Skip to main content

Questions tagged [software-assistance]

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

Filter by
Sorted by
Tagged with
2 votes
1 answer
17 views

Error running USPEX with VASP locally

I am a beginner in USPEX, particularly trying to run EX01. However, I am running into the following errors: ...
sourav guha's user avatar
1 vote
0 answers
17 views

(AMBER) Questioning how mask works in MMPBSA

Note: this question was also posted on the AMBER mailing list, but I reposted this question here because I needed answers for this question quickly. Sorry if this is violating any rules... Dear AMBER ...
Leo's user avatar
  • 67
4 votes
0 answers
105 views

A problem to compile the Quantum ESPRESSO with external libraries

I try to compile the Quantum ESPRESSO (QE) using the following external libraries: fftw-3.3.10, lapack-3.12.0, ...
SFriendly's user avatar
  • 1,007
2 votes
0 answers
32 views

Compilation error of quantum espresso [closed]

During installation of quantum espresso 7.3.1, I am getting error mentioned in the code block below: [to be added later] I am using cmake version 3.22 and latest ...
Rafi Ullah's user avatar
4 votes
1 answer
44 views

siesta 5.0 compilation issues with spack

I installed spack and a more recent gcc (v13). I followed the steps in the doc. I started with the installation of the serial version using: $ spack install siesta -mpi build_type=Debug However, ...
Boubacar's user avatar
  • 103
2 votes
0 answers
39 views

How to install and run daltonproject with dalton project?

I have downloaded and installed daltonproject as well as dalton program but when I try to run a script through Python I got this error: ...
diamond999's user avatar
6 votes
1 answer
198 views

Using the same input (MINP) file, why does MRCC fail with a "normal" fort.55 file, but succeeds with a longer fort.55 file that has duplicate entries?

I have the following fort.55 file: ...
Jaafar Mehrez's user avatar
6 votes
1 answer
140 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
3 votes
0 answers
121 views

Installing Material Studio on Linux (CentOs cluster) for a non-root user

I am a beginner and want to install Material Studio in CentOs (version 7) cluster. Is there anyone have detailed tutorial or information for installing Material Studio in linux? My tries: I used ...
Martin's user avatar
  • 31
2 votes
2 answers
220 views

Does any one know about Quantum Espresso and Burai?

Can some one please help me in installing Quantum Espresso? Is the software available for Windows or it only for Linux? And I read that Burai is GUI for Quantum Espresso, is it?
PriZarah's user avatar
  • 409
4 votes
0 answers
101 views

How to Change the Color Palette of Atoms in ASE GUI

I know that there is a configuration file called gui.py that would be initialized if it is placed in a directory like ...
Jaafar Mehrez's user avatar
2 votes
0 answers
30 views

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
190 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
48 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
18 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
200 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
3 votes
1 answer
379 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 -Free Palestine's user avatar
3 votes
1 answer
286 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
  • 1,056
8 votes
1 answer
417 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
409 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
261 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
993 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
  • 2,209
7 votes
1 answer
2k 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
323 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
1k 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
270 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 - No Free Time's user avatar
3 votes
2 answers
264 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 - No Free Time's user avatar
3 votes
1 answer
90 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
75 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
897 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
35 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
700 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
281 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
862 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
402 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
  • 2,067
4 votes
1 answer
146 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
508 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
  • 1,371
5 votes
1 answer
244 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
  • 991
3 votes
1 answer
1k 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
  • 2,067
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
586 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
4k 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
215 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
  • 2,067
5 votes
1 answer
719 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
  • 2,067
6 votes
0 answers
377 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
  • 2,067
7 votes
2 answers
839 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
  • 2,067
3 votes
1 answer
753 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
  • 2,067
3 votes
1 answer
174 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
  • 2,067
5 votes
1 answer
135 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
  • 2,067
7 votes
0 answers
561 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