Questions tagged [atomic-simulation-environment]
For questions about the Atomic Simulation Environment (ASE) tools and Python modules
45
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Layer detection in a crystal structure
The situation here, I have two images from a Monte Carlo Basin Hopping where silicon (in yellow) is getting replaced by germanium (in blue). Both have 32 germanium atoms at Si/Ge = 2.5; only the Ge ...
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Quantum ESPRESSO won't work in ASE
I am trying to use Quantum ESPRESSO in ASE, but I keep getting the following error. When I run pw.x directly from the terminal, it works, so Quantum ESPRESSO ...
- 111
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1
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How to determine the lattice vector direction and magnitude in ASE
I am using the ASE library to compute the distance matrix with minimum image convention. In that, I have got the positions of all atoms in the cell.
Now I wish to calculate the distance between each ...
- 105
3
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1
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Error in running Python file using ASE library
I am trying to run a Python script using ASE library, I have installed ASE using this page and run my Python script using this library on my terminal. I have made a virtual env named 'MLC_env' and ...
- 105
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2
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How to run simulation box relaxation with EAM callculator in ASE
I am trying to use EAM calculator in ASE. I want to perform simulation box relaxation with EAM potential. The code is working fine with EMT but fails in EAM as stress property is not implemented with ...
- 3,834
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Calculate DOS with Quantum Espresso and ASE
I am unable to do a Quantum Espresso "nscf" calculation using ASE. I have created a "mwe" to show the problem, followed by the output. I will be grateful if someone helps me solve ...
- 153
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how to incorporate size polydispersity in colloidal suspensions
Basically, I'm working on spherical colloids and investigating the phase behavior of these monodisperse colloids using Monte Carlo simulations (Fortran 77 coding). Now I want to introduce size ...
- 21
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Assign elements correctly in LAMMPS output (xyz)
I am trying to do LAMMPS calculations but I have noticed that when I dump to .xyz that ASE cannot read the elements because they are simply not output! Is there a ...
- 10.6k
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Generate quantum espresso spin-polarized input using ASE
I am trying to create the espresso input for magnetic calculation, reading the data from a cif file.
The ase code for the same is:
...
- 153
2
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Continuous Coordination Number Definition
I am interesting in quantifying the coordination number of some atoms in metals and am curious what approaches to defining a coordination number are possible for an atom. In particular, I am curious ...
- 10.6k
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How to terminate a surface with hydrogens
I am trying to study surface reconstructions of metal oxides using Quantum ESPRESSO. For this, I am creating slabs using python tools: ASE, Pymatgen, and catgen. However, I am unable to terminate the ...
- 731
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Atomic Simulation Environment (ASE) is unable to read a big trajectory file [closed]
The problem that I face is the ASE software can't read the trajectory file and throws this error ValueError: buffer is smaller than requested size. My assumption is ...
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Getting Internal Calculator Data in ASE [closed]
I am using the framework ASE to do computational chemistry calculations. I am using the calculator GPAW with it.
How do I extract data that is internal to the calculator? I mostly want to get the ...
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199
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Space group issue with XYZ, VASP formats in VESTA [closed]
I am facing an issue while converting .cif/.vesta files into .xyz and ...
- 41
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196
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How to calculate the surface area of a stepped surface slab in a unit cell? [closed]
I am trying to calculate the surface energies of Ni fcc (111) and (311) surfaces, therefore I need to calculate the surface areas. I use periodic slabs to model these surfaces. For a flat fcc (111) ...
- 161
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1
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Translate INCAR to Python script using ASE
I am considering using ASE to translate my old work into a Python script. I already have the INCAR and POSCAR KPOINTS files. Is it possible to let ASE read these files and generate Python scripts that ...
- 1,915
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The standard format and parser of VASP output files
I see a lot of post-processing tools for VASP, including ASE, VASPKIT,Pymagten and some other customized codes. They all read the VASP output files like a normal text file. Sometimes I would meet ...
- 1,915
3
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How could I generate the parameter of 'selective dynamics' in POSCAR with ASE?
I often use selective dynamics to do structure optimization in VASP, but I am not sure how to do it when using ASE, it seems I could use the constraint class to tell ASE what I want to do.
My question ...
- 1,915
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Python ASE: How to stack a nanocrystal on top of a graphene slab? [closed]
I'm trying to model a 2D TMD (transition metal dichalcogenide) nanocrystal on a graphene substrate. I know how to generate 2D TMDs through the MX2 module, and I certainly know how to make graphene on ...
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What is the principle of generating INCAR tags in ASE?
I am wondering if there is a detailed explanation about how ASE chooses the INCAR tags, since VASP already provides default values for a lot of tags, does ASE choose the default values?
There are a ...
- 1,915
5
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331
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Why calculation of coordination numbers from Element-specific RDFs (ASE) doesn't make sense? [closed]
The link to the trajectory is here.I am using the module and similar code of the ASAP calculator from ASE. The problem is as follows, the running Coordination Number doesn't match the number of atoms ...
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4
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1
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265
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RAMAN calculation with SIESTA and ASE-SIESTA
I have been using the ASE-SIESTA-PyNAO module to attempt some RAMAN/IR mode calculations on graphene (if anyone has any experience with this please send me a message maybe we can chat about it). At no ...
- 1,317
10
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2
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ASE convesion of Trajectory file to XDATCAR
The issue here is while converting a TRAJ file to POSCAR, it works. But, for TRAJ to XDATCAR, it shows TypeError: images should be a sequence of Atoms objects. (...
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How to calculate displacement in each coordinate and wrap w.r.t. lattice parameter?
The problem is my box is not orthorhombic (base angles different than 90 degrees). So, I am getting wrong results with the formula,
...
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2k
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4
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1
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173
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Are all the atom tags equal to 0 for ase.build.surface() objects?
I'm looking to build a surface slab in Atomic Simulation Environment (ASE) for CeO2 (fluorite structure). Using ase.build.surface( ) allowed modelling the surface. I would now like to run a relaxation ...
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1
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254
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How to define the a, b, c vectors in the cut function in ASE
I am testing an example of the 'cut' function in ASE cut. In this example, the surface Al(111) is created using vectors (1, -1, 0) and (0, 1, -1) included in the "cut" function. But I am not ...
- 1,935
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524
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Best way to read forces and positions and energies into Atomic Simulation Environment (ASE)?
My current procedure is to create a .xyz file out of my MD run for a crystal structure. I can read the energy and also each atomic position. But I want to add forces. If I add forces as the additional ...
- 211
8
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73
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Constructing an anisotropic crystal in WulffPack [closed]
I am trying to create an $\ce{LiFePO4}$ crystal in WulffPack. I have the surface energies of seven different surfaces from the paper [1]. When I input the same to WulffPack, it creates a structure ...
- 81
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Periodic Boundary Conditions in Atomistic Simulation Environment
Consider the following atoms object.
atoms_al = ase.build.fcc111('Al', size=(1,2,2), vacuum=16.0, orthogonal=True)
To set the periodic boundary conditions along the ...
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6
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Downloading ASE (Atomic Simulation Environment) on older versions of Python
I'm trying to install something called ASE that models atomic structures. I have ASE currently installed on python 3.7, however I need to run scripts that can import and recognize ASE in an older ...
Malena Rybacki
8
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1
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problem using GPAW in Google Colab
I am trying to follow the following: https://peterschindler.github.io/
This is searchable on the internet and it shows how to use GPAW as an ASE calculator. The installation is done by
...
- 1,121
8
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Read a data file into the atoms object in ASE
There isn't that many tutorials on Atomic Simulation Environment on the net and among those I saw, the atoms object is always built explicitly within Python.
What if I have a data file containing the ...
- 1,121
7
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319
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How to discard molecules at the boundary in the Atomic Simulation Environment (ASE)?
When building a supercell for a molecular crystal with the Atomic Simulation Environment, it seems that the program takes into account periodic boundary conditions when replicating the unit cell. How ...
- 1,453
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How do you write an .xyz file in the Atomic Simulation Environment?
I built a supercell of a molecular crystal and wish to write an .xyz file in ASE. How do I do that? The molecule has three different types of elements, C, H, and N.
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How to sort a supercell for a molecular crystal?
I am trying to build a supercell of the following (below) molecular crystal from its .cif file. How do I sort a supercell here according to each molecule in the supercell? I'm not tethered to a ...
- 1,453
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ASE: why do I get warnings about "monoclinic" and "orthorhombic" not being interpreted?
I am trying to use ASE (Atomic Simulation Environment) to build a supercell of some molecular crystals and then output the result to a file with the atoms given in a specified order for each molecule, ...
- 1,453
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How to sort using ase.build.sort?
I am trying to sort a set of Cu atoms in a fcc (non primitive) crystal structure according to their Z cordinate. I am using ase.build.sort to do this with the help ...
10
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How to build the [111] slab model of NiSe2 with different terminations with ASE tool?
The following figure is the bulk structure of NiSe$_2$ downloaded from the materials project database.
Now I want to study the properties of its [111] plane. In detail, I cut the slab with atomic ...
- 14.6k
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How to include individual PBC box dimensions in xyz file format compatible with VMD
I am using ASE to write an xyz file. Each frame in the file has a different PBC (periodic boundary condition). Currently, a frame starts like this:
...
- 1,083
8
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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 ...
- 1,919
12
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641
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Moving from VASP to CASTEP for bulk crystal and surface calculations
Can someone that works with CASTEP and VASP explain to me how a workflow might change between the two programs? I am very familiar with VASP but have not used CASTEP before.
As an example, assuming ...
- 10.6k
31
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19
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7k
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What are the freely available crystal-structure visualization softwares?
I use VESTA mostly for crystal structure visualizations.
What other options are available?
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What are the pre/post processing tools available for VASP?
I am aware of pyPROCAR and VASPKIT. Are there any other tools supporting VASP
- 8,612
17
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Computational tools for automatic creation of surface slab models of complex systems
I am looking for computational tools that can be used to automatize the generation surface slab models of latices of oxides, layered oxides, perovskites etc.
I have found a promising Python package, ...
- 1,677