Hello,
I have problem in visualizing dump files when I use dump_modify command. I use these commands:
dump myphase all custom 10 NiTi_tensile.xyz type x y z
dump_modify myphase region box2
run 1000
After running, the dump file contains 100 frames and its okay. But when I visualize this file by VMD, it shows only 1 frame. I have this problem only when I use dump_modify command.when I use " dump myphase all custom 10 NiTi_tensile.xyz type x y z " alone, everything is OK. ( I use LAMMPS trajectory to load the dump to VMD )
I cannot find the problem. let me know your opinion please.
Nazanin
Hello,
I have problem in visualizing dump files when I use dump_modify command. I
use these commands:
dump myphase all custom 10 NiTi_tensile.xyz type x y z
dump_modify myphase region box2
run 1000
After running, the dump file contains 100 frames and its okay. But when I
visualize this file by VMD, it shows only 1 frame. I have this problem only
when I use dump_modify command.when I use " dump myphase all custom 10
NiTi_tensile.xyz type x y z " alone, everything is OK. ( I use LAMMPS
trajectory to load the dump to VMD )
I cannot find the problem. let me know your opinion please.
this is not a LAMMPS issue but a VMD issue.
please re-read the VMD documentation. it will
tell you that VMD will only read trajectories
where each frame has the same number of atoms.
if this is not given it will stop.
there are some workarounds with limitations,
that were discussed on the vmd-l mailing list,
i.e. should show up in the mailing list archive.
axel.
Nazanin,
Try and use OVITO to visualize your system. You can download OVITO at http://www.ovito.org/
You need to re-write the output in different format for OVITO to work well.
Use the command below to get 100 different output files and OVITO will be able to import all of them and run the trajectory across board.
dump myphase all custom 10 NiTi_tensile.xyz.* type x y z
dump_modify myphase region box2
run 1000
OVITO should produce 100 files with names NiTi_tensile.xyz.0 NiTi_tensile.xyz.10 , NiTi_tensile.xyz.20, NiTi_tensile.xyz.30,… NiTi_tensile.xyz.1000.
When you finish installing OVITO. Run OVITO and go to;
(1) File ----> Import data
(2) Pick the NiTi_tensile.xyz.0 file " Do not load yet"
(3) Make sure you select “Automatic file detection” and ovito will identify them as .xyz.*
(4) From the dialog options, select “load multiple file”
(5) from the menu list below, configure OVITO to identify each column by selecting the following option.
integer Atom type
float Position X
float Position Y
float Position Z
(6) Load
OVITO should load all the files with extension .0 to .1000.
You can then run the movie using the forward arrow >
I did a test and it works. Let me know if you have any problem.
Suleiman.
Hello Nazanin,
You can also keep the original format of writing your system into a single dump file and OVITO will still run fine. On the right side of the window, OVITO will tell you the total number of atoms at different time steps as it runs through the animation.
Use the same procedure that I described in the earlier e-mail, but this time, just select the single file NiTi_tensile.xyz and after opening this, select “File contains multiple snapshot” and after making all the setting for Atom type X Y Z then you can load the trajectory. You should get the same animation as you would when printing out different dump files for each snapshot.
Suleiman.