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Questions tagged [geometry]

Questions about molecular or lattice geometry.

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1 answer
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How are z-matrices represented in the various matter modeling packages?

Is there a standardized format that is commonly used across molecular simulation (or QM) software packages to store z-matrix information about a molecule? For instance, in CHARMM, which is a Molecular ...
Hemanth Haridas's user avatar
3 votes
0 answers
49 views

Convert VASP Outcar to extxyz with hershfeld charge and virial data for all frames using ASE?

I have VASP AIMD Outcar file with Hirshfeld charge per each atom. I hope to convert this outcar file to extxyz file for MACE or NequIP MD framework training. Outcar file contains 800 frames (or images ...
exsonic01's user avatar
  • 873
2 votes
0 answers
36 views

Calculating geometric features using Zeo++?

I am currently engaged in research involving metal-organic frameworks (MOFs) and I am seeking assistance with calculating specific geometric features using Zeo++. The features I am interested in are ...
harsh's user avatar
  • 223
5 votes
2 answers
260 views

Gaussian 16: Relaxed scan using Jacobi coordinates expressed using generalized internal coordinates

For teaching porpouses, I would like to make a relaxed scan for an A-BC system (for example, the isomerization of of H-NC to H-CN or CH3-NC to CH3-CN) with Gaussian 16 using generalized internal ...
PAEP's user avatar
  • 195
11 votes
1 answer
374 views

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 ...
Nike Dattani - No Free Time's user avatar
3 votes
1 answer
93 views

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 ...
S R Maiti's user avatar
  • 7,011
5 votes
0 answers
45 views

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 ...
Shaun Han's user avatar
  • 1,885
6 votes
1 answer
100 views

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. ...
Sam Zhuang's user avatar
4 votes
0 answers
89 views

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 ...
S R Maiti's user avatar
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6 votes
1 answer
248 views

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: <...
John's user avatar
  • 268
5 votes
1 answer
237 views

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 ...
Vladislav Gladkikh's user avatar
9 votes
1 answer
186 views

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. ...
Vladislav Gladkikh's user avatar
5 votes
1 answer
90 views

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 ...
S R Maiti's user avatar
  • 7,011
2 votes
1 answer
264 views

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: ...
leire's user avatar
  • 183
4 votes
3 answers
675 views

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 ...
user avatar
5 votes
1 answer
69 views

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 ...
leire's user avatar
  • 183
7 votes
3 answers
1k views

Print chemical formula from list of atoms in Python?

Lets consider the following code which uses the Mole object: ...
Nike Dattani - No Free Time's user avatar
4 votes
1 answer
356 views

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: ...
Anastasia Bitter's user avatar
4 votes
1 answer
184 views

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, ...
Atom's user avatar
  • 1,005
3 votes
2 answers
442 views

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 ...
Camps's user avatar
  • 23.4k
6 votes
1 answer
114 views

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 ...
More Anonymous's user avatar
8 votes
1 answer
733 views

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 ...
Andrea Pellegrini's user avatar
6 votes
2 answers
739 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?
sarra6's user avatar
  • 579
10 votes
1 answer
1k 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 ...
sarra6's user avatar
  • 579
11 votes
1 answer
265 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 ...
Hitanshu Sachania's user avatar
7 votes
2 answers
3k views

Converting input file into XYZ format using ASE

Here is my code: ...
Saha_1994's user avatar
  • 969
2 votes
1 answer
49 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 ...
DJA's user avatar
  • 851
14 votes
2 answers
407 views

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 ...
Ariel's user avatar
  • 141
9 votes
1 answer
180 views

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 ...
mhdadk's user avatar
  • 229
13 votes
1 answer
2k views

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 ...
Collodial_machine 's user avatar
9 votes
1 answer
321 views

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 ...
Mriganka Parasar's user avatar
20 votes
7 answers
6k views

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: ...
Jose Pinto's user avatar
12 votes
1 answer
315 views

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 ...
user avatar
11 votes
1 answer
248 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 ...
Greg's user avatar
  • 1,807
9 votes
1 answer
404 views

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 ...
Savir's user avatar
  • 1,051
15 votes
3 answers
734 views

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 ...
Michael Brunsteiner's user avatar
5 votes
1 answer
625 views

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 ...
Anoop A Nair's user avatar
  • 4,496
19 votes
4 answers
1k views

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 ...
Tristan Maxson's user avatar
10 votes
0 answers
635 views

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 ...
DoubleKx's user avatar
  • 1,070
5 votes
1 answer
1k views

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 ...
Giu's user avatar
  • 477
16 votes
3 answers
4k 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)?
M_Fisher's user avatar
  • 631
18 votes
2 answers
993 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 ...
Bereau's user avatar
  • 861
4 votes
1 answer
108 views

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' ?
Alfred's user avatar
  • 1,939
10 votes
2 answers
633 views

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?
Alfred's user avatar
  • 1,939