Python smooth_path Examples

Example #1

File: basesystem.py Project: sniblett402/pele

    def smooth_path(self, images, **kwargs):
        """return a smoothed path between two configurations.

        used for movies
        
        See Also
        --------
        pele.landscape.smooth_path
        """
        from pele.landscape import smooth_path
        try:
            interpolator = self.params.double_ended_connect.local_connect_params.NEBparams.interpolator
        except (KeyError, AttributeError):
            interpolator = None
        return smooth_path(images, self.get_mindist(), interpolator=interpolator)        

Example #2

File: basesystem.py Project: spraharsh/pele

    def smooth_path(self, images, **kwargs):
        """return a smoothed path between two configurations.

        used for movies
        
        See Also
        --------
        pele.landscape.smooth_path
        """
        from pele.landscape import smooth_path
        try:
            interpolator = self.params.double_ended_connect.local_connect_params.NEBparams.interpolator
        except (KeyError, AttributeError):
            interpolator = None
        return smooth_path(images,
                           self.get_mindist(),
                           interpolator=interpolator)

Example #3

    def test1(self):
        natoms = 13
        m1 = np.random.uniform(-1, 1, natoms * 3)
        ts = np.random.uniform(-1, 1, natoms * 3)
        m2 = np.random.uniform(-1, 1, natoms * 3)
        path = [m1, ts, m2]

        density = 5.
        spath = smooth_path(path, crap_mindist, density=density)

        d1 = crap_mindist(m1, ts)[0]
        d2 = crap_mindist(ts, m2)[0]
        dmax = max(d1, d2)
        for x1, x2 in zip(spath[:-1], spath[1:]):
            d = crap_mindist(x1, x2)[0]
            self.assertGreater(d, 0)
            self.assertLess(d, dmax)

        self.assertGreaterEqual(len(spath), 2 * density)

Example #4

File: test_smooth_path.py Project: Mahdisadjadi/pele

 def test1(self):
     natoms = 13
     m1 = np.random.uniform(-1,1,natoms*3)
     ts = np.random.uniform(-1,1,natoms*3)
     m2 = np.random.uniform(-1,1,natoms*3)
     path = [m1, ts, m2]
     
     density = 5.
     spath = smooth_path(path, crap_mindist, density=density)
     
     d1 = crap_mindist(m1,ts)[0]
     d2 = crap_mindist(ts,m2)[0]
     dmax = max(d1, d2)
     for x1, x2 in izip(spath[:-1], spath[1:]):
         d = crap_mindist(x1, x2)[0]
         self.assertGreater(d, 0)
         self.assertLess(d, dmax)
     
     self.assertGreaterEqual(len(spath), 2*density)

Example #5

File: pspin_spherical_system.py Project: smcantab/pele

 def smooth_path(self, path, **kwargs):
     mindist = self.get_mindist()
     return smooth_path(path, mindist, **kwargs)

Example #6

 def smooth_path(self, images, **kwargs):
     mindist = self.get_mindist()
     path = smooth_path(images, mindist, interpolator=interpolate_spins)
     return path

Example #7

 def smooth_path(self, path, **kwargs):
     mindist = self.get_mindist()
     return smooth_path(path, mindist, **kwargs)

Example #8

File: aasystem.py Project: spraharsh/pele

 def smooth_path(self, path, **kwargs):
     mindist = self.get_mindist()
     return smooth_path(path,
                        mindist,
                        interpolator=self.aasystem.interpolate,
                        **kwargs)

Example #9

File: heisenberg_spin_system.py Project: Mahdisadjadi/pele

 def smooth_path(self, images, **kwargs):
     mindist = self.get_mindist()
     path = smooth_path(images, mindist, interpolator=interpolate_spins)
     return path

Example #10

File: aasystem.py Project: pele-python/pele

 def smooth_path(self, path, **kwargs):
     mindist = self.get_mindist()
     return smooth_path(path, mindist, interpolator=self.aasystem.interpolate, **kwargs)

Example #11

File: connect_no_system_class.py Project: Mahdisadjadi/pele

nts = nmin - 1
print "the path has %d minima and %d transition states" % (nmin, nts)
eofs = "path.EofS"
print "saving energies to", eofs
with open(eofs, "w") as fout:
    for i in range(len(S)):
        fout.write("%f %f\n" % (S[i], energies[i]))

xyzfile = "path.xyz"
print "saving path in xyz format to", xyzfile
with open(xyzfile, "w") as fout:
    for m in mints:
        write_xyz(fout, m.coords, title=str(m.energy))

xyzfile = "path.smooth.xyz"
print "saving smoothed path in xyz format to", xyzfile
clist = [m.coords for m in mints]
smoothed = smooth_path(clist, mindist)
with open(xyzfile, "w") as fout:
    for coords in smoothed:
        write_xyz(fout, coords)

if False:
    try:
        import matplotlib.pyplot as plt

        plt.plot(S, energies)
        plt.show()
    except ImportError:
        print "problem plotting with pyplot, skipping"

Example #12

File: connect_no_system_class.py Project: spraharsh/pele

nts = nmin - 1
print("the path has %d minima and %d transition states" % (nmin, nts))
eofs = "path.EofS"
print("saving energies to", eofs)
with open(eofs, "w") as fout:
    for i in range(len(S)):
        fout.write("%f %f\n" % (S[i], energies[i]))

xyzfile = "path.xyz"
print("saving path in xyz format to", xyzfile)
with open(xyzfile, "w") as fout:
    for m in mints:
        write_xyz(fout, m.coords, title=str(m.energy))

xyzfile = "path.smooth.xyz"
print("saving smoothed path in xyz format to", xyzfile)
clist = [m.coords for m in mints]
smoothed = smooth_path(clist, mindist)
with open(xyzfile, "w") as fout:
    for coords in smoothed:
        write_xyz(fout, coords)

if False:
    try:
        import matplotlib.pyplot as plt

        plt.plot(S, energies)
        plt.show()
    except ImportError:
        print("problem plotting with pyplot, skipping")