Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/USER-MOLFILE/README
66c5617afbe6efficient_neuronet

Last Change
Raw File

README
View Options

This package provides a C++ interface class to the VMD molfile
plugins, http://www.ks.uiuc.edu/Research/vmd/plugins/molfile, and a
set of LAMMPS classes that use this interface.
Molfile plugins provide a consistent programming interface to read and
write file formats commonly used in molecular simulations. This
package only provides the interface code, not the plugins; these can
be taken as precompiled binaries directly from a VMD installation that
matches the platform of your LAMMPS executable. Using the plugin
interface one can add support for additional file formats to LAMMPS
simply by telling LAMMPS where to find a suitable plugin without
having to recompile or change LAMMPS directly. The plugins bundled
with VMD are usually installed in a directory inside the VMD
installation tree named "plugins/<VMDARCH>/molfile".
To be able to dynamically load and execute the plugins from inside
LAMMPS, you need to link with a system library containing functions
like dlopen(), dlsym() and so on for dynamic linking of executable
code into an executable. This library is defined by setting the
molfile_SYSLIB variable in USER-MOLFILE/Makefile.lammps. For Linux
and most current unix-like operating systems, this can be kept at the
default setting of "-ldl" (on some platforms this library is called
"-ldld"). For compilation on Windows, a slightly different mechanism
is used that is part of the Windows programming environment and this
library is not needed.
NOTE: while the programming interface (API) to the molfile plugins is
backward compatible (i.e. you can expect to be able to compile this
package for plugins from newer VMD packages), the binary interface
(ABI) is not. So it is necessary to compile this package with the
molfile plugin header files (vmdplugin.h and molfile_plugin.h) taken
from the _same_ VMD installation that the (binary) plugin files are
taken from. These header files can be found inside the VMD
installation tree under: "plugins/include". For your convenience,
this package ships with a set of header files compatible with VMD 1.9
and 1.9.1 (the current version in June 2012) and should be compilable
with VMD versions back to about version 1.8.4
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
c4science · Help