That's an interesting puzzle; I can reproduce your results on my machine.  
Clearly, something is being discretized differently in the two cases, but off 
the top of my head I can't see what would cause this.

Presumably, both results converge to one another as you increase the 
resolution, so at the end of the day it won't matter, but it is a bit 
annoying...

On Apr 14, 2014, at 12:45 AM, Andrey Panov <pa...@canopus.iacp.dvo.ru> wrote:
> After simulating a trivial example with MEEP, I have found that the results 
> of 
> the computation of the electric (magnetic, electric+magnetic) field energy in 
> a 
> cube obtained using libctl and C++ interfaces slightly (~0.1-1%) differ. This 
> examle is a 16x16x16 cube with PML boundaries and isotropic constant epsilon; 
> a 
> continuous-wave point dipole as a source. The energy is calculated in the 
> 4x4x4 
> cube at the center. Epsilon averaging is not used. The libctl and C++ files 
> are 
> attached here. I think that all the comutations are done by the same libmeep 
> and should be identical or have discrepancies on the order of 1e-16.
> 
> My system is Slackware Linux 14.1 x86_64 with gcc-4.8.2, I tried this on AMD 
> and 
> Intel core 5 CPU. I have installed the latest relesad versions of Meep, 
> Guile, 
> Libctl. Everything is compiled with "-O2 -fPIC" options, Meep has not MPI 
> support.

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