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mkmat / Z1plus-code

Supplementary scripts for Z1+ users
https://github.com/mkmat/Z1plus-code
MIT License
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Question regarding converting LAMMP data file and dump file to config.Z1 #1

Closed peter-zhang-chem closed 3 months ago

peter-zhang-chem commented 4 months ago

Dear MK,

I have a LAMMPS data file and a LAMMPs dump file that I'd like to convert to config.Z1 file for analysis. However, inputting the dump file directly in Z1+ program resulted in crashing. I tried to use the script available in the repo to extract the backbone and generate the config.Z1 file; however, I got no output.

Here I attached the test files here. Can you please give me a couple of pointers of how to generate the correct input for the Z1+ program? Thanks!

peter-zhang-chem commented 4 months ago

Following up on my question, I was able to use Z1+import-lammps.pl to generate a config.Z1 file.

mkmat commented 4 months ago

Dear Peter (if I may),

Thanks for your message. It seems you solved your problem. I didn't download the

files you sent, but do you know what caused your problem? I would then add

this information to the github site.

Eventually, your dump file had unsorted IDs or Z1+ was not able to

recognize the chains as this information is only contained in the data file?

All the best, Martin

--

Martin Kröger Prof Computational Polymer Physics, PD Dr habil website www.complexfluids.ethz.chhttp://www.complexfluids.ethz.ch

Swiss Federal Institute of Technology, ETH Zurich Leopold-Ruzicka-Weg 4, HCP F 48.2, CH-8093 ZURICH, Switzerland phone +41-44-632-6622 fax -1076

Google Scholar EUCO-BAAAAAJ ORCID 0000-0003-1402-6714 Scopus 56416643300

From: Peter Zhang @.***> Sent: 04 April 2024 01:20:16 To: mkmat/Z1plus-code Cc: Subscribed Subject: Re: [mkmat/Z1plus-code] Question regarding converting LAMMP data file and dump file to config.Z1 (Issue #1)

Following up on my question, I was able to use Z1+import-lammps.pl to generate a config.Z1 file.

— Reply to this email directly, view it on GitHubhttps://github.com/mkmat/Z1plus-code/issues/1#issuecomment-2035796760, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGFK5YLTRCHHCYC36WJE57TY3SFDBAVCNFSM6AAAAABFWGT2XWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZVG44TMNZWGA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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peter-zhang-chem commented 4 months ago

Hey!

Thank you for the timely response. I will have to look into the extract-backbone.pl script for to see what might be the issue. I input the same .data and dump file for the extract-backbone.pl and Z1+import-lammps.pl - and extract-backbone.pl was not able to run correctly to output the config.Z1 file. Right now I am trying to analyzing/understand the output I got from the analysis - so I will get back to you at a later time regarding what might have happened with the extract-backbone.pl.

Thanks!

Peter

mkmat commented 4 months ago

Dear Peter,

Let me know if I should have a look at your files.

Probably it is about the formatting of data and dump

files and it could be sufficient if you post the first 10

lines of a dump file and the part of the data file

until the say 20th line after 'Atoms' by email.

Greetings, Martin

--

Martin Kröger Prof Computational Polymer Physics, PD Dr habil website www.complexfluids.ethz.chhttp://www.complexfluids.ethz.ch

Swiss Federal Institute of Technology, ETH Zurich Leopold-Ruzicka-Weg 4, HCP F 48.2, CH-8093 ZURICH, Switzerland phone +41-44-632-6622 fax -1076

Google Scholar EUCO-BAAAAAJ ORCID 0000-0003-1402-6714 Scopus 56416643300

From: Peter Zhang @.***> Sent: 04 April 2024 16:56:54 To: mkmat/Z1plus-code Cc: Kroeger Martin; Comment Subject: Re: [mkmat/Z1plus-code] Question regarding converting LAMMP data file and dump file to config.Z1 (Issue #1)

Hey!

Thank you for the timely response. I will have to look into the extract-backbone.pl script for to see what might be the issue. I input the same .data and dump file for the extract-backbone.pl and Z1+import-lammps.pl - and extract-backbone.pl was not able to run correctly to output the config.Z1 file. Right now I am trying to analyzing/understand the output I got from the analysis - so I will get back to you at a later time regarding what might have happened with the extract-backbone.pl.

Thanks!

Peter

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peter-zhang-chem commented 4 months ago

Dear Martin,

Ok, that'd be great!

Here is beginning portion of the data file:

LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.7 on Thu Apr 04 11:43:30 EDT 2024
 9024 atoms
 8960 bonds
 0 angles
 0 dihedrals
 0 impropers
 3 atom types
 1 bond types
 0 angle types
 0 dihedral types
 0 improper types
 -381.353540 1118.646460  xlo xhi
 -325.649424 1174.350576  ylo yhi
 -344.678904 1155.321096  zlo zhi

# Pair Coeffs
#
# 1  A
# 2  C
# 3  G

# Bond Coeffs
#
# 1  

 Masses

 1 39.948002 # A
 2 12.010700 # C
 3 69.723000 # G

 Atoms # full

1 1 2 0.000000 103.589508 164.201080 471.432495 # C CYT
2 2 1 0.000000 102.579193 158.147980 471.438110 # A ADE
3 3 3 0.000000 102.035980 153.521759 474.633545 # G GUA
4 4 2 0.000000 102.872406 151.734192 480.493103 # C CYT
5 5 1 0.000000 102.498383 147.463348 484.110962 # A ADE
6 6 3 0.000000 101.344696 143.881531 488.439941 # G GUA
7 7 2 0.000000 102.650482 139.132507 490.965698 # C CYT
8 8 1 0.000000 106.925201 139.131836 495.002686 # A ADE
9 9 3 0.000000 111.695648 141.219269 498.194336 # G GUA
10 10 2 0.000000 116.481354 140.336823 501.122437 # C CYT
11 11 1 0.000000 121.827545 137.300018 500.431091 # A ADE
12 12 3 0.000000 126.666168 134.139893 502.225952 # G GUA
13 13 2 0.000000 130.583771 130.122253 503.335876 # C CYT
14 14 1 0.000000 129.694427 124.575012 502.921265 # A ADE
15 15 3 0.000000 131.787445 119.330780 502.795776 # G GUA
16 16 2 0.000000 134.016510 114.287109 500.142273 # C CYT
17 17 1 0.000000 139.271881 111.263916 499.137024 # A ADE
18 18 3 0.000000 144.555756 109.422485 500.863159 # G GUA
19 19 2 0.000000 146.606049 106.436554 505.548035 # C CYT
20 20 1 0.000000 144.243561 105.940399 510.782593 # A ADE

and here is the beginning portion of the dump file:

ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
9024
ITEM: BOX BOUNDS pp pp pp
-381.354 1118.65
-325.334 1174.67
-344.769 1155.23
ITEM: ATOMS id type xu yu zu
 1 1 103.59 164.201 471.432
mkmat commented 4 months ago

Dear Peter,

I must admit, I am only reading the email but did not have a look at my code, but

here is what I see from the email as possible problems:

data-file:

Atoms with a preceding blank, usually there is no blank before Atoms. Same for Masses and Bonds.

The # C CYT after the coordinates, I do not remember if I interpreted these columns as ix iy iz

because usually, the data file has id mol type q x y z ix iy iz while you have ix iy iz replaced by

some arbitrary text. Finally, what is the 2nd column in the Atoms section? Is it mol and

has each atom its own mol ID?

1 1 2 0.000000 103.589508 164.201080 471.432495 # C CYT

2 2 1 0.000000 102.579193 158.147980 471.438110 # A ADE

dump-file:

Most likely the problem is here, there is no "mol" in the dump-file.

ITEM: ATOMS id type xu yu zu

I agree, that the bond information is in the data file so that in principle a code

can retrieve this information from the data file and then use it to interpret the dump

file. Has you data file also a Bonds section?

If so, then I can give it try and please send me your data file and the first two

snapshots of your dump trajectory. I could write a code to handle your relatively

unconventional data and dump files. Were they generated by lammps?

All the best, Martin

--

Martin Kröger Prof Computational Polymer Physics, PD Dr habil website www.complexfluids.ethz.chhttp://www.complexfluids.ethz.ch

Swiss Federal Institute of Technology, ETH Zurich Leopold-Ruzicka-Weg 4, HCP F 48.2, CH-8093 ZURICH, Switzerland phone +41-44-632-6622 fax -1076

Google Scholar EUCO-BAAAAAJ ORCID 0000-0003-1402-6714 Scopus 56416643300

From: Peter Zhang @.***> Sent: 04 April 2024 20:18:23 To: mkmat/Z1plus-code Cc: Kroeger Martin; Comment Subject: Re: [mkmat/Z1plus-code] Question regarding converting LAMMP data file and dump file to config.Z1 (Issue #1)

Dear Martin,

Ok, that'd be great!

Here is beginning portion of the data file:

LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.7 on Thu Apr 04 11:43:30 EDT 2024 9024 atoms 8960 bonds 0 angles 0 dihedrals 0 impropers 3 atom types 1 bond types 0 angle types 0 dihedral types 0 improper types -381.353540 1118.646460 xlo xhi -325.649424 1174.350576 ylo yhi -344.678904 1155.321096 zlo zhi

Pair Coeffs

#

1 A

2 C

3 G

Bond Coeffs

#

1

Masses

1 39.948002 # A 2 12.010700 # C 3 69.723000 # G

Atoms # full

1 1 2 0.000000 103.589508 164.201080 471.432495 # C CYT 2 2 1 0.000000 102.579193 158.147980 471.438110 # A ADE 3 3 3 0.000000 102.035980 153.521759 474.633545 # G GUA 4 4 2 0.000000 102.872406 151.734192 480.493103 # C CYT 5 5 1 0.000000 102.498383 147.463348 484.110962 # A ADE 6 6 3 0.000000 101.344696 143.881531 488.439941 # G GUA 7 7 2 0.000000 102.650482 139.132507 490.965698 # C CYT 8 8 1 0.000000 106.925201 139.131836 495.002686 # A ADE 9 9 3 0.000000 111.695648 141.219269 498.194336 # G GUA 10 10 2 0.000000 116.481354 140.336823 501.122437 # C CYT 11 11 1 0.000000 121.827545 137.300018 500.431091 # A ADE 12 12 3 0.000000 126.666168 134.139893 502.225952 # G GUA 13 13 2 0.000000 130.583771 130.122253 503.335876 # C CYT 14 14 1 0.000000 129.694427 124.575012 502.921265 # A ADE 15 15 3 0.000000 131.787445 119.330780 502.795776 # G GUA 16 16 2 0.000000 134.016510 114.287109 500.142273 # C CYT 17 17 1 0.000000 139.271881 111.263916 499.137024 # A ADE 18 18 3 0.000000 144.555756 109.422485 500.863159 # G GUA 19 19 2 0.000000 146.606049 106.436554 505.548035 # C CYT 20 20 1 0.000000 144.243561 105.940399 510.782593 # A ADE

and here is the beginning portion of the dump file:

ITEM: TIMESTEP 0 ITEM: NUMBER OF ATOMS 9024 ITEM: BOX BOUNDS pp pp pp -381.354 1118.65 -325.334 1174.67 -344.769 1155.23 ITEM: ATOMS id type xu yu zu 1 1 103.59 164.201 471.432

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peter-zhang-chem commented 4 months ago

Dear Martin,

Hey sorry for the belated response.

  1. Regarding the data file: The atoms in data file has the following format:

    1 molecule-tag atom-type q x y z nx ny nz  (nx,ny,nz are optional -
...                                    see "true flag" input command)
...                
N molecule-tag atom-type q x y z nx ny nz  (N = # of atoms)

    Yea, the space before atoms, masses, and bonds is weird - I generated these files from VMD.

  2. Yes, I have a Bonds section in the .data file.

  3. Thank you so much for your time - I have attached the .data file and the dump file with first 2 frames here. dump-data-files.zip

mkmat commented 4 months ago

Dear Peter,

Sorry for the late response. Let me check your data file first.

I just do not remember if Z1+ returns a lammps data file for the

primitive network or not. Such lammps data file you can visualize

using vmd or ovito, for example. I usually use matlab for myself,

but the blender figures were done by Clarisse Luap, I forwarded

your message. Using matlab (or r) you can in any case read

directly the Z1-formatted files and visualize them quite easily.

It should even be not be difficult using python and matplotlib.

If I find time I could try to set up a python script. Let me know if

Clarisse does not respond and if you have any of the mentioned

softwares. Until later,

Martin

--

Martin Kröger Prof Computational Polymer Physics, PD Dr habil website www.complexfluids.ethz.chhttp://www.complexfluids.ethz.ch

Swiss Federal Institute of Technology, ETH Zurich Leopold-Ruzicka-Weg 4, HCP F 48.2, CH-8093 ZURICH, Switzerland phone +41-44-632-6622 fax -1076

Google Scholar EUCO-BAAAAAJ ORCID 0000-0003-1402-6714 Scopus 56416643300

From: Peter Zhang @.***> Sent: 17 April 2024 16:37:30 To: mkmat/Z1plus-code Cc: Kroeger Martin; Comment Subject: Re: [mkmat/Z1plus-code] Question regarding converting LAMMP data file and dump file to config.Z1 (Issue #1)

Dear Martin,

Hey sorry for the belated response.

  1. Regarding the data file: The atoms in data file has the following format:

1 molecule-tag atom-type q x y z nx ny nz (nx,ny,nz are optional - ... see "true flag" input command) ... N molecule-tag atom-type q x y z nx ny nz (N = # of atoms)

Yea, the space before atoms, masses, and bonds is weird - I generated these files from VMD.

  1. Yes, I have a Bonds section in the .data file.

  2. Thank you so much for your time - I have attached the .data file and the dump file with first 2 frames here. dump-data-files.ziphttps://github.com/mkmat/Z1plus-code/files/15012544/dump-data-files.zip

— Reply to this email directly, view it on GitHubhttps://github.com/mkmat/Z1plus-code/issues/1#issuecomment-2061416814, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGFK5YPU7GTB66CBORJ5XE3Y52CKVAVCNFSM6AAAAABFWGT2XWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRRGQYTMOBRGQ. You are receiving this because you commented.Message ID: @.***>

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peter-zhang-chem commented 4 months ago

Dear Martin,

Thank you. I do not think Z1+ returns a lammps data file. Here are the list of files I got from Z1+ output.

I have all the programs you mentioned - currently I am using python to plot values of my interest from the Z1+summary.dat file. It would be awesome to visualize the primitive network used by Z1+ to calculate these values.

And thank you so much, I will wait to see if Clarisse Luap gets back to me.

Peter

mkmat commented 4 months ago

Dear Peter,

I see. So then I will eventually also write a script that creates a lammps data file

from the Z1+SP.dat file, which contains the primitive path network. I will think

about it and let you know. Please ask back in a few days!

All the best, Martin

--

Martin Kröger Prof Computational Polymer Physics, PD Dr habil website www.complexfluids.ethz.chhttp://www.complexfluids.ethz.ch

Swiss Federal Institute of Technology, ETH Zurich Leopold-Ruzicka-Weg 4, HCP F 48.2, CH-8093 ZURICH, Switzerland phone +41-44-632-6622 fax -1076

Google Scholar EUCO-BAAAAAJ ORCID 0000-0003-1402-6714 Scopus 56416643300

From: Peter Zhang @.***> Sent: 18 April 2024 19:53:42 To: mkmat/Z1plus-code Cc: Kroeger Martin; Comment Subject: Re: [mkmat/Z1plus-code] Question regarding converting LAMMP data file and dump file to config.Z1 (Issue #1)

Dear Martin,

Thank you. I do not think Z1+ returns a lammps data file. Here are the list of files I got from Z1+ output.

I have all the programs you mentioned - currently I am using python to plot values of my interest from the Z1+summary.dat file. It would be awesome to visualize the primitive network used by Z1+ to calculate these values.

And thank you so much, I will wait to see if Clarisse Luap gets back to me.

Peter

— Reply to this email directly, view it on GitHubhttps://github.com/mkmat/Z1plus-code/issues/1#issuecomment-2064745766, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGFK5YIOL5HFALHZONACRW3Y6ACCNAVCNFSM6AAAAABFWGT2XWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRUG42DKNZWGY. You are receiving this because you commented.Message ID: @.***>

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peter-zhang-chem commented 4 months ago

Thank you so much for your time and this really useful program, Martin! I will check back with you in a few days!

peter-zhang-chem commented 3 months ago

Dear Martin,

I hope you are well. Just wanted to check in with you regarding the script for creating lammps data file from the Z1+SP.dat file.

Thank you!

Peter

mkmat commented 3 months ago

Dear Peter,

Thanks for your message. I thought I answered already. Is what is written on the Z1+ github

https://github.com/mkmat/Z1plus-code

not what you are looking for? Please let me know, I forgot everything in the meantime ..

Martin

[cid:80e06dd2-b770-4bc5-872e-89a4ee9aaf84]

--

Martin Kröger Prof Computational Polymer Physics, PD Dr habil website www.complexfluids.ethz.chhttp://www.complexfluids.ethz.ch

Swiss Federal Institute of Technology, ETH Zurich Leopold-Ruzicka-Weg 4, HCP F 48.2, CH-8093 ZURICH, Switzerland phone +41-44-632-6622 fax -1076

Google Scholar EUCO-BAAAAAJ ORCID 0000-0003-1402-6714 Scopus 56416643300

From: Peter Zhang @.***> Sent: 03 May 2024 15:26:41 To: mkmat/Z1plus-code Cc: Kroeger Martin; Comment Subject: Re: [mkmat/Z1plus-code] Question regarding converting LAMMP data file and dump file to config.Z1 (Issue #1)

Dear Martin,

I hope you are well. Just wanted to check in with you regarding the script for creating lammps data file from the Z1+SP.dat file.

Thank you!

Peter

— Reply to this email directly, view it on GitHubhttps://github.com/mkmat/Z1plus-code/issues/1#issuecomment-2093019508, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGFK5YJSAIQM6OWKJZRKFJTZAOGBDAVCNFSM6AAAAABFWGT2XWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJTGAYTSNJQHA. You are receiving this because you commented.Message ID: @.***>

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peter-zhang-chem commented 3 months ago

Hey Martin,

Thank you! I was able to visualize the shortest path configuration in vmd using the Z1+SP-to-data.pl.

Peter