Tag atoms by Indices

This Cube tags atoms based on specified atom indices. You can find the atom indices (starting at 0) for your molecule, on the ‘3D Modelling’ tab and chose the labels:index. Atom indices are specified as integers separated by spaces. Make sure that the number of atoms specified with ‘Atom Indices’ agrees with the ‘Expected Number of Tagged Atoms.’

Main Parameters

Parameter Name

Associated Port

Port Type

Atom Indices

Atom Tag String

Expected Number of Tagged Atoms

Calculation Parameters

  • Constrain the tagged atoms (boolean) : If True, then a field is added to the record which will constrain these atoms during a psi4 optimization. If False, then the atoms are just tagged.
    Default: False
  • Atom Indices (string) : Indices of atoms you want tagged with numbers separated by a space, such as ‘1 2 3 4’.
  • Atom Tag String (string) : String used to tag atoms.
    Default: atom_tag
  • CPUs (integer) : The number of CPUs to run this cube with
    Default: 1 Min: 1 Max: 128
  • Cube Metrics (string) : Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Temporary Disk Space (MiB) (decimal) : The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 Min: 128.0 Max: 8589934592
  • Expected Number of Tagged Atoms (integer) : Specify the number of atoms you expected to be tagged by this Cube.
    Default: 4
  • GPUs (integer) : The number of GPUs to run this cube with
    Default: 0 Max: 16
  • Instance Tags (string) : Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (string) : The type of instance that this cube needs to be run on
  • Memory (MiB) (decimal) : The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 Min: 256.0 Max: 8589934592
  • Metric Period (decimal) : How often to sample metrics, in seconds
    Default: 60 Min: 1 Max: 300
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required

Field parameters

  • Extended Log Field (Field Type: StringVec) : Message extended log field
    Default: Extended Log Field
  • Input Molecule Field (Field Type: Chem.Mol) : Primary Molecule Field to use as input to the Cube
  • Log Field (Field Type: String) : Message log field
    Default: Log Field
  • Output Molecule Field (Field Type: Chem.Mol) : Primary Molecule Field to use as output to the Cube

Hardware Parameters

Machine hardware requirements

  • Memory (MiB) (decimal) : The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 Min: 256.0 Max: 8589934592
  • Temporary Disk Space (MiB) (decimal) : The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 Min: 128.0 Max: 8589934592
  • GPUs (integer) : The number of GPUs to run this cube with
    Default: 0 Max: 16
  • CPUs (integer) : The number of CPUs to run this cube with
    Default: 1 Min: 1 Max: 128
  • Instance Type (string) : The type of instance that this cube needs to be run on
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (string) : Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters

  • Metric Period (decimal) : How often to sample metrics, in seconds
    Default: 60 Min: 1 Max: 300
  • Cube Metrics (string) : Set of metrics to be collected

    Choices: cpu, disk, memory, network

Tip

filename: psi4-orion/psi4_orion/psi4_cube_gopt.py