| 352 |  |  | 
| 353 | JM | JM | 
| 354 |  |  | 
| 355 |  |  | 
| 356 |  | >>>> From Andrea | 
| 357 |  |  | 
| 358 |  | Chapter 3 | 
| 359 |  | -------- | 
| 360 |  |  | 
| 361 |  | Almost all of the 'math mode' text is dropped down as subscripts | 
| 362 |  |  | 
| 363 |  | divide chapter 3 more clearly into 2 sections? | 
| 364 |  | (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and | 
| 365 |  | then 3.19 and 3.20 are informational again - rearrange subsections?) | 
| 366 |  |  | 
| 367 |  | 3.1 - don't need a link to the outside of the document (remove it) | 
| 368 |  | - link to htdig is broken | 
| 369 |  |  | 
| 370 |  | 3.2.1 - link at bottom to source code points to section 3.2.1 | 
| 371 |  | (ie, to itself) - link should point to cvs code archive | 
| 372 |  |  | 
| 373 |  | 3.2.2.1  - ('upgrading from an earlier version') belongs under | 
| 374 |  | the cvs part, ie, should be 3.2.1.1 | 
| 375 |  |  | 
| 376 |  | 3.3 - remove reference to 'diags' section under MITgcm | 
| 377 |  | - remove reference to 'exe' and 'bin' sections also | 
| 378 |  | (remove the .cvsignore file under these directories in cvs) | 
| 379 |  | - add a 'jobs' section, and a description as examples of run scripts | 
| 380 |  | - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions | 
| 381 |  | - under 'tools' add a reference to 'build_options'. refer to the 'optfiles' | 
| 382 |  | - under 'tools' the adjoint points to section 5 - this is now section 8 | 
| 383 |  | (but should be a floating reference) | 
| 384 |  | - under 'utils' add a reference to exch2 - stuff for different resolutions | 
| 385 |  | - the description of the pkg section refers directly to | 
| 386 |  | section 3. should be section 6 (actually should be a floating reference) | 
| 387 |  |  | 
| 388 |  | 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10) | 
| 389 |  | 3.4.1 - links to the following experiments don't exist or are broken: | 
| 390 |  | exp2 - should link to section 3.9 | 
| 391 |  | hs94.cs-32x32x5 - link to section 3.12 | 
| 392 |  | add 'convection' to the list, link to section 3.13 | 
| 393 |  | add 'plume on slope` to the list, link to section 3.14 | 
| 394 |  | add '??' link to section 3.15 | 
| 395 |  | add 'dic_example on slope` to the list, link to section 3.16 | 
| 396 |  | add '??' link to section 3.17 | 
| 397 |  | add 'offline' and link to section 3.18 | 
| 398 |  | clean up others and make links where they are needed | 
| 399 |  | 3.4.2 - text suggests to see section 2 for details about what is in the 'code' | 
| 400 |  | and 'input' directories - should refer to the examples in this section | 
| 401 |  | - add 'build' bullet - this is where the model is compiled and exectuable lives | 
| 402 |  |  | 
| 403 |  | 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options | 
| 404 |  | as the place where they live (add a link?) | 
| 405 |  |  | 
| 406 |  | 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the | 
| 407 |  | 'data' file in the input directory or by the data.[pkg name] file for any | 
| 408 |  | package running. And there is some default behavior when the 'state' dumps | 
| 409 |  | are written. | 
| 410 |  | 3.6.1.2 - needs to be moved to inside section 3.6.2 | 
| 411 |  |  | 
| 412 |  | 3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18) | 
| 413 |  | underneath this one and leave the text for 3.7 in place | 
| 414 |  |  | 
| 415 |  | All the 'overview' sections need some reference to the name of the experiment in | 
| 416 |  | the verification directory | 
| 417 |  |  | 
| 418 |  | 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript | 
| 419 |  | - is this experiment in the list from section 3.4??? | 
| 420 |  | 3.10.3.1 - refers to figures and equations, links are broken | 
| 421 |  |  | 
| 422 |  | 3.11.3.2 - line 43: link to equation is broken | 
| 423 |  | - line 51-53: link to equation is broken | 
| 424 |  | - there is some mess of text hanging around the end of this section. remove? reformat? | 
| 425 |  |  | 
| 426 |  | 3.12.4.1 - line 34 - link to equation is broken | 
| 427 |  | - lines 60,61 - 1st (take out the 'r' in the superscript) | 
| 428 |  |  | 
| 429 |  | 3.13.2 - link to theta-equation is broken | 
| 430 |  | 3.13.5.4 -- ALL of the bold links to variable names are broken | 
| 431 |  | line 34: link to equation is broken | 
| 432 |  |  | 
| 433 |  | 3.15.1 - reference to 'fourth experiment' should be removed | 
| 434 |  |  | 
| 435 |  | 3.16.4 - strange formatting, presence of '>' symbols - remove them | 
| 436 |  |  | 
| 437 |  | 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4 | 
| 438 |  | 3.17.3.1 - nothing filled in under file input/data - needs description | 
| 439 |  |  | 
| 440 |  | 3.18.2 - point to section 2 for details - need hyperlink | 
| 441 |  |  | 
| 442 |  | 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true! | 
| 443 |  | section 3.5 has the 'build' directory in the example | 
| 444 |  |  | 
| 445 |  | 3.20.1 - link to doc at end of section points to this section | 
| 446 |  | 3.20.2 - link to doc at end of section points to this section | 
| 447 |  |  | 
| 448 |  | offline - duplicate inputs, what is it, tidy up cfc v. | 
| 449 |  | other offline. JM thinks these need tidying up. | 
| 450 | >>>> From Ed | >>>> From Ed | 
| 451 |  |  | 
| 452 | Here are the remaining bits for Chap 4 : | Here are the remaining bits for Chap 4 : | 
| 570 |  |  | 
| 571 | andrea | andrea | 
| 572 |  |  | 
|  | >>>> From Andrea |  | 
|  |  |  | 
|  | Chapter 3 |  | 
|  | -------- |  | 
|  |  |  | 
|  | Almost all of the 'math mode' text is dropped down as subscripts |  | 
|  |  |  | 
|  | divide chapter 3 more clearly into 2 sections? |  | 
|  | (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and |  | 
|  | then 3.19 and 3.20 are informational again - rearrange subsections?) |  | 
|  |  |  | 
|  | 3.1 - don't need a link to the outside of the document (remove it) |  | 
|  | - link to htdig is broken |  | 
|  |  |  | 
|  | 3.2.1 - link at bottom to source code points to section 3.2.1 |  | 
|  | (ie, to itself) - link should point to cvs code archive |  | 
|  |  |  | 
|  | 3.2.2.1  - ('upgrading from an earlier version') belongs under |  | 
|  | the cvs part, ie, should be 3.2.1.1 |  | 
|  |  |  | 
|  | 3.3 - remove reference to 'diags' section under MITgcm |  | 
|  | - remove reference to 'exe' and 'bin' sections also |  | 
|  | (remove the .cvsignore file under these directories in cvs) |  | 
|  | - add a 'jobs' section, and a description as examples of run scripts |  | 
|  | - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions |  | 
|  | - under 'tools' add a reference to 'build_options'. refer to the 'optfiles' |  | 
|  | - under 'tools' the adjoint points to section 5 - this is now section 8 |  | 
|  | (but should be a floating reference) |  | 
|  | - under 'utils' add a reference to exch2 - stuff for different resolutions |  | 
|  | - the description of the pkg section refers directly to |  | 
|  | section 3. should be section 6 (actually should be a floating reference) |  | 
|  |  |  | 
|  | 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10) |  | 
|  | 3.4.1 - links to the following experiments don't exist or are broken: |  | 
|  | exp2 - should link to section 3.9 |  | 
|  | hs94.cs-32x32x5 - link to section 3.12 |  | 
|  | add 'convection' to the list, link to section 3.13 |  | 
|  | add 'plume on slope` to the list, link to section 3.14 |  | 
|  | add '??' link to section 3.15 |  | 
|  | add 'dic_example on slope` to the list, link to section 3.16 |  | 
|  | add '??' link to section 3.17 |  | 
|  | add 'offline' and link to section 3.18 |  | 
|  | clean up others and make links where they are needed |  | 
|  | 3.4.2 - text suggests to see section 2 for details about what is in the 'code' |  | 
|  | and 'input' directories - should refer to the examples in this section |  | 
|  | - add 'build' bullet - this is where the model is compiled and exectuable lives |  | 
|  |  |  | 
|  | 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options |  | 
|  | as the place where they live (add a link?) |  | 
|  |  |  | 
|  | 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the |  | 
|  | 'data' file in the input directory or by the data.[pkg name] file for any |  | 
|  | package running. And there is some default behavior when the 'state' dumps |  | 
|  | are written. |  | 
|  | 3.6.1.2 - needs to be moved to inside section 3.6.2 |  | 
|  |  |  | 
|  | 3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18) |  | 
|  | underneath this one and leave the text for 3.7 in place |  | 
|  |  |  | 
|  | All the 'overview' sections need some reference to the name of the experiment in |  | 
|  | the verification directory |  | 
|  |  |  | 
|  | 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript |  | 
|  | - is this experiment in the list from section 3.4??? |  | 
|  | 3.10.3.1 - refers to figures and equations, links are broken |  | 
|  |  |  | 
|  | 3.11.3.2 - line 43: link to equation is broken |  | 
|  | - line 51-53: link to equation is broken |  | 
|  | - there is some mess of text hanging around the end of this section. remove? reformat? |  | 
|  |  |  | 
|  | 3.12.4.1 - line 34 - link to equation is broken |  | 
|  | - lines 60,61 - 1st (take out the 'r' in the superscript) |  | 
|  |  |  | 
|  | 3.13.2 - link to theta-equation is broken |  | 
|  | 3.13.5.4 -- ALL of the bold links to variable names are broken |  | 
|  | line 34: link to equation is broken |  | 
|  |  |  | 
|  | 3.15.1 - reference to 'fourth experiment' should be removed |  | 
|  |  |  | 
|  | 3.16.4 - strange formatting, presence of '>' symbols - remove them |  | 
|  |  |  | 
|  | 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4 |  | 
|  | 3.17.3.1 - nothing filled in under file input/data - needs description |  | 
|  |  |  | 
|  | 3.18.2 - point to section 2 for details - need hyperlink |  | 
|  |  |  | 
|  | 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true! |  | 
|  | section 3.5 has the 'build' directory in the example |  | 
|  |  |  | 
|  | 3.20.1 - link to doc at end of section points to this section |  | 
|  | 3.20.2 - link to doc at end of section points to this section |  | 
|  |  |  | 
|  | offline - duplicate inputs, what is it, tidy up cfc v. |  | 
|  | other offline. JM thinks these need tidying up. |  | 
|  |  |  | 
| 573 |  |  | 
| 574 | 9. Model uses | 9. Model uses | 
| 575 | Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... | Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |