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Questions tagged [atomic-simulation-environment]

For questions about the Atomic Simulation Environment (ASE) tools and Python modules

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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. ...
Rubi Agrawal's user avatar
3 votes
0 answers
28 views

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 ...
Emu's user avatar
  • 31
3 votes
0 answers
37 views

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 ...
Muhammad Hasan's user avatar
5 votes
2 answers
151 views

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: ...
Muhammad Hasan's user avatar
1 vote
0 answers
26 views
+100

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: ...
Atom's user avatar
  • 1,005
5 votes
1 answer
114 views

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 ...
harsh's user avatar
  • 223
3 votes
0 answers
26 views

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 ...
Joyal sunny's user avatar
4 votes
0 answers
36 views

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,...
Rob Lut's user avatar
  • 41
3 votes
0 answers
34 views

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 ...
cinder_shot's user avatar
5 votes
0 answers
62 views

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 ...
harsh's user avatar
  • 223
3 votes
1 answer
51 views

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: ...
Atom's user avatar
  • 1,005
5 votes
0 answers
30 views

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 ...
Rubi Agrawal's user avatar
5 votes
1 answer
67 views

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. ...
Rubi Agrawal's user avatar
3 votes
0 answers
46 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
5 votes
0 answers
209 views

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 $\overset{\circ}{\mathrm{A}}$...
ARKA PRAVA SARKAR's user avatar
6 votes
1 answer
109 views

Build supercell in ASE with forces and stress

This is my configuration in extended xyz format ...
Pranav kumar's user avatar
  • 4,268
7 votes
1 answer
252 views

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 ...
Camps's user avatar
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5 votes
1 answer
77 views

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 ...
Rubi Agrawal's user avatar
4 votes
0 answers
66 views

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 ...
Jaafar Mehrez's user avatar
3 votes
1 answer
130 views

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 ...
Rubi Agrawal's user avatar
3 votes
1 answer
100 views

Making Deuterium POTCAR file for optimization in VASP software

How to make Deuterium POTCAR file? i have Hydrogen POTCAR file.
Rubi Agrawal's user avatar
1 vote
0 answers
94 views

Disappearing vacuum layer when relaxing bilayered hBN with VASP

I'm doing geometry optimization of bilayer h-BN, a 72-atom supercell (6x6x1) with vacuum thickness of 20 Å, and I set the parameters in INCAR as below: ...
Meifeng WANG's user avatar
1 vote
0 answers
46 views

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. ...
Nana Kofi Boakye's user avatar
7 votes
1 answer
563 views

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 ...
Mikke Mus's user avatar
  • 263
2 votes
1 answer
49 views

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.
Rubi Agrawal's user avatar
2 votes
1 answer
117 views

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 ...
Pradip Si's user avatar
2 votes
1 answer
68 views

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!
rahman62's user avatar
  • 153
3 votes
0 answers
91 views

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 ...
sachin hegde's user avatar
5 votes
1 answer
164 views

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 ...
sachin hegde's user avatar
1 vote
2 answers
157 views

ModuleNotFoundError: No module named 'ase.mep'

I am trying to find the transition path using NEB method in ASE. However when i try to import the ase.mep module, i am getting the following error 'ModuleNotFoundError: No module named 'ase.mep'' Can ...
sachin hegde's user avatar
4 votes
2 answers
161 views

How to model adsorbate layer on a monolayer graphene surface using ASE

My surface is a monolayer graphene. I want to add a layer of water as adsorbate and the parameters are height = 3.31 Angstroms on top of the slab; Coverage = 24/72; The orientation is: The hydrogen ...
sachin hegde's user avatar
3 votes
0 answers
52 views

Beginning in molecular simulation world

I want to do a simulation of an atom (type atom is not important) bouncing inside a spherical surface (the material of the surface is not important too) (i.e. starting from an initial velocity, the ...
eraldcoil's user avatar
  • 201
6 votes
1 answer
181 views

How to convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA software?

Convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA
Rubi Agrawal's user avatar
5 votes
2 answers
125 views

ASE: How to plot the irreducible Brillouin zone and this bandpath from a bandpath object

I am using ASE (Atomic Simulation Environment) for theoretical chemistry and I see an option to plot the irreducible Brillouin zone and this bandpath but I can't figure out how. I'm not a programmer. ...
Samaray's user avatar
  • 61
1 vote
1 answer
38 views

ASE reading cell dimensions from XYZ file generated by I-Py

I have an xyz file formatted in the following way (just a snapshot of the 192 atoms is shown) its cell information is given in # ...
KugelBlitz's user avatar
4 votes
1 answer
211 views

Random velocity generation

How to generate random velocities in the geometry coordinates of a surface (POSCAR file) using the Boltzmann distribution law with Atomic Simulation Environment (ASE) or other codes for Molecular ...
Rubi Agrawal's user avatar
3 votes
1 answer
153 views

Print full stress tensor in ASE to calculate Green Kubo viscosity

I would like to print out the off diagonal components of the full stress tensor in ASE. The goal is then to calculate the Green Kubo viscosity. One should use the ensemble average of the off diagonal ...
Marco Di Gennaro's user avatar
2 votes
0 answers
104 views

Water simulation in ASE/LAMMPS

I want to simulate some water in MD with ASE and a LammpsLib calculator. I set up a minimal Lammps calculator and I try to calculate the energy per atom of an isolated molecule, and a 3x3x3 supercell. ...
Marco Di Gennaro's user avatar
3 votes
0 answers
193 views

Read and run lammps water model in ASE

I want to read a lammps data file in ASE, for instance the TIP3P or the SPC model. The lammps examples provide the input script and the data file, which work perfectly. ASE is not able to read the <...
Marco Di Gennaro's user avatar
2 votes
0 answers
63 views

What is the best model to calculate the free energies using ASE thermochemistry?

I am trying to calculate the free energy of adsorption of a small molecule on a 2D material. After adsorption, I am using the thermochemistry module of the Atomic Simulation Environment to calculate ...
ansonthms's user avatar
  • 981
4 votes
0 answers
108 views

ASE/XTB: zero temperature and stress in MD simulation

I want to see how the volume and pressure of my cell is changing during a MD relaxation in ASE. I used the atom.get_volume() and ...
Marco Di Gennaro's user avatar
3 votes
0 answers
60 views

Are then any material property solvers (from Charge Density) available in python? [duplicate]

I am looking to predict properties like the Bulk Modulus, total energy, etc., all from the charge density I have as input (CHGCAR file)
Pranoy Ray's user avatar
  • 1,635
4 votes
1 answer
224 views

ASE: Shape mismatch when using FrechetCellFilter filter

I want to use a FrechetCellFilter into a MD simulation with ASE to make sure both the atomic forces and unit cell are simultaneously minimised. I encounter a ...
Marco Di Gennaro's user avatar
4 votes
2 answers
565 views

How to put adsorbate on the surface by ASE

I would like to make formate-adsorbed surface on Cu(111). I have prepared the Cu(111) by ASE: ...
Tommy Wang's user avatar
5 votes
1 answer
170 views

How to read multiple Atoms objects from a single file using ASE

I am trying to read Atoms objects from the file "data.txt", which contains multiple configurations. Each configuration has a different cell. ...
user174967's user avatar
4 votes
1 answer
98 views

How to get displacements along VASP NEB trajectory?

I am performing an NEB calculation with VASP and VTST. I would like to visualize the atoms along the path and to calculate their displacements. When I have a single relaxation's XDATCAR, I can unwrap ...
kpoint's user avatar
  • 139
4 votes
1 answer
305 views

Run ASE MD in parallel

I would like to run my MD simulation in parallel on a cluster (16 CPUs per node). From the ASE doc we can see that: ASE will automatically run in parallel, if it can import an MPI communicator from ...
Marco Di Gennaro's user avatar
3 votes
0 answers
225 views

How to check the units from ASE get_forces() function?

Here is a little python code that loops through a molecular dynamics trajectory (performed with the ASE package) and outputs the forces on the atoms at each frame: ...
breadcrumbs's user avatar
5 votes
1 answer
230 views

Fix layers of a slab

How do you fix the bottom layers of a slab to mimic a bulk material in ASE? Any functional that takes the slab object and writes a POSCAR with selective dynamics will be deeply appreciated. Thank you.
Nana Kofi Boakye's user avatar
2 votes
0 answers
257 views

ASE write extxyz question

I'm trying to convert vasp outcar to extxyz using ase read and write. But how can I control what contents to print out from comment line and data columns? For example, I hope to convert vasp AIMD ...
exsonic01's user avatar
  • 873