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ubsuny / 23-Homework7G5

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how to Initialize the cluster geometry to an ideal case? #24

Closed reshnashrestha closed 11 months ago

poojashresthacode commented 11 months ago

run simulation for a simple box

a = 0.2

r_na = np.array([[0, 0, 0], [a, a, 0]]) r_cl = np.array([[a, 0, 0], [0, a, 0]])

cluster = Cluster(r_na, r_cl) The code initializes the molecular cluster by placing sodium and chlorine ions in a specific initial geometry (simple box configuration). The Cluster class is then used to represent and work with this initial configuration throughout the simulation and optimization process.

reshnashrestha commented 11 months ago

Oh its helpful and the code is available i the compphys minmax nacl.ipynb?

tirthbha commented 11 months ago

@reshnashrestha Actually, to initialize the cluster geometry means starting the simulation with the ions (Na+ and Cl-, in our case) arranged in a geometric configuration that is close to what we would expect for the minimum energy structure.

poojashresthacode commented 11 months ago

@@.***> can you please describe, how can we know the initial positions of those ions.

From: tirthbha @.> Sent: Tuesday, November 28, 2023 11:21 AM To: ubsuny/23-Homework7G5 @.> Cc: Pooja Shrestha @.>; Comment @.> Subject: Re: [ubsuny/23-Homework7G5] how to Initialize the cluster geometry to an ideal case? (Issue #24)

@reshnashresthahttps://github.com/reshnashrestha Actually, to initialize the cluster geometry means starting the simulation with the ions (Na+ and Cl-, in our case) arranged in a geometric configuration that is close to what we would expect for the minimum energy structure.

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tirthbha commented 11 months ago

@poojashresthacode Take cubic structure as a configuration. Consider (0,0,0) as origin for first Na+ ion, then choose alternate position for the chloride just as shown in the Figure 4 of Paper (mentioned in the HW) where big circles represent Na+ ions and small represents Cl- ions.