Psi4 QM Vacuum Entropy Floe

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Solution-based/Small Molecule Lead-opt/QM Analysis

  • Task-based/Quantum Mechanics/Energetic Analysis

  • Role-based/Computational Chemist

  • Product-based/Quantum Mechanics/Psi4

Description

This floe uses a finite difference method to compute the Hessian from Psi4 single point gradients. Those Hessians are used to compute an entropic contribution to the free energy at room temperature (298 K).

The method and basis set that was used for the geometry optimization of the input structure(s) should be used for the Hessian calculation in this floe. Any dataset created in a Psi4 floe has the field Psi4 Method/Basis from that calculation.

The default behavior of this floe is to treat each input record as a different conformer of the same molecule. Then a single record is output with the entropic contribution to the gas phase free energy. However, if you would like to compute vacuum entropies for more than one molecule, make sure that all conformers of that molecule have the same value in a structure ID field which can be specified below.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Database Molecules (in): Dataset containing records with optimized conformers, such as output from a local minima search.

  • Required

  • Type: data_source

Outputs

Psi4 Entropy Output (out): Dataset containing records with Psi4 calculated entropies.

  • Required

  • Type: dataset_out

  • Default: psi4_vacuum_entropy

Failure Output (psi4_entropy_failure): Dataset to store records which fail during this floe.

  • Required

  • Type: dataset_out

  • Default: psi4_vacuum_entropy_failures

Psi4 Calculation Parameters

Psi4 Hamiltonian for Property Calculation (psi4_prop_method): Method used for Psi4 property calculation. Must be the same as used for geometry optimization on input dataset.

  • Type: string

  • 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’]

Psi4 Basis Set (psi4_prop_basis): Basis set used for Psi4 gradient calculation. Must be the same as used for geometry optimization on input dataset. Default empty basis set (‘’) goes with HF3c, which has one built in.

  • Type: string

  • 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’]

Psi4 #Threads (psi4_prop_nthreads): Number of CPUs for Psi4 calculations

  • Type: integer

  • Default: 8

Psi4 Memory (psi4_prop_memory): Memory for Psi4 calculations in MBs

  • Type: decimal

  • Default: 14400

Optional Hessian Parameters

Maximum Initial Gradient (maximum_grad): Hessian calculations require the initial structure to be a local minima. If the maximum gradient is above this threshold then the calculation will fail.

  • Type: decimal

  • Default: 0.001

Structure Index (structure_id_field): If this integer field is present, it is interpreted as molecule identifier.

Multiple incoming records with same value of this integer field, will be interpreted as conformer ensemble for that molecule. If this field is not present, all structures will be assumed as conformer ensemble of the same molecule.

  • Type: field_parameter

  • Default: structure id