Questions tagged [geometry]
Questions about molecular or lattice geometry.
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Inconsistencies in a famous point group table
The original resource
"Tables for Group Theory" By Peter Atkins, Mark Child and Courtenay Phillips (1970). I have been using this 2008 version, in which Pg. 37 has the following table:
Some ...
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How to calculate the distortion of molecule?
I have a set of molecules that are generated from a regular cyclohexane and have varying amounts of substitutions and double bonds. I need to compute the amount of distortion that each of these ...
- 2,612
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1
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Cubic spline interpolation through a series of images
Cubic spline interpolation is used in a lot of methods like Nudged Elastic Band (NEB), or String or Growing String Method (GSM) either to reparameterize the path, or to estimate the position of the ...
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How to transform a perturbed surface structure to a reference surface structure?
Say I have a bulk FCC Pt structure obtained from Materials Project with a lattice constant a = 3.94 Å. I first did DFT to relax the bulk structure, and the optimized lattice constant becomes for ...
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Trouble finding pdfs of "Tables of Interatomic Distances and Configuration in Molecules and Ions" series books
I am currently trying to find molecular geometry data prior to 1960, and it seems like
"Tables of Interatomic Distances and Configuration in Molecules and Ions (1958). Special publication No. 11. ...
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0
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Is it possible to generate atom-mapped xyz files from reaction SMILES for NEB?
There are SMILES that represent reactions happening (e.g. C=C.O>>CCO representing water addition to ethylene). And I know that there are atom-mapping ...
- 6,436
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Why am I getting "AttributeError" when running this Python function?
I installed chemcoord (link to documentation) on MacOS in a fresh Python 3.7 virtual environment. When I tried to run the first line of code from the tutorial:
<...
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How to get rotation matrix elements from root integer notation?
For example, I am reading a paper, where they put one layer on top of another, and in order to minimize the lattice mismatch, they transform unit cells of both layers.
They report it in a root integer ...
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How to stack graphene and hBN on top of each other?
I read in papers (e.g. link) about AA stacking, where C atoms are above the B and N atoms, and AB stacking where one C atom is above the N or B atom, while the other C atom is above the h-BN hexagon.
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5
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Hessian used for calculating GDIIS error vectors
GDIIS (Geometry optimisation with Direct Inversion of Iterative Subspace) is a well known method used by many QM codes for geometry optimisation. It is inspired from the almost universal DIIS method ...
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How do I know which is the asymmetric unit of a unit cell?
I need the number of independent atoms in the asymmetric unit
I have to introduce them in this form:
...
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What is the bond length of O2--?
I need the bond length in Å for $\ce{O_2^{--}}$ from this geometry database page (type "O2--" for the input).
I get a bunch of possible values. I don't know much about those yet but after ...
iwab
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Is there a program to compare different structures?
I am looking for a program that can compare different structures and determine if they are equal or not. After performing DFT calculations, the obtained structures may be identical but for reasons ...
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Print chemical formula from list of atoms in Python?
Lets consider the following code which uses the Mole object:
...
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4
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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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4
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List of properties of molecules categorized by the number of atoms?
Is there an online database having information on molecules with a certain number of atoms? For example, properties of tri-atomic molecules?
There is this table that I got from NIST which gives a few, ...
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How to merge two files (molecule structure and file property) into one?
I've run some calculations with the xtb software. From its output I got XYZ and MOL files ...
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6
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Slope of the potential when both molecules "touch"?
My aim is to model the potential energy surface for two colliding H2 molecules. More specifically, I needed the order of magnitude of the slope of the potential at the moment when two colliding H2 ...
- 405
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Restart potential energy scan in Gaussian with additional scan points
I have finished a scan of a bond length, but I need to continue the coordinate scan adding more points to the same scan.
I thought of writing a second input file from the last geometry, relaunching ...
6
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2
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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?
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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 ...
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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 ...
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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 ...
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2
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Translating fractional coordinates resulting from conventional cell and primitive cell
I have calculated the band structure of some material where the unit cell was the conventional one (i.e. the lattice vectors are orthogonal). I'm trying now to calculate the same band structure only ...
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References related to the molecular distance geometry problem (estimating true distances based on noisy distances)
One aspect of the molecular distance geometry problem (MDGP) described in this PDF, can be written as follows:
"Given observations of noisy distances between atoms in a molecule, estimate the ...
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Extracting molecular structure from CIF file using VESTA or Mercury
I am trying to extract XYZ coordinates from a CIF file for a molecule to use in DFT calculations. I have Mercury and Vesta installed on my computer. Whenever I open the files, I get the following ...
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How do I create geometry files for carbon nanoribbons and molecular junctions for DFTB+?
I am currently learning DFTB+ using the tutorials on the official website :
Carbon Nanoribbons : https://dftbplus-recipes.readthedocs.io/en/latest/defect/carbon2d-elec.html#zigzag-nanoribbon
...
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Convert XYZ coordinates to Z-matrix
I want to make a python script that will load an xyz file. From the xyz parameters, I need to find the distance between atoms, angle and dihedral between atoms.
The file xyz have this structure:
...
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Functional group detection from geometry
I am currently looking for an efficient way to detect common functional groups - that is, characterize whether a molecule is an alcohol, an aromatic compound, etc. - in a larger database consisting of ...
user430
11
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1
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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 ...
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What is the "formula unit surface area"?
Firstly, sorry if this question is too basic for this community but seriously I couldn't find any answer. Does it mean the multiplication of the in-plane lattice constants? For example, lets say ...
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Rotation of crystal structure to match another structure of the same compound/polymorph
Say, I have two crystal structures of a particular organic molecule, the crystal structures are basically identical, apart from a rotation and redefinition of the lattice vectors/angles, a simple ...
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Is there a difference in performance when the symmetry is specified via ibrav in Quantum ESPRESSO?
I have been using cif2cell for converting CIF files into quantum ESPRESSO input files. But cif2cell always keeps the ibrav value to be zero and indicates the CELL_PARAMETERS. As per the quantum ...
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How to explain Miller indices to someone outside nanomaterials?
I often find that when talking to experimentalists outside of the field of nanomaterials, it is nearly impossible to explain Miller indices concisely. As this often comes up during talks from other ...
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Constraining coordination or bond lengths for certain atoms in VASP [closed]
I have a structure composed of many MX4 tetrahedral units. When doing MD on this structure I find that just one M atom moves into a trigonal planar coordination (MX3). I was wondering how to set ...
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How to calculate RMSD with GLIDE?
I need to calculate the RMSD between a co-crystallized ligand and my ligands and a non-co-crystallized ligand with GLIDE but I don't know how. Could someone explain to me how to do it? Many thanks in ...
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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)?
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2
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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 ...
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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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What are the methods that can be used to ensure that an optimized geometry is a local minimum?
Usually it is suggested to do a phonon calculation. What are the other ways?
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