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Questions tagged [software-assistance]

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

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4 votes
1 answer
30 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, ...
2 votes
0 answers
34 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: ...
6 votes
1 answer
189 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: ...
6 votes
1 answer
121 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. ...
3 votes
0 answers
75 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 ...
2 votes
2 answers
151 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?
4 votes
0 answers
78 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 ...
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
5 votes
1 answer
161 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: ...
2 votes
0 answers
41 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?
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?
5 votes
0 answers
183 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 ...
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:
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 ...
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 ...
3 votes
1 answer
347 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 ...
3 votes
1 answer
260 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 ...
8 votes
1 answer
411 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 ...
4 votes
0 answers
351 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 ...
6 votes
1 answer
250 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: <...
7 votes
2 answers
812 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 ...
5 votes
1 answer
319 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: ...
3 votes
1 answer
959 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 ...
4 votes
1 answer
144 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 ...
3 votes
1 answer
306 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 ...
3 votes
0 answers
825 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 ...
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: <...
2 votes
1 answer
250 views

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

CCSD(T) works after an RHF calculation: Input: ...
3 votes
2 answers
262 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: ...
3 votes
1 answer
86 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. ...
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 ...
3 votes
1 answer
491 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 ...
3 votes
1 answer
844 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 ...
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.) &...
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 ...
7 votes
1 answer
602 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: ...
2 votes
0 answers
674 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 ...
5 votes
1 answer
235 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 ...
3 votes
1 answer
265 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 ...
2 votes
0 answers
399 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 ...
3 votes
1 answer
974 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 ...
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 ...
3 votes
0 answers
555 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 ...
4 votes
1 answer
204 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 ...
5 votes
1 answer
690 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 ...
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, ...
6 votes
0 answers
360 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?
5 votes
1 answer
131 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 ...
3 votes
1 answer
155 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 ...
3 votes
1 answer
738 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 ...