db = system.create_database()
pot = system.get_potential()
bh = system.get_basinhopping(database=db)
bh.run(50)
min1 = db.minima()[0]
coords = min1.coords
print()
print("Done with basinghopping, performing frequency analysis")
print()
#min1 = db.transition_states()[0]
# determine point group order of system
determine_pgorder = PointGroupOrderCluster(system.get_compare_exact())
pgorder = determine_pgorder(min1.coords)
# free energy from symmetry
Fpg = old_div(np.log(pgorder), beta)
# get the hession
e, g, hess = pot.getEnergyGradientHessian(min1.coords)
# TODO: go to reduced coordinates here
# get the eigenvalues
freqs2 = normalmode_frequencies(hess)
# analyze eigenvalues
n, lnf = logproduct_freq2(freqs2, 6)
Ffrq = (n * np.log(beta) + 0.5 * lnf / beta)
open a dialog box to change the parameters
"""
if checked is None:
return
if not hasattr(self, "_paramsdlg"):
self._paramsdlg = DlgParams(self._params, parent=self)
self._paramsdlg.show()
if __name__ == "__main__":
from OpenGL.GLUT import glutInit
import sys
glutInit()
app = QtGui.QApplication(sys.argv)
from pele.systems import LJCluster
natoms = 13
system = LJCluster(natoms)
system.params.double_ended_connect.local_connect_params.NEBparams.iter_density = 5.
x1, e1 = system.get_random_minimized_configuration()[:2]
db = system.create_database()
match = system.get_compare_exact()
min1 = db.addMinimum(e1, x1)
com = match.measure.get_com(x1)
match.transform.translate(x1, -com)
wnd = NormalmodeBrowser(app=app, system=system)
wnd.set_coords(x1)
wnd.show()
sys.exit(app.exec_())
pot = system.get_potential() bh = system.get_basinhopping(database=db) bh.run(50) min1 = db.minima()[0] coords = min1.coords print print "Done with basinghopping, performing frequency analysis" print #min1 = db.transition_states()[0] # determine point group order of system determine_pgorder = PointGroupOrderCluster(system.get_compare_exact()) pgorder = determine_pgorder(min1.coords) # free energy from symmetry Fpg = np.log(pgorder)/beta # get the hession e, g, hess = pot.getEnergyGradientHessian(min1.coords) # TODO: go to reduced coordinates here # get the eigenvalues freqs2 = normalmode_frequencies(hess) # analyze eigenvalues n, lnf = logproduct_freq2(freqs2, 6) Ffrq = (n*np.log(beta) + 0.5*lnf /beta)