Questions tagged [atomic-simulation-environment]
For questions about the Atomic Simulation Environment (ASE) tools and Python modules
81
questions
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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 #
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4
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172
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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 ...
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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 ...
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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. ...
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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 <...
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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 ...
- 911
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64
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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 ...
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Are then any material property solvers (from Charge Density) available in python?
I am looking to predict properties like the Bulk Modulus, total energy, etc., all from the charge density I have as input (CHGCAR file)
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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 ...
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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:
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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.
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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 ...
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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 ...
- 667
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101
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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:
...
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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.
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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 ...
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Tool to extract rings from zeolite structures
I am trying to reproduce the work done in this paper https://doi.org/10.1021/acscatal.7b00588.
In this direction, I have been successful in optimizing the unit cells of the zeolites. For further steps,...
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Python code for combining two surfaces to form an interface
I have two surfaces named POSCAR1 and POSCAR2. I want to stack the surface of POSCAR2 on POSCAR1 to form an interface and also to match their lattice constants. I tried a solution here by adding it ...
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How to Create a 2D Structure of Boron (Brophene) using ASE?
Unlike Graphene and MoS2, For borophene, I didn't find any inbuilt function in ASE. I have tried to make it, but i failed. So If anyone could help me, it will be great help.
Since brophene has ...
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84
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Generate a bimetallic surface in ASE
I am trying to generate a 50-50 Pt-Au fcc(111) bimetallic surface in ASE for DFT calcualtions. However, I am unable to figure out the procedure. Any help regarding the procedure will be great. Thanks
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How to read a poscar file which is a surface and add adsorbates using ASE
I have a POSCAR file containing Co, Cr, Fe, Ni elements. It is a slab of 6 layers. The first 3 layers are mobile whiles the last three layers are fixed. I would like to add adsorbates at the FCC ...
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How do you write an .xyz file with the information of cell as comment in the Atomic Simulation Environment?
I want to convert the OUTCAR file to a file of xyz (not extxyz) format.
The informaiton of lattice (or cell) is stored in the comment line (like extxyz format).
Can this be done with the help of ase ?
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Saving forces from ASE Molecular Dynamics calculations
I have run some molecular dynamics calculations with a pretrained machine-learning potential (M3GNet) which uses the ASE MolecularDynamics calculator. My goal is to compare the results (energies and ...
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Basic MD in ASE
I am testing ASE with a basic H2 MD simulation.
I am reading the input file from a xyz file (generated with Packmol), I set pbc True .
Then, I relax the system with BFGS and move to NVT and NPT ...
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Clustering Algorithms with Periodic Boundary Conditions
I've been working on a project that involves the clustering of data with periodic boundary conditions. Like simulation of extra-framework water species.
Specifically, I am looking for clustering ...
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317
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Visualise bonds in ASE
I want to visualize an MD trajectory produced with ASE.
ase.visualize.view produces an output for atoms and trajectories. I am not able to show the bonds between atoms.
For atoms, I can use this in ...
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Copper FCC structure using ASE (Atomic Simulation Environment) library in python
I want to create a FCC structure using ASE (atomic simulation environment). I have define the all the required parameter correctly but at the time when i add GPAW calculator. The output of the program ...
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Create a SMILES from ASE Atoms
I am trying to create a SMILES representation starting from a .xyz molecule description (positions + symbols) read as ASE Atoms.
How can I convert a given molecule as a SMILES string ?
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Loading Gromacs Trajectories using ASE (Atomic-Silumation-Environment)
I am trying to study some trajectories generated using Gromacs. I have been given tpr and pdb files of the simulation. What might be the most effective way to load them in ASE? Or is there way to ...
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Atomic Simulation Environment (ASE) Modelling. Adding additional layer
Beginners here, to ASE. I've create a 2x2x2 supercell of TiO2 from unit cell (.cif file obtained from LegacyMaterialsProject ) using ASE. The script code is attached as follows. The outcome is shown ...
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Use Atomic Simulation Environment to set DFT+U parameters with Quantum Espresso
I wish to set the DFT+U parameters (ideally with the Liechtenstein’s formulation) using ASE and the Quantum Espresso calculator. I have seen that the format for QE has been updated to give the Hubbard ...
- 2,015
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Ionic relaxation with ASE (Atomic Simulation Environment)
I want to do an ionic relaxation of just the ions inside my unit cell (not the cell dimensions), with Quantum Espresso through ASE. However, I have only been able to find structure optimization ...
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How to build a unit cell in ASE?
As a basic example, I want to build a defect MgO unit cell within ASE. From VASP the input is simple:
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- 2,015
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Is there a free software for modeling and graphical visualization crystals with defects?
At real situation, it can happen, that a crystal can have defects, for instance, some of them are point defects — Schottky, Frenkel defects, line defects — dislocations, planar defects — grain ...
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ASE: Receiving error on implimenting ase cellpar_to_cell method [closed]
I am getting the following error while implementing ase cell method. I am not able to understand where is it going wrong, although I think it has to do something with the values I am getting for cell.
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Layer detection in a crystal structure
Context
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 distribution ...
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Quantum ESPRESSO won't work in ASE [closed]
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 ...
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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 ...
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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 ...
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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 ...
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190
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Calculate DOS with Quantum Espresso and ASE [closed]
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 ...
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how to incorporate size polydispersity in colloidal suspensions [closed]
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 ...
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Assign elements correctly in LAMMPS output (xyz) [closed]
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 ...
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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:
...
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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 ...
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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 ...
- 911
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423
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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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53
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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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Space group issue with XYZ, VASP formats in VESTA [closed]
I am facing an issue while converting .cif/.vesta files into .xyz and ...
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