johahu / molsim Goto Github PK

• #12
  parameters use at least the following:
  ∆t = 0.014 tend = 1000
• #13
• #14

I'm not so sure how I feel about the build instructions. They are not wrong, but very specific.
For example, these environment variables make everything sound more complicated than it is. I would just go with an example build folder called build.
Also, for the cmake command, I would just say cmake instead of specifying the full path, since this would not work if CMake is installed in a different place. Then -S $(pwd) is not really needed when you already say that this command should be executed in the root folder. And -DCMAKE_EXPORT_COMPILE_COMMANDS=ON is only needed for the clang-tidy analysis I believe.

The code frame in its current state is not very suitable as a base for building up
a molecular dynamics simulator. Refactor it, especially concerning the following
issues:

• #16
  It should be possible to iterate over the particles as well as the particle pairs in a simple way.
  → Which software design patterns are suitable?
  During this course, we will use different methods for I/O and for calculating
  the force between particles.
  → What might be an easy and extensible way to do that?
• #17
  Also, pay attention where you use copies or references!
  → This is highlighted by the output produced by the constructor and destruc-
  tor of the Particle.
• #18
  → What can you do with a system like Doxygen, what is it useful for?
  → Document the interfaces and implementations you created with Doxygen.
  → Set the main page of your Doxygen documentation to your projects’ Readme
  file.
  → Do not commit the Doxygen output to your repository.
• #19
  Required features are:
  → Create the documentation by calling make doc doxygen.
  → Exclude the Doxygen target from the all / default target.
  → An CMake Option to disable creating the Doxygen target.
  (Useful if you build your code on a machine that does not have Doxygen).
• #20
  → Consider using the latest Clang compiler: https://apt.llvm.org/.
  → State which compiler you used in your report

As we discussed in the meeting, the basic algorithm of the molecular dynamics
simulation consists of the following steps:

• #3
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• #8
• #9

1. Don't initialize PaticleContainer with a hardcoded value

2. "This constructor does more than allocating memory. It already creates capacity number of particles. If you only want to allocate memory, std::vector<>.reserve() would be the method to call" ParticleContainer.h

Create a custom CMake variable such that the user can disable the doxygen setup and still run your main program even when doxygen is not installed on their system.