Questions tagged [aimd]
Questions about ab-initio molecular dynamics (AIMD).
41
questions
1
vote
0
answers
16
views
Avarage bond distance as a function of time step in aimd
I am trying to reproduce a plot of average bond distance vs time steps in aimd for the compound Na2AgSb using the data from the paper "Decoupling thermoelectric transport coefficients of Dirac ...
- 31
6
votes
1
answer
105
views
How to fix values of LANGEVIN_GAMMA in VASP?
While running MD simulation in NpT ensemble in VASP, when using a Langevin thermostat (MDALGO=3), it is prescribed to set the LANGEVIN_GAMMA tag. However, I need help determining my system's ...
- 61
4
votes
1
answer
74
views
How do I know that a MD simulation (NPT ensemble) reach equilibrium?
I need to run MD (NPT ensemble) to find out lattice parameters at different temperature. Below is the input file for 300 K.
...
- 835
3
votes
0
answers
45
views
How do I fill my simulation box with molecules efficiently?
I am using VASP for DFT simulations so far and want to start with AIMD of solid liquid interfaces. Now I stand before the problem of how to fill my cell appropriately with molecules. So far I have ...
- 483
4
votes
1
answer
101
views
Average value of lattice parameters from cell trajectory
Is there any post processing tools by which I can get average value of lattice parameters from cell trajectory? For example: I ran 'vc-cp' (CPMD) in quantum espresso (for Silicon) and Si.cel file is ...
- 835
2
votes
0
answers
42
views
Convergence issue of Temperature Dependent Lattice constant using CPMD
I am trying to find out temperature dependent lattice constant (Silicon) using CPMD (NPT-MD). If I want the lattice parameters at 300 K, should I set temp 300 K in both &cell and &ion card? I ...
- 835
2
votes
0
answers
22
views
is it possible to extract the co-ordination number vs simulation time from VASP AIMD calculations?
is there any script or software available for extracting the co-ordination number for each step from AIMD results.
- 51
4
votes
0
answers
55
views
How to plot temperature dependent Phonon dispersion using Quantum Espresso?
Would someone please suggest me how can I plot temperature dependent phonon dispersion using Quantum Espresso? The paper (10.48550/arXiv.2211.15571) plotted phonon dispersion at different temperatures ...
- 835
3
votes
0
answers
57
views
Mean square displacement (MSD) graph from AIMD simulation
To get the slope from MSD graph, how to do the fitting if the graph is not perfectly linear? Do we need to do fitting only in the linear region?
- 51
4
votes
0
answers
74
views
Optical properties (temperature dependent dielectric constant) calculation using AIMD/CPMD: Is it possible with Quantum ESPRESSO?
I am trying to find dielectric constant using the mentioned method (10.48550/arXiv.2211.15571). They implement AIMD in VASP. Actually, I am familier with Quantum Espresso (not VASP) and using QE, I ...
- 835
4
votes
1
answer
95
views
Calculating the heat capacity at constant pressure of a solid in its liquid state using AIMD as implemented in VASP
I am trying to calculate the heat capacity at constant pressure of Silicon in its liquid state. For the same, I am using the example given in VASPwiki https://www.vasp.at/wiki/index.php/Liquid_Si_-...
- 916
6
votes
2
answers
246
views
Are there scripts available for AIMD?
I need to determine which of two electrolyte is the best for a hydrogen fuel cell. As far as I understand, the first thing to do is to compute their ionic diffusion coefficient and to compare (the ...
- 61
4
votes
0
answers
37
views
Query regarding individual polarization calculation using CP2K
I am seeking assistance in calculating the individual polarization matrix from CP2K. While utilizing the Polar input under FORCE_EVAL -> PROPERTIES -> LINRES -> POLAR, I observed that the ...
3
votes
1
answer
189
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 ...
- 587
2
votes
0
answers
199
views
Prerelaxation before AIMD with VASP
I am investigating a bulk structure by ab initio molecular dynamics (AIMD) implemented in VASP.
I was wondering, how to choose the initial geometry (= POSCAR file) to run the AIMD simulation. In the ...
- 313
2
votes
1
answer
24
views
Geometry of H2O in the v=1 vibrational state for AIMD simulation
This is a follow-up to my recent question: Algorithm for finding the v=1 state of an H2O molecule
I want the geometry (atomic positions) of the H2O molecule in the v=1 state. How are initial ...
- 147
2
votes
1
answer
103
views
Equilibrating Surface Temperature Through NVT Ensemble Ab Initio Molecular Dynamics
In my AIMD simulations with the NVT ensemble at T= 300K (Nosé–Hoover thermostat)for a Pd (111) surface (2*2, 6 layers) and vacuum sizes of 14 Å and 18 Å, All other INCAR tags are same(only NGZ for 14Å ...
- 587
2
votes
1
answer
475
views
Choice of SMASS for AIMD simulations in VASP
How can one verify that the values (0, 1, 2, and 3) in the SMASS parameter correspond appropriately to the NVT ensemble(Nose-Hoover thermostat) in the context of an ab initio molecular dynamics ...
- 587
2
votes
1
answer
273
views
Absorption enthaply at different temprature in VASP software via ab initio molecular dynamics
Can we calculate the absorption enthalpy at different temperature in VASP software via ab initio molecular dynamics? If yes, how?
- 587
3
votes
0
answers
47
views
How to perform atomistic spin dynamics (ASD) Ab Initio Molecular Dynamics (AIMD) using VASP?
I have tried normal AIMD simulation using VASP for Non magnetic materials. Now, I am interested to perform the molecular dynamics simulations for the finite temperature for Magnetic materials to ...
- 31
3
votes
0
answers
47
views
Normal coordinate analysis in TRAVIS
I have run a few AIMD calculations of some impurities trapped in a solid using CP2K and TRAVIS to simulate the resulting infrared spectrum. While the infrared spectrum was simulated well, there is no ...
- 485
3
votes
0
answers
116
views
I need molecular dynamics simulations input file for hexagonal heterostructures in quantum espresso [closed]
I m a material science student of PhD and search alot and make some input files for AIMD simulation but I didn't get the best output if anyone have the input file please provide me
- 31
3
votes
0
answers
36
views
How to estimate the minimal distance between atoms for which a pseudopotential-based AIMD gets forces correctly?
I am doing ab initio molecular dynamics in VASP. As far as I know, pseudopotentials approximate all-electron potential far from the nucleus, and deviate from it near the nucleus.
When some of my atoms ...
2
votes
0
answers
43
views
AIMD simulation of a silica slab and a electrolyte placed in the vacuum region
Can someone share a VASP input file as a template that I can use to equillibrate a system as mentioned in the title. I created one but I am not sure if that is correct or not.
...
- 541
1
vote
0
answers
80
views
How to calculate constraint force for angle constraint in CP2K NVT MD simulation? [closed]
I am running a CP2K NVT molecular dynamics simulation and want to apply an angle constraint between three atoms. In my previous simulations, I used a bond constraint between two atoms, and it was easy ...
- 1,641
5
votes
1
answer
139
views
Are thermostat parameters transferable between AIMD and classical MD?
I need to run several large systems using AIMD. I would like to benchmark same phase transition phenomenon using different thermostats (like Nose vs Langevin). For that it is crucial that I pick most ...
- 615
5
votes
1
answer
193
views
How to simulate the electron transfer during OER with AIMD?
I am trying to simulate the electron transfer from adsorbed H2O molecule to the electrode with AIMD. I guess I need to set up an external electric field, so the electron inside the H2O molecule would ...
- 2,077
3
votes
1
answer
206
views
Discrepancy in forces between AIMD and relaxation
I am a bit perplexed to see substantive differences in forces (as taken from OUTCAR with ASE) computed when I take AIMD frames and run static electronic relaxations on each one (no additional ionic ...
- 1,658
6
votes
2
answers
1k
views
Is AIMD classified as MD or DFT?
As far as I know, we need force fields such as Tersoff/Coulomb potentials when performing MD simulations. In AIMD, we use pseudopotentials similar to DFT.
Which method should we classify AIMD to: a ...
- 2,197
6
votes
0
answers
216
views
Regarding use of GCMC to add water molecules
I am working on a goethite system, and wish to fill the unit cell with water molecules for AIMD simulation using quantum espresso. For this, some papers[1],[2] indicated the use of Grand Canonical ...
- 1,003
7
votes
1
answer
304
views
Simulating autoionization of small molecules using DFT or AIMD
From what I'm reading, simulation of auto-ionization in liquid substances is hard to do using gas phase DFT or AIMD [1][2][3]. I am using ORCA to do my work and I must confess that I'm shocked to see ...
- 327
4
votes
1
answer
2k
views
Why does the temperature fluctuate severely during the AIMD using an NVT ensemble?
I am trying to raise the temperature of my model and keep the temperature at 300K, with an NVT ensemble and Nose-Hoover thermostat.
I am doing this job with VASP, here is the ...
- 2,077
11
votes
1
answer
564
views
Steps to obtain ionic diffusivity using AIMD
I read a paper and the authors wrote they use AIMD to estimate the ionic diffusivity of materials. I wonder steps to obtain the value at different temperatures. What are the input and output of ...
- 2,197
11
votes
1
answer
291
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 ...
- 5,195
7
votes
2
answers
313
views
What is the real reason behind the minimization of the system at the beginning of a Car-Parrinello MD calculation?
I've been studying MD and more specifically about Car-Parrinello Molecular Dynamics and I'm not entirely sure if I understood the meaning behind the minimization.
This is the way I understand it: The ...
7
votes
2
answers
237
views
How to take periodic snapshots while running a simulation in VASP?
Same question, rephrased:
What is the procedure to take snapshots at fixed intervals while running an AIMD or DFT Simulation in VASP?
OR
Which parameter in the INCAR file do I modify to achieve ...
- 1,637
13
votes
0
answers
732
views
How to build amorphous Al2O3 using the AIMD method implemented in VASP? [closed]
I want to build amorphous $\ce{Al_2O_3}$ with the AIMD (ab initio molecular dynamics) method implemented in VASP.
I'm thinking of this process in three steps:
Build initial supercell
Melt
Quench
I ...
- 15.3k
10
votes
2
answers
701
views
Choosing RAM, CPU time, # of cores, and other parameters for an MD run
I did an AIMD run in VASP using 64 cores (32 cores/node) and 250 GB of memory (125 GB/node) for 5 ps (1 fs time step). The calculation took 12.6 hours to complete. CPU efficiency was 99.7% and memory ...
- 1,080
10
votes
1
answer
2k
views
AIMD and velocity scaling in VASP
Typically one does velocity scaling to "heat" their sample with MD.
How do we do this in VASP? Is it by setting the SMASS=-1 and ...
- 1,080
10
votes
2
answers
314
views
What are some methods for modeling bulk phase infrared spectra?
I am interested in predicting the infrared spectra of bulk phase molecules, it seems that AIMD (ab initio molecular dynamics) is the current best approach. I have found a tutorial on using CP2K to do ...
- 1,232
22
votes
3
answers
2k
views
What are the types of ab initio Molecular Dynamics?
I am new to the world of Molecular Dynamics, and am curious to know exactly what is considered to be an ab initio Molecular Dynamics (AIMD) method, and how do they work?
The seminal work by Roberto ...
- 4,879