November 2021 Commit Log

Number of Commits:
132
Number of Active Developers:
2
sbu062 2021-11-30 13:23 Rev.: 11844

preliminary title

43 lines of code changed in 1 file:

sbu062 2021-11-30 13:07 Rev.: 11843

just first notes

27 lines of code changed in 1 file:

sbu062 2021-11-30 12:37 Rev.: 11842

doc structure for friprop 22

5 lines of code changed in 1 file:

sbu062 2021-11-29 22:24 Rev.: 11841

added serverbot service for systemd

22 lines of code changed in 1 file:

sbu062 2021-11-29 13:14 Rev.: 11840

additional doxygen notes

6 lines of code changed in 1 file:

sbu062 2021-11-29 12:54 Rev.: 11839

use single backend function (SGR_r) for all

3 lines of code changed in 1 file:

sbu062 2021-11-29 12:09 Rev.: 11838

fix unit on specific growth rate

1 lines of code changed in 1 file:

sbu062 2021-11-29 12:07 Rev.: 11837

fix unit on specific growth rate

2 lines of code changed in 2 files:

hje044 2021-11-29 11:54 Rev.: 11836

Makefile updated to be OS-agnostic. NetCDF libraries now pulled based on operating system

42 lines of code changed in 3 files:

sbu062 2021-11-26 10:29 Rev.: 11835

save rate data with arbitrary rate unit by `rate_unit_scale`

27 lines of code changed in 1 file:

sbu062 2021-11-26 09:33 Rev.: 11834

use arbitrary rate scale set by `rate_unit_scale` for growth rate in CMD and GUI

38 lines of code changed in 2 files:

sbu062 2021-11-26 08:20 Rev.: 11833

additional notes on rate time scales, show rate scale in CMD mode

19 lines of code changed in 3 files:

sbu062 2021-11-26 07:37 Rev.: 11832

doc: `rate_unit_scale` description

5 lines of code changed in 1 file:

sbu062 2021-11-25 18:45 Rev.: 11831

need single time scale abbreviations, public parameter

3 lines of code changed in 3 files:

sbu062 2021-11-25 17:07 Rev.: 11830

calculate and plot with any rate unit: h-1, min-1 etc. controlled by new `rate_unit_scale` parameter

65 lines of code changed in 5 files:

sbu062 2021-11-25 14:49 Rev.: 11829

set enumerators public or private

16 lines of code changed in 2 files:

sbu062 2021-11-25 13:56 Rev.: 11828

arbitrary time unit for Y scale in SGR

6 lines of code changed in 2 files:

sbu062 2021-11-25 10:13 Rev.: 11827

specific growth rate can be calculated for any arbitrary time interval, standard minute

22 lines of code changed in 3 files:

sbu062 2021-11-25 09:21 Rev.: 11826

doxygen comments only

10 lines of code changed in 1 file:

sbu062 2021-11-24 22:26 Rev.: 11825

doc: help doc on specific growth rate

2 lines of code changed in 2 files:

sbu062 2021-11-24 22:21 Rev.: 11824

unit is hour

1 lines of code changed in 1 file:

sbu062 2021-11-24 22:18 Rev.: 11823

plot specific growth rate in CMD mode

68 lines of code changed in 1 file:

sbu062 2021-11-24 21:48 Rev.: 11822

specific growth rate: option to rescale SGR to min

36 lines of code changed in 2 files:

sbu062 2021-11-24 21:14 Rev.: 11821

fix forgotten `kind` parameter

2 lines of code changed in 1 file:

sbu062 2021-11-24 19:05 Rev.: 11820

plot specific growth rate in GUI mode

57 lines of code changed in 2 files:

sbu062 2021-11-24 18:37 Rev.: 11819

(SGR_blockdata) calculates specific growth rate array from block data as (blockrate)

40 lines of code changed in 1 file:

sbu062 2021-11-24 18:24 Rev.: 11818

need specific growth rate that works with integer times as time speps, display specific growth rate in `stats` command

26 lines of code changed in 2 files:

sbu062 2021-11-24 18:07 Rev.: 11817

latex formula added

4 lines of code changed in 1 file:

sbu062 2021-11-24 13:14 Rev.: 11816

initial version of specific growth rate, Houde & Scheckter, 1981; needs testing

15 lines of code changed in 1 file:

sbu062 2021-11-23 23:00 Rev.: 11815

debug mode visible

10 lines of code changed in 1 file:

sbu062 2021-11-23 22:55 Rev.: 11814

interface starts with model title string

8 lines of code changed in 3 files:

sbu062 2021-11-23 12:49 Rev.: 11813

got rid of simgut, fully switched to fishmet

29 lines of code changed in 7 files:

sbu062 2021-11-23 12:17 Rev.: 11812

set `stats_output_long` in CMD mode

12 lines of code changed in 1 file:

sbu062 2021-11-17 12:27 Rev.: 11811

report general output stats file format, long or short, in GUI mode

8 lines of code changed in 2 files:

sbu062 2021-11-17 12:18 Rev.: 11810

report long or short general stats format in CMD mode

7 lines of code changed in 1 file:

sbu062 2021-11-17 11:23 Rev.: 11809

report general output stats file in GUI mode

3 lines of code changed in 1 file:

sbu062 2021-11-16 10:29 Rev.: 11808

doc: default value of `stats_output_long`

3 lines of code changed in 2 files:

sbu062 2021-11-16 09:59 Rev.: 11807

implemented long and short output stats file format controlled by `stats_output_long` configuration parameter

86 lines of code changed in 6 files:

sbu062 2021-11-16 09:09 Rev.: 11806

need separate arrays for input parameters and output statistics

56 lines of code changed in 1 file:

sbu062 2021-11-15 18:21 Rev.: 11805

added `smr_oxygen_temp` and `smr_oxygen_o2` to general output stats

8 lines of code changed in 1 file:

sbu062 2021-11-15 17:59 Rev.: 11804

array-based parameters added to general stats output: `transport_pattern_t_` and `transport_pattern_r_`

16 lines of code changed in 1 file:

sbu062 2021-11-15 13:45 Rev.: 11803

better var labels for CSV

2 lines of code changed in 1 file:

sbu062 2021-11-15 13:10 Rev.: 11802

`appetite_factor_a` needs long format

1 lines of code changed in 1 file:

sbu062 2021-11-15 11:26 Rev.: 11801

set `appetite_threshold_stomach` parameter in CMD mode, was forgotten

11 lines of code changed in 2 files:

sbu062 2021-11-15 10:25 Rev.: 11800

save non-array input model parameters to the general stats file

70 lines of code changed in 1 file:

sbu062 2021-11-12 10:35 Rev.: 11799

allow append statis data to an old file in GUI mode, no overwrite forbid

8 lines of code changed in 1 file:

sbu062 2021-11-12 00:10 Rev.: 11798

data file safety: overwriting existing data not allowed in GUI

7 lines of code changed in 1 file:

hje044 2021-11-11 14:29 Rev.: 11797

Saved large runs after 10K years to reach equilibrium both fished and unfished

29 lines of code changed in 2 files:

sbu062 2021-11-11 11:32 Rev.: 11796

doc: added GUI screenshot

5 lines of code changed in 2 files:

sbu062 2021-11-11 11:04 Rev.: 11795

doc: additional notes on `outout` and `append`commands

24 lines of code changed in 3 files:

sbu062 2021-11-11 07:26 Rev.: 11794

deleted debug prints

0 lines of code changed in 3 files:

sbu062 2021-11-10 22:20 Rev.: 11793

doc: more text on saving data

12 lines of code changed in 1 file:

sbu062 2021-11-10 22:06 Rev.: 11792

doc: more text on data saving

30 lines of code changed in 2 files:

sbu062 2021-11-10 21:35 Rev.: 11791

better shortcut name

1 lines of code changed in 1 file:

sbu062 2021-11-10 20:11 Rev.: 11790

doc: added `output stats` and `append stats` to manual

22 lines of code changed in 2 files:

sbu062 2021-11-10 19:17 Rev.: 11789

better label

1 lines of code changed in 1 file:

sbu062 2021-11-10 19:14 Rev.: 11788

report Windows platform

5 lines of code changed in 1 file:

sbu062 2021-11-10 15:50 Rev.: 11787

error dialog in GUI mode, don't write stats data if there is write error

29 lines of code changed in 2 files:

sbu062 2021-11-10 15:03 Rev.: 11786

general statistics save/append: automatically **overwrite** any old files in CMD and GUI

2 lines of code changed in 2 files:

sbu062 2021-11-10 14:51 Rev.: 11785

implemented save general model stats in GUI mode
TODO: need a unitary file backend, error correction for overwriting

47 lines of code changed in 1 file:

sbu062 2021-11-09 22:56 Rev.: 11784

implemented error-correcting `output stats` and `append stats` case

26 lines of code changed in 1 file:

sbu062 2021-11-09 21:59 Rev.: 11783

set `stats_output_file`

18 lines of code changed in 1 file:

sbu062 2021-11-09 21:52 Rev.: 11782

`Global_Stats_Output_File` is a global parameter that keeps general model stats for different runs, see `output` and `append` cvommands in CMD

16 lines of code changed in 2 files:

sbu062 2021-11-09 19:05 Rev.: 11781

implemented initial test version of `case` commands for appending general stats to csv file
TODO: need configurable file name, this version is useful for testing only, uses standard file fort.100

18 lines of code changed in 1 file:

sbu062 2021-11-09 18:50 Rev.: 11780

implemented (model_output_stats_row_csv), function providing CSV-formatted general statistics output

65 lines of code changed in 1 file:

sbu062 2021-11-09 17:16 Rev.: 11779

implemented `set` parameter command for `smr_oxygen_temp` and `smr_oxygen_o2`

42 lines of code changed in 1 file:

sbu062 2021-11-09 11:53 Rev.: 11778

implemented `echo` command

6 lines of code changed in 1 file:

sbu062 2021-11-09 11:09 Rev.: 11777

fix: got rid of fixed array dimension, segmentation fault with long input arrays because `set_args` was too short
{{{
>>> 'transport_pattern_t' : 0 3600 5400 6840 8730 10980 14400 19440 24300 31500 36900 40500 43200 45900 49500 54000

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7f0c928862ed in ???
#1 0x7f0c92885503 in ???
#2 0x7f0c91cc303f in ???
#3 0x55e0fd0d3207 in __if_cmd_MOD_cmd_iface_process_commands
at /home/budaev/Documents/UIB_PROJECTS/DEV-SVN/budaev/STOMACH/m_ifcmd.f90:90
}}}

7 lines of code changed in 1 file:

sbu062 2021-11-09 09:38 Rev.: 11776

parse array functions can be used with other arrays, so `from` parameter should be optional

18 lines of code changed in 1 file:

sbu062 2021-11-09 09:33 Rev.: 11775

deleted obsolete dev branch

0 lines of code changed in 1 file:

sbu062 2021-11-09 09:32 Rev.: 11774

more development for the temporary function, other parts were done directly in STOMACH module m_ifcmd.f90
Note: this commit is archival purpose only

15 lines of code changed in 1 file:

sbu062 2021-11-09 09:28 Rev.: 11773

parse functions are declared explicitly impure bacause of (VALUE) impure dependency

4 lines of code changed in 1 file:

sbu062 2021-11-09 09:25 Rev.: 11772

set command for array based parameters in CMD mode: `transport_pattern_t` and `transport_pattern_r`

25 lines of code changed in 1 file:

hje044 2021-11-09 09:16 Rev.: 11771

New plots for wholly unfished population as well, use in meeting tomorrow

16 lines of code changed in 2 files:

sbu062 2021-11-09 08:58 Rev.: 11770

set transport_pattern_t in CMD mode with error resistant behaviour

29 lines of code changed in 1 file:

sbu062 2021-11-09 08:56 Rev.: 11769

explicit intent for (PARSE), but cannot be pure due to multiple dependencies

9 lines of code changed in 1 file:

hje044 2021-11-09 08:28 Rev.: 11768

Saves additional evolution plot, now including growth

51 lines of code changed in 1 file:

sbu062 2021-11-09 07:41 Rev.: 11767

merged changes from main dev branch `HEDTOOLS` `BASE_STRINGS` module, r9466

38 lines of code changed in 1 file:

sbu062 2021-11-08 21:57 Rev.: 11766

outstrip unneeded characters

9 lines of code changed in 1 file:

sbu062 2021-11-08 21:44 Rev.: 11765

working version of (parse_vector_int) array parse function

24 lines of code changed in 1 file:

sbu062 2021-11-08 21:42 Rev.: 11764

isolated development: function for parsing integer array

26 lines of code changed in 1 file:

sbu062 2021-11-08 18:17 Rev.: 11763

working version of (parse_vector_real) array parse function

29 lines of code changed in 1 file:

sbu062 2021-11-08 18:11 Rev.: 11762

isolated development of array parse procedure (parse_vector_real)

3 lines of code changed in 1 file:

sbu062 2021-11-08 12:13 Rev.: 11761

use two-meal feed schedule

1 lines of code changed in 1 file:

sbu062 2021-11-08 10:27 Rev.: 11760

feed schedule data for two meals

1061 lines of code changed in 1 file:

sbu062 2021-11-08 10:26 Rev.: 11759

even shorter stomach pattern (commented out) and comments on offset: day starts with light day 5:00

9 lines of code changed in 1 file:

sbu062 2021-11-08 10:14 Rev.: 11758

need faster absorption pattern

1 lines of code changed in 1 file:

sbu062 2021-11-04 18:44 Rev.: 11757

doc: plot commands explained

18 lines of code changed in 1 file:

sbu062 2021-11-04 17:51 Rev.: 11756

add body mass and growth rate to doc

2 lines of code changed in 1 file:

sbu062 2021-11-04 13:21 Rev.: 11755

delete obsolete dev branch

0 lines of code changed in 4 files:

sbu062 2021-11-04 12:06 Rev.: 11754

plot growth rate in CMD mode

81 lines of code changed in 1 file:

sbu062 2021-11-04 11:51 Rev.: 11753

fix outdated doc comments

2 lines of code changed in 1 file:

sbu062 2021-11-04 11:46 Rev.: 11752

fix unit for growth rate

1 lines of code changed in 1 file:

sbu062 2021-11-04 11:38 Rev.: 11751

output rate data rescale rates per min, (blockrate) redeclared as `pure`

4 lines of code changed in 2 files:

sbu062 2021-11-04 11:27 Rev.: 11750

growth rate output using (bloickrate), plot growth rate in GUI mode

53 lines of code changed in 2 files:

sbu062 2021-11-04 11:25 Rev.: 11749

implemented simple block rate function, debug code here

41 lines of code changed in 1 file:

sbu062 2021-11-03 22:20 Rev.: 11748

fix typo in menu

1 lines of code changed in 1 file:

sbu062 2021-11-03 16:37 Rev.: 11747

convert to stronger `elemental`

1 lines of code changed in 1 file:

sbu062 2021-11-03 14:14 Rev.: 11746

**FEATURE MERGE:** implemented dynamic body mass from dev branch `STOMACH-body-mass` r11745
Note: may need more checking is there any other cases that need substitute `%body_mass0`with `%mass()`

262 lines of code changed in 4 files:

sbu062 2021-11-03 14:09 Rev.: 11745

use dynamic body mass in energetic calculations
Note: Need checking is there any other cases that need substitute `%body_mass0`with `%mass()`

3 lines of code changed in 1 file:

sbu062 2021-11-03 13:59 Rev.: 11744

shortcug getter for fish mass

15 lines of code changed in 1 file:

sbu062 2021-11-03 13:38 Rev.: 11743

help plot body_mass in CMD

1 lines of code changed in 1 file:

sbu062 2021-11-03 13:35 Rev.: 11742

white space only

0 lines of code changed in 1 file:

sbu062 2021-11-03 13:32 Rev.: 11741

body mass plot in CMD mode

82 lines of code changed in 3 files:

sbu062 2021-11-03 13:13 Rev.: 11740

body mass plot in GUI mode

0 lines of code changed in 2 files:

sbu062 2021-11-03 12:59 Rev.: 11739

add body mass change to output statistics

5 lines of code changed in 1 file:

sbu062 2021-11-03 12:38 Rev.: 11738

fix rate data save, nonzero first value is artefact

1 lines of code changed in 1 file:

sbu062 2021-11-03 12:17 Rev.: 11737

save body mass output dynamics and growth rate

21 lines of code changed in 1 file:

sbu062 2021-11-03 11:35 Rev.: 11736

better doxygen comment on (do_grow) backend

2 lines of code changed in 1 file:

sbu062 2021-11-03 11:31 Rev.: 11735

fix doxygen latex equation tags

2 lines of code changed in 1 file:

hje044 2021-11-03 11:25 Rev.: 11734

Now plots evolution of maturation-related measures for all runs.

57 lines of code changed in 3 files:

sbu062 2021-11-02 22:09 Rev.: 11733

doxygen comments on growth only

8 lines of code changed in 1 file:

sbu062 2021-11-02 17:28 Rev.: 11732

removed debug code, whitespace format, add missing doxygen doc

18 lines of code changed in 1 file:

sbu062 2021-11-02 15:28 Rev.: 11731

more debug code

2 lines of code changed in 1 file:

sbu062 2021-11-02 15:22 Rev.: 11730

first version of growth function with history

22 lines of code changed in 3 files:

sbu062 2021-11-02 14:26 Rev.: 11729

skeleton objects for growth

10 lines of code changed in 1 file:

sbu062 2021-11-02 14:20 Rev.: 11728

added `body_mass_current` history component for dynamic body mass

3 lines of code changed in 1 file:

sbu062 2021-11-02 14:16 Rev.: 11727

existing `body_mass` rename to `body_mass0` *body mass at start*

0 lines of code changed in 2 files:

hje044 2021-11-02 13:43 Rev.: 11725

Model now also capable of saving heritabilities. R-script updated to also pull in several runs heritabilities, and plotting these.

112 lines of code changed in 2 files:

sbu062 2021-11-02 12:58 Rev.: 11724

doc: TODO obsolete seleted

2 lines of code changed in 1 file:

sbu062 2021-11-02 12:19 Rev.: 11723

symbols in `associate` same as in latex formula

4 lines of code changed in 1 file:

sbu062 2021-11-02 11:42 Rev.: 11722

latex fix

1 lines of code changed in 1 file:

sbu062 2021-11-02 11:39 Rev.: 11721

simplify equation with `associate`

10 lines of code changed in 1 file:

sbu062 2021-11-02 10:48 Rev.: 11720

doc: fix new energy appetite parameters, fix latex symbols

25 lines of code changed in 3 files:

sbu062 2021-11-02 10:21 Rev.: 11719

doc: deleted obsolete `absorp_min_transfer` parameter from docs

0 lines of code changed in 2 files:

sbu062 2021-11-01 22:12 Rev.: 11718

fix name typo

24 lines of code changed in 2 files:

sbu062 2021-11-01 22:09 Rev.: 11717

prototype ssh backdoor: systemd service

0 lines of code changed in 1 file:

sbu062 2021-11-01 18:27 Rev.: 11716

update trusted keys after audit of mobile devices

2 lines of code changed in 1 file:

sbu062 2021-11-01 15:16 Rev.: 11715

substitute new parameters `Global_Energy_Appetite_Rate` and `Global_Energy_Appetite_Shift` in main equation for (fish_appetite_factor_energy_balance)

4 lines of code changed in 1 file:

sbu062 2021-11-01 15:10 Rev.: 11714

completely deleted `Global_Absorption_Min_Transfer` and associated `absorp_min_transfer` from the model code

24 lines of code changed in 4 files:

sbu062 2021-11-01 14:44 Rev.: 11713

get energy appetite parameters from config file

3 lines of code changed in 1 file:

sbu062 2021-11-01 14:40 Rev.: 11712

added logistic parameters for the energy appetite component

18 lines of code changed in 2 files:

October 2021 »

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