13
Incidentally, I initiated some discussions along these lines in these questions for HF-DFT (also called 'density-corrected' DFT) here,
and here. I'm familiar with Quantum ESPRESSO, so I can detail a procedure with QE. If you want to generate a Hartree-Fock density, you can just turn on a hybrid functional (say HSE06) and turn up the fraction of exact ...
11
Due to the enhanced coulomb interaction and the quantum confinement effect in the two-dimensional limit, the optical properties should be investigated with the GW+BSE method.
The practical calculation flow is the following if you are considering using VASP
Perform a ground state DFT or hybrid calculation.
Based on previous converged charge density and ...
11
The VASP manual is always the first resource to check, you can find it here. As a beginner, following "Getting Started" should help you greatly, from how to install the code, some details of the background theory, and how to run simple calculations.
8
I assume that you have relaxed your geometry structure. The single point energy calculation also called the self-consistent field calculation (SCFC), the central quantities outputted by it are:
Total energy
Charge density
Wavefunction
In particular, the charge density and the wavefunction are the two key quantities to perform non-self-consistent ...
6
Since you know how to use Avogadro to create XYZ files, a very simple solution to your problem is to simply create the XYZ file then use an xyz2gen script to convert fron XYZ format to the GEN format you seek. This is an example of a script that converts from XYZ to DFTB+ format.
The beauty of the GEN format of DFTB+ is that with only a few lines, you can &...
5
You could do this by just modifying the first line of the file.
But here are some more general purpose utilities you could use (note it requires the re module)
def read_xyz(
filename,
scale=1.):
""" Read xyz file
Params:
filename (str) - name of xyz file to read
Returns:
geom ((natoms,4) np.ndarray) - ...
4
So this question is related to the recent discussion in Procedure to classify errors in Kohn-Sham DFT where I already gave the general procedure: get the density from some level of theory, and use it to run a single-point DFT calculation.
This question was about how to do this in Q-Chem; it's actually quite simple. Here's an example input for a calculation ...
4
One way could be as follow.
Download software PACKMOL.
Download the examples files (tar.gz or zip).
Modify the file solvprotein-comment.inp: removing the info about the protein, and the ions and define the number of water molecules and the size of the droplet:
#
# Protein solvated by water and ions
#
# All atoms from diferent molecules will be at least 2....
3
If your structure is relaxed. The total energy can be calculated with a self-consistent calculation.
An INCAR template you may refer to:
System:
ISTART=0
ICHARG=2
ENCUT=500
EDIFF=1E-6
NELM=300
ISMEAR=0
SIGMA=0.05
IALGO=38
##Spin-related
#ISPIN=2
#MAGMOM=17*0
#LSORBIT=.TRUE.
#SAXIS= 0 0 1
#ISYM=0
##Output:
...
3
It should be easy to achieve what you want with a bash script. For a file named test.xyz, it can be achieved with:
fname=test.xyz
nlines=`wc -l $fname | awk '{print $1}'`
natoms=$((nlines-2))
sed -i "1s/.*/$natoms/" $fname
This follows the logic given in the answer by @Prasanta. It should be easy to change this to a script taking the filename as ...
3
More a comment than an answer, note that e.g., for methane
5
C 0.92745 -0.05402 0.04264
H 2.01965 -0.05402 0.04264
H 0.56338 0.81142 0.60065
H 0.56338 -0.96998 0.51313
H 0.56338 -0.00348 -0.98585
the first line including 5 (in this example) ...
2
This is a strange type question. First, there is something wrong with the xyz file having total 5 columns.
For you answer,
Find total row number (let it be r)
calculate r-2 (since the format of the xyz is that after the total number of atoms, there is a gap followed by atomic coordinates. The end of atomic coordinate specifications ends the file)
replace ...
1
If I'm interpreting the manual correctly, it is not possible to define a complex external potential in CP2K. It specifies that the VALUES keyword to define the corresponding PARAMETERS of your potential has to be real. I don't know anything about the internal code of CP2K, so I don't know if this would be a simple modification of the code to accept complex ...
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