Author: bugman
Date: Tue Apr 2 12:26:26 2013
New Revision: 19300
URL: http://svn.gna.org/viewcvs/relax?rev=19300&view=rev
Log:
Merged revisions 19297 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r19297 | bugman | 2013-04-02 11:44:35 +0200 (Tue, 02 Apr 2013) | 78 lines
Manually merged r19291, r19292, r19293, r19294, r19295, r19296 from the 2.2
line to trunk.
The command used was:
svn merge -r19290:19296 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/2.2
.
.....
------------------------------------------------------------------------
r19296 | bugman | 2013-04-02 11:41:09 +0200 (Tue, 02 Apr 2013) | 5 lines
Changed paths:
M /branches/2.2/test_suite/system_tests/scripts/bug_20674_jw_mapping.py
Fix for the Jw.test_bug_20674_jw_mapping system test.
The parameter f_eta is for consistency testing and not J(w) mapping.
------------------------------------------------------------------------
r19295 | bugman | 2013-04-02 11:39:55 +0200 (Tue, 02 Apr 2013) | 5 lines
Changed paths:
M /branches/2.2/test_suite/system_tests/scripts/bug_20674_jw_mapping.py
Converted the bug_20674_jw_mapping.py system test script to use the
self._execute_uf() interface.
This allows the script to be used in the GUI.
------------------------------------------------------------------------
r19294 | bugman | 2013-04-02 11:33:22 +0200 (Tue, 02 Apr 2013) | 5 lines
Changed paths:
M /branches/2.2/test_suite/system_tests/scripts/consistency_tests.py
M
/branches/2.2/test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py
M /branches/2.2/test_suite/system_tests/scripts/jw_mapping.py
M
/branches/2.2/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
System test speed ups - decreased the number of Monte Carlo simulations
in many tests.
Running 500 simulation optimisations in a system test is a total waste of
time!
------------------------------------------------------------------------
r19293 | bugman | 2013-04-02 11:27:32 +0200 (Tue, 02 Apr 2013) | 5 lines
Changed paths:
M /branches/2.2/specific_analyses/jw_mapping.py
Fix for the J(w) mapping analysis matching that of r19284 for the
consistency testing.
The overfit_deselect() method is now identical to that of the consistency
testing analysis.
------------------------------------------------------------------------
------------------------------------------------------------------------
r19292 | bugman | 2013-04-02 11:23:09 +0200 (Tue, 02 Apr 2013) | 8 lines
Changed paths:
M /branches/2.2/test_suite/system_tests/jw_mapping.py
A
/branches/2.2/test_suite/system_tests/scripts/bug_20674_jw_mapping.py (from
/branches/2.2/test_suite/system_tests/scripts/bug_20674_ct_analysis_failure.py:19284)
Created the Jw.bug_20674_jw_mapping system test.
This is a modification of the Ct.test_bug_20674_ct_analysis_failure
system test for catching bug
#20674 (https://gna.org/bugs/?20674). The test script was duplicated and
the small modifications
made to convert it into the J(w) mapping analysis. This now reveals the
same bug but for the J(w)
mapping analysis.
------------------------------------------------------------------------
r19291 | bugman | 2013-04-02 11:11:11 +0200 (Tue, 02 Apr 2013) | 5 lines
Changed paths:
M /branches/2.2/specific_analyses/model_free/main.py
Fix for the model-free analysis specific overfit_deselect() method.
The tests for the presence of dipolar relaxation was not correct and was
non-functional.
------------------------------------------------------------------------
.....
........
Added:
branches/relax_disp/test_suite/system_tests/scripts/bug_20674_jw_mapping.py
- copied unchanged from r19297,
trunk/test_suite/system_tests/scripts/bug_20674_jw_mapping.py
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/specific_analyses/jw_mapping.py
branches/relax_disp/specific_analyses/model_free/main.py
branches/relax_disp/test_suite/system_tests/jw_mapping.py
branches/relax_disp/test_suite/system_tests/scripts/consistency_tests.py
branches/relax_disp/test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py
branches/relax_disp/test_suite/system_tests/scripts/jw_mapping.py
branches/relax_disp/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Apr 2 12:26:26 2013
@@ -1,1 +1,1 @@
-/trunk:1-19289
+/trunk:1-19298
Modified: branches/relax_disp/specific_analyses/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/jw_mapping.py?rev=19300&r1=19299&r2=19300&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/jw_mapping.py (original)
+++ branches/relax_disp/specific_analyses/jw_mapping.py Tue Apr 2 12:26:26
2013
@@ -274,7 +274,7 @@
def overfit_deselect(self, data_check=True, verbose=True):
- """Deselect spins which _have insufficient data to support
calculation.
+ """Deselect spins which have insufficient data to support
calculation.
@keyword data_check: A flag to signal if the presence of base
data is to be checked for.
@type data_check: bool
@@ -292,32 +292,68 @@
# Loop over spin data.
deselect_flag = False
+ spin_count = 0
for spin, spin_id in spin_loop(return_id=True):
# Skip deselected spins.
if not spin.select:
continue
- # Check if data exists.
- if not hasattr(spin, 'ri_data'):
- warn(RelaxDeselectWarning(spin_id, 'missing relaxation
data'))
+ # The interatomic data.
+ interatoms = return_interatom_list(spin_id)
+
+ # Loop over the interatomic data.
+ dipole_relax = False
+ for i in range(len(interatoms)):
+ # No dipolar relaxation mechanism.
+ if not interatoms[i].dipole_pair:
+ continue
+
+ # The surrounding spins.
+ if spin_id != interatoms[i].spin_id1:
+ spin_id2 = interatoms[i].spin_id1
+ else:
+ spin_id2 = interatoms[i].spin_id2
+ spin2 = return_spin(spin_id2)
+
+ # Dipolar relaxation flag.
+ dipole_relax = True
+
+ # No relaxation mechanism.
+ if not dipole_relax or not hasattr(spin, 'csa') or spin.csa ==
None:
+ warn(RelaxDeselectWarning(spin_id, 'an absence of relaxation
mechanisms'))
spin.select = False
deselect_flag = True
continue
- # Require 3 or more data points.
- else:
- # Count the points.
+ # Data checks.
+ if data_check:
+ # The number of relaxation data points.
data_points = 0
- for id in cdp.ri_ids:
- if id in spin.ri_data and spin.ri_data[id] != None:
- data_points += 1
-
- # Not enough.
+ if hasattr(cdp, 'ri_ids') and hasattr(spin, 'ri_data'):
+ for id in cdp.ri_ids:
+ if id in spin.ri_data and spin.ri_data[id] != None:
+ data_points += 1
+
+ # Relaxation data must exist!
+ if not hasattr(spin, 'ri_data'):
+ warn(RelaxDeselectWarning(spin_id, 'missing relaxation
data'))
+ spin.select = False
+ deselect_flag = True
+ continue
+
+ # Require 3 or more data points.
if data_points < 3:
warn(RelaxDeselectWarning(spin_id, 'insufficient
relaxation data, 3 or more data points are required'))
spin.select = False
deselect_flag = True
continue
+
+ # Increment the spin number.
+ spin_count += 1
+
+ # No spins selected, so fail hard to prevent the user from going any
further.
+ if spin_count == 0:
+ warn(RelaxWarning("No spins are selected therefore the
optimisation or calculation cannot proceed."))
# Final printout.
if verbose and not deselect_flag:
Modified: branches/relax_disp/specific_analyses/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/model_free/main.py?rev=19300&r1=19299&r2=19300&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/model_free/main.py (original)
+++ branches/relax_disp/specific_analyses/model_free/main.py Tue Apr 2
12:26:26 2013
@@ -2019,10 +2019,10 @@
spin2 = return_spin(spin_id2)
# Dipolar relaxation flag.
- dipole_relax = False
+ dipole_relax = True
# No relaxation mechanism.
- if not dipole_relax and not hasattr(spin, 'csa') or spin.csa ==
None:
+ if not dipole_relax or not hasattr(spin, 'csa') or spin.csa ==
None:
warn(RelaxDeselectWarning(spin_id, 'an absence of relaxation
mechanisms'))
spin.select = False
deselect_flag = True
Modified: branches/relax_disp/test_suite/system_tests/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/jw_mapping.py?rev=19300&r1=19299&r2=19300&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/jw_mapping.py (original)
+++ branches/relax_disp/test_suite/system_tests/jw_mapping.py Tue Apr 2
12:26:26 2013
@@ -40,6 +40,13 @@
# Create the data pipe.
self.interpreter.pipe.create('jw', 'jw')
+
+
+ def test_bug_20674_jw_mapping(self):
+ """Catch U{bug #20674<https://gna.org/bugs/?20674>}, but for the
J(w) mapping analysis."""
+
+ # Execute the script.
+ self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bug_20674_jw_mapping.py')
def test_calc(self):
Modified:
branches/relax_disp/test_suite/system_tests/scripts/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/consistency_tests.py?rev=19300&r1=19299&r2=19300&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/scripts/consistency_tests.py
(original)
+++ branches/relax_disp/test_suite/system_tests/scripts/consistency_tests.py
Tue Apr 2 12:26:26 2013
@@ -46,7 +46,7 @@
self._execute_uf(uf_name='calc')
# Monte Carlo simulations.
-self._execute_uf(uf_name='monte_carlo.setup', number=500)
+self._execute_uf(uf_name='monte_carlo.setup', number=5)
self._execute_uf(uf_name='monte_carlo.create_data')
self._execute_uf(uf_name='calc')
self._execute_uf(uf_name='monte_carlo.error_analysis')
Modified:
branches/relax_disp/test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py?rev=19300&r1=19299&r2=19300&view=diff
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py
Tue Apr 2 12:26:26 2013
@@ -68,7 +68,7 @@
minimise('simplex', scaling=False, constraints=False)
# Monte Carlo simulations.
-monte_carlo.setup(number=500)
+monte_carlo.setup(number=5)
monte_carlo.create_data()
monte_carlo.initial_values()
minimise('simplex', scaling=False, constraints=False)
Modified: branches/relax_disp/test_suite/system_tests/scripts/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/jw_mapping.py?rev=19300&r1=19299&r2=19300&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/scripts/jw_mapping.py
(original)
+++ branches/relax_disp/test_suite/system_tests/scripts/jw_mapping.py Tue Apr
2 12:26:26 2013
@@ -40,7 +40,7 @@
self._execute_uf(uf_name='calc')
# Monte Carlo simulations.
-self._execute_uf(uf_name='monte_carlo.setup', number=500)
+self._execute_uf(uf_name='monte_carlo.setup', number=5)
self._execute_uf(uf_name='monte_carlo.create_data')
self._execute_uf(uf_name='calc')
self._execute_uf(uf_name='monte_carlo.error_analysis')
Modified:
branches/relax_disp/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py?rev=19300&r1=19299&r2=19300&view=diff
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
Tue Apr 2 12:26:26 2013
@@ -34,7 +34,7 @@
results.write(file='devnull', dir=None, compress_type=1, force=True)
# Monte Carlo simulation setup.
-monte_carlo.setup(number=200)
+monte_carlo.setup(number=5)
monte_carlo.create_data(method='back_calc')
monte_carlo.initial_values()
r19300 - in /branches/relax_disp: ./ specific_analyses/ specific_analyses/model_free/ test_suite/system_tests/ test_suite/sy...