Questions tagged [software-assistance]
Questions asking for assistance with the use or compilation of a software.
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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 ...
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3
votes
1
answer
88
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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 ...
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8
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1
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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 ...
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4
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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
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1
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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:
<...
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7
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2
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647
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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
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1
answer
251
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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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3
votes
1
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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 ...
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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 ...
- 33.1k
3
votes
1
answer
181
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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 ...
- 2,602
3
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0
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588
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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 ...
- 33.1k
10
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3
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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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3
votes
0
answers
580
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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 ...
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2
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1
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166
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Why does CCSD work, but not CCSD(T), after reading an FCIDUMP in PySCF?
CCSD(T) works after an RHF calculation:
Input:
...
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2
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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:
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- 33.1k
3
votes
1
answer
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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. ...
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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 ...
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3
votes
1
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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 ...
- 33.1k
3
votes
1
answer
465
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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 ...
CommunityBot
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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.) &...
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6
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4
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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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7
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1
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434
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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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2
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0
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385
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Autodock prepare_receptor4.py script gives error while converting pdb files to pdbqt files
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 ...
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5
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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 ...
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3
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177
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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 ...
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0
answers
308
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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 ...
- 1,938
3
votes
1
answer
653
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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
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810
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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
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0
answers
353
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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 ...
- 15k
4
votes
1
answer
135
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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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5
votes
1
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456
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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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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
206
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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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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 ...
- 10.7k
3
votes
1
answer
59
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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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3
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553
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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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9
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1
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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-...
- 6,467
6
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0
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471
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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 ...
- 33.1k
7
votes
0
answers
313
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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 ...
- 33.1k
8
votes
1
answer
74
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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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16
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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 ...
- 15k
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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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9
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1
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767
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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 ...
- 15k
8
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1
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293
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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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461
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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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86
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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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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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212
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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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99
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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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6
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499
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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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