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f | 1 | { | f | 1 | { |
2 | "author": "Freese, Jan Philip", | 2 | "author": "Freese, Jan Philip", | ||
3 | "author_email": "", | 3 | "author_email": "", | ||
4 | "creator_user_id": "17755db4-395a-4b3b-ac09-e8e3484ca700", | 4 | "creator_user_id": "17755db4-395a-4b3b-ac09-e8e3484ca700", | ||
5 | "doi": "10.35097/1275", | 5 | "doi": "10.35097/1275", | ||
6 | "doi_date_published": "2023", | 6 | "doi_date_published": "2023", | ||
7 | "doi_publisher": "", | 7 | "doi_publisher": "", | ||
8 | "doi_status": "True", | 8 | "doi_status": "True", | ||
9 | "groups": [], | 9 | "groups": [], | ||
10 | "id": "471c2679-04d4-4cfc-b3d0-69e5e0a25993", | 10 | "id": "471c2679-04d4-4cfc-b3d0-69e5e0a25993", | ||
11 | "isopen": false, | 11 | "isopen": false, | ||
12 | "license_id": "CC BY-NC-SA 4.0 | 12 | "license_id": "CC BY-NC-SA 4.0 | ||
13 | Attribution-NonCommercial-ShareAlike", | 13 | Attribution-NonCommercial-ShareAlike", | ||
14 | "license_title": "CC BY-NC-SA 4.0 | 14 | "license_title": "CC BY-NC-SA 4.0 | ||
15 | Attribution-NonCommercial-ShareAlike", | 15 | Attribution-NonCommercial-ShareAlike", | ||
16 | "metadata_created": "2023-08-04T08:50:25.626092", | 16 | "metadata_created": "2023-08-04T08:50:25.626092", | ||
t | 17 | "metadata_modified": "2023-08-04T09:04:07.652830", | t | 17 | "metadata_modified": "2023-08-04T09:29:01.252759", |
18 | "name": "rdr-doi-10-35097-1275", | 18 | "name": "rdr-doi-10-35097-1275", | ||
19 | "notes": "Abstract: This code has been used for the numerical | 19 | "notes": "Abstract: This code has been used for the numerical | ||
20 | experiments in the thesis \"Numerical homogenization of time-dependent | 20 | experiments in the thesis \"Numerical homogenization of time-dependent | ||
21 | Maxwell's equations with dispersion effects\" by Jan Philip Freese, | 21 | Maxwell's equations with dispersion effects\" by Jan Philip Freese, | ||
22 | see https://www.doi.org/10.5445/IR/1000129214.\r\nTechnicalRemarks: # | 22 | see https://www.doi.org/10.5445/IR/1000129214.\r\nTechnicalRemarks: # | ||
23 | Readme\r\nThis code was used for the numerical experiments of the PhD | 23 | Readme\r\nThis code was used for the numerical experiments of the PhD | ||
24 | thesis \"Numerical homogenization of time-dependent Maxwell's | 24 | thesis \"Numerical homogenization of time-dependent Maxwell's | ||
25 | equations with dispersion effects\" by P. Freese (cf. Section 7.2, | 25 | equations with dispersion effects\" by P. Freese (cf. Section 7.2, | ||
26 | Section 7.3) https://www.doi.org/10.5445/IR/1000129214. \r\nThe | 26 | Section 7.3) https://www.doi.org/10.5445/IR/1000129214. \r\nThe | ||
27 | computations are done in C++ using the Finite Element library | 27 | computations are done in C++ using the Finite Element library | ||
28 | deal.II.\r\n\r\n## Requirements\r\n- In order to run the code you need | 28 | deal.II.\r\n\r\n## Requirements\r\n- In order to run the code you need | ||
29 | **deal.II** (release 9.1.1), cf. https://www.dealii.org/9.1.1\r\n- For | 29 | **deal.II** (release 9.1.1), cf. https://www.dealii.org/9.1.1\r\n- For | ||
30 | the experiments on the macroscopic level (Section 7.3) you need to | 30 | the experiments on the macroscopic level (Section 7.3) you need to | ||
31 | compile deal.II using **Trilinos** (version 12.17) and **p4est** | 31 | compile deal.II using **Trilinos** (version 12.17) and **p4est** | ||
32 | (version 2.2), cf. | 32 | (version 2.2), cf. | ||
33 | https://www.dealii.org/9.1.1/external-libs/trilinos.html and | 33 | https://www.dealii.org/9.1.1/external-libs/trilinos.html and | ||
34 | https://www.dealii.org/9.1.1/external-libs/p4est.html\r\n- To get the | 34 | https://www.dealii.org/9.1.1/external-libs/p4est.html\r\n- To get the | ||
35 | full functionality of the scripts a **Bash** shell has to be used and | 35 | full functionality of the scripts a **Bash** shell has to be used and | ||
36 | at least **cmake** (version 3.13.0) is needed\r\n- For the | 36 | at least **cmake** (version 3.13.0) is needed\r\n- For the | ||
37 | visualization of the data you need **Matlab** (version R2020a Update | 37 | visualization of the data you need **Matlab** (version R2020a Update | ||
38 | 2) and **Paraview** (version 5.8.1-RC1)\r\n\r\n## Structure\r\nThe | 38 | 2) and **Paraview** (version 5.8.1-RC1)\r\n\r\n## Structure\r\nThe | ||
39 | structure is as follows: \r\n\r\n- The folder **executables** contains | 39 | structure is as follows: \r\n\r\n- The folder **executables** contains | ||
40 | Bash scripts for all figures and tables separately. All figures from | 40 | Bash scripts for all figures and tables separately. All figures from | ||
41 | Section 7.2 may be computed using the | 41 | Section 7.2 may be computed using the | ||
42 | `compute_all_micro_figures_and_tables.sh` at ones. Similarly, the | 42 | `compute_all_micro_figures_and_tables.sh` at ones. Similarly, the | ||
43 | figures from Section 7.3 are computed using the | 43 | figures from Section 7.3 are computed using the | ||
44 | `compute_all_macro_figures_and_tables.sh` script. Moreover, the | 44 | `compute_all_macro_figures_and_tables.sh` script. Moreover, the | ||
45 | `distclean.sh` script runs the `deal.II` distclean command in all | 45 | `distclean.sh` script runs the `deal.II` distclean command in all | ||
46 | programs.\r\n- The folder **matlab_plot_files** contains Matlab | 46 | programs.\r\n- The folder **matlab_plot_files** contains Matlab | ||
47 | scripts for the convergence plots and related tables\r\n- The folder | 47 | scripts for the convergence plots and related tables\r\n- The folder | ||
48 | **paraview_plot_files** contains Paraview states to generate the | 48 | **paraview_plot_files** contains Paraview states to generate the | ||
49 | solution plots\r\n- In **programs** the actual source code is stored | 49 | solution plots\r\n- In **programs** the actual source code is stored | ||
50 | within three different programs that are\r\n - | 50 | within three different programs that are\r\n - | ||
51 | **hmm_for_Maxwell_conductivity_memory_variable:** Code that applies | 51 | **hmm_for_Maxwell_conductivity_memory_variable:** Code that applies | ||
52 | the Heterogeneous Multiscale Method combined with the memory variable | 52 | the Heterogeneous Multiscale Method combined with the memory variable | ||
53 | technique as explained in Section 6.2.3\r\n - | 53 | technique as explained in Section 6.2.3\r\n - | ||
54 | **hmm_for_Maxwell_conductivity_recursive_convolution:** Code that | 54 | **hmm_for_Maxwell_conductivity_recursive_convolution:** Code that | ||
55 | applies the Heterogeneous Multiscale Method combined with the | 55 | applies the Heterogeneous Multiscale Method combined with the | ||
56 | recursive convolution technique as explained in Section 6.2.2\r\n - | 56 | recursive convolution technique as explained in Section 6.2.2\r\n - | ||
57 | **microproblem_conductivity:** Code that solves the microscopic cell | 57 | **microproblem_conductivity:** Code that solves the microscopic cell | ||
58 | problems\r\n- In **results** the results of the computations are | 58 | problems\r\n- In **results** the results of the computations are | ||
59 | stored according to the sub structure of the **programs** | 59 | stored according to the sub structure of the **programs** | ||
60 | folder\r\n\r\n\r\n## Howto\r\nIn order to run the program, open a | 60 | folder\r\n\r\n\r\n## Howto\r\nIn order to run the program, open a | ||
61 | terminal session in the folder **executables** and run one of the Bash | 61 | terminal session in the folder **executables** and run one of the Bash | ||
62 | scripts providing at least the additional argument:\r\n\r\n- **Number | 62 | scripts providing at least the additional argument:\r\n\r\n- **Number | ||
63 | of kernels (-n)**: One should usually use one job for each processor | 63 | of kernels (-n)**: One should usually use one job for each processor | ||
64 | core on the machine\r\n\r\nUse a command like\r\n\r\n```bash\r\n | 64 | core on the machine\r\n\r\nUse a command like\r\n\r\n```bash\r\n | ||
65 | bash figure*.sh -n number_of_kernels\r\n```\r\nIt may be mandatory to | 65 | bash figure*.sh -n number_of_kernels\r\n```\r\nIt may be mandatory to | ||
66 | provide the location of your deal.II installation as well. This is | 66 | provide the location of your deal.II installation as well. This is | ||
67 | done by providing another argument:\r\n\r\n- **Path to deal (-D)**: | 67 | done by providing another argument:\r\n\r\n- **Path to deal (-D)**: | ||
68 | Path to the deal.II installation\r\n\r\nUse a command | 68 | Path to the deal.II installation\r\n\r\nUse a command | ||
69 | like\r\n\r\n```bash\r\n bash figure*.sh -n number_of_kernels -D | 69 | like\r\n\r\n```bash\r\n bash figure*.sh -n number_of_kernels -D | ||
70 | path_to_deal\r\n```\r\n\r\nIf you can not execute the Bash scripts, | 70 | path_to_deal\r\n```\r\n\r\nIf you can not execute the Bash scripts, | ||
71 | you have to build the program and copy/edit the config/source files | 71 | you have to build the program and copy/edit the config/source files | ||
72 | yourself. Still, the necessary information is found in the bash | 72 | yourself. Still, the necessary information is found in the bash | ||
73 | scripts, so just use a text editor to open those files and execute the | 73 | scripts, so just use a text editor to open those files and execute the | ||
74 | steps by hand.\r\n\r\n### Example\r\nIf you unpack this code within | 74 | steps by hand.\r\n\r\n### Example\r\nIf you unpack this code within | ||
75 | the **examples** folder of **deal.II** you can simply use the | 75 | the **examples** folder of **deal.II** you can simply use the | ||
76 | following example code to run the Bash script (generating data for | 76 | following example code to run the Bash script (generating data for | ||
77 | Figure 7.2 and Table 7.1 with 4 kernels)\r\n\r\n```bash\r\n bash | 77 | Figure 7.2 and Table 7.1 with 4 kernels)\r\n\r\n```bash\r\n bash | ||
78 | figure_7_2_table_7_1.sh -n 4 -D ../../../../\r\n``` \r\n## | 78 | figure_7_2_table_7_1.sh -n 4 -D ../../../../\r\n``` \r\n## | ||
79 | Visualization\r\n\r\n### Matlab\r\nThe Matlab scripts are used to | 79 | Visualization\r\n\r\n### Matlab\r\nThe Matlab scripts are used to | ||
80 | generate the plots and tables. The tables are directly prompted to the | 80 | generate the plots and tables. The tables are directly prompted to the | ||
81 | Matlab output.\r\n\r\n### Paraview\r\nTo load the state files in | 81 | Matlab output.\r\n\r\n### Paraview\r\nTo load the state files in | ||
82 | Paraview, select `File->Load State...`. Select the respective `.pvsm` | 82 | Paraview, select `File->Load State...`. Select the respective `.pvsm` | ||
83 | file of the figure you want to plot. As `Load State Data File Options` | 83 | file of the figure you want to plot. As `Load State Data File Options` | ||
84 | choose `Search files under specified directory` and select the | 84 | choose `Search files under specified directory` and select the | ||
85 | `results` folder. Paraview should find the files itself.\r\n\r\n## | 85 | `results` folder. Paraview should find the files itself.\r\n\r\n## | ||
86 | Remarks\r\n- The scripts `figure_7_19_table_7_9.sh` and | 86 | Remarks\r\n- The scripts `figure_7_19_table_7_9.sh` and | ||
87 | `figure_7_21_table_7_10.sh` save reference solutions that are used to | 87 | `figure_7_21_table_7_10.sh` save reference solutions that are used to | ||
88 | compute the errors between different levels of refinement. These | 88 | compute the errors between different levels of refinement. These | ||
89 | solutions are stored in | 89 | solutions are stored in | ||
90 | `programs/hmm_for_Maxwell_conductivity_recursive_convolution/data/`. | 90 | `programs/hmm_for_Maxwell_conductivity_recursive_convolution/data/`. | ||
91 | If you want to run these scripts a second time you either have to | 91 | If you want to run these scripts a second time you either have to | ||
92 | delete the solutions (and compute the solutions again) or you have to | 92 | delete the solutions (and compute the solutions again) or you have to | ||
93 | set the `Output.Reference_Solution` flag in the respective config file | 93 | set the `Output.Reference_Solution` flag in the respective config file | ||
94 | in | 94 | in | ||
95 | rams/hmm_for_Maxwell_conductivity_recursive_convolution/config_files/` | 95 | rams/hmm_for_Maxwell_conductivity_recursive_convolution/config_files/` | ||
96 | to false (which makes the computation even faster).\r\n- Be aware | 96 | to false (which makes the computation even faster).\r\n- Be aware | ||
97 | that, depending on your computer, the computations may take several | 97 | that, depending on your computer, the computations may take several | ||
98 | hours or days.", | 98 | hours or days.", | ||
99 | "num_resources": 0, | 99 | "num_resources": 0, | ||
100 | "num_tags": 7, | 100 | "num_tags": 7, | ||
101 | "orcid": "", | 101 | "orcid": "", | ||
102 | "organization": { | 102 | "organization": { | ||
103 | "approval_status": "approved", | 103 | "approval_status": "approved", | ||
104 | "created": "2023-01-12T13:30:23.238233", | 104 | "created": "2023-01-12T13:30:23.238233", | ||
105 | "description": "RADAR (Research Data Repository) is a | 105 | "description": "RADAR (Research Data Repository) is a | ||
106 | cross-disciplinary repository for archiving and publishing research | 106 | cross-disciplinary repository for archiving and publishing research | ||
107 | data from completed scientific studies and projects. The focus is on | 107 | data from completed scientific studies and projects. The focus is on | ||
108 | research data from subjects that do not yet have their own | 108 | research data from subjects that do not yet have their own | ||
109 | discipline-specific infrastructures for research data management. ", | 109 | discipline-specific infrastructures for research data management. ", | ||
110 | "id": "013c89a9-383c-4200-8baa-0f78bf1d91f9", | 110 | "id": "013c89a9-383c-4200-8baa-0f78bf1d91f9", | ||
111 | "image_url": "radar-logo.svg", | 111 | "image_url": "radar-logo.svg", | ||
112 | "is_organization": true, | 112 | "is_organization": true, | ||
113 | "name": "radar", | 113 | "name": "radar", | ||
114 | "state": "active", | 114 | "state": "active", | ||
115 | "title": "RADAR", | 115 | "title": "RADAR", | ||
116 | "type": "organization" | 116 | "type": "organization" | ||
117 | }, | 117 | }, | ||
118 | "owner_org": "013c89a9-383c-4200-8baa-0f78bf1d91f9", | 118 | "owner_org": "013c89a9-383c-4200-8baa-0f78bf1d91f9", | ||
119 | "private": false, | 119 | "private": false, | ||
120 | "production_year": "2020", | 120 | "production_year": "2020", | ||
121 | "publication_year": "2023", | 121 | "publication_year": "2023", | ||
122 | "publishers": [ | 122 | "publishers": [ | ||
123 | { | 123 | { | ||
124 | "publisher": "Karlsruhe Institute of Technology" | 124 | "publisher": "Karlsruhe Institute of Technology" | ||
125 | } | 125 | } | ||
126 | ], | 126 | ], | ||
127 | "relationships_as_object": [], | 127 | "relationships_as_object": [], | ||
128 | "relationships_as_subject": [], | 128 | "relationships_as_subject": [], | ||
129 | "repository_name": "RADAR (Research Data Repository)", | 129 | "repository_name": "RADAR (Research Data Repository)", | ||
130 | "resources": [], | 130 | "resources": [], | ||
131 | "services_used_list": "", | 131 | "services_used_list": "", | ||
132 | "source_metadata_created": "2023", | 132 | "source_metadata_created": "2023", | ||
133 | "source_metadata_modified": "", | 133 | "source_metadata_modified": "", | ||
134 | "state": "active", | 134 | "state": "active", | ||
135 | "subject_areas": [ | 135 | "subject_areas": [ | ||
136 | { | 136 | { | ||
137 | "subject_area_additional": "", | 137 | "subject_area_additional": "", | ||
138 | "subject_area_name": "Mathematics" | 138 | "subject_area_name": "Mathematics" | ||
139 | } | 139 | } | ||
140 | ], | 140 | ], | ||
141 | "tags": [ | 141 | "tags": [ | ||
142 | { | 142 | { | ||
143 | "display_name": "Maxwell equations", | 143 | "display_name": "Maxwell equations", | ||
144 | "id": "98156513-fec2-4cdd-a7f5-009d09d07160", | 144 | "id": "98156513-fec2-4cdd-a7f5-009d09d07160", | ||
145 | "name": "Maxwell equations", | 145 | "name": "Maxwell equations", | ||
146 | "state": "active", | 146 | "state": "active", | ||
147 | "vocabulary_id": null | 147 | "vocabulary_id": null | ||
148 | }, | 148 | }, | ||
149 | { | 149 | { | ||
150 | "display_name": "Sobolev equation", | 150 | "display_name": "Sobolev equation", | ||
151 | "id": "56300516-677f-4334-9759-69aae3733fd4", | 151 | "id": "56300516-677f-4334-9759-69aae3733fd4", | ||
152 | "name": "Sobolev equation", | 152 | "name": "Sobolev equation", | ||
153 | "state": "active", | 153 | "state": "active", | ||
154 | "vocabulary_id": null | 154 | "vocabulary_id": null | ||
155 | }, | 155 | }, | ||
156 | { | 156 | { | ||
157 | "display_name": "heterogeneous multiscale method", | 157 | "display_name": "heterogeneous multiscale method", | ||
158 | "id": "adeb9aac-5b40-4e5a-a837-0d0e8ca7dac3", | 158 | "id": "adeb9aac-5b40-4e5a-a837-0d0e8ca7dac3", | ||
159 | "name": "heterogeneous multiscale method", | 159 | "name": "heterogeneous multiscale method", | ||
160 | "state": "active", | 160 | "state": "active", | ||
161 | "vocabulary_id": null | 161 | "vocabulary_id": null | ||
162 | }, | 162 | }, | ||
163 | { | 163 | { | ||
164 | "display_name": "homogenization", | 164 | "display_name": "homogenization", | ||
165 | "id": "cfd788ea-6d76-4b36-b651-dfd5957ac999", | 165 | "id": "cfd788ea-6d76-4b36-b651-dfd5957ac999", | ||
166 | "name": "homogenization", | 166 | "name": "homogenization", | ||
167 | "state": "active", | 167 | "state": "active", | ||
168 | "vocabulary_id": null | 168 | "vocabulary_id": null | ||
169 | }, | 169 | }, | ||
170 | { | 170 | { | ||
171 | "display_name": "memory variable", | 171 | "display_name": "memory variable", | ||
172 | "id": "5a7560f8-5ad8-4ab2-9379-40ff0044138d", | 172 | "id": "5a7560f8-5ad8-4ab2-9379-40ff0044138d", | ||
173 | "name": "memory variable", | 173 | "name": "memory variable", | ||
174 | "state": "active", | 174 | "state": "active", | ||
175 | "vocabulary_id": null | 175 | "vocabulary_id": null | ||
176 | }, | 176 | }, | ||
177 | { | 177 | { | ||
178 | "display_name": "recursive convolution", | 178 | "display_name": "recursive convolution", | ||
179 | "id": "531506e5-7ac8-4076-8c7d-4f34a19f867f", | 179 | "id": "531506e5-7ac8-4076-8c7d-4f34a19f867f", | ||
180 | "name": "recursive convolution", | 180 | "name": "recursive convolution", | ||
181 | "state": "active", | 181 | "state": "active", | ||
182 | "vocabulary_id": null | 182 | "vocabulary_id": null | ||
183 | }, | 183 | }, | ||
184 | { | 184 | { | ||
185 | "display_name": "time-integration", | 185 | "display_name": "time-integration", | ||
186 | "id": "f3979ae6-2486-4b06-8418-476c0aa58409", | 186 | "id": "f3979ae6-2486-4b06-8418-476c0aa58409", | ||
187 | "name": "time-integration", | 187 | "name": "time-integration", | ||
188 | "state": "active", | 188 | "state": "active", | ||
189 | "vocabulary_id": null | 189 | "vocabulary_id": null | ||
190 | } | 190 | } | ||
191 | ], | 191 | ], | ||
192 | "title": "Numerical experiments to \"numerical homogenization of | 192 | "title": "Numerical experiments to \"numerical homogenization of | ||
193 | time-dependent maxwell's equations with dispersion effects\"", | 193 | time-dependent maxwell's equations with dispersion effects\"", | ||
194 | "type": "vdataset", | 194 | "type": "vdataset", | ||
195 | "url": "https://doi.org/10.35097/1275" | 195 | "url": "https://doi.org/10.35097/1275" | ||
196 | } | 196 | } |