146 lines
8.5 KiB
Groff
146 lines
8.5 KiB
Groff
LAMMPS (10 Feb 2021)
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# Charge regulation lammps for simple weak electrolyte
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units real
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atom_style charge
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neighbor 10.0 bin
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read_data data.chreg-acid-real
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Reading data file ...
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orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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219 atoms
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read_data CPU = 0.002 seconds
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#real units
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variable sigma equal 7.2 # particle diameter 0.72 nm
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variable temperature equal 298 # temperature 298 K
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variable kb index 0.0019872067 # kB in Kcal/mol/K
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variable epsilon equal ${kb}*${temperature}
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variable epsilon equal 0.0019872067*${temperature}
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variable epsilon equal 0.0019872067*298
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variable tunit equal 2000 # time unit is 2000 fs
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variable timestep equal 0.005*${tunit}
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variable timestep equal 0.005*2000
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variable cut_long equal 12.5*${sigma}
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variable cut_long equal 12.5*7.2
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variable nevery equal 100
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variable nmc equal 100
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variable pH equal 7.0
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variable pKa equal 6.0
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variable pIm equal 3.0
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variable pIp equal 3.0
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variable cut_lj equal 2^(1.0/6.0)*${sigma}
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variable cut_lj equal 2^(1.0/6.0)*7.2
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velocity all create ${temperature} 8008 loop geom
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velocity all create 298 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 8.08172674782749 ${cut_long}
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pair_style lj/cut/coul/long 8.08172674782749 90
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pair_coeff * * ${epsilon} ${sigma}
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pair_coeff * * 0.5921875966 ${sigma}
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pair_coeff * * 0.5921875966 7.2
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kspace_style pppm 1.0e-3
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dielectric 78
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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 $(v_temperature) $(v_temperature) $(v_tunit) 123
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fix fT all langevin 298 $(v_temperature) $(v_tunit) 123
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fix fT all langevin 298 298 $(v_tunit) 123
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fix fT all langevin 298 298 2000 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 0.1 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 0.1 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 0.1 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 0.1 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 0.1 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 0.1 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 0.1 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 ${timestep}
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timestep 10
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run 2000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (../kspace.cpp:339)
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G vector (1/distance) = 0.019408615
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grid = 8 8 8
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stencil order = 5
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estimated absolute RMS force accuracy = 0.00012527706
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estimated relative force accuracy = 3.7726815e-07
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using double precision KISS FFT
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3d grid and FFT values/proc = 1053 128
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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 (../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 = 100
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ghost atom cutoff = 100
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binsize = 50, bins = 8 8 8
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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) = 3.624 | 3.624 | 3.624 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 -6.4798431 298 0 0 1 99 0 0 109 10
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100 -7.6327126 304.68909 100 73 15 85 0 0 94 9
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200 -6.1699041 272.19597 200 156 24 76 0 0 87 11
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300 -7.7876571 288.90801 300 240 20 80 0 0 87 7
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400 -6.3239918 274.65708 400 315 16 84 0 0 90 6
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500 -5.3978659 257.49208 500 398 15 85 0 0 93 8
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600 -5.6433949 322.52048 600 477 18 82 0 0 90 8
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700 -6.5351367 269.20244 700 558 18 82 0 0 91 9
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800 -6.2093085 315.21326 800 638 24 76 0 0 83 7
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900 -7.0795998 311.93228 900 719 28 72 0 0 82 10
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1000 -6.4668438 281.72674 1000 796 27 73 0 0 81 8
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1100 -6.2377994 318.48594 1100 875 25 75 0 0 84 9
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1200 -6.6305072 304.9091 1200 950 23 77 0 0 87 10
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1300 -5.9624552 286.05027 1300 1029 22 78 0 0 86 8
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1400 -4.4695814 261.81053 1400 1111 20 80 0 0 90 10
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1500 -5.6928652 293.72403 1500 1191 24 76 0 0 86 10
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1600 -6.8715413 290.47065 1600 1275 22 78 0 0 90 12
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1700 -6.5067505 292.74735 1700 1356 25 75 0 0 85 10
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1800 -5.3902702 307.79012 1800 1434 22 78 0 0 83 5
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1900 -5.1407153 318.48918 1900 1510 21 79 0 0 87 8
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2000 -4.9514719 281.87771 2000 1589 25 75 0 0 82 7
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Loop time of 0.562889 on 4 procs for 2000 steps with 189 atoms
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Performance: 3069.876 ns/day, 0.008 hours/ns, 3553.097 timesteps/s
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99.6% CPU use with 4 MPI tasks x no 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 | 0.008399 | 0.010383 | 0.011765 | 1.2 | 1.84
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Kspace | 0.17501 | 0.17543 | 0.1757 | 0.1 | 31.17
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Neigh | 0.001833 | 0.0021325 | 0.002293 | 0.4 | 0.38
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Comm | 0.023099 | 0.024255 | 0.026645 | 0.9 | 4.31
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Output | 0.000465 | 0.000546 | 0.000783 | 0.0 | 0.10
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Modify | 0.3464 | 0.34669 | 0.34698 | 0.0 | 61.59
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Other | | 0.003452 | | | 0.61
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Nlocal: 47.2500 ave 57 max 41 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Nghost: 285.750 ave 303 max 263 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Neighs: 403.500 ave 548 max 324 min
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Histogram: 2 0 0 1 0 0 0 0 0 1
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Total # of neighbors = 1614
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Ave neighs/atom = 8.5396825
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Neighbor list builds = 2081
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Dangerous builds = 0
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Total wall time: 0:00:00
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