Improved documentation of the small cosmo volume test case and added Gadget-2...

Improved documentation of the small cosmo volume test case and added Gadget-2 equivalent parameter file.

examples/SmallCosmoVolume/Gadget2/README

+This parameter file can be used to run the exact same example
+with the Gadget-2 code.
+
+The Gadget code has to be compiled with at least the following options:
+ - PERIODIC
+ - HAVE_HDF5

examples/SmallCosmoVolume/Gadget2/small_cosmo_volume.param

+
+% System of units
+
+UnitLength_in_cm         3.08567758e24      %  1.0 Mpc
+UnitMass_in_g            1.98848e43         %  1.0e10 solar masses 
+UnitVelocity_in_cm_per_s 1e5                %  1 km/sec 
+GravityConstantInternal  4.300927e+01       %  Same value as SWIFT
+
+%  Relevant files
+InitCondFile  	   small_cosmo_volume
+OutputDir          data/
+
+EnergyFile         energy.txt
+InfoFile           info.txt
+TimingsFile        timings.txt
+CpuFile            cpu.txt
+
+RestartFile        restart
+SnapshotFileBase   box
+
+OutputListFilename dummy
+
+% CPU time -limit
+
+TimeLimitCPU      360000  % = 10 hours
+ResubmitOn        0
+ResubmitCommand   my-scriptfile  
+
+
+% Code options
+
+ICFormat                 3
+SnapFormat               3
+ComovingIntegrationOn    1
+
+TypeOfTimestepCriterion  0
+OutputListOn             0
+PeriodicBoundariesOn     1
+
+%  Caracteristics of run
+
+TimeBegin             0.019607843 % z = 50.
+TimeMax	              1.          % z = 0.
+
+Omega0	              0.276
+OmegaLambda           0.724
+OmegaBaryon           0.0455
+HubbleParam           0.703
+BoxSize               100.        % Mpc / h
+
+% Output frequency
+
+TimeBetSnapshot        1.02
+TimeOfFirstSnapshot    0.02
+
+CpuTimeBetRestartFile     36000.0    ; here in seconds
+TimeBetStatistics         0.02
+
+NumFilesPerSnapshot       1
+NumFilesWrittenInParallel 1
+
+% Accuracy of time integration
+
+ErrTolIntAccuracy      0.025 
+MaxRMSDisplacementFac  0.25
+CourantFac             0.1     
+MaxSizeTimestep        0.01
+MinSizeTimestep        1e-6
+
+
+% Tree algorithm, force accuracy, domain update frequency
+
+ErrTolTheta            	     0.3
+TypeOfOpeningCriterion	     1
+ErrTolForceAcc         	     0.005
+TreeDomainUpdateFrequency    0.01
+
+%  Further parameters of SPH
+
+DesNumNgb              48
+MaxNumNgbDeviation     1.
+ArtBulkViscConst       0.8
+InitGasTemp            0.        
+MinGasTemp             0.
+
+% Memory allocation
+
+PartAllocFactor       1.6
+TreeAllocFactor       0.8
+BufferSize            30  
+
+% Softening lengths
+
+MinGasHsmlFractional 0.001
+
+SofteningGas       0
+SofteningHalo      0.0625        # 62.5 kpc / h = 1/25 of mean inter-particle separation
+SofteningDisk      0
+SofteningBulge     0           
+SofteningStars     0
+SofteningBndry     0
+
+SofteningGasMaxPhys       0
+SofteningHaloMaxPhys      0.0625   # 62.5 kpc / h = 1/25 of mean inter-particle separation
+SofteningDiskMaxPhys      0
+SofteningBulgeMaxPhys     0           
+SofteningStarsMaxPhys     0
+SofteningBndryMaxPhys     0
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examples/SmallCosmoVolume/README

@@ -6,4 +6,4 @@ The ICs have been generated to run with Gadget-2 so we need to switch
 on the options to cancel the h-factors and a-factors at reading time.
 
 MD5 checksum of the ICs:
-2a9c603ffb1f6d29f3d98a3ecb9d3238  small_cosmo_volume.hdf5
+08736c3101fd738e22f5159f78e6022b  small_cosmo_volume.hdf5

examples/SmallCosmoVolume/small_cosmo_volume.yml

 # Define the system of units to use internally. 
 InternalUnitSystem:
-  UnitMass_in_cgs:     1.98848e43    # 10^10 M_sun in grams
-  UnitLength_in_cgs:   3.08567758e24 # Mpc in centimeters
-  UnitVelocity_in_cgs: 1e5           # km/s in centimeters per second
+  UnitMass_in_cgs:     1.98848e43    # 10^10 M_sun
+  UnitLength_in_cgs:   3.08567758e24 # 1 Mpc
+  UnitVelocity_in_cgs: 1e5           # 1 km/s
   UnitCurrent_in_cgs:  1             # Amperes
   UnitTemp_in_cgs:     1             # Kelvin
 
 # Structure finding options
 StructureFinding:
-  config_file_name:     stf_input_6dfof_dmonly_sub.cfg  # Name of the STF config file.
-  basename:             ./stf                           # Common part of the name of output files.
-  output_time_format:   0                               # Specifies the frequency format of structure finding. 0 for simulation steps (delta_step) and 1 for simulation time intervals (delta_time).
-  scale_factor_first:   0.92                            # Scale-factor of the first snaphot (cosmological run)
-  time_first:           0.01                            # Time of the first structure finding output (in internal units).
-  delta_step:           1000                            # Time difference between consecutive structure finding outputs (in internal units) in simulation steps.
-  delta_time:           1.02                            # Time difference between consecutive structure finding outputs (in internal units) in simulation time intervals.
+  config_file_name:     stf_input_6dfof_dmonly_sub.cfg
+  basename:             ./stf
+  output_time_format:   1
+  scale_factor_first:   0.02
+  delta_time:           1.02
 
-# WMAP9 cosmology
-Cosmology:
+Cosmology:                      # WMAP9 cosmology
   Omega_m:        0.276
   Omega_lambda:   0.724
   Omega_b:        0.0455
   h:              0.703
-  a_begin:        0.0196078
-  a_end:          1.0
+  a_begin:        0.019607843	# z_ini = 50.
+  a_end:          1.0		# z_end = 0.
 
 # Parameters governing the time integration
 TimeIntegration:
@@ -34,9 +31,9 @@ TimeIntegration:
 Gravity:
   eta:          0.025         
   theta:        0.3           
-  comoving_softening:     0.08
-  max_physical_softening: 0.08
-  mesh_side_length:         32
+  comoving_softening:     0.0889     # 1/25th of the mean inter-particle separation: 88.9 kpc
+  max_physical_softening: 0.0889     # 1/25th of the mean inter-particle separation: 88.9 kpc
+  mesh_side_length:       64
   
 # Parameters governing the snapshots
 Snapshots:

examples/SmallCosmoVolume/stf_input_6dfof_dmonly_sub.cfg

@@ -104,7 +104,7 @@ Allowed_kinetic_potential_ratio=0.2
 #run unbinding of field structures, aka halos
 Bound_halos=0
 #simple Plummer softening length when calculating gravitational energy. If cosmological simulation with period, is fraction of interparticle spacing
-Softening_length=0.
+Softening_length=0.04
 #don't keep background potential when unbinding
 Keep_background_potential=0