root / ase / md / md.py @ 1
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| 1 | 1 | tkerber | """Molecular Dynamics."""
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| 2 | 1 | tkerber | |
| 3 | 1 | tkerber | import numpy as np |
| 4 | 1 | tkerber | |
| 5 | 1 | tkerber | from ase.optimize.optimize import Dynamics |
| 6 | 1 | tkerber | from ase.data import atomic_masses |
| 7 | 1 | tkerber | from ase.md.logger import MDLogger |
| 8 | 1 | tkerber | |
| 9 | 1 | tkerber | |
| 10 | 1 | tkerber | class MolecularDynamics(Dynamics): |
| 11 | 1 | tkerber | """Base-class for all MD classes."""
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| 12 | 1 | tkerber | def __init__(self, atoms, timestep, trajectory, logfile=None, |
| 13 | 1 | tkerber | loginterval=1):
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| 14 | 1 | tkerber | Dynamics.__init__(self, atoms, logfile=None, trajectory=trajectory) |
| 15 | 1 | tkerber | self.dt = timestep
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| 16 | 1 | tkerber | self.masses = self.atoms.get_masses() |
| 17 | 1 | tkerber | self.masses.shape = (-1, 1) |
| 18 | 1 | tkerber | if logfile:
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| 19 | 1 | tkerber | self.attach(MDLogger(dyn=self, atoms=atoms, logfile=logfile), |
| 20 | 1 | tkerber | interval=loginterval) |
| 21 | 1 | tkerber | |
| 22 | 1 | tkerber | def run(self, steps=50): |
| 23 | 1 | tkerber | """Integrate equation of motion."""
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| 24 | 1 | tkerber | f = self.atoms.get_forces()
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| 25 | 1 | tkerber | |
| 26 | 1 | tkerber | if not self.atoms.has('momenta'): |
| 27 | 1 | tkerber | self.atoms.set_momenta(np.zeros_like(f))
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| 28 | 1 | tkerber | |
| 29 | 1 | tkerber | for step in xrange(steps): |
| 30 | 1 | tkerber | f = self.step(f)
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| 31 | 1 | tkerber | self.nsteps += 1 |
| 32 | 1 | tkerber | self.call_observers()
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| 33 | 1 | tkerber | |
| 34 | 1 | tkerber | def get_time(self): |
| 35 | 1 | tkerber | return self.nsteps * self.dt |