What are saddle points?

Who took cubic structure in your group? I am facing an issue, nan"divide by zero encountered in divide" for potential calculations. I took those 8 indices, and they are all, (a,0,0), (0,0,a), etc. and I considered all indices to be at most "a" apart. Did I take those indices wrong, or am I missing something?
Thank you.

As shown in the picture, it seems like Cl and Na ions have formed three bonds which is not correct. What is the correct interpretation?

Do we need to do all of our work in a jupyter notebook, or is a regular python file okay?

This paper will let you know some important configurations for our task that will aid to understand the structure type.
Source:
J. P. Rose and R. S. Berry, ‘‘Towards Elucidating the Interplay of Structure and Dynamics in Clusters: Small KCl Clusters as Models,’’ J. Chem. Phys. 96, 517–538 ~1992!.

I have chosen a planar rectangle as one of the 7 configurations, how would we expect to assign the values of a and b (a=length and b=width)? Are we allowed to choose randomly? Because there are no specific values for these terms in the paper?

I will appreciated your responses.

I have completed the over all tasks under this topic and the my work is summarized in:
cubic_rectangular_configurations.md

Is this the the potential energy function for the Na4Cl4 cluster that we are going to use for it optimization?

I have chosen MIT license for this homework.

Hello, dear members of the G#4,
I just want to make sure that I understood correctly about this HW, So all we need to do is to find the positions of the Na and Cl molecules and then make 2 arrays out of them and use the code provided, to find out the potential energy. Once we find the potential energy, we have to run the optimization code and once we run that it will give us the minimum energy. Is that the whole plan?
Thank you.

Should we provide seperate files for each configuration, or is having them all in one per task okay?

Should we include separate image files of plots and results or just keep them all in our python/notebook files?

Hi all,
Do we have to know the structure of tetramer configurations and search for the position of Na and Cl ion to be used for optimization. For different structure, what is the difference that we have to do to implement the code. Paper shows that the binding energy per ions for given configurations are different, so how we approach to get that value?

Using a random guess method I got this configuration which looks like number 5

With

Is this reasonable? I'm not even trying to focus on 5 I just got here on accident so this is more curiosity than anything

For the exact same code (for configuration 3) I get this plot when running in a jupyter notebook

Which is not great, but running locally in Spyder I get this

Which looks like the rectangular configuration for me. Any idea why this is?

@WildJimmy How far have you finished your tasks? Just to remind we have due by tomorrow.

Hello,
who is working on the cubic and pentagon configurations??

for your info, the paper mentioned is available at
https://pubs-aip-org.gate.lib.buffalo.edu/aapt/ajp/article/66/3/231/1044856/Evolving-few-ion-clusters-of-Na-and-Cl

Hello, I got different energy in my case than the paper, what could be the reason? Could it be the reason that may be our a,b, etc, values are different? What you think? Any help would be appreciated.

The ion-ion potential in K.Michaelian paper is:

and the one found in the Compphys minmax is:

and in the paper, the potential formula is referenced to:

For this homework, which formula should we follow? @laserlab may be you can provide some lead.

If you encountered the problem of getting the interactive plot in the Jupyter notebook, you could replace the first line %matplotlib notebook with %matplotlib inline as shown in the figure.

I assume that we will do the following steps to carry out this task:
To determine the equilibrium configurations of Na4Cl4 clusters for tetramers and plot their configurations with energies, we can proceed with the following steps:

1. Define the potential energy function for the Na4Cl4 cluster.
   For our case the potential energy is of the form:
   
   The potential energy function parameters for the Na4Cl4 cluster are defined as follows:

• $\ A_{ij} = 423.80 \ eV$
• $\ \rho = 0.317 \ Å$
• $\ \frac{e^2}{4 \pi \epsilon_0} = 1.44 \ eV·nm$

3. Initialize the cluster geometry to an ideal case.
4. Use an optimization algorithm to minimize the energy and find the equilibrium configuration.
   Note: We will use CG algorithm for the optimization.
   What about you guys?
5. Plot the equilibrium configurations using scatter plots and label them with their energies.

Correction to my views and your suggestions will really be appreciated

Who are the other group members?

Right now I'm messing around with trying to just randomly get some of the more complex configurations. By random I literally mean using

r_na = np.random.rand(4,3)
r_cl = np.random.rand(4,3)

Which actually gets me somewhere, but I usually end up with either structures 2 or 3 which is not entirely useful. Do you think running this on a loop until I reach (around) a set equilibrium energy would be fruitful? This is the tactic I'm debating to make this at least a little more methodical

Let's discuss here, which 2 configurations are we choosing.

When using the initial positions provided by the professor for structure 7, I end up with a plot like this

Has anyone else had this issue? This is not the form of in the paper and it needs some additional tuning correct?

Is anyone doing the 4 and 5 structure? If so, what are their coordinates?

Fig. 4. The lowest energy configurations found for the cluster size of four
ion pairs along with their respective binding energies ~eV/ion pair!.

As the title says, should we flesh out the docstrings for each function for each function in the initial python file to include inputs, outputs, etc. or is this not necessary for this assignment?

who should be the main responsible for the repository ?

Sometimes when using the random guess method (as described in #54) I get a configuration that looks like this

Is this valid? I know we're not looking for it but I'm curious if this actually works or if it's just kind of a fluke. It happens reasonably often

This the first configuration among 7, with optimized potential -28.69 eV. [G1]

Your suggestions and corrections will be appreciated

Why did you lynt the main NaCl file?

What exactly is the difference between different configuration? It seems that the final potential energy after optimization is different ? Any idea how we start with the initial ideal position ?

I would like to choose these configurations: Binding energies:
-6.9788 eV/ion pair and -6.8696

As described in hw task, no unit tests are necessary, what's the point of unittesting.yml?