Changeset 719

Timestamp:

03/02/10 11:11:07 (2 years ago)

Author:

apdavison

Message:

Added the ability to set the atol and rtol parameters of NEURON's cvode solver in the extra_params argument of setup() (patch from Johannes Partzsch).

Location:

trunk

Files:

• doc/installation.txt (modified) (2 diffs)
• src/neuron/__init__.py (modified) (1 diff)
• src/recording/__init__.py (modified) (1 diff)

trunk/doc/installation.txt

@@ -34 +34 @@
     loading membrane mechanisms from /home/andrew/dev/pyNN/hoc/i686/.libs/libnrnmech.so
     Additional mechanisms from files
-     adexp.mod alphaisyn.mod alphasyn.mod expisyn.mod hh_traub.mod netstim2.mod refrac.mod reset.mod stdwa_guetig.mod stdwa_softlimits.mod stdwa_songabbott.mod stdwa_symm.mod tmgsyn.mod vecstim.mod
+     adexp.mod alphaisyn.mod alphasyn.mod expisyn.mod hh_traub.mod netstim2.mod refrac.mod reset.mod
+     stdwa_guetig.mod stdwa_softlimits.mod stdwa_songabbott.mod stdwa_symm.mod tmgsyn.mod vecstim.mod
 
 If your model relies on other NMODL mechanisms, call the ``load_mechanisms()`` function with the path to the directory containing the ``.mod`` files.
@@ -99 +100 @@
 This will install PyNEST to your Python ``site-packages`` directory, and may require root privileges.
 If you wish to install it elsewhere, see the full installation instructions.
+Make sure you have the GNU Scientific Library (GSL) installed,
+otherwise some PyNN standard models (e.g. ``IF_cond_exp``) will not be available.
 
 Now try it out::

trunk/src/neuron/__init__.py

@@ -58 +58 @@
     if extra_params.has_key('use_cvode'):
         simulator.state.cvode.active(int(extra_params['use_cvode']))
+        if extra_params.has_key('rtol'):
+            simulator.state.cvode.rtol(float(extra_params['rtol']))
+        if extra_params.has_key('atol'):
+            simulator.state.cvode.atol(float(extra_params['atol']))
     return rank()
 

trunk/src/recording/__init__.py

@@ -110 +110 @@
         data_array = self._get(gather, compatible_output)
         id_offset = self.population and self.population.first_id or 0
-        data_array[:,0] -= id_offset # relies on fact that id is always first column
+        if data_array.size > 0:
+            data_array[:,0] -= id_offset # relies on fact that id is always first column
         self._data_size = data_array.shape[0]
         return data_array