Performs a classical propagation of a system on a potential energy surface (PES) given its initial conditions. Time propagation is perform with leapfrog algorithm.

A file named input_file.py is requiered with all the information to perform the molecular dynamcics. A template can be found in input_file_example. It has the following general form:

input_file={
        'nat' : 4,                                   # Number of particles in the system.
        'mintraj' : 1,                               # Initial trajectory.
        'maxtraj' : 10,                              # Final trajectory.
        'initial_cond' : 'initial-conditions-A.dat', # File with initial conditions.
        'mass' : [12e0, 15e0, 1e0, 1e0],             # Masses of the particles (amu).
        'tfin' : 100,                                # Final propagation time.
        'tstep' : 0.1,                               # Time step for leapfrog propagation.
        'it_print' : 10,                             # Printing interval.
        'atoms' : ['C', 'O', 'H', 'H'],              # List with the atomic symbol of the particles.
        'random_init_cond' : True,                   # True = Random indexes for selecting initial conditions.
                                                     # False = Sequencial indexes.
        }

def check_end(t, XP):
  '''
  Function to decide whether a trayectory ended or not.
  It is usefull if the trajectory will be stopped if some distance breaks, for example.
  '''
  
  end = False
  return end

For a system of N particles, each initial condition is expressed as a 2*3*N vector, where the first 3*N elements are the positions of each particles and the following 3*N elements their momentum.

Initial conditions must be provided in atomic units.

Your PES is called through a function named potxyz where a vector of positions (in atomic units) is input and the energy and derivatives with respect to each coordinate are returned (all of them in atomic units).

If your PES is a Fortran code, compile it through f2py with a module name pes (-m pes).

To run the molecular dynamics trajectories execute:

python MD.py

Several files will be created:

• end-conditions: File with position and momenta of the system at the end of the propagation.
• traj_<id>.xyz: File where <id> trajectory is printed if it_print != 0.
• Standard output: Prints the trajectory currently propagating as well as initial and final energy to check its conservation.