Author: bugman
Date: Fri Jul 25 15:26:45 2014
New Revision: 24753
URL: http://svn.gna.org/viewcvs/relax?rev=24753&view=rev
Log:
Merged revisions 24739-24743,24751-24752 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r24739 | bugman | 2014-07-25 12:14:00 +0200 (Fri, 25 Jul 2014) | 21 lines
Reverted r24024, the deletion of the
Relax_disp.test_hansen_cpmg_data_to_lm63_3site system test.
See the thread at
http://thread.gmane.org/gmane.science.nmr.relax.scm/21774/focus=6300 for the
request that this deletion be reverted. This is the only system test for
the 'LM63 3-site'
dispersion model using real data. Having this test allows for better
coverage of the code.
The command used was:
svn merge -r24024:r24023 .
.....
r24024 | tlinnet | 2014-06-17 12:32:34 +0200 (Tue, 17 Jun 2014) | 4 lines
Changed paths:
M /trunk/test_suite/system_tests/relax_disp.py
Removed systemtest test_hansen_cpmg_data_to_lm63_3site.
This was a temporary implementation and has been replaced with systemtest:
Relax_disp.test_lm63_3site_synthetic
.....
........
r24740 | bugman | 2014-07-25 12:14:44 +0200 (Fri, 25 Jul 2014) | 5 lines
Updated the Relax_disp.test_hansen_cpmg_data_to_lm63_3site system test.
This is for the changes to the optimisation user functions.
........
r24741 | bugman | 2014-07-25 12:18:44 +0200 (Fri, 25 Jul 2014) | 6 lines
Updated the checks in the Relax_disp.test_hansen_cpmg_data_to_lm63_3site
system test.
The values were incorrect due to a bug in relax and a non-optimal minfx
setting
(https://gna.org/bugs/?22210 and https://gna.org/bugs/?22211).
........
r24742 | bugman | 2014-07-25 13:35:34 +0200 (Fri, 25 Jul 2014) | 7 lines
Fix for a fatal bug for the prompt UI on MS Windows.
The improvements in the tab completion support for the prompt UI on Mac OS
X systems (r24421) was
fatal for certain Python readline modules on MS Windows, as
readline.__doc__ can be None. This is
now correctly handled.
........
r24743 | bugman | 2014-07-25 13:39:33 +0200 (Fri, 25 Jul 2014) | 16 lines
Reverted r24736 as this was fatal for the relax information printout - the
modules are required.
The command used was:
svn merge -r24736:r24735 .
.....
r24736 | bugman | 2014-07-25 11:20:21 +0200 (Fri, 25 Jul 2014) | 5 lines
Changed paths:
M /trunk/dep_check.py
Clean up of the dep_check module - all imported and unused modules are
now deleted as well.
This cleans up the module namespace of the unused imports.
.....
........
r24751 | bugman | 2014-07-25 15:08:57 +0200 (Fri, 25 Jul 2014) | 5 lines
Decreased the precision the Relax_disp.test_hansen_cpmg_data_to_lm63_3site
system test.
This is to allow the test to pass on Mac OS X systems.
........
r24752 | bugman | 2014-07-25 15:13:11 +0200 (Fri, 25 Jul 2014) | 7 lines
Unit test fix for Mac OS X.
This is for the test_ns_mmq_2site_korzhnev_2005_15n_dq_data_complex128 test
of
test_suite.unit_tests._lib._dispersion.test_matrix_exponential.Test_matrix_exponential.
The
tests no longer check for exact values, but use the assertAlmostEqual()
calls instead.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/dep_check.py
branches/frame_order_cleanup/prompt/interpreter.py
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_dispersion/test_matrix_exponential.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Jul 25 15:26:45 2014
@@ -1 +1 @@
-/trunk:1-24737
+/trunk:1-24752
Modified: branches/frame_order_cleanup/dep_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/dep_check.py?rev=24753&r1=24752&r2=24753&view=diff
==============================================================================
--- branches/frame_order_cleanup/dep_check.py (original)
+++ branches/frame_order_cleanup/dep_check.py Fri Jul 25 15:26:45 2014
@@ -40,7 +40,6 @@
if float(numpy.version.version[:3]) < 1.6:
sys.stderr.write("Version %s of the 'numpy' dependency is not
supported, numpy >= 1.6 is required.\n" % numpy.version.version)
sys.exit()
- del numpy
except ImportError:
sys.stderr.write("The dependency 'numpy' has not been installed.\n")
sys.exit()
@@ -48,7 +47,6 @@
# Command line option parser.
try:
import optparse
- del optparse
except ImportError:
sys.stderr.write("The dependency 'Optik' has not been installed.\n")
sys.exit()
@@ -56,7 +54,6 @@
# Minfx python package check.
try:
import minfx
- del minfx
except ImportError:
sys.stderr.write("The dependency 'minfx' has not been installed (see
https://gna.org/projects/minfx/).\n")
sys.exit()
@@ -66,7 +63,6 @@
# Bmrblib python package check.
try:
import bmrblib
- del bmrblib
bmrblib_module = True
except ImportError:
bmrblib_module = False
@@ -74,7 +70,6 @@
# wx module.
try:
import wx
- del wx
wx_module = True
except ImportError:
wx_module = False
@@ -84,7 +79,6 @@
# epydoc module.
try:
import epydoc
- del epydoc
epydoc_module = True
except ImportError:
epydoc_module = False
@@ -95,8 +89,6 @@
if 'TERM' in os.environ and os.environ['TERM'] == 'xterm':
os.environ['TERM'] = 'linux'
import readline
- del os
- del readline
readline_module = True
except ImportError:
readline_module = False
@@ -104,7 +96,6 @@
# matplotlib module.
try:
import matplotlib
- del matplotlib
matplotlib_module = True
except ImportError:
matplotlib_module = False
@@ -112,7 +103,6 @@
# runpy module.
try:
import runpy
- del runpy
runpy_module = True
except ImportError:
runpy_module = False
@@ -120,7 +110,6 @@
# profile module (python development packages required).
try:
import profile
- del profile
profile_module = True
except ImportError:
profile_module = False
@@ -128,7 +117,6 @@
# profile C module (python development packages required).
try:
import cProfile
- del cProfile
cprofile_module = True
except ImportError:
cprofile_module = False
@@ -136,7 +124,6 @@
# BZ2 compression module.
try:
import bz2
- del bz2
bz2_module = True
except ImportError:
message = sys.exc_info()[1]
@@ -146,7 +133,6 @@
# Gzip compression module.
try:
import gzip
- del gzip
gzip_module = True
except ImportError:
message = sys.exc_info()[1]
@@ -156,7 +142,6 @@
# IO module.
try:
import io
- del io
io_module = True
except ImportError:
message = sys.exc_info()[1]
@@ -166,7 +151,6 @@
# Scipy import.
try:
import scipy
- del scipy
scipy_module = True
except:
scipy_module = False
@@ -182,7 +166,6 @@
# mpi4py.
try:
import mpi4py
- del mpi4py
mpi4py_module = True
except ImportError:
message = sys.exc_info()[1]
@@ -201,7 +184,6 @@
# PyMOL.
try:
import pymol
- del pymol
pymol_module = True
except ImportError:
message = sys.exc_info()[1]
@@ -225,12 +207,10 @@
else:
xml_version = ''
xml_type = ''
- del xml
# subprocess module.
try:
import subprocess
- del subprocess
subprocess_module = True
except ImportError:
message = sys.exc_info()[1]
@@ -240,7 +220,6 @@
# ctypes module.
try:
import ctypes
- del ctypes
ctypes_module = True
except ImportError:
message = sys.exc_info()[1]
@@ -248,7 +227,6 @@
ctypes_module_message = message.args[0]
try:
from ctypes import Structure
- del Structure
ctypes_structure_module = True
except ImportError:
message = sys.exc_info()[1]
@@ -265,7 +243,6 @@
try:
from target_functions import relax_fit
from target_functions.relax_fit import setup
- del relax_fit
del setup
C_module_exp_fn = True
except ImportError:
Modified: branches/frame_order_cleanup/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/prompt/interpreter.py?rev=24753&r1=24752&r2=24753&view=diff
==============================================================================
--- branches/frame_order_cleanup/prompt/interpreter.py (original)
+++ branches/frame_order_cleanup/prompt/interpreter.py Fri Jul 25 15:26:45
2014
@@ -264,7 +264,7 @@
if dep_check.readline_module:
readline.set_completer(Tab_completion(name_space=locals()).finish)
readline.set_completer_delims(' \t\n`~!@#$%^&*()=+{}\\|;:",<>/?')
- if 'libedit' in readline.__doc__:
+ if readline.__doc__ != None and 'libedit' in readline.__doc__:
readline.parse_and_bind("bind ^I rl_complete")
else:
readline.parse_and_bind("tab: complete")
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py?rev=24753&r1=24752&r2=24753&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py Fri
Jul 25 15:26:45 2014
@@ -3011,6 +3011,70 @@
self.assertAlmostEqual(spin71.phi_ex, 0.0553787825650613, 5)
self.assertAlmostEqual(spin71.kex/1000, 2781.72292994154/1000, 5)
self.assertAlmostEqual(spin71.chi2, 17.0776399916287, 5)
+
+
+ def test_hansen_cpmg_data_to_lm63_3site(self):
+ """Optimisation of Dr. Flemming Hansen's CPMG data to the LM63
dispersion model.
+
+ This uses the data from Dr. Flemming Hansen's paper at
http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed
relaxation time period.
+ """
+
+ # Base data setup.
+ self.setup_hansen_cpmg_data(model='LM63 3-site')
+
+ # Alias the spins.
+ spin70 = return_spin(":70")
+ spin71 = return_spin(":71")
+
+ # The R20 keys.
+ r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
+ r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
+
+ ## Set the initial parameter values.
+ spin70.r2 = {r20_key1: 7.570370921220954, r20_key2:
8.694446951909107}
+ spin70.phi_ex_B = 0.14872003058250227
+ spin70.phi_ex_C = 0.1319419923472704
+ spin70.kB = 4103.672910444741
+ spin70.kC = 7029.001690726248
+ spin71.r2 = {r20_key1: 5.1347793381636, r20_key2: 7.156573986051575}
+ spin71.phi_ex_B = 0.04013553485505605
+ spin71.phi_ex_C = 0.020050748406928887
+ spin71.kB = 4045.3007136121364
+ spin71.kC = 3586.38798270774
+
+ #self.interpreter.relax_disp.r20_from_min_r2eff(force=False)
+ #self.interpreter.minimise.grid_search(lower=None, upper=None,
inc=41, constraints=True, verbosity=1)
+
+ # Low precision optimisation.
+ self.interpreter.minimise.execute(min_algor='simplex',
line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-25,
grad_tol=None, max_iter=10000000, constraints=True, scaling=True, verbosity=1)
+
+ # Printout.
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value
(:71)"))
+ print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)",
spin70.r2[r20_key1], spin71.r2[r20_key1]))
+ print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)",
spin70.r2[r20_key2], spin71.r2[r20_key2]))
+ print("%-20s %20.15g %20.15g" % ("phi_ex_B", spin70.phi_ex_B,
spin71.phi_ex_B))
+ print("%-20s %20.15g %20.15g" % ("phi_ex_C", spin70.phi_ex_C,
spin71.phi_ex_C))
+ print("%-20s %20.15g %20.15g" % ("kB", spin70.kB, spin71.kB))
+ print("%-20s %20.15g %20.15g" % ("kC", spin70.kC, spin71.kC))
+ print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2))
+
+ # Checks for residue :70.
+ self.assertAlmostEqual(spin70.r2[r20_key1], 6.7436230253685, 5)
+ self.assertAlmostEqual(spin70.r2[r20_key2], 6.57406813008828, 6)
+ self.assertAlmostEqual(spin70.phi_ex_B, 0.206304023079778, 5)
+ self.assertAlmostEqual(spin70.phi_ex_C, 0.106428983339627, 5)
+ self.assertAlmostEqual(spin70.kB/1000, 4723.09897652589/1000, 6)
+ self.assertAlmostEqual(spin70.kC/1000, 4723.09876196409/1000, 6)
+ self.assertAlmostEqual(spin70.chi2, 363.534044873483, 5)
+
+ # Checks for residue :71.
+ self.assertAlmostEqual(spin71.r2[r20_key1], 4.96612095596752, 5)
+ self.assertAlmostEqual(spin71.phi_ex_B, 0.00398262266512895, 5)
+ self.assertAlmostEqual(spin71.phi_ex_C, 0.0555791581291262, 5)
+ self.assertAlmostEqual(spin71.kB/1000, 1323.33195689832/1000, 5)
+ self.assertAlmostEqual(spin71.kC/1000, 3149.58971568059/1000, 5)
+ self.assertAlmostEqual(spin71.chi2, 16.2620934464368)
def test_hansen_cpmg_data_to_ns_cpmg_2site_3D(self):
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_dispersion/test_matrix_exponential.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_lib/_dispersion/test_matrix_exponential.py?rev=24753&r1=24752&r2=24753&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_dispersion/test_matrix_exponential.py
(original)
+++
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_dispersion/test_matrix_exponential.py
Fri Jul 25 15:26:45 2014
@@ -238,7 +238,7 @@
diff_A_neg_imag_sum = sum(diff_A_neg_imag)
# Test that the sum difference is zero.
- self.assertEqual(diff_A_pos_real_sum , 0.0)
- self.assertEqual(diff_A_pos_imag_sum , 0.0)
- self.assertEqual(diff_A_neg_real_sum , 0.0)
- self.assertEqual(diff_A_neg_imag_sum , 0.0)
+ self.assertAlmostEqual(diff_A_pos_real_sum, 0.0)
+ self.assertAlmostEqual(diff_A_pos_imag_sum, 0.0)
+ self.assertAlmostEqual(diff_A_neg_real_sum, 0.0)
+ self.assertAlmostEqual(diff_A_neg_imag_sum, 0.0)
r24753 - in /branches/frame_order_cleanup: ./ prompt/ test_suite/system_tests/ test_suite/unit_tests/_lib/_dispersion/