Overview#

Several example input files are provided in the examples/ directory to demonstrate ChemNetworks capabilities across different trajectory formats, system sizes, and analysis types. Each example directory contains an input.cn file, one or more trajectory files, and a ref_files.tgz archive of reference output for validation.

For a detailed, line-by-line explanation of an input file, see the tutorial explaining the Water-LiCl example.

water-licl_lammpstrj#

A box of water molecules with dissolved lithium and chloride ions, read from a LAMMPS trajectory. This example defines four separate Z-matrix blocks to capture water-water hydrogen bonds, Li-Cl ion pairs, Li-water coordination, and Cl-water coordination. It demonstrates the [GRAPH.WRITE] sub-block syntax for organizing output commands. See the full walkthrough for a detailed explanation.

1k-water-100-frame_groxtc#

A 1,000 water molecule system read from combined GRO and XTC files. This example uses SCALE = 10 to convert the standard GROMACS unit of nanometer coordinates to angstroms. It also demonstrates several graph analyses applied in sequence: merge_equal_nodes, degree, betweenness, and connected_components. The ADD.ATTRIBUTE.NODE.NODE command is used to rename atom types from the GRO format (OW, HW1, HW2) to simpler names (O, H).

35k-waters-1-step_gro#

A large system of 35,000 water molecules analyzed for a single timestep in GRO format. This example tests scalability with an atom count that exceeds the GRO format's standard index maximum (99,999). Periodic boundary conditions are enabled when PBC.DIM is set, provided the box lengths are non-zero.

2-waters-10k-steps_xyz#

A minimal two-molecule water system tracked over 10,000 timesteps in XYZ format. This system is used when testing MPI distribution of many timesteps and to check timestep overhead.

dspaces_spce#

An SPC/E water model read from the DSpaces trajectory format. This example contains a LAMMPS input file script that demonstrates the DataSpaces dump format for a customized version of LAMMPS. This dump format writes coordinate data to a shared memory space that is then read by ChemNetworks directly.

integer-lattice_xyz#

A synthetic 3x3x3 integer lattice demonstrating a nine-row Z-matrix that identifies 3x3 slices of a cube.