dpd.cpp

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/*
 * Copyright (C) 2010-2022 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
 *  Implementation of dpd.hpp.
 */
#include "config/config.hpp"
 
#ifdef DPD
 
#include "dpd.hpp"
 
#include "BoxGeometry.hpp"
#include "cell_system/CellStructure.hpp"
#include "cells.hpp"
#include "nonbonded_interactions/nonbonded_interaction_data.hpp"
#include "random.hpp"
#include "system/System.hpp"
#include "thermostat.hpp"
 
#include <utils/Vector.hpp>
#include <utils/math/sqr.hpp>
#include <utils/math/tensor_product.hpp>
#include <utils/matrix.hpp>
 
#include <boost/mpi/collectives/reduce.hpp>
 
#include <algorithm>
#include <cmath>
#include <cstdint>
#include <functional>
 
/** Return a random uniform 3D vector with the Philox thermostat.
 *  Random numbers depend on
 *  1. dpd_rng_counter (initialized by seed) which is increased on integration
 *  2. Salt (decorrelates different counters)
 *  3. Two particle IDs (order-independent, decorrelates particles, gets rid of
 *     seed-per-node)
 */
Utils::Vector3d dpd_noise(DPDThermostat const &dpd, int pid1, int pid2) {
  return Random::noise_uniform<RNGSalt::SALT_DPD>(
      dpd.rng_counter(), dpd.rng_seed(), (pid1 < pid2) ? pid2 : pid1,
      (pid1 < pid2) ? pid1 : pid2);
}
Utils::Vector3d dpd_noise(DPDThermostat const &dpd, int pid1, int pid2) {…}
 
void dpd_init(double kT, double time_step) {
  auto &nonbonded_ias = *System::get_system().nonbonded_ias;
  auto const max_type = nonbonded_ias.get_max_seen_particle_type();
  for (int type_a = 0; type_a <= max_type; type_a++) {
    for (int type_b = type_a; type_b <= max_type; type_b++) {
      auto &ia_params = nonbonded_ias.get_ia_param(type_a, type_b);
 
      ia_params.dpd.radial.pref =
          sqrt(24.0 * kT * ia_params.dpd.radial.gamma / time_step);
      ia_params.dpd.trans.pref =
          sqrt(24.0 * kT * ia_params.dpd.trans.gamma / time_step);
    }
  }
}
void dpd_init(double kT, double time_step) {…}
 
static double weight(int type, double r_cut, double k, double r) {
  if (type == 0) {
    return 1.;
  }
  return 1. - pow((r / r_cut), k);
}
static double weight(int type, double r_cut, double k, double r) {…}
 
Utils::Vector3d dpd_pair_force(DPDParameters const &params,
                               Utils::Vector3d const &v, double dist,
                               Utils::Vector3d const &noise) {
  if (dist < params.cutoff) {
    auto const omega = weight(params.wf, params.cutoff, params.k, dist);
    auto const omega2 = Utils::sqr(omega);
 
    auto const f_d = params.gamma * omega2 * v;
    auto const f_r = params.pref * omega * noise;
 
    return f_r - f_d;
  }
 
  return {};
}
Utils::Vector3d dpd_pair_force(DPDParameters const &params, {…}
 
Utils::Vector3d
dpd_pair_force(Particle const &p1, Particle const &p2, DPDThermostat const &dpd,
               BoxGeometry const &box_geo, IA_parameters const &ia_params,
               Utils::Vector3d const &d, double dist, double dist2) {
  if (ia_params.dpd.radial.cutoff <= 0.0 && ia_params.dpd.trans.cutoff <= 0.0) {
    return {};
  }
 
  auto const v21 =
      box_geo.velocity_difference(p1.pos(), p2.pos(), p1.v(), p2.v());
  auto const noise_vec =
      (ia_params.dpd.radial.pref > 0.0 || ia_params.dpd.trans.pref > 0.0)
          ? dpd_noise(dpd, p1.id(), p2.id())
          : Utils::Vector3d{};
 
  auto const f_r = dpd_pair_force(ia_params.dpd.radial, v21, dist, noise_vec);
  auto const f_t = dpd_pair_force(ia_params.dpd.trans, v21, dist, noise_vec);
 
  /* Projection operator to radial direction */
  auto const P = tensor_product(d / dist2, d);
  /* This is equivalent to P * f_r + (1 - P) * f_t, but with
   * doing only one matrix-vector multiplication */
  auto const force = P * (f_r - f_t) + f_t;
  return force;
}
dpd_pair_force(Particle const &p1, Particle const &p2, DPDThermostat const &dpd, {…}
 
static auto dpd_viscous_stress_local() {
  auto &system = System::get_system();
  auto const &box_geo = *system.box_geo;
  auto const &nonbonded_ias = *system.nonbonded_ias;
  auto &cell_structure = *system.cell_structure;
  system.on_observable_calc();
 
  Utils::Matrix<double, 3, 3> stress{};
  cell_structure.non_bonded_loop([&stress, &box_geo, &nonbonded_ias](
                                     Particle const &p1, Particle const &p2,
                                     Distance const &d) {
    auto const v21 =
        box_geo.velocity_difference(p1.pos(), p2.pos(), p1.v(), p2.v());
 
    auto const &ia_params = nonbonded_ias.get_ia_param(p1.type(), p2.type());
    auto const dist = std::sqrt(d.dist2);
 
    auto const f_r = dpd_pair_force(ia_params.dpd.radial, v21, dist, {});
    auto const f_t = dpd_pair_force(ia_params.dpd.trans, v21, dist, {});
 
    /* Projection operator to radial direction */
    auto const P = tensor_product(d.vec21 / d.dist2, d.vec21);
    /* This is equivalent to P * f_r + (1 - P) * f_t, but with
     * doing only one matrix-vector multiplication */
    auto const f = P * (f_r - f_t) + f_t;
 
    stress += tensor_product(d.vec21, f);
  });
 
  return stress;
}
static auto dpd_viscous_stress_local() {…}
 
Utils::Vector9d dpd_pressure_local() {
  auto const local_stress = dpd_viscous_stress_local();
  return -Utils::flatten(local_stress);
}
Utils::Vector9d dpd_pressure_local() {…}
 
/**
 * @brief Viscous stress tensor of the DPD interaction.
 *
 * This calculates the total viscous stress contribution of the
 * DPD interaction. It contains only the dissipative contributions
 * of the interaction without noise. It's calculated as the
 * sum over all pair virials as
 * \f[
 *    \sigma^{\nu\mu} = V^{-1}\sum_i \sum_{j < i} r_{i,j}^{\nu} (- \gamma_{i,j}
 * v_{i,j})^{\mu} \f] where \f$\gamma_{i,j}\f$ is the (in general tensor valued)
 * DPD friction coefficient for particles i and j, \f$v_{i,j}\f$, \f$r_{i,j}\f$
 * are their relative velocity and distance and \f$V\f$ is the box volume.
 *
 * @return Stress tensor contribution.
 */
Utils::Vector9d dpd_stress(boost::mpi::communicator const &comm) {
  auto const &box_geo = *System::get_system().box_geo;
  auto const local_stress = dpd_viscous_stress_local();
  std::remove_const_t<decltype(local_stress)> global_stress{};
 
  boost::mpi::reduce(comm, local_stress, global_stress, std::plus<>(), 0);
 
  return Utils::flatten(global_stress) / box_geo.volume();
}
Utils::Vector9d dpd_stress(boost::mpi::communicator const &comm) {…}
 
#endif // DPD