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After the model structure is established, the calculation can be started. Click Calculate in the undefined column of the calculation module to see the following figure.
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In Setup, we can see that the basic tasks of Dmol3 mainly include: single point energy calculation, structural optimization, dynamic calculation, transition state search, transition state optimization, transition state confirmation, elastic constant calculation and so on. (The new version of MS has more tasks).
First we choose geometric optimization, and then click more. We can see that we can choose the criteria for calculating convergence, including energy, maximum force and maximum displacement. Quality mainly includes coarse, medium and fine, corresponding to different convergence criteria. The higher the general convergence standard, the better the calculation accuracy and the longer the calculation time. In order to meet the calculation accuracy requirements of different systems, the data can also be directly converted into specific energy, Max. Force and maximum. Displacement.
Maximum number of iterations specifies the maximum number of geometric optimization cycles. If the set number of cycles is reached, the calculation will stop even if the convergence criteria are not met. Generally, the number of secondary cycles can be adjusted to 100 or even more.
The maximum step length refers to the maximum step length of each optimized atomic motion.
When "optimize cell" is selected, it means that cell parameters will be optimized in addition to the atomic position. If you only need to optimize the atomic position, you don't need to check this box.
Note: The lower right corner of each panel is helpful. This is the official manual file provided by Materials Studio, which is very important. You should check it often. Click on the help of each panel, and descriptions of all parameters on that panel will appear.
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The figure above describes other parameters in the settings bar. Quality is to control the total electron convergence accuracy, including coarse, medium and fine, and the specific value corresponds to the electron column of this panel.
Functional Functional is a very important option, and the commonly used principal functional is shown in the above figure. For different systems, the required function combination is different, and the corresponding accuracy is also different. Generally, the best function combination method can be tested by itself, or you can directly refer to the function combination of similar systems in the literature.
DFT-D correction is to add long-range interactions to describe weak interactions such as hydrogen bonds and van der Waals forces. Commonly used options are: Tkatenko-Scheffler (TS) (GGA-PBE, GGA-BLYP, B3LYP), grimm(GGA-PBE, GGA-BLYP, B3LYP) and OBS (GGA). The choice of weak interaction is related to specific system elements, as shown in the following figure:
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Spin Unlimited: When selected, it means that the calculation will be carried out in different orbits for different spins. This is the so-called "spin infinity" or "spin polarization" calculation. If unchecked, the calculation will use the same orbit for the alpha and beta spins. This is called "spin-limited" or "non-spin-polarized" calculation. The default value is unchecked.
Use formal spin as initial value: When selected, the initial value of unpaired electron number representing each atom will be taken from the formal spin introduced for each atom. This initial value will be optimized in the future calculation process.
Metal: If selected, it means that the system is metal and needs heat treatment, and Brillouin zone is densely sampled. If unchecked, the K-point interval used by default will be thicker and smearing will not be used. Suitable for periodic systems.
Use Symmetry: When selected, it indicates that symmetry information should be used in the calculation. Molecular dynamics simulation or calculation involving transient search or confirmation cannot use symmetric information.
Multiplicity: Spin multiplicity has the following options: Auto, Single, Double, Triple, Quadruple, Quadruple, Hexuple, Split and Octuple. When Auto Auto is selected, DMol3 will try to determine the spin state of the ground state by performing spin free calculation.
Charge: The total charge of a specified molecule or cell.
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As shown in the above figure, you can set the parameters related to the electronic Hamiltonian on the "Electronics" tab.
Integration Precision: Specifies the precision used in the numerical integration of Hamiltonian. Available options are: coarse, medium and fine, with specific values corresponding to the quality in the setting bar of this panel.
SCF tolerance: self-consistent convergence criterion. Specifies the threshold used to determine whether the self-consistent calculation converges. Option and related convergence thresholds are: Coase (10-4), medium (10-5) and fine (10-6). You can also change the convergence criterion according to the SCF tolerance in the lower right corner of the system, and then you can also change the maximum self-consistent cycle number of Max. SCF loop, and specify the maximum number of SCF iterations allowed for energy calculation. If the SCF does not converge after the specified number of iterations, the calculation will be terminated.
K-point set: defines the number of integral points used to integrate wave functions in reciprocal space. You can choose gamma single point (1× 1× 1), coarse, medium and fine, or you can enter different k points in more k points in the lower right corner, which is only applicable to periodic systems. The same series of systems need to use the same K point.
Core therapy: nuclear therapy, with the following four optional types:
All-electronic (default): the core electrons are not specially processed, and all electrons are included in the computing system for processing.
Effective Core Potential (ECP): The core electron is replaced by a single effective potential, and the relativistic correction is introduced in the core processing.
All-electron Relativity: All electrons in the system are treated, and relativistic effect is introduced in the treatment of core electrons.
DFT Semi-core Pseudopoint (DSPP): A single effective potential is used to replace the core electrons, and relativistic correction is introduced in the core processing.
Note: ECP and DSPP are both heavy elements after processing 2 1, DSPP is specially developed for DMol3 module, and ECP is derived from Hartree-Fock potential.
Basis set: Specifies the atomic orbital basis set to be used in the calculation. Mainly includes the following contents:
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Basic file: basic group file, which specifies the version of the basic group file to be used: 3.5 and 4.4. Among them, 4.4 is a newly optimized basis set, which can slightly improve the heat of formation, and was proposed by Delley in 2006. 3.5 is the original version, which is the default value.
Orbital Truncation Mass Atomic Orbital Truncation Radius: Specifies the finite range truncation of atomic basis groups. The accuracy of track cut-off determines the size of limited range cut-off and depends on the track cut-off scheme. It can be divided into three types: coarse, medium and fine, and you can also enter different values in Orbital Cutoff in More in the lower right corner.
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Harris Approximation Harris Approximation: When selected, specifies that Harris non-uniform approximation is used in the calculation. This greatly reduces the required calculation time, but also reduces the calculation accuracy. Harris approximation is only suitable for spin-limited calculation using LDA functional, and there is no solvent effect.
Use solvent model: when selected, COSMO solvent model will be specified, and more details can be set on the solvent tab of DMol3 electronic options dialog box. Harris approximation is not available when using solvation model.
Multipole expansion: specifies the maximum angular momentum function used for multipole representation of charge density. Mainly divided into: monopole, dipole, quadrupole, octupole and hexapole.
Charge: Specifies the value f, which is used to mix the charge density between the current iteration and the previous iteration. The allowable value is 0.0.
Rotation: Specifies the value used to blend the rotation density between the current iteration and the previous iteration. The allowed values are 0.0 to 1.0.
Use diis (Direct Inversion of Iterative Subspace): When selected, it means that DIIS (Direct Inversion of Iterative Subspace) will be used to accelerate SCF convergence.
DIIS Size: Specifies the maximum size of the subspace of the DIIS procedure. If SCF does not converge to the default number of history records, increasing this value sometimes leads to a significant improvement in SCF convergence. It is not recommended to use less than 4 history records. The allowed values are 1 to 10.
Use preprocessor Use preprocessor: When selected, it means that the charge density preprocessor is turned on, which can suppress the charge density oscillation between successive SCF cycles. This can accelerate convergence, especially for large-scale systems or surface or interface calculations.
Q0: Specifies the reference wave vector that attenuates the charge density oscillation by Bohr reciprocal. The allowed values are 0.5 to 20.
Use smear hot placeholder: When selected, it means that hot placeholder will be applied to track placeholder to accelerate convergence. The smearing parameters allow electrons to trail on all orbits according to the specified energy difference δ e, which is similar to the physical thermal occupancy phenomenon. This method can greatly accelerate the convergence speed of SCF iteration by allowing orbital relaxation. It will lead to the mixture of virtual track and occupying track, so there will be fractional occupying of some tracks. The larger the smear value (in Hartree), the faster the convergence, but the more inaccurate the calculation results. Generally, systems that converge easily are not recommended.
Apply dipole plate correction Apply dipole unit correction: When selected, external potential is added to the vacuum area of the unit. This potential counteracts the non-zero dipole moment of the battery caused by polar adsorbents in the battery (or adsorbents only on one side of the battery). This correction is especially helpful for the calculation of work function.
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