Questions tagged [software]

For questions about matter modeling software. Questions can be about usage or recommendations.

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7
votes
1answer
117 views

How do the various programs read or write integrals in FCIDUMP format?

The FCIDUMP format was created by Peter Knowles and Nick Handy circa 1989 and now allows many electronic structure software packages to interact with each other. ...
4
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0answers
24 views

Calculating emission spectrum of organic compounds by DFT. Can someone elaborate in terms of calculating it for aggregatrion induced emission?

I am planning for the calculation of emission spectra of organic compounds showing the phenomenon of aggregation-induced emission (AIE). Can someone help me get started?
11
votes
1answer
159 views

What units are used in Gaussian 16 for dipole derivatives output?

I ran a frequency analysis employing Gaussian 16 on MP2/6-31+G(d,p) level of theory with the keyword iop(7/33=1) in order to have access to dipole derivatives with ...
14
votes
3answers
544 views

Is the DYNAMO code developed by LAMMPS still available?

In 2013 it was stated that v8.8 of DYNAMO was the version mostly used for the last 10-12 years. However I am struggling to find the code repository. It was developed by the LAMMPS developers and is ...
15
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3answers
278 views

What are some codes available for Dynamical Mean Field Theory (DMFT)?

One particularly field of matter modeling is that of strongly correlated materials, heavy-fermion compounds with partially filled 4f or 5f orbitals. In brief, these are materials whose complex ...
8
votes
3answers
92 views

How do you generate 3D electron density from fchk file without the Gaussian software?

I'm trying to reproduce some results from a paper with fchk output files containing DFT calculations. The paper details how to produce the 3D electron density using Gaussian software, but since I don'...
10
votes
1answer
82 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. ...
11
votes
1answer
133 views

Functional group detection from geometry

I am currently looking for an efficient way to detect common functional groups - that is, characterize whether a molecule is an alcohol, an aromatic compound, etc. - in a larger database consisting of ...
28
votes
9answers
645 views

Is there a free package with robust CASSCF functionality?

Among free software packages, which one has robust CASSCF functionality? The FCI solver can be implemented in either way, e.g., direct solver, DMRG, etc.
16
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2answers
395 views

How should I organize and keep track of a huge number of calculations systematically?

Doing matter modeling generates vast amounts of data. We might most probably be working on different projects simultaneously. We definitely will have to revisit old data for revisions, post-processing,...
26
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12answers
705 views

What are the freely available crystal-structure visualization softwares?

I use VESTA mostly for crystal structure visualizations. What other options are available?
13
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4answers
273 views

Is python sufficient for serious tensor network or DMRG calculations?

There are enough tensor-network/DMRG packages that support python (ALPS, OpenMPS, pyUni10) that it would seem (to an outsider) that it's possible to do some substantial work with DMRG without messing ...
27
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9answers
4k views

Which Linux distribution is best for Matter Modeling?

In some science fields there are efforts to provide customized distributions, so you can get a productive environment with minimum set-up overhead. For example, in high energy particle physics, we ...
13
votes
1answer
261 views

GUI for DFT calculations

I am a beginner in DFT. Can someone suggest a good DFT software with a GUI for simulating dipole moments and optical absorption spectra in an organic crystal? I have tried the Burai GUI of Quantum ...
7
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0answers
52 views

Excited states using ORMAS flag in GAMESS

I am trying to calculate the excited states using single reference CISD on $\ce{CH3OH},$ using ORMAS' CI-X option in GAMESS. As a test example I am using the $\ce{CH3OH}$ that has 2 core, 7 occ. ...
12
votes
1answer
92 views

Recent developments in QM/MM for Molecular Dynamics

I am looking for new QM/MM methodologies which have recently developed and implemented into MD packages. Any applications or molecular systems studies with these methods can be used as an example as ...
9
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0answers
81 views

Is there any code that runs WHAM starting from histograms rather than time series?

I'm looking for a way to run the Weighted Histogram Analsys Method, but I don't have a time series to feed to the code as usually happens, but rather I have histograms coming from the debiasing of a ...
11
votes
4answers
714 views

How to make the input generator plugin work in Avogadro 2 on GNU/Linux?

It seems Avogadro was phased out in Ubuntu 20.04 (Focal Fossa) and derivatives like Mint 20 (Ulyana). Now the version available in the repositories is Avogadro 2. If you had Avogadro installed in 18....
8
votes
1answer
75 views

What software can perform block analysis on time sequence data?

I have a .xyz file for a trajectory and I want to perform block analysis on it, and to find the decorrelation time and to perform analysis on that as well. What ...
18
votes
1answer
261 views

How to set up a local server for iQmol on macOS?

I'm trying to set up iQmol as a tool to submit calculations to Q-Chem on our lab machines to make access to it easier for OChem students. Unfortunately, it is not working properly "from the box&...
7
votes
2answers
76 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 ...
4
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1answer
72 views

Excited determinants, electronic partition function and thermochemistry calculation

While studying statistical thermodynamics I came across the partition functions, which connect the quantum world to the macroscopic world. I understand that partition functions are used to calculate ...
24
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4answers
302 views

What are the main computational frameworks used in materials modeling?

What are the main computational frameworks used in materials modeling? Software packages can include those designed to run on both classical and quantum devices.
9
votes
1answer
62 views

What software is a software for RNA tertiary structure prediction?

It seems that the prediction of protein folding is a pretty advanced area. Are there options based on some GDT-like measure? For me, it has relevance in connection with the origin of life (cf. RNA ...
9
votes
1answer
68 views

What software can do RNA secondary structure prediction?

This question is a follow-up to this previous question. I have learnt there that there are reasonable ways to predict RNA tertiary structure. Here I inquire about how to predict RNA secondary ...
13
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0answers
124 views

Empirically determining thermostat damping factor

Is there a way to determine an appropriate thermostat damping factor given a timestep size and a numerical integration method? I am computing a set of simulations in LAMMPS, using ReaxFF, tracking ...
6
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0answers
92 views

Fix deposit and USER-REAXC: pre-allocating memory for atoms when using LAMMPS with ReaxFF

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. ...
9
votes
1answer
86 views

What do the parameters at the top of an FCIDUMP file mean?

A while ago I wrote a simple program that takes in an FCIDUMP file (generated by MOLRPO) and can determine matrix elements (or ...
27
votes
2answers
445 views

How is Julia used in Materials Modeling?

What are the main uses and applications of Julia in Materials Modeling? Python for example is used in codes such as kwant, ...
13
votes
3answers
205 views

Is there a (free) GUI to setup transport calculations using SIESTA?

I am very interested in doing transport calculation with SIESTA. My problem is that it is a little hard for me to understand and setup the input files to be used with TranSIESTA (the module that do ...
30
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5answers
3k views

What is a good replacement for Gaussian?

When I started studying computational chemistry (circa 2007), my supervisor used to tell me about the controversy surrounding Gaussian, Inc. regarding the banning of researchers involved in the ...
10
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2answers
124 views

Programs/Libraries for calculating solvent excluded surface and excluded volume

Given the 3D structure of a molecule (e.g. as *.mol) and a probe radius r, I want to calculate the solvent excluded surface (SES)...
21
votes
5answers
4k views

What software will allow me to combine two images?

I have seen in many presentations and publications, things like a human on a molecule (for example). What software can do this? It's for a presentation I'm doing.
9
votes
1answer
140 views

How to calculate FCI matrix elements from an FCIDUMP file

I'm interested in writing a simple program (as an exercise) that takes an FCIDUMP file (e.g. from a Molpro calculation) and can determine FCI matrix elements (e.g. to construct the entire FCI matrix ...
10
votes
1answer
86 views

How to determine occupied and closed orbitals for a Molpro CASSCF calculation?

I am currently working with Molpro, to which I am completely new, trying to run some calculations on $\ce{PdO}$. From literature I have gathered that the ground state is given by $^3\Sigma^-$ state, ...
19
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5answers
2k views

What software is available to do molecular dynamics on Windows?

Is there a Windows-based molecular dynamics simulation software which is easy to use?
5
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0answers
28 views

Interpreting Critic2 charge analysis in metallic systems

I'm using Critic2 software to perform post-processing of the charge density of metallic alloys. With the charge density obtained from the Self-Consistent-Field calculation (for that I'm using Quantum ...
6
votes
0answers
35 views

What could be the possible causes of the energy difference in the following calculating using Octopus (TDDFT) code?

I am trying to do a simple ground state energy calculation of methane molecule using the Octopus (TDDFT) code. The example is already available in the octopus manual. ...
9
votes
1answer
155 views

How are molecular orbitals constructed from the coefficients and basis set?

When an SCF calculation is done in a QM program, the MO coefficients of the solution are printed into the output. Now, graphical softwares can plot 3D molecular orbitals from these coefficients, ...
17
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2answers
2k views

Calculating HSE06 band structures on Quantum ESPRESSO

I am currently trying to figure out how to compute band structures for my system, using the hybrid functional HSE06. I'm doing this on Quantum Espresso. As I understand, there are a handful of ways to ...
9
votes
4answers
239 views

What programs can do electron integrals and SCF calculations with more than one CPU?

Similar to this question which asks for each answer to provide one software that can do CASSCF: I am interested in software that can do integrals, SCF (Hartree-Fock), and the integral transformation, ...
11
votes
0answers
103 views

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 ...
7
votes
1answer
34 views

The number of long-range interaction pairs in Tinker

I tested MM calculation of a benzene molecule with Tinker. The following is the xyz file used for the input. ...
7
votes
0answers
299 views

Is there any code for local-orbital ab initio tight binding molecular dynamics other than fireball? [closed]

I was searching for a local-orbital ab-initio tight binding implementation of molecular dynamics and Ive found a code called fireball. Ive tried to compile it but the code seems to be buggy and there ...
16
votes
2answers
107 views

Methods for visualising aromaticity

I was wondering what tools there are for visualising aromaticity and anti-aromaticity in molecules, to what quantum chemistry programs they are interfaced, and what other relevant features they have. ...
11
votes
3answers
745 views

How to build a nanocluster?

What are the software tools (if possible open source) or methods we can use for constructing a nanocluster, most preferably with high symmetry such as icosahedron, octahedron, cuboctahedron etc. ?
6
votes
1answer
53 views

How to calculate Transport coeffiecients for 0 D systems?

I would like to calculate the thermal transport coefficients like Thermal Conductivity, Seebeck coefficient etc for thermoelectric 0 D systems (quantum dots, nanoclusters ..etc). For bulk materials, ...
6
votes
1answer
48 views

Understanding QuantumEspresso Toolbox through Maestro

Anyone here uses Quantum Espresso through Maestro can tell me a bit more about the calculation panel setting: I understand that -npools option must be divisible by ...
6
votes
1answer
48 views

Band structure output from Exciting - what are the X units?

I'm using Exciting Code to calculate some electronic band structures. Starting with the example of Si I get sensible output and can plot BAND.OUT and BAND-QP.OUT using PLOT-gwbands.py or directly in ...
17
votes
1answer
308 views

Alternatives to VEDA 4 vibrational energy distribution analysis software?

Said software is useful when you need to assign the peaks in vibrational spectra to different vibrational modes found in a hessian calculation for a given molecule, as described in Jamróz, Michał H. “...