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Added initialization of NetCDF encounter data file variables
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@daminton
daminton committed Dec 2, 2022
1 parent 5bcf737 commit 3154dfa
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71 changes: 71 additions & 0 deletions src/encounter/encounter_io.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@

submodule (encounter_classes) s_encounter_io
use swiftest
use netcdf
contains

module subroutine encounter_io_dump_storage_list(self, param)
Expand All @@ -26,12 +27,70 @@ module subroutine encounter_io_initialize_output(self, param)
!! author: David A. Minton
!!
!! Initialize a NetCDF encounter file system and defines all variables.
use, intrinsic :: ieee_arithmetic
implicit none
! Arguments
class(encounter_io_parameters), intent(inout) :: self !! Parameters used to identify a particular NetCDF dataset
class(swiftest_parameters), intent(in) :: param !! Current run configuration parameters
! Internals
integer(I4B) :: nvar, varid, vartype
real(DP) :: dfill
real(SP) :: sfill
logical :: fileExists
character(len=STRMAX) :: errmsg
integer(I4B) :: ndims

dfill = ieee_value(dfill, IEEE_QUIET_NAN)
sfill = ieee_value(sfill, IEEE_QUIET_NAN)

! Check if the file exists, and if it does, delete it
inquire(file=param%outfile, exist=fileExists)
if (fileExists) then
open(unit=LUN, file=self%outfile, status="old", err=667, iomsg=errmsg)
close(unit=LUN, status="delete")
end if

call check( nf90_create(self%outfile, NF90_NETCDF4, self%ncid), "encounter_io_initialize_output nf90_create" )

call check( nf90_def_dim(self%ncid, ENCID_DIMNAME, NF90_UNLIMITED, self%encid_dimid), "encounter_io_initialize_output nf90_def_dim encid_dimid" )
call check( nf90_def_dim(self%ncid, STR_DIMNAME, NAMELEN, self%str_dimid), "encounter_io_initialize_output nf90_def_dim str_dimid" ) ! Dimension for string variables (aka character arrays)
call check( nf90_def_dim(self%ncid, TIME_DIMNAME, NF90_UNLIMITED, self%time_dimid), "encounter_io_initialize_output nf90_def_dim time_dimid" ) ! 'y' dimension

select case (param%out_type)
case("NETCDF_FLOAT")
self%out_type = NF90_FLOAT
case("NETCDF_DOUBLE")
self%out_type = NF90_DOUBLE
end select

call check( nf90_def_var(self%ncid, TIME_DIMNAME, self%out_type, self%time_dimid, self%time_varid), "encounter_io_initialize_output nf90_def_var time_varid" )
call check( nf90_def_var(self%ncid, ENCID_DIMNAME, NF90_INT, self%encid_dimid, self%encid_varid), "encounter_io_initialize_output nf90_def_var encid_varid" )
call check( nf90_def_var(self%ncid, NENC_VARNAME, NF90_INT, self%time_dimid, self%nenc_varid), "encounter_io_initialize_output nf90_def_var nenc_varid" )
call check( nf90_def_var(self%ncid, ID1_VARNAME, NF90_INT, [self%encid_dimid, self%time_dimid], self%id1_varid), "encounter_io_initialize_output nf90_def_var id1_varid" )
call check( nf90_def_var(self%ncid, ID2_VARNAME, NF90_INT, [self%encid_dimid, self%time_dimid], self%id2_varid), "encounter_io_initialize_output nf90_def_var id2_varid" )
call check( nf90_def_var(self%ncid, X1X_VARNAME, self%out_type, [self%encid_dimid, self%time_dimid], self%x1x_varid), "encounter_io_initialize_output nf90_def_var x1x_varid" )
call check( nf90_def_var(self%ncid, X1Y_VARNAME, self%out_type, [self%encid_dimid, self%time_dimid], self%x1y_varid), "encounter_io_initialize_output nf90_def_var x1y_varid" )
call check( nf90_def_var(self%ncid, X1Z_VARNAME, self%out_type, [self%encid_dimid, self%time_dimid], self%x1z_varid), "encounter_io_initialize_output nf90_def_var x1z_varid" )
call check( nf90_def_var(self%ncid, X2X_VARNAME, self%out_type, [self%encid_dimid, self%time_dimid], self%x2x_varid), "encounter_io_initialize_output nf90_def_var x2x_varid" )
call check( nf90_def_var(self%ncid, X2Y_VARNAME, self%out_type, [self%encid_dimid, self%time_dimid], self%x2y_varid), "encounter_io_initialize_output nf90_def_var x2y_varid" )
call check( nf90_def_var(self%ncid, X2Z_VARNAME, self%out_type, [self%encid_dimid, self%time_dimid], self%x2z_varid), "encounter_io_initialize_output nf90_def_var x2z_varid" )
call check( nf90_def_var(self%ncid, V1X_VARNAME, self%out_type, [self%encid_dimid, self%time_dimid], self%v1x_varid), "encounter_io_initialize_output nf90_def_var v1x_varid" )
call check( nf90_def_var(self%ncid, V1Y_VARNAME, self%out_type, [self%encid_dimid, self%time_dimid], self%v1y_varid), "encounter_io_initialize_output nf90_def_var v1y_varid" )
call check( nf90_def_var(self%ncid, V1Z_VARNAME, self%out_type, [self%encid_dimid, self%time_dimid], self%v1z_varid), "encounter_io_initialize_output nf90_def_var v1z_varid" )
call check( nf90_def_var(self%ncid, V2X_VARNAME, self%out_type, [self%encid_dimid, self%time_dimid], self%v2x_varid), "encounter_io_initialize_output nf90_def_var v2x_varid" )
call check( nf90_def_var(self%ncid, V2Y_VARNAME, self%out_type, [self%encid_dimid, self%time_dimid], self%v2y_varid), "encounter_io_initialize_output nf90_def_var v2y_varid" )
call check( nf90_def_var(self%ncid, V2Z_VARNAME, self%out_type, [self%encid_dimid, self%time_dimid], self%v2z_varid), "encounter_io_initialize_output nf90_def_var v2z_varid" )
call check( nf90_def_var(self%ncid, LEVEL_VARNAME, NF90_INT, [self%encid_dimid, self%time_dimid], self%level_varid), "encounter_io_initialize_output nf90_def_var level_varid" )


! Take the file out of define mode
call check( nf90_enddef(self%ncid), "encounter_io_initialize_output nf90_enddef" )

return

667 continue
write(*,*) "Error creating encounter output file. " // trim(adjustl(errmsg))
call util_exit(FAILURE)
end subroutine encounter_io_initialize_output


Expand All @@ -44,6 +103,18 @@ module subroutine encounter_io_open_file(self, param, readonly)
class(encounter_io_parameters), intent(inout) :: self !! Parameters used to identify a particular NetCDF dataset
class(swiftest_parameters), intent(in) :: param !! Current run configuration parameters
logical, optional, intent(in) :: readonly !! Logical flag indicating that this should be open read only
! Internals
integer(I4B) :: mode, status
character(len=NF90_MAX_NAME) :: str_dim_name
character(len=STRMAX) :: errmsg

mode = NF90_WRITE
if (present(readonly)) then
if (readonly) mode = NF90_NOWRITE
end if

write(errmsg,*) "netcdf_open nf90_open ",trim(adjustl(param%outfile))
call check( nf90_open(self%outfile, mode, self%ncid), errmsg)

return
end subroutine encounter_io_open_file
Expand Down
38 changes: 38 additions & 0 deletions src/modules/encounter_classes.f90
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Expand Up @@ -17,6 +17,24 @@ module encounter_classes
public

integer(I4B), parameter :: SWEEPDIM = 3
!! NetCDF dimension and variable names for the enounter save object
character(*), parameter :: ENCID_DIMNAME = "encounter"
character(*), parameter :: NENC_VARNAME = "nenc"
character(*), parameter :: ID1_VARNAME = "id1"
character(*), parameter :: ID2_VARNAME = "id2"
character(*), parameter :: X1X_VARNAME = "x1x"
character(*), parameter :: X1Y_VARNAME = "x1y"
character(*), parameter :: X1Z_VARNAME = "x1z"
character(*), parameter :: X2X_VARNAME = "x2x"
character(*), parameter :: X2Y_VARNAME = "x2y"
character(*), parameter :: X2Z_VARNAME = "x2z"
character(*), parameter :: V1X_VARNAME = "v1x"
character(*), parameter :: V1Y_VARNAME = "v1y"
character(*), parameter :: V1Z_VARNAME = "v1z"
character(*), parameter :: V2X_VARNAME = "v2x"
character(*), parameter :: V2Y_VARNAME = "v2y"
character(*), parameter :: V2Z_VARNAME = "v2z"
character(*), parameter :: LEVEL_VARNAME = "level"

type :: encounter_list
integer(I8B) :: nenc = 0 !! Total number of encounters
Expand Down Expand Up @@ -48,6 +66,26 @@ module encounter_classes
end type encounter_storage

type, extends(netcdf_parameters) :: encounter_io_parameters
character(STRMAX) :: outfile = "encounter.nc" !! Encounter output file name
integer(I4B) :: encid_dimid !! NetCDF ID for the encounter pair index dimension
integer(I4B) :: encid_varid !! NetCDF ID for the encounter pair index variable
integer(I4B) :: nenc_varid !! NetCDF ID for the number of encounters variable
integer(I4B) :: id1_varid !! NetCDF ID for the id1 of the encounter variable
integer(I4B) :: id2_varid !! NetCDF ID for the id2 of the encounter variable
integer(I4B) :: x1x_varid !! NetCDF ID for the body1 x position variable
integer(I4B) :: x1y_varid !! NetCDF ID for the body1 y position variable
integer(I4B) :: x1z_varid !! NetCDF ID for the body1 z position variable
integer(I4B) :: x2x_varid !! NetCDF ID for the body2 x position variable
integer(I4B) :: x2y_varid !! NetCDF ID for the body2 y position variable
integer(I4B) :: x2z_varid !! NetCDF ID for the body2 z position variable
integer(I4B) :: v1x_varid !! NetCDF ID for the body1 x velocity variable
integer(I4B) :: v1y_varid !! NetCDF ID for the body1 y velocity variable
integer(I4B) :: v1z_varid !! NetCDF ID for the body1 z velocity variable
integer(I4B) :: v2x_varid !! NetCDF ID for the body2 x velocity variable
integer(I4B) :: v2y_varid !! NetCDF ID for the body2 y velocity variable
integer(I4B) :: v2z_varid !! NetCDF ID for the body2 z velocity variable
integer(I4B) :: level_varid !! NetCDF ID for the recursion level variable

contains
procedure :: initialize => encounter_io_initialize_output !! Initialize a set of parameters used to identify a NetCDF output object
procedure :: open => encounter_io_open_file !! Opens a NetCDF file
Expand Down
7 changes: 7 additions & 0 deletions src/modules/swiftest_classes.f90
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Expand Up @@ -496,6 +496,13 @@ end subroutine abstract_step_system
end interface

interface

module subroutine check(status, call_identifier)
implicit none
integer, intent (in) :: status !! The status code returned by a NetCDF function
character(len=*), intent(in), optional :: call_identifier
end subroutine check

module subroutine discard_pl(self, system, param)
implicit none
class(swiftest_pl), intent(inout) :: self !! Swiftest massive body object
Expand Down
2 changes: 1 addition & 1 deletion src/netcdf/netcdf.f90
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Expand Up @@ -12,7 +12,7 @@
use netcdf
contains

subroutine check(status, call_identifier)
module subroutine check(status, call_identifier)
!! author: Carlisle A. Wishard, Dana Singh, and David A. Minton
!!
!! Checks the status of all NetCDF operations to catch errors
Expand Down

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