# All Questions

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18 views

### SCAN-RVV10 geometry optimization

I'm using SCAN-RVV10 to optimize hexagonal-BN but optimized geometry not looking true as the calculated interlayer distance is far smaller than the experimental value(exp=3.35, calc=3.20)(SCAN-RVV10 ...
9 views

### Using “soft” constrains / bias in geometry optimization?

I study molecules weakly bound to nanoclusters and surfaces. During geometry optimization, I often run into problems like for example a small metal cluster behave nicely and has a given, stable ...
158 views

### How to calculate DFT energy with density from another level of theory?

I need to calculate the DFT energy given the density of another level of theory, for example Hartree Fock. $E[\rho_{HF}]$ This is sometimes used to fix various electron delocalization errors in ...
21 views

### What are the input parameters of VASP for 2D material geometry optimization?

Apparently, my input parameters are not good for geometry relaxation of 2D materials using VASP. ...
22 views

### What are some examples where TD-DFT was successful and where it fell short in describing photophysical or photochemical processes?

Time-dependent Density Functional Theory has been around for quite a while now, Runge, Erich; Gross, E. K. U. (1984). "Density-Functional Theory for Time-Dependent Systems". Physical Review ...
17 views

### Bulding host-guest polymer system for molecular dynamics

I'm thinking of running MD simulation of poling process (heating and cooling in external electric field) of host-guest polymer system: organic chromophore in polymer matrix (PMMA or polycarbonate). So,...
33 views

### Cannot import both numpy and LAMMPS to python after installing with conda

I installed the module LAMMPS by using this command conda install -c conda-forge lammps I want to import LAMMPS to python code, but it says: ...
46 views

### Unable to recreate data for benzene from paper in GROMACS 2020.5

I have been trying to simulate benzene in OPLSS-AA forcefield as per this paper: https://pubs.acs.org/doi/10.1021/ct2002122. I have been at a loss, since I believe I have everything running as per the ...
84 views

### What novel drugs are developed via CADD?

Virtual screening , protein ligand docking, MD simulation, FEP free energy calculations and the QM/MM approach have all been widely applied in optimization for drug discovery. Which drugs that have ...
17 views

### Thermo-calc: Calculate precipitation driving force by parallel tangent construction

I want to calculate the difference in Gibbs free energies between a Zr-Cu-Al liquid (composition - Zr 65 Cu 27.5 Al 7.5 at%) and the CuZr2 solid phase as a function of temperature (300 - 1000 K). In ...
78 views

### Symmetry-preserving low-level structural relaxation

I would like some suggestions on how to do structural relaxation (while I'm at it, let me list some synonyms for search exposure - geometry optimization, structural refinement, energy minimization etc)...
62 views

### How to evaluate the exciton velocity?

I have calculated the exciton wave functions using the GW-BSE method: $$\tag{1}|S\rangle = \sum_{cv\mathbf{k}} A_{cv\mathbf{k}} |cv\mathbf{k}\rangle$$ where $c$ for conduction and $v$ for valence ...
23 views

### Effect of temperature on density of states effective mass

The experimental study shows that Density of state effective mass is calculated at 300K while in theoretical study DFT yield Density of state effective mass at 0K .Why there is so much temperature ...
68 views

### VASP error when trying to do calculations in the presence of an electric field

I am trying to observe the effect of the electric field on 2D materials. I applied electric field by introducing three tags: ...
141 views

### Number of KPOINTS in irreducible part of Brillouin zone

I want to investigate the comparison of Total Energy per cell with respect to the number of KPOINTS in irreducible part of Brillouin zone but I do not know how to calculate the number of KPOINTS with ...
174 views

### How to perform band-structure unfolding in VASP?

I have created a band structure for 3x3x1 doped-supercell using VASP, and I obtained the figure below. Now I want to do band-unfolding. What are the simplest ways ...
96 views

### Single point energy calculation in VASP

I want to do single point energy calculations in VASP for $\ce{Mg2Si}$ so what should be initial steps to do? What are tags required in INCAR sufficient to do this ...
52 views

### How does one project out the translations and rotations from a hessian?

I've recently written a simple code to numerically compute the hessian of some function (at a point). Most electronic structure packages will compute the hessian and then project out the translations ...
102 views

### Procedure to classify errors in Kohn-Sham DFT

I was reading this paper which basically outlines the two main types of errors that one encounters in Kohn-Sham DFT : Density-based errors and Functional-based errors. I understand the practical ...
64 views

### What are some materials known to be able to keep being pulled thinner and thinner like gold? [closed]

This question is similar to but different compared to: What mathematics/computation heavy resources are available for understanding materials behaviour?. I know bitumen is one such material, as shown ...
56 views

### What are some of the advantages and disadvantages when using shape consistent pseudopotentials as compared to energy consistent pseduopotentials

From the literature as well as the answer to the question What is the meaning of energy-consistent and shape-consistent in the context of pseudopotentials? I can see that the key difference between ...
79 views

### What is a good practical way to determine whether or not I need to use a multiconfigurational method?

I’m planning to run a calculation of single electron transfer where my system goes from singlet to triplet biradical (presumably). So I’m wondering how to decide if I need to use milticonfigurational ...
93 views

### What is static correlation, actually?

My question is inspired by this question and also this one. I have come across the term static correlation multiple times. Introduction to Computational Chemistry by Frank Jensen describes static (or ...
71 views

### Molecular Dynamics Simulations in VASP

I want to run molecular dynamics (MD) simulations with VASP for Mg2Si to investigate the simulation time vs ENCUT and KPOINTS, ...
478 views

### Total energy from KS-DFT: How reliable is it and why?

As the title suggests, my question is fundamental - How reliable are the total energy values from Kohn-Sham Density Functional Theory, and why. I acknowledge that absolute values of energies are ...
150 views

### Extracting the coordinates of a super cell in Vesta or Avogadro

I am trying to use a program such as Vesta or Avogadro to build a super cell from a .cif file for a molecular crystal. In neither program can I seem to figure out how to order the output of the ...
55 views

### Phonon Frequencies and Free Energy with respect to polymorphs

I have a material that can crystallize in either a cubic or tetragonal polymorph depending on the synthesis. I used DFPT in VASP and calculated the phonon band structures. I see that the cubic has all ...
52 views

### Why are Norm-conserving Pseudopotentials considered so important?

So I am aware that a norm-conserving pseudopotential enforces the conditions that: Inside the cut-off radius, the norm of each pseudo-wavefunction is identical to its corresponding all-electron ...
154 views

### Gaussian-type orbitals vs Slater-type orbitals in terms of computational efficiency

When creating molecular orbitals via the linear combination of atomic orbitals method I am told that Slater orbitals provide a more accurate representation whilst Gaussian orbitals are computationally ...
102 views

### How to calculate the formation energy of a monolayer using VASP?

I want to calculate the formation energy of WS2 monolayer unit cell using VASP. I am wandering if you could show me the detailed ...
44 views

### Excited state energy gradient during geometry optimization of a target excited state

During the geometry optimization of the ground state of a molecule, we try to optimize the energy gradient with respect to the nuclear positions such that the system remains in its lowest energy state....
88 views

### What is the meaning of energy-consistent and shape-consistent in the context of pseudopotentials?

I am trying to use pseudopotentials to model scattering from heavy molecules. However, I am confused by some of the terminologies of pseudopotentials/ECPs: Norm-conserving according to Wikipedia and ...
23 views

### How do I get exact percentage of spin-polarization in Quantum ESPRESSO?

I am investigating a near half-metallic / high-spin polarization material. I ran an SCF calculation with nspin = 2, with some starting magnetization. So now I ...
54 views

### 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 ...
60 views

### How to fix gauge in Quantum Espresso?

I am trying to use Quantum Espresso to manually calculate the Berry phase using the Berry connection, due to evolution along a closed loop in k-space. I want to do this manually instead of using ...
55 views

### Calculating the surface state with Wannier tools

Currently I met a problem when I calculate the surface state of a topologically non-trivial thin film system. I did a DFT calculation and fit the result with wannier function. The fitting looks pretty ...
170 views

### Mismatched number of normal modes calculation in GAMESS

I am trying to calculate normal modes frequency matrix using HESSIAN calculation in GAMESS. Since we know that number of normal modes for a non-linear molecule is 3N-5 where N is the number of atoms. ...
50 views

### Two-stage unbinding & binding energies with DFT

I'm trying to calculate the stability of the product of a coordinate bonding process of molecules A and B in the polarizable continuum solvent model (PCM, solvent set to water). I'm getting energies ...
64 views

### Can I do a “constrained” geometry optimization in Quantum ESPRESSO, such that certain dopants appear in certain positions even after relaxation?

I am studying the magnetic properties of bulk ZnO, so I am doping it with transition metal elements in order to observe the magnetic spectrum. I replace a Zn atom with a transition metal element at ...
46 views

### In VASP, which option is better for monolayer relaxation: ISIF=3 or ISIF=4?

Since I have started working on monolayers I was using the ISIF=3 tag for relaxation, this was after recompiling VASP with the modified "...
96 views

### Has it been researched whether face centered cubic carbon is stable? [closed]

According to this paper, carbon has a face centered cubic phase which is a metallic form. My question is: Has it been researched whether face centered cubic carbon is stable? Reasons why I'm ...
80 views

### Bash script to extract lattice parameters from CONTCAR

I am using VASP to calculate material properties. I want to know how to extract the lattice parameters from my cells automatically with a script. I know about the method with VESTA (described here How ...
40 views

### How can I calculate and plot the Molecular orbitals (MO's) from the Gaussian wavefunction file?

This a follow-up question to my previous question. And as per the answer one could create M.O orbitals from the primitives. As a new user of Gaussian, is there any method (or algorithm) to followed so ...
90 views

### Has there been research on improving the strength of graphene-based materials?

I read that brittle materials tend to have an observed strength much less than its theoretical strength because they tend to have surface cracks and whatever tension is applied gets greatly magnified ...
36 views

### Reading complex potential into CP2K

Is it possible to read a complex potential into CP2K? I have generated a potential using FDTD at a given frequency, which results in a complex result. The potential is to be read in to a real time ...
39 views

### Value of density of state effective mass and transport effective mass to calculate conductivity

How can density of state effective mass and transport effective mass can be defined to calculate conductivity for a cubic system with parabolic but anisotropic dispersion relation? What will be the ...
60 views

### How do I interpret the Gaussian16 wavefunction file?

I'm new to gaussian16. The wave function file that I obtain as a result of the "Energy" calculation. It consists of five distinct parts : PART 1 : ...
73 views

### Finding parameters for a molecule in various forcefields

Let's say I want to run a simulation for benzene in GROMACS using parameters from a certain force-field. I logged on to the Automated Topology Builder, I looked up benzene, and I found an ITP file for ...