Merge branch 'master' into removed_variable_shadowing

configure.ac

@@ -627,7 +627,7 @@ fi
 # Hydro scheme.
 AC_ARG_WITH([hydro],
    [AS_HELP_STRING([--with-hydro=<scheme>],
-      [Hydro dynamics to use @<:@gadget2, minimal, hopkins, default, gizmo, shadowfax default: gadget2@:>@]
+      [Hydro dynamics to use @<:@gadget2, minimal, hopkins, default, gizmo, shadowfax debug default: gadget2@:>@]
    )],
    [with_hydro="$withval"],
    [with_hydro="gadget2"]
@@ -639,6 +639,9 @@ case "$with_hydro" in
    minimal)
       AC_DEFINE([MINIMAL_SPH], [1], [Minimal SPH])
    ;; 
+   debug)
+      AC_DEFINE([DEBUG_INTERACTIONS_SPH], [1], [Debug SPH])
+   ;; 
    hopkins)
       AC_DEFINE([HOPKINS_PE_SPH], [1], [Pressure-Entropy SPH])
    ;; 

examples/SedovBlast_3D/sedov.yml

@@ -32,4 +32,5 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./sedov.hdf5          # The file to read
+  h_scaling:           3.33
 

src/debug.c

@@ -21,16 +21,15 @@
  ******************************************************************************/
 
 /* Config parameters. */
-#include "../config.h"
+
+/* This object's header. */
+#include "debug.h"
 
 /* Some standard headers. */
 #include <float.h>
 #include <stdio.h>
 #include <unistd.h>
 
-/* This object's header. */
-#include "debug.h"
-
 /* Local includes. */
 #include "active.h"
 #include "cell.h"
@@ -41,7 +40,9 @@
 #include "space.h"
 
 /* Import the right hydro definition */
-#if defined(MINIMAL_SPH)
+#if defined(DEBUG_INTERACTIONS_SPH)
+#include "./hydro/DebugInteractions/hydro_debug.h"
+#elif defined(MINIMAL_SPH)
 #include "./hydro/Minimal/hydro_debug.h"
 #elif defined(GADGET2_SPH)
 #include "./hydro/Gadget2/hydro_debug.h"

src/debug.h

@@ -19,6 +19,9 @@
 #ifndef SWIFT_DEBUG_H
 #define SWIFT_DEBUG_H
 
+/* Config parameters. */
+#include "../config.h"
+
 /* Includes. */
 #include "cell.h"
 #include "part.h"

src/engine.c

@@ -2086,7 +2086,7 @@ static inline void engine_make_external_gravity_dependencies(
     struct scheduler *sched, struct task *gravity, struct cell *c) {
 
   /* init --> external gravity --> kick */
-  scheduler_addunlock(sched, c->drift_gpart, gravity);
+  scheduler_addunlock(sched, c->super->drift_gpart, gravity);
   scheduler_addunlock(sched, gravity, c->super->kick2);
 }
 

src/hydro.h

@@ -27,7 +27,11 @@
 #include "kernel_hydro.h"
 
 /* Import the right functions */
-#if defined(MINIMAL_SPH)
+#if defined(DEBUG_INTERACTIONS_SPH)
+#include "./hydro/DebugInteractions/hydro.h"
+#include "./hydro/DebugInteractions/hydro_iact.h"
+#define SPH_IMPLEMENTATION "Debug SELF/PAIR"
+#elif defined(MINIMAL_SPH)
 #include "./hydro/Minimal/hydro.h"
 #include "./hydro/Minimal/hydro_iact.h"
 #define SPH_IMPLEMENTATION "Minimal version of SPH (e.g. Price 2010)"

src/hydro/DebugInteractions/hydro.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (c) 2017 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program 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 Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+#ifndef SWIFT_DEBUG_INTERACTIONS_HYDRO_H
+#define SWIFT_DEBUG_INTERACTIONS_HYDRO_H
+
+/**
+ * @file DebugInteractions/hydro.h
+ * @brief Empty SPH implementation used solely to test the SELF/PAIR routines.
+ */
+
+#include "hydro_properties.h"
+#include "hydro_space.h"
+#include "part.h"
+
+#include <float.h>
+
+/**
+ * @brief Returns the internal energy of a particle
+ *
+ * @param p The particle of interest
+ */
+__attribute__((always_inline)) INLINE static float hydro_get_internal_energy(
+    const struct part *restrict p) {
+
+  return 0.f;
+}
+
+/**
+ * @brief Returns the pressure of a particle
+ *
+ * @param p The particle of interest
+ */
+__attribute__((always_inline)) INLINE static float hydro_get_pressure(
+    const struct part *restrict p) {
+
+  return 0.f;
+}
+
+/**
+ * @brief Returns the entropy of a particle
+ *
+ * @param p The particle of interest
+ */
+__attribute__((always_inline)) INLINE static float hydro_get_entropy(
+    const struct part *restrict p) {
+
+  return 0.f;
+}
+
+/**
+ * @brief Returns the sound speed of a particle
+ *
+ * @param p The particle of interest
+ */
+__attribute__((always_inline)) INLINE static float hydro_get_soundspeed(
+    const struct part *restrict p) {
+
+  return 0.f;
+}
+
+/**
+ * @brief Returns the density of a particle
+ *
+ * @param p The particle of interest
+ */
+__attribute__((always_inline)) INLINE static float hydro_get_density(
+    const struct part *restrict p) {
+
+  return 0.f;
+}
+
+/**
+ * @brief Returns the mass of a particle
+ *
+ * @param p The particle of interest
+ */
+__attribute__((always_inline)) INLINE static float hydro_get_mass(
+    const struct part *restrict p) {
+  return 0.f;
+}
+
+/**
+ * @brief Returns the time derivative of internal energy of a particle
+ *
+ * We assume a constant density.
+ *
+ * @param p The particle of interest
+ */
+__attribute__((always_inline)) INLINE static float hydro_get_internal_energy_dt(
+    const struct part *restrict p) {
+  return 0.f;
+}
+
+/**
+ * @brief Returns the time derivative of internal energy of a particle
+ *
+ * We assume a constant density.
+ *
+ * @param p The particle of interest.
+ * @param du_dt The new time derivative of the internal energy.
+ */
+__attribute__((always_inline)) INLINE static void hydro_set_internal_energy_dt(
+    struct part *restrict p, float du_dt) {}
+
+/**
+ * @brief Computes the hydro time-step of a given particle
+ *
+ * @param p Pointer to the particle data
+ * @param xp Pointer to the extended particle data
+ *
+ */
+__attribute__((always_inline)) INLINE static float hydro_compute_timestep(
+    const struct part *restrict p, const struct xpart *restrict xp,
+    const struct hydro_props *restrict hydro_properties) {
+
+  return FLT_MAX;
+}
+
+/**
+ * @brief Does some extra hydro operations once the actual physical time step
+ * for the particle is known.
+ *
+ * @param p The particle to act upon.
+ * @param dt Physical time step of the particle during the next step.
+ */
+__attribute__((always_inline)) INLINE static void hydro_timestep_extra(
+    struct part *p, float dt) {}
+
+/**
+ * @brief Prepares a particle for the density calculation.
+ *
+ * Zeroes all the relevant arrays in preparation for the sums taking place in
+ * the variaous density tasks
+ *
+ * @param p The particle to act upon
+ * @param hs #hydro_space containing hydro specific space information.
+ */
+__attribute__((always_inline)) INLINE static void hydro_init_part(
+    struct part *restrict p, const struct hydro_space *hs) {
+
+  for (int i = 0; i < 256; ++i) p->ids_ngbs_density[i] = -1;
+  p->num_ngb_density = 0;
+
+  p->density.wcount = 0.f;
+  p->density.wcount_dh = 0.f;
+}
+
+/**
+ * @brief Finishes the density calculation.
+ *
+ * Multiplies the density and number of neighbours by the appropiate constants
+ * and add the self-contribution term.
+ *
+ * @param p The particle to act upon
+ */
+__attribute__((always_inline)) INLINE static void hydro_end_density(
+    struct part *restrict p) {
+
+  /* Some smoothing length multiples. */
+  const float h = p->h;
+  const float h_inv = 1.0f / h;                       /* 1/h */
+  const float h_inv_dim = pow_dimension(h_inv);       /* 1/h^d */
+  const float h_inv_dim_plus_one = h_inv_dim * h_inv; /* 1/h^(d+1) */
+
+  /* Final operation on the density (add self-contribution). */
+  p->density.wcount += kernel_root;
+  p->density.wcount_dh -= hydro_dimension * kernel_root;
+
+  /* Finish the calculation by inserting the missing h-factors */
+  p->density.wcount *= h_inv_dim;
+  p->density.wcount_dh *= h_inv_dim_plus_one;
+}
+
+/**
+ * @brief Sets all particle fields to sensible values when the #part has 0 ngbs.
+ *
+ * @param p The particle to act upon
+ * @param xp The extended particle data to act upon
+ */
+__attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
+    struct part *restrict p, struct xpart *restrict xp) {
+
+  /* Some smoothing length multiples. */
+  const float h = p->h;
+  const float h_inv = 1.0f / h;                 /* 1/h */
+  const float h_inv_dim = pow_dimension(h_inv); /* 1/h^d */
+
+  /* Re-set problematic values */
+  p->density.wcount = kernel_root * kernel_norm * h_inv_dim;
+  p->density.wcount_dh = 0.f;
+}
+
+/**
+ * @brief Prepare a particle for the force calculation.
+ *
+ * Computes viscosity term, conduction term and smoothing length gradient terms.
+ *
+ * @param p The particle to act upon
+ * @param xp The extended particle data to act upon
+ * @param ti_current The current time (on the timeline)
+ * @param timeBase The minimal time-step size
+ */
+__attribute__((always_inline)) INLINE static void hydro_prepare_force(
+    struct part *restrict p, struct xpart *restrict xp) {}
+
+/**
+ * @brief Reset acceleration fields of a particle
+ *
+ * Resets all hydro acceleration and time derivative fields in preparation
+ * for the sums taking place in the variaous force tasks
+ *
+ * @param p The particle to act upon
+ */
+__attribute__((always_inline)) INLINE static void hydro_reset_acceleration(
+    struct part *restrict p) {
+
+  for (int i = 0; i < 256; ++i) p->ids_ngbs_force[i] = -1;
+  p->num_ngb_force = 0;
+
+  p->force.h_dt = 0.f;
+}
+
+/**
+ * @brief Sets the values to be predicted in the drifts to their values at a
+ * kick time
+ *
+ * @param p The particle.
+ * @param xp The extended data of this particle.
+ */
+__attribute__((always_inline)) INLINE static void hydro_reset_predicted_values(
+    struct part *restrict p, const struct xpart *restrict xp) {}
+
+/**
+ * @brief Predict additional particle fields forward in time when drifting
+ *
+ * @param p The particle
+ * @param xp The extended data of the particle
+ * @param dt The drift time-step.
+ * @param t0 The time at the start of the drift
+ * @param t1 The time at the end of the drift
+ * @param timeBase The minimal time-step size
+ */
+__attribute__((always_inline)) INLINE static void hydro_predict_extra(
+    struct part *restrict p, const struct xpart *restrict xp, float dt) {}
+
+/**
+ * @brief Finishes the force calculation.
+ *
+ * Multiplies the forces and accelerationsby the appropiate constants
+ *
+ * @param p The particle to act upon
+ */
+__attribute__((always_inline)) INLINE static void hydro_end_force(
+    struct part *restrict p) {}
+
+/**
+ * @brief Kick the additional variables
+ *
+ * @param p The particle to act upon
+ * @param xp The particle extended data to act upon
+ * @param dt The time-step for this kick
+ */
+__attribute__((always_inline)) INLINE static void hydro_kick_extra(
+    struct part *restrict p, struct xpart *restrict xp, float dt) {}
+
+/**
+ *  @brief Converts hydro quantity of a particle at the start of a run
+ *
+ * Requires the density to be known
+ *
+ * @param p The particle to act upon
+ */
+__attribute__((always_inline)) INLINE static void hydro_convert_quantities(
+    struct part *restrict p, struct xpart *restrict xp) {}
+
+/**
+ * @brief Initialises the particles for the first time
+ *
+ * This function is called only once just after the ICs have been
+ * read in to do some conversions.
+ *
+ * @param p The particle to act upon
+ * @param xp The extended particle data to act upon
+ */
+__attribute__((always_inline)) INLINE static void hydro_first_init_part(
+    struct part *restrict p, struct xpart *restrict xp) {
+
+  p->time_bin = 0;
+  xp->v_full[0] = p->v[0];
+  xp->v_full[1] = p->v[1];
+  xp->v_full[2] = p->v[2];
+
+  hydro_reset_acceleration(p);
+  hydro_init_part(p, NULL);
+}
+
+#endif /* SWIFT_DEBUG_INTERACTIONS_HYDRO_H */

src/hydro/DebugInteractions/hydro_debug.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (c) 2017 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program 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 Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+#ifndef SWIFT_DEBUG_INTERACTIONS_HYDRO_DEBUG_H
+#define SWIFT_DEBUG_INTERACTIONS_HYDRO_DEBUG_H
+
+/**
+ * @file DebugInteractions/hydro_debug.h
+ * @brief Empty SPH implementation used solely to test the SELF/PAIR routines.
+ */
+
+__attribute__((always_inline)) INLINE static void hydro_debug_particle(
+    const struct part* p, const struct xpart* xp) {
+  printf(
+      "x=[%.3e,%.3e,%.3e], "
+      "v=[%.3e,%.3e,%.3e],v_full=[%.3e,%.3e,%.3e] \n a=[%.3e,%.3e,%.3e],\n "
+      "h=%.3e, wcount=%.3f, wcount_dh=%.3e, dh/dt=%.3e time_bin=%d\n",
+      p->x[0], p->x[1], p->x[2], p->v[0], p->v[1], p->v[2], xp->v_full[0],
+      xp->v_full[1], xp->v_full[2], p->a_hydro[0], p->a_hydro[1], p->a_hydro[2],
+      p->h, p->density.wcount, p->density.wcount_dh, p->force.h_dt,
+      p->time_bin);
+}
+
+#endif /* SWIFT_DEBUG_INTERACTIONS_HYDRO_DEBUG_H */

src/hydro/DebugInteractions/hydro_iact.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (c) 2017 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program 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 Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+#ifndef SWIFT_DEBUG_INTERACTIONS_HYDRO_IACT_H
+#define SWIFT_DEBUG_INTERACTIONS_HYDRO_IACT_H
+
+/**
+ * @file DebugInteractions/hydro_iact.h
+ * @brief Empty SPH implementation used solely to test the SELF/PAIR routines.
+ */
+
+/**
+ * @brief Density loop
+ */
+__attribute__((always_inline)) INLINE static void runner_iact_density(
+    float r2, float *dx, float hi, float hj, struct part *pi, struct part *pj) {
+
+  float wi, wi_dx;
+  float wj, wj_dx;
+
+  /* Get r and r inverse. */
+  const float r = sqrtf(r2);
+
+  /* Compute the kernel function for pi */
+  const float hi_inv = 1.f / hi;
+  const float ui = r * hi_inv;
+  kernel_deval(ui, &wi, &wi_dx);
+
+  /* Compute contribution to the number of neighbours */
+  pi->density.wcount += wi;
+  pi->density.wcount_dh -= (hydro_dimension * wi + ui * wi_dx);
+
+  /* Compute the kernel function for pj */
+  const float hj_inv = 1.f / hj;
+  const float uj = r * hj_inv;
+  kernel_deval(uj, &wj, &wj_dx);
+
+  /* Compute contribution to the number of neighbours */
+  pj->density.wcount += wj;
+  pj->density.wcount_dh -= (hydro_dimension * wj + uj * wj_dx);
+
+  /* Update ngb counters */
+  pi->ids_ngbs_density[pi->num_ngb_density] = pj->id;
+  ++pi->num_ngb_density;
+  pj->ids_ngbs_density[pj->num_ngb_density] = pi->id;
+  ++pj->num_ngb_density;
+}
+
+/**
+ * @brief Density loop (non-symmetric version)
+ */
+__attribute__((always_inline)) INLINE static void runner_iact_nonsym_density(
+    float r2, float *dx, float hi, float hj, struct part *pi, struct part *pj) {
+
+  float wi, wi_dx;
+
+  /* Get r and r inverse. */
+  const float r = sqrtf(r2);
+
+  /* Compute the kernel function */
+  const float hi_inv = 1.0f / hi;
+  const float ui = r * hi_inv;
+  kernel_deval(ui, &wi, &wi_dx);
+
+  /* Compute contribution to the number of neighbours */
+  pi->density.wcount += wi;
+  pi->density.wcount_dh -= (hydro_dimension * wi + ui * wi_dx);
+
+  /* Update ngb counters */
+  pi->ids_ngbs_density[pi->num_ngb_density] = pj->id;
+  ++pi->num_ngb_density;
+}
+
+/**
+ * @brief Force loop
+ */
+__attribute__((always_inline)) INLINE static void runner_iact_force(
+    float r2, float *dx, float hi, float hj, struct part *pi, struct part *pj) {
+
+  /* Update ngb counters */
+  pi->ids_ngbs_force[pi->num_ngb_force] = pj->id;
+  ++pi->num_ngb_force;
+  pj->ids_ngbs_force[pj->num_ngb_force] = pi->id;
+  ++pj->num_ngb_force;
+}
+
+/**
+ * @brief Force loop (non-symmetric version)
+ */
+__attribute__((always_inline)) INLINE static void runner_iact_nonsym_force(
+    float r2, float *dx, float hi, float hj, struct part *pi, struct part *pj) {
+
+  /* Update ngb counters */
+  pi->ids_ngbs_force[pi->num_ngb_force] = pj->id;
+  ++pi->num_ngb_force;
+}
+
+#endif /* SWIFT_DEBUG_INTERACTIONS_HYDRO_IACT_H */

src/hydro/DebugInteractions/hydro_io.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (c) 2017 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program 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 Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+#ifndef SWIFT_DEBUG_INTERACTIONS_HYDRO_IO_H
+#define SWIFT_DEBUG_INTERACTIONS_HYDRO_IO_H
+
+/**
+ * @file DebugInteractions/hydro_io.h
+ * @brief Empty SPH implementation used solely to test the SELF/PAIR routines.
+ */
+
+#include "adiabatic_index.h"
+#include "hydro.h"
+#include "io_properties.h"
+#include "kernel_hydro.h"
+
+/**
+ * @brief Specifies which particle fields to read from a dataset
+ *
+ * @param parts The particle array.
+ * @param list The list of i/o properties to read.
+ * @param num_fields The number of i/o fields to read.
+ */
+void hydro_read_particles(struct part* parts, struct io_props* list,
+                          int* num_fields) {
+
+  *num_fields = 4;
+
+  /* List what we want to read */
+  list[0] = io_make_input_field("Coordinates", DOUBLE, 3, COMPULSORY,
+                                UNIT_CONV_LENGTH, parts, x);
+  list[1] = io_make_input_field("Velocities", FLOAT, 3, COMPULSORY,
+                                UNIT_CONV_SPEED, parts, v);
+  list[2] = io_make_input_field("SmoothingLength", FLOAT, 1, COMPULSORY,
+                                UNIT_CONV_LENGTH, parts, h);
+  list[3] = io_make_input_field("ParticleIDs", ULONGLONG, 1, COMPULSORY,
+                                UNIT_CONV_NO_UNITS, parts, id);
+}
+
+float convert_u(struct engine* e, struct part* p) {
+
+  return hydro_get_internal_energy(p);
+}