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runIMR.m
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runIMR.m
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%% Runfile for inertial microcavitation rheometry
% Authors:
% Jon Estrada
% Brown Solid Mechanics, PhD '17
% Carlos Barajas
% Umich Mechanical Engineering BS '16
clear; close all;
warning('off','all')
%% Set up the file paths
%For CCV, file path is different
%general folder
addpath(genpath('/gpfs/data/cf5/jbestrad/FL_Cav_Data/'));
%data folder
fp = '/gpfs/data/cf5/jbestrad/FL_Cav_Data/160420/11kPa_PA/';
%fp = '/gpfs/data/cf5/jbestrad/FL_Cav_Data/160420/water/';
%fp = '/gpfs/data/cf5/jbestrad/FL_Cav_Data/160511/collagen/1/';
%fp = '/gpfs/data/cf5/jbestrad/FL_Cav_Data/170403/Collagen/';
%fp = '/gpfs/data/cf5/jbestrad/FL_Cav_Data/170411/Collagen/20170302p1/';
%For Local comp usage (i.e. single runs)
%general folder
%addpath(genpath('V:\data\jbestrad\FL_Cav_Data\'));
%data folder
%fp = 'V:\data\jbestrad\FL_Cav_Data\160420\water\';
%fp = 'V:\data\jbestrad\FL_Cav_Data\170411\Collagen\20170302p1/';
%fp = 'C:\Users\Jon\Brown Google Drive\RESEARCH DATA\FL Cav Data\160420\11kPa_PA\';
%Load the file RofTdata.mat, which contains vars Rnew and t
%Rnew has size [num_expts num_video_frames]
load([fp 'RofTdata.mat']);
%There are 4 choices of model:
%linkv (linear Kelvin-Voigt)
%neoHook (neo-Hookean Kelvin-Voigt)
%sls (Standard Linear Solid)
%nhzen (neo-Hookean Standard Solid)
model = 'neoHook';
savename = '170821_sweep';
%'170727_softsweep_coarse';%'170413_collagenKVcoarse';
%Parallel pool creation
% curCluster = parcluster('local');
% curCluster.NumWorkers = 8;
% saveProfile(curCluster);
% pool = parpool(8);
%Set time duration for the simulation (s)
tspan = 2.25E-4;%1.3E-4;
allRmax = max(Rnew,[],2);
%Set the index choice of experiments
%expts = [12 14:19]; %water
%expts = [2,3,4,5,8,10,14,15,16,18,20,23,24]; %collagen
expts = 6;
%Set the range of G and mu (most conveniently done as powers of 10)
G_ooms = 1:0.2:5;%3.0:0.1:4.0; %soft PA %3.65:0.05:4.15 stiff PA
mu_ooms = -1.4:0.05:-0.9;%[-inf -4:0.25:-1.25 -1.05];%[-1.65:0.05:-0.9]%-2.25:0.25:-0.5%[-inf -1.65:0.05:-0.9];
G1_ooms = inf;
%Note, mu/G1 should go to 0 in the limit, so G1 for K-V models should be infinite
%% Run IMR
for expt = expts
mkdir([fp num2str(expt)]);
cd([fp num2str(expt)]);
%%
soln_mx = cell(length(G_ooms),length(mu_ooms),length(G1_ooms));
P_inf = 101325; % (Pa) Atmospheric Pressure
rho = 998.2; % (Kg/m^3) Material Density
Uc = sqrt(P_inf/rho); % Characteristic velocity
Tgrad = 1; %1 Temperature transfer bt bubble and material
Cgrad = 1;%1; %1 Vapor-non-condensible gas diffusion
Tmgrad = 0; %0 Off means cold liquid assumption
%%
for k = 1:length(G1_ooms)
for j= 1:length(mu_ooms)
tic
parfor i=1:length(G_ooms)
soln_mx{i,j,k} = struct('G',10^G_ooms(i),'mu',10^mu_ooms(j),'G1',10^G1_ooms(k),...
'tcs_star',[],'Rratios',[],'tmaxs_star',[],'t2',[],'R2',[],'U',[],'P',[],'J',[],'T',[],'C',[],...
'Cdel',[],'tdel',[],'Tdel',[]);
G = soln_mx{i,j,k}.G;
mu = soln_mx{i,j,k}.mu;
G1 = soln_mx{i,j,k}.G1;
[R0,t0] = calcR0(Rnew(expt,:)*1E-6,t); %need to get the inital radius from a fit (R)
eqR = median(Rnew(expt,62:end))*10^-6;
R_eq = eqR/R0;
% Bisection method to get initial partial pressure of the non-condensible gas
% Initial guess (purely empirical) and range (e.g. ~226 for
% 11kPa, 92 for 1.3kPa, 20.6 for water)
P_guess = 226;
P = [8, 400];
R_eq_lims = [IMRCalc_Req(R0,Tgrad,Cgrad,P(1),G,G1,mu), IMRCalc_Req(R0,Tgrad,Cgrad,P(2),G,G1,mu)];
R_eqf = IMRCalc_Req(R0,Tgrad,Cgrad,P_guess,G,G1,mu);
error = 1;
while abs(error) > 0.00001
if R_eq > R_eqf
P(1) = P_guess;
R_eq_lims(1) = IMRCalc_Req(R0,Tgrad,Cgrad,P_guess,G,G1,mu);
else
P(2) = P_guess;
R_eq_lims(2) = IMRCalc_Req(R0,Tgrad,Cgrad,P_guess,G,G1,mu);
end
P_guess = mean(P);
R_eqf = IMRCalc_Req(R0,Tgrad,Cgrad,P_guess,G,G1,mu);
error = abs(R_eq-R_eqf);
end
%%
NT = 500; % Mesh points in bubble, resolution should be >=500
NTM = 10; % Mesh points in the material, should be 10
Pext_type = 'IC'; %'IC' for Flynn, 'ga' for gaussian bubble growth
if strcmp(Pext_type,'IC')
Pext_Amp_Freq = [P_guess; 0];%[226; 0]; % Tune first number to match equi radii
elseif strcmp(Pext_type,'ga')
Pext_Amp_Freq = [P_guess; dt; tw;];
end
disptime = 0; % 1 = Displays time to complete simulation
Dim = 1; % 1 = displays results in dimensional form
comp = 1; % 0 uses Rayleigh-Plesset, 1 uses Keller-Miksis
%%
if strcmp(Pext_type,'ga')
Rmax = R0;
R0 = eqR;
end
tic
%Variables:
%t2 = simulation time
%R2 = simulation radius
%R2dot = velocity of bubble wall
%P = bubble pressure
%S = stress integral
%T = temperature inside bubble
%C = relative concentration of vapor
%Tm = temperature of wall
[t2, R2, R2dot, P, S, T, C, Tm, tdel, Tdel, Cdel] = IMRsolver...
(model, G, G1, mu, tspan, R0, NT, NTM, ...
Pext_type, Pext_Amp_Freq , disptime, Tgrad, Tmgrad, Cgrad, Dim, comp);
toc
%%
Rdiff = diff(R2);
inc_idx = find(Rdiff>0);
diffzeros_idx = find(Rdiff(1:(end-1)).*Rdiff(2:(end))<0)+1;
localmax_idx = [1; diffzeros_idx(2:2:end)];
localmin_idx = diffzeros_idx(1:2:end);
Rratios = R2(localmax_idx)/R2(1);
tcs = t2(localmin_idx);
tcs_star = tcs*Uc/R0;
tmaxs_star = t2(localmax_idx)*Uc/R0;
%tpeaksall_star = [0; reshape([tcs_star,tmaxs_star(2:end)],size(diffzeros_idx))];
soln_mx{i,j,k}.tcs_star = tcs_star;
soln_mx{i,j,k}.Rratios = Rratios;
soln_mx{i,j,k}.tmaxs_star = tmaxs_star;
soln_mx{i,j,k}.t2 = t2;
soln_mx{i,j,k}.R2 = R2;
soln_mx{i,j,k}.U = U;
soln_mx{i,j,k}.P = P;
soln_mx{i,j,k}.J = J;
%soln_mx{i,j,k}.T = T;
%soln_mx{i,j,k}.C = C;
soln_mx{i,j,k}.Cdel = Cdel;
soln_mx{i,j,k}.tdel = tdel;
soln_mx{i,j,k}.Tdel = Tdel;
[i j k]
end
toc
%If you want to save intermediate files during runs, uncomment this line
%save([savename 'G_' num2str(G_ooms(i)) '.mat'],'soln_mx','G_ooms','mu_ooms','Rnew','t');
end
end
save([savename '.mat'],'soln_mx','G_ooms','mu_ooms','Rnew','t');
cd(fp)
end
%%
% sz = size(soln_mx);
% sG1 = sz(1);
% try
% sM = sz(2);
% catch
% sM = 1;
% end
% try
% sG = sz(3);
% catch
% sG = 1;
% end
%%
%
% LSQ = cell(sG1,sM,sG);
% LSQminidx = [inf 0 0 0];
% try
% for i=1:sG1
% %figure(i)
% for j=1:sM
% for k=1:sG
%
% %figure(10000*i+100*j+k)
% %figure(10000*i+100+k)
% %figure(505)
%
% [R2max idx] = max(soln_mx{i,j,k}.R2);
%
% hold on;
%
% t2 = soln_mx{i,j,k}.t2-soln_mx{i,j,k}.t2(idx);
% R2 = soln_mx{i,j,k}.R2;
% %plot(t2,R2,'Color',[(i-1)/sG1(1) (k-1)/sG(1) (j-1)/sM(1)]);
%
% [R0,t0] = calcR0(Rnew(expt,:)*1E-6,t);
% t2exp=t-t0;
% R2exp=Rnew(expt,:)*1E-6;
% %plot(t2exp,R2exp, ' *');
%
% distRmat = bsxfun(@minus,R2,R2exp);
% disttmat = bsxfun(@minus,t2,t2exp);
% distmat = sqrt(disttmat.^2+distRmat.^2);
% weight = ones(1,101);
% %weight([1:10 18:end]) = 0; %for fitting the first peak
% %weight([1:10 19:26]) = 0; %for ignoring the second peak
% weight([1:9 70:end]) = 0;
%
%
% LSQ{i,j,k} = nansum(weight.*min(distmat,[],1));
%
% if LSQ{i,j,k}<LSQminidx(1)
% LSQminidx = [LSQ{i,j,k} i j k];
% end
% end
% % for n=k:-1:1
% % [maxRNHZ(n) idx(n)] = max(soln_mx{i,j,n}.R2);
% % end
%
% end
%
% end
% catch
% end
%
% i=LSQminidx(2); j=LSQminidx(3); k=LSQminidx(4);
% log10([soln_mx{i,j,k}.G soln_mx{i,j,k}.mu soln_mx{i,j,k}.G1])
% [k j i]
% %%
% %k=7; j=8; i=16;
% %figure(9999); hold on;
% R2 = soln_mx{i,j,k}.R2;
% [R2max idx] = max(soln_mx{i,j,k}.R2);
% t2 = soln_mx{i,j,k}.t2-soln_mx{i,j,k}.t2(idx);
% %plot(t2,R2);%,'Color','red');
% %plot(t2/max(R2)*10,R2/max(R2)./(1-((1-0.1301).*(exp(-t2/max(R2)*10/1.15))+0.1301)));%,'Color','red');
% %hold on; scatter(t2exp,R2exp,16,[0 0 0],'filled');
%
% [R2max idx] = max(soln_mx{i,j,k}.R2);
%
% %save('dataprocoutputs.mat','t2' , 'R2','U','P','Z', 'T','C', 'Tm','tdel','Tdel','Cdel');
% end