ToDo-List

PALM workshop (May 22-25, 2018)

Category	What to do?	Name
Web docu	Restructure entire PALM docu	Farah
Web docu	Update palmrun description	Siggi
Web docu	Update links to palmrun description, remove/rename traces to mbuild, mrun, subjob	tba
Web docu	Update installation/requirements description	Helge
Web docu	Complete and check existing PALM error messages (Remaining Numbers without description: PA0149, 226, 228, 234, 245-270, 296-301, 309, 319-321, 327, 328, 330, 334-338, 460-464, UI0002; the error message itself is sufficient for many of these -> mark them in a special way?)	tba
Web docu	Check consistency of parameter lists (namelist pages and alphabetical list)	tba
Web docu	Update links from manual to Tutorial (new: PALM seminar material)	tba
Web docu	Revise description of timeseries output	tba
Web docu	Update VAPOR page	Tobias
Tickets	Sort tickets of component "General" into appropriate components (change title and keywords where needed, create new components where necessary)	tba
PALM code	Check for double-use of error numbers	tba
PALM code	Clean up / extend location messages	tba
PALM code	Comment variables/parameters in declaration sections	tba
PALM code	Known bug: W* and Z_I in the first line of the run control file don't correspond to the values in the last run control output line of the previous run.	Sebastian
PALM code	Known bug: Restart crashes in sum_up_3d_data if an _av quantity is given in the restart run NAMELIST file (_p3dr) but not in the initial run NAMELIST file (_p3d) --> Implement check?!
Scripts	Write new script to find the next unused of free error number	Helge
Scripts	Finalize first version of new palmplot script (python)	Helge
Scripts	Remove deprecated vapor scripts	Tobias
Discussion	Parameter file inconsistencies. Settings for data output are not consistent within the parameter file. For example, 3d/2d/pr output variables are explicitly declared, but timeseries are always the same (confusing for users). Also, differentiation between data_output and data_output_pr is confusing. A possible solution would be to use data_output exclusively and include profiles, e.g. for pt this then would read "pt", "pt_xy", "pt_pr", etc. I would leave this as it is. Several quantities only exist as profiles, so it don't make sense to add a _pr to all of them. It should be enough to add (better) hints in the docu. Siggi	group
Discussion	Discuss the treatment of package parameters, regarding their appearance in rrd_global and wrd_global. Discuss the general treatment / separation of inipar and d3par parameters.	Sebastian / work in progress
PALM code	Revise variable/dimension names and attributes in the NetCDF data input and PIDS input according to the [UC]² data policy	tba
PALM code	Make use of already implemented 'long_name' attribute of variables, i.e. give possibility to assign a long_name for user defined variables	tba
PALM code	Make proper use of global attributes; especially do not write time average interval in title if there exists a specific attribute (time_avg) for this.
PALM code	Add georeferencing (lat/lon) and global attributes according to [UC]² data policyto NetCDF output	tba
PALM code	Extend plant canopy model to handle basal area (trunks, branches)	Björn
homepage	replace the provisional picture (showing Kelvin-Helmholtz waves) by a nicer one from an urban canopy simulation	Tobias
test suite	Design test cases for microphysic and lagrangian particles	Johannes

Documentation

Page (e. g. wiki/doc/app/userint)	What to do?	Name
wiki/doc/tec/1d_model	Description of 1d model
wiki/doc/tec/cloud_physics	Description of cloud physics module	Johannes
<page>	Write descriptions for exercises 6-14 (divide all exercises into Tutorial exercises and Advanced exercises), Advanced examples->Research project examples
wiki/doc/	Description of statistical methods (computation of fluxes and variances, horizontal averaging, etc.)
wiki/doc/tec/wtm	Write documentation for wind turbine parametrization code	Björn Witha
	Add additions/correction page for the Maronga et al. 2015 paper so that we can incorporate them in the next model description paper
Tutorial	Various exercises and general presentation are since long time listed as "under construction". Links have been removed for now.
	* Data visualization with VAPOR (see also comment in "Tools")
	* Data visualization with DVR
	* Exercise 6: Cumulus cloud from cloud droplets
	* Exercise 7: Ocean mixed layer
	* Exercise 8: Atmosphere-ocean coupling
	* Exercise 9: Canopy flow
	* Exercise 12: Non-cyclic boundary conditions
	* Exercise 13: Turbulence recycling
	* Exercise 14: Using DVR
	* Example: Footprints
	* Example: Stable boundary layer (GABLS3)
	* Cloud Physics up to date?

Source Code

Program parts	What to do?	Name
	develop new GUI for parameter file generation
PALM code	code clearing and restructuring following programmer guidelines of DWD/DMI	all, Siggi
<page>	Avoid collecting of 2D data on PE0 (topography data, surface coupling layer)	Matthias
<page>	Subgrid-scale saturation fluctuation for Lagrangian cloud model	Johannes
data_output	implement output of scalar and momentum fluxes calculated by temporal EC
PALM code	Create temporary job sub-directories via mrun (does not work properly with the FORTRAN system call function) There is currently no proper solution for this. Postponed.
Example runs	Modify the "building" example run (example_building_p3d), since topography is allowed with WS-scheme	Tobias
PALM code	For reference_state='horizontal_average' round the averaged profile (e.g. 3.3 digits) to make runs repeatable	Siggi
PALM code	Avoid repeating code blocks in data_output routines and use subroutines instead
PALM code	Avoid unnecessary grid checks when using multi grid solver	??
PALM code	make simple random number generator available for general usage	Johannes
PALM code	Implement and homogenize output of cloud-physical variables derived from bulk and Lagrangian cloud physics (e.g., qc, ql, qr, lpt, pt)	Johannes
PALM code/ documentation	Change the name specific humidity to mixing ratio! We don't compute specific humidities.	Johannes
data_output	In profile output define zu and zw only once instead of define a vertical dimension for each individual variable (e.g. zpt, zw"u, zw"v, ...)
data_output	When calculating vertical cross sections averaged along x or y, leave out topography
data_output	Do not output ghost points in masked output	Siggi
PALM code	Separate option "cyclic_fill" from restart run to avoid unwanted effects (e.g. surface heat flux value in namelist of a run using "cyclic_fill" will always be overwritten by the value used in the precursor run).	Björn / Tobias
PALM code	define dimensions of data_output, data_output_pr, etc. as variables (avoid fixed numbers in code)
PALM code	Implement a more flexible y-shift method for non-cyclic but also for cyclic runs	Simon
PALM code	Particle code: unify allocation of particle arrays within lpm_droplet_collision, lpm_droplet_condensation, ... (REAL(wp), DIMENSION(:), ALLOCATABLE or REAL(wp), DIMENSION(prt_count(k,j,i)))	Johannes
PALM code	Implement PALM error messages in parallel random number generator module	Helge
PALM code	Review summation of "1E-5_wp" in lines 164/167 in diffusivities.f90 (r2119), see ticket:393	Tobias
data_output	Set missing values/fill values inside topography and define these missing values as attributes in NetCDF file.	Matthias
PALM code	for consistency reasons, implement "initial gradient" top boundary conditions for the mixing ratio too	Johannes
RRTMG coupling	allow for dry runs with RRTMG (might lead to unrealistic results if the atmosphere is considered totally dry!)	Björn
1d-model	fix 1d model to work without Coriolis force why is this required? Siggi
PALM code	allow more flexible vertical grid stretching, e.g. for having near-surface stretching, constant grid spacing above and again stretching in the free atmosphere	Sebastian
check parameters	with psolver=multigrid, check that the subdomains can be divived by 2 at least once (see documentation of the multigrid). Is this still a problem? Needs to be checked.	Siggi
Spectra output	Check and possibly revise spectra normalization with wavenumber	Matthias
Initialization	It needs to be clarified that the initial wind profile constructed by ug_surface, ug_vertical_gradient etc. describes the forcing by the geostrophic wind (pressure gradient), and at the same time depicts the initial actual-wind profile. just add better hints in docu	Siggi
PALM scripts	Not all SCRIPTS bash based yet.	Helge
palmrun	make working directory independent from installation directory	Siggi
NAMELISTs	it should be possible to give output levels in real coordinates (m) instead of grid level, output should then be done for the nearest grid point	Sebastian
data_output	all output checks should be done BEFORE the first time step, and not when the first output is done
Nesting output	additional output of nesting information is required (e.g. in header): for root domain: number of nested domains, name of nested domains, number of nesting levels; for each domain: position of the nest domains given in grid index number range, e.g. (20..40,10:15), also position of lower left corners in physical coordinates?
PALM code	routine global_min_max does not work for mode 'min', 'max', and 'minmax'.	Tobias
PALM code	discuss using Fortran Intrinsic Function "SUM" instead of loops as done many times in the code	all (KS)
initializing_actions	discuss use of initializing_actions='user', because its usage requires good code knowledge and the advantage over using 'set_constant_profiles' and later overwriting variables in user_init_3d_model.f90 is not clear just give better explanations in the docu. Siggi	all (KS)
PALM code	Revise Fortran NAMELIST names (e.g. &inipar --> &initialization_parameters)	Björn see r2932
PALM code	Revise vertical loops in plant-canopy model in order to get rid-off 2D-index array pch_index	Matthias

Code performance

	define setups for scaling / benchmark runs	Björn, Siggi, Fabian
	carry out runs to determine PALM's weak/strong scaling behaviour + parallel efficiency, this might be good to be carried out during the test phase of the HLRNIV	?
	debug ex_lsm_clearsky and reincorporate it to standard test cases	Björn, Katrin

Tools

-	new plotting tool based on python to replace palmplot	Helge
-	extend PALM grid finder for nesting configurations	Hiwi
-	tool for finding vertical grid configuration with grid stretching (maybe as part of palm_gf)	Katrin+HiWi?
-	development and implementation of an automatic mechanism to test source code modifications	Helge
Vapor	remove deprecated vapor scripts. Users try to use them but they are highly specialized for our IMUK system and the old HLRN2 complex (deprecated). Also update documentation (see above).	Tobias