PALM chapter 3.5.5

3.5.4 User-defined output quantities

A very typical request of users is the calculation and output of quantities which are not part of PALM's standard output. The basic user interface includes a number of subroutines which allow the calculation of user-defined quantities and output of these quantities as time series, (horizontally averaged) vertical profile, 2d cross section or 3d volume data. The respective subroutines contain sample code lines (written as comment lines) for defining, calculating and output of such quantities.

Output times, averaging intervals, etc. are steered by the same variables as used for the standard PALM output quantities, e.g. dt_data_output.

The rest of this chapter explains step-by-step how to modify/extend the default file user_interface.f90 in order to generate the respective output.

Output of vertical profiles

This example shows the output of the quantity "turbulent resolved-scale horizontal momentum flux" (u*v*). If more than one user-defined quantity shall be output, the following steps have to be carried out in the same way for each of the quantities.

The quantity has to be given a unique string identifier, e.g. 'u*v*'. This identifier must be different from the identifiers used for the PALM standard output (see list in description of parameter data_output_pr). To switch on output of this quantity, the user has to assign the string identifier to the parameter data_output_pr_user, eg.:

data_output_pr_user = 'u*v*',
For the quantity, an identification number, a physical unit, and the vertical grid on which it is defined (u- or w-grid), has to be assigned (subroutine user_check_data_output_pr):

CASE ( 'u*v*' )
index = pr_palm + 1 ! identification number
dopr_index(var_count) = index
dopr_unit(var_count) = 'm2/s2' ! physical unit
hom(:,2,index,:) = SPREAD( zu, 2, statistic_regions+1 ) ! vertical grid

Here only the those parts in red color have to be given by the user appropriately.
The identification number (index) must be within the range [ pr_palm+1 , pr_palm+max_pr_user ], where max_pr_user is the number of user-defined profiles as given by parameter data_output_pr_user in the respective PALM run. The physical unit has to be given with respect to the NetCDF conventions. If no unit is given, PALM will abort. The vertical grid has to be either zu (u-grid) or zw (w-grid).
The quantity has to be calculated for all gridpoints (subroutine user_statistics):

!$OMP DO
    DO i = nxl, nxr
       DO j = nys, nyn
          DO k = nzb_s_outer(j,i)+1, nzt
             sums_l(k,pr_palm+1,tn) = sums_l(k,pr_palm+1,tn) +           &
                   ( 0.5 * ( u(k,j,i) + u(k,j,i+1) ) - hom(k,1,1,sr) ) * &
                   ( 0.5 * ( v(k,j,i) + v(k,j+1,i) ) - hom(k,1,2,sr) ) * &
                                              * rmask(j,i,sr)
ENDDO
ENDDO
ENDDO

Once again, only those parts in red have to be adjusted by the user.
The turbulent resolved-scale momentum flux u*v* is defined as the product of the deviations of the horizontal velocities from their respective horizontally averaged mean values. These mean values are stored in array hom(..,1,1,sr) and hom(..,1,2,sr) for the u- and v-component, respectively. Since due to the staggered grid, u and v are not defined at the same gridpoints, they have to be interpolated appropriately (here to the center of the gridbox). The result of the calculation is stored in array sums_l. The second index of this array is the identification number of the profile which must match the one given in the previous step 2.

Output of timeseries

still to be added

Output of 2d cross sections or 3d volume data

This example shows the output of the quantity "square of the u-component" (Note: this quantity could of course easily be calculated from the u-component by postprocessing the PALM output so that calculation within PALM is not necessarily required). If more than one user-defined quantity shall be output, the following steps have to be carried out in the same way for each of the quantities.

The quantity has to be given a unique string identifier, e.g. 'u2'. This identifier must be different from the identifiers used for the PALM standard output (see list in description of parameter data_output). To switch on output of this quantity, the user has to assign the string identifier to the parameter data_output_user, eg.:

data_output_user = 'u2', 'u2_xy_av'

The pure string 'u2' switches on the output of instantaneous 3d volume data. Output of cross section data and time averaged data is switched on by additionally appending the strings '_xy', '_xz', '_yz', and/or '_av' (for a detailed explanation see parameter data_output).
In order to store the quantities' grid point data within PALM, a 3d data array has to be declared in module user:

REAL, DIMENSION(:,:,:), ALLOCATABLE :: u2, u2_av

The second array u2_av is needed in case that output of time averaged data is requested. It is used to store the sum of the data of the respective time levels over which the average has to be carried out.
The data array has to be allocated in subroutine user_init:

ALLOCATE( u2(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )

In case that output of time averaged data is requested, the array containing the sum has possibly to be read from the restart file (local filename BININ) by executing the following code in user_init:

   IF ( initializing_actions == 'read_restart_data' ) THEN
     READ ( 13 ) field_chr
    DO WHILE ( TRIM( field_chr ) /= '*** end user ***' )

      SELECT CASE ( TRIM( field_chr ) )

             CASE ( 'u2_av' )
              ALLOCATE( u2_av(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
              READ ( 13 ) u2_av

           CASE DEFAULT
            PRINT*, '+++ user_init: unknown variable named "', &
                      TRIM( field_chr ), '" found in'
          PRINT*, '               data from prior run on PE ', myid
            CALL local_stop

      END SELECT
   ENDDO
   ENDIF
The quantity has to be given a unit (subroutine user_check_data_output):

CASE ( 'u2' )
unit = 'm2/s2'

Otherwise, PALM will abort.
The vertical grid on which the quantity is defined (given by the levels 'zu' or 'zw', on which the u- or w-component of the velocity are defined) has to be specified for the NetCDF output files in subroutine user_define_netcdf_grid:

CASE ( 'u2', 'u2_xy', 'u2_xz', 'u2_yz' )
grid = 'zu'

As the example shows, this grid has to be defined for the 3d volume data as well as for all of the three cross sections.
After each timestep, the quantity has to be calculated at all gridpoints and to be stored. This has to be done in subroutine user_actions at location 'after_integration':

    CASE ( 'after_integration' )
!
!--    Enter actions to be done after every time integration (before
!--    data output)
!--    Sample for user-defined output:
       DO i = nxl-1, nxr+1
          DO j = nys-1, nyn+1
             DO k = nzb, nzt+1
                u2(k,j,i) = u(k,j,i)**2
             ENDDO
          ENDDO
       ENDDO
In case that output of time-averaged data is requested, the sum- and average-operations as well as the allocation of the sum-array have to be carried out in subroutine user_3d_data_averaging:

    IF ( mode == 'allocate' ) THEN
...
       CASE ( 'u2' )
          IF ( .NOT. ALLOCATED( u2_av ) ) THEN
             ALLOCATE( u2_av(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
          ENDIF
          u2_av = 0.0
...
    ELSEIF ( mode == 'sum' ) THEN
...
       CASE ( 'u2' )
          DO i = nxl-1, nxr+1
             DO j = nys-1, nyn+1
                DO k = nzb, nzt+1
                   u2_av(k,j,i) = u2_av(k,j,i) + u2(k,j,i)
                ENDDO
             ENDDO
          ENDDO
...
    ELSEIF ( mode == 'average' ) THEN
...
       CASE ( 'u2' )
          DO i = nxl-1, nxr+1
             DO j = nys-1, nyn+1
                DO k = nzb, nzt+1
                   u2_av(k,j,i) = u2_av(k,j,i) / REAL( average_count_3d )
                ENDDO
             ENDDO
          ENDDO
For output of 2d cross sections, the gridpoint data of the quantity has to be resorted to array local_pf in subroutine user_data_output_2d. Also the vertical grid, on which the quantity is defined, has to be set again:

    CASE ( 'u2_xy', 'u2_xz', 'u2_yz' )
       IF ( av == 0 ) THEN
          DO i = nxl-1, nxr+1
             DO j = nys-1, nyn+1
                DO k = nzb, nzt+1
                   local_pf(i,j,k) = u2(k,j,i)
                ENDDO
             ENDDO
          ENDDO
       ELSE
          DO i = nxl-1, nxr+1
             DO j = nys-1, nyn+1
                DO k = nzb, nzt+1
                   local_pf(i,j,k) = u2_av(k,j,i)
                ENDDO
             ENDDO
          ENDDO
       ENDIF

       grid = 'zu'

The ELSE case is only needed in case that output of time-averaged data is requested.
For output of 3d volume data, the gridpoint data of the quantity has to be resorted to array local_pf in subroutine user_data_output_3d. Also the vertical grid, on which the quantity is defined, has to be set again:

    CASE ( 'u2' )
       IF ( av == 0 ) THEN
          DO i = nxl-1, nxr+1
             DO j = nys-1, nyn+1
                DO k = nzb, nz_do
                   local_pf(i,j,k) = u2(k,j,i)
                ENDDO
             ENDDO
          ENDDO
       ELSE
          DO i = nxl-1, nxr+1
             DO j = nys-1, nyn+1
                DO k = nzb, nz_do
                   local_pf(i,j,k) = u2_av(k,j,i)
                ENDDO
             ENDDO
          ENDDO
       ENDIF

       grid = 'zu'

The ELSE case is only needed in case that output of time-averaged data is requested.
In case of job chains, the sum array has to be written to the (binary) restart file (local filename BINOUT) in subroutine user_last_actions:

    IF ( ALLOCATED( u2_av ) ) THEN
       WRITE ( 14 ) 'u2_av               '; WRITE ( 14 ) u2_av
    ENDIF

Otherwise, the calculated time-average may be wrong.

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