ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #2585 from tc387/charge_regulation2

Browse Source 
Add fix charge/regulation to MC package
This commit is contained in:
Axel Kohlmeyer
2021-04-12 18:49:03 -04:00
committed by GitHub
parent 0ca9f2e8a0 82e1c4fb12
commit 9bc353e5bd
20 changed files with 3492 additions and 2 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
doc/src/Commands_fix.rst
View File

@ -46,6 +46,7 @@ OPT.
* :doc:`bond/react <fix_bond_react>` * :doc:`bond/react <fix_bond_react>`
* :doc:`bond/swap <fix_bond_swap>` * :doc:`bond/swap <fix_bond_swap>`
* :doc:`box/relax <fix_box_relax>` * :doc:`box/relax <fix_box_relax>`
* :doc:`charge/regulation <fix_charge_regulation>`
* :doc:`client/md <fix_client_md>` * :doc:`client/md <fix_client_md>`
* :doc:`cmap <fix_cmap>` * :doc:`cmap <fix_cmap>`
* :doc:`colvars <fix_colvars>` * :doc:`colvars <fix_colvars>`

6
doc/src/Packages_details.rst
View File

@ -586,7 +586,7 @@ MC package
Several fixes and a pair style that have Monte Carlo (MC) or MC-like Several fixes and a pair style that have Monte Carlo (MC) or MC-like
attributes. These include fixes for creating, breaking, and swapping attributes. These include fixes for creating, breaking, and swapping
bonds, for performing atomic swaps, and performing grand-canonical MC bonds, for performing atomic swaps, and performing grand-canonical MC
(GCMC) in conjunction with dynamics. (GCMC) or similar processes in conjunction with dynamics.
**Supporting info:** **Supporting info:**
@ -594,8 +594,12 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
* :doc:`fix atom/swap <fix_atom_swap>` * :doc:`fix atom/swap <fix_atom_swap>`
* :doc:`fix bond/break <fix_bond_break>` * :doc:`fix bond/break <fix_bond_break>`
* :doc:`fix bond/create <fix_bond_create>` * :doc:`fix bond/create <fix_bond_create>`
* :doc:`fix bond/create/angle <fix_bond_create>`
* :doc:`fix bond/swap <fix_bond_swap>` * :doc:`fix bond/swap <fix_bond_swap>`
* :doc:`fix charge/regulation <fix_charge_regulation>`
* :doc:`fix gcmc <fix_gcmc>` * :doc:`fix gcmc <fix_gcmc>`
* :doc:`fix tfmc <fix_tfmc>`
* :doc:`fix widom <fix_widom>`
* :doc:`pair_style dsmc <pair_dsmc>` * :doc:`pair_style dsmc <pair_dsmc>`
* https://lammps.sandia.gov/movies.html#gcmc * https://lammps.sandia.gov/movies.html#gcmc

1
doc/src/fix.rst
View File

@ -189,6 +189,7 @@ accelerated styles exist.
* :doc:`bond/react <fix_bond_react>` - apply topology changes to model reactions * :doc:`bond/react <fix_bond_react>` - apply topology changes to model reactions
* :doc:`bond/swap <fix_bond_swap>` - Monte Carlo bond swapping * :doc:`bond/swap <fix_bond_swap>` - Monte Carlo bond swapping
* :doc:`box/relax <fix_box_relax>` - relax box size during energy minimization * :doc:`box/relax <fix_box_relax>` - relax box size during energy minimization
* :doc:`charge/regulation <fix_charge_regulation>` - Monte Carlo sampling of charge regulation
* :doc:`client/md <fix_client_md>` - MD client for client/server simulations * :doc:`client/md <fix_client_md>` - MD client for client/server simulations
* :doc:`cmap <fix_cmap>` - enables CMAP cross-terms of the CHARMM force field * :doc:`cmap <fix_cmap>` - enables CMAP cross-terms of the CHARMM force field
* :doc:`colvars <fix_colvars>` - interface to the collective variables "Colvars" library * :doc:`colvars <fix_colvars>` - interface to the collective variables "Colvars" library

276
doc/src/fix_charge_regulation.rst Normal file
View File

@ -0,0 +1,276 @@
.. index:: fix charge/regulation
fix charge/regulation command
=============================
Syntax
""""""
.. parsed-literal::
fix ID group-ID charge/regulation cation_type anion_type keyword value(s)
* ID, group-ID are documented in fix command
* charge/regulation = style name of this fix command
* cation_type = atom type of free cations
* anion_type = atom type of free anions
* zero or more keyword/value pairs may be appended
.. parsed-literal::
keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
*pH* value = pH of the solution
*pKa* value = acid dissociation constant
*pKb* value = base dissociation constant
*pIp* value = chemical potential of free cations
*pIm* value = chemical potential of free anions
*pKs* value = solution self-dissociation constant
*acid_type* = atom type of acid groups
*base_type* = atom type of base groups
*lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers)
*temp* value = temperature
*tempfixid* value = fix ID of temperature thermostat
*nevery* value = invoke this fix every nevery steps
*nmc* value = number of charge regulation MC moves to attempt every nevery steps
*xrd* value = cutoff distance for acid/base reaction
*seed* value = random # seed (positive integer)
*tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0")
*group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups.
*onlysalt* values = flag charge_cation charge_anion.
flag = yes or no (yes: the fix performs only ion insertion/deletion, no: perform acid/base dissociation and ion insertion/deletion)
charge_cation, charge_anion = value of cation/anion charge, must be an integer (only specify if flag = yes)
*pmcmoves* values = pmcA pmcB pmcI - MC move fractions for acid ionization (pmcA), base ionization (pmcB) and free ion exchange (pmcI)
Examples
""""""""
.. code-block:: LAMMPS
fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT
fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0
Description
"""""""""""
This fix performs Monte Carlo (MC) sampling of charge regulation and
exchange of ions with a reservoir as discussed in :ref:`(Curk1) <Curk1>`
and :ref:`(Curk2) <Curk2>`. The implemented method is largely analogous
to the grand-reaction ensemble method in :ref:`(Landsgesell)
<Landsgesell>`. The implementation is parallelized, compatible with
existing LAMMPS functionalities, and applicable to any system utilizing
discrete, ionizable groups or surface sites.
Specifically, the fix implements the following three types of MC moves,
which discretely change the charge state of individual particles and
insert ions into the systems: :math:`\mathrm{A} \rightleftharpoons
\mathrm{A}^-+\mathrm{X}^+`, :math:`\mathrm{B} \rightleftharpoons
\mathrm{B}^++\mathrm{X}^-`, and :math:`\emptyset \rightleftharpoons
Z^-\mathrm{X}^{Z^+}+Z^+\mathrm{X}^{-Z^-}`. In the former two types of
reactions, Monte Carlo moves alter the charge value of specific atoms
(:math:`\mathrm{A}`, :math:`\mathrm{B}`) and simultaneously insert a
counterion to preserve the charge neutrality of the system, modeling the
dissociation/association process. The last type of reaction performs
grand canonical MC exchange of ion pairs with a (fictitious) reservoir.
In our implementation "acid" refers to particles that can attain charge
:math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`,
whereas the MC exchange of free ions allows any integer charge values of
:math:`{Z^+}` and :math:`{Z^-}`.
Here we provide several practical examples for modeling charge
regulation effects in solvated systems. An acid ionization reaction
(:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be
defined via a single line in the input file
.. code-block:: LAMMPS
fix acid_reaction all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0
where the fix attempts to charge :math:`\mathrm{A}` (discharge
:math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and
insert (delete) a proton (atom type 2). Besides, the fix implements
self-ionization reaction of water :math:`\emptyset \rightleftharpoons
\mathrm{H}^++\mathrm{OH}^-`. However, this approach is highly
inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of
both protons and hydroxyl ions is low, resulting in a relatively low
acceptance rate of MC moves.
A more efficient way is to allow salt ions to participate in ionization
reactions, which can be easily achieved via
.. code-block:: LAMMPS
fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
where particles of atom type 4 and 5 are the salt cations and anions,
both at chemical potential pI=2.0, see :ref:`(Curk1) <Curk1>` and
:ref:`(Landsgesell) <Landsgesell>` for more details.
Similarly, we could have simultaneously added a base ionization reaction
(:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
.. code-block:: LAMMPS
fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0
where the fix will attempt to charge :math:`\mathrm{B}` (discharge
:math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and
insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. If
neither the acid or the base type is specified, for example,
.. code-block:: LAMMPS
fix salt_reaction all charge/regulation 4 5 pIp 2.0 pIm 2.0
the fix simply inserts or deletes an ion pair of a free cation (atom
type 4) and a free anion (atom type 5) as done in a conventional
grand-canonical MC simulation.
The fix is compatible with LAMMPS sub-packages such as *molecule* or
*rigid*. That said, the acid and base particles can be part of larger
molecules or rigid bodies. Free ions that are inserted to or deleted
from the system must be defined as single particles (no bonded
interactions allowed) and cannot be part of larger molecules or rigid
bodies. If *molecule* package is used, all inserted ions have a molecule
ID equal to zero.
Note that LAMMPS implicitly assumes a constant number of particles
(degrees of freedom). Since using this fix alters the total number of
particles during the simulation, any thermostat used by LAMMPS, such as
NVT or Langevin, must use a dynamic calculation of system
temperature. This can be achieved by specifying a dynamic temperature
compute (e.g. dtemp) and using it with the desired thermostat, e.g. a
Langevin thermostat:
.. code-block:: LAMMPS
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
The chemical potential units (e.g. pH) are in the standard log10
representation assuming reference concentration :math:`\rho_0 =
\mathrm{mol}/\mathrm{l}`. Therefore, to perform the internal unit
conversion, the length (in nanometers) of the LAMMPS unit length must be
specified via *lunit_nm* (default is set to the Bjerrum length in water
at room temperature *lunit_nm* = 0.71nm). For example, in the dilute
ideal solution limit, the concentration of free ions will be
:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`.
The temperature used in MC acceptance probability is set by *temp*. This
temperature should be the same as the temperature set by the molecular
dynamics thermostat. For most purposes, it is probably best to use
*tempfixid* keyword which dynamically sets the temperature equal to the
chosen MD thermostat temperature, in the example above we assumed the
thermostat fix-ID is *fT*. The inserted particles attain a random
velocity corresponding to the specified temperature. Using *tempfixid*
overrides any fixed temperature set by *temp*.
The *xrd* keyword can be used to restrict the inserted/deleted
counterions to a specific radial distance from an acid or base particle
that is currently participating in a reaction. This can be used to
simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* /
2, where *L* is the smallest box dimension, the radial restriction is
automatically turned off and free ion can be inserted or deleted
anywhere in the simulation box.
If the *tag yes* is used, every inserted atom gets a unique tag ID,
otherwise, the tag of every inserted atom is set to 0. *tag yes* might
cause an integer overflow in very long simulations since the tags are
unique to every particle and thus increase with every successful
particle insertion.
The *pmcmoves* keyword sets the relative probability of attempting the
three types of MC moves (reactions): acid charging, base charging, and
ion pair exchange. The fix only attempts to perform particle charging
MC moves if *acid_type* or *base_type* is defined. Otherwise fix only
performs free ion insertion/deletion. For example, if *acid_type* is not
defined, *pmcA* is automatically set to 0. The vector *pmcmoves* is
automatically normalized, for example, if set to *pmcmoves* 0 0.33 0.33,
the vector would be normalized to [0,0.5,0.5].
The *only_salt* option can be used to perform multivalent
grand-canonical ion-exchange moves. If *only_salt yes* is used, no
charge exchange is performed, only ion insertion/deletion (*pmcmoves* is
set to [0,0,1]), but ions can be multivalent. In the example above, an
MC move would consist of three ion insertion/deletion to preserve the
charge neutrality of the system.
The *group* keyword can be used to add inserted particles to a specific
group-ID. All inserted particles are automatically added to group *all*.
Output
""""""
This fix computes a global vector of length 8, which can be accessed by
various output commands. The vector values are the following global
quantities:
* 1 = cumulative MC attempts
* 2 = cumulative MC successes
* 3 = current # of neutral acid atoms
* 4 = current # of -1 charged acid atoms
* 5 = current # of neutral base atoms
* 6 = current # of +1 charged base atoms
* 7 = current # of free cations
* 8 = current # of free anions
Restrictions
""""""""""""
This fix is part of the MC package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
The :doc:`atom_style <atom_style>`, used must contain the charge
property, for example, the style could be *charge* or *full*. Only
usable for 3D simulations. Atoms specified as free ions cannot be part
of rigid bodies or molecules and cannot have bonding interactions. The
scheme is limited to integer charges, any atoms with non-integer charges
will not be considered by the fix.
All interaction potentials used must be continuous, otherwise the MD
integration and the particle exchange MC moves do not correspond to the
same equilibrium ensemble. For example, if an lj/cut pair style is used,
the LJ potential must be shifted so that it vanishes at the cutoff. This
can be easily achieved using the :doc:`pair_modify <pair_modify>`
command, i.e., by using: *pair_modify shift yes*.
.. note::
Region restrictions are not yet implemented.
Related commands
""""""""""""""""
:doc:`fix gcmc <fix_gcmc>`,
:doc:`fix atom/swap <fix_atom_swap>`
Default
"""""""
pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0;
acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery =
100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
[1/3, 1/3, 1/3], group-ID = all
----------
.. _Curk1:
**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Coarse-grained simulation of charge regulation using LAMMPS", preprint (2021).
.. _Curk2:
**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL (2021)
.. _Landsgesell:
**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007-3020 (2020).

28
doc/utils/sphinx-config/false_positives.txt
View File

@ -261,6 +261,7 @@ bitmask
bitrate bitrate
bitrates bitrates
Bitzek Bitzek
Bjerrum
Blaise Blaise
blanchedalmond blanchedalmond
blocksize blocksize
@ -504,6 +505,8 @@ coulgauss
coulombic coulombic
Coulombic Coulombic
Coulombics Coulombics
counterion
counterions
Courant Courant
covalent covalent
covalently covalently
@ -732,6 +735,7 @@ DRUDE
dsf dsf
dsmc dsmc
dt dt
dtemp
dtgrow dtgrow
dtheta dtheta
dtshrink dtshrink
@ -880,6 +884,7 @@ equilibrates
equilibrating equilibrating
equilibration equilibration
Equilibria Equilibria
equilibria
equilization equilization
equipartitioning equipartitioning
Ercolessi Ercolessi
@ -1216,6 +1221,7 @@ hbnewflag
hbond hbond
hcp hcp
heatconduction heatconduction
Hebbeker
Hebenstreit Hebenstreit
Hecht Hecht
Heenen Heenen
@ -1283,6 +1289,7 @@ hy
hydrophobicity hydrophobicity
hydrostatic hydrostatic
hydrostatically hydrostatically
hydroxyl
Hynninen Hynninen
Hyoungki Hyoungki
hyperdynamics hyperdynamics
@ -1373,6 +1380,7 @@ ints
inv inv
invariants invariants
inversed inversed
ionizable
ionocovalent ionocovalent
iostreams iostreams
iparam iparam
@ -1552,6 +1560,7 @@ Koning
Kooser Kooser
Korn Korn
Koskinen Koskinen
Kosovan
Koster Koster
Kosztin Kosztin
Kp Kp
@ -1598,6 +1607,7 @@ Lamoureux
Lanczos Lanczos
Lande Lande
Landron Landron
Landsgesell
langevin langevin
Langevin Langevin
Langston Langston
@ -1735,10 +1745,13 @@ lpsapi
lrt lrt
lsfftw lsfftw
ltbbmalloc ltbbmalloc
Lua
lubricateU lubricateU
lucy lucy
Lua
Luding Luding
Luijten
lunit
Lunkad
Lussetti Lussetti
Lustig Lustig
lval lval
@ -2029,6 +2042,7 @@ multiscale
multisectioning multisectioning
multithreading multithreading
Multithreading Multithreading
multivalent
Mundy Mundy
Murdick Murdick
Murtola Murtola
@ -2074,6 +2088,7 @@ Nanoletters
nanomechanics nanomechanics
nanometer nanometer
nanometers nanometers
nanoparticle
nanoparticles nanoparticles
Nanotube Nanotube
nanotube nanotube
@ -2183,6 +2198,7 @@ nm
Nm Nm
Nmax Nmax
nmax nmax
nmc
Nmin Nmin
nmin nmin
Nmols Nmols
@ -2317,6 +2333,7 @@ OMP
oneAPI oneAPI
onelevel onelevel
oneway oneway
onlysalt
onn onn
ons ons
OO OO
@ -2401,6 +2418,8 @@ pbc
pc pc
pchain pchain
Pchain Pchain
pcmoves
pmcmoves
Pdamp Pdamp
pdb pdb
pdf pdf
@ -2445,6 +2464,7 @@ phosphide
Phs Phs
Physica Physica
physik physik
pI
Piaggi Piaggi
picocoulomb picocoulomb
picocoulombs picocoulombs
@ -2456,7 +2476,9 @@ pid
piecewise piecewise
Pieniazek Pieniazek
Pieter Pieter
pIm
pimd pimd
pIp
Piola Piola
Pisarev Pisarev
Pishevar Pishevar
@ -2471,6 +2493,9 @@ ploop
PloS PloS
plt plt
plumedfile plumedfile
pKa
pKb
pKs
pmb pmb
Pmolrotate Pmolrotate
Pmoltrans Pmoltrans
@ -2799,6 +2824,7 @@ rst
rstyle rstyle
Rubensson Rubensson
Rubia Rubia
Rud
Rudd Rudd
Rudra Rudra
Rudranarayan Rudranarayan

36
examples/USER/misc/charge_regulation/README Normal file
View File

@ -0,0 +1,36 @@
This directory has two input scripts that illustrates how to use fix
charge_regulation in LAMMPS to perform coarse-grained molecular dynamics
(MD) simulations with incorporation of charge regulation effects. The
charge regulation is implemented via Monte Carlo (MC) sampling following
the reaction ensemble MC approach, producing a MC/MD hybrid tool for
modeling charge regulation in solvated systems.
The script `in.chreg-acid` 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
output.
The script `in.chreg-polymer` sets up a weak poly-electrolyte 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 output.

235
examples/USER/misc/charge_regulation/data.chreg-acid Normal file
View File

@ -0,0 +1,235 @@
LAMMPS data file generated by get_input.py
219 atoms
3 atom types
-2.5000000000000000e+01 2.5000000000000000e+01 xlo xhi
-2.5000000000000000e+01 2.5000000000000000e+01 ylo yhi
-2.5000000000000000e+01 2.5000000000000000e+01 zlo zhi
Masses
1 1
2 1
3 1
Atoms
1 1 0 2.5983275747497636 -8.368052973860795 20.001288664343484
2 1 -1 -18.182868728594865 -8.079792367885453 8.253737231981816
3 1 -1 -17.437350808966414 8.120411567445771 10.747650340639332
4 1 -1 6.502476583291578 -23.497326620756837 19.948223080086798
5 1 -1 -22.528179279677296 -18.783433570718127 -17.964657736688018
6 1 -1 -9.713496019164342 18.97235576760402 -19.495620818582825
7 1 -1 -12.831976006720659 0.12265736526942561 -21.679396938423718
8 1 -1 20.909063679212295 -2.16535062758771 0.46197866620165584
9 1 -1 23.86211981166997 24.024928465132284 10.534067202515907
10 1 -1 -0.5289298325031275 23.820222457999776 -2.657199543669442
11 1 -1 9.57021229491361 11.973871502198485 3.4206509716759186
12 1 -1 -10.201559985782705 7.557482594092384 12.07004973873643
13 1 -1 4.898458045226889 2.0169997859717945 -20.765285372762087
14 1 -1 -24.086606883730077 4.424991619615298 -4.204294764756856
15 1 -1 3.6837161829600795 -4.763233144818308 -12.75873457519811
16 1 -1 -12.217842496816345 -17.720229208905618 -13.556354139556914
17 1 -1 -21.456229140133704 -7.423996317612119 -6.94398044071275
18 1 -1 13.697298849253912 8.503639732052164 8.085487457359058
19 1 -1 -5.764222710061347 11.49890485049034 -5.1113880296575935
20 1 -1 3.9944161041544426 16.928204188257893 -14.875635895409372
21 1 -1 4.509525276444776 16.63590711792657 -22.21846494992397
22 1 -1 22.115374932704306 -18.97293932558108 -23.982486000144267
23 1 -1 14.169061011408473 -16.69837647199978 13.779039228068108
24 1 -1 17.186846147657228 8.827459489898189 23.055435051390333
25 1 -1 2.9822901981431045 -16.83687718528342 -21.278623587083484
26 1 -1 16.657554689423897 -1.6217275605348647 -11.315859420404218
27 1 -1 19.215533149393543 -15.512634977936068 7.2701088767584565
28 1 -1 -8.886744157248422 -24.09644410100167 4.013016013803799
29 1 -1 20.99918340066754 4.4716257356730225 0.3847245765737597
30 1 -1 1.3442294253060716 5.601341425720583 -14.918594492786674
31 1 -1 -6.962977050326831 20.470183675946515 -16.37885865567279
32 1 -1 -9.98531733187143 9.52233798117566 -24.979630708193724
33 1 -1 -17.327989778292306 5.761352103841766 5.720220488689204
34 1 -1 5.168359673466362 -23.698812306679418 2.6199762372169744
35 1 -1 18.978042448492154 6.41188742965139 6.31975357155018
36 1 -1 -16.38534911663758 -14.8262205163943 4.125239045887575
37 1 -1 7.974455406459249 -18.88332583451115 11.00721254217055
38 1 -1 13.779816416416402 1.8581999350851426 9.104219696003227
39 1 -1 -23.90949397031401 -3.346877828308571 -10.228782973473443
40 1 -1 21.61647622174447 8.443955423089903 -19.12066464239769
41 1 -1 -8.823979405515548 14.461154001848172 16.061704411241706
42 1 -1 -2.4406878944912513 12.5535360118296 20.606764200087852
43 1 -1 -18.459404356124697 15.260951448001258 21.187332685021346
44 1 -1 2.2354003384439878 -23.350013178190736 11.369307324043625
45 1 -1 15.595889705552018 -6.6075680254604805 5.434256329408505
46 1 -1 -17.528243443870238 4.109747707896265 -1.4167331089310942
47 1 -1 2.161977144405782 -16.511059804921263 -12.186191310598671
48 1 -1 -8.685671837367341 -7.0743613044263185 -1.1561844713769105
49 1 -1 15.62258718398045 -6.559293763708908 20.556775995508488
50 1 -1 -6.965207014475155 -14.348784897390543 -14.421447863144754
51 1 -1 -12.099361509567913 -24.62785640990423 -15.839126670614329
52 1 -1 6.673854222058246 7.83575773885061 -9.714128155619994
53 1 -1 -17.413453800948826 12.386754276446203 -16.882300786608994
54 1 -1 21.8966589175091 12.485943283688762 -14.553421680298634
55 1 -1 -8.37629917390651 -24.783875012947064 7.454467809536389
56 1 -1 14.081149297694104 -21.719204113108943 -17.447225564400064
57 1 -1 4.681992702049627 1.9719544892622558 -7.823736613205725
58 1 -1 4.353171917533494 15.86928389762705 24.669680272563014
59 1 -1 23.31502072066573 -4.685724298328946 2.459643890128799
60 1 -1 7.0470920520598455 23.016693234922386 -13.139471333592677
61 1 -1 11.725555941181668 -15.809323171320772 -1.6292879532275037
62 1 -1 -20.36388898925061 -12.084932320023162 -22.816700826388757
63 1 -1 -2.492146614764735 -0.7314052253623018 -15.89959178250266
64 1 -1 -22.45303825831233 -11.27996814407809 -9.553770912146142
65 1 -1 24.76771926037101 20.128947543233757 10.528974830883733
66 1 -1 11.326213670190818 -11.624187194192492 -9.687726413467862
67 1 -1 -5.712764220166093 15.778887306376163 -0.9263244618113831
68 1 -1 -15.073201136996362 -12.372916148178115 -5.461704510273556
69 1 -1 -5.82976670348781 -4.57812040989473 9.0443548565365
70 1 -1 -5.429195387856279 1.4542054472230177 -7.397291151203568
71 1 -1 -23.385555726942343 -11.924588975396505 3.8215294321466153
72 1 -1 -1.0694104826815725 2.999945633116507 3.67092922106918
73 1 -1 12.134312161994352 1.9747455475585376 -14.895893366599623
74 1 -1 21.30950120583112 18.97294626436546 -17.520867878211376
75 1 -1 -24.356703356157063 3.594879254976714 17.172993705171677
76 1 -1 12.634233603338409 24.373499564220822 4.561976273909789
77 1 -1 -10.740243207970495 19.345205140729554 -3.3368424800818097
78 1 -1 -3.027848793907552 10.604939843027267 7.493012332728249
79 1 -1 5.000539296336658 11.770088203844622 17.227492055930185
80 1 -1 1.1585200269400353 -24.45822157176123 -12.515688997756257
81 1 -1 1.9163088584430596 -14.064330279670672 11.302445490552905
82 1 -1 -20.857041355570576 21.292791787236673 17.397470691573346
83 1 -1 -24.50473305235651 -12.741459355708756 -1.9325218065560357
84 1 -1 2.658628688373309 -1.1131226252194608 7.491603553398086
85 1 -1 -18.515435126408363 24.20642384141299 14.466889392835121
86 1 -1 19.63928177206153 9.942655640416291 8.691463646789934
87 1 -1 -7.69626451160762 11.762517043363786 -7.457263991495665
88 1 -1 1.051431093064835 -11.460307039827766 16.90304637479744
89 1 -1 0.9157815447227939 23.656751182559688 -6.538587603918376
90 1 -1 23.330169435555234 -7.293893221439802 -10.739388379883973
91 1 -1 1.3454906653067376 0.3584300740797559 8.837879234629618
92 1 -1 -21.93056639286312 -10.890279576013356 -10.412914392053596
93 1 -1 21.9136101677979 -10.780221720642636 11.543925933359859
94 1 -1 1.213289938136601 -7.171863230861625 20.734527885288102
95 1 -1 23.102370131877777 21.949933206350458 0.29281565885028016
96 1 -1 -18.917780884063298 -0.03244735062602544 23.633906995676227
97 1 -1 7.583004866601307 10.74178675512821 -4.857297835527785
98 1 -1 -7.4910066746799835 -14.168364618485734 -6.426540836249767
99 1 -1 -20.672200987670426 -8.746789722660697 11.011389790610103
100 1 -1 -18.662115132221917 -21.356740361991612 -8.735991534410413
101 2 1 11.900973676882046 6.591531431964558 19.018193594877637
102 2 1 -23.433591822114983 -18.956429005519567 4.8373984358422994
103 2 1 -11.825475204099472 -3.8206287568445134 3.1167558949026173
104 2 1 -17.49780467176259 -23.115560141825554 9.614132296727426
105 2 1 10.88916113281772 4.512200980010334 18.685489050240854
106 2 1 -22.04662313800728 23.973268925992897 -23.417792740205652
107 2 1 -13.57041123540546 17.3687874050987 21.186270978357783
108 2 1 6.586851196789095 16.27860887432974 -3.638909639278946
109 2 1 8.191448685630277 6.828880619305412 -6.347576950950089
110 2 1 -15.723292856220288 -20.484673256634117 -15.14713811293425
111 2 1 18.58081219522701 19.060706710849452 -10.295676869062909
112 2 1 -21.09194001526127 -7.739334786748358 5.417635948058724
113 2 1 -14.10404878784055 -15.769737592448523 -18.881834262561505
114 2 1 -14.644589058195612 8.84169065013063 8.611654925486256
115 2 1 -11.719050253933538 -4.9700119000832 -0.9846728956163453
116 2 1 19.498247505274143 -10.418045613133986 -22.12098182226518
117 2 1 21.857683401772697 20.157098661061575 -13.652393197742995
118 2 1 -17.623414455798407 21.873813778550875 -6.533965802006303
119 2 1 7.231785003326529 -13.925962842972222 5.360080190636602
120 2 1 -7.509430039873415 19.13541714591672 -16.23545960168472
121 2 1 -4.048249209544995 13.126195473202351 -7.156541250053138
122 2 1 -20.26837137264583 21.46366988603839 15.603080527043964
123 2 1 -4.478253524569759 -3.1812369811955783 -18.52918159641348
124 2 1 21.541019047040052 13.514999235394065 -1.8086547561089752
125 2 1 -15.223319907923727 -5.958117989814905 -7.194967640819577
126 2 1 -20.87181173003304 -7.66780336209651 20.518235718821714
127 2 1 -3.7444846073700297 21.014628245718292 7.197818215477007
128 2 1 -5.904222844268787 7.656315546673127 -1.3911802017487425
129 2 1 -21.49072414090769 -23.123923448235523 10.49453669763092
130 2 1 24.90628307456096 7.081046671281136 -14.422530828641655
131 2 1 -12.173002002514222 -23.250366655717176 -5.145802772598103
132 2 1 -19.68809858318764 4.476541650697328 6.249229323733747
133 2 1 16.85550827580734 -0.8462194407221624 18.011901711631936
134 2 1 17.289399533444858 -11.99379336569853 11.875868193611936
135 2 1 19.532020913911126 -23.053375288330326 -4.9162076250112605
136 2 1 -12.432304028989998 5.029488375070969 7.535325299264009
137 2 1 14.934807008644 8.086694342170496 19.68691014849572
138 2 1 -7.088283921093918 -23.094109864922018 16.57088328184242
139 2 1 14.77413976080318 21.343550134324772 13.996489344579572
140 2 1 -14.606423208703657 -6.928316926567433 -22.717483260149475
141 2 1 -17.139771555632173 14.533410346451518 -21.83064865887975
142 2 1 4.261830086466784 15.518968841247663 -17.791505649414617
143 2 1 -9.814793042774223 -5.120956154726329 14.054454130549104
144 2 1 8.313311590434793 3.9666876022475606 -20.677101093823236
145 2 1 10.603190079756637 -2.62347089527481 1.6661989541795634
146 2 1 -17.763718339721695 1.2541370478041287 -21.55649971308305
147 2 1 -8.538066365356812 14.81814356892842 -4.478673557614034
148 2 1 -5.809558827384787 14.611789154829552 13.287687188309562
149 2 1 8.986830839040898 -17.43898584267833 -18.08640526127862
150 2 1 -13.315275244526854 8.890431200255954 -8.708179477452443
151 2 1 -0.5407152591412618 -23.67970550599055 -24.1586910560046
152 2 1 -19.79961109336906 -16.10906604558887 -5.879899717095562
153 2 1 -23.626316306846658 9.337407355717588 -9.640842288307239
154 2 1 -18.847256196659333 -16.303517291166603 -10.786416046984721
155 2 1 13.567770091716845 -24.4927974402177 8.896906985984664
156 2 1 13.652894892068794 -24.87567116574863 21.89026113439551
157 2 1 -8.575912713332162 9.92386172372207 5.029537530028822
158 2 1 20.69339436974964 1.129252448454178 0.3584458063532807
159 2 1 -0.9971941518705947 18.317397852358788 6.795424830570379
160 2 1 23.155704681402298 15.458725773368961 17.01599672991628
161 2 1 22.278634187244123 14.642946508468171 20.543957651530896
162 2 1 9.771629496835963 -21.696904301438853 -5.259678202922196
163 2 1 5.253009955872763 17.911287158418148 15.769047957152992
164 2 1 -20.759038961257414 5.59089552770853 -12.383953925685166
165 2 1 3.2163819108147145 -4.948608591009169 -17.85036103684716
166 2 1 20.637631925250837 9.109955226257064 6.177181979863878
167 2 1 5.306344093540837 12.647347581939556 23.229957406774105
168 2 1 -24.15187998806597 17.263903348029615 -17.141028077545826
169 2 1 -15.705280442832997 -15.655358704303895 -10.488762557871972
170 2 1 -6.601131108664461 -22.50322976595015 -5.672942609306119
171 2 1 22.869179482568555 13.369592422303498 -9.378437532422556
172 2 1 -23.151055417980903 -3.928919101213168 -11.117061489640207
173 2 1 1.3592343286386246 -18.552063924235036 -15.346172149331993
174 2 1 10.23567488314778 -18.14207926130103 -1.6884247085891886
175 2 1 12.595888032974493 -1.7416169207452157 -21.786811832485718
176 2 1 -0.14792438162408672 17.11748549051584 1.2788726677139053
177 2 1 24.349235298880274 -8.664350854740949 12.4309854455257
178 2 1 -18.827147816604253 -18.80258748867273 -1.6980553939283212
179 2 1 -9.048793002383698 -1.788614428205263 -11.841289777017172
180 2 1 -22.49667217853208 -22.112076711777533 10.01393503943838
181 2 1 -16.183333848138453 1.3098533508906556 0.8096413611556166
182 2 1 -4.007575369376703 -24.447854073342157 -19.683971619997376
183 2 1 8.79123015290173 -15.890906503248287 -23.45721570121758
184 2 1 -8.557898021171628 -21.985380426316674 22.626382729361595
185 2 1 7.143974673263372 16.57516065778192 0.5907315164854055
186 2 1 7.05280226857041 6.658154377550723 17.993436860997946
187 2 1 20.98391844656716 -3.7711929542825544 -22.37222924252256
188 2 1 -8.856382807041598 -16.421301042649826 -7.682473719905396
189 2 1 -14.381919492441797 -7.667674808763277 -10.178028203828621
190 2 1 -22.93472549116592 10.072854607637751 3.756868463885592
191 2 1 9.458987867260412 17.23200182595278 -0.03503381482496337
192 2 1 11.013603635791974 19.842184408029837 -5.83598462187852
193 2 1 23.28897987479008 2.835578651649044 -20.512845011389647
194 2 1 -18.86161127148128 8.956542530565656 14.193388541103026
195 2 1 13.688477473034126 -15.973205475346514 10.952445409682397
196 2 1 2.1058159557459497 2.740725960214597 -23.72037436968614
197 2 1 20.982351847235442 7.072739454450108 -24.07322254392252
198 2 1 5.962360707177609 -19.424513569281604 22.469955103109243
199 2 1 -17.13607356062674 20.038457022813326 12.94227215395123
200 2 1 11.592617137491743 22.283887092702138 2.339699650677858
201 2 1 -1.3864952037065237 19.199632510575505 -7.684210221911414
202 2 1 -22.44476570586083 -19.66385674506424 -8.981660607669522
203 2 1 0.36547911522815824 -7.628556098996082 16.326944822668068
204 2 1 -9.766164330974753 24.38435844399602 -14.352553497163
205 2 1 -0.6310792726759544 -5.625399375968325 13.665993163571486
206 2 1 2.6795300975636103 -0.37097710463575595 15.575183407667495
207 2 1 10.68508361399715 24.638181487800373 -17.538711281692827
208 2 1 18.30809729940504 18.39121662193474 18.285926328751984
209 2 1 -11.52561870836783 -11.871004571782223 12.890674390475048
210 3 -1 16.038097437687007 -0.8308290507120688 9.140710202344948
211 3 -1 -12.071581865552927 23.77532123232212 -6.250109721970887
212 3 -1 24.179073767023887 19.6390206210449 22.20321951706368
213 3 -1 22.899159789805424 8.918385700451317 -1.1269016129923664
214 3 -1 -10.48576153865241 5.691510884812594 21.955276995406933
215 3 -1 6.272776670877239 10.035821052072265 22.22030412319301
216 3 -1 14.689947575936934 -7.785907120217196 0.5033983092114553
217 3 -1 23.173937996535116 -21.041572031861037 -21.057283440516468
218 3 -1 -6.015120142466472 6.3962924962024985 21.58241945230285
219 3 -1 -0.77667042466472 0.3962848125024985 1.582473830285

235
examples/USER/misc/charge_regulation/data.chreg-acid-real Normal file
View File

@ -0,0 +1,235 @@
LAMMPS data file generated by get_input.py
219 atoms
3 atom types
-180 180 xlo xhi
-180 180 ylo yhi
-180 180 zlo zhi
Masses
1 20
2 20
3 20
Atoms
1 1 0 18.70795854 -60.24998141 144.0092784
2 1 -1 -130.9166548 -58.17450505 59.42690807
3 1 -1 -125.5489258 58.46696329 77.38308245
4 1 -1 46.8178314 -169.1807517 143.6272062
5 1 -1 -162.2028908 -135.2407217 -129.3455357
6 1 -1 -69.93717134 136.6009615 -140.3684699
7 1 -1 -92.39022725 0.88313303 -156.091658
8 1 -1 150.5452585 -15.59052452 3.326246397
9 1 -1 171.8072626 172.9794849 75.84528386
10 1 -1 -3.808294794 171.5056017 -19.13183671
11 1 -1 68.90552852 86.21187482 24.628687
12 1 -1 -73.4512319 54.41387468 86.90435812
13 1 -1 35.26889793 14.52239846 -149.5100547
14 1 -1 -173.4235696 31.85993966 -30.27092231
15 1 -1 26.52275652 -34.29527864 -91.86288894
16 1 -1 -87.96846598 -127.5856503 -97.6057498
17 1 -1 -154.4848498 -53.45277349 -49.99665917
18 1 -1 98.62055171 61.22620607 58.21550969
19 1 -1 -41.50240351 82.79211492 -36.80199381
20 1 -1 28.75979595 121.8830702 -107.1045784
21 1 -1 32.46858199 119.7785312 -159.9729476
22 1 -1 159.2306995 -136.6051631 -172.6738992
23 1 -1 102.0172393 -120.2283106 99.20908244
24 1 -1 123.7452923 63.55770833 165.9991324
25 1 -1 21.47248943 -121.2255157 -153.2060898
26 1 -1 119.9343938 -11.67643844 -81.47418783
27 1 -1 138.3518387 -111.6909718 52.34478391
28 1 -1 -63.98455793 -173.4943975 28.8937153
29 1 -1 151.1941205 32.1957053 2.770016951
30 1 -1 9.678451862 40.32965827 -107.4138803
31 1 -1 -50.13343476 147.3853225 -117.9277823
32 1 -1 -71.89428479 68.56083346 -179.8533411
33 1 -1 -124.7615264 41.48173515 41.18558752
34 1 -1 37.21218965 -170.6314486 18.86382891
35 1 -1 136.6419056 46.16558949 45.50222572
36 1 -1 -117.9745136 -106.7487877 29.70172113
37 1 -1 57.41607893 -135.959946 79.2519303
38 1 -1 99.2146782 13.37903953 65.55038181
39 1 -1 -172.1483566 -24.09752036 -73.64723741
40 1 -1 155.6386288 60.79647905 -137.6687854
41 1 -1 -63.53265172 104.1203088 115.6442718
42 1 -1 -17.57295284 90.38545929 148.3687022
43 1 -1 -132.9077114 109.8788504 152.5487953
44 1 -1 16.09488244 -168.1200949 81.85901273
45 1 -1 112.2904059 -47.57448978 39.12664557
46 1 -1 -126.2033528 29.5901835 -10.20047838
47 1 -1 15.56623544 -118.8796306 -87.74057744
48 1 -1 -62.53683723 -50.93540139 -8.324528194
49 1 -1 112.4826277 -47.2269151 148.0087872
50 1 -1 -50.1494905 -103.3112513 -103.8344246
51 1 -1 -87.11540287 -177.3205662 -114.041712
52 1 -1 48.0517504 56.41745572 -69.94172272
53 1 -1 -125.3768674 89.18463079 -121.5525657
54 1 -1 157.6559442 89.89879164 -104.7846361
55 1 -1 -60.30935405 -178.4439001 53.67216823
56 1 -1 101.3842749 -156.3782696 -125.6200241
57 1 -1 33.71034745 14.19807232 -56.33090362
58 1 -1 31.34283781 114.2588441 177.621698
59 1 -1 167.8681492 -33.73721495 17.70943601
60 1 -1 50.73906277 165.7201913 -94.6041936
61 1 -1 84.42400278 -113.8271268 -11.73087326
62 1 -1 -146.6200007 -87.0115127 -164.2802459
63 1 -1 -17.94345563 -5.266117623 -114.4770608
64 1 -1 -161.6618755 -81.21577064 -68.78715057
65 1 -1 178.3275787 144.9284223 75.80861878
66 1 -1 81.54873843 -83.6941478 -69.75163018
67 1 -1 -41.13190239 113.6079886 -6.669536125
68 1 -1 -108.5270482 -89.08499627 -39.32427247
69 1 -1 -41.97432027 -32.96246695 65.11935497
70 1 -1 -39.09020679 10.47027922 -53.26049629
71 1 -1 -168.3760012 -85.85704062 27.51501191
72 1 -1 -7.699755475 21.59960856 26.43069039
73 1 -1 87.36704757 14.21816794 -107.2504322
74 1 -1 153.4284087 136.6052131 -126.1502487
75 1 -1 -175.3682642 25.88313064 123.6455547
76 1 -1 90.96648194 175.4891969 32.84622917
77 1 -1 -77.3297511 139.285477 -24.02526586
78 1 -1 -21.80051132 76.35556687 53.9496888
79 1 -1 36.00388293 84.74463507 124.0379428
80 1 -1 8.341344194 -176.0991953 -90.11296078
81 1 -1 13.79742378 -101.263178 81.37760753
82 1 -1 -150.1706978 153.3081009 125.261789
83 1 -1 -176.434078 -91.73850736 -13.91415701
84 1 -1 19.14212656 -8.014482902 53.93954558
85 1 -1 -133.3111329 174.2862517 104.1616036
86 1 -1 141.4028288 71.58712061 62.57853826
87 1 -1 -55.41310448 84.69012271 -53.69230074
88 1 -1 7.57030387 -82.51421069 121.7019339
89 1 -1 6.593627122 170.3286085 -47.07783075
90 1 -1 167.9772199 -52.51603119 -77.32359634
91 1 -1 9.68753279 2.580696533 63.63273049
92 1 -1 -157.900078 -78.41001295 -74.97298362
93 1 -1 157.7779932 -77.61759639 83.11626672
94 1 -1 8.735687555 -51.63741526 149.2886008
95 1 -1 166.3370649 158.0395191 2.108272744
96 1 -1 -136.2080224 -0.233620925 170.1641304
97 1 -1 54.59763504 77.34086464 -34.97254442
98 1 -1 -53.93524806 -102.0122253 -46.27109402
99 1 -1 -148.8398471 -62.976886 79.28200649
100 1 -1 -134.367229 -153.7685306 -62.89913905
101 2 1 85.68701047 47.45902631 136.9309939
102 2 1 -168.7218611 -136.4862888 34.82926874
103 2 1 -85.14342147 -27.50852705 22.44064244
104 2 1 -125.9841936 -166.432033 69.22175254
105 2 1 78.40196016 32.48784706 134.5355212
106 2 1 -158.7356866 172.6075363 -168.6081077
107 2 1 -97.70696089 125.0552693 152.541151
108 2 1 47.42532862 117.2059839 -26.2001494
109 2 1 58.97843054 49.16794046 -45.70255405
110 2 1 -113.2077086 -147.4896474 -109.0593944
111 2 1 133.7818478 137.2370883 -74.12887346
112 2 1 -151.8619681 -55.72321046 39.00697883
113 2 1 -101.5491513 -113.5421107 -135.9492067
114 2 1 -105.4410412 63.66017268 62.00391546
115 2 1 -84.37716183 -35.78408568 -7.089644848
116 2 1 140.387382 -75.00992841 -159.2710691
117 2 1 157.3753205 145.1311104 -98.29723102
118 2 1 -126.8885841 157.4914592 -47.04455377
119 2 1 52.06885202 -100.2669325 38.59257737
120 2 1 -54.06789629 137.7750035 -116.8953091
121 2 1 -29.14739431 94.50860741 -51.527097
122 2 1 -145.9322739 154.5384232 112.3421798
123 2 1 -32.24342538 -22.90490626 -133.4101075
124 2 1 155.0953371 97.30799449 -13.02231424
125 2 1 -109.6079033 -42.89844953 -51.80376701
126 2 1 -150.2770445 -55.20818421 147.7312972
127 2 1 -26.96028917 151.3053234 51.82429115
128 2 1 -42.51040448 55.12547194 -10.01649745
129 2 1 -154.7332138 -166.4922488 75.56066422
130 2 1 179.3252381 50.98353603 -103.842222
131 2 1 -87.64561442 -167.4026399 -37.04977996
132 2 1 -141.7543098 32.23109989 44.99445113
133 2 1 121.3596596 -6.092779973 129.6856923
134 2 1 124.4836766 -86.35531223 85.50625099
135 2 1 140.6305506 -165.9843021 -35.3966949
136 2 1 -89.51258901 36.2123163 54.25434215
137 2 1 107.5306105 58.22419926 141.7457531
138 2 1 -51.03564423 -166.277591 119.3103596
139 2 1 106.3738063 153.673561 100.7747233
140 2 1 -105.1662471 -49.88388187 -163.5658795
141 2 1 -123.4063552 104.6405545 -157.1806703
142 2 1 30.68517662 111.7365757 -128.0988407
143 2 1 -70.66650991 -36.87088431 101.1920697
144 2 1 59.85584345 28.56015074 -148.8751279
145 2 1 76.34296857 -18.88899045 11.99663247
146 2 1 -127.898772 9.029786744 -155.2067979
147 2 1 -61.47407783 106.6906337 -32.24644961
148 2 1 -41.82882356 105.2048819 95.67134776
149 2 1 64.70518204 -125.5606981 -130.2221179
150 2 1 -95.86998176 64.01110464 -62.69889224
151 2 1 -3.893149866 -170.4938796 -173.9425756
152 2 1 -142.5571999 -115.9852755 -42.33527796
153 2 1 -170.1094774 67.22933296 -69.41406448
154 2 1 -135.7002446 -117.3853245 -77.66219554
155 2 1 97.68794466 -176.3481416 64.0577303
156 2 1 98.30084322 -179.1048324 157.6098802
157 2 1 -61.74657154 71.45180441 36.21267022
158 2 1 148.9924395 8.130617629 2.580809806
159 2 1 -7.179797893 131.8852645 48.92705878
160 2 1 166.7210737 111.3028256 122.5151765
161 2 1 160.4061661 105.4292149 147.9164951
162 2 1 70.35573238 -156.217711 -37.86968306
163 2 1 37.82167168 128.9612675 113.5371453
164 2 1 -149.4650805 40.2544478 -89.16446826
165 2 1 23.15794976 -35.62998186 -128.5225995
166 2 1 148.5909499 65.59167763 44.47571026
167 2 1 38.20567747 91.06090259 167.2556933
168 2 1 -173.8935359 124.3001041 -123.4154022
169 2 1 -113.0780192 -112.7185827 -75.51909042
170 2 1 -47.52814398 -162.0232543 -40.84518679
171 2 1 164.6580923 96.26106544 -67.52475023
172 2 1 -166.687599 -28.28821753 -80.04284273
173 2 1 9.786487166 -133.5748603 -110.4924395
174 2 1 73.69685916 -130.6229707 -12.1566579
175 2 1 90.69039384 -12.53964183 -156.8650452
176 2 1 -1.065055548 123.2458955 9.207883208
177 2 1 175.3144942 -62.38332615 89.50309521
178 2 1 -135.5554643 -135.3786299 -12.22599884
179 2 1 -65.15130962 -12.87802388 -85.25728639
180 2 1 -161.9760397 -159.2069523 72.10033228
181 2 1 -116.5200037 9.430944126 5.8294178
182 2 1 -28.85454266 -176.0245493 -141.7245957
183 2 1 63.2968571 -114.4145268 -168.891953
184 2 1 -61.61686575 -158.2947391 162.9099557
185 2 1 51.43661765 119.3411567 4.253266919
186 2 1 50.78017633 47.93871152 129.5527454
187 2 1 151.0842128 -27.15258927 -161.0800505
188 2 1 -63.76595621 -118.2333675 -55.31381078
189 2 1 -103.5498203 -55.20725862 -73.28180307
190 2 1 -165.1300235 72.52455317 27.04945294
191 2 1 68.10471264 124.0704131 -0.252243467
192 2 1 79.29794618 142.8637277 -42.01908928
193 2 1 167.6806551 20.41616629 -147.6924841
194 2 1 -135.8036012 64.48710622 102.1923975
195 2 1 98.55703781 -115.0070794 78.85760695
196 2 1 15.16187488 19.73322691 -170.7866955
197 2 1 151.0729333 50.92372407 -173.3272023
198 2 1 42.92899709 -139.8564977 161.7836767
199 2 1 -123.3797296 144.2768906 93.18435951
200 2 1 83.46684339 160.4439871 16.84583748
201 2 1 -9.982765467 138.2373541 -55.3263136
202 2 1 -161.6023131 -141.5797686 -64.66795638
203 2 1 2.63144963 -54.92560391 117.5540027
204 2 1 -70.31638318 175.5673808 -103.3383852
205 2 1 -4.543770763 -40.50287551 98.39515078
206 2 1 19.2926167 -2.671035153 112.1413205
207 2 1 76.93260202 177.3949067 -126.2787212
208 2 1 131.8183006 132.4167597 131.6586696
209 2 1 -82.9844547 -85.47123292 92.81285561
210 3 -1 115.4743016 -5.981969165 65.81311346
211 3 -1 -86.91538943 171.1823129 -45.00079
212 3 -1 174.0893311 141.4009485 159.8631805
213 3 -1 164.8739505 64.21237704 -8.113691614
214 3 -1 -75.49748308 40.97887837 158.0779944
215 3 -1 45.16399203 72.25791157 159.9861897
216 3 -1 105.7676225 -56.05853127 3.624467826
217 3 -1 166.8523536 -151.4993186 -151.6124408
218 3 -1 -43.30886503 46.05330597 155.3934201
219 3 -1 -5.592027058 2.85325065 11.39381158

264
examples/USER/misc/charge_regulation/data.chreg-polymer Normal file
View File

@ -0,0 +1,264 @@
##A Weak PE Chain of N=80
160 atoms
79 bonds
5 atom types
1 bond types
-50 50 xlo xhi
-50 50 ylo yhi
-50 50 zlo zhi
Masses
1 1.0
2 1.0
3 1.0
4 1.0
5 1.0
Atoms
# atom_id molecule_id atom_type charge x y z
1 1 1 -1 0 0 -48.37753795169063
2 1 1 -1 0 0 -47.255075903381254
3 1 1 -1 0 0 -46.13261385507188
4 1 1 -1 0 0 -45.01015180676251
5 1 1 -1 0 0 -43.887689758453135
6 1 1 -1 0 0 -42.76522771014376
7 1 1 -1 0 0 -41.64276566183439
8 1 1 -1 0 0 -40.520303613525016
9 1 1 -1 0 0 -39.39784156521564
10 1 1 -1 0 0 -38.27537951690627
11 1 1 -1 0 0 -37.1529174685969
12 1 1 -1 0 0 -36.030455420287524
13 1 1 -1 0 0 -34.90799337197815
14 1 1 -1 0 0 -33.78553132366878
15 1 1 -1 0 0 -32.663069275359405
16 1 1 -1 0 0 -31.54060722705003
17 1 1 -1 0 0 -30.41814517874066
18 1 1 -1 0 0 -29.295683130431286
19 1 1 -1 0 0 -28.173221082121913
20 1 1 -1 0 0 -27.05075903381254
21 1 1 -1 0 0 -25.928296985503167
22 1 1 -1 0 0 -24.805834937193794
23 1 1 -1 0 0 -23.68337288888442
24 1 1 -1 0 0 -22.560910840575048
25 1 1 -1 0 0 -21.438448792265675
26 1 1 -1 0 0 -20.3159867439563
27 1 1 -1 0 0 -19.19352469564693
28 1 1 -1 0 0 -18.071062647337556
29 1 1 -1 0 0 -16.948600599028183
30 1 1 -1 0 0 -15.82613855071881
31 1 1 -1 0 0 -14.703676502409436
32 1 1 -1 0 0 -13.581214454100063
33 1 1 -1 0 0 -12.45875240579069
34 1 1 -1 0 0 -11.336290357481317
35 1 1 -1 0 0 -10.213828309171944
36 1 1 -1 0 0 -9.091366260862571
37 1 1 -1 0 0 -7.968904212553198
38 1 1 -1 0 0 -6.846442164243825
39 1 1 -1 0 0 -5.723980115934452
40 1 1 -1 0 0 -4.601518067625079
41 1 1 -1 0 0 -3.4790560193157063
42 1 1 -1 0 0 -2.3565939710063333
43 1 1 -1 0 0 -1.2341319226969603
44 1 1 -1 0 0 -0.11166987438758724
45 1 1 -1 0 0 1.0107921739217858
46 1 1 -1 0 0 2.133254222231159
47 1 1 -1 0 0 3.255716270540532
48 1 1 -1 0 0 4.378178318849905
49 1 1 -1 0 0 5.500640367159278
50 1 1 -1 0 0 6.623102415468651
51 1 1 -1 0 0 7.745564463778024
52 1 1 -1 0 0 8.868026512087397
53 1 1 -1 0 0 9.99048856039677
54 1 1 -1 0 0 11.112950608706143
55 1 1 -1 0 0 12.235412657015516
56 1 1 -1 0 0 13.357874705324889
57 1 1 -1 0 0 14.480336753634262
58 1 1 -1 0 0 15.602798801943635
59 1 1 -1 0 0 16.725260850253008
60 1 1 -1 0 0 17.84772289856238
61 1 1 -1 0 0 18.970184946871754
62 1 1 -1 0 0 20.092646995181127
63 1 1 -1 0 0 21.2151090434905
64 1 1 -1 0 0 22.337571091799873
65 1 1 -1 0 0 23.460033140109246
66 1 1 -1 0 0 24.58249518841862
67 1 1 -1 0 0 25.704957236727992
68 1 1 -1 0 0 26.827419285037365
69 1 1 -1 0 0 27.949881333346738
70 1 1 -1 0 0 29.07234338165611
71 1 1 -1 0 0 30.194805429965484
72 1 1 -1 0 0 31.317267478274857
73 1 1 -1 0 0 32.43972952658423
74 1 1 -1 0 0 33.5621915748936
75 1 1 -1 0 0 34.684653623202976
76 1 1 -1 0 0 35.80711567151235
77 1 1 -1 0 0 36.92957771982172
78 1 1 -1 0 0 38.052039768131095
79 1 1 -1 0 0 39.17450181644047
80 1 1 -1 0 0 40.29696386474984
81 0 2 1 -27.886422274724097 27.72001798427955 38.68169635811057
82 0 2 1 29.812255760623188 17.871838747003693 -29.094648426460257
83 0 2 1 -13.23881351410531 13.28123966828678 -24.422176415560116
84 0 2 1 4.9465650593939685 -37.7521903558826 -15.115417767729575
85 0 2 1 34.82527943387106 29.457664434004897 -25.565595338061254
86 0 2 1 46.35660570786446 -7.161776614070412 -20.2471250527001
87 0 2 1 39.20854546781531 34.96815569014278 13.893531822586723
88 0 2 1 -7.797240698180197 0.07861219105048889 48.686453603015224
89 0 2 1 43.92391845355516 -39.42362941705827 22.448930565867585
90 0 2 1 -40.371744364329984 -17.743039071967246 -15.08153047835009
91 0 2 1 -21.573165497710058 -0.5844447399891948 -45.73596994149077
92 0 2 1 -19.882394451769102 -7.392447895357577 30.733607063808876
93 0 2 1 -17.393031309514107 26.882975097407467 -47.64059480000892
94 0 2 1 25.652222561671735 1.0229206994719107 -14.959030208952043
95 0 2 1 26.075045766879313 19.902341017250052 46.70284805469666
96 0 2 1 39.91980369168496 0.753749460187592 -26.203575929573407
97 0 2 1 13.777613371273958 7.112171629839359 -33.5270487721399
98 0 2 1 18.944534687271826 20.090215089875286 -34.381335468790574
99 0 2 1 -23.801856387842435 -42.275962146864586 -8.322936238250279
100 0 2 1 -31.386991395893826 29.83894468611787 8.937114269513422
101 0 2 1 -41.07090001085809 49.59339931450579 6.666864232174753
102 0 2 1 -46.58911504232167 -32.46068937927039 19.40424197066872
103 0 2 1 -39.94659416571965 -36.28203465180086 5.841020764632312
104 0 2 1 -26.027467090120137 -41.05522015175137 -1.1145958296128313
105 0 2 1 37.09602855959457 23.76087951027276 45.09142423198867
106 0 2 1 -27.78138413517528 -48.97344929918942 45.91491289356401
107 0 2 1 4.468912883622387 -5.217782298407556 6.381420595433383
108 0 2 1 36.758686966564525 48.425582881586166 -25.909273336802997
109 0 2 1 -27.045102667146036 -19.713951008254117 4.339232870380627
110 0 2 1 -5.984280016624311 -49.45311479123866 36.35727783065221
111 0 2 1 27.833389147163018 -47.80144978082761 -47.71458334276804
112 0 2 1 -23.628507668044364 -30.353876765128685 36.174277933133254
113 0 2 1 -40.93360714431151 40.1336490864843 -27.035347797435495
114 0 2 1 6.3523980881104976 -28.636485436097082 -10.671354350535445
115 0 2 1 42.765716958607086 -32.85779663523676 -1.9682360265562124
116 0 2 1 -33.68069757415453 16.800769050458484 -6.273374390373085
117 0 2 1 13.909148568042937 4.921040289518388 12.111069913598996
118 0 2 1 6.728324076730296 -48.44092815223126 -35.92436883370601
119 0 2 1 -18.121173967321912 -15.76903395165283 2.2495451015454933
120 0 2 1 -11.75253233489407 -45.82569982175387 -12.477142440015896
121 0 2 1 1.9713864197144133 17.961034900064007 32.97992150691711
122 0 2 1 -3.993384770632943 -47.63120435620297 27.75490859098018
123 0 2 1 -0.32208279553454844 -47.30616152402566 -22.751109302380367
124 0 2 1 -0.135777029397957 23.88599790464609 -31.87440560354473
125 0 2 1 -6.123924906817393 -2.038519565120424 45.4809181974626
126 0 2 1 -29.622588299895046 42.40404115712096 6.640479709229595
127 0 2 1 -11.694512971272673 19.983258641775762 -38.152427411711145
128 0 2 1 -20.93721440637313 39.46397829322392 -45.52708262202337
129 0 2 1 34.13340147809369 36.14268504987945 -23.978137043267044
130 0 2 1 -37.422309952611485 29.181841318883087 27.55677757161692
131 0 2 1 30.11314373799594 18.721794400471353 1.5553303682670574
132 0 2 1 -7.3563467211571805 46.84253369205935 -39.84708490437832
133 0 2 1 -3.695927445484358 2.494403998274727 -7.634369981832755
134 0 2 1 44.09701173592077 17.717328437831043 31.54108326477207
135 0 2 1 48.070189931616795 10.601166369398662 -28.28574863896286
136 0 2 1 -7.044858382811761 -42.080663380241766 -1.4369925734636553
137 0 2 1 -12.485032488076918 23.87106169116919 6.178803347562642
138 0 2 1 -15.613232443702309 10.103630885941392 -20.447182948810916
139 0 2 1 28.610332347774147 37.08335835592116 -19.90280831362493
140 0 2 1 25.853920233242505 -27.768648181803655 24.971357611943475
141 0 2 1 9.256159541363296 -23.562096053197934 -4.722701100419371
142 0 2 1 39.96929397877305 -11.88228547846326 -28.70638149104603
143 0 2 1 -37.98545134633291 -23.50528193202669 -10.939982626098441
144 0 2 1 25.40017763114089 -47.49220127581256 15.1783064865064
145 0 2 1 28.073596076651768 3.6631266774864386 31.54355751177208
146 0 2 1 -19.596457173068703 46.79824882013442 -12.302655772327597
147 0 2 1 -36.46192411958321 -2.785830672302666 -25.1901381125736
148 0 2 1 -27.377389198969894 11.295792272951147 39.32842550184691
149 0 2 1 32.24967019136358 -20.517755791016402 31.20590722085157
150 0 2 1 47.70698618147787 9.75462874031868 -28.267447889542563
151 0 2 1 17.157803106328345 -27.48141290657965 7.7670687016760525
152 0 2 1 15.089833959419678 5.342811012118396 27.35336620165029
153 0 2 1 9.836963929211372 -11.047378229392443 -20.960811370690678
154 0 2 1 44.66600586278604 14.949733274456321 -29.328965994323575
155 0 2 1 -21.006260382140685 8.492712712433658 -46.31580169190271
156 0 2 1 -29.970979487850748 -36.46250489415931 26.914372830947457
157 0 2 1 -1.0821372755756329 -8.453379951300242 -19.95665062432509
158 0 2 1 -24.033653425909772 -39.51330620205049 20.067656167683793
159 0 2 1 27.747287624384626 -21.904990435351312 -10.819345241055956
160 0 2 1 -40.86737066410612 -25.609300376714796 -21.128139356809783
Bonds
# bond_id bond_type atom1_id atom2_id
1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5
5 1 5 6
6 1 6 7
7 1 7 8
8 1 8 9
9 1 9 10
10 1 10 11
11 1 11 12
12 1 12 13
13 1 13 14
14 1 14 15
15 1 15 16
16 1 16 17
17 1 17 18
18 1 18 19
19 1 19 20
20 1 20 21
21 1 21 22
22 1 22 23
23 1 23 24
24 1 24 25
25 1 25 26
26 1 26 27
27 1 27 28
28 1 28 29
29 1 29 30
30 1 30 31
31 1 31 32
32 1 32 33
33 1 33 34
34 1 34 35
35 1 35 36
36 1 36 37
37 1 37 38
38 1 38 39
39 1 39 40
40 1 40 41
41 1 41 42
42 1 42 43
43 1 43 44
44 1 44 45
45 1 45 46
46 1 46 47
47 1 47 48
48 1 48 49
49 1 49 50
50 1 50 51
51 1 51 52
52 1 52 53
53 1 53 54
54 1 54 55
55 1 55 56
56 1 56 57
57 1 57 58
58 1 58 59
59 1 59 60
60 1 60 61
61 1 61 62
62 1 62 63
63 1 63 64
64 1 64 65
65 1 65 66
66 1 66 67
67 1 67 68
68 1 68 69
69 1 69 70
70 1 70 71
71 1 71 72
72 1 72 73
73 1 73 74
74 1 74 75
75 1 75 76
76 1 76 77
77 1 77 78
78 1 78 79
79 1 79 80

36
examples/USER/misc/charge_regulation/in.chreg-acid Normal file
View File

@ -0,0 +1,36 @@
# Charge regulation lammps for simple weak electrolyte
units lj
atom_style charge
neighbor 3.0 bin
read_data data.chreg-acid
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_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
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

44
examples/USER/misc/charge_regulation/in.chreg-acid-real Normal file
View File

@ -0,0 +1,44 @@
# Charge regulation lammps for simple weak electrolyte
units real
atom_style charge
neighbor 10.0 bin
read_data data.chreg-acid-real
#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 tunit equal 2000 # time unit is 2000 fs
variable timestep equal 0.005*${tunit}
variable cut_long equal 12.5*${sigma}
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}
velocity all create ${temperature} 8008 loop geom
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
pair_coeff * * ${epsilon} ${sigma}
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_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
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}
run 2000

33
examples/USER/misc/charge_regulation/in.chreg-polymer Normal file
View File

@ -0,0 +1,33 @@
# Charge regulation lammps for a polymer chain
units lj
atom_style full
neighbor 3.0 bin
read_data data.chreg-polymer
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

125
examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 Normal file
View File

@ -0,0 +1,125 @@
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

125
examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 Normal file
View File

@ -0,0 +1,125 @@
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

131
examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 Normal file
View File

@ -0,0 +1,131 @@
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

131
examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 Normal file
View File

@ -0,0 +1,131 @@
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

145
examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 Normal file
View File

@ -0,0 +1,145 @@
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

145
examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 Normal file
View File

@ -0,0 +1,145 @@
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 2 by 2 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 = 1053 128
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) = 3.624 | 3.624 | 3.624 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 -7.6327126 304.68909 100 73 15 85 0 0 94 9
200 -6.1699041 272.19597 200 156 24 76 0 0 87 11
300 -7.7876571 288.90801 300 240 20 80 0 0 87 7
400 -6.3239918 274.65708 400 315 16 84 0 0 90 6
500 -5.3978659 257.49208 500 398 15 85 0 0 93 8
600 -5.6433949 322.52048 600 477 18 82 0 0 90 8
700 -6.5351367 269.20244 700 558 18 82 0 0 91 9
800 -6.2093085 315.21326 800 638 24 76 0 0 83 7
900 -7.0795998 311.93228 900 719 28 72 0 0 82 10
1000 -6.4668438 281.72674 1000 796 27 73 0 0 81 8
1100 -6.2377994 318.48594 1100 875 25 75 0 0 84 9
1200 -6.6305072 304.9091 1200 950 23 77 0 0 87 10
1300 -5.9624552 286.05027 1300 1029 22 78 0 0 86 8
1400 -4.4695814 261.81053 1400 1111 20 80 0 0 90 10
1500 -5.6928652 293.72403 1500 1191 24 76 0 0 86 10
1600 -6.8715413 290.47065 1600 1275 22 78 0 0 90 12
1700 -6.5067505 292.74735 1700 1356 25 75 0 0 85 10
1800 -5.3902702 307.79012 1800 1434 22 78 0 0 83 5
1900 -5.1407153 318.48918 1900 1510 21 79 0 0 87 8
2000 -4.9514719 281.87771 2000 1589 25 75 0 0 82 7
Loop time of 0.562889 on 4 procs for 2000 steps with 189 atoms
Performance: 3069.876 ns/day, 0.008 hours/ns, 3553.097 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.008399 | 0.010383 | 0.011765 | 1.2 | 1.84
Kspace | 0.17501 | 0.17543 | 0.1757 | 0.1 | 31.17
Neigh | 0.001833 | 0.0021325 | 0.002293 | 0.4 | 0.38
Comm | 0.023099 | 0.024255 | 0.026645 | 0.9 | 4.31
Output | 0.000465 | 0.000546 | 0.000783 | 0.0 | 0.10
Modify | 0.3464 | 0.34669 | 0.34698 | 0.0 | 61.59
Other | | 0.003452 | | | 0.61
Nlocal: 47.2500 ave 57 max 41 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 285.750 ave 303 max 263 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 403.500 ave 548 max 324 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 1614
Ave neighs/atom = 8.5396825
Neighbor list builds = 2081
Dangerous builds = 0
Total wall time: 0:00:00

1379
src/MC/fix_charge_regulation.cpp Normal file
View File

File diff suppressed because it is too large Load Diff

118
src/MC/fix_charge_regulation.h Normal file
View File

@ -0,0 +1,118 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Tine Curk (tcurk5@gmail.com) and Jiaxing Yuan (yuanjiaxing123@hotmail.com)
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(charge/regulation,FixChargeRegulation)
#else
#ifndef LMP_FIX_CHARGE_REGULATION_H
#define LMP_FIX_CHARGE_REGULATION_H
#include "fix.h"
namespace LAMMPS_NS {
class FixChargeRegulation : public Fix {
public:
FixChargeRegulation(class LAMMPS *, int, char **);
~FixChargeRegulation();
int setmask();
void init();
void pre_exchange();
void forward_acid();
void backward_acid();
void forward_base();
void backward_base();
void forward_ions();
void forward_ions_multival();
void backward_ions();
void backward_ions_multival();
int get_random_particle(int, double, double, double *);
int insert_particle(int, double, double, double *);
double energy_full();
int particle_number(int, double);
int particle_number_xrd(int, double, double, double *);
double compute_vector(int n);
void assign_tags();
void options(int, char **);
void setThermoTemperaturePointer();
double memory_usage();
private:
int exclusion_group, exclusion_group_bit;
int nevery, seed; // begin MC cycle every nevery MD timesteps, random seed
int nmc; // MC move attempts per cycle
double llength_unit_in_nm ; // LAMMPS unit of length in nm, needed since chemical potentials are in units of mol/l
double pH, pKa, pKb, pKs, pI_plus, pI_minus; // chemical potentials and equilibrium constant in log10 base
double c10pH, c10pKa, c10pKb, c10pOH, c10pI_plus, c10pI_minus; // 10 raised to chemical potential value, in units of concentration [mol/liter]
double pmcmoves[3]; // mc move attempt probability: acid, base, ion pair exchange
double pmcc; // mc move cumulative attempt probability
int npart_xrd; // # of particles (ions) within xrd
int npart_xrd2; // # of particles (ions) within xrd
double vlocal_xrd; // # local volume within xrd
bool only_salt_flag; // true if performing only salt insertion/deletion, no acid/base dissociation.
bool add_tags_flag; // true if each inserted atom gets its unique atom tag
int groupbitall; // group bitmask for inserted atoms
int ngroups; // number of group-ids for inserted atoms
char **groupstrings; // list of group-ids for inserted atoms
// counters
unsigned long int nacid_attempts, nacid_successes, nbase_attempts, nbase_successes, nsalt_attempts, nsalt_successes;
int nacid_neutral, nacid_charged, nbase_neutral, nbase_charged, ncation, nanion; // particle type counts
int cr_nmax; // max number of local particles
double reservoir_temperature;
double beta, sigma, volume, volume_rx; // inverse temperature, speed, total volume, reacting volume
int salt_charge[2]; // charge of salt ions: [0] - cation, [1] - anion
int salt_charge_ratio; // charge ratio when using multivalent ion exchange
double xlo, xhi, ylo, yhi, zlo, zhi; // box size
double energy_stored; // full energy of old/current configuration
int triclinic; // 0 = orthog box, 1 = triclinic
double *sublo, *subhi; // triclinic size
int *ptype_ID; // particle ID array
double overlap_cutoffsq; // square distance cutoff for overlap
int overlap_flag;
int acid_type, cation_type, base_type, anion_type; // reacting atom types
int reaction_distance_flag; // radial reaction restriction flag
double reaction_distance; // max radial distance from acid/base for ion insertion
class Pair *pair;
class Compute *c_pe; // energy compute pointer
class RanPark *random_equal; // random number generator
class RanPark *random_unequal; // random number generator
char *idftemp; // pointer to the temperature fix
double *target_temperature_tcp; // current temperature of the thermostat
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
Self-explanatory.
*/