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exercises:common:neb [2022/09/08 15:21] – jglanexercises:common:neb [2022/09/08 21:16] (current) – [Nudged elastic band] jglan
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 ====== Nudged elastic band====== ====== Nudged elastic band======
-This exercise is adopted from [[exercises:2019_uzh_acpc2:ex03 | here ]], which is initially created by Kristjan Eimre and Jinggang Lan+Regtest see: 
  
 +[[https://github.com/cp2k/cp2k/tree/master/tests/NEB|cp2k/tests/NEB/]] 
 +
 +Manual see: 
 +
 +[[https://manual.cp2k.org/cp2k-2022_1-branch/CP2K_INPUT/MOTION/BAND.html | %MOTION%BAND]]
 +
 +Reference: 
 +
 +[[https://aip.scitation.org/doi/10.1063/1.1323224 | J. Chem. Phys. 113, 9978 (2000)]] for IT-NEB;
 +
 +[[https://aip.scitation.org/doi/10.1063/1.1329672 | J. Chem. Phys. 113, 9901 (2000)]] for CI-NEB
 +===== Introduction =====
 +Consider a potential energy surface (PES) as below, the goal is to find the saddle point, transition structure between reactant and prodcut. The commonly-used algorithms include [[https://manual.cp2k.org/cp2k-2022_1-branch/CP2K_INPUT/MOTION/BAND.html|NEB]],[[https://manual.cp2k.org/cp2k-2022_1-branch/CP2K_INPUT/MOTION/GEO_OPT/TRANSITION_STATE.html|DIMER]] etc
 +
 +{{:exercises:common:pes.jpg?400|}}
 +
 +<note>Maxima or Saddle Points (maximum in one direction but minimum in other directions) have one or more negative (imaginary) frequencies.
 +</note>
 +
 +Mathematically, the saddle point should fulfill the requirements: 
 +
 +1. The gradient should be zero, $\frac{dE}{dr} = 0 $
 +
 +2. The sign of Hessian should be negative,  $\frac{d^2E}{dr^2} < 0 $
 +
 +3. Only ONE negative (imaginary) frequency
 +
 +
 +
 +
 +===== Exercies =====
  
 In this exercise, we will study the $S_N2$ nucleophilic substitution reaction  In this exercise, we will study the $S_N2$ nucleophilic substitution reaction 
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 For energy and force evaluation, we will use the Parameterization Method 6 (PM6), which is a relatively inexpensive semiempirical model for electronic structure evaluation. For accurate reaction characterizations, ab initio methods, such as DFT or higher level, should be used. For energy and force evaluation, we will use the Parameterization Method 6 (PM6), which is a relatively inexpensive semiempirical model for electronic structure evaluation. For accurate reaction characterizations, ab initio methods, such as DFT or higher level, should be used.
  
-===== NEB activation barrier ===== 
  
 In order to find the activation barrier for the reaction we will use the NEB method. The NEB method provides a way to find the minimum energy path (MEP) between two different conformations of the system corresponding local potential energy minima. The MEP is a one-dimensional path on the $3N$-dimensional potential energy landscape and every point on the MEP is a potential energy minimum in all directions perpendicular to the path. MEP passes at least one saddle point and the energy of the highest saddle point is the peak of the activation barrier of the reaction. In order to find the activation barrier for the reaction we will use the NEB method. The NEB method provides a way to find the minimum energy path (MEP) between two different conformations of the system corresponding local potential energy minima. The MEP is a one-dimensional path on the $3N$-dimensional potential energy landscape and every point on the MEP is a potential energy minimum in all directions perpendicular to the path. MEP passes at least one saddle point and the energy of the highest saddle point is the peak of the activation barrier of the reaction.
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 These sections show for every replica geometry along the NEB trajectory, the distance to its neighbors and its energy. The final section corresponds to the converged NEB trajectory. These sections show for every replica geometry along the NEB trajectory, the distance to its neighbors and its energy. The final section corresponds to the converged NEB trajectory.
  
-<note>**TASK 2** +
-  * Run the NEB calculation +
-  * Find the activation barrier of the reaction in eV. +
-</note>+
  
exercises/common/neb.1662650509.txt.gz · Last modified: 2022/09/08 15:21 by jglan