Name changes from FLASH2 to FLASH3

Below are the translations between FLASH2 and FLASH3 routines and constant names. The routines and parameters listed here are not a complete list of the a unit's API, just a reference for some of the more name changes. The names are also not one for one substitutes! For example a function in FLASH2 like dbaseBlockCoord has become a subroutine Grid_getBlkCenterCoords in FLASH3. The arguments are also often slightly different so one should check the FLASH3 documentation to verify all the correct arguments are passed. Finally, some of the implementation may not be exactly the same in the two corresponding functions. The list below gives a good starting point for comparison.

FLASH 2                                 FLASH 3

Routine Name Changes
evolve                                  Driver_evolveFlash
abort_flash                             Driver_abortFlash, Driver_abortFlashC
end_flash                               Driver_finalizeFlash
init_flash                              Driver_initFlash


convert_var_prim_to_cons                (gr_primitiveToConserve or flash_convert_cc_hook)
convert_var_cons_to_prim                (gr_conserveToPrimitive or flash_unconvert_cc_hook)
                                        -- There should be no need to call these directly.
                                           Conversion for AMR interpolation is handled
                                           transparently within the Grid unit, in particular
                                           inside Grid_fillGuardCells, based on runtime
                                           parameters convertToConsvdForMeshCalls and
                                           convertToConsvdInMeshInterp (see under Grid unit)

In F3 Driver stores some values that were stored in the dbase in F2

Config Parameter Name Changes
dtini, dt_init                          dtinit
reason: consistency, now all dt parameters are dtmax, dtmin, dtinit

***DBASE - MESH - GRID unit
dBaseLocalBlockCount			        Grid_getLocalNumBlocks
dBaseNodeType				            Grid_getListOfBlocks !pass arg to find nodetype
                                            FLASH2 type    |  FLASH3 argument
                                             1                LEAF
					                         2                PARENT 
dBaseKeyNumber				            No longer needed - get index directly from Flash.h
dBaseVarName				            get directly from Flash.h
dBaseFluxName				            get directly from Flash.h
dBaseGetCellVolume			            Grid_getCellVolume
dBaseGetDataPtrSingleBlock		        Grid_getBlkPtr
dBaseReleaseDataPtrSingleBlock		    Grid_releaseBlkPtr
dBasePutData				            Grid_putPointData/_putRowData/_putPlaneData/_putBlockData

In F3 there are accessor functions for values that were stored in the dbase
Others are #defined constants in Flash.h
dBasePropertyInteger('MyPE')		    Grid_getMyPE(MyPE)
dBasePropertyInteger('MasterProcessor')	in constants.h as MASTER_PE
dBasePropertyInteger			        not needed: in Flash.h
dBasePropertyReal			            not needed: in Flash.h

In F3 we can use non-fixed-blocksizes, so you need to be careful about assuming
NXB being constant across blocks.  Within each block, you can calculate as such:
    call Grid_getBlkIndexLimits(blockId,blkLimits,blkLimitsGC)
    NXB = blkLimits(HIGH,IAXIS) - blkLimits(LOW,IAXIS) + 1
    NYB = blkLimits(HIGH,JAXIS) - blkLimits(LOW,JAXIS) + 1
But note that you probably want to call these N?B something like sizeX to avoid confusion
with anything that might still exist in Flash.h

For Guardcells, ideally you should calculate a different value for each direction,
which is constant by block
    IGUARD = blkLimitsGC(LOW,IAXIS) - blkLimits(LOW,IAXIS)
    JGUARD = blkLimitsGC(LOW,JAXIS) - blkLimits(LOW,JAXIS)

Similarly, the maximum length of a vector in each coordinate direction used to be determined
like this, where k2d =0 if it is a one-dimensional problem:
    jHi_gc = NYB + 2*NGUARD * k2d
Now, calculate it simply as shown below, since blockExtent is zero if the dimension is not 
    jHi_gc = blkLimitsGC(HIGH,JAXIS)

dBaseBlockSize				Grid_getBlkPhysicalSize
dBaseBlockCoord				Grid_getBlkCenterCoords
dBaseNeighborBlocklist	                Grid_getBlkBC
dBaseNeighborType			Grid_getBlkBC (see constants.h for definitions of boundaries)
					  Flash2 values  | FLASH3  
					  <= -20         | .NOT. NOT_BOUNDARY
	                                  nbrs(1)        | nbrs(LOW,IAXIS)
	                                  nbrs(2)        | nbrs(HIGH,IAXIS)
	                                  nbrs(3)        | nbrs(LOW,JAXIS)
	                                  nbrs(4)        | nbrs(HIGH,JAXIS)
	                                  nbrs(5)        | nbrs(LOW,KAXIS)
	                                  nbrs(6)        | nbrs(HIGH,KAXIS)
dBaseGetCoords				Grid_getCellCoords  OR (if variable=znl,zn,znr)
					Grid_getDeltas      (if variable=dz)
dBaseRefinementLevel			Grid_getListOfBlocks (with optional argument and REFINEMENT)

NOTE:  Previous arguments to dBaseGetCoords are translated thus:
    xCoord,yCoord,zCoord        	IAXIS,JAXIS,KAXIS 
    zn (zone center)			CENTER
    znl					LEFT_EDGE
    znr                                 RIGHT_EDGE

NOTE : These routines were very specific to paramesh's interaction with hydro so we have made
!them internal to the Hydro unit					
dBaseGetBoundaryFluxes			hy_getTemporaryData 
dBasePutBoundaryFluxes			hy_putTemporaryData

!refinement done a little differently, look at Grid_markRefineDerefine, 
					Grid_markBlkRefine and Grid_markBlkDerefine

mesh_mark_grid_refinement		Grid_markRefineDerefine Grid_markBlkRefine
mesh_refine_derefine			Grid_markRefineDerefine Grid_markBlkDerefine
mark_grid_refinement			Grid_markRefineDerefine
ref_marking,amr_test_refinement		gr_markRefineDerefine

init_mesh				Grid_init and Grid_initDomain
update_grid_refinement			Grid_updateRefinement
mesh_flux_conserve			Grid_conserveFluxes

					Internal Subroutines - user shouldn't touch
divide_domain				gr_createDomain !plus more
create_block				gr_createBlock
find_neighbors				gr_searchNeighbors

Config Parameter Name Changes    
refine_cutoff                           refine_cutoff_1, refine_cutoff_2, ..., refine_cutoff_4
derefine_cutoff                         derefine_cutoff_1, derefine_cutoff_2, ..., derefine_cutoff_4
refine_filter                           refine_filter_1, refine_filter_2, ..., refine_filter_4
msgbuffer [TRUE]			msgbuf [INTEGER] [1]
        Buffer small messages		        Valid Values: Unconstrained
						triggers consolication of MPI messages. 1 indicates to "consolidate"
						Paramesh2 specific, should always stay at 1
conserved_var                           convertToConsvdForMeshCalls    (old logic, like conserved_var), or

init_eos				Eos_init
eos_types				look in Eos.h for definitions
eos, eos1d				Eos
eos3d					Eos_wrapped

NOTE:  in FLASH2, the default mode for Eos was EOS_REMODE -- this is replaced
   in FLASH3 by mode MODE_DENS_EI.  See description in routine Eos_wrapped
   The eos mode is now a runtime parameter which is defined in the Grid unit,
   however, all units are free to use different modes if they need to.					

Config Parameter Name Changes    
eos_mode [INTEGER]			eosMode [STRING],
                 			eosModeInit [STRING]   (during Grid initialization only)
                                        (These are meant to let the *Grid* unit know how to call
                                         Eos[_wrapped]; other code units, esp. physics units, are
                                         not required to use them.)
tstep_hydro				Hydro_computeDt
init_hydro				Hydro_init
hydro					Hydro
shock_detect				Hydro_detectShock

					Internal Functions - user shouldn't touch
hydro_sweep				hy_sweep
hydro_sweep				hy_block - additional function in F3
hydro_1d				hydro_1d
update_soln				hy_updateSoln

***MHD 8Wave
init_hydro, mhd_init			MHD_init
hydro, mhd_3d				MHD

					Internal Functions - user shouldn't touch
mhd_tstep				mhd_setTimestep

***IO Unit

Routine Name Changes
wr_integrals				IO_writeIntegralQuantities
checkpoint_wr				IO_writeCheckpoint
checkpoint_re				IO_readCheckpoint
plotfile				IO_writePlotfile
output_initial				IO_outputInitial
output					IO_output
particleplot				IO_writeParticles

user_var				Grid_computeUserVars

Config Parameter Name Changes	 
trstrt		 			checkpointFileIntervalTime
nrstrt					checkpointFileIntervalStep
cpNumber				checkpointFileNumber
tplot					plotFileIntervalTime
nplot					plotFileIntervalStep
ptNumber				plotFileNumber

use physical_constants			#include "PhysicalConstants.h"
init_constants_db			PhysicalConstants_init
get_constant_from_db			PhysicalConstants_get
list_measurement_units_db		PhysicalConstants_listUnits
list_constants_db			PhysicalConstants_list
destroy_constants_db			not used 
					Internal subroutines.  User should not call
add_constant_to_db			pc_addConstant			
add_unit_to_db				pc_addUnit

stamp_logfile				Logfile_stamp, Logfile_stampMessage
break_logfile				Logfile_break
create_logfile				Logfile_create
write_perfmon_summary			Logfile_writeSummary, Timers_getSummary

init_mfluid_db				Multispecies_init
add_fluid_to_db				not used.  Use Multispecies_setProperty
get_fluid_property			Multispecies_getProperty
set_fluid_property			Multispecies_setProperty
get_mfluid_property			Multispecies_getProperty
n_fluids				not used - NSPECIES is #defined in Flash.h
find_fluid_index (f, i)			not used - get index directly from Flash.h
					(example #define AIR_SPEC 12)   

query_mfluid_sum			Multispecies_getSum
query_mfluid_suminv			Multispecies_getSumInv
query_mfluid_sumsqr			Multispecies_getSumSqr
query_mfluid_sumfrc			Multispecies_getSumFrac
					Multispecies_getAvg !new in F3
NOTE that the order of arguments has changed -- the weights are now
  optional and at the end in F3
list_mfluid_db				Multispecies_list
init_mat				Simulation_initSpecies

In F2, 
!     Name                    F2              type           F3 Multispecies_setProperty integer
!     ----                    ------          ----           -------------------------
!     "name"                  name            string        Name is given by index in Flash.h
!     "short name"            chem. symbol    string        no equivalent
!     "num total"             A               real          A
!     "num positive"          Z               real          Z
!     "num neutral"           N               real          N
!     "num negative"          E               real          E
!     "binding energy"        Eb              real          EB
!     "adiabatic index"       gamma           real          GAMMA

get_parm_from_context			RuntimeParameters_get
use runtime_parameters			#include "RuntimeParameters.h"
global_parm_context			not used (only one context now)
add_parm_to_context			RuntimeParameters_add
create_parm_context			RuntimeParameters_init !plus more in F3
set_parm_in_context			RuntimeParameters_set
get_parm_type_from_context		no equiv.  use RuntimeParameters_get
get_n_*_parms_in_context		RuntimeParameters_getNum
get_num_parms_in_context		RuntimeParameters_getNum

					!internal function user shouldn't touch
bcast_parm_context			rp_bcastParameters

init_block				Simulation_initBlock and Simulation_init
init_mat				Simulation_initSpecies

timer_start				Timers_start
timer_stop				Timers_stop


***Dbase defined quantities/Flash.h defined quantities
The Flash.h header file is a key file in FLASH3 which 
replaces much of the functionality of the dBase in FLASH2.
The Flash.h header file is well commented, please see it for more

ionmax					NSPECIES

paramFile.txt				setup_params


ParticleData                            Particles_data
InitParticles                           Particles_init
InitParticlePositions                   Particles_initPositions
ParticleFilter                          -- not yet implemented in FLASH3 --
ParticleTimestep                        Particles_computeDt
ParticleUpdateGravity                   Particles_updateGridVar
UpdateParticleAttributes	        Particles_updateAttributes
MapMeshToParticles			Particles_mapFromMesh
MapParticlesToMesh                      Particles_mapToMeshOneBlk -- This 
                                        function uses a different algorithm
                                        and unlike FLASH2 handles one block
                                        at a time.         

IO/IOParticles Config
ptplot					particleFileIntervalTime
nppart					particleFileIntervalStep
pptNumber				particleFileNumber

removed ppstruct - particle attributes are now all real values

F2					F3

GravAccelAllBlocks			Gravity_accelListOfBlocks
GravAccelOneBlock			Gravity_accelListOfBlocks

GravPotentialAllBlocks			Gravity_potentialListOfBlocks
GravPotentialOneBlock			Gravity_potentialListOfBlocks

GravAccelOneRow				Gravity_accelOneRow

InitGravity				Gravity_init

GravityTimestep				Gravity_computeDt	


GravAccelOneLevel                      These functions don't exist anymore.