Author: bugman
Date: Thu Jan 24 16:08:02 2013
New Revision: 18308
URL: http://svn.gna.org/viewcvs/relax?rev=18308&view=rev
Log:
Merged revisions 18301-18307 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18301 | bugman | 2013-01-24 13:00:31 +0100 (Thu, 24 Jan 2013) | 7 lines
Big data store clean up fix for the N-state model.
The N-state model specific base_data_loop() method now skips deselected
interatomic data containers
and spins. This prevents a lot of junk data being created in the data
pipe, for example back
calculated and Monte Carlo simulation RDC and PCS data.
........
r18302 | bugman | 2013-01-24 14:16:51 +0100 (Thu, 24 Jan 2013) | 5 lines
Added new checks in the N_state_model.test_metal_pos_opt system test.
These are for structures which should not be in the deselected spins and
interatomic containers
........
r18303 | bugman | 2013-01-24 14:21:42 +0100 (Thu, 24 Jan 2013) | 5 lines
The N-state model _check_rdcs() method now skips deselected interatomic
data containers.
A FIXME comment has also been added to highlight a possible future problem.
........
r18304 | bugman | 2013-01-24 14:43:43 +0100 (Thu, 24 Jan 2013) | 3 lines
Small docstring fix.
........
r18305 | bugman | 2013-01-24 14:45:07 +0100 (Thu, 24 Jan 2013) | 6 lines
Added some consistency to the specific analysis API base class.
The return_data() method argument has been changed from 'spin' to
'data_id', as the data from the
base_data_loop() methods are often not spin containers.
........
r18306 | bugman | 2013-01-24 14:49:52 +0100 (Thu, 24 Jan 2013) | 5 lines
Fixes for the relaxation curve-fitting specific return_data() method.
Strangely, it appears as if this method is never used.
........
r18307 | bugman | 2013-01-24 16:05:54 +0100 (Thu, 24 Jan 2013) | 5 lines
Made the chi2 value check less stringent in the
N_state_model.test_metal_pos_opt system test.
For some bizarre reason, the calc() call in the GUI is less precise.
........
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/specific_fns/api_base.py
branches/frame_order_testing/specific_fns/n_state_model.py
branches/frame_order_testing/specific_fns/relax_fit.py
branches/frame_order_testing/test_suite/system_tests/n_state_model.py
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Jan 24 16:08:02 2013
@@ -1,1 +1,1 @@
-/trunk:1-18299
+/trunk:1-18307
Modified: branches/frame_order_testing/specific_fns/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/api_base.py?rev=18308&r1=18307&r2=18308&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/api_base.py (original)
+++ branches/frame_order_testing/specific_fns/api_base.py Thu Jan 24 16:08:02
2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2012 Edward d'Auvergne
#
+# Copyright (C) 2004-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -117,7 +117,7 @@
"""Create the Monte Carlo data.
@keyword data_id: The data identification information, as yielded
by the base_data_loop() generator method.
- @type data_id: str
+ @type data_id: anything
@return: The Monte Carlo simulation data.
@rtype: list of floats
"""
@@ -523,13 +523,13 @@
return self.PARAMS.get_conv_factor(param)
- def return_data(self, spin):
+ def return_data(self, data_id=None):
"""Return the data points used in optimisation.
- @param spin: The SpinContainer object.
- @type spin: SpinContainer instance
- @return: The array of relaxation data values.
- @rtype: list of float
+ @keyword data_id: The data identification information, as yielded
by the base_data_loop() generator method.
+ @type data_id: anything
+ @return: The array of data values.
+ @rtype: list of float
"""
# Not implemented.
@@ -571,13 +571,13 @@
return param
- def return_error(self, data_id):
+ def return_error(self, data_id=None):
"""Return the error points corresponding to the data points used in
optimisation.
- @param data_id: The data identification information, as yielded by
the base_data_loop() generator method.
- @type data_id: str
- @return: The array of relaxation data error values.
- @rtype: list of float
+ @keyword data_id: The data identification information, as yielded
by the base_data_loop() generator method.
+ @type data_id: anything
+ @return: The array of data error values.
+ @rtype: list of float
"""
# Not implemented.
@@ -708,7 +708,7 @@
"""Pack the Monte Carlo simulation data.
@param data_id: The data identification information, as yielded
by the base_data_loop() generator method.
- @type data_id: str
+ @type data_id: anything
@param sim_data: The Monte Carlo simulation data.
@type sim_data: list of float
"""
Modified: branches/frame_order_testing/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/n_state_model.py?rev=18308&r1=18307&r2=18308&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/n_state_model.py (original)
+++ branches/frame_order_testing/specific_fns/n_state_model.py Thu Jan 24
16:08:02 2013
@@ -412,7 +412,12 @@
@return: True if the RDCs should be used, False otherwise.
"""
+ # Skip deselected interatomic data containers.
+ if not interatom.select:
+ return False
+
# Skip deselected spins.
+ # FIXME: These checks could be fatal in the future if a user has
good RDCs and one of the two spins are deselected!
if not spin1.select or not spin2.select:
return False
@@ -1797,6 +1802,10 @@
# Loop over the interatomic data containers.
for interatom in interatomic_loop():
+ # Skip deselected data.
+ if not interatom.select:
+ continue
+
# Re-initialise the data structure.
data = [interatom, None, None]
@@ -1826,6 +1835,10 @@
# Loop over the spins.
for spin in spin_loop():
+ # Skip deselected data.
+ if not spin.select:
+ continue
+
# Re-initialise the data structure.
data = [spin, None, None]
@@ -2451,7 +2464,7 @@
@keyword data_id: The list of spin ID, data type, and alignment
ID, as yielded by the base_data_loop() generator method.
@type data_id: str
@return: The Monte Carlo simulation data errors.
- @rtype: list of floats
+ @rtype: list of float
"""
# Initialise the MC data structure.
Modified: branches/frame_order_testing/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/relax_fit.py?rev=18308&r1=18307&r2=18308&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/relax_fit.py (original)
+++ branches/frame_order_testing/specific_fns/relax_fit.py Thu Jan 24
16:08:02 2013
@@ -850,15 +850,19 @@
print("No spins have been deselected.")
- def return_data(self, spin):
+ def return_data(self, data_id=None):
"""Function for returning the peak intensity data structure.
- @param spin: The spin container.
- @type spin: SpinContainer instance
- @return: The peak intensity data structure.
- @rtype: list of float
- """
-
+ @keyword data_id: The spin identification string, as yielded by
the base_data_loop() generator method.
+ @type data_id: str
+ @return: The peak intensity data structure.
+ @rtype: list of float
+ """
+
+ # Get the spin container.
+ spin = return_spin(data_id)
+
+ # Return the peak intensities.
return spin.intensities
Modified:
branches/frame_order_testing/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/n_state_model.py?rev=18308&r1=18307&r2=18308&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/n_state_model.py
(original)
+++ branches/frame_order_testing/test_suite/system_tests/n_state_model.py Thu
Jan 24 16:08:02 2013
@@ -572,12 +572,22 @@
'Tm': [ 0.000125066528687, -0.000564062193363,
-0.000607973317902, 0.000090266635200, 0.000174865797403,
0.002488010156480, 0.000830246873289, 0.000762523870219,
-0.000096933008248, 0.000742665143642, -0.000215152849719],
'Er': [-0.481445160767000, -0.361046693640000,
-0.370098680342000, -0.413514467402000, -0.410802287329000,
-1.081011578870000, -0.963176128222000, -0.745366702244000,
-0.674570724880000, -0.751320872646000, -0.684906087274000,
-0.461253969271000, -0.443680922437000, -0.344056233315000,
-0.328118573270000, -0.395048353548000, -0.356220572284000,
-0.324533952261000, -0.411777498713000, -0.511811581196000,
-1.018565433020000, -0.959481602761000, -0.734022165690000,
-0.660034918889000, -0.709085634512000, -0.878775632044000,
-0.553464480425000, -0.765371835675000, -1.548006987460000]
}
+ spin_deselect_blacklist = ['pcs_bc', 'pcs_sim']
+
# Loop over the align IDs.
for tag in ['Dy', 'Tb', 'Tm', 'Er']:
i = 0
for spin, spin_id in spin_loop(return_id=True):
# Deselected spin.
if not spin.select:
+ print("Checking the deselected spin '%s'" % spin_id)
+
+ # Check that the container is clean.
+ for name in spin_deselect_blacklist:
+ print(" Checking the blacklisted object %s." %
name)
+ self.assert_(not hasattr(spin, name))
+
+ # Skip the rest of the checks.
continue
# No PCS.
@@ -608,12 +618,22 @@
'Tm': [-0.057386340972700, -0.045650398398700,
-0.074873514450400, 0.099056143214600, 0.021275817005300,
0.037132036464200, 0.047340390362400, 0.128745838536000,
0.010906407989400],
'Er': [ 22.944150028900001, 23.363231565100001,
25.948323446000000, 6.955380304960000, 1.784067087050000,
7.228324193240000, 8.271072502000001, -7.403618580470000]
}
+ interatom_deselect_blacklist = ['rdc_bc', 'rdc_sim']
+
# Loop over the align IDs.
for tag in ['Dy', 'Tm', 'Er']:
i = 0
for interatom in interatomic_loop():
# Deselected interatomic container.
if not interatom.select:
+ print("Checking the deselected interatom '%s-%s'" %
(interatom.spin_id1, interatom.spin_id2))
+
+ # Check that the container is clean.
+ for name in interatom_deselect_blacklist:
+ print(" Checking the blacklisted object %s." %
name)
+ self.assert_(not hasattr(interatom, name))
+
+ # Skip the rest of the checks.
continue
# No RDC.
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py?rev=18308&r1=18307&r2=18308&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
(original)
+++
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
Thu Jan 24 16:08:02 2013
@@ -113,7 +113,7 @@
cdp.paramagnetic_centre[0] = cdp.paramagnetic_centre[0] + 0.02
print("Shifted position: [%.3f, %.3f, %.3f]\n" %
(cdp.paramagnetic_centre[0], cdp.paramagnetic_centre[1],
cdp.paramagnetic_centre[2]))
self._execute_uf(uf_name='calc')
-print("Chi2: %s" % cdp.chi2)
+print("Chi2: %.15f" % cdp.chi2)
if cdp.chi2 < 1e-15:
raise RelaxError("The chi2 value cannot be zero here!")
@@ -121,15 +121,16 @@
x, y, z = cdp.paramagnetic_centre
self._execute_uf(uf_name='n_state_model.select_model', model='population')
self._execute_uf(uf_name='calc')
-print("Chi2: %s" % cdp.chi2)
+print("Chi2: %.15f" % cdp.chi2)
chi2 = cdp.chi2
if cdp.chi2 < 1e-15:
raise RelaxError("The chi2 value cannot be zero here!")
self._execute_uf(uf_name='paramag.centre', fix=True)
self._execute_uf(uf_name='calc')
-print("Chi2: %s" % cdp.chi2)
-if abs(cdp.chi2 - chi2) > 1e-15:
- raise RelaxError("The chi2 value must match the previous value of %s." %
chi2)
+print("Chi2: %.15f" % cdp.chi2)
+if abs(cdp.chi2 - chi2) > 1e-10:
+ print "%.15g" % abs(cdp.chi2 - chi2)
+ raise RelaxError("The chi2 value must match the previous value of
%.15f." % chi2)
self._execute_uf(uf_name='n_state_model.select_model', model='fixed')
self._execute_uf(uf_name='paramag.centre', fix=False)
self._execute_uf(uf_name='calc')
r18308 - in /branches/frame_order_testing: ./ specific_fns/ test_suite/system_tests/ test_suite/system_tests/scripts/n_state...