Readme for 10.17634/122626-7
 
The files are in MATLAB format. Here "..." labels the elements in mat files.
 
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The common/generally required information for plotting the 3D data are
1. the time are denoted as "te" with the unit in ms, or te_af_bec for the time after t_bec.
2. The spatial axis are named as "x", "y" and "z" for longitudinal and transeverse directions.
3. The length unit is "aho".
To visualize the density plot for a wavefuntion "u":
[X,Y,Z] = meshgrid(x,y,z);
figure,
[faces,verts] = isosurface(X*aho*1e6,Y*aho*1e6,Z*aho*1e6,abs(u).^2,1000);
    patch('Vertices', verts, 'Faces', faces,'FaceColor','g','edgecolor', 'none','FaceAlpha',0.2);
        [faces,verts] = isosurface(X*aho*1e6,Y*aho*1e6,Z*aho*1e6,abs(u).^2,50);
    patch('Vertices', verts, 'Faces', faces,'FaceColor','y','edgecolor', 'none','FaceAlpha',0.125);
    view(3); axis xy equal;
    camlight head; lighting phong;
    xlim([-1 1] * 125);
where 1000 and 50 are isovalue for the green and yellow isosurface in the plots (see method).
With the same command, one could also use it to plot the intensity of velocity filed to visualize the vortices/defects with a given isovalue.
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The other plots please refer the command in each instructions.

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* File Name: Fig_1_a.mat
  The wavefunctions in figure 1. The c-field wavefunctions are named as "ui" and "uf" in the matlab file for initial and final profiles.
  The spatial axes are included as "x", "y" and "z" in the same file. 
 
* File Name: Fig_1_b-fast.mat
  The c-field wavefunctions at te= 18, 45, 114 and 726 ms for tau_R= 18 ms in "ut" sequed by its orde, and the spatial axese are included as "x", "y" and "z" in the same file with the length unit "aho". 
  To recover the full wavefunctions for each time, please use the MATLAB commands:
    [X,Y,Z] = meshgrid(x,y,z); 
    u = reshape(ut(jj,:),size(X));
  where jj is the sequence number of desired moment.
 
* File Name: Fig_1_b-typical.mat
  The c-field wavefunctions at te= 48, 120, 318 and 720 ms for tau_R= 18 ms in "ut" sequenced by its order, and the spatial axes are included as "x", "y" and "z" in the same file with the length unit "aho". 
  To recover the full wavefunctions for each time, please use the MATLAB commands:
    [X,Y,Z] = meshgrid(x,y,z); 
    u = reshape(ut(jj,:),size(X));
  where jj is the sequence number of desired moment.
 
* File Name: Fig_1_b-slow.mat
  The c-field wavefunctions at te= 240, 330, 402 and 720 ms in "ut" sequenced by its order, and the spatial axes are included as "x", "y" and "z" in the same file with the length unit "aho". 
  To recover the full wavefunctions for each time, please use the MATLAB commands:
    [X,Y,Z] = meshgrid(x,y,z); 
    u = reshape(ut(jj,:),size(X));
  where jj is the sequence number of desired moment.
 
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* File Name: Fig_2.mat
  There are 6 c-field wavefunctions at te= 0, 28, 29, 30, 31 and 32 ms for tau_R= 84 ms in "ut" sequenced by its orde, and the spatial axes are included as "x", "y" and "z" in the same file with the length unit "aho". 
  To recover the full wavefunctions for each time, please use the MATLAB commands:
    [X,Y,Z] = meshgrid(x,y,z); 
    u = reshape(ut(jj,:),size(X));
  where jj is the sequence number of desired moment.
 
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* File Name: Fig_3_a_to_d.rar:
  A package file consists with 12 mat file for Figure 3 panels (a) to (d):
  In the series of 'Fig_3_#_##uKs.mat', there is a "N0" element in each mat file for # panels and dT/dt = ##.
  Each "N0" has two rows for simulation data.
  The first and second rows are the horizontal (time) axis and vertical (mean PO condensate number) axis respectively.
  While the statistic error between different realizations of a ramp duration is small, such information is not included.
 
  In the series of 'Fig_3_#_expt_##uKs.mat', there is a "N0_expt" element.
  The first and second rows are the horizontal (time) axis and vertical (condensate number) axis respectively for # panels and dT/dt = ##.
  The third and fourth rows are the upper and lower error bar for the vertical axes.
 
* File Name: Fig_3_e.mat
  Composed by two elements: "tauR" and "tauG" for horizontal and vertical axis.
  "tauR" is the ramp duration, and "tauG" is the growth time scale extracted from the fit of the PO condensate number growth curves.
  "tauR" is a 1 * 11 array in the unit of ms.
  "tauG" is a 3 * 11 array in the unit of ms. The first row are the vertical values.
  The second and third rows are the upper and lower bounds for confidential zone of the fit.
 
* File Name: Fig_3_f.mat
  Composed by two elements: "tauR" and "tbec" for horizontal and vertical axis.
  "tauR" is the ramp duration, and "tbec" is the moment that the PO condensate number reaches the 5% of the final equilibrium total particle number.
  "tauR" is a 1 * 11 array in the unit of ms.
  "tbec" is a 3 * 11 array in the unit of ms. The errorbar of tbec is negligible here.
  The second and third rows are the upper and lower bounds for the t_bec defined by 7% and 3% fraction of the final total particle number.
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* File Name: Fig_4_a.mat
  The evolution of mean number of defects, "Nv", for 6 different tau_R with its statistic error.
  There are 6 "Nv_###" in this mat file. Each "Nv_###" corresponds to the evolution for tau_R=###, and there are 3 columns inside it.
  The first column is the evolution time after t_bec, namely, te - t_bec.
  The second and third columns are the mean number of defects and corresponding statistic error, respectively.
 
* File Name: FIg_4_b.mat
  This file contains 5 data elements:
  "dTdt", "Nv", "tau_R" for simulation data, and 
  "dTdt_epxt" and "Nv_expt" for experimental data.
  For the horizontal axis: "dTdt" and "tau_R" are 1 * 11 arrays and "dTdt_expt" is an 1 * 12 arrays.
  For the vertical axis:
  "Nv" is a 6 * 11 array, the top three rows and bottom three rows are information of number of defects with the statistic error.
  In each set of three rows, the first row is the mean number of defects, and the 2nd and 3rd rows are the upper and lower errors respectively.
  Similar to "Nv", "Nv_expt" composed with 3 rows as well, the first row is the mean number of defects, and the 2nd and 3rd rows are the upper and lower errors respectively.
 
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* File Name: Fig_5_experiment
  The absorption images of experimental data
 
* File Name: Fig_5_simulation.mat
  There are c-field wavefunctions of 3 different realization of tau_R= 84 ms at te= 342 ms in "ut", and the spatial axes are included as x, y and z in the same file with the length unit aho. 
  To recover the full wavefunctions for each time, please use the MATLAB commands:
    [X,Y,Z] = meshgrid(x,y,z); 
    u = reshape(ut(jj,:),size(X));
  where jj is the sequence number of desired run.
 
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* File Name: Fig_6_a.mat
  There are 15 elements in this mat file in 7 categories:
  1. "Dx" the horizontal axis of the plot in micro-meter.
  2. "g1_error_x" the x input for the errorband.
  3. "g1_ini", the initial g1 profile. Using 'plot(Dx,g1_ini);' to plot the data.     
  4. "g1_eqbm_####", a 6 * 399 array the equilibrium g1 for corresponding scaled time with #### = 'fast', 'middle', and 'slow'.
     The first index ranging from 1 to 6 labels the corresponding sequence in Fig. 6 a from top to bottom.
     Using 'plot(Dx,g1_eqbm_####(jj,:));' for jj = 1 to 6 to plot the data.     
  5. "g1_eqbm_####_error", a 6 * 794 array for the corresponding error of g1_eqbm_#### in patch form, which is compatible down to MATLAB 2014 at least.
     Using 
        'patch(g1_error_x,g1_eqbm_####_error(jj,:),'y')'
     to get the errorband with an outline stroke for jj = 1 to 6.
  6. "g1_####", a 6 * 399 array the dynamical g1 for corresponding scaled time with #### = 'fast', 'middle', and 'slow.
     Using 'plot(Dx,g1_####(jj,:));' for jj = 1 to 6 to plot the data.     
  7. "g1_####_error",  a 6 * 794 array for the corresponding error of dynamical g1_#### in patch form.
     Using 
        'patch(g1_error_x,g1_####_error(jj,:),'y')'
     to get the errorband with an outline stroke for jj = 1 to 6.
 
* File Name: Fig_6_b.mat
  There are 7 elements in this mat file in 3 categories:
  1. "te_tauG_error" is a 1*5 array recording the the deviation of (t -t_bec) / tau_G for tau_R = 84, 144, 300, 600 and 1440 ms in order.
      It is the combination of the uncertainty in identifying t_bec and the fitting error for _tau_G, shown in Fig. 1 (e) and (f).
  2. Three "lcoh_#" for correlation length in the unit micro-meter
  3. Three corresponding "te_tbec_tauG_#" elements for scaled time,
  where # denotes corresponding tau_R.
   
* File Name: Fig_6_c.mat
  There are 11 elements in this mat file in 4 categories:
  1. "te_tauG_error" is a 1*5 array recording the the deviation of (t -t_bec) / tau_G for tau_R = 84, 144, 300, 600 and 1440 ms in order.
     It is the combination of the uncertainty in identifying t_bec and the fitting error for _tau_G, shown in Fig. 1 (e) and (f).
  2. "N0_#" for the evolution of condensate number.
  3. "rPO_#" for the evolution of r_PO, the ratio of first and second largest eigenvalue of the one-particle density matrix.
  4. "te_tbec_tauG_#" elements for scaled time,
  where # denotes corresponding tau_R.
 
  Suggesting plotting command without horizontal errorbar (use compatible errorbar command for your own matlab):
   tauR = #
   figure, 
    eval(['errorbar(te_tbec_tauG_' num2str(tauR) ',dlcoh_' num2str(tauR) '(1,:),dlcoh_' num2str(tauR) '(2,:),dlcoh_' num2str(tauR) '(3,:))'])  
 
* File Name: Fig_6_d.mat
  There are 11 elements in this mat file in 3 categories:
  1. "te_tauG_error" is a 1*5 array recording the the deviation of (t -t_bec) / tau_G for tau_R = 84, 144, 300, 600 and 1440 ms in order.
     It is the combination of the uncertainty in identifying t_bec and the fitting error for _tau_G, shown in Fig. 1 (e) and (f).
  2. "dlcoh_#" for delta l_{coh} defined in Eq. (1).
  3. Three corresponding "te_tbec_tauG_#" elements for scaled time,
  where # denotes corresponding tau_R.
  
  Suggesting plotting command withour horizontal errorbar (use compatible errorbar command for your own matlab):
   tauR = #
   figure, 
   eval(['errorbar(te_tbec_tauG_' num2str(tauR) ',dlcoh_' num2str(tauR) '(1,:),dlcoh_' num2str(tauR) '(2,:),dlcoh_' num2str(tauR) '(3,:))'])