Movies in .xyz format

Vasp transition state theory tools

Moderator: moderators

Post Reply
anirudhnk
Posts: 39
Joined: Thu Dec 09, 2021 5:49 pm

Movies in .xyz format

Post by anirudhnk »

Dear Prof. Henkelman,

Sorry if this is a question not relevant to the forum, but I tried searching online and couldn't get an answer.

The movies created using nebmovie.pl are in .xyz format. How could I convert them to a format that is preferred for journal publications such as .avi or .mpeg? Please excuse if this is not the right forum.

Thank you.
graeme
Site Admin
Posts: 2260
Joined: Tue Apr 26, 2005 4:25 am
Contact:

Re: Movies in .xyz format

Post by graeme »

I am not an expert on this. Of course you can just post the xyz or XDATCAR file for others to view, but if you want an actual movie, maybe try jmol, vmd, or vesta. My students will know better than I will about how to make fancy movies.
anirudhnk
Posts: 39
Joined: Thu Dec 09, 2021 5:49 pm

Re: Movies in .xyz format

Post by anirudhnk »

Thank you for your reply.

Yes I use Jmol to visualize the movies - but they happen to be in .xyz format. Please find attached a movie.
Attachments
movie.xyz.zip
(31.62 KiB) Downloaded 909 times
zongtang
Posts: 9
Joined: Wed Nov 04, 2020 5:59 pm

Re: Movies in .xyz format

Post by zongtang »

Hello,

Just came up with a question for the same topic.
Recently, I tried nebmovie.pl to make a movie.xyz file to visualize.

1) The file I got is a series coordinates from the CONTCAR/POSCAR files like the following, which is different the format from the last post.
2) Also the latest script generated a file with movie instead of movie.xyz, although I don't think it is an issue to open with jmol.
3) The issue is that with jmol, I could only see the first image for my movie and I could not play the animation;
could you please let me know if this is a way to generate a movie with the same format as that from the last post ?

Thanks a lot.

Zongtang


=========================== my format
O Li Ni Mn Co F H
1.000000000000000
14.8793487549000005 0.0000000000000000 0.0000000000000000
0.0046245916000000 14.2570163856000001 0.0000000000000000
0.0963566257000000 -0.0207429075000000 19.9999993630999988
O Li Ni Mn Co F H
124 63 48 6 6 1 4
Selective dynamics
Direct
0.0743239984487007 0.0990211009702817 0.2884388482854858 T T T
0.0814814012974273 0.2952559813613808 0.2846819554150704 T T T
0.0645867816909727 0.4903179256985337 0.2810705759526723 T T T
0.0676102132512025 0.7065157329643914 0.2806262189853563 T T T
0.0735294735528581 0.8999835844522277 0.2841778409965620 T T T
0.4035540617573366 0.0962763721185094 0.2843045558247344 T T T
0.4136569506013608 0.2950893786841103 0.2838557879217913 T T T
0.3954108209087713 0.4881641585869489 0.2821651908543701 T T T
0.4071114479304818 0.7032903846455727 0.2801827132365674 T T T
0.4103624599988664 0.8943679637200106 0.2808327316943995 T T T
0.7382276912665360 0.1067287915281670 0.2823015725599314 T T T
0.7511223199853160 0.3041629040079560 0.2833038001637684 T T T
0.7472010308922612 0.5007270030752624 0.2790845882979348 T T T
0.7436388147438029 0.7044782144445085 0.2816806267566165 T T T
0.7381889415453280 0.8991998060067267 0.2834555219866719 T T T
0.0055619290000024 0.9900826080000016 0.3966118219999970 F F F
0.0058404560000014 0.2007044080000000 0.4000199919999972 F F F
-----

========================= format from the last post
137
F: 0.007888 ... E: 0
Ge 12.10031110804062 12.10290463110334 12.10161735456573
Ge 12.09766848261308 4.36832332911005 4.37064835887443
Ge 4.37460312848546 12.10290566329512 4.37329385455718
Ge 4.37361401983808 4.37281375776258 12.10062736020326
Ge 14.94533870337352 7.21794731282763 4.37408108270631
Ge 14.94361517078563 14.94278553803385 12.10352904600676
Ge 7.21297475440745 4.37469839522801 14.93999526983230
Ge 7.21328999422178 12.10665044794592 7.21752213883662
Ge 14.94453336956988 12.10664960406172 14.94030855998986
Ge 4.37651274758276 14.94277843124976 7.21659346134345
Ge 12.10302641570069 14.94224328340833 14.94067236954484
Ge 8.23743946451405 0.51125180399070 11.07752401317719
Ge 8.23571452900093 8.23608901827014 3.35293654451885
Ge 3.35241708053555 3.35113158320752 3.35372591775264
Ge 3.35340305361659 11.08122328785218 11.08042712428693
Ge 11.08074161079615 3.35113112818566 11.07943696634999
Ge 11.08338521132997 11.08571228195340 3.35636853706718
Ge 0.51404260378644 11.07933762940341 8.24105887973625
Ge 0.51372956523419 3.34738469783379 0.50949724001621
Ge 8.23651938458490 3.34738635037853 8.24074458980803
Ge 11.07994958347318 8.23609380863024 0.50870123799311
Ge 3.34978817661776 8.23784004334208 8.24036876422121
Ge 0.51334523527639 8.23783379723869 11.07680476124096
Ge 0.51335866352409 0.51178708565559 3.35101089159712
Ge 8.23444469819941 11.08203963031117 0.50742622536328
Ge 11.07802826215727 0.51179196027195 8.24038134770096
Ge 3.35050534629788 0.51125709481165 0.51042502254723
anirudhnk
Posts: 39
Joined: Thu Dec 09, 2021 5:49 pm

Re: Movies in .xyz format

Post by anirudhnk »

Dear Prof. Henkelman,

Surprisingly i also have an issue with making the movie. When i used nebmovie.pl, i got files such as p0.xyz, p1.xyz and p2.xyz instead of the earlier movie.xyz file. Could you please help with this?

Thank you
graeme
Site Admin
Posts: 2260
Joined: Tue Apr 26, 2005 4:25 am
Contact:

Re: Movies in .xyz format

Post by graeme »

It looks like we have turned off writing of .xyz movies by default. There is a flag at the top of the script that can turn that back on. If I remember correctly, the issue is that the cell structure is written in POSCAR files but not (nessecarily) xyz files.
zongtang
Posts: 9
Joined: Wed Nov 04, 2020 5:59 pm

Re: Movies in .xyz format

Post by zongtang »

Thank you, Prof. Henkelman.
I turned back on "$xyzflag = 1; # turn off xyz writing, by default" and this issue was fixed.
anirudhnk
Posts: 39
Joined: Thu Dec 09, 2021 5:49 pm

Re: Movies in .xyz format

Post by anirudhnk »

Could you let me know how did you do it?

I tried the same (turned back on) but get an error: Illegal division by zero at /home/anandak4/bin/pos2con.pl line 160.
Illegal division by zero at /home/anandak4/bin/Vasp.pm line 168.

Thank you.
zongtang
Posts: 9
Joined: Wed Nov 04, 2020 5:59 pm

Re: Movies in .xyz format

Post by zongtang »

please check out the attached for the modification for the file of nebmovie.pl. Default was 0 instead of 1.
Attachments
capture.JPG
capture.JPG (25.96 KiB) Viewed 20828 times
anirudhnk
Posts: 39
Joined: Thu Dec 09, 2021 5:49 pm

Re: Movies in .xyz format

Post by anirudhnk »

Thanks for your reply.

If you meant just going to bin/nebmovie.pl and manually changing the value from 0 to 1, yes i tried that. But im still getting the same error as before.
Post Reply