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Applied edits/optimizations suggested by Axel. Further simplifified/fixed MC acceptance equations, few clarifications to documentation.

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tc387
2021-02-10 13:24:30 -06:00
parent 4421843604
commit 60113a6ddf
6 changed files with 193 additions and 168 deletions
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5
examples/USER/misc/charge_regulation/README
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@ -2,6 +2,7 @@ This directory has two input scripts that illustrates how to use fix charge_regu
The script `in_acid.chreg` sets up a simple weak acid electrolyte (pH=7,pKa=6,pI=3). Four different types of MC moves are implemented: acid protonation & de-protonation, and monovalent ion pair insertion and deletion. Note here we have grouped all free monovalent ions into a single type, a physically natural choice on the level of coarse-grained primitive electrolyte models, which increases the calculation performance but has no effects on thermodynamic observables. The variables such as pH, pKa, pI, and lb at the top of the input script can be adjusted to play with various simulation parameters. The cumulative MC attempted moves and cumulative number of accepted moves, as well as, current number of neutral and charged acid particles, neutral and charged base particles (in this example always 0), and the current number of free cations and anions in the system are printed in the `log_acid.lammps`.
The script `in_polymer.chreg` sets up a weak polyelectrolyte chain of N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 and salt pI=3. In this example, we choose to treat salt ions, protons, and hydroxyl ions separately, which results in 5 types of MC moves: acid [type 1] protonation & de-protonation (with protons [type 4] insertion & deletion), acid [type 1] protonation & de-protonation (with salt cation [type 2] insertion & deletion), water self-ionization (insertion and deletion of proton [type4] and hydroxyl ion [type 5] pair), insertion and deletion of monovalent salt pair [type 2 and type 3] , insertion and deletion
Of a proton [type4] and salt anion [type 3]. The current number of neutral and charged acid particles, the current number of free salt cations and anions, and the current number of protons and hydroxyl ions are printed in the `log_polymer.lammps`.
The script `in_polymer.chreg` sets up a weak polyelectrolyte chain of N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 and monovalent salt chemical potential pI=3. In this example, we choose to treat salt ions, protons, and hydroxyl ions separately, which results in 5 types of MC moves: acid [type 1] protonation & de-protonation (with protons [type 4] insertion & deletion), acid [type 1] protonation & de-protonation (with salt cation [type 2] insertion & deletion), water self-ionization (insertion and deletion of proton [type4] and hydroxyl ion [type 5] pair), insertion and deletion of monovalent salt pair [type 2 and type 3] , insertion and deletion
Of a proton [type4] and salt anion [type 3].
The current number of neutral and charged acid particles, the current number of free salt cations and anions, and the current number of protons and hydroxyl ions are printed in the `log_polymer.lammps`.

7
examples/USER/misc/charge_regulation/in_acid.chreg
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@ -24,7 +24,7 @@ pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
pair_coeff * * 1.0 1.0 ${cut_lj} # charges
kspace_style ewald 1.0e-3
dielectric 1.0
pair_modify shift no
pair_modify shift yes
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
fix fnve all nve
@ -33,8 +33,9 @@ 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 ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} 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]
log log_acid.lammps
timestep 0.005
run 10000
run 20000

12
examples/USER/misc/charge_regulation/in_polymer.chreg
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@ -14,7 +14,7 @@ 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 no
pair_modify shift yes
dielectric 1.0
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
@ -24,12 +24,14 @@ 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
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
fix chareg3 all charge_regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20
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]
log log_polymer.lammps
timestep 0.005
run 10000
run 20000