Added files for minimal implementation of SPH

src/Makefile.am

@@ -47,6 +47,8 @@ AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
 noinst_HEADERS = approx_math.h atomic.h cycle.h error.h inline.h kernel.h vector.h \
 		 runner_doiact.h runner_doiact_grav.h units.h intrinsics.h \
 		 hydro.h hydro_io.h gravity.h \
+		 hydro/Minimal/hydro.h hydro/Minimal/hydro_iact.h hydro/Minimal/hydro_io.h \
+                 hydro/Minimal/hydro_debug.h hydro/Minimal/hydro_part.h
 		 hydro/Default/hydro.h hydro/Default/hydro_iact.h hydro/Default/hydro_io.h \
                  hydro/Default/hydro_debug.h hydro/Default/hydro_part.h \
 		 hydro/Gadget2/hydro.h hydro/Gadget2/hydro_iact.h hydro/Gadget2/hydro_io.h \

src/const.h

@@ -66,7 +66,9 @@
 #define const_iepsilon6 (const_iepsilon3* const_iepsilon3)
 
 /* SPH variant to use */
-#define GADGET2_SPH
+#define MINIMAL_SPH
+//#define GADGET2_SPH
+//#define DEFAULT_SPH
 
 /* System of units */
 #define const_unit_length_in_cgs 1   /* 3.08567810e16  /\* 1Mpc *\/ */

src/hydro/Minimal/hydro.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (c) 2015 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/>.
+ *
+ ******************************************************************************/
+
+/**
+ * @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(
+    struct part* p, struct xpart* xp) {
+
+  /* CFL condition */
+  float dt_cfl = 2.f * const_cfl * kernel_gamma * p->h / p->force.v_sig;
+
+  /* Limit change in u */
+  float dt_u_change = (p->force.u_dt != 0.0f)
+                          ? fabsf(const_max_u_change * p->u / p->force.u_dt)
+                          : FLT_MAX;
+
+  return fminf(dt_cfl, fminf(dt_h_change, dt_u_change));
+}
+
+/**
+ * @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
+ */
+__attribute__((always_inline))
+    INLINE static void hydro_init_part(struct part* p) {
+  p->density.wcount = 0.f;
+  p->density.wcount_dh = 0.f;
+  p->rho = 0.f;
+  p->rho_dh = 0.f;
+  p->density.div_v = 0.f;
+  p->density.curl_v[0] = 0.f;
+  p->density.curl_v[1] = 0.f;
+  p->density.curl_v[2] = 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
+ * @param time The current time
+ */
+__attribute__((always_inline))
+    INLINE static void hydro_end_density(struct part* p, float time) {
+
+  /* Some smoothing length multiples. */
+  const float h = p->h;
+  const float ih = 1.0f / h;
+  const float ih2 = ih * ih;
+  const float ih4 = ih2 * ih2;
+
+  /* Final operation on the density. */
+  p->rho = ih * ih2 * (p->rho + p->mass * kernel_root);
+  p->rho_dh = (p->rho_dh - 3.0f * p->mass * kernel_root) * ih4;
+  p->density.wcount =
+      (p->density.wcount + kernel_root) * (4.0f / 3.0 * M_PI * kernel_gamma3);
+  p->density.wcount_dh =
+      p->density.wcount_dh * ih * (4.0f / 3.0 * M_PI * kernel_gamma3);
+}
+
+/**
+ * @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 time The current time
+ */
+__attribute__((always_inline))
+INLINE static void hydro_prepare_force(struct part* p, struct xpart* xp, float time) {
+
+  /* Some smoothing length multiples. */
+  const float h = p->h;
+  const float ih = 1.0f / h;
+  const float ih2 = ih * ih;
+  const float ih4 = ih2 * ih2;
+
+  /* Pre-compute some stuff for the balsara switch. */
+  const float normDiv_v = fabs(p->density.div_v / p->rho * ih4);
+  const float normCurl_v = sqrtf(p->density.curl_v[0] * p->density.curl_v[0] +
+                                 p->density.curl_v[1] * p->density.curl_v[1] +
+                                 p->density.curl_v[2] * p->density.curl_v[2]) /
+                           p->rho * ih4;
+
+  /* Compute this particle's sound speed. */
+  const float u = p->u;
+  const float fc = p->force.c =
+      sqrtf(const_hydro_gamma * (const_hydro_gamma - 1.0f) * u);
+
+  /* Compute the P/Omega/rho2. */
+  xp->omega = 1.0f + 0.3333333333f * h * p->rho_dh / p->rho;
+  p->force.POrho2 = u * (const_hydro_gamma - 1.0f) / (p->rho * xp->omega);
+
+  /* Balsara switch */
+  p->force.balsara = normDiv_v / (normDiv_v + normCurl_v + 0.0001f * fc * ih);
+
+  /* Viscosity parameter decay time */
+  const float tau = h / (2.f * const_viscosity_length * p->force.c);
+
+  /* Viscosity source term */
+  const float S = fmaxf(-normDiv_v, 0.f);
+
+  /* Compute the particle's viscosity parameter time derivative */
+  const float alpha_dot = (const_viscosity_alpha_min - p->alpha) / tau +
+                          (const_viscosity_alpha_max - p->alpha) * S;
+
+  /* Update particle's viscosity paramter */
+  p->alpha += alpha_dot * (p->t_end - p->t_begin);
+}
+
+/**
+ * @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* p) {
+
+  /* Reset the acceleration. */
+  p->a_hydro[0] = 0.0f;
+  p->a_hydro[1] = 0.0f;
+  p->a_hydro[2] = 0.0f;
+
+  /* Reset the time derivatives. */
+  p->force.u_dt = 0.0f;
+  p->h_dt = 0.0f;
+  p->force.v_sig = 0.0f;
+}
+
+/**
+ * @brief Predict additional particle fields forward in time when drifting
+ *
+ * @param p The particle
+ * @param xp The extended data of the particle
+ * @param t0 The time at the start of the drift
+ * @param t1 The time at the end of the drift
+ */
+__attribute__((always_inline)) INLINE static void hydro_predict_extra(
+    struct part* p, struct xpart* xp, float t0, float t1) {
+  float u, w;
+
+  const float dt = t1 - t0;
+
+  /* Predict internal energy */
+  w = p->force.u_dt / p->u * dt;
+  if (fabsf(w) < 0.01f) /* 1st order expansion of exp(w) */
+    u = p->u *=
+        1.0f + w * (1.0f + w * (0.5f + w * (1.0f / 6.0f + 1.0f / 24.0f * w)));
+  else
+    u = p->u *= expf(w);
+
+  /* Predict gradient term */
+  p->force.POrho2 = u * (const_hydro_gamma - 1.0f) / (p->rho * xp->omega);
+}
+
+/**
+ * @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* p) {}
+
+/**
+ * @brief Kick the additional variables
+ *
+ * @param p The particle to act upon
+ * @param dt The time-step for this kick
+ */
+__attribute__((always_inline))
+    INLINE static void hydro_kick_extra(struct part* p, float dt) {}
+
+/**
+ * @brief Converts hydro quantity of a particle
+ *
+ * Requires the density to be known
+ *
+ * @param p The particle to act upon
+ */
+__attribute__((always_inline))
+    INLINE static void hydro_convert_quantities(struct part* p) {}

src/hydro/Minimal/hydro_debug.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (c) 2016 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/>.
+ *
+ ******************************************************************************/
+
+__attribute__((always_inline))
+    INLINE static void hydro_debug_particle(struct part* p, 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=%d, m=%.3e, dh_drho=%.3e, rho=%.3e, t_begin=%.3e, t_end=%.3e\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, (int)p->density.wcount, p->mass, p->rho_dh, p->rho, p->t_begin,
+      p->t_end);
+}

src/hydro/Minimal/hydro_io.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (c) 2016 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/>.
+ *
+ ******************************************************************************/
+
+/**
+ * @brief Reads the different particles to the HDF5 file
+ *
+ * @param h_grp The HDF5 group in which to read the arrays.
+ * @param N The number of particles on that MPI rank.
+ * @param N_total The total number of particles (only used in MPI mode)
+ * @param offset The offset of the particles for this MPI rank (only used in MPI
+ *mode)
+ * @param parts The particle array
+ *
+ */
+__attribute__((always_inline)) INLINE static void hydro_read_particles(
+    hid_t h_grp, int N, long long N_total, long long offset,
+    struct part* parts) {
+
+  /* Read arrays */
+  readArray(h_grp, "Coordinates", DOUBLE, N, 3, parts, N_total, offset, x,
+            COMPULSORY);
+  readArray(h_grp, "Velocities", FLOAT, N, 3, parts, N_total, offset, v,
+            COMPULSORY);
+  readArray(h_grp, "Masses", FLOAT, N, 1, parts, N_total, offset, mass,
+            COMPULSORY);
+  readArray(h_grp, "SmoothingLength", FLOAT, N, 1, parts, N_total, offset, h,
+            COMPULSORY);
+  readArray(h_grp, "InternalEnergy", FLOAT, N, 1, parts, N_total, offset, u,
+            COMPULSORY);
+  readArray(h_grp, "ParticleIDs", ULONGLONG, N, 1, parts, N_total, offset, id,
+            COMPULSORY);
+  readArray(h_grp, "Acceleration", FLOAT, N, 3, parts, N_total, offset, a_hydro,
+            OPTIONAL);
+  readArray(h_grp, "Density", FLOAT, N, 1, parts, N_total, offset, rho,
+            OPTIONAL);
+}
+
+/**
+ * @brief Writes the different particles to the HDF5 file
+ *
+ * @param h_grp The HDF5 group in which to write the arrays.
+ * @param fileName The name of the file (unsued in MPI mode).
+ * @param xmfFile The XMF file to write to (unused in MPI mode).
+ * @param N The number of particles on that MPI rank.
+ * @param N_total The total number of particles (only used in MPI mode)
+ * @param mpi_rank The MPI rank of this node (only used in MPI mode)
+ * @param offset The offset of the particles for this MPI rank (only used in MPI
+ *mode)
+ * @param parts The particle array
+ * @param us The unit system to use
+ *
+ */
+__attribute__((always_inline)) INLINE static void hydro_write_particles(
+    hid_t h_grp, char* fileName, FILE* xmfFile, int N, long long N_total,
+    int mpi_rank, long long offset, struct part* parts, struct UnitSystem* us) {
+
+  /* Write arrays */
+  writeArray(h_grp, fileName, xmfFile, "Coordinates", DOUBLE, N, 3, parts,
+             N_total, mpi_rank, offset, x, us, UNIT_CONV_LENGTH);
+  writeArray(h_grp, fileName, xmfFile, "Velocities", FLOAT, N, 3, parts,
+             N_total, mpi_rank, offset, v, us, UNIT_CONV_SPEED);
+  writeArray(h_grp, fileName, xmfFile, "Masses", FLOAT, N, 1, parts, N_total,
+             mpi_rank, offset, mass, us, UNIT_CONV_MASS);
+  writeArray(h_grp, fileName, xmfFile, "SmoothingLength", FLOAT, N, 1, parts,
+             N_total, mpi_rank, offset, h, us, UNIT_CONV_LENGTH);
+  writeArray(h_grp, fileName, xmfFile, "InternalEnergy", FLOAT, N, 1, parts,
+             N_total, mpi_rank, offset, u, us, UNIT_CONV_ENERGY_PER_UNIT_MASS);
+  writeArray(h_grp, fileName, xmfFile, "ParticleIDs", ULONGLONG, N, 1, parts,
+             N_total, mpi_rank, offset, id, us, UNIT_CONV_NO_UNITS);
+  writeArray(h_grp, fileName, xmfFile, "Acceleration", FLOAT, N, 3, parts,
+             N_total, mpi_rank, offset, a_hydro, us, UNIT_CONV_ACCELERATION);
+  writeArray(h_grp, fileName, xmfFile, "Density", FLOAT, N, 1, parts, N_total,
+             mpi_rank, offset, rho, us, UNIT_CONV_DENSITY);
+}

src/hydro/Minimal/hydro_part.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@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/>.
+ *
+ ******************************************************************************/
+
+/* Extra particle data not needed during the SPH loops over neighbours. */
+struct xpart {
+
+  /* Old position, at last tree rebuild. */
+  double x_old[3];
+
+  /* Velocity at the last full step. */
+  float v_full[3];
+
+  /* Old density. */
+  float omega;
+
+} __attribute__((aligned(xpart_align)));
+
+/* Data of a single particle. */
+struct part {
+
+  /* Particle position. */
+  double x[3];
+
+  /* Particle predicted velocity. */
+  float v[3];
+
+  /* Particle acceleration. */
+  float a_hydro[3];
+
+  /* Particle cutoff radius. */
+  float h;
+
+  /* Change in smoothing length over time. */
+  float h_dt;
+
+  /* Particle time of beginning of time-step. */
+  float t_begin;
+
+  /* Particle time of end of time-step. */
+  float t_end;
+
+  /* Particle internal energy. */
+  float u;
+
+  /* Particle density. */
+  float rho;
+
+  /* Derivative of the density with respect to this particle's smoothing length.
+   */
+  float rho_dh;
+
+  /* Particle viscosity parameter */
+  float alpha;
+
+  /* Store density/force specific stuff. */
+  // union {
+
+  struct {
+
+    /* Particle velocity divergence. */
+    float div_v;
+
+    /* Derivative of particle number density. */
+    float wcount_dh;
+
+    /* Particle velocity curl. */
+    float curl_v[3];
+
+    /* Particle number density. */
+    float wcount;
+
+  } density;
+
+  struct {
+
+    /* Balsara switch */
+    float balsara;
+
+    /* Aggregate quantities. */
+    float POrho2;
+
+    /* Change in particle energy over time. */
+    float u_dt;
+
+    /* Signal velocity */
+    float v_sig;
+
+    /* Sound speed */
+    float c;
+
+  } force;
+  //};
+
+  /* Particle mass. */
+  float mass;
+
+  /* Particle ID. */
+  unsigned long long id;
+
+  /* Pointer to corresponding gravity part. */
+  struct gpart* gpart;
+
+} __attribute__((aligned(part_align)));