atom/vtk output format

Submitted by ahobbs on Wed, 01/16/2013 - 10:08

I'm trying to use the new atom/vtk dump format...

According to the documentation the syntax is

dump ID group-ID style N file args

where atom/vtk args = none

I've tried the following:

dump dmp all atom/vtk 800 post/dump*.vtk

But I get the error: Invalid dump style (output.cpp:399)

Any suggestions from the LIGGGHTS gurus? Also with no arguments what exactly is exported with the atom/vtk output?

Forums:

AGl | Wed, 01/16/2013 - 10:49

The format is correct. You just need to be sure, liggghts is linked against vtk shared library. "make ubuntuVTK" should do the job.

ahobbs | Wed, 01/16/2013 - 13:53

is there any documentation or tutorial how this is done? I've run sudo make ubuntuVTK from the LIGGGHTS/src directory but I get all sorts of missing header file messages.

ahobbs | Wed, 01/16/2013 - 17:07

I've installed the headers, but I wonder if something else is still missing.
Here's the output of my error:

ahobbs@astec-win7-2:~/LIGGGHTS/LIGGGHTS-ASTEC/src$ sudo make ubuntuVTK
grep: angle_*.h: No such file or directory
grep: dihedral_*.h: No such file or directory
grep: improper_*.h: No such file or directory
make[1]: Entering directory `/home/ahobbs/LIGGGHTS/LIGGGHTS-ASTEC/src/Obj_ubuntuVTK'
mpic++ -g -O2 -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized -DLAMMPS_GZIP -DLAMMPS_VTK -I/usr/include/vtk-5.2 -I/usr/include/eigen2 -c dump_atom_vtk.cpp
In file included from dump_atom_vtk.cpp:29:0:
dump_atom_vtk.h:42:25: fatal error: vtkCellArray.h: No such file or directory
compilation terminated.
make[1]: *** [dump_atom_vtk.o] Error 1
make[1]: Leaving directory `/home/ahobbs/LIGGGHTS/LIGGGHTS-ASTEC/src/Obj_ubuntuVTK'
make: *** [ubuntuVTK] Error 2

ckloss's picture

ckloss | Fri, 01/18/2013 - 11:14

Hi Andrew,

you might have to change the makefile according to which Version of VTK you have installed. This line of the makefile

VTK_INC = -I/usr/include/vtk-5.2 -I/usr/include/eigen2

depends on the version of VTK lib you have installed (might be different than 5.2)

Cheers Christoph

ahobbs | Sat, 01/19/2013 - 21:53

I've edited the makefiles to match the VTK version (5.8). I'm still getting some errors:

ahobbs@astec-win7-2:~/LIGGGHTS/LIGGGHTS-ASTEC/src$ sudo make ubuntuVTK
[sudo] password for ahobbs:
grep: angle_*.h: No such file or directory
grep: dihedral_*.h: No such file or directory
grep: improper_*.h: No such file or directory
make[1]: Entering directory `/home/ahobbs/LIGGGHTS/LIGGGHTS-ASTEC/src/Obj_ubuntuVTK'
mpic++ -g -O2 -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized -DLAMMPS_GZIP -DLAMMPS_VTK -I/usr/include/vtk-5.8 -I/usr/include/eigen2 -c dump_atom_vtk.cpp
In file included from /usr/include/c++/4.7/backward/strstream:52:0,
from /usr/include/vtk-5.8/vtkIOStream.h:112,
from /usr/include/vtk-5.8/vtkSystemIncludes.h:40,
from /usr/include/vtk-5.8/vtkIndent.h:24,
from /usr/include/vtk-5.8/vtkObjectBase.h:43,
from /usr/include/vtk-5.8/vtkObject.h:41,
from /usr/include/vtk-5.8/vtkCellArray.h:35,
from dump_atom_vtk.h:42,
from dump_atom_vtk.cpp:29:
/usr/include/c++/4.7/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
In file included from dump_atom_vtk.cpp:29:0:
dump_atom_vtk.h:59:22: fatal error: Eigen/Core: No such file or directory
compilation terminated.
make[1]: *** [dump_atom_vtk.o] Error 1
make[1]: Leaving directory `/home/ahobbs/LIGGGHTS/LIGGGHTS-ASTEC/src/Obj_ubuntuVTK'
make: *** [ubuntuVTK] Error 2

ahobbs | Mon, 01/21/2013 - 09:31

I've installed eigen2 (eigen3 wouldn't install on my version of ubuntu), and I think it has compiled ok. However I still get the invalid dump style when using:
dump dmp all atom/vtk 800 post/dump*.vtk