ls1-MarDyn is a massively parallel Molecular Dynamics (MD) code for large systems. Its main target is the simulation of thermodynamics and nanofluidics. ls1-MarDyn is designed with a focus on performance and easy extensibility.
Together with ADIOS (PR #192), the option to set a name for the single sites were introduced.
This name should be something like the element or functional group which is modeled by the respective site.
It could later be used for some kind of automated selection of the color during visualization.
With issue #310 it was revealed that the name was not handled correctly if not set in the xml file. After fixing this bug, a warning is now printed if the name is not given. To get rid of these warnings, this PR introduces site names in the xml files if possible.
In some cases, it is not really feasible to set meaningful site names, e.g. for the Stoll CO2 model, which simplifies the 3 elements by just 2 sites. Therefore, one site does not represent a single element (e.g. C or O) or a functional group (e.g. methyl or methylene group).
Furthermore, some documentation regarding the xml structure of the sites was added.
Description
Together with ADIOS (PR #192), the option to set a name for the single sites were introduced. This name should be something like the element or functional group which is modeled by the respective site. It could later be used for some kind of automated selection of the color during visualization.
With issue #310 it was revealed that the name was not handled correctly if not set in the xml file. After fixing this bug, a warning is now printed if the name is not given. To get rid of these warnings, this PR introduces site names in the xml files if possible. In some cases, it is not really feasible to set meaningful site names, e.g. for the Stoll CO2 model, which simplifies the 3 elements by just 2 sites. Therefore, one site does not represent a single element (e.g. C or O) or a functional group (e.g. methyl or methylene group).
Furthermore, some documentation regarding the xml structure of the sites was added.