Coverage for examples/hydrocorr.py: 100%

1""" Example of how to calculate the two hydrodynamic correlation functions  

2  

3 1: the transverse current correlation function (jacf), and  

4 2: the longitudinal density correlation function (dacf) 

5 

6 The system is a simple Lennard-Jones system at the liquid state point. 

7 

8 The correlation functions are stored in the files jacf.dat and dacf.dat when calling the calculator read method 

9 1st column is time, remaining columns are correlation function values at the different wavevectors k = 2*pi*n/L  

10 where n is the wave number and L the system box length in the x-direction.  

11 

12 It is recommended to use a simple cubic box for these calculations. 

13 

14 """ 

15 

16import gamdpy as gp 

17import os 

18 

19# Setup configuration: FCC Lattice 

20configuration = gp.Configuration(D=3, compute_flags={'W':True}) 

21configuration.make_lattice(gp.unit_cells.FCC, cells=[8, 8, 8], rho=0.8) 

22configuration['m'] = 1.0 

23configuration.randomize_velocities(temperature=0.9) 

24 

25# Setup pair potential: Single component 12-6 Lennard-Jones 

26pair_func = gp.apply_shifted_potential_cutoff(gp.LJ_12_6_sigma_epsilon) 

27sig, eps, cut = 1.0, 1.0, 2.5 

28pair_pot = gp.PairPotential(pair_func, params=[sig, eps, cut], max_num_nbs=1000) 

29 

30# Setup integrator: NVT 

31integrator = gp.integrators.NVT(temperature=0.9, tau=0.2, dt=0.005) 

32 

33# Setup runtime actions, i.e. actions performed during simulation of timeblocks 

34runtime_actions = [gp.TrajectorySaver(), 

35 gp.ScalarSaver(16, {'W':True}), 

36 gp.MomentumReset(100)] 

37 

38# Setup Simulation.  

39sim = gp.Simulation(configuration, pair_pot, integrator, runtime_actions, 

40 num_timeblocks=2048, steps_per_timeblock=32, 

41 storage='memory') 

42 

43print('Simulation created') 

44 

45hydrocorr = gp.CalculatorHydrodynamicCorrelations(configuration, dtsample=32*0.005, nwaves=10) 

46 

47# Run simulation 

48for _ in sim.run_timeblocks(): 

49 hydrocorr.update() 

50 

51print(sim.summary()) 

52 

53hydrocorr.read() 

54