Questions tagged [geometry-optimization]
Questions about finding the molecular or material geometry that has the lowest energy.
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questions
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59 views
Geometry optimization using DFT
I have been attempting to optimize the structure of a Si nanowire using SIESTA. The original structure fed into the optimization is as follows.
Once it is optimized, the structure would change to ...
6
votes
2answers
244 views
Geometry optimization with Moller-Plesset MP4
Can we optimize a molecular structure using Moller-Plesset MP4 method on GAUSSIAN software? If yes what keyword do we have to add?
6
votes
1answer
84 views
How to eliminate imaginary frequencies during a Gaussian geometry optimization?
When conducting a minimization on Gaussian software, What are the procedures used to eliminate imaginary frequencies if we have already found a stationary point? Are there any keywords that would help ...
3
votes
0answers
28 views
Simple Pt111 slab not converging using Quantum Espresso
I would like to perform a "vc-relax" calculation on a simple 3x4x5 $\ce{Pt}111$ slab, this calculation is running well but as soon as I add the ESM ...
5
votes
1answer
51 views
Variable Cell Optimization of Halfnium Crystal
Reference: Density Functional Theory: A Practical Introduction, David Sholl, Janice A. Steckel, Chapter 2, Page No. 46
Hf is experimentally observed to be an hcp metal with c/a 1.58. Perform ...
11
votes
1answer
146 views
How would one find a material's equilibrium structure at any specific temperature?
Let's take an example of a simple FCC material, a binary alloy. Above absolute zero K, the alloy will start to disorder and become an FCC solid solution. The alloy would develop defects as it ...
5
votes
2answers
154 views
SCF not converging during RHF/STO-3G geometry optimisation
I'm new in the field of QM methods and I've run into a problem for which I can't find a solution online.
I have tried with different basis sets, I've raised the maximum number of iterations and number ...
3
votes
1answer
67 views
How to do a proper relaxation of the multicomponent structure?
I have a beta Ti (Space Group 229) structure with 16 atoms, I prepared 15 disordered TiNb structures with 5 atoms of Nb. I did it using VASPKIT. However, before the ...
2
votes
1answer
44 views
Determining the geometry of UOx and WOx for (x=1-3)
Is there a way to work out the geometries for the $\ce{UO_x}$ and $\ce{WO_x}$ species for ($x=1-3$).
I know that deducing the multiplicity (the number of unpaired electrons) in d and f block ...
5
votes
0answers
54 views
How to calculate energy gradient and Hessian with respect to only a few internal coordinates using Gaussian?
I would like to form the (numerical) gradient and the Hessian of the total electronic energy with respect only to a few internal coordinates (namely, the six intermolecular coordinates of a weakly ...
14
votes
2answers
263 views
What's the best quantum chemistry output parser for the command line?
This question is about tools like Open Babel. Are there any good command-line parsers for quantum chemistry program outputs? A good Python library could come in as a close second.
I am interested e.g. ...
5
votes
1answer
61 views
Define a geometry region using 'for' loop in MuMax3
I was trying to define regions using a 'for' loop.
Please find the regions:
...
6
votes
2answers
441 views
Analytic Hessian at the level of full CI?
This is a follow-up question to my previous question: Computing analytic derivatives of molecular Hamiltonians obtained from solving Hartree-Fock equations.
After looking at various quantum chemistry ...
9
votes
2answers
93 views
Is it possible to do a Gaussian redundant scan with some fixed bonds?
I'm trying to do a redundant PES scan of a hydrogen abstraction in a Gaussian job while maintaining the rest of the system fixed. I need to scan the coordinate where H5 approaches to H6, maintaining ...
5
votes
2answers
77 views
How to use fractional numbers as arguments for keywords in Gaussian input?
I have used both Gaussian09 and Gaussian16 and one thing that seemed unusual to me is that I was unable to enter any fractional number as one of the arguments for a keyword in the Gaussian input file.
...
11
votes
1answer
133 views
Why does Gaussian ignore the opt=maxcycles keyword for optimizations?
I have been using both Gaussian09 and Gaussian16 recently to optimize some metal complexes. The Gaussian manual (for both versions) indicates that the maximum number of steps in a geometry ...
6
votes
0answers
75 views
How to optimize the geometry of beta PHB in VASP?
I would like to calculate the elastic constants of beta PHB. From this paper. I know that it has P3221 space group. The beta PHB has upward and downward chains, which exist at one lattice site with 50%...
11
votes
1answer
304 views
Choice of coordinate system for geometry optimization
For geometry optimization, most QM codes tend to use internal coordinates. Most codes also support Cartesian coordinates. I have always heard the usual "use Cartesian as a last resort, always use ...
14
votes
5answers
719 views
Are dispersion correction methods for DFT (such as D3) useful for geometry optimization?
For what I know the DFT-D3 method or similar corrections that take into account dispersion effect, add this type of contribution through calculation of atom pairwise interactions at the end of an ...
6
votes
1answer
84 views
Gaussian: Transition state convergence question
I am running a TS computation in Gaussian 16. It performs several steps.
At the end of each there is a summary on whether Maximum Force, ...
22
votes
3answers
1k views
Geometry optimization: what happens in the algorithm?
Geometry optimization using density functional theory (DFT) is done by moving the atoms of a molecule to get the most stable structure with the lowest possible ground state energy. My question is what ...
9
votes
1answer
157 views
SCAN-RVV10 geometry optimization
I'm using SCAN-RVV10 to optimize the hexagonal-BN but the optimized geometry doesn't look true as the calculated interlayer distance is far smaller than the experimental value(exp=3.35 Aangstrom, calc=...
9
votes
0answers
97 views
Using "soft" constraints / bias in geometry optimization?
I study molecules weakly bound to nanoclusters and surfaces.
During geometry optimization, I often run into problems like for example a small metal cluster behave nicely and has a given, stable ...
8
votes
1answer
89 views
What are the input parameters of VASP for 2D material geometry optimization?
Apparently, my input parameters are not good for geometry relaxation of 2D materials using VASP.
...
6
votes
2answers
102 views
Symmetry-preserving low-level structural relaxation
I would like some suggestions on how to do structural relaxation (while I'm at it, let me list some synonyms for search exposure - geometry optimization, structural refinement, energy minimization etc)...
12
votes
1answer
78 views
Excited state energy gradient during geometry optimization of a target excited state
During the geometry optimization of the ground state of a molecule, we try to optimize the energy
gradient with respect to the nuclear positions such that the system remains in its lowest energy
state....
10
votes
1answer
96 views
Can I do a "constrained" geometry optimization in Quantum ESPRESSO, such that certain dopants appear in certain positions even after relaxation?
I am studying the magnetic properties of bulk ZnO, so I am doping it with transition metal elements in order to observe the magnetic spectrum. I replace a Zn atom with a transition metal element at ...
5
votes
1answer
95 views
Dispersion correction and band structure
Let's say I optimized geometry with PBE+D3. I want to carry out band structure calculation with HSE06, should I add the dispersion correction to the band structure calculation or not?
I tried both and ...
6
votes
1answer
64 views
Understanding QuantumEspresso Toolbox through Maestro
Anyone here uses Quantum Espresso through Maestro can tell me a bit more about the calculation panel setting:
I understand that -npools option must be divisible by ...
15
votes
1answer
248 views
Is it right to neglect very small imaginary frequencies?
I'm running a DFT optimization (B3LYP/def2-TZVP) and frequencies in ORCA for a molecule. And I get one or two very small (1-6 cm^-1) imaginary frequencies which corresponds to a slight bend of the ...
7
votes
1answer
46 views
Relax vs VC-Relax for interstitial incorporation energy
In order to model an interstitial trapped in a metal lattice, and the associated incorporation energy, which should be used - "relax" or "vc-relax"? I want to understand the ...
16
votes
1answer
402 views
Why is CPHF/CPKS necessary for calculating second derivatives?
This question is coming from an answer to one of my previous questions. During optimizations, QM programs usually compute the gradient(first derivative) analytically, and take a guess of the hessian (...
12
votes
1answer
187 views
Geometric optimization taking a long time. Are my convergence criteria too tight in CP2K?
I have been having trouble with the VIBRATIONAL_ANALYSIS routine. Namely, the routine keeps timing out. I am trying to find the vibrational modes of Pyridine in a non periodic system, as well as $\ce{...
10
votes
1answer
70 views
How to define a nonconventional geometry to obtain exchange spring hysteresis loop structure using MuMax3?
I have tried to simulate the hysteresis loop for the exchange spring structure using Mumax3. I have already simulated the hysteresis loop for the conventional bilayer soft-hard structure. Please find ...
12
votes
2answers
228 views
Comparing calculations in plane wave and atomic orbital bases for the same functional
Let's say I have two codes. One is plane wave, and the other is using atomic orbitals as basis sets. How can I compare these two codes with the same functional? And let's say I want to optimise the ...
6
votes
2answers
114 views
How can I increase the default maximum limit on step size for convergence in quantum ESPRESSO?
When trying to manually optimise the geometry of the crystal, I've faced an issue wherein the code stopped the convergence process after just 100 steps (which was the default maximum). Is there a way ...
10
votes
2answers
315 views
Should I do vc-relax with nspin=2 in Quantum Espresso for magnetic samples?
I'm a beginner when it comes to DFT and Quantum Espresso.
Consider I have a lattice which has associated magnetic properties. So for geometric optimization should I take into account the magnetic ...
11
votes
1answer
2k views
When should "vc-relax" be performed over "relax" calculations in Quantum ESPRESSO?
I'm new to Quantum ESPRESSO and I have read that there are several scenarios when relax calculations are preferred over vc-relax calculations, for example in maintaining vacuum while modelling surface....
10
votes
2answers
399 views
Analytic gradient for DLPNO-CCSD
Is there a formula for analytical gradients (for geometry optimization) for the DLPNO-CCSD method? I ask because I know that it is not implemented in ORCA. Maybe PNO-CCSD is implemented in MRCC or ...
14
votes
1answer
178 views
Is there a software that has implemented forces of TDDFT calculations for solids?
I'd like to investigate the structural relaxations of the excited state for periodic systems. BSE and TDDFT are two promising methods for this purpose. While there is a discussion on forces with BSE ...
13
votes
5answers
2k views
Can I use two different codes?
Can I use one code for geometry optimization and another code for a single point calculation on that optimized geometry? Can one publish results like that?
13
votes
3answers
644 views
Geometry optimization for n-layers in VASP
What is the best way to optimize monolayer geometry in VASP?
Should the same method be used for an n-layer (n=2,3,4,5)?
12
votes
2answers
155 views
Permissible amount of forces on ions in a relaxed structure
An equilibrium structure would be at a local minimum but that doesn't happen with all relaxation calculations. Relaxed structures tend to have some resultant forces on ions. What amount of these ...
11
votes
1answer
196 views
How would you report the lattice parameters of an alloy, modelled using a supercell
There is a whole lot of literature behind ab initio modelling of alloys with statistical site occupancies. These include VCA, SQS, CPA, supercell approach, etc. This question does not aim to compare ...
17
votes
2answers
937 views
Logic of published geometry optimization results without checking phonons
I see that in many papers where optimization results presented, they do not mention phonons and their force convergence criterion is 0.01 eV/A. Can you publish a result like that? And is not this ...
10
votes
1answer
232 views
How do I predict the structure of a nanoparticle with Calypso and Quantum ESPRESSO?
I want to create a nanoparticle of CuO and predict it's structure. I've done unit cell relaxation with Quantum ESPRESSO. One tool to predict nanocluster structure is Calypso which is PSO-based. I'm ...
15
votes
3answers
146 views
Candidate structures for global minimum determination
What are the best packages that can generate candidate structures for quantum chemical optimization (DFT or CCSD) to find the global minimum? I am working on the gas-phase small inorganic clusters (...
9
votes
2answers
269 views
Is there a possibility to change the initial crystal system during full geometric relaxation?
One of the challenges of modelling completely new material using DFT is the selection of initial geometry. Usually, an experimental structure (cif) which appears to be similar to the new material in ...
8
votes
0answers
112 views
ASE's fmax and FHI-AIMS's relax_geometry bfgs "tolerance". Are they same? [closed]
They look like the same thing, but their definitions are confusing. Additionally, while it's possible to use 'tolerance'< 0.05 in AIMS easily, in ASE, some structures never optimize if you choose ...
