126 lines
7.7 KiB
Groff
126 lines
7.7 KiB
Groff
LAMMPS (10 Feb 2021)
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using 1 OpenMP thread(s) per MPI task
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# Charge regulation lammps for simple weak electrolyte
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units lj
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atom_style charge
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neighbor 3.0 bin
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read_data data.chreg-acid
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Reading data file ...
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orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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219 atoms
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read_data CPU = 0.003 seconds
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variable cut_long equal 12.5
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variable nevery equal 100
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variable nmc equal 100
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variable pH equal 7.0
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variable pKa equal 6.0
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variable pIm equal 3.0
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variable pIp equal 3.0
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variable cut_lj equal 2^(1.0/6.0)
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variable lunit_nm equal 0.72 # in the units of nm
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velocity all create 1.0 8008 loop geom
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pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
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pair_style lj/cut/coul/long 1.12246204830937 ${cut_long}
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pair_style lj/cut/coul/long 1.12246204830937 12.5
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pair_coeff * * 1.0 1.0
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kspace_style ewald 1.0e-3
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pair_modify shift yes
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######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
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fix fnve all nve
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compute dtemp all temp
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compute_modify dtemp dynamic yes
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fix fT all langevin 1.0 1.0 1.0 123
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fix_modify fT temp dtemp
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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
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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
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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
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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
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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
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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
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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
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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
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thermo 100
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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]
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timestep 0.005
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run 2000
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Ewald initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
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G vector (1/distance) = 0.14221027
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estimated absolute RMS force accuracy = 0.0010128126
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estimated relative force accuracy = 0.0010128126
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KSpace vectors: actual max1d max3d = 257 5 665
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kxmax kymax kzmax = 5 5 5
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0 atoms in group FixChargeRegulation:exclusion_group:chareg
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WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 15.5
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ghost atom cutoff = 15.5
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binsize = 7.75, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 11.91 | 11.91 | 11.91 Mbytes
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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]
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0 -0.049662059 1 0 0 1 99 0 0 109 10
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100 -0.053672881 0.99159291 100 71 16 84 0 0 92 8
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200 -0.053383027 0.90935145 200 156 26 74 0 0 85 11
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300 -0.040471335 0.97937429 300 240 21 79 0 0 87 8
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400 -0.036188123 1.0837424 400 319 14 86 0 0 92 6
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500 -0.057294925 1.0507526 500 407 10 90 0 0 98 8
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600 -0.056009748 1.0669354 600 487 15 85 0 0 92 7
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700 -0.069686562 0.99202496 700 567 14 86 0 0 96 10
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800 -0.054695624 1.0592933 800 647 25 75 0 0 82 7
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900 -0.058693653 0.97870458 900 728 27 73 0 0 83 10
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1000 -0.062352957 1.0008923 1000 805 24 76 0 0 84 8
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1100 -0.065011926 0.91691048 1100 886 22 78 0 0 87 9
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1200 -0.080463686 0.98879304 1200 963 23 77 0 0 88 11
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1300 -0.062146141 1.0566033 1300 1047 21 79 0 0 88 9
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1400 -0.046980246 1.0847512 1400 1129 17 83 0 0 94 11
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1500 -0.042935292 1.0075805 1500 1203 24 76 0 0 86 10
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1600 -0.056075891 0.94173489 1600 1277 23 77 0 0 90 13
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1700 -0.042279161 1.1126317 1700 1355 28 72 0 0 82 10
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1800 -0.036842528 1.0255327 1800 1436 24 76 0 0 83 7
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1900 -0.038816022 0.93883373 1900 1511 23 77 0 0 86 9
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2000 -0.047008287 0.98904085 2000 1592 26 74 0 0 81 7
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Loop time of 11.6365 on 1 procs for 2000 steps with 188 atoms
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Performance: 74249.079 tau/day, 171.873 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.24337 | 0.24337 | 0.24337 | 0.0 | 2.09
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Kspace | 4.6009 | 4.6009 | 4.6009 | 0.0 | 39.54
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Neigh | 0.023451 | 0.023451 | 0.023451 | 0.0 | 0.20
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Comm | 0.027729 | 0.027729 | 0.027729 | 0.0 | 0.24
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Output | 0.0007813 | 0.0007813 | 0.0007813 | 0.0 | 0.01
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Modify | 6.7345 | 6.7345 | 6.7345 | 0.0 | 57.87
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Other | | 0.005713 | | | 0.05
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Nlocal: 188.000 ave 188 max 188 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 597.000 ave 597 max 597 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2196.00 ave 2196 max 2196 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2196
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Ave neighs/atom = 11.680851
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Neighbor list builds = 2059
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Dangerous builds = 0
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Total wall time: 0:00:11
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