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--- howto:ic-qmmm [2017/09/29 15:26] – [Print options] dgolze
+++ howto:ic-qmmm [2024/01/03 13:11] – oschuett
@@ Line 1: / Line 1: @@
-====== How to run IC-QM/MM simulations for interface systems ======
+This page has been moved to: https://manual.cp2k.org/trunk/methods/qm_mm/builtin.html
-===== Introduction =====
-The image charge (IC) augmented QM/MM model in CP2K is designed for the simulation of adsorbate-metal systems. The adsorbate is treated by QM whereas the metallic substrate is described by classical force fields, see <imgref fig:nitrobenz>.  The interactions between metal and adsorbate are described at the MM level of theory accounting for the polarization of metal and adsorbate by an IC approach. The charge distribution $\rho_m$ in the metal is modeled by a set of Gaussian charges (image charges) centered at the metal atoms,
-<imgcaption fig:nitrobenz |Nitrobenzene molecule on Au111. Separation in subsystems for IC-QM/MM.>{{ icqmmm.png?300x200}}</imgcaption>
-\begin{equation}
- \rho_m(\mathbf{r})= \sum_{a}{c_a g_a(\mathbf{r,R}_a)},
- \label{eq:rhom}
-\end{equation}
-where $\mathbf{R}_\mathrm{a}$ is the position of metal atom $a$ and $g_a$ the spherical Gaussian function located at $a$. The expansion coefficients $c_a$ are unknown and determined in a self-consistent procedure imposing the constant-potential condition within a metal, i.e. the sum of $V_H(\mathbf{r})$ generated by the charge density $\rho(\mathbf{r})$ of the molecule and $V_m(\mathbf{r})$ generated by $\rho_m$ has to be constant within the metal,
-\begin{equation}
- V_{H}(\mathbf{r})+V_m(\mathbf{r})=\int \frac{\rho(\mathbf{r}')+\rho_m(\mathbf{r}')}{|\mathbf{r}'-\mathbf{r}|}
- d\mathbf{r}'=V_0.
- \label{eq:const_pot}
-\end{equation}
-In this expression $V_0$ is a constant potential that can be different from zero, if an external potential is applied.
- The implementation is embedded in the Gaussian and plane waves scheme of CP2K and thus naturally suited for periodic systems. Details of the theory and implementation are described in [[doi>10.1021/ct400698y | J. Chem. Theory Comput., 9, 5086 (2013)]].\\
-===== Basic input =====
-The IC method is specified in the [[inp>FORCE_EVAL/QMMM|QMMM]] section by
-<code cp2k>
-&QMMM
- :
- :
- &IMAGE_CHARGE
-  MM_ATOM_LIST 1..576
-  EXT_POTENTIAL 0.0
- &END IMAGE_CHARGE
-&END QMMM
-</code>
-The keyword [[inp>FORCE_EVAL/QMMM/IMAGE_CHARGE#MM_ATOM_LIST|MM_ATOM_LIST]] defines the list of MM atoms that carrying an image charge. These are typically all metal atoms. [[inp>FORCE_EVAL/QMMM/IMAGE_CHARGE#EXT_POTENTIAL|EXT_POTENTIAL]] corresponds to $V_0$ above and is set to 0.0V by default. Note that the QM and MM box must have the same size for an IC-QM/MM calculation.
-===== Print options =====
-Detailed energy information and the normalized IC coefficients $q_a$ can be printed out by [[inp>FORCE_EVAL/QMMM/PRINT/IMAGE_CHARGE_INFO|IMAGE_CHARGE_INFO]]. The normalized IC coefficients are defined as $q_a =  c_a\left(\frac{\alpha}{\pi}\right)^{-\frac{3}{2}}$, where $\alpha$ is the width of the Gaussian.
-<code cp2k>
-&QMMM
- :
- :
- &PRINT
-  &IMAGE_CHARGE_INFO
-  &END
- &END PRINT
-&END QMMM
-</code>
-===== Advanced input options =====
-Additional keywords that can be set in [[inp>FORCE_EVAL/QMMM/IMAGE_CHARGE|IMAGE_CHARGE]] are:
-<code cp2k>
-&IMAGE_CHARGE
-  MM_ATOM_LIST 1..576
-  EXT_POTENTIAL 0.0
-  WIDTH 3.5
-  IMAGE_MATRIX_METHOD MME
-  DETERM_COEFF CALC_MATRIX
-  RESTART_IMAGE_MATRIX .false.
-&END IMAGE_CHARGE
-</code>
- [[inp>FORCE_EVAL/QMMM/IMAGE_CHARGE#WIDTH|WIDTH]] refers to the width $\alpha$ of the Gaussian $g_a$, which is the only adjustable parameter in our IC model. The energies and gradients do not depend on $\alpha$ for values larger than 3.0 Å$^{-2}$. Small values of $\alpha$ correspond to very broad Gaussians, which will lead to technical artifacts. Extremely large values are not recommended, too.\\
-[[inp>FORCE_EVAL/QMMM/IMAGE_CHARGE#IMAGE_MATRIX_METHOD|IMAGE_MATRIX_METHOD]] determines how the IC matrix $T_{ab}$, Eq. 11 in [[doi>10.1021/ct400698y | J. Chem. Theory Comput., 9, 5086 (2013)]], is calculated. "GPW" corresponds to the algorithm shown in Fig. 1 in J. Chem. Theory Comput., 9, 5086 (2013), whereas "MME" is an integral scheme that has been recently implemented and that is significantly faster. \\
-[[inp>FORCE_EVAL/QMMM/IMAGE_CHARGE#DETERM_COEFF|DETERM_COEFF]] specifies how the expansion coefficients $c_a$ are determined. With CALC_MATRIX, $T_{ab}$ is calculated and the linear set of equations is solved. ITERATIVE avoids calculation of $T_{ab}$ in each SCF step by using an iterative conjugate gradient scheme. The new integral scheme MME evaluates the matrix $T_{ab}$ very quickly, i.e. the iterative solutions is not required here, thus set always CALC_MATRIX. \\
-[[inp>FORCE_EVAL/QMMM/IMAGE_CHARGE#RESTART_IMAGE_MATRIX|RESTART_IMAGE_MATRIX]] can be used to restart $T_{ab}$ for an MD simulation if ITERATIVE is set. \\
-**Note that setting of these additional keywords is typically not required.** The default settings are fine.
-===== Typical setup =====
-The typical setup for an IC-QM/MM simulation is as follows
-   * adsorbed molecules described by DFT
-   * metal is constrained or described by an embedded atom model (EAM)
-   * Interactions between QM and MM:
-     * Pauli repulsion, dispersion etc. modeled by force fields e.g. Lennard Jones
-     *electrostatic interaction/induction: IC model
-===== Example input files =====
-The first input example is a single guanine molecule on an Au111 surface using a modified Born-Mayer potential to describe Pauli repulsion and dispersion between molecule and metal. The second example is a single water molecule on Pt111. The interactions between water and metal are modeled by the Siepmann-Sprik potential, see [[doi>10.1063/1.469429 | J. Chem. Phys., 102, 511 (1995)]].
-   * Guanine@Au111: {{:howto:au111_guanine.tar.gz|Au111_guanine.tar.gz}}
-   * H2O@Pt111: {{:howto:pt111_1h2O.tar.gz|Pt111_1H2O.tar.gz}}