| 538 |  |  | 
| 539 | the master package diagram does not appear in the document | the master package diagram does not appear in the document | 
| 540 |  |  | 
|  | pkg/ptracers doesn't seem to have any documentation (see packages list below) |  | 
|  | martin volunteered - get martin to ask steph |  | 
|  |  |  | 
|  |  |  | 
| 541 | Master list of packages (add this to beginning of chap 6) | Master list of packages (add this to beginning of chap 6) | 
| 542 |  |  | 
| 543 | admtlm/               - autodiff (chapter 5) | admtlm/               - autodiff (chapter 5) | 
| 562 | ebm/                  - (check with PH) | ebm/                  - (check with PH) | 
| 563 | ecco/                 - chapter 8 | ecco/                 - chapter 8 | 
| 564 | embed_files/          - add something to chapter 7 | embed_files/          - add something to chapter 7 | 
|  | ex3/                  - move to contrib (EH) |  | 
| 565 | exch2/                - 6.2.2 | exch2/                - 6.2.2 | 
| 566 | exf/                  - 6.3.4 | exf/                  - 6.3.4 | 
| 567 | fizhi/                - 6.4.3 | fizhi/                - 6.4.3 | 
| 568 | flt/                  - in chapter 2 (JM check) | flt/                  - (PH check) | 
| 569 | gchem/                - 6.7.1 | gchem/                - 6.7.1 | 
| 570 | generic_advdiff/      - in chapter 2 (JM check) | generic_advdiff/      - in chapter 2 (JM check) | 
| 571 | ggl90/                - nothing, (Martin?) | ggl90/                - nothing, (Martin?) | 
| 572 | gmredi/               - in chapter 2 (JM check). also need | gmredi/               - in chapter 2 (JM check). also need | 
| 573 | Ferrari & Mc tapering | Ferrari & Mc transition zone stuff (Samar doing this) | 
| 574 |  | get dfer to read this | 
| 575 | grdchk/               - grdchk (chapter 5 - check with PH) | grdchk/               - grdchk (chapter 5 - check with PH) | 
| 576 | gridalt/              - 6.2.4 | gridalt/              - 6.2.4 | 
| 577 | kpp/                  - 6.3.2 | kpp/                  - 6.3.2 | 
| 578 | land/                 - 6.4.2 (not connected to code - JM to fix) | land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix) | 
| 579 | matrix/               - Samar | matrix/               - Samar | 
| 580 | mdsio/                - 7.3.1 | mdsio/                - 7.3.1 | 
| 581 | mnc/                  - 7.2.1 | mnc/                  - 7.2.1 | 
| 584 | mom_vecinv/           - in chapter 2 (JM check) | mom_vecinv/           - in chapter 2 (JM check) | 
| 585 | monitor/              - 7.4 | monitor/              - 7.4 | 
| 586 | my82/                 - nothing, (martin?) | my82/                 - nothing, (martin?) | 
| 587 | obcs/                 - 6.3 (needs a check) | obcs/                 - 6.3 (needs a check - ask PH to read) | 
| 588 | ocn_compon_interf/    - 6.6 (no content yet) | ocn_compon_interf/    - 6.6 (no content yet) | 
| 589 | offline/              - nothing, tutorials that need work but no package   section entry | offline/              - nothing, tutorials that need work but no package   section entry | 
| 590 |  | trivial to document (CNH to do) | 
| 591 | opps/                 - nothing, (martin?) | opps/                 - nothing, (martin?) | 
| 592 | pp81/                 - nothing, (martin?) | pp81/                 - nothing, (martin?) | 
| 593 | profiles/             - GAEL | profiles/             - GAEL | 
| 594 | ptracers/             - JM + SD to write something | ptracers/             - JM + SD + Martin to write something (nothing for this | 
| 595 | rbcs/                 - talk to steph | at the moment) | 
| 596 | runclock/             - runclock | AM has diagnostics table for this. | 
| 597 | rw/                   - not sure | rbcs/                 - CNH to talk to steph | 
| 598 |  | runclock/             - runclock - CNH | 
| 599 |  | rw/                   - not sure - going to stay says JMC. quick IO calls | 
| 600 |  | JMC to write a quick note for that. | 
| 601 | sbo/                  - text in sbo_descruption.tex but not linked into | sbo/                  - text in sbo_descruption.tex but not linked into | 
| 602 | part6 | part6 - CNH | 
| 603 | seaice/               - 6.5.2 - no equations, dimitris has promised some | seaice/               - 6.5.2 - no equations, dimitris has promised some | 
| 604 | shap_filt/            - chapter 2, JM to check | shap_filt/            - chapter 2, JM to check | 
| 605 | shelfice/             - nothing yet (martin?) | shelfice/             - nothing yet (martin?) | 
| 606 | solver/               - empty | solver/               - empty (go away?) | 
| 607 | sphere/               - chapter 5 or 8 (PH to check) | sphere/               - chapter 5 or 8 (PH to check) | 
| 608 | therm_seaice/         - empty | therm_seaice/         - empty (go away?) | 
| 609 | thsice/               - 6.5.1 (JM to update?) | thsice/               - 6.5.1 (JM to update?) | 
| 610 | timeave/              - retiring...... | timeave/              - retiring...... | 
| 611 | zonal_filt/           - chapter 2 (JM to check) | zonal_filt/           - chapter 2 (JM to check) | 
| 612 |  |  | 
| 613 | Possible for chap 7 - Daniels grafix/ stuff | list an expeiment which uses package? CNH | 
|  |  |  | 
|  | Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. |  | 
| 614 |  |  | 
| 615 | Figure 6.8 is missing | [DONE]Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. | 
| 616 |  |  | 
| 617 | 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 | 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 | 
| 618 | Figure 6.8 is missing | Figure 6.8 is missing |