September 2021 Commit Log

Number of Commits:
124
Number of Active Developers:
2
sbu062 2021-09-29 10:20 Rev.: 11541

better proc name

4 lines of code changed in 1 file:

sbu062 2021-09-29 08:27 Rev.: 11540

newer screenshot gui

0 lines of code changed in 1 file:

sbu062 2021-09-28 18:52 Rev.: 11539

not needed

0 lines of code changed in 1 file:

sbu062 2021-09-28 13:14 Rev.: 11538

better label for zoom limits dialog

6 lines of code changed in 1 file:

sbu062 2021-09-28 12:52 Rev.: 11537

need even bigger format string for final energy

1 lines of code changed in 1 file:

sbu062 2021-09-28 12:42 Rev.: 11536

zoom plot function for (do_plot_output_total_evacuation)

9 lines of code changed in 1 file:

sbu062 2021-09-28 12:35 Rev.: 11535

zoom plot function for (do_plot_output_energy_balance)

10 lines of code changed in 1 file:

sbu062 2021-09-28 12:28 Rev.: 11534

zoom plot function for (do_plot_output_total_midgut_absorption)

9 lines of code changed in 1 file:

sbu062 2021-09-28 12:21 Rev.: 11533

zoom plot function for (do_plot_output_total_midgut)

10 lines of code changed in 1 file:

sbu062 2021-09-28 12:16 Rev.: 11532

zoom plot function for (do_plot_output_appetite) and (do_plot_output_total_stomach)

18 lines of code changed in 1 file:

sbu062 2021-09-28 12:08 Rev.: 11531

zoom plot function for (do_plot_output_total_provided)

8 lines of code changed in 1 file:

sbu062 2021-09-28 12:05 Rev.: 11530

zoom plot function for (do_plot_output_total_not_ingested)

12 lines of code changed in 1 file:

sbu062 2021-09-28 11:59 Rev.: 11529

zoom plot function for (do_plot_output_rate_absorption)

6 lines of code changed in 1 file:

sbu062 2021-09-28 11:16 Rev.: 11528

zoom plot function for (do_plot_output_rate_ingested)

7 lines of code changed in 1 file:

sbu062 2021-09-28 11:01 Rev.: 11527

header docs on zoom set procs

8 lines of code changed in 1 file:

sbu062 2021-09-28 10:54 Rev.: 11526

declare `pure` or `impure` for procs

2 lines of code changed in 1 file:

sbu062 2021-09-28 10:40 Rev.: 11525

test top-level doc for trac

0 lines of code changed in 1 file:

sbu062 2021-09-28 10:32 Rev.: 11524

don't need separate file here

0 lines of code changed in 1 file:

sbu062 2021-09-28 10:26 Rev.: 11523

need yo set range also as `11-12`

1 lines of code changed in 1 file:

sbu062 2021-09-28 09:27 Rev.: 11522

merged r11418 and r11520 from DEV: improvements to (TOSTR)

137 lines of code changed in 2 files:

sbu062 2021-09-28 09:22 Rev.: 11521

merged r11520 from v1: long integer (kind 16) version of (TOSTR)

62 lines of code changed in 1 file:

sbu062 2021-09-28 09:19 Rev.: 11520

implemented long integer (kind 16) version of (TOSTR)

62 lines of code changed in 1 file:

hje044 2021-09-27 15:58 Rev.: 11519

Improved efficiency in writing results, and added a makefile

68 lines of code changed in 4 files:

sbu062 2021-09-27 15:18 Rev.: 11518

move time slot indicator in zoom mode to X time axis

5 lines of code changed in 1 file:

sbu062 2021-09-27 15:05 Rev.: 11517

implemented arbitrary plot zoom for n ingested (do_plot_output_total_ingested)

59 lines of code changed in 1 file:

sbu062 2021-09-27 13:47 Rev.: 11516

need long integer version for (TOSTR) generic function

60 lines of code changed in 1 file:

sbu062 2021-09-27 12:57 Rev.: 11515

implemented graphical zoom limits with modified set procedure

46 lines of code changed in 1 file:

sbu062 2021-09-27 11:52 Rev.: 11514

started zoom window set procedure

67 lines of code changed in 1 file:

sbu062 2021-09-24 11:35 Rev.: 11513

output rate data on autorun

2 lines of code changed in 1 file:

sbu062 2021-09-24 10:00 Rev.: 11512

migrate volume to mass

3 lines of code changed in 1 file:

sbu062 2021-09-23 18:40 Rev.: 11511

MID_GUT now MIDGUT

8 lines of code changed in 2 files:

sbu062 2021-09-23 18:38 Rev.: 11510

do not delete data, csv are all autodeleted on `distclean` or `clean_data`

86402 lines of code changed in 3 files:

sbu062 2021-09-23 13:05 Rev.: 11509

list columns of csv data file as in (output_arrays_save_csv)

2 lines of code changed in 1 file:

sbu062 2021-09-23 13:00 Rev.: 11508

doc: move away from volume to mass in all docs and scripts

66 lines of code changed in 7 files:

sbu062 2021-09-23 13:00 Rev.: 11507

rename (st_food_item_volume) to (st_food_item_mass)

18 lines of code changed in 4 files:

sbu062 2021-09-23 10:19 Rev.: 11506

unify class names: midgut

21 lines of code changed in 1 file:

sbu062 2021-09-23 10:02 Rev.: 11505

doc: need lowercase objects for doxygen

8 lines of code changed in 2 files:

sbu062 2021-09-22 09:47 Rev.: 11504

fix typo

1 lines of code changed in 1 file:

sbu062 2021-09-22 09:30 Rev.: 11503

volume variable and object names go to mass except `midgut_volume` to `midgut_capacity` and `stomach_volume` to `stomach_capacity`
Note: needs testing replicability with fixed seed against previous version
{{{
integer :: i
call random_seed(put= (/ (0, i = 1, 33) /) )
}}}

415 lines of code changed in 8 files:

sbu062 2021-09-16 14:13 Rev.: 11502

TEST change to HRP precision model in (appetite_energy)

6 lines of code changed in 1 file:

sbu062 2021-09-15 15:18 Rev.: 11501

explicit no food to the end of 24 h period

84960 lines of code changed in 1 file:

sbu062 2021-09-15 14:51 Rev.: 11500

one meal feeding schedule

35 lines of code changed in 1 file:

sbu062 2021-09-15 14:45 Rev.: 11499

stomach pattern data from Grove
Grove, D.J. et al. (1978) Satiation amount, frequency of feeding and gastric emptying rate in Salmo gairdneri. J. Fish Biol. 12, 507–516

10 lines of code changed in 1 file:

sbu062 2021-09-15 13:33 Rev.: 11498

cubic splines give much better interpolation than polynominals

9 lines of code changed in 2 files:

sbu062 2021-09-14 12:20 Rev.: 11497

need very long format for very steep appetite function parameter

2 lines of code changed in 1 file:

sbu062 2021-09-14 11:32 Rev.: 11496

setup feeding schedule in file fom Malta exp 1

1453 lines of code changed in 2 files:

sbu062 2021-09-14 11:14 Rev.: 11495

mark UI code pieces for easier folding less clutter

6 lines of code changed in 1 file:

sbu062 2021-09-14 11:07 Rev.: 11494

feedig schedule as in Malta experiments

1 lines of code changed in 1 file:

sbu062 2021-09-13 11:49 Rev.: 11493

add energy appetite factor to debugging output switched at `IS_LOGGING_DEBUG`

28 lines of code changed in 2 files:

sbu062 2021-09-13 11:26 Rev.: 11492

appetite function (fish_appetite_probability_ingestion): now testing appetite defined by maximum value of appetite factor components, debug code and notes still there

33 lines of code changed in 2 files:

sbu062 2021-09-11 07:28 Rev.: 11491

doc: global and grained access to UI modules

29 lines of code changed in 2 files:

sbu062 2021-09-11 06:58 Rev.: 11490

fine-gained invocation for interface modules
Note: isolation of interface modules is needed to make other additional interfaces more easily, or delete dependencies on GUI for server-only build

7 lines of code changed in 1 file:

sbu062 2021-09-10 18:31 Rev.: 11489

list TEG members

2 lines of code changed in 1 file:

sbu062 2021-09-10 18:28 Rev.: 11488

add new user to shared roster group TEG

5 lines of code changed in 1 file:

sbu062 2021-09-10 18:22 Rev.: 11487

show list of users at the end

6 lines of code changed in 1 file:

sbu062 2021-09-10 18:16 Rev.: 11486

better numbers

2 lines of code changed in 1 file:

sbu062 2021-09-10 18:14 Rev.: 11485

switch fully yo internal authentication for XMPP

6 lines of code changed in 1 file:

sbu062 2021-09-10 14:27 Rev.: 11484

first debugging version of energy appetite component based on difference, logistic in terms of SMR function units
Note debug code only in m_simulate.f90

83 lines of code changed in 2 files:

sbu062 2021-09-10 10:58 Rev.: 11483

add Andrea to TEG group

1 lines of code changed in 1 file:

sbu062 2021-09-09 20:37 Rev.: 11482

doc: better text for gross energy

10 lines of code changed in 2 files:

sbu062 2021-09-09 20:20 Rev.: 11481

better swap i

1 lines of code changed in 1 file:

sbu062 2021-09-09 12:18 Rev.: 11480

done save cumulative mass ingested in GUI mode

2 lines of code changed in 1 file:

sbu062 2021-09-09 11:43 Rev.: 11479

doc: document the new `mass_ingested` command

2 lines of code changed in 2 files:

sbu062 2021-09-09 11:39 Rev.: 11478

plot either N or mass of food ingested in CMD mode

54 lines of code changed in 1 file:

sbu062 2021-09-09 11:10 Rev.: 11477

plot either N or mass of food ingested in GUI mode

60 lines of code changed in 1 file:

sbu062 2021-09-09 08:55 Rev.: 11476

add parameter for feed gross energy

24 lines of code changed in 4 files:

sbu062 2021-09-09 08:30 Rev.: 11475

added save plot for total evacuated, forgotten before

4 lines of code changed in 1 file:

sbu062 2021-09-08 21:00 Rev.: 11474

doc: note on SMR parameters

5 lines of code changed in 1 file:

sbu062 2021-09-08 19:14 Rev.: 11473

doc: better table

7 lines of code changed in 1 file:

sbu062 2021-09-08 19:06 Rev.: 11472

added autogenerated smr function to manual

4 lines of code changed in 2 files:

sbu062 2021-09-08 16:05 Rev.: 11471

implemented smr function plot (plot_smr_function) in CMD mode

45 lines of code changed in 1 file:

sbu062 2021-09-08 15:51 Rev.: 11470

implemanted smr parameter plotting procedure (do_plot_smr_function) for GUI mode

52 lines of code changed in 1 file:

sbu062 2021-09-08 14:39 Rev.: 11469

doc: more doc on energetics

47 lines of code changed in 1 file:

sbu062 2021-09-08 14:02 Rev.: 11468

started documenting energetics

45 lines of code changed in 2 files:

sbu062 2021-09-08 14:02 Rev.: 11467

doc: added implementation comments for energetics

47 lines of code changed in 2 files:

sbu062 2021-09-08 09:47 Rev.: 11466

implemenmted (do_plot_output_energy_balance) to plot energy balance in GUI mode

79 lines of code changed in 1 file:

sbu062 2021-09-08 08:40 Rev.: 11465

final module name for `m_subst.f90` stub must be `DISLIN` as in substituted module

2 lines of code changed in 1 file:

sbu062 2021-09-08 08:37 Rev.: 11464

disable `m_subst.f90` stub test r11463: revert to r11462
`svn merge -r HEAD:11462 .`

3 lines of code changed in 2 files:

sbu062 2021-09-08 08:32 Rev.: 11463

enable `m_subst.f90` stub for DISLIN to test if it works if DISLIN is disabled at build

3 lines of code changed in 2 files:

sbu062 2021-09-08 08:31 Rev.: 11462

add messages the go to std out in DISLIN stub

7 lines of code changed in 1 file:

sbu062 2021-09-08 05:04 Rev.: 11461

added stub substitution module, now for DISLIN allowing to build components without UI

32 lines of code changed in 1 file:

sbu062 2021-09-07 22:27 Rev.: 11460

better name

3 lines of code changed in 1 file:

sbu062 2021-09-07 22:13 Rev.: 11459

debug output

4 lines of code changed in 1 file:

sbu062 2021-09-07 22:12 Rev.: 11458

added units to doxygen doc

2 lines of code changed in 1 file:

sbu062 2021-09-07 22:05 Rev.: 11457

(energy2mass) function to reverse-calculate the body mas from the whole-body energy

17 lines of code changed in 1 file:

sbu062 2021-09-07 19:15 Rev.: 11456

mark global output variables that depend on `Global_Temperature`

2 lines of code changed in 1 file:

sbu062 2021-09-07 17:57 Rev.: 11455

(fish_whole_body_energy_trout) calculates whole body energy content, based on Ivar attached file `Rainbowtrout data Energetics and nutrient content.xlsx`
> Date: Wed, 1 Sep 2021 06:09:10 +0000
> From: Ivar Rønnestad <Ivar.Ronnestad@uib.no>
> To: Sergei Budaev <Sergey.Budaev@uib.no>
> Subject: Rainbow trout generic data for energetics
>
>
> Sergey,
> Please use these data for the initial runs.
>
> IvarR
> We can have a chat, so I can briefly go through what the data means, when will you be available (today)?
>
> **************************************************
> Ivar Rønnestad, PhD, Professor
> Department of Biological Sciences, University of Bergen, Bergen, NORWAY
>
> Cell: +47 926 47 219

33 lines of code changed in 1 file:

sbu062 2021-09-07 17:52 Rev.: 11454

set `body_mass` in CMD interface
note: forgotten, must have been implemented before

9 lines of code changed in 1 file:

sbu062 2021-09-07 16:55 Rev.: 11453

add stub AMR to overall energy balance

2 lines of code changed in 1 file:

sbu062 2021-09-07 16:48 Rev.: 11452

stub for AMR calculation function, now fixed linear metabolic scope amr=k*smr

15 lines of code changed in 1 file:

sbu062 2021-09-07 15:57 Rev.: 11451

unify names of backend procedures: those pertaining to MIDGUT normally start from `fish_midgut_`

17 lines of code changed in 2 files:

sbu062 2021-09-07 12:55 Rev.: 11450

move (energy_update) from MIDGUT up to FISH class is more logical

6 lines of code changed in 1 file:

sbu062 2021-09-07 12:39 Rev.: 11449

plot energy balance in CMD mode

81 lines of code changed in 2 files:

sbu062 2021-09-07 11:32 Rev.: 11448

better model stats output, debug code removed

17 lines of code changed in 1 file:

sbu062 2021-09-07 10:37 Rev.: 11447

can use arbitrary start value for energy balance in (fish_midgut_energy_balance_update), also fix bug with *smr* in *O2* rather than energy *kJ* units

14 lines of code changed in 1 file:

sbu062 2021-09-07 10:25 Rev.: 11446

any temperature can be used in (fish_midgut_energy_balance_update) as an optional parameter

14 lines of code changed in 1 file:

sbu062 2021-09-07 02:40 Rev.: 11445

add energy balance to model output arrays, add to save csv

26 lines of code changed in 1 file:

sbu062 2021-09-06 14:22 Rev.: 11444

debug code for (fish_midgut_energy_balance_update)

25 lines of code changed in 1 file:

sbu062 2021-09-06 14:22 Rev.: 11443

(fish_midgut_energy_balance_update) calculation checked correct

24 lines of code changed in 1 file:

sbu062 2021-09-06 07:54 Rev.: 11442

do energy balance update subroutine: start value zero now, update balance at step *i* from value at *i-1*

9 lines of code changed in 1 file:

sbu062 2021-09-06 07:43 Rev.: 11441

(fish_midgut_energy_balance_calc) should be subroutine (fish_midgut_energy_balance_update)

4 lines of code changed in 1 file:

sbu062 2021-09-03 21:29 Rev.: 11440

first working version of (fish_midgut_energy_balance_calc), needs testing

9 lines of code changed in 1 file:

sbu062 2021-09-03 13:45 Rev.: 11439

incomplete: started (fish_midgut_energy_balance_calc)

31 lines of code changed in 1 file:

sbu062 2021-09-03 12:59 Rev.: 11438

new history stack component: `energy_balance_curr`

3 lines of code changed in 1 file:

sbu062 2021-09-03 10:24 Rev.: 11437

`DEBUG_ABSORP_CUMULATE_MISMATCH` debug check for mismatch between cimumative absorption calculated in fish object and simulate output arrays

13 lines of code changed in 1 file:

sbu062 2021-09-02 21:12 Rev.: 11436

deleted obsolete `Global_Energy_Reserves`

0 lines of code changed in 4 files:

sbu062 2021-09-02 20:59 Rev.: 11435

whitespace only

1 lines of code changed in 1 file:

sbu062 2021-09-02 20:20 Rev.: 11434

fix typo in unit

1 lines of code changed in 1 file:

sbu062 2021-09-02 18:21 Rev.: 11433

DEBUG: need both raw smr-O2 and energy kJ

5 lines of code changed in 1 file:

sbu062 2021-09-02 17:23 Rev.: 11432

white space only

1 lines of code changed in 1 file:

sbu062 2021-09-02 16:35 Rev.: 11431

test energy overall outputs for simulation

9 lines of code changed in 1 file:

sbu062 2021-09-02 15:58 Rev.: 11430

function (feed_energy) calculates energy content of a feed mass, default content 23.0

19 lines of code changed in 1 file:

sbu062 2021-09-02 15:42 Rev.: 11429

better oxygen energy function name

2 lines of code changed in 1 file:

sbu062 2021-09-02 15:33 Rev.: 11428

added notes on parameters, with units

17 lines of code changed in 2 files:

sbu062 2021-09-02 14:48 Rev.: 11427

trivial unit conversion

7 lines of code changed in 1 file:

sbu062 2021-09-02 14:36 Rev.: 11426

comment fixed value

1 lines of code changed in 1 file:

sbu062 2021-09-02 14:33 Rev.: 11425

fix ratio

1 lines of code changed in 1 file:

sbu062 2021-09-02 14:21 Rev.: 11424

cleaner expression

2 lines of code changed in 1 file:

sbu062 2021-09-02 14:18 Rev.: 11423

function (o2vol) to calculate oxygen volume

11 lines of code changed in 1 file:

sbu062 2021-09-02 13:54 Rev.: 11422

functions for O2 energetic equivalent in kJ (energy2o2) and oxygen (o2mass)
--This line,yonsill be ignored--

M STOMACH/m_common.f90

22 lines of code changed in 1 file:

sbu062 2021-09-01 14:07 Rev.: 11421

(fish_smr_dep_temp_bodymass_van_deurs_fiksen) is now obsolete

0 lines of code changed in 1 file:

sbu062 2021-09-01 13:53 Rev.: 11420

reformat long lines, program style

32 lines of code changed in 3 files:

sbu062 2021-09-01 08:58 Rev.: 11419

use the new `is_cleanup` parameter to (TOSTR) for cleaner output in (model_output_stats_txt) backend

22 lines of code changed in 2 files:

sbu062 2021-09-01 08:36 Rev.: 11418

added `is_cleanup` parameter to (TOSTR) FALSE results in verbatim format

195 lines of code changed in 7 files:

August 2021 »

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