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Questions tagged [software-assistance]

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

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16 votes
2 answers
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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 ...
Tyberius's user avatar
  • 15.5k
15 votes
1 answer
3k 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 ...
S R Maiti's user avatar
  • 6,991
11 votes
2 answers
2k 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: ...
fireball.1's user avatar
  • 1,083
11 votes
1 answer
304 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 ...
sgp45's user avatar
  • 602
11 votes
1 answer
2k 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 ...
Roni Saiba's user avatar
11 votes
1 answer
347 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 ...
megamence's user avatar
  • 4,171
11 votes
0 answers
321 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 ...
Bri's user avatar
  • 341
11 votes
0 answers
153 views

Setting multiple new atype/dtype/itype with LAMMPS fix bond/create [closed]

When creating a new bond in a LAMMPS simulation with the command fix/bond create it is likely new angles/dihedrals/impropers be need to be set. This can be done with the atype/dtype/itype arguments ...
Matt's user avatar
  • 351
10 votes
3 answers
4k 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: <...
Paul Eugenio's user avatar
10 votes
1 answer
504 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. ...
Till's user avatar
  • 589
9 votes
1 answer
3k 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-...
Jack's user avatar
  • 2,057
9 votes
1 answer
1k 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 ...
Parmeet Singh EP 066's user avatar
8 votes
1 answer
406 views

How may I install the latest version of a software?

This is a follow-up of my previous question here: How to address 'saveGraphic: Method not found' error in automating the generation of figures in avogadro using Python?, at which I was told to ...
Aimun Jawed's user avatar
8 votes
2 answers
3k 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 ...
sarah bnm's user avatar
8 votes
1 answer
221 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 ...
Hypersphere's user avatar
8 votes
1 answer
1k 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, ...
Paul Eugenio's user avatar
8 votes
1 answer
1k 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 ...
S R Maiti's user avatar
  • 6,991
8 votes
1 answer
444 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 ...
Till's user avatar
  • 589
8 votes
1 answer
119 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 ...
Chi Kou's user avatar
  • 5,833
8 votes
1 answer
298 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 ...
Jason M Gray's user avatar
8 votes
2 answers
139 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: ...
Binh Thien's user avatar
  • 2,095
8 votes
1 answer
559 views

Modelling water using the TIP3P flexible system [closed]

I am modelling water using a TIP3P flexible system. I am using the pair, bond and angle parameters given on the LAMMPS webpage. I am trying to run an $NPT$ simulation at $298\,K$ and $1 \,\mathrm{atm}$...
megamence's user avatar
  • 4,171
8 votes
1 answer
84 views

Error when using pycotem to index an electron diffraction pattern?

In the pycotem code, this error comes up when using the Diffraction GUI. ...
user3679's user avatar
  • 151
8 votes
0 answers
343 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. ...
geo's user avatar
  • 455
7 votes
2 answers
799 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 ...
Jack's user avatar
  • 2,057
7 votes
1 answer
1k views

How do I install Quantum ESPRESSO on Linux?

People, can someone please help me how to solve this problem with QE 7.0 installation:
Everson Gomes's user avatar
7 votes
2 answers
4k 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 ...
RoyBatty's user avatar
  • 367
7 votes
1 answer
2k 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 ...
Nilabja Kanti Sarkar's user avatar
7 votes
1 answer
670 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 ...
user avatar
7 votes
1 answer
588 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: ...
epsilon02fft's user avatar
  • 1,522
7 votes
0 answers
521 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 ...
Gargi Biswas's user avatar
7 votes
0 answers
127 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: ...
user3679's user avatar
  • 151
7 votes
0 answers
813 views

Calculating band structure with HSE using Open_grid (Quantum ESPRESSO) [closed]

I have executed the SCF calculation and obtained the results. After which I used kmesh.pl to extract k-points. I was able to run wannier calculations but there was an error Checking info from wannier....
Hepsibah Priyadarshini.C's user avatar
6 votes
4 answers
3k 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 ...
Parmeet Singh EP 066's user avatar
6 votes
2 answers
235 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 ...
madhusudana's user avatar
6 votes
1 answer
263 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/). ...
sgp45's user avatar
  • 602
6 votes
1 answer
106 views

wannier90 compilation error (MPI)

I tried to build wannier90 for parallel execution in a fedora system. However, I encounter with the following issue repetitively. ...
wenusara satheekshana's user avatar
6 votes
1 answer
248 views

Why am I getting "AttributeError" when running this Python function?

I installed chemcoord (link to documentation) on MacOS in a fresh Python 3.7 virtual environment. When I tried to run the first line of code from the tutorial: <...
John's user avatar
  • 268
6 votes
0 answers
354 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?
Jack's user avatar
  • 2,057
6 votes
0 answers
625 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 ...
カイル's user avatar
6 votes
0 answers
93 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 ...
Nithyadevi's user avatar
6 votes
0 answers
293 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 ...
sgp45's user avatar
  • 602
5 votes
2 answers
160 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. ...
S R Maiti's user avatar
  • 6,991
5 votes
1 answer
150 views

What is the problem in my gaussian input?

I want to obtain the single point energy of a Ni-complex molecule, with a mixed basis set using the Gen keyword. The input is: ...
Saeed Hp's user avatar
5 votes
1 answer
668 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 ...
Jack's user avatar
  • 2,057
5 votes
1 answer
128 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 ...
Jack's user avatar
  • 2,057
5 votes
1 answer
310 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: ...
Wychh's user avatar
  • 2,167
5 votes
1 answer
228 views

How to download METADISE code?

I have a (possibly trivial) question regarding the METADISE code. I can find the documentation related to this code, but I cannot find the download page or tarball anywhere. Can someone kindly share ...
ansonthms's user avatar
  • 981
5 votes
1 answer
1k 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 ...
Giu's user avatar
  • 477
5 votes
0 answers
173 views

How do I install Quantum ESPRESSO on Windows 10? [closed]

Cross posted on LinkedIn Struggling to install Quantum Espresso on Windows 10 for vital DFT calculations due to missing GitHub libraries. Seeking assistance from the LinkedIn community. If you have ...
86_ Kamran Elyas's user avatar