Move files to directories

diff --git a/Kalibrace.m b/Kalibrace/Kalibrace.m
similarity index 100%
rename from Kalibrace.m
rename to Kalibrace/Kalibrace.m

diff --git a/round_deviation.m b/Kalibrace/round_deviation.m
similarity index 100%
rename from round_deviation.m
rename to Kalibrace/round_deviation.m

diff --git a/altminimize.m b/altminimize.m
deleted file mode 100644 (file)
index a0182ba..0000000
--- a/altminimize.m
+++ /dev/null
@@ -1,25 +0,0 @@
-function x = altminimize(objfun, x_0, tol = 0.01, max_iter = 2)
-
-       s = size(x_0);
-       if s(1) ~= 1 && s(2) ~= 1
-               printf("x_0 must be given as an array of parameters!\n");
-               return ;
-       elseif (s(2) ~= 1)
-               x = x_0';
-       else
-               x = x_0;
-       end
-
-       Y = zeros(size(x));
-       change = (tol + 1) * ones(size(x));
-       while (max(abs(change)) > tol)
-               for i=1:length(x)
-                       y0 = x(i);
-                       x(i) = 0;
-                       Y(i) = 1;
-                       x(i) = minimize(@(y) objfun(x + y*Y), y0, tol);
-                       change(i) = (y0 - x(i)) / min(y0, x(i))
-                       Y(i) = 0;
-               end
-       end
-end

diff --git a/alternating_min.m b/functions/alternating_min.m
similarity index 100%
rename from alternating_min.m
rename to functions/alternating_min.m

diff --git a/basic_model.m b/functions/basic_model.m
similarity index 100%
rename from basic_model.m
rename to functions/basic_model.m

diff --git a/batch_sim.m b/functions/batch_sim.m
similarity index 100%
rename from batch_sim.m
rename to functions/batch_sim.m

diff --git a/estimateDP.m b/functions/estimateDP.m
similarity index 100%
rename from estimateDP.m
rename to functions/estimateDP.m

diff --git a/grad.m b/functions/grad.m
similarity index 100%
rename from grad.m
rename to functions/grad.m

diff --git a/objfun.m b/functions/objfun.m
similarity index 100%
rename from objfun.m
rename to functions/objfun.m

diff --git a/simulate_cell.m b/functions/simulate_cell.m
similarity index 99%
rename from simulate_cell.m
rename to functions/simulate_cell.m
index ab3993e966f8dab4586b1afac99f566ed06a545d..7a5097ab0393e7ca658a48d182597a7ea0112e19 100644 (file)
--- a/simulate_cell.m
+++ b/functions/simulate_cell.m
@@ -13,7 +13,7 @@ function simulate_cell(full_path, conditions)
                                temperature                     % temp
                                outer_vol                       % volume from which the gas expands inside
        %}
                                temperature                     % temp
                                outer_vol                       % volume from which the gas expands inside
        %}

-               
+

        %{
        figure
        surf(t, x, p);
        %{
        figure
        surf(t, x, p);

diff --git a/steepest_grad.m b/functions/steepest_grad.m
similarity index 100%
rename from steepest_grad.m
rename to functions/steepest_grad.m

diff --git a/main.m b/main.m
deleted file mode 100644 (file)
index ac06a79..0000000
--- a/main.m
+++ /dev/null
@@ -1,271 +0,0 @@
-clear all
-close all
-
-pkg load optim
-%{
-classdef Membrane
-  properties
-    D double {mustBePositive}
-    P double {mustBePositive}
-    S double {mustBePositive}
-
-    r double {mustBePositive}
-    d double {mustBePositive}
-    A double {mustBePositive}
-    l double {mustBePositive}
-
-    material char
-  endproperties
-endclassdef
-
-classdef MembraneSimulation
-  properties
-    membrane Membrane
-
-    tstep double {mustBePositive}
-    xstep double {mustBePositive}
-
-    tend double {mustBePositive}
-    tc double {mustBeNonnegative} = 0.5
-
-    pmax double {mustBePositive}
-    pvac double {mustBeNonnegative} = 0
-
-    T double {mustBePositive} = 0
-
-  endproperties
-  methods
-    function [t, p] = simulate();
-      D = membrane.D
-      P = membrane.P
-      l = membrane.l
-      A = membrane.A
-    endfunction
-  endmethods
-endclassdef
-%}
-
-
-[fname,path]=uigetfile;
-data=importdata([path fname], '\t', 2);
-
-datasize=size(data.data);
-t=data.data(:,1)';
-p1=data.data(:,datasize(2))';
-p2=data.data(:,datasize(2)-1)';
-
-pvac = min([p1 p2]);
-pmax = max(p1);
-
-xm=find(p1>0.5*max(p1),1,'first');
-tstart = t(xm);
-
-l = 350e-6;
-d = 32e-3;
-A = d^2/4*pi;
-V0 = 616e-9;
-V1 = 872e-9;
-V2 = 684e-9;
-
-
-
-pars_cur = [1e-3, 3.5e-5, tstart, 100, 3e-10, 3e-13, 3.5e-4, 32e-3, V0, V1, V2, pmax, 0.3];
-
-function [tmod, p] = cellmod(pars)
-  % cellmod(tstep, xstep, tstart, tend, D, P, l, d, V0, V1, V2, pmax, tc=0.5, pvac=0, T = 298, all)
-
-  tstep = pars(1);
-  xstep = pars(2);
-  tstart = pars(3);
-  tend = pars(4);
-  D = pars(5);
-  P = pars(6);
-  l = pars(7);
-  d = pars(8);
-  V0 = pars(9);
-  V1 = pars(10);
-  V2 = pars(11);
-  pmax = pars(12);
-
-
-  if length(pars)<16
-    all = false;
-  else
-    all = pars(16);
-  end
-
-  if length(pars)<15
-    T = 298;
-  else
-    T = pars(15);
-  end
-
-  if length(pars)<14
-    pvac = 0;
-  else
-    pvac = pars(14);
-  end
-
-  if length(pars)<13
-    tc = 0.5;
-  else
-    tc = pars(13);
-  end
-
-  A = d^2/4*pi;
-
-       R = 8.314;
-
-       m = floor(l/xstep)+1;
-       xstep = l/m;
-
-       n1 = floor(tc/tstep)+1;
-       tstep1 = tc/n1;
-
-  if tend>tc
-    n2 = floor( (tend-tc)/tstep);
-    tstep2 = (tend-tc)/n2;
-    p = zeros(n1+n2-1, m);
-  else
-    tstep2 = tstep;
-    p = zeros(n1, m);
-  end
-
-  % criterium for numerical stability
-  crit = D*max([tstep1, tstep2])/xstep^2;
-  while crit>1  % Meaning error grows
-    if tstep1 > tstep2
-      tstep1 = tstep1/2;
-      n1 = n1*2;
-    else
-      tstep2 = tstep2/2;
-      if tend > tc
-        n2 = n2*2;
-      end
-    endif
-    crit = D*max([tstep1, tstep2])/xstep^2;
-  end
-
-  tstep1;
-  tstep2;
-
-  tmod(1) = 0;
-
-       p(1, :) = pvac;
-       p(1,1) = pmax;
-
-       for j=1:n1
-               p(j+1, 2:end-1) = p(j, 2:end-1) + ...
-                       D*tstep1/xstep^2*( p(j, 1:end-2) - 2*p(j, 2:end-1) + p(j, 3:end));
-               p(j+1, 1) = p(j, 1) + tstep1/2/xstep*P*R*T*A/(V0+V1)*...
-                       ( -3*p(j, 1) + 4*p(j, 2) - p(j, 3) );
-               p(j+1, m) = p(j, m) - tstep1/2/xstep*P*R*T*A/V2*...
-                       ( p(j, m-2) - 4*p(j, m-1) + 3*p(j, m) );
-
-               tmod(j+1) = tmod(j) + tstep1;
-       end
-  if tend > tc
-    for j=n1+1:n1+n2-1
-      p(j+1, 2:end-1) = p(j, 2:end-1) + ...
-        D*tstep1/xstep^2*( p(j, 1:end-2) - 2*p(j, 2:end-1) + p(j, 3:end));
-      p(j+1, 1) = p(j, 1) + tstep2/2/xstep*P*R*T*A/V1*...
-        ( -3*p(j, 1) + 4*p(j, 2) - p(j, 3) );
-      p(j+1, m) = p(j, m) - tstep2/2/xstep*P*R*T*A/V2*...
-        ( p(j, m-2) - 4*p(j, m-1) + 3*p(j, m) );
-
-      tmod(j+1) = tmod(j) + tstep2;
-    end
-  end
-
-  tmod = [0 tstart tmod+tstart];
-  p = [pvac*ones(2,size(p,2)); p];
-
-  if all<0.5
-    p = [p(:,1) p(:,end)]; %Erasing all but the boundary (cell) pressures
-  endif
-end
-
-function Obj = objfun(model, pars, exp)
-       xexp = exp(:,1);
-       yexp = exp(:,2:end);
-
-       [xmod, ymod] = model(pars);
-
-       ymod_interpol = interp1(xmod, ymod, xexp);
-
-       valid = ~isnan(ymod_interpol) & (yexp>0);
-
-       Obj = 1/sum(sum(valid)) * sum(sum( (yexp(valid) - ymod_interpol(valid)).^2 ./ yexp(valid) ));
-end
-
-function grad = grad(field, pars, ind, step = 0.001)
-  grad = zeros(size(pars));
-  temp_pars = pars;
-  for i = ind
-    j = j+1;
-
-    temp_pars_pos = pars;
-    temp_pars_pos(i) = temp_pars_pos(i)*(1+step);
-
-    val_pos = field(temp_pars_pos);
-
-    temp_pars_neg = pars;
-    temp_pars_neg(i) = temp_pars_neg(i)*(1-step);
-
-    val_neg = field(temp_pars_neg);
-
-    grad(i) = (val_pos - val_neg)/(temp_pars_pos(i) - temp_pars_neg(i));
-  endfor
-end
-
-tolobj = 1e-4;
-
-curobjfun = @(pars) objfun(@cellmod, pars, [t; p1; p2]');
-
-
-pars_prev = pars_cur;
-pars_prev(5:6) = pars_prev(5:6)*1.01;
-gradF_prev = grad(curobjfun, pars_prev, [5 6]);
-F_prev = curobjfun(pars_prev);
-
-krit = tolobj+1;
-
-optstep = 1;
-
-while F_prev>tolobj
-
-
-       gradF_cur = grad(curobjfun, pars_cur, [5 6])
-
-       pars_cur = pars_cur - optstep * numhessian(curobjfun, pars_cur, [5 6]) \ gradF_cur
-       F_cur = curobjfun(pars_cur)
-%{
-       while F_cur > F_prev
-               optstep = optstep/2;
-               pars_cur = pars_prev - optstep * gradF;
-               F_cur = curobjfun(pars_cur);
-       endwhile
-
-       krit = abs(F_prev - F_cur)
-       F_cur
-       optstep
-       pars_cur
-       gradF_cur
-%}
-       F_prev = F_cur;
-       gradF_prev = gradF_cur;
-       pars_prev = pars_cur;
-
-end
-
-%{
-p1mod = p(:,1);
-p2mod = p(:,end);
-
-t = (0:0.01:tend);
-x = (0: 10e-6 : 350e-6);
-
-[X,T] = meshgrid(x,t);
-
-surf(X,T,p)
-%}

diff --git a/octave-workspace b/octave-workspace
deleted file mode 100644 (file)
index 84c5b3b..0000000
Binary files a/octave-workspace and /dev/null differ

diff --git a/allmin.m b/others/allmin.m
similarity index 100%
rename from allmin.m
rename to others/allmin.m

diff --git a/draw_hist.m b/others/draw_hist.m
similarity index 100%
rename from draw_hist.m
rename to others/draw_hist.m

diff --git a/expl_sol_model.m b/others/expl_sol_model.m
similarity index 100%
rename from expl_sol_model.m
rename to others/expl_sol_model.m

diff --git a/halving_int.m b/others/halving_int.m
similarity index 100%
rename from halving_int.m
rename to others/halving_int.m

diff --git a/hessgrad.m b/others/hessgrad.m
similarity index 100%
rename from hessgrad.m
rename to others/hessgrad.m

diff --git a/membrane.m b/others/membrane.m
similarity index 100%
rename from membrane.m
rename to others/membrane.m