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Fixed array order problems for dimension id arrays in the NetCDF file
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@daminton
daminton committed Aug 27, 2021
1 parent 0ad8959 commit 31d87fe
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Showing 2 changed files with 78 additions and 63 deletions.
18 changes: 18 additions & 0 deletions python/swiftest/swiftest/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -710,6 +710,24 @@ def swiftest2xr(param):
return ds


def clean_string_values(param, ds):
"""
Cleans up the string values in the DataSet that have artifacts as a result of coming from NetCDF Fortran
Parameters
----------
param : dict
ds : xarray dataset
Returns
-------
dscleanstring : xarray dataset with the strings cleaned up
"""

dscleanstring = ds
return dscleanstring


def swiftest_particle_stream(f):
"""
Reads in a Swiftest particle.dat file and returns a single frame of particle data as a datastream
Expand Down
123 changes: 60 additions & 63 deletions src/netcdf/netcdf.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,6 @@ module subroutine netcdf_initialize_output(self, param)
call check( nf90_def_dim(self%ncid, ID_DIMNAME, NF90_UNLIMITED, self%id_dimid) ) ! 'x' dimension
call check( nf90_def_dim(self%ncid, TIME_DIMNAME, NF90_UNLIMITED, self%time_dimid) ) ! 'y' dimension
call check( nf90_def_dim(self%ncid, STR_DIMNAME, NAMELEN, self%str_dimid) ) ! Dimension for string variables (aka character arrays)
self%dimids = [self%time_dimid, self%id_dimid, self%str_dimid]

select case (param%out_type)
case(NETCDF_FLOAT_TYPE)
Expand All @@ -68,39 +67,39 @@ module subroutine netcdf_initialize_output(self, param)
call check( nf90_def_var(self%ncid, ID_DIMNAME, NF90_INT, self%id_dimid, self%id_varid) )
call check( nf90_def_var(self%ncid, NPL_VARNAME, NF90_INT, self%time_dimid, self%npl_varid) )
call check( nf90_def_var(self%ncid, NTP_VARNAME, NF90_INT, self%time_dimid, self%ntp_varid) )
call check( nf90_def_var(self%ncid, NAME_VARNAME, NF90_CHAR, [self%id_dimid, self%str_dimid], self%name_varid) )
call check( nf90_def_var(self%ncid, NAME_VARNAME, NF90_CHAR, [self%str_dimid, self%id_dimid], self%name_varid) )
if ((param%out_form == XV) .or. (param%out_form == XVEL)) then
call check( nf90_def_var(self%ncid, XHX_VARNAME, self%out_type, self%dimids, self%xhx_varid) )
call check( nf90_def_var(self%ncid, XHY_VARNAME, self%out_type, self%dimids, self%xhy_varid) )
call check( nf90_def_var(self%ncid, XHZ_VARNAME, self%out_type, self%dimids, self%xhz_varid) )
call check( nf90_def_var(self%ncid, VHX_VARNAME, self%out_type, self%dimids, self%vhx_varid) )
call check( nf90_def_var(self%ncid, VHY_VARNAME, self%out_type, self%dimids, self%vhy_varid) )
call check( nf90_def_var(self%ncid, VHZ_VARNAME, self%out_type, self%dimids, self%vhz_varid) )
call check( nf90_def_var(self%ncid, XHX_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%xhx_varid) )
call check( nf90_def_var(self%ncid, XHY_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%xhy_varid) )
call check( nf90_def_var(self%ncid, XHZ_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%xhz_varid) )
call check( nf90_def_var(self%ncid, VHX_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%vhx_varid) )
call check( nf90_def_var(self%ncid, VHY_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%vhy_varid) )
call check( nf90_def_var(self%ncid, VHZ_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%vhz_varid) )
end if

if ((param%out_form == EL) .or. (param%out_form == XVEL)) then
call check( nf90_def_var(self%ncid, A_VARNAME, self%out_type, self%dimids, self%a_varid) )
call check( nf90_def_var(self%ncid, E_VARNAME, self%out_type, self%dimids, self%e_varid) )
call check( nf90_def_var(self%ncid, INC_VARNAME, self%out_type, self%dimids, self%inc_varid) )
call check( nf90_def_var(self%ncid, CAPOM_VARNAME, self%out_type, self%dimids, self%capom_varid) )
call check( nf90_def_var(self%ncid, OMEGA_VARNAME, self%out_type, self%dimids, self%omega_varid) )
call check( nf90_def_var(self%ncid, CAPM_VARNAME, self%out_type, self%dimids, self%capm_varid) )
call check( nf90_def_var(self%ncid, A_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%a_varid) )
call check( nf90_def_var(self%ncid, E_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%e_varid) )
call check( nf90_def_var(self%ncid, INC_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%inc_varid) )
call check( nf90_def_var(self%ncid, CAPOM_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%capom_varid) )
call check( nf90_def_var(self%ncid, OMEGA_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%omega_varid) )
call check( nf90_def_var(self%ncid, CAPM_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%capm_varid) )
end if

call check( nf90_def_var(self%ncid, GMASS_VARNAME, self%out_type, self%dimids, self%Gmass_varid) )
if (param%lrhill_present) call check( nf90_def_var(self%ncid, RHILL_VARNAME, self%out_type, self%dimids, self%rhill_varid) )
if (param%lclose) call check( nf90_def_var(self%ncid, RADIUS_VARNAME, self%out_type, self%dimids, self%radius_varid) )
call check( nf90_def_var(self%ncid, GMASS_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%Gmass_varid) )
if (param%lrhill_present) call check( nf90_def_var(self%ncid, RHILL_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%rhill_varid) )
if (param%lclose) call check( nf90_def_var(self%ncid, RADIUS_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%radius_varid) )
if (param%lrotation) then
call check( nf90_def_var(self%ncid, IP1_VARNAME, self%out_type, self%dimids, self%Ip1_varid) )
call check( nf90_def_var(self%ncid, IP2_VARNAME, self%out_type, self%dimids, self%Ip2_varid) )
call check( nf90_def_var(self%ncid, IP3_VARNAME, self%out_type, self%dimids, self%Ip3_varid) )
call check( nf90_def_var(self%ncid, ROTX_VARNAME, self%out_type, self%dimids, self%rotx_varid) )
call check( nf90_def_var(self%ncid, ROTY_VARNAME, self%out_type, self%dimids, self%roty_varid) )
call check( nf90_def_var(self%ncid, ROTZ_VARNAME, self%out_type, self%dimids, self%rotz_varid) )
call check( nf90_def_var(self%ncid, IP1_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%Ip1_varid) )
call check( nf90_def_var(self%ncid, IP2_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%Ip2_varid) )
call check( nf90_def_var(self%ncid, IP3_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%Ip3_varid) )
call check( nf90_def_var(self%ncid, ROTX_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%rotx_varid) )
call check( nf90_def_var(self%ncid, ROTY_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%roty_varid) )
call check( nf90_def_var(self%ncid, ROTZ_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%rotz_varid) )
end if
if (param%ltides) then
call check( nf90_def_var(self%ncid, K2_VARNAME, self%out_type, self%dimids, self%k2_varid) )
call check( nf90_def_var(self%ncid, Q_VARNAME, self%out_type, self%dimids, self%Q_varid) )
call check( nf90_def_var(self%ncid, K2_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%k2_varid) )
call check( nf90_def_var(self%ncid, Q_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%Q_varid) )
end if
if (param%lenergy) then
call check( nf90_def_var(self%ncid, KE_ORB_VARNAME, self%out_type, self%time_dimid, self%KE_orb_varid) )
Expand Down Expand Up @@ -146,7 +145,6 @@ module subroutine netcdf_open(self, param)
call check( nf90_inq_varid(self%ncid, NTP_VARNAME, self%ntp_varid))
call check( nf90_inq_varid(self%ncid, NAME_VARNAME, self%name_varid))

!call check( nf90_inq_varid(self%ncid, NAME_VARNAME, self%name_varid))
if ((param%out_form == XV) .or. (param%out_form == XVEL)) then
call check( nf90_inq_varid(self%ncid, XHX_VARNAME, self%xhx_varid))
call check( nf90_inq_varid(self%ncid, XHY_VARNAME, self%xhy_varid))
Expand Down Expand Up @@ -235,66 +233,66 @@ module subroutine netcdf_write_frame_base(self, iu, param)
call check( nf90_put_var(iu%ncid, iu%id_varid, self%id(j), start=[idslot]) )
name = trim(adjustl(self%name(j)))
strlen = len(name)
call check( nf90_put_var(iu%ncid, iu%name_varid, name, start=[idslot, 1], count=[1, strlen]) )
call check( nf90_put_var(iu%ncid, iu%name_varid, name, start=[1, idslot], count=[strlen, 1]) )
if ((param%out_form == XV) .or. (param%out_form == XVEL)) then
call check( nf90_put_var(iu%ncid, iu%xhx_varid, self%xh(1, j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%xhy_varid, self%xh(2, j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%xhz_varid, self%xh(3, j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%vhx_varid, self%vh(1, j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%vhy_varid, self%vh(2, j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%vhz_varid, self%vh(3, j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%xhx_varid, self%xh(1, j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%xhy_varid, self%xh(2, j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%xhz_varid, self%xh(3, j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%vhx_varid, self%vh(1, j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%vhy_varid, self%vh(2, j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%vhz_varid, self%vh(3, j), start=[idslot, tslot]) )
end if
if ((param%out_form == EL) .or. (param%out_form == XVEL)) then
call check( nf90_put_var(iu%ncid, iu%a_varid, self%a(j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%e_varid, self%e(j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%inc_varid, self%inc(j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%capom_varid, self%capom(j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%omega_varid, self%omega(j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%capm_varid, self%capm(j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%a_varid, self%a(j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%e_varid, self%e(j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%inc_varid, self%inc(j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%capom_varid, self%capom(j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%omega_varid, self%omega(j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%capm_varid, self%capm(j), start=[idslot, tslot]) )
end if
select type(pl => self)
class is (swiftest_pl) ! Additional output if the passed polymorphic object is a massive body
call check( nf90_put_var(iu%ncid, iu%Gmass_varid, pl%Gmass(j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%Gmass_varid, pl%Gmass(j), start=[idslot, tslot]) )
if (param%lrhill_present) then
call check( nf90_put_var(iu%ncid, iu%rhill_varid, pl%rhill(j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%rhill_varid, pl%rhill(j), start=[idslot, tslot]) )
end if
if (param%lclose) then
call check( nf90_put_var(iu%ncid, iu%radius_varid, pl%radius(j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%radius_varid, pl%radius(j), start=[idslot, tslot]) )
end if
if (param%lrotation) then
call check( nf90_put_var(iu%ncid, iu%Ip1_varid, pl%Ip(1, j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%Ip2_varid, pl%Ip(2, j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%Ip3_varid, pl%Ip(3, j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%rotx_varid, pl%rot(1, j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%roty_varid, pl%rot(2, j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%rotz_varid, pl%rot(3, j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%Ip1_varid, pl%Ip(1, j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%Ip2_varid, pl%Ip(2, j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%Ip3_varid, pl%Ip(3, j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%rotx_varid, pl%rot(1, j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%roty_varid, pl%rot(2, j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%rotz_varid, pl%rot(3, j), start=[idslot, tslot]) )
end if
if (param%ltides) then
call check( nf90_put_var(iu%ncid, iu%k2_varid, pl%k2(j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%Q_varid, pl%Q(j), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%k2_varid, pl%k2(j), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%Q_varid, pl%Q(j), start=[idslot, tslot]) )
end if
end select
end do
end associate
class is (swiftest_cb)
idslot = self%id + 1
call check( nf90_put_var(iu%ncid, iu%id_varid, id, start=[idslot]) )
call check( nf90_put_var(iu%ncid, iu%id_varid, self%id, start=[idslot]) )
name = trim(adjustl(self%name))
strlen = len(name)
call check( nf90_put_var(iu%ncid, iu%name_varid, name, start=[idslot, 1], count=[1, strlen]) )
call check( nf90_put_var(iu%ncid, iu%Gmass_varid, self%Gmass, start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%radius_varid, self%radius, start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%name_varid, name, start=[1, idslot], count=[strlen, 1]) )
call check( nf90_put_var(iu%ncid, iu%Gmass_varid, self%Gmass, start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%radius_varid, self%radius, start=[idslot, tslot]) )
if (param%lrotation) then
call check( nf90_put_var(iu%ncid, iu%Ip1_varid, self%Ip(1), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%Ip2_varid, self%Ip(2), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%Ip3_varid, self%Ip(3), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%rotx_varid, self%rot(1), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%roty_varid, self%rot(2), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%rotz_varid, self%rot(3), start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%Ip1_varid, self%Ip(1), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%Ip2_varid, self%Ip(2), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%Ip3_varid, self%Ip(3), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%rotx_varid, self%rot(1), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%roty_varid, self%rot(2), start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%rotz_varid, self%rot(3), start=[idslot, tslot]) )
end if
if (param%ltides) then
call check( nf90_put_var(iu%ncid, iu%k2_varid, self%k2, start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%Q_varid, self%Q, start=[tslot, idslot]) )
call check( nf90_put_var(iu%ncid, iu%k2_varid, self%k2, start=[idslot, tslot]) )
call check( nf90_put_var(iu%ncid, iu%Q_varid, self%Q, start=[idslot, tslot]) )
end if
end select

Expand Down Expand Up @@ -346,5 +344,4 @@ module subroutine netcdf_write_hdr_system(self, iu, param)
end subroutine netcdf_write_hdr_system



end submodule s_netcdf

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