Removed ENGINE shear torque calculation

doc/sphinx/particles.rst

@@ -535,7 +535,7 @@ Lattice Boltzmann (LB) swimmers
  system = espressomd.System()
 
  system.part.add(id=1, pos=[2, 0, 0], rotation=[1, 1, 1], swimming={
- 'f_swim': 0.01, 'mode': 'pusher', 'dipole_length': 2.0, 'rotational_friction': 20})
+ 'f_swim': 0.01, 'mode': 'pusher', 'dipole_length': 2.0})
 
 For an explanation of the parameters ``v_swim`` and ``f_swim`` see the previous
 item. In lattice Boltzmann self-propulsion is less trivial than for regular MD,
@@ -549,11 +549,7 @@ nature of the particle's flow field by using one of the modes: ``pusher`` or
 ``puller``. You will also need to specify a ``dipole_length`` which determines
 the distance of the source of propulsion from the particle's center. Note that
 you should not put this distance to zero; |es| (currently) does not support
-mathematical dipole flow fields. The key ``rotational_friction`` can be used to
-set the friction that causes the orientation of the particle to change in shear
-flow. The torque on the particle is determined by taking the cross product of
-the difference between the fluid velocity at the center of the particle and at
-the source point and the vector connecting the center and source.
+mathematical dipole flow fields.
 
 You may ask: "Why are there two methods ``v_swim`` and ``f_swim`` for the
 self-propulsion using the lattice Boltzmann algorithm?" The answer is
@@ -566,10 +562,3 @@ reaches a constant speed (given by ``v_swim``) this monopolar moment is gone
 and the flow field is zero! In contrast, ``f_swim`` always, i.e., while
 accelerating *and* while swimming at constant force possesses a dipolar flow
 field.
-
-.. warning::
-
- Please note that even though swimming is interoperable with the
- CPU version of LB it is only supported on *one* MPI
- rank, i.e. ``n_nodes`` = 1.
-

doc/tutorials/06-active_matter/06-active_matter.tex

@@ -230,13 +230,7 @@ \subsection{\label{sub:lattice}Self-Propulsion with Hydrodynamics}
 flow,~\textit{e.g.}, a swimmer in a Posseuille flow. If the thermostat is
 switched on, the rotational degrees of freedom will also be thermalized, but
 there is still no contribution of rotation due to `external' flow fields. A
-rather unsatisfying solution to this problem is offered by the
-\codees{rotational_friction} option, which allows one to include the effect of
-fluid flow on the rotation. The algorithm computes the difference in fluid flow
-velocity between the center of the particle and the coupling point, and takes
-the cross product of that with the dipole length. This quantity is then
-converted into a torque using the \codees{rotational_friction}. It is
-recommended to use an alternative means of obtaining rotations in your LB
+It is recommended to use an alternative means of obtaining rotations in your LB
 swimming simulations. For example, by constructing a raspberry
 particle~\cite{lobaskin04,chatterji05,fischer15,degraaf15,degraaf16b}.
 

src/core/Particle.hpp

@@ -34,6 +34,18 @@ enum : uint8_t {
  ROTATION_Z = 4u
 };
 
+struct ParticleParametersSwimming {
+ bool swimming = false;
+ double f_swim = 0.;
+ double v_swim = 0.;
+ int push_pull = 0;
+ double dipole_length = 0.;
+
+ template <class Archive> void serialize(Archive &ar, long int /* version */) {
+ ar &swimming &f_swim &v_swim &push_pull &dipole_length;
+ }
+};
+
 /** Properties of a particle which are not supposed to
  * change during the integration, but have to be known
  * for all ghosts. Ghosts are particles which are
@@ -156,6 +168,10 @@ struct ParticleProperties {
  Utils::Vector3d ext_torque = {0, 0, 0};
 #endif
 #endif
+
+#ifdef ENGINE
+ ParticleParametersSwimming swim;
+#endif
 };
 
 /** Positional information on a particle. Information that is
@@ -240,27 +256,6 @@ struct ParticleLocal {
  Utils::Vector3i i = {0, 0, 0};
 };
 
-struct ParticleParametersSwimming {
-// ifdef inside because we need this type for some MPI prototypes
-#ifdef ENGINE
- bool swimming = false;
- double f_swim = 0.;
- double v_swim = 0.;
- int push_pull = 0;
- double dipole_length = 0.;
- Utils::Vector3d v_center;
- Utils::Vector3d v_source;
- double rotational_friction = 0.;
-#endif
-
- template <typename Archive> void serialize(Archive &ar, long int) {
-#ifdef ENGINE
- ar &swimming &f_swim &v_swim &push_pull &dipole_length &v_center &v_source
- &rotational_friction;
-#endif
- }
-};
-
 /** Struct holding all information for one particle. */
 struct Particle {
  int &identity() { return p.identity; }
@@ -292,9 +287,6 @@ struct Particle {
  ret.m = m;
  ret.f = f;
  ret.l = l;
-#ifdef ENGINE
- ret.swim = swim;
-#endif
 
  return ret;
  }
@@ -346,10 +338,6 @@ struct Particle {
  */
  IntList el;
 #endif
-
-#ifdef ENGINE
- ParticleParametersSwimming swim;
-#endif
 };
 
 #endif

src/core/communication.cpp

@@ -67,7 +67,6 @@
 
 #include "serialization/IA_parameters.hpp"
 #include "serialization/Particle.hpp"
-#include "serialization/ParticleParametersSwimming.hpp"
 
 #include <utils/Counter.hpp>
 #include <utils/u32_to_u64.hpp>

src/core/cuda_common_cuda.cu

@@ -52,9 +52,6 @@ std::vector<float> particle_forces_host;
 CUDA_energy energy_host;
 
 std::vector<float> particle_torques_host;
-#ifdef ENGINE
-std::vector<CUDA_v_cs> host_v_cs;
-#endif
 
 /**cuda streams for parallel computing on cpu and gpu */
 cudaStream_t stream[1];
@@ -187,9 +184,6 @@ void gpu_change_number_of_part_to_comm() {
  particle_data_device = nullptr;
  }
 
-#ifdef ENGINE
- host_v_cs.clear();
-#endif
 #ifdef ROTATION
  particle_torques_host.clear();
 #endif
@@ -210,9 +204,6 @@ void gpu_change_number_of_part_to_comm() {
  cudaHostAllocWriteCombined));
  particle_forces_host.resize(3 *
  global_part_vars_host.number_of_particles);
-#ifdef ENGINE
- host_v_cs.resize(global_part_vars_host.number_of_particles);
-#endif
 #if (defined DIPOLES || defined ROTATION)
  particle_torques_host.resize(3 *
  global_part_vars_host.number_of_particles);
@@ -352,23 +343,6 @@ void copy_forces_from_GPU(ParticleRange particles) {
  }
 }
 
-#if defined(ENGINE) && defined(CUDA)
-// setup and call kernel to copy v_cs to host
-void copy_v_cs_from_GPU(ParticleRange particles) {
- if (global_part_vars_host.communication_enabled == 1 &&
- global_part_vars_host.number_of_particles) {
- // Copy result from device memory to host memory
- if (this_node == 0) {
- cuda_safe_mem(cudaMemcpy2D(
- host_v_cs.data(), sizeof(CUDA_v_cs), particle_data_device,
- sizeof(CUDA_particle_data), sizeof(CUDA_v_cs),
- global_part_vars_host.number_of_particles, cudaMemcpyDeviceToHost));
- }
- cuda_mpi_send_v_cs(particles, host_v_cs);
- }
-}
-#endif
-
 void clear_energy_on_GPU() {
  if (!global_part_vars_host.communication_enabled)
  // || !global_part_vars_host.number_of_particles )

src/core/cuda_interface.cpp

@@ -77,13 +77,14 @@ static void pack_particles(ParticleRange particles,
 #endif
 
 #ifdef ENGINE
- buffer[i].swim.v_swim = static_cast<float>(part.swim.v_swim);
- buffer[i].swim.f_swim = static_cast<float>(part.swim.f_swim);
+ buffer[i].swim.v_swim = static_cast<float>(part.p.swim.v_swim);
+ buffer[i].swim.f_swim = static_cast<float>(part.p.swim.f_swim);
  buffer[i].swim.director = buffer[i].director;
 
- buffer[i].swim.push_pull = part.swim.push_pull;
- buffer[i].swim.dipole_length = static_cast<float>(part.swim.dipole_length);
- buffer[i].swim.swimming = part.swim.swimming;
+ buffer[i].swim.push_pull = part.p.swim.push_pull;
+ buffer[i].swim.dipole_length =
+ static_cast<float>(part.p.swim.dipole_length);
+ buffer[i].swim.swimming = part.p.swim.swimming;
 #endif
  i++;
  }
@@ -162,38 +163,6 @@ void cuda_mpi_send_forces(ParticleRange particles,
  }
 }
 
-#if defined(ENGINE) && defined(CUDA)
-namespace {
-void set_v_cs(ParticleRange particles, const std::vector<CUDA_v_cs> &v_cs) {
- int ind = 0;
- for (auto &p : particles) {
- for (int i = 0; i < 3; i++) {
- p.swim.v_center[i] = v_cs[ind].v_cs[0 + i];
- p.swim.v_source[i] = v_cs[ind].v_cs[3 + i];
- }
- ind++;
- }
-}
-} // namespace
-
-void cuda_mpi_send_v_cs(ParticleRange particles,
- std::vector<CUDA_v_cs> host_v_cs) {
- // first collect number of particles on each node
- auto const n_part = particles.size();
-
- // call slave functions to provide the slave data
- if (this_node > 0) {
- std::vector<CUDA_v_cs> buffer(n_part);
-
- Utils::Mpi::scatter_buffer(buffer.data(), n_part, comm_cart);
- set_v_cs(particles, buffer);
- } else {
- Utils::Mpi::scatter_buffer(host_v_cs.data(), n_part, comm_cart);
- set_v_cs(particles, host_v_cs);
- }
-}
-#endif // ifdef ENGINE
-
 /** Takes a CUDA_energy struct and adds it to the core energy struct.
 This cannot be done from inside cuda_common_cuda.cu:copy_energy_from_GPU()
 because energy.hpp indirectly includes on mpi.h while .cu files may not depend

src/core/cuda_interface.hpp

@@ -28,17 +28,6 @@
 #include <utils/Span.hpp>
 #include <utils/Vector.hpp>
 
-#ifdef ENGINE
-// velocities which need to be copied from the GPU to the CPU to calculate a
-// torque
-typedef struct {
-
- // center and source velocity of the md part
- float v_cs[6];
-
-} CUDA_v_cs;
-#endif
-
 // Parameters for swimmers
 #ifdef ENGINE
 struct CUDA_ParticleParametersSwimming {
@@ -156,13 +145,6 @@ void cuda_mpi_send_forces(ParticleRange particles,
 void cuda_bcast_global_part_params();
 void cuda_copy_to_device(void *host_data, void *device_data, size_t n);
 void cuda_copy_to_host(void *host_device, void *device_host, size_t n);
-
-#ifdef ENGINE
-void copy_v_cs_from_GPU(ParticleRange particles);
-void cuda_mpi_send_v_cs(ParticleRange particles,
- std::vector<CUDA_v_cs> host_v_cs);
-#endif
-
 #endif /* ifdef CUDA */
 
 #endif /* ifdef CUDA_INTERFACE_HPP */

src/core/forces_inline.hpp

@@ -94,8 +94,8 @@ inline ParticleForce external_force(Particle const &p) {
 #ifdef ENGINE
  // apply a swimming force in the direction of
  // the particle's orientation axis
- if (p.swim.swimming) {
- f.f += p.swim.f_swim * p.r.calc_director();
+ if (p.p.swim.swimming) {
+ f.f += p.p.swim.f_swim * p.r.calc_director();
  }
 #endif
 

src/core/ghosts.cpp

@@ -183,10 +183,6 @@ static int calc_transmit_size(GhostCommunication &ghost_comm,
  if (data_parts & GHOSTTRANS_FORCE)
  n_buffer_new += sizeof(ParticleForce);
 
-#ifdef ENGINE
- if (data_parts & GHOSTTRANS_SWIMMING)
- n_buffer_new += sizeof(ParticleParametersSwimming);
-#endif
  int count = 0;
  for (auto const &pl : ghost_comm.part_lists)
  count += pl->n;
@@ -231,12 +227,6 @@ static void prepare_send_buffer(CommBuf &send_buffer,
  if (data_parts & GHOSTTRANS_FORCE) {
  archiver << part.f;
  }
-
-#ifdef ENGINE
- if (data_parts & GHOSTTRANS_SWIMMING) {
- archiver << part.swim;
- }
-#endif
  }
  }
  }
@@ -311,12 +301,6 @@ static void put_recv_buffer(CommBuf &recv_buffer,
  if (data_parts & GHOSTTRANS_FORCE) {
  archiver >> part.f;
  }
-
-#ifdef ENGINE
- if (data_parts & GHOSTTRANS_SWIMMING) {
- archiver >> part.swim;
- }
-#endif
  }
  }
  }
@@ -368,11 +352,6 @@ static void cell_cell_transfer(GhostCommunication &ghost_comm,
  }
  if (data_parts & GHOSTTRANS_FORCE)
  part2.f += part1.f;
-
-#ifdef ENGINE
- if (data_parts & GHOSTTRANS_SWIMMING)
- part2.swim = part1.swim;
-#endif
  }
  }
  }

src/core/ghosts.hpp

@@ -134,9 +134,7 @@ enum : unsigned {
  /// transfer \ref ParticleForce
  GHOSTTRANS_FORCE = 16u,
  /// resize the receiver particle arrays to the size of the senders
- GHOSTTRANS_PARTNUM = 64u,
- /// transfer \ref ParticleParametersSwimming
- GHOSTTRANS_SWIMMING = 128u
+ GHOSTTRANS_PARTNUM = 64u
 };
 
 /** \name Data Types */