Questions tagged [atomic-simulation-environment]
For questions about the Atomic Simulation Environment (ASE) tools and Python modules
136 questions
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Partial Hessian vibrational analysis (PHVA) of adsorption in MOFs
I have been probing acid sites in metal-organic frameworks (MOFs) by performing the partial Hessian vibrational analysis (PHVA) which provides information about characteristic vibrational modes that ...
4
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Creating a surface with ASE (Atomic simulation Environment)
I want to create the (4×2) Rutile TiO2(110) surface and the surface slab consisting of five TiO2 trilayers (or 15 atomic layers)
I did that, but I don't if it is correct or not!
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Convergence issue for ions with GPAW
How best to do relaxation on charged molecules (plus and minus one electron) from the initial geometry of the relaxed neutral system? Two examples are CCOCCOCC(F)F and CCS(=O)(=O)C=C, where the former ...
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ASE-driven NWChem: How to include a Mulliken charges calculation?
I want to include the calculation of Mulliken charges into ASE-driven NWChem.
This is the input file I am using.
giving this error:
...
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Why does increasing the cell size affect the energy of molecules?
At the moment I'm performing various convergence tests of a cation-solvent-anion complex in ASE using the GPAW calculator, and found strange results for energy vs. vacuum padding as shown in the ...
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How can I restart a job in VASP software?
I'm running an AIMD (Ab initio molecular dynamics) calculation in the NVE ensemble with a specific initial kinetic energy (without using temperature control). My job stopped before the simulation time ...
- 617
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How to apply k/q point symmetries in Brillioun Zone on transmission function of near field radiation heat transfer
Basically, I want to find out the near field radiation transmission function between two graphene, set at Temperature(T1) and Temperature(T2). As you can see in the figure d is the separation distance ...
- 935
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How to find magnitude of k (wave vector) in hexagonal lattice cell(graphene)?
I want to calculate magnitude of k point(in Brillouin zone) of graphene which has hexagonal unit cell. The lattice parameters of graphene are given below:
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ASE calculating Poisson's ratio
I'm new to ASE and as a beginner project I'm trying to calculate Poisson's Ratio.
I have the following code:
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73
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ASE apply strains to entire cell
I'm just starting out with ASE, and wanted to write a program to calculate the Poisson's ratio for a material, by applying strains to a unit cell. I have written the following code:
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Is there a scriptable tool to determine whether two periodic structures are the same?
I'm doing some material search, in which I remove 2-4 atoms from a medium sized (~20 atoms) unit cell. I need to find all different combinations that are unique with respect to the translational, ...
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Read ase trajectory file by another (free) software
ase produces nice trajectory file, .traj. However, only "ase gui" can read the ".traj" file.
Is there another (free) sofware that can be used for reading ase traj-files ?
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Convergence Issue using GPAW for Anatase and Rutile
I am quite new to simulation and trying to calculate band structures for Anatase and Rutile. To do so I start with convergence tests in order to find appropriate cutoff energies and k-point meshes. ...
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Placing an atom along the line of the dipole moment of another molecule in ASE/GPAW
I have a solvent molecule, ethylene carbonate (EC), that I have calculated the dipole moment of. I want to place a Na atom at an appropriate distance from EC along the line of the dipole moment (in ...
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Calculating lattice constant using QE with ASE
I'm trying to follow simple example of determining the lattice constant (https://wiki.fysik.dtu.dk/ase/tutorials/eos/eos.html), but using QE instead of EMT. Here is ASE code I use:
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ASE EquationOfState error
I am running QE with ASE using Ubuntu WSL and trying to recreate simple case of calculating lattice constant (https://wiki.fysik.dtu.dk/ase/tutorials/eos/eos.html). Here is part of the code that is ...
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Why is ACAT not identifying the difference between 2 bridge sites on a surface slab?
I am using ACAT (Alloy Catalysis Automated Toolkit) to determine the unique adsorption sites on a 4x4x4 slab of Re3Pd. I've used the following code to identify these unique sites:
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Running Quantum Espresso from ASE
On my Windows Subsystem for Linux I compiled QE and I can execute simple test script from terminal. However, if I try to run QE using ASE I get the following error:
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How to Implement a Custom Calculator in ASE for a System with Two Particle Types?
I'm new to ASE and currently working on a simulation involving two types of particles, A and B, with quantities NA and NB respectively, within a simulation box of dimensions (4,4,4) in x, y, and z ...
3
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What are the specific differences between these two notations of supercell denoted by (√3×√3)R30∘ and (√3×√3)?
I am studying the super-cell structures in crystallography and came across two different notations:
(√3×√3)R30∘ and (√3×√3). I would like to understand whether these two notations represent the same ...
- 617
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BCC issues Iron Slab in ase
I've been having issues trying to optimise a 3x3 bcc slab of iron in ase. When modelled as an fcc struture it isn't problematic but given that iron is bcc it's naturally important I have it run as bcc....
3
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172
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How to use ASE to combine several MD trajectories into 1 trajectory
I have several continuous MD trajectories. How can I combine them into one trajectory to summarize all?
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How to calculate height of the center of the H2 molecule from surface via ASE?
I have XDATCAR file, i want to calculate graph of time vs height of the H2 molecule(center of the H2 molecule) from surface.
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- 617
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Rich editing of ASE images
I want to produce some images related to graphene-like materials.
I was able to draw them using ASE visualize module after constructing the atomistic model. However ...
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Is there any tool/website available by which I can generate VASP input files?
I am familiar with QE input files, but totally new in VASP. I know by using the quantum espresso input generator(https://www.materialscloud.org/work/tools/qeinputgenerator), we can use CIF file
to get ...
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How to make Quantum espresso input file from Vesta?
here is the CIF file of CaCO3 (http://www.crystallography.net/cod/1010962.html). I have opened it using Vesta and get the following data:
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- 935
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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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- 1,115
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problem calculating formation energy per atom using vasp
Using the below code I am trying to calculate the formation energy per atom and bandgap given the cif file. the values that are present in the material project.
but I got these values which are wrong ...
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How to model NiTe2 (011) plane using ASE
I have modeled the (011) plane of NiTe2 using ASE by cutting through bulk ,by the code given below
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Phonon dispersion calculation of graphene with ASE
I'm trying to use the package ase.phonons to calculate the dispersion relation bands and the DOS, I followed the example of the documentation for Al and went well for the diamond case. For some reason,...
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How to extract the displacement eigenvectors from a phonon calculation?
I'm an undergraduate student using GPAW/ASE for research, and am currently working with the phonon module. I can extract the modes, but aside from using phonopy I can't seem to find a way to get the ...
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Problem with using VASP with ase on a GPU
I am a newbie using VASP, currently I am trying to calculate the formation energy per atom and pre bandgap using DFT with VASP on a GPU machine.
I wrote the following script for calculating the ...
- 241
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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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- 1,115
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How can calculate length or coordinate of any molecule in different quantum state [like (rotational quantum state)j=2] with any software or code?
How can one determine the bond length of a diatomic or tri-atomic molecule(rot. state J=3 and vib. state v=2) from its ground state bond length (x angstrom) using computational tools or programming ...
- 617
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How to convert all structure coordinates in .traj file to separate .txt files (e.g. POSCAR format files)?
I am using the ACAT code for generating the structures.
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- 617
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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 ...
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231
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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 $\overset{\circ}{\mathrm{A}}$...
6
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Build supercell in ASE with forces and stress
This is my configuration in extended xyz format
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Better SIESTA workflows system?
Normally, I run all my SIESTA calculations manually and then go to post-processing the results, also manually.
I would like to know which of the tools below is "better" (more complete?) in ...
- 24.2k
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How can one create various arrangements of two or more types of atoms (like O, N etc.) with distinct coverages on a metal surface?
How can I modify the procedure described in this answer to achieve adsorption of two or more types of atoms on a surface, each with distinct coverages?
Is there an extension to the described method ...
- 617
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How to Change the Color Palette of Atoms in ASE GUI
I know that there is a configuration file called gui.py that would be initialized if it is placed in a directory like ...
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Controlling Initial Velocities in NVE Trajectory Simulations with VASP
"I've determined the initial velocities of the surface following its equilibration at 300 K in the NVT ensemble. Now, I aim to conduct AIMD (NVE ensemble)with the metal surface (initially defined ...
- 617
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Making Deuterium POTCAR file for optimization in VASP software
How to make Deuterium POTCAR file? i have Hydrogen POTCAR file.
- 617
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Interstitial and vacancy defects
I'm trying to insert interstitial defects in an FCC crystal with 32 atoms. And also a quick way of inserting a vacancy or doing a substitutional defect. Any code for this would be deeply appreciated. ...
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pyscf: Why should the choice of pseudopotential determine the total energy, and not the physics?
I have limited experience with DFT, but as an exercise I have written a DFT program of an atom (from scratch using nothing more than python built in functions and numpy) by following Richard Martin's ...
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How to make initial trajectory for incident A2 molecule on any surface?
I want to write code to simulate the impingement of any molecule on a surface at different (r, theta, and phi) angles in XYZ format.
- 617
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How to make a super cell for molecular crystal with PBC
I am trying to build a supercell for molecular crystals from a .cif file. With the ASE package, the supercell has the perfect PBC, but the atom sequence is very random and might be difficult to match ...
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2
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1
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Visualizing magnetic moments of Quantum espresso input/output files
I am looking for a software/website that can visualize atomic structure of my quantum espresso input/output files with magnetic moments. Any help will be highly appreciated.
Thanks in advance!
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How to model the final state for NEB calculations in ASE
I want to find the transition state properties (activation energy, reaction rate and few thermodynamic properties). I found out that NEB can do the transition state search. I have already created the ...
- 163
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How to use ase gui to visualize the geometry optimization (through graphs and animation)?
How can I visualize the geometry optimization? I want to see the plot of potential energy through various iterations to reach the minimum value. I would also like to see the animation of the atoms ...
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