initial commit of turing pattern generator - #1

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hbozhao wants to merge 153 commits into

cgrambow:masterfrom

Commits on Apr 12, 2019

Add training module
Colin Grambow
committed
b18114f
Add training script
Colin Grambow
committed
684f322

Commits on Apr 15, 2019

Implement data parsing
Colin Grambow
committed
567ce20
initial commit of turing pattern generator
Hongbo Zhao
committed
a270227

Commits on Apr 18, 2019

fix bugs and debugging of the solver
Hongbo Zhao
committed
05ca016

Commits on Apr 26, 2019

move rungpu condition to after defintion of yall
Hongbo Zhao
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5337429
generate turing result using cpu
Hongbo Zhao
committed
8eb6fcc

Commits on Apr 27, 2019

spinodal decomposition
Hongbo Zhao
committed
b79482d

Commits on May 1, 2019

add the option to reinitialize for each instance
Hongbo Zhao
committed
c4f0839
fix bugs in turing_cpu reinitialize
Hongbo Zhao
committed
ce3f39e
in turing_cpu, better loading of result to plot samples
Hongbo Zhao
committed
fa4c1d8
pca analysis of turing pattern
Hongbo Zhao
committed
7e5278f

Commits on May 5, 2019

update odeimexez on the usage of event function
Hongbo Zhao
committed
335eee6
update turing_ps and turing_cpu after odeimexez update
Hongbo Zhao
committed
2a0bffa
generate turing patterns that are close to steady state
Hongbo Zhao
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2dd6e0e
slight modifcation to spdecomp.m for generating spdecomp patterns
Hongbo Zhao
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6eae434
fix bug in odeimexez, apply transform when et aborts the iteration
Hongbo Zhao
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82af5f5
post processing of turing pattern
Hongbo Zhao
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a102293

Commits on May 8, 2019

post processing
Hongbo Zhao
committed
8c6f707
fix bug in post processing video
Hongbo Zhao
committed
6b5e4d6

Commits on May 13, 2019

plot dispersion curve
Hongbo Zhao
committed
96d218a

Commits on Jun 28, 2019

add DDFT scripts
Hongbo Zhao
committed
56d323a

Commits on Jun 29, 2019

start adding FSA to odeimex
Hongbo Zhao
committed
70046d8

Commits on Jul 1, 2019

add moerodeoptions, fix bugs, add output function in odeimex
Hongbo Zhao
committed
ad37036
add InterpFcn in odeimex and add ntrp15s
Hongbo Zhao
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622831c
test another kernel
Hongbo Zhao
committed
b970294

Commits on Jul 2, 2019

create a nucleus from DDFT
Hongbo Zhao
committed
c1f2076
start working on Krylov-based DDFT solver
Hongbo Zhao
committed
530756e

Commits on Jul 3, 2019

updaet solver_DDFT, and moreode*, seems to work
Hongbo Zhao
committed
91131e4
update solver_DDFT
Hongbo Zhao
committed
e2ba7a5
roi diffuse shape function
Hongbo Zhao
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bcfb49b
DDFT_nucleation study nucleation
Hongbo Zhao
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0366d53

Commits on Jul 6, 2019

work on solver_DDFT and IP_DDFT
Hongbo Zhao
committed
7ea11aa
add a few lines in DDFT_nucleation for IP test
Hongbo Zhao
committed
e12586a

Commits on Jul 7, 2019

fix bugs in IP_DDFT and solver_DDFT
Hongbo Zhao
committed
5ec85d7
decrease gmrestol and increase restart in solver_DDFT
Hongbo Zhao
committed
4cd60d7
update DDFT_nucleation, try using real space representation for C
Hongbo Zhao
committed
d2d39f6
use the options of sensFcnMultiplier to directly multiply omega with dF in sensFcn
Hongbo Zhao
committed
859a520

Commits on Jul 8, 2019

fix bugs in solver_DDFT
Hongbo Zhao
committed
533c177
add fminunc option, add Cspace=isotropic option, increase weight by 100 in IP_DDFT
Hongbo Zhao
committed
e0c6e91
update DDFT_nucleation scripts
Hongbo Zhao
committed
b0adbe4
IP_DDFT_debug, plot val and gradient along the search direction
Hongbo Zhao
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f82c82f

Commits on Jul 9, 2019

fix bug in roi_circle
Hongbo Zhao
committed
37a11b7

Commits on Jul 10, 2019

add x_guess input in IP_DDFT, continue from previous run in DDFT_nucleation2
Hongbo Zhao
committed
09e6520

Commits on Jul 11, 2019

continue DDFT_nucleation2 from the previous run
Hongbo Zhao
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7b95fbd
add the mode of eval (output model solution) and fval and exitflag output in IP_DDFT
Hongbo Zhao
committed
30d4325
add history_production, producing figures for DDFT IP (need more work)
Hongbo Zhao
committed
c25a631
visualize DDFT_nucleation2, update DDFT_nucleation2_helper to do optim loop
Hongbo Zhao
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5e087bf

Commits on Jul 14, 2019

update IP_DDFT, add tspan and eval options
Hongbo Zhao
committed
5af0e2b
add DDFT_nucleation3, a larger alpha, small n0 for nucleation event
Hongbo Zhao
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317d33b
try alternate between 2 datasets DDFT_nucleation3
Hongbo Zhao
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64efb7c

Commits on Jul 16, 2019

update solver_DDFT to allow empty C and mu in params
Hongbo Zhao
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9555e50
switch to custom_EvenPoly for Cspace=isotropic in IP_DDFT
Hongbo Zhao
committed
8285010
DDFT_nucleation_PFC, use PFC kernel
Hongbo Zhao
committed
d47fe29
update IP_DDFT, parameter prescreening and isotropic Cspace, highest order must be negative
Hongbo Zhao
committed
834adad
add DDFT_nucleation4 fit DDFT to a 4-th order PFC
Hongbo Zhao
committed
e688147
fix critical bug in jacobian_mult in solver_DDFT, for loop index wrong, vectorize jacobian_mult over columns of xi, FSA now works for DDFT
Hongbo Zhao
committed
834156a
add FDcoeff to compute 1D finite difference coefficient
Hongbo Zhao
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c90e58f
rewrite Cspace=isotropic, add Cspace=FD
Hongbo Zhao
committed
5e85688
use parser in solver_DDFT, add option and moreoptions in params, update IP_DDFT
Hongbo Zhao
committed
8ef80df
DDFT_nucleation6
Hongbo Zhao
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0e8d85f
DDFT_nucleation6 and 7
Hongbo Zhao
committed
2664bcc

Commits on Jul 17, 2019

add Cspace='isotropic_CmE', add optimizing mu params in IP_DDFT
Hongbo Zhao
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67dfd83
update and add DDFT_nucleation(4,9)
Hongbo Zhao
committed
8656cfa

Commits on Jul 19, 2019

DDFT_nucleation15, based on 13, with a different initial guess
Hongbo Zhao
committed
1f422b8
if mu is optimized, the constant term in C is removed in IP_DDFT
Hongbo Zhao
committed
70a568b
add the option to optimize D as well
Hongbo Zhao
committed
a565a77
add DDFT_nucleation17 and 18 to test optimizing mu, C, and D at the same time with full data
Hongbo Zhao
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3cdd8c2
DDFT_nucleation19, use 10 frames
Hongbo Zhao
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3cd783e
add the option of discrete IP in IP_DDFT, update 19
Hongbo Zhao
committed
ae2013f
fix bug in IP_DDFT about the default of D, and set tspan for solver_DDFT equal to tdata when discrete
Hongbo Zhao
committed
cbbb9ea

Commits on Jul 20, 2019

add mode in IP_DDFT, prepare for post processing
Hongbo Zhao
committed
af428a5
add DDFT_nucleation files
Hongbo Zhao
committed
0bdab36

Commits on Jul 22, 2019

in IP_DDFT, mode=eval, output modified params and meta for postprocessing
Hongbo Zhao
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2a98340
update history_production after IP_DDFT update
Hongbo Zhao
committed
699a60b
update DDFT_nucleation13 for visualization
Hongbo Zhao
committed
7b8e3a9
update history_production to rescale and shift mu and C
Hongbo Zhao
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b2851ff

Commits on Jul 23, 2019

two more files with different initial conditions
Hongbo Zhao
committed
7db47cf
Merge branch 'master' of https://github.com/hbozhao/reacdiff
Hongbo Zhao
committed
f8957e8
add mu_positive option in IP_DDFT, doesn't seem to work at least yet
Hongbo Zhao
committed
852a5c8

Commits on Jul 25, 2019

add mode='sens' in IP_DDFT
Hongbo Zhao
committed
f7712aa
add Cspace='isotropic_cutoff', add assign_suppress options in IP_DDFT
Hongbo Zhao
committed
fb0fc3f

Commits on Jul 27, 2019

in IP_DDFT, remove isotropic_cutoff, add istropic_cos_cutoff and isotropic_poly_cutoff/scale, based on scaled Legendre on [0,1]
Hongbo Zhao
committed
81eac81
DDFT_nucleation26 and 27, try isotropic_poly_scale
Hongbo Zhao
committed
b103af4

Commits on Jul 28, 2019

add istropic_even option in IP_DDFT to use even legendrepolynomials only
Hongbo Zhao
committed
a1bcf79
DDFT_nucleation28, try isotropic_poly_scale with isotropic_even = true
Hongbo Zhao
committed
9b74119
update IP_DDFT, remove shifting by 1 for isotropic_poly, add 29 to test it
Hongbo Zhao
committed
36f7fe3
Revert "update IP_DDFT, remove shifting by 1 for isotropic_poly, add 29 to test it"
Hongbo Zhao
committed
d70e888
add isotropic_hermite_scale in IP_DDFT
Hongbo Zhao
committed
dbefb76
add DDFT_nucleation29 t try isotropic_hermite_scale
Hongbo Zhao
committed
4eb1de1

Commits on Jul 29, 2019

upload DDFT_nucleation* on HZ-BazantLab
Hongbo Zhao
committed
54a5892
DDFT_nucleation30/31 to test isotropic_hermite_scale with discrete images and mu
Hongbo Zhao
committed
a932236
more DDFT_nucleation32/33 on adding mu while isotropic_hermite_scale
Hongbo Zhao
committed
1db12c0

Commits on Jul 31, 2019

visualization of DDFT_nucleation23
Hongbo Zhao
committed
912931b
add optional cutoff/scaling for Cspace=isotropic in IP_DDFT
Hongbo Zhao
committed
102e1e9
DDFT_nucleation34 try isotropic with scaling by k0
Hongbo Zhao
committed
cc72c43
add Cspace=isotropic_laguerre_scale
Hongbo Zhao
committed
c726c25
DDFT_nucleation36, sensitivity analysis using isotropic_hermite_scale
hbozhao
committed
5c4c022
Merge branch 'master' of https://github.com/hbozhao/reacdiff
Hongbo Zhao
committed
f32919b
update IP_DDFT, now cutoff can be used for all Cspace=isotropic*, add relevant Cfunc output pp
Hongbo Zhao
committed
9d2e663
in history_production, generalize C to all isotropic*, fix bugs
Hongbo Zhao
committed
ff857f8
add DDFT_nucleation30 visualization
Hongbo Zhao
committed
6d41919
small updates to DDFT_nucleation files
Hongbo Zhao
committed
b043639

Commits on Aug 2, 2019

add isotropic_fourier_scale in IP_DDFT
Hongbo Zhao
committed
b686b25
update IP_DDFT, add mode='pp'
Hongbo Zhao
committed
3aaeeba
add history_func, copied from history_production to plot functions in history only
Hongbo Zhao
committed
2825717
begin working on mainFigure
Hongbo Zhao
committed
ab3dd92
update DDFT_nucleation, add 35: laguerre poly (failed), 37: sensitivity using fourier_
Hongbo Zhao
committed
b8005e6
fix bug in IP_DDFT regarding isotropic_fourier_scale
Hongbo Zhao
committed
fe826c0
update history_production, use history_func
Hongbo Zhao
committed
230a877
DDFT_nucleation38 try Laguerre polynomials for sensitivity analysis
Hongbo Zhao
committed
7c29608

Commits on Aug 3, 2019

update DDFT_nucleation26/38 to show C2 error bar
Hongbo Zhao
committed
a9b7b34

Commits on Aug 5, 2019

calculate sensitivity (eigenvalue etc) using 1D approx
Hongbo Zhao
committed
e9781a5
update mainFig and history_func
Hongbo Zhao
committed
9420010
update DDFT_nucleation36/38 (sensitivity) visualization
Hongbo Zhao
committed
aee2537

Commits on Aug 13, 2019

update mainFig and utility function
Hongbo Zhao
committed
d0a790f

Commits on Aug 14, 2019

DDFT_nucleation39, using initial and final frames only
Hongbo Zhao
committed
f7b4006
Merge branch 'master' of https://github.com/hbozhao/reacdiff
Hongbo Zhao
committed
bb4b5d8
critical bug in ASA (adjoint jacobian) for solver_DDFT (reconfirm), Laplacian and mu' don't commute
Hongbo Zhao
committed
34701fe
add DDFT_nucleation40, try Cspace = k again after fixing ASA bug
Hongbo Zhao
committed
0d5958a
update mainFig, (remove yyaxis right in the bottom row)
Hongbo Zhao
committed
6470f69

Commits on Sep 22, 2019

update mainFig's subplot spacing, figure saved as DDFT_mainFig_v4
Hongbo Zhao
committed
817f412

Commits on Nov 23, 2019

add DDFT_nucleation41, redo DDFT_nucleation32 with a different x_guess
Hongbo Zhao
committed
6e4d6f4

Commits on Nov 25, 2019

add option of (commented now) shifting C2 such that C2(0) matches the truth
Hongbo Zhao
committed
56aebdc
highlight the difference between row 3 (model) and row 1 (data) using mydecorrstretch (based on decorrstretch)
Hongbo Zhao
committed
bbfa6de
fix bug in history_production, add the option of showModelSolution, now you can turn off showing model prediction (which takes too long if not saved)
Hongbo Zhao
committed
9c91978
plot the result of DDFT_nucleation32 and 41
Hongbo Zhao
committed
4acb8fd

Commits on Nov 26, 2019

in history_production, save nonexistent model prediction to result as y
Hongbo Zhao
committed
3225464
update mainFig subplot positions, used to produce DDFT_mainFig_v5 on 11/25/2019
Hongbo Zhao
committed
8ebd596
update history_production, add stparg option, fix xlabel
Hongbo Zhao
committed
dd3f5df
visualize DDFT_nucleation41 result
Hongbo Zhao
committed
38ddee6

Commits on May 17, 2020

add user-defined option in Cspace 'user'
Hongbo Zhao
committed
693b6ec
add DDFT_nucleation30_DILI, perform DILI based on nucleation30, (mainFig d), C only
Hongbo Zhao
committed
28fc081
DDFT_nucleation30_DILI, fix bug, change back to normalized hermite function (not scaled by eigenvalue)
Hongbo Zhao
committed
680b8da
add mode='fgh' in IP_DDFT (for DILI)
Hongbo Zhao
committed
ab57b75

Commits on May 28, 2020

update DDFT_nucleation30_DILI visualization to generate Fig. 2 in expip_v0.tex, for meeting with Martin on 05/26
Hongbo Zhao
committed
ded8b76

Commits on Jan 4, 2021

add presentation_RD, to generate figure for slide
Hongbo Zhao
committed
9389b61
fux bugs in solver_DDFT
Hongbo Zhao
committed
91034b8

Commits on Jan 5, 2021

fix bug in solver_DDFT about user options setting
Hongbo Zhao
committed
c7f2837

Commits on Jan 15, 2021

update presentation_RD.m
Hongbo
committed
00c2015

Commits on Jan 16, 2021

add presentation_RD_nucleus, present crystallization starting from a nucleus
Hongbo Zhao
committed
e8c66d4
update presentation_RD_nucleus, running model and exporting
Hongbo
committed
c6ad219
write C3 into an image in presentation_RD_nucleus
Hongbo Zhao
committed
bcd99bb
add history_production and history_func, add offset and muderiv options
Hongbo Zhao
committed
4912d8a
add history_movie, turn history into a movie
Hongbo Zhao
committed
39afacc
update IP_DDFT, add loss in fgh mode
Hongbo Zhao
committed
4bd5f7c
update visualization, generate history movie, dark mode
Hongbo Zhao
committed
b35cdaf

Commits on Dec 30, 2021

add DDFT_nucleation42 created on bgs
Hongbo
committed
730e6c8
Merge branch 'master' of github.com:hbozhao/reacdiff
Hongbo
committed
345ba88
add files on workstation
Hongbo Zhao
committed
231476e
add DDFT_nucleus.mat on workstation
Hongbo Zhao
committed
ae88762
commit changes on home PC
Hongbo Zhao
committed
ced5709
commit changes on MIT laptop
hbozhao
committed
0ee2cc5