Gaussian Geometry Optimization Cube

Cube to geometry optimize the input conformer. Assumes a single conformer molecule.

Related Cubes

Calculation Parameters

  • Gaussian Basis Set (basis) type: string: Basis set used for property calculation with Gaussian
    Default: 6-31G
    Choices: 3-21G, 6-31G, 6-31G*, 6-31+G*, 6-31G**, 6-31+G**, 6-311G**, 6-311+G**, 6-311G(2d,2p), def2SVP, def2TZVP, def2TZVPP, aug-cc-pvdz, aug-cc-pvtz, “”
  • Checkpoint Increment (hours) (checkpoint_increment) type: decimal: Checkpoint files are saved to a collection at this increment.

    If something happens to stop the calculation these saved checkpoint files will be used to restart the calculation automatically. | Default: 0.6 , Min: 0.001, Max: 5.0

  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Cube Metrics (cube_metrics) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Temporary Disk Space (MiB) (disk_space) type: 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 (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • Memory (MiB) (memory_mb) type: 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
  • Gaussian Method (method) type: string: Method used for this Gaussian calculation
    Default: HF
    Choices: HF, B3LYP, B3LYP - GD3, B3LYP - GD3BJ, B2PLYP, B2PLYPD3, M06, M062X, M06L, MN15, MN15L, PW6B95D3, CAM-B3LYP, CAM-B3LYP - GD3, CAM-B3LYP - GD3BJ, WB97X, wB97XD, LC-wHPBE, PBE1PBE, MP2, PW91PW91, PM6
  • Metric Period (metric_period) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Multiplicity Choice(s) (multiplicity_choices) type: integer: Chose multiplicities to be used on your calculations.
    Default: [1, 2, 3]
    Choices: 1, 2, 3, 4, 5, 6
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Remove Implicit Hydrogens (remove_implicit_hydrogens) type: boolean: If True, implicit hydrogens are removed from the molecule before the formal charge is calculated. This is recommended when a molecule was created from an XYZ file or similar, since bond orders based on coordinates can lead to extra implicit hydrogens If false, the Cube will fail if the molecule does have implicit hydrogens.
    Default: False
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Gaussian Solvent Environment (solvent) type: string: Solvent environment used for this Gaussian calculation
    Default: Gas Phase
    Choices: Gas Phase, Water IEFPCM, Water CPCM, Water SMD, DMSO IEFPCM, DMSO CPCM, DMSO SMD, Octanol IEFPCM, Octanol CPCM, Octanol SMD
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Save Log files (store_log_file) type: boolean: Save output log files for all calculations, they are always saved for failed calculations.
    Default: False

Field parameters

  • Gaussian Energy Field (energy_field) type: Field Type: Float: Field created during Floes to store Gaussian Energy
    Default: Gaussian Energy (kcal/mol)
  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • Input Molecule Field (in_mol_field) type: Field Type: Chem.Mol: Primary Molecule Field to use as input to the Cube
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • Output Molecule Field (out_mol_field) type: Field Type: Chem.Mol: Primary Molecule Field to use as output to the Cube
  • ID Field (record_id_field) type: Field Type: String: Field to store record’s ID
    Default: Record UUID

Hardware Parameters

Machine hardware requirements
  • Memory (MiB) (memory_mb) type: 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
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • Temporary Disk Space (MiB) (disk_space) type: 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 (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters
  • Metric Period (None) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Cube Metrics (None) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network

Parallel Gaussian Geometry Optimization Cube

The parallel version adds these extra parameters.

  • Number of messages to distribute at a time (item_count) type: integer: The maximum number of messages to bundle together for a parallel cube.
    Default: 1 , Min: 1, Max: 65535
  • Maximum Failures (max_failures) type: integer: The maximum number of times to attempt processing a work item
    Default: 10 , Min: 1, Max: 100
  • Autoscale this Cube (autoscale) type: boolean: If True, let Orion manage the parallelism of this Cube
    Default: True
  • Maximum number of Cubes (max_parallel) type: integer: The maximum number of concurrently running copies of this Cube
    Default: 1000 , Min: 1
  • Minimum number of Cubes (min_parallel) type: integer: The minimum number of concurrently running copies of this Cube
    Default: 0