I have a very basic question on dump files. I find references in various visualization packages to “lammpa dump files”. However, when I search “dump files” in the Lammps documentation, I am directed to the dump command, which really seems to be an operation to create anyone of a number of files of different types and options. For instance with a dump command, you can create atom, cfg,custom, .dcd. and other file options, some with no options, some with many. It looks like which the format of a “dump file” varies, starting with a type of file, and offering various output options. So, when a visualization program states it reads “LAMMPS dump files”, with no additional explanation, are they referring to a specific format from the dump command, something else, or is it a vague reference? Specifically, I am trying to use OVITO to look at trajectory files., and also Atomeye. I have a bunch of .dcd files. Neither OVITO not Atomeye. Both can read .cfg files. Dcd files are binary and machine or system dependent. Therefore I think it needs to be transformed to something else. Is there any program than can read a .dcd file and convert it to something else, e.g. a .cfg file? I am assuming you would have to run it (e.g. Python), or compile ti form source code and create a system specific program to perform the conversion for the binary file to be read. If there isn’t one, is the only way to get one is to write one from interpreting the LAMMPS source code for the two files types?
I have a very basic question on dump files. I find references in various
visualization packages to “lammpa dump files”. However, when I search
“dump files” in the Lammps documentation, I am directed to the dump
command, which really seems to be an operation to create anyone of a number
of files of different types and options. For instance with a dump command,
you can create atom, cfg,custom, .dcd. and other file options, some with no
options, some with many. It looks like which the format of a “dump file”
varies, starting with a type of file, and offering various output options.
So, when a visualization program states it reads “LAMMPS dump files”, with
no additional explanation, are they referring to a specific format from the
dump command, something else, or is it a vague reference?
in this context "LAMMPS dump files" refers to the "native" format, i.e.
dump style "atom" and dump style "custom".
Specifically, I am trying to use OVITO to look at trajectory files., and
also Atomeye. I have a bunch of .dcd files. Neither OVITO not Atomeye.
Both can read .cfg files. Dcd files are binary and machine or system
dependent. Therefore I think it needs to be transformed to something
else. Is there any program than can read a .dcd file and convert it to
something else, e.g. a .cfg file?
yes, LAMMPS could do it, if you install/configure/compile the USER-MOLFILE
package.
have a look at the rerun command. you need to set up your simulation as
you have before, but then you can replace your pair style with pair style
zero, to avoid recomputing everything. please be aware that this will
likely mess up the time step numbers, since DCD format files are extremely
minimal.
as an alternative, you may look into using VMD, which reads DCD format
files natively, however, you likely want to reconstruct some additional
topology and atom/element information information, since DCD files itself
do not store that information, but only coordinates.
another option would be to look into teaching Ovito to read DCD files. a
simple approach for that would be to adapt the code in the USER-MOLFILE
package, which passes the heavy lifting of processing many different file
formats to VMD molfile plugins. another option is to utilize the dcdplugin
source code from the VMD molfile plugin directly (which has a ton of
helpful comments, and can handle DCD files from several different platforms
and fortran compilers and byteswap them on the fly)
axel.