dps density

Calculate a one-dimensional mass- or charge-density profile.

Synopsis and options

usage: dps density [-h] -s FILE -f FILE [-n FILE] -o FILE [-x {x,y,z}] [-tp {mass,charge}]
                   [-b START_TIME] [-e END_TIME] [-dt DELTA_TIME] [--bin-width BIN_WIDTH]
                   [-selfit SELECTION_FIT] [-sel SELECTION_CALCULATE [SELECTION_CALCULATE ...]]
                   [--center-mode {frame,block,none}] [--blocks BLOCKS] [-nc]
                   [-t DENSE_PHASE_THRESHOLD]

Calculate a one-dimensional mass- or charge-density profile.

Input:
  -s FILE, --run-input FILE
                        Input DROPPS run file (.tpr) containing the system and simulation
                        settings. (required)
  -f FILE, --input FILE
                        Input trajectory file (.xtc). (required)
  -n FILE, --index FILE
                        Optional index file (.ndx) defining additional atom groups. (default:
                        None)

Output:
  -o FILE, --output FILE
                        Output density-profile file (.xvg); the extension is added if omitted.
                        (required)

Parameters:
  -h, --help            Show this help message and exit.
  -x {x,y,z}, --axis {x,y,z}
                        Axis along which to calculate the density profile. (default: z)
  -tp {mass,charge}, --type {mass,charge}
                        Density quantity to calculate. (default: mass)
  -b START_TIME, --start-time START_TIME
                        First trajectory time to analyze, in ns. (default: None)
  -e END_TIME, --end-time END_TIME
                        Last trajectory time to analyze, in ns. (default: None)
  -dt DELTA_TIME, --delta-time DELTA_TIME
                        Approximate interval between analyzed frames, in ns. (default: None)
  --bin-width BIN_WIDTH
                        Requested density-bin width, in nm. (default: 0.05)
  -selfit SELECTION_FIT, --selection-fit SELECTION_FIT
                        Index group used to locate the dense phase; if omitted, prompt
                        interactively. (default: None)
  -sel SELECTION_CALCULATE [SELECTION_CALCULATE ...], --selection-calculate SELECTION_CALCULATE [SELECTION_CALCULATE ...]
                        Index groups whose density profiles are written; if omitted, prompt
                        interactively. (default: None)
  --center-mode {frame,block,none}
                        Slab centering strategy: frame aligns each analyzed frame; block uses one
                        center per contiguous --blocks segment; none applies no shift. (default:
                        frame)
  --blocks BLOCKS       Number of contiguous groups used by --center-mode block. (default: 5)
  -nc, --no-center      Compatibility alias for --center-mode none. (default: False)
  -t DENSE_PHASE_THRESHOLD, --dense-phase-threshold DENSE_PHASE_THRESHOLD
                        Dense-phase threshold as a fraction of the maximum reference density.
                        (default: 0.5)

Examples:
  dps density -s run.tpr -f run.xtc -o density.xvg -x z

Note

This page is generated from the DROPPS 1.0 argument parser. Run dps density -h in the installed environment for the same reference at the command line.