Questions tagged [software]
For questions about matter modeling software. Questions can be about usage or recommendations.
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Benchmarks for optimised Math Libraries across platforms
Are there any benchmarks of low-level and high-level math operations from different Math libraries on corresponding architectures?
Here are a few packages:
LAPACK / BLAS + ATLAS (stock version from ...
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Raman Spectra in Quantum Espresso
Does anyone have any experience simulating Raman spectra in Quantum ESPRESSO? Following the example 15 that comes with QE, I have attempted to simulate the Raman spectrum of MgO. I know the lraman ...
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DFT code for simulating thousands of atoms in a supercell
I'm trying to simulate a supercell that contains thousands of atoms with the DFT method, but it seems VASP couldn't handle such a large system, its parallel efficiency is relatively low, when I try to ...
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How to run SCRF in Gaussian with extra basis?
I want to run a SCRF calculation in Gaussian for a molecule. This has been done as standard with several geometries without issue using the aug-cc-pvtz basis and ...
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List of programs for post-CCSD(T) calculations
Implementations of CCSD(T) are almost too numerous to list, but CCSDT and CCSDT(Q) are much more rare. I have compiled a list of such programs below, and I would be interested to hear if anyone is ...
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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 ...
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Extracting bond information from the xyz positions of atoms?
I have xyz positions of my atoms in a .txt file, how can I extract information about bonding using VMD?
I want to create a LAMMPS input file that contains not only ...
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RPA calculations with Hybrid Functionals
When doing RPA calculations as explained here, if I want to calculate it with hybrid PBE0 should I put LHFCALC = .TRUE. for just step 1 or step 1, step 3 and step 4?...
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How to export .xyz files from VESTA of crystal viewed along different crystallographic axes
I've only been able to export atomic coordinates for a crystal when looking down the c axis, but I need to do so along the a and b axis as well. I've tried changing the Projection Vector in the ...
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How to calculate molecular orbitals of octaoxygen under high pressure?
This question about octaoxygen:
Why is octaoxygen diamagnetic?,
was asked in chemistry, but I really don't have an answer in terms of molecular orbitals. I think it could be a mixing of the O$_2$'s $\...
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How can the GGA functionals in libxc be evaluated?
For pedagogical reasons, I started adding libxc to the atomic DFT dftatom. In this program only spherical symmetric charges. That means that the final potential is just radial.
To my understanding, if ...
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Translate INCAR to Python script using ASE
I am considering using ASE to translate my old work into a Python script. I already have the INCAR and POSCAR KPOINTS files. Is it possible to let ASE read these files and generate Python scripts that ...
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How to predict protonation state of molecules in water?
I'm interested in predicting the protonation and tautomer state of organic molecules (typically CHNOS) at near pH 7 in water. I've used tools like Schrodinger's Epik / LigPrep before, but they ...
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Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules?
There are programs out there which calculate the binding affinity between a ligand and a target protein (Autodock 4, Autodock Vina, Chimera... etc). Is there any analogous program that can be used to ...
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Autodock Vina Error on Chimera: Service "local" unavailable
I was confronted with an error, upon trying to dock a minimized ligand to a target protein, that the "service 'local' [is] unavailable". I then realized ...
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Recommendation of open source software that could build Heterostructure models visually?
I am looking for open-source software that could help me to build Heterostructure models visually, I've been working with BIOVIA Materials Studio before, but I got no valid license now, so I'd like to ...
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Unrecognized or duplicated keyword error using ORCA
I wanted to run ORCA 5.0.2 with the following input:
...
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What software can be used for Crystal Surface Calculations?
I have been unable to find software for making surface calculations, so I currently perform surface calculations in LAMMPS by creating crystal structures in python, before rotating and cutting them ...
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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 ...
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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 ...
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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 ...
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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 ...
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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, ...
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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,...
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How to efficiently adjust the AMIX_MAG and BMIX_MAG parameter in VASP calculations?
I'm trying to calculate the magnetic anisotropy energy of Cr2O3 by comparing the total energy difference of the system in different spin configurations (in-plane and out-of-plane). However, when ...
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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 ...
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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 ...
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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-...
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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 ...
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Simulate drain current gate voltage for QDFET [closed]
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 ...
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How can I add double bonds to Triazine-derivatives for OpenBabel generation of pdbqt files? [closed]
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 ...
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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 ...
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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:
...
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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?
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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 ...
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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?
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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?
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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'...
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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,...
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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 ...
ewf
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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 ...
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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
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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 ...
user430
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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