18 votes

Is it necessary to optimize structures obtained from a cif file?

It depends somewhat on the properties you are interested in. Meaningful vibrational modes, for example, require that your geometry is an energy minimum for the method you are using. Since the ...
Tyberius's user avatar
  • 15.4k
16 votes
Accepted

What exactly is the "Optimizer" in CP2K geometry optimization?

The question says: I am having trouble understanding the difference between the optimizer options (CG, BFGS, LBFGS). These are three optimization algorithms that evidently are implemented in CP2K ...
Nike Dattani's user avatar
  • 34.7k
16 votes
Accepted

What is the cutting edge for open-source Force-Field generation?

ForceBalance ForceBalance is one approach which aims at making it easier to create force fields from a combination of theoretical and experimental data. I believe it's within the OpenMM framework. The ...
Cody Aldaz's user avatar
  • 7,997
15 votes
Accepted

How much does the initial geometry affect the final geometry in optimization calculations?

Alot Optimizations are all about finding the minimum in something. Typically in geometry optimization, it is about finding the minimum in energy. At a minimum the derivative of energy with respect to ...
B. Kelly's user avatar
  • 4,326
14 votes

What exactly is the "Optimizer" in CP2K geometry optimization?

Optimizer refers to the algorithm used for finding the minimum of a function. In this specific case the optimizer is referring to "geometry optimization" which seeks to find the local minimum of the ...
Cody Aldaz's user avatar
  • 7,997
12 votes

Is it necessary to optimize structures obtained from a cif file?

This is a very intriguing question. I'll answer assuming that your CIF is formed by a molecule-based crystal. The structure in such CIF has been obtained usually by the X-ray diffraction technique. ...
SalvaCardona's user avatar
  • 1,590
11 votes

What is the cutting edge for open-source Force-Field generation?

ForceBalance Cody is right, ForceBalance is designed for the task of generating custom force fields. Force fields have a lot of variability in their functional forms, representation of parameters (as ...
Lee-Ping Wang's user avatar
9 votes

How much does the initial geometry affect the final geometry in optimization calculations?

I won't go over what Charlie Crown already described in his answer, but if you don't have experimental data, you can try starting off with the experimental structure of a similar compound that has the ...
Kevin J. May's user avatar
  • 3,121
9 votes
Accepted

Hexagonal lattice optimization

This can be readily done using the Atomic Simulation Environment (ASE), if you are comfortable with Python. A tutorial for this exact purpose is described here. Another example using ASE can be found ...
Andrew Rosen's user avatar
  • 7,301
8 votes

Why is line search not popular in quasi-Newton geometry optimisers?

A trust region method is not really a replacement for a line-search optimisation, the methods are complementary. A line-search optimiser would usually proceed by taking a trial step in the direction ...
Phil Hasnip's user avatar
  • 7,022
8 votes

Relation between lattice parameter and energy for relaxations

For system with small strain condition, energy of strained system can be written in Taylor series as $$E(\epsilon)=E(0)+\frac{V_0}{2}\sum_{ijk}C_{ijkl}\epsilon_{ij}\epsilon_{kl}+...$$ In Voigt ...
Pragyandipta Mishra's user avatar
8 votes
Accepted

What's the Theory Behind Nudged Elastic Band?

The Nudged Elastic Band (NEB) method is a way to find the Minimum Energy Path (MEP) between a set of reactants and products. Some variants, like the Climbing Image (CI-NEB), also specifically find ...
Tyberius's user avatar
  • 15.4k
8 votes
Accepted

What's the Difference between Lattice Statics and Lattice Dynamics?

Lattice statics refer more to the minimum energy lattice structure such as spacegroup, lattice constant, bond distances, or any other property you can derive from a geometric standpoint on that ...
Tristan Maxson's user avatar
7 votes

How to do lattice optimization, encut optimization and Kpoint optimization in VASP?

You can start with this bash script for Aluminum to begin Note: Make sure to fix two quantities while changing third one among INCAR,...
Pranav kumar's user avatar
  • 3,969
7 votes
Accepted

How to extract lattice constants a and c from relaxed hexagonal structure using VASP?

The CONTCAR file contains the final position and velocities from a VASP run. You can find out more information from this vasp wiki page or from VASP manual. Please note, the 3rd 4th and 5th lines are ...
Aritra Mukhopadhyaya's user avatar
7 votes
Accepted

Use of genetic algorithm based methods for geometry optimization

The paper you cite has certainly left a legacy, but it is by now almost 30 years old! I think its main insight is in applying physics-agnostic, information-theoretic ideas to atomistic coordinates. (...
Shern Ren Tee's user avatar
7 votes

Is it ok to start from an identity matrix Hessian guess for optimisation?

This is a difficult question to answer, because it really depends what you mean by "OK". There is certainly no fundamental problem with an initial guess Hessian which is the identity matrix, ...
Phil Hasnip's user avatar
  • 7,022
6 votes

How can I build the wheels necessary for a quick installation of PySCFad on a "compute node"?

I finally got it working! Explanation of the error The above procedure installed the "main" branch of "pyscf_properties" rather than the "ad" branch. It seems that due ...
Nike Dattani's user avatar
  • 34.7k
6 votes

What is the X in Almlöf and Taylor's "Unified treatment of energy derivatives?"

Question "Jan Almlöf and Peter R. Taylor (link) provides little further detail, by defining U=exp(X), but not providing details how X can be calculated here." Answer $X$ is literally ...
Nike Dattani's user avatar
  • 34.7k
4 votes

Which lattice parameter should be used, the one obtained by vc-relax or the optimized value acquired through the Birch-Murnaghen equation?

I will personally recommend to use the result (lattice parameter) after the fit with the Birch-Murnaghan equation, that what people do especially the bulk modulus will be included as a result and ...
M06-2x's user avatar
  • 896
4 votes

Relation between lattice parameter and energy for relaxations

I don't have a chance to give a complete answer and this may not be as fitting since you are intending to use a planewave based code, but this paper [1] gives a good description of computing the ...
2 votes

How much energy difference could be used to distinguish optimized results from different initial geometries for the same structure?

The question makes no sense, since a solid state system might have different phases, or a molecule might have different conformers. They may all be proper local minima of the energy functional, and ...
Susi Lehtola's user avatar
  • 18.4k
2 votes

Where/when did the fields of Operations Research and Spin Physics or Molecular Dynamics begin to cross-pollinate?

The cross-pollination and exchange of ideas between the operations research and physics communities in the context of Ising optimization methods can be traced back to several key papers and ...
Jaafar Mehrez's user avatar
2 votes

Gaussian enzyme optimization fails, possible memory error?

I tried to solve the problem. Here what I did. In the input, the first part, try to select the number of CPU or Gaussian will take the default=1, and in your case you need a lot of CPUs as you can ...
Abd-Elazeem Mohamed's user avatar
2 votes

Problems with restarting an optimization file in Gaussian

The excerpt you pasted states that the SCF calculation failed, and one cannot tell when this happened. Was it at the initial geometry? You may get the calculation to work with SCF=XQC. However, I have ...
Susi Lehtola's user avatar
  • 18.4k
2 votes

Optimizing (DFT/MP2) small molecule dimers

Summarizing the OP's comment that describes how they managed to remove negative (imaginary) frequencies for their system: Ensure correct symmetry of the molecular geometry Include D3 dispersion for ...
2 votes

GAUSSIAN 16 Error with CCSD(T)

Non-gradient optimizations only work in internal coordinates, and if you only want the last H to optimize, you cannot have the B1 variable to also define atom 2.
Frank Jensen's user avatar
  • 1,716
1 vote

GAUSSIAN 16 Error with CCSD(T)

Are there any extra empty lines after the final line you've posted? In my experience, you need to add a few empty lines at the end of your input file if you want the calculation to work. In other ...
isolated matrix's user avatar
1 vote

How do you project the Hessian along a certain vector?

The comments by Tyberius were accepted as a solution by the OP, this answer is to remove the question from the "unanswered" queue. I'll delete this Community Wiki answer if Tyberius does ...

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