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opt

opt

This keyword controls the search for geometry minima, transition states, and reaction paths.

Options

type
Value Min: Searches for the geometry minimum.
NEB: Uses the Nudged Elastic Band (NEB) algorithm to search for the reaction path and transition state.
Dimer: Uses the dimer algorithm to locate the transition state, given the reactant and product geometries.
Default Min

Specify the type of geometry optimization to perform:

  • For Min, the initial structure must be provided in mol. The optimization process is saved to x-opt-traj.xyz, and the final optimized minimum is written to x-opt.xyz.
  • For NEB and Dimer, two structures must be provided in mol and mol2, representing the reactant and product poses, respectively. Typically, NEB is used first to quickly find a reasonable path and transition state. If NEB fails to converge, the resulting structures can then be used in a Dimer search. Dimer is computationally cheaper than NEB, but it requires high-quality reactant and product structures.
  • For NEB, the reaction path is saved to x-opt-traj.xyz, and the final transition state is written to x-opt.xyz.
  • For Dimer, the transition state is saved to x-opt.xyz. Note that x-opt-traj.xyz is not the reaction path—it simply records the optimization steps, similar to Min.

max_step

The maximum number of geometry optimization steps.

Value An integer
Default 1000
energy_cov

The energy convergence threshold. When the energy change falls below this value, the energy criterion is considered satisfied.

Value A real number
Default 1.E-4
grad_cov
Value A real number
Default 1.E-3

The gradient convergence threshold. This value determines four specific convergence criteria:

Maximum gradient component grad_cov
RMS gradient: grad_cov * 2/3
Maximum atomic displacement grad_cov * 4
RMS atomic displacement grad_cov * 8/3

When all four conditions are met, the gradient criterion is considered satisfied.

max_dr

The maximum atomic displacement allowed in a single optimization step. If the molecule is highly flexible (i.e., the potential energy surface is very flat), or if the structure—particularly a transition state—is close to a stationary point but not yet converged, setting a smaller max_dr value (e.g., 0.1) can be very helpful.

Value A real number
Default 0.5
num_images

The number of images used in the NEB transition state search.
This number should not be set too small (e.g., 5), as it may lead to an inaccurate reaction path.

Value An integer
Default 10
neb_k
Value A real number
Default 0.01

The force constant used in NEB transition state search.
For a given system, the optimal value of neb_k should be determined through trial and error.

fix_atoms
Value Atom range
Default None

Specifies the atoms to be fixed during geometry optimization.
For example: atoms 2, 5, 6, 7, 8, 9, 23, and 26 will remain fixed throughout the optimization.

fix_bond
Value 2 integers
Default None

Specifies the bonds to be fixed during geometry optimization.
For example: bonds (1, 4) and (2, 6) will remain fixed throughout the optimization.

fix_angle
Value 3 integers
Default None

Specifies the angles to be fixed during geometry optimization.
For example: angles (1, 4, 5) and (2, 6, 7) will remain fixed throughout the optimization.

fix_torsion
Value 4 integers
Default None

Specifies the torsions to be fixed during geometry optimization. For example: torsions (1, 4, 5, 9) and (2, 6, 7, 12) will remain fixed throughout the optimization.

Theoretical Background

Minimum

A minimum is defined as a stable isomer on the potential energy surface (PES) of a molecule, where the gradients on all atoms are zero.
The optimization result strongly depends on the initial structure; different starting geometries may lead to different isomers.

Transition State

A transition state is a short-lived atomic configuration that represents a maximum along one direction and a minimum along all others on the potential energy surface. The gradients on all atoms are also zero.
In Qbics, the transition state can be located using the NEB or dimer method. Only the (unoptimized) reactant and product structures are required—no exact Hessian needs to be computed.

A recommended strategy is:

  • Use a low-cost method, such as xTB, to identify a reasonable reaction path and transition state using the NEB method (type neb).
  • Then, refine the transition state using a standard DFT method with the dimer approach (type dimer), even if the initial NEB result has not fully converged.

This strategy is illustrated below:

Input Examples

Example: Minimum Structure of Aspirin

Search for the minimum structure of aspirin at the B3LYP/def2-SVP level of theory:

Example: Minimum Structure with Constraints

Search for the minimum structure of the molecule "1UML" with one bond and one torsion fixed, using the xTB level of theory: 

opt
    fix_bond 7 51
    fix_torsion 2 9 12 13
end

mol
    1uml.xyz
end

task
    opt xtb
end

Check the applied constraints during the optimization:

Example: Transition State of SN2 Reaction

Search for the transition state of an SN2 reaction using the NEB algorithm at the B3LYP/def2-SVP level of theory:

The reaction path is provided in ts-1-opt-traj.xyz:

The energies can be found in the output file ts-1.out:

In the table, structure 0 and 1 correspond to the reactant and product, respectively. Structure 6 represents the transition state, which is also saved in ts-1-opt.xyz.
You can replace b3lyp with xtb to perform the calculation more quickly.
You can also try type dimer, which is computationally cheaper than NEB, but requires high-quality reactant and product structures.

Example: Transion State of Decarboxylation Reaction

Search for the transition state of the following decarboxylation reaction using the NEB algorithm at the B3LYP/def2-SVP level of theory:

The structures in a1.xyz and a2.xyz are shown below. They are placed arbitrarily without prior optimization.

The optimized transition state (ts-2-opt.xyz) and the reaction path (ts-2-opt-traj.xyz) are shown below:

Example: Transition State of Pd(OAc)-Catalyzed Nucleopalladation

Search for the transition state of the following Pd(OAc)-catalyzed nucleopalladation using the DIMER algorithm at the B3LYP/def2-SVP level of theory: 

mol
    a1.xyz
end

mol2
    a2.xyz
end

scf
    charge  0 
    spin2p1 1
end

opt
    type dimer
end

basis
    def2-svp
end

pseudopotential
    def2-ecp # Since Pd is used, you need to use ECP.
end


task
    opt b3lyp 
end

The structures in a1.xyz and a2.xyz are shown below. They are arranged arbitrarily without prior optimization.

The optimized transition state is provided in ts-3-opt.xyz, as shown below: