Questions tagged [reference-request]
This tag is for questions looking for a single specific, or a small number of (citable) references.
163
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Free energy calculations for lammps
Is there any tutorial or reference available to perform free enegy calculations (umbrella sampling; thermodynamic integration; free energy perturbation; widom's particle insertion method) etc. With ...
- 11
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Updated book/chapter or review article with broad perspective on computational chemistry
I really like Frank Jensen's "Introduction to Computational Chemistry" because it provides a broad perspective, starting from first principles and extending to surveys of current methods for ...
8
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87
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How to go from zero to hero in Machine Learning for materials modelling
I am interested in exploring the use of machine learning tools to accelerate molecular dynamics simulation probably by training machine learning potentials. While I have found some papers that apply ...
- 443
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Evaluating analytic gradients for overlap integrals
I have been working on a toy HF code for some time. From this reference I am trying to work out an analytic expression for the first derivatives of overlap integrals.
The original expression for ...
- 2,762
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Method for Energy Computation of Protein Structures
So far i have found only one paper that describes how we can compute protein energy while doing MD simulation:
Nishikawa, Ken, Motohisa Oobatake, and Tatsuo Ooi. "Method for Energy Computation ...
- 2,352
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Indirect to direct band gap transition in SUPERCELLS?
My compound under investigation are cubic and construct corresponding 2x2x2 supercell. Properties like optical and mechanical seem to be correct as expected. However a problem arises in their ...
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Factorization of a closed shell Slater determinant into spatial and spin part
I'm studying the HF method, so I have a non-relativistic time-independent Hamiltonian.
Since in the Hamiltonian, there is no spin, we have:
$$
\left[\hat{H}, \hat{S}_z \right] = 0 \quad \text{and} \...
- 165
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Trouble finding pdfs of "Tables of Interatomic Distances and Configuration in Molecules and Ions" series books
I am currently trying to find molecular geometry data prior to 1960, and it seems like
"Tables of Interatomic Distances and Configuration in Molecules and Ions (1958). Special publication No. 11. ...
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How to calculate the Eliashberg spectral function in VASP?
I want to calculate a superconducting critical temperature.
I see in papers like this one: link that they calculate $T_c$ in Quantum Espresso. They use the formula (Eq. 2 in that paper):
$$T_c=\frac{\...
10
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1
answer
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Time Evolution of the Hartree-Fock Wave Function
The Hartree-Fock Hamiltonian is given by
$$
\hat{H} = \sum_i \hat{h}_i + \frac{1}{2}\sum_i\sum_j \left[\hat{J}_{ij} - \hat{K}_{ij}\right]
$$
and by choosing a basis, the Hamiltonian can be written in ...
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Where can I find the source code from the book "The Art of Molecular Dynamics Simulation"?
I need the source code (written in C programming language) for the following book:
The Page-xiii of the book says:
Software availability
Readers interested in ...
- 2,352
3
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answer
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Molecular integrals in spherical harmonics?
I have been trying to write a basic HF code that can compute the MOs and total energy of a molecule. I followed the following reference for overlap and kinetic integrals. During a conversation with a ...
- 2,762
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Hartree Fock method
Currently, I'm studying (again from zero and more in detail) Hartree Fock (HF) method, specifically the Restricted Hartree Fock (RHF).
I'm following two books:
"Introduction to Computational ...
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Interaction energy of two cartesian quadrupoles?
I am looking for a complete description of the interaction of two traceless cartesian quadrupoles. Even just an implementation online would be quite useful. The problem I am having is many of the ...
- 3,524
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Can you supply me with some book names on MC protein simulation?
Is there any book written on protein simulation specifically using the Monte Carlo technique (i.e., not QM or MD)?
If so, can you supply me with some names of such books?
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What is a 'mover' in molecular dynamics?
Movers
What is a 'mover' in molecular dynamics?
Can you supply me with reading material on 'mover'?
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Which researchers in electrical engineering do work related to DFT?
I would like to gain knowledge about how DFT calculations can be specifically used in the subject of electrical engineering. It would really help if people in the community can direct me towards ...
- 1,127
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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 ...
- 2,101
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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 ...
- 1,124
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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, ...
- 2,281
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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 $\...
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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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118
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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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28
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Book that can interpret molecular properties of organic coumpounds? [closed]
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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Literature applying molecular docking into MD-simulated structures of proteins
This is quite surprising, at least for me, that many papers performed molecular docking of an unsimulated (original) protein structure and MD simulation of a protein in a timescale to check the ...
- 231
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Methods to build tight-binding models for realistic materials [closed]
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 ...
user5405
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527
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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 ...
user5405
8
votes
1
answer
530
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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 ...
user5405
4
votes
1
answer
130
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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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77
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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?
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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 ...
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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 ...
- 10.8k
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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 ...
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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 ...
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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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0
answers
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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-...
- 2,352
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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....
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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 ...
- 2,262
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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 ...
- 2,262
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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 \...
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139
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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 ...
- 10.8k