0.052179167 0.99512151 39 41 261 220 0 0
7300 0.053258707 1.0171204 43 37 256 219 0 0
7400 0.026037532 0.93786837 45 35 259 224 0 0
7500 0.029731213 1.0172281 46 34 250 216 0 0
7600 0.023118288 0.95628439 42 38 262 224 0 0
7700 0.037021854 0.99991854 42 38 263 225 0 0
7800 0.050404736 1.0130826 40 40 260 220 0 0
7900 0.035658921 0.95772506 40 40 259 219 0 0
8000 0.034426806 1.0028052 40 40 254 214 0 0
8100 0.041427611 1.0347682 40 40 256 216 0 0
8200 0.05986843 0.9804614 38 42 262 220 0 0
8300 0.041419023 1.0613186 37 43 264 221 0 0
8400 0.065701758 1.0511531 40 40 256 216 0 0
8500 0.091954526 0.97190676 37 43 257 214 0 0
8600 0.056982532 1.017813 35 45 252 207 0 0
8700 0.075615111 1.0148527 29 51 263 212 0 0
8800 0.066070082 1.0259454 33 47 260 213 0 0
8900 0.055054194 1.0183535 37 43 247 204 0 0
9000 0.063070816 1.0266115 39 41 244 203 0 0
9100 0.10174156 0.99457684 34 46 246 200 0 0
9200 0.071667261 1.033159 33 47 249 202 0 0
9300 0.05520096 0.99821492 38 42 243 201 0 0
9400 0.050355422 0.99148522 37 43 243 200 0 0
9500 0.062314961 1.0042937 36 44 252 208 0 0
9600 0.061148899 1.0052132 37 43 254 211 0 0
9700 0.078695273 1.0175164 37 43 252 209 0 0
9800 0.067487202 1.0110138 35 45 258 213 0 0
9900 0.070340779 0.99640142 31 49 263 214 0 0
10000 0.037252172 0.99863894 32 48 259 211 0 0
Loop time of 23.0419 on 1 procs for 10000 steps with 550 atoms
Performance: 187484.206 tau/day, 433.991 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5444 | 2.5444 | 2.5444 | 0.0 | 11.04
Bond | 0.025075 | 0.025075 | 0.025075 | 0.0 | 0.11
Kspace | 4.7385 | 4.7385 | 4.7385 | 0.0 | 20.56
Neigh | 0.2058 | 0.2058 | 0.2058 | 0.0 | 0.89
Comm | 0.073087 | 0.073087 | 0.073087 | 0.0 | 0.32
Output | 0.003464 | 0.003464 | 0.003464 | 0.0 | 0.02
Modify | 15.417 | 15.417 | 15.417 | 0.0 | 66.91
Other | | 0.03479 | | | 0.15
Nlocal: 550.000 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1023.00 ave 1023 max 1023 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9644.00 ave 9644 max 9644 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9644
Ave neighs/atom = 17.534545
Ave special neighs/atom = 0.85090909
Neighbor list builds = 7576
Dangerous builds = 0
Total wall time: 0:00:23