Building a Non-Ideal HCP Lattice in MD Simulation

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To build a non-ideal hexagonal close-packed (hcp) lattice for molecular dynamics (MD) simulation, the user is seeking advice on converting negative lattice basis values to positive. One suggested method involves adding a z-lattice vector, such as using 1 minus the negative value to achieve a positive result. This approach can help in adjusting the lattice parameters effectively. The discussion emphasizes the importance of maintaining valid lattice configurations in simulations. Proper handling of negative values is crucial for accurate modeling in MD simulations.
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Dear Friends,

I'm trying to bulid a non-ideal hcp lattice in order to use in MD simualtion. I have12 lattice basis. but 2 of them are negative values. Can anyone tell me how I can convert the negative values to positive?

0.66667 0.33333 -0.0416
0.66667 0.33333 -0.1668
 
I think you could add a z-lattice vector, i.e. take 1-0.0416 instead of -0.0416.
 
Thread 'Unexpected irregular reflection signal from a high-finesse cavity'

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I am observing an irregular, aperiodic noise pattern in the reflection signal of a high-finesse optical cavity (finesse ≈ 20,000). The cavity is normally operated using a standard Pound–Drever–Hall (PDH) locking configuration, where an EOM provides phase modulation. The signals shown in the attached figures were recorded with the modulation turned off. Under these conditions, when scanning the laser frequency across a cavity resonance, I expected to observe a simple reflection dip. Instead...
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