initial commit of turing pattern generator#1

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hbozhao wants to merge 153 commits intocgrambow:masterfrom

Commits on Apr 12, 2019

Add training module
Colin Grambow
committed
Add training script
Colin Grambow
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Commits on Apr 15, 2019

Implement data parsing
Colin Grambow
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initial commit of turing pattern generator
Hongbo Zhao
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Commits on Apr 18, 2019

fix bugs and debugging of the solver
Hongbo Zhao
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Commits on Apr 26, 2019

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

Commits on Apr 27, 2019

spinodal decomposition
Hongbo Zhao
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Commits on May 1, 2019

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

Commits on May 5, 2019

update odeimexez on the usage of event function
Hongbo Zhao
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update turing_ps and turing_cpu after odeimexez update
Hongbo Zhao
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generate turing patterns that are close to steady state
Hongbo Zhao
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slight modifcation to spdecomp.m for generating spdecomp patterns
Hongbo Zhao
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fix bug in odeimexez, apply transform when et aborts the iteration
Hongbo Zhao
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post processing of turing pattern
Hongbo Zhao
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Commits on May 8, 2019

post processing
Hongbo Zhao
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fix bug in post processing video
Hongbo Zhao
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Commits on May 13, 2019

plot dispersion curve
Hongbo Zhao
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Commits on Jun 28, 2019

add DDFT scripts
Hongbo Zhao
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Commits on Jun 29, 2019

start adding FSA to odeimex
Hongbo Zhao
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Commits on Jul 1, 2019

add moerodeoptions, fix bugs, add output function in odeimex
Hongbo Zhao
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add InterpFcn in odeimex and add ntrp15s
Hongbo Zhao
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test another kernel
Hongbo Zhao
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Commits on Jul 2, 2019

create a nucleus from DDFT
Hongbo Zhao
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start working on Krylov-based DDFT solver
Hongbo Zhao
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Commits on Jul 3, 2019

updaet solver_DDFT, and moreode*, seems to work
Hongbo Zhao
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update solver_DDFT
Hongbo Zhao
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roi diffuse shape function
Hongbo Zhao
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DDFT_nucleation study nucleation
Hongbo Zhao
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Commits on Jul 6, 2019

work on solver_DDFT and IP_DDFT
Hongbo Zhao
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add a few lines in DDFT_nucleation for IP test
Hongbo Zhao
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Commits on Jul 7, 2019

fix bugs in IP_DDFT and solver_DDFT
Hongbo Zhao
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decrease gmrestol and increase restart in solver_DDFT
Hongbo Zhao
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update DDFT_nucleation, try using real space representation for C
Hongbo Zhao
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use the options of sensFcnMultiplier to directly multiply omega with dF in sensFcn
Hongbo Zhao
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Commits on Jul 8, 2019

fix bugs in solver_DDFT
Hongbo Zhao
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add fminunc option, add Cspace=isotropic option, increase weight by 100 in IP_DDFT
Hongbo Zhao
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update DDFT_nucleation scripts
Hongbo Zhao
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IP_DDFT_debug, plot val and gradient along the search direction
Hongbo Zhao
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Commits on Jul 9, 2019

fix bug in roi_circle
Hongbo Zhao
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Commits on Jul 10, 2019

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

Commits on Jul 11, 2019

continue DDFT_nucleation2 from the previous run
Hongbo Zhao
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add the mode of eval (output model solution) and fval and exitflag output in IP_DDFT
Hongbo Zhao
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add history_production, producing figures for DDFT IP (need more work)
Hongbo Zhao
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visualize DDFT_nucleation2, update DDFT_nucleation2_helper to do optim loop
Hongbo Zhao
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Commits on Jul 14, 2019

update IP_DDFT, add tspan and eval options
Hongbo Zhao
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add DDFT_nucleation3, a larger alpha, small n0 for nucleation event
Hongbo Zhao
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try alternate between 2 datasets DDFT_nucleation3
Hongbo Zhao
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Commits on Jul 16, 2019

update solver_DDFT to allow empty C and mu in params
Hongbo Zhao
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switch to custom_EvenPoly for Cspace=isotropic in IP_DDFT
Hongbo Zhao
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DDFT_nucleation_PFC, use PFC kernel
Hongbo Zhao
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update IP_DDFT, parameter prescreening and isotropic Cspace, highest order must be negative
Hongbo Zhao
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add DDFT_nucleation4 fit DDFT to a 4-th order PFC
Hongbo Zhao
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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
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add FDcoeff to compute 1D finite difference coefficient
Hongbo Zhao
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rewrite Cspace=isotropic, add Cspace=FD
Hongbo Zhao
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use parser in solver_DDFT, add option and moreoptions in params, update IP_DDFT
Hongbo Zhao
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DDFT_nucleation6
Hongbo Zhao
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DDFT_nucleation6 and 7
Hongbo Zhao
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Commits on Jul 17, 2019

add Cspace='isotropic_CmE', add optimizing mu params in IP_DDFT
Hongbo Zhao
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update and add DDFT_nucleation(4,9)
Hongbo Zhao
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Commits on Jul 19, 2019

Commits on Jul 20, 2019

add mode in IP_DDFT, prepare for post processing
Hongbo Zhao
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add DDFT_nucleation files
Hongbo Zhao
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Commits on Jul 22, 2019

in IP_DDFT, mode=eval, output modified params and meta for postprocessing
Hongbo Zhao
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update history_production after IP_DDFT update
Hongbo Zhao
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update DDFT_nucleation13 for visualization
Hongbo Zhao
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update history_production to rescale and shift mu and C
Hongbo Zhao
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Commits on Jul 23, 2019

two more files with different initial conditions
Hongbo Zhao
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Merge branch 'master' of https://github.com/hbozhao/reacdiff
Hongbo Zhao
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add mu_positive option in IP_DDFT, doesn't seem to work at least yet
Hongbo Zhao
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Commits on Jul 25, 2019

add mode='sens' in IP_DDFT
Hongbo Zhao
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add Cspace='isotropic_cutoff', add assign_suppress options in IP_DDFT
Hongbo Zhao
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Commits on Jul 27, 2019

Commits on Jul 28, 2019

add istropic_even option in IP_DDFT to use even legendrepolynomials only
Hongbo Zhao
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DDFT_nucleation28, try isotropic_poly_scale with isotropic_even = true
Hongbo Zhao
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update IP_DDFT, remove shifting by 1 for isotropic_poly, add 29 to test it
Hongbo Zhao
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Revert "update IP_DDFT, remove shifting by 1 for isotropic_poly, add 29 to test it"
Hongbo Zhao
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add isotropic_hermite_scale in IP_DDFT
Hongbo Zhao
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add DDFT_nucleation29 t try isotropic_hermite_scale
Hongbo Zhao
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Commits on Jul 29, 2019

upload DDFT_nucleation* on HZ-BazantLab
Hongbo Zhao
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DDFT_nucleation30/31 to test isotropic_hermite_scale with discrete images and mu
Hongbo Zhao
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more DDFT_nucleation32/33 on adding mu while isotropic_hermite_scale
Hongbo Zhao
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Commits on Jul 31, 2019

visualization of DDFT_nucleation23
Hongbo Zhao
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add optional cutoff/scaling for Cspace=isotropic in IP_DDFT
Hongbo Zhao
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DDFT_nucleation34 try isotropic with scaling by k0
Hongbo Zhao
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add Cspace=isotropic_laguerre_scale
Hongbo Zhao
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DDFT_nucleation36, sensitivity analysis using isotropic_hermite_scale
hbozhao
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Merge branch 'master' of https://github.com/hbozhao/reacdiff
Hongbo Zhao
committed
update IP_DDFT, now cutoff can be used for all Cspace=isotropic*, add relevant Cfunc output pp
Hongbo Zhao
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in history_production, generalize C to all isotropic*, fix bugs
Hongbo Zhao
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add DDFT_nucleation30 visualization
Hongbo Zhao
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small updates to DDFT_nucleation files
Hongbo Zhao
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Commits on Aug 2, 2019

add isotropic_fourier_scale in IP_DDFT
Hongbo Zhao
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update IP_DDFT, add mode='pp'
Hongbo Zhao
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add history_func, copied from history_production to plot functions in history only
Hongbo Zhao
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begin working on mainFigure
Hongbo Zhao
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update DDFT_nucleation, add 35: laguerre poly (failed), 37: sensitivity using fourier_
Hongbo Zhao
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fix bug in IP_DDFT regarding isotropic_fourier_scale
Hongbo Zhao
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update history_production, use history_func
Hongbo Zhao
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DDFT_nucleation38 try Laguerre polynomials for sensitivity analysis
Hongbo Zhao
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Commits on Aug 3, 2019

update DDFT_nucleation26/38 to show C2 error bar
Hongbo Zhao
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Commits on Aug 5, 2019

calculate sensitivity (eigenvalue etc) using 1D approx
Hongbo Zhao
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update mainFig and history_func
Hongbo Zhao
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update DDFT_nucleation36/38 (sensitivity) visualization
Hongbo Zhao
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Commits on Aug 13, 2019

update mainFig and utility function
Hongbo Zhao
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Commits on Aug 14, 2019

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

Commits on Sep 22, 2019

update mainFig's subplot spacing, figure saved as DDFT_mainFig_v4
Hongbo Zhao
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Commits on Nov 23, 2019

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

Commits on Nov 25, 2019

Commits on Nov 26, 2019

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

Commits on May 17, 2020

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

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

Commits on Jan 4, 2021

add presentation_RD, to generate figure for slide
Hongbo Zhao
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fux bugs in solver_DDFT
Hongbo Zhao
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Commits on Jan 5, 2021

fix bug in solver_DDFT about user options setting
Hongbo Zhao
committed

Commits on Jan 15, 2021

update presentation_RD.m
Hongbo
committed

Commits on Jan 16, 2021

Commits on Dec 30, 2021

add DDFT_nucleation42 created on bgs
Hongbo
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Merge branch 'master' of github.com:hbozhao/reacdiff
Hongbo
committed
add files on workstation
Hongbo Zhao
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add DDFT_nucleus.mat on workstation
Hongbo Zhao
committed
commit changes on home PC
Hongbo Zhao
committed
commit changes on MIT laptop
hbozhao
committed