1 """Using filters, trajectories and python dynamics 
   2 """
   3 
   4 from Dacapo import Dacapo
   5 from ASE import Atom, ListOfAtoms
   6 from ASE.Filters.Subset import Subset
   7 from ASE.Dynamics.ConjugateGradient import ConjugateGradient
   8 from ASE.Dynamics.MDMin import MDMin
   9 from ASE.Dynamics.LineMinimizers.LM1 import LM1
  10 from ASE.Trajectories import NetCDFTrajectory
  11 import os
  12 
  13 os.system('rm -f CO_in_a_box.nc CO_in_a_box.txt dynamics.nc dynamics.txt')
  14 
  15 atoms = ListOfAtoms([Atom('C', (2, 2, 2),tag=1),
  16                      Atom('O', (3.1, 2, 2))],
  17                      cell=(4, 3.5, 3.5), periodic=1)
  18 
  19 calc = Dacapo(planewavecutoff=300,   # in eV
  20               nbands=6,            # 1 extra empty bands
  21               out='CO_in_a_box.nc',txtout='CO_in_a_box.txt')
  22 
  23 atoms.SetCalculator(calc)
  24 
  25 energy = atoms.GetPotentialEnergy()
  26 forces = atoms.GetCartesianForces()
  27 
  28 print 'Initial energy:',energy
  29 print 'Initial abs force:',max(max(forces))
  30 
  31 calc.SetNetCDFFile('dynamics.nc')
  32 calc.SetTxtFile('dynamics.txt')
  33 
  34 # for efficiency keep dacapo running between steps
  35 calc.StayAliveOn()
  36 
  37 # Setup the filter constraining the fixed atoms
  38 subset = Subset(atoms, mask=[atom.GetTag() != 1 for atom in atoms])
  39 
  40 # Setup the minimizer
  41 # use MDMin and not ConjugateGradient because of a 
  42 # problem combining StayAliveOn and this minimizer, 
  43 # dyn = ConjugateGradient(subset, fmax=0.05,lineMin=LM1(0.05))
  44 # dyn.SetVerbosity(1)
  45 dyn = MDMin(subset, fmax=0.2,dt=0.08)
  46 
  47 
  48 # Create a trajectory for the minimization path
  49 path = NetCDFTrajectory('CO-trajectory.nc', atoms)
  50 # Put the initial state in the trajectory:
  51 path.Update()
  52 
  53 # attach the trajectory to the dynamics
  54 dyn.Attach(path)
  55 
  56 # Find the ground state
  57 dyn.Converge()
  58 
  59 energy = atoms.GetPotentialEnergy()
  60 forces = atoms.GetCartesianForces()
  61 print 'Final energy:', energy
  62 print 'Final abs forces:',max(max(forces))