Author: bugman
Date: Fri Mar 22 17:27:57 2013
New Revision: 19000
URL: http://svn.gna.org/viewcvs/relax?rev=19000&view=rev
Log:
Next block of the manual merger of the frame_order_testing branch.
The commands used were:
svn merge -r18650:18651
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18651:18652
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18652:18653
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18653:18654
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18654:18655
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18655:18656
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18657:18658
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18719:18720
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18729:18730
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
The console messages were:
[edau@localhost relax-trunk]$ svn merge -r18650:18651
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
[edau@localhost relax-trunk]$ svn merge -r18651:18652
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18652 into '.':
U auto_analyses/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18652:18653
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18653 into '.':
G auto_analyses/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18653:18654
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18654 into '.':
G auto_analyses/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18654:18655
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18655 into '.':
U maths_fns/frame_order/__init__.py
[edau@localhost relax-trunk]$ svn merge -r18655:18656
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18656 into '.':
U test_suite/system_tests/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18657:18658
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18658 into '.':
A test_suite/shared_data/frame_order/displacements/optimisation.log.bz2
[edau@localhost relax-trunk]$ svn merge -r18719:18720
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18720 into '.':
A sample_scripts/frame_order
[edau@localhost relax-trunk]$ svn merge -r18729:18730
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18730 into '.':
U specific_fns/frame_order.py
[edau@localhost relax-trunk]$
Added:
trunk/sample_scripts/frame_order/
- copied from r18720,
branches/frame_order_testing/sample_scripts/frame_order/
trunk/test_suite/shared_data/frame_order/displacements/optimisation.log.bz2
- copied unchanged from r18658,
branches/frame_order_testing/test_suite/shared_data/frame_order/displacements/optimisation.log.bz2
Modified:
trunk/auto_analyses/frame_order.py
trunk/maths_fns/frame_order/__init__.py
trunk/specific_fns/frame_order.py
trunk/test_suite/system_tests/frame_order.py
Modified: trunk/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=19000&r1=18999&r2=19000&view=diff
==============================================================================
--- trunk/auto_analyses/frame_order.py (original)
+++ trunk/auto_analyses/frame_order.py Fri Mar 22 17:27:57 2013
@@ -226,7 +226,7 @@
# The free rotor model.
if model == 'free rotor':
- incs += [None, None, self.grid_inc, self.grid_inc]
+ incs += [self.grid_inc, self.grid_inc, self.grid_inc,
self.grid_inc]
# The torsionless isotropic cone model.
if model == 'iso cone, torsionless':
@@ -269,6 +269,12 @@
rigid_pipe = get_pipe(self.pipe_name_dict['rigid'])
# Copy the average position parameters from the rigid model.
+ if hasattr(rigid_pipe, 'ave_pos_x'):
+ cdp.ave_pos_x = rigid_pipe.ave_pos_x
+ if hasattr(rigid_pipe, 'ave_pos_y'):
+ cdp.ave_pos_y = rigid_pipe.ave_pos_y
+ if hasattr(rigid_pipe, 'ave_pos_z'):
+ cdp.ave_pos_z = rigid_pipe.ave_pos_z
if model not in ['free rotor', 'iso cone, free rotor']:
cdp.ave_pos_alpha = rigid_pipe.ave_pos_alpha
cdp.ave_pos_beta = rigid_pipe.ave_pos_beta
@@ -447,8 +453,14 @@
format_vect = " %-20s %20s\n"
# Average position.
- if hasattr(cdp, 'ave_pos_alpha') or hasattr(cdp, 'ave_pos_beta') or
hasattr(cdp, 'ave_pos_gamma'):
- sys.stdout.write("\nAverage moving domain position Euler
angles:\n")
+ if hasattr(cdp, 'ave_pos_x') or hasattr(cdp, 'ave_pos_alpha') or
hasattr(cdp, 'ave_pos_beta') or hasattr(cdp, 'ave_pos_gamma'):
+ sys.stdout.write("\nAverage moving domain position:\n")
+ if hasattr(cdp, 'ave_pos_x'):
+ sys.stdout.write(format_float % ('x:', cdp.ave_pos_x))
+ if hasattr(cdp, 'ave_pos_y'):
+ sys.stdout.write(format_float % ('y:', cdp.ave_pos_y))
+ if hasattr(cdp, 'ave_pos_z'):
+ sys.stdout.write(format_float % ('z:', cdp.ave_pos_z))
if hasattr(cdp, 'ave_pos_alpha'):
sys.stdout.write(format_float % ('alpha:', cdp.ave_pos_alpha))
if hasattr(cdp, 'ave_pos_beta'):
Modified: trunk/maths_fns/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/maths_fns/frame_order/__init__.py?rev=19000&r1=18999&r2=19000&view=diff
==============================================================================
--- trunk/maths_fns/frame_order/__init__.py (original)
+++ trunk/maths_fns/frame_order/__init__.py Fri Mar 22 17:27:57 2013
@@ -26,10 +26,6 @@
from copy import deepcopy
from math import acos, ceil, pi, sqrt
from numpy import array, dot, float32, float64, ones, transpose, uint8, zeros
-try:
- from numpy import float16
-except ImportError:
- float16 = float32
from numpy.linalg import norm
# relax module imports.
@@ -1892,7 +1888,7 @@
m = len(dims)
# Initialise.
- self.sobol_angles = zeros((n, m), float16)
+ self.sobol_angles = zeros((n, m), float32)
# Loop over the points.
for i in range(n):
Modified: trunk/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/frame_order.py?rev=19000&r1=18999&r2=19000&view=diff
==============================================================================
--- trunk/specific_fns/frame_order.py (original)
+++ trunk/specific_fns/frame_order.py Fri Mar 22 17:27:57 2013
@@ -2371,8 +2371,13 @@
if not hasattr(interatom, 'rdc_err'):
raise RelaxError("The RDC errors are missing for interatomic
data container between spins '%s' and '%s'." % (spin_id1, spin_id2))
+ # Handle missing data.
+ if align_id not in interatom.rdc_err:
+ mc_errors.append(None)
+
# Append the data.
- mc_errors.append(interatom.rdc_err[align_id])
+ else:
+ mc_errors.append(interatom.rdc_err[align_id])
# The PCS data.
elif data_id[0] == 'pcs':
@@ -2386,8 +2391,13 @@
if not hasattr(spin, 'pcs_err'):
raise RelaxError("The PCS errors are missing for spin '%s'."
% spin_id)
+ # Handle missing data.
+ if align_id not in spin.pcs_err:
+ mc_errors.append(None)
+
# Append the data.
- mc_errors.append(spin.pcs_err[align_id])
+ else:
+ mc_errors.append(spin.pcs_err[align_id])
# Return the errors.
return mc_errors
Modified: trunk/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/frame_order.py?rev=19000&r1=18999&r2=19000&view=diff
==============================================================================
--- trunk/test_suite/system_tests/frame_order.py (original)
+++ trunk/test_suite/system_tests/frame_order.py Fri Mar 22 17:27:57 2013
@@ -315,7 +315,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'iso_cone_free_rotor.py')
- self.check_chi2(48.623418841452626)
+ self.check_chi2(31.400316262936347)
def test_cam_iso_cone_free_rotor_pcs(self):
@@ -333,7 +333,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(pcs=False)
self.interpreter.run(script_file=self.cam_path+'iso_cone_free_rotor.py')
- self.check_chi2(17.282846954724896)
+ self.check_chi2(0.058871004304276831)
def test_cam_iso_cone_free_rotor2(self):
@@ -1138,7 +1138,7 @@
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'rigid_test.py')
# Check the chi2 value.
- self.assertAlmostEqual(cdp.chi2, 94337.6680299)
+ self.assertAlmostEqual(cdp.chi2, 94337.620142880114)
def test_rigid_data_to_iso_cone_model(self):
@@ -1151,7 +1151,7 @@
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'rigid_test.py')
# Check the chi2 value.
- self.assertAlmostEqual(cdp.chi2, 175.440396354)
+ self.assertAlmostEqual(cdp.chi2, 177.13243371265614)
def test_rigid_data_to_iso_cone_free_rotor_model(self):
@@ -1164,7 +1164,7 @@
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'rigid_test.py')
# Check the chi2 value.
- self.assertAlmostEqual(cdp.chi2, 101224.40326971974)
+ self.assertAlmostEqual(cdp.chi2, 101218.55718817962)
def test_rigid_data_to_iso_cone_torsionless_model(self):
@@ -1177,7 +1177,7 @@
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'rigid_test.py')
# Check the chi2 value.
- self.assertAlmostEqual(cdp.chi2, 2.80180329697)
+ self.assertAlmostEqual(cdp.chi2, 2.7993179077540402)
def test_rigid_data_to_rigid_model(self):
@@ -1203,7 +1203,7 @@
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'rigid_test.py')
# Check the chi2 value.
- self.assertAlmostEqual(cdp.chi2, 0.968768022709)
+ self.assertAlmostEqual(cdp.chi2, 0.96883720077954039)
def test_rigid_data_to_pseudo_ellipse_model(self):
@@ -1216,7 +1216,7 @@
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'rigid_test.py')
# Check the chi2 value.
- self.assertAlmostEqual(cdp.chi2, 175.440396354)
+ self.assertAlmostEqual(cdp.chi2, 177.13243371265639)
def test_rigid_data_to_pseudo_ellipse_torsionless_model(self):
@@ -1229,4 +1229,4 @@
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'rigid_test.py')
# Check the chi2 value.
- self.assertAlmostEqual(cdp.chi2, 2.80180329697)
+ self.assertAlmostEqual(cdp.chi2, 2.7993179077540522)
r19000 - in /trunk: auto_analyses/ maths_fns/frame_order/ sample_scripts/frame_order/ specific_fns/ test_suite/shared_data/f...