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The science
Dry granular flow through an orifice does not depend on the head of material (unlike a liquid, v ~ sqrt(2 g h)). The empirical Beverloo law gives the mass flow W = C rho_b sqrt(g) (D - k d)^(5/2) with bulk density rho_b ~ 1500 kg/m3, C ~ 0.58, k ~ 1.4, orifice diameter D and grain diameter d. Because W is constant, the timer's upper bulb empties linearly: T = M / W.
The heap at the bottom grows as a cone at the material's angle of repose (about 33 degrees here, the same value as the 3D page): the apex height follows from V = integral of 2 pi r h(r) dr with h(r) = h_c - r tan(phi). Smaller gravity (Moon, Mars) lowers W as sqrt(g), so a Moon timer runs about 2.4 times longer.
Simplifications: no discrete grains (a continuum fill level), the Beverloo constants are typical not measured values, the flow does not stop for very small orifices (D < ~2.5 d, where real hourglasses jam), and a simple bulb outline is used.
What to try
- Halve the neck diameter: the time grows by about 2^2.5 = 5.7.
- Use the Moon preset: time scales as 1/sqrt(g).
- Coarser sand (bigger d) reduces the effective opening D - 1.4 d.
- Watch the upper mass drain on a straight line, not a curve.