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implement compute_array

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This commit is contained in:
srtee
2022-05-02 23:24:00 +10:00
parent eb5d867adf
commit 0855d62bfd
9 changed files with 126 additions and 259 deletions
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116
src/ELECTRODE/fix_electrode_conp.cpp
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@ -22,8 +22,8 @@
#include "compute.h"
#include "domain.h"
#include "electrode_accel_interface.h"
#include "electrode_matrix.h"
#include "electrode_math.h"
#include "electrode_matrix.h"
#include "electrode_vector.h"
#include "error.h"
#include "force.h"
@ -73,7 +73,7 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
ffield = false;
thermo_time = 0.;
scalar_flag = 1;
vector_flag = 1;
array_flag = 1;
top_group = 0;
intelflag = false;
tfflag = false;
@ -222,7 +222,8 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
"Cannot write elastance matrix if reading capacitance matrix "
"from file");
num_of_groups = static_cast<int>(groups.size());
size_vector = num_of_groups;
size_array_rows = num_of_groups;
size_array_cols = 2 + 2 * num_of_groups;
// check groups are consistent
int *mask = atom->mask;
@ -260,12 +261,6 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
// 0 1 2 3 return 4 if successful
// fix_modify fxupdate set v [group] [var]
// fix_modify fxupdate set qsb [group] [var]
// 0 1 2 3 4 return 5 if successful
// fix_modify fxupdate set mc [group1] [group2] [var]
// fix_modify fxupdate set me [group1] [group2] [var]
int FixElectrodeConp::modify_param(int narg, char **arg)
{
if (strcmp(arg[0], "tf") == 0) {
@ -306,49 +301,6 @@ int FixElectrodeConp::modify_param(int narg, char **arg)
timer_flag = utils::logical(FLERR, arg[1], false, lmp);
return 2;
} else if (strcmp(arg[0], "set") == 0) {
if (strcmp(arg[1], "v") == 0 || strcmp(arg[1], "qsb") == 0) {
if (narg != 4)
error->all(FLERR,
fmt::format("Incorrect number of arguments for fix_modify set {}", arg[1]));
int outputgrp = groupnum_from_name(arg[2]);
int outputvar = input->variable->find(arg[3]);
if (outputvar < 0)
error->all(FLERR,
fmt::format("Variable {} for fix_modify electrode does not exist", arg[3]));
if (!input->variable->internalstyle(outputvar))
error->all(FLERR,
fmt::format("Variable {} for fix_modify electrode is invalid style", arg[3]));
if (strcmp(arg[1], "v") == 0)
setvars_types.push_back(V);
else
setvars_types.push_back(QSB);
setvars_groups.push_back(outputgrp);
setvars_vars.push_back(outputvar);
return 4;
} else if (strcmp(arg[1], "mc") == 0 || strcmp(arg[1], "me") == 0) {
if (narg != 5)
error->all(FLERR,
fmt::format("Incorrect number of arguments for fix_modify set {}", arg[1]));
int outputgrpi = groupnum_from_name(arg[2]);
int outputgrpj = groupnum_from_name(arg[3]);
int outputgrpij = outputgrpi * num_of_groups + outputgrpj;
int outputvar = input->variable->find(arg[4]);
if (outputvar < 0)
error->all(FLERR,
fmt::format("Variable {} for fix_modify electrode does not exist", arg[4]));
if (!input->variable->internalstyle(outputvar))
error->all(FLERR,
fmt::format("Variable {} for fix_modify electrode is invalid style", arg[4]));
if (strcmp(arg[1], "mc") == 0)
setvars_types.push_back(MC);
else
setvars_types.push_back(ME);
setvars_groups.push_back(outputgrpij);
setvars_vars.push_back(outputvar);
return 5;
} else
error->all(FLERR, "Invalid set option for fix_modify electrode");
} else
error->all(FLERR, "Invalid argument for fix_modify electrode");
return 0;
@ -452,10 +404,6 @@ void FixElectrodeConp::setup_post_neighbor()
int *mask = atom->mask;
tagint *tag = atom->tag;
// setvars asserts:
assert(setvars_groups.size() == setvars_vars.size());
assert(setvars_groups.size() == setvars_types.size());
// if Thomas-Fermi, make sure all electrode atoms have parameters
if (tfflag) {
int unset_tf = 0;
@ -539,8 +487,8 @@ void FixElectrodeConp::setup_post_neighbor()
compute_macro_matrices();
MPI_Barrier(world);
if (timer_flag && (comm->me == 0))
utils::logmesg(lmp,
fmt::format("SD-vector and macro matrices time: {:.4g} s\n", MPI_Wtime() - start));
utils::logmesg(
lmp, fmt::format("SD-vector and macro matrices time: {:.4g} s\n", MPI_Wtime() - start));
// initial charges and b vector
update_charges();
@ -789,9 +737,7 @@ void FixElectrodeConp::update_charges()
gather_elevec(charge_iele);
MPI_Allreduce(MPI_IN_PLACE, &sb_charges.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world);
update_setvars(QSB);
update_psi(); // use for equal-style and conq
update_setvars(V); // push psi into 'fix_modify set' vars
update_psi(); // use for equal-style and conq
for (int g = 0; g < num_of_groups; g++)
for (int j = 0; j < ngroup; j++) { charge_iele[j] += sd_vectors[g][j] * group_psi[g]; }
@ -820,34 +766,6 @@ void FixElectrodeConp::update_psi()
/* ---------------------------------------------------------------------- */
void FixElectrodeConp::update_setvars(int vtype)
{
int num_of_vars = static_cast<int>(setvars_groups.size());
for (int v = 0; v < num_of_vars; v++) {
if (vtype != setvars_types[v]) continue;
switch (vtype) {
case V:
input->variable->internal_set(setvars_vars[v], group_psi[setvars_groups[v]]);
break;
case QSB:
input->variable->internal_set(setvars_vars[v], sb_charges[setvars_groups[v]]);
break;
case MC: {
int groupi = setvars_groups[v] / num_of_groups;
int groupj = setvars_groups[v] % num_of_groups;
input->variable->internal_set(setvars_vars[v], macro_capacitance[groupi][groupj]);
} break;
case ME: {
int groupi = setvars_groups[v] / num_of_groups;
int groupj = setvars_groups[v] % num_of_groups;
input->variable->internal_set(setvars_vars[v], macro_elastance[groupi][groupj]);
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixElectrodeConp::compute_macro_matrices()
{
macro_capacitance =
@ -902,9 +820,6 @@ void FixElectrodeConp::compute_macro_matrices()
}
}
}
update_setvars(MC);
update_setvars(ME);
}
/* ---------------------------------------------------------------------- */
@ -915,9 +830,22 @@ double FixElectrodeConp::compute_scalar()
}
/* ---------------------------------------------------------------------- */
double FixElectrodeConp::compute_vector(int i)
double FixElectrodeConp::compute_array(int i, int j)
{
return group_psi[i];
if (i < 0 || i >= num_of_groups) error->all(FLERR, "invalid fix electrode array row reference");
if (j < 0)
error->all(FLERR, "invalid fix electrode array column reference");
else if (j == 0)
return group_psi[i];
else if (j == 1)
return sb_charges[i];
else if (j <= num_of_groups + 1)
return macro_capacitance[i][j - 2];
else if (j <= 2 * num_of_groups + 1)
return macro_elastance[i][j - num_of_groups - 2];
else
error->all(FLERR, "invalid fix electrode array column reference");
return 0.; // avoid -Wreturn-type warning
}
/* ---------------------------------------------------------------------- */