Compute deformation gradient in matrix form

[efaulhaber]

Turns out, computing the deformation gradient in matrix form takes pretty much the same time as computing only one entry of the matrix. Thus, computing the whole gradient in matrix form is about 4x faster (in 2D) than computing every single entry.

Benchmarks are based on #36, but this PR can be merged independently.
Before:

julia> pixie_include("examples/solid/oscillating_beam_2d.jl", tspan=(0.0, 1.0));
[...]
────────────────────────────────────────────────────────────────────────────────────────────────────
Pixie simulation finished.  Final time: 1.0  Time steps: 2973 (accepted), 3168 (total)
────────────────────────────────────────────────────────────────────────────────────────────────────

 ────────────────────────────────────────────────────────────────────────────────────
              Pixie.jl                      Time                    Allocations      
                                   ───────────────────────   ────────────────────────
         Tot / % measured:              33.0s /  99.8%           1.68MiB /   0.2%    

 Section                   ncalls     time    %tot     avg     alloc    %tot      avg
 ────────────────────────────────────────────────────────────────────────────────────
 rhs!                       28.6k    32.9s  100.0%  1.15ms   3.67KiB  100.0%    0.13B
   update containers        28.6k    24.4s   74.1%   853μs      752B   20.0%    0.03B
     precompute pk1         28.6k    24.4s   74.0%   853μs     0.00B    0.0%    0.00B
     ~update containers~    28.6k   16.2ms    0.0%   569ns      752B   20.0%    0.03B
   container interaction    28.6k    8.52s   25.9%   298μs     0.00B    0.0%    0.00B
   ~rhs!~                   28.6k   8.09ms    0.0%   283ns   2.94KiB   80.0%    0.11B
   reset ∂u/∂t              28.6k   3.60ms    0.0%   126ns     0.00B    0.0%    0.00B
   update nhs               28.6k    636μs    0.0%  22.3ns     0.00B    0.0%    0.00B
 ────────────────────────────────────────────────────────────────────────────────────

julia> using BenchmarkTools

julia> @benchmark Pixie.deformation_gradient($1, $(semi.neighborhood_searches[1][1]), $particle_container)
BenchmarkTools.Trial: 10000 samples with 10 evaluations.
 Range (min … max):  1.458 μs …  4.026 μs  ┊ GC (min … max): 0.00% … 0.00%
 Time  (median):     1.495 μs              ┊ GC (median):    0.00%
 Time  (mean ± σ):   1.498 μs ± 41.374 ns  ┊ GC (mean ± σ):  0.00% ± 0.00%

               ▂▃▆▆█▃                                         
  ▂▂▂▂▂▂▂▂▂▂▃▃▄███████▆▅▄▃▂▂▂▂▂▂▂▂▂▂▂▂▁▁▂▁▁▁▂▁▁▁▁▁▁▂▂▁▁▂▁▁▁▂ ▃
  1.46 μs        Histogram: frequency by time        1.59 μs <

 Memory estimate: 0 bytes, allocs estimate: 0.

After:

julia> pixie_include("examples/solid/oscillating_beam_2d.jl", tspan=(0.0, 1.0));
[...]
────────────────────────────────────────────────────────────────────────────────────────────────────
Pixie simulation finished.  Final time: 1.0  Time steps: 2973 (accepted), 3168 (total)
────────────────────────────────────────────────────────────────────────────────────────────────────

 ────────────────────────────────────────────────────────────────────────────────────
              Pixie.jl                      Time                    Allocations      
                                   ───────────────────────   ────────────────────────
         Tot / % measured:              15.4s /  99.5%           1.69MiB /   0.2%    

 Section                   ncalls     time    %tot     avg     alloc    %tot      avg
 ────────────────────────────────────────────────────────────────────────────────────
 rhs!                       28.6k    15.3s  100.0%   537μs   3.67KiB  100.0%    0.13B
   container interaction    28.6k    8.44s   55.0%   295μs     0.00B    0.0%    0.00B
   update containers        28.6k    6.88s   44.9%   241μs      752B   20.0%    0.03B
     precompute pk1         28.6k    6.86s   44.8%   240μs     0.00B    0.0%    0.00B
     ~update containers~    28.6k   19.8ms    0.1%   692ns      752B   20.0%    0.03B
   ~rhs!~                   28.6k   8.07ms    0.1%   282ns   2.94KiB   80.0%    0.11B
   reset ∂u/∂t              28.6k   3.48ms    0.0%   122ns     0.00B    0.0%    0.00B
   update nhs               28.6k    634μs    0.0%  22.2ns     0.00B    0.0%    0.00B
 ────────────────────────────────────────────────────────────────────────────────────

julia> using BenchmarkTools

julia> @benchmark Pixie.deformation_gradient($1, $(semi.neighborhood_searches[1][1]), $particle_container)
BenchmarkTools.Trial: 10000 samples with 211 evaluations.
 Range (min … max):  352.659 ns … 506.550 ns  ┊ GC (min … max): 0.00% … 0.00%
 Time  (median):     362.993 ns               ┊ GC (median):    0.00%
 Time  (mean ± σ):   363.593 ns ±   4.560 ns  ┊ GC (mean ± σ):  0.00% ± 0.00%

                ▃█▃▅▇▃▄▃▄▃▄▁                                     
  ▁▁▁▁▁▁▁▁▁▁▂▃▄▆████████████▆▆▄▃▃▂▁▂▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ ▃
  353 ns           Histogram: frequency by time          384 ns <

 Memory estimate: 0 bytes, allocs estimate: 0.

[LasNikas]

Very good! This small modification has such a big impact.
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