Merge branch 'master' into 'faster_rebuilds'

# Conflicts:
#   src/part.c

README.md

+SWIFT: SPH WIth Fine-grained inter-dependent Tasking
+====================================================
+
+[![Build Status](https://gitlab.cosma.dur.ac.uk/jenkins/job/GNU%20SWIFT%20build/badge/icon)](https://gitlab.cosma.dur.ac.uk/jenkins/job/GNU%20SWIFT%20build/)
+
+SWIFT is a gravity and SPH solver designed to run cosmological simulations
+on peta-scale machines, scaling well up to 10's of thousands of compute
+node.
+
+More general information about SWIFT is available on the project
+[webpages](http://www.swiftsim.com).
+
+For information on how to _run_ SWIFT, please consult the onboarding guide
+available [here](http://www.swiftsim.com/onboarding.pdf). This includes
+dependencies, and a few examples to get you going.
+
+We suggest that you use the latest release branch of SWIFT, rather than the
+current master branch as this will change rapidly. We do, however, like to
+ensure that the master branch will build and run.
+
+This GitHub repository is designed to be an issue tracker, and a space for
+the public to submit patches through pull requests. It is synchronised with
+the main development repository that is available on the
+[ICC](http://icc.dur.ac.uk)'s GitLab server which is available
+[here](https://gitlab.cosma.dur.ac.uk/swift/swiftsim).
+
+Please feel free to submit issues to this repository, or even pull
+requests. We will try to deal with them as soon as possible, but as the
+core development team is quite small this could take some time.
+
+Contribution Guidelines
+-----------------------
+
+The SWIFT source code uses a variation of the 'Google' formatting style.
+The script 'format.sh' in the root directory applies the clang-format-3.8
+tool with our style choices to all the SWIFT C source file. Please apply
+the formatting script to the files before submitting a pull request.
+
+Please check that the test suite still runs with your changes applied before
+submitting a pull request and add relevant unit tests probing the correctness
+of new modules. An example of how to add a test to the suite can be found by
+considering the tests/testGreeting case.
+
+Any contributions that fail any of the automated tests will not be accepted.
+Contributions that include tests of the proposed modules (or any current ones!)
+are highly encouraged.
+
+```
+ Welcome to the cosmological hydrodynamical code
+    ______       _________________
+   / ___/ |     / /  _/ ___/_  __/
+   \__ \| | /| / // // /_   / /   
+  ___/ /| |/ |/ // // __/  / /    
+ /____/ |__/|__/___/_/    /_/     
+ SPH With Inter-dependent Fine-grained Tasking
+
+ Website: www.swiftsim.com
+ Twitter: @SwiftSimulation
+
+See INSTALL.swift for install instructions.
+
+Usage: swift [OPTION]... PARAMFILE
+       swift_mpi [OPTION]... PARAMFILE
+
+Valid options are:
+  -a                Pin runners using processor affinity.
+  -c                Run with cosmological time integration.
+  -C                Run with cooling.
+  -d                Dry run. Read the parameter file, allocate memory but does not read
+                    the particles from ICs and exit before the start of time integration.
+                    Allows user to check validity of parameter and IC files as well as memory limits.
+  -D                Always drift all particles even the ones far from active particles. This emulates
+                    Gadget-[23] and GIZMO's default behaviours.
+  -e                Enable floating-point exceptions (debugging mode).
+  -f          {int} Overwrite the CPU frequency (Hz) to be used for time measurements.
+  -g                Run with an external gravitational potential.
+  -G                Run with self-gravity.
+  -M                Reconstruct the multipoles every time-step.
+  -n          {int} Execute a fixed number of time steps. When unset use the time_end parameter to stop.
+  -P  {sec:par:val} Set parameter value and overwrites values read from the parameters file. Can be used more than once.
+  -s                Run with hydrodynamics.
+  -S                Run with stars.
+  -t          {int} The number of threads to use on each MPI rank. Defaults to 1 if not specified.
+  -T                Print timers every time-step.
+  -v           [12] Increase the level of verbosity:
+                    1: MPI-rank 0 writes,
+                    2: All MPI-ranks write.
+  -y          {int} Time-step frequency at which task graphs are dumped.
+  -Y          {int} Time-step frequency at which threadpool tasks are dumped.
+  -h                Print this help message and exit.
+
+See the file examples/parameter_example.yml for an example of parameter file.
+```

examples/EAGLE_100/eagle_100.yml

@@ -37,15 +37,18 @@ Statistics:
 
 # Parameters for the self-gravity scheme
 Gravity:
-  eta:                   0.025    # Constant dimensionless multiplier for time integration. 
-  epsilon:               0.001   # Softening length (in internal units).
-  theta:                 0.85      # Opening angle (Multipole acceptance criterion)
-  
+  eta:                    0.025    # Constant dimensionless multiplier for time integration. 
+  theta:                  0.85      # Opening angle (Multipole acceptance criterion)
+  comoving_softening:     0.0026994 # Comoving softening length (in internal units).
+  max_physical_softening: 0.0007    # Physical softening length (in internal units).
+
 # Parameters for the hydrodynamics scheme
 SPH:
   resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
   CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  minimal_temperature:   100      # (internal units)
 
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./EAGLE_ICs_100.hdf5     # The file to read
+  cleanup_h_factors: 1                 # Remove the h-factors inherited from Gadget

examples/EAGLE_100/run.sh

@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -s -t 16 eagle_100.yml 2>&1 | tee output.log
+../swift -c -s -t 16 eagle_100.yml 2>&1 | tee output.log
 

examples/EAGLE_12/eagle_12.yml

@@ -38,16 +38,18 @@ Statistics:
 
 # Parameters for the self-gravity scheme
 Gravity:
-  eta:                   0.025    # Constant dimensionless multiplier for time integration.
-  epsilon:               0.001    # Softening length (in internal units).
-  theta:                 0.85     # Opening angle (Multipole acceptance criterion)
+  eta:                    0.025     # Constant dimensionless multiplier for time integration.
+  theta:                  0.85      # Opening angle (Multipole acceptance criterion)
+  comoving_softening:     0.0026994 # Comoving softening length (in internal units).
+  max_physical_softening: 0.0007    # Physical softening length (in internal units).
   
 # Parameters for the hydrodynamics scheme
 SPH:
   resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
   CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  minimal_temperature:   100      # (internal units)
 
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./EAGLE_ICs_12.hdf5     # The file to read
-
+  cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget

examples/EAGLE_12/run.sh

@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -s -t 16 eagle_12.yml 2>&1 | tee output.log
+../swift -c -s -t 16 eagle_12.yml 2>&1 | tee output.log
 

examples/EAGLE_25/eagle_25.yml

@@ -38,16 +38,19 @@ Statistics:
 
 # Parameters for the self-gravity scheme
 Gravity:
-  eta:                   0.025    # Constant dimensionless multiplier for time integration. 
-  epsilon:               0.001    # Softening length (in internal units).
-  theta:                 0.85     # Opening angle (Multipole acceptance criterion)
-  
+  eta:                    0.025    # Constant dimensionless multiplier for time integration. 
+  theta:                  0.85     # Opening angle (Multipole acceptance criterion)
+  comoving_softening:     0.0026994 # Comoving softening length (in internal units).
+  max_physical_softening: 0.0007    # Physical softening length (in internal units).
+
 # Parameters for the hydrodynamics scheme
 SPH:
   resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
   CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  minimal_temperature:   100      # (internal units)
 
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./EAGLE_ICs_25.hdf5     # The file to read
+  cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
 

examples/EAGLE_25/run.sh

@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -s -t 16 eagle_25.yml 2>&1 | tee output.log
+../swift -c -s -t 16 eagle_25.yml 2>&1 | tee output.log
 

examples/EAGLE_50/eagle_50.yml

@@ -37,16 +37,19 @@ Statistics:
 
 # Parameters for the self-gravity scheme
 Gravity:
-  eta:                   0.025    # Constant dimensionless multiplier for time integration.
-  epsilon:               0.001    # Softening length (in internal units).
-  theta:                 0.85     # Opening angle (Multipole acceptance criterion)
+  eta:                    0.025    # Constant dimensionless multiplier for time integration.
+  theta:                  0.85     # Opening angle (Multipole acceptance criterion)
+  comoving_softening:     0.0026994 # Comoving softening length (in internal units).
+  max_physical_softening: 0.0007    # Physical softening length (in internal units).
 
 # Parameters for the hydrodynamics scheme
 SPH:
   resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
   CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  minimal_temperature:   100      # (internal units)
 
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./EAGLE_ICs_50.hdf5     # The file to read
+  cleanup_h_factors: 1                # Remove the h-factors inherited from Gadget
 

examples/EAGLE_50/run.sh

@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -s -t 16 eagle_50.yml 2>&1 | tee output.log
+../swift -c -s -t 16 eagle_50.yml 2>&1 | tee output.log
 

examples/EAGLE_6/eagle_6.yml

@@ -28,7 +28,7 @@ TimeIntegration:
 # Parameters governing the snapshots
 Snapshots:
   basename:            eagle # Common part of the name of output files
-  time_first:          0.    # Time of the first output (in internal units)
+  time_first:          1.    # Time of the first output (in internal units)
   delta_time:          1e-3  # Time difference between consecutive outputs (in internal units)
   compression:         4
 
@@ -38,16 +38,19 @@ Statistics:
 
 # Parameters for the self-gravity scheme
 Gravity:
-  eta:                   0.025    # Constant dimensionless multiplier for time integration.
-  epsilon:               0.001    # Softening length (in internal units).
-  theta:                 0.85     # Opening angle (Multipole acceptance criterion)
+  eta:                    0.025    # Constant dimensionless multiplier for time integration.
+  theta:                  0.85     # Opening angle (Multipole acceptance criterion)
+  comoving_softening:     0.0026994 # Comoving softening length (in internal units).
+  max_physical_softening: 0.0007    # Physical softening length (in internal units).
   
 # Parameters for the hydrodynamics scheme
 SPH:
   resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
   CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  minimal_temperature:   100      # (internal units)
 
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./EAGLE_ICs_6.hdf5     # The file to read
+  cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
 

examples/EAGLE_6/run.sh

@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -s -t 16 eagle_6.yml 2>&1 | tee output.log
+../swift -c -s -t 16 eagle_6.yml 2>&1 | tee output.log
 

examples/EvrardCollapse_3D/evrard.yml

@@ -31,11 +31,10 @@ SPH:
 
 # Parameters for the self-gravity scheme
 Gravity:
-  eta:                   0.025    # Constant dimensionless multiplier for time integration.
-  epsilon:               0.001      # Softening length (in internal units).
-  theta:                 0.9
-  a_smooth:              1.25     # (Optional) Smoothing scale in top-level cell sizes to smooth the long-range forces over (this is the default value).
-  r_cut:                 4.5      # (Optional) Cut-off in number of top-level cells beyond which no FMM forces are computed (this is the default value).
+  eta:                    0.025    # Constant dimensionless multiplier for time integration.
+  theta:                  0.9
+  comoving_softening:     0.001    # Comoving softening length (in internal units).
+  max_physical_softening: 0.001    # Physical softening length (in internal units).
 
 # Parameters related to the initial conditions
 InitialConditions:

examples/EvrardCollapse_3D/makeIC.py

@@ -18,9 +18,24 @@
 ################################################################################
 
 import h5py
+import argparse as ap
 from numpy import *
 
-# Generates a swift IC file for the Evrard collapse
+parser = ap.ArgumentParser(
+    description="Generates a swift IC file for the Evrard collapse"
+)
+
+parser.add_argument(
+    "-n",
+    "--nparts",
+    help="""
+         Number of particles to be used in the Evrard collapse.
+         """,
+    required=False,
+    default=100000
+)
+
+args = vars(parser.parse_args())
 
 # Parameters
 gamma = 5. / 3.      # Gas adiabatic index
@@ -28,7 +43,7 @@ M = 1.  # total mass of the sphere
 R = 1.               # radius of the sphere
 u0 = 0.05 / M        # initial thermal energy
 fileName = "evrard.hdf5" 
-numPart = 100000
+numPart = int(args["nparts"])
 
 r = R * sqrt(random.random(numPart))
 phi = 2. * pi * random.random(numPart)

examples/SedovBlast_3D/sedov.yml

@@ -31,6 +31,6 @@ SPH:
 
 # Parameters related to the initial conditions
 InitialConditions:
-  file_name:  ./sedov.hdf5          # The file to read
-  h_scaling:           3.33
+  file_name:                    ./sedov.hdf5          
+  smoothing_length_scaling:     3.33
 

examples/SquareTest_2D/run.sh

@@ -11,4 +11,4 @@ fi
 ../swift -s -t 1 square.yml 2>&1 | tee output.log
 
 # Plot the solution
-python plotSolution.py 40
+python plotSolution.py 5

examples/analyse_dump_cells.py

@@ -39,9 +39,11 @@ zcol = 2
 xwcol = 3
 ywcol = 4
 zwcol = 5
-localcol = 18
 supercol = 15
-activecol = 16
+topcol = 16
+activecol = 17
+localcol = 19
+mpicol = 20
 
 #  Command-line arguments.
 if len(sys.argv) < 5:
@@ -59,11 +61,12 @@ for i in range(4, len(sys.argv)):
 
     #  Read the file.
     data = pl.loadtxt(sys.argv[i])
-    #print data
+    if len(data) == 0 or len(data) == 20:
+        continue
 
-    #  Select cells that are on the current rank and are super cells.
+    #  Select cells that are on the current rank and are top-level cells.
     rdata = data[data[:,localcol] == 1]
-    tdata = rdata[rdata[:,supercol] == 1]
+    tdata = rdata[rdata[:,topcol] == 1]
 
     #  Separation of the cells is in data.
     xwidth = tdata[0,xwcol]

examples/main.c

@@ -484,7 +484,7 @@ int main(int argc, char *argv[]) {
 #endif
 
   /* Common variables for restart and IC sections. */
-  int clean_h_values = 0;
+  int clean_smoothing_length_values = 0;
   int flag_entropy_ICs = 0;
 
   /* Work out where we will read and write restart files. */
@@ -609,20 +609,32 @@ int main(int argc, char *argv[]) {
     if (myrank == 0 && with_cosmology) cosmology_print(&cosmo);
 
     /* Initialise the hydro properties */
-    if (with_hydro) hydro_props_init(&hydro_properties, params);
+    if (with_hydro)
+      hydro_props_init(&hydro_properties, &prog_const, &us, params);
     if (with_hydro) eos_init(&eos, params);
 
     /* Initialise the gravity properties */
-    if (with_self_gravity) gravity_props_init(&gravity_properties, params);
+    if (with_self_gravity)
+      gravity_props_init(&gravity_properties, params, &cosmo);
 
     /* Read particles and space information from (GADGET) ICs */
     char ICfileName[200] = "";
     parser_get_param_string(params, "InitialConditions:file_name", ICfileName);
     const int replicate =
         parser_get_opt_param_int(params, "InitialConditions:replicate", 1);
-    clean_h_values =
-        parser_get_opt_param_int(params, "InitialConditions:cleanup_h", 0);
+    clean_smoothing_length_values = parser_get_opt_param_int(
+        params, "InitialConditions:cleanup_smoothing_lengths", 0);
+    const int cleanup_h = parser_get_opt_param_int(
+        params, "InitialConditions:cleanup_h_factors", 0);
+    const int generate_gas_in_ics = parser_get_opt_param_int(
+        params, "InitialConditions:generate_gas_in_ics", 0);
+    if (generate_gas_in_ics && flag_entropy_ICs)
+      error("Can't generate gas if the entropy flag is set in the ICs.");
+    if (generate_gas_in_ics && !with_cosmology)
+      error("Can't generate gas if the run is not cosmological.");
     if (myrank == 0) message("Reading ICs from file '%s'", ICfileName);
+    if (myrank == 0 && cleanup_h)
+      message("Cleaning up h-factors (h=%f)", cosmo.h);
     fflush(stdout);
 
     /* Get ready to read particles of all kinds */
@@ -630,25 +642,27 @@ int main(int argc, char *argv[]) {
     double dim[3] = {0., 0., 0.};
     int periodic = 0;
     if (myrank == 0) clocks_gettime(&tic);
+#if defined(HAVE_HDF5)
 #if defined(WITH_MPI)
 #if defined(HAVE_PARALLEL_HDF5)
     read_ic_parallel(ICfileName, &us, dim, &parts, &gparts, &sparts, &Ngas,
                      &Ngpart, &Nspart, &periodic, &flag_entropy_ICs, with_hydro,
                      (with_external_gravity || with_self_gravity), with_stars,
-                     myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL,
-                     nr_threads, dry_run);
+                     cleanup_h, cosmo.h, myrank, nr_nodes, MPI_COMM_WORLD,
+                     MPI_INFO_NULL, nr_threads, dry_run);
 #else
     read_ic_serial(ICfileName, &us, dim, &parts, &gparts, &sparts, &Ngas,
                    &Ngpart, &Nspart, &periodic, &flag_entropy_ICs, with_hydro,
                    (with_external_gravity || with_self_gravity), with_stars,
-                   myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL, nr_threads,
-                   dry_run);
+                   cleanup_h, cosmo.h, myrank, nr_nodes, MPI_COMM_WORLD,
+                   MPI_INFO_NULL, nr_threads, dry_run);
 #endif
 #else
     read_ic_single(ICfileName, &us, dim, &parts, &gparts, &sparts, &Ngas,
                    &Ngpart, &Nspart, &periodic, &flag_entropy_ICs, with_hydro,
                    (with_external_gravity || with_self_gravity), with_stars,
-                   nr_threads, dry_run);
+                   cleanup_h, cosmo.h, nr_threads, dry_run);
+#endif
 #endif
     if (myrank == 0) {
       clocks_gettime(&toc);
@@ -659,14 +673,18 @@ int main(int argc, char *argv[]) {
 
 #ifdef SWIFT_DEBUG_CHECKS
     /* Check once and for all that we don't have unwanted links */
-    if (!with_stars) {
+    if (!with_stars && !dry_run) {
       for (size_t k = 0; k < Ngpart; ++k)
         if (gparts[k].type == swift_type_star) error("Linking problem");
     }
-    if (!with_hydro) {
+    if (!with_hydro && !dry_run) {
       for (size_t k = 0; k < Ngpart; ++k)
         if (gparts[k].type == swift_type_gas) error("Linking problem");
     }
+
+    /* Check that the other links are correctly set */
+    if (!dry_run)
+      part_verify_links(parts, gparts, sparts, Ngas, Ngpart, Nspart, 1);
 #endif
 
     /* Get the total number of particles across all nodes. */
@@ -690,8 +708,9 @@ int main(int argc, char *argv[]) {
 
     /* Initialize the space with these data. */
     if (myrank == 0) clocks_gettime(&tic);
-    space_init(&s, params, dim, parts, gparts, sparts, Ngas, Ngpart, Nspart,
-               periodic, replicate, with_self_gravity, talking, dry_run);
+    space_init(&s, params, &cosmo, dim, parts, gparts, sparts, Ngas, Ngpart,
+               Nspart, periodic, replicate, generate_gas_in_ics,
+               with_self_gravity, talking, dry_run);
 
     if (myrank == 0) {
       clocks_gettime(&toc);
@@ -700,6 +719,11 @@ int main(int argc, char *argv[]) {
       fflush(stdout);
     }
 
+    /* Check that the matter content matches the cosmology given in the
+     * parameter file. */
+    if (with_cosmology && with_self_gravity && !dry_run)
+      space_check_cosmology(&s, &cosmo, myrank);
+
 /* Also update the total counts (in case of changes due to replication) */
 #if defined(WITH_MPI)
     N_long[0] = s.nr_parts;
@@ -819,7 +843,7 @@ int main(int argc, char *argv[]) {
 
 /* Initialise the table of Ewald corrections for the gravity checks */
 #ifdef SWIFT_GRAVITY_FORCE_CHECKS
-  if (periodic) gravity_exact_force_ewald_init(e.s->dim[0]);
+  if (s.periodic) gravity_exact_force_ewald_init(e.s->dim[0]);
 #endif
 
 /* Init the runner history. */
@@ -836,7 +860,7 @@ int main(int argc, char *argv[]) {
 #endif
 
     /* Initialise the particles */
-    engine_init_particles(&e, flag_entropy_ICs, clean_h_values);
+    engine_init_particles(&e, flag_entropy_ICs, clean_smoothing_length_values);
 
     /* Write the state of the system before starting time integration. */
     engine_dump_snapshot(&e);
@@ -845,10 +869,10 @@ int main(int argc, char *argv[]) {
 
   /* Legend */
   if (myrank == 0)
-    printf("# %6s %14s %14s %14s %9s %12s %12s %12s %16s [%s] %6s\n", "Step",
-           "Time", "Scale-factor", "Time-step", "Time-bins", "Updates",
-           "g-Updates", "s-Updates", "Wall-clock time", clocks_getunit(),
-           "Props");
+    printf("# %6s %14s %14s %10s %14s %9s %12s %12s %12s %16s [%s] %6s\n",
+           "Step", "Time", "Scale-factor", "Redshift", "Time-step", "Time-bins",
+           "Updates", "g-Updates", "s-Updates", "Wall-clock time",
+           clocks_getunit(), "Props");
 
   /* File for the timers */
   if (with_verbose_timers) timers_open_file(myrank);
@@ -1000,6 +1024,24 @@ int main(int argc, char *argv[]) {
            (double)runner_hist_bins[k]);
 #endif
 
+  /* Write final time information */
+  if (myrank == 0) {
+
+    /* Print some information to the screen */
+    printf("  %6d %14e %14e %10.5f %14e %4d %4d %12zu %12zu %12zu %21.3f %6d\n",
+           e.step, e.time, e.cosmology->a, e.cosmology->z, e.time_step,
+           e.min_active_bin, e.max_active_bin, e.updates, e.g_updates,
+           e.s_updates, e.wallclock_time, e.step_props);
+    fflush(stdout);
+
+    fprintf(e.file_timesteps,
+            "  %6d %14e %14e %14e %4d %4d %12zu %12zu %12zu %21.3f %6d\n",
+            e.step, e.time, e.cosmology->a, e.time_step, e.min_active_bin,
+            e.max_active_bin, e.updates, e.g_updates, e.s_updates,
+            e.wallclock_time, e.step_props);
+    fflush(e.file_timesteps);
+  }
+
   /* Write final output. */
   engine_drift_all(&e);
   engine_print_stats(&e);

examples/parameter_example.yml

@@ -30,15 +30,19 @@ SPH:
   h_max:                 10.      # (Optional) Maximal allowed smoothing length in internal units. Defaults to FLT_MAX if unspecified.
   max_volume_change:     1.4      # (Optional) Maximal allowed change of kernel volume over one time-step.
   max_ghost_iterations:  30       # (Optional) Maximal number of iterations allowed to converge towards the smoothing length.
-
+  initial_temperature:   0        # (Optional) Initial temperature (in internal units) to set the gas particles at start-up. Value is ignored if set to 0.
+  minimal_temperature:   0        # (Optional) Minimal temperature (in internal units) allowed for the gas particles. Value is ignored if set to 0.
+  H_mass_fraction:       0.76     # (Optional) Hydrogen mass fraction used for initial conversion from temp to internal energy.
+  
 # Parameters for the self-gravity scheme
 Gravity:
-  eta:          0.025    # Constant dimensionless multiplier for time integration.
-  theta:        0.7      # Opening angle (Multipole acceptance criterion)
-  epsilon:      0.1      # Softening length (in internal units).
-  a_smooth:     1.25     # (Optional) Smoothing scale in top-level cell sizes to smooth the long-range forces over (this is the default value).
-  r_cut_max:    4.5      # (Optional) Cut-off in number of top-level cells beyond which no FMM forces are computed (this is the default value).
-  r_cut_min:    0.1      # (Optional) Cut-off in number of top-level cells below which no truncation of FMM forces are performed (this is the default value).
+  eta:          0.025               # Constant dimensionless multiplier for time integration.
+  theta:        0.7                 # Opening angle (Multipole acceptance criterion)
+  comoving_softening:     0.0026994 # Comoving softening length (in internal units).
+  max_physical_softening: 0.0007    # Physical softening length (in internal units).
+  a_smooth:     1.25                # (Optional) Smoothing scale in top-level cell sizes to smooth the long-range forces over (this is the default value).
+  r_cut_max:    4.5                 # (Optional) Cut-off in number of top-level cells beyond which no FMM forces are computed (this is the default value).
+  r_cut_min:    0.1                 # (Optional) Cut-off in number of top-level cells below which no truncation of FMM forces are performed (this is the default value).
 
 # Parameters for the task scheduling
 Scheduler:
@@ -81,12 +85,14 @@ Statistics:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  SedovBlast/sedov.hdf5 # The file to read
-  cleanup_h:   0                    # (Optional) Clean the values of h that are read in. Set to 1 to activate.
-  h_scaling:  1.                    # (Optional) A scaling factor to apply to all smoothing lengths in the ICs.
+  generate_gas_in_ics:         0    # (Optional) Generate gas particles from the DM-only ICs (e.g. from panphasia).
+  cleanup_h_factors:           0    # (Optional) Clean up the h-factors used in the ICs (e.g. in Gadget files).
+  cleanup_smoothing_lengths:   0    # (Optional) Clean the values of the smoothing lengths that are read in to remove stupid values. Set to 1 to activate.
+  smoothing_length_scaling:    1.   # (Optional) A scaling factor to apply to all smoothing lengths in the ICs.
   shift_x:    0.                    # (Optional) A shift to apply to all particles read from the ICs (in internal units).
   shift_y:    0.
   shift_z:    0.
-  replicate:  2                     # (Optional) Replicate all particles along each axis a given number of times. Default 1.
+  replicate:  2                     # (Optional) Replicate all particles along each axis a given integer number of times. Default 1.
 
 # Parameters controlling restarts
 Restarts:

examples/process_cells

@@ -48,7 +48,7 @@ echo "Number of steps = $steps"
 
 #  And process them,
 echo "Processing cell dumps files..."
-#echo $files | xargs -P $NPROCS -n 4 /bin/bash -c "${SCRIPTHOME}/process_cells_helper $NX $NY $NZ \$0 \$1 \$2 \$3"
+echo $files | xargs -P $NPROCS -n 4 /bin/bash -c "${SCRIPTHOME}/process_cells_helper $NX $NY $NZ \$0 \$1 \$2 \$3"
 
 #  Create summary.
 grep "top cells" step*-active-cells.dat | sort -h > active_cells.log

src/Makefile.am

@@ -65,11 +65,13 @@ AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
 nobase_noinst_HEADERS = align.h approx_math.h atomic.h barrier.h cycle.h error.h inline.h kernel_hydro.h kernel_gravity.h \
 		 kernel_long_gravity.h vector.h cache.h runner_doiact.h runner_doiact_vec.h runner_doiact_grav.h runner_doiact_fft.h \
                  runner_doiact_nosort.h units.h intrinsics.h minmax.h kick.h timestep.h drift.h adiabatic_index.h io_properties.h \