Python Database.transition_states方法代码示例

# 需要导入模块: from pele.storage import Database [as 别名]
# 或者: from pele.storage.Database import transition_states [as 别名]
class TestOptimCollagen(unittest.TestCase):
    """test a known value for a large database"""
    def setUp(self):
        from pele.utils.optim_compatibility import OptimDBConverter
        from pele.storage import Database
        ndof = 10 # wrong, but who cares.
        self.db = Database()
        current_dir = os.path.dirname(__file__)
        converter = OptimDBConverter(self.db, ndof=ndof, mindata=current_dir+"/collagen.min.data", 
                                     tsdata=current_dir+"/collagen.ts.data", assert_coords=False)
        converter.convert_no_coords()
    
    def test1(self):
        m1 = self.db.getMinimum(1)
        m2 = self.db.getMinimum(2)
        m3 = self.db.getMinimum(3)
        m4 = self.db.getMinimum(4)
        
        rcalc = RateCalculation(self.db.transition_states(), [m1], [m2], T=0.592)
        rcalc.compute_rates()
        self.assertAlmostEqual(rcalc.get_rate_AB(), 7106337458., delta=1e4)
        self.assertAlmostEqual(rcalc.get_rate_BA(), 1955395816., delta=1e4)
        
        rcalc = RateCalculation(self.db.transition_states(), [m1,m3], [m2, m4], T=0.592)
        rcalc.compute_rates()
        self.assertAlmostEqual(rcalc.get_rate_AB(), 8638736600., delta=1e4)
        self.assertAlmostEqual(rcalc.get_rate_BA(), 3499625167., delta=1e4)
        
        rla = RatesLinalg(self.db.transition_states(), [m1], [m2], T=0.592)
        rAB = rla.compute_rates()
        self.assertAlmostEqual(rAB, 7106337458., delta=1e4)
        
        rla = RatesLinalg(self.db.transition_states(), [m1, m3], [m2, m4], T=0.592)
        rAB = rla.compute_rates()
        self.assertAlmostEqual(rAB, 8638736600., delta=1e4)

# 需要导入模块: from pele.storage import Database [as 别名]
# 或者: from pele.storage.Database import transition_states [as 别名]
    def test1(self):
        current_dir = os.path.dirname(__file__)
        db = Database()
        converter = OptimDBConverter(db, 
                                     mindata=os.path.join(current_dir, "min.data"),
                                     tsdata=os.path.join(current_dir, "ts.data"),
                                     pointsmin=os.path.join(current_dir, "points.min"),
                                     pointsts=os.path.join(current_dir, "points.ts"),
                                     endianness="<")
        converter.convert()
        self.assertEqual(db.number_of_minima(), 2)
        self.assertEqual(db.number_of_transition_states(), 1)
        
        ts = db.transition_states()[0]
        self.assertAlmostEqual(ts.coords[0], 1.548324, 5)
        self.assertAlmostEqual(ts.coords[2], 0.18178001, 5)
        self.assertAlmostEqual(ts.coords[-1], -0.50953229, 5)
        self.assertEqual((180,), ts.coords.shape)

        m = db.minima()[0]
        print(repr(m.coords))
        self.assertAlmostEqual(m.coords[0], 1.53700142, 5)
        self.assertAlmostEqual(m.coords[2], 0.87783657, 5)
        self.assertAlmostEqual(m.coords[-1], -0.50953229, 5)
        self.assertEqual((180,), m.coords.shape)

# 需要导入模块: from pele.storage import Database [as 别名]
# 或者: from pele.storage.Database import transition_states [as 别名]
 def test2(self):
     from pele.utils.tests.test_disconnectivity_graph import create_random_database
     
     db = create_random_database(nmin=20, nts=15)
     
     delete=False
     mdata = tempfile.NamedTemporaryFile(delete=delete, suffix=".min.data")
     tsdata = tempfile.NamedTemporaryFile(delete=delete, suffix=".ts.data")
     pm = tempfile.NamedTemporaryFile(delete=delete)
     pts = tempfile.NamedTemporaryFile(delete=delete)
     print(mdata.name, tsdata.name)
     writer = WritePathsampleDB(db,
                                mindata=mdata.name,
                                tsdata=tsdata.name,
                                pointsmin=pm.name,
                                pointsts=pts.name,
                                endianness="<")
     
     writer.write_db()
     
     newdb = Database()
     reader = OptimDBConverter(newdb,
                               mindata=mdata.name,
                               tsdata=tsdata.name,
                               pointsmin=pm.name,
                               pointsts=pts.name,
                               endianness="<")
     reader.convert()
     
     for m1, m2 in zip(db.minima(), newdb.minima()):
         self.assertAlmostEqual(m1.energy, m2.energy)
         _base_test.assert_arrays_almost_equal(self, m1.coords, m2.coords)
     
     for ts1, ts2 in zip(db.transition_states(), newdb.transition_states()):
         self.assertAlmostEqual(ts1.energy, ts2.energy)
         _base_test.assert_arrays_almost_equal(self, ts1.coords, ts2.coords)
         self.assertAlmostEqual(ts1.minimum1.energy, ts2.minimum1.energy)
         self.assertAlmostEqual(ts1.minimum2.energy, ts2.minimum2.energy)

# 需要导入模块: from pele.storage import Database [as 别名]
# 或者: from pele.storage.Database import transition_states [as 别名]
print len(A), "A minima"
print len(B), "B minima"

        
        

print A[0].energy
print B[0].energy

#rate_constants = reduce_rates(rate_constants, B, A=A)


print "computing rates from minima data"
T = .05
print "temperature", T
pele_rates = RateCalculation(db.transition_states(), A, B, T=T, use_fvib=True)
pele_rates._make_kmc_graph()
rates = pele_rates.rate_constants
weights = pele_rates._get_equilibrium_occupation_probabilities()
rate_norm = np.exp(-pele_rates.max_log_rate)
#Peq = pele_rates._get_equilibrium_occupation_probabilities()

print "reducing rates"
rate_constants = reduce_rates(rates, B, A=A)



print "max rate constant", max(rates.itervalues())
print "min rate constant", min(rates.itervalues())

if False:

# 需要导入模块: from pele.storage import Database [as 别名]
# 或者: from pele.storage.Database import transition_states [as 别名]
class TestDB(unittest.TestCase):
    def setUp(self):
        self.db = Database()
        self.nminima = 10
        for i in range(self.nminima):
            e = float(i)
            self.db.addMinimum(e, [e])
        
        
        self.nts = 3
        self.db.addTransitionState(0., [0.], self.db.minima()[0], self.db.minima()[1], eigenval=0., eigenvec=[0.])
        self.db.addTransitionState(0., [0.], self.db.minima()[1], self.db.minima()[2], eigenval=0., eigenvec=[0.])
        self.db.addTransitionState(0., [0.], self.db.minima()[0], self.db.minima()[2], eigenval=0., eigenvec=[0.])

    def test_size(self):
        self.assertEqual(len(self.db.minima()), self.nminima)
        
    def test_energy(self):
        m = self.db.minima()[0]
        self.assertEqual(m.energy, 0.)

    def test_coords(self):
        m = self.db.minima()[0]
        self.assertEqual(m.coords, [0.])

    def test_sizets(self):
        self.assertEqual(len(self.db.transition_states()), self.nts)
    def test_energyts(self):
        ts = self.db.transition_states()[0]
        self.assertEqual(ts.energy, 0.)

    def test_coordsts(self):
        ts = self.db.transition_states()[0]
        self.assertEqual(ts.coords, [0.])
    
    def test_remove_minimum(self):
        m = self.db.minima()[0]
        self.db.removeMinimum(m)
        self.assertEqual(len(self.db.minima()), self.nminima-1)
        self.assertNotIn(m, self.db.minima())
        
        # m should have 2 minima.  both of those should be gone
        self.assertEqual(len(self.db.transition_states()), self.nts-2)

    def test_remove_ts(self):
        ts = self.db.transition_states()[0]
        self.db.remove_transition_state(ts)
        self.assertEqual(self.db.number_of_transition_states(), self.nts-1)
        self.assertNotIn(ts, self.db.transition_states())
        
        # m should have 2 minima.  both of those should be gone
        self.assertEqual(self.db.number_of_minima(), self.nminima)


    def test_getTransitionState(self):
        m1 = self.db.minima()[0]
        m2 = self.db.minima()[1]
        m3 = self.db.minima()[-1]
        self.assertIsNotNone(self.db.getTransitionState(m1, m2))
        self.assertIsNone(self.db.getTransitionState(m1, m3))
    
    def test_getMinimum(self):
        m = self.db.minima()[0]
        self.assertEqual(m, self.db.getMinimum(m._id))
        
    def test_minimum_adder(self):
        ma = self.db.minimum_adder()
        ma(101., [101.])
        self.assertEqual(len(self.db.minima()), self.nminima+1)
    
    def test_merge_minima(self):
        m1 = self.db.minima()[0]
        m2 = self.db.minima()[1]
        self.db.mergeMinima(m1, m2)
        self.assertEqual(len(self.db.minima()), self.nminima-1)
        # transition states shouldn't be deleted
        self.assertEqual(len(self.db.transition_states()), self.nts)
    
    def test_number_of_minima(self):
        self.assertEqual(self.nminima, self.db.number_of_minima())
    
    def test_number_of_transition_states(self):
        self.assertEqual(self.nts, self.db.number_of_transition_states())
    
    def test_highest_energy_minimum(self):
        m1 = self.db._highest_energy_minimum()
        m2 = self.db.minima()[-1]
        self.assertEqual(m1, m2)
    
    def test_maximum_number_of_minima(self):
        m = self.db.addMinimum(-1., [-1.], max_n_minima=self.nminima)
        self.assertEqual(self.nminima, self.db.number_of_minima())
        self.assertIn(m, self.db.minima())

    def test_maximum_number_of_minima_largestE(self):
        e = float(self.nminima + 1)
        m = self.db.addMinimum(e, [e], max_n_minima=self.nminima)
        self.assertEqual(self.nminima, self.db.number_of_minima())
        self.assertIsNone(m)
        
#.........这里部分代码省略.........

# 需要导入模块: from pele.storage import Database [as 别名]
# 或者: from pele.storage.Database import transition_states [as 别名]
db = Database(db="tip4p_8.sqlite", createdb=False)

graph = TSGraph(db)

dg = DisconnectivityGraph(graph.graph, db.minima(), subgraph_size=20)
dg.calculate()
dg.plot()

for m in db.minima():
    if m.pgorder != 2:
        print m.pgorder
    m.free_energy = m.energy + kbT * 0.5*m.fvib + kbT*np.log(m.pgorder)

 
for ts in db.transition_states():
#    if ts.pgorder != 2:
    print ts.pgorder
    #assert ts.pgorder == 2    

    ts.free_energy = ts.energy + kbT * 0.5*ts.fvib + kbT*np.log(ts.pgorder) + kbT*np.log(kbT)
    if ts.free_energy > ts.minimum1.free_energy or ts.free_energy > ts.minimum2.free_energy:        
        print "warning, free energy of transition state lower than minimum"
        print ts.free_energy, ts.minimum1.free_energy, ts.minimum2.free_energy
        print ts.energy, ts.minimum1.energy, ts.minimum2.energy
        
    
dg_F = DisconnectivityGraph(graph.graph, db.minima(), energy_attribute="free_energy", subgraph_size=20)
dg_F.calculate()
dg_F.plot()