Author: bugman
Date: Fri Mar 22 11:46:15 2013
New Revision: 18942
URL: http://svn.gna.org/viewcvs/relax?rev=18942&view=rev
Log:
Next block of the manual merger of the frame_order_testing branch.
The commands used were:
svn merge -r15024:15025
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15025:15026
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15026:15027
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15027:15028
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15028:15029
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15029:15030
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
Again much conflict resolution was required.
Added:
trunk/generic_fns/domain.py
- copied unchanged from r15028,
branches/frame_order_testing/generic_fns/domain.py
trunk/prompt/domain.py
- copied unchanged from r15027,
branches/frame_order_testing/prompt/domain.py
Modified:
trunk/generic_fns/__init__.py
trunk/generic_fns/align_tensor.py
trunk/specific_fns/frame_order.py
Modified: trunk/generic_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/__init__.py?rev=18942&r1=18941&r2=18942&view=diff
==============================================================================
--- trunk/generic_fns/__init__.py (original)
+++ trunk/generic_fns/__init__.py Fri Mar 22 11:46:15 2013
@@ -30,6 +30,7 @@
'dasha',
'diffusion_tensor',
'dipole_pair',
+ 'domain',
'eliminate',
'exp_info',
'fix',
Modified: trunk/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/align_tensor.py?rev=18942&r1=18941&r2=18942&view=diff
==============================================================================
--- trunk/generic_fns/align_tensor.py (original)
+++ trunk/generic_fns/align_tensor.py Fri Mar 22 11:46:15 2013
@@ -34,7 +34,6 @@
from data.align_tensor import AlignTensorList
from generic_fns.angles import wrap_angles
from generic_fns import pipes
-from generic_fns.mol_res_spin import spin_loop
from physical_constants import g1H, h_bar, kB, mu0, return_gyromagnetic_ratio
from relax_errors import RelaxError, RelaxNoTensorError, RelaxStrError,
RelaxTensorError, RelaxUnknownParamCombError, RelaxUnknownParamError
from relax_io import write_data
@@ -1842,16 +1841,18 @@
"""
-def set_domain(tensor=None, domain=None, spin_id=None):
+def set_domain(tensor=None, domain=None):
"""Set the domain label for the given tensor.
- @param tensor: The alignment tensor label.
- @type tensor: str
- @param domain: The domain label.
- @type domain: str
- @keyword spin_id: The spin ID string.
- @type spin_id: None or str
- """
+ @param tensor: The alignment tensor label.
+ @type tensor: str
+ @param domain: The domain label.
+ @type domain: str
+ """
+
+ # Check that the domain is defined.
+ if not hasattr(cdp, 'domain') or domain not in cdp.domain.keys():
+ raise RelaxError("The domain '%s' has not been defined. Please use
the domain user function." % domain)
# Test if alignment tensor data exists.
if not hasattr(cdp, 'align_tensors') or len(cdp.align_tensors) == 0 or
not hasattr(cdp, 'align_ids'):
@@ -1869,16 +1870,6 @@
if not match:
raise RelaxNoTensorError('alignment', tensor)
- # Label the spins by domain.
- if spin_id != None:
- for spin in spin_loop(spin_id):
- # Initialise.
- if not hasattr(spin, 'domain'):
- spin.domain = {}
-
- # Set the domain.
- spin.domain[tensor] = domain
-
def svd(basis_set=0, tensors=None):
"""Function for calculating the singular values of all the loaded
tensors.
Modified: trunk/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/frame_order.py?rev=18942&r1=18941&r2=18942&view=diff
==============================================================================
--- trunk/specific_fns/frame_order.py (original)
+++ trunk/specific_fns/frame_order.py Fri Mar 22 11:46:15 2013
@@ -961,6 +961,10 @@
# Test if the current data pipe exists.
pipes.test()
+
+ # Check that the domain is defined.
+ if not hasattr(cdp, 'domain') or domain not in cdp.domain.keys():
+ raise RelaxError("The domain '%s' has not been defined. Please
use the domain user function." % domain)
# Test if the reference domain exists.
exists = False
@@ -1322,23 +1326,17 @@
@type sim_index: None or int
"""
- # Assemble the parameter vector.
- param_vector = self._assemble_param_vector()
-
- # Get the data structures for optimisation using the tensors as base
data sets.
- full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self._minimise_setup_tensors()
-
- # Set up the optimisation function.
- target = frame_order.Frame_order(model=cdp.model,
full_tensors=full_tensors, red_tensors=red_tensors,
red_errors=red_tensor_err, full_in_ref_frame=full_in_ref_frame)
+ # Set up the target function for direct calculation.
+ model, param_vector, data_types, scaling_matrix =
self._target_fn_setup(sim_index=sim_index)
# Make a single function call. This will cause back calculation and
the data will be stored in the class instance.
- chi2 = target.func(param_vector)
+ chi2 = model.func(param_vector)
# Set the chi2.
cdp.chi2 = chi2
# Store the back-calculated tensors.
- self._store_bc_tensors(target)
+ self._store_bc_tensors(model)
def create_mc_data(self, data_id=None):
r18942 - in /trunk: generic_fns/ prompt/ specific_fns/