Changeset 553 for palm/trunk/DOC
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- Sep 1, 2010 2:09:06 PM (14 years ago)
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palm/trunk/DOC/tec/technical_documentation.html
r544 r553 1 <!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en"> 2 <html><head> 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 <meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type"> <meta content="Mozilla/4.73 [en] (X11; U; HP-UX B.10.20 9000/782) [Netscape]" name="GENERATOR"> <meta content="Siegfried Raasch" name="Author"> <meta content="parallel LES model" name="Keywords"><title>PALM technical/numerical documentation</title></head><body><font size="+4">PALM 30 </font>a 31 <b>pa</b>rallelized 32 <b>L</b>ES <b>m</b>odel 33 <br><hr width="100%"> 34 <br><font size="+2">technical/numerical documentation</font> 35 <br> 36 <br> 37 <br><table nosave="" cellpadding="0" cellspacing="0"> <caption> <br> </caption><tbody> 38 </tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br> 39 </span></td> </tr> 40 <tr nosave=""> <td nosave=""><b>Last 41 change of this document</b>: </td> <td nosave=""><b>$Id$</b></td> </tr> 42 </tbody> 43 </table><hr width="100%"> 44 <p><font size="+2">Table of contents</font> 45 <br> 46 <br> 47 </p><ul> <a href="#Kapitel1.0">1.0</a> 48 History of changes <p><a href="#Kapitel2.0">2.0</a> 49 How to change the source 50 code and how to document modifications<br> 51 </p> <p><a href="#Kapitel3.0">3.0</a> 52 Description of selected model numerics<br> 53 </p> 54 </ul><b></b><br> 55 56 <h2><a name="Kapitel1.0"></a>1.0 57 History of changes</h2> 58 The following table documents all changes to the PALM repository since 2009. Older changes can be found <a href="tec_doc_1998-2008.html">here</a>.<br> 59 <br> 60 Entries in the fifth column specify the type of the change: 61 change 62 of existing code (C), new code (N) or bugfix (B). More detailed 63 information 64 about the changes may sometimes be found in the header comment lines of the 65 respective 66 routines. 67 <br> 68 <br> 69 <table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2"> 70 <tbody> 71 <tr> 72 <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br> 73 </td> 74 <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br> 75 </td> 76 <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br> 77 </td> 78 <td style="width: 40px;"><big><span style="font-weight: bold;">last release</span></big><br> 79 </td> 80 <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br> 81 </td> 82 <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br> 83 </td> 84 <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br> 85 </td> 86 </tr> 87 88 89 90 91 92 93 94 95 96 <tr> 97 <td style="vertical-align: top;">17/08/10<br> 98 </td> 99 <td style="vertical-align: top;">BM<br> 100 </td> 101 <td style="vertical-align: top;">544<br> 102 </td> 103 <td style="vertical-align: top;">3.7a<br> 104 </td> 105 <td style="vertical-align: top;">B/C/N<br> 106 </td> 107 <td style="vertical-align: top;">adjustments for lcxt4; bugfix (mbuild): loading of user-defined modules; new .mrun.config.lcxt4 for Cray XT4 in Bergen/Norway<br> 108 </td> 109 <td style="vertical-align: top;">mrun, mbuild, subjob<br> 110 </td> 111 </tr> 112 113 <tr> 114 <td style="vertical-align: top;">15/06/10<br> 115 </td> 116 <td style="vertical-align: top;">RH<br> 117 </td> 118 <td style="vertical-align: top;">540<br> 119 </td> 120 <td style="vertical-align: top;">3.7a<br> 121 </td> 122 <td style="vertical-align: top;">C<br> 123 </td> 124 <td style="vertical-align: top;">ssh from compute nodes to login 125 nodes on hosts lcsgih/lcsgib is done using the names 126 hicegate0/bicegate0 instead of the IP addresses<br> 127 </td> 128 <td style="vertical-align: top;">mrun<br> 129 </td> 130 </tr> 131 <tr> 132 <td style="vertical-align: top;">21/04/10<br> 133 </td> 134 <td style="vertical-align: top;">RH<br> 135 </td> 136 <td style="vertical-align: top;">532<br> 137 </td> 138 <td style="vertical-align: top;">3.7a<br> 139 </td> 140 <td style="vertical-align: top;">C<br> 141 </td> 142 <td style="vertical-align: top;"> 143 Large scale vertical motion (subsidence/ascent) can be added as 144 additional source to the prognostic equation for humidity/passive scalar<br> 145 <br> 146 character length for dopr_unit enlarged<br> 147 <br> 148 Adjustment of the NCL scripts<span style="font-family: Courier New,Courier,monospace;"> </span>to allow for output of png files <br> 149 </td> 150 <td style="vertical-align: top;">modules, prognostic_equations<br> 151 <br> 152 .ncl.config.default, cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl<br> 153 </td> 154 </tr> 155 <tr> 156 <td style="vertical-align: top;"><br> 157 </td> 158 <td style="vertical-align: top;"><br> 159 </td> 160 <td style="vertical-align: top;"><br> 161 </td> 162 <td style="vertical-align: top;"><br> 163 </td> 164 <td style="vertical-align: top;">B<br> 165 </td> 166 <td style="vertical-align: top;">Bugfix: unit of hyp changed to dbar<br> 167 </td> 168 <td style="vertical-align: top;">check_parameters<br> 169 </td> 170 </tr> 171 <tr> 172 <td style="vertical-align: top;">01/04/10<br> 173 </td> 174 <td style="vertical-align: top;">RH<br> 175 </td> 176 <td style="vertical-align: top;">530<br> 177 </td> 178 <td style="vertical-align: top;">3.7a<br> 179 </td> 180 <td style="vertical-align: top;">B<br> 181 </td> 182 <td style="vertical-align: top;">Bugfix: treatment of special character * in NCL variables containing lists corrected<br> 183 </td> 184 <td style="vertical-align: top;">palmplot<br> 185 </td> 186 </tr> 187 <tr> 188 <td style="vertical-align: top;">31/03/10<br> 189 </td> 190 <td style="vertical-align: top;">RH<br> 191 </td> 192 <td style="vertical-align: top;">529<br> 193 </td> 194 <td style="vertical-align: top;">3.7a<br> 195 </td> 196 <td style="vertical-align: top;">C<br> 197 </td> 198 <td style="vertical-align: top;">List of variable names have to specified using blank separated lists and single quotes<br> 199 </td> 200 <td style="vertical-align: top;">palmplot<br> 201 </td> 202 </tr> 203 <tr> 204 <td style="vertical-align: top;">30/03/10<br> 205 </td> 206 <td style="vertical-align: top;">RH<br> 207 </td> 208 <td style="vertical-align: top;">526<br> 209 </td> 210 <td style="vertical-align: top;">3.7a<br> 211 </td> 212 <td style="vertical-align: top;">C<br> 213 </td> 214 <td style="vertical-align: top;">Adjustment of the NCL scripts and <span style="font-family: Courier New,Courier,monospace;">palmplot </span>to allow for special characters in NetCDF variable names <br> 215 </td> 216 <td style="vertical-align: top;">palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl<br> 217 </td> 218 </tr> 219 <tr> 220 <td style="vertical-align: top;">30/03/10<br> 221 </td> 222 <td style="vertical-align: top;">SR<br> 223 </td> 224 <td style="vertical-align: top;">525<br> 225 </td> 226 <td style="vertical-align: top;">3.7a<br> 227 </td> 228 <td style="vertical-align: top;">B<br> 229 </td> 230 <td style="vertical-align: top;">Bugfix: "/" in netcdf profile variable names replaced by ":"<br> 231 </td> 232 <td style="vertical-align: top;">check_parameters<br> 233 </td> 234 </tr> 235 <tr> 236 <td style="vertical-align: top;">19/03/10<br> 237 </td> 238 <td style="vertical-align: top;">SR<br> 239 </td> 240 <td style="vertical-align: top;">520<br> 241 </td> 242 <td style="vertical-align: top;">3.7a<br> 243 </td> 244 <td style="vertical-align: top;">N<br> 245 </td> 246 <td style="vertical-align: top;">NetCDF4 support for particle 247 data. Total number of particles is allowed to increase during the run, 248 when netcdf_data_format > <span style="font-style: italic;">2</span> is used.<br> 249 </td> 250 <td style="vertical-align: top;">advec_particles, check_open, netcdf<br> 251 </td> 252 </tr> 253 <tr> 254 <td style="vertical-align: top;"><br> 255 </td> 256 <td style="vertical-align: top;"><br> 257 </td> 258 <td style="vertical-align: top;"><br> 259 </td> 260 <td style="vertical-align: top;"><br> 261 </td> 262 <td style="vertical-align: top;">C<br> 263 </td> 264 <td style="vertical-align: top;">Special characters like * and " 265 are now allowed for NetCDF variable names. Replacement of these 266 characters has been removed (routine clean_netcdf_varname removed)<br> 267 </td> 268 <td style="vertical-align: top;"><br> 269 </td> 270 </tr> 271 <tr> 272 <td style="vertical-align: top;">18/03/10<br> 273 </td> 274 <td style="vertical-align: top;">SR<br> 275 </td> 276 <td style="vertical-align: top;">516<br> 277 </td> 278 <td style="vertical-align: top;">3.7a<br> 279 </td> 280 <td style="vertical-align: top;">N<br> 281 </td> 282 <td style="vertical-align: top;">Simple installation method has been documented (see chapter 5.0). Respective scripts and configuration files have been updated.<br> 283 </td> 284 <td style="vertical-align: top;">palm_simple_install, palm_simple_run<br> 285 </td> 286 </tr> 287 <tr> 288 <td style="vertical-align: top;"><br> 289 </td> 290 <td style="vertical-align: top;"><br> 291 </td> 292 <td style="vertical-align: top;"><br> 293 </td> 294 <td style="vertical-align: top;"><br> 295 </td> 296 <td style="vertical-align: top;">B<br> 297 </td> 298 <td style="vertical-align: top;">opt=1 is forced for PGI-compiler in routine<span style="font-family: Courier New,Courier,monospace;"> buoyancy </span>by compiler-directive. Otherwise, program aborts with SIGFPE.<br> 299 </td> 300 <td style="vertical-align: top;">buoyancy<br> 301 </td> 302 </tr> 303 <tr> 304 <td style="vertical-align: top;">16/03/10<br> 305 </td> 306 <td style="vertical-align: top;">RH<br> 307 </td> 308 <td style="vertical-align: top;">513<br> 309 </td> 310 <td style="vertical-align: top;">3.7a<br> 311 </td> 312 <td style="vertical-align: top;">N<br> 313 </td> 314 <td style="vertical-align: top;">NCL scripts can be run with the shell script <span style="font-family: Courier New,Courier,monospace;">palmplot.</span><br> 315 </td> 316 <td style="vertical-align: top;">palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl<br> 317 </td> 318 </tr> 319 <tr> 320 <td style="vertical-align: top;">12/03/10<br> 321 </td> 322 <td style="vertical-align: top;">SR<br> 323 </td> 324 <td style="vertical-align: top;">509<br> 325 </td> 326 <td style="vertical-align: top;">3.7a<br> 327 </td> 328 <td style="vertical-align: top;">B<br> 329 </td> 330 <td style="vertical-align: top;">bugfix for rev 504: remode_md was given a wrong value<br> 331 </td> 332 <td style="vertical-align: top;">mbuild<br> 333 </td> 334 </tr> 335 <tr> 336 <td style="vertical-align: top;">08/03/10<br> 337 </td> 338 <td style="vertical-align: top;">SR<br> 339 </td> 340 <td style="vertical-align: top;">506<br> 341 </td> 342 <td style="vertical-align: top;">3.7a<br> 343 </td> 344 <td style="vertical-align: top;">C<br> 345 </td> 346 <td style="vertical-align: top;">hack for better usage of <span style="font-weight: bold;">mrun</span> on Kyoto computing center machine (<span style="font-family: Courier New,Courier,monospace;">lckyoto</span>)<br> 347 </td> 348 <td style="vertical-align: top;">mrun<br> 349 </td> 350 </tr> 351 <tr> 352 <td style="vertical-align: top;">03/03/10<br> 353 </td> 354 <td style="vertical-align: top;">SR<br> 355 </td> 356 <td style="vertical-align: top;">504<br> 357 </td> 358 <td style="vertical-align: top;">3.7a<br> 359 </td> 360 <td style="vertical-align: top;">C<br> 361 </td> 362 <td style="vertical-align: top;"><span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> is now directly called within <span style="font-weight: bold;">mrun</span> and must not be given by an output command in the configuration file any more. Please remove the respective output command (<span style="font-family: Courier New,Courier,monospace;">OC:combine_plot_fields.x</span>) from your configuration file!<br> 363 <br> 364 Utility programs (<span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span>, <span style="font-family: Courier New,Courier,monospace;">interpret_config</span>) are created by <span style="font-weight: bold;">mbuild</span> separately for each block in the configuration file. Depending on option <span style="font-family: Courier New,Courier,monospace;">-K</span>, <span style="font-weight: bold;">mrun</span> is using the utility programs for the respective block.<br> 365 <br> 366 Utility programs are also compiled in parallel, depending on variable <span style="font-family: Courier New,Courier,monospace;">%mopts</span> in the configuration file..<br> 367 <br> 368 Default configuration files updated.<br> 369 </td> 370 <td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br> 371 </td> 372 </tr> 373 <tr> 374 <td style="vertical-align: top;">02/03/10<br> 375 </td> 376 <td style="vertical-align: top;">SR<br> 377 </td> 378 <td style="vertical-align: top;">496<br> 379 </td> 380 <td style="vertical-align: top;">3.7a<br> 381 </td> 382 <td style="vertical-align: top;">C<br> 383 </td> 384 <td style="vertical-align: top;">Particle data for restart runs are only written if environment variable <span style="font-family: Courier New,Courier,monospace;">write_binary</span> = <span style="font-style: italic;">.T.</span>, i.e. particle data are now handled in the same way as the other restart data.<br> 385 </td> 386 <td style="vertical-align: top;">palm<br> 387 </td> 388 </tr> 389 <tr> 390 <td style="vertical-align: top;">01/03/10<br> 391 </td> 392 <td style="vertical-align: top;">SR<br> 393 </td> 394 <td style="vertical-align: top;">494<br> 395 </td> 396 <td style="vertical-align: top;">3.7a<br> 397 </td> 398 <td style="vertical-align: top;">N<br> 399 </td> 400 <td style="vertical-align: top;">Output in NetCDF4-format.<br> 401 <br> 402 NetCDF4 allows for parallel I/O. Also, variables are not limited in 403 size any more (i.e. arrays can be larger than 2GB). The new 404 d3par-parameter <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span>.can be used to select among the different NetCDF file formats (<span style="font-style: italic;">1</span>: classic format, <span style="font-style: italic;">2</span>: 64-bit-offset format (this is now the default), <span style="font-style: italic;">3</span>: NetCDF4/HDF5 format, <span style="font-style: italic;">4</span>: NetCDF4 format with NF90_CLASSIC_MODEL bit set). Setting <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span> > <span style="font-style: italic;">2</span> 405 only affects 2d- and 3d-output, i.e. there is no parallel output for 406 profiles, time series, spectra, and particles. Parallel output of 407 particle data may realized in the future.<br> 408 <br> 409 In case of parallel output, all PEs write into one file, which means that postprocessing the data with <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> 410 (merging data from single files - one per PE - into one file) is not 411 neccessary. In this case, flag files are automatically set, telling <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> that nothing is to be done.<br> 412 <br> 413 Using NetCDF4 format requires a NetCDF4/HDF library. Respective 414 settings for -I, -L, and -l compiler/loader options for the SGI-ICE at 415 HLRN can be found in the new example configuration file <span style="font-family: Courier New,Courier,monospace;">..../trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4</span><br> 416 <br> 417 <span style="font-weight: bold;">Attention:</span><br> 418 So far, NetCDF parallel I/O has only been tested a little. Further 419 performance optimizations may be required, especially in case of large 420 data sets (e.g. data chunking, or lustre file system settings with <span style="font-family: Courier New,Courier,monospace;">lfs setstripe</span>). <span style="font-weight: bold;">Please report bugs and performance problems immediately!</span><br> 421 <br> 422 <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br> 423 <br> 424 Modules to be loaded for compilation (mbuild) or job execution (mrun) can/should now be given in the configuration file (<span style="font-family: Courier New,Courier,monospace;">.mrun.config</span>) using variable <span style="font-family: Courier New,Courier,monospace;">modules</span>. Example:<br> 425 <br> 426 <span style="font-family: Courier New,Courier,monospace;"> %modules ifort/11.0.069:netcdf lcsgih parallel</span><br> 427 <br> 428 This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br> 429 <br> 430 <span style="font-weight: bold;">WARNING:</span><br> 431 <span style="font-weight: bold;">All fixed settings of modules in the scripts mbuild, mrun, and subjob have been removed! Please set the <span style="font-family: Courier New,Courier,monospace;">modules</span> variable appropriately and remove the mpilib variable in your configuration file.<br> 432 <br> 433 </span>Compilation time can be reduced be using parallel make. The 434 number of allowed simultaneous compiler calls (threads) is set in the 435 configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br> 436 <br> 437 <span style="font-family: Courier New,Courier,monospace;"> %mopts -j:4 lcsgih parallel</span><br> 438 <br> 439 allows a maximum of 4 routines to be compiled simultaneously (provided 440 that the makefile does not show any dependencies between these 441 routines).<span style="font-weight: bold;"><br> 442 </span> 443 </td> 444 <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br> 445 <br> 446 combine_plot_fields<br> 447 <br> 448 mbuild, mrun, subjob<br> 449 </td> 450 </tr> 451 <tr> 452 <td style="vertical-align: top;"><br> 453 </td> 454 <td style="vertical-align: top;"><br> 455 </td> 456 <td style="vertical-align: top;"><br> 457 </td> 458 <td style="vertical-align: top;"><br> 459 </td> 460 <td style="vertical-align: top;">C<br> 461 </td> 462 <td style="vertical-align: top;">d3par-parameters <span style="font-family: Courier New,Courier,monospace;">netcdf_64bit</span> and <span style="font-family: Courier New,Courier,monospace;">netcdf_64bit_3d</span> have been removed. Use the new d3par-variable <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span> = <span style="font-style: italic;">2</span> 463 for choosing the NetCDF 64bit-offset format (this is the default from 464 now on). The offset-format can not be set independently for the 465 3d-output-data any more.<br> 466 <br> 467 d3par-parameters <span style="font-family: Courier New,Courier,monospace;">netcdf_format_mask</span>, <span style="font-family: Courier New,Courier,monospace;">netcdf_format_mask_av</span>, and variables <span style="font-family: Courier New,Courier,monospace;">nc_format_mask</span>, <span style="font-family: Courier New,Courier,monospace;">format_parallel_io</span> removed. They are replaced by the new parameter <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span>. This change concerns the masked data output, which is still not documented.<br> 468 </td> 469 <td style="vertical-align: top;">check_open, close_file,<br> 470 data_output_mask, header, init_masks, modules, parin<br> 471 <br> 472 </td> 473 </tr> 474 <tr> 475 <td style="vertical-align: top;"><br> 476 </td> 477 <td style="vertical-align: top;"><br> 478 </td> 479 <td style="vertical-align: top;"><br> 480 </td> 481 <td style="vertical-align: top;"><br> 482 </td> 483 <td style="vertical-align: top;">B<br> 484 </td> 485 <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br> 486 <br> 487 Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br> 488 </td> 489 <td style="vertical-align: top;">user_statistics<br> 490 <br> 491 trunk/UTIL/Makefile<br> 492 </td> 493 </tr> 494 <tr> 495 <td style="vertical-align: top;">05/02/10<br> 496 </td> 497 <td style="vertical-align: top;">SR<br> 498 </td> 499 <td style="vertical-align: top;">485<br> 500 </td> 501 <td style="vertical-align: top;">3.7a<br> 502 </td> 503 <td style="vertical-align: top;">B<br> 504 </td> 505 <td style="vertical-align: top;"><span style="font-family: Courier New,Courier,monospace;">ngp_3d</span>, <span style="font-family: Courier New,Courier,monospace;">ngp_3d_inner</span> 506 changed to 64 bit. Otherwise, on large grids > 2*10**9 grid points 507 some global statistics (e.g. total kinetic energy) have wrong values.<br> 508 </td> 509 <td style="vertical-align: top;">init_3d_model, modules<br> 510 </td> 511 </tr> 512 <tr> 513 <td style="vertical-align: top;">05/02/10<br> 514 </td> 515 <td style="vertical-align: top;">SR<br> 516 </td> 517 <td style="vertical-align: top;">484<br> 518 </td> 519 <td style="vertical-align: top;">3.7a<br> 520 </td> 521 <td style="vertical-align: top;">B<br> 522 </td> 523 <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br> 524 </td> 525 <td style="vertical-align: top;">many<br> 526 </td> 527 </tr> 528 <tr> 529 <td style="vertical-align: top; width: 27px;">05/02/10<br> 530 </td> 531 <td style="vertical-align: top; width: 38px;">SR<br> 532 </td> 533 <td style="vertical-align: top; width: 42px;">483<br> 534 </td> 535 <td style="vertical-align: top; width: 40px;">3.7a<br> 536 </td> 537 <td style="vertical-align: top; width: 27px;">N<br> 538 </td> 539 <td style="vertical-align: top; width: 497px;"><span style="font-family: Courier New,Courier,monospace;">compare_palm_logs </span>is additionally compiled with <span style="font-weight: bold;">mbuild</span> <span style="font-family: Courier New,Courier,monospace;">-u</span> . (<span style="font-family: Courier New,Courier,monospace;">Makefile</span> in <span style="font-family: Courier New,Courier,monospace;">trunk/UTIL</span>)<br> 540 <br> 541 make options (<span style="font-family: Courier New,Courier,monospace;">mopts</span>) to be set by configuration file implemented. (<span style="font-weight: bold;">mrun</span>, <span style="font-weight: bold;">mbuild</span>)<br> 542 <br> 543 <span style="font-family: Courier New,Courier,monospace;">humidity</span> = <span style="font-style: italic;">.T.</span> can be used for runs with topography. <span style="font-family: Courier New,Courier,monospace;">wall_humidityflux</span> and<br><span style="font-family: Courier New,Courier,monospace;"> 544 wall_scalarflux</span> are the corresponding new inipar parameters.<br> 545 (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>, <span style="font-family: Courier New,Courier,monospace;">parin</span>)<br> 546 <br> 547 Large scale vertical motion (subsidence/ascent) can be added as 548 additional source to the prognostic equation for potential temperature. 549 See new parameters <span style="font-family: Courier New,Courier,monospace;">large_scale_subsidence</span>, <span style="font-family: Courier New,Courier,monospace;">ws_vertical_gradient</span>, and <span style="font-family: Courier New,Courier,monospace;">ws_vertical_gradient_level</span>. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, <span style="font-family: Courier New,Courier,monospace;">header</span>, <span style="font-family: Courier New,Courier,monospace;">Makefile</span>, <span style="font-family: Courier New,Courier,monospace;">modules</span>, <span style="font-family: Courier New,Courier,monospace;">parin</span>, <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>, <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, <span style="font-family: Courier New,Courier,monospace;">subsidence</span>, <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br> 550 <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br> 551 <br> 552 A simple method for installing and running palm (with limited features) has been added. (<span style="font-family: Courier New,Courier,monospace;">Makefile</span>, new scripts <span style="font-weight: bold;">palm_simple_install</span>, <span style="font-weight: bold;">palm_simple_run</span>)<br> 553 <br> 554 Masked data output has been implemented but it is not documented in the 555 user manual so far. This feature can already use NetCDF4 file format. 556 (check_open, check_parameters, close_file, modules, netcdf, parin, 557 time_integration, user_parin, new: data_output_mask, init_masks, 558 user_data_output_mask)<br> 559 </td> 560 <td style="vertical-align: top; width: 189px;">check_open, check 561 parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun, 562 netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br> 563 <br><span style="font-weight: bold;"> 564 new:</span> data_output_mask, init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br> 565 <br> 566 </td> 567 </tr> 568 <tr> 569 <td style="vertical-align: top; width: 27px;"><br> 570 </td> 571 <td style="vertical-align: top; width: 38px;"><br> 572 </td> 573 <td style="vertical-align: top; width: 42px;"><br> 574 </td> 575 <td style="vertical-align: top; width: 40px;"><br> 576 </td> 577 <td style="vertical-align: top; width: 27px;">C<br> 578 </td> 579 <td style="vertical-align: top; width: 497px;">2d-decomposition is default for Cray-XT machines. (<span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>)<br> 580 <br><span style="font-family: Courier New,Courier,monospace;"> 581 var_ts</span> is replaced by <span style="font-family: Courier New,Courier,monospace;">dots_max</span>. (<span style="font-family: Courier New,Courier,monospace;">modules</span>, <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br> 582 <br> 583 Every cloud droplet has now an own weighting factor and can be deleted 584 due to collisions. Condensation and collision of cloud droplets are 585 adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br> 586 <br> 587 Collision efficiency for large cloud droplets has changed according to table of Rogers and Yau. (<span style="font-family: Courier New,Courier,monospace;">collision_efficiency</span>)<br> 588 </td> 589 <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br> 590 </td> 591 </tr> 592 <tr> 593 <td style="vertical-align: top; width: 27px;"><br> 594 </td> 595 <td style="vertical-align: top; width: 38px;"><br> 596 </td> 597 <td style="vertical-align: top; width: 42px;"><br> 598 </td> 599 <td style="vertical-align: top; width: 40px;"><br> 600 </td> 601 <td style="vertical-align: top; width: 27px;">B<br> 602 </td> 603 <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br> 604 <br> 605 Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br> 606 <br> 607 Dimension of array <span style="font-family: Courier New,Courier,monospace;">stat</span> in cascade change to prevent type problems with mpi2 libraries. (<span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>)<br> 608 <br> 609 Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br> 610 <br> 611 Bugfix: exchange of ghost points for <span style="font-family: Courier New,Courier,monospace;">prho</span> included. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br> 612 <br> 613 Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br> 614 <br> 615 Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br> 616 <br> 617 Bugfix: initial data assignments to some dvrp arrays changed due to error messages from gfortran compiler. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br> 618 <br> 619 Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br> 620 <br> 621 Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br> 622 <br> 623 Bugfix in calculation of collision efficiency. (<span style="font-family: Courier New,Courier,monospace;">collision_efficiency</span>)<span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;"></span><br> 624 </td> 625 <td style="vertical-align: top; width: 189px;">advec_particles, 626 calc_precipitation, collision_efficiency, disturb_field, header, 627 modules, poisfft_hybrid, subjob, sum_up_3d_data, 628 time_integration<br> 629 <br> 630 </td> 631 </tr> 632 <tr> 633 <td style="vertical-align: top; width: 27px;">23/09/09<br> 634 </td> 635 <td style="vertical-align: top; width: 38px;">SR<br> 636 </td> 637 <td style="vertical-align: top; width: 42px;">392<br> 638 </td> 639 <td style="vertical-align: top; width: 40px;">3.7<br> 640 </td> 641 <td style="vertical-align: top; width: 27px;">N<br> 642 </td> 643 <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most 644 important changes:</span> 645 atmosphere-ocean coupling has been improved and steering of 646 dvr-software is more user-friendly now. Beside that, the release 647 contains a lot of optimizations, changes, and bugfixes which have 648 accumulated over the last months.<br> 649 650 <br> 651 652 The atmosphere-ocean coupling allows to use independent precursor runs 653 in order to account for different spin-up times. The time when coupling 654 has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>. 655 The precursor ocean run has to be started using new <span style="font-weight: bold;">mrun</span> option "<span style="font-family: Courier New,Courier,monospace;">-y</span>" in 656 order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all 657 output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>, 658 <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, 659 <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>, 660 <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>, 661 <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>, 662 <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>, 663 <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>, 664 <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>, 665 <span style="font-family: Courier New,Courier,monospace;">header</span>, 666 <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>, 667 <span style="font-family: Courier New,Courier,monospace;">modules</span>, 668 <span style="font-family: Courier New,Courier,monospace;">mrun</span>, 669 <span style="font-family: Courier New,Courier,monospace;">parin</span>, 670 <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, 671 <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>, 672 <span style="font-family: Courier New,Courier,monospace;">time_integration</span>, 673 <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br> 674 675 <br> 676 677 Clipping of dvrp output implemented. Default colourtable for particles 678 implemented, particle attributes (color, dvrp_size) can be set with new 679 parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>, 680 <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>, 681 <span style="font-family: Courier New,Courier,monospace;">color_interval</span>, 682 <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>. 683 Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span> 684 and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>. 685 (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>, 686 <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>, 687 <span style="font-family: Courier New,Courier,monospace;">modules</span>, 688 <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>, 689 <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br> 690 691 <br> 692 693 Polygon reduction for topography and ground plate isosurface. Reduction 694 level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br> 695 696 <br> 697 698 Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span> 699 / <span style="font-family: Courier New,Courier,monospace;">bc_ns</span> 700 in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br> 701 702 <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span> 703 for speed optimization. This gives a significant speedup of more than 704 10%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, 705 <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>, 706 <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>, 707 <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>, 708 <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br> 709 710 <br> 711 712 Scripts have been adapted for machine lck (Yonsei Univ.). (<span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, <span style="font-family: Courier New,Courier,monospace;">subjob</span>)<br> 713 714 <br> 715 716 Additional timestep criterion in case of simulations with plant canopy. 717 (<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br> 718 719 <br> 720 721 Check for illegal entries in <span style="font-family: Courier New,Courier,monospace;">section_xy</span>|<span style="font-family: Courier New,Courier,monospace;">xz</span>|<span style="font-family: Courier New,Courier,monospace;">yz</span> that 722 exceed <span style="font-family: Courier New,Courier,monospace;">nz+1</span>|<span style="font-family: Courier New,Courier,monospace;">ny+1</span>|<span style="font-family: Courier New,Courier,monospace;">nx+1</span>. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br> 723 724 <br> 725 726 External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, 727 <span style="font-family: Courier New,Courier,monospace;">header</span>, 728 <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>, 729 <span style="font-family: Courier New,Courier,monospace;">modules</span>, 730 <span style="font-family: Courier New,Courier,monospace;">parin</span>, 731 <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>, 732 <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, 733 <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br> 734 735 <br> 736 737 New topography case '<span style="font-style: italic;">single_street_canyon</span>'. 738 (<span style="font-family: Courier New,Courier,monospace;">header</span>, 739 <span style="font-family: Courier New,Courier,monospace;">init_grid</span>, 740 <span style="font-family: Courier New,Courier,monospace;">modules</span>, 741 <span style="font-family: Courier New,Courier,monospace;">parin</span>, 742 <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, 743 <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>, 744 <span style="font-family: Courier New,Courier,monospace;">user_header</span>, 745 <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>, 746 <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br> 747 748 <br> 749 750 Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>. 751 (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, 752 <span style="font-family: Courier New,Courier,monospace;">header</span>, 753 <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>, 754 <span style="font-family: Courier New,Courier,monospace;">modules</span>, 755 <span style="font-family: Courier New,Courier,monospace;">parin</span>, 756 <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, 757 <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br> 758 759 <br> 760 761 Option for user defined 2D data output in xy cross sections at z=<span style="font-family: Courier New,Courier,monospace;">nzb</span>+1. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>, 762 <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br> 763 764 <br> 765 766 xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>, 767 <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, 768 <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>, 769 <span style="font-family: Courier New,Courier,monospace;">modules</span>, 770 <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>, 771 <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>, 772 <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td> 773 <td style="vertical-align: top; width: 189px;">average_3d_data, 774 check_for_restart, check_parameters, data_output_2d, data_output_3d, 775 data_output_dvrp, data_output_profiles, data_output_ptseries, 776 data_output_spectra, data_output_tseries, diffusion_u, diffusion_v, 777 diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model, 778 header, mbuild, modules, mrun, package_parin, parin, 779 prognostic_equations, read_3d_binary, read_var_list, subjob, 780 sum_up_3d_data, surface_coupler, timestep, time_integration, 781 user_check_parameters, user_data_output_2d, user_data_output_dvrp, 782 user_header, user_init_grid, write_3d_binary, write_var_list<br> 783 784 <br> 785 786 <span style="font-weight: bold;">new:</span> 787 set_particle_attributes, set_slicer_attributes_dvrp</td> 788 </tr> 789 <tr> 790 <td style="vertical-align: top; width: 27px;"><br> 791 </td> 792 <td style="vertical-align: top; width: 38px;"><br> 793 </td> 794 <td style="vertical-align: top; width: 42px;"><br> 795 </td> 796 <td style="vertical-align: top; width: 40px;"><br> 797 </td> 798 <td style="vertical-align: top; width: 27px;">C<br> 799 </td> 800 <td style="vertical-align: top; width: 497px;">Output of messages replaced by 801 message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>, 802 <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>, 803 <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>, 804 <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>, 805 <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>, 806 <span style="font-family: Courier New,Courier,monospace;">check_open</span>, 807 <span style="font-family: Courier New,Courier,monospace;">coriolis</span>, 808 <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>, 809 <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>, 810 <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>, 811 <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>, 812 <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>, 813 <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>, 814 <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>, 815 <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>, 816 <span style="font-family: Courier New,Courier,monospace;">header</span>, 817 <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>, 818 <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>, 819 <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>, 820 <span style="font-family: Courier New,Courier,monospace;">init_grid</span>, 821 <span style="font-family: Courier New,Courier,monospace;">init_particles</span>, 822 <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>, 823 <span style="font-family: Courier New,Courier,monospace;">netcdf</span>, 824 <span style="font-family: Courier New,Courier,monospace;">parin</span>, 825 <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>, 826 <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>, 827 <span style="font-family: Courier New,Courier,monospace;">poismg</span>, 828 <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>, 829 <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, 830 <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>, 831 <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>, 832 <span style="font-family: Courier New,Courier,monospace;">timestep</span>, 833 <span style="font-family: Courier New,Courier,monospace;">user_actions</span>, 834 <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>, 835 <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>, 836 <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>, 837 <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>, 838 <span style="font-family: Courier New,Courier,monospace;">user_parin</span>, 839 <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>, 840 <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br> 841 842 <br> 843 844 Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>, 845 <span style="font-family: Courier New,Courier,monospace;">close_file</span>, 846 <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>, 847 <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>, 848 <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>, 849 <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>, 850 <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>, 851 <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>, 852 <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br> 853 854 <br> 855 856 __lcmuk changed to __lc to avoid problems with Intel compiler on 857 sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br> 858 859 <br> 860 861 For extended NetCDF files, the updated title attribute includes an 862 update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br> 863 864 <br> 865 866 In case of restart runs without extension, initial profiles are not 867 written to NetCDF-file anymore. So far, time axis always started at 868 t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>, 869 <span style="font-family: Courier New,Courier,monospace;">modules</span>, 870 <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, 871 <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br> 872 873 <br> 874 875 <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to 876 '<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill 877 can now <br> 878 879 be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>. 880 (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, 881 <span style="font-family: Courier New,Courier,monospace;">header</span>, 882 <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br> 883 884 <br> 885 886 2 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br> 887 888 <br> 889 890 A link to the webspage appendix_a.html is printed for further 891 information about possible reasons of the error that appeared. (message)<br> 892 893 <br> 894 895 Temperature gradient criterion for estimating the boundary layer height 896 replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br> 897 898 <br> 899 900 NetCDF unit attribute in timeseries output in case of statistic regions 901 added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br> 902 903 <br> 904 905 Maximum number of tails is calculated from maximum number of particles 906 and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>. 907 (<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br> 908 909 <br> 910 911 Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span> 912 is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>, 913 <span style="font-family: Courier New,Courier,monospace;">header</span>, 914 <span style="font-family: Courier New,Courier,monospace;">modules</span>) 915 <br> 916 917 <br> 918 919 First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also 920 defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br> 921 922 <br> 923 924 Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span> 925 moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span> 926 to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>. 927 (<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br> 928 929 <br> 930 931 <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span> 932 moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span> 933 to <span style="font-family: Courier New,Courier,monospace;">inipar</span> 934 (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, 935 <span style="font-family: Courier New,Courier,monospace;">header</span>, 936 <span style="font-family: Courier New,Courier,monospace;">parin</span>, 937 <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, 938 <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>, 939 <span style="font-family: Courier New,Courier,monospace;">user_header</span>, 940 <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>, 941 <span style="font-family: Courier New,Courier,monospace;">user_parin</span>, 942 <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br> 943 944 <br> 945 946 Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span> 947 changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br> 948 949 <br> 950 951 Adjustments for runs on lcxt4 (necessary due to a software update on 952 CRAY) and for coupled runs on ibmy. (<span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">subjob</span>)</td> 953 <td style="vertical-align: top; width: 189px;">advec_particles, 954 advec_s_bc, 955 buoyancy, calc_spectra, check_for_restart, check_open, 956 check_parameters, close_file, coriolis, cpu_log, data_output_2d, 957 data_output_3d, data_output_dvrp, data_output_profiles, 958 data_output_ptseries, data_output_spectra, data_output_tseries, 959 eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model, 960 init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid, 961 message, mrun, netcdf, package_parin, parin, plant_canopy_model, 962 poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob, 963 surface_coupler, temperton_fft, timestep, 964 user_actions,user_check_parameters, user_data_output_dvrp, 965 user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy, 966 user_parin, user_read_restart_data, user_spectra, write_var_list </td> 967 </tr> 968 <tr> 969 <td style="vertical-align: top; width: 27px;"><br> 970 </td> 971 <td style="vertical-align: top; width: 38px;"><br> 972 </td> 973 <td style="vertical-align: top; width: 42px;"><br> 974 </td> 975 <td style="vertical-align: top; width: 40px;"><br> 976 </td> 977 <td style="vertical-align: top; width: 27px;">B<br> 978 </td> 979 <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic 980 pressure profile in case of ocean runs is now calculated in 5 iteration 981 steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br> 982 983 <br> 984 985 Bugfix: wrong sign in buoyancy production of ocean part in case of not 986 using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>). 987 (<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br> 988 989 <br> 990 991 Bugfix: output of averaged 2d/3d quantities requires that an avaraging 992 interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br> 993 994 <br> 995 996 Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>. 997 (<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br> 998 999 <br> 1000 1001 Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>. 1002 (<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br> 1003 1004 <br> 1005 1006 Bugfix for extended NetCDF files: In order to avoid 'data mode' errors 1007 if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span> 1008 is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span> 1009 and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span> 1010 calls. This implies a possible performance loss; an alternative 1011 strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br> 1012 1013 <br> 1014 1015 Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br> 1016 1017 <br> 1018 1019 Bugfix: zero initialization of arrays within buildings for '<span style="font-style: italic;">cyclic_fill</span>'. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br> 1020 1021 <br> 1022 1023 Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span> 1024 => <span style="font-family: Courier New,Courier,monospace;">s_av</span> 1025 for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>, 1026 <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br> 1027 1028 <br> 1029 1030 Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span> 1031 becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br> 1032 1033 <br> 1034 1035 Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br> 1036 1037 <br> 1038 1039 Bugfix: error in check, if particles moved further than one subdomain 1040 length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br> 1041 1042 <br> 1043 1044 Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span> 1045 is only written to file if its third index is > 0, arrays for tails 1046 are allocated with a minimum size of 10 tails if there is no tail 1047 initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>, 1048 <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br> 1049 1050 <br> 1051 1052 Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br> 1053 1054 <br> 1055 1056 Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span> 1057 changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on 1058 NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br> 1059 1060 <br> 1061 1062 Bugfix: output of particle time series only if particle advection is 1063 switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br> 1064 1065 <br> 1066 1067 Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span> 1068 = <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>. 1069 (<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br> 1070 1071 <br> 1072 1073 Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and 1074 z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br> 1075 1076 <br> 1077 1078 Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br> 1079 1080 <br> 1081 1082 If the inversion height calculated by the prerun is zero, 1083 inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br> 1084 1085 <br> 1086 1087 Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br> 1088 1089 <br> 1090 1091 Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span> 1092 removed from the restart file, because otherwise, no change from a 1093 fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, 1094 <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br> 1095 1096 <br> 1097 1098 Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span> 1099 in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td> 1100 <td style="vertical-align: top; width: 189px;">advec_particles, 1101 check_parameters, cpu_log, data_output_2d, data_output_3d, header, 1102 init_3d_model, init_particles, init_ocean, modules, netcdf, 1103 prandtl_fluxes, production_e, read_var_list, time_integration, 1104 user_last_actions, write_var_list<br> 1105 1106 </td> 1107 </tr> 1108 <tr> 1109 <td style="vertical-align: top; width: 27px;">02/02/09<br> 1110 </td> 1111 <td style="vertical-align: top; width: 38px;">SR<br> 1112 </td> 1113 <td style="vertical-align: top; width: 42px;">228<br> 1114 </td> 1115 <td style="vertical-align: top; width: 40px;">3.6<br> 1116 </td> 1117 <td style="vertical-align: top; width: 27px;">N<br> 1118 </td> 1119 <td style="vertical-align: top; width: 497px;">This 1120 release contains further additions, changes, and bugfixes for the 1121 SGI-ICE system, as well as important changes like the splitting of the 1122 user-interface into single files, a complete revision of the 1123 pre-compiling mechanism allowing to use different make-depositories 1124 simultaneously, and a revision of the reading-mechanism from restart 1125 files, which has no more restrictions in case that the previous and 1126 current run have different domain/subdomain sizes. A new handling of 1127 all kind of output messages is introduced with this release and will be 1128 applied to all existing messages within the next releases.<br> 1129 1130 <br> 1131 1132 <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;"> 1133 1134 <br> 1135 1136 Restart runs on SGI-ICE are working. (mrun)<br> 1137 1138 2d-decomposition is default on SGI-ICE systems. (init_pegrid)<br> 1139 1140 <br> 1141 1142 Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this 1143 case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option 1144 "<span style="font-style: italic;">-K parallel</span>" for coupling. 1145 Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and 1146 <span style="font-family: Courier New,Courier,monospace;">subjob</span> 1147 for lcxt4.<br> 1148 1149 <br> 1150 1151 DVRP arguments changed to single precision, mode pathlines added.<br> 1152 1153 <br> 1154 1155 User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br> 1156 1157 <br> 1158 1159 User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td> 1160 <td style="vertical-align: top; width: 189px;">check_for_restart, 1161 check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop, 1162 modules, package_parin, palm, surface_coupler, timestep<br> 1163 1164 <br> 1165 1166 Makefile, mbuild, mrun, subjob<br> 1167 1168 <br> 1169 1170 <span style="font-weight: bold;">new:</span><br> 1171 1172 init_coupling, user_additional_routines, user_check_parameters</td> 1173 </tr> 1174 <tr> 1175 <td style="vertical-align: top; width: 27px;"><br> 1176 </td> 1177 <td style="vertical-align: top; width: 38px;"><br> 1178 </td> 1179 <td style="vertical-align: top; width: 42px;"><br> 1180 </td> 1181 <td style="vertical-align: top; width: 40px;"><br> 1182 </td> 1183 <td style="vertical-align: top; width: 27px;">C<br> 1184 </td> 1185 <td style="vertical-align: top; width: 497px;">User interface has been 1186 split into single files.<br> 1187 1188 <br> 1189 1190 Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span> 1191 changed to INTEGER(8) in order to avoid "out of range" problems, which 1192 result in measured negative time intervals. (cpu_log, local_tremain, 1193 local_tremain_ini)<br> 1194 1195 <br> 1196 1197 Reading mechanism from restart files 1198 completely revised. The subdomain/total domain size is now allowed to 1199 vary arbitrarily between the current and previous run. (read_var_list, 1200 read_3d_binary, user_read_restart_data)<br> 1201 1202 <br> 1203 1204 Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>) 1205 completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>). 1206 One depository per block (given in the config-file) is created. Always 1207 all files from the source directory are copied to the respective 1208 depository. No additional file checks are done any more (mrun version 1209 2.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option 1210 "<span style="font-family: Courier New,Courier,monospace;">-K</span>". 1211 (mbuild, mrun)<br> 1212 1213 <br> 1214 1215 Output messages (including required stop of execution) can now be 1216 handled with the new subroutine <span style="font-family: Courier New,Courier,monospace;">message</span>. 1217 All output messages will be replaced by this routine step by step 1218 within the next revisions.<br> 1219 1220 <br> 1221 1222 Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is 1223 explicitly set for better reading, although this has been already done 1224 in boundary_conds. (advec_s_bc)<br> 1225 1226 <br> 1227 1228 Origin of the xy-coordinate system shifted from the center of the first 1229 grid cell (indices <span style="font-family: Courier New,Courier,monospace;">i=0</span>, <span style="font-family: Courier New,Courier,monospace;">j=0</span>) to the 1230 south-left corner of this cell. (netcdf) Topography definition 1231 according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>. 1232 (init_grid, modules, user_header, user_init_grid, user_parin)</td> 1233 <td style="vertical-align: top; width: 189px;">advec_s_bc, 1234 check_parameters, cpu_log, init_grid, local_stop, local_tremain, 1235 local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list, 1236 user_read_restart_data<br> 1237 1238 <br> 1239 1240 Makefile, mbuild, mrun<br> 1241 1242 <br> 1243 1244 <span style="font-weight: bold;">removed:</span><br> 1245 1246 user_interface<br> 1247 1248 <br> 1249 1250 <span style="font-weight: bold;">new:</span><br> 1251 1252 message, 1253 user_3d_data_averaging, user_actions, user_advec_particles, 1254 user_check_data_output, user_check_data_output_pr, user_data_output_2d, 1255 user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid, 1256 user_dvrp_coltab, user_header, user_init_3d_model, user_init, 1257 user_init_grid, user_init_particles, user_init_plant_canopy, 1258 user_last_actions, user_parin, user_parin, user_particle_attributes, 1259 user_read_restart_data, user_spectra, user_statistics</td> 1260 </tr> 1261 <tr> 1262 <td style="vertical-align: top; width: 27px;"><br> 1263 </td> 1264 <td style="vertical-align: top; width: 38px;"><br> 1265 </td> 1266 <td style="vertical-align: top; width: 42px;"><br> 1267 </td> 1268 <td style="vertical-align: top; width: 40px;"><br> 1269 </td> 1270 <td style="vertical-align: top; width: 27px;">B<br> 1271 </td> 1272 <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is 1273 reallocated in case that multigrid is used. (calc_spectra)<br> 1274 1275 <br> 1276 1277 Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics, 1278 inflow_turbulence, timestep)<br> 1279 1280 <br> 1281 1282 Size of <span style="font-family: Courier New,Courier,monospace;">pf3d 1283 </span>adjusted to the required output size (1 gridpoint less, 1284 along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>) 1285 in the NF90_PUT_VAR statement caused segmentation fault with the INTEL 1286 compiler. (combine_plot_fields)<br> 1287 1288 <br> 1289 1290 Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in 1291 case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>. 1292 (header)<br> 1293 1294 <br> 1295 1296 Inconsistency 1297 removed: as the thermal stratification is not taken into account for 1298 the evaluation of the wall fluxes at vertical walls, the eddy viscosity 1299 <span style="font-family: Courier New,Courier,monospace;">km</span> 1300 must not be used for the evaluation of the velocity gradients <span style="font-family: Courier New,Courier,monospace;">dudy</span>, <span style="font-family: Courier New,Courier,monospace;">dwdy</span>, <span style="font-family: Courier New,Courier,monospace;">dvdx</span> and <span style="font-family: Courier New,Courier,monospace;">dwdx</span>. 1301 (production_e)<br> 1302 1303 <br> 1304 1305 Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in 1306 case of oceans runs. (sort_particles)<br> 1307 1308 <br> 1309 1310 Bugfix: no output of particle concentration and radius unless particles 1311 have been started. (data_output_2d)<br> 1312 1313 <br> 1314 1315 Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span> 1316 from restart files ignored if total numbers of grid points do not 1317 match. (read_3d_binary)<br> 1318 1319 <br> 1320 1321 Bugfix: abort in case that absolute temperature is below zero. 1322 (init_cloud_physics)</td> 1323 <td style="vertical-align: top; width: 189px;">advec_particles, 1324 calc_spectra, check_for_restart, cpu_statistics, data_output_2d, 1325 header, inflow_turbulence, init_cloud_physics, production_e, 1326 read_3d_binary, timestep<br> 1327 1328 <br> 1329 1330 combine_plot_fields</td> 1331 </tr> 1332 </tbody> 1333 </table> 1334 <b><blink></blink></b><br> 1335 <br> 1336 <h2><a name="Kapitel2.0"></a>2.0 How 1337 to change the source 1338 code and how to document modifications<br> 1339 </h2>Currently 1340 (Sep 23rd, 2009), only selected users are allowed to commit changes to 1341 the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br> 1342 <br> 1343 <ol> 1344 <li>Change source code in your current working copy. Document changes in the respective file headers unter "<span style="font-family: Courier New,Courier,monospace;">Current revisions:</span>". 1345 Additionally, document all changes in a local file (e.g. 1346 ~/palm/current_version/CURRENT_MODIFICATIONS), including the files that 1347 have been changed. Classify changes in three cases, new (N), changed 1348 (C), and bugfix (B). <span style="font-weight: bold;">Try to be as short and as precise as possible in describing the changes!</span><br> 1349 <br> 1350 </li> 1351 <li>Test the changed version, unless it works sufficiently.<br> 1352 <br> 1353 </li> 1354 1355 <li>Commit the changes to the repository<br> 1356 <br> 1357 <span style="font-family: Courier New,Courier,monospace;"> svn commit -m "message string" trunk<br> 1358 </span><br> 1359 where "<span style="font-family: Courier New,Courier,monospace;">message string</span>" is a short, <span style="font-weight: bold;">meaningful</span> summary of the changes.<br> 1360 <br> 1361 Alternatively, in case that you have made quite a lot of changes, you 1362 can also give the contents of your file CURRENT_MODIFICATIONS as the 1363 log message:<br> 1364 <br> 1365 <span style="font-family: Courier New,Courier,monospace;"> svn commit -F CURRENT_MODIFICATIONS trunk</span><br> 1366 <br> 1367 </li> 1368 1369 <li>Enter the changes into the technical documentation (under <span style="font-family: Courier New,Courier,monospace;">.../trunk/DOC/tec/technical_documentation.html</span>).<br> 1370 <br> 1371 </li> 1372 <li>Move the change comments in the file headers from "Current 1373 revisions:" to "Former revisions:". Set the current svn id in front of 1374 that.<br> 1375 <br> 1376 <span style="font-weight: bold;">Example:</span><br> 1377 <br> 1378 <span style="font-weight: bold;">before move:</span><br> 1379 <br> 1380 <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;"> 1381 <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;"> 1382 <span style="font-family: Courier New,Courier,monospace;">! <span style="font-weight: bold;">new dummy argument abcd</span></span><span style="font-family: Courier New,Courier,monospace;"></span><br style="font-family: Courier New,Courier,monospace;"> 1383 <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;"> 1384 <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;"> 1385 <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;"> 1386 <span style="font-family: Courier New,Courier,monospace;">! ￜId: init_3d_model.f90 <span style="color: rgb(51, 102, 255); font-weight: bold;">425 2010-02-06 13:37:48Z raasch</span> ￜ</span><br style="font-family: Courier New,Courier,monospace;"> 1387 <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;"> 1388 <span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;">! 407 2009-12-01 15:01:15Z maronga</span><br style="font-family: Courier New,Courier,monospace;"> 1389 <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br> 1390 <br> 1391 <span style="font-weight: bold;">after move:</span><br> 1392 <br> 1393 <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;"> 1394 1395 <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;"> 1396 1397 <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;"> 1398 1399 <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;"> 1400 1401 <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;"> 1402 1403 <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;"> 1404 1405 <span style="font-family: Courier New,Courier,monospace;">! ￜId: </span><span style="font-family: Courier New,Courier,monospace;">init_3d_model.f90 425 2010-02-06 13:37:48Z raasch</span><span style="font-family: Courier New,Courier,monospace;"> ￜ<br> 1406 !</span><br style="font-family: Courier New,Courier,monospace;"> 1407 <span style="font-family: Courier New,Courier,monospace;">! </span><span style="font-family: Courier New,Courier,monospace; color: rgb(51, 102, 255); font-weight: bold;">425 2010-02-06 13:37:48Z raasch</span><span style="font-family: Courier New,Courier,monospace;"><span style="font-weight: bold; color: rgb(51, 51, 255);"></span><br> 1408 ! </span><span style="font-family: Courier New,Courier,monospace; font-weight: bold;">new dummy argument abcd</span><br style="font-family: Courier New,Courier,monospace;"> 1409 1410 <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;"> 1411 1412 <span style="font-family: Courier New,Courier,monospace;">! 407 2009-12-01 15:01:15Z maronga</span><br style="font-family: Courier New,Courier,monospace;"> 1413 1414 <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br> 1415 <br> 1416 <span style="font-family: Times New Roman,Times,serif;">Note that the "<span style="font-family: Courier New,Courier,monospace;">ￜ</span>" 1417 in this example should read "$", but "$" cannot be used here, because 1418 otherwise svn would replace these entries after every change to this 1419 technical documentation.</span><br> 1420 </span><br> 1421 </li> 1422 <li>Commit the changes in the technical documentation and the file headers:<br> 1423 <br> 1424 <span style="font-family: Courier New,Courier,monospace;"> svn commit -m "last commit documented" trunk</span><br> 1425 <br> 1426 <br> 1427 </li> 1428 </ol> 1429 1430 <h2> 1431 <a name="Kapitel3.0"></a>3.0 Description 1432 of selected parts of the 1433 model source code</h2> 1434 <b></b> 1435 <p>This section gives links to existing descriptions about special 1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> 2 <HTML> 3 <HEAD> 4 <META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8"> 5 <TITLE>PALM technical/numerical documentation</TITLE> 6 <META NAME="GENERATOR" CONTENT="OpenOffice.org 3.0 (Unix)"> 7 <META NAME="AUTHOR" CONTENT="Siegfried Raasch"> 8 <META NAME="CREATED" CONTENT="0;0"> 9 <META NAME="CHANGED" CONTENT="20100901;15562900"> 10 <META NAME="KEYWORDS" CONTENT="parallel LES model"> 11 </HEAD> 12 <BODY LANG="en-US" DIR="LTR"> 13 <P STYLE="margin-bottom: 0in"><FONT SIZE=7>PALM </FONT>a 14 <B>pa</B>rallelized <B>L</B>ES <B>m</B>odel 15 </P> 16 <HR> 17 <P STYLE="margin-bottom: 0in"><BR><FONT SIZE=5>technical/numerical 18 documentation</FONT> <BR> <BR> 19 </P> 20 <P ALIGN=CENTER STYLE="margin-bottom: 0in"> 21 </P> 22 <TABLE CELLPADDING=0 CELLSPACING=0> 23 <TR> 24 <TD> 25 <P><B>Current fixed release:</B></P> 26 </TD> 27 <TD> 28 <P><B>3.7a</B></P> 29 </TD> 30 </TR> 31 <TR> 32 <TD> 33 <P><B>Last change of this document</B>: </P> 34 </TD> 35 <TD> 36 <P><B>$Id: technical_documentation.html 544 2010-08-17 10:44:58Z 37 maronga $</B></P> 38 </TD> 39 </TR> 40 </TABLE> 41 <HR> 42 <P><FONT SIZE=5>Table of contents</FONT> <BR> <BR> 43 </P> 44 <UL> 45 <P><A HREF="#Kapitel1.0">1.0</A> History of changes 46 </P> 47 <P><A HREF="#Kapitel2.0">2.0</A> How to change the source code 48 and how to document modifications</P> 49 <P><A HREF="#Kapitel3.0">3.0</A> Description of selected model 50 numerics<BR> </P> 51 </UL> 52 <P><BR><BR> 53 </P> 54 <H2><A NAME="Kapitel1.0"></A>1.0 History of changes</H2> 55 <P STYLE="margin-bottom: 0in">The following table documents all 56 changes to the PALM repository since 2009. Older changes can be found 57 <A HREF="tec_doc_1998-2008.html">here</A>.<BR><BR>Entries in the 58 fifth column specify the type of the change: change of existing 59 code (C), new code (N) or bugfix (B). More detailed information about 60 the changes may sometimes be found in the header comment lines of the 61 respective routines. <BR> 62 </P> 63 <TABLE WIDTH=1223 BORDER=1 CELLPADDING=2 CELLSPACING=3> 64 <COL WIDTH=37> 65 <COL WIDTH=56> 66 <COL WIDTH=68> 67 <COL WIDTH=62> 68 <COL WIDTH=36> 69 <COL WIDTH=518> 70 <COL WIDTH=393> 71 <TR> 72 <TD WIDTH=37> 73 <P><FONT SIZE=4><B>date</B></FONT></P> 74 </TD> 75 <TD WIDTH=56> 76 <P><FONT SIZE=4><B>author</B></FONT></P> 77 </TD> 78 <TD WIDTH=68> 79 <P><FONT SIZE=4><B>svn revision</B></FONT></P> 80 </TD> 81 <TD WIDTH=62> 82 <P><FONT SIZE=4><B>last release</B></FONT></P> 83 </TD> 84 <TD WIDTH=36> 85 <P><FONT SIZE=4><B>type</B></FONT></P> 86 </TD> 87 <TD WIDTH=518> 88 <P><FONT SIZE=4><B>description</B></FONT></P> 89 </TD> 90 <TD WIDTH=393> 91 <P><FONT SIZE=4><B>affected routines</B></FONT></P> 92 </TD> 93 </TR> 94 <TR> 95 <TD WIDTH=37 SDVAL="40187" SDNUM="1033;0;MM/DD/YY"> 96 <P STYLE="font-weight: normal"><FONT SIZE=3>01/09/10</FONT></P> 97 </TD> 98 <TD WIDTH=56> 99 <P STYLE="font-weight: normal"><FONT SIZE=3>CH</FONT></P> 100 </TD> 101 <TD WIDTH=68 SDVAL="553" SDNUM="1033;"> 102 <P STYLE="font-weight: normal"><FONT SIZE=3>553</FONT></P> 103 </TD> 104 <TD WIDTH=62> 105 <P STYLE="font-weight: normal"><FONT SIZE=3>3.7a</FONT></P> 106 </TD> 107 <TD WIDTH=36> 108 <P STYLE="font-weight: normal"><FONT SIZE=3>C</FONT></P> 109 </TD> 110 <TD WIDTH=518> 111 <P STYLE="font-weight: normal"><FONT SIZE=3>d3dpar-parameters for 112 masked output <FONT FACE="Courier New, monospace">data_output_mask_*, 113 data_output_mask_user_*, mask_*_x, mask_*_y, mask_*_z, 114 mask_*_x_loop, mask_*_y_loop </FONT><FONT FACE="Times New Roman, serif">and 115 </FONT><FONT FACE="Courier New, monospace">mask_*_z_loop </FONT>have 116 been replaced by corresponding arrays <FONT FACE="Courier New, monospace">data_output_masks, 117 data_output_masks_user, mask_x, mask_y, mask_z, mask_x_loop, 118 mask_y_loop </FONT><FONT FACE="Times New Roman, serif">and</FONT><FONT FACE="Courier New, monospace"> 119 mask_z_loop</FONT></FONT></P> 120 <P STYLE="font-weight: normal"><FONT SIZE=3>inipar-parameter <FONT FACE="Courier New, monospace">masks</FONT> 121 has been removed. </FONT> 122 </P> 123 <P STYLE="font-weight: normal"><FONT SIZE=3>The changes concern 124 the masked data output, which is still not documented.</FONT></P> 125 </TD> 126 <TD WIDTH=393> 127 <P STYLE="font-weight: normal"><FONT SIZE=3>check_parameters, 128 init_masks, modules, parin, user_parin</FONT></P> 129 </TD> 130 </TR> 131 <TR> 132 <TD WIDTH=37> 133 <P>17/08/10</P> 134 </TD> 135 <TD WIDTH=56> 136 <P>BM</P> 137 </TD> 138 <TD WIDTH=68> 139 <P>544</P> 140 </TD> 141 <TD WIDTH=62> 142 <P>3.7a</P> 143 </TD> 144 <TD WIDTH=36> 145 <P>B/C/N</P> 146 </TD> 147 <TD WIDTH=518> 148 <P>adjustments for lcxt4; bugfix (mbuild): loading of user-defined 149 modules; new .mrun.config.lcxt4 for Cray XT4 in Bergen/Norway</P> 150 </TD> 151 <TD WIDTH=393> 152 <P>mrun, mbuild, subjob</P> 153 </TD> 154 </TR> 155 <TR> 156 <TD WIDTH=37> 157 <P>15/06/10</P> 158 </TD> 159 <TD WIDTH=56> 160 <P>RH</P> 161 </TD> 162 <TD WIDTH=68> 163 <P>540</P> 164 </TD> 165 <TD WIDTH=62> 166 <P>3.7a</P> 167 </TD> 168 <TD WIDTH=36> 169 <P>C</P> 170 </TD> 171 <TD WIDTH=518> 172 <P>ssh from compute nodes to login nodes on hosts lcsgih/lcsgib is 173 done using the names hicegate0/bicegate0 instead of the IP 174 addresses</P> 175 </TD> 176 <TD WIDTH=393> 177 <P>mrun</P> 178 </TD> 179 </TR> 180 <TR> 181 <TD WIDTH=37> 182 <P>21/04/10</P> 183 </TD> 184 <TD WIDTH=56> 185 <P>RH</P> 186 </TD> 187 <TD WIDTH=68> 188 <P>532</P> 189 </TD> 190 <TD WIDTH=62> 191 <P>3.7a</P> 192 </TD> 193 <TD WIDTH=36> 194 <P>C</P> 195 </TD> 196 <TD WIDTH=518> 197 <P>Large scale vertical motion (subsidence/ascent) can be added as 198 additional source to the prognostic equation for humidity/passive 199 scalar<BR> <BR>character length for dopr_unit 200 enlarged<BR><BR>Adjustment of the NCL scripts to allow for output 201 of png files 202 </P> 203 </TD> 204 <TD WIDTH=393> 205 <P>modules, prognostic_equations<BR><BR>.ncl.config.default, 206 cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl</P> 207 </TD> 208 </TR> 209 <TR> 210 <TD WIDTH=37> 211 <P><BR> 212 </P> 213 </TD> 214 <TD WIDTH=56> 215 <P><BR> 216 </P> 217 </TD> 218 <TD WIDTH=68> 219 <P><BR> 220 </P> 221 </TD> 222 <TD WIDTH=62> 223 <P><BR> 224 </P> 225 </TD> 226 <TD WIDTH=36> 227 <P>B</P> 228 </TD> 229 <TD WIDTH=518> 230 <P>Bugfix: unit of hyp changed to dbar</P> 231 </TD> 232 <TD WIDTH=393> 233 <P>check_parameters</P> 234 </TD> 235 </TR> 236 <TR> 237 <TD WIDTH=37> 238 <P>01/04/10</P> 239 </TD> 240 <TD WIDTH=56> 241 <P>RH</P> 242 </TD> 243 <TD WIDTH=68> 244 <P>530</P> 245 </TD> 246 <TD WIDTH=62> 247 <P>3.7a</P> 248 </TD> 249 <TD WIDTH=36> 250 <P>B</P> 251 </TD> 252 <TD WIDTH=518> 253 <P>Bugfix: treatment of special character * in NCL variables 254 containing lists corrected</P> 255 </TD> 256 <TD WIDTH=393> 257 <P>palmplot</P> 258 </TD> 259 </TR> 260 <TR> 261 <TD WIDTH=37> 262 <P>31/03/10</P> 263 </TD> 264 <TD WIDTH=56> 265 <P>RH</P> 266 </TD> 267 <TD WIDTH=68> 268 <P>529</P> 269 </TD> 270 <TD WIDTH=62> 271 <P>3.7a</P> 272 </TD> 273 <TD WIDTH=36> 274 <P>C</P> 275 </TD> 276 <TD WIDTH=518> 277 <P>List of variable names have to specified using blank separated 278 lists and single quotes</P> 279 </TD> 280 <TD WIDTH=393> 281 <P>palmplot</P> 282 </TD> 283 </TR> 284 <TR> 285 <TD WIDTH=37> 286 <P>30/03/10</P> 287 </TD> 288 <TD WIDTH=56> 289 <P>RH</P> 290 </TD> 291 <TD WIDTH=68> 292 <P>526</P> 293 </TD> 294 <TD WIDTH=62> 295 <P>3.7a</P> 296 </TD> 297 <TD WIDTH=36> 298 <P>C</P> 299 </TD> 300 <TD WIDTH=518> 301 <P>Adjustment of the NCL scripts and <FONT FACE="Courier New, Courier, monospace">palmplot 302 </FONT>to allow for special characters in NetCDF variable names 303 </P> 304 </TD> 305 <TD WIDTH=393> 306 <P>palmplot, .ncl.config.default, cross_sections.ncl, 307 profiles.ncl, timeseries.ncl, spectra.ncl</P> 308 </TD> 309 </TR> 310 <TR> 311 <TD WIDTH=37> 312 <P>30/03/10</P> 313 </TD> 314 <TD WIDTH=56> 315 <P>SR</P> 316 </TD> 317 <TD WIDTH=68> 318 <P>525</P> 319 </TD> 320 <TD WIDTH=62> 321 <P>3.7a</P> 322 </TD> 323 <TD WIDTH=36> 324 <P>B</P> 325 </TD> 326 <TD WIDTH=518> 327 <P>Bugfix: "/" in netcdf profile variable names replaced 328 by ":"</P> 329 </TD> 330 <TD WIDTH=393> 331 <P>check_parameters</P> 332 </TD> 333 </TR> 334 <TR> 335 <TD WIDTH=37> 336 <P>19/03/10</P> 337 </TD> 338 <TD WIDTH=56> 339 <P>SR</P> 340 </TD> 341 <TD WIDTH=68> 342 <P>520</P> 343 </TD> 344 <TD WIDTH=62> 345 <P>3.7a</P> 346 </TD> 347 <TD WIDTH=36> 348 <P>N</P> 349 </TD> 350 <TD WIDTH=518> 351 <P>NetCDF4 support for particle data. Total number of particles is 352 allowed to increase during the run, when netcdf_data_format > <I>2</I> 353 is used.</P> 354 </TD> 355 <TD WIDTH=393> 356 <P>advec_particles, check_open, netcdf</P> 357 </TD> 358 </TR> 359 <TR> 360 <TD WIDTH=37> 361 <P><BR> 362 </P> 363 </TD> 364 <TD WIDTH=56> 365 <P><BR> 366 </P> 367 </TD> 368 <TD WIDTH=68> 369 <P><BR> 370 </P> 371 </TD> 372 <TD WIDTH=62> 373 <P><BR> 374 </P> 375 </TD> 376 <TD WIDTH=36> 377 <P>C</P> 378 </TD> 379 <TD WIDTH=518> 380 <P>Special characters like * and " are now allowed for NetCDF 381 variable names. Replacement of these characters has been removed 382 (routine clean_netcdf_varname removed)</P> 383 </TD> 384 <TD WIDTH=393> 385 <P><BR> 386 </P> 387 </TD> 388 </TR> 389 <TR> 390 <TD WIDTH=37> 391 <P>18/03/10</P> 392 </TD> 393 <TD WIDTH=56> 394 <P>SR</P> 395 </TD> 396 <TD WIDTH=68> 397 <P>516</P> 398 </TD> 399 <TD WIDTH=62> 400 <P>3.7a</P> 401 </TD> 402 <TD WIDTH=36> 403 <P>N</P> 404 </TD> 405 <TD WIDTH=518> 406 <P>Simple installation method has been documented (see chapter 407 5.0). Respective scripts and configuration files have been 408 updated.</P> 409 </TD> 410 <TD WIDTH=393> 411 <P>palm_simple_install, palm_simple_run</P> 412 </TD> 413 </TR> 414 <TR> 415 <TD WIDTH=37> 416 <P><BR> 417 </P> 418 </TD> 419 <TD WIDTH=56> 420 <P><BR> 421 </P> 422 </TD> 423 <TD WIDTH=68> 424 <P><BR> 425 </P> 426 </TD> 427 <TD WIDTH=62> 428 <P><BR> 429 </P> 430 </TD> 431 <TD WIDTH=36> 432 <P>B</P> 433 </TD> 434 <TD WIDTH=518> 435 <P>opt=1 is forced for PGI-compiler in routine <FONT FACE="Courier New, Courier, monospace">buoyancy 436 </FONT>by compiler-directive. Otherwise, program aborts with 437 SIGFPE.</P> 438 </TD> 439 <TD WIDTH=393> 440 <P>buoyancy</P> 441 </TD> 442 </TR> 443 <TR> 444 <TD WIDTH=37> 445 <P>16/03/10</P> 446 </TD> 447 <TD WIDTH=56> 448 <P>RH</P> 449 </TD> 450 <TD WIDTH=68> 451 <P>513</P> 452 </TD> 453 <TD WIDTH=62> 454 <P>3.7a</P> 455 </TD> 456 <TD WIDTH=36> 457 <P>N</P> 458 </TD> 459 <TD WIDTH=518> 460 <P>NCL scripts can be run with the shell script <FONT FACE="Courier New, Courier, monospace">palmplot.</FONT></P> 461 </TD> 462 <TD WIDTH=393> 463 <P>palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl</P> 464 </TD> 465 </TR> 466 <TR> 467 <TD WIDTH=37> 468 <P>12/03/10</P> 469 </TD> 470 <TD WIDTH=56> 471 <P>SR</P> 472 </TD> 473 <TD WIDTH=68> 474 <P>509</P> 475 </TD> 476 <TD WIDTH=62> 477 <P>3.7a</P> 478 </TD> 479 <TD WIDTH=36> 480 <P>B</P> 481 </TD> 482 <TD WIDTH=518> 483 <P>bugfix for rev 504: remode_md was given a wrong value</P> 484 </TD> 485 <TD WIDTH=393> 486 <P>mbuild</P> 487 </TD> 488 </TR> 489 <TR> 490 <TD WIDTH=37> 491 <P>08/03/10</P> 492 </TD> 493 <TD WIDTH=56> 494 <P>SR</P> 495 </TD> 496 <TD WIDTH=68> 497 <P>506</P> 498 </TD> 499 <TD WIDTH=62> 500 <P>3.7a</P> 501 </TD> 502 <TD WIDTH=36> 503 <P>C</P> 504 </TD> 505 <TD WIDTH=518> 506 <P>hack for better usage of <B>mrun</B> on Kyoto computing center 507 machine (<FONT FACE="Courier New, Courier, monospace">lckyoto</FONT>)</P> 508 </TD> 509 <TD WIDTH=393> 510 <P>mrun</P> 511 </TD> 512 </TR> 513 <TR> 514 <TD WIDTH=37> 515 <P>03/03/10</P> 516 </TD> 517 <TD WIDTH=56> 518 <P>SR</P> 519 </TD> 520 <TD WIDTH=68> 521 <P>504</P> 522 </TD> 523 <TD WIDTH=62> 524 <P>3.7a</P> 525 </TD> 526 <TD WIDTH=36> 527 <P>C</P> 528 </TD> 529 <TD WIDTH=518> 530 <P><FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT> 531 is now directly called within <B>mrun</B> and must not be given by 532 an output command in the configuration file any more. Please 533 remove the respective output command (<FONT FACE="Courier New, Courier, monospace">OC:combine_plot_fields.x</FONT>) 534 from your configuration file!<BR><BR>Utility programs 535 (<FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>, 536 <FONT FACE="Courier New, Courier, monospace">interpret_config</FONT>) 537 are created by <B>mbuild</B> separately for each block in the 538 configuration file. Depending on option <FONT FACE="Courier New, Courier, monospace">-K</FONT>, 539 <B>mrun</B> is using the utility programs for the respective 540 block.<BR><BR>Utility programs are also compiled in parallel, 541 depending on variable <FONT FACE="Courier New, Courier, monospace">%mopts</FONT> 542 in the configuration file..<BR><BR>Default configuration files 543 updated.</P> 544 </TD> 545 <TD WIDTH=393> 546 <P>mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*</P> 547 </TD> 548 </TR> 549 <TR> 550 <TD WIDTH=37> 551 <P>02/03/10</P> 552 </TD> 553 <TD WIDTH=56> 554 <P>SR</P> 555 </TD> 556 <TD WIDTH=68> 557 <P>496</P> 558 </TD> 559 <TD WIDTH=62> 560 <P>3.7a</P> 561 </TD> 562 <TD WIDTH=36> 563 <P>C</P> 564 </TD> 565 <TD WIDTH=518> 566 <P>Particle data for restart runs are only written if environment 567 variable <FONT FACE="Courier New, Courier, monospace">write_binary</FONT> 568 = <I>.T.</I>, i.e. particle data are now handled in the same way 569 as the other restart data.</P> 570 </TD> 571 <TD WIDTH=393> 572 <P>palm</P> 573 </TD> 574 </TR> 575 <TR> 576 <TD WIDTH=37> 577 <P>01/03/10</P> 578 </TD> 579 <TD WIDTH=56> 580 <P>SR</P> 581 </TD> 582 <TD WIDTH=68> 583 <P>494</P> 584 </TD> 585 <TD WIDTH=62> 586 <P>3.7a</P> 587 </TD> 588 <TD WIDTH=36> 589 <P>N</P> 590 </TD> 591 <TD WIDTH=518> 592 <P>Output in NetCDF4-format.<BR><BR>NetCDF4 allows for parallel 593 I/O. Also, variables are not limited in size any more (i.e. arrays 594 can be larger than 2GB). The new d3par-parameter 595 <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>.can 596 be used to select among the different NetCDF file formats (<I>1</I>: 597 classic format, <I>2</I>: 64-bit-offset format (this is now the 598 default), <I>3</I>: NetCDF4/HDF5 format, <I>4</I>: NetCDF4 format 599 with NF90_CLASSIC_MODEL bit set). Setting <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT> 600 > <I>2</I> only affects 2d- and 3d-output, i.e. there is no 601 parallel output for profiles, time series, spectra, and particles. 602 Parallel output of particle data may realized in the future.<BR><BR>In 603 case of parallel output, all PEs write into one file, which means 604 that postprocessing the data with <FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT> 605 (merging data from single files - one per PE - into one file) is 606 not neccessary. In this case, flag files are automatically set, 607 telling <FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT> 608 that nothing is to be done.<BR><BR>Using NetCDF4 format requires a 609 NetCDF4/HDF library. Respective settings for -I, -L, and -l 610 compiler/loader options for the SGI-ICE at HLRN can be found in 611 the new example configuration file 612 <FONT FACE="Courier New, Courier, monospace">..../trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4</FONT><BR><BR><B>Attention:</B><BR>So 613 far, NetCDF parallel I/O has only been tested a little. Further 614 performance optimizations may be required, especially in case of 615 large data sets (e.g. data chunking, or lustre file system 616 settings with <FONT FACE="Courier New, Courier, monospace">lfs 617 setstripe</FONT>). <B>Please report bugs and performance problems 618 immediately!</B><BR><BR><FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT> 619 outputs cpu-time needed for file merging.<BR><BR>Modules to be 620 loaded for compilation (mbuild) or job execution (mrun) can/should 621 now be given in the configuration file (<FONT FACE="Courier New, Courier, monospace">.mrun.config</FONT>) 622 using variable <FONT FACE="Courier New, Courier, monospace">modules</FONT>. 623 Example:<BR><BR> <FONT FACE="Courier New, Courier, monospace">%modules 624 ifort/11.0.069:netcdf lcsgih 625 parallel</FONT><BR><BR>This method replaces the (undocumented) 626 <FONT FACE="Courier New, Courier, monospace">mpilib</FONT>-variable.<BR><BR><B>WARNING:</B><BR><B>All 627 fixed settings of modules in the scripts mbuild, mrun, and subjob 628 have been removed! Please set the </B><FONT FACE="Courier New, Courier, monospace"><B>modules</B></FONT><B> 629 variable appropriately and remove the mpilib variable in your 630 configuration file.<BR><BR></B>Compilation time can be reduced be 631 using parallel make. The number of allowed simultaneous compiler 632 calls (threads) is set in the configuration file using variable 633 <FONT FACE="Courier New, Courier, monospace">mopt</FONT>, e.g.<BR><BR> 634 <FONT FACE="Courier New, Courier, monospace">%mopts -j:4 635 lcsgih parallel</FONT><BR><BR>allows a maximum of 4 routines to be 636 compiled simultaneously (provided that the makefile does not show 637 any dependencies between these routines).</P> 638 </TD> 639 <TD WIDTH=393> 640 <P>check_open, check_parameters, close_file, data_output_2d, 641 data_output_3d, header, modules, netcdf, 642 parin<BR><BR>combine_plot_fields<BR><BR>mbuild, mrun, subjob</P> 643 </TD> 644 </TR> 645 <TR> 646 <TD WIDTH=37> 647 <P><BR> 648 </P> 649 </TD> 650 <TD WIDTH=56> 651 <P><BR> 652 </P> 653 </TD> 654 <TD WIDTH=68> 655 <P><BR> 656 </P> 657 </TD> 658 <TD WIDTH=62> 659 <P><BR> 660 </P> 661 </TD> 662 <TD WIDTH=36> 663 <P>C</P> 664 </TD> 665 <TD WIDTH=518> 666 <P>d3par-parameters <FONT FACE="Courier New, Courier, monospace">netcdf_64bit</FONT> 667 and <FONT FACE="Courier New, Courier, monospace">netcdf_64bit_3d</FONT> 668 have been removed. Use the new d3par-variable <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT> 669 = <I>2</I> for choosing the NetCDF 64bit-offset format (this is 670 the default from now on). The offset-format can not be set 671 independently for the 3d-output-data any more.<BR><BR>d3par-parameters 672 <FONT FACE="Courier New, Courier, monospace">netcdf_format_mask</FONT>, 673 <FONT FACE="Courier New, Courier, monospace">netcdf_format_mask_av</FONT>, 674 and variables <FONT FACE="Courier New, Courier, monospace">nc_format_mask</FONT>, 675 <FONT FACE="Courier New, Courier, monospace">format_parallel_io</FONT> 676 removed. They are replaced by the new parameter 677 <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>. 678 This change concerns the masked data output, which is still not 679 documented.</P> 680 </TD> 681 <TD WIDTH=393> 682 <P>check_open, close_file,<BR>data_output_mask, header, 683 init_masks, modules, parin</P> 684 </TD> 685 </TR> 686 <TR> 687 <TD WIDTH=37> 688 <P><BR> 689 </P> 690 </TD> 691 <TD WIDTH=56> 692 <P><BR> 693 </P> 694 </TD> 695 <TD WIDTH=68> 696 <P><BR> 697 </P> 698 </TD> 699 <TD WIDTH=62> 700 <P><BR> 701 </P> 702 </TD> 703 <TD WIDTH=36> 704 <P>B</P> 705 </TD> 706 <TD WIDTH=518> 707 <P>Bugfix in trunk/UTIL/Makefile: forgot to compile for 708 interpret_config.<BR><BR>Bugfix: timeseries data have to be 709 collected by PE0 (user_statistics).</P> 710 </TD> 711 <TD WIDTH=393> 712 <P>user_statistics<BR><BR>trunk/UTIL/Makefile</P> 713 </TD> 714 </TR> 715 <TR> 716 <TD WIDTH=37> 717 <P>05/02/10</P> 718 </TD> 719 <TD WIDTH=56> 720 <P>SR</P> 721 </TD> 722 <TD WIDTH=68> 723 <P>485</P> 724 </TD> 725 <TD WIDTH=62> 726 <P>3.7a</P> 727 </TD> 728 <TD WIDTH=36> 729 <P>B</P> 730 </TD> 731 <TD WIDTH=518> 732 <P><FONT FACE="Courier New, Courier, monospace">ngp_3d</FONT>, 733 <FONT FACE="Courier New, Courier, monospace">ngp_3d_inner</FONT> 734 changed to 64 bit. Otherwise, on large grids > 2*10**9 grid 735 points some global statistics (e.g. total kinetic energy) have 736 wrong values.</P> 737 </TD> 738 <TD WIDTH=393> 739 <P>init_3d_model, modules</P> 740 </TD> 741 </TR> 742 <TR> 743 <TD WIDTH=37> 744 <P>05/02/10</P> 745 </TD> 746 <TD WIDTH=56> 747 <P>SR</P> 748 </TD> 749 <TD WIDTH=68> 750 <P>484</P> 751 </TD> 752 <TD WIDTH=62> 753 <P>3.7a</P> 754 </TD> 755 <TD WIDTH=36> 756 <P>B</P> 757 </TD> 758 <TD WIDTH=518> 759 <P>Typo in file headers removed ("current" instead of 760 "actual").</P> 761 </TD> 762 <TD WIDTH=393> 763 <P>many</P> 764 </TD> 765 </TR> 766 <TR> 767 <TD WIDTH=37> 768 <P>05/02/10</P> 769 </TD> 770 <TD WIDTH=56> 771 <P>SR</P> 772 </TD> 773 <TD WIDTH=68> 774 <P>483</P> 775 </TD> 776 <TD WIDTH=62> 777 <P>3.7a</P> 778 </TD> 779 <TD WIDTH=36> 780 <P>N</P> 781 </TD> 782 <TD WIDTH=518> 783 <P><FONT FACE="Courier New, Courier, monospace">compare_palm_logs 784 </FONT>is additionally compiled with <B>mbuild</B> <FONT FACE="Courier New, Courier, monospace">-u</FONT> 785 . (<FONT FACE="Courier New, Courier, monospace">Makefile</FONT> in 786 <FONT FACE="Courier New, Courier, monospace">trunk/UTIL</FONT>)<BR><BR>make 787 options (<FONT FACE="Courier New, Courier, monospace">mopts</FONT>) 788 to be set by configuration file implemented. (<B>mrun</B>, 789 <B>mbuild</B>)<BR><BR><FONT FACE="Courier New, Courier, monospace">humidity</FONT> 790 = <I>.T.</I> can be used for runs with topography. 791 <FONT FACE="Courier New, Courier, monospace">wall_humidityflux</FONT> 792 and<BR><FONT FACE="Courier New, Courier, monospace">wall_scalarflux</FONT> 793 are the corresponding new inipar parameters.<BR>(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>, 794 <FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>, 795 <FONT FACE="Courier New, Courier, monospace">parin</FONT>)<BR><BR>Large 796 scale vertical motion (subsidence/ascent) can be added as 797 additional source to the prognostic equation for potential 798 temperature. See new parameters <FONT FACE="Courier New, Courier, monospace">large_scale_subsidence</FONT>, 799 <FONT FACE="Courier New, Courier, monospace">ws_vertical_gradient</FONT>, 800 and <FONT FACE="Courier New, Courier, monospace">ws_vertical_gradient_level</FONT>. 801 (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>, 802 <FONT FACE="Courier New, Courier, monospace">header</FONT>, 803 <FONT FACE="Courier New, Courier, monospace">Makefile</FONT>, 804 <FONT FACE="Courier New, Courier, monospace">modules</FONT>, 805 <FONT FACE="Courier New, Courier, monospace">parin</FONT>, 806 <FONT FACE="Courier New, Courier, monospace">prognostic_equations</FONT>, 807 <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>, 808 <FONT FACE="Courier New, Courier, monospace">subsidence</FONT>, 809 <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Scripts 810 have been updated for Cray-XT5 machine (lcxt5m) and 811 Hitachi-machine (lckyoto).<BR><BR>A simple method for installing 812 and running palm (with limited features) has been added. 813 (<FONT FACE="Courier New, Courier, monospace">Makefile</FONT>, new 814 scripts <B>palm_simple_install</B>, <B>palm_simple_run</B>)<BR><BR>Masked 815 data output has been implemented but it is not documented in the 816 user manual so far. This feature can already use NetCDF4 file 817 format. (check_open, check_parameters, close_file, modules, 818 netcdf, parin, time_integration, user_parin, new: 819 data_output_mask, init_masks, user_data_output_mask)</P> 820 </TD> 821 <TD WIDTH=393> 822 <P>check_open, check parameters, close_file, header, 823 init_3d_model, Makefile, mbuild, modules, mrun, netcdf, parin, 824 prognostic_equations, read_var_list, time_integration, user_parin, 825 write_var_list<BR><BR><B>new:</B> data_output_mask, 826 init_masks, palm_simple_install, palm_simple_run, subsidence, 827 user_data_output_mask</P> 828 </TD> 829 </TR> 830 <TR> 831 <TD WIDTH=37> 832 <P><BR> 833 </P> 834 </TD> 835 <TD WIDTH=56> 836 <P><BR> 837 </P> 838 </TD> 839 <TD WIDTH=68> 840 <P><BR> 841 </P> 842 </TD> 843 <TD WIDTH=62> 844 <P><BR> 845 </P> 846 </TD> 847 <TD WIDTH=36> 848 <P>C</P> 849 </TD> 850 <TD WIDTH=518> 851 <P>2d-decomposition is default for Cray-XT machines. 852 (<FONT FACE="Courier New, Courier, monospace">init_pegrid</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">var_ts</FONT> 853 is replaced by <FONT FACE="Courier New, Courier, monospace">dots_max</FONT>. 854 (<FONT FACE="Courier New, Courier, monospace">modules</FONT>, 855 <FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Every 856 cloud droplet has now an own weighting factor and can be deleted 857 due to collisions. Condensation and collision of cloud droplets 858 are adjusted accordingly. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Collision 859 efficiency for large cloud droplets has changed according to table 860 of Rogers and Yau. (<FONT FACE="Courier New, Courier, monospace">collision_efficiency</FONT>)</P> 861 </TD> 862 <TD WIDTH=393> 863 <P>advec_particles, collision_efficiency, init_3d_model, 864 init_pegrid, modules</P> 865 </TD> 866 </TR> 867 <TR> 868 <TD WIDTH=37> 869 <P><BR> 870 </P> 871 </TD> 872 <TD WIDTH=56> 873 <P><BR> 874 </P> 875 </TD> 876 <TD WIDTH=68> 877 <P><BR> 878 </P> 879 </TD> 880 <TD WIDTH=62> 881 <P><BR> 882 </P> 883 </TD> 884 <TD WIDTH=36> 885 <P>B</P> 886 </TD> 887 <TD WIDTH=518> 888 <P>Bugfix for generating serial jobs. (<B>subjob</B>)<BR><BR>Bugfix: 889 index problem concerning gradient_level indices removed. 890 (<FONT FACE="Courier New, Courier, monospace">header</FONT>)<BR><BR>Dimension 891 of array <FONT FACE="Courier New, Courier, monospace">stat</FONT> 892 in cascade change to prevent type problems with mpi2 libraries. 893 (<FONT FACE="Courier New, Courier, monospace">poisfft_hybrid</FONT>)<BR><BR>Loop 894 was split to make runs reproducible when using ifort compiler. 895 (<FONT FACE="Courier New, Courier, monospace">disturb_field</FONT>)<BR><BR>Bugfix: 896 exchange of ghost points for <FONT FACE="Courier New, Courier, monospace">prho</FONT> 897 included. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)<BR><BR>Bugfix 898 in calculation of time-averaged surface heatfluxes. 899 (<FONT FACE="Courier New, Courier, monospace">sum_up_3d_data</FONT>)<BR><BR>Bugfix 900 in calculation of precipitation_rate. 901 (<FONT FACE="Courier New, Courier, monospace">calc_precipitation</FONT>)<BR><BR>Bugfix: 902 initial data assignments to some dvrp arrays changed due to error 903 messages from gfortran compiler. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Bugfix 904 in calculation of cloud droplet velocity. 905 (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix 906 in transfer of particles at south/left edge. 907 (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix 908 in calculation of collision efficiency. (<FONT FACE="Courier New, Courier, monospace">collision_efficiency</FONT>)</P> 909 </TD> 910 <TD WIDTH=393> 911 <P>advec_particles, calc_precipitation, collision_efficiency, 912 disturb_field, header, modules, poisfft_hybrid, subjob, 913 sum_up_3d_data, time_integration</P> 914 </TD> 915 </TR> 916 <TR> 917 <TD WIDTH=37> 918 <P>23/09/09</P> 919 </TD> 920 <TD WIDTH=56> 921 <P>SR</P> 922 </TD> 923 <TD WIDTH=68> 924 <P>392</P> 925 </TD> 926 <TD WIDTH=62> 927 <P>3.7</P> 928 </TD> 929 <TD WIDTH=36> 930 <P>N</P> 931 </TD> 932 <TD WIDTH=518> 933 <P><B>Most important changes:</B> atmosphere-ocean coupling has 934 been improved and steering of dvr-software is more user-friendly 935 now. Beside that, the release contains a lot of optimizations, 936 changes, and bugfixes which have accumulated over the last 937 months.<BR><BR>The atmosphere-ocean coupling allows to use 938 independent precursor runs in order to account for different 939 spin-up times. The time when coupling has to be started is given 940 by new inipar parameter <FONT FACE="Courier New, Courier, monospace">coupling_start_time</FONT>. 941 The precursor ocean run has to be started using new <B>mrun</B> 942 option "<FONT FACE="Courier New, Courier, monospace">-y</FONT>" 943 in order to add the appendix "<FONT FACE="Courier New, Courier, monospace">_O</FONT>" 944 to all output files. (<FONT FACE="Courier New, Courier, monospace">check_for_restart</FONT>, 945 <FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>, 946 <FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>, 947 <FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>, 948 <FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>, 949 <FONT FACE="Courier New, Courier, monospace">data_output_ptseries</FONT>, 950 <FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>, 951 <FONT FACE="Courier New, Courier, monospace">data_output_tseries</FONT>, 952 <FONT FACE="Courier New, Courier, monospace">header</FONT>, 953 <FONT FACE="Courier New, Courier, monospace">init_coupling</FONT>, 954 <FONT FACE="Courier New, Courier, monospace">modules</FONT>, <FONT FACE="Courier New, Courier, monospace">mrun</FONT>, 955 <FONT FACE="Courier New, Courier, monospace">parin</FONT>, 956 <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>, 957 <FONT FACE="Courier New, Courier, monospace">surface_coupler</FONT>, 958 <FONT FACE="Courier New, Courier, monospace">time_integration</FONT>, 959 <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Clipping 960 of dvrp output implemented. Default colourtable for particles 961 implemented, particle attributes (color, dvrp_size) can be set 962 with new parameters <FONT FACE="Courier New, Courier, monospace">particle_color</FONT>, 963 <FONT FACE="Courier New, Courier, monospace">particle_dvrpsize</FONT>, 964 <FONT FACE="Courier New, Courier, monospace">color_interval</FONT>, 965 <FONT FACE="Courier New, Courier, monospace">dvrpsize_interval</FONT>. 966 Slicer attributes (dvrp) are set with new routine 967 <FONT FACE="Courier New, Courier, monospace">set_slicer_attributes_dvrp</FONT> 968 and are controlled with existing parameters <FONT FACE="Courier New, Courier, monospace">slicer_range_limits</FONT>. 969 (<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>, 970 <FONT FACE="Courier New, Courier, monospace">data_output_dvrp</FONT>, 971 <FONT FACE="Courier New, Courier, monospace">modules</FONT>, 972 <FONT FACE="Courier New, Courier, monospace">set_slicer_attributes_dvrp</FONT>, 973 <FONT FACE="Courier New, Courier, monospace">user_data_output_dvrp</FONT>)<BR><BR>Polygon 974 reduction for topography and ground plate isosurface. Reduction 975 level for buildings can be chosen with parameter cluster_size. 976 (<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>)<BR><BR>Variables 977 <FONT FACE="Courier New, Courier, monospace">bc_lr</FONT> / <FONT FACE="Courier New, Courier, monospace">bc_ns</FONT> 978 in most subroutines replaced by LOGICAL variables 979 <FONT FACE="Courier New, Courier, monospace">bc_lr_cyc</FONT>,<BR><FONT FACE="Courier New, Courier, monospace">bc_ns_cyc</FONT> 980 for speed optimization. This gives a significant speedup of more 981 than 10%. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>, 982 <FONT FACE="Courier New, Courier, monospace">diffusion_u</FONT>, 983 <FONT FACE="Courier New, Courier, monospace">diffusion_v</FONT>, 984 <FONT FACE="Courier New, Courier, monospace">diffusion_w</FONT>, 985 <FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Scripts 986 have been adapted for machine lck (Yonsei Univ.). (<FONT FACE="Courier New, Courier, monospace">mrun</FONT>, 987 <FONT FACE="Courier New, Courier, monospace">mbuild</FONT>, 988 <FONT FACE="Courier New, Courier, monospace">subjob</FONT>)<BR><BR>Additional 989 timestep criterion in case of simulations with plant canopy. 990 (<FONT FACE="Courier New, Courier, monospace">timestep</FONT>)<BR><BR>Check 991 for illegal entries in <FONT FACE="Courier New, Courier, monospace">section_xy</FONT>|<FONT FACE="Courier New, Courier, monospace">xz</FONT>|<FONT FACE="Courier New, Courier, monospace">yz</FONT> 992 that exceed <FONT FACE="Courier New, Courier, monospace">nz+1</FONT>|<FONT FACE="Courier New, Courier, monospace">ny+1</FONT>|<FONT FACE="Courier New, Courier, monospace">nx+1</FONT>. 993 (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>External 994 pressure gradient can be used as driving force. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>, 995 <FONT FACE="Courier New, Courier, monospace">header</FONT>, 996 <FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>, 997 <FONT FACE="Courier New, Courier, monospace">modules</FONT>, 998 <FONT FACE="Courier New, Courier, monospace">parin</FONT>, 999 <FONT FACE="Courier New, Courier, monospace">prognostic_equations</FONT>, 1000 <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>, 1001 <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>New 1002 topography case '<I>single_street_canyon</I>'. (<FONT FACE="Courier New, Courier, monospace">header</FONT>, 1003 <FONT FACE="Courier New, Courier, monospace">init_grid</FONT>, 1004 <FONT FACE="Courier New, Courier, monospace">modules</FONT>, 1005 <FONT FACE="Courier New, Courier, monospace">parin</FONT>, 1006 <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>, 1007 <FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT>, 1008 <FONT FACE="Courier New, Courier, monospace">user_header</FONT>, 1009 <FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>, 1010 <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Option 1011 to predefine a target bulk velocity for <FONT FACE="Courier New, Courier, monospace">conserve_volume_flow</FONT>. 1012 (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>, 1013 <FONT FACE="Courier New, Courier, monospace">header</FONT>, 1014 <FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>, 1015 <FONT FACE="Courier New, Courier, monospace">modules</FONT>, 1016 <FONT FACE="Courier New, Courier, monospace">parin</FONT>, 1017 <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>, 1018 <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Option 1019 for user defined 2D data output in xy cross sections at z=<FONT FACE="Courier New, Courier, monospace">nzb</FONT>+1. 1020 (<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>, 1021 <FONT FACE="Courier New, Courier, monospace">user_data_output_2d</FONT>)<BR><BR>xy 1022 cross section output of surface heatfluxes (sensible and latent). 1023 (<FONT FACE="Courier New, Courier, monospace">average_3d_data</FONT>, 1024 <FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>, 1025 <FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>, 1026 <FONT FACE="Courier New, Courier, monospace">modules</FONT>, 1027 <FONT FACE="Courier New, Courier, monospace">read_3d_binary</FONT>, 1028 <FONT FACE="Courier New, Courier, monospace">sum_up_3d_data</FONT>, 1029 <FONT FACE="Courier New, Courier, monospace">write_3d_binary</FONT>)</P> 1030 </TD> 1031 <TD WIDTH=393> 1032 <P>average_3d_data, check_for_restart, check_parameters, 1033 data_output_2d, data_output_3d, data_output_dvrp, 1034 data_output_profiles, data_output_ptseries, data_output_spectra, 1035 data_output_tseries, diffusion_u, diffusion_v, diffusion_w, 1036 init_coupling, init_dvrp, init_grid, init_3d_model, header, 1037 mbuild, modules, mrun, package_parin, parin, prognostic_equations, 1038 read_3d_binary, read_var_list, subjob, sum_up_3d_data, 1039 surface_coupler, timestep, time_integration, 1040 user_check_parameters, user_data_output_2d, user_data_output_dvrp, 1041 user_header, user_init_grid, write_3d_binary, write_var_list<BR><BR><B>new:</B> 1042 set_particle_attributes, set_slicer_attributes_dvrp</P> 1043 </TD> 1044 </TR> 1045 <TR> 1046 <TD WIDTH=37> 1047 <P><BR> 1048 </P> 1049 </TD> 1050 <TD WIDTH=56> 1051 <P><BR> 1052 </P> 1053 </TD> 1054 <TD WIDTH=68> 1055 <P><BR> 1056 </P> 1057 </TD> 1058 <TD WIDTH=62> 1059 <P><BR> 1060 </P> 1061 </TD> 1062 <TD WIDTH=36> 1063 <P>C</P> 1064 </TD> 1065 <TD WIDTH=518> 1066 <P>Output of messages replaced by message handling routine. 1067 (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>, 1068 <FONT FACE="Courier New, Courier, monospace">advec_s_bc</FONT>, 1069 <FONT FACE="Courier New, Courier, monospace">buoyancy</FONT>, 1070 <FONT FACE="Courier New, Courier, monospace">calc_spectra</FONT>, 1071 <FONT FACE="Courier New, Courier, monospace">check_for_restart</FONT>, 1072 <FONT FACE="Courier New, Courier, monospace">check_open</FONT>, 1073 <FONT FACE="Courier New, Courier, monospace">coriolis</FONT>, 1074 <FONT FACE="Courier New, Courier, monospace">cpu_log</FONT>, 1075 <FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>, 1076 <FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>, 1077 <FONT FACE="Courier New, Courier, monospace">data_output_dvrp</FONT>, 1078 <FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>, 1079 <FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>, 1080 <FONT FACE="Courier New, Courier, monospace">fft_xy</FONT>, 1081 <FONT FACE="Courier New, Courier, monospace">flow_statistics</FONT>, 1082 <FONT FACE="Courier New, Courier, monospace">header</FONT>, 1083 <FONT FACE="Courier New, Courier, monospace">init_1d_model</FONT>, 1084 <FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>, 1085 <FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>, 1086 <FONT FACE="Courier New, Courier, monospace">init_grid</FONT>, 1087 <FONT FACE="Courier New, Courier, monospace">init_particles</FONT>, 1088 <FONT FACE="Courier New, Courier, monospace">init_pegrid</FONT>, 1089 <FONT FACE="Courier New, Courier, monospace">netcdf</FONT>, <FONT FACE="Courier New, Courier, monospace">parin</FONT>, 1090 <FONT FACE="Courier New, Courier, monospace">plant_canopy_model</FONT>, 1091 <FONT FACE="Courier New, Courier, monospace">poisfft_hybrid</FONT>, 1092 <FONT FACE="Courier New, Courier, monospace">poismg</FONT>, 1093 <FONT FACE="Courier New, Courier, monospace">read_3d_binary</FONT>, 1094 <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>, 1095 <FONT FACE="Courier New, Courier, monospace">surface_coupler</FONT>, 1096 <FONT FACE="Courier New, Courier, monospace">temperton_fft</FONT>, 1097 <FONT FACE="Courier New, Courier, monospace">timestep</FONT>, 1098 <FONT FACE="Courier New, Courier, monospace">user_actions</FONT>, 1099 <FONT FACE="Courier New, Courier, monospace">user_data_output_dvrp</FONT>, 1100 <FONT FACE="Courier New, Courier, monospace">user_dvrp_coltab</FONT>, 1101 <FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>, 1102 <FONT FACE="Courier New, Courier, monospace">user_init_plant_canopy</FONT>, 1103 <FONT FACE="Courier New, Courier, monospace">user_parin</FONT>, 1104 <FONT FACE="Courier New, Courier, monospace">user_read_restart_data</FONT>, 1105 <FONT FACE="Courier New, Courier, monospace">user_spectra</FONT>)<BR><BR>Output 1106 of NetCDF messages with aid of message handling routine. 1107 (<FONT FACE="Courier New, Courier, monospace">check_open</FONT>, 1108 <FONT FACE="Courier New, Courier, monospace">close_file</FONT>, 1109 <FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>, 1110 <FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>, 1111 <FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>, 1112 <FONT FACE="Courier New, Courier, monospace">data_output_ptseries</FONT>, 1113 <FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>, 1114 <FONT FACE="Courier New, Courier, monospace">data_output_tseries</FONT>, 1115 <FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>__lcmuk 1116 changed to __lc to avoid problems with Intel compiler on sgi-ice. 1117 (<FONT FACE="Courier New, Courier, monospace">poisfft</FONT>)<BR><BR>For 1118 extended NetCDF files, the updated title attribute includes an 1119 update of time_average_text where appropriate. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>In 1120 case of restart runs without extension, initial profiles are not 1121 written to NetCDF-file anymore. So far, time axis always started 1122 at t=0. (<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>, 1123 <FONT FACE="Courier New, Courier, monospace">modules</FONT>, 1124 <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>, 1125 <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">initializing_actions</FONT>='<I>read_data_for_recycling</I>' 1126 renamed to '<I>cyclic_fill</I>'. A cyclic fill can now <BR>be used 1127 independent of <FONT FACE="Courier New, Courier, monospace">turbulent_inflow</FONT>. 1128 (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>, 1129 <FONT FACE="Courier New, Courier, monospace">header</FONT>, 1130 <FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>2 1131 NetCDF error numbers changed. (<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>)<BR><BR>A 1132 link to the webspage appendix_a.html is printed for further 1133 information about possible reasons of the error that appeared. 1134 (message)<BR><BR>Temperature gradient criterion for estimating the 1135 boundary layer height replaced by the gradient criterion of 1136 Sullivan et al. (1998). (<FONT FACE="Courier New, Courier, monospace">flow_statistics</FONT>)<BR><BR>NetCDF 1137 unit attribute in timeseries output in case of statistic regions 1138 added. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Maximum 1139 number of tails is calculated from maximum number of particles and 1140 <FONT FACE="Courier New, Courier, monospace">skip_particles_for_tail</FONT>. 1141 (<FONT FACE="Courier New, Courier, monospace">init_particles</FONT>)<BR><BR>Value 1142 of <FONT FACE="Courier New, Courier, monospace">vertical_particle_advection</FONT> 1143 is allowed to differ for each particle group. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>, 1144 <FONT FACE="Courier New, Courier, monospace">header</FONT>, 1145 <FONT FACE="Courier New, Courier, monospace">modules</FONT>) 1146 <BR><BR>First constant in array <FONT FACE="Courier New, Courier, monospace">den</FONT> 1147 also defined as type double. (<FONT FACE="Courier New, Courier, monospace">eqn_state_seawater</FONT>)<BR><BR>Parameter 1148 <FONT FACE="Courier New, Courier, monospace">dvrp_psize</FONT> 1149 moved from <FONT FACE="Courier New, Courier, monospace">particles_par</FONT> 1150 to <FONT FACE="Courier New, Courier, monospace">dvrp_graphics_par</FONT>. 1151 (<FONT FACE="Courier New, Courier, monospace">package_parin</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">topography_grid_convention</FONT> 1152 moved from <FONT FACE="Courier New, Courier, monospace">userpar</FONT> 1153 to <FONT FACE="Courier New, Courier, monospace">inipar</FONT> 1154 (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>, 1155 <FONT FACE="Courier New, Courier, monospace">header</FONT>, <FONT FACE="Courier New, Courier, monospace">parin</FONT>, 1156 <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>, 1157 <FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT>, 1158 <FONT FACE="Courier New, Courier, monospace">user_header</FONT>, 1159 <FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>, 1160 <FONT FACE="Courier New, Courier, monospace">user_parin</FONT>, 1161 <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Default 1162 value of <FONT FACE="Courier New, Courier, monospace">grid_matching</FONT> 1163 changed to '<I>strict</I>'. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Adjustments 1164 for runs on lcxt4 (necessary due to a software update on CRAY) and 1165 for coupled runs on ibmy. (<FONT FACE="Courier New, Courier, monospace">mrun</FONT>, 1166 <FONT FACE="Courier New, Courier, monospace">subjob</FONT>)</P> 1167 </TD> 1168 <TD WIDTH=393> 1169 <P>advec_particles, advec_s_bc, buoyancy, calc_spectra, 1170 check_for_restart, check_open, check_parameters, close_file, 1171 coriolis, cpu_log, data_output_2d, data_output_3d, 1172 data_output_dvrp, data_output_profiles, data_output_ptseries, 1173 data_output_spectra, data_output_tseries, eqn_state_seawater, 1174 fft_xy, flow_statistics, header, init_1d_model, init_3d_model, 1175 init_dvrp, init_grid, init_particles, init_pegrid, message, mrun, 1176 netcdf, package_parin, parin, plant_canopy_model, poisfft, 1177 poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob, 1178 surface_coupler, temperton_fft, timestep, 1179 user_actions,user_check_parameters, user_data_output_dvrp, 1180 user_dvrp_coltab, user_header, user_init_grid, 1181 user_init_plant_canopy, user_parin, user_read_restart_data, 1182 user_spectra, write_var_list 1183 </P> 1184 </TD> 1185 </TR> 1186 <TR> 1187 <TD WIDTH=37> 1188 <P><BR> 1189 </P> 1190 </TD> 1191 <TD WIDTH=56> 1192 <P><BR> 1193 </P> 1194 </TD> 1195 <TD WIDTH=68> 1196 <P><BR> 1197 </P> 1198 </TD> 1199 <TD WIDTH=62> 1200 <P><BR> 1201 </P> 1202 </TD> 1203 <TD WIDTH=36> 1204 <P>B</P> 1205 </TD> 1206 <TD WIDTH=518> 1207 <P>Bugfix: Initial hydrostatic pressure profile in case of ocean 1208 runs is now calculated in 5 iteration steps. (<FONT FACE="Courier New, Courier, monospace">init_ocean</FONT>)<BR><BR>Bugfix: 1209 wrong sign in buoyancy production of ocean part in case of not 1210 using the reference density (only in 3D routine <FONT FACE="Courier New, Courier, monospace">production_e</FONT>). 1211 (<FONT FACE="Courier New, Courier, monospace">production_e</FONT>)<BR><BR>Bugfix: 1212 output of averaged 2d/3d quantities requires that an avaraging 1213 interval has been set, respective error message is included. 1214 (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>Bugfix: 1215 Output on unit 14 only if requested by <FONT FACE="Courier New, Courier, monospace">write_binary</FONT>. 1216 (<FONT FACE="Courier New, Courier, monospace">user_last_actions</FONT>)<BR><BR>Bugfix 1217 to avoid zero division by <FONT FACE="Courier New, Courier, monospace">km_neutral</FONT>. 1218 (<FONT FACE="Courier New, Courier, monospace">production_e</FONT>)<BR><BR>Bugfix 1219 for extended NetCDF files: In order to avoid 'data mode' errors if 1220 updated attributes are larger than their original size, 1221 <FONT FACE="Courier New, Courier, monospace">NF90_PUT_ATT</FONT> 1222 is called in 'define mode' enclosed by <FONT FACE="Courier New, Courier, monospace">NF90_REDEF</FONT> 1223 and <FONT FACE="Courier New, Courier, monospace">NF90_ENDDEF</FONT> 1224 calls. This implies a possible performance loss; an alternative 1225 strategy would be to ensure equal attribute size in a job chain. 1226 (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Bugfix: 1227 correction of initial volume flow for non-flat topography. 1228 (<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Bugfix: 1229 zero initialization of arrays within buildings for '<I>cyclic_fill</I>'. 1230 (<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Bugfix: 1231 <FONT FACE="Courier New, Courier, monospace">to_be_resorted</FONT> 1232 => <FONT FACE="Courier New, Courier, monospace">s_av</FONT> for 1233 time-averaged scalars. (<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>, 1234 <FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>)<BR><BR>Bugfix: 1235 avoid that <FONT FACE="Courier New, Courier, monospace">ngp_2dh_s_inner</FONT> 1236 becomes zero. (<FONT FACE="Courier New, Courier, monospace">init_3_model</FONT>)<BR><BR>Typographical 1237 error: unit of wpt in dots_unit. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Bugfix: 1238 error in check, if particles moved further than one subdomain 1239 length. This check must not be applied for newly released 1240 particles. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix: 1241 several tail counters are initialized, <FONT FACE="Courier New, Courier, monospace">particle_tail_coordinates</FONT> 1242 is only written to file if its third index is > 0, arrays for 1243 tails are allocated with a minimum size of 10 tails if there is no 1244 tail initially. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>, 1245 <FONT FACE="Courier New, Courier, monospace">init_particles</FONT>)<BR><BR>Bugfix: 1246 pressure included for profile output. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>Bugfix: 1247 Type of <FONT FACE="Courier New, Courier, monospace">count</FONT> 1248 and <FONT FACE="Courier New, Courier, monospace">count_rate</FONT> 1249 changed to default <FONT FACE="Courier New, Courier, monospace">INTEGER</FONT> 1250 on NEC machines. (<FONT FACE="Courier New, Courier, monospace">cpu_log</FONT>)<BR><BR>Bugfix: 1251 output of particle time series only if particle advection is 1252 switched on. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)<BR><BR>Bugfix: 1253 qsws was calculated in case of <FONT FACE="Courier New, Courier, monospace">constant 1254 heatflux</FONT> = <FONT FACE="Courier New, Courier, monospace">.FALSE.</FONT>. 1255 (<FONT FACE="Courier New, Courier, monospace">prandtl_fluxes</FONT>)<BR><BR>Bugfix: 1256 averaging along z is not allowed for 2d quantities (e.g. u* and 1257 z0). (<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>)<BR><BR>Typographical 1258 errors. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>If 1259 the inversion height calculated by the prerun is zero, 1260 inflow_damping_height must be explicitly specified. 1261 (<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Small 1262 bugfix concerning 3d 64bit netcdf output format. (<FONT FACE="Courier New, Courier, monospace">header</FONT>)<BR><BR>Bugfix: 1263 <FONT FACE="Courier New, Courier, monospace">dt_fixed</FONT> 1264 removed from the restart file, because otherwise, no change from a 1265 fixed to a variable timestep would be possible in restart runs. 1266 (<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>, 1267 <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Bugfix: 1268 initial setting of <FONT FACE="Courier New, Courier, monospace">time_coupling</FONT> 1269 in coupled restart runs. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)</P> 1270 </TD> 1271 <TD WIDTH=393> 1272 <P>advec_particles, check_parameters, cpu_log, data_output_2d, 1273 data_output_3d, header, init_3d_model, init_particles, init_ocean, 1274 modules, netcdf, prandtl_fluxes, production_e, read_var_list, 1275 time_integration, user_last_actions, write_var_list</P> 1276 </TD> 1277 </TR> 1278 <TR> 1279 <TD WIDTH=37> 1280 <P>02/02/09</P> 1281 </TD> 1282 <TD WIDTH=56> 1283 <P>SR</P> 1284 </TD> 1285 <TD WIDTH=68> 1286 <P>228</P> 1287 </TD> 1288 <TD WIDTH=62> 1289 <P>3.6</P> 1290 </TD> 1291 <TD WIDTH=36> 1292 <P>N</P> 1293 </TD> 1294 <TD WIDTH=518> 1295 <P>This release contains further additions, changes, and bugfixes 1296 for the SGI-ICE system, as well as important changes like the 1297 splitting of the user-interface into single files, a complete 1298 revision of the pre-compiling mechanism allowing to use different 1299 make-depositories simultaneously, and a revision of the 1300 reading-mechanism from restart files, which has no more 1301 restrictions in case that the previous and current run have 1302 different domain/subdomain sizes. A new handling of all kind of 1303 output messages is introduced with this release and will be 1304 applied to all existing messages within the next releases.<BR><BR><B>New 1305 features are:</B><BR><BR>Restart runs on SGI-ICE are working. 1306 (mrun)<BR>2d-decomposition is default on SGI-ICE systems. 1307 (init_pegrid)<BR><BR>Ocean-atmosphere coupling realized with 1308 MPI-1. mrun adjusted for this case (-Y option). Check that PALM is 1309 called with <FONT FACE="Courier New, Courier, monospace">mrun</FONT>-option 1310 "<I>-K parallel</I>" for coupling. Adjustments in <FONT FACE="Courier New, Courier, monospace">mrun</FONT>, 1311 <FONT FACE="Courier New, Courier, monospace">mbuild</FONT>, and 1312 <FONT FACE="Courier New, Courier, monospace">subjob</FONT> for 1313 lcxt4.<BR><BR>DVRP arguments changed to single precision, mode 1314 pathlines added.<BR><BR>User can add additional routines in files 1315 <FONT FACE="Courier New, Courier, monospace">user_additional_routines</FONT>.<BR><BR>User 1316 can check user parameters and deduce further quantities in 1317 <FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT></P> 1318 </TD> 1319 <TD WIDTH=393> 1320 <P>check_for_restart, check_parameters, data_output_dvrp, 1321 init_dvrp, init_pegrid, local_stop, modules, package_parin, palm, 1322 surface_coupler, timestep<BR><BR>Makefile, mbuild, mrun, 1323 subjob<BR><BR><B>new:</B><BR>init_coupling, 1324 user_additional_routines, user_check_parameters</P> 1325 </TD> 1326 </TR> 1327 <TR> 1328 <TD WIDTH=37> 1329 <P><BR> 1330 </P> 1331 </TD> 1332 <TD WIDTH=56> 1333 <P><BR> 1334 </P> 1335 </TD> 1336 <TD WIDTH=68> 1337 <P><BR> 1338 </P> 1339 </TD> 1340 <TD WIDTH=62> 1341 <P><BR> 1342 </P> 1343 </TD> 1344 <TD WIDTH=36> 1345 <P>C</P> 1346 </TD> 1347 <TD WIDTH=518> 1348 <P>User interface has been split into single files.<BR><BR>Type of 1349 variables <FONT FACE="Courier New, Courier, monospace">count</FONT> 1350 and <FONT FACE="Courier New, Courier, monospace">count_rate</FONT> 1351 changed to INTEGER(8) in order to avoid "out of range" 1352 problems, which result in measured negative time intervals. 1353 (cpu_log, local_tremain, local_tremain_ini)<BR><BR>Reading 1354 mechanism from restart files completely revised. The 1355 subdomain/total domain size is now allowed to vary arbitrarily 1356 between the current and previous run. (read_var_list, 1357 read_3d_binary, user_read_restart_data)<BR><BR>Precompilation 1358 mechanism (<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>) 1359 completely revised: the source-tarfile remains in the source 1360 directory (<FONT FACE="Courier New, Courier, monospace">trunk/SOURCE</FONT>). 1361 One depository per block (given in the config-file) is created. 1362 Always all files from the source directory are copied to the 1363 respective depository. No additional file checks are done any more 1364 (mrun version 2.1). The depository name used contains the 1365 conditions given by <FONT FACE="Courier New, Courier, monospace">mrun</FONT>-option 1366 "<FONT FACE="Courier New, Courier, monospace">-K</FONT>". 1367 (mbuild, mrun)<BR><BR>Output messages (including required stop of 1368 execution) can now be handled with the new subroutine <FONT FACE="Courier New, Courier, monospace">message</FONT>. 1369 All output messages will be replaced by this routine step by step 1370 within the next revisions.<BR><BR>Neumann boundary condition at 1371 <FONT FACE="Courier New, Courier, monospace">k=nzb</FONT> is 1372 explicitly set for better reading, although this has been already 1373 done in boundary_conds. (advec_s_bc)<BR><BR>Origin of the 1374 xy-coordinate system shifted from the center of the first grid 1375 cell (indices <FONT FACE="Courier New, Courier, monospace">i=0</FONT>, 1376 <FONT FACE="Courier New, Courier, monospace">j=0</FONT>) to the 1377 south-left corner of this cell. (netcdf) Topography definition 1378 according to new user parameter <FONT FACE="Courier New, Courier, monospace">topography_grid_convention</FONT>. 1379 (init_grid, modules, user_header, user_init_grid, user_parin)</P> 1380 </TD> 1381 <TD WIDTH=393> 1382 <P>advec_s_bc, check_parameters, cpu_log, init_grid, local_stop, 1383 local_tremain, local_tremain_ini, modules, netcdf, read_3d_binary, 1384 read_var_list, user_read_restart_data<BR><BR>Makefile, mbuild, 1385 mrun<BR><BR><B>removed:</B><BR>user_interface<BR><BR><B>new:</B><BR>message, 1386 user_3d_data_averaging, user_actions, user_advec_particles, 1387 user_check_data_output, user_check_data_output_pr, 1388 user_data_output_2d, user_data_output_3d, user_data_output_dvrp, 1389 user_define_netcdf_grid, user_dvrp_coltab, user_header, 1390 user_init_3d_model, user_init, user_init_grid, 1391 user_init_particles, user_init_plant_canopy, user_last_actions, 1392 user_parin, user_parin, user_particle_attributes, 1393 user_read_restart_data, user_spectra, user_statistics</P> 1394 </TD> 1395 </TR> 1396 <TR> 1397 <TD WIDTH=37> 1398 <P><BR> 1399 </P> 1400 </TD> 1401 <TD WIDTH=56> 1402 <P><BR> 1403 </P> 1404 </TD> 1405 <TD WIDTH=68> 1406 <P><BR> 1407 </P> 1408 </TD> 1409 <TD WIDTH=62> 1410 <P><BR> 1411 </P> 1412 </TD> 1413 <TD WIDTH=36> 1414 <P>B</P> 1415 </TD> 1416 <TD WIDTH=518> 1417 <P>Bugfix: array <FONT FACE="Courier New, Courier, monospace">d</FONT> 1418 is reallocated in case that multigrid is used. 1419 (calc_spectra)<BR><BR>Bugfixes for nonparallel execution. 1420 (check_for_restart, cpu_statistics, 1421 inflow_turbulence, timestep)<BR><BR>Size of <FONT FACE="Courier New, Courier, monospace">pf3d 1422 </FONT>adjusted to the required output size (1 gridpoint less, 1423 along all three dimensions), because output of a subset of the 1424 data (<FONT FACE="Courier New, Courier, monospace">pf3d(nxa:nxe...)</FONT>) 1425 in the NF90_PUT_VAR statement caused segmentation fault with the 1426 INTEL compiler. (combine_plot_fields)<BR><BR>Bugfix: error in <FONT FACE="Courier New, Courier, monospace">zu</FONT> 1427 index in case of <FONT FACE="Courier New, Courier, monospace">section_xy=-1</FONT>. 1428 (header)<BR><BR>Inconsistency removed: as the thermal 1429 stratification is not taken into account for the evaluation of the 1430 wall fluxes at vertical walls, the eddy viscosity <FONT FACE="Courier New, Courier, monospace">km</FONT> 1431 must not be used for the evaluation of the velocity gradients 1432 <FONT FACE="Courier New, Courier, monospace">dudy</FONT>, <FONT FACE="Courier New, Courier, monospace">dwdy</FONT>, 1433 <FONT FACE="Courier New, Courier, monospace">dvdx</FONT> and <FONT FACE="Courier New, Courier, monospace">dwdx</FONT>. 1434 (production_e)<BR><BR>Bugfix in calculating <FONT FACE="Courier New, Courier, monospace">k</FONT> 1435 index in case of oceans runs. (sort_particles)<BR><BR>Bugfix: no 1436 output of particle concentration and radius unless particles have 1437 been started. (data_output_2d)<BR><BR>Bugfix: reading of 1438 <FONT FACE="Courier New, Courier, monospace">spectrum_x|y</FONT> 1439 from restart files ignored if total numbers of grid points do not 1440 match. (read_3d_binary)<BR><BR>Bugfix: abort in case that absolute 1441 temperature is below zero. (init_cloud_physics)</P> 1442 </TD> 1443 <TD WIDTH=393> 1444 <P>advec_particles, calc_spectra, check_for_restart, 1445 cpu_statistics, data_output_2d, header, inflow_turbulence, 1446 init_cloud_physics, production_e, read_3d_binary, 1447 timestep<BR><BR>combine_plot_fields</P> 1448 </TD> 1449 </TR> 1450 </TABLE> 1451 <P><BR> <BR> 1452 </P> 1453 <H2><A NAME="Kapitel2.0"></A>2.0 How to change the source code 1454 and how to document modifications</H2> 1455 <P>Currently (Sep 23rd, 2009), only selected users are allowed to 1456 commit changes to the repository. Rules given below are preliminary, 1457 until we have switched to the "trac"-System.</P> 1458 <OL> 1459 <LI><P>Change source code in your current working copy. Document 1460 changes in the respective file headers unter "<FONT FACE="Courier New, Courier, monospace">Current 1461 revisions:</FONT>". Additionally, document all changes in a 1462 local file (e.g. ~/palm/current_version/CURRENT_MODIFICATIONS), 1463 including the files that have been changed. Classify changes in 1464 three cases, new (N), changed (C), and bugfix (B). <B>Try to be as 1465 short and as precise as possible in describing the changes!</B></P> 1466 <LI><P>Test the changed version, unless it works sufficiently.</P> 1467 <LI><P>Commit the changes to the repository<BR><BR> <FONT FACE="Courier New, Courier, monospace">svn 1468 commit -m "message string" trunk<BR></FONT><BR>where 1469 "<FONT FACE="Courier New, Courier, monospace">message string</FONT>" 1470 is a short, <B>meaningful</B> summary of the 1471 changes.<BR><BR>Alternatively, in case that you have made quite a 1472 lot of changes, you can also give the contents of your file 1473 CURRENT_MODIFICATIONS as the log message:<BR><BR> <FONT FACE="Courier New, Courier, monospace">svn 1474 commit -F CURRENT_MODIFICATIONS trunk</FONT></P> 1475 <LI><P>Enter the changes into the technical documentation (under 1476 <FONT FACE="Courier New, Courier, monospace">.../trunk/DOC/tec/technical_documentation.html</FONT>).</P> 1477 <LI><P>Move the change comments in the file headers from "Current 1478 revisions:" to "Former revisions:". Set the current 1479 svn id in front of that.<BR><BR><B>Example:</B><BR><BR><B>before 1480 move:</B><BR><BR><FONT FACE="Courier New, Courier, monospace">! 1481 Current revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1482 -----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1483 </FONT><FONT FACE="Courier New, Courier, monospace"><B>new dummy 1484 argument abcd</B></FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1485 Former revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1486 -----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1487 ￜId: init_3d_model.f90 </FONT><FONT COLOR="#3366ff"><FONT FACE="Courier New, Courier, monospace"><B>425 1488 2010-02-06 13:37:48Z raasch</B></FONT></FONT><FONT FACE="Courier New, Courier, monospace"> 1489 ￜ</FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1490 407 2009-12-01 15:01:15Z maronga</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1491 var_ts is replaced by dots_max </FONT><BR><BR><B>after move:</B><BR><BR><FONT FACE="Courier New, Courier, monospace">! 1492 Current revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1493 -----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1494 </FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1495 Former revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1496 -----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1497 ￜId: init_3d_model.f90 425 2010-02-06 13:37:48Z raasch</FONT> 1498 <FONT FACE="Courier New, Courier, monospace">ￜ<BR>!</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1499 </FONT><FONT COLOR="#3366ff"><FONT FACE="Courier New, Courier, monospace"><B>425 1500 2010-02-06 13:37:48Z raasch</B></FONT></FONT><FONT FACE="Courier New, Courier, monospace"><BR>! 1501 </FONT><FONT FACE="Courier New, Courier, monospace"><B>new dummy 1502 argument abcd</B></FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1503 407 2009-12-01 15:01:15Z maronga</FONT><BR><FONT FACE="Courier New, Courier, monospace">! 1504 var_ts is replaced by dots_max<BR><BR></FONT><FONT FACE="Times New Roman, Times, serif">Note 1505 that the "</FONT><FONT FACE="Courier New, Courier, monospace">ￜ</FONT><FONT FACE="Times New Roman, Times, serif">" 1506 in this example should read "$", but "$" cannot 1507 be used here, because otherwise svn would replace these entries 1508 after every change to this technical documentation.</FONT></P> 1509 <LI><P>Commit the changes in the technical documentation and the 1510 file headers:<BR><BR> <FONT FACE="Courier New, Courier, monospace">svn 1511 commit -m "last commit documented" trunk</FONT><BR><BR><BR> 1512 </P> 1513 </OL> 1514 <H2><A NAME="Kapitel3.0"></A>3.0 Description of selected parts 1515 of the model source code</H2> 1516 <P>This section gives links to existing descriptions about special 1436 1517 parts of the PALM code, e.g. special numerical methods that are used 1437 1518 (including mathematical background). Documents are stored in single 1438 1519 files with different formats. Some are in German (sorry for the 1439 inconvenience). 1440 < br> 1441 < /p><ul> <li> <a name="UPS"></a>upstream-spline1442 advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a> 1443 , only in German)</li> <li> <a name="Cloud_physics"></a>cloud 1444 physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a> 1445 )</li> 1446 <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br> 1447 </li>1448 <li>Runge-Kutta 1449 time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>1450 , only in German)</li> 1451 1452 </ul><br>1453 1454 <br> 1455 <br> 1456 < br> 1457 < br> 1458 < br> 1459 < br> 1460 < br> 1461 </ body></html>1520 inconvenience). <BR> 1521 </P> 1522 <UL> 1523 <LI><P STYLE="margin-bottom: 0in"><A NAME="UPS"></A>upstream-spline 1524 advection scheme ( <A HREF="methods/upstream_spline/ups.pdf">.pdf</A> 1525 , only in German) 1526 </P> 1527 <LI><P STYLE="margin-bottom: 0in"><A NAME="Cloud_physics"></A>cloud 1528 physics module ( <A HREF="methods/cloud_physics/cloud_physics.pdf">.pdf</A> 1529 ) 1530 </P> 1531 <LI><P STYLE="margin-bottom: 0in"><A NAME="Bitkompression"></A>data 1532 compression with <A HREF="methods/bit_compression/bit_compression.html">bit 1533 shifting method</A> (only in German)</P> 1534 <LI><P>Runge-Kutta time integration scheme ( <A HREF="methods/runge_kutta/runge_kutta.pdf">.pdf</A> 1535 , only in German) 1536 </P> 1537 </UL> 1538 <P><BR> <BR> <BR> <BR> <BR> <BR> 1539 <BR> <BR> 1540 </P> 1541 </BODY> 1542 </HTML>
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