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diamond.cpp
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diamond.cpp
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/*
Copyright (C) 2010-2018 The ESPResSo project
Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
Max-Planck-Institute for Polymer Research, Theory Group
This file is part of ESPResSo.
ESPResSo is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
ESPResSo is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
/** \file
* This file contains everything needed to create a start-up configuration
* of (partially charged) diamond structure polymer chains with counterions
* and salt molecules, assigning velocities to the particles and
* cross-linking the polymers if necessary.
*
* The corresponding header file is diamond.hpp.
*/
#include <cmath>
#include <cstddef>
#include "PartCfg.hpp"
#include "bonded_interactions/bonded_interaction_data.hpp"
#include "communication.hpp"
#include "constraints.hpp"
#include "constraints/ShapeBasedConstraint.hpp"
#include "diamond.hpp"
#include "global.hpp"
#include "integrate.hpp"
#include "polymer.hpp"
#include "random.hpp"
int create_counterions(PartCfg &partCfg, int const N_CI, int part_id,
int const mode, double const shield, int const max_try,
double const val_CI, int const type_CI) {
Utils::Vector3d pos;
int cnt1 = 0;
int max_cnt = 0;
for (int n = 0; n < N_CI; ++n) {
for (cnt1 = 0; cnt1 < max_try; ++cnt1) {
pos[0] = box_geo.length()[0] * d_random();
pos[1] = box_geo.length()[1] * d_random();
pos[2] = box_geo.length()[2] * d_random();
if ((mode != 0) or (mindist(partCfg, pos) > shield))
break;
}
if (cnt1 >= max_try)
throw std::runtime_error(
"Too many failed attempts finding valid position.");
if (place_particle(part_id, pos.data()) == ES_PART_ERROR)
throw std::runtime_error("Failed to place particle.");
set_particle_q(part_id, val_CI);
set_particle_type(part_id, type_CI);
part_id++;
max_cnt = std::max(cnt1, max_cnt);
}
return max_cnt;
}
int create_diamond(PartCfg &partCfg, double const a, double const bond_length,
int const MPC, int const N_CI, double const val_nodes,
double const val_cM, double const val_CI, int const cM_dist,
int const nonet) {
Utils::Vector3d pos;
double const off = bond_length / sqrt(3);
auto const dnodes =
a / 4. * Utils::Vector<Utils::Vector3d, 8>{{0, 0, 0}, {1, 1, 1},
{2, 2, 0}, {0, 2, 2},
{2, 0, 2}, {3, 3, 1},
{1, 3, 3}, {3, 1, 3}};
static constexpr int dchain[16][5] = {
{0, 1, +1, +1, +1}, {1, 2, +1, +1, -1}, {1, 3, -1, +1, +1},
{1, 4, +1, -1, +1}, {2, 5, +1, +1, +1}, {3, 6, +1, +1, +1},
{4, 7, +1, +1, +1}, {5, 0, +1, +1, -1}, {5, 3, +1, -1, +1},
{5, 4, -1, +1, +1}, {6, 0, -1, +1, +1}, {6, 2, +1, -1, +1},
{6, 4, +1, +1, -1}, {7, 0, +1, -1, +1}, {7, 2, -1, +1, +1},
{7, 3, +1, +1, -1}};
int const type_bond = 0;
int const type_node = 0;
int const type_cM = 1;
int const type_nM = 1;
int const type_CI = 2;
int part_id = 0;
/* place 8 tetra-functional nodes */
for (auto &dnode : dnodes) {
for (int i = 0; i < 3; ++i) {
pos[i] = dnode[i];
}
if (place_particle(part_id, pos.data()) == ES_PART_ERROR)
return -3;
set_particle_q(part_id, val_nodes);
set_particle_type(part_id, type_node);
part_id++;
}
/* place intermediate monomers on chains connecting the nodes */
for (auto const &chain : dchain) {
for (int k = 1; k <= MPC; ++k) {
for (int j = 0; j < 3; ++j)
pos[j] = dnodes[chain[0]][j] + k * chain[2 + j] * off;
if (place_particle(part_id, pos.data()) == ES_PART_ERROR)
throw std::runtime_error("Failed to place particle.");
set_particle_q(part_id, (k % cM_dist == 0) ? val_cM : 0.0);
set_particle_type(part_id, (k % cM_dist == 0) ? type_cM : type_nM);
int bond[2];
bond[0] = type_bond;
if (k == 1) {
if (nonet != 1) {
bond[1] = chain[0];
add_particle_bond(part_id, bond);
}
} else {
bond[1] = part_id - 1;
add_particle_bond(part_id, bond);
}
if ((k == MPC) && (nonet != 1)) {
bond[1] = chain[1];
add_particle_bond(part_id, bond);
}
part_id++;
}
}
/* place counterions (if any) */
if (N_CI > 0)
create_counterions(partCfg, N_CI, part_id, 1, 0.0, 30000, val_CI, type_CI);
return 0;
}