Closed reshnashrestha closed 11 months ago
Oh its helpful and the code is available i the compphys minmax nacl.ipynb?
@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.
@@.***> 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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@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.
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.