nebm fs: corrected variables; added test; refining params

Author: davidcortesortuno

fidimag/common/chain_method_integrators.py

@@ -160,10 +160,10 @@ def __init__(self, ChainObj,
                  # band, forces, distances, rhs_fun, action_fun,
                  # n_images, n_dofs_image,
                  maxSteps=1000,
-                 maxCreep=5, actionTol=1e-10, forcesTol=1e-6,
-                 etaScale=1.0, dEta=2, minEta=0.001,
+                 maxCreep=6, actionTol=1e-10, forcesTol=1e-6,
+                 etaScale=1e-6, dEta=4., minEta=1e-6,
                  # perturbSeed=42, perturbFactor=0.1,
-                 nTrail=10, resetMax=20
+                 nTrail=13, resetMax=20
                  ):
         # super(FSIntegrator, self).__init__(band, rhs_fun)
 
@@ -188,17 +188,16 @@ def __init__(self, ChainObj,
         self.n_dofs_image = self.ChainObj.n_dofs_image
         # self.forces_prev = np.zeros_like(band).reshape(n_images, -1)
         # self.G :
-        self.forces = self.ChainObj.forces
+        self.forces = self.ChainObj.G
         self.distances = self.ChainObj.distances
-        self.forces_old = np.zeros_like(self.ChainObj.forces)
+        self.forces_old = np.zeros_like(self.ChainObj.G)
 
         # self.band should be just a reference to the band in the ChainObj
         self.band = self.ChainObj.band
-        self.band_old = np.zeros_like(self.band)
+        self.band_old = np.copy(self.band)
 
     def run_for(self, n_steps):
 
-        t = 0.0
         nStart = 0
         exitFlag = False
         totalRestart = True
@@ -214,19 +213,25 @@ def run_for(self, n_steps):
 
         INNER_DOFS = slice(self.n_dofs_image, -self.n_dofs_image)
 
+        # Save data of energies on every step
+        self.ChainObj.tablewriter.save()
+        self.ChainObj.tablewriter_dm.save()
+
+        np.save(self.ChainObj.name + '_init.npy', self.ChainObj.band)
+
         while not exitFlag:
 
             if totalRestart:
-                if self.step > 0:
+                if self.i_step > 0:
                     print('Restarting')
                 self.band[:] = self.band_old
 
                 # Compute from self.band. Do not update the step at this stage:
                 # This step updates the forces and distances in the G array of the nebm module,
                 # using the current band state self.y
-                # TODO: remove time from chain method rhs
-                #       make a specific function to update G??
-                self.rhs(t, self.y)
+                # TODO: make a specific function to update G??
+                print('Computing forces')
+                self.ChainObj.nebm_step(self.band, ensure_zero_extrema=True)
                 self.action = self.ChainObj.compute_action()
 
                 # self.step += 1
@@ -250,13 +255,17 @@ def run_for(self, n_steps):
                 self.trailAction
 
                 self.ChainObj.nebm_step(self.band, ensure_zero_extrema=True)
-                self.action = self.ChainObj.action_fun()
+                self.action = self.ChainObj.compute_action()
 
                 self.trailAction[nStart] = self.action
                 nStart = next(trailPool)
 
                 self.i_step += 1
 
+                # Save data of energies on every step
+                self.ChainObj.tablewriter.save()
+                self.ChainObj.tablewriter_dm.save()
+
                 # Getting averages of forces from the INNER images in the band (no extrema)
                 # (forces are given by vector G in the chain method code)
                 # TODO: we might use all band images, not only inner ones, although G is zero at the extrema
@@ -268,10 +277,14 @@ def run_for(self, n_steps):
                 # Average step difference between trailing action and new action
                 deltaAction = (np.abs(self.trailAction[nStart] - self.action)) / self.nTrail
 
+                # print('trail Actions', self.trailAction)
+
                 # Print log
                 print(f'Step {self.i_step}  ⟨RMS(G)〉= {mean_rms_G_norms_per_image:.5e}  ',
                       f'deltaAction = {deltaAction:.5e}  Creep n = {creepCount:>3}  resetC = {resetCount:>3}  ',
-                      f'eta = {eta:>5.4e}')
+                      f'eta = {eta:>5.4e}  '
+                      f'action = {self.action:>5.4e}  action_old = {self.action_old:>5.4e}'
+                      )
 
                 # 10 seems like a magic number; we set here a minimum number of evaulations
                 if (nStart > self.nTrail * 10) and (deltaAction < self.actionTol):
@@ -291,17 +304,25 @@ def run_for(self, n_steps):
                     eta = eta / (self.dEta * self.dEta)
 
                     # If eta is too small, reset and start again
-                    if (eta < 1e-3):
-                        print('')
+                    if (eta < self.minEta):
+                        # print('')
                         resetCount += 1
                         # bestAction = self.action_old
-                        self.refine_path(self.ChainObj.distances, self.band)  # Resets the path to equidistant structures (smoothing  kinks?)
+                        print('Refining path')
+                        self.refine_path(self.ChainObj.path_distances, self.band)  # Resets the path to equidistant structures (smoothing  kinks?)
                         # PathChanged[:] = True
 
                         if resetCount > self.resetMax:
-                            print('Failed to converge!')
-                    # Otherwise, just 
+                            print('Failed to converge! Reached max number of restarts')
+                            exitFlag = True
+                            break  # creep loop
+
+                        totalRestart = True
+                        break  # creep loop
+
+                    # Otherwise, just start again with smaller alpha 
                     else:
+                        print('Decreasing alpha')
                         self.band[:] = self.band_old
                         self.forces[:] = self.forces_old
                 # If action decreases, move to next creep step
@@ -318,20 +339,22 @@ def run_for(self, n_steps):
             # END creep while loop
 
             # After creep loop:
-            self.eta = self.eta * self.dEta
+            eta = eta * self.dEta
             resetCount = 0
 
+        np.save(self.ChainObj.name + '.npy', self.ChainObj.band)
+
     # Taken from the string method class
-    def refine_path(self, distances, band):
+    def refine_path(self, path_distances, band):
         """
         """
-        new_dist = np.linspace(distances[0], distances[-1], distances.shape[0])
+        new_dist = np.linspace(path_distances[0], path_distances[-1], path_distances.shape[0])
         # Restructure the string by interpolating every spin component
         # print(self.integrator.y[self.n_dofs_image:self.n_dofs_image + 10])
         bandrs = band.reshape(self.n_images, self.n_dofs_image)
         for i in range(self.n_dofs_image):
 
-            cs = si.CubicSpline(distances, bandrs[:, i])
+            cs = si.CubicSpline(path_distances, bandrs[:, i])
             bandrs[:, i] = cs(new_dist)
 
     # def set_options(self):

fidimag/common/hubert_minimiser.py

@@ -264,6 +264,7 @@ def minimise(self,
                     exitFlag = True
                     break  # creep loop
 
+                # TODO: check if we need to use last spin state here
                 if self.totalE > self.totalE_last:  # If E increases, decrease eta so minimise slower
                     # print('Decreasing eta')
                     self.creepCount = 0

fidimag/common/nebm_FS.py

@@ -113,7 +113,7 @@ def __init__(self, sim,
                  name='unnamed',
                  climbing_image=None,
                  openmp=False,
-                 integrator='sundials'  # or scipy
+                 # integrator='sundials'  # or scipy
                  ):
 
         super(NEBM_FS, self).__init__(sim,
@@ -127,7 +127,7 @@ def __init__(self, sim,
                                       )
 
         # We need the gradient norm to calculate the action
-        self.gradientENorm = np.zeros_like(self.n_images)
+        self.gradientENorm = np.zeros(self.n_images)
 
         # Initialisation ------------------------------------------------------
         # See the NEBMBase class for details
@@ -136,7 +136,7 @@ def __init__(self, sim,
 
         self.initialise_energies()
 
-        self.initialise_integrator(integrator=integrator)
+        self.initialise_integrator()
 
         self.create_tablewriter()
 
@@ -236,9 +236,9 @@ def compute_effective_field_and_energy(self, y):
         the relaxation function
         """
 
-        self.gradientE = self.gradientE.reshape(self.n_images, -1)
+        self.gradientE.shape = (self.n_images, -1)
 
-        y = y.reshape(self.n_images, -1)
+        y.shape = (self.n_images, -1)
 
         # Do not update the extreme images
         for i in range(1, len(y) - 1):
@@ -253,13 +253,17 @@ def compute_effective_field_and_energy(self, y):
 
             self.energies[i] = self.sim.compute_energy()
 
+        # TODO: move this calc to the action function
         # Compute the gradient norm per every image
-        Gnorms2 = np.sum(self.gradientE.reshape(-1, 3)**2, axis=1)
+        Gnorms2 = np.sum(self.gradientE**2, axis=1) / self.n_images
         # Compute the root mean square per image
-        self.gradientENorm[:] = np.sqrt(np.mean(Gnorms2.reshape(self.n_images, -1), axis=1))
+        self.gradientENorm[:] = np.sqrt(Gnorms2)
 
-        y = y.reshape(-1)
-        self.gradientE = self.gradientE.reshape(-1)
+        # DEBUG:
+        # print('gradEnorm', self.gradientENorm)
+
+        y.shape = (-1)
+        self.gradientE.shape = (-1)
 
     def compute_tangents(self, y):
         nebm_clib.compute_tangents(self.tangents, y, self.energies,
@@ -327,7 +331,10 @@ def compute_action(self):
 
         # TODO: we can use a better quadrature such as Gaussian
         # notice that the gradient norm here is using the RMS
-        action = spi.trapezoid(self.gradientENorm, self.distances)
+        action = spi.trapezoid(self.gradientENorm, self.path_distances)
+
+        # DEBUG:
+        # print('action from gradE', action)
 
         # The spring term in the action is added as |F_k|^2 / (2 * self.k) = self.k * x^2 / 2
         # (CHECK) This assumes the spring force is orthogonal to the force gradient (after projection)
@@ -341,10 +348,13 @@ def compute_action(self):
         dist_minus_norm = self.distances[:-1]
         # dY_plus_norm = distances[i];
         # dY_minus_norm = distances[i - 1];
-        springF2 = self.k * ((dist_plus_norm - dist_minus_norm)**2)
+        springF2 = self.k[1:-1] * ((dist_plus_norm - dist_minus_norm)**2)
         # CHECK: do we need to scale?
         action += np.sum(springF2) / (self.n_images - 2)
 
+        # DEBUG:
+        # print('action spring term', np.sum(springF2) / (self.n_images - 2))
+
         return action
 
     def compute_min_action(self):

tests/tes_oommf.py tests/test_oommf.pytests/tes_oommf.py renamed to tests/test_oommf.py

@@ -0,0 +1,111 @@
+import pytest
+
+# FIDIMAG:
+from fidimag.micro import Sim
+from fidimag.common import CuboidMesh
+from fidimag.micro import UniformExchange, UniaxialAnisotropy
+from fidimag.common.nebm_FS import NEBM_FS
+import numpy as np
+
+# Material Parameters
+# Parameters
+A = 1e-12
+Kx = 1e5
+# Strong anisotropy
+Ms = 3.8e5
+
+
+"""
+We will define two particles using a 4 sites mesh, letting the
+sites in the middle as Ms = 0
+
+"""
+
+
+def two_part(pos):
+
+    x = pos[0]
+
+    if x > 6 or x < 3:
+        return Ms
+    else:
+        return 0
+
+# Finite differences mesh
+mesh = CuboidMesh(nx=3, ny=1, nz=1, dx=3, dy=3, dz=3, unit_length=1e-9)
+
+# Simulation Function
+def relax_string(maxst, simname, init_im, interp, save_every=10000):
+    """
+    """
+
+    # Prepare simulation
+    # We define the cylinder with the Magnetisation function
+    sim = Sim(mesh)
+    sim.Ms = two_part
+
+    # sim.add(UniformExchange(A=A))
+
+    # Uniaxial anisotropy along x-axis
+    sim.add(UniaxialAnisotropy(Kx, axis=(1, 0, 0)))
+
+    # Define many initial states close to one extreme. We want to check
+    # if the images in the last step, are placed mostly in equally positions
+    # init_images = init_im
+
+    # Number of images between each state specified before (here we need only
+    # two, one for the states between the initial and intermediate state
+    # and another one for the images between the intermediate and final
+    # states). Thus, the number of interpolations must always be
+    # equal to 'the number of initial states specified', minus one.
+    interpolations = interp
+
+    nebm = NEBM_FS(sim, init_im, interpolations=interpolations, name=simname)
+
+    # dt = integrator.stepsize means after every integrator step, the images
+    # are rescaled. We can run more integrator steps if we decrease the
+    # stepsize, e.g. dt=1e-3 and integrator.stepsize=1e-4
+    nebm.integrator.maxSteps = 33
+    nebm.integrator.run_for(maxst,
+                            # save_vtks_every=save_every,
+                            # save_npys_every=save_every,
+                            )
+
+    return nebm
+
+
+def mid_m(pos):
+    if pos[0] > 4:
+        return (0.5, 0, 0.2)
+    else:
+        return (-0.5, 0, 0.2)
+
+
+def test_energy_barrier_2particles_string():
+    # Initial images: we set here a rotation interpolating
+    init_im = [(-1, 0, 0), (1, 0, 0)]
+    interp = [13]
+
+    barriers = []
+
+    # Define different ks for multiple simulations
+    # krange = ['1e8']
+
+    string = relax_string(10,
+                          'nebmfs_2particles_k1e8_10-10int',
+                          init_im,
+                          interp,
+                          save_every=5000,
+                          )
+
+    _file = np.loadtxt('string_2particles_k1e8_10-10int_energy.ndt')
+    barriers.append((np.max(_file[-1][1:]) - _file[-1][1]) / 1.602e-19)
+
+    print('Energy barrier is:', barriers[-1])
+    assert np.abs(barriers[-1] - 0.016019) < 1e-5
+
+    print(barriers)
+
+
+if __name__ == '__main__':
+    test_energy_barrier_2particles_string()