Merge branch 'master' of gitlab.cosma.dur.ac.uk:swift/swiftsim into engine_exchange_strays

Conflicts:
	src/engine.c
	src/space.c
	src/space.h

examples/BigCosmoVolume/makeIC.py

@@ -64,7 +64,7 @@ v = inputFile["/PartType0/Velocities"][:,:]
 m = inputFile["/PartType0/Masses"][:]
 h = inputFile["/PartType0/SmoothingLength"][:]
 u = inputFile["/PartType0/InternalEnergy"][:]
-ids = np.array(range(np.size(u)), dtype='L')
+ids = np.array(range(np.size(u)), dtype='L') + 1
 
 # Downsample
 print "Downsampling..."

examples/BigPerturbedBox/makeIC_fcc.py

@@ -111,6 +111,6 @@ ds[()] = h
 ds = grp.create_dataset('InternalEnergy', (numPart,1), 'f')
 ds[()] = u
 ds = grp.create_dataset('ParticleIDs', (numPart, 1), 'L')
-ds[()] = ids
+ds[()] = ids + 1
 
 file.close()

examples/GreshoVortex/makeIC.py

@@ -82,7 +82,7 @@ for i in range(L):
             else:
                 P = P + 3. + 4.*log(2.)
             u[index] = P / ((gamma - 1.)*rho)
-            ids[index] = partId
+            ids[index] = partId + 1
             partId = partId + 1
 
 

examples/Makefile.am

@@ -63,13 +63,15 @@ swift_fixdt_mpi_LDADD =  ../src/.libs/libswiftsim_mpi.a $(HDF5_LDFLAGS) $(HDF5_L
 
 # Scripts to generate ICs
 EXTRA_DIST = UniformBox/makeIC.py \
+	     UniformDMBox/makeIC.py \
 	     PerturbedBox/makeIC.py \
 	     SedovBlast/makeIC.py SedovBlast/makeIC_fcc.py SedovBlast/solution.py \
 	     SodShock/makeIC.py SodShock/solution.py SodShock/glass_001.hdf5 SodShock/glass_002.hdf5 SodShock/rhox.py \
 	     CosmoVolume/getIC.sh \
 	     BigCosmoVolume/makeIC.py \
 	     BigPerturbedBox/makeIC_fcc.py \
-             GreshoVortex/makeIC.py GreshoVortex/solution.py
+             GreshoVortex/makeIC.py GreshoVortex/solution.py \
+             MultiTypes/makeIC.py
 
 
 # Scripts to plot task graphs

examples/MultiTypes/makeIC.py

+###############################################################################
+ # This file is part of SWIFT.
+ # Copyright (c) 2013 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
+ #                    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/>.
+ # 
+ ##############################################################################
+
+import h5py
+import sys
+from numpy import *
+
+# Generates a swift IC file containing a cartesian distribution of DM particles
+# with a density of 1
+
+# Parameters
+periodic= 1           # 1 For periodic box
+boxSize = 1.
+Lgas = int(sys.argv[1])  # Number of particles along one axis
+rhoGas = 2.              # Density
+P = 1.                   # Pressure
+gamma = 5./3.            # Gas adiabatic index
+rhoDM = 1.
+Ldm = int(sys.argv[2])  # Number of particles along one axis
+
+fileName = "multiTypes.hdf5"
+
+#---------------------------------------------------
+numGas = Lgas**3
+massGas = boxSize**3 * rhoGas / numGas
+internalEnergy = P / ((gamma - 1.)*rhoGas)
+
+numDM = Ldm**3
+massDM = boxSize**3 * rhoDM / numDM
+
+#--------------------------------------------------
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = boxSize
+grp.attrs["NumPart_Total"] =  [numGas, numDM, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numGas, numDM, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, massDM, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = 0
+
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = periodic
+
+
+# Gas Particle group
+grp = file.create_group("/PartType0")
+
+v  = zeros((numGas, 3))
+ds = grp.create_dataset('Velocities', (numGas, 3), 'f')
+ds[()] = v
+v = zeros(1)
+
+m = full((numGas, 1), massGas)
+ds = grp.create_dataset('Masses', (numGas,1), 'f')
+ds[()] = m
+m = zeros(1)
+
+h = full((numGas, 1), 1.1255 * boxSize / Lgas)
+ds = grp.create_dataset('SmoothingLength', (numGas,1), 'f')
+ds[()] = h
+h = zeros(1)
+
+u = full((numGas, 1), internalEnergy)
+ds = grp.create_dataset('InternalEnergy', (numGas,1), 'f')
+ds[()] = u
+u = zeros(1)
+
+ids = linspace(0, numGas, numGas, endpoint=False).reshape((numGas,1))
+ds = grp.create_dataset('ParticleIDs', (numGas, 1), 'L')
+ds[()] = ids + 1
+x      = ids % Lgas;
+y      = ((ids - x) / Lgas) % Lgas;
+z      = (ids - x - Lgas * y) / Lgas**2;
+coords = zeros((numGas, 3))
+coords[:,0] = z[:,0] * boxSize / Lgas + boxSize / (2*Lgas)
+coords[:,1] = y[:,0] * boxSize / Lgas + boxSize / (2*Lgas)
+coords[:,2] = x[:,0] * boxSize / Lgas + boxSize / (2*Lgas)
+ds = grp.create_dataset('Coordinates', (numGas, 3), 'd')
+ds[()] = coords
+
+
+
+
+
+# DM Particle group
+grp = file.create_group("/PartType1")
+
+v  = zeros((numDM, 3))
+ds = grp.create_dataset('Velocities', (numDM, 3), 'f')
+ds[()] = v
+v = zeros(1)
+
+m = full((numDM, 1), massDM)
+ds = grp.create_dataset('Masses', (numDM,1), 'f')
+ds[()] = m
+m = zeros(1)
+
+ids = linspace(0, numDM, numDM, endpoint=False).reshape((numDM,1))
+ds = grp.create_dataset('ParticleIDs', (numDM, 1), 'L')
+ds[()] = ids + Lgas**3 + 1
+x      = ids % Ldm;
+y      = ((ids - x) / Ldm) % Ldm;
+z      = (ids - x - Ldm * y) / Ldm**2;
+coords = zeros((numDM, 3))
+coords[:,0] = z[:,0] * boxSize / Ldm + boxSize / (2*Ldm)
+coords[:,1] = y[:,0] * boxSize / Ldm + boxSize / (2*Ldm)
+coords[:,2] = x[:,0] * boxSize / Ldm + boxSize / (2*Ldm)
+ds = grp.create_dataset('Coordinates', (numDM, 3), 'd')
+ds[()] = coords
+
+file.close()

examples/PerturbedBox/makeIC.py

@@ -103,6 +103,6 @@ ds[()] = h
 ds = grp.create_dataset('InternalEnergy', (numPart,1), 'f')
 ds[()] = u
 ds = grp.create_dataset('ParticleIDs', (numPart, 1), 'L')
-ds[()] = ids
+ds[()] = ids + 1
 
 file.close()

examples/SedovBlast/makeIC.py

@@ -69,7 +69,7 @@ for i in range(L):
             m[index] = mass
             h[index] = 1.1255 * boxSize / L
             u[index] = internalEnergy
-            ids[index] = index
+            ids[index] = index + 1
             if sqrt((x - boxSize/2.)**2 + (y - boxSize/2.)**2 + (z - boxSize/2.)**2) < 2.01 * boxSize/L:
                 u[index] = u[index] + E0 / (33. * mass)
                 print "Particle " , index , " set to detonate."

examples/SedovBlast/makeIC_fcc.py

@@ -72,7 +72,7 @@ for i in range(L):
                 m[index] = mass
                 h[index] = 1.1255 * hbox
                 u[index] = internalEnergy
-                ids[index] = index
+                ids[index] = index + 1
                 if sqrt((x - boxSize/2.)**2 + (y - boxSize/2.)**2 + (z - boxSize/2.)**2) < 1.2 * hbox:
                     u[index] = u[index] + E0 / (28. * mass)
                     print "Particle " , index , " set to detonate."

examples/SodShock/makeIC.py

@@ -86,8 +86,8 @@ h = append(h1, h2,0)
 u = append(u1, u2,0)
 m = append(m1, m2,0)
 ids = zeros(numPart, dtype='L')
-for i in range(numPart):
-    ids[i] = i
+for i in range(1, numPart+1):
+    ids[i-1] = i
 
 #Final operations
 h /= 2

examples/UniformBox/makeIC.py

@@ -86,7 +86,7 @@ u = zeros(1)
 
 ids = linspace(0, numPart, numPart, endpoint=False).reshape((numPart,1))
 ds = grp.create_dataset('ParticleIDs', (numPart, 1), 'L')
-ds[()] = ids
+ds[()] = ids + 1
 x      = ids % L;
 y      = ((ids - x) / L) % L;
 z      = (ids - x - L * y) / L**2;

examples/UniformBox/makeICbig.py

@@ -98,7 +98,7 @@ for n in range(n_iterations):
     u = zeros(1)
 
     ids = linspace(offset, offset+N, N, endpoint=False).reshape((N,1))
-    ds_id[offset:offset+N] = ids
+    ds_id[offset:offset+N] = ids + 1
     x      = ids % L;
     y      = ((ids - x) / L) % L;
     z      = (ids - x - L * y) / L**2;
@@ -130,10 +130,8 @@ u = full((remainder, 1), internalEnergy)
 ds_u[offset:offset+remainder] = u
 u = zeros(1)
 
-print "Done", offset+remainder,"/", numPart
-
 ids = linspace(offset, offset+remainder, remainder, endpoint=False).reshape((remainder,1))
-ds_id[offset:offset+remainder] = ids
+ds_id[offset:offset+remainder] = ids + 1
 x      = ids % L;
 y      = ((ids - x) / L) % L;
 z      = (ids - x - L * y) / L**2;
@@ -143,6 +141,7 @@ coords[:,1] = y[:,0] * boxSize / L + boxSize / (2*L)
 coords[:,2] = x[:,0] * boxSize / L + boxSize / (2*L)
 ds_x[offset:offset+remainder,:] = coords
 
+print "Done", offset+remainder,"/", numPart
 
 
 

examples/UniformDMBox/makeIC.py

+###############################################################################
+ # This file is part of SWIFT.
+ # Copyright (c) 2013 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
+ #                    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/>.
+ # 
+ ##############################################################################
+
+import h5py
+import sys
+from numpy import *
+
+# Generates a swift IC file containing a cartesian distribution of DM particles
+# with a density of 1
+
+# Parameters
+periodic= 1           # 1 For periodic box
+boxSize = 1.
+rho = 1.
+L = int(sys.argv[1])  # Number of particles along one axis
+fileName = "uniformDMBox_%d.hdf5"%L 
+
+#---------------------------------------------------
+numPart = L**3
+mass = boxSize**3 * rho / numPart
+
+#--------------------------------------------------
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = boxSize
+grp.attrs["NumPart_Total"] =  [0, numPart, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [0, numPart, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, mass, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = 0
+
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = periodic
+
+#Particle group
+grp = file.create_group("/PartType1")
+
+v  = zeros((numPart, 3))
+ds = grp.create_dataset('Velocities', (numPart, 3), 'f')
+ds[()] = v
+v = zeros(1)
+
+m = full((numPart, 1), mass)
+ds = grp.create_dataset('Masses', (numPart,1), 'f')
+ds[()] = m
+m = zeros(1)
+
+ids = linspace(0, numPart, numPart, endpoint=False).reshape((numPart,1))
+ds = grp.create_dataset('ParticleIDs', (numPart, 1), 'L')
+ds[()] = ids + 1
+x      = ids % L;
+y      = ((ids - x) / L) % L;
+z      = (ids - x - L * y) / L**2;
+coords = zeros((numPart, 3))
+coords[:,0] = z[:,0] * boxSize / L + boxSize / (2*L)
+coords[:,1] = y[:,0] * boxSize / L + boxSize / (2*L)
+coords[:,2] = x[:,0] * boxSize / L + boxSize / (2*L)
+ds = grp.create_dataset('Coordinates', (numPart, 3), 'd')
+ds[()] = coords
+
+file.close()

examples/main.c

@@ -58,8 +58,9 @@
 
 int main(int argc, char *argv[]) {
 
-  int c, icount, j, k, N, periodic = 1;
-  long long N_total = -1;
+  int c, icount, periodic = 1;
+  size_t Ngas = 0, Ngpart = 0;
+  long long N_total[2] = {0, 0};
   int nr_threads = 1, nr_queues = -1;
   int dump_tasks = 0;
   int data[2];
@@ -67,6 +68,7 @@ int main(int argc, char *argv[]) {
   double h_max = -1.0, scaling = 1.0;
   double time_end = DBL_MAX;
   struct part *parts = NULL;
+  struct gpart *gparts = NULL;
   struct space s;
   struct engine e;
   struct UnitSystem us;
@@ -354,14 +356,14 @@ int main(int argc, char *argv[]) {
   if (myrank == 0) clocks_gettime(&tic);
 #if defined(WITH_MPI)
 #if defined(HAVE_PARALLEL_HDF5)
-  read_ic_parallel(ICfileName, dim, &parts, &N, &periodic, myrank, nr_nodes,
+  read_ic_parallel(ICfileName, dim, &parts, &Ngas, &periodic, myrank, nr_nodes,
                    MPI_COMM_WORLD, MPI_INFO_NULL);
 #else
-  read_ic_serial(ICfileName, dim, &parts, &N, &periodic, myrank, nr_nodes,
+  read_ic_serial(ICfileName, dim, &parts, &Ngas, &periodic, myrank, nr_nodes,
                  MPI_COMM_WORLD, MPI_INFO_NULL);
 #endif
 #else
-  read_ic_single(ICfileName, dim, &parts, &N, &periodic);
+  read_ic_single(ICfileName, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic);
 #endif
 
   if (myrank == 0) {
@@ -372,24 +374,35 @@ int main(int argc, char *argv[]) {
   }
 
 #if defined(WITH_MPI)
-  long long N_long = N;
-  MPI_Reduce(&N_long, &N_total, 1, MPI_LONG_LONG, MPI_SUM, 0, MPI_COMM_WORLD);
+  long long N_long[2] = {Ngas, Ngpart};
+  MPI_Reduce(&N_long, &N_total, 2, MPI_LONG_LONG, MPI_SUM, 0, MPI_COMM_WORLD);
+  if (myrank == 0)
+    message("Read %lld gas particles and %lld DM particles from the ICs",
+            N_total[0], N_total[1]);
 #else
-  N_total = N;
+  N_total[0] = Ngas;
+  N_total[1] = Ngpart - Ngas;
+  message("Read %lld gas particles and %lld DM particles from the ICs",
+	  N_total[0], N_total[1]);
 #endif
-  if (myrank == 0) message("Read %lld particles from the ICs", N_total);
 
   /* Apply h scaling */
   if (scaling != 1.0)
-    for (k = 0; k < N; k++) parts[k].h *= scaling;
+    for (size_t k = 0; k < Ngas; k++) parts[k].h *= scaling;
 
   /* Apply shift */
-  if (shift[0] != 0 || shift[1] != 0 || shift[2] != 0)
-    for (k = 0; k < N; k++) {
+  if (shift[0] != 0 || shift[1] != 0 || shift[2] != 0) {
+    for (size_t k = 0; k < Ngas; k++) {
       parts[k].x[0] += shift[0];
       parts[k].x[1] += shift[1];
       parts[k].x[2] += shift[2];
     }
+    for (size_t k = 0; k < Ngpart; k++) {
+      gparts[k].x[0] += shift[0];
+      gparts[k].x[1] += shift[1];
+      gparts[k].x[2] += shift[2];
+    }
+  }
 
   /* Set default number of queues. */
   if (nr_queues < 0) nr_queues = nr_threads;
@@ -399,7 +412,8 @@ int main(int argc, char *argv[]) {
 
   /* Initialize the space with this data. */
   if (myrank == 0) clocks_gettime(&tic);
-  space_init(&s, dim, parts, N, periodic, h_max, myrank == 0);
+  space_init(&s, dim, parts, gparts, Ngas, Ngpart, periodic, h_max,
+             myrank == 0);
   if (myrank == 0 && verbose) {
     clocks_gettime(&toc);
     message("space_init took %.3f %s.", clocks_diff(&tic, &toc),
@@ -415,6 +429,7 @@ int main(int argc, char *argv[]) {
     message("highest-level cell dimensions are [ %i %i %i ].", s.cdim[0],
             s.cdim[1], s.cdim[2]);
     message("%zi parts in %i cells.", s.nr_parts, s.tot_cells);
+    message("%zi gparts in %i cells.", s.nr_gparts, s.tot_cells);
     message("maximum depth is %d.", s.maxdepth);
     // message( "cutoffs in [ %g %g ]." , s.h_min , s.h_max ); fflush(stdout);
   }
@@ -482,9 +497,10 @@ int main(int argc, char *argv[]) {
 
   if (myrank == 0) {
     message(
-        "Running on %lld particles until t=%.3e with %i threads and %i "
-        "queues (dt_min=%.3e, dt_max=%.3e)...",
-        N_total, time_end, e.nr_threads, e.sched.nr_queues, e.dt_min, e.dt_max);
+        "Running on %lld gas particles and %lld DM particles until t=%.3e with "
+        "%i threads and %i queues (dt_min=%.3e, dt_max=%.3e)...",
+        N_total[0], N_total[1], time_end, e.nr_threads, e.sched.nr_queues,
+        e.dt_min, e.dt_max);
     fflush(stdout);
   }
 
@@ -499,7 +515,7 @@ int main(int argc, char *argv[]) {
         clocks_getunit());
 
   /* Let loose a runner on the space. */
-  for (j = 0; !engine_is_done(&e); j++) {
+  for (int j = 0; !engine_is_done(&e); j++) {
 
 /* Repartition the space amongst the nodes? */
 #ifdef WITH_MPI

src/Makefile.am

@@ -46,9 +46,9 @@ AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
 # Include files for distribution, not installation.
 nobase_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 minmax.h \
-		 gravity.h \
-		 gravity/Default/gravity.h gravity/Default/runner_iact_grav.h \
-		 gravity/Default/gravity_part.h \
+		 gravity.h gravity_io.h \
+		 gravity/Default/gravity.h gravity/Default/gravity_iact.h gravity/Default/gravity_io.h \
+		 gravity/Default/gravity_debug.h gravity/Default/gravity_part.h  \
 	 	 hydro.h hydro_io.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 \

src/cell.c

@@ -376,9 +376,9 @@ void cell_split(struct cell *c) {
 
   int i, j;
   const int count = c->count, gcount = c->gcount;
-  struct part* parts = c->parts;
-  struct xpart* xparts = c->xparts;
-  struct gpart* gparts = c->gparts;
+  struct part *parts = c->parts;
+  struct xpart *xparts = c->xparts;
+  struct gpart *gparts = c->gparts;
   int left[8], right[8];
   double pivot[3];
 

src/common_io.c

@@ -359,7 +359,9 @@ FILE* prepareXMFfile() {
 
   if (tempFile == NULL) error("Unable to open temporary file.");
 
-  for (int i = 0; fgets(buffer, 1024, tempFile) != NULL && i < counter - 3; i++) {
+  int i = 0;
+  while (fgets(buffer, 1024, tempFile) != NULL && i < counter - 3) {
+    i++;
     fprintf(xmfFile, "%s", buffer);
   }
   fprintf(xmfFile, "\n");
@@ -471,4 +473,90 @@ void writeXMFline(FILE* xmfFile, char* fileName, char* name, long long N,
   fprintf(xmfFile, "</Attribute>\n");
 }
 
+/**
+ * @brief Prepare the DM particles (in gparts) read in for the addition of the
+ * other particle types
+ *
+ * This function assumes that the DM particles are all at the start of the
+ * gparts array
+ *
+ * @param gparts The array of #gpart freshly read in.
+ * @param Ndm The number of DM particles read in.
+ */
+void prepare_dm_gparts(struct gpart* gparts, size_t Ndm) {
+
+  /* Let's give all these gparts a negative id */
+  for (size_t i = 0; i < Ndm; ++i) {
+
+    /* 0 or negative ids are not allowed */
+    if (gparts[i].id <= 0) error("0 or negative ID for DM particle");
+
+    gparts[i].id = -gparts[i].id;
+  }
+}
+
+/**
+ * @brief Copy every #part into the corresponding #gpart and link them.
+ *
+ * This function assumes that the DM particles are all at the start of the
+ * gparts array and adds the hydro particles afterwards
+ *
+ * @param parts The array of #part freshly read in.
+ * @param gparts The array of #gpart freshly read in with all the DM particles
+ *at the start
+ * @param Ngas The number of gas particles read in.
+ * @param Ndm The number of DM particles read in.
+ */
+void duplicate_hydro_gparts(struct part* parts, struct gpart* gparts,
+                            size_t Ngas, size_t Ndm) {
+
+  for (size_t i = 0; i < Ngas; ++i) {
+
+    /* Duplicate the crucial information */
+    gparts[i + Ndm].x[0] = parts[i].x[0];
+    gparts[i + Ndm].x[1] = parts[i].x[1];
+    gparts[i + Ndm].x[2] = parts[i].x[2];
+
+    gparts[i + Ndm].v_full[0] = parts[i].v[0];
+    gparts[i + Ndm].v_full[1] = parts[i].v[1];
+    gparts[i + Ndm].v_full[2] = parts[i].v[2];
+
+    gparts[i + Ndm].mass = parts[i].mass;
+
+    /* Link the particles */
+    gparts[i + Ndm].part = &parts[i];
+    parts[i].gpart = &gparts[i + Ndm];
+  }
+}
+
+/**
+ * @brief Copy every DM #gpart into the dmparts array.
+ *
+ * @param gparts The array of #gpart containing all particles.
+ * @param Ntot The number of #gpart.
+ * @param dmparts The array of #gpart containg DM particles to be filled.
+ * @param Ndm The number of DM particles.
+ */
+void collect_dm_gparts(struct gpart* gparts, size_t Ntot, struct gpart* dmparts,
+                       size_t Ndm) {
+
+  size_t count = 0;
+
+  /* Loop over all gparts */
+  for (size_t i = 0; i < Ntot; ++i) {
+
+    /* And collect the DM ones */
+    if (gparts[i].id < 0) {
+      memcpy(&dmparts[count], &gparts[i], sizeof(struct gpart));
+      dmparts[count].id = -dmparts[count].id;
+      count++;
+    }
+  }
+
+  /* Check that everything is fine */
+  if (count != Ndm)
+    error("Collected the wrong number of dm particles (%zd vs. %zd expected)",
+          count, Ndm);
+}
+
 #endif