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added qtotal keyword

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This commit is contained in:
Shern Tee
2023-05-31 14:50:55 +00:00
parent 7d8866891a
commit 59bdb136dc
6 changed files with 168 additions and 14 deletions
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17
doc/src/fix_electrode.rst
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@ -45,7 +45,7 @@ Syntax
rng_v = integer used to initialize random number generator
* zero or more keyword/value pairs may be appended
* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv*
* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv* or *qtotal*
.. parsed-literal::
@ -68,6 +68,8 @@ Syntax
filename = file from which to read elastance matrix
*read_inv* value = filename
filename = file from which to read inverted matrix
*qtotal* value = number or *v_* equal-style variable
add overall potential so that all electrode charges add up to *qtotal*
Examples
""""""""
@ -249,6 +251,19 @@ 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.
.. versionchanged:: qtotal
The keyword *qtotal* causes *fix electrode/conp* and *fix electrode/thermo*
to add an overall potential to all electrodes so that the total charge on
the electrodes is a specified amount (which may be an equal-style variable).
For example, if a user wanted to simulate a solution of excess cations
such that the total electrolyte charge is +2, setting *qtotal -2* would cause
the total electrode charge to be -2, so that the simulation box remains overall
electroneutral. Since *fix electrode/conq* constrains the total charges of
individual electrodes, and since *symm on* constrains the total charge of all
electrodes to be zero, either option is incompatible with the *qtotal* keyword
(even if *qtotal* is set to zero).
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

31
examples/PACKAGES/electrode/graph-il/in.nonneut Normal file
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@ -0,0 +1,31 @@
# electrodes, overall non-neutral
# for graphene-ionic liquid supercapacitor
boundary p p f # slab calculation
include settings.mod # styles, groups, computes and fixes
kspace_modify slab 3.0
# make an extra anion
variable qmodify index 1
variable vdiff index 1
# these values can be changed, e.g. ${LAMMPS_EXECUTABLE} -i in.nonneut -var qmodify 0.9 -var vdiff -2
# fix electrode/* needs equal style variables:
variable qmodify_equal equal v_qmodify
variable vdiff_equal equal v_vdiff
create_atoms 4 single 16.1 17.2 0
set atom 3777 charge $(-v_qmodify)
fix c top electrode/conp v_vdiff_equal 1.979 couple bot 0 etypes on qtotal v_qmodify_equal
# to test electrode/thermo:
# variable vbot equal 0
# fix c top electrode/thermo v_vdiff_equal 1.979 couple bot v_vbot etypes on qtotal v_qmodify_equal temp 310 100 12309 # symm on
variable dv equal f_c[1]-f_c[2]
variable qelec equal c_qbot+c_qtop
compute qall all reduce sum v_q # total system charge
thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_c[1] f_c[2] v_dv v_qelec c_qall
run 500

33
examples/PACKAGES/electrode/graph-il/in.nonneut2 Normal file
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@ -0,0 +1,33 @@
# electrodes, overall non-neutral
# for graphene-ionic liquid supercapacitor
boundary p p f # slab calculation
include settings.mod # styles, groups, computes and fixes
kspace_modify slab 3.0
# make an extra anion
variable qmodify index 1
variable vdiff index 1
# these values can be changed, e.g. ${LAMMPS_EXECUTABLE} -i in.nonneut -var qmodify 0.9 -var vdiff -2
create_atoms 4 single 16.1 17.2 0
set atom 3777 charge $(-v_qmodify)
fix c top electrode/conp v_vtop 1.979 couple bot v_vbot etypes on # symm on
# to test electrode/thermo:
#fix c top electrode/thermo v_vtop 1.979 couple bot v_vbot etypes on temp 310 100 12309 symm off
#but it looks like update_psi() is hardwired to impose electroneutrality
variable csum equal f_c[1][2]+f_c[1][3]+f_c[2][2]+f_c[2][3]
variable cdiff equal 0.5*(f_c[1][2]-f_c[2][3])
variable qdeficit equal v_qmodify-f_c[1][1]-f_c[2][1]-v_cdiff*v_vdiff
variable vphi equal v_qdeficit/v_csum
variable vtop equal v_vphi+0.5*v_vdiff
variable vbot equal v_vphi-0.5*v_vdiff
variable dv equal v_vtop-v_vbot
variable qelec equal c_qbot+c_qtop
compute qall all reduce sum v_q # total system charge
thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_c[1] f_c[2] v_dv v_qelec c_qall
run 500

86
src/ELECTRODE/fix_electrode_conp.cpp
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@ -103,20 +103,23 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
mult_time = 0;
n_call = n_cg_step = 0;
qtotal = 0.;
qtotal_var_style = VarStyle::UNSET;
// read fix command
fixname = std::string(arg[0]);
groups = std::vector<int>(1, igroup);
group_bits = std::vector<int>(1, groupbit);
group_psi_var_names = std::vector<std::string>(1);
group_psi_var_styles = std::vector<VarStyle>(1, VarStyle::CONST);
group_psi = std::vector<double>(1);
group_psi_const = std::vector<double>(1);
etypes_neighlists = false;
if (strstr(arg[3], "v_") == arg[3]) {
std::string vname = arg[3];
group_psi_var_names[0] = vname.substr(2);
group_psi_var_styles[0] = VarStyle::EQUAL;
} else
group_psi[0] = utils::numeric(FLERR, arg[3], false, lmp);
group_psi_const[0] = utils::numeric(FLERR, arg[3], false, lmp);
char *eta_str = arg[4];
eta = utils::numeric(FLERR, eta_str, false, lmp);
int iarg = 5;
@ -132,12 +135,12 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
std::string vname = arg[iarg];
group_psi_var_names.push_back(vname.substr(2));
group_psi_var_styles.push_back(VarStyle::EQUAL);
group_psi.push_back(0.);
group_psi_const.push_back(0.);
} else {
std::string null;
group_psi_var_names.push_back(null);
group_psi_var_styles.push_back(VarStyle::CONST);
group_psi.push_back(utils::numeric(FLERR, arg[iarg], false, lmp));
group_psi_const.push_back(utils::numeric(FLERR, arg[iarg], false, lmp));
}
} else if ((strcmp(arg[iarg], "algo") == 0)) {
if (!default_algo) error->one(FLERR, fmt::format("Algorithm can be set once, only"));
@ -195,6 +198,19 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
thermo_temp = force->boltz / force->qe2f * 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);
} else if ((strcmp(arg[iarg], "qtotal") == 0)) {
if (iarg + 2 > narg) error->all(FLERR, "Need one argument after qtotal keyword");
if (strcmp(this->style, "electrode/conq") == 0)
error->all(FLERR, "qtotal keyword not available for electrode/conq");
++iarg;
if (strstr(arg[iarg], "v_") == arg[iarg]) {
std::string vname = arg[iarg];
qtotal_var_name = vname.substr(2);
qtotal_var_style = VarStyle::EQUAL;
} else {
qtotal = utils::numeric(FLERR, arg[iarg], false, lmp);
qtotal_var_style = VarStyle::CONST;
}
// toggle parameters
} else if ((strcmp(arg[iarg], "etypes") == 0)) {
etypes_neighlists = utils::logical(FLERR, arg[++iarg], false, lmp);
@ -208,6 +224,12 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
iarg++;
}
if (qtotal_var_style != VarStyle::UNSET) {
if (symm) error->all(FLERR, "{} cannot use qtotal keyword with symm on", this->style);
}
// computatonal potential
group_psi = std::vector<double>(groups.size());
// union of all coupled groups
std::string union_group = "conp_group";
std::string group_cmd = union_group + " union";
@ -225,6 +247,7 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
if (need_elec_vector) elec_vector = new ElectrodeVector(lmp, igroup, igroup, eta, false);
assert(groups.size() == group_bits.size());
assert(groups.size() == group_psi.size());
assert(groups.size() == group_psi_const.size());
assert(groups.size() == group_psi_var_styles.size());
assert(groups.size() == group_psi_var_names.size());
assert(igroup == elyt_vector->igroup);
@ -396,7 +419,8 @@ void FixElectrodeConp::init()
for (char *fix_id : integrate_ids)
error->warning(
FLERR,
"Electrode atoms are integrated by fix {}, but fix electrode is using a matrix method. For "
"Electrode atoms are integrated by fix {}, but fix electrode is using a matrix method. "
"For "
"mobile electrodes use the conjugate gradient algorithm without matrix ('algo cg').",
fix_id);
}
@ -475,6 +499,7 @@ void FixElectrodeConp::setup_post_neighbor()
// get equal-style variable ids:
group_psi_var_ids = std::vector<int>(num_of_groups, -1);
for (int g = 0; g < num_of_groups; g++) {
assert(group_psi_var_styles[g] != VarStyle::UNSET);
if (group_psi_var_styles[g] == VarStyle::CONST) continue;
const char *var_name = group_psi_var_names[g].c_str();
int var_id = input->variable->find(var_name);
@ -485,6 +510,16 @@ void FixElectrodeConp::setup_post_neighbor()
fmt::format("Variable '{}' for fix electrode is not equal-style", var_name));
group_psi_var_ids[g] = var_id;
}
if (qtotal_var_style == VarStyle::EQUAL) {
const char *var_name = qtotal_var_name.c_str();
int var_id = input->variable->find(var_name);
if (var_id < 0)
error->all(FLERR, fmt::format("Variable '{}' for fix electrode does not exist", var_name));
if (!input->variable->equalstyle(var_id))
error->all(FLERR,
fmt::format("Variable '{}' for fix electrode is not equal-style", var_name));
qtotal_var_id = var_id;
}
// pair and list setups:
@ -834,6 +869,8 @@ void FixElectrodeConp::update_charges()
}
MPI_Allreduce(MPI_IN_PLACE, &sb_charges.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world);
update_psi(); // use for equal-style and conq
if (qtotal_var_style != VarStyle::UNSET)
update_psi_qtotal(); // use for qtotal; same for thermo
for (int g = 0; g < num_of_groups; g++)
for (int j = 0; j < nlocalele; j++) q_local[j] += sd_vectors[g][list_iele[j]] * group_psi[g];
MPI_Barrier(world);
@ -936,12 +973,22 @@ std::vector<double> FixElectrodeConp::gather_ngroup(std::vector<double> x_local)
}
/* ----------------------------------------------------------------------
ensure total electrode charge is 0 if symm
ensure total electrode charge is 0 if symm and qtotal if qtotal is used
------------------------------------------------------------------------- */
std::vector<double> FixElectrodeConp::constraint_correction(std::vector<double> x)
{
return constraint_projection(x);
if (symm || qtotal_var_style != VarStyle::UNSET) {
if (qtotal_var_style == VarStyle::EQUAL) qtotal = input->variable->compute_equal(qtotal_var_id);
double sum = 0.;
for (double xi : x) sum += xi;
MPI_Allreduce(MPI_IN_PLACE, &sum, 1, MPI_DOUBLE, MPI_SUM, world);
if (qtotal_var_style != VarStyle::UNSET) sum -= qtotal;
sum /= ngroup;
for (double &xi : x) xi -= sum;
return x;
}
return x;
}
/* ----------------------------------------------------------------------
@ -950,7 +997,7 @@ std::vector<double> FixElectrodeConp::constraint_correction(std::vector<double>
std::vector<double> FixElectrodeConp::constraint_projection(std::vector<double> x)
{
if (symm) {
if (symm || qtotal_var_style != VarStyle::UNSET) {
double sum = 0.;
for (double xi : x) sum += xi;
MPI_Allreduce(MPI_IN_PLACE, &sum, 1, MPI_DOUBLE, MPI_SUM, world);
@ -1008,13 +1055,28 @@ std::vector<double> FixElectrodeConp::times_elastance(std::vector<double> x)
void FixElectrodeConp::update_psi()
{
for (int g = 0; g < num_of_groups; g++) {
if (group_psi_var_styles[g] == VarStyle::CONST) continue;
group_psi[g] = input->variable->compute_equal(group_psi_var_ids[g]);
if (group_psi_var_styles[g] == VarStyle::CONST)
group_psi[g] = group_psi_const[g];
else
group_psi[g] = input->variable->compute_equal(group_psi_var_ids[g]);
}
}
/* ---------------------------------------------------------------------- */
void FixElectrodeConp::update_psi_qtotal()
{
if (qtotal_var_style == VarStyle::EQUAL) qtotal = input->variable->compute_equal(qtotal_var_id);
double q_current = 0.;
for (int i = 0; i < num_of_groups; i++) {
q_current += sb_charges[i];
for (int j = 0; j < num_of_groups; j++) q_current += macro_capacitance[i][j] * group_psi[j];
}
double add_psi = (qtotal - q_current) / macro_capacitance_sum;
for (int i = 0; i < num_of_groups; i++) group_psi[i] += add_psi;
}
/* ---------------------------------------------------------------------- */
void FixElectrodeConp::compute_macro_matrices()
{
assert(algo == Algo::MATRIX_INV);
@ -1070,6 +1132,10 @@ void FixElectrodeConp::compute_macro_matrices()
}
}
}
macro_capacitance_sum = 0.;
for (int i = 0; i < num_of_groups; i++)
for (int j = 0; j < num_of_groups; j++) macro_capacitance_sum += macro_capacitance[i][j];
}
/* ---------------------------------------------------------------------- */

10
src/ELECTRODE/fix_electrode_conp.h
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@ -71,7 +71,7 @@ class FixElectrodeConp : public Fix {
protected:
enum class Algo { MATRIX_INV, MATRIX_CG, CG };
enum class VarStyle { CONST, EQUAL };
enum class VarStyle { CONST, EQUAL, UNSET };
virtual void update_psi();
virtual void pre_update(){};
virtual void recompute_potential(std::vector<double>, std::vector<double>){};
@ -80,6 +80,7 @@ class FixElectrodeConp : public Fix {
virtual void compute_macro_matrices();
std::vector<double> ele_ele_interaction(const std::vector<double> &);
std::vector<double> group_psi;
std::vector<double> group_psi_const; // needed to undo qtotal psi updates
std::vector<int> group_bits;
std::vector<int> groups;
int num_of_groups;
@ -101,6 +102,10 @@ class FixElectrodeConp : public Fix {
std::string fixname; // used by electrode/ffield to set up internal efield
bool intelflag;
inline virtual void intel_pack_buffers() {}
double qtotal;
std::string qtotal_var_name;
int qtotal_var_id;
VarStyle qtotal_var_style;
private:
std::string output_file_inv, output_file_mat, output_file_vec;
@ -143,6 +148,9 @@ class FixElectrodeConp : public Fix {
std::vector<double> gather_ngroup(std::vector<double>);
std::vector<double> gather_elevec_local(ElectrodeVector *);
void set_charges(std::vector<double>);
// qtotal
double macro_capacitance_sum;
void update_psi_qtotal();
// fix-specific electrode ID storage system:

5
src/ELECTRODE/fix_electrode_thermo.cpp
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@ -47,7 +47,8 @@ FixElectrodeThermo::FixElectrodeThermo(LAMMPS *lmp, int narg, char **arg) :
if (thermo_time < SMALL) error->all(FLERR, "Keyword temp not set or zero in electrode/thermo");
thermo_random = new RanMars(lmp, thermo_init);
if (group_psi_var_styles[0] == VarStyle::CONST) delta_psi_0 = group_psi[1] - group_psi[0];
if (group_psi_var_styles[0] == VarStyle::CONST)
delta_psi_0 = group_psi_const[1] - group_psi_const[0];
}
/* ----------------------------------------------------------------------- */
@ -102,7 +103,7 @@ void FixElectrodeThermo::update_psi()
double const delta_psi = group_psi_old[1] - group_psi_old[0];
// target potential difference from input parameters
if (group_psi_var_styles[0] != VarStyle::CONST) {
if (group_psi_var_styles[0] == VarStyle::EQUAL) {
delta_psi_0 = input->variable->compute_equal(group_psi_var_ids[1]) -
input->variable->compute_equal(group_psi_var_ids[0]);
}