December 2019 Commit Log

Number of Commits:
245
Number of Active Developers:
5
sbu062 2019-12-20 13:42 Rev.: 9191

added long integer version to (APPEND), merged from dev branch r9162
- This must go to next minor revision 1.4

492 lines of code changed in 1 file:

sbu062 2019-12-20 13:26 Rev.: 9190

long integer 64 bit version of CSV_IO (append), merged from STOMACH r9162
- this must go to next minor version 1.4, new feature

483 lines of code changed in 1 file:

sbu062 2019-12-20 12:41 Rev.: 9189

portability, merged r9188, as in HEDTOOLS r9185

1491 lines of code changed in 29 files:

sbu062 2019-12-20 11:58 Rev.: 9188

improved portability for Windows, use macros for platform-specific tools (`grep`, `cut`,`uname`etc.) as in HEDTOOLS r9185

71 lines of code changed in 1 file:

sbu062 2019-12-20 11:31 Rev.: 9187

merged latest changes in HEDTOOLS r9185

384 lines of code changed in 4 files:

sbu062 2019-12-20 11:30 Rev.: 9186

remove dependency on Linux tools, merged r9185

20 lines of code changed in 2 files:

sbu062 2019-12-20 11:25 Rev.: 9185

improve portability for Windows, deleted dependency on Linux tools `grep` and `cut`

10 lines of code changed in 1 file:

sbu062 2019-12-19 12:58 Rev.: 9184

fixed `echo` in autogenerated code macro, use GNU-compatible `echo.exe` on Windows, see r9179

23 lines of code changed in 1 file:

sbu062 2019-12-19 11:49 Rev.: 9183

fix autogenerated code on Windows 10, see r9179, merged r9180

59 lines of code changed in 1 file:

sbu062 2019-12-19 11:40 Rev.: 9182

Fixed build on Windows 10: echo quirks
- merged from SB r9179 and r9181
- redefine `echo` under shell command to refer to a third-party `echo.exe` command under Windows; Windows 10 does not automatically use third-party echo under `shell echo` macro, it uses built-in echo

101 lines of code changed in 3 files:

sbu062 2019-12-19 11:32 Rev.: 9181

Fixed build on Windows 10 with third-party GNU-compatible `echo` as in r9179

56 lines of code changed in 1 file:

sbu062 2019-12-19 10:52 Rev.: 9180

report what is used for `ECHO`

1 lines of code changed in 1 file:

sbu062 2019-12-19 10:46 Rev.: 9179

redefine `echo` under shell command to refer to a third-party echo.exe command under Windows
- quirk: Windows 10 does not automatically use third-party echo under `shell echo` macro, it uses built-in echo

58 lines of code changed in 1 file:

sbu062 2019-12-19 10:41 Rev.: 9178

revert to double qoted echo shell commands

47 lines of code changed in 1 file:

sbu062 2019-12-19 10:21 Rev.: 9177

redefine `echo` under shell command to refer to a third-party echo.exe command under Windows
- quirk: Wiondows 10 does not automatically use third-party echo under `shell echo` macro, it uses built-in

53 lines of code changed in 1 file:

nfijg 2019-12-19 10:06 Rev.: 9176

redefine ECHO to refer to echo.exe on Windows 10, it always forces use of built-in echo command

43 lines of code changed in 1 file:

nfijg 2019-12-19 09:53 Rev.: 9175

set echo platform-specific

3 lines of code changed in 1 file:

sbu062 2019-12-18 20:33 Rev.: 9174

better name

0 lines of code changed in 25 files:

sbu062 2019-12-18 20:13 Rev.: 9173

added GNU binary tools for building HEDTOOLS on Windows platform

0 lines of code changed in 25 files:

nfijg 2019-12-18 12:15 Rev.: 9171

quiting works on windows 10

0 lines of code changed in 2 files:

sbu062 2019-12-18 11:31 Rev.: 9168

Makefile double quotes may not work on all platformssuch as Windows 10
- parentheses must use escaping, e.g. '\('

43 lines of code changed in 1 file:

sbu062 2019-12-17 20:35 Rev.: 9167

portability, array constructor

2 lines of code changed in 1 file:

sbu062 2019-12-17 20:30 Rev.: 9166

debug disabled

1 lines of code changed in 1 file:

sbu062 2019-12-17 20:29 Rev.: 9165

debug file parameter

5 lines of code changed in 1 file:

sbu062 2019-12-17 20:19 Rev.: 9164

comments fix

3 lines of code changed in 1 file:

sbu062 2019-12-17 20:17 Rev.: 9163

comments fixed

6 lines of code changed in 1 file:

sbu062 2019-12-17 20:12 Rev.: 9162

long integer 64 bit version of CSV_IO (append)

484 lines of code changed in 2 files:

sbu062 2019-12-17 19:46 Rev.: 9161

deleted old debug write procedure (debug_step_write_out) and all related debug counters

1 lines of code changed in 1 file:

sbu062 2019-12-17 19:27 Rev.: 9160

now invoked (detailed_csv_output_) routines in debug mode

24 lines of code changed in 1 file:

sbu062 2019-12-17 18:14 Rev.: 9159

debugging columns must be local to main running procedure

3 lines of code changed in 1 file:

sbu062 2019-12-17 18:11 Rev.: 9158

done csv record saving procedures, detailed raw data

51 lines of code changed in 1 file:

sbu062 2019-12-17 16:59 Rev.: 9157

continue filling csv procedure [work in bus]

44 lines of code changed in 1 file:

sbu062 2019-12-17 15:24 Rev.: 9156

error reporting (csv_file_error_report) is module-global

13 lines of code changed in 1 file:

sbu062 2019-12-17 15:17 Rev.: 9155

filling skeleton

32 lines of code changed in 1 file:

sbu062 2019-12-17 13:53 Rev.: 9154

continue skeleton (detailed_csv_output_open)

6 lines of code changed in 1 file:

sbu062 2019-12-17 13:45 Rev.: 9153

continue skeleton for debug detailed data out to csv

24 lines of code changed in 1 file:

sbu062 2019-12-17 13:32 Rev.: 9152

filling skeleton

34 lines of code changed in 1 file:

sbu062 2019-12-17 13:13 Rev.: 9151

skeleton subroutines for writing detailed step data to CSV

21 lines of code changed in 1 file:

tla051 2019-12-17 11:39 Rev.: 9147

add INPUT FILE temperature environment

0 lines of code changed in 1 file:

tla051 2019-12-17 11:38 Rev.: 9146

last working code

114 lines of code changed in 4 files:

lhi088 2019-12-16 10:20 Rev.: 9144

tidied up code and comments

197 lines of code changed in 5 files:

sbu062 2019-12-16 09:55 Rev.: 9143

reduce clutter in doxygen doc

3 lines of code changed in 1 file:

sbu062 2019-12-15 11:55 Rev.: 9142

fix help

2 lines of code changed in 1 file:

sbu062 2019-12-14 20:03 Rev.: 9141

fix help screen

4 lines of code changed in 1 file:

sbu062 2019-12-14 19:52 Rev.: 9140

done plotting command for n of feed items encountered

74 lines of code changed in 1 file:

sbu062 2019-12-14 19:36 Rev.: 9139

added plotting commands for n foods not ingested

82 lines of code changed in 1 file:

sbu062 2019-12-14 19:17 Rev.: 9138

added total n of food items provided/encountered to model output arrays

30 lines of code changed in 1 file:

sbu062 2019-12-14 17:27 Rev.: 9137

combine (output_arrays_add_not_ingested) into (output_arrays_add_ingested)

17 lines of code changed in 1 file:

sbu062 2019-12-14 17:16 Rev.: 9136

added n food items not ingested wasted to model output arrays, food scheduling saved in output csv file

80 lines of code changed in 1 file:

sbu062 2019-12-14 16:18 Rev.: 9135

debug output option disabled

1 lines of code changed in 1 file:

sbu062 2019-12-14 16:16 Rev.: 9134

additional command line options to force run

4 lines of code changed in 1 file:

sbu062 2019-12-14 16:12 Rev.: 9133

small fixes formatting

30 lines of code changed in 1 file:

sbu062 2019-12-14 15:44 Rev.: 9132

read food_provision_pattern, loop-based version

8 lines of code changed in 1 file:

sbu062 2019-12-14 14:19 Rev.: 9131

read food_provision_pattern, first preliminary non-loop version

23 lines of code changed in 1 file:

sbu062 2019-12-14 13:51 Rev.: 9130

done food sheduling parameter reporting in GUI mode

30 lines of code changed in 2 files:

sbu062 2019-12-14 13:42 Rev.: 9129

implemented read parameters for food provisioning scheduler
- print parameters done for CMD not GUI

36 lines of code changed in 4 files:

sbu062 2019-12-14 13:21 Rev.: 9128

food provision patterning parameters substituted by array, this makes it possible to define various patterns
- patterning array is 2 elements for two-step pattern as before

13 lines of code changed in 3 files:

sbu062 2019-12-14 13:08 Rev.: 9127

food scheduling now based on global scheduling array
- sheduling array setting parameters still fixed in
COMMONDATA, need parameter file read and cmd set code

13 lines of code changed in 2 files:

sbu062 2019-12-14 12:13 Rev.: 9126

debug code deleted, diff check okay
- enabled version 2, array-based code as it better vectorizes

5 lines of code changed in 2 files:

sbu062 2019-12-14 12:10 Rev.: 9125

developing global provisioning pattern in form of a global logical array
- debug code here

39 lines of code changed in 3 files:

sbu062 2019-12-14 11:35 Rev.: 9124

put two-interval food scheduling to (schedule) method, scheduling parameters set as fixed for debug: need reading setting code

26 lines of code changed in 2 files:

sbu062 2019-12-14 11:20 Rev.: 9123

comments only

13 lines of code changed in 1 file:

sbu062 2019-12-14 10:36 Rev.: 9122

made two-interval checking function for food scheduling

22 lines of code changed in 1 file:

sbu062 2019-12-13 13:06 Rev.: 9121

fix autorun, `.csv` extension was not appended due to ninitialised tag string

5 lines of code changed in 1 file:

sbu062 2019-12-13 12:29 Rev.: 9120

added model file tag in unattended mode

27 lines of code changed in 3 files:

sbu062 2019-12-13 08:51 Rev.: 9119

parameter abbreviations from setting shown in `show parameters` command, option to not show progress bar in CMD mode

66 lines of code changed in 3 files:

sbu062 2019-12-12 15:52 Rev.: 9118

better format

3 lines of code changed in 2 files:

sbu062 2019-12-12 15:02 Rev.: 9117

fix format

1 lines of code changed in 1 file:

sbu062 2019-12-12 14:59 Rev.: 9116

progress bar in cmd mode done

40 lines of code changed in 3 files:

sbu062 2019-12-12 14:43 Rev.: 9115

added prototype progress bar in txt mode

5 lines of code changed in 1 file:

sbu062 2019-12-12 11:26 Rev.: 9114

better startup info screen

8 lines of code changed in 1 file:

sbu062 2019-12-12 10:56 Rev.: 9113

plot appetite in plot help

1 lines of code changed in 1 file:

sbu062 2019-12-12 10:45 Rev.: 9112

added overall appetite plotting to CMD interface

65 lines of code changed in 1 file:

sbu062 2019-12-12 10:35 Rev.: 9111

added fish appetite to model output arrays

18 lines of code changed in 1 file:

sbu062 2019-12-12 10:33 Rev.: 9110

delete output csv on distclean

1 lines of code changed in 1 file:

sbu062 2019-12-11 20:50 Rev.: 9109

added plot appetite factor function

41 lines of code changed in 1 file:

sbu062 2019-12-11 20:38 Rev.: 9108

save output arrays in batch run mode

1 lines of code changed in 1 file:

sbu062 2019-12-11 19:43 Rev.: 9107

test modules from https://people.sc.fsu.edu/~jburkardt

44390 lines of code changed in 6 files:

sbu062 2019-12-11 12:12 Rev.: 9106

small reformat cmd help screens

10 lines of code changed in 1 file:

sbu062 2019-12-11 12:02 Rev.: 9105

added plotting commands help

27 lines of code changed in 1 file:

sbu062 2019-12-11 11:41 Rev.: 9104

TIMERS updated to latest r9099

25 lines of code changed in 1 file:

sbu062 2019-12-11 11:36 Rev.: 9103

added comment on cpu time

0 lines of code changed in 2 files:

sbu062 2019-12-11 11:34 Rev.: 9102

addet comment note

25 lines of code changed in 1 file:

sbu062 2019-12-11 11:12 Rev.: 9100

added a demo/test program for TIMERS module

29 lines of code changed in 1 file:

sbu062 2019-12-11 11:10 Rev.: 9099

merged latest fixes in TIMERS module r9098

6 lines of code changed in 2 files:

sbu062 2019-12-11 11:06 Rev.: 9098

fix kind

3 lines of code changed in 1 file:

sbu062 2019-12-11 10:32 Rev.: 9097

use consistent name TIMERS

0 lines of code changed in 3 files:

sbu062 2019-12-11 10:27 Rev.: 9096

dapted module for general use, merged r9095

2 lines of code changed in 1 file:

sbu062 2019-12-11 10:24 Rev.: 9095

delete (show) method to avoid extra dependencies that are not needed outside of AHA context

1 lines of code changed in 1 file:

sbu062 2019-12-10 22:19 Rev.: 9094

tolerance must be private, unused outside

1 lines of code changed in 1 file:

sbu062 2019-12-10 22:00 Rev.: 9093

added STOPWATCH module and timing reporting; process incorrect command input

204 lines of code changed in 3 files:

sbu062 2019-12-10 21:27 Rev.: 9092

STOPWATCH module, copied from the AHA model

40 lines of code changed in 1 file:

sbu062 2019-12-10 17:58 Rev.: 9091

fix file name extension

17 lines of code changed in 1 file:

sbu062 2019-12-10 17:10 Rev.: 9090

minor fix output

2 lines of code changed in 1 file:

sbu062 2019-12-10 16:49 Rev.: 9089

need trim for fixed string

9 lines of code changed in 3 files:

sbu062 2019-12-10 16:24 Rev.: 9088

user-adjustable plot save with error correction

32 lines of code changed in 2 files:

sbu062 2019-12-10 15:30 Rev.: 9087

DISLIN_Save_FMT is not fixed now, must be adjustable in `set` command

14 lines of code changed in 3 files:

sbu062 2019-12-10 15:24 Rev.: 9086

adjuet write outputs, global save format

18 lines of code changed in 2 files:

sbu062 2019-12-10 13:46 Rev.: 9085

implemented (plot_output_total_midgut_absorption)

65 lines of code changed in 1 file:

sbu062 2019-12-10 13:35 Rev.: 9084

implemented (plot_output_total_midgut)

77 lines of code changed in 1 file:

sbu062 2019-12-10 13:27 Rev.: 9083

(plot_output_total_stomach) implemented

77 lines of code changed in 1 file:

sbu062 2019-12-10 13:09 Rev.: 9082

plotting command to save midgut mm pattern and total ingested

28 lines of code changed in 1 file:

sbu062 2019-12-10 12:32 Rev.: 9081

(plot_output_total_ingested) now plots squeezed model output array, maximum points MAX_POINTS_PLOT

35 lines of code changed in 2 files:

sbu062 2019-12-10 10:01 Rev.: 9080

(plot_output_total_ingested) to plot output array cumulative ingested

25 lines of code changed in 1 file:

sbu062 2019-12-10 09:23 Rev.: 9079

better help screen

23 lines of code changed in 1 file:

sbu062 2019-12-10 09:01 Rev.: 9078

rename record variable, shorter to fit

16 lines of code changed in 1 file:

sbu062 2019-12-10 08:56 Rev.: 9077

debug code deleted, intel compiler bug report comment deleted
- ifort test pass

0 lines of code changed in 1 file:

sbu062 2019-12-10 08:53 Rev.: 9076

(output_arrays_save_csv) reimplemented to build records rather than use high-levet matrix write
- This is a work around against Intel Fortran bug segmentation fault
- high-level matrix write pcall still here for debugging, fiff test pass

78 lines of code changed in 1 file:

sbu062 2019-12-10 08:19 Rev.: 9075

csv modules moved to within procedure scope rather than module scope

8 lines of code changed in 3 files:

sbu062 2019-12-10 08:05 Rev.: 9074

rename for consistency

4 lines of code changed in 2 files:

sbu062 2019-12-10 08:03 Rev.: 9073

save csv functions moved to SIMULATE
- they may be called from GUI also

47 lines of code changed in 2 files:

sbu062 2019-12-10 07:54 Rev.: 9072

save output arrays procedure copied (should move) to SIMULATE module

38 lines of code changed in 1 file:

sbu062 2019-12-09 23:50 Rev.: 9071

more comments on intel compiler bug

2 lines of code changed in 1 file:

sbu062 2019-12-09 23:42 Rev.: 9070

intel compiler bug report

17 lines of code changed in 1 file:

sbu062 2019-12-09 23:40 Rev.: 9069

obsolete conflicting (average) not needed as there is better implementation from AHA model

0 lines of code changed in 1 file:

sbu062 2019-12-09 23:06 Rev.: 9068

implemented midgut absorption plot command in CMD

19 lines of code changed in 2 files:

sbu062 2019-12-09 22:31 Rev.: 9067

implemented `save output_arrays` command in CMD mode

28 lines of code changed in 2 files:

sbu062 2019-12-09 22:13 Rev.: 9066

added complete reset functionality with reread of config files
- this requires reallocation of grid arrays in (read_parameters_file)

41 lines of code changed in 2 files:

sbu062 2019-12-09 20:38 Rev.: 9065

(output_arrays_init) called only at runtime

3 lines of code changed in 3 files:

sbu062 2019-12-09 20:16 Rev.: 9064

need to reinit output array objects before each run because timesteps can change

7 lines of code changed in 2 files:

sbu062 2019-12-09 19:23 Rev.: 9063

small reformat help screen

4 lines of code changed in 1 file:

sbu062 2019-12-09 19:20 Rev.: 9062

save commands parsed separately

28 lines of code changed in 1 file:

sbu062 2019-12-09 18:35 Rev.: 9061

use global parameter for dislin basename

3 lines of code changed in 2 files:

sbu062 2019-12-09 18:30 Rev.: 9060

saving plots does not require graphic capabilities, (disfin) not needed for calling (qplot)

3 lines of code changed in 1 file:

sbu062 2019-12-09 16:59 Rev.: 9059

added save plot in pdf

9 lines of code changed in 1 file:

sbu062 2019-12-09 16:51 Rev.: 9058

in (plot_stomach_pattern) use any arbitrary metafile format

5 lines of code changed in 1 file:

sbu062 2019-12-09 16:46 Rev.: 9057

(x11fnt) causes warnings on non-X11 platforms, on X11, no warnings if xfonts-75dpi package is installed
- `sudo apt-get install xfonts-75dpi` on Linux

0 lines of code changed in 1 file:

sbu062 2019-12-09 16:40 Rev.: 9056

comments fixed

3 lines of code changed in 1 file:

sbu062 2019-12-09 16:33 Rev.: 9055

plot stomach pattern in CMD mode

67 lines of code changed in 2 files:

sbu062 2019-12-09 14:56 Rev.: 9054

enable or disable extended logging in (test_run)

8 lines of code changed in 1 file:

sbu062 2019-12-09 14:49 Rev.: 9053

delete obsolete debug code

0 lines of code changed in 1 file:

sbu062 2019-12-09 14:47 Rev.: 9052

done set parameters in command line interface

174 lines of code changed in 1 file:

nzlcj 2019-12-09 13:57 Rev.: 9051

Coded together. Add timestep to ind information. Made large array that holds all individuals over time. Added time to csv writing procedure (butn ot binary).

27 lines of code changed in 3 files:

sbu062 2019-12-09 13:02 Rev.: 9050

use (parse_int) function, addad (parse_real)

23 lines of code changed in 1 file:

sbu062 2019-12-09 12:54 Rev.: 9049

(parse_int) is integer parse parameter function

17 lines of code changed in 1 file:

lhi088 2019-12-09 12:48 Rev.: 9048

104 lines of code changed in 4 files:

sbu062 2019-12-09 12:48 Rev.: 9047

skeleton parse parameters

27 lines of code changed in 1 file:

sbu062 2019-12-09 12:19 Rev.: 9046

check and report availability of GUI windows, X or Windows

8 lines of code changed in 2 files:

sbu062 2019-12-09 12:13 Rev.: 9045

(graphics_is_available) determines if X is enabled on Linux/Unix or runtime platform is Windows

27 lines of code changed in 1 file:

sbu062 2019-12-09 11:10 Rev.: 9044

done skeleton for parsing parameters in CMD mode: show parameters not needed by dafault

22 lines of code changed in 2 files:

sbu062 2019-12-09 10:57 Rev.: 9043

need compacting commands for parsing

2 lines of code changed in 1 file:

sbu062 2019-12-09 10:52 Rev.: 9042

skeleton command line interface

74 lines of code changed in 3 files:

sbu062 2019-12-09 09:43 Rev.: 9041

are impurehis line, and those below, will be ignored--

M STOMACH/m_runtime.f90

1 lines of code changed in 1 file:

sbu062 2019-12-09 09:40 Rev.: 9040

windows style command line parameter /run added

6 lines of code changed in 2 files:

sbu062 2019-12-09 09:35 Rev.: 9039

cmd parameter to run model at startup in command line mode

19 lines of code changed in 1 file:

sbu062 2019-12-08 14:34 Rev.: 9038

dislin example draw

66 lines of code changed in 1 file:

sbu062 2019-12-08 14:26 Rev.: 9037

dislin test progress bar

42 lines of code changed in 1 file:

sbu062 2019-12-06 20:12 Rev.: 9036

fix, eaten at the first step initializes global counter to 1 not 0

10 lines of code changed in 1 file:

sbu062 2019-12-06 19:59 Rev.: 9035

added counter for total number of food items eaten to model output arrays

65 lines of code changed in 1 file:

sbu062 2019-12-06 18:47 Rev.: 9034

fix case

1 lines of code changed in 1 file:

sbu062 2019-12-06 17:02 Rev.: 9033

synchronized CSV_IO with the latest v1.3

117 lines of code changed in 1 file:

sbu062 2019-12-06 16:45 Rev.: 9032

autogenerate GUI VBA script on Windows platform

2 lines of code changed in 1 file:

sbu062 2019-12-06 16:37 Rev.: 9031

single quotes produce error in vb script

4 lines of code changed in 1 file:

sbu062 2019-12-06 16:23 Rev.: 9030

command line option to force the GUI mode

28 lines of code changed in 3 files:

sbu062 2019-12-06 15:55 Rev.: 9029

any number of command line arguments can be used

23 lines of code changed in 2 files:

sbu062 2019-12-06 15:25 Rev.: 9028

minor rearrange modules
- build and run test okay

8 lines of code changed in 5 files:

sbu062 2019-12-06 14:56 Rev.: 9027

obsolete test code, now called in RUNTIME

0 lines of code changed in 1 file:

sbu062 2019-12-06 14:43 Rev.: 9026

rearrange module calls

3 lines of code changed in 5 files:

sbu062 2019-12-06 14:29 Rev.: 9025

SIMULATE is called from RUNTIME, so output arrays and related procs moved to SIMULATE from RUNTIME
- builds and runs tested ok

110 lines of code changed in 4 files:

sbu062 2019-12-06 13:51 Rev.: 9024

added the SIMULATE module that will contain actual simulation code
- need a separate module depending on RUNTIME, that is called from
user interface modules. RUNTIME calls user interface routines
and cannot be called from them (circular)
- build and run testse ok

138 lines of code changed in 4 files:

sbu062 2019-12-06 12:43 Rev.: 9023

newer version of CSV_IO from HEDTOOLS 1.3, old version copied manually and mon-mergable deleted

119 lines of code changed in 1 file:

sbu062 2019-12-06 12:35 Rev.: 9022

fix module name, renamed by Laura

103 lines of code changed in 3 files:

sbu062 2019-12-06 12:26 Rev.: 9021

sync with Laura's code r9019, CSV_IO updated to v1.3

0 lines of code changed in 5 files:

sbu062 2019-12-06 12:14 Rev.: 9020

autogenerate Microsoft VBS script to run the model in GUI mode suppressing terminal window
- Windows shortcut should refer to the vbs script rather than model.exe

19 lines of code changed in 1 file:

lhi088 2019-12-06 11:53

7090 lines of code changed in 8 files:

sbu062 2019-12-06 11:31 Rev.: 9011

updated CSV_IO to later version 1.3 r9008 (merged from SB r9010)

117 lines of code changed in 1 file:

sbu062 2019-12-06 11:28 Rev.: 9010

updated CSV_IO to later version 1.3 r9008

117 lines of code changed in 1 file:

sbu062 2019-12-06 11:06 Rev.: 9008

synchronized stand-alone CSV_IO with HEDTOOLS 1.3

122 lines of code changed in 2 files:

sbu062 2019-12-06 09:27 Rev.: 9007

doc: r9006, added example with derived type inline conversion to array

61 lines of code changed in 1 file:

sbu062 2019-12-06 09:24 Rev.: 9006

doc: added example of inline saving to CSV implementing inline conversion of derived type array to matrix

61 lines of code changed in 1 file:

sbu062 2019-12-06 08:55 Rev.: 9005

added another demo showing how to use derived types with arrays, CSV_MATRIX_SAVE example with inline type to array conversion
- merged r9004

79 lines of code changed in 3 files:

sbu062 2019-12-06 08:48 Rev.: 9004

example of inline data save code, commented out so far, merged r9003

10 lines of code changed in 1 file:

sbu062 2019-12-06 08:46 Rev.: 9003

added example of inline data save code, with implied loops and reshape, this code is commented out

10 lines of code changed in 1 file:

sbu062 2019-12-06 08:27 Rev.: 9002

fixed bug: `ind` must not go inside (save_individuals_csv) and (save_individuals_bin), should be input argument `inds`, merged from r9001

83 lines of code changed in 2 files:

sbu062 2019-12-06 08:23 Rev.: 9001

fixed bug `ind` is global array of individuals, but **inds** arbument should be used in (save_individuals_csv) and (save_individuals_bin)

27 lines of code changed in 1 file:

sbu062 2019-12-06 08:17 Rev.: 9000

demo program showing how to convert a derived type array to a simple array, for writing to CSV output

79 lines of code changed in 1 file:

sbu062 2019-12-06 08:16 Rev.: 8999

added compile command, easier use

3 lines of code changed in 1 file:

sbu062 2019-12-05 18:09 Rev.: 8998

added ignore file and attributes

0 lines of code changed in 1 file:

sbu062 2019-12-05 15:52 Rev.: 8997

added average absorption to csv output

5 lines of code changed in 1 file:

sbu062 2019-12-05 15:48 Rev.: 8996

basically repeat previous rename at r8995

2 lines of code changed in 1 file:

sbu062 2019-12-05 15:45 Rev.: 8995

rename component with a shorter name, added more data to csv output

8 lines of code changed in 1 file:

sbu062 2019-12-05 15:34 Rev.: 8994

reformat tab indents only

5 lines of code changed in 1 file:

sbu062 2019-12-05 15:32 Rev.: 8993

save all arrays into single csv file

7 lines of code changed in 1 file:

sbu062 2019-12-05 15:22 Rev.: 8992

better name, update is by time step

4 lines of code changed in 1 file:

sbu062 2019-12-05 14:45 Rev.: 8991

merged bug fix r8990, missing reallocation of arrays

11 lines of code changed in 1 file:

sbu062 2019-12-05 14:43 Rev.: 8990

fix wrong allocation of `tmp_data`, they have another dimension in the second part, surv_traits

11 lines of code changed in 1 file:

sbu062 2019-12-05 14:27 Rev.: 8989

merged data saving subroutines to the main branch

6846 lines of code changed in 4 files:

sbu062 2019-12-05 14:18 Rev.: 8988

(save_individuals_csv) is done

53 lines of code changed in 1 file:

sbu062 2019-12-05 14:05 Rev.: 8987

fix bug, must use inds from input argument

37 lines of code changed in 1 file:

sbu062 2019-12-05 13:53 Rev.: 8986

added column names to the output file

12 lines of code changed in 1 file:

sbu062 2019-12-05 13:46 Rev.: 8985

added individual save subroutine using CSV, first non-array data components of ind

5149 lines of code changed in 2 files:

sbu062 2019-12-05 13:26 Rev.: 8984

added actual binary write code for collected_data

1319 lines of code changed in 2 files:

sbu062 2019-12-05 13:17 Rev.: 8983

data from ind_def data structures are collected into the global 3D data box

103 lines of code changed in 2 files:

sbu062 2019-12-05 11:43 Rev.: 8982

skeleton for (save_individuals)

0 lines of code changed in 2 files:

sbu062 2019-12-05 11:39 Rev.: 8981

added parmeter somacost

0 lines of code changed in 2 files:

sbu062 2019-12-05 10:41 Rev.: 8979

save output arrays in (test_run) in CSV
- BASE_STRINGS imports only (lowercase) to avoid compiler warning on ambiguous interface

10 lines of code changed in 1 file:

sbu062 2019-12-05 10:30 Rev.: 8978

minor fix comment

2 lines of code changed in 1 file:

sbu062 2019-12-05 10:27 Rev.: 8977

calculate mean volume of absorbed food

1 lines of code changed in 1 file:

sbu062 2019-12-05 10:26 Rev.: 8976

doxygen comments only fixed

13 lines of code changed in 1 file:

sbu062 2019-12-05 10:18 Rev.: 8975

(average) function code copied from the AHA model r8510 `m_common.f90`

155 lines of code changed in 1 file:

sbu062 2019-12-05 10:09 Rev.: 8974

added time step update code for total volume absorped
- long objects put under `associate` construct

7 lines of code changed in 1 file:

sbu062 2019-12-05 09:47 Rev.: 8973

small note

2 lines of code changed in 1 file:

sbu062 2019-12-05 09:44 Rev.: 8972

output arrays converted to data structure OUTPUT_ARRAYS_STEP_DEF

26 lines of code changed in 1 file:

sbu062 2019-12-05 07:35 Rev.: 8971

(write_out_debug) procedure substitutes WRITE_OUT block in (test_run)

11 lines of code changed in 1 file:

sbu062 2019-12-04 18:00 Rev.: 8970

minor reformat

2 lines of code changed in 1 file:

sbu062 2019-12-04 17:56 Rev.: 8969

optional time step in (output_arrays_update)

16 lines of code changed in 1 file:

sbu062 2019-12-04 17:47 Rev.: 8968

better names

10 lines of code changed in 1 file:

sbu062 2019-12-04 14:35 Rev.: 8967

debug write code deleted

0 lines of code changed in 1 file:

sbu062 2019-12-04 14:33 Rev.: 8966

pure subroutine cannot modify globals

1 lines of code changed in 1 file:

sbu062 2019-12-04 14:28 Rev.: 8965

(build_output_arrays) for updating output data for each time step
- cannot incorporate the backend code into THE_FISH module because RUNTIME is the last in hierarchy and depends on THE_FISH
- debug write code here, test pass, `diff`

18 lines of code changed in 1 file:

sbu062 2019-12-04 14:17 Rev.: 8964

update output arrays,, so far inline for testing
- write test pass, compares with raw okay
- need OO subroutine

3 lines of code changed in 1 file:

sbu062 2019-12-04 13:44 Rev.: 8963

minor comment forgotten

3 lines of code changed in 1 file:

sbu062 2019-12-04 13:42 Rev.: 8962

in (system_model_output_arrays_set) added optional raw global default number of time steps

15 lines of code changed in 1 file:

sbu062 2019-12-04 13:35 Rev.: 8961

init procedures for model output arrays
- may need to pass them as arguments into interface modules, arrays should be okay

42 lines of code changed in 1 file:

sbu062 2019-12-04 13:34 Rev.: 8960

also delete temporary fortran write files

1 lines of code changed in 1 file:

nzlcj 2019-12-04 13:22 Rev.: 8959

Coded together. Added constant somatic growth cost. Tried to put survival in right place but it surival is only 0, why? Added sorting into males and females in new ind array.

33 lines of code changed in 1 file:

sbu062 2019-12-04 13:09 Rev.: 8958

global parameter `Global_Run_Model_Hours` with read and display procedures

20 lines of code changed in 5 files:

sbu062 2019-12-04 12:53 Rev.: 8957

global output arrays defined

15 lines of code changed in 1 file:

sbu062 2019-12-04 12:52 Rev.: 8956

global (appetite) function

29 lines of code changed in 1 file:

sbu062 2019-12-04 12:07 Rev.: 8955

revert from debug code to r8951
- `svn merge -r HEAD:8951 . `

1 lines of code changed in 2 files:

sbu062 2019-12-04 12:03 Rev.: 8954

debug code, checking food item deletion from mid-gut

11 lines of code changed in 2 files:

lhi088 2019-12-04 11:46 Rev.: 8953

98 lines of code changed in 1 file:

lhi088 2019-12-04 11:32 Rev.: 8952

Tidied up the code. Made separate parameter file. tried to implement body mass, and two-fold cost of males.

63 lines of code changed in 2 files:

sbu062 2019-12-04 11:02 Rev.: 8951

minor reformat and comments update

5 lines of code changed in 2 files:

sbu062 2019-12-04 08:59 Rev.: 8950

fix comments

4 lines of code changed in 1 file:

sbu062 2019-12-03 19:38 Rev.: 8949

comment only

2 lines of code changed in 1 file:

sbu062 2019-12-03 19:26 Rev.: 8948

added `Global_Maximum_Duration_Midgut` parameter with data input and reporting

25 lines of code changed in 6 files:

sbu062 2019-12-03 14:44 Rev.: 8947

deleted debug array printing code, step subroutines still not elemental for further testing

3 lines of code changed in 2 files:

sbu062 2019-12-03 14:35 Rev.: 8946

preliminary version of (check_disappear) with fixed food item age threshold

5 lines of code changed in 1 file:

sbu062 2019-12-03 14:02 Rev.: 8945

#71 `absorped` data component is not used as `processed` so need not add `delta_vol`, debug code disabled, (destruct_eaten) now obsolete

17 lines of code changed in 1 file:

sbu062 2019-12-03 12:56 Rev.: 8944

absorption limited to those food items that are below limit

2 lines of code changed in 1 file:

sbu062 2019-12-03 12:33 Rev.: 8943

done check function (is_absorbed_full), debug code here

46 lines of code changed in 1 file:

sbu062 2019-12-03 08:40 Rev.: 8942

better name

5 lines of code changed in 3 files:

sbu062 2019-12-02 22:18 Rev.: 8941

`absorped` is cleaner name than `processed`

9 lines of code changed in 2 files:

sbu062 2019-12-02 22:07 Rev.: 8940

data component `volume_0` should be in mid-gut-specific class FOOD_ITEM_EATEN_MG
- was unused in FOOD_ITEM_EATEN
- needs more checking but seems okay

23 lines of code changed in 1 file:

sbu062 2019-12-02 21:22 Rev.: 8939

reuse lower order (zero) init method

17 lines of code changed in 1 file:

sbu062 2019-12-02 15:48 Rev.: 8938

debugging absorption, debug code is here

219 lines of code changed in 2 files:

sbu062 2019-12-02 12:17 Rev.: 8937

comments on (appetite_midgut)

5 lines of code changed in 1 file:

sbu062 2019-12-02 11:42 Rev.: 8936

(decide_eat) now linked to MID_GUT class, global appetite is set to multiplication of stomach and mid-gut appetite factors

22 lines of code changed in 2 files:

sbu062 2019-12-02 10:49 Rev.: 8935

appetite factor for midgut done. appetite component of skeleton base type obsolete

62 lines of code changed in 2 files:

sbu062 2019-12-02 10:48 Rev.: 8934

much smaller absorption

1 lines of code changed in 1 file:

sbu062 2019-12-02 10:08 Rev.: 8933

delete mercurial settings

0 lines of code changed in 1 file:

sbu062 2019-12-02 10:07 Rev.: 8932

add config for code::blocks

199 lines of code changed in 1 file:

sbu062 2019-12-02 10:04 Rev.: 8931

comments on generic interface (decide_eat)

4 lines of code changed in 1 file:

sbu062 2019-12-02 09:49 Rev.: 8930

comment on version.h

8 lines of code changed in 1 file:

November 2019 »

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