Fix origin collection in LAMMPS general triclinic boxes.
Safer floating point zero box length detection.
Fixed minimum value detection in neighbor listing. Only matters if you're doing inv_dist.
Removed dead PBC edge attribute setting from graph edge creation. Logic moved to a graph util.
Remove spurious double edge creation when using ADD.EDGES.FROM_FILE.
Change label_node_block documentation language.
Fix MIC distances for boolean wrapped distance calculations.
Remove dead GRAPH.ADD.ATRIBUTE.EDGE.EDGE pe_lj.
Fix off by one error in modularity optimization.
Use MIC util in steinhardt calculation.
Properly scale PBCs when PBC.DIM = read
Validate Z-matrix reference row existence
Avoid crash when writing attribute histogram of empty graph
Pass directedness to edge id collector in write_edge_graph
Grab correct PBCs in steinhardt analysis
Throw an error if negative node indicies are read from .nds or .edg files.
Store trajectory file cursor at GRAPH.ADD.NODES.TRAJECTORY level to prevent multiple graph blocks advancing the same
cursor erroneously on the same timestep.
Allow negative dihedral angles, use IUPAC sign conventions.
Initialize coordinate matrix if TOTAL zmatrix command is used.
Add MPI execution to input file tutorial
Fix edge case in neighborlist results vector
Change line tokenizer pre-allocation. Larger size, moved to instantiation.
Allocate a single string stream in the zmatrix search.
Preallocate vectors in pe_lj and inv_dist
Prevent negation of 2-body constraints due to neighbor listing
Use edge ids instead of node pairs to avoid issues with parallel edges.
Remove doubled remark line from PDB file writer
Add note on == comparitors in delete_edges/nodes analysis doc
Avoid division by zero when PBCs are set to zero, either in 2D trajectories, or when PBCs are disabled in a dimension
Add references to igraph docs in analysis commands docs (#303)
Add type-aware attr comparisons
Prevent ROW = SUM, or other future TOTAL commands from being used in ROW commands
Add optional argument to ADD.EDGES/NODES.FROM_FILE that specifies the delimiters used in that file.
Add a walkthrough on a GROMACS example
Update dev guide IO references to the Utils::IO filename helper and remove the stale Count_Lines_In_File entry.
Remove inv_dist Z-matrix constraint from the not/none docs and error message.
Add MIC support to dev walkthrough of new zmatrix commands.
Remove the single node-attribute updating and unused variables from observers
Remove unused variables from the Z-matrix commands, trajectory readers, etc.
Persist the trajectory file cursors across timesteps so readers resume from the last read frame instead of skipping
the file from the beginning every frame.
Use inclusive distance bounds
Fix multi-frame gro and multi-frame lammpstrj general triclinic parsing.
Validate pe_lj sigma and epsilon are positive. Fix the optional argument parsing
Replace in_avail() stream-parsing with LineTokenizer across all input file components
Consolidate the numeric/string/boolean attribute type switches into Utils::Graph visitor helpers with_attr_value
and with_attr_column.
Replace ghost particle approach with minimum image convention (MIC) for periodic boundary conditions (PBCs) (#279)
Remove PBC.CUTOFF setting, add_ghosts analysis, and delete_ghosts analysis
Support triclinic (non-orthogonal) cells via upper-triangular box matrix (Initial work towards #2)
Apply MIC to all distance, angle, and dihedral calculations
Apply MIC to neighbor lists
Apply MIC to edge attributes
Update tutorial and all relevant docs
Update ghost node ghost_of attribute when deleting or merging nodes. Only relevant if analyses were run before the
last ZMATRIX_SEARCH. (#274) Superceded by MIC changes in #279