Mathematica incorrectly imports a table

Question

I am trying to calculate the eigenvalues of a large matrix (10^4x10^4), which is formed by summing a matrix containing advective terms and a matrix containing diffusive terms. I am using the following simple script:

add = "address/n=50l=50/";
adv = Transpose[Import[add <> "u_B.dat", "Table"]];

diff = Transpose[Import[add<>"diffusion.dat", "Table"]];

ans = 303*adv + diff // Eigenvalues;
Sort[ans]

Mathematica imports the diffusion matrix as a one dimensional array for some reason, and as such cannot transpose it or calculate eigenvalues. I have used this code for various (smaller) resolutions/matrix sizes and it worked fine. I really do not understand why this matrix is suddenly being imported as a one dimensional object.

----------Edit 2---------

Here is a link to the diffusion file: https://www.dropbox.com/s/gx8sokt2zggiq99/diffusion.dat?dl=0

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Here are the first few elements of the first row. There are 10^4 rows and 10^4 columns in the file (adv has the same)

  -9.9999999999997868      -2.0718235518950072      -0.7368652300812841      -0.3366733737341420      -0.1785767012502300      -0.1046968732429871      -0.0659813101416420      -0.0439219818289296      -0.0305217022632576      -0.0219581437532483      -0.0162554151475518      -0.0123258483194475      -0.0095389926277596      -0.0075132770178053      -0.0060091173707776      -0.0048712446774423      -0.0039962212568781      -0.0033134493535647      -0.0027736997195499      -0.0023419799843653      -0.0019929858760674      -0.0017081324330329      -0.0014735758787324      -0.0012788706178710      -0.0011160417221390      -0.0009789342582586      -0.0008627502850535      -0.0007637149330716      -0.0006788326779994      -0.0006057073883789      -0.0005424080705597      -0.0004873676971277      -0.0004393062644368      -0.0003971718205800      -0.0003600948026407      -0.0003273525133293      -0.0002983412085359      -0.0002725540935550      -0.0002495637478567      -0.0002290081574144      -0.0002105794044882      -0.0001940145717756      -0.0001790883002599      -0.0001656067401675      -0.0001534025872206      -0.0001423309440523      -0.0001322659628047      -0.0001230979832230      -0.0001147311994253      -0.0001070816570830       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000       0.0000000000000000

Answer 1

I can't tell you why this is occurring, but there are 4 lines which are each short by one number. You can see the line numbers below: 9850, 9900, 9950, 1000.

diffusion = Import["diffusion.dat", "Table"];

(* save the import in case its needed later *)
DumpSave["diffusion.mx", diffusion];

(* is it nxn? *)
Dimensions@diffusion

(* {10000} *)

(* no, what lengths are present? *)
Length /@ diffusion // Union

(* {9999,10000} *)

(* where are the short lines? *)
lengths = Table[{n, Length[diffusion[[n]]]}, {n, Length[diffusion]}];
Select[lengths, #[[2]] == 9999 &]

(* {{9850,9999},{9900,9999},{9950,9999},{10000,9999}} *)

Edit: Further, this can be used to examine line 9850 as a string:

stream = OpenRead["diffusion.dat"];

Skip[stream, "String", 9849];

rec9850 = ReadList[stream, "String", 1]

In a section of that string you will see a run-together number:

Sorry, another edit, but this problem is too interesting. Assuming this run-together at the minus sign is the issue, it can be corrected by putting a space in front of all the minus signs:

SetStreamPosition[stream, 0];

strings = ReadList[stream, "String"];

correctedStrings = StringReplace[#, "-" -> " -"] & /@ strings;

diffusion2 = 
  ReadList[StringToStream[#], "Number"] & /@ correctedStrings;

diffusion2 // Dimensions

(* {10000,10000} *)

And:

eigenValues = Eigenvalues[diffusion2];

Histogram[eigenValues, PlotTheme -> "Scientific"]