Questions tagged [software-assistance]

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

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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 ...
Jack's user avatar
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4 votes
1 answer
124 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
4 votes
0 answers
151 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
4 votes
0 answers
508 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
3 votes
1 answer
224 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
149 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
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3 votes
2 answers
247 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
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3 votes
1 answer
594 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
1 answer
774 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
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3 votes
1 answer
175 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
798 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
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3 votes
1 answer
83 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
3 votes
1 answer
395 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
3 votes
1 answer
787 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
3 votes
1 answer
200 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
1 answer
89 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
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3 votes
0 answers
32 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
  • 816
3 votes
0 answers
672 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
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3 votes
0 answers
409 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
3 votes
1 answer
632 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
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2 votes
1 answer
205 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
  • 33.6k
2 votes
0 answers
499 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
2 votes
0 answers
357 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
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1 vote
1 answer
67 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
1 vote
1 answer
984 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
1 vote
0 answers
20 views

Log_linearization [migrated]

Can any one please suggest me how to log-linearize the utility maximization of the Ricardian households in a closed economy DSGE model. The equation is bellow :
Yetsedaw Emagne's user avatar

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