Psi4 Geometry Optimization

This cube performs geometry optimization using Psi4.

Related Cubes

Calculation Parameters

  • Basis used by Psi4 (basis) type: string: Basis set used for geometry optimization by Psi4.
    Default: “”
    Choices: “”, minix, 6-31G, 6-31G*, 6-31+G*, 6-31G**, 6-31+G**, 6-311G**, 6-311+G**, 6-311G(2d,2p), def2-SVP, def2-SVPD, def2-TZVP, def2-TZVPD, def2-TZVPP, def2-TZVPPD, DZVP, cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, aug-cc-pVTZ, LanL2DZ
  • 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
  • Optimization Engine (engine) type: string: Choose an optimization engine from OptKing or GeomeTRIC.
    Default: Psi4 OptKing
    Choices: Psi4 OptKing, Psi4 GeomeTRIC
  • Geometry Convergence Criteria (g_convergence) type: string: The convergence criteria used for geometry optimization as defined by Psi4.

    If not defined, the default will be chosen as based on the optimization engine: QCHEM for OptKing and GAU_TIGHT for geomeTRIC. | Default: “” | Choices: “”, GAU_LOOSE, GAU, GAU_TIGHT, GAU_VERYTIGHT, QCHEM, NWCHEM_LOOSE, TURBOMOLE

  • 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
  • Maximum number of geometry optimization steps (max_gopt_steps) type: integer: Maximum number of steps during a single geometry optimization calculation.
    Default: 100 , Max: 200
  • 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
  • Method used by Psi4 (method) type: string: Method used for geometry optimization by Psi4.
    Default: HF3c
    Choices: HF3c, PBEh3c, HF, HF-D3, B3LYP, B3LYP-D3BJ, B3LYP-D3MBJ, B2PLYP-D3BJ, M06, M06-2X, M06-L, MN15-D3BJ, MN15-L, PW6B95-D3BJ, CAM-B3LYP, CAM-B3LYP-D3BJ, WB97X, WB97X-D, WB97M-D3BJ, B97M-D3BJ, PBE, PBE0
  • 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
  • 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: When On, implicit hydrogens are removed from the molecule before the formal charge is calculated. If Off, 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
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Save Psi4 Log File (store_log_file) type: boolean: The log file generated from Psi4 is saved. It will be available as a floe report when the floe is complete.
    Default: False
  • Store Psi4 optimization history (store_opt_history) type: boolean: Add Psi4 optimization history to output record
    Default: False

Field parameters

  • Energy Field (energy_field) type: Field Type: Float: Field to store Psi4 Energies.
    Default: Psi4 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.

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 Psi4 Geometry Optimization

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