removed remaining Scientific.LA deps

Removed dead code

MMTK/Geometry.py

@@ -17,7 +17,6 @@ import numpy
 
 from Scientific.Geometry import Vector
 
-
 # Error type
 class GeomError(Exception):
     pass
@@ -789,8 +788,8 @@ def superpositionFit(confs):
     k = 2.*k
     for i in range(4):
         k[i, i] = k[i, i] + possq - numpy.add.reduce(pos*pos)
-    from Scientific import LA
-    e, v = LA.eigenvectors(k)
+    e, v = numpy.linalg.eig(k)
+    v = numpy.transpose(v)
     i = numpy.argmin(e)
     v = v[i]
     if v[0] < 0: v = -v

MMTK/NormalModes/Core.py

@@ -5,65 +5,23 @@
 
 __docformat__ = 'restructuredtext'
 
-import numpy
-
-from MMTK import Units, ParticleProperties, Visualization
 import copy
 
-#
-# Import LAPACK routines or equivalents
-#
+import numpy
 
-eigh = None
+from MMTK import ParticleProperties, Visualization
 
-# Use symeig (http://mdp-toolkit.sourceforge.net/symeig.html)
-# if it is installed and if NumPy is used (symeig works only
-# with NumPy). Symeig uses the LAPACK routine dsyevr, which
-# uses less memory than dsyevd. It is also said to be faster,
-# but in my tests on the Mac it turned out to be slightly slower.
+dgesdd = None
 try:
-    from numpy.linalg import eigh
+    from numpy.linalg.lapack_lite import dgesdd
 except ImportError:
     pass
 
-dsyevd = None
-dgesdd = None
-try:
-    from numpy.linalg.lapack_lite import dsyevd, dgesdd, LapackError
-except ImportError: pass
-if dsyevd is None:
-    try:
-        # PyLAPACK
-        from lapack_dsy import dsyevd, LapackError
-    except ImportError: pass
 if dgesdd is None:
     try:
         # PyLAPACK
         from lapack_dge import dgesdd
     except ImportError: pass
-if dsyevd is None:
-    from numpy.linalg import eigh
-if dsyevd:
-    n = 1
-    array = numpy.zeros((n, n), numpy.float)
-    ev = numpy.zeros((n,), numpy.float)
-    work = numpy.zeros((1,), numpy.float)
-    int_types = [numpy.int, numpy.int8, numpy.int16, numpy.int32]
-    try:
-        int_types.append(numpy.int64)
-        int_types.append(numpy.int128)
-    except AttributeError:
-        pass
-    for int_type in int_types:
-        iwork = numpy.zeros((1,), int_type)
-        try:
-            dsyevd('V', 'L', n, array, n, ev, work, -1, iwork, -1, 0)
-            break
-        except LapackError:
-            pass
-    del n, array, ev, work, iwork, int_types
-
-del array_package
 
 #
 # Class for a single mode
@@ -251,32 +209,13 @@ class NormalModes(object):
             return eigenvalues
 
         # Calculate eigenvalues and eigenvectors of self.array
-        if eigh is not None:
-            _symmetrize(self.array)
-            ev, modes = eigh(self.array, overwrite_a=True)
-            self.array = numpy.transpose(modes)
-        elif dsyevd is None:
-            ev, modes = Heigenvectors(self.array)
-            ev = ev.real
-            modes = modes.real
-            self.array = modes.T
-        else:
-            ev = numpy.zeros((self.nmodes,), numpy.float)
-            work = numpy.zeros((1,), numpy.float)
-            iwork = numpy.zeros((1,), int_type)
-            results = dsyevd('V', 'L', self.nmodes, self.array, self.nmodes,
-                             ev, work, -1, iwork, -1, 0)
-            lwork = int(work[0])
-            liwork = iwork[0]
-            work = numpy.zeros((lwork,), numpy.float)
-            iwork = numpy.zeros((liwork,), int_type)
-            results = dsyevd('V', 'L', self.nmodes, self.array, self.nmodes,
-                             ev, work, lwork, iwork, liwork, 0)
-            if results['info'] > 0:
-                raise ValueError('Eigenvalue calculation did not converge')
+        _symmetrize(self.array)
+        ev, modes = numpy.linalg.eigh(self.array, overwrite_a=True)
+        self.array = numpy.transpose(modes)
 
         if self.basis is not None:
             self.array = numpy.dot(self.array, self.basis)
+            
         return ev
 
     def _setupBasis(self):

MMTK/Trajectory.py

@@ -11,7 +11,7 @@ __docformat__ = 'restructuredtext'
 
 import numpy
 
-from MMTK import Collections, Units, Universe, Utility, \
+from MMTK import Collections, Units, Utility, \
                  ParticleProperties, Visualization
 from Scientific.Geometry import Vector
 import copy, os, sys
@@ -935,10 +935,9 @@ class RigidBodyTrajectory(object):
 
         quaternions = numpy.zeros((steps, 4), numpy.float)
         fit = numpy.zeros((steps,), numpy.float)
-        from numpy.linalg import eig
         for i in range(steps):
-            e, v = eig(k[i])
-            v = v.T
+            e, v = numpy.linalg.eig(k[i])
+            v = numpy.transpose(v)
             j = numpy.argmin(e)
             if e[j] < 0.:
                 fit[i] = 0.