Questions tagged [software-assistance]
Questions asking for assistance with the use or compilation of a software.
73
questions
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
13
votes
1
answer
2k
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Why does Gaussian ignore the opt=maxcycles keyword for optimizations?
I have been using both Gaussian09 and Gaussian16 recently to optimize some metal complexes. The Gaussian manual (for both versions) indicates that the maximum number of steps in a geometry ...
- 6,436
11
votes
2
answers
2k
views
How to include individual PBC box dimensions in xyz file format compatible with VMD
I am using ASE to write an xyz file. Each frame in the file has a different PBC (periodic boundary condition). Currently, a frame starts like this:
...
- 1,083
11
votes
1
answer
194
views
Pycalphad most efficient way to gather equilibirum phase data for set of alloy compositions?
What's the most efficient way to get the equilibrium phases and phase fractions for a set of alloy compositions? For context, I'm coming from Thermo-Calc/TC-Python where I would just loop through the ...
- 693
11
votes
1
answer
1k
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Calculating RMSF in VMD
As a part of my coursework I have to calculate root mean square of fluctuation (RMSF) of a protein trajectory over the last 5 nanoseconds of simulation. I have used the inbuilt ...
- 433
11
votes
1
answer
302
views
Unable to recreate data for benzene from paper in GROMACS 2020.5
I have been trying to simulate benzene in OPLSS-AA forcefield as per this paper: https://pubs.acs.org/doi/10.1021/ct2002122. I have been at a loss, since I believe I have everything running as per the ...
- 4,141
11
votes
0
answers
268
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I ran TDDFT on some small molecules. For some files, the ORCA output files cut short and contain no absorption data. What could be the reason? [closed]
Below is just the end of the output file, and the top of the input file. This is for the molecule FDICTF. The calculation did not run out of time. I ran a batch of 15 molecules, all with same ...
- 331
11
votes
0
answers
143
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Setting multiple new atype/dtype/itype with LAMMPS fix bond/create [closed]
When creating a new bond in a LAMMPS simulation with the command fix/bond create it is likely new angles/dihedrals/impropers be need to be set. This can be done with the atype/dtype/itype arguments ...
- 331
10
votes
3
answers
3k
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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:
<...
- 643
10
votes
1
answer
387
views
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.
...
- 589
9
votes
1
answer
2k
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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-...
- 1,938
9
votes
1
answer
783
views
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 ...
- 1,631
8
votes
1
answer
379
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 ...
- 151
8
votes
1
answer
209
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Avogadro for Linux -- Input Generators and Submitting Job to QM software?
Regarding input generators for a Linux (Linux Mint 20.1 Xfce) version of Avogadro2, I have managed to get this working using the Flatpak version and copying the input generator python scripts from ...
- 121
8
votes
1
answer
1k
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How to get the .47 file from ORCA for natural bonding orbital analysis
I am trying to perform NBO analysis with relaxed density matrix with the open-source program JANPA. I am following the guide here. The first step is to get the NBO input .47 file from Orca v4.2.1. The ...
- 6,436
8
votes
1
answer
294
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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 ...
- 589
8
votes
1
answer
109
views
How to solve this Bandup software problem?
I have compiled the Bandup software using this command : ./build -compiler gfortran. After that, I tried to follow the tutorial inside the directory ...
- 5,643
8
votes
1
answer
240
views
Reading in E-field with CP2K
I have figured out a way to input a custom electric field in a .cube format, but I am not sure I am doing it in the proper way. Currently my file contains information for the magnitude of the electric ...
- 693
8
votes
2
answers
130
views
Vacancy with USPEX
I am using USPEX code. I would like to create structures with vacancies. I defined in the file "INPUT.txt" vacancy as Vc, but it stopped and said:
...
- 2,025
8
votes
1
answer
460
views
Modelling water using the TIP3P flexible system [closed]
I am modelling water using a TIP3P flexible system. I am using the pair, bond and angle parameters given on the LAMMPS webpage. I am trying to run an $NPT$ simulation at $298\,K$ and $1 \,\mathrm{atm}$...
- 4,141
8
votes
1
answer
74
views
Error when using pycotem to index an electron diffraction pattern?
In the pycotem code, this error comes up when using the Diffraction GUI.
...
- 151
8
votes
0
answers
283
views
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. ...
- 445
7
votes
2
answers
650
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 ...
- 1,938
7
votes
2
answers
3k
views
Converting SDF to PDBQT using OpenBabel
I want to convert several molecules from sdf format to pdbqt using OpenBabel.
However, I can't find ...
- 367
7
votes
1
answer
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 ...
- 79
7
votes
1
answer
1k
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How to sort using ase.build.sort?
I am trying to sort a set of Cu atoms in a fcc (non primitive) crystal structure according to their Z cordinate. I am using ase.build.sort to do this with the help ...
7
votes
1
answer
899
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, ...
- 643
7
votes
1
answer
436
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:
...
- 1,095
7
votes
0
answers
317
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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 ...
- 101
7
votes
0
answers
101
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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:
...
- 151
7
votes
0
answers
719
views
Calculating band structure with HSE using Open_grid (Quantum ESPRESSO) [closed]
I have executed the SCF calculation and obtained the results. After which I used kmesh.pl to extract k-points. I was able to run wannier calculations but there was an error
Checking info from wannier....
6
votes
4
answers
2k
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 ...
- 1,631
6
votes
2
answers
219
views
Excited state normal mode frequency doesn't match for NH3
I am trying to optimize the geometry of excited state NH3 and get the corresponding normal modes for excited states. I am trying to get the frequencies as mentioned in this reference. They claim to ...
- 345
6
votes
1
answer
234
views
Pycalphad "Failed while parsing" Yttrium from light alloys database
The code in question is just 2 lines used to import the "COST507 database for light alloys" (downloaded from the opencalphad homepage http://www.opencalphad.com/).
...
- 693
6
votes
1
answer
509
views
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 ...
Malena Rybacki
6
votes
1
answer
198
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:
<...
- 268
6
votes
0
answers
209
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?
- 1,938
6
votes
0
answers
480
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 ...
- 61
6
votes
0
answers
86
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 ...
- 455
6
votes
0
answers
217
views
Why does Thermo-Calc one axis equilibrium calculation get stuck in never ending loop? [closed]
I've been trying to run a Thermo-Calc one axis equilibrium calculation on some quaternary alloys in the TCHEA4 database. Most of the calculations work fine, but for some alloys it gets stuck in a loop ...
- 693
5
votes
2
answers
131
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.
...
- 6,436
5
votes
1
answer
466
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 ...
- 1,938
5
votes
1
answer
102
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 ...
- 1,938
5
votes
1
answer
253
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:
...
- 2,003
5
votes
1
answer
169
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 ...
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5
votes
1
answer
932
views
How to calculate RMSD with GLIDE?
I need to calculate the RMSD between a co-crystallized ligand and my ligands and a non-co-crystallized ligand with GLIDE but I don't know how. Could someone explain to me how to do it? Many thanks in ...
- 457
5
votes
0
answers
318
views
Cannot import both numpy and LAMMPS to python after installing with conda [closed]
I installed the module LAMMPS by using this command
conda install -c conda-forge lammps
I want to import LAMMPS to python code, but it says:
...
- 2,025
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votes
0
answers
213
views
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 ...
- 1,658
4
votes
1
answer
136
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 ...
- 1,938
4
votes
1
answer
112
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 ...
