Merge pull request #28 from jschueller/sundials5

Sundials 5.x port
Also contains lots of updates to line endings, now everything is LF.

CHANGELOG

@@ -1,5 +1,8 @@
 --- CHANGELOG ---
 
+--- Assimulo-3.2.8 ---
+    * Sundials 5.x port
+
 --- Assimulo-3.2.7 ---
     * Resolved deprecation warnings visible when using numpy 1.20.
     * Resolved deprecation warnings visible when creating an ndarray from ragged nested sequences.

doc/sphinx/source/museum.rst

@@ -1,38 +1,38 @@
-
-
-=============
-The Museum
-=============
-
-Assimulo includes an ODE solver museum. Integrators written in FORTRAN and C 
-were developped at least since the mid-sixties. Many of those are hard to access 
-others are only available as print-outs.
-
-``The harsch requirement that a useful numerical method must 
-permit an efficient, robust, and reliable implementation has
-withered the beautiful flowers which bloomed on thousands of journal pages.`` [Stetter93]_
-
-
-Following this motto, the Assimulo Museum aims at  showing these flowers at least in an herbarium.
-
-At the moment the Assimulo Museum includes
-
-    * DASP3  (scan)
-    * ODASSL
-
-    wrapping is in preperation for
-
-    * METAN1
-    * EULEX
-    * DIFFSUB
-    * MEXAX
-
-.. note::
-
-   Codes marked by (scan) are reconstructed from a scan and an OCR process. They are tested but
-   still they might include bugs due to the reconstruction process.
-
-   All other codes are original and untouched.
-
-.. [Stetter93] Hans Stetter In: Mathematics of Computation 1943-1993: A half-century
-   of computational mathematics: Mathematics of Computations 50th Aniversary Symposium. August 9-13, 1993. Vancouver, Britisch-Columbia, CA.)
+
+
+=============
+The Museum
+=============
+
+Assimulo includes an ODE solver museum. Integrators written in FORTRAN and C 
+were developped at least since the mid-sixties. Many of those are hard to access 
+others are only available as print-outs.
+
+``The harsch requirement that a useful numerical method must 
+permit an efficient, robust, and reliable implementation has
+withered the beautiful flowers which bloomed on thousands of journal pages.`` [Stetter93]_
+
+
+Following this motto, the Assimulo Museum aims at  showing these flowers at least in an herbarium.
+
+At the moment the Assimulo Museum includes
+
+    * DASP3  (scan)
+    * ODASSL
+
+    wrapping is in preperation for
+
+    * METAN1
+    * EULEX
+    * DIFFSUB
+    * MEXAX
+
+.. note::
+
+   Codes marked by (scan) are reconstructed from a scan and an OCR process. They are tested but
+   still they might include bugs due to the reconstruction process.
+
+   All other codes are original and untouched.
+
+.. [Stetter93] Hans Stetter In: Mathematics of Computation 1943-1993: A half-century
+   of computational mathematics: Mathematics of Computations 50th Aniversary Symposium. August 9-13, 1993. Vancouver, Britisch-Columbia, CA.)

examples/cvode_basic_backward.py

@@ -1,70 +1,70 @@
-#!/usr/bin/env python 
-# -*- coding: utf-8 -*-
-
-# Copyright (C) 2010 Modelon AB
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-import numpy as N
-import nose
-from assimulo.solvers import CVode
-from assimulo.problem import Explicit_Problem
-
-def run_example(with_plots=True):
-    """
-    The same as example :doc:`EXAMPLE_cvode_basic`  but now integrated backwards in time.
-    
-    on return:
-    
-       - :dfn:`exp_mod`    problem instance
-    
-       - :dfn:`exp_sim`    solver instance
-       
-    """
-    #Define the rhs
-    def f(t,y):
-        ydot = -y[0]
-        return N.array([ydot])
-
-    #Define an Assimulo problem
-    exp_mod = Explicit_Problem(f,t0=5, y0=0.02695, name = r'CVode Test Example (reverse time): $\dot y = - y$ ')
-
-    #Define an explicit solver
-    exp_sim = CVode(exp_mod) #Create a CVode solver
-
-    #Sets the parameters
-    exp_sim.iter  = 'Newton' #Default 'FixedPoint'
-    exp_sim.discr = 'BDF' #Default 'Adams'
-    exp_sim.atol = [1e-8] #Default 1e-6
-    exp_sim.rtol = 1e-8 #Default 1e-6
-    exp_sim.backward = True
-
-    #Simulate
-    t, y = exp_sim.simulate(0) #Simulate 5 seconds (t0=5 -> tf=0)
-
-    #Plot
-    if with_plots:
-        import pylab as P
-        P.plot(t, y, color="b")
-        P.title(exp_mod.name)
-        P.ylabel('y')
-        P.xlabel('Time')
-        P.show()
-
-    #Basic test
-    nose.tools.assert_almost_equal(float(y[-1]), 4.00000000, 3)
-
-    return exp_mod, exp_sim
-
-if __name__=='__main__':
-    mod,sim = run_example()
+#!/usr/bin/env python 
+# -*- coding: utf-8 -*-
+
+# Copyright (C) 2010 Modelon AB
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, version 3 of the License.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+import numpy as N
+import nose
+from assimulo.solvers import CVode
+from assimulo.problem import Explicit_Problem
+
+def run_example(with_plots=True):
+    """
+    The same as example :doc:`EXAMPLE_cvode_basic`  but now integrated backwards in time.
+    
+    on return:
+    
+       - :dfn:`exp_mod`    problem instance
+    
+       - :dfn:`exp_sim`    solver instance
+       
+    """
+    #Define the rhs
+    def f(t,y):
+        ydot = -y[0]
+        return N.array([ydot])
+
+    #Define an Assimulo problem
+    exp_mod = Explicit_Problem(f,t0=5, y0=0.02695, name = r'CVode Test Example (reverse time): $\dot y = - y$ ')
+
+    #Define an explicit solver
+    exp_sim = CVode(exp_mod) #Create a CVode solver
+
+    #Sets the parameters
+    exp_sim.iter  = 'Newton' #Default 'FixedPoint'
+    exp_sim.discr = 'BDF' #Default 'Adams'
+    exp_sim.atol = [1e-8] #Default 1e-6
+    exp_sim.rtol = 1e-8 #Default 1e-6
+    exp_sim.backward = True
+
+    #Simulate
+    t, y = exp_sim.simulate(0) #Simulate 5 seconds (t0=5 -> tf=0)
+
+    #Plot
+    if with_plots:
+        import pylab as P
+        P.plot(t, y, color="b")
+        P.title(exp_mod.name)
+        P.ylabel('y')
+        P.xlabel('Time')
+        P.show()
+
+    #Basic test
+    nose.tools.assert_almost_equal(float(y[-1]), 4.00000000, 3)
+
+    return exp_mod, exp_sim
+
+if __name__=='__main__':
+    mod,sim = run_example()