def test(): # pragma: no cover
from pele.systems import LJCluster
from pele.transition_states import GeneralizedDimer
from pele.transition_states import FindTransitionState
from pele.utils.xyz import read_xyz
system = LJCluster(13)
x = system.get_random_configuration()
x = read_xyz(open("tests/lj18_ts.xyz", "r")).coords.flatten()
dimer = GeneralizedDimer(x.copy(), system.get_potential(),
rotational_steps=40,
dimer=False,
leig_kwargs=dict(iprint=10, maxstep=2.,
tol=.1,
),
translator_kwargs=dict(iprint=1,
verbosity=10,
),
)
ret = dimer.run()
print(ret)
print("\n\nnow the same with the old version")
searcher = FindTransitionState(x.copy(), system.get_potential(), iprint=1, verbosity=10)
# print ret
ret = searcher.run()
print(ret)
def test_ts(self):
from pele.utils.xyz import read_xyz
path = os.path.dirname(os.path.abspath(__file__))
xyz = read_xyz(open(path + "/lj18_ts.xyz", "r"))
x = xyz.coords.flatten()
vec = np.random.rand(x.size)
vec /= np.linalg.norm(vec)
self.eigpot = LowestEigPot(x,
self.pot,
orthogZeroEigs=self.system.
get_orthogonalize_to_zero_eigenvectors(),
first_order=self.first_order)
e1 = self.eigpot.getEnergy(vec)
e, g = self.eigpot.getEnergyGradient(vec)
gnum = self.eigpot.NumericalDerivative(vec, eps=1e-4)
gnum -= np.dot(gnum, vec)
self.assertLess(old_div(np.max(np.abs(g - gnum)), np.max(np.abs(g))),
1e-3)
self.assertAlmostEqual(e, e1, delta=e * 1e-4)
self.assertAlmostEqual(
1.,
np.dot(g, gnum) / np.linalg.norm(g) / np.linalg.norm(gnum), 3)
def setUp(self):
self.pot = _lj_cpp.LJ()
self.natoms = 13
self.xrandom = np.random.uniform(-1, 1, [3 * self.natoms]) * 5.0
current_dir = os.path.dirname(__file__)
xyz = read_xyz(open(current_dir + "/_lj13_gmin.xyz", "r"))
self.xmin = xyz.coords.reshape(-1).copy()
self.Emin = float(xyz.title)
def setUp(self):
self.pot = _lj_cpp.LJ()
self.natoms = 13
self.xrandom = np.random.uniform(-1, 1, [3 * self.natoms]) * 5.
current_dir = os.path.dirname(__file__)
xyz = read_xyz(open(current_dir + "/_lj13_gmin.xyz", "r"))
self.xmin = xyz.coords.reshape(-1).copy()
self.Emin = float(xyz.title)
def setUp(self):
current_dir = os.path.dirname(__file__)
xyz = read_xyz(open(current_dir + "/_morse13_min.xyz", "r"))
self.xmin = xyz.coords.reshape(-1).copy()
self.Emin, rho, r0, A = map(float, xyz.title.split()[1::2])
self.natoms = self.xmin.size / 3
self.xrandom = np.random.uniform(-1, 1, [3 * self.natoms]) * 5.
self.pot = _morse_cpp.Morse(rho=rho, r0=r0, A=A)
def setUp(self):
current_dir = os.path.dirname(__file__)
xyz = read_xyz(open(current_dir + "/_morse13_min.xyz", "r"))
self.xmin = xyz.coords.reshape(-1).copy()
self.Emin, rho, r0, A = map(float, xyz.title.split()[1::2])
self.natoms = self.xmin.size / 3
self.xrandom = np.random.uniform(-1, 1, [3 * self.natoms]) * 5.0
self.pot = _morse_cpp.Morse(rho=rho, r0=r0, A=A)
def test2(self):
# get the path of the file directory
path = os.path.dirname(os.path.abspath(__file__))
xyz = read_xyz(open(path + "/lj18_ts.xyz", "r"))
x = xyz.coords.flatten()
dimer = self.make_dimer(x)
res = dimer.run()
self.assertTrue(res.success)
self.assertLess(res.nsteps, 5)
def test2(self):
# get the path of the file directory
path = os.path.dirname(os.path.abspath(__file__))
xyz = read_xyz(open(path+"/lj18_ts.xyz", "r"))
x = xyz.coords.flatten()
dimer = self.make_dimer(x)
res = dimer.run()
self.assertTrue(res.success)
self.assertLess(res.nsteps, 5)
def setUp(self):
np.random.seed(0)
self.natoms = 13
nlist = [[i, j] for i in range(self.natoms) for j in range(i + 1, self.natoms)]
nlist = np.array(nlist, dtype=np.int64).reshape(-1)
self.pot = _lj_cpp.LJNeighborList(nlist)
self.xrandom = np.random.uniform(-1, 1, [3 * self.natoms]) * 5.
current_dir = os.path.dirname(__file__)
xyz = read_xyz(open(current_dir + "/_lj13_gmin.xyz", "r"))
self.xmin = xyz.coords.reshape(-1).copy()
self.Emin = float(xyz.title)
def setUp(self):
np.random.seed(0)
self.natoms = 13
nlist = [[i, j] for i in xrange(self.natoms) for j in xrange(i + 1, self.natoms)]
nlist = np.array(nlist, dtype=np.int64).reshape(-1)
self.pot = _lj_cpp.LJNeighborList(nlist)
self.xrandom = np.random.uniform(-1, 1, [3 * self.natoms]) * 5.0
current_dir = os.path.dirname(__file__)
xyz = read_xyz(open(current_dir + "/_lj13_gmin.xyz", "r"))
self.xmin = xyz.coords.reshape(-1).copy()
self.Emin = float(xyz.title)
def test_fcc():
from pele.utils.xyz import read_xyz
fname = "fcc100-coords.8x8x8.xyz"
pot = SuttonChen(rcut=3.2, boxvec=[8.]*3, c=144.41, n=12, m=6)
pot = SuttonChen(rcut=3.2, boxvec=[8.]*3, c=34.408, n=10, m=8)
xyz = read_xyz(open(fname, "r"))
x = xyz.coords.flatten()
e, g = pot.getEnergyGradient(x)
print "energy", e
print "norm grad", np.linalg.norm(g)
print "rms grad", np.linalg.norm(g) / np.sqrt(g.size)
def test_fcc(): # pragma: no cover
from pele.utils.xyz import read_xyz
fname = "fcc100-coords.8x8x8.xyz"
# pot = SuttonChen(rcut=3.2, boxvec=[8.] * 3, c=144.41, n=12, m=6)
pot = SuttonChen(rcut=3.2, boxvec=[8.] * 3, c=34.408, n=10, m=8)
xyz = read_xyz(open(fname, "r"))
x = xyz.coords.flatten()
e, g = pot.getEnergyGradient(x)
print("energy", e)
print("norm grad", np.linalg.norm(g))
print("rms grad", old_div(np.linalg.norm(g), np.sqrt(g.size)))
def setUp(self):
np.random.seed(1)
current_dir = os.path.dirname(__file__)
xyz = read_xyz(open(current_dir + "/_blj13_min.xyz", "r"))
self.xmin = xyz.coords.reshape(-1).copy()
ntypeA, self.Emin, rcut, epsAA, sigAA, epsBB, sigBB, epsAB, sigAB = list(map(float, xyz.title.split()[1::2]))
ntypeA = int(ntypeA)
self.rcut = rcut
natoms = self.xmin.size // 3
self.pot = BLJCut(natoms, ntypeA, rcut=rcut, sigAA=sigAA, epsAA=epsAA,
epsBB=epsBB, sigBB=sigBB, epsAB=epsAB, sigAB=sigAB)
self.xrandom = np.random.uniform(-1, 1, self.xmin.size) * 5.
def setUp(self):
np.random.seed(1)
current_dir = os.path.dirname(__file__)
xyz = read_xyz(open(current_dir + "/_blj13_min.xyz", "r"))
self.xmin = xyz.coords.reshape(-1).copy()
ntypeA, self.Emin, rcut, epsAA, sigAA, epsBB, sigBB, epsAB, sigAB = map(float, xyz.title.split()[1::2])
ntypeA = int(ntypeA)
self.rcut = rcut
natoms = self.xmin.size / 3
self.pot = BLJCut(natoms, ntypeA, rcut=rcut, sigAA=sigAA, epsAA=epsAA,
epsBB=epsBB, sigBB=sigBB, epsAB=epsAB, sigAB=sigAB)
self.xrandom = np.random.uniform(-1, 1, self.xmin.size) * 5.
def test1(self):
d = os.path.dirname(__file__)
fname = os.path.join(d, "coords.lj75.gmin.xyz")
xyz = read_xyz(open(fname, "r"))
coords = xyz.coords.reshape(-1)
print fname
self.assertEqual(coords.size, 75 * 3)
permlist = [range(75)]
match = ExactMatchAtomicCluster(permlist=permlist, can_invert=True)
calculator = PointGroupOrderCluster(match)
pgorder = calculator(coords)
# print pgorder
self.assertEqual(pgorder, 20)
def test1(self):
d = os.path.dirname(__file__)
fname = os.path.join(d, "coords.lj75.gmin.xyz")
xyz = read_xyz(open(fname, "r"))
coords = xyz.coords.reshape(-1)
print(fname)
self.assertEqual(coords.size, 75*3)
permlist = [list(range(75))]
match = ExactMatchAtomicCluster(permlist=permlist, can_invert=True)
calculator = PointGroupOrderCluster(match)
pgorder = calculator(coords)
# print pgorder
self.assertEqual(pgorder, 20)
def water(xyzfile): # TIP4P-16.xyz"
ref = xyz.read_xyz(open(xyzfile))
xyz.write_xyz(open("test.xyz", "w"), coords=ref.coords)
# lookup table for atom masses
mass_lookup = {'O': 16., 'H': 1.}
rb_sites = []
for atomtype, x, i in zip(ref.atomtypes, ref.coords, xrange(len(ref.atomtypes))):
# every 3rd atom, define a new reigid molecule
if i % 3 == 0:
rb = rigidbody.RigidFragment()
rb_sites.append(rb)
rb.add_atom(atomtype, x, mass_lookup[atomtype])
# finalize the rigid body setup
for rb in rb_sites:
rb.finalize_setup()
return rb_sites, ref
def test_ts(self):
from pele.utils.xyz import read_xyz
path = os.path.dirname(os.path.abspath(__file__))
xyz = read_xyz(open(path + "/lj18_ts.xyz", "r"))
x = xyz.coords.flatten()
vec = np.random.rand(x.size)
vec /= np.linalg.norm(vec)
self.eigpot = LowestEigPot(x, self.pot,
orthogZeroEigs=self.system.get_orthogonalize_to_zero_eigenvectors(),
first_order=self.first_order)
e1 = self.eigpot.getEnergy(vec)
e, g = self.eigpot.getEnergyGradient(vec)
gnum = self.eigpot.NumericalDerivative(vec, eps=1e-4)
gnum -= np.dot(gnum, vec)
self.assertLess(np.max(np.abs(g-gnum)) / np.max(np.abs(g)), 1e-3)
self.assertAlmostEqual(e, e1, delta=e * 1e-4)
self.assertAlmostEqual(1., np.dot(g, gnum) / np.linalg.norm(g) / np.linalg.norm(gnum), 3)
def test(): # pragma: no cover
from pele.systems import LJCluster
from pele.transition_states import GeneralizedDimer
from pele.transition_states import FindTransitionState
from pele.utils.xyz import read_xyz
system = LJCluster(13)
x = system.get_random_configuration()
x = read_xyz(open("tests/lj18_ts.xyz", "r")).coords.flatten()
dimer = GeneralizedDimer(
x.copy(),
system.get_potential(),
rotational_steps=40,
dimer=False,
leig_kwargs=dict(
iprint=10,
maxstep=2.,
tol=.1,
),
translator_kwargs=dict(
iprint=1,
verbosity=10,
),
)
ret = dimer.run()
print(ret)
print("\n\nnow the same with the old version")
searcher = FindTransitionState(x.copy(),
system.get_potential(),
iprint=1,
verbosity=10)
# print ret
ret = searcher.run()
print(ret)
from __future__ import print_function
from builtins import zip
from builtins import range
import numpy as np
from pele.potentials import LJ
from pele.utils import xyz
from pele.angleaxis import rigidbody
from pele.optimize import lbfgs_py
# read in coordinates from xyz file
ref = xyz.read_xyz(open("water.xyz"))
xyz.write_xyz(open("test.xyz", "w"), coords=ref.coords)
# lookup table for atom masses
mass_lookup = {'O': 16., 'H': 1.}
#ref.coords[:] *= 3
# now define a new rigid body system
rb_sites = []
for atomtype, x, i in zip(ref.atomtypes, ref.coords,
range(len(ref.atomtypes))):
# every 3rd atom, define a new reigid molecule
if i % 3 == 0:
rb = rigidbody.RigidFragment()
rb_sites.append(rb)
rb.add_atom(atomtype, x, mass_lookup[atomtype])
# finalize the rigid body setup
for rb in rb_sites:
rb.finalize_setup()
import numpy as np
from pele.potentials import LJ
from pele.utils import xyz
from pele.angleaxis import rigidbody
from pele.optimize import lbfgs_py
# read in coordinates from xyz file
ref = xyz.read_xyz(open("TIP4P-16.xyz"))
xyz.write_xyz(open("test.xyz", "w"), coords=ref.coords)
# lookup table for atom masses
mass_lookup = {'O': 16., 'H': 1.}
#ref.coords[:] *= 3
# now define a new rigid body system
rb_sites = []
for atomtype, x, i in zip(ref.atomtypes, ref.coords,
xrange(len(ref.atomtypes))):
# every 3rd atom, define a new reigid molecule
if i % 3 == 0:
rb = rigidbody.RigidFragment()
rb_sites.append(rb)
rb.add_atom(atomtype, x, mass_lookup[atomtype])
# finalize the rigid body setup
for rb in rb_sites:
rb.finalize_setup()
# define a new rigid body system
rbsystem = rigidbody.RBSystem()
rbsystem.add_sites(rb_sites)
import numpy as np
from pele.potentials import LJ
from pele.utils import xyz
from pele.angleaxis import rigidbody
from pele.optimize import lbfgs_py
# read in coordinates from xyz file
ref = xyz.read_xyz(open("water.xyz"))
xyz.write_xyz(open("test.xyz", "w"), coords = ref.coords)
# lookup table for atom masses
mass_lookup = {'O': 16., 'H': 1.}
#ref.coords[:] *= 3
# now define a new rigid body system
rb_sites = []
for atomtype, x, i in zip(ref.atomtypes, ref.coords, xrange(len(ref.atomtypes))):
# every 3rd atom, define a new reigid molecule
if i%3 == 0:
rb = rigidbody.RigidFragment()
rb_sites.append(rb)
rb.add_atom(atomtype, x, mass_lookup[atomtype])
# finalize the rigid body setup
for rb in rb_sites:
rb.finalize_setup()
# define a new rigid body system
rbsystem = rigidbody.RBSystem()
rbsystem.add_sites(rb_sites)
