Questions tagged [software-assistance]

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

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Reactor design DCPLS parapmeter

I have the following error in the design of reactor in Aspen+. How can I solve this issue
Laman Alipashayeva's user avatar
5 votes
1 answer
135 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
2 votes
0 answers
26 views

How to compile VASP for non-colinear calculations?

How to compile VASP for non-colinear calculations? How to compile VASP without the flag -DNGXhalf and -DNGZhalf?
sangeeta's user avatar
1 vote
0 answers
17 views

Removing "say XYZ.PRF:" name in winplotr in Fullprof?

I am facing difficulty on removing text like XYZ.PRF:, when we run fullprof in External applications in WinPLOTR. Is there some way to remove it?
Anshul Sharma's user avatar
5 votes
0 answers
126 views

How do I install Quantum ESPRESSO on Windows 10?

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
3 votes
1 answer
235 views

How to compile Quantum ESPRESSO on CentOS 7?

I am trying to install Quantum ESPRESSO on a cluster running on CentOS 7. I do not have admin privilege on this cluster. The compilation with make always exits with ...
Abdul Muhaymin's user avatar
3 votes
1 answer
185 views

Comparison between the ordering of Molecular Orbital coefficients between Gaussian and PySCF

I am trying to compare the Molecular Orbital coefficients obtained from PySCF and G09 program. Below is the PySCF and Gaussian input and output. I am using 3-21G basis and RHF method for both the ...
Pro's user avatar
  • 934
8 votes
1 answer
396 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
4 votes
0 answers
210 views

Why VESTA displays much more atoms beyond the cell boundaries?

I was trying to follow this recipe, NanoCrystal / Graphene Heterostructure in VESTA step by step but instead of an Au nanocrystal, I put a small graphene nanoflake approximately 3.35 Å on top of ...
Vladislav Gladkikh's user avatar
6 votes
1 answer
233 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
3 votes
1 answer
893 views

Why Windows is not showing in the Dual-Boot menu and boot into Ubuntu directly? [closed]

It's been more than a month that I installed Ubuntu 20.04 on a desktop along side with windows (Probably 10 or 11) that was already on the desktop. Now I noticed that the computer boot directly into ...
Camilla's user avatar
  • 2,049
7 votes
1 answer
847 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
3 votes
1 answer
249 views

Error in running Python file using ASE library

I am trying to run a Python script using ASE library, I have installed ASE using this page and run my Python script using this library on my terminal. I have made a virtual env named 'MLC_env' and ...
Formal_this's user avatar
3 votes
1 answer
904 views

ORCA: Getting the error "mpirun noticed that process rank 0 with PID 383161 on node exited on signal 11 (Segmentation fault)."

I am getting a segmentation fault error when running the following input file below. The calculation runs fine in gas phase and CPCM modes, but fails with SMD. What could be the issue? Some are saying ...
learner254's user avatar
2 votes
1 answer
216 views

Why does CCSD work, but not CCSD(T), after reading an FCIDUMP in PySCF?

CCSD(T) works after an RHF calculation: Input: ...
Nike Dattani's user avatar
  • 34.7k
3 votes
2 answers
253 views

Is this "internal error" reproducible when compiling OpenMolcas on other Intel compilers?

The procedure I've been following to build OpenMolcas with an Intel Fortran compiler in the Compute Canada environment is as follows: ...
Nike Dattani's user avatar
  • 34.7k
3 votes
1 answer
85 views

Error when trying to compile (after everything else has been done) GAMESS on Windows/WSL

I requested a copy of GAMESS, downloaded it, installed ATLAS because the config file said "please download a math library" and built ATLAS. I then tried to compile it using the compall file. ...
Kanghun Kim's user avatar
1 vote
1 answer
71 views

How do I install the beta5 version of PSI4 on my WebMO Basic server?

Installing the basic version of PSI4 on my personal LG Gram 360 (with a Windows OS), used as a my-own WebMO Basic server, was done according to the WebMO tutorial. I then tried to compute the energy ...
Kanghun Kim's user avatar
3 votes
1 answer
709 views

problem with the installation of g16 with gaussview under Linux

I don't know how to install the g16 with gv under Linux. According to the internet the installation seems to require a file called a tar.gz which I don't find in the g16 folder. I have a lot of files ...
diamond999's user avatar
3 votes
0 answers
33 views

Problem with installation of Multiwell Software package and open mpi [closed]

I'm trying to install Multiwell including Thermo. The manual says under 1.4. that I have to install openmpi before. So I followed the instructions from the multiwell manual but get an error at 8.) &...
Andrea's user avatar
  • 856
2 votes
0 answers
574 views

Autodock prepare_receptor4.py script gives error while converting pdb files to pdbqt files [closed]

Cross-posted on Chemistry.SE. I am trying to make pdbqt files from pdb files for Docking with Autodock vina but getting errors while running the prepare_receptor4.py script present in the mgltools ...
user3765252's user avatar
3 votes
1 answer
226 views

QUANTUM ESPRESSO, How to force ./configure to use intel oneAPI compilers?

I recently installed Intel® oneAPI Base Toolkit and Intel® oneAPI HPC Toolkit using the cimmands: sudo yum install intel-basekit sudo yum install intel-hpckit The ...
Derive D1's user avatar
  • 135
3 votes
0 answers
734 views

Installation of GaussView on Linux Ubuntu 20.04.2 ARM [closed]

Has someone made some experience with installing GaussView for Linux on an Ubuntu ARM64 virtuelle maschine? I work with an Mac M1 Chip MacBook Pro and GaussView is the only program I need to run on ...
Andrea's user avatar
  • 856
2 votes
0 answers
381 views

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

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 ...
Jack's user avatar
  • 1,997
4 votes
1 answer
135 views

How to install the optional LAMMPS package DPD-REACT in MacOS?

I have installed LAMMPS on my mac-pro (OS Monetery), using this. I installed Homebrew and then LAMMPS. I need to install DPD-REACT package. I tried ...
Delaram Nematollahi's user avatar
3 votes
1 answer
441 views

Domain decomposition error while applying bonded restraints - GROMACS

GROMACS version:version 2021.3-MODIFIED GROMACS modification: Yes Hi, I have a small system with 87 residues of a protein. And I want to maintain the tertiary structure of the protein, so I came up ...
Vasista's user avatar
  • 1,291
5 votes
1 answer
209 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
  • 921
3 votes
1 answer
865 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 ...
Jack's user avatar
  • 1,997
1 vote
1 answer
1k 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 ...
Avrana's user avatar
  • 79
3 votes
0 answers
479 views

Segmentation fault with ORCA-3.0.1 [closed]

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 ...
TobiR's user avatar
  • 343
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
4 votes
1 answer
186 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 ...
Jack's user avatar
  • 1,997
5 votes
1 answer
615 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
  • 1,997
6 votes
0 answers
310 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
  • 1,997
7 votes
2 answers
750 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
  • 1,997
3 votes
1 answer
677 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 ...
Jack's user avatar
  • 1,997
3 votes
1 answer
118 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 ...
Jack's user avatar
  • 1,997
5 votes
1 answer
120 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
  • 1,997
7 votes
0 answers
446 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
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
  • 1,997
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
6 votes
0 answers
575 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
10 votes
3 answers
3k 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
8 votes
1 answer
401 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
6 votes
0 answers
90 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
4 votes
0 answers
547 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: ...
ali farajimohammad's user avatar
7 votes
1 answer
540 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
  • 1,392
8 votes
1 answer
82 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
5 votes
2 answers
152 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
  • 6,741
8 votes
2 answers
2k 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