Code

Project in SciComp - Fall 2020#26

Code

Open

jfloouf wants to merge 148 commits intoURDME:masterURDME/urdme:masterfrom jfloouf:masterjfloouf/urdme:masterCopy head branch name to clipboard

+12,374-55

Commits

Commits on Oct 30, 2020

• Added project underfolder, added stenglib files, changed URDME startup.m to include those, added windows compiler to make files

  jfloouf

  committed
  36f642b

  Copy full SHA for 36f642b

Commits on Nov 2, 2020

• Fixed make file for tprod.c for Mingw64

  jfloouf

  committed
  6a5b6ef

  Copy full SHA for 6a5b6ef

• bla

  Chrishij

  committed
  58918c9

  Copy full SHA for 58918c9

• Merge branch 'master' of https://github.com/jfloouf/urdme

  Chrishij

  committed
  cb99681

  Copy full SHA for cb99681

Commits on Nov 6, 2020

• PDE-proj start

  Show description for fc38de5
  Chrishij

  committed
  fc38de5

  Copy full SHA for fc38de5

Commits on Nov 8, 2020

• U_dead

  AliceGrafBrolund

  committed
  bcc8e6c

  Copy full SHA for bcc8e6c

Commits on Nov 9, 2020

• Added BC that calcs distance from origin, started saving runs in saveData-folder, some plotting scripts

  jfloouf

  committed
  238b421

  Copy full SHA for 238b421

• Removed some temporary code

  jfloouf

  committed
  8177904

  Copy full SHA for 8177904

• dying cells

  AliceGrafBrolund

  committed
  1d3d186

  Copy full SHA for 1d3d186

Commits on Nov 12, 2020

• death+degradation works

  AliceGrafBrolund

  committed
  00627b8

  Copy full SHA for 00627b8

• Lot of simulations results, some crap code and started on assemble_Mgamma code

  jfloouf

  committed
  6bfa5bb

  Copy full SHA for 6bfa5bb

• Profilerate

  Show description for 93659da
  Chrishij

  committed
  93659da

  Copy full SHA for 93659da

• Non errorness assemble_Mgamma function, under dev

  jfloouf

  committed
  d6f9bf8

  Copy full SHA for d6f9bf8

Commits on Nov 13, 2020

• Small improvements

  Show description for 59ec168
  Chrishij

  committed
  59ec168

  Copy full SHA for 59ec168

• Implementing sdof_m movement

  Show description for a7c7719
  Chrishij

  committed
  a7c7719

  Copy full SHA for a7c7719

• Changed assemble_Mgamma function, some patching functions

  jfloouf

  committed
  da0ac4f

  Copy full SHA for da0ac4f

Commits on Nov 17, 2020

• Newest: Implemeting Movement

  Show description for ae0140d
  Chrishij

  committed
  ae0140d

  Copy full SHA for ae0140d

• add initial condition

  

  Rebecca Persson

  committed
  d35362f

  Copy full SHA for d35362f

• Reworked visualization of Data, removed unneeded saveData files

  jfloouf

  committed
  9bb1cf0

  Copy full SHA for 9bb1cf0

• Cleaned up in folders, updated structure

  jfloouf

  committed
  8512c73

  Copy full SHA for 8512c73

• Some minor changes in Copy2_AvascularTumour, fixed assemble_Mgamma hardcoding

  jfloouf

  committed
  06649c7

  Copy full SHA for 06649c7

• Added initialCondition function to Copy1_AvascularTumour, fixed some viz

  jfloouf

  committed
  c2d7d9d

  Copy full SHA for c2d7d9d

• Made some changes to Pr viz

  jfloouf

  committed
  7f785cb

  Copy full SHA for 7f785cb

• Small changes

  Show description for c9f7e11
  Chrishij

  committed
  c9f7e11

  Copy full SHA for c9f7e11

• add 6th initial condition

  

  Rebecca Persson

  committed
  797a6b4

  Copy full SHA for 797a6b4

• add 6th initial condition, fix notation

  

  Rebecca Persson

  committed
  eec0898

  Copy full SHA for eec0898

• Added experimental scatterbar3 for Pr viz

  jfloouf

  committed
  d4814ad

  Copy full SHA for d4814ad

• Changed Pr viz to better one, added function for additional, wack 3D bar plot

  jfloouf

  committed
  34aacee

  Copy full SHA for 34aacee

Commits on Nov 18, 2020

• Latest: Plotting functions

  Show description for a64b720
  Chrishij

  committed
  a64b720

  Copy full SHA for a64b720

• New New:

  Show description for fef6b6f
  Chrishij

  committed
  fef6b6f

  Copy full SHA for fef6b6f

• New New:

  Show description for de1f63e
  Chrishij

  committed
  de1f63e

  Copy full SHA for de1f63e

• Rearranged the pressure plotting, fixed quiver plot for pressure plot, changed some in saveData and plotting of data

  jfloouf

  committed
  8e2f1ab

  Copy full SHA for 8e2f1ab

• implementing movement

  Show description for 0d01060
  AliceGrafBrolund

  committed
  0d01060

  Copy full SHA for 0d01060

Commits on Nov 19, 2020

• Made changes to Mgamma assembling yet again due to possible error, some changes in plotting methods

  jfloouf

  committed
  c99a511

  Copy full SHA for c99a511

• Added some useful things in plot scripts

  jfloouf

  committed
  33ab2d0

  Copy full SHA for 33ab2d0

• Grows

  Show description for e58dcd3
  AliceGrafBrolund

  committed
  e58dcd3

  Copy full SHA for e58dcd3

Commits on Nov 20, 2020

• growing sdof

  Show description for 5e68957
  AliceGrafBrolund

  committed
  5e68957

  Copy full SHA for 5e68957

Commits on Nov 23, 2020

• growing sdof+dead appearance

  Show description for fe40728
  AliceGrafBrolund

  committed
  fe40728

  Copy full SHA for fe40728

Commits on Nov 24, 2020

• Gradient colors

  Show description for aa2cd65
  AliceGrafBrolund

  committed
  aa2cd65

  Copy full SHA for aa2cd65

Commits on Nov 27, 2020

• Copy2 update

  

  Rebecca Persson

  committed
  652a917

  Copy full SHA for 652a917

• TumorGraphics

  Show description for a30a044
  Chrishij

  committed
  a30a044

  Copy full SHA for a30a044

• Fixed merge conflicts, added some Mgamma_assemble changes and a Copy3_AvascularTumour where bdof_m were analyzed

  jfloouf

  committed
  08199a5

  Copy full SHA for 08199a5

• Changed/added .gitignore

  jfloouf

  committed
  eb975c5

  Copy full SHA for eb975c5

• U_new

  Show description for a7c5b01
  AliceGrafBrolund

  committed
  a7c5b01

  Copy full SHA for a7c5b01

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  AliceGrafBrolund

  committed
  1ed486b

  Copy full SHA for 1ed486b

• New Euler Stepping

  Show description for 88eebaa
  Chrishij

  committed
  88eebaa

  Copy full SHA for 88eebaa

Commits on Nov 30, 2020

• Cleaned up in rep, removed unused or old scripts

  jfloouf

  committed
  5ecce58

  Copy full SHA for 5ecce58

• New code

  Show description for 6884ae1
  Chrishij

  committed
  6884ae1

  Copy full SHA for 6884ae1

• relaxation_exp

  AliceGrafBrolund

  committed
  217e690

  Copy full SHA for 217e690

• code for label

  AliceGrafBrolund

  committed
  235e153

  Copy full SHA for 235e153

Commits on Dec 1, 2020

• Some more runs with basePr=1 in saveData, some changes in plotFunctions

  jfloouf

  committed
  c26e70e

  Copy full SHA for c26e70e

• experiments, better visuals

  Show description for 8e10ebc
  AliceGrafBrolund

  committed
  8e10ebc

  Copy full SHA for 8e10ebc

• Breakup of AvascularTumor

  Chrishij

  committed
  b60570d

  Copy full SHA for b60570d

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  Chrishij

  committed
  8265f78

  Copy full SHA for 8265f78

• Better visuals

  AliceGrafBrolund

  committed
  5ae4f45

  Copy full SHA for 5ae4f45

• Calcs_updated

  Chrishij

  committed
  42de0a6

  Copy full SHA for 42de0a6

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  AliceGrafBrolund

  committed
  f053960

  Copy full SHA for f053960

• Added some runs, a flipped_mesh function

  jfloouf

  committed
  5f4667d

  Copy full SHA for 5f4667d

• Better visuals igen

  AliceGrafBrolund

  committed
  80ddd1b

  Copy full SHA for 80ddd1b

• New calc file

  Chrishij

  committed
  c8460f4

  Copy full SHA for c8460f4

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  Chrishij

  committed
  e831142

  Copy full SHA for e831142

• add basic mesh2, poimesh2

  

  Rebecca Persson

  authored and

  Rebecca Persson

  committed
  f92aa5b

  Copy full SHA for f92aa5b

• Division of Avascular Tumor

  Show description for 18266f2
  Chrishij

  committed
  18266f2

  Copy full SHA for 18266f2

• figure added

  Show description for 59737f3
  AliceGrafBrolund

  committed
  59737f3

  Copy full SHA for 59737f3

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  AliceGrafBrolund

  committed
  82d75d6

  Copy full SHA for 82d75d6

• figure added-nrVoxels

  AliceGrafBrolund

  committed
  a01385c

  Copy full SHA for a01385c

• Update dof_calc

  Chrishij

  committed
  59a3264

  Copy full SHA for 59a3264

• Create AvascExp

  Chrishij

  committed
  9ffa59c

  Copy full SHA for 9ffa59c

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  Chrishij

  committed
  ec8c6e2

  Copy full SHA for ec8c6e2

• right inits

  AliceGrafBrolund

  committed
  ca04991

  Copy full SHA for ca04991

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  AliceGrafBrolund

  committed
  26b62d8

  Copy full SHA for 26b62d8

Commits on Dec 2, 2020

• small changes

  AliceGrafBrolund

  committed
  4da2d64

  Copy full SHA for 4da2d64

Commits on Dec 4, 2020

• Big Restructuring

  Show description for 7028035
  Chrishij

  committed
  7028035

  Copy full SHA for 7028035

• Resolve

  Chrishij

  committed
  960a76f

  Copy full SHA for 960a76f

• Update Still.m

  AliceGrafBrolund

  committed
  f9bd34a

  Copy full SHA for f9bd34a

• Updated new code

  Show description for 7e547cd
  Chrishij

  committed
  7e547cd

  Copy full SHA for 7e547cd

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  Chrishij

  committed
  0ab2758

  Copy full SHA for 0ab2758

Commits on Dec 8, 2020

• Newest For-loop changes

  Chrishij

  committed
  64e5a6b

  Copy full SHA for 64e5a6b

• update poimesh2

  

  Rebecca Persson

  committed
  c632098

  Copy full SHA for c632098

Commits on Dec 9, 2020

• Changes in Copy3AT, added dwnsclATProblem, changes in different plot functions, some more saveData

  jfloouf

  committed
  eacffc7

  Copy full SHA for eacffc7

Commits on Dec 10, 2020

• Latest version: Working timestep

  Chrishij

  committed
  8b34b0c

  Copy full SHA for 8b34b0c

Commits on Dec 14, 2020

• Create 2020-12-14(newdt_noscale).gif

  AliceGrafBrolund

  committed
  bc17793

  Copy full SHA for bc17793

• Create 2020-12-12(newdt_noscale_normal).gif

  AliceGrafBrolund

  committed
  779a98e

  Copy full SHA for 779a98e

Commits on Dec 15, 2020

• Create 2020-12-15_relax(newdt_noscale).gif

  AliceGrafBrolund

  committed
  e500e7f

  Copy full SHA for e500e7f

• Pictures

  Chrishij

  committed
  33aa177

  Copy full SHA for 33aa177

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  Chrishij

  committed
  12b4d72

  Copy full SHA for 12b4d72

• gifs Tend100 no scale

  AliceGrafBrolund

  committed
  53c7332

  Copy full SHA for 53c7332

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  AliceGrafBrolund

  committed
  d93a020

  Copy full SHA for d93a020

• New pics

  Chrishij

  committed
  3f2c00e

  Copy full SHA for 3f2c00e

• More pics

  Chrishij

  committed
  ddec299

  Copy full SHA for ddec299

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  Chrishij

  committed
  d2cb125

  Copy full SHA for d2cb125

• Create 2020-12-15_relax(newdt_scale).gif

  AliceGrafBrolund

  committed
  2a4e3a2

  Copy full SHA for 2a4e3a2

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  AliceGrafBrolund

  committed
  98f372a

  Copy full SHA for 98f372a

• better colourscale oxy

  AliceGrafBrolund

  committed
  d4604cd

  Copy full SHA for d4604cd

• Create 2020-12-15_Oxynormal_scaled.gif

  AliceGrafBrolund

  committed
  c1ef73b

  Copy full SHA for c1ef73b

Commits on Dec 16, 2020

• 1_T200 pics

  Chrishij

  committed
  08a5dd7

  Copy full SHA for 08a5dd7

• Code for downscaled problem, som vizualisations, savedata and images

  jfloouf

  committed
  1016a75

  Copy full SHA for 1016a75

• More pics

  Chrishij

  committed
  2c72bc3

  Copy full SHA for 2c72bc3

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  Chrishij

  committed
  be4a42d

  Copy full SHA for be4a42d

• update

  AliceGrafBrolund

  committed
  cf8816d

  Copy full SHA for cf8816d

• more updates

  AliceGrafBrolund

  committed
  e1761a8

  Copy full SHA for e1761a8

Commits on Dec 18, 2020

• New pics

  AliceGrafBrolund

  committed
  074373e

  Copy full SHA for 074373e

Commits on Dec 23, 2020

• update test_gamma, assemble_Mgamma2

  

  Rebecca Persson

  authored and

  Rebecca Persson

  committed
  016a551

  Copy full SHA for 016a551

• Made changes in downscalde problem code, som visualization-stuff, test code for Dirichlet and Neumann comparison

  jfloouf

  committed
  77da1e8

  Copy full SHA for 77da1e8

Commits on Jan 4, 2021

• parameter variation figures

  AliceGrafBrolund

  committed
  aaba163

  Copy full SHA for aaba163

Commits on Jan 7, 2021

• figures and script for schematic figure

  AliceGrafBrolund

  committed
  57c6840

  Copy full SHA for 57c6840

Commits on Jan 11, 2021

• scripts for relaxation and still growth experiments

  AliceGrafBrolund

  committed
  ee593b4

  Copy full SHA for ee593b4

• New January

  Show description for 48124a9
  Chrishij

  committed
  48124a9

  Copy full SHA for 48124a9

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  Chrishij

  committed
  4b0a04d

  Copy full SHA for 4b0a04d

• Latest changes in the Copies of avasscularTumour, changes in downscaledProblem and a lot of saveData

  jfloouf

  committed
  9431fcb

  Copy full SHA for 9431fcb

• Cleaned up version

  Show description for 68235c1
  Chrishij

  committed
  68235c1

  Copy full SHA for 68235c1

• Even newer more enhanced

  Chrishij

  committed
  92bc018

  Copy full SHA for 92bc018

Commits on Jan 12, 2021

• Incorporated new Robin BC in PDE (more or less), some additional .m-files needed for this, plotting scripts and some saveData for different runs

  jfloouf

  committed
  ecc4210

  Copy full SHA for ecc4210

• Small fix in still growth script+figures

  AliceGrafBrolund

  committed
  5cb985c

  Copy full SHA for 5cb985c

• New layout of code

  Chrishij

  committed
  bda92ea

  Copy full SHA for bda92ea

• comments and cleanup, copy1

  

  Rebecca Persson

  committed
  b52cd81

  Copy full SHA for b52cd81

• Added AvascularTumour_RobinBC script with comments

  jfloouf

  committed
  3e2d215

  Copy full SHA for 3e2d215

• Clean up in code and repositories

  jfloouf

  committed
  e9971e7

  Copy full SHA for e9971e7

• Faster PDE-code

  Chrishij

  committed
  a637389

  Copy full SHA for a637389

• updated pics

  AliceGrafBrolund

  committed
  64a33d3

  Copy full SHA for 64a33d3

• Merge branch 'PDE-Proj' of https://github.com/jfloouf/urdme into PDE-Proj

  AliceGrafBrolund

  committed
  2232426

  Copy full SHA for 2232426

• cutoff_bdof figures

  AliceGrafBrolund

  committed
  e14d039

  Copy full SHA for e14d039

Commits on Jan 13, 2021

• Some changes in AvascularTumour_RobinBC and plots

  jfloouf

  committed
  4e804a2

  Copy full SHA for 4e804a2

• Added more plotting scripts, changes in main tumour script

  jfloouf

  committed
  9746346

  Copy full SHA for 9746346

Commits on Jan 14, 2021

• Undergoing analysis of how to incorporate the BC into the PDE-model

  jfloouf

  committed
  afc2a30

  Copy full SHA for afc2a30

• Nothing really, made a figure for the presentation

  jfloouf

  committed
  e99ac21

  Copy full SHA for e99ac21

• Humm humm

  jfloouf

  committed
  2768be7

  Copy full SHA for 2768be7

• Generated some more report images

  jfloouf

  committed
  e576f45

  Copy full SHA for e576f45

• Yoyo

  jfloouf

  committed
  d9a6b6b

  Copy full SHA for d9a6b6b

Commits on Jan 15, 2021

• Update AvascularTumour_Relaxation.m

  AliceGrafBrolund

  committed
  b2fe3d2

  Copy full SHA for b2fe3d2

• AvascTumour code

  Show description for fe7fc15
  Chrishij

  committed
  fe7fc15

  Copy full SHA for fe7fc15

• Cleaned up code, added relevant comments; removed saveData, images and misc

  jfloouf

  committed
  5ef850e

  Copy full SHA for 5ef850e

• Fixed conflicts with .mex-files

  jfloouf

  committed
  2d3bf7a

  Copy full SHA for 2d3bf7a

• Minor fixes

  jfloouf

  committed
  7f77d6d

  Copy full SHA for 7f77d6d

• Restructured code

  Chrishij

  committed
  0bf787f

  Copy full SHA for 0bf787f

• Cleaned up joined model code

  jfloouf

  committed
  4a47180

  Copy full SHA for 4a47180

• Minor fix

  jfloouf

  committed
  73dc49f

  Copy full SHA for 73dc49f

• Resolved conflicts

  jfloouf

  committed
  8b690b8

  Copy full SHA for 8b690b8

• Scripts for relaxation and still growth experiments

  AliceGrafBrolund

  committed
  9589f10

  Copy full SHA for 9589f10

Commits on Jan 20, 2021

• Commented code

  Show description for 89306b4
  AliceGrafBrolund

  committed
  89306b4

  Copy full SHA for 89306b4

• Update AvascularTumour_commented.m

  AliceGrafBrolund

  committed
  272a587

  Copy full SHA for 272a587

Commits on Jan 22, 2021

• Update AvascularTumour_commented.m

  AliceGrafBrolund

  committed
  ced2481

  Copy full SHA for ced2481

• Update AvascularTumour_commented.m

  AliceGrafBrolund

  committed
  c868075

  Copy full SHA for c868075

Commits on Jan 29, 2021

• FINAL

  Show description for 0c21932
  Chrishij

  committed
  0c21932

  Copy full SHA for 0c21932

• Update AvascularTumour.m

  AliceGrafBrolund

  committed
  6e86f2d

  Copy full SHA for 6e86f2d

• Merge branch 'PDE-Proj'

  AliceGrafBrolund

  committed
  578a1c9

  Copy full SHA for 578a1c9

• Reordered Final

  Chrishij

  committed
  a0bad1f

  Copy full SHA for a0bad1f

• rename

  AliceGrafBrolund

  committed
  1b13d57

  Copy full SHA for 1b13d57