Author: bugman
Date: Thu Aug 11 17:32:59 2011
New Revision: 14367
URL: http://svn.gna.org/viewcvs/relax?rev=14367&view=rev
Log:
Merged revisions 14361-14366 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r14361 | bugman | 2011-08-11 16:38:36 +0200 (Thu, 11 Aug 2011) | 5 lines
Bug fix for the data.align_tensor.calc_eta() function - divide by zeros are
now avoided.
When Azz is zero, eta is now set to NaN.
........
r14362 | bugman | 2011-08-11 16:41:38 +0200 (Thu, 11 Aug 2011) | 3 lines
Typo fix in the unused and incomplete dfunc function.
........
r14363 | bugman | 2011-08-11 16:45:31 +0200 (Thu, 11 Aug 2011) | 5 lines
Bug fix for the data.align_tensor.calc_R() function - divide by zeros are
now avoided.
When Aa is zero, Ar is now set to NaN.
........
r14364 | bugman | 2011-08-11 16:56:16 +0200 (Thu, 11 Aug 2011) | 5 lines
Fix for the test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149 model-free
system test on MS Windows.
The te parameter check was too strict.
........
r14365 | bugman | 2011-08-11 17:04:28 +0200 (Thu, 11 Aug 2011) | 3 lines
Another divide by zero problem is being caught in the RDC Q-factor code.
........
r14366 | bugman | 2011-08-11 17:13:28 +0200 (Thu, 11 Aug 2011) | 3 lines
The dipolar_constant() and pcs_constant() functions now catch division by
zero problems.
........
Modified:
branches/gui_testing/ (props changed)
branches/gui_testing/data/align_tensor.py
branches/gui_testing/generic_fns/rdc.py
branches/gui_testing/maths_fns/relax_fit.c
branches/gui_testing/physical_constants.py
branches/gui_testing/test_suite/system_tests/model_free.py
Propchange: branches/gui_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Aug 11 17:32:59 2011
@@ -1,1 +1,1 @@
-/1.3:1-14355
+/1.3:1-14366
Modified: branches/gui_testing/data/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/data/align_tensor.py?rev=14367&r1=14366&r2=14367&view=diff
==============================================================================
--- branches/gui_testing/data/align_tensor.py (original)
+++ branches/gui_testing/data/align_tensor.py Thu Aug 11 17:32:59 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2004, 2006-2010 Edward d'Auvergne
#
+# Copyright (C) 2003-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -29,6 +29,7 @@
# relax module imports.
from data_classes import Element
+from float import nan
from maths_fns.rotation_matrix import R_to_euler_zyz
from relax_errors import RelaxError
from relax_xml import fill_object_contents, xml_to_object
@@ -265,6 +266,10 @@
@rtype: float
"""
+ # Zero Azz value, so return NaN.
+ if A_diag[2, 2] == 0:
+ return nan
+
# Return eta.
return (A_diag[0, 0] - A_diag[1, 1]) / A_diag[2, 2]
@@ -761,6 +766,10 @@
@rtype: float
"""
+ # Zero Aa value, so return NaN.
+ if Aa == 0:
+ return nan
+
# Return R.
return Ar / Aa
Modified: branches/gui_testing/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/generic_fns/rdc.py?rev=14367&r1=14366&r2=14367&view=diff
==============================================================================
--- branches/gui_testing/generic_fns/rdc.py (original)
+++ branches/gui_testing/generic_fns/rdc.py Thu Aug 11 17:32:59 2011
@@ -31,6 +31,7 @@
from warnings import warn
# relax module imports.
+from float import nan
from generic_fns import grace, pipes
from generic_fns.align_tensor import get_tensor_index
from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
@@ -301,7 +302,10 @@
D = dj * cdp.align_tensors[cdp.align_ids.index(align_id)].A_diag
Da = 1.0/3.0 * (D[2, 2] - (D[0, 0]+D[1, 1])/2.0)
Dr = 1.0/3.0 * (D[0, 0] - D[1, 1])
- R = Dr / Da
+ if Da == 0:
+ R = nan
+ else:
+ R = Dr / Da
norm = 2.0 * (Da)**2 * (4.0 + 3.0*R**2)/5.0
if Da == 0.0:
norm = 1e-15
Modified: branches/gui_testing/maths_fns/relax_fit.c
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/maths_fns/relax_fit.c?rev=14367&r1=14366&r2=14367&view=diff
==============================================================================
--- branches/gui_testing/maths_fns/relax_fit.c (original)
+++ branches/gui_testing/maths_fns/relax_fit.c Thu Aug 11 17:32:59 2011
@@ -1,5 +1,5 @@
/*
- * Copyright (C) 2006 Edward d'Auvergne
+ * Copyright (C) 2006-2011 Edward d'Auvergne
*
* This file is part of the program relax.
*
@@ -140,7 +140,7 @@
/* Temp Declarations */
double aaa[MAXPARAMS] = {1.0, 2.0};
int i;
- double* params;
+ double *params;
/* Parse the function arguments, the only argument should be the
parameter array */
if (!PyArg_ParseTuple(args, "O", ¶ms_arg))
Modified: branches/gui_testing/physical_constants.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/physical_constants.py?rev=14367&r1=14366&r2=14367&view=diff
==============================================================================
--- branches/gui_testing/physical_constants.py (original)
+++ branches/gui_testing/physical_constants.py Thu Aug 11 17:32:59 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2007-2009 Edward d'Auvergne
#
+# Copyright (C) 2007-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -29,6 +29,7 @@
from string import ascii_letters, digits, upper
# relax module imports.
+from float import nan
from relax_errors import RelaxError
@@ -101,6 +102,10 @@
@type r: float
"""
+ # Catch zero bond lengths, returning NaN.
+ if r == 0:
+ return nan
+
# Calculate and return the value.
return - mu0 / (4.0*pi) * gx * gh * h_bar / r**3
@@ -132,6 +137,10 @@
@param r: The distance between the two nuclei.
@type r: float
"""
+
+ # Catch zero bond lengths, returning NaN.
+ if r == 0:
+ return nan
# Calculate and return the value.
return mu0 / (4.0*pi) * 15.0 * kB * T / Bo**2 / r**3
Modified: branches/gui_testing/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/test_suite/system_tests/model_free.py?rev=14367&r1=14366&r2=14367&view=diff
==============================================================================
--- branches/gui_testing/test_suite/system_tests/model_free.py (original)
+++ branches/gui_testing/test_suite/system_tests/model_free.py Thu Aug 11
17:32:59 2011
@@ -2569,7 +2569,7 @@
# te correlation time.
if type(te) == float:
- self.assertAlmostEqual(spin.te / 1e-12, te, 6, msg=mesg)
+ self.assertAlmostEqual(spin.te / 1e-12, te, 5, msg=mesg)
elif te == None:
self.assertEqual(spin.te, None, msg=mesg)
r14367 - in /branches/gui_testing: ./ data/ generic_fns/ maths_fns/ test_suite/system_tests/