June 2021 Commit Log

Number of Commits:
89
Number of Active Developers:
3
aru047 2021-06-30 10:40 Rev.: 11293

EPC value added to female performance

16 lines of code changed in 2 files:

sbu062 2021-06-29 09:40 Rev.: 11292

function to calculate stomach volume from fish mass
use Salgado, A., Salgado, I., & Valdebenito, I. (2018). A direct and straightforward method for measurement real maximum fish stomach volume to improve aquaculture feeding research. Latin American Journal of Aquatic Research, 46(5), 880–889. https://doi.org/10.3856/vol46-issue5-fulltext-3

15 lines of code changed in 1 file:

sbu062 2021-06-25 14:31 Rev.: 11291

autodetect bash array upper limit

1 lines of code changed in 1 file:

sbu062 2021-06-25 14:14 Rev.: 11290

process raw csv data by multiple dielcycle group using bash array

27 lines of code changed in 2 files:

nfijg 2021-06-25 11:04 Rev.: 11289

added count and print of number of fathers in generation

230 lines of code changed in 2 files:

sbu062 2021-06-25 08:28 Rev.: 11288

add steps ranges for dielcycles

8 lines of code changed in 1 file:

sbu062 2021-06-24 11:53 Rev.: 11287

need full path to `xsend` for reliable work

1 lines of code changed in 1 file:

sbu062 2021-06-24 11:33 Rev.: 11286

change for simulation experiments data with G=1, 1000 behaviour columns

1 lines of code changed in 1 file:

sbu062 2021-06-23 19:52 Rev.: 11285

intel fortran requires strict commas in format specifier

2 lines of code changed in 1 file:

sbu062 2021-06-23 19:39 Rev.: 11284

use format for better output

4 lines of code changed in 1 file:

sbu062 2021-06-23 12:22 Rev.: 11283

report debug status in version tag

11 lines of code changed in 1 file:

sbu062 2021-06-23 12:10 Rev.: 11282

fix feeding offset application, not to day-light pattern

3 lines of code changed in 1 file:

sbu062 2021-06-23 11:46 Rev.: 11281

feeding offset should not be independently applied, but start new at each day

4 lines of code changed in 1 file:

nfijg 2021-06-21 13:46 Rev.: 11280

found and corrected double density-dependent suppression of feeding in fgain

31 lines of code changed in 2 files:

nfijg 2021-06-18 14:03 Rev.: 11279

even lower generational deviations in ShalFood and HighFaM

8 lines of code changed in 2 files:

sbu062 2021-06-18 11:40 Rev.: 11278

increased `MAX_FOOD_ITEMS_INDEX` to avoid array overflow
this fixes occasional `DEBUG_CHECK_MAX_MIDGUT` condifion

1 lines of code changed in 1 file:

nfijg 2021-06-17 11:11 Rev.: 11277

dampened environmental eviations in ShalFood, HighFaM and HighMort generations to avoid restarts

27 lines of code changed in 2 files:

sbu062 2021-06-15 12:17 Rev.: 11276

use stomach volume data from Grove et al., 1978 equation p. 514

233 lines of code changed in 3 files:

sbu062 2021-06-14 12:22 Rev.: 11275

report either version or 'FFA_MODEL_OUTPUT_TAG' on the last line in GUI

9 lines of code changed in 1 file:

sbu062 2021-06-14 11:42 Rev.: 11274

reset commands are redundant in GUI, but add load food provision pattern from csv

6 lines of code changed in 1 file:

sbu062 2021-06-14 10:12 Rev.: 11273

report provisioning pattern if pattern data file is not found

22 lines of code changed in 2 files:

sbu062 2021-06-12 09:09 Rev.: 11272

doc: move to tips and tricks

55 lines of code changed in 1 file:

sbu062 2021-06-12 08:53 Rev.: 11271

doc: added python example scheduling

20 lines of code changed in 1 file:

sbu062 2021-06-12 07:39 Rev.: 11270

doc: add example scheduling configuration from csv file

39 lines of code changed in 1 file:

sbu062 2021-06-12 07:12 Rev.: 11269

get feed scheduling from the last column of csv file

11 lines of code changed in 2 files:

sbu062 2021-06-11 22:35 Rev.: 11268

merged all latest changes from r11253

5153 lines of code changed in 24 files:

sbu062 2021-06-11 20:41 Rev.: 11267

report feed scheduling file status when reporting global parameters

26 lines of code changed in 2 files:

sbu062 2021-06-11 20:08 Rev.: 11266

`food_provision_file_repeat` controls if arbitrary food scheduling from file propagates across all 24-h periods or not

43 lines of code changed in 7 files:

sbu062 2021-06-11 19:36 Rev.: 11265

allow feed scheduling from file to be applied only once or propagate to all 24h periods in (food_provisioning_get_file)

40 lines of code changed in 2 files:

sbu062 2021-06-11 18:15 Rev.: 11264

file-based scheduling is more logical to go after config-based pattern

4 lines of code changed in 1 file:

sbu062 2021-06-11 17:52 Rev.: 11263

doc: document `food_provision_file_name` parameter

22 lines of code changed in 1 file:

sbu062 2021-06-11 17:31 Rev.: 11262

command to set `food_provision_file_name` in CMD mode

30 lines of code changed in 1 file:

nfijg 2021-06-11 14:02 Rev.: 11261

added prints of vertical distributions of GOS and inds each age in final generations

175 lines of code changed in 2 files:

sbu062 2021-06-11 13:17 Rev.: 11260

set and reset food provision schedule in GUI mode

34 lines of code changed in 1 file:

sbu062 2021-06-11 12:50 Rev.: 11259

show food provision file in print parameters function when appropriate

39 lines of code changed in 3 files:

sbu062 2021-06-11 12:33 Rev.: 11258

merged fix r11253: not closing file after data read

3 lines of code changed in 1 file:

sbu062 2021-06-11 12:28 Rev.: 11257

fixed bug r11253: close file after data reading

0 lines of code changed in 2 files:

sbu062 2021-06-11 12:20 Rev.: 11256

code formats

9 lines of code changed in 2 files:

sbu062 2021-06-11 12:13 Rev.: 11255

merged fix r11253: not closing CSV file after data read

2 lines of code changed in 1 file:

sbu062 2021-06-11 11:56 Rev.: 11254

propagated fix r11253: not closing file after reading data

6 lines of code changed in 5 files:

sbu062 2021-06-11 11:46 Rev.: 11253

fixed bug not closing CSV data after reading, could cause errors on multiple rereads

4 lines of code changed in 3 files:

sbu062 2021-06-11 09:29 Rev.: 11252

WORK: integrating (food_provisioning_get_file) into SIMULATE module
- added parameter `Global_Food_Pattern_File`
- call (food_provisioning_get_file) in SIMULATE
- some tests

42 lines of code changed in 5 files:

sbu062 2021-06-11 05:05 Rev.: 11251

`FILE_NAME_LEN` should be used for maximum length because it is limited by file name length, perhaps can be even longer

2 lines of code changed in 1 file:

sbu062 2021-06-11 04:59 Rev.: 11250

need separate parameter to define file name string length
Note: still need checking if all file name vars are consistent

6 lines of code changed in 2 files:

sbu062 2021-06-11 04:46 Rev.: 11249

scheme must be in fixed format

2 lines of code changed in 1 file:

sbu062 2021-06-11 04:39 Rev.: 11248

better comment

3 lines of code changed in 1 file:

sbu062 2021-06-11 04:36 Rev.: 11247

better description comment

3 lines of code changed in 1 file:

sbu062 2021-06-10 20:44 Rev.: 11246

(food_provisioning_get_file) gets any arbitrary food provisioning pattern from minute-interval data from CSV file

61 lines of code changed in 1 file:

nfijg 2021-06-10 19:26 Rev.: 11245

fixed some bugs in file prints in SR03

98 lines of code changed in 2 files:

sbu062 2021-06-10 10:48 Rev.: 11244

doc: document the `feed_start_offset` parameter

17 lines of code changed in 3 files:

sbu062 2021-06-10 10:21 Rev.: 11243

more appropriate to print `feed_start_offset` after `food_provision_pattern`

8 lines of code changed in 2 files:

sbu062 2021-06-10 10:15 Rev.: 11242

control `feed_start_offset` in GUI interface

11 lines of code changed in 1 file:

sbu062 2021-06-10 10:02 Rev.: 11241

control `feed_start_offset` in command line CMD interface

14 lines of code changed in 2 files:

sbu062 2021-06-10 09:52 Rev.: 11240

implamented dayly offset for feeding as an independent process controlled by (schedule_2_int)

26 lines of code changed in 4 files:

sbu062 2021-06-10 07:05 Rev.: 11239

realistic body mass; feeding pattern to three meals a day (240)

4 lines of code changed in 1 file:

sbu062 2021-06-09 20:17 Rev.: 11238

`rm` uses platform specific command

11 lines of code changed in 1 file:

sbu062 2021-06-09 09:08 Rev.: 11237

added `/O3` optimization flag on Windows

1 lines of code changed in 1 file:

sbu062 2021-06-08 13:24 Rev.: 11236

merged r11234 and previous fixes to build

25 lines of code changed in 1 file:

sbu062 2021-06-08 12:38 Rev.: 11235

`O2` and higher optimization does not work on Windows Intel Fortran, propagate fix r11234

234 lines of code changed in 57 files:

sbu062 2021-06-08 12:25 Rev.: 11234

Windows ifort glitch: `O2` and higher optimizations do not work on W10, only O1 seems to work. O2 and higher produce access violation crash

6 lines of code changed in 1 file:

sbu062 2021-06-08 09:28 Rev.: 11233

delete dependence of living cost on smr, very small effect and potentially slow down simulation
Note: this applies changes r11231:r11232
applied diff `svn diff -r 11226:11232 m_body.f90` for all branches

80 lines of code changed in 40 files:

sbu062 2021-06-08 09:14 Rev.: 11232

deleted obsolete doxygen comments after r11231

0 lines of code changed in 1 file:

sbu062 2021-06-08 08:57 Rev.: 11231

delete dependence of living cost on smr, very small effect and potentially slow down simulation

2 lines of code changed in 1 file:

sbu062 2021-06-08 07:03 Rev.: 11230

revert wrong commit from `HEDG`

4 lines of code changed in 3 files:

sbu062 2021-06-08 07:00 Rev.: 11229

fix exponent as in r11226

170 lines of code changed in 34 files:

sbu062 2021-06-08 06:51 Rev.: 11228

fix exponent as in r11226

16 lines of code changed in 8 files:

sbu062 2021-06-08 06:33 Rev.: 11227

fix power factor as in r11226
patch
{{{
Index: m_body.f90
===================================================================
--- m_body.f90 (revision 11225)
+++ m_body.f90 (working copy)
@@ -1139,7 +1139,8 @@
!! Kleiber's law: `metabolic rate = mass**3/4`
!! TODO: Get rid of the old model cost, do dependent on SMR mainly.
stepcost = this%body_mass * LIVING_COST / LIFESPAN + &
- (this%smr/SIGMA)**3/4 * this%body_mass * LIVING_COST / LIFESPAN
+ (this%smr/SIGMA)**(3.0_SRP/4.0_SRP) * this%body_mass * &
+ LIVING_COST / LIFESPAN

end function body_mass_calculate_cost_living_step

}}}


2 lines of code changed in 1 file:

sbu062 2021-06-08 04:34 Rev.: 11226

fix bug in exponent
{{{
Index: m_body.f90
===================================================================
--- m_body.f90 (revision 11225)
+++ m_body.f90 (working copy)
@@ -1139,7 +1139,8 @@
!! Kleiber's law: `metabolic rate = mass**3/4`
!! TODO: Get rid of the old model cost, do dependent on SMR mainly.
stepcost = this%body_mass * LIVING_COST / LIFESPAN + &
- (this%smr/SIGMA)**3/4 * this%body_mass * LIVING_COST / LIFESPAN
+ (this%smr/SIGMA)**(3.0_SRP/4.0_SRP) * this%body_mass * &
+ LIVING_COST / LIFESPAN

end function body_mass_calculate_cost_living_step

}}}

2 lines of code changed in 1 file:

sbu062 2021-06-08 04:20 Rev.: 11225

fix comments, duplicate deleted

5 lines of code changed in 1 file:

sbu062 2021-06-08 04:08 Rev.: 11224

The `max`condition dependent on (cost_factor_food_smr) never needed, can delete both function and `COST_FACTOR_FORAGING_SMR`

0 lines of code changed in 4 files:

aru047 2021-06-07 19:21 Rev.: 11222

last simulations for short-lived species

43 lines of code changed in 4 files:

nfijg 2021-06-07 14:44 Rev.: 11221

added panic to SRcorrplots RESPONSE and MODULATION

133 lines of code changed in 1 file:

nfijg 2021-06-07 13:58 Rev.: 11220

added panic to SRcorrplotsAPPRAISAL

30 lines of code changed in 1 file:

nfijg 2021-06-07 13:33 Rev.: 11219

added panic info in SRageneurons

75 lines of code changed in 3 files:

aru047 2021-06-07 10:18 Rev.: 11218

short-lived species, last simulations for paper 1

1308 lines of code changed in 2 files:

aru047 2021-06-07 10:11 Rev.: 11217

long simulations part 2, 200 000 generations

1320 lines of code changed in 6 files:

nfijg 2021-06-05 15:45 Rev.: 11216

removed print to file 39 POSgenome

51 lines of code changed in 4 files:

sbu062 2021-06-05 07:46 Rev.: 11215

doc: typo

1 lines of code changed in 1 file:

sbu062 2021-06-05 07:36 Rev.: 11214

doc: `body_mass` in model parameters

5 lines of code changed in 1 file:

nfijg 2021-06-03 20:54 Rev.: 11213

reshuffled more parameters

34 lines of code changed in 5 files:

nfijg 2021-06-03 19:56 Rev.: 11212

moved several parameters from i101-fishparameters.txt to iCommonfish_SNG.txt

424 lines of code changed in 5 files:

sbu062 2021-06-03 14:17 Rev.: 11211

script to recode internal GOS for complexity analysis

39 lines of code changed in 1 file:

sbu062 2021-06-03 09:47 Rev.: 11210

repeat r11209: need even longer record to fit all values

117 lines of code changed in 39 files:

sbu062 2021-06-03 09:32 Rev.: 11209

need even longer record to fit all values
This avoids crashes in simulations with very long history

3 lines of code changed in 1 file:

sbu062 2021-06-02 13:18 Rev.: 11208

need extra length for the record to avoid writing data to non-existent space beyond last character, useful against huge history crashing

40 lines of code changed in 57 files:

nfijg 2021-06-02 08:53 Rev.: 11207

2GOS

38 lines of code changed in 1 file:

nfijg 2021-06-02 08:52 Rev.: 11206

two setup-files: setup2GOS and setup3GOS

67 lines of code changed in 4 files:

sbu062 2021-06-01 23:14 Rev.: 11205

collected merge from main dev branch r11204

286 lines of code changed in 8 files:

sbu062 2021-06-01 22:59 Rev.: 11204

need longer `max_size_record` for saving very large data sets, otherwise can sometimes crash

12 lines of code changed in 1 file:

May 2021 »

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