Questions tagged [geometry-optimization]
Questions about finding the molecular or material geometry that has the lowest energy.
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siesta: gold atomic layer splitting during geometry optimization of MoS2 and gold heterostructure
The heterstructure was made by placing three layers of gold on top of a MoS2 monolayer with a (111) surface orientation of gold crystal,the (111) surfaces of metals are strained to match the optimized ...
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Geometry optimization of two or more different interacting molecules
My question is concerned with the initial tweaking of two or more different molecules to get the optimized geometry. For example, I have one water molecule and a carbon nanotube with similar length ...
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Are there any software packages to find the minimum number of constraints to fix a molecule structure?
I wanted to know if there are any modules or packages which help in identifying the bonds which should be fixed to make the molecule rigid. For example in $\ce{H2O}$ there are just three (trivial), $\...
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Physical Properties from Variable Cell Relax Calculations in Quantum ESPRESSO
I want to know what physical quantities can I calculate using the output file of variables cell relax calculations (vc-relax) in Quantum ESPRESSO or using its post processing tools.
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How to implement constrained optimisation with Lagrange multiplier?
I am trying to implement a version of the Lagrange multiplier in delocalised internal coordinates as described by Jon Baker (J. Comput. Chem. 18, 1997, 1079). A description of the method that's not ...
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How may I get reasonable lattice constants of hybrid halide perovskite material ((BA)2PbBr4 here) using SIESTA?
I am relaxing the structures of hybrid halide perovskite material,(BA)2PbBr4 here. I tried to use GGA-PBE or LDA-PW92 exchange functionals, and pseudopotential files come from ...
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Issue in Converging a FCC Pd crystal on VASP, errors in body text
I have been struggling optimizing a specific structure in VASP. But I keep getting errors, and it only runs for like 3 seconds. These are a few errors I get. Sometimes it doesn't have the final one ...
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What software is fit for calculating an atomic and electronic structure of a newly formed nanocluster after injecting impurities into an initial one?
Let's suppose there is a nanocluster and its structrure is known. The problem is to inject impurities into this nanocluster. The impurities can be injected in different quantitites but consist only of ...
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Geometry optimization with background charges in Gaussian with charge keyword
Gaussian requires the opt=z-matrix option when performing geometry optimization with the charge keyword. As can be seen in the following section from Gaussian's website:
To perform geometry ...
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Negative phonon calculation
Hi everyone I'm here again to ask you if you know what I can modify to improve my phonon calculation of rutile
I think my issues are rooted in not-so-good cell optimizations, I optimize my starting ...
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Spin-orbit coupling(SOC) in geometry optimisation
When I tried including SOC during the optimization of InBi lattice constants, the lattice constant increased from 4.6 Å (without SOC) to more than 6 Å (with SOC), which seems like an 'incorrect' ...
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Consequences of starting a new relaxation calculation from the final coordinates of an interrupted run
In order to address oscillating total force during an ongoing relaxation calculation in Quantum ESPRESSO, I've found it effective to interrupt the current run and commence a new relaxation calculation ...
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Geometry optimisation with low frequency modes
I am currently running a transition state (TS) optimisation in ORCA. One of the issues that I am seeing is that whenever the Hessian (updated or calculated) has an eigenvalue with small magnitude (i.e....
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Correct method for structure optimization using DFT tools
Lets's say I want to start off DFT calculations for a material whose experimental cell constants are known. So I have two ways to get the correct structure to later on calculate, say, band structure ...
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How can i do a variable cell relaxation under the influence of constant field in GPAW?
As a continuation of my previous question, I would like to do variable cell relaxation of BaTiO3 under the influence of a constant electric field. The script I've used is given below:
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Convergence Issues in VASP Relaxation Calculations
I'm encountering convergence issues in my VASP relaxation calculations, specifically related to the message 'BRIONS problems: POTIM should be increased.' I've tried adjusting POTIM, but I'm still ...
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ASE GPAW variable cell relaxation
Ive been trying to do a vc relax using GPAW and ASE on the BaTiO3 unitcell. The input file is as below:
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Is it possible to do a vc-relax calculation using GPAW?
I wanted to do a variable-cell relaxation calculation using GPAW (similar to the one present in quantum ESPRESSO). It would be nice if I could get pointers on how to approach this.
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Help regarding Geometry Optimization of a bimetallic surface
I am trying to perform a geometry optimization (GEO_OPT) of a FCC 111 Pt$_{0.5}$Au$_{0.5}$ bimetallic surface (10x10x3) generated from ASE, with a lattice parameter of 3.9 $\overset{\circ}{\mathrm{A}}$...
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MOPAC: Is there a simple way to display geometry trajectories
I would like to display MOPAC geometry trajectories for structure minimization and transition state searching.
Is there a simple way to achieve that ? Avogadro can display only final geometry from ...
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Different QM and MM gradients in geometry optimization
I calculated the single point energy of some small molecule using the PM7 method (with COSMO solvation model) in MOPAC and calculated the gradients. Then I calculated MM potential energy with ...
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Si Thin film phonon dispersion with negative frequency
I have a Si slab of thickness 0.5nm for which I want to calculate the phonon dispersion. The unitcell has 5 atomic layers and 10 Si atoms with vacuum of 10A in z-direction (a 2x2 supercell is shown ...
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Prerelaxation before AIMD with VASP
I am investigating a bulk structure by ab initio molecular dynamics (AIMD) implemented in VASP.
I was wondering, how to choose the initial geometry (= POSCAR file) to run the AIMD simulation. In the ...
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Making Deuterium POTCAR file for optimization in VASP software
How to make Deuterium POTCAR file? i have Hydrogen POTCAR file.
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Why is this geometry optimization in Gaussian not working for a system containing an amino acid, a water molecule and a metal (Pb) ion?
I started optimising a system containing amino acid residue, water molecule and a toxic metal ion, in proving a supposed reaction steps that might take place in inhibiting enzyme activity. The ...
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What is the best way to optimize molecules with 8000 atoms. This includes C,H,O,N,Si
My molecule includes C,H,O,N,Si
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How do I do a PES (potential energy surface) scan for the excited electronic state?
I know how to do a PES scan for a ground electronic state. But for the nth-excited state, is it the same (i.e. an excited state optimization and just rotating the dihedral to simulate the ...
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Disappearing vacuum layer when relaxing bilayered hBN with VASP [closed]
I'm doing geometry optimization of bilayer h-BN, a 72-atom supercell (6x6x1) with vacuum thickness of 20 Å, and I set the parameters in INCAR as below:
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Which is the best way to plot E_tot vs Lattice graph for structures with two lattice parameters?
I made the graph using the ratio between the parameters x E_tot (trigonal structure), but I would like to know if there is a better way to do this.
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Singlet excited state optimization gaussian issue
I hope someone here can help me with some TD-DFT calculations. I am trying to calculate the excited state optimised structures and energies of some Germanium compounds. Firstly, I run a TD calculation ...
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Incorporating Phonon Calculations as a Criterion for Geometrical Relaxation
In the context of first-principles calculations, such as DFT, lattice vibrations are often determined through phonon calculations, providing valuable insights into the stability and dynamics of ...
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Large energy differences across successive geometry optimization steps in SIESTA
I am trying to calculate adsorption energies of acetophenone on a 6x6x3 nickel surface with about 12 Angstrom of vacuum above it using SIESTA 5.
I have arranged the molecule so that the ring plane is ...
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Wrong lattice parameter of CeO2 after structure relaxation with VASP
I am calculating the lattice parameter of CeO2 with VASP, but the optimized lattice parameter is wrong according to many references (Physical Review B 75, 035109 (2007); The Journal of Chemical ...
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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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Computing proton-proton potentials for infinite periodic materials
For electronic structure calculation, when optimizing the wavefunction for an infinite periodic material, the proton-proton energy is needed to monitor the convergence of the SCF loop.
How is the ...
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Constrained geometry optmization: Molecule interacts with its surroundings
I have a water cluster(suppose) generated from MD run. Now, I want to optimize the geometry of only one water molecule of interest using QC methods (e.g. B3LYP/6-31+G(d,p)). I intend that the water ...
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Discrepancy between Force Convergence in Geometrical Optimization and SCF Calculation in VASP: Reasons and Troubleshooting Suggestions
During a geometrical optimization of ions and lattice parameters in VASP, the forces acting on atoms were minimized to less than 0.01 eV/Å. However, when performing the subsequent self-consistent ...
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Structural phase transition under uniaxial strain
I am trying calculate a strain-induced phase transition in some weakly correlated crystalline material using Quantum ESPRESSO (QE). The compound has two (experimentally observed) phases, one of which ...
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Optimal choice between ISIF = 3 and ISIF = 4 for lattice parameter and atomic position relaxation in VASP calculations
In my VASP calculations, I am interested in simultaneously optimizing both the lattice parameters and atomic positions of my system.
I understand that using ISIF = 3 allows for relaxation of both ...
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How to pre-optimize metal-organic complexes in RDKit using UFF?
I have run into a particular problem while trying to automate my input file generation for ORCA calculations. Apparently, I either do not fully understand how SMILES strings work, or I am demanding ...
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Quantum Espresso optimization calculation not converging
I have been trying to optimize the geometry of a copper based metal halide perovskite. I opened the CIF file using BURAI GUI and generated the VC-RELAX input file.
I have increased the steps to be 200 ...
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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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How many non-redundant internal coordinates are needed for optimisation of linear molecule?
I have been working to implement optimisation in internal coordinates (for a transition state search software I am working on). However, the implementation details are almost always glossed over in ...
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UseSym Keyword in ORCA fails to find appropriate number of SALCs
I am trying to run some geometry optimizations in ORCA 5.0.4 and I am using the UseSym keyword to ensure that my molecules retain Cs Symmetry during optimization. ...
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ORCA crashes because of RI approximation?
I am doing a geometry optimization for a cationic imidazolate-zinc complex.
I'm trying to run an optimization using this input file. It uses the RI approximation.
ORCA seems to be running fine until ...
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Is it okay to use semi-empirical methods to optimize structures if I perform high-level energy calculations?
For non-covalent systems comprised of small-molecule monomers, folks are usually interested in understanding the interaction and binding energies of small (gas-phase) clusters ... things like $\ce{X(...
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How to select charge and multiplicity for macro-molecules?
In optimising proteins with DFT/B3LYP, how can we detect the charge and multiplicity of the protein?
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Cannot optimize hexa aqua Cu(II) and Fe(III)
I try to optimize very simple systems - hexa aqua Cu(II) and hexa aqua Fe(III) - in Gaussian 16. The inputs are provided in the end of the post. Unfortunately, the geometry optimization never finishes ...
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