barakhirshberg / molecularsimulations Goto Github PK

In the init description of Simulation class parameters, the kinetic energy K is described as an array instead of a float.

K : numpy.ndarray, optional
            Kinetic energy. The default is None.

should be:

K : float, optional
            Kinetic energy. The default is None.

As referenced in the documentation, 'mass' property of the main class simulation is an np.ndarray with shape (Natoms, 1).
However, when no R is assigned, the class sets the default property of mass to be a scalar instead of an np.ndarray of the same value.

Current code: self.mass = 1.6735575E-27 #H mass in kg as default
It should be self.mass=np.array([1.6735575E-27]).

evaluateForce() should be evalForce().

If one wants to use the output files within the scope of running the simulation they must remember to flush the file before reading from it:
self.file.flush

Due to recent misunderstandings, a clarification on the usage of kwargs would be beneficial.

Add a warning to apply boundary condition right before each calculation of the force.

self.E is being referenced without being defined.

Hey Barak,

I'm going through the course notes to refresh my memory, in my opinion, in the solution of the last active learning, you should add a further explanation why the expression in the bracket (line 2) is reduce to line 3. specifically I think you should add why the first term (left term in the bracket) is equal to zero.

The link to github in the header leads to https://github.com/BarakHirshberg/book, which is broken

you cal -> you can