Questions tagged [software]

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

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9
votes
1answer
169 views

What software can I use for gas adsorption calculations?

We are from a new research group working on matter modelling. Currently our work has focused mainly on classical Molecular Dynamics (MD), Lattice Dynamics (LD) and ab-initio methods. For these, we ...
18
votes
9answers
4k views

GUIs for Quantum Chemistry... Where are they?

I have a general and maybe a little silly / funny question. Why don't most CompChem or QuantumChem software have a GUI? SIESTA is trying with Simune as far as I know, but even proprietary software ...
6
votes
0answers
33 views

Benchmarking Monte Carlo simulations of polymers

I have written a simulation engine in C++ to run a Monte Carlo simulation of polymers on a lattice. My code basically plants a polymer on a lattice, and performs certain Monte Carlo moves, including ...
28
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15answers
1k views

What are the freely available crystal-structure visualization softwares?

I use VESTA mostly for crystal structure visualizations. What other options are available?
6
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1answer
54 views

Frequency error in Gaussian CASSCF(10,10)

I am stuck in calculating the frequencies of one optimised geometry for naphthalene CASSCF(10,10) with Gaussian 16. I have optimised its geometry and checked the active space is the pi system of it, ...
15
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5answers
438 views

What are some open-source all-electron DFT alternatives to Wien2K?

Since the beginning of the century, Wien2K has proven to be a very powerful player in computational condensed matter and materials physics. Wien2K is an all-electron periodic DFT code based on the ...
17
votes
1answer
179 views

Empirically determining thermostat damping factor

Is there a way to empirically determine an appropriate thermostat damping factor given a timestep size and a numerical integration method? For example, I would like one for the surface and the ...
9
votes
1answer
87 views

What's the Theory Behind Nudged Elastic Band?

I'm interested in doing some calculations to model the interstitial addition of nitrogen into a structure and I'm thinking of using Nudged Elastic Band to do it. From what I have read you start with ...
9
votes
0answers
91 views

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

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 one would usually do, but rather I have histograms coming from the de-biasing ...
6
votes
1answer
55 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 ...
5
votes
1answer
87 views

Modify ORCA orbitals for CASSCF

I have run a HF calculation on naphthalene and I have checked the MOs that have been obtained. Now, I have to select my active and inactive orbitals for CASCF(10,10). As there are 34 occupied orbitals,...
8
votes
1answer
61 views

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 ...
12
votes
7answers
2k views

How do I extract a molecular structure from a CIF file?

When I open a CIF file of a crystal structure in a typical molecular editor like Avogadro, then I just see a few symmetry-unique atoms scattered around the unit cell. But I don't see the full molecule ...
5
votes
1answer
42 views

What is the meaning of Coulomb Subtraction?

Specifically, in the General Utility Lattice Program (GULP) 2003 paper, in the methods section on Two-body Short-range Interactions we have the following: For covalently bonded atoms, it is often ...
3
votes
0answers
22 views

Discrete Lattice polymer simulations

I am trying to develop phase coexistence curves for generic polymers. Of course, I can use standard Flory theory free energy functionals to do this, but I want to define my nearest neighbor polymer-...
5
votes
2answers
326 views

Soil Modelling: Getting accurate Thermal Conductivity values

Context: We perform a lot of CFD (Computational Fluid Dynamics) modelling for our clients (geothermal, construction, general underground engineering, etc) where we have to model temperature flows and ...
4
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0answers
36 views

Simulate drain current gate voltage for QDFET

I've modeled a QDFET transistor of sorts at an atomic scale, as it's not a standard MOSFET, and was wondering how to do a drain current/gate voltage simulation. I don't really have any idea how to ...
12
votes
1answer
266 views

Comparing GAMESS, OpenMOLCAS and Psi4

Over the years many open-source ab initio packages have been developed and the diversity in subroutines, methods and portability (ability to interface with other software) is quite varied for ...
10
votes
2answers
106 views

Can you list some useful code snippets for processing quantum ESPRESSO output files?

I know that this is quite general. But we have all written code for processing output files from various dft codes. The functionality of which, may range from analysing time traces to finding ...
5
votes
2answers
215 views

More matter modeling codes or better codes?

We face a reality that we have many codes to do matter modeling simulations (as described here). This is good. But, how good is it, really? For any beginner in computational modeling it is very ...
5
votes
0answers
58 views

How can I add double bonds to Triazine-derivatives for OpenBabel generation of pdbqt files?

The double bonds are initially present at the sdf file but disappear or are misplaced after .pdbqt conversion. I tried all kinds of combinations using renumbering ...
5
votes
1answer
91 views

How to run multiples VASP files named as POSCAR-XYZ

Is it possible to direct VASP to read a POSCAR-xyz file instead of reading the default POSCAR? For example, I want to run VASP in the Quantum ESPRESSO format: ...
8
votes
0answers
54 views

What could be the possible causes of the energy difference in the following calculation using Octopus (TDDFT) code? [closed]

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. ...
5
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0answers
69 views

How to extract Cartesian gradient with more digits than 8 using Gaussian? [closed]

I would like to obtain the Cartesian gradient from a Gaussian formatted checkpoint file with more digits than 8 (specified in scientific notation). Is there any way to do this?
7
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0answers
55 views

How can I calculate the exchange energy for a molecule in PySCF? [closed]

I am trying to generate exchange energy separately in pyscf but didn't see a way to do that. For correlation energy, it's fairly simple but do you have any idea how to calculate exchange energy?
19
votes
2answers
448 views

What is a chemputer?

I first saw the term "chemputer" when reading about the work of Neil Ostlund (who you may know as one of the authors of the famous book "Modern Quantum Chemistry"). Based on the ...
4
votes
0answers
37 views

Convert PSP8 pseudopotential files to UPF format

Is there a way to convert psp8 pseudopotential files (used for abinit) to UPF format (used for Quantum ESPRESSO)? I noticed there is the upfconv.x utility in ...
13
votes
5answers
2k views

Can I use two different codes?

Can I use one code for geometry optimization and another code for a single point calculation on that optimized geometry? Can one publish results like that?
10
votes
1answer
139 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. ...
31
votes
2answers
720 views

How is Julia used in matter modeling?

What are the main uses and applications of Julia in matter modeling? Python for example is used in many codes, not to mention workflow automation and data processing. Are there any available codes or ...
8
votes
1answer
77 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. ...
8
votes
1answer
180 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
votes
0answers
36 views

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

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
263 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
565 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
votes
3answers
403 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 ...
9
votes
2answers
211 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'...
12
votes
1answer
158 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
776 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
votes
2answers
415 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,...
13
votes
4answers
368 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 ...
28
votes
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 ...
14
votes
1answer
542 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 ...
12
votes
1answer
102 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 ...
11
votes
4answers
1k 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
78 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
284 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
330 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
votes
1answer
89 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 ...
26
votes
4answers
358 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.