howto:gfn1xtb
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howto:gfn1xtb [2022/07/19 10:27] – ahehn | howto:gfn1xtb [2022/07/19 12:03] – ahehn | ||
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====== How to run a GFN1-xTB calculation ====== | ====== How to run a GFN1-xTB calculation ====== | ||
- | This is a short tutorial on how to run GFN1-XTB computations. The details on the theory and the original implementation by Grimme can be found in [[https:// | + | This is a short tutorial on how to run GFN1-xTB computations. The details on the theory and the original implementation by Grimme can be found in [[https:// |
- | Please cite this paper if you were to use the GFN1-XTB module. | + | Please cite this paper if you were to use the GFN1-xTB module. |
===== Brief theory recap ===== | ===== Brief theory recap ===== | ||
- | The semi-empirical GFN1-xTB energy expression comprises contributions due to electronic (el), atom-pairwise repulsion (rep), dispersion (disp), and halogen-bonding (XB) terms, | + | The semi-empirical GFN1-xTB energy expression comprises contributions due to electronic (EL), atom-pairwise repulsion (REP), dispersion (DISP), and halogen-bonding (XB) terms, |
- | \begin{equation}\label{gfnxtb1_energy_expression} | + | \begin{equation}\label{gfnxtb1_plus_nonbonded} |
\begin{aligned} | \begin{aligned} | ||
- | E_{\rm{\tiny{GFN1-xTB}}} = E_{\rm{\tiny{EL}}} + E_{\rm{\tiny{REP}}} + E_{\rm{\tiny{DISP}}} + E_{\rm{\tiny{XB}}} + E_{\rm{\tiny{NONBOND}}}\, . | + | E_{\rm{\tiny{GFN1-xTB}}} = E_{\rm{\tiny{EL}}} + E_{\rm{\tiny{REP}}} + E_{\rm{\tiny{DISP}}} + E_{\rm{\tiny{XB}}} \, . |
\end{aligned} | \end{aligned} | ||
\end{equation} | \end{equation} | ||
Line 18: | Line 18: | ||
\begin{equation}\label{electronic_energy} | \begin{equation}\label{electronic_energy} | ||
\begin{aligned} | \begin{aligned} | ||
- | E_{\rm{\tiny{el}}} = \sum_i^{\rm{\tiny{occ}}} n_i \langle \Psi_i | h_0 | \Psi_i \rangle + \frac{1}{2} \sum_{A,B} \sum_{{l}^A}\sum_{{l' | + | E_{\rm{\tiny{EL}}} = \sum_i^{\rm{\tiny{occ}}} n_i \langle \Psi_i | h_0 | \Psi_i \rangle + \frac{1}{2} \sum_{A,B} \sum_{{l}^A}\sum_{{l' |
\end{aligned} | \end{aligned} | ||
\end{equation} | \end{equation} | ||
Line 40: | Line 40: | ||
\begin{equation}\label{repulsion} | \begin{equation}\label{repulsion} | ||
\begin{aligned} | \begin{aligned} | ||
- | E_{\rm{\tiny{rep}}} = \sum_{AB} \frac{Z_A^{\rm{\tiny{eff}}} Z_B^{\rm{\tiny{eff}}} }{R_{AB}} \exp^{- (\alpha_A \alpha_B)^{1/ | + | E_{\rm{\tiny{REP}}} = \sum_{AB} \frac{Z_A^{\rm{\tiny{eff}}} Z_B^{\rm{\tiny{eff}}} }{R_{AB}} \exp^{- (\alpha_A \alpha_B)^{1/ |
\end{aligned} | \end{aligned} | ||
\end{equation} | \end{equation} | ||
Line 47: | Line 47: | ||
3. Dispersion is included by the well-established D3 method in the BJ-damping scheme[[https:// | 3. Dispersion is included by the well-established D3 method in the BJ-damping scheme[[https:// | ||
- | 4. Corrections for element-specific interactions are possible using either a halogen-bonding correction term (XB) or a generic nonbonding potential correction (NONBOND). | + | 4. Corrections for element-specific interactions are possible using either a halogen-bonding correction term (XB) or a generic nonbonding potential correction (NONBOND). |
+ | |||
+ | \begin{equation}\label{gfnxtb1_energy_expression} | ||
+ | \begin{aligned} | ||
+ | E_{\rm{\tiny{GFN1-xTB+NONBOND}}} = E_{\rm{\tiny{GFN1-xTB}}} + E_{\rm{\tiny{NONBOND}}} \, . | ||
+ | \end{aligned} | ||
+ | \end{equation} | ||
Line 57: | Line 63: | ||
* '' | * '' | ||
* '' | * '' | ||
+ | * '' | ||
The additional keywords '' | The additional keywords '' | ||
Line 65: | Line 72: | ||
==== GFN1-xTB ground-state energy for ==== | ==== GFN1-xTB ground-state energy for ==== | ||
+ | The following input is an examplary standard input for calculating GFN1-xTB ground-state energies. | ||
+ | |||
+ | <code - periodic.inp> | ||
+ | |||
+ | &GLOBAL | ||
+ | RUN_TYPE | ||
+ | PROJECT_NAME xtb | ||
+ | PRINT_LEVEL | ||
+ | PREFERRED_DIAG_LIBRARY SL | ||
+ | &END GLOBAL | ||
+ | & | ||
+ | | ||
+ | &DFT | ||
+ | &QS | ||
+ | | ||
+ | & | ||
+ | CHECK_ATOMIC_CHARGES F ! Keyword to check if Mulliken charges are physically reasonable | ||
+ | DO_EWALD | ||
+ | USE_HALOGEN_CORRECTION T ! Element-specific correction for halogen interactions (Cl, Br) with (O, N) | ||
+ | & | ||
+ | &END QS | ||
+ | &SCF | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | | ||
+ | | ||
+ | & | ||
+ | &END SCF | ||
+ | & | ||
+ | &SUBSYS | ||
+ | & | ||
+ | COORD_FILE_FORMAT | ||
+ | COORD_FILE_NAME | ||
+ | CONNECTIVITY OFF | ||
+ | & | ||
+ | &END CENTER_COORDINATES | ||
+ | & | ||
+ | &CELL | ||
+ | ABC 21.64 21.64 21.64 | ||
+ | ALPHA_BETA_GAMMA 90.0 90.0 90.0 | ||
+ | PERIODIC XYZ | ||
+ | &END CELL | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | |||
+ | </ | ||
+ | |||
+ | The so-obtained output is listing information on the chosen system-specific parameters. Note that parameters can be changed manually by adding a '' | ||
+ | |||
+ | <code - cp2k> | ||
+ | |||
+ | ##### ##### | ||
+ | # | ||
+ | # | ||
+ | # | ||
+ | # | ||
+ | # | ||
+ | #### # ##### # ## ## | ||
+ | |||
+ | |||
+ | xTB| Parameter file xTB_parameters | ||
+ | xTB| Basis expansion STO-NG | ||
+ | xTB| Basis expansion STO-NG for Hydrogen | ||
+ | xTB| Halogen interaction potential | ||
+ | xTB| Halogen interaction potential cutoff radius | ||
+ | xTB| Nonbonded interactions | ||
+ | xTB| D3 Dispersion: Parameter | ||
+ | xTB| Huckel constants ks kp kd 1.850 | ||
+ | xTB| Huckel constants ksp k2sh 2.080 2.850 | ||
+ | xTB| Mataga-Nishimoto exponent | ||
+ | xTB| Repulsion potential exponent | ||
+ | xTB| Coordination number scaling kcn(s) kcn(p) kc | ||
+ | xTB| Electronegativity scaling | ||
+ | xTB| Halogen potential scaling kxr kx2 1.300 0.440 | ||
+ | |||
+ | </ | ||
+ | |||
+ | Analogously to any other self-consistent field optimization (SCF) method, the output also includes the energy and convergence during the SCF steps with the finally converged GFN1-xTB energy. | ||
+ | |||
+ | <code - cp2k> | ||
+ | |||
+ | SCF WAVEFUNCTION OPTIMIZATION | ||
+ | |||
+ | ----------------------------------- OT --------------------------------------- | ||
+ | Minimizer | ||
+ | in the iterative subspace | ||
+ | | ||
+ | safer DIIS on | ||
+ | Preconditioner : FULL_SINGLE_INVERSE : inversion of | ||
+ | H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T | ||
+ | Precond_solver : DEFAULT | ||
+ | stepsize | ||
+ | eps_taylor | ||
+ | ----------------------------------- OT --------------------------------------- | ||
+ | |||
+ | Step | ||
+ | ------------------------------------------------------------------------------ | ||
+ | 1 OT DIIS | ||
+ | 2 OT DIIS | ||
+ | 3 OT DIIS | ||
+ | 4 OT DIIS | ||
+ | 5 OT DIIS | ||
+ | 6 OT DIIS | ||
+ | 7 OT DIIS | ||
+ | 8 OT DIIS | ||
+ | 9 OT DIIS | ||
+ | 10 OT DIIS | ||
+ | 11 OT DIIS | ||
+ | 12 OT DIIS | ||
+ | 13 OT DIIS | ||
+ | 14 OT DIIS | ||
+ | 15 OT DIIS | ||
+ | |||
+ | *** SCF run converged in 15 steps *** | ||
+ | |||
+ | |||
+ | Core Hamiltonian energy: | ||
+ | Repulsive potential energy: | ||
+ | Electronic energy: | ||
+ | DFTB3 3rd order energy: | ||
+ | Dispersion energy: | ||
+ | |||
+ | Total energy: | ||
+ | |||
+ | outer SCF iter = 1 RMS gradient = | ||
+ | outer SCF loop converged in 1 iterations or 15 steps | ||
+ | |||
+ | </ | ||
==== Adding a generic correction potential ==== | ==== Adding a generic correction potential ==== | ||
+ | |||
+ | It is possible to add a generic non bonded correction potential. The potential form can be chosen freely and needs to be specified by adding the keyword '' | ||
+ | |||
+ | <code - periodic_with_generic_correction_potential.inp> | ||
+ | |||
+ | &GLOBAL | ||
+ | RUN_TYPE | ||
+ | PROJECT_NAME xtb | ||
+ | PRINT_LEVEL | ||
+ | PREFERRED_DIAG_LIBRARY SL | ||
+ | &END GLOBAL | ||
+ | & | ||
+ | | ||
+ | &DFT | ||
+ | &QS | ||
+ | | ||
+ | & | ||
+ | CHECK_ATOMIC_CHARGES F | ||
+ | DO_EWALD | ||
+ | USE_HALOGEN_CORRECTION T | ||
+ | DO_NONBONDED T ! Possible option to include a generic non-bonded potential | ||
+ | & | ||
+ | &GENPOT | ||
+ | ATOMS Kr Br | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | RCUT 40.5 | ||
+ | &END GENPOT | ||
+ | & | ||
+ | & | ||
+ | &END QS | ||
+ | &SCF | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | | ||
+ | | ||
+ | & | ||
+ | &END SCF | ||
+ | & | ||
+ | &SUBSYS | ||
+ | & | ||
+ | COORD_FILE_FORMAT | ||
+ | COORD_FILE_NAME | ||
+ | CONNECTIVITY OFF | ||
+ | & | ||
+ | &END CENTER_COORDINATES | ||
+ | & | ||
+ | &CELL | ||
+ | ABC 21.64 21.64 21.64 | ||
+ | ALPHA_BETA_GAMMA 90.0 90.0 90.0 | ||
+ | PERIODIC XYZ | ||
+ | &END CELL | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | |||
+ | </ | ||
+ | |||
+ |
howto/gfn1xtb.txt · Last modified: 2024/01/03 13:22 by oschuett