The VAMPIRE version 6.0 source code at [1] has:
Line 139: // Set system dimensions !Angstroms
Line 141: cs::system_dimensions[0] = 100.0;
Line 142: cs::system_dimensions[1] = 100.0;
Line 143: cs::system_dimensions[2] = 100.0;
I believe dimensions:system-size is set internally by default to 100 angstroms by that code. To check if it still generates the same number of atoms (the 6,625 in your case), you might try putting in your input file:
dimensions:system-size=100 !A
Kind Regards,
Gavin
VAMPIRE user