def setup_aatopology(self):
GMIN.initialize()
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = old_div(coords.size, 6)
print("I have %d water molecules in the system"%nrigid)
print("The initial energy is", pot.getEnergy(coords))
water = create_base()
system = RBTopology()
system.add_sites([deepcopy(water) for i in range(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.15
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in range(nrigid-1):
self.draw_bonds.append((2*i, 2*i+1))
self.draw_bonds.append((2*i, 2*i+2))
return system
def setup_aatopology(self):
GMIN.initialize()
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = coords.size / 6
print "I have %d PAP molecules in the system" % nrigid
print "The initial energy is", pot.getEnergy(coords)
water = create_pap()
system = RBTopology()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.1
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid):
self.draw_bonds.append((3 * i, 3 * i + 1))
self.draw_bonds.append((3 * i, 3 * i + 2))
return system
def __init__(self, *args, **kwargs):
AppBasinHopping.__init__(self, *args, **kwargs)
self.quenchRoutine = mylbfgs
self.potential = GMINPotential(GMIN)
self.quenchParameters["tol"] = 1e-4
self.quenchParameters["M"] = 80
self.quenchParameters["maxErise"] = 0.1
self.quenchRoutine = mylbfgs
def check_converged(E, coords):
if (E < (parameters.TARGET + parameters.EDIFF)):
fl = open("stat.dat", "a")
print("#found minimum")
t1 = time.clock()
timespent = t1 - t0
fl.write("#quenches, functioncalls, time\n")
fl.write("%d %d %f\n" % (opt.stepnum, potential.ncalls, timespent))
fl.close()
exit()
# initialize GMIN
GMIN.initialize()
# create a potential which calls GMIN
potential = GMINPotential(GMIN)
# get the initial coorinates
coords = potential.getCoords()
coords = np.random.random(coords.shape)
# create takestep routine
# we combine a normal step taking
group = takestep.BlockMoves()
step1 = takestep.AdaptiveStepsize(OXDNATakestep(displace=parameters.displace,
rotate=0.),
frequency=50)
step2 = takestep.AdaptiveStepsize(OXDNATakestep(displace=0.,
rotate=parameters.rotate),
frequency=50)
group.addBlock(100, step1)
