Merge branch 'master' into mark_tasks_in_drift

AUTHORS

@@ -10,3 +10,4 @@ Tom Theuns 		tom.theuns@durham.ac.uk
 Richard G. Bower	r.g.bower@durham.ac.uk
 Stefan Arridge		stefan.arridge@durham.ac.uk
 Massimiliano Culpo	massimiliano.culpo@googlemail.com
+Yves Revaz   		yves.revaz@epfl.ch

doc/Doxyfile.in

@@ -763,7 +763,8 @@ INPUT                  =  @top_srcdir@ @top_srcdir@/src @top_srcdir@/tests @top_
 INPUT		       += @top_srcdir@/src/hydro/Minimal
 INPUT		       += @top_srcdir@/src/gravity/Default
 INPUT		       += @top_srcdir@/src/riemann
-INPUT		       += @top_srcdir@/src/cooling/const_lambda
+INPUT		       += @top_srcdir@/src/potential/point_mass
+INPUT		       += @top_srcdir@/src/cooling/const_du
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

examples/Disk-Patch/GravityOnly/disk-patch.yml → examples/DiscPatch/GravityOnly/disc-patch.yml

@@ -19,7 +19,7 @@ Statistics:
   
 # Parameters governing the snapshots
 Snapshots:
-  basename:            Disk-Patch # Common part of the name of output files
+  basename:            Disc-Patch # Common part of the name of output files
   time_first:          0.         # Time of the first output (in internal units)
   delta_time:          8.         # Time difference between consecutive outputs (in internal units)
 
@@ -33,11 +33,11 @@ SPH:
 
 # Parameters related to the initial conditions
 InitialConditions:
-  file_name:  Disk-Patch.hdf5       # The file to read
+  file_name:  Disc-Patch.hdf5       # The file to read
 
 # External potential parameters
-Disk-PatchPotential:
+DiscPatchPotential:
   surface_density: 10.
   scale_height:    100.
-  z_disk:          300.
+  z_disc:          300.
   timestep_mult:   0.03

examples/Disk-Patch/GravityOnly/makeIC.py → examples/DiscPatch/GravityOnly/makeIC.py

@@ -26,7 +26,7 @@ import random
 
 # Generates N particles in a box of [0:BoxSize,0:BoxSize,-2scale_height:2scale_height]
 # see Creasey, Theuns & Bower, 2013, for the equations:
-# disk parameters are: surface density sigma
+# disc parameters are: surface density sigma
 #                      scale height b
 # density: rho(z) = (sigma/2b) sech^2(z/b)
 # isothermal velocity dispersion = <v_z^2? = b pi G sigma
@@ -79,7 +79,7 @@ N       = int(sys.argv[1])  # Number of particles
 rho = 2.              # Density
 P = 1.                # Pressure
 gamma = 5./3.         # Gas adiabatic index
-fileName = "Disk-Patch.hdf5" 
+fileName = "Disc-Patch.hdf5" 
 
 
 #---------------------------------------------------

examples/Disk-Patch/GravityOnly/run.sh → examples/DiscPatch/GravityOnly/run.sh

 #!/bin/bash
 
 # Generate the initial conditions if they are not present.
-if [ ! -e Isothermal.hdf5 ]
+if [ ! -e Disc-Patch.hdf5 ]
 then
-    echo "Generating initial conditions for the disk-patch example..."
+    echo "Generating initial conditions for the disc-patch example..."
     python makeIC.py 1000
 fi
 
-../../swift -g -t 2 disk-patch.yml
+../../swift -g -t 2 disc-patch.yml

examples/Disk-Patch/GravityOnly/test.pro → examples/DiscPatch/GravityOnly/test.pro

@@ -8,7 +8,7 @@ iplot = 1 ; if iplot = 1, make plot of E/Lz conservation, else, simply compare f
 @physunits
 
 indir    = './'
-basefile = 'Disk-Patch_'
+basefile = 'Disc-Patch_'
 
 ; set properties of potential
 uL   = phys.pc                  ; unit of length

examples/Disk-Patch/HydroStatic/README → examples/DiscPatch/HydroStatic/README

-Generates and evolves a disk-patch, where gas is in hydrostatic
+Generates and evolves a disc-patch, where gas is in hydrostatic
 equilibrium with an imposed external gravitational force, using the
 equations from Creasey, Theuns & Bower, 2013, MNRAS, Volume 429,
 Issue 3, p.1922-1948.
@@ -10,11 +10,11 @@ To generate ICs ready for a scientific run:
 2) Generate pre-ICs by running the 'makeIC.py' script.
 
 3) Run SWIFT with an isothermal EoS, no cooling nor feedback, and the
-disk-patch potential switched on and using the parameters from
-'disk-patch-icc.yml'
+disc-patch potential switched on and using the parameters from
+'disc-patch-icc.yml'
 
 4) The ICs are then ready to be run for a science problem. Rename the last 
-output to 'Disk-Patch-dynamic.hdf5'. These are now the ICs for the actual test.
+output to 'Disc-Patch-dynamic.hdf5'. These are now the ICs for the actual test.
 
-When running SWIFT with the parameters from 'disk-patch.yml' and an
-ideal gas EoS on these ICs the disk should stay in equilibrium.
+When running SWIFT with the parameters from 'disc-patch.yml' and an
+ideal gas EoS on these ICs the disc should stay in equilibrium.

examples/Disk-Patch/HydroStatic/disk-patch-icc.yml → examples/DiscPatch/HydroStatic/disc-patch-icc.yml

@@ -19,7 +19,7 @@ Statistics:
   
 # Parameters governing the snapshots
 Snapshots:
-  basename:            Disk-Patch   # Common part of the name of output files
+  basename:            Disc-Patch   # Common part of the name of output files
   time_first:          0.           # Time of the first output (in internal units)
   delta_time:          12.          # Time difference between consecutive outputs (in internal units)
 
@@ -33,12 +33,12 @@ SPH:
 
 # Parameters related to the initial conditions
 InitialConditions:
-  file_name:  Disk-Patch.hdf5       # The file to read
+  file_name:  Disc-Patch.hdf5       # The file to read
 
 # External potential parameters
-Disk-PatchPotential:
+DiscPatchPotential:
   surface_density: 10.
   scale_height:    100.
-  z_disk:          200.
+  z_disc:          200.
   timestep_mult:   0.03
   growth_time:     5.

examples/Disk-Patch/HydroStatic/disk-patch.yml → examples/DiscPatch/HydroStatic/disc-patch.yml

@@ -19,7 +19,7 @@ Statistics:
   
 # Parameters governing the snapshots
 Snapshots:
-  basename:           Disk-Patch-dynamic # Common part of the name of output files
+  basename:           Disc-Patch-dynamic # Common part of the name of output files
   time_first:         968.               # Time of the first output (in internal units)
   delta_time:         24.                 # Time difference between consecutive outputs (in internal units)
 
@@ -33,11 +33,11 @@ SPH:
 
 # Parameters related to the initial conditions
 InitialConditions:
-  file_name:  Disk-Patch-dynamic.hdf5       # The file to read
+  file_name:  Disc-Patch-dynamic.hdf5       # The file to read
 
 # External potential parameters
-Disk-PatchPotential:
+DiscPatchPotential:
   surface_density: 10.
   scale_height:    100.
-  z_disk:          200.
+  z_disc:          200.
   timestep_mult:   0.03

examples/Disk-Patch/HydroStatic/makeIC.py → examples/DiscPatch/HydroStatic/makeIC.py

@@ -25,9 +25,9 @@ import math
 import random
 import matplotlib.pyplot as plt
 
-# Generates a disk-patch in hydrostatic equilibrium
+# Generates a disc-patch in hydrostatic equilibrium
 # see Creasey, Theuns & Bower, 2013, for the equations:
-# disk parameters are: surface density sigma
+# disc parameters are: surface density sigma
 #                      scale height b
 # density: rho(z) = (sigma/2b) sech^2(z/b)
 # isothermal velocity dispersion = <v_z^2? = b pi G sigma
@@ -79,7 +79,7 @@ Radius  = 100.         # maximum radius of particles [kpc]
 G       = const_G 
 
 # File
-fileName = "Disk-Patch.hdf5" 
+fileName = "Disc-Patch.hdf5" 
 
 #---------------------------------------------------
 mass           = 1
@@ -145,7 +145,7 @@ mass           = 0.*h + pmass
 entropy_flag   = 0
 vel            = 0 + 0 * pos
 
-# move centre of disk to middle of box
+# move centre of disc to middle of box
 pos[:,:]     += boxSize/2
 
 

examples/Disk-Patch/HydroStatic/test.pro → examples/DiscPatch/HydroStatic/test.pro

@@ -8,7 +8,7 @@ iplot = 1 ; if iplot = 1, make plot of E/Lz conservation, else, simply compare f
 @physunits
 
 indir    = './'
-basefile = 'Disk-Patch_'
+basefile = 'Disc-Patch_'
 
 ; set properties of potential
 uL   = phys.pc                  ; unit of length

examples/ExternalPointMass/externalPointMass.yml

@@ -38,7 +38,7 @@ InitialConditions:
   shift_z:    50.
 
 # External potential parameters
-PointMass:
+PointMassPotential:
   position_x:      50.     # location of external point mass in internal units
   position_y:      50.
   position_z:      50.	

examples/MultiTypes/multiTypes.yml

@@ -35,7 +35,7 @@ InitialConditions:
   file_name:  ./multiTypes.hdf5     # The file to read
 
 # External potential parameters
-PointMass:
+PointMassPotential:
   position_x:      50.     # location of external point mass in internal units
   position_y:      50.
   position_z:      50.	

examples/UniformBox_3D/uniformBox.yml

@@ -33,11 +33,3 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./uniformBox.hdf5     # The file to read
-
-
-  # External potential parameters
-PointMass:
-  position_x:      50.     # location of external point mass in internal units
-  position_y:      50.
-  position_z:      50.	
-  mass:            1e10     # mass of external point mass in internal units

examples/main.c

@@ -439,9 +439,9 @@ int main(int argc, char *argv[]) {
   if (with_external_gravity && myrank == 0) potential_print(&potential);
 
   /* Initialise the cooling function properties */
-  struct cooling_data cooling;
-  if (with_cooling) cooling_init(params, &us, &prog_const, &cooling);
-  if (with_cooling && myrank == 0) cooling_print(&cooling);
+  struct cooling_function_data cooling_func;
+  if (with_cooling) cooling_init(params, &us, &prog_const, &cooling_func);
+  if (with_cooling && myrank == 0) cooling_print(&cooling_func);
 
   /* Construct the engine policy */
   int engine_policies = ENGINE_POLICY | engine_policy_steal;
@@ -457,7 +457,7 @@ int main(int argc, char *argv[]) {
   struct engine e;
   engine_init(&e, &s, params, nr_nodes, myrank, nr_threads, with_aff,
               engine_policies, talking, &us, &prog_const, &hydro_properties,
-              &potential, &cooling);
+              &potential, &cooling_func);
   if (myrank == 0) {
     clocks_gettime(&toc);
     message("engine_init took %.3f %s.", clocks_diff(&tic, &toc),

examples/parameter_example.yml

@@ -66,7 +66,7 @@ DomainDecomposition:
 # Parameters related to external potentials --------------------------------------------
   
 # Point mass external potentials
-PointMass:
+PointMassPotential:
   position_x:      50.      # location of external point mass (internal units)
   position_y:      50.
   position_z:      50.
@@ -82,12 +82,12 @@ IsothermalPotential:
   timestep_mult:   0.03     # Dimensionless pre-factor for the time-step condition
 
 # Disk-patch potential parameters
-Disk-PatchPotential:
-  surface_density: 10.      # Surface density of the disk (internal units)
-  scale_height:    100.     # Scale height of the disk (internal units)
-  z_disk:          200.     # Disk height (internal units)
+DiscPatchPotential:
+  surface_density: 10.      # Surface density of the disc (internal units)
+  scale_height:    100.     # Scale height of the disc (internal units)
+  z_disc:          200.     # Position of the disc along the z-axis (internal units)
   timestep_mult:   0.03     # Dimensionless pre-factor for the time-step condition
-  growth_time:     5.       # (Optional) Time for the disk to grow to its final size (multiple of the dynamical time)
+  growth_time:     5.       # (Optional) Time for the disc to grow to its final size (multiple of the dynamical time)
 
 # Parameters related to cooling function  ----------------------------------------------
 

src/Makefile.am

@@ -42,8 +42,8 @@ endif
 include_HEADERS = space.h runner.h queue.h task.h lock.h cell.h part.h const.h \
     engine.h swift.h serial_io.h timers.h debug.h scheduler.h proxy.h parallel_io.h \
     common_io.h single_io.h multipole.h map.h tools.h partition.h clocks.h parser.h \
-    physical_constants.h physical_constants_cgs.h potentials.h version.h \
-    hydro_properties.h threadpool.h cooling.h
+    physical_constants.h physical_constants_cgs.h potential.h version.h \
+    hydro_properties.h riemann.h threadpool.h cooling.h cooling_struct.h
 
 
 # Common source files
@@ -51,11 +51,11 @@ AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
     serial_io.c timers.c debug.c scheduler.c proxy.c parallel_io.c \
     units.c common_io.c single_io.c multipole.c version.c map.c \
     kernel_hydro.c tools.c part.c partition.c clocks.c parser.c \
-    physical_constants.c potentials.c hydro_properties.c \
+    physical_constants.c potential.c hydro_properties.c \
     runner_doiact_fft.c threadpool.c cooling.c
 
 # Include files for distribution, not installation.
-nobase_noinst_HEADERS = approx_math.h atomic.h cycle.h error.h inline.h kernel_hydro.h kernel_gravity.h \
+nobase_noinst_HEADERS = align.h approx_math.h atomic.h cycle.h error.h inline.h kernel_hydro.h kernel_gravity.h \
 		 kernel_long_gravity.h vector.h runner_doiact.h runner_doiact_grav.h runner_doiact_fft.h \
                  units.h intrinsics.h minmax.h kick.h timestep.h drift.h adiabatic_index.h io_properties.h \
 		 dimension.h equation_of_state.h \
@@ -71,9 +71,13 @@ nobase_noinst_HEADERS = approx_math.h atomic.h cycle.h error.h inline.h kernel_h
                  hydro/Gadget2/hydro_debug.h hydro/Gadget2/hydro_part.h \
 		 hydro/Gizmo/hydro.h hydro/Gizmo/hydro_iact.h hydro/Gizmo/hydro_io.h \
                  hydro/Gizmo/hydro_debug.h hydro/Gizmo/hydro_part.h \
-	         riemann.h riemann/riemann_hllc.h riemann/riemann_trrs.h \
+	         riemann/riemann_hllc.h riemann/riemann_trrs.h \
 		 riemann/riemann_exact.h riemann/riemann_vacuum.h \
-	         cooling/const_du/cooling.h cooling/const_lambda/cooling.h
+	         potential/none/potential.h potential/point_mass/potential.h \
+                 potential/isothermal/potential.h potential/disc_patch/potential.h \
+		 cooling/none/cooling.h cooling/none/cooling_struct.h \
+	         cooling/const_du/cooling.h cooling/const_du/cooling_struct.h \
+                 cooling/const_lambda/cooling.h cooling/const_lambda/cooling_struct.h 
 
 
 # Sources and flags for regular library