Coverage for examples/write_to_lammps.py: 95%

1""" Example of writing a configuration to a LAMMPS dump file. """ 

2import os 

3 

4import gamdpy as gp 

5 

6# Setup configuration: FCC Lattice 

7configuration = gp.Configuration(D=3) 

8configuration.make_lattice(gp.unit_cells.FCC, cells=[8, 8, 8], rho=0.973) 

9configuration['m'] = 1.0 

10configuration.randomize_velocities(temperature=0.7) 

11 

12# Write initial configuration to LAMMPS dump file 

13lmp_dump = gp.configuration_to_lammps(configuration) 

14print(lmp_dump, file=open('dump.initial', 'w')) 

15 

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

17pair_func = gp.apply_shifted_potential_cutoff(gp.LJ_12_6_sigma_epsilon) 

18sig, eps, cut = 1.0, 1.0, 2.5 

19pair_pot = gp.PairPotential(pair_func, params=[sig, eps, cut], max_num_nbs=1000) 

20 

21# Setup integrator: NVT 

22integrator = gp.integrators.NVT(temperature=0.7, tau=0.2, dt=0.005) 

23 

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

25runtime_actions = [gp.TrajectorySaver(), 

26 gp.ScalarSaver(), 

27 gp.MomentumReset(100)] 

28 

29 

30# Setup Simulation. 

31sim = gp.Simulation(configuration, pair_pot, integrator, runtime_actions, 

32 num_timeblocks=100, steps_per_timeblock=1000, 

33 storage='memory') 

34 

35# Delete old dump file if it exists 

36dump_filename = 'dump.lammps' 

37if os.path.exists(dump_filename): 

38 os.remove(dump_filename) 

39 

40# Run simulation and write configuration to LAMMPS dump file on the fly 

41for block in sim.run_timeblocks(): 

42 lmp_dump = gp.configuration_to_lammps(sim.configuration, timestep=sim.steps_per_block*block) 

43 print(lmp_dump, file=open(dump_filename, 'a')) 

44 

45# Open dump file in ovito with 

46# ovito dump.lammps 

47# 

48# Open in VMD with 

49# vmd -lammpstrj dump.lammps