latest fromj Ivar
Cc: Ivar Rønnestad <ivar.ronnestad@uib.no>
Reply-To: ivar.ronnestad@uib.no
Subject: Ivar Rønnestad shared "D1.4 Intermediary Report" with you.
Date: Sun, 31 Oct 2021 18:42:21 +0000
Sender: Ivar Rønnestad <no-reply@sharepointonline.com>
Ivar Rønnestad shared a file with you
Dear all,
Please find in the link an updated version of the report/Deliverable, based on the comments of Elisa with no track changes. It is also available in Sharepoint.
D1.4 Intermediary Report
This link only works for the direct recipients of this message.
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50797 lines of code changed in 1 file:
audit for auth keys
62 lines of code changed in 1 file:
note on efficiency
22 lines of code changed in 1 file:
CMD interface fix: missed volume in save plot commands: `stomach_volume` and `midgut_volume`
6 lines of code changed in 2 files:
**important** REVERT: get back to absorption algorithm as in r11569
only `DO_ABSORP` is back, new parameters untouched and not setleted, need more testing
25 lines of code changed in 1 file:
latest version
> From: Elisa Ravagnan <elra@norceresearch.no>
> Date: Thursday, 28 October 2021 at 10:48
> To: Ivar Rønnestad <Ivar.Ronnestad@uib.no>, Sergei Budaev <Sergey.Budaev@uib.no>
> Subject: iFishIENCi D1.4
> Hi,
> Is this the final version to revise?
> [cid:image001.jpg@01D7CBF6.B9742930] (Invalid URL)
>
> This version I was able to open in Word desktop app.
>
> Best
> Elisa
>
> Elisa Ravagnan, PhD
> Senior Research Scientist
> NORCE Environment, Marine Ecology
> +47 46 90 22 55 (work)
> +47 40 46 20 90 (mobile)
> Nygårdsgaten 112, 5008 Bergen, Norway
> www.norceresearch.no<http://www.norceresearch.no
89998 lines of code changed in 1 file:
ssh config file
6 lines of code changed in 1 file:
proxychains config for SOCKS
65 lines of code changed in 2 files:
links on Microsoft docs
0 lines of code changed in 2 files:
better name
0 lines of code changed in 2 files:
agent: socks5 proxy via ssh
0 lines of code changed in 2 files:
backdoor agent: brief manual on Windows10 tunneling
0 lines of code changed in 1 file:
arrow fixed
0 lines of code changed in 4 files:
gateway ports try tunnel
1 lines of code changed in 1 file:
working config for ssh Windows, localhoist connects
8 lines of code changed in 1 file:
default config file for Windows ssh server
3 lines of code changed in 1 file:
move all host configs to a dedicated place
0 lines of code changed in 10 files:
Fixed a bug which added negative growth to smaller individuals, eventually leading to crashing the population
35 lines of code changed in 2 files:
suggestions from Jarl incorporated
29 lines of code changed in 1 file:
delete silly
906 lines of code changed in 2 files:
some fixes
55 lines of code changed in 1 file:
finally all slides
9409 lines of code changed in 1 file:
now 35 pages
39639 lines of code changed in 1 file:
20 slides is it too much?
13324 lines of code changed in 1 file:
intro slides done
3878 lines of code changed in 1 file:
started presentation for climate sustainability seminar
2326 lines of code changed in 1 file:
littlt more on vpn
13 lines of code changed in 1 file:
emphasis only
174 lines of code changed in 1 file:
my lovely dash
12 lines of code changed in 1 file:
wording
12 lines of code changed in 1 file:
trend it almost sudden
12 lines of code changed in 1 file:
added thank to Bruce
> From: Bruce Schneier <schneier@schneier.com>
> To: Sergey Budaev <sbudaev@gmail.com>
> Subject: Re: need an advice on text
> Date: Sat, 23 Oct 2021 09:42:28 -0400
>
> I only had time to skim it, but it looks good.
>
> Good luck.
16 lines of code changed in 1 file:
smal fix, sent paper to Bruce
12 lines of code changed in 1 file:
more small
12 lines of code changed in 1 file:
small rephrase
12 lines of code changed in 1 file:
on PIV
12 lines of code changed in 1 file:
small fix subtitle
58 lines of code changed in 1 file:
popups
19 lines of code changed in 1 file:
minir: certificate
12 lines of code changed in 1 file:
small fix - educating users
164 lines of code changed in 1 file:
small change
12 lines of code changed in 1 file:
more fixes, all small
14 lines of code changed in 1 file:
crucial point on adding security incentives
12 lines of code changed in 1 file:
small added changes
12 lines of code changed in 1 file:
minor fixes after sending out the link https://tegsvn.uib.no:5443/upload/ac5550e7f0d04136283aad69f0b92893700917a5/6NnTMxwh6osEX6CiG8GF4PIOZsI5x62xEK26igT5/silly-jail-rev.docx
42 lines of code changed in 1 file:
new updates after a second reading
59 lines of code changed in 1 file:
report: combined with Joseph's changes, some fixes
94245 lines of code changed in 1 file:
more on ssh proxy jump
23 lines of code changed in 1 file:
some changes after sending out to TEG
32 lines of code changed in 1 file:
first of silly jail report
101 lines of code changed in 1 file:
fix port was wrong
107 lines of code changed in 2 files:
prototype ssh backdoor: better draft
68 lines of code changed in 2 files:
prototype ssh backdoor: outline
84 lines of code changed in 2 files:
prototype ssh backdoor: notes on client connect
0 lines of code changed in 1 file:
prototype ssh backdoor: note how to connect from frontend to endpoint agent
2 lines of code changed in 1 file:
prototype ssh backdoor: add some brief doc, need more detail and systemd unit config
0 lines of code changed in 2 files:
prototype ssh backdoor: need clientalive and proxy on frontend
3 lines of code changed in 1 file:
prototype ssh backdoor: default ssh server config for frontend proxy
3 lines of code changed in 1 file:
prototype ssh backdoor: full config for the endpoint agent
install on SysV init system:
1. make symlinks for rc.d:
`update-rc.d gator-tunnel-endpoint defaults`
2. enable daemon:
`update-rc.d gator-tunnel-endpoint enable`
3. start/restart/check daemon
`service gator-tunnel-endpoint start`
`service gator-tunnel-endpoint status`
0 lines of code changed in 2 files:
prototype ssh backdoor: ssh config needs root access for endpoint agent host
0 lines of code changed in 2 files:
prototype ssh backdoor: default ssh server config on endpoint agent host
0 lines of code changed in 1 file:
doc: missing cross-reference
2 lines of code changed in 1 file:
doc: duplicate text removed
11 lines of code changed in 2 files:
doc: missing cross-reference
2 lines of code changed in 1 file:
doc: added cross-reference links to all pparameters of the configuration file
Note: config file parameters must be in `[[lowercase]]` to reduce errors, all other cross-references remain `[[UPPERCASE]]` for better visibility
87 lines of code changed in 2 files:
Added biomass plot to R-script
17 lines of code changed in 2 files:
doc: fix txt
7 lines of code changed in 1 file:
doc: more on feed protocol
8 lines of code changed in 1 file:
doc: fix some symbols
20 lines of code changed in 1 file:
doc: pasted biological bases from report
26 lines of code changed in 1 file:
doc: note formatted rightly
4 lines of code changed in 1 file:
doc: symbols were conciding for gut capacity and gross energytomach
4 lines of code changed in 1 file:
doc: fix fig 1, there is no logistic curve in midgut delay
0 lines of code changed in 1 file:
doc: fix title level
1 lines of code changed in 1 file:
doc: fix plot titles
18 lines of code changed in 1 file:
doc: fix and cleanup parameters of the model list
25 lines of code changed in 2 files:
doc: fix list of variables and parameters
3 lines of code changed in 1 file:
report: small changes evening
3 lines of code changed in 1 file:
doc: filled box 1 with model symbols
93 lines of code changed in 2 files:
report: no need to refer to Ivar's version in file name
87428 lines of code changed in 2 files:
report: cleanup sections 4, 5, 6
3 lines of code changed in 1 file:
report: added table of main parameters
4 lines of code changed in 1 file:
keywords check
8409 lines of code changed in 1 file:
report: latest version from sharepoint
21178 lines of code changed in 1 file:
R loads parameters too, and now plots several runs alongside each other. Saved results include evolving traits, which R now plots over the years.
123 lines of code changed in 3 files:
report: newest version from morning
572 lines of code changed in 1 file:
doc: fix interpolation, DDPI long obsolete for splines from r11498
11 lines of code changed in 1 file:
doc: fix and reformat
7 lines of code changed in 1 file:
doc: copied pieces on appetite model from fishmet report
68 lines of code changed in 1 file:
Checking whether commit works by Andrea.
1 lines of code changed in 1 file:
doc: pasted model intro from latest deliverable report
45 lines of code changed in 3 files:
report: latest changes from aquabiotech sharepoint
329 lines of code changed in 1 file:
fodt outdated
0 lines of code changed in 1 file:
report: added keywords
27656 lines of code changed in 1 file:
converted to word xml, note that conversion won't work with save-changes
27655 lines of code changed in 1 file:
Removing old folder with wrong name.
0 lines of code changed in 12 files:
Committing after Debug folder has been created by visual studio to see if it also appears and need to be delete in svn.
1 lines of code changed in 1 file:
5 lines of code changed in 1 file:
0 lines of code changed in 12 files:
Trying to set up the files correctly, deleting these and will create new ones.
0 lines of code changed in 3 files:
Starting life history model with Andrea and Christian.
0 lines of code changed in 3 files:
use FishMet name for model
21 lines of code changed in 2 files:
report: rename file
0 lines of code changed in 2 files:
small morning changes
113 lines of code changed in 1 file:
report: small adjust for Windows version glitch
180 lines of code changed in 1 file:
added appetite function plot
0 lines of code changed in 1 file:
report: done appetite
250 lines of code changed in 1 file:
report: section 5 to appetite
1276 lines of code changed in 1 file:
report: more text
199 lines of code changed in 1 file:
report: figs in metafile format
0 lines of code changed in 3 files:
report: done text on model outline
2228 lines of code changed in 1 file:
report: write outline of the model
7744 lines of code changed in 1 file:
rates better per minute, both GUI and CMD
11 lines of code changed in 3 files:
updated outline in text as r11591
20215 lines of code changed in 1 file:
report: update outline as r11590
0 lines of code changed in 1 file:
appetite arrows should appear badly on pdf, need 0.5 mm thick
0 lines of code changed in 1 file:
report: updated screenshots
2206 lines of code changed in 1 file:
report: new combined screenshots
0 lines of code changed in 1 file:
report: copy screenshote from STOMACH
0 lines of code changed in 2 files:
report: add more emf resources
0 lines of code changed in 2 files:
report: need emf files for insertion to main docx
0 lines of code changed in 1 file:
updated figure 3 from generated emf
20656 lines of code changed in 1 file:
report: fix tags
174 lines of code changed in 1 file:
report fishmet: add date and revision tags to text
236 lines of code changed in 1 file:
Fixed bug in calculating skipspawnthreshold, number of spawn skippers now much more realistic, and no more negative gonad growth. Also added R functionality to read data when only a single run was made.
67 lines of code changed in 3 files:
!FishMet report, initial version sent by Ivar
> Date: Mon, 11 Oct 2021 11:50:43 +0000
> From: Ivar Rønnestad <Ivar.Ronnestad@uib.no>
> To: Sergei Budaev <Sergey.Budaev@uib.no>
> Subject: Re: Can we talk today regarding the reporting
>
>
> The report enclosed as promised
>
> IvarR
92919 lines of code changed in 1 file:
improve title line
2 lines of code changed in 2 files:
need more precision in parameters at Michaelis-Meneten function view
2 lines of code changed in 2 files:
need consistent symbols with other docs
10 lines of code changed in 2 files:
show Michaelis-Meneten equation in absorption pattern plot
13 lines of code changed in 2 files:
started latex formula for Michaelis-Meneten in GUI
6 lines of code changed in 1 file:
set `absorp_min_transfer` in GUI with bug fixes in table edit values: mismatched row col coordinates
57 lines of code changed in 1 file:
set `absorp_min_transfer` in CMD mode
10 lines of code changed in 1 file:
doc: document the new parameter `absorp_min_transfer`
11 lines of code changed in 1 file:
added absorption threshold parameter `Global_Absorption_Min_Transfer` with `absorp_min_transfer`
33 lines of code changed in 4 files:
`DO_ABSORP` change: change **absorption** algorithm: in `DO_ABSORP`: absorption starts with all food items that are in the stomach rather than those that appeared fully in the midgut; `SELECT_ABSORP` sets the limit of emergence proportion in the midgat, for testing `0.5`
24 lines of code changed in 1 file:
**important** disable `GET_CUMULATE`, independent calculation of cumulative absorption for cross-checking; use standard `food_mass_absorb_cum` object component, the last array element
16 lines of code changed in 1 file:
R now capable of importing and combining multiple .nc files
64 lines of code changed in 2 files:
Now saves standard deviation, and avoids overwriting previous runs
95 lines of code changed in 2 files:
gnuplot is sufficient
1 lines of code changed in 1 file:
use gnuplot for simple example pls
20 lines of code changed in 2 files:
show latex formula in appetite function plot
19 lines of code changed in 2 files:
test parameters: stomach capacity as in exp.1, shorten stomach transport to 50%, accelerate appetite
5 lines of code changed in 1 file:
doc: add `appetite_threshold_stomach` to manual
8 lines of code changed in 1 file:
added separate parameter for `appetite_threshold_stomach`
27 lines of code changed in 4 files:
Cleaned up remnants of csv saving paradigm, and added legend to netCDF file. Also included new function to calculate standard deviation to be implemented in saving the results.
84 lines of code changed in 3 files:
have optional parameter, use default global time step, this is for consistency between (output_arrays_add_ingested) and (output_arrays_update_step)
1 lines of code changed in 1 file:
UI label helpful for clarity
2 lines of code changed in 1 file:
move (do_ingest) up into the class hierarchy to `FISH`, now (add_midgut) method can be called from (do_ingest) directly without confusion
Test results with fixed random seed:
{{{
integer :: i
call random_seed(put= (/ (0, i = 1, 33) /) )
}}}
---------------------------
Test results:
{{{
General model output statistics (r11557)
- Simulation duration, hours : 24
- Total N of food items ingested : 516
- Total mass of food ingested, g : 23.2200
- Total cumulative absorption,g : 0.0000
- Total energy intake from food, kJ : 0.0000
- Total maintenance (at SMR), mg O2*: 1111.4769
- Total maintenance energy, kJ* : 15.0939
- Energy budget at the end, kJ : -75.4686
- Body mass equivalent of energy, g*: -6.4780
- Total mass evacuated, g : 0.0000
- Total N of food items provided : 900
- Ingestion ratio ingested/provided : 0.5733
}}}
---------------------------
{{{
General model output statistics (r11554)
- Simulation duration, hours : 24
- Total N of food items ingested : 516
- Total mass of food ingested, g : 23.2200
- Total cumulative absorption,g : 0.0000
- Total energy intake from food, kJ : 0.0000
- Total maintenance (at SMR), mg O2*: 1111.4769
- Total maintenance energy, kJ* : 15.0939
- Energy budget at the end, kJ : -75.4686
- Body mass equivalent of energy, g*: -6.4780
- Total mass evacuated, g : 0.0000
- Total N of food items provided : 900
- Ingestion ratio ingested/provided : 0.5733
}}}
8 lines of code changed in 1 file:
long running model
4 lines of code changed in 2 files:
netCDF file now also contains the parameters used in the saved run
59 lines of code changed in 2 files:
fix strange bug in GUI: initialising `Global_Interval_Food_Pattern` to FALSE
the problem was that after the second or third run in GUI with feed pattern from CSV, global step-wise feed pattern was broken and TRUE throughout the whole run, although should be FALSE, need more testing with higher feed rate
4 lines of code changed in 1 file:
Added netCDF saving functionality to the fortran script, and rewrote R-script to load 3d netCDF data instead
131 lines of code changed in 4 files:
cleanup time_steps reuse existing variable
4 lines of code changed in 1 file:
move (add_midgut) call to (decide_eat) is more logical
Note that it cannot for now move to the backend (do_ingest) as the latter is `STOMACH` class
6 lines of code changed in 2 files:
`target_value` parameter in (decide_eat) is long obsolete
4 lines of code changed in 2 files:
fix appetite function call in (decide_eat)
1 lines of code changed in 1 file:
tweak drawing
0 lines of code changed in 1 file:
more details of model on main image: energy, activity
0 lines of code changed in 1 file:
newer cmd screenshot, unix
0 lines of code changed in 1 file:
better scrinshot windows
0 lines of code changed in 1 file:
`plots_scale_relative` now `plot_scale_relative` as shorter label neede for GUI to fit on Windows
13 lines of code changed in 7 files:
add unix screenshot, unused so far
0 lines of code changed in 1 file:
button for graphical zoom window
6 lines of code changed in 1 file: