Questions tagged [software-assistance]

Questions asking for assistance with the use or compilation of a software.

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Why does the GPU version of VASP consume a lot of time on STRESS calculation?

I am trying to compare the CPU and GPU versions of VASP.6.3.0, it seems that the GPU version consumes a lot of time on the STRESS item, does it represent the time for calculation stress tensor? Here ...
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2 votes
1 answer
98 views

NCORE bigger than 1 when performing phonon/vibrational calculation(IBRION=5) in VASP?

When I try to calculate the vibration frequency of TiO2, I set IBRION=5 in VASP, but it turns out I couldn't use NCORE>1 in this situation, once I use NCORE>1, VASP would run for only one ionic ...
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1 vote
1 answer
123 views

Repeated error in Quantum Espresso "Error in routine potinit (1)"

I have been trying to perform some calculations in Quantum espresso on mono-layer Borophene. Initially, I have optimized the structure which succeeds. Subsequently, I am trying to use this optimized ...
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3 votes
0 answers
89 views

Segmentation fault with ORCA-3.0.1

I would like to use ORCA-3.0.1 under the following Linux version: 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux and Intel version ...
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  • 343
6 votes
3 answers
483 views

Unable to install P4Vasp

I am currently learning how to use VASP and was looking at how to get the DOS plots. I have been recommended to use P4VASP but due to some reason I am not able to install it on my Ubuntu 20.04. When I ...
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4 votes
1 answer
56 views

Using pseudo-hydrogen in VASP results in the wrong format in CONTCAR

I am using VASP to do the simulation of a slab, I used some pseudohydrogen to passivate the bottom side of the slab. After the structure optimization calculation, the ...
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  • 1,601
5 votes
1 answer
82 views

The standard format and parser of VASP output files

I see a lot of post-processing tools for VASP, including ASE, VASPKIT,Pymagten and some other customized codes. They all read the VASP output files like a normal text file. Sometimes I would meet ...
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  • 1,601
6 votes
0 answers
43 views

The workflow of VASP [closed]

I am trying to understand the workflow of VASP, so I make a simple diagram to show how VASP updates the related file during iteration. Did I make it right?
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7 votes
2 answers
231 views

Does SCF calculation have to be done before calculating DOS?

The standard procedure to calculate DOS or band structure is: Structure optimization, SCF calculation, non-SCF calculation. According to the vasp wiki, it is because: Mind: Since the charge density ...
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  • 1,601
3 votes
1 answer
122 views

How could I generate the parameter of 'selective dynamics' in POSCAR with ASE?

I often use selective dynamics to do structure optimization in VASP, but I am not sure how to do it when using ASE, it seems I could use the constraint class to tell ASE what I want to do. My question ...
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3 votes
1 answer
24 views

How to keep the freedom of an atom along a specific direction in VASP?

I am trying to relax my model's structure by letting some atoms could move freely along some specific direction, in VASP, I could set selective dynamics, but it seems I could only adjust the freedom ...
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5 votes
1 answer
47 views

What is vaspcmd in job.sh of the official VASP examples?

There is job.sh script in a lot of official VASP examples, for example: Graphite MBD binding energy. it is used to help submit job on supercomputer But in the script, it usually uses ...
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7 votes
0 answers
57 views

Pymol is not opening after startup [closed]

I installed open-source pymol software using miniconda4 which have been installed successfully. I worked with the software, but whenever I am shutting down my PC and again restarted, the >pymol ...
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8 votes
1 answer
313 views

What is the detailed difference between Vasp_std and Vasp_ncl?

I am trying to figure out the difference between vasp_std, vasp_gam, and vasp_ncl. I find some related details on the Vasp forum, I think vasp_gam makes some customized optimization for the gamma-...
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  • 1,601
7 votes
1 answer
265 views

How do I compile Quantum Espresso with HDF5 support? (Linux)

I've previously installed the Quantum Espresso (QEsp) binaries using "apt install" on an Ubuntu 16.04.7 LTS distro. This has worked fine, except that calculations don't produce .hdf5 output, ...
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6 votes
0 answers
124 views

How do you perform parallelization of NEB-TS in ORCA? [closed]

I have tried running a NEB-TS calculation in orca with %pal nprocs 32, but I get an error saying ...
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8 votes
2 answers
848 views

Installing Quantum Espresso on an Apple M1 processor possible?

I'm attempting to make QEspresso's pw program on a new 2021 MacBook Air, which has an M1 processor. While ./configure does not throw any errors, running 'make pw' fails with the following output: <...
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8 votes
1 answer
107 views

How to use VEDA to analyze vibrational energy distribution?

In my bachelor thesis, I am trying to use the VEDA program to analyze the vibrational energy distribution to associate different vibrations to the calculated modes from gaussian. I am stuck now ...
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6 votes
0 answers
50 views

Why does the GUI not run after the installation of FullProf Suite? [closed]

I installed Fullprof_Suite_March2021_Linux64.tgz in Ubuntu 18.04. I also installed "libmotif-common" libraries. But all the GUIs are not opening. Why is ...
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4 votes
0 answers
136 views

How to compile VASP without the flags -DNGXhalf and -DNGZhalf? [closed]

I'm trying to do spin-orbit coupling calculations with VASP but when I started to run them, I got this error: ...
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6 votes
0 answers
216 views

Error while installing ShengBTE

I am trying to install the thirdorder script that is mean to work in tandem with ShengBTE on an Ubuntu OS, but I'm getting the following error: ...
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8 votes
1 answer
57 views

Error when using pycotem to index an electron diffraction pattern?

In the pycotem code, this error comes up when using the Diffraction GUI. ...
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  • 151
5 votes
2 answers
92 views

How to use fractional numbers as arguments for keywords in Gaussian input?

I have used both Gaussian09 and Gaussian16 and one thing that seemed unusual to me is that I was unable to enter any fractional number as one of the arguments for a keyword in the Gaussian input file. ...
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  • 5,544
6 votes
1 answer
845 views

Emission and absorption UV-Visible spectrum using GAUSSIAN-09

I am currently studying the UV-visible spectrum of ethylene using GAUSSIAN-09. I optimized the ground state(# opt b3lyp/6-31g geom=connectivity) then used the ...
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8 votes
1 answer
308 views

Error while doing a band structure calculation in Quantum ESPRESSO

I have been using BURAI GUI of Quantum ESPRESSO to calculate the optical properties of ZnSe quantum dots. But first I wanted to calculate the electronic band structure. After running the calculation ...
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7 votes
0 answers
56 views

Convert standard image file format to py4DSTEM datacube? [closed]

I want to analyze a diffraction pattern. Py4dSTEM is asking for a datacube to start with. I thought it might be able to convert an image to this format: ...
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  • 151
12 votes
1 answer
610 views

Why does Gaussian ignore the opt=maxcycles keyword for optimizations?

I have been using both Gaussian09 and Gaussian16 recently to optimize some metal complexes. The Gaussian manual (for both versions) indicates that the maximum number of steps in a geometry ...
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10 votes
1 answer
88 views

Pycalphad most efficient way to gather equilibirum phase data for set of alloy compositions?

What's the most efficient way to get the equilibrium phases and phase fractions for a set of alloy compositions? For context, I'm coming from Thermo-Calc/TC-Python where I would just loop through the ...
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  • 611
6 votes
1 answer
167 views

Pycalphad "Failed while parsing" Yttrium from light alloys database

The code in question is just 2 lines used to import the "COST507 database for light alloys" (downloaded from the opencalphad homepage http://www.opencalphad.com/). ...
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  • 611
6 votes
1 answer
205 views

Downloading ASE (Atomic Simulation Environment) on older versions of Python

I'm trying to install something called ASE that models atomic structures. I have ASE currently installed on python 3.7, however I need to run scripts that can import and recognize ASE in an older ...
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8 votes
1 answer
163 views

Avogadro for Linux -- Input Generators and Submitting Job to QM software?

Regarding input generators for a Linux (Linux Mint 20.1 Xfce) version of Avogadro2, I have managed to get this working using the Flatpak version and copying the input generator python scripts from ...
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7 votes
2 answers
1k views

Converting SDF to PDBQT using OpenBabel

I want to convert several molecules from sdf format to pdbqt using OpenBabel. However, I can't find ...
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  • 367
6 votes
2 answers
198 views

Excited state normal mode frequency doesn't match for NH3

I am trying to optimize the geometry of excited state NH3 and get the corresponding normal modes for excited states. I am trying to get the frequencies as mentioned in this reference. They claim to ...
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8 votes
1 answer
79 views

How to solve this Bandup software problem?

I have compiled the Bandup software using this command : ./build -compiler gfortran. After that, I tried to follow the tutorial inside the directory ...
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  • 5,501
5 votes
0 answers
174 views

Cannot import both numpy and LAMMPS to python after installing with conda [closed]

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: ...
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  • 1,550
11 votes
1 answer
207 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 ...
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  • 3,787
7 votes
1 answer
431 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 ...
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8 votes
1 answer
444 views

How to get the .47 file from ORCA for natural bonding orbital analysis

I am trying to perform NBO analysis with relaxed density matrix with the open-source program JANPA. I am following the guide here. The first step is to get the NBO input .47 file from Orca v4.2.1. The ...
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  • 5,544
11 votes
2 answers
826 views

How to include individual PBC box dimensions in xyz file format compatible with VMD

I am using ASE to write an xyz file. Each frame in the file has a different PBC (periodic boundary condition). Currently, a frame starts like this: ...
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  • 1,083
10 votes
1 answer
185 views

How to create a Potential Energy Surface in Chemcraft?

The Chemcraft website says that it is possible to create a potential energy surface. Nevertheless, it doesn't work for my Gaussian scan job. ...
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  • 589
11 votes
1 answer
480 views

Calculating RMSF in VMD

As a part of my coursework I have to calculate root mean square of fluctuation (RMSF) of a protein trajectory over the last 5 nanoseconds of simulation. I have used the inbuilt ...
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6 votes
0 answers
103 views

Why does Thermo-Calc one axis equilibrium calculation get stuck in never ending loop? [closed]

I've been trying to run a Thermo-Calc one axis equilibrium calculation on some quaternary alloys in the TCHEA4 database. Most of the calculations work fine, but for some alloys it gets stuck in a loop ...
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  • 611
8 votes
1 answer
155 views

Reading in E-field with CP2K

I have figured out a way to input a custom electric field in a .cube format, but I am not sure I am doing it in the proper way. Currently my file contains information for the magnitude of the electric ...
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5 votes
0 answers
120 views

Q-Chem gives "Hessian Appears to have all zero or negative eigenvalues" error when calculating Frequencies [closed]

I have troubles with obtaining spectra for selected molecules in different DFT functionals. I calculate IR spectra for my target molecules (gold complexes with C/H/N/O/S/Au composition) to find how ...
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8 votes
2 answers
113 views

Vacancy with USPEX

I am using USPEX code. I would like to create structures with vacancies. I defined in the file "INPUT.txt" vacancy as Vc, but it stopped and said: ...
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  • 1,550
16 votes
2 answers
1k views

Open Source PyMol Conda Package: UnsatisfiableError

I'm having an issue installing the open-source version of Pymol using Anaconda on Windows. I have Python 3.8.3 installed and when I try to add the package with Conda using ...
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  • 14k
4 votes
1 answer
114 views

PySCF: 2-index and 3-index matrix

The 4-index 2-electron integral can be obtained for the He atom with the following code: ...
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  • 1,769
8 votes
0 answers
174 views

Fix deposit and USER-REAXC: pre-allocating memory for atoms when using LAMMPS with ReaxFF [closed]

I would like to use "fix deposit" with ReaxFF to add atoms to a simulation in which I deposit molecules on a surface. I have built working scripts for my system with other force fields. ...
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  • 445
5 votes
1 answer
397 views

How to calculate RMSD with GLIDE?

I need to calculate the RMSD between a co-crystallized ligand and my ligands and a non-co-crystallized ligand with GLIDE but I don't know how. Could someone explain to me how to do it? Many thanks in ...
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  • 457
11 votes
0 answers
191 views

I ran TDDFT on some small molecules. For some files, the ORCA output files cut short and contain no absorption data. What could be the reason? [closed]

Below is just the end of the output file, and the top of the input file. This is for the molecule FDICTF. The calculation did not run out of time. I ran a batch of 15 molecules, all with same ...
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