Input and output files

The model works with a set of files, which are all located in the temporary working directory and which are either expected at the beginning of the run (the so-called input files) or which are produced during the run and/or at the end of the simulation (output files). The following table lists all default files addressed by the model. They are arranged according to the associated FORTRAN unit (unit number). The unit 90 is used for different files, which are opened only briefly and uniquely in the model and closed directly afterwards. Unit numbers 101 - 109, 111 - 113, 116, 118 and 121-160 refer to data files which have netCDF format. These are not opened by a FORTRAN-OPEN-statement but by a corresponding netCDF call (NF90_CREATE or NF90_OPEN). These files are only created on machines where a netCDF library is available.

The file names described in the list correspond to the names indicated in the respective OPEN instruction, i.e. the files are expected and saved under these names in the temporary working directory of the model. By default, file names are always written in capital letters. The third column indicates whether it is an input or output file (I and/or O). The netCDF files can be both input and output files (I/O). If restart jobs shall append data to an existing netCDF file (created by a previous job of the job chain), the respective file has to be given as an input file (see more details about the PALM-netCDF-output).

On parallel computers, many of the files are read and/or written by the central processing element 0 (PE0) only. These files have processor-independent content (and therefore they can be read or written by other PEs just as well). However, certain files have processor-dependent content. For the binary output of data for restart runs (local file BINOUT), for example, each PE outputs only the data of its subdomain. So each processing element writes into its own file with its own file name. These files lie in a subdirectory of the temporary working directory. Their names are built from the underline ("_") and the four digit processor ID. The data written for restart runs would be e.g. on the files BINOUT/_0000 (PE0), BINOUT/_0001 (PE1), BINOUT/_0002 (PE2) etc. Such files, which have processor-dependent content on parallel computers, are marked in the following list by the fact, that to the file name a line ("/") is attached. If appropriate output files are to be copied through palmrun to permanent files, and/or files with processor-dependent content are supposed to be copied as input files into the temporary working directory of the model, you have to indicate a special file attribute in the appropriate file connection statement (see arpe?, flpe? in the palmrun description). Then the permanent file name will be interpreted as a directory name, in which the input files are expected and/or to which output files are written. The file names in these directories are always named _0000, _0001, _0002 etc.

For internal use, the model may open a set of further files, which are not defined by the user but contain no usable information and therefore are not included in this list.

Depending on the configuration of the underlying file-system (e.g. Lustre) and the capacity of the I/O-hardware, simultaneous output to a larger number of files, i.e. if a larger number of PEs is used (>1000), may lead to severe problems as job aborts or even to a complete crash of the whole system. In order to circumvent this problem, the maximum number of parallel I/O streams (i.e. the number of files which are simultaneously written), can be limited by using the palmrun-option -w <max # of streams>, where <max # of streams> should be smaller or equal 256 (on the SGI-ICE of HLRN-II). The (parallel) output is then done in a sequential order for blocks of 256 PEs.

In case of coupled atmosphere-ocean runs, both the atmosphere and the ocean executable use the same temporary working directory. However, each executable requires its own, unique set of files for I/O. In order to distinguish between atmosphere and ocean files, coupled atmosphere-ocean runs use the following filename convention. The atmosphere executable uses the set of normal filenames given in the table below. The ocean executable uses a set of modified filenames that have the string '_O' added to their normal name. The coupled ocean filenames are given in brackets in the table below where applicable. The string '_O' is simply appended to most filenames; exceptions are highlighted in bold face. (Note: uncoupled ocean runs use the normal set of filenames without '_O'.)

Unit	Name	I/O	Format	Explanation / File content
11	PARIN (PARIN_O)	I	ASCII/ NAMELIST	Parameter for model steering. This file is needed by the model in each case. A simple example shows a parameter set for the CBL.
13	BININ/ (BININ_O/)	I	Binary	Binary data, which are read in by the model at the beginning of a restart run. The appropriate file must have been written by the preceding job of the job chain (see BINOUT). This file contains the initial parameters of the job chain, arrays of the prognostic and diagnostic variables as well as those parameters and variables for plots of horizontally averaged vertical profiles (see data_output_pr), which have been determined by the job chain so far. Concerning runs on several processors it has to be noted that each processing element reads its own file and the file content is processor-dependent. The number of processors which can be used must not be changed during a job chain and/or if a job chain is continued. Knowledge of the file structure is usually not necessary, because the file is produced and also read again by the model, but it can be useful for error determination in case of read errors. Therefore the file structure is described in the following. The first record of this file contains a version number (ten character string) of the subroutine, which output the data that follows (write_var_list.f90). This number has to agree with the version number subroutine which is reading the file (read_var_list.f90) in case of a restart run. Otherwise the model run is aborted. Version numbers are changed whenever new code revisions require a change of the file format. Starting from the second record, all initial parameters follow (exception: initializing_actions), whereby each parameter fills two records. In the first record the name of the parameter is saved as a character string (30 characters long, short names are filled by trailing blanks, longer names are cut off at the end), in the second record the value (or the values) of the parameter follow. The sequence of parameters on the file may be arbitrary, however the first and second variable must be nz and statistic_regions. If a variable with unknown name is found the model run is aborted. At the end of the initial parameters a record with the string '***end***' follows (filled up with trailing blanks up to a length of 30 characters). Afterwards the fields of the prognostic and diagnostic variables follow. This part of the file also begins with a record consisting of a character string of length 10, which contains the version number of the subroutine that wrote the arrays that follow (write_3d_binary.f90). It must agree with the number of the reading subroutine (read_3d_binary.f90). The following record contains the number of processors which were used in the model run producing this file, the processor ID of the special processor, which creates the file, as well as the lower and upper array indices of the subdomain belonging to this processing element. If no complete agreement with the values of the current model run exists, then this is aborted. This examination must be made in particular on parallel computers because the jobs of a job chain always have to use the same number of processors and the same virtual processor grid. After these tests the individual arrays as well as parameters and variables for plots of horizontally averaged vertical profiles follow. Like the initialization parameters, they consist of two records. In the first record, the name of the array or the variable (character string, consisting of 20 characters, filled with trailing blanks) is located, in the second one its values follow. The sequence of the individual variables may be arbitrary again. The parameters for the plot and the respective variables are only read in if for the run parameter use_prior_plot1d_parameters = .T. is selected, otherwise they will be skipped. At the end of the file there has to be a record with the character string '***end***' (filled up with trailing blanks up to a length of 20 characters).
14	BINOUT/ (BINOUT_O/)	O	Binary	Binary data, which are written by the model at the end of the run and possibly needed by restart runs for the initialization. This output file is then read in as file BININ. It contains the initial parameters of the model run, arrays of the prognostic and diagnostic variables as well as those parameters determined so far during a job chain and variables for plots of horizontally averaged vertical profiles (see data_output_pr). With runs on several processors it has to be noted that each processing element writes its own file and the file content is processor-dependent. A specification of the file format can be found in the description of the file BININ. The file BINOUT is written by the model only if, with the help of the palmrun-configuration file, the environment variable write_binary is assigned to the true (see example). With large grid point numbers the file BINOUT (or the files residing in directory BINOUT/) will be very large and should be stored (if available) on the archive system of the remote computer.
15	RUN_CONTROL (RUN_CONTROL_O)	O	ASCII	This file contains the so-called time step control output of the model. At certain temporal intervals, which are described by the run parameter dt_run_control, a line with the values of certain control parameters is written into this file. Additionally, such a control line is always written, whenever the time step of the model changes. All data and quantities always refer to the entire model domain. If the 1D-model is switched on for the initialization of the 3D-models, then control lines are likewise written into this file at certain temporal intervals (see dt_run_control_1d). By default, the file RUN_CONTROL only lists information about the selected model parameters at the beginning of the initial run. These informations are written at the beginnning of a run. They correspond to those of the file HEADER (however without data concerning the consumed CPU time, because these are only known at the end of a run). With the run parameter force_print_header it can be achieved that this information is also written at the beginning of the file RUN_CONTROL at restart runs. The individual columns of the 1D - time step control output have the following meaning (listed by the respective heading of the appropriate column in the file): ITER. Number of time steps accomplished so far. HH:MM:SS Time (in hours: minutes: seconds). DT Time step (in s). UMAX Maximum absolute wind velocity (u-component) (in m/s). VMAX Maximum absolute wind velocity (v-component) (in m/s). U* Friction velocity (in m/s). ALPHA Angle of the wind vector (to the x-axis) at the top of the constant flux layer (k=1) (in degrees). ENERG. Kinetic energy of the 1D-model (in m2/s2), averaged over all grid points. The individual columns of the 3D - time step control output have the following meaning (listed by the respective heading of the appropriate column in the file): RUN Serial-number of the job in the job chain. The initial run has the number 0, restart runs accordingly have larger numbers. ITER. Number of time steps accomplished since starting time t=0 of the initial run. HH:MM:SS Time (in hours: minutes: seconds) since starting time t=0 of the initial run. DT (E) Time step (in s). The following character indicates the reason of timestep limititaion: (A) - timestep limitation due to advection (CFL criterion), (D) due to diffusion criterion, (S) due to diffusion criterion at energy-balance surfaces (see land surface and urban surface), (P) due to precipitaton (see bulk cloud model), (X) timestep is limited by dt_max, (F) timestep dt is fixed to a constant value. This does not apply for the default Runge-Kutta timestep scheme. UMAX Maximum absolute wind velocity (u-component) (in m/s). If at the appropriate output time a random disturbance was added to the horizontal velocity field (see create_disturbances), the character D will appear directly after the velocity value. VMAX Maximum absolute wind velocity (v-component) (in m/s). If at the appropriate output time a random disturbance was added to the horizontal velocity field (see create_disturbances), the character D will appear directly after the velocity value. WMAX Maximum absolute wind velocity (w-component) (in m/s). U* Horizontal average of the friction velocity (in m/s). W* Convective velocity scale (in m/s). The assumed boundary layer height is determined via the heat flux minimum criterion. THETA* Characteristic temperature of the constant flux layer (in K). Z_I Height of the convective boundary layer (in m), determined via the criterion of the heat flux minimum. ENERG. Average resolved total energy of the flow field (in m2/s2), normalized with the total number of grid points. DISTENERG Average resolved disturbance energy of flow field (in m2/s2), normalized with the total number of grid points. Please note: For small number of horizontal grid points it is possible that DISTENERG > ENERG, which can be attributed to insufficient statistics. However, this is not physical since the ENERG is composed of DISTENERG and the kinetic energy of the mean flow. DIVOLD Divergence of the velocity field (sum of the absolute values) (in 1/s) before call of the pressure solver, normalized with the total number of grid points. DIVNEW Divergence of the velocity field (sum of the absolute values) (in 1/s) after call of the pressure solver, normalized with the total number of grid points. UMAX (KJI) Indices of the grid point with the maximum absolute u-component of the wind velocity (sequence: k, j, i). VMAX (KJI) Indices of the grid point with the maximum absolute v-component of the wind velocity (sequence: k, j, i). WMAX (KJI) Indices of the grid point with the maximum absolute w-component of the wind velocity (sequence: k, j, i). ADVECX Distance (in km) the coordinate system has been moved in x-direction with Galilei-Transformation switched on (see galilei_transformation). ADVECY Distance (in km) the coordinate system has been moved in y-direction with Galilei-Transformation switched on (see galilei_transformation). MGCYC Number of multigrid cycles used if psolver='multigrid' (see psolver and mg_cycles).
16	LIST_PROFIL (LIST_PROFIL_O)	O	ASCII	This file contains horizontally (and possibly temporally) averaged vertical profiles of some model variables. The quantities saved are set model-internally and can not be determined by the user. At each output time (see dt_dopr_listing) two tables are written to the file consecutively. The first contains variables which are defined on the scalar / u-v-grid-levels, the second table contains variables which are defined on the w-grid-levels. If subdomains were defined with the initialization parameter statistic_regions for additional statistic evaluation, then the tables described above are written for each individual subdomain. The name of the respective subdomain (see region) appears in the header of the respective table. In each case the tables consist of a header, followed by the profiles arranged next to each other in columns. The header contains some basic information about the respective run (model version, run identifier consisting of basic file name and number of the job in the job chain, executing computer, date, time of the beginning of the run, name of the subdomain, output time, kind of averaging). On the u-v-level the following columns are written: k Vertical grid point index. zu Height of the grid point level (in m). u u-component of the wind velocity (in m/s). du Deviation of the u-component from the initial profile at the time t=0 (initialization profile) (in m/s). v v-component of the wind velocity (in m/s). dv Deviation of the v-component from the initial profile at the time t=0 (initialization profile) (in m/s). pt Potential temperature (in K). dpt Deviation of potential temperature from the initial profile at the time t=0 (initialization profile) (in K). e Turbulent kinetic energy (subgrid-scale) (in m2/s2). Km Turbulent diffusion coefficient for momentum (in m2/s). Kh Turbulent diffusion coefficient for heat (in m2/s). l Mixing length (in m). On the w-level the following columns are written: k Vertical grid point index. zw Height of the grid point level (in m). w'pt' Vertical subgrid-scale kinematic heat flux (in K m/s). wpt Vertical total ( subgrid-scale + resolved) kinematic heat flux (in K m/s). w'u' u-component of the vertical subgrid-scale momentum flux (in m2/s2). wu u-component of the total vertical momentum flux ( subgrid-scale + resolved) (in m2/s2). w'v' v-component of the vertical subgrid-scale momentum flux (in m2/s2). wv v-component of the total vertical momentum flux ( subgrid-scale + resolved) (in m2/s2).
17	LIST_PROFIL_1D (LIST_PROFIL_1D_O)	O	ASCII	This file contains the vertical profiles calculated by the 1D-model within initial runs. The quantities saved are set model-internally and cannot be determined by the user. At the respective output times (see dt_pr_1d) a table with the following information is written to the file: The table header contains some basic information of the respective run (model version, run identifier consisting of basic file name and number of the job in the job chain (this number should always be 00, because the 1D-model is only switched on at initial runs), executing computer, date, time of the beginning of the run, output time). Afterwards, the following columns appear: k Vertical grid point index. zu Height of the grid point level (in m). u u-component of the wind velocity (in m/s). v v-component of the wind velocity (in m/s). pt Potential temperature (in K). e Turbulent kinetic energy (in m2/s2). rif Flux Richardson number. Km Turbulent diffusion coefficient for momentum (in m2/s). Kh Turbulent diffusion coefficient for heat (in m2/s). l Mixing length (in m).
18	CPU_MEASURES (CPU_MEASURES_O)	O	ASCII	Time measurements are accomplished through the subroutine cpu_log.f90. The file CPU_MEASURES contains a header with some basic information of the respective run (model version, run identifier consisting of basic file name and number of the job in the job chain, executing computer, date, time of the beginning of the run) and afterwards two tables with data of CPU times which have been consumed by certain model parts. The model parts analyzed in the first table do not overlap and the CPU times needed for them therefore approximately add up to the “total” value given in the first line of this table. In the second table (heading: special measures) overlaps (in particular with the parts described in the first table) are possible. For each model part it is indicated in the following columns how much CPU time was needed (absolutely and relative), and how often it was called. With runs on several processors, the average values of all processors are indicated. In the case of parallel runs, information for those processors with the largest and smallest CPU time follow as well as the standard deviation of all PEs from the average value. With good parallelization, the CPU times on the individual processors should differ only little from each other and the standard deviation should be small.
19	HEADER (HEADER_O)	O	ASCII	Information about the selected model parameters (physical and numerical values) as well as general information about the run. This file contains the values of all important steering parameters (numerical procedures, computing grid and model dimensions, boundary conditions, physical dimension, turbulence quantities, actions during the simulation, 1D-model-parameters) as well as data concerning the selected plot and list outputs. The headlines of the file list the program version used, date and time of the beginning of the run, the name of the executing computer, the run identifier (corresponds to the selected base file name) and the number of the run (number of the restart run). With parallel runs the number of processors as well as the assigned virtual processor net also appear. After these headlines run time and time step information appear (point of starting time, related to t=0 of the initial run, end-time, time actually reached, CPU time, etc.). If a model run is incorrectly terminated (e.g. run time error or excess of the permitted CPU time), information over the time reached and the necessary CPU time is missing (to understand: the file HEADER is written twice by the model; once briefly after beginning of the simulation (naturally here the information over the time reached is missing etc.) and then briefly before the normal end of the simulation. The second, now complete output overwrites the first output.). At the end of the file, information about the values of user parameters (see Optional software packages? and user-defined parameters?) can be output by the user with the help of the subroutine user_header (located in the file user_interface.f90). If no user parameters were found, the string '*** no user-defined variables found' appears at the end of the file. If user parameters were indicated, the string 'user-defined variables and actions' is printed, followed by information about the user-defined subdomains for which profiles and time series are output. All further information to appear here must be provided by the user (by appropriate WRITE statements in user_header).
21	PLOT2D_XY (PLOT2D_XY_O)	O	Binary	This file contains data of the two-dimensional horizontal cross sections written by the model (see data_output). With parallel runs and choice of data_output_2d_on_each_pe = .T. each processing element writes the data of its subdomain to a separate file with the name PLOT2D_XY_<processor-Id>, whereby <processor-Id> is a four digit number (e.g. PLOT2D_XY_0000). After PALM has finished, the contents of these individual files are sampled into one final file using the program combine_plot_fields.x (automatically activated by palmrun). The tool writes informative messages about the actions accomplished into the job protocol (e.g., even if no files were found). By the call of combine_plot_fields.x possibly existing files of the other cross sections (xz and/or yz) and three-dimensional arrays (see PLOT3D_DATA) are also combined. Further information about the output of plots of two-dimensional cross sections is found in the description of the run parameter data_output.
22	PLOT2D_XZ (PLOT2D_XZ_O)	O	Binary	This file contains the data of the xz cross sections written by the model. The description of the local file PLOT2D_XY applies to this file, respectively.
23	PLOT2D_YZ (PLOT2D_YZ_O)	O	Binary	This file contains the data of the yz cross sections written by the model. The description of the local file PLOT2D_XY applies to this file, respectively.
24	STG_PROFILES	I	ASCII	This file contains column-separated vertical profiles needed as input for the synthetic turbulence generator. The first line consists of a header which is ignored by PALM. The profiles contained in the file are: k vertical grid point L(u,y) length scale of u along y-direction L(u,z) length scale of u along z-direction T(u) time scale of u L(v,y) length scale of v along y-direction L(v,z) length scale of v along z-direction T(v) time scale of v L(w,y) length scale of w along y-direction L(w,z) length scale of w along z-direction T(w) time scale of w uu Reynolds stress component R11 uv Reynolds stress component R12 vv Reynolds stress component R22 uw Reynolds stress component R13 vw Reynolds stress component R23 ww Reynolds stress component R33 U mean wind speed along x-direction V mean wind speed along y-direction W mean wind speed along z-direction TKE mean subgrid-scale turbulent kinetic energy See STG_PROFILES​ for an example input file.
25	SURFACE_DATA_BIN	=	Binary	These files contain unstructured surface output data at pre-defined output timesteps. These data need to be further processed in order to convert into Paraview-readable ASCII files. A suitable tool to do this will be provided soon.
26	SURFACE_DATA_AV_BIN	=	Binary	These files contain unstructured surface output data (time-averaged) at pre-defined output timesteps. These data need to be further processed in order to convert into Paraview-readable ASCII files. A suitable tool to do this will be provided soon.
30	PLOT3D_DATA (PLOT3D_DATA_O)	O	Binary	This file contains the data of the three-dimensional arrays (see data_output) in netCDF format. The specific netCDF format (e.g. classic, 64-bit offset, netcdf4, etc.) depends on the setting of d3par-parameter netcdf_data_format. With parallel runs and netcdf_data_format < 5, each processing element first writes the data of its subdomain in FORTRAN binary format to a separate file named PLOT3D_DATA_<Processor-Id>, where <Processor-Id> is a four digit number (e.g. PLOT3D_DATA_0000). After PALM has finished, contents of these files are collected by the helper routine combine_plot_fields.x (automatically executed by palmrun). This tool expects the files of the individual processing elements under the names described above and outputs the combined data in netCDF format into the final file named PLOT3D_DATA. The tool writes informative messages about the accomplished actions into the job protocol (also if no files were found). Helper routine combine_plot_fields.x also collects files containing two-dimensional data (see e.g. PLOT2D_XY). With netcdf_data_format > 4 PALM directly writes the data of the subdomains into one single file using parallel I/O (MPI I/O), which makes a call of combine_plot_fields.x obsolete.
80	PARTICLE_INFOS/ PARTICLE_INFOS_O/	O	ASCII	This file is created in case of particle transport (see the particles package). It contains statistical information about the number of particles used and about the number of particles exchanged between each single PE. This information is output after every timestep if switched on by parameter write_particle_statistics.
85	PARTICLE_DATA/ PARTICLE_DATA_O/	O	Binary	This file is created if particle transport is switched on (see the particles package) and contains all particle data for one or several output times (see dt_write_particle_data). The first record of this file contains an identification string (PALM version number, run identifier, etc., 80 characters long). The second record also contains a version string (80 characters long) followed by two records with particle group information and a record containing the index bounds of the 3d subdomain arrays (see palm/trunk/SOURCE/check_open.f90@4182#L553​). Then, for each output time, two records follow, where the first one gives the output time and the second one the number of particles that are output for the subdomain. After that, particle data is output, one record for each model grid box (if particles exist in that box) of the respective subdomain. See palm/trunk/SOURCE/lagrangian_particle_model_mod.f90@4182#L2364​ for the respective output statements. A FORTRAN TYPE structure is used for storing the particle attributes. See palm/trunk/SOURCE/mod_particle_attributes.f90@4182#L77​ for the detailed TYPE structure.
	SPININ/	I	Binary	Binary data for storing spinup surface data.
	SPINOUT/	O	Binary	Binary data for storing spinup surface data.
88	SVFIN/ SVFIN_O/	I	Binary	Binary data for storing surface view factors needed by the RTM.
89	SVFOUT/ SVFOUT_O/	I	Binary	Binary data for storing surface view factors needed by the RTM.
90	PARTICLE_RESTART _DATA_IN/	I	Binary	Binary data, which are read in by the model at the beginning of a restart run). The appropriate file must have been written by the preceding job of the job chain (see PARTICLE_RESTART_DATA_OUT). This file is needed if particle transport is switched on (see the particles package) and contains all particle information (particle positions, velocities, etc.) from the end of the preceding run. Concerning runs on several processors it has to be noted that each processing element reads its own file and that the file content is processor-dependent. The number of processors which can be used must not be changed during a job chain and/or if a job chain is continued. The first record of this file contains a version number (four character string) of the subroutine, which output the data that follows (write_particles, see end of file advec_particles.f90). This number has to agree with the version number of the subroutine which is reading the file (init_parrticles.f90) in case of a restart run. Otherwise the model run is aborted. Version numbers are changed whenever new code revisions require a change of the file format. Some general information like the number of particles stored in the file, the number of particle groups, etc. are stored in the second record. The third record includes the particles to be released at the source and the fourth record contains all current particles. In case that particle tails are used (see maximum_number_of_tailpoints), a further record may follow, which contains the particle tail information. A FORTRAN TYPE structure is used for storing the particle attributes. For detailed informations about the file format see the corresponding READ statements in file init_particles.f90.
90	PARTICLE_RESTART _DATA_OUT/	O	Binary	Binary data, which are output at the end of the run and possibly needed by restart runs) for the initialization. This output file is then read as file PARTICLE_RESTART_DATA_IN. The file is only written if particle transport is switched on (see the particles package). For a more detailed description of the file structure see PARTICLE_RESTART_DATA_IN.
90	LSF_DATA	I	ASCII	The file contains column-separated surface variables shf, qsws, pt_surface, q_surface, surface_pressure and profiles of ug, vg, w_subs, td_lsa_lpt, td_lsa_q (large scale advection tendencies), td_sub_lpt, td_sub_q (large scale subsidence tendencies) at different time steps. The data is usually provided by measurements or larger scale models. In case of large_scale_forcing = .T. the subroutine lsf_init in large_scale_forcing_nudging_mod​ which is called in module_interface_init​ reads the surface and profile information in a free floating point format. The hash character (#) is used as a special steering character. The data in the file has to be organized in the following way: The file has to begin with exactly three lines beginning with a # where for example header information can be stored. The first line not beginning with a # contains surface data which must be column separated and in the following sequence: time, shf, qsws, pt_surface, q_surface, surface_pressure. At least one blank line after the surface data must follow to indicate the end of the surface data. A line beginning with # time indicates the beginning of a profile data set at time step time. Profile data following # time has to be column separated and in the following sequence: height information z, ug, vg, w_subs, td_lsa_lpt, td_lsa_q, td_sub_lpt, td_sub_q A sketch of the layout of LSF_DATA​ is attached. The height information does not have to match PALM's grid. A linear, vertical interpolation to the zu-grid of PALM is conducted in lsf_init. A linear, temporal interpolation of the surface and profile data is conducted in the subroutines ls_forcing_surf, ls_forcing_vert and ls_advec, which are all implemented in large_scale_forcing_nudging_mod​. An example parameter file (p3d) with large scale forcing can be found here.
90	NUDGING_DATA	I	ASCII	The file contains column-separated profiles of the prognostic variable u, v, w, lpt, q originating from measurements or larger scale models which are to be used for nudging. Additionally, height information and the nudging time scale tnudge have to be provided. In case of nudging = .T. the subroutine nudge_init in large_scale_forcing_nudging_mod​ which is called in module_interface_init​ reads the profile information in a free floating point format. The hash character (#) is used as a special steering character. The data in the file has to be organized in the following way: The file can begin with an arbitrary number of lines beginning with a # where for example header information can be stored. A line beginning with # time indicates the beginning of a profile data set at time step time. Profile data following # time has to be column separated and in the following sequence: height information z, nudging time scale tnudge, prognostic variables u, v, w, lpt, q. A sketch of the layout of NUDGING_DATA​ is attached. The height information does not have to match PALM's grid. A linear, vertical interpolation to the zu-grid of PALM is conducted in nudge_init. A linear, temporal interpolation of the profile data is conducted in the subroutine nudge. If quantities are set to -999999.9 for all heights and all time levels, no nudging is applied to them. An example parameter file (p3d) with nudging can be found here.
90	TOPOGRAPHY_DATA	I	ASCII	Two-dimensional rastered topography height information (in m above ground). In case of topography = 'read_from_file' the subroutine init_grid reads the topography height information (in m above ground) for each grid point in a free floating point format. The ASCII file format is ​ESRI grid - also known as ​ARC/INFO ASCII GRID - without the header. The data on file are laid out naturally, i.e. in W-E orientation horizontally and in S-N orientation vertically, they must thus be organized as follows: each line contains height information in m from i = 0, ..., nx, the top line contains height information in m for j = ny (North), the bottom line for j = 0 (South), individual data must be separated by at least one blank. Layout sketch: N (0,ny) (1,ny) (2,ny) ... (nx,ny) top of file (0,ny-1) (1,ny-1) (2,ny-1) ... (nx,ny-1) W (0,ny-2) (1,ny-2) (2,ny-2) ... (nx,ny-2) E : : (0,0) (1,0) (2,0) ... (nx,0) bottom of file S Example for a 50m tall building surrounded by a 12.5m tall podium on flat ground: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12.5 12.5 12.5 12.5 12.5 12.5 12.5 12.5 12.5 12.5 0 0 0 12.5 12.5 12.5 12.5 12.5 12.5 12.5 12.5 12.5 12.5 0 0 0 12.5 12.5 50 50 50 50 50 50 12.5 12.5 0 0 0 12.5 12.5 50 50 50 50 50 50 12.5 12.5 0 0 0 12.5 12.5 50 50 50 50 50 50 12.5 12.5 0 0 0 12.5 12.5 50 50 50 50 50 50 12.5 12.5 0 0 0 12.5 12.5 50 50 50 50 50 50 12.5 12.5 0 0 0 12.5 12.5 50 50 50 50 50 50 12.5 12.5 0 0 0 12.5 12.5 12.5 12.5 12.5 12.5 12.5 12.5 12.5 12.5 0 0 0 12.5 12.5 12.5 12.5 12.5 12.5 12.5 12.5 12.5 12.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 These data must exactly match the horizontal grid. Due to the staggered grid, the topography may be displaced by -0.5 dx in x-direction and -0.5 dy in y-direction depending on the parameter topography_grid_convention. See also the example in trunk/EXAMPLES/topo_file/. Alternatively, the user may add code to the user interface subroutine user_init_grid. Please note, topography information can also be provide in netCDF format via file #PIDS_STATIC.
	PIDS_STATIC	I	netCDF	Static input file following PALM-input-data-standard. The static input file contains all static information, such as topography, geographical latitude and longitude, surface property and vegetation information. More detailed information on individual input variables is provided here.
	PIDS_DYNAMIC	I	netCDF	Dynamic input file following PALM-input-data-standard. The dynamic input file contains dynamic information on the initial state of the atmosphere or time-dependent boundary conditions. More detailed information on individual input variables is provided here.
	PIDS_RAD	I	netCDF	Radiation input file following PALM-input-data-standard. The radiation input file contains static and dynamic information on radiation properties such as trace gas profiles or sky-view factors. More detailed information on individual input variables is provided here.
	PIDS_CHEM	I	netCDF	Chemistry input file following PALM-input-data-standard. The radiation input file contains static and dynamic information on chemical species and emissions. More detailed information on individual input variables is provided here.
	PIDS_VM	I	netCDF	Input file to setup virtual measurement locataions. The input file contains the coordiate information of a measurment, its type, the sampled variables, as well as further attributes. The radiation input file contains static and dynamic information on chemical species and emissions. More detailed information on individual input variables is provided here.
90	WTM_DATA	I	ASCII	This file includes input data for the wind turbine model. The tabulated data is from the publicly available NREL 5 MW reference turbine (see Jonkman et al. 2009: Technical Report NREL/TP-500-38060, doi:10.2172/947422).
101	DATA_2D_XY_NETCDF (DATA_2D_XY_NETCDF_O)	I/O	Binary/ netCDF	This file contains data of the two-dimensional horizontal cross sections (see data_output) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
102	DATA_2D_XZ_NETCDF (DATA_2D_XZ_NETCDF_O)	I/O	Binary/ netCDF	This file contains data of the two-dimensional vertical (xz) cross sections (see data_output) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
103	DATA_2D_YZ_NETCDF (DATA_2D_YZ_NETCDF_O)	I/O	Binary/ netCDF	This file contains data of the two-dimensional vertical (yz) cross sections (see data_output) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
104	DATA_1D_PR_NETCDF (DATA_1D_PR_NETCDF_O)	I/O	Binary/ netCDF	This file contains data of the horizontally averaged vertical profiles (see data_output_pr) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
105	DATA_1D_TS_NETCDF (DATA_1D_TS_NETCDF_O)	I/O	Binary/ netCDF	This file contains data of the time series (see dt_dots) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
106	DATA_3D_NETCDF (DATA_3D_NETCDF_O)	I/O	Binary/ netCDF	This file contains data of the 3d-volume data (see data_output) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
107	DATA_1D_SP_NETCDF (DATA_1D_SP_NETCDF_O)	I/O	Binary/ netCDF	This file contains data of the horizontal spectra (see data_output_sp) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
108	DATA_PRT_NETCDF/ (DATA_PRT_NETCDF_O/)	I/O	Binary/ netCDF	This file contains data of the particle data (see dt_prel) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed informations.
109	DATA_1D_PTS_NETCDF (DATA_1D_PTS_NETCDF_O/)	I/O	Binary/ netCDF	This file contains data of the time series of particle quantities (see dt_prel) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). For a list of available output quantities see dt_dopts. In case of using more than one particle group (see number_of_particle_groups), separate time series are output for each of the groups. The long names of the variables in the netCDF file containing the respective time series all end with the string ' PG ## ' , where ## is the number of the particle group (01, 02, etc.). See the description of PALM-netCDF-output for more detailed information.
111	DATA_2D_XY_AV_NETCDF (DATA_2D_XY_AV_NETCDF_O)	I/O	Binary/ netCDF	This file contains data of the temporally averaged two-dimensional horizontal cross sections (see data_output) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
112	DATA_2D_XZ_AV_NETCDF (DATA_2D_XZ_AV_NETCDF_O)	I/O	Binary/ netCDF	This file contains data of the temporally averaged two-dimensional vertical (xz) cross sections (see data_output) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
113	DATA_2D_YZ_AV_NETCDF (DATA_2D_YZ_AV_NETCDF_O)	I/O	Binary/ netCDF	This file contains data of the temporally averaged two-dimensional vertical (yz) cross sections (see data_output) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
116	DATA_3D_AV_NETCDF (DATA_3D_AV_NETCDF_O)	I/O	Binary/ netCDF	This file contains data of the temporally averaged 3d-volume data (see data_output) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
118	DATA_AGT_NETCDF	O	NetCDF	This file contains all output data from the Multi Agent System (MAS) in NetCDF format. Each variable other than time (1D, contains what the name suggests) has two dimensions (time and agent_number) so that at each output time step all agent variables are output for each agent. The variables are: unique agent ID (ag_id) agent position (ag_x, ag_y) wind speed at agent position (ag_wind) temperature at agent position (ag_temp) agent group (ag_group, see number_of_agent_groups) Very important: Due to agent data structure, agents may not always be sorted in the same succession. E.g. ag_id( time=i, agent_number= j) is not guaranteed to be the same as ag_id( time=i+1, agent_number= j). Thus, if individual agent data is needed, sorting by ag_id in postprocessing is required. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL or Pythons ​matplotlib). For further information, have a look at the parameters dim_size_agtnum_manual, dim_size_factor_agtnum and dt_write_agent_data.
119	NAVIGATION_DATA	I	Binary	This file contains the navigation data from the Agent Preprocessing Tool in Fortran binary format.
199	DATA_1D_FL_NETCDF	I/O	Binary/ netCDF	This file contains data of the space-time series obtained from virtual flight measurements (see virtual_flight_parameters) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
201	DATA_MASK_01_NETCDF (DATA_MASK_01_NETCDF_O)	I/O	Binary/ netCDF	This file contains the masked data of location 1 (see data_output_masks) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
202	DATA_MASK_02_NETCDF (DATA_MASK_02_NETCDF_O)	I/O	Binary/ netCDF	This file contains the masked data of location 2 (see data_output_masks) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
...	...	I/O	Binary/ netCDF	This file contains the masked data of location ... (see data_output_masks) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
201 + 2 * max_masks (max_masks=50 by default)	DATA_MASK_01_AV_NETCDF (DATA_MASK_01_AV_NETCDF_O)	I/O	Binary/ netCDF	This file contains the temporally averaged masked data of location 1 (see data_output_masks) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
202 + 2 * max_masks (max_masks=50 by default)	DATA_MASK_02_AV_NETCDF (DATA_MASK_02_AV_NETCDF_O)	I/O	Binary/ netCDF	This file contains the temporally averaged masked data of location 2 (see data_output_masks) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
...	...	I/O	Binary/ netCDF	This file contains the temporally averaged masked data of location ... (see data_output_masks) in netCDF format. The data in this file can be visualized by any graphic software which provides a netCDF interface (e.g. NCL, ​ferret or ​ncview). See the description of PALM-netCDF-output for more detailed information.
401	TURBINE_PARAMETERS01	O	ASCII	This file contains control data for the first wind turbine for every model time step: Time simulated time in s RSpeed rotor speed in rad/s GSpeed generator speed in rad/s GenTorque generator torque in Nm AeroTorque aerodynamic torque in Nm Pitch pitch angle of the rotor blades in ° Power(Gen) electrical generator power in W Power(Rot) mechanical power (rotor) in W RotThrust rotor thrust in N WDirection wind direction (0° = west) YawOrient yaw angle (0° = perpendicular to x axis)
402	TURBINE_PARAMETERS02	O	ASCII	This file contains control data for the second wind turbine for every model time step
...	...	O	ASCII	This file contains control data for the ... wind turbine for every model time step