Questions tagged [optimization]
For questions related to theory or application of optimization techniques in matter modeling. If your question is about a specific type of optimization like geometry optimization, we have the "geometry-optimization" and "geometry" tags. Another related tag is the "numerical-convergence" tag.
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How to estimate TFLOPS for calculation in Quantum Espresso?
My question is related to this. But I am more interested in knowing if there is a way to estimate computational requirements in terms of TFLOPS.
I was talking to someone who works in hardware design, ...
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Unexpected behavior when running LAMMPS from Python
I am trying to run a series of LAMMPS input files to parameterize a system, and then using the residuals to optimize the Force Field parameters. I am able to generate the input files and run them ...
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Can we build two graphite sheets as an input file in Gaussian?
I want to optimize a system containing a metal ion in between two graphite sheets. For that can I use Gaussian software? If so how can I create the input file with two graphite sheets?
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SIESTA basis set optimization (Enthalpy vs total energy)
Using SIESTA for bulk Si (not optimized, downloaded from materialsproject.org), I am trying to optimize the DZP basis set using the PAO.EnergyShift parameter. ...
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Find the outermost peak of a function to calculate the cutoff radius for pseudopotential calculation
Problem presentation
The problem mentioned in this paper about norm conserving potentials. I cite ...
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284
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LBFGS -- Incomplete Convergence due to BadIntpln [closed]
I am doing energy minimization of a molecular system in TINKER. While doing so, I am getting the error in the title of this question. What might be my problem?
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How does the line search in geometry optimisations work?
I am trying to write a Newton-Raphson geometry optimisation script in python (Current version of my code) using the energy, gradient and Hessian from Gaussian 16. In order to reach a minimum, I would ...
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Which lattice parameter should be used, the one obtained by vc-relax or the optimized value acquired through the Birch-Murnaghen equation?
To determine the lattice parameter of a material, I did a VC-RELAX calculation using Quantum ESPRESSO, and I also applied the Birch-Murnaghen equation to obtain the optimized lattice parameter. ...
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Use of genetic algorithm based methods for geometry optimization
What are the benefits or pitfalls in using a GA based optimizer for geometry optimization instead of a more traditional Hessian based algorithm?
It can be argued that performing single point energy ...
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How realistic is the use of classical analog electronic computers in solving the Schrödinger, Hartree-Fock, and Kohn-Sham equations?
Classical binary computer
The classical binary computers, on which a Hartree-Fock (or density functional theory) calculation can be executed, already allows seeing a limit in their progress, mainly in ...
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What is the X in Almlöf and Taylor's "Unified treatment of energy derivatives?"
I have been studying the possible methods for basis set optimizations. One notable paper is "Energy-optimized GTO basis sets for LCAO Calculations. A Gradient Approach" by Knut Faegri Jr. ...
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Why is line search not popular in quasi-Newton geometry optimisers?
One of the most important quasi-Newton optimisation methods is the BFGS (which uses an iterated Hessian update scheme to avoid recalculation of the actual Hessian). Most numerical optimisation ...
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How can I build the wheels necessary for a quick installation of PySCFad on a "compute node"?
The following is the procedure I have been following:
Install PySCFad
...
3
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1
answer
116
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How do you project the Hessian along a certain vector?
I have been trying to understand the Gaussian optimiser (Berny optimiser algorithm) from what has been written in their manual. So far, I have understood most of it, but one part has been giving me ...
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ORCA failed during NEB-TS ONIOM [closed]
Thanks in advance for any help provided. I was trying to find the transition state of a diels alder reaction and considering my system's bulkiness I wanted to try a NEB calculation considering part of ...
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1
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Gaussian enzyme optimization fails, possible memory error?
I started to optimise a selected cavity of the enzyme with a metal ion using Gaussian 09 software. The basis set used for C,H,N and O atoms was 6-311+G(d) and for the Cd2+ ion was def2-tzvp. And, ...
- 409
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1
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Is it ok to start from an identity matrix Hessian guess for optimisation?
I am attempting to implement an algorithm for transition state finding (in Python, but that's not important). The algorithm is called BITSS (Binary Image-pair Transition State Search). It defines a ...
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169
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Gaussian error in optimization [closed]
I want to optimize an enzyme in the presence of a metal ion.
I started the optimization for the system in the ground state with DFT (B3LYP) method using 6-31G(d) basis set.
But, this gave an error
<...
- 409
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Gaussian calculation error when optimizing an enzyme bound with a metal ion? [closed]
I want to optimize an enzyme with a metal ion bound to the active site of the enzyme.
Using PyMOL software I placed the metal ion in the active site of the enzyme and the metal-enzyme structure was ...
- 409
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1
answer
425
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Problems with restarting an optimization file in Gaussian
I'm trying to do a geometry optimization of a paraquat molecule ontop of a goldbulk consisting of four layers. Two of those layers are fixed. The input file looks like the following:
...
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What are the types of density matrix mixing methods?
I would like to know what are the different types of mixing procedures to be applied to the density matrix (Broyden mixing, Pulay mixing) and their pros and cons?
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Optimizing (DFT/MP2) small molecule dimers
I'm attempting to optimize n-alkane dimers using MP2/DFT in Gaussian09. However the first one or two frequencies are always negative. Can these modes be ignored or do I need to do a tighter ...
6
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2
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Relation between lattice parameter and energy for relaxations
We have been wanting to do relaxation of lattice parameters as a function of the energy. I want to know the mathematical expression for this, and also the theoretical background related to this method....
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What's the Theory Behind Nudged Elastic Band?
I'm interested in doing some calculations to model the interstitial addition of nitrogen into a structure and I'm thinking of using Nudged Elastic Band to do it.
From what I have read you start with ...
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What's the Difference between Lattice Statics and Lattice Dynamics?
For example, in something like the General Utility Lattice Program, you perform structural optimisation and then use phonons to calculate properties like elastic constants etc.
The latter part seems ...
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How to do lattice optimization, encut optimization and Kpoint optimization in VASP?
What is the procedure to do lattice optimization, encut optimization and kpoint optimization in VASP?
Thank you in advance.
- 539
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1
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How much energy difference could be used to distinguish optimized results from different initial geometries for the same structure?
Is there a threshold? Could I say that my final geometries are the same with 'energy difference = 0.05 meV/atom' ?
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How to extract lattice constants a and c from relaxed hexagonal structure using VASP?
Taking a bulk WS$_2$ (bilayer) structure and relaxing it with ISIF=3 and IVDW=10 (DFT-D2 method) using the VASP code. Then ...
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2
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What is the cutting edge for open-source Force-Field generation?
The adoption of atom-typing allowed for the creation of incredibly widely used force-fields (FF) such as GROMOS/AMBER/OPLS and many more. Because of the assumptions required in Molecular Mechanical (...
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2
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654
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How much does the initial geometry affect the final geometry in optimization calculations?
This might be a stupid question but to what extent will the initial configuration of a bulk phase geometry optimization calculation affect the final geometry? Most places say to start with ...
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What exactly is the "Optimizer" in CP2K geometry optimization?
I'm just now starting to use the program CP2K, and I am having trouble understanding the difference between the optimizer options (CG, BFGS, LBFGS). I have seen ...
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2
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Is it necessary to optimize structures obtained from a cif file?
Crystallographic Information Files (CIF) are, in general, obtained from experimental measurements. Since the information originated from real samples, is it mandatory to relax the structure in order ...
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1
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Hexagonal lattice optimization
I have downloaded POSCAR file for "WS2" from "materials project website". I want to do lattice optimization, draw "Energy versus lattice parameters" curves, and calculate Bulk modulus through Birch–...
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Where/when did the fields of Operations Research and Spin Physics or Molecular Dynamics begin to cross-pollinate?
Operations Research is a field of mathematics in which optimal or near-optimal solutions are sought for complicated problems.
In the modeling of materials, we often optimize Ising models, in which the ...