merged master

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/EAGLE_25/README

@@ -13,4 +13,4 @@ The particle load of the main EAGLE simulation can be reproduced by
 running these ICs on 64 cores.
 
 MD5 checksum of the ICs: 
-ada2c728db2bd2d77a20c4eef52dfaf1  EAGLE_ICs_25.hdf5
+02cd1c353b86230af047b5d4ab22afcf  EAGLE_ICs_25.hdf5

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

@@ -35,8 +35,9 @@ 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.	
   mass:            1e10     # mass of external point mass in internal units
+  timestep_mult:   1e-2

examples/SedovBlast_1D/sedov.yml

@@ -21,7 +21,7 @@ Snapshots:
 
 # Parameters governing the conserved quantities statistics
 Statistics:
-  delta_time:          1e-3 # Time between statistics output
+  delta_time:          1e-5 # Time between statistics output
 
 # Parameters for the hydrodynamics scheme
 SPH:

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

@@ -541,7 +541,7 @@ int main(int argc, char *argv[]) {
 
       /* Make sure output file is empty, only on one rank. */
       char dumpfile[30];
-      snprintf(dumpfile, 30, "thread_info_MPI-step%d.dat", j);
+      snprintf(dumpfile, 30, "thread_info_MPI-step%d.dat", j + 1);
       FILE *file_thread;
       if (myrank == 0) {
         file_thread = fopen(dumpfile, "w");
@@ -593,7 +593,7 @@ int main(int argc, char *argv[]) {
 
 #else
       char dumpfile[30];
-      snprintf(dumpfile, 30, "thread_info-step%d.dat", j);
+      snprintf(dumpfile, 30, "thread_info-step%d.dat", j + 1);
       FILE *file_thread;
       file_thread = fopen(dumpfile, "w");
       /* Add some information to help with the plots */