This is the repository of shape matching algorithm Iterative Rotations and Assignments (IRA)

Last update: Nov 14, 2022

Overview

Description

This is the repository of shape matching algorithm Iterative Rotations and Assignments (IRA), described in the publication [1].

Directory contents

/IRA: Contains the IRA software, see also the README in /IRA.

/benchmark_test: Contains data and other software used for benchmark tests from [1]. See also the README in /benchmark_test folder.

Compile and run

To run IRA, you need to compile it. See README in /IRA subdirectory.

References

[1] Gunde M., Salles N., Hemeryck A., Martin Samos L. IRA: A shape matching approach for recognition and comparison of generic atomic patterns, Journal of Chemical Information and Modeling (2021), DOI: https://doi.org/10.1021/acs.jcim.1c00567, HAL: hal-03406717, arXiv: 2111.00939

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Comments

ira_eq.x doesn't work.

Hi , @mgoonde .

I am a student working on a project of Off-lattice Kinetic Monte Carlo. I found your paper and source code with excitement. As you mentioned in the paper(IRA: A shape matching approach for recognition and comparison of generic atomic patterns), in self-Learning KMC, atomic assignment is unknown amd number of atoms unset. Traditional optimal method like SVD and assignment method like Hungarian algorithm cannot work on my system. So I downloaded your code and tried.

However, there was something wrong after I combined two .xyz system and executed ira_eq.x.

First, variable hd_fin not defined. To be honest, I don't know what it means. So i changed hd_out = hd_fin to hd_out = hd

Second, the way you permute the coordinates is not recognized by my machine, it goes , whenerver there is a permutation operation. So I changed it from coords1(:,:) = coords1(:,nint(d_o(2,:))) to do i = 1, nat1 coords1(:,i) = coords1_tmp(:,nint(d_o(2,i))) end do So does the array typ1/typ2/coords2

After doing these rescue measures, I ran your example ./ira_eq.x < temp_ira. temp_ira is combined from benchmark_test/data/lj_clusters/xyz/47.xyz, same structure file in run_single.sh, and the randomized one. The two xyz structures didn't found scattered using ovito. The result goes infinity.

I don't know what is wrong and I am not that farmiliar with fortran. So I appreciate your help about it. Best wishes.

opened by FanMover 1

Releases(IRA_v1.5.0)

IRA_v1.5.0(May 12, 2022)

The second release of IRA code. Improvements are made on performance (speed), and in the unification of routines dealing with equal and nonequal number of atoms. An interface to python is also added. For complete list of changes see the version_history file.
Source code(tar.gz)
Source code(zip)
v1.0.0(Nov 18, 2021)

The source code of IRA is released, without the data and scripts used for the benchmark tests in the original publication.
Source code(tar.gz)
Source code(zip)

This is the repository of shape matching algorithm Iterative Rotations and Assignments (IRA)

Related tags

Overview

Description

Directory contents

Compile and run

References

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Comments

ira_eq.x doesn't work.

Releases(IRA_v1.5.0)

IRA_v1.5.0(May 12, 2022)

v1.0.0(Nov 18, 2021)

Owner

MAMMASMIAS Consortium

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