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Make documentation of ELECTRODE fixes more complete by listing more warnings and describing options more fully.
Use utils::logical for toggle (on/off) options.
With the changes in etypes to auto-detect electrode types it makes more sense to make it an on/off toggle as well, so that we don't have inconsistent keyword types.
This commit is contained in:
Shern Tee
2022-10-12 12:00:46 +00:00
committed by Ludwig Ahrens-Iwers
parent ea7e0fbb6c
commit 5f285e6aa3
10 changed files with 206 additions and 97 deletions
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258
doc/src/fix_electrode_conp.rst
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@ -31,26 +31,21 @@ Syntax
* ID, group-ID are documented in fix command * ID, group-ID are documented in fix command
* mode = electrode/conp or electrode/conq or electrode/thermo * mode = electrode/conp or electrode/conq or electrode/thermo
* potential = electrode potential (number, or equal-style variable) * potential = electrode potential (can be an equal-style variable, see below)
* charge = electrode charge * charge = electrode charge (can be an equal-style variable, see below)
* eta = reciprocal width of electrode charge smearing * eta = reciprocal width of electrode charge Gaussian distribution
* T_v = temperature of thermo-potentiostat * T_v = temperature of thermo-potentiostat
* tau_v = time constant of thermo-potentiostat * tau_v = time constant of thermo-potentiostat
* rng_v = integer used to initialize random number generator * rng_v = integer used to initialize thermo-potentiostat random number generator
* Optional keywords and values:
.. parsed-literal:: .. parsed-literal::
*algo mat_inv/mat_cg value/cg value* *algo mat_inv/mat_cg tol/cg tol*
specify the algorithm used to compute the electrode charges specify the algorithm used to compute the electrode charges
*symm(etry) on/off*
turn on/off charge neutrality constraint for the electrodes
*couple group-ID value* *couple group-ID value*
group-ID = group of atoms treated as additional electrode group-ID = group of atoms treated as additional electrode
value = electric potential or charge on this electrode value = electric potential or charge on this electrode
*etypes*
construct optimized neighbor lists (types of the electrode must be exclusive to them)
*ffield on/off*
turn on/off finite-field implementation
*write_mat filename* *write_mat filename*
write elastance matrix to file write elastance matrix to file
*write_inv filename* *write_inv filename*
@ -59,6 +54,12 @@ Syntax
read elastance matrix from file read elastance matrix from file
*read_inv filename* *read_inv filename*
read inverted matrix from file read inverted matrix from file
*symm(etry) on/off*
turn on/off charge neutrality constraint for the electrodes
*ffield on/off*
turn on/off finite-field implementation
*etypes on/off*
turn on/off type-based optimized neighbor lists (electrode and electrolyte types may not overlap)
Examples Examples
"""""""" """"""""
@ -66,32 +67,81 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
fix fxconp bot electrode/conp -1.0 1.805 couple top 1.0 couple ref 0.0 write_inv inv.csv symm on fix fxconp bot electrode/conp -1.0 1.805 couple top 1.0 couple ref 0.0 write_inv inv.csv symm on
fix fxconp electrodes electrode/conq 0.0 1.805 fix fxconp electrodes electrode/conq 0.0 1.805 algo cg 1e-5
fix fxconp bot electrode/thermo -1.0 1.805 temp 298 100 couple top 1.0 fix fxconp bot electrode/thermo -1.0 1.805 temp 298 100 couple top 1.0
Description Description
""""""""""" """""""""""
fix electrode/conp mode implements a constant potential method (CPM) The *electrode* fixes implement the constant potential method (CPM)
(:ref:`Siepmann <Siepmann>`, :ref:`Reed <Reed3>`). Charges of groups specified (:ref:`Siepmann <Siepmann>`, :ref:`Reed <Reed3>`), and modern variants, to
via group-ID and optionally with the `couple` keyword are adapted to meet their respective accurately model electrified, conductive electrodes. This is primarily useful
potential at every time step. An arbitrary number of electrodes can be set but for studying electrode-electrolyte interfaces, especially at high potential
the respective groups may not overlap. Electrode charges have a Gaussian charge differences or ionicities, with non-planar electrodes such as nanostructures or
distribution with reciprocal width eta. nanopores, and to study dynamic phenomena such as charging or discharging time
scales or conductivity or ionic diffusivities.
Three algorithms are available to minimize the energy: Each *electrode* fix allows users to set additional electrostatic relationships
via matrix inversion (*algo mat_inv*) :ref:`(Wang) <Wang5>`, or with the conjugate gradient between the specified groups which model useful electrostatic configurations:
method either using a matrix for the electrode-electrode interaction (*algo
mat_cg value*) or computing the interaction directly (*algo cg value*). This
method requires a threshold value to set the accuracy.
fix electrode/conq enforces a total charge specified in the input on each electrode. The energy is * *electrode/conp* sets potentials or potential differences between electrodes
minimized w.r.t. the charge distribution within the electrode.
fix electrode/thermo implements a thermo-potentiostat :ref:`(Deissenbeck) * (resulting in changing electrode total charges)
<Deissenbeck>`. Temperature and time constant of the thermo-potentiostat need
to be specified using the temp keyword. Currently, only two electrodes are possible with * *electrode/conq* sets the total charge on each electrode
this style. This fix is not compatible with the conjugate gradient algorithms.
* (resulting in changing electrode potentials)
* *electrode/thermo* sets a thermopotentiostat :ref:`(Deissenbeck)<Deissenbeck>` between two electrodes
* (resulting in changing charges and potentials with appropriate average potential difference and thermal variance)
The first group-ID provided to each fix specifies the first electrode group, and
more group(s) are added using the *couple* keyword for each additional group.
While *electrode/thermo* only accepts two groups, *electrode/conp* and
*electrode/conq* accept any number of groups, up to LAMMPS's internal
restrictions (see Restrictions below). Electrode groups must not overlap, i.e.
the fix will issue an error if any particle is detected to belong to at least
two electrode groups.
CPM involves updating charges on groups of electrode particles, per time step,
so that the system's total energy is minimized with respect to those charges.
From basic electrostatics, this is equivalent to making each group conductive,
or imposing an equal electrostatic potential on every particle in the same group
(hence the name CPM). The charges are usually modelled as a Gaussian
distribution to make the charge-charge interaction matrix invertible
(:ref:`Gingrich <Gingrich>`). The keyword *eta* specifies the distribution's
width in units of inverse length.
Three algorithms are available to minimize the energy, varying in how matrices
are pre-calculated before a run to provide computational speedup. These
algorithms can be selected using the keyword *algo*:
* *algo mat_inv* pre-calculates the capacitance matrix
and obtains the charge configuration in one matrix-vector calculation per time step
* *algo mat_cg* pre-calculates the elastance matrix (inverse of capacitance matrix)
and obtains the charge configuration using a conjugate gradient solver
in multiple matrix-vector calculations per time step
* *algo cg* does not perform any pre-calculation and obtains the charge configuration
using a conjugate gradient solver and multiple calculations of the electric potential per time step.
For both *cg* methods, the command must specify the conjugate gradient
tolerance. *fix electrode/thermo* currently only supports the *mat_inv*
algorithm.
For *fix electrode/conp*, the keyword *symm* can be set *on* (or *off*) to turn
on (or turn off) the constraint requiring total electrode charge to be zero.
With *symm off*, the potentials specified are absolute potentials, but the
charge configurations satisfying them may add up to an overall non-zero, varying
charge for the electrodes (and thus the simulation box). With *symm on*, the
total charge over all electrode groups is constrained to zero.
The *symm* keyword is not allowed for *electrode/conq*, for which overall
neutrality is explicitly obeyed or violated by the user input, and for
*electrode/thermo*, for which overall neutrality is always automatically
imposed.
For all three fixes, any potential (or charge for *conq*) can be specified as an For all three fixes, any potential (or charge for *conq*) can be specified as an
equal-style variable prefixed with "v\_". For example, the following code will equal-style variable prefixed with "v\_". For example, the following code will
@ -105,15 +155,16 @@ course of the simulation:
Note that these fixes only parse their supplied variable name when starting a Note that these fixes only parse their supplied variable name when starting a
run, and so these fixes will accept equal-style variables defined *after* the run, and so these fixes will accept equal-style variables defined *after* the
fix definition, including variables dependent on the fix's own output. For an fix definition, including variables dependent on the fix's own output. This is
advanced example of this see the in.conq2 input file in the directory useful, for example, in the fix's internal finite-field commands (see below).
For an advanced example of this see the in.conq2 input file in the directory
examples/PACKAGES/electrode/graph-il. examples/PACKAGES/electrode/graph-il.
This fix necessitates the use of a long range solver that calculates and provides the matrix This fix necessitates the use of a long range solver that calculates and
of electrode-electrode interactions and a vector of electrode-electrolyte provides the matrix of electrode-electrode interactions and a vector of
interactions. The Kspace styles *ewald/electrode*, *pppm/electrode* and electrode-electrolyte interactions. The Kspace styles *ewald/electrode*,
*pppm/electrode/intel* are created specifically for this task *pppm/electrode* and *pppm/electrode/intel* are created specifically for this
:ref:`(Ahrens-Iwers) <Ahrens-Iwers>`. task :ref:`(Ahrens-Iwers) <Ahrens-Iwers>`.
For systems with non-periodic boundaries in one or two directions dipole For systems with non-periodic boundaries in one or two directions dipole
corrections are available with the :doc:`kspace_modify <kspace_modify>`. For corrections are available with the :doc:`kspace_modify <kspace_modify>`. For
@ -135,6 +186,49 @@ moderate mesh size but requires more memory.
kspace_modify amat onestep/twostep kspace_modify amat onestep/twostep
For all versions of the fix, the keyword-value *ffield on* enables the
finite-field mode (:ref:`Dufils <Dufils>`, :ref:`Tee <Tee>`), which uses an
electric field across a periodic cell instead of non-periodic boundary
conditions to impose a potential difference between the two electrodes bounding
the cell. The fix (with name *fix-ID*) detects which of the two electrodes is
"on top" (has the larger maximum *z*-coordinate among all particles). Assuming
the first electrode group is on top, it then issues the following commands
internally:
.. code-block:: LAMMPS
variable fix-ID_ffield_zfield equal (f_fix-ID[2]-f_fix-ID[1])/lz
efield fix-ID_efield all efield 0.0 0.0 v_fix-ID_ffield_zfield
which implements the required electric field as the potential difference divided
by cell length. The internal commands use variable so that the electric field
will correctly vary with changing potentials in the correct way (for example
with equal-style potential difference or with *fix electrode/conq*). This
keyword requires two electrodes and will issue an error with any other number of
electrodes.
For all versions of the fix, the keyword-value *etypes on* enables type-based
optimized neighbor lists. With this feature enabled, LAMMPS provides the fix
with an occasional neighborlist restricted to electrode-electrode interactions
for calculating the electrode matrix, and a perpetual neighborlist restricted to
electrode-electrolyte interactions for calculating the electrode potentials,
using particle types to list only desired interactions, and typically resulting
in 5--10\% less computational time. Without this feature the fix will simply
use the active pair style's neighborlist. This feature cannot be enabled if any
electrode particle has the same type as any electrolyte particle (which would be
unusual in a typical simulation) and the fix will issue an error in that case.
..
(if we merge the overlap_etypes branch)
This feature will provide minimal benefit if any electrode particle has the same type as any
electrolyte particle, since it will be impossible for LAMMPS to list only electrode-electrolyte
neighbor pairs and discard other neighbor pairs from the provided perpetual neighborlist.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix currently does not write any information to restart files.
The *fix_modify tf* option enables the Thomas-Fermi metallicity model The *fix_modify tf* option enables the Thomas-Fermi metallicity model
(:ref:`Scalfi <Scalfi>`) and allows parameters to be set for each atom type. (:ref:`Scalfi <Scalfi>`) and allows parameters to be set for each atom type.
@ -144,7 +238,8 @@ The *fix_modify tf* option enables the Thomas-Fermi metallicity model
fix_modify ID tf type length voronoi fix_modify ID tf type length voronoi
If this option is used parameters must be set for all atom types of the electrode. If this option is used parameters must be set for all atom types of the
electrode.
The *fix_modify timer* option turns on (off) additional timer outputs in the log The *fix_modify timer* option turns on (off) additional timer outputs in the log
file, for code developers to track optimization. file, for code developers to track optimization.
@ -156,8 +251,8 @@ file, for code developers to track optimization.
---------- ----------
These fixes compute a global (extensive) scalar, a global (intensive) vector, These fixes compute a global (extensive) scalar, a global (intensive) vector,
and a global array, which can be accessed by various and a global array, which can be accessed by various :doc:`output commands
:doc:`output commands <Howto_output>`. <Howto_output>`.
The global scalar outputs the energy added to the system by this fix, which is The global scalar outputs the energy added to the system by this fix, which is
the negative of the total charge on each electrode multiplied by that the negative of the total charge on each electrode multiplied by that
@ -167,48 +262,46 @@ The global vector outputs the potential on each electrode (and thus has *N*
entries if the fix manages *N* electrode groups), in :doc:`units <units>` of entries if the fix manages *N* electrode groups), in :doc:`units <units>` of
electric field multiplied by distance (thus volts for *real* and *metal* units). electric field multiplied by distance (thus volts for *real* and *metal* units).
The electrode groups' ordering follows the order in which they were input in the The electrode groups' ordering follows the order in which they were input in the
fix command using *couple*. The global vector output is useful for fix command using *couple*. The global vector output is useful for *fix
*fix electrode/conq* and *fix electrode/thermo*, electrode/conq* and *fix electrode/thermo*, where potential is dynamically
where potential is dynamically updated based on electrolyte configuration updated based on electrolyte configuration instead of being directly set.
instead of being directly set.
The global array has *N* rows and *2N+1* columns, where the fix manages *N* The global array has *N* rows and *2N+1* columns, where the fix manages *N*
electrode groups managed by the fix. For the *I*-th row of the array, the electrode groups managed by the fix. For the *I*-th row of the array, the
elements are: elements are:
* array[I][1] = total charge that group *I* would have had *if it were at 0 V * array[I][1] = total charge that group *I* would have had *if it were at 0 V
applied potential* applied potential* * array[I][2 to *N* + 1] = the *N* entries of the *I*-th
* array[I][2 to *N* + 1] = the *N* entries of the *I*-th row of the electrode row of the electrode capacitance matrix (definition follows) * array[I][*N* +
capacitance matrix (definition follows) 2 to *2N* + 1] = the *N* entries of the *I*-th row of the electrode elastance
* array[I][*N* + 2 to *2N* + 1] = the *N* entries of the *I*-th row of the electrode matrix (the inverse of the electrode capacitance matrix)
elastance matrix (the inverse of the electrode capacitance matrix)
The :math:`N \times N` electrode capacitance matrix, denoted :math:`\mathbf{C}` The :math:`N \times N` electrode capacitance matrix, denoted :math:`\mathbf{C}`
in the following equation, summarizes how the total charge induced on each electrode in the following equation, summarizes how the total charge induced on each
(:math:`\mathbf{Q}` as an *N*-vector) is related to the potential on each electrode (:math:`\mathbf{Q}` as an *N*-vector) is related to the potential on
electrode, :math:`\mathbf{V}`, and the charge-at-0V :math:`\mathbf{Q}_{0V}` each electrode, :math:`\mathbf{V}`, and the charge-at-0V :math:`\mathbf{Q}_{0V}`
(which is influenced by the local electrolyte structure): (which is influenced by the local electrolyte structure):
.. math:: .. math::
\mathbf{Q} = \mathbf{Q}_{0V} + \mathbf{C} \cdot \mathbf{V} \mathbf{Q} = \mathbf{Q}_{0V} + \mathbf{C} \cdot \mathbf{V}
The charge-at-0V, electrode capacitance and elastance matrices are internally used to The charge-at-0V, electrode capacitance and elastance matrices are internally
calculate the potentials required to induce the specified total electrode charges used to calculate the potentials required to induce the specified total
in *fix electrode/conq* and *fix electrode/thermo*. With the *symm on* option, electrode charges in *fix electrode/conq* and *fix electrode/thermo*. With the
the electrode capacitance matrix would be singular, and thus its last row is *symm on* option, the electrode capacitance matrix would be singular, and thus
replaced with *N* copies of its top-left entry (:math:`\mathbf{C}_{11}`) for its last row is replaced with *N* copies of its top-left entry
invertibility. (:math:`\mathbf{C}_{11}`) for invertibility.
The global array output is mainly useful for quickly determining the 'vacuum The global array output is mainly useful for quickly determining the 'vacuum
capacitance' of the system (capacitance with only electrodes, no electrolyte), capacitance' of the system (capacitance with only electrodes, no electrolyte),
and can also be used for advanced simulations setting the potential as some and can also be used for advanced simulations setting the potential as some
function of the charge-at-0V (such as in the in.conq2 example mentioned above). function of the charge-at-0V (such as the `in.conq2` example mentioned above).
Please cite :ref:`(Ahrens-Iwers2022) <Ahrens-Iwers2>` in any publication that uses Please cite :ref:`(Ahrens-Iwers2022) <Ahrens-Iwers2>` in any publication that
this implementation. uses this implementation. Please cite also the publication on the combination
Please cite also the publication on the combination of the CPM with pppm if you of the CPM with PPPM if you use *pppm/electrode* :ref:`(Ahrens-Iwers)
use *pppm/electrode* :ref:`(Ahrens-Iwers) <Ahrens-Iwers>`. <Ahrens-Iwers>`.
---------- ----------
@ -218,6 +311,14 @@ Restrictions
For algorithms that use a matrix for the electrode-electrode interactions, For algorithms that use a matrix for the electrode-electrode interactions,
positions of electrode particles have to be immobilized at all times. positions of electrode particles have to be immobilized at all times.
With *ffield off* (i.e. the default), the box geometry is expected to be
*z*-non-periodic (i.e. *boundary p p f*), and this fix will issue an error if
the box is *z*-periodic. With *ffield on*, the box geometry is expected to be
*z*-periodic, and this fix will issue an error if the box is *z*-non-periodic.
TODO: will fix check if *kspace_modify slab* is enabled or does it silently give
wrong results?
The parallelization for the fix works best if electrode atoms are evenly The parallelization for the fix works best if electrode atoms are evenly
distributed across processors. For a system with two electrodes at the bottom distributed across processors. For a system with two electrodes at the bottom
and top of the cell this can be achieved with *processors * * 2*, or with the and top of the cell this can be achieved with *processors * * 2*, or with the
@ -230,6 +331,22 @@ line
which avoids an error if the script is run on an odd number of processors (such which avoids an error if the script is run on an odd number of processors (such
as on just one processor for testing). as on just one processor for testing).
The fix creates an additional group named *[fix-ID]_group* which is the union of
all electrode groups supplied to LAMMPS. This additional group counts towards
LAMMPS's limitation on the total number of groups (currently 32), which may not
allow scripts that use that many groups to run with this fix.
The matrix-based algorithms (*algo mat_inv* and *algo mat_cg*) currently store
an interaction matrix (either elastance or capacitance) of *N* by *N* doubles
for each MPI process. This memory requirement may be prohibitive for large
electrode groups. The fix will issue a warning if it expects to use more than
0.5 GiB of memory.
Default
"""""""
The default keyword-option settings are *algo mat_inv*, *symm off*, *etypes off*
and *ffield off*.
---------- ----------
.. include:: accel_styles.rst .. include:: accel_styles.rst
@ -244,14 +361,14 @@ as on just one processor for testing).
**(Reed)** Reed *et al.*, J. Chem. Phys. 126, 084704 (2007). **(Reed)** Reed *et al.*, J. Chem. Phys. 126, 084704 (2007).
.. _Wang5:
**(Wang)** Wang *et al.*, J. Chem. Phys. 141, 184102 (2014).
.. _Deissenbeck: .. _Deissenbeck:
**(Deissenbeck)** Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021). **(Deissenbeck)** Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021).
.. _Gingrich:
**(Gingrich)** Gingrich, `MSc thesis` <https://gingrich.chem.northwestern.edu/papers/ThesiswCorrections.pdf>` (2010).
.. _Ahrens-Iwers: .. _Ahrens-Iwers:
**(Ahrens-Iwers)** Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021). **(Ahrens-Iwers)** Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).
@ -260,6 +377,14 @@ as on just one processor for testing).
**(Hu)** Hu, J. Chem. Theory Comput. 10, 5254 (2014). **(Hu)** Hu, J. Chem. Theory Comput. 10, 5254 (2014).
.. _Dufils:
**(Dufils)** Dufils *et al.*, Phys. Rev. Letters 123, 195501 (2019).
.. _Tee:
**(Tee)** Tee and Searles, J. Chem. Phys. 156, 184101 (2022).
.. _Scalfi: .. _Scalfi:
**(Scalfi)** Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020). **(Scalfi)** Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020).
@ -267,4 +392,3 @@ as on just one processor for testing).
.. _Ahrens-Iwers2: .. _Ahrens-Iwers2:
**(Ahrens-Iwers2022)** Ahrens-Iwers *et al.*, J. Chem. Phys. 157, 084801 (2022). **(Ahrens-Iwers2022)** Ahrens-Iwers *et al.*, J. Chem. Phys. 157, 084801 (2022).

2
examples/PACKAGES/electrode/au-aq/in.ffield
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@ -4,7 +4,7 @@
boundary p p p # ffield uses periodic z-boundary and no slab boundary p p p # ffield uses periodic z-boundary and no slab
include settings.mod # styles, groups, computes and fixes include settings.mod # styles, groups, computes and fixes
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot

2
examples/PACKAGES/electrode/au-aq/in.tf
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@ -6,7 +6,7 @@
boundary p p p # ffield uses periodic z-boundary and no slab boundary p p p # ffield uses periodic z-boundary and no slab
include settings.mod # styles, groups, computes and fixes include settings.mod # styles, groups, computes and fixes
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on
fix_modify conp tf 6 1.0 18.1715745 fix_modify conp tf 6 1.0 18.1715745
fix_modify conp tf 7 1.0 18.1715745 fix_modify conp tf 7 1.0 18.1715745

2
examples/PACKAGES/electrode/graph-il/in.conq
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@ -5,7 +5,7 @@ boundary p p f # slab calculation
include settings.mod # styles, groups, computes and fixes include settings.mod # styles, groups, computes and fixes
kspace_modify slab 3.0 kspace_modify slab 3.0
fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes # conq doesn't take symm option fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # conq doesn't take symm option
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2]

2
examples/PACKAGES/electrode/graph-il/in.conq2
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@ -5,7 +5,7 @@ boundary p p f # slab calculation
include settings.mod # styles, groups, computes and fixes include settings.mod # styles, groups, computes and fixes
kspace_modify slab 3.0 kspace_modify slab 3.0
fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes on
variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge
variable qex_top equal 1.0-f_conp[2][1] # difference between desired and 0V charge variable qex_top equal 1.0-f_conp[2][1] # difference between desired and 0V charge

2
examples/PACKAGES/electrode/graph-il/in.etypes
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@ -5,7 +5,7 @@ boundary p p f # slab calculation
include settings.mod # styles, groups, computes and fixes include settings.mod # styles, groups, computes and fixes
kspace_modify slab 3.0 kspace_modify slab 3.0
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop

2
examples/PACKAGES/electrode/graph-il/in.ffield
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@ -4,7 +4,7 @@
boundary p p p # ffield uses periodic z-boundary and no slab boundary p p p # ffield uses periodic z-boundary and no slab
include settings.mod # styles, groups, computes and fixes include settings.mod # styles, groups, computes and fixes
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes ffield yes fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on ffield yes
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop

2
examples/PACKAGES/electrode/graph-il/in.ramp
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@ -6,7 +6,7 @@ include settings.mod # styles, groups, computes and fixes
kspace_modify slab 3.0 kspace_modify slab 3.0
variable v equal ramp(2,4) variable v equal ramp(2,4)
fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v

4
examples/PACKAGES/electrode/graph-il/in.thermo
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@ -6,9 +6,9 @@ include settings.mod # styles, groups, computes and fixes
kspace_modify slab 3.0 kspace_modify slab 3.0
unfix nvt # remove NVT thermostat included from "settings.mod" unfix nvt # remove NVT thermostat included from "settings.mod"
fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes temp 500 100 7 # temp tau rng fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 # temp tau rng
# to compare to regular constant potential, switch previous line to this: # to compare to regular constant potential, switch previous line to this:
#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes symm on #fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on
fix nve electrolyte nve fix nve electrolyte nve
# note ionic liquid does not reach 500K immediately # note ionic liquid does not reach 500K immediately

27
src/ELECTRODE/fix_electrode_conp.cpp
View File

@ -136,16 +136,6 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
group_psi_var_styles.push_back(VarStyle::CONST); group_psi_var_styles.push_back(VarStyle::CONST);
group_psi.push_back(utils::numeric(FLERR, arg[iarg], false, lmp)); group_psi.push_back(utils::numeric(FLERR, arg[iarg], false, lmp));
} }
} else if ((strncmp(arg[iarg], "symm", 4) == 0)) {
if (iarg + 2 > narg) error->all(FLERR, "Need yes/no command after symm keyword");
char *symm_arg = arg[++iarg];
if ((strcmp(symm_arg, "yes") == 0) || (strcmp(symm_arg, "on") == 0)) {
symm = true;
} else if ((strcmp(symm_arg, "no") == 0) || (strcmp(symm_arg, "off") == 0)) {
symm = false;
} else {
error->all(FLERR, "Invalid argument after symm keyword");
}
} else if ((strcmp(arg[iarg], "algo") == 0)) { } else if ((strcmp(arg[iarg], "algo") == 0)) {
if (!default_algo) error->one(FLERR, fmt::format("Algorithm can be set once, only")); if (!default_algo) error->one(FLERR, fmt::format("Algorithm can be set once, only"));
default_algo = false; default_algo = false;
@ -195,8 +185,6 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
} else { } else {
error->all(FLERR, "Illegal fix electrode/conp command with read"); error->all(FLERR, "Illegal fix electrode/conp command with read");
} }
} else if ((strcmp(arg[iarg], "etypes") == 0)) {
etypes_neighlists = true;
} else if ((strcmp(arg[iarg], "temp") == 0)) { } else if ((strcmp(arg[iarg], "temp") == 0)) {
if (iarg + 4 > narg) error->all(FLERR, "Need three arguments after temp command"); if (iarg + 4 > narg) error->all(FLERR, "Need three arguments after temp command");
if (strcmp(this->style, "electrode/thermo") != 0) if (strcmp(this->style, "electrode/thermo") != 0)
@ -204,16 +192,13 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
thermo_temp = force->boltz / force->qe2f * utils::numeric(FLERR, arg[++iarg], false, lmp); thermo_temp = force->boltz / force->qe2f * utils::numeric(FLERR, arg[++iarg], false, lmp);
thermo_time = utils::numeric(FLERR, arg[++iarg], false, lmp); thermo_time = utils::numeric(FLERR, arg[++iarg], false, lmp);
thermo_init = utils::inumeric(FLERR, arg[++iarg], false, lmp); thermo_init = utils::inumeric(FLERR, arg[++iarg], false, lmp);
// toggle parameters
} else if ((strcmp(arg[iarg], "etypes") == 0)) {
etypes_neighlists = utils::logical(FLERR, arg[++iarg], false, lmp);
} else if ((strncmp(arg[iarg], "symm", 4) == 0)) {
symm = utils::logical(FLERR, arg[++iarg], false, lmp);
} else if ((strcmp(arg[iarg], "ffield") == 0)) { } else if ((strcmp(arg[iarg], "ffield") == 0)) {
if (iarg + 2 > narg) error->all(FLERR, "Need yes/no command after ffield keyword"); ffield = utils::logical(FLERR, arg[++iarg], false, lmp);
char *ffield_arg = arg[++iarg];
if ((strcmp(ffield_arg, "yes") == 0) || (strcmp(ffield_arg, "on") == 0)) {
ffield = true;
} else if ((strcmp(ffield_arg, "no") == 0) || (strcmp(ffield_arg, "off") == 0)) {
ffield = false;
} else {
error->all(FLERR, "Invalid argument after ffield keyword");
}
} else { } else {
error->all(FLERR, "Illegal fix electrode/conp command"); error->all(FLERR, "Illegal fix electrode/conp command");
} }