Newest Questions
4,805 questions
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Why does the magnetic structure change after non-collinear AFM band calculation in SIESTA?
I'm performing a non-collinear antiferromagnetic (AFM) band structure calculation using SIESTA on a Mn-based compound. However, I noticed that after the calculation, the magnetic structure changed: ...
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Getting the order of execution of functions in LAMMPS
I have written an MD code myself to model a system of interacting charged particles. I am using Nose-Hoover thermostat. To validate my results, I have also modeled the same system in LAMMPS taking ...
- 183
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Why double hybrid functionals produce different results in different packages?
I'm calculating the single-point energy of the Nitrogen dimer using a double-hybrid functional called "mPW2PLYP". This is a widely known double hybrid functional available for use in ...
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13
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The best choice of the Extension Shell in the Partial Hessian Vibrational Analysis (PHVA)
I am interested in vibrational analysis (Hessian) for the QM part of a QM/MM system, with the MM part being frozen. This is (usually) done using the Partial Hessian Vibrational Analysis (PHVA). If I ...
- 703
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does anyone has the Potential file for the U - Zr Alloy?
Does anyone have the interatomic potential file for the U-ZR alloys? If yes, please share with me
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3
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1
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Different results from two different integral routines
I've been working on a Hartree-Fock code called Planck, where I've implemented overlap and kinetic integrals using three different methods: THO, OS, and Hermite, following Chapter 9 of Molecular ...
- 4,144
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47
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Is there a typo in this open shell CCSD formula from Scuseria?
In Scuseria (1991), the author provides an implementation of open-shell restricted Hartree-Fock coupled-cluster singles-doubles in the Appendix.
Equation A.5 is given as:
$$
\begin{equation}
v^{\...
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107
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What is the method to examine atomic bonds and hydrogen interactions after an optimization calculation?
I am currently working on a project to construct an energy profile for a reaction, which involves many optimization calculations. As a result, I need to verify numerous structures and ensure the ...
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27
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Calculating the IR spectrum of a system in an arbitrary vibrational state with propagation-based methods
In the context of nuclear quantum dynamics, there are two ways of computing an IR spectrum for the vibrational ground state $|\Psi_0 \rangle$:
energy differences and transition dipole moments, or
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5
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572
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After optimizing all of my structures, I discovered that one of them needs tighter convergence criteria. Is it mandatory for all to be re-done?
I'm working on optimizing a transition state for proton transfer and C-N bond cleavage.
I successfully obtained a transition state with a negative frequency corresponding to the expected process. ...
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How to Calculate Quantum capacitance from DOS(VASP-DFT) of Graphene 4x4 monolayer?
My query might be very basic but I am not able to figure out where I am going wrong in calculating Quantum capacitance for the Graphene 4x4 monolayer.I am using vasp to calculate Density of states.
My ...
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How to consider LHE and RHE for a given system in tbtrans (SIESTA)?
I am working on Janus MXenes right now. I want to use TBTrans-3.2 to compute the systems' transport properties. Could you please clarify which part will be the scattering region (SR) and how to take ...
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There are problems when calculating the projected transmission rate using tbtrans
I am calculating a four-electrode single-molecule device based on a graphene-naphthalene molecule-graphene structure, which has a total of 338 atoms. I have already calculated the transmission rate. ...
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I encountered the problem of band crossings when using TBTrans to calculate the projected transmission
I'm calculating a four-electrode single-molecule device based on a graphene-naphthalene molecule-graphene structure, which consists of a total of 338 atoms. I've already calculated the transmission ...
- 21
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Problem when performing the calculation of projected transmission using TBTrans
I am calculating a four-electrode single-molecule device based on graphene-naphthalene molecule-graphene, which has a total of 338 atoms. I have already calculated the transmission rate. When using ...
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How may I make a heterostructure from two different crystal structures with different shapes?
I have two different crystal structure and I want to create a heterostructure but the problem is that the shape of their unit cell is different. I know how to combine them if their unit cell are same....
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61
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Using libmsym for symmetrizing Molecular Orbitals
I have written a Hartree-Fock code (mostly as a learning exercise, and to use it as a tool in my lessons) that utilizes the libmsym library (following the advice here) to identify the symmetry of ...
- 4,144
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Symmetry error in slab relaxation calculation with quantum espresso pw.x
I´m doing ralaxation calculations in some slabs to compute adsortion energies of Li in several adsortion sites. In some outputs from QE pw.x I get the following error:
...
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NEB convegence problem with LUA engine in siesta
I am having problems to converge NEB calculations with LUA engine within SIESTA. The NEB forces remain high after many days of calculations. Many of my NEB calculations so far never converge. I tried ...
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How does CRYSTAL14 properties use fort.98 to generate 3D charge density from ECH3?
I’m using the properties program from CRYSTAL14, and I want to understand how the ECH3 function processes the fort.98 file to compute the 3D charge density grid (i.e., the values written in DENS_CUBE....
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204
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How to specify isotopes in PySCF?
I'm using Qiskit-Nature with PySCF driver to calculate PES of simple molecules. And my question is about PySCF.
If there is a way to specify isotopes of atoms in PySCF, how may I do it?
PS: I've ...
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9
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91
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Recent Advances in Density Functional Theory (Mathematical Side)
I have been learning DFT with resources such as Engel and Dreizler's book, and it seems that higher level mathematics such as functional analysis appear frequently, especially in the more foundational ...
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How to read LAMMPS trajectory file when the number of atoms is not same as that in topology file?
I'm running a LAMMPS simulation with 2197 atoms, when writing the trajectory file, I only write the information of atoms that enter a specific region in the simulation box. Because of this the number ...
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63
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How to find the symmetry unique atoms of a molecule with a specified point group by any software or tool?
Suppose, for cyclopropane, the highest point group is D3h. However, I want to define it to its subgroup C2v for my NwChem calculation. But for specifying a different point group NwChem requires the ...
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34
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Omega variant of B2PLYP functional in case of charge-separated (zwitterionic) ground state
I wonder if B2PLYP and wB2PLYP functionals are similar for the normal ground state but wB2PLYP might be better in the case of charge-separated (zwitterionic) ground state?
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91
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How do I input k-path in the bands.in file?
I use seek k-path website to find the suggested k-path and its coordinates for band structure calculation. Following is the input file (bands.in)
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49
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How do I find the updated cell parameters?
After performing relax-vc calculations for any system, I would like to find the cell parameters celldm(1), celldm(2), celldm(3), etc. using my output file. But I don't understand which of the values ...
- 193
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220
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How to Keep Spin Vectors Fixed in Non-Collinear Antiferromagnetic SIESTA Calculations？
When using SIESTA to perform structural relaxation on non-collinear antiferromagnetic systems, I would like to incorporate magnetic effects while ensuring that the spin directions of certain atoms ...
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How can I access the original xlo/xhi box bounds from a LAMMPS dump file in MDAnalysis?
I'm working with a LAMMPS trajectory in MDAnalysis using the default LAMMPSDUMP format, like this:
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Fourier transform expression of the coulomb interaction between the sheets(graphene)
Do you know any expression which can present the Fourier form of coulomb interaction between two graphene sheets separated by vacuum (as the figure above)?
Here S(w) is the transmission equation. ...
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53
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Understanding the [13s8p/6s3p] contraction scheme for Mg⁺ and its reduction to [12s7p/5s2p]
Pacchioni et al. [1] used a [13s8p/6s3p] basis set for Mg⁺ in early cluster model calculations. The context is embedding, here is the list of primitives for the basis as given in the appendix:
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Elec: transfer matrix has 0 elements. The self-energy cannot be calculated. Please check your electrode electronic structure
Here I added my electrode and scattering zone files. I would like to ask if there is any problem with the settings here. Z is the transport direction, xy is the periodic direction, and here I set the ...
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Combining AI Methods with PXRD structure detemination : Seeking Software for Direct Method-Generated Electron Density Maps or Phase Retrieval
I am currently working on integrating AI approaches with PXRD (Powder X-ray Diffraction) to analyze crystal structures. I am looking for recommendations on software that can export electron density ...
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Question about Band Structure Oscillations in Siesta Results
I have a question regarding the band structure results calculated using Siesta. I am currently comparing the band structure of a doped monolayer Bi system (48 Bi atoms + 2 Sb atoms in a 50-atom ...
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What is the correct process to calculate band structure along z-direction for 2D materials?
I am doing a Magnetoresistance study using 2d materials. I am using MXene ferromagnetic material which has layered structure with a finite thickness. MXene has a hexagonal structure. I calculated the ...
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Calculating Potential Alignment Term
I want to calculate defect formation energy for CsPbI3 where one of the Pb is substituted with Zn to create a defect. I have seen the questions here and here but not able to find the exact answer. ...
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Calculating transition dipole moment between two excited states in GAUSSIAN
I am trying to calculate the transition dipole moment between the two excited states with GAUSSIAN software and to extract the transition density between the excited states for later calculations. ...
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3
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727
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Programs for file transfer/visualization between remote cluster and laptop
I understand there have been many questions asked about what software to use to view your output data. I am more interested in programs that allow simpler transportation of files from my remote ...
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POSCAR & INCAR to get Nitrogen defect formation energy
I previously used an hpc structure for Zr in order to get its defect formation energy. However, now that i want to do this for Nitrogen, I am confused as to what symmetry and what my POSCAR & ...
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Creating a polymer chain in WebMO's QOOL system
Im not sure if this is the right place to ask this, but in my chemistry class we're using this quantum online organic laboratory hosted by WebMD. I wanted to figure out how to model a polymer chain in ...
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Correct process to calculate ZrN with defects
I have been using VASP to calculate properties of a ZrN supercell with various defects and I do a lot of calculations so I made a script to do several calculations at once to optimize my process.
What ...
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Quantum Espresso NEB String Length Dramatically Increasing Without Energy Changes (HfO2, neb.x)
Dear Matter Modeling Community,
I'm using QE 7.4.1 and trying to do NEB with neb.x. The system is HfO2 and I'm studying polarization changes. I've encountered an ...
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van Hove correlation function plot from VASP output
How to plot self and distinct van Hove correlation functions from VASP AIMD trajectory files (XDATCAR)?
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How may I know how thermal expansion happens as a function of temperature, with AIMD?
I wanted to know how the volume changes with the temperature, with respect to the changes in lattice parameter for gamma Uranium. But when I use ISIF =3, it will ...
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Have I found a way to restart perturbative coupled cluster calculations in MRCC?
Preamble
More than 6 years ago I started the thread "Restarts during perturbative corrections" on the MRCC forum. Mihaly Kallay, the lead author of MRCC wrote:
"Dear Nike,
...
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Standing excitons in boron-doped diamond
I am dealing with standing excitons in boron-doped diamond. These excitons arise due to a local disturbance of the dielectric constant in the region of the boron atom. If anyone considered the ...
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Installing SIESTA using SPACK
I am following the instruction from here to install SIESTA using SPACK.
The command spack repo list, return, as expected:
...
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Optical properties calculation considering vector potential
I’ve been calculating optical properties using Quantum ESPRESSO and Yambo, which include only instantaneous and longitudinal electron-electron interactions (scaler potential). Now, I'm interested in ...
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Are PAO.Basis and PAO.BasisSizes able to be used with the same or different tag in the SIESTA input file?
The system we are working on contains a variety of atom types; for some, PAO.Basis is available on the website, but for others, it is not. As a result, we must use <...
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How can we test a code for an algorithm that is implemented for the first time?
I have been implementing a density functional tight binding software from scratch to experiment with it. I based myself off papers describing the theory and two concrete implementations that I could ...
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