Author: bugman
Date: Sun Sep 3 10:28:49 2006
New Revision: 2553
URL: http://svn.gna.org/viewcvs/relax?rev=2553&view=rev
Log:
Merged the 'nan_catch_test' branch (r2552) into the 1.2 line (r2552).
The command used was:
svn merge svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2@2552
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/nan_catch_test@2552
This branch was created as a branch off the 1.2 line at r2528. It was in
response to bug #6503
(https://gna.org/bugs/?func=detailitem&item_id=6503) and the subsequent
discussions in the threads
starting at https://mail.gna.org/public/relax-devel/2006-08/msg00000.html
(Message-id: <7f080ed10608020558o47fd0260s9579f663147ab84@xxxxxxxxxxxxxx>) and
https://mail.gna.org/public/relax-devel/2006-08/msg00029.html (Message-id:
<7f080ed10608082240r114cf35an60af62836fcc81bf@xxxxxxxxxxxxxx>).
The two functions 'isnan()' and 'isinf()' have been created to fix the bug.
These are however not
currently functional. In addition bug #6510
(https://gna.org/bugs/?func=detailitem&item_id=6510)
has been fixed.
Added:
1.2/float.py
- copied unchanged from r2552, branches/nan_catch_test/float.py
Modified:
1.2/errors.py
1.2/generic_fns/pdb.py
1.2/minimise/line_search/backtrack.py
1.2/relax
1.2/specific_fns/model_free.py
Modified: 1.2/errors.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/errors.py?rev=2553&r1=2552&r2=2553&view=diff
==============================================================================
--- 1.2/errors.py (original)
+++ 1.2/errors.py Sun Sep 3 10:28:49 2006
@@ -597,4 +597,21 @@
self.text = "The colour " + `colour` + " is invalid."
if Debug:
self.save_state()
-
+
+
+ # Value errors.
+ ###############
+
+ # Infinity.
+ class RelaxInfError(BaseError):
+ def __init__(self, name):
+ self.text = "The invalid " + name + " floating point value of
infinity has occurred."
+ if Debug:
+ self.save_state()
+
+ # NaN (Not a Number).
+ class RelaxNaNError(BaseError):
+ def __init__(self, name):
+ self.text = "The invalid " + name + " floating point value of
NaN (Not a Number) has occurred."
+ if Debug:
+ self.save_state()
Modified: 1.2/generic_fns/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/generic_fns/pdb.py?rev=2553&r1=2552&r2=2553&view=diff
==============================================================================
--- 1.2/generic_fns/pdb.py (original)
+++ 1.2/generic_fns/pdb.py Sun Sep 3 10:28:49 2006
@@ -156,6 +156,10 @@
print "The PDB file " + `self.file_path` + " cannot be
found, no structures will be loaded."
return
+ # Test that the nuclei have been correctly set.
+ if self.heteronuc == self.proton:
+ raise RelaxError, "The proton and heteronucleus are set to the
same atom."
+
# Data creation.
################
@@ -256,9 +260,21 @@
# Get the heteronucleus position.
posX = pdb_res.atoms[self.heteronuc].position.array
+ # Calculate the XH bond vector.
+ vector = posH - posX
+
+ # Normalisation factor.
+ norm_factor = sqrt(dot(vector, vector))
+
+ # Test for zero length.
+ if norm_factor == 0.0:
+ if self.print_flag:
+ print "The XH bond vector for residue " +
`self.relax.data.res[self.run][j].num` + " is of zero length."
+ self.relax.data.res[self.run][j].xh_vect.append(None)
+
# Calculate the normalised vector.
- vector = posH - posX
- self.relax.data.res[self.run][j].xh_vect.append(vector /
sqrt(dot(vector, vector)))
+ else:
+
self.relax.data.res[self.run][j].xh_vect.append(vector / norm_factor)
# Print out.
if self.print_flag:
Modified: 1.2/minimise/line_search/backtrack.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/minimise/line_search/backtrack.py?rev=2553&r1=2552&r2=2553&view=diff
==============================================================================
--- 1.2/minimise/line_search/backtrack.py (original)
+++ 1.2/minimise/line_search/backtrack.py Sun Sep 3 10:28:49 2006
@@ -23,7 +23,7 @@
from Numeric import dot
-def backtrack(func, args, x, f, g, p, a_init=1.0, rho=0.5, c=1e-4):
+def backtrack(func, args, x, f, g, p, a_init=1.0, rho=0.5, c=1e-4,
max_iter=500):
"""Backtracking line search.
Procedure 3.1, page 41, from 'Numerical Optimization' by Jorge Nocedal
and Stephen J. Wright,
@@ -63,8 +63,9 @@
# Initialise values.
a = a_init
f_count = 0
+ i = 0
- while 1:
+ while i <= max_iter:
fk = apply(func, (x + a*p,)+args)
f_count = f_count + 1
@@ -73,3 +74,6 @@
return a, f_count
else:
a = rho*a
+
+ # Increment the counter.
+ i = i + 1
Modified: 1.2/relax
URL:
http://svn.gna.org/viewcvs/relax/1.2/relax?rev=2553&r1=2552&r2=2553&view=diff
==============================================================================
--- 1.2/relax (original)
+++ 1.2/relax Sun Sep 3 10:28:49 2006
@@ -67,6 +67,7 @@
from colour import Colour
from data import Data
from errors import RelaxErrors
+from float import Float
from io import IO
from generic_fns.main import Generic
from prompt.gpl import gpl
@@ -110,6 +111,9 @@
# File operation functions.
self.IO = IO(self)
+ # Floating point number functions.
+ self.float = Float()
+
# Colour operations.
self.colour = Colour()
Modified: 1.2/specific_fns/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/model_free.py?rev=2553&r1=2552&r2=2553&view=diff
==============================================================================
--- 1.2/specific_fns/model_free.py (original)
+++ 1.2/specific_fns/model_free.py Sun Sep 3 10:28:49 2006
@@ -2373,6 +2373,14 @@
self.f_count = self.f_count + fc
self.g_count = self.g_count + gc
self.h_count = self.h_count + hc
+
+ # Catch infinite chi-squared values.
+ #if self.relax.float.isinf(self.func):
+ # raise RelaxInfError, 'chi-squared'
+
+ # Catch chi-squared values of NaN.
+ #if self.relax.float.isnan(self.func):
+ # raise RelaxNaNError, 'chi-squared'
# Scaling.
if scaling:
r2553 - in /1.2: errors.py float.py generic_fns/pdb.py minimise/line_search/backtrack.py relax specific_fns/model_free.py