All Questions
Tagged with computational-physics computational-chemistry
15
questions
2
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1
answer
205
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Need help with the python code: Calculating Madelung constant CsCl crystal structure
Need help with the code to estimate the Madelung constant for CsCl lattice:
Cs at (0,0,0)
Cl at (0.5, 0.5, 0.5)
Answer: Converged value I am getting is 0.465. ...
- 21
-1
votes
1
answer
68
views
Does it make any sense to acquire some sort of knowledge about manufacturing or engineering for computational design optimization? [closed]
Does it make any sense to acquire some sort of knowledge about manufacturing or engineering for computational design optimization?
I've viewed computational science to be an abstract science ...
- 427
2
votes
0
answers
45
views
Calculating the species mass consumption from implicit reaction-term in diffusion-reaction equation
The 1D diffusion equation with a chemical source term has the following form:
$$\frac{\partial Y}{\partial t} = D \frac{\partial^2 Y}{\partial x^2} - k Y,$$
where $Y$ is the molar concentration of the ...
- 21
0
votes
1
answer
1k
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Who can explain the minimum image convention in molecular dynamic simulations?
How to choose the cutoff radius so that the atoms do not interact with its periodic image? Especially when simulating macromolecules (proteins).
2
votes
1
answer
258
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Applications of Julia in Chemistry and Molecular Physics?
I was wondering if there are any Theoretical & Computational Chemistry (MM, QM) codes or publications out there that are based primarily on the Julia programming language?
- 121
40
votes
23
answers
10k
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Good examples of "two is easy, three is hard" in computational sciences
I recently encountered a formulation of the meta-phenomenon: "two is easy, three is hard" (phrased this way by Federico Poloni), which can be described, as follows:
When a certain problem is ...
- 8,702
1
vote
1
answer
67
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What are the things I should keep in mind before doing an analysis of my gromacs simulation?
I did a liquid argon simulation at 100k. I forgot during analysis that I need to accommodate for the Periodic Boundary Conditions before doing any analysis which included distance. What are other such ...
- 131
1
vote
1
answer
280
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Oil/Water interface simulation using GROMACS
I would like to perform a decane/water(tip4p) interface simulation using GROMACS to analyse the fluctuation of the interface over a long period of time (50ps - 1ns).
Though I have a rough idea on ...
1
vote
0
answers
68
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Parallelizing molecular simulation with full configuration energy
First, let just me stress that I'm not a an expert in computation chemistry, so now the problem:
We have GCMC molecular simulation, in the Grand Canonical ensemble, using the standard metropolis ...
- 11
5
votes
1
answer
1k
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What determines the usual chemistry textbook plots of atom orbitals?
In elementary chemistry textbooks you often have pictures like the following one:
Are there any conventions how to get them?
I am not sure, but I guess that it are contour plots with only one iso-...
- 231
2
votes
1
answer
1k
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Is the Finite Volume Method conservative when the source term depends on the variable?
I trying to do a simulation where there are two quantities, $\Delta\theta(x,t) = \theta(x,t) - \theta_{o}$ and $\Delta\nu(x,t) = \nu(x,t) - \nu_{o}$. These quantities are chemical concentrations ...
user19247
8
votes
0
answers
588
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DIIS method to accelerate SCF convergence for stretched geometries
I am implementing from scratch an Hartree-Fock calculation in the STO-3G basis set to perform Born-Oppenheimer molecular dynamics. I have a Restricted Hartree-Fock procedure that can reproduce very ...
user18279
1
vote
0
answers
99
views
Time dependent self-consistent equations
I am facing the following problem. I need to solve numerically a set of coupled equations
$$i\frac{d}{dt}f_{n}^{(i)}(t) = \left[U\cdot n(n-1) + \mu\cdot n\right]f_{n}^{(i)}(t) - \sqrt{n+1}\Phi_i^{*}\...
- 203
3
votes
1
answer
2k
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Computer Build for Scientific Computing
I am currently a .NET software developer(SQL Server, ASP.NET, C#, MVC & Web Forms). In my spare time I'm researching different areas of environmental science. E.g.(Hydrology, Ecology, Atmospheric ...
3
votes
1
answer
82
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Is there any numerical application whose performance heavily depends on the division operation?
I am an undergraduate student majoring in computer science.
Recently, I am interested in the division operation, which is not directly supported by some architectures. While some architectures ...
- 131