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yuxiangwang321 / ContactAngleCalculator

A TCL code for the calculation of contact angle of droplet wetting on solid substrates
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Is this tool applicable to other cases? #2

Open YimingWANG585 opened 2 weeks ago

YimingWANG585 commented 2 weeks ago

Hi Yuxiang,

I am recently learning about the contact angle calculating and I read your article: 'ContactAngleCalculator: An Automated, Parametrized, and Flexible Code for Contact Angle Estimation in Visual Molecular Dynamics' which is publised in 2022. Your work is very useful to me, I appreciate a lot for having this chance to read this article and thank for all the contributions you've made for contact angle calculator.

I have downloaded the support information and all the data through:yuxiangwang321/ContactAngleCalculator: A TCL code for the calculation of contact angle of droplet wetting on solid substrates (github.com) The bcwt.psf and bcwt.dcd files are prepared in advance and as you mentioned in your article, this example is for the 'water droplet wetting on a bare crystalline cellulose surface', I understand that the bcwt.psf includes the water structure information and bcwt.dcd includes the trajectory information, but they are only for 'water droplet wetting on a bare crystalline cellulose surface' case. I was just wondering is it proper to use this example to calculate the contact angle for this case: 'liquid metal GaInSn wetting on the stainless steel(316L)'? if no, does this mean I need to prepare the .psf and .dcd files firstly? This question may be silly, sorry for that, I have no knowledge about the MD or VMD.....

Looking forward to your reply! Thank you in advance.

Best regards Yiming

yuxiangwang321 commented 2 weeks ago

Hi Yiming,

Thank you for using the code.

First, you question is very good and typical, definitely not silly.

Then, you don't need to convert you file format, .dcd and .psf are just examples in the paper.

The code could be used in your case if your liquid mixture is very homogeneous, but you need to do some treatments to your file. The code only deals with liquid consisting of one substance not mixture by defaut, but this could be overcome. You can rename the atom names of GaInSn in your liquid metal mixture, and create a unique name for all them, for example change both In and Sn to Ga. By doing this, your previous mixture now is only one substance (Ga). Then, you set parameter "atomNumberInMol" to 1.

One thing you have to do is to determine the parameter "dropletMolNumDensity", see the paper for its definition. You can get this value by doing a liquid metal cell simulation in NPT, then calculate the number density in unit atom_number/A^3. For parameters "sphereFactor, thicknessFactor, sliceFactor", you can try the values in the paper first. I suggest you understand the defintions of these parameters, then you may know how to adjust them in your case.

I hope these can help you. Best regards, Yuxiang

On Fri, 11 Oct 2024 at 12:36, YimingWANG585 @.***> wrote:

Hi Yuxiang,

I am recently learning about the contact angle calculating and I read your article: 'ContactAngleCalculator: An Automated, Parametrized, and Flexible Code for Contact Angle Estimation in Visual Molecular Dynamics' which is publised in 2022. Your work is very useful to me, I appreciate a lot for having this chance to read this article and thank for all the contributions you've made for contact angle calculator.

I have downloaded the support information and all the data through:yuxiangwang321/ContactAngleCalculator: A TCL code for the calculation of contact angle of droplet wetting on solid substrates (github.com) https://github.com/yuxiangwang321/ContactAngleCalculator The bcwt.psf and bcwt.dcd files are prepared in advance and as you mentioned in your article, this example is for the 'water droplet wetting on a bare crystalline cellulose surface', I understand that the bcwt.psf includes the water structure information and bcwt.dcd includes the trajectory information, but they are only for 'water droplet wetting on a bare crystalline cellulose surface' case. I was just wondering is it proper to use this example to calculate the contact angle for this case: 'liquid metal GaInSn wetting on the stainless steel(316L)'? if no, does this mean I need to prepare the .psf and .dcd files firstly? This question may be silly, sorry for that, I have no knowledge about the MD or VMD.....

Looking forward to your reply! Thank you in advance.

Best regards Yiming

— Reply to this email directly, view it on GitHub https://github.com/yuxiangwang321/ContactAngleCalculator/issues/2, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOCW3KKIUD3NCIBAF2UGE2DZ24TQLAVCNFSM6AAAAABPX57ZFSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU4DAMJZHE2TQMA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

YimingWANG585 commented 2 weeks ago

Hi Yuxiang,

Thanks for your quick reply! I have to mention that before reading your article, I have no knowledge about the codes or cell simulations, etc. My major focuses on the MHD effect when liquid metal working under the magnetic environment, the contact angle is an important factor to my research, that's why I found your article extremelly useful. But to be honest It's a bit hard for me to understand very well all your explainations...

1.You mentioned: 'Then, you don't need to convert you file format, .dcd and .psf are just examples in the paper.'. -----I actually don't have any structure information nor trajectory information files for my own case=( What I would like to ask is: 1) could I use thees two files (bcwt.psf and bcwt.dcd) directly for my case liquid metal GaInSn wetting on SS? 2)if no, I don't know how could I produce these files, by which software, and how to define the structure and the trajectory? could you please give some recommendations?....

  1. You mentioned "The code could be used in your case if your liquid mixture is very homogeneous, but you need to do some treatments to your file. The code only deals with liquid consisting of one substance not mixture by defaut, but this could be overcome. You can rename the atom names of GaInSn in your liquid metal mixture, and create a unique name for all them, for example change both In and Sn to Ga. By doing this, your previous mixture now is only one substance (Ga). Then, you set parameter "atomNumberInMol" to 1. " -----Does this 'file' means the code file (.tcl) and all these 'treatments' should be done in this code file too?

Thanks for the parameters' explanations. I was also wondering about what does 'Frame' mean? What kind of difference would cause by defining different 'first frame' and 'last frame'? I understand I will know these difference by trying different values, but I will appricate it a lot if you could give me some simple explanations in advance=)

These's a lot for me to study, but luckily I can speed up based on your contributions and support!

Best regards Yiming

yuxiangwang321 commented 2 weeks ago

Hi Yiming,

I see that. You need to learn MD first, then do the data analysis. It is too early to answer these questions if you have no MD experience and data.

I have no idea about the metal system MD simulations, you may have to search resources online yourself. I started to learn MD in 2020 from a level lower than you, I know it is very hard to learn by oneself. You can join a training group, there would be many learners following an experienced instructor. I recommend the one I used to join, the instructor is also an expert of metal simulation.

Don't worry, you will finally be a MD master! [image: 2024-10-12_140800.jpg]

Cheers, Yuxiang

On Sat, 12 Oct 2024 at 00:58, YimingWANG585 @.***> wrote:

Hi Yuxiang,

Thanks for your quick reply! I have to mention that before reading your article, I have no knowledge about the codes or cell simulations, etc. My major focuses on the MHD effect when liquid metal working under the magnetic environment, the contact angle is an important factor to my research, that's why I found your article extremelly useful. But to be honest It's a bit hard for me to understand very well all your explainations...

1.You mentioned: 'Then, you don't need to convert you file format, .dcd and .psf are just examples in the paper.'. -----I actually don't have any structure information nor trajectory information files for my own case=( What I would like to ask is: 1) could I use thees two files (bcwt.psf and bcwt.dcd) directly for my case liquid metal GaInSn wetting on SS? 2)if no, I don't know how could I produce these files, by which software, and how to define the structure and the trajectory? could you please give some recommendations?....

  1. You mentioned "The code could be used in your case if your liquid mixture is very homogeneous, but you need to do some treatments to your file. The code only deals with liquid consisting of one substance not mixture by defaut, but this could be overcome. You can rename the atom names of GaInSn in your liquid metal mixture, and create a unique name for all them, for example change both In and Sn to Ga. By doing this, your previous mixture now is only one substance (Ga). Then, you set parameter "atomNumberInMol" to 1. " -----Does this 'file' means the code file (.tcl) and all these 'treatments' should be done in this code file too?

Thanks for the parameters' explanations. I was also wondering about what does 'Frame' mean? What kind of difference would cause by defining different 'first frame' and 'last frame'? I understand I will know these difference by trying different values, but I will appricate it a lot if you could give me some simple explanations in advance=)

These's a lot for me to study, but luckily I can speed up based on your contributions and support!

Best regards Yiming

— Reply to this email directly, view it on GitHub https://github.com/yuxiangwang321/ContactAngleCalculator/issues/2#issuecomment-2407475721, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOCW3KKGK2VXL2WFCIHCU3LZ27KRLAVCNFSM6AAAAABPX57ZFSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBXGQ3TKNZSGE . You are receiving this because you commented.Message ID: @.***>