Questions tagged [reference-request]
This tag is for questions looking for a single specific, or a small number of (citable) references.
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Where can I find the MASTANI-2014 tutorial files?
There was a two-week summer school on Density Functional Theory using Quantum ESPRESSO in the summer of 2014 organized by The Abdus Salam International Centre for Theoretical Physics (ICTP), jointly ...
- 457
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Why are maximally localized Wannier functions supposed to be real?
I am computing maximally localized Wannier functions (MLWFs) for several high-pressure phases of a system I am studying using wannier90. For some of these calculations, I see that the imaginary part ...
- 1,244
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Reference textbooks for calculating pressures/stress/strain/tensors?
Is there a good reference textbook for calculating pressures/stress/strain/tensors in materials - vapor, liquids and solids? Pure physics is fine, but it would be a bonus if it also included force-...
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High school student that wants to do DFT calculations
I originally asked this on Physics.SE but was suggested to ask here instead.
I'm a high school student interested in material simulation. I want to do a project involving density functional theory to ...
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Original reference for gapped chiral fermion k·p model?
In eq. 1 of this reference, the authors present the following Hamiltonian for the 2-band gapped chiral fermion model that can describe many systems including various semiconductors, N-layer graphene, ...
- 2,131
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I'm considering to take an introduction course with textbook "Materials Science and Engineering: An Introduction", as a beginner QE user. Is it okay?
People, I am a beginner in material modeling (I am studing solid state in Quantum ESPRESSO) and I am having a lot of difficulty with basic terms like "k-points", "Miller Indices", &...
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Simple models for the energetic stabilization associated with damped polarizabilities of anions in solution
For many molecules, the gas-phase molecular polarizability, $\alpha_{gas}$ is approximately the same as that in the liquid, $\alpha_{liq.}$. For instance, $\ce{H2O}$, has roughly the same average $\...
- 3,249
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Improving my programming for computational chemistry/physics
What are some good textbooks or online resources to improve my skills in C++, C and Fortran, specifically for computational chemistry.
For example, I am interested in learning about parallelisation ...
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Books on machine learning and condensed matter? [closed]
What are the best books on the use of machine learning in condensed matter, focusing on density functional theory and many-body physics?
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Great value introductory computational drug design literature?
Anyone know introductory computational drug design literature of great value.
I found plenty from web stores, but some of these cost €100 or more. I'm not sure if all of them are as worthwhile.
...
- 217
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Book that can interpret molecular properties of organic coumpounds?
I'm new in the field of research and modelling matter.
I got results from DFT calculations but I don't know how to interpret them and I wonder if anyone can suggest to me books for interpreting ...
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Methods to build tight-binding models for realistic materials
I am aware that a standard way to build tight-binding models for realistic crystalline systems is by using the Maximally-localized Wannier Functions (MLWFs) as implemented in the Wannier90 Fortran ...
- 543
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How does charge mixing work?
When doing DFT calculations on certain magnetic materials, convergence can be difficult. This problem can be solved by changing the mixing parameters (e.g. AMIN and BMIX in the INCAR file of VASP). My ...
- 543
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1
answer
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Learning how the DFT codes work
I am a beginning PhD student studying topological materials and strongly-correlated systems, such as high Tc superconductivity. I am using density functional theory in my work. I am wondering what I ...
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List of properties of molecules categorized by the number of atoms?
Is there an online database having information on molecules with a certain number of atoms? For example, properties of tri-atomic molecules?
There is this table that I got from NIST which gives a few, ...
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Finding the Configuration State Functions of Atoms
Is there a book or tabulated work where the configuration state functions of atoms have been documented? Just as useful would be information about computer programs that are able to predict the CSFs.
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Good books about green's function method [closed]
I am trying to learn to do Green's function calculations. Are there any good introductory books about the Green's function method?
- 305
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What does it mean by "scale mismatch" and "bridging of scales"?
As far as I understood, molecular simulation works in two types of scales:
temporal scale - how much time is required to simulate the model.
spatial scale - how much memory-space is required to ...
- 1,267
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Repository of Common Surfaces
Are there any repositories of crystal surfaces? Due to orientation / termination of surfaces, occasionally it is non-trivial to decide how exactly to cut a surface for things such as oxides. I ...
- 10.6k
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Attempts to define atomic energies based on electron density?
The concept of an atom in a molecule is undefined in quantum mechanics. Consequently, very useful properties like atomic charges, bond orders, and so on cannot be rigorously defined. There are many ...
- 3,249
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Slope of the potential when both molecules "touch"?
My aim is to model the potential energy surface for two colliding H2 molecules. More specifically, I needed the order of magnitude of the slope of the potential at the moment when two colliding H2 ...
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Definition of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins
What are the definitions of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins?
Examples will be highly appreciated.
Also, please, back them up ...
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What do we simulate with molecular simulation of proteins in the theoretical research?
I know that the following can be simulated:
secondary/tertiary structure prediction
protein-surface/protein-protein interaction tests
protein-ligand binding test
I wonder if references or ...
- 1,267
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Is there a system of multiple interacting quantum particles for which the density can be obtained analytically?
I know that it is impossible for real electrons and nuclei. In the Kohn and Sham approach, a system of interacting electrons is approximated by a system of non-interacting Kohn-Sham particles in an ...
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Interlink among different length scales of simulation and modelling techniques [closed]
I found this figure:
In the following paper:
A Review on Multiscale Modelling and Simulation for Polymer Nanocomposites
However, I am skeptical about its correctness, as this paper is not peer-...
- 1,267
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153
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What is the best cell shape to calculate the energy of a free atom with a periodic DFT code (VASP)?
I want to study the adsorption energies of many different atoms to some surfaces. For that, I need to calculate the energies of free atoms (adsorbates) in a vacuum.
I understand that I am supposed to ...
4
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Recommendation for some papers on simulation of metallic metal
I want to simulate the collision between two gas giants, the inner layer of gas giant contains the layer of metallic hydrogen and a solid core, if two gas giants collide then the abrubt variation of ...
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Can you recommend a molecular modeling book targeted at polymers or biomolecules that supplies programming examples? [closed]
I know one book -
Molecular Simulation of Fluids Theory, Algorithms, and Object-Orientation; Richard J. Sadus.
This book supplies source code. However, it is not targeted at polymers or biomolecules....
- 1,267
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What are some recent significant developments/studies in theoretical nonlinear chemical dynamics?
During my undergraduate studies, I was introduced to oscillatory and nonlinear reactions, which are essentially chemical reactions oscillating far away from equilibrium conditions - A very visual ...
- 2,052
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Is it incorrect to use a NVT ensemble for Non-equilibrium MD simulation?
I am getting some conflicting results on this topic while searching for literature online, so I am asking this question here with respect to a simplified experimental setup. If we are trying to ...
- 2,052
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Is it possible to calculate the dipole polarizability in the presence of a nonzero electric field?
One common way of calculating a dipole polarizability from electronic structure is by calculating the following derivative by finite difference:
$$
\mathbf{\mu}=\left(\frac{\partial U}{\partial \...
- 3,249
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DFT+U for RPA Ground State
For RPA calculations in VASP, a four step process can be utilized where the first step is to compute the occupied orbitals at either the GGA or hybrid GGA level.
I am curious with materials that are ...
- 10.6k
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Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules? [closed]
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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The effect of different mediums on the molecular orbital energies [closed]
I want to study the effect of different mediums, gas and various solvents, on the energy of the 10th highest molecular orbital of multiple quinones, which I obtained by a Gaussian software calculation....
- 517
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How can I get started on DFT?
This question is simply:
How can we use DFT in the field of electrochemistry?
What are the best resources (Books, reviews, papers, software ...) to learn about using DFT in electrochemistry? ...
- 1,317
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How to interpret density of states and band structure of a material? [closed]
I am new on the VASP platform, and have learned how to calculate any material's DOS and Band structure.
However, I don't know how to interpret these properties. Can you recommend resources that ...
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Which molecules have multi-reference character?
I'm using WebMO to construct molecules that have high multireference character, but I cannot seem to find any, or perhaps I'm not building them correctly on WebMO; I know singlet biradicals generally ...
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How does a beginner condensed matter theorist working on real materials, get up to speed?
I asked this on Physics.SE and got recommended here.
More precisely, as a condensed matter theory PhD student, I am often overwhelmed by the wide variety of chemical formulas that experimentalists ...
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What are the types of PT applied to electronic structure methods?
The motivation for this question is similar in nature to the series of questions on different methods :
What are the types of SCF?
What are the types of MCSCF?
What are the types of Quantum Monte ...
user784
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How are structure descriptors used in regression or machine learning?
I am currently working on prediction of UV-vis spectra from structure of molecules. I have read multiple papers where structure descriptors were used as inputs for machine learning to find various ...
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Are there any benchmark test sets for UV-vis absorption maxima?
In computational chemistry, I have come across many test sets which are used to benchmark a new method. For example, the G2 test set for thermochemical calculations (heats of formation). There is the ...
- 6,216
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546
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VASP GW PAW Pseudopotentials
What is the difference between the GW and non-GW potentials in VASP. While it is clear that the GW potentials should be used with GW calculations, the documentation also states that these potentials ...
- 10.6k
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How can we calculate the Gibbs free energy from first principles?
I am trying to calculate the Gibbs free energy for a bulk material. Since DFT ground state calculations give the energy at 0K, a temperature dependent part has to be added in this to obtain correct ...
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Where can I find/generate force-field parameters for common inorganic anions in water?
I have to do simulations of some inorganic anions, specifically $\ce{PO4^3-}$ (ortho-phosphate), $\ce{CO3^2-}$ (carbonate), $\ce{SO4^2-}$ (sulfate), in an aqueous enviornment. However, I am having a ...
- 6,216
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References for Electrostatics Calculations Used in Molecular Dynamics
I'm looking for classic references that describe the usual electrostatic contributions which have to be calculated in molecular dynamics simulations. I find it very hard to apprehend what different ...
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Large dataset with conductivities of materials and chemical compounds? [closed]
I'm looking for a fairly large (>100k) dataset of chemical compounds (and materials) that has conductivities. I've looked at PubMed, but couldn't find conductivities.
I would ideally like to avoid ...
6
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1
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How can scanning tunneling microscopy images (constant current and dI/dV conductivity) be simulated? What's under the hood in software packages?
Scanning tunneling microscopy comes in several flavors; vanilla (traditional STM) is constant current where the tip height is varied to maintain a constant current at a set constant bias1 and the ...
- 1,994
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Good books about computational chemistry of solid state materials for newbie
At the University, I chose the organic chemistry path and to better understand my experimental works I started studying computational chemistry on my own. There are a lot of books in this field, but I ...
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References related to the molecular distance geometry problem (estimating true distances based on noisy distances)
One aspect of the molecular distance geometry problem (MDGP) described in this PDF, can be written as follows:
"Given observations of noisy distances between atoms in a molecule, estimate the ...
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Linearized Augmented Plane Wave Method vs. Pseudopotential Methods
While reviewing some DFT literature, I have come across a few papers utilizing the LAPW (Linearized
Augmented Plane Wave) method, but I am interested in understanding why exactly one would use these ...
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