def getPairLJ(natoms=38):
from pygmin.systems import LJCluster
system = LJCluster(natoms)
ret1 = system.get_random_minimized_configuration()
ret2 = system.get_random_minimized_configuration()
coords1, coords2 = ret1[0], ret2[0]
E1, E2 = ret1[1], ret2[1]
mindist = system.get_mindist()
mindist(coords1, coords2)
return coords1, coords2, system.get_potential(), mindist, E1, E2
def getPairLJ(natoms=38):
from pygmin.systems import LJCluster
system = LJCluster(natoms)
ret1 = system.get_random_minimized_configuration()
ret2 = system.get_random_minimized_configuration()
coords1, coords2 = ret1[0], ret2[0]
E1, E2 = ret1[1], ret2[1]
mindist = system.get_mindist()
mindist(coords1, coords2)
return coords1, coords2, system.get_potential(), mindist, E1, E2
def spawnlj(**kwargs):
from pygmin.systems import LJCluster
from pygmin.config import config
import os
natoms = 13
sys = LJCluster(natoms)
db = sys.create_database()
x1, E1 = sys.get_random_minimized_configuration()[:2]
x2, E2 = sys.get_random_minimized_configuration()[:2]
m1 = db.addMinimum(E1, x1)
m2 = db.addMinimum(E2, x2)
optim = "/home/js850/git/OPTIM/source/build/OPTIM"
optim = config.get("exec", "OPTIM")
optim = os.path.expandvars(os.path.expanduser(optim))
spawner = SpawnOPTIM_LJ(x1, x2, sys, OPTIM=optim, **kwargs)
spawner.run()
spawner.load_results(db)
def spawnlj(**kwargs):
from pygmin.systems import LJCluster
from pygmin.config import config
import os
natoms = 13
sys = LJCluster(natoms)
db = sys.create_database()
x1, E1 = sys.get_random_minimized_configuration()[:2]
x2, E2 = sys.get_random_minimized_configuration()[:2]
m1 = db.addMinimum(E1, x1)
m2 = db.addMinimum(E2, x2)
optim = "/home/js850/git/OPTIM/source/build/OPTIM"
optim = config.get("exec", "OPTIM")
optim = os.path.expandvars(os.path.expanduser(optim))
spawner = SpawnOPTIM_LJ(x1, x2, sys, OPTIM=optim, **kwargs)
spawner.run()
spawner.load_results(db)
def plot_hist(hess):
import pylab as pl
pl.hist(np.log10(np.abs(hess.reshape(-1))))
pl.show()
if __name__ == "__main__":
from pygmin.systems import LJCluster
natoms = 30
system = LJCluster(natoms)
pot = system.get_potential()
coords = system.get_random_configuration()
xmin = system.get_random_minimized_configuration()[0]
e, g, h = pot.getEnergyGradientHessian(xmin)
evals = get_eigvals(h)
print evals
quencher = system.get_minimizer(tol=10.)
coords = quencher(coords)[0]
e, g, h = pot.getEnergyGradientHessian(coords)
w1, v1 = get_smallest_eig(h)
print w1
w, v = get_smallest_eig_arpack(h)
print w
w2, v2 = get_smallest_eig_sparse(h)
print w2, w2 / w1
w3, v3 = get_smallest_eig_nohess(coords, system)
print w3, w3 / w1
app = QtGui.QApplication(sys.argv)
from pygmin.systems import LJCluster
pl.ion()
natoms = 13
system = LJCluster(natoms)
system.params.double_ended_connect.local_connect_params.NEBparams.iter_density = 5.
dbname = "lj%dtest.db" % (natoms,)
db = system.create_database(dbname)
#get some minima
if False:
bh = system.get_basinhopping(database=db)
bh.run(10)
minima = db.minima()
else:
x1, e1 = system.get_random_minimized_configuration()[:2]
x2, e2 = system.get_random_minimized_configuration()[:2]
min1 = db.addMinimum(e1, x1)
min2 = db.addMinimum(e2, x2)
minima = [min1, min2]
# connect some of the minima
nmax = min(3, len(minima))
m1 = minima[0]
for m2 in minima[1:nmax]:
connect = system.get_double_ended_connect(m1, m2, db)
connect.connect()
def start():
wnd.start()
print >> sys.stderr, "started decrunner"
if __name__ == "__main__":
from OpenGL.GLUT import glutInit
import sys
import pylab as pl
app = QtGui.QApplication(sys.argv)
from pygmin.systems import LJCluster
pl.ion()
natoms = 113
system = LJCluster(natoms)
system.params.double_ended_connect.local_connect_params.NEBparams.iter_density = 5.
x1, e1 = system.get_random_minimized_configuration()[:2]
x2, e2 = system.get_random_minimized_configuration()[:2]
db = system.create_database()
min1 = db.addMinimum(e1, x1)
min2 = db.addMinimum(e2, x2)
wnd = ConnectViewer(system, db, min1=min1, min2=min2, app=app)
# decrunner = DECRunner(system, db, min1, min2, outstream=wnd.textEdit_writer)
glutInit()
wnd.show()
from PyQt4.QtCore import QTimer
QTimer.singleShot(10, start)
sys.exit(app.exec_())
print "times", n, time1, time2, time3, time4
sys.stdout.flush()
def plot_hist(hess):
import pylab as pl
pl.hist(np.log10(np.abs(hess.reshape(-1))))
pl.show()
if __name__ == "__main__":
from pygmin.systems import LJCluster
natoms = 30
system = LJCluster(natoms)
pot = system.get_potential()
coords = system.get_random_configuration()
xmin = system.get_random_minimized_configuration()[0]
e, g, h = pot.getEnergyGradientHessian(xmin)
evals = get_eigvals(h)
print evals
quencher = system.get_minimizer(tol=10.)
coords = quencher(coords)[0]
e, g, h = pot.getEnergyGradientHessian(coords)
w1, v1 = get_smallest_eig(h)
print w1
w, v = get_smallest_eig_arpack(h)
print w
w2, v2 = get_smallest_eig_sparse(h)
print w2, w2/w1
w3, v3 = get_smallest_eig_nohess(coords, system)
print w3, w3/w1