Questions tagged [software-assistance]
Questions asking for assistance with the use or compilation of a software.
76
questions
10
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1
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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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- 406
5
votes
0
answers
229
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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 ...
- 33.6k
7
votes
0
answers
114
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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:
...
- 15.2k
7
votes
1
answer
560
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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 ...
- 10.8k
5
votes
2
answers
142
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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.
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- 15.2k
13
votes
1
answer
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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 ...
- 15.2k
11
votes
1
answer
235
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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 ...
- 1,728
6
votes
1
answer
243
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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/).
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- 1,728
8
votes
1
answer
210
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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 ...
- 33.6k
7
votes
2
answers
4k
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Converting SDF to PDBQT using OpenBabel
I want to convert several molecules from sdf format to pdbqt using OpenBabel.
However, I can't find ...
- 21
6
votes
2
answers
223
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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 ...
- 15.2k
8
votes
1
answer
112
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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 ...
- 33.6k
11
votes
1
answer
321
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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
5
votes
0
answers
328
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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:
...
- 33.6k
8
votes
1
answer
501
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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 $1 \,\mathrm{atm}$...
- 33.6k
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 ...
- 10.8k
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 ...
- 33.6k
11
votes
0
answers
148
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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 ...
- 33.6k
6
votes
0
answers
255
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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 ...
- 33.6k
8
votes
1
answer
264
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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 ...
- 2,544
11
votes
2
answers
2k
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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:
...
- 15.2k
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 ...
- 7,957
7
votes
0
answers
757
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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....
- 33.6k
8
votes
2
answers
133
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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:
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- 33.6k
11
votes
0
answers
289
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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 ...
- 33.6k
5
votes
1
answer
1k
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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 ...
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