Impossible to open the project file

jacqueline-nguyen commented 1 year ago

I've tried to open a new project with a file.xyz but "Error code: 2" showed up. Please kindly show me how to fix this.

Slookeur commented 1 year ago

Hello, sorry too little to help, I would need a copy of your XYZ file to see what is going on.

S.

jacqueline-nguyen commented 1 year ago

Dear Dr. Sebastien Le Roux, Thank you for being supportive. Please kindly find attached herewith the file. By the way, I study the structure of a monatomic system in general, with no specific species of atom, and all quantities are measured in reduced units. Is it possible to apply radius cutoff and some other quantities in reduced units in ATOMES?

On Wed, Jul 26, 2023 at 4:50 PM Sébastien Le Roux @.***> wrote:

Hello, sorry too little to help, I would need a copy of your XYZ file to see what is going on.

S.

— Reply to this email directly, view it on GitHub https://github.com/Slookeur/Atomes/issues/16#issuecomment-1651399484, or unsubscribe https://github.com/notifications/unsubscribe-auth/AH73TOQAONYA7OQJ6RYSKYLXSDR5HANCNFSM6AAAAAA2X4HYM4 . You are receiving this because you authored the thread.Message ID: @.***>

-- Best regards,

Nguyễn Tố Nga

Slookeur commented 1 year ago

Hello, It seems your file was too big to be transmitted via email, I suggest that you put the file on a cloud somewhere and send me a download link, alternatively you can edit the file and send a single configuration (MD step) providing that the number of atoms in your system is not the reason the file is so big. You might want to check yourself if the structure of the file follow the XYZ standard, using an example provided on this page:

https://isaacs.sourceforge.io/ex.html

Also I am sorry but I do not understand what you mean by 'reduced' unit, if you think about fractional coordinates, ie. coordinates expressed in terms of the unit cell parameters, then no problem atomes will deal with it. Otherwise I would appreciate more information it.

jacqueline-nguyen commented 1 year ago

Dear Dr. Sebatien Le Roux,

Thank you for your great support. I seem to have figured out the problem. As I studied a 2D monatomic system, I named the atom species A generally. In this case, ATOMES seems to not recognize the atom species so it does not load the configuration. When I changed the name of the atoms to Pt or another specific name, with other specific criteria of atomic mass, bond type, and atomic radius, ATOMES finally worked well. Please follow the link below to find the two files, one is the original file with an unspecific atomic name A, and the other file contains specific atom species of Pt. https://drive.google.com/drive/folders/1l31gAcJOxenDPjjI8OdUCvBjCaQprp45?usp=sharing

Also I am sorry but I do not understand what you mean by 'reduced' unit,

if you think about fractional coordinates, ie. coordinates expressed in terms of the unit cell parameters, then no problem atomes will deal with it. Otherwise I would appreciate more information it.

As I work with a simple monatomic system in which the interatomic potential is a variation of Lennard-Jones' potential, the units used in all calculations are in Lennard-Jones' reduced units. Namely, energy is in ε which is the depth of the Lennard-Jones potential minimum, length is in σ - atomic diameter, temperature is in ε/kB and time is in τ0 = σ √(m/ε) with m is the atomic mass. Meanwhile, in ATOMES the quantities such as atomic radius or cutoff radius are in Angstrom, i.e. the studied model needs to consist of specific species of atoms (with specific atomic mass and radius) to convert reduced units into regular units.

If that is the case, do I probably have to find another tool other than ATOMES to study the structure of the model?

On Thu, Jul 27, 2023 at 4:11 PM Sébastien Le Roux @.***> wrote:

Hello, It seems you file was to boo big to be transmitted via email, I suggest that you put the file on a cloud somewhere and send me a download link, alternatively you can edit the file a send a single configuration (MD step) providing the number of atoms in you system is no the reason the file is so big. You might want to check your self if the structure of the file follow the XYZ standard, using an example provided on this page:

https://isaacs.sourceforge.io/ex.html

Also I am sorry but I do not understand what you mean by 'reduced' unit, if you think about fractional coordinates, ie. coordinates expressed in terms of the unit cell parameters, then no problem atomes will deal with it. Otherwise I would appreciate more information it.

— Reply to this email directly, view it on GitHub https://github.com/Slookeur/Atomes/issues/16#issuecomment-1653214583, or unsubscribe https://github.com/notifications/unsubscribe-auth/AH73TOX2J3QRSZSEI4BAYQLXSIWEXANCNFSM6AAAAAA2X4HYM4 . You are receiving this because you authored the thread.Message ID: @.***>

-- Best regards,

Nguyễn Tố Nga

Slookeur commented 1 year ago

Hello, I think you have more than one issue with your file, first the number of atoms (lines of coordinates) 6400 does not match the number on the first line 6399, this is the first reason for error. It should not even be possible to read your 'Pt' file to begin with, to read it you need to modify the number of atoms to 6400.

For the time being it is indeed require to have a known chemical species in the file that contains the atomic coordinates. I will work on this to make it possible to have unknown species.

For the unit length, are you referring to atomic length ? Atomic length are not standards units for the XYZ file format, therefore I did not make it optional to read this kind of coordinates, for the XYZ format that is, if you can transform your coordinates file in VASP or CPMD format then the native unit length is indeed atomic length and Atomes handles it just fine.

jacqueline-nguyen commented 1 year ago

Dear Dr. Sebastien Le Roux,

Thank you for your time and consideration.

I think you have more than one issue with your file, first the number of atoms (lines of coordinates) 6400 does not match the number on the first line 6399, this is the first reason for error. It should not even be possible to read your 'Pt' file to begin with, to read it you need to modify the number of atoms to 6400.

Yes, you're correct! The number of atoms is 6399, and I edited it in the file attached herewith. https://drive.google.com/drive/folders/13j4IwbVabkyJdAtseg7q-CqvVphlUsqn?usp=sharing

For the time being it is indeed require to have a known chemical species in the file that contains the atomic coordinates. I will work on this to make it possible to have unknown species.

I fully appreciate your great support and I hope to be able to use the latest version of A.T.O.M.E.S that would not require a specific chemical species in the model as soon as possible.

For the unit length, are you referring to atomic length ? Atomic length are not standards units for the XYZ file format, therefore I did not make it optional to read this kind of coordinates, for the XYZ format that is, if you can transform your coordinates file in VASP or CPMD format then the native unit length is indeed atomic length and Atomes handles it just fine.

I converted the file.xyz to file.vasp. However, A.T.O.M.E.S still reports an error: impossible to process input file data. https://drive.google.com/drive/folders/13j4IwbVabkyJdAtseg7q-CqvVphlUsqn?usp=sharing

-- Best regards,

Nguyễn Tố Nga (PhD. Student) Comp. Phys. Lab HCM City Univ. of Technology Vietnam National Univ. - HCM City 268 Ly Thuong Kiet Street, District 10, HCM City, Vietnam

Slookeur commented 6 months ago

Hello, just noticed that your problem was not dealt with, here are few things that you should do:

Install the latest release of atomes.
Change the chemical species to a standard one (I am working on the other option).
Edit your coordinate file: the number of line is good but not the number of atomes on the first line of the file.
Not sure how relevant this is but all z coordinates are equal to 0.0.
No need to use VASP format.

Slookeur / Atomes

Impossible to open the project file #16