Questions tagged [charge-density]

Questions about charge density.

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Calculating the electrostatic potential of a molecule: what is a good 3D Poisson equation solver? [closed]

I was wondering if anybody can recommend an easy-to-use library/program to solve the 3D Poisson equation $\nabla^2 V(r,\theta,\phi) = \rho(r,\theta,\phi)$ with vanishing solutions at infinity: $$V(r,\...
Emil Zak's user avatar
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12 votes
1 answer
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What can we learn by inspecting charge densities calculated with DFT?

The charge density is an important physical quantity obtained from first-principles calculations based on density functional theory (DFT). Much useful information about the investigated materials can ...
Jack's user avatar
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11 votes
2 answers
1k views

Effect of ISYM tag on Partial Density of States (VASP version < 6)

This is from the entry for LORBIT in the VASP Wiki. For LORBIT >= 11 and ...
Hitanshu Sachania's user avatar
11 votes
1 answer
774 views

Charge density convergence within VASP using spin polarized DFT+U

I am noticing a possible convergence problem in a magnetic $U$ system I am studying. In the OSZICAR file I often see the rms(c) value go to about ...
Tristan Maxson's user avatar
11 votes
0 answers
117 views

Should augmented basis be used for Hirshfeld charges? [closed]

I'm calculating condensed Fukui functions to explain the reactivity of my molecules. The manual for Multiwfn suggests using atomic dipole moment corrected Hirshfeld charges for it. However I get ...
Roman's user avatar
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10 votes
1 answer
1k views

Best software to plot Charge densities

I have obtained cube files of charge density difference using Quantum Espresso. I am trying to plot these as a contour plot in an aesthetically pleasing manner with good quality. I'm aware that ...
ansonthms's user avatar
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10 votes
1 answer
2k views

What's the difference between charge density and the electron localization function (ELF)?

The following figure is the electron localization function (ELF) for monolayer LaBr$_2$. The ELF is calculated to reflect the bonding character in SL LaBr$_2$. As shown in the figure, ELF shows two ...
Jack's user avatar
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8 votes
1 answer
319 views

HSE06 Starting Guess

In CASTEP, can you start with a converged density for a lower level of theory for a starting guess for HSE06? If you can, what functional is suggested or is it something that will cause more headache ...
Tristan Maxson's user avatar
8 votes
0 answers
318 views

Why do I get negative charge density values in the core of atoms when I perform DFT calculations with PAW? [closed]

We are all aware of the fact that negative charge densities in the atomic cores are an artefact of Density Functional theory Calculations using Projector Augmented Wave (PAW) method. But what is the ...
Pranoy Ray's user avatar
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7 votes
1 answer
212 views

How to obtain electron charge density per unit volume about a water molecule using SlowQuant?

@Nike Dattani's answer to How to “get my feet wet” in Density Functional Theory by simulating a water molecule using Python recommends SlowQuant. I've used the install instructions for Linux on my ...
uhoh's user avatar
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6 votes
2 answers
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How to use Multiwfn software (for charge density and ELF analysis)?

I am interested to learn the use of multifwn software. I have windows OS. Mostly I am interested to see the charge density and ELF, particularly in non-atomic locations. Can anyone guide me, starting ...
Sak's user avatar
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6 votes
1 answer
544 views

Can a file in the Gaussian CUBE format be voxelized?

My aim is to voxelize a CHGCAR file. I am trying to build up a workflow to do the same. With the aid of the Matter Modeling community members, I have figured out a way to convert a CHGCAR file into ...
Pranoy Ray's user avatar
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6 votes
2 answers
593 views

How to calculate the individual atomic charge from a cube file of charge density?

I have a cube file of charge density. The unit cell consists two silicon atoms. If I use a python code to calculate the net charge of the system, it results around 24, which is ok because the ...
Sak's user avatar
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6 votes
1 answer
387 views

Total number of electrons from DOS and PDOS - what's the theory behind it?

Let say we need to determine the total number of electrons of an FCC material (let say, two silicon atoms in the unit cell, using numerical/mathematical approach. How can we get the total number of ...
Sak's user avatar
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6 votes
1 answer
144 views

Charge density wave and band inversion

Is there any connection between charge density wave and band inversion? Or is there any system in which band inversion follows the same mechanism as the CDW? I am just trying to find a connection ...
Alisufyan's user avatar
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6 votes
1 answer
441 views

How to extract information from Charge Density Different?

I would like to learn more about Charge density different and would like suggestion for how to get any information from the Charge Density Different plots. How accurate it is and if anyone have ...
Ngan Huynh's user avatar
6 votes
1 answer
162 views

Where are the atoms located in a charge density calculation using DFT?

The charge density (electron distribution) is calculated self-consistently by employing DFT, so a question arises here: where are the atoms located, or are their positions fixed?
Shalini's user avatar
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6 votes
1 answer
176 views

Interpreting Critic2 charge analysis in metallic systems

I'm using Critic2 software to perform post-processing of the charge density of metallic alloys. With the charge density obtained from the Self-Consistent-Field calculation (for that I'm using Quantum ...
Anibal Bezerra's user avatar
5 votes
1 answer
543 views

How to calculate the charge density using Quantum Espresso?

How do I modify the input file below to calculate the charge density (DENS) using Quantum Espresso? Input file: ...
Caroline Santos 's user avatar
5 votes
1 answer
240 views

Bader charge calculation in Quantum ESPRESSO DFT

I am searching for calculating Bader charge using Quantum ESPRESSO. I am using pseudopotential based DFT calculation. And I have charge density files (cube and XSF formats). My objective is to ...
Sak's user avatar
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5 votes
0 answers
75 views

Can the electron charge density of two material systems be similar?

Broadly given two electron charge density (ECD) fields, is it possible to distinguish between the elements present in both the systems? Since the ECD does not explicitly present any information on the ...
Pranoy Ray's user avatar
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5 votes
0 answers
109 views

Color of isosurface in charge density visualization

I am trying to visualize the charge density of a crystal through VESTA. However the intersection surface of the isosurface and the boundary turns into blue, which is certainly not included in my ...
蕭力諶's user avatar
  • 411
5 votes
0 answers
128 views

How to calculate the number of interstital electrons from Quantum Espresso charge density outputs? [closed]

I have calculated the charge densities (in 1D, 2D and 3D formats) with the help of Quantum Espresso DFT. The system (/material) is simple, two atoms in an unit cell. However, I want to determine the ...
Sak's user avatar
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5 votes
0 answers
88 views

"Failed" running DDEC6 Atomic Charge when using Palladium (Pd) cluster model [closed]

I have a problem with running DDEC6 when I used Palladium (Pd) cluster, the main issue was that there were no DDEC6_even_templered_net_atomic_charges.xyz files came ...
Paratee's user avatar
  • 51
4 votes
1 answer
238 views

Does integrating PDOS give total charge of a system?

Suppose you have a two atom cubic cell, and you have calculated the atomic PDOS. Does integrating the atomic PDOS and summing them to Fermi energy give exactly the total charge of a system?
Sak's user avatar
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4 votes
1 answer
59 views

Can the Electron Charge Density (ECD) have negative values and why?

In certain charge densities I am getting negative values, in the place where the atomic cores would be. I do not have access to the vasp.xml or OUTCAR files, so there is no way to determine whether ...
Pranoy Ray's user avatar
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4 votes
1 answer
303 views

Is there any free software that helps to know specific charge densities or ELFs at any position of the material?

Can anyone suggest some free software that can visualize the charge density and/or electron localization function (ELF)? More importantly, can we determine/know those values (charge density and/or ELF)...
Sak's user avatar
  • 889
4 votes
0 answers
182 views

orca_vpot problem

I'm trying to calculate the electrostatic potential of a molecule. When I try to use the orca_vpot tool, I am facing some difficulties detailed below. The first ...
vifontenelle's user avatar
3 votes
0 answers
23 views

Assistance Needed in Replicating Charge Density Difference Plot for g-C3N4/Pt System

I'm currently facing a challenge in replicating the charge density difference (CDD) plot showcased in Figure 7(b) of this paper. Specifically, I'm attempting to reproduce the CDD plot for the ...
Nidhi Tiwari's user avatar
3 votes
0 answers
190 views

Why is my post-processing calculation using Quantum ESPRESSO not complete after 9 hours? [closed]

I'm working on an i7 laptop with the parallel version of Quantum ESPRESSO (8 processors are running). I ran a post-processing calculation by ...
Camilla's user avatar
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3 votes
0 answers
1k views

PDOS calculation with Quantum Espresso (need help for further analysis) [closed]

I have two silicon in an unit cell, for a test calculation. Each silicon as 12 electrons in the pseudopotential (1s is frozen). I have done the partial density of states (PDOS) calculation using DFT ...
Sak's user avatar
  • 889
3 votes
0 answers
49 views

Is there any relation between electride and an electron localization function (ELF)?

I would like to know if there is any correlation between the ELF values with materials in the electronic phase, versus with the electride phase?
Sak's user avatar
  • 889
2 votes
1 answer
547 views

2D charge density contour plot (how to get arbitrary 'Z' values in the plot using python)

I need to generate a contour plot from a file (named abc.gnu) which has X, Y and Z columns of data. It has 1000000 rows of data. I have got the contour plot with a python code (shown at the end). What ...
Sak's user avatar
  • 889
2 votes
1 answer
75 views

What is the basic equation for total charge calculation from a 3D cube file of charge density file?

I have a 3D charge density file, calculated from Quantum Espresso DFT. If someone calculates the total charge (number of electrons) of an unit cell from that cube file (using a numerical approximation ...
Sak's user avatar
  • 889
2 votes
0 answers
19 views

CDD on the surface of a slab and in other types of (finite) systems

What would be the appropriate method of calculating the difference in charges for this type of system? For composite systems it is usually something like: $$ \Delta\rho = \rho_{system}-\sum_{i=1}^{N}\...
Gabriel Elyas's user avatar
2 votes
0 answers
113 views

|psi|^2 calculation (1D) for diamond structure silicon not showing full dataset for all bands: Quantum ESPRESSO [closed]

Dear Quantum ESPRESSO users, I was trying to calculate the |psi|^2 calculation (1D) for diamond structure silicon at a single kpoint (gamma point). I have used the semicore pseudopotential that ...
Sak's user avatar
  • 889
2 votes
0 answers
79 views

How to plot a charge density from a CHGCAR file in Python? [duplicate]

I can convert a CHGCAR file on the NxNxN grid into a 3D array of shape (N,N,N) for better handling, if that helps. At the end of the day, I want plot/visualize the ...
Pranoy Ray's user avatar
  • 1,631
1 vote
1 answer
86 views

Interstitial charge from a cube file: Need help in python coding

I have a test material- two silicon atoms in an unit cell. This particular structure shows evidence of having interstitial charge between the two atoms. I need to find out the amount of this ...
Sak's user avatar
  • 889
1 vote
0 answers
397 views

VASP DOS WARNING: charge density file is incomplete ERROR: charge density could not be read from file CHGCAR for ICHARG>10 [closed]

I'm working with a system of 192 atoms. I've already relaxed the structure (with ISIF=2 and ISMEAR=0) and achieved the required ...
Trivaani Yadav's user avatar
1 vote
0 answers
190 views

How to perform Bader charge analysis in QUANTUM ESPRESSO? [closed]

Suppose I have a test calculation, for two atoms in an unit cell. I have the charge density files in 1D and 3D, calculated using pseudopotential approach. How can I do the Bader analysis with QUANTUM ...
Sak's user avatar
  • 889
1 vote
0 answers
70 views

Inelastica Pakage [closed]

I'm use the Inelastica package to compute MPSH states and analyze the (HOMO/LUMO). For that, I run the Eigenchannels command with : ...
Hananab's user avatar
  • 369
0 votes
0 answers
26 views

What (executable) command to calculate charge density using quantum espresso? [duplicate]

I'm trying to calculate the charge density of a structure using quantum espresso, I've already used the DENS.X and DEN.X commands, but in both tests the executable not found error appears. Can someone ...
Caroline Santos 's user avatar