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2 | "author": "Kadasch and S\u00fchring", | 2 | "author": "Kadasch and S\u00fchring", | ||
3 | "author_email": "suehring@muk.uni-hannover.de", | 3 | "author_email": "suehring@muk.uni-hannover.de", | ||
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5 | "doi": "10.25835/0084787", | 5 | "doi": "10.25835/0084787", | ||
6 | "doi_date_published": "2020-11-05", | 6 | "doi_date_published": "2020-11-05", | ||
7 | "doi_publisher": "LUIS", | 7 | "doi_publisher": "LUIS", | ||
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15 | "license_title": "CC0-1.0", | 15 | "license_title": "CC0-1.0", | ||
16 | "maintainer": "Matthias S\u00fchring", | 16 | "maintainer": "Matthias S\u00fchring", | ||
17 | "maintainer_email": "suehring@muk.uni-hannover.de", | 17 | "maintainer_email": "suehring@muk.uni-hannover.de", | ||
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22 | "notes": "Source code, setup files and analysis scripts", | 22 | "notes": "Source code, setup files and analysis scripts", | ||
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29 | \r\n\r\nhttps://www.muk.uni-hannover.de/\r\n\r\n", | 29 | \r\n\r\nhttps://www.muk.uni-hannover.de/\r\n\r\n", | ||
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77 | "description": "# Mesoscale nesting interface of the PALM model | 49 | "description": "# Mesoscale nesting interface of the PALM model | ||
78 | system 6.0 \u2014 Simulation setups\r\n\r\nIn this document, we | 50 | system 6.0 \u2014 Simulation setups\r\n\r\nIn this document, we | ||
79 | describe how to produce the simulation results and analyses documented | 51 | describe how to produce the simulation results and analyses documented | ||
80 | in our article \"Mesoscale nesting interface of the PALM model system | 52 | in our article \"Mesoscale nesting interface of the PALM model system | ||
81 | 6.0\" submitted to the journal Geoscientific Model Development. In | 53 | 6.0\" submitted to the journal Geoscientific Model Development. In | ||
82 | particular, we explain how we configured the model, processed the | 54 | particular, we explain how we configured the model, processed the | ||
83 | mesoscale input, and produced the figures for the publication. | 55 | mesoscale input, and produced the figures for the publication. | ||
84 | Everything that is needed to run PALM and reproduce the simulations | 56 | Everything that is needed to run PALM and reproduce the simulations | ||
85 | documented in our manuscript is contained in this package. | 57 | documented in our manuscript is contained in this package. | ||
86 | \r\n\r\nEckhard Kadasch and Matthias S\u00fchring, November | 58 | \r\n\r\nEckhard Kadasch and Matthias S\u00fchring, November | ||
87 | 2020\r\n\r\n\r\n## 1 Package contents\r\n\r\nFor the simulations, we | 59 | 2020\r\n\r\n\r\n## 1 Package contents\r\n\r\nFor the simulations, we | ||
88 | used revision 4564 of the PALM model system 6.0, which we included in | 60 | used revision 4564 of the PALM model system 6.0, which we included in | ||
89 | this package. To reproduce the simulations please download\r\n\r\n- | 61 | this package. To reproduce the simulations please download\r\n\r\n- | ||
90 | PALM source code files (trunk.zip),\r\n- Analysis scripts | 62 | PALM source code files (trunk.zip),\r\n- Analysis scripts | ||
91 | (analysis_scripts.zip), and\r\n- Job configurations and dynamic driver | 63 | (analysis_scripts.zip), and\r\n- Job configurations and dynamic driver | ||
92 | (jobs.zip).\r\n\r\nAfter extracting them at a location of your choice | 64 | (jobs.zip).\r\n\r\nAfter extracting them at a location of your choice | ||
93 | using\r\n\r\n unzip trunk.zip\r\n unzip analysis_scripts.zip\r\n | 65 | using\r\n\r\n unzip trunk.zip\r\n unzip analysis_scripts.zip\r\n | ||
94 | unzip jobs.zip -d ./trunk\r\n\r\nyou will find the following | 66 | unzip jobs.zip -d ./trunk\r\n\r\nyou will find the following | ||
95 | contents:\r\n\r\n ./analysis_scripts/ \u2014 post-processing and | 67 | contents:\r\n\r\n ./analysis_scripts/ \u2014 post-processing and | ||
96 | visualization scripts\r\n ./trunk/\r\n JOBS/\r\n | 68 | visualization scripts\r\n ./trunk/\r\n JOBS/\r\n | ||
97 | setup_LOD_1/ \u2014 PALM job directory for simulation with LOD-1 | 69 | setup_LOD_1/ \u2014 PALM job directory for simulation with LOD-1 | ||
98 | boundary conditions\r\n setup_LOD_1/USERCODE/ \u2013 PALM | 70 | boundary conditions\r\n setup_LOD_1/USERCODE/ \u2013 PALM | ||
99 | usercode changes to enforce LOD-1 boundary conditions\r\n | 71 | usercode changes to enforce LOD-1 boundary conditions\r\n | ||
100 | setup_LOD_2/INPUT/ \u2014 PALM job directory for simulation with LOD-2 | 72 | setup_LOD_2/INPUT/ \u2014 PALM job directory for simulation with LOD-2 | ||
101 | boundary conditions\r\n SOURCE/ \u2014 PALM model code | 73 | boundary conditions\r\n SOURCE/ \u2014 PALM model code | ||
102 | files\r\n UTIL/\r\n inifor/ \u2014 INIFOR | 74 | files\r\n UTIL/\r\n inifor/ \u2014 INIFOR | ||
103 | preprocessor code files\r\n ...\r\n ...\r\n\r\nYou | 75 | preprocessor code files\r\n ...\r\n ...\r\n\r\nYou | ||
104 | can find detailed instructions about the model installation in the | 76 | can find detailed instructions about the model installation in the | ||
105 | [PALM installation | 77 | [PALM installation | ||
106 | https://palm.muk.uni-hannover.de/trac/wiki/doc/install).\r\n\r\n\r\n## | 78 | https://palm.muk.uni-hannover.de/trac/wiki/doc/install).\r\n\r\n\r\n## | ||
107 | 2 Model setup and input data generation\r\n\r\nThis package includes | 79 | 2 Model setup and input data generation\r\n\r\nThis package includes | ||
108 | the PALM and INIFOR setups used for our simulation runs under | 80 | the PALM and INIFOR setups used for our simulation runs under | ||
109 | `trunk/JOBS/setup_LOD_1/INPUT` and `trunk/JOBS/setup_LOD_2/INPUT`. | 81 | `trunk/JOBS/setup_LOD_1/INPUT` and `trunk/JOBS/setup_LOD_2/INPUT`. | ||
110 | These folders contain, in particular, the two kinds of Namelist files, | 82 | These folders contain, in particular, the two kinds of Namelist files, | ||
111 | namely `setup_LOD_x_p3d` and `setup_LOD_x_inifor`, which control PALM | 83 | namely `setup_LOD_x_p3d` and `setup_LOD_x_inifor`, which control PALM | ||
112 | and INIFOR, respectively. To reproduce the simulations, you need to | 84 | and INIFOR, respectively. To reproduce the simulations, you need to | ||
113 | carry out the following steps:\r\n\r\n1. Generate the dynamic driver | 85 | carry out the following steps:\r\n\r\n1. Generate the dynamic driver | ||
114 | file (already included) using INIFOR and\r\n2. Run PALM using the | 86 | file (already included) using INIFOR and\r\n2. Run PALM using the | ||
115 | respective job configurations\r\n\r\n\r\n### 2.1 Generating dynamic | 87 | respective job configurations\r\n\r\n\r\n### 2.1 Generating dynamic | ||
116 | drivers using INIFOR\r\n\r\nINIFOR computes dynamic boundary | 88 | drivers using INIFOR\r\n\r\nINIFOR computes dynamic boundary | ||
117 | conditions from the output of the COSMO model. In the present case, we | 89 | conditions from the output of the COSMO model. In the present case, we | ||
118 | used COSMO analysis data by the German Meteorological Service | 90 | used COSMO analysis data by the German Meteorological Service | ||
119 | (Deutscher Wetterdienst, DWD), which we obtained through DWD's [Pamore | 91 | (Deutscher Wetterdienst, DWD), which we obtained through DWD's [Pamore | ||
120 | interface](https://www.dwd.de/DE/leistungen/pamore/pamore.html) | 92 | interface](https://www.dwd.de/DE/leistungen/pamore/pamore.html) | ||
121 | (registration required). With this package, we provide both the | 93 | (registration required). With this package, we provide both the | ||
122 | generated dynamic driver (under | 94 | generated dynamic driver (under | ||
123 | `/trunk/JOBS/setup_LOD_2/INPUT/setup_LOD_2_dynamic`) as well as the | 95 | `/trunk/JOBS/setup_LOD_2/INPUT/setup_LOD_2_dynamic`) as well as the | ||
124 | steps to produce them. Hence, you may reproduce the simulations | 96 | steps to produce them. Hence, you may reproduce the simulations | ||
125 | without obtaining the analysis data first. For generating the dynamic | 97 | without obtaining the analysis data first. For generating the dynamic | ||
126 | driver, the COSMO data has to be converted into the netCDF format as | 98 | driver, the COSMO data has to be converted into the netCDF format as | ||
127 | described in the [INIFOR | 99 | described in the [INIFOR | ||
128 | /trac/wiki/doc/app/iofiles/inifor#RequirednetCDFvariables).\r\n\r\nFor | 100 | /trac/wiki/doc/app/iofiles/inifor#RequirednetCDFvariables).\r\n\r\nFor | ||
129 | the manuscript, we carried out a simulation with spatially | 101 | the manuscript, we carried out a simulation with spatially | ||
130 | heterogeneous boundary conditions, here referred to as `setup_LOD_2`, | 102 | heterogeneous boundary conditions, here referred to as `setup_LOD_2`, | ||
131 | and a reference simulation with spatially averaged one-dimensional | 103 | and a reference simulation with spatially averaged one-dimensional | ||
132 | boundary conditions, which we refer to as `setup_LOD_1`. Here, LOD | 104 | boundary conditions, which we refer to as `setup_LOD_1`. Here, LOD | ||
133 | stands for the level of detail. For the simulation with LOD-1 boundary | 105 | stands for the level of detail. For the simulation with LOD-1 boundary | ||
134 | conditions, we carried out the averaging online within the PALM code. | 106 | conditions, we carried out the averaging online within the PALM code. | ||
135 | This functionality is contained within the user code files in the | 107 | This functionality is contained within the user code files in the | ||
136 | input directory `setup_LOD_1/USERCODE/`. (Meanwhile, we also added | 108 | input directory `setup_LOD_1/USERCODE/`. (Meanwhile, we also added | ||
137 | this averaging feature directly in INIFOR, which is available since | 109 | this averaging feature directly in INIFOR, which is available since | ||
138 | PALM revision r4606.)\r\n\r\nTo use them for both simulations, link | 110 | PALM revision r4606.)\r\n\r\nTo use them for both simulations, link | ||
139 | the LOD-2 driver to the LOD-1 setup:\r\n\r\n ln -s {path | 111 | the LOD-2 driver to the LOD-1 setup:\r\n\r\n ln -s {path | ||
140 | to}/trunk/JOBS/setup_LOD_2/INPUT/setup_LOD_2_dynamic {path | 112 | to}/trunk/JOBS/setup_LOD_2/INPUT/setup_LOD_2_dynamic {path | ||
141 | to}/trunk/JOBS/setup_LOD_1/INPUT/setup_LOD_1_dynamic\r\n\r\nWe | 113 | to}/trunk/JOBS/setup_LOD_1/INPUT/setup_LOD_1_dynamic\r\n\r\nWe | ||
142 | generated the dynamic driver for both the LOD-1 and LOD-2 setup | 114 | generated the dynamic driver for both the LOD-1 and LOD-2 setup | ||
143 | using:\r\n\r\n inifor --path path/to/dataset --date 20160507 | 115 | using:\r\n\r\n inifor --path path/to/dataset --date 20160507 | ||
144 | --hhl-file path/to/dataset/hhl.nc -o GMD_driver --init-mode profile | 116 | --hhl-file path/to/dataset/hhl.nc -o GMD_driver --init-mode profile | ||
145 | --elevation 50.0 --namelist | 117 | --elevation 50.0 --namelist | ||
146 | trunk/JOBS/setup_LOD_2/INPUT/setup_LOD_2_inifor\r\n\r\nNote that the | 118 | trunk/JOBS/setup_LOD_2/INPUT/setup_LOD_2_inifor\r\n\r\nNote that the | ||
147 | final driver files need to follow the naming convention `{job | 119 | final driver files need to follow the naming convention `{job | ||
148 | name}_dynamic` for PALM to use the correct driver.\r\n\r\nYou can find | 120 | name}_dynamic` for PALM to use the correct driver.\r\n\r\nYou can find | ||
149 | a detailed description of all available command-line arguments in the | 121 | a detailed description of all available command-line arguments in the | ||
150 | [INIFOR | 122 | [INIFOR | ||
151 | .muk.uni-hannover.de/trac/wiki/doc/app/iofiles/inifor).\r\n\r\n\r\n### | 123 | .muk.uni-hannover.de/trac/wiki/doc/app/iofiles/inifor).\r\n\r\n\r\n### | ||
152 | 2.2 Running PALM\r\n\r\nAfter you generated the dynamic driver(s) and | 124 | 2.2 Running PALM\r\n\r\nAfter you generated the dynamic driver(s) and | ||
153 | copied them into the respective job directories, you may proceed with | 125 | copied them into the respective job directories, you may proceed with | ||
154 | starting the PALM simulation runs using the `palmrun` command:\r\n\r\n | 126 | starting the PALM simulation runs using the `palmrun` command:\r\n\r\n | ||
155 | palmrun -c {host_identifier} -r {run_identifier} ...\r\n\r\nwhere | 127 | palmrun -c {host_identifier} -r {run_identifier} ...\r\n\r\nwhere | ||
156 | `{host_identifier}` selects the configuration for the simulation | 128 | `{host_identifier}` selects the configuration for the simulation | ||
157 | computer and `{run_identifier}` refers to the particular mode setup, | 129 | computer and `{run_identifier}` refers to the particular mode setup, | ||
158 | in our case either `setup_LOD_1` or `setup_LOD_2`.\r\n\r\nYou can | 130 | in our case either `setup_LOD_1` or `setup_LOD_2`.\r\n\r\nYou can | ||
159 | learn more about the host and case configuration in the [`palmrun` | 131 | learn more about the host and case configuration in the [`palmrun` | ||
160 | ps://palm.muk.uni-hannover.de/trac/wiki/doc/app/palmrun).\r\n\r\nAfter | 132 | ps://palm.muk.uni-hannover.de/trac/wiki/doc/app/palmrun).\r\n\r\nAfter | ||
161 | the successful run, you will find the simulation results in the output | 133 | the successful run, you will find the simulation results in the output | ||
162 | directory of the respective job, e.g. under | 134 | directory of the respective job, e.g. under | ||
163 | `{path_to_output}/{run_identifier}/OUTPUT/`. \r\n\r\n\r\n## 3 | 135 | `{path_to_output}/{run_identifier}/OUTPUT/`. \r\n\r\n\r\n## 3 | ||
164 | Analyzing and visualizing results\r\n\r\nIn the following, we give an | 136 | Analyzing and visualizing results\r\n\r\nIn the following, we give an | ||
165 | overview of the analysis tools and plotting scripts we used to | 137 | overview of the analysis tools and plotting scripts we used to | ||
166 | visualize the model results. The scripts are written in NCL (NCAR | 138 | visualize the model results. The scripts are written in NCL (NCAR | ||
167 | Command Language, version 6.6.2, 2019, | 139 | Command Language, version 6.6.2, 2019, | ||
168 | [doi:10.5065/D6WD3XH5](http://dx.doi.org/10.5065/D6WD3XH5)) and can be | 140 | [doi:10.5065/D6WD3XH5](http://dx.doi.org/10.5065/D6WD3XH5)) and can be | ||
169 | found under `analysis_scripts/`.\r\n\r\n- Figure 7: `Fig_7.ncl` - | 141 | found under `analysis_scripts/`.\r\n\r\n- Figure 7: `Fig_7.ncl` - | ||
170 | dynamic input file (`setup_LOD_1`)\r\n- Figure 8: `Fig_8.ncl` - PALM | 142 | dynamic input file (`setup_LOD_1`)\r\n- Figure 8: `Fig_8.ncl` - PALM | ||
171 | 3D output for averaged quantities (`setup_LOD_1`)\r\n- Figure 9: | 143 | 3D output for averaged quantities (`setup_LOD_1`)\r\n- Figure 9: | ||
172 | `Fig_9.ncl` - PALM 3D output for instantaneous quantities | 144 | `Fig_9.ncl` - PALM 3D output for instantaneous quantities | ||
173 | (`setup_LOD_1`)\r\n- Figure 10: `Fig_10.ncl` - PALM time series file | 145 | (`setup_LOD_1`)\r\n- Figure 10: `Fig_10.ncl` - PALM time series file | ||
174 | as well as COSMO output files for radiation\r\n- Figure 11: | 146 | as well as COSMO output files for radiation\r\n- Figure 11: | ||
175 | `Fig_11.ncl` - PALM 3D output for instantaneous quantities | 147 | `Fig_11.ncl` - PALM 3D output for instantaneous quantities | ||
176 | (LOD=1)\r\n- Figure 12: `Fig_12.ncl` - PALM 3D output for | 148 | (LOD=1)\r\n- Figure 12: `Fig_12.ncl` - PALM 3D output for | ||
177 | instantaneous quantities (LOD=1)\r\n- Figure 13: `Fig_13.ncl` - | 149 | instantaneous quantities (LOD=1)\r\n- Figure 13: `Fig_13.ncl` - | ||
178 | dynamic input file (`setup_LOD_1`)\r\n- Figure 14: `Fig_14.ncl` - PALM | 150 | dynamic input file (`setup_LOD_1`)\r\n- Figure 14: `Fig_14.ncl` - PALM | ||
179 | time series file, PALM 2D output for averaged quantities, PALM 3D | 151 | time series file, PALM 2D output for averaged quantities, PALM 3D | ||
180 | output for averaged quantities (`setup_LOD_1`)\r\n- Figure 15: | 152 | output for averaged quantities (`setup_LOD_1`)\r\n- Figure 15: | ||
181 | `Fig_15.ncl` - PALM time series file, PALM 2D output for averaged | 153 | `Fig_15.ncl` - PALM time series file, PALM 2D output for averaged | ||
182 | quantities, PALM 3D output for averaged quantities | 154 | quantities, PALM 3D output for averaged quantities | ||
183 | (`setup_LOD_1`)\r\n- Figure 16: `Fig_16.ncl` - PALM time series file, | 155 | (`setup_LOD_1`)\r\n- Figure 16: `Fig_16.ncl` - PALM time series file, | ||
184 | PALM 2D output for averaged quantities, PALM 3D output for averaged | 156 | PALM 2D output for averaged quantities, PALM 3D output for averaged | ||
185 | quantities (`setup_LOD_1`)\r\n- Figure 17: `Fig_17.ncl` - PALM time | 157 | quantities (`setup_LOD_1`)\r\n- Figure 17: `Fig_17.ncl` - PALM time | ||
186 | series file, PALM 2D output for averaged quantities, PALM 3D output | 158 | series file, PALM 2D output for averaged quantities, PALM 3D output | ||
187 | for averaged quantities (`setup_LOD_1`)\r\n- Figure 18: `Fig_18.ncl` - | 159 | for averaged quantities (`setup_LOD_1`)\r\n- Figure 18: `Fig_18.ncl` - | ||
188 | PALM 3D output for averaged quantities (`setup_LOD_1` + | 160 | PALM 3D output for averaged quantities (`setup_LOD_1` + | ||
189 | `setup_LOD_2`), COSMO output files\r\n- Figure 19: `Fig_19.ncl` - PALM | 161 | `setup_LOD_2`), COSMO output files\r\n- Figure 19: `Fig_19.ncl` - PALM | ||
190 | 3D output for averaged quantities (`setup_LOD_1`), COSMO output | 162 | 3D output for averaged quantities (`setup_LOD_1`), COSMO output | ||
191 | files\r\n- Figure 20: `Fig_20.ncl` - PALM monitoring files for CPU | 163 | files\r\n- Figure 20: `Fig_20.ncl` - PALM monitoring files for CPU | ||
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317 | ], | 282 | ], | ||
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319 | "title": "Supplementary material to 'Mesoscale nesting interface of | 284 | "title": "Supplementary material to 'Mesoscale nesting interface of | ||
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321 | "type": "vdataset", | 286 | "type": "vdataset", | ||
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