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Messages - Sacho

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Dear Constanze

I have a problem about the Voronoi analysis.
How to determine the value of absolute and relative face area threshold, and the edge length threshold?


Support Forum / Re: Steinhardt order parameters
« on: July 21, 2019, 04:45:14 PM »
Dear Alexander

I downloaded the C++ code you wrote for calculating the Steinhardt parameters. But I encountered some problems during the compilation process.

1.   I installed the boost library, but there is always an error that appears in the twenty-fourth line of the CmakeLists.txt file,as shown in the attachment. I can't check the cause of this error. Are there specific requirements for installing the path and directory name of the boost library? Or are there other places to pay attention to?
2.   Can you send me the final running program? I want to calculate the bond order parameters to represent the structure.


Dear Constanze

Thank you for helping me.Best wish to you.


Dear Constanze

I am a newbie and some problems may be stupid. I want to know if the atom corresponding to the atomic number before the CNA index in the output file is the same as the input file. Because I want to count the CNA index for each atom type. If they are not the same, what should I do?

Thanks, best wish for you.

Dear Constanze
I have another problem. Is there a difference between the CAN index and HA index?

for HA index: (i) The second index represents whether or not they are near-neighbor (ii) The second index represents the number of near neighbors they have in common. (iii) The third index is for the number of nearest-neighbor bonds among the shared neighbors. (iv) A fourth index is used to distinguish configurations with the same first three indices but with a different topology.

According the literature [Faken and Jonsson, Comput. Mater. Sci. 2, 279], the bonded pairs of type 555 are characteristic of Icosahedral order , but in HA index, the 1551 and 1541 pairs are icosahedral order. Based on the definition of both, I think that 55x and 54x in CAN index is same as the 155x and 154x, is this right? If it is right, the type 55x and 54x in CAN index can represent the five-fold symmetry based motifs, that is, the icosahedral order degree.


Dear Constanze
Thanks very much. My promble has been solved, you are right, I want ro calculate the bong angle distribution for a specific bond pair. Your work is great.

Dear Constanze
Thanks. I used the PTM under your suggestion, but the result is same as the CAN, as shown in the attachment. From its liquid structural factor curve, it has a pre-peak and a second peak with a shoulder. According to the literature, there should be icosahedral clusters. This alloy is a ternary system. Is it useful to calculate the bond angle distribution or bond order parameter?

Dear Constanze
I want to get the bond angle distribution centered on each atom, I saw your previous reply and want to ask you the code to solve this problem. The “firstly and secondly” in the last question is that I want to ask if the steps are correct. If it is right, I will use it.
Best wishes to you


Thank you for your careful answer.
I am sorry to make the problem not clear. I am doing some metal liquid structural characterization, I want to get the local cluster changes with temperature. So I tried to use the CNA method, but I can't get the result I want, as shown below, I don’t know how to solve it. And I also used the Voronoi analysis, the results showed that the distribution of clusters is very scattered, and the maximum number of clusters is less than one percent. Maybe you can give me some help and advice for cluster analysis. Thanks again.

Hello, can this program get a bond angle distribution centered on each atom? If I want to get the angle distribution of a specific bond pair1-2-3, firstly,create bonds between 1 and 2,between 2 and 3. Secondly,modify the part of the script where you iterate over all particles,code show as below:

create_bonds_mod = CreateBondsModifier(mode=CreateBondsModifier.Mode.Pairwise)
create_bonds_mod.set_pairwise_cutoff('Type 1', 'Type 2', 2.3)
create_bonds_mod.set_pairwise_cutoff('Type 2', 'Type 3', 2.3)

tprop = data.particles["Particle Type"]
for particle_index in range(data.number_of_particles):
    if (tprop[particle_index] == 2_type_id):
        angle_cosine_histogram_1 += np.histogram(angle_cosines, bins=bin_count, range=(-1.0,1.0))[0]
        angle_cosine_histogram_2 += np.histogram(angle_cosines, bins=bin_count, range=(-1.0,1.0))[0]

Is this right?
Thank you very much.

Support Forum / Questions about common neighbor analysis
« on: July 11, 2019, 09:30:00 AM »
I have two questions
one is the result of program that was showed by Alexander Stukowski nine months ago, I don't know if the result after the program is running is correct and the code and results are placed in the attachment,and the meaning of each line is not very clear for me,it has cna index and counts,why are there many cnd index in every line?If I want to get a statistical result of a structure type, what else do I need to add to the program?

And another question is whether these analysis methods consider periodic boundary conditions,incluing cna ,bong angle analysisand Voronoi analysis?

Thanks very much

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