diff --git a/doc/src/fix_electrode.rst b/doc/src/fix_electrode.rst index 5685482a71..d807da7fd2 100644 --- a/doc/src/fix_electrode.rst +++ b/doc/src/fix_electrode.rst @@ -70,6 +70,8 @@ Syntax 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* + *eta* value = d_propname + d_propname = a custom double vector defined via fix property/atom Examples """""""" @@ -264,6 +266,11 @@ 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). +The keyword *eta* takes the name of a custom double vector defined via fix +property/atom. The values will be used instead of the standard eta value. The +property/atom fix must be for vector of double values and use the *ghost on* +option. + Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/examples/PACKAGES/electrode/madelung/data.eta b/examples/PACKAGES/electrode/madelung/data.eta new file mode 100644 index 0000000000..b05700a4ab --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/data.eta @@ -0,0 +1,34 @@ +LAMMPS data file via write_data, version 24 Dec 2020, timestep = 0 + +4 atoms +3 atom types + +0 1 xlo xhi +0 1 ylo yhi +-10 10 zlo zhi + +Masses + +1 196.966553 +2 196.966553 +3 1.0 + +Pair Coeffs # lj/cut/coul/long + +1 0 0 +2 0 0 +3 0 0 + +Atoms # full + +1 1 1 0.00 0.00 0.00 -2.00 # bottom electrode +2 2 2 0.00 0.00 0.00 2.00 # top electrode +3 3 3 0.50 0.00 0.00 -1.00 # bottom electrolyte +4 3 3 -0.50 0.00 0.00 1.00 # top electrolyte + +ETA + +1 2.0 +2 2.0 +3 0 +4 0 diff --git a/examples/PACKAGES/electrode/madelung/data.eta_mix b/examples/PACKAGES/electrode/madelung/data.eta_mix new file mode 100644 index 0000000000..9322ebd662 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/data.eta_mix @@ -0,0 +1,34 @@ +LAMMPS data file via write_data, version 24 Dec 2020, timestep = 0 + +4 atoms +3 atom types + +0 1 xlo xhi +0 1 ylo yhi +-10 10 zlo zhi + +Masses + +1 196.966553 +2 196.966553 +3 1.0 + +Pair Coeffs # lj/cut/coul/long + +1 0 0 +2 0 0 +3 0 0 + +Atoms # full + +1 1 1 0.00 0.00 0.00 -2.00 # bottom electrode +2 2 2 0.00 0.00 0.00 2.00 # top electrode +3 3 3 0.50 0.00 0.00 -1.00 # bottom electrolyte +4 3 3 -0.50 0.00 0.00 1.00 # top electrolyte + +ETA + +1 0.5 +2 3.0 +3 0 +4 0 diff --git a/examples/PACKAGES/electrode/madelung/eval.py b/examples/PACKAGES/electrode/madelung/eval.py index 2f5a355d9b..feda0e384e 100644 --- a/examples/PACKAGES/electrode/madelung/eval.py +++ b/examples/PACKAGES/electrode/madelung/eval.py @@ -1,7 +1,7 @@ #!/usr/env/python3 -import sys import os.path as op +import sys def rel_error(out, ref): @@ -49,5 +49,5 @@ for label, ref, out in out_lines: error = rel_error(out, ref) lines.append(f"{label}: {out:.5f}, {error:.5f}\n") -with open("madelung.txt", 'a') as f: +with open("madelung.txt", "a") as f: f.writelines(lines) diff --git a/examples/PACKAGES/electrode/madelung/in.eta b/examples/PACKAGES/electrode/madelung/in.eta new file mode 100644 index 0000000000..d928f8fed0 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.eta @@ -0,0 +1,17 @@ +atom_style full +units real +boundary p p f + +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc +pair_style lj/cut/coul/long 12 + +fix feta all property/atom d_eta ghost yes +read_data data.eta fix feta NULL ETA + +include "settings_eta.mod" + +fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.eta_cg b/examples/PACKAGES/electrode/madelung/in.eta_cg new file mode 100644 index 0000000000..e04db318d5 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.eta_cg @@ -0,0 +1,17 @@ +atom_style full +units real +boundary p p f + +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc +pair_style lj/cut/coul/long 12 + +fix feta all property/atom d_eta ghost yes +read_data data.eta_mix fix feta NULL ETA + +include "settings_eta.mod" + +fix conp bot electrode/conp 0 2 couple top 1 symm on algo cg 1e-6 eta d_eta + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.eta_mix b/examples/PACKAGES/electrode/madelung/in.eta_mix new file mode 100644 index 0000000000..d4bcf71225 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.eta_mix @@ -0,0 +1,17 @@ +atom_style full +units real +boundary p p f + +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc +pair_style lj/cut/coul/long 12 + +fix feta all property/atom d_eta ghost on +read_data data.eta_mix fix feta NULL ETA + +include "settings_eta.mod" + +fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/plate_cap.py b/examples/PACKAGES/electrode/madelung/plate_cap.py index 62d52fe102..fcca166869 100755 --- a/examples/PACKAGES/electrode/madelung/plate_cap.py +++ b/examples/PACKAGES/electrode/madelung/plate_cap.py @@ -3,7 +3,6 @@ import numpy as np from scipy.special import erf -ETA = 2 SQRT2 = np.sqrt(2) COULOMB = 332.06371 # Coulomb constant in Lammps 'real' units QE2F = 23.060549 @@ -17,14 +16,14 @@ def lattice(length): return np.array(np.meshgrid(x, y)).T.reshape(-1, 2) -def a_element(r): +def a_element(r, eta): """Coulomb contribution of two Gaussians""" - return erf(ETA / SQRT2 * r) / r + return erf(eta * r) / r -def b_element(r, q): +def b_element(r, q, eta): """Coulomb contribution of a Gaussian with a point charge""" - return q * erf(ETA * r) / r + return q * erf(eta * r) / r a = 1 # nearest neighbor distance i.e. lattice constant / sqrt(2) @@ -36,59 +35,65 @@ v = np.array([-0.5, 0.5]) * (QE2F / COULOMB) # distances to images within electrode and to opposite electrode distances = a * np.linalg.norm(lattice(LENGTH), axis=1) -opposite_distances = np.sqrt(np.square(distances) + distance_plates ** 2) +opposite_distances = np.sqrt(np.square(distances) + distance_plates**2) -# self interaction and within original box -A_11 = np.sqrt(2 / np.pi) * ETA -A_12 = erf(ETA * distance_plates / SQRT2) / distance_plates +for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]: + eta_mix = np.prod(eta_elec) / np.sqrt(np.sum(np.square(eta_elec))) + # self interaction and within original box + A_11 = np.sqrt(2 / np.pi) * eta_elec[0] + A_22 = np.sqrt(2 / np.pi) * eta_elec[1] + A_12 = erf(eta_mix * distance_plates) / distance_plates -# interaction with periodic images -A_11 += 4 * np.sum(a_element(distances)) -A_12 += 4 * np.sum(a_element(opposite_distances)) -A = np.array([[A_11, A_12], [A_12, A_11]]) -inv = np.linalg.inv(A) -e = np.array([1, 1]) -inv -= np.matmul(inv, np.matmul(np.outer(e, e), inv)) / np.dot(e, np.dot(inv, e)) + # interaction with periodic images + A_11 += 4 * np.sum(a_element(distances, eta_elec[0] / SQRT2)) + A_22 += 4 * np.sum(a_element(distances, eta_elec[1] / SQRT2)) + A_12 += 4 * np.sum(a_element(opposite_distances, eta_mix)) + A = np.array([[A_11, A_12], [A_12, A_22]]) + inv = np.linalg.inv(A) + e = np.array([1, 1]) + inv -= np.matmul(inv, np.matmul(np.outer(e, e), inv)) / np.dot(e, np.dot(inv, e)) -# electrode-electrolyte interaction -b = [] -for x in x_elec: - bi = 0 - for y, q in zip(x_elyt, q_elyt): - d = abs(y - x) - bi += b_element(d, q) - image_distances = np.sqrt(np.square(distances) + d ** 2) - bi += 4 * np.sum(b_element(image_distances, q)) - b.append(bi) -b = np.array(b) + # electrode-electrolyte interaction + b = [] + for x, eta in zip(x_elec, eta_elec): + bi = 0 + for y, q in zip(x_elyt, q_elyt): + d = abs(y - x) + bi += b_element(d, q, eta) + image_distances = np.sqrt(np.square(distances) + d**2) + bi += 4 * np.sum(b_element(image_distances, q, eta)) + b.append(bi) + b = np.array(b) -# electrolyte-electrolyte energy -elyt_11 = 4 * np.sum(1 / distances) -distance_elyt = x_elyt[1] - x_elyt[0] -elyt_12 = 1 / distance_elyt + 4 * np.sum( - 1 / np.sqrt(np.square(distances) + distance_elyt ** 2) -) -elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]]) -energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt)) - -# electrode charges and energy -q = np.dot(inv, v - b) -energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt) - -print( - "length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A" -) -print( - ", ".join( - [ - str(LENGTH), - f"{energy:.8f}", - f"{q[0]:.10f}", - f"{q[1]:.10f}", - f"{inv[0, 0]:.10f}", - f"{inv[0, 1]:.10f}", - f"{b[0]:.8f}", - f"{b[1]:.8f}", - ] + # electrolyte-electrolyte energy + elyt_11 = 4 * np.sum(1 / distances) + distance_elyt = x_elyt[1] - x_elyt[0] + elyt_12 = 1 / distance_elyt + 4 * np.sum( + 1 / np.sqrt(np.square(distances) + distance_elyt**2) ) -) + elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]]) + energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt)) + + # electrode charges and energy + q = np.dot(inv, v - b) + energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt) + + with open(f"plate_cap{name}.csv", "w") as f: + f.write( + "length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A\n" + ) + f.write( + ", ".join( + [ + str(LENGTH), + f"{energy:.8f}", + f"{q[0]:.10f}", + f"{q[1]:.10f}", + f"{inv[0, 0]:.10f}", + f"{inv[0, 1]:.10f}", + f"{b[0]:.8f}", + f"{b[1]:.8f}", + ] + ) + + "\n" + ) diff --git a/examples/PACKAGES/electrode/madelung/settings_eta.mod b/examples/PACKAGES/electrode/madelung/settings_eta.mod new file mode 100644 index 0000000000..aee63bf2e9 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/settings_eta.mod @@ -0,0 +1,19 @@ + +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +group bot type 1 +group top type 2 + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop + diff --git a/examples/PACKAGES/electrode/madelung/test.sh b/examples/PACKAGES/electrode/madelung/test.sh index edac04f5b1..a558ee6711 100644 --- a/examples/PACKAGES/electrode/madelung/test.sh +++ b/examples/PACKAGES/electrode/madelung/test.sh @@ -7,17 +7,27 @@ if [ ! -f $lmpbin ]; then fi ref_out="plate_cap.csv" -if [ ! -f $ref_out ]; then +ref_mix_out="plate_cap_eta_mix.csv" +if [ ! -f $ref_out ] || [ ! -f $ref_mix_out ]; then echo "Generating reference data" - python3 plate_cap.py > $ref_out + python3 plate_cap.py fi echo "Running Lammps inputs" +# w/o eta mixing rm -rf madelung.txt && touch madelung.txt -for file in in.*; do +for file in in.eta in.ewald-ew3dc in.ewald-ew2d in.pppm-ew3dc in.cg; do printf "\n$file\n" >> madelung.txt rm -f out.csv inv.csv vec.csv $lmpbin -i $file &> /dev/null python3 eval.py $ref_out out.csv inv.csv vec.csv done + +# with eta mixing +for file in in.eta_mix in.eta_cg; do + printf "\n$file\n" >> madelung.txt + rm -f out.csv inv.csv vec.csv + $lmpbin -i $file &> /dev/null + python3 eval.py $ref_mix_out out.csv inv.csv vec.csv +done cat madelung.txt diff --git a/src/ELECTRODE/electrode_matrix.cpp b/src/ELECTRODE/electrode_matrix.cpp index 7be9119c62..d917fb1f97 100644 --- a/src/ELECTRODE/electrode_matrix.cpp +++ b/src/ELECTRODE/electrode_matrix.cpp @@ -43,6 +43,7 @@ ElectrodeMatrix::ElectrodeMatrix(LAMMPS *lmp, int electrode_group, double eta) : groupbit = group->bitmask[igroup]; ngroup = group->count(igroup); this->eta = eta; + etaflag = false; tfflag = false; } @@ -72,6 +73,14 @@ void ElectrodeMatrix::setup_tf(const std::map &tf_types) /* ---------------------------------------------------------------------- */ +void ElectrodeMatrix::setup_eta(int index) +{ + etaflag = true; + eta_index = index; +} + +/* ---------------------------------------------------------------------- */ + void ElectrodeMatrix::compute_array(double **array, bool timer_flag) { // setting all entries of coulomb matrix to zero @@ -115,8 +124,6 @@ void ElectrodeMatrix::pair_contribution(double **array) int nlocal = atom->nlocal; int newton_pair = force->newton_pair; - double const etaij = eta * eta / sqrt(2.0 * eta * eta); // see mw ewald theory eq. (29)-(30) - // neighbor list will be ready because called from post_neighbor inum = list->inum; ilist = list->ilist; @@ -135,6 +142,7 @@ void ElectrodeMatrix::pair_contribution(double **array) xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; + double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta; itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; @@ -152,6 +160,9 @@ void ElectrodeMatrix::pair_contribution(double **array) jtype = type[j]; if (rsq < cutsq[itype][jtype]) { + double const eta_j = etaflag ? atom->dvector[eta_index][j] : eta; + double const etaij = eta_i * eta_j / sqrt(eta_i * eta_i + eta_j * eta_j); + r = sqrt(rsq); rinv = 1.0 / r; aij = rinv; @@ -178,7 +189,10 @@ void ElectrodeMatrix::self_contribution(double **array) const double preta = MY_SQRT2 / MY_PIS; for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { array[mpos[i]][mpos[i]] += preta * eta - selfint; } + if (mask[i] & groupbit) { + double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta; + array[mpos[i]][mpos[i]] += preta * eta_i - selfint; + } } /* ---------------------------------------------------------------------- */ diff --git a/src/ELECTRODE/electrode_matrix.h b/src/ELECTRODE/electrode_matrix.h index 8499cfdb34..1c64d8a4c4 100644 --- a/src/ELECTRODE/electrode_matrix.h +++ b/src/ELECTRODE/electrode_matrix.h @@ -30,6 +30,7 @@ class ElectrodeMatrix : protected Pointers { ElectrodeMatrix(class LAMMPS *, int, double); void setup(const std::unordered_map &, class Pair *, class NeighList *); void setup_tf(const std::map &); + void setup_eta(int); void compute_array(double **, bool); int igroup; @@ -39,6 +40,8 @@ class ElectrodeMatrix : protected Pointers { double **cutsq; double g_ewald, eta; bool tfflag; + bool etaflag; + int eta_index; std::map tf_types; std::unordered_map tag_to_iele; bool assigned; diff --git a/src/ELECTRODE/electrode_vector.cpp b/src/ELECTRODE/electrode_vector.cpp index 245ba57727..a2eaf784c5 100644 --- a/src/ELECTRODE/electrode_vector.cpp +++ b/src/ELECTRODE/electrode_vector.cpp @@ -29,6 +29,7 @@ #include "neigh_list.h" #include "pair.h" +#include #include #include @@ -47,6 +48,7 @@ ElectrodeVector::ElectrodeVector(LAMMPS *lmp, int sensor_group, int source_group source_grpbit = group->bitmask[source_group]; this->eta = eta; tfflag = false; + etaflag = false; kspace_time_total = 0; pair_time_total = 0; @@ -93,6 +95,14 @@ void ElectrodeVector::setup_tf(const std::map &tf_types) /* ---------------------------------------------------------------------- */ +void ElectrodeVector::setup_eta(int index) +{ + etaflag = true; + eta_index = index; +} + +/* ---------------------------------------------------------------------- */ + void ElectrodeVector::compute_vector(double *vector) { MPI_Barrier(world); @@ -121,7 +131,6 @@ void ElectrodeVector::compute_vector(double *vector) void ElectrodeVector::pair_contribution(double *vector) { - double const etaij = eta * MY_ISQRT2; double **x = atom->x; double *q = atom->q; int *type = atom->type; @@ -142,6 +151,7 @@ void ElectrodeVector::pair_contribution(double *vector) double const xtmp = x[i][0]; double const ytmp = x[i][1]; double const ztmp = x[i][2]; + double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta; int itype = type[i]; int *jlist = firstneigh[i]; int jnum = numneigh[i]; @@ -158,18 +168,22 @@ void ElectrodeVector::pair_contribution(double *vector) double const rsq = delx * delx + dely * dely + delz * delz; int jtype = type[j]; if (rsq >= cutsq[itype][jtype]) continue; + double const eta_j = etaflag ? atom->dvector[eta_index][j] : eta; + double etaij; + if (i_in_sensor && j_in_sensor) + etaij = eta_i * eta_j / sqrt(eta_i * eta_i + eta_j * eta_j); + else if (i_in_sensor) + etaij = eta_i; + else { + assert(j_in_sensor); + etaij = eta_j; + } double const r = sqrt(rsq); double const rinv = 1.0 / r; double aij = rinv; aij *= ElectrodeMath::safe_erfc(g_ewald * r); - if (invert_source) - aij -= ElectrodeMath::safe_erfc(eta * r) * rinv; - else - aij -= ElectrodeMath::safe_erfc(etaij * r) * rinv; - if (i_in_sensor) { - vector[i] += aij * q[j]; - //} else if (j_in_sensor) { - } + aij -= ElectrodeMath::safe_erfc(etaij * r) * rinv; + if (i_in_sensor) { vector[i] += aij * q[j]; } if (j_in_sensor && (!invert_source || !i_in_sensor)) { vector[j] += aij * q[i]; } } } @@ -189,9 +203,10 @@ void ElectrodeVector::self_contribution(double *vector) for (int ii = 0; ii < inum; ii++) { int const i = ilist[ii]; + double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta; bool const i_in_sensor = (mask[i] & groupbit); bool const i_in_source = !!(mask[i] & source_grpbit) != invert_source; - if (i_in_sensor && i_in_source) vector[i] += (preta * eta - selfint) * q[i]; + if (i_in_sensor && i_in_source) vector[i] += (preta * eta_i - selfint) * q[i]; } } diff --git a/src/ELECTRODE/electrode_vector.h b/src/ELECTRODE/electrode_vector.h index e7f637dd2d..a4f274a049 100644 --- a/src/ELECTRODE/electrode_vector.h +++ b/src/ELECTRODE/electrode_vector.h @@ -29,6 +29,7 @@ class ElectrodeVector : protected Pointers { ~ElectrodeVector() override; void setup(class Pair *, class NeighList *, bool); void setup_tf(const std::map &); + void setup_eta(int); void compute_vector(double *); int igroup, source_group; @@ -39,6 +40,8 @@ class ElectrodeVector : protected Pointers { double **cutsq; double g_ewald, eta; bool tfflag; + bool etaflag; + int eta_index; std::map tf_types; class Pair *pair; class NeighList *list; diff --git a/src/ELECTRODE/fix_electrode_conp.cpp b/src/ELECTRODE/fix_electrode_conp.cpp index 13866cd394..a87642182b 100644 --- a/src/ELECTRODE/fix_electrode_conp.cpp +++ b/src/ELECTRODE/fix_electrode_conp.cpp @@ -97,6 +97,7 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : top_group = 0; intelflag = false; tfflag = false; + etaflag = false; timer_flag = false; update_time = 0; @@ -211,6 +212,19 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : qtotal = utils::numeric(FLERR, arg[iarg], false, lmp); qtotal_var_style = VarStyle::CONST; } + } else if ((strcmp(arg[iarg], "eta") == 0)) { + if (iarg + 2 > narg) error->all(FLERR, "Need two arguments after eta command"); + etaflag = true; + int is_double, cols; + eta_index = atom->find_custom(arg[++iarg] + 2, is_double, cols); + if (eta_index == -1) + error->all(FLERR, "eta keyword requires name of previously defined property"); + if (!is_double) error->all(FLERR, "eta keyword requires double-valued property/atom vector"); + if (cols != 0) error->all(FLERR, "eta keyword requires property/atom vector not an array"); + if (!atom->nextra_border) + error->all(FLERR, + "There is no fix with ghost on, but the eta keyword requires a property/atom " + "fix with ghost on"); // toggle parameters } else if ((strcmp(arg[iarg], "etypes") == 0)) { etypes_neighlists = utils::logical(FLERR, arg[++iarg], false, lmp); @@ -520,8 +534,10 @@ void FixElectrodeConp::setup_post_neighbor() evscale = force->qe2f / force->qqrd2e; elyt_vector->setup(pair, vec_neighlist, timer_flag); + if (etaflag) elyt_vector->setup_eta(eta_index); if (need_elec_vector) { elec_vector->setup(pair, mat_neighlist, timer_flag); + if (etaflag) elec_vector->setup_eta(eta_index); if (tfflag) elec_vector->setup_tf(tf_types); } @@ -556,7 +572,8 @@ void FixElectrodeConp::setup_post_neighbor() if (etypes_neighlists) neighbor->build_one(mat_neighlist, 0); auto array_compute = std::unique_ptr(new ElectrodeMatrix(lmp, igroup, eta)); array_compute->setup(tag_to_iele, pair, mat_neighlist); - if (tfflag) { array_compute->setup_tf(tf_types); } + if (etaflag) array_compute->setup_eta(eta_index); + if (tfflag) array_compute->setup_tf(tf_types); array_compute->compute_array(elastance, timer_flag); } // write_mat before proceeding if (comm->me == 0 && write_mat) { @@ -1186,7 +1203,7 @@ double FixElectrodeConp::self_energy(int eflag) // corrections to energy due to self interaction double const qqrd2e = force->qqrd2e; int const nlocal = atom->nlocal; - double const pre = eta / sqrt(MY_2PI) * qqrd2e; + double const pre = 1. / sqrt(MY_2PI) * qqrd2e; int *mask = atom->mask; int *type = atom->type; double *q = atom->q; @@ -1194,7 +1211,8 @@ double FixElectrodeConp::self_energy(int eflag) for (int i = 0; i < nlocal; i++) { if (groupbit & mask[i]) { double const q2 = q[i] * q[i]; - double e = pre * q2; + double ieta = etaflag ? atom->dvector[eta_index][i] : eta; + double e = ieta * pre * q2; if (tfflag && (groupbit & mask[i])) e += 0.5 * qqrd2e * q2 * tf_types[type[i]]; energy += e; if (eflag) { @@ -1234,6 +1252,7 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag) double xtmp = x[i][0]; double ytmp = x[i][1]; double ztmp = x[i][2]; + double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta; int itype = type[i]; int *jlist = firstneigh[i]; int jnum = numneigh[i]; @@ -1242,7 +1261,6 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag) int const j = jlist[jj] & NEIGHMASK; bool j_in_ele = groupbit & mask[j]; if (!(i_in_ele || j_in_ele)) continue; - double eta_ij = (i_in_ele && j_in_ele) ? eta / MY_SQRT2 : eta; double delx = xtmp - x[j][0]; double dely = ytmp - x[j][1]; @@ -1251,6 +1269,16 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag) int jtype = type[j]; if (rsq < force->pair->cutsq[itype][jtype]) { + double const eta_j = etaflag ? atom->dvector[eta_index][j] : eta; + double eta_ij; + if (i_in_ele && j_in_ele) + eta_ij = eta_i * eta_j / sqrt(eta_i * eta_i + eta_j * eta_j); + else if (i_in_ele) + eta_ij = eta_i; + else { + assert(j_in_ele); + eta_ij = eta_j; + } double r2inv = 1.0 / rsq; double r = sqrt(rsq); double erfc_etar = 0.; diff --git a/src/ELECTRODE/fix_electrode_conp.h b/src/ELECTRODE/fix_electrode_conp.h index 689a44053c..fa972c0acc 100644 --- a/src/ELECTRODE/fix_electrode_conp.h +++ b/src/ELECTRODE/fix_electrode_conp.h @@ -138,6 +138,8 @@ class FixElectrodeConp : public Fix { int get_top_group(); // used by ffield int top_group; // used by ffield bool tfflag; + int eta_index; // index of atom property for eta + bool etaflag; // eta specified as atom property bool timer_flag; std::map tf_types; // cg