Author: bugman
Date: Tue Jun 19 12:58:44 2012
New Revision: 16953
URL: http://svn.gna.org/viewcvs/relax?rev=16953&view=rev
Log:
The model-free analysis is now fully using the new interatomic data container
design.
Modified:
branches/interatomic/specific_fns/model_free/mf_minimise.py
Modified: branches/interatomic/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/specific_fns/model_free/mf_minimise.py?rev=16953&r1=16952&r2=16953&view=diff
==============================================================================
--- branches/interatomic/specific_fns/model_free/mf_minimise.py (original)
+++ branches/interatomic/specific_fns/model_free/mf_minimise.py Tue Jun 19
12:58:44 2012
@@ -36,7 +36,7 @@
from generic_fns import diffusion_tensor, pipes
from generic_fns.diffusion_tensor import diff_data_exists
from generic_fns.interatomic import interatomic_loop, return_interatom
-from generic_fns.mol_res_spin import count_spins, exists_mol_res_spin_data,
return_spin_from_index, spin_loop
+from generic_fns.mol_res_spin import count_spins, exists_mol_res_spin_data,
return_spin, return_spin_from_index, spin_loop
from maths_fns.mf import Mf
from multi import Processor_box
from multi_processor_commands import MF_grid_command, MF_memo,
MF_minimise_command
@@ -979,7 +979,7 @@
return A, b
- def _minimise_data_setup(self, data_store, min_algor, num_data_sets,
min_options, spin=None, sim_index=None):
+ def _minimise_data_setup(self, data_store, min_algor, num_data_sets,
min_options, spin=None, spin_id=None, sim_index=None):
"""Set up all the data required for minimisation.
@param data_store: A data storage container.
@@ -992,6 +992,8 @@
@type min_options: list
@keyword spin: The spin data container.
@type spin: SpinContainer instance
+ @keyword spin_id: The spin ID string.
+ @type spin_id: str
@keyword sim_index: The optional MC simulation index.
@type sim_index: int
@return: An insane tuple. The full tuple is
(ri_data, ri_data_err, equations, param_types, param_values, r, csa, num_frq,
frq, num_ri, remap_table, noe_r1_table, ri_types, num_params,
xh_unit_vectors, diff_type, diff_params)
@@ -1023,12 +1025,11 @@
# Set up the data for the back_calc function.
if min_algor == 'back_calc':
- # The data.
+ # The spin data.
data_store.ri_data = [0.0]
data_store.ri_data_err = [0.000001]
data_store.equations = [spin.equation]
data_store.param_types = [spin.params]
- data_store.r = [spin.r]
data_store.csa = [spin.csa]
data_store.num_frq = [1]
data_store.frq = [[min_options[3]]]
@@ -1036,12 +1037,29 @@
data_store.remap_table = [[0]]
data_store.noe_r1_table = [[None]]
data_store.ri_types = [[min_options[2]]]
- data_store.gx = [return_gyromagnetic_ratio(spin.heteronuc_type)]
- data_store.gh = [return_gyromagnetic_ratio(spin.proton_type)]
- if data_store.model_type != 'local_tm' and cdp.diff_tensor.type
!= 'sphere':
- data_store.xh_unit_vectors = [spin.xh_vect]
- else:
- data_store.xh_unit_vectors = [None]
+ data_store.gx = [return_gyromagnetic_ratio(spin.isotope)]
+
+ # The interatomic data.
+ interatoms = return_interatom(spin_id)
+ for i in range(len(interatoms)):
+ # No relaxation mechanism.
+ if not interatoms[i].dipole_pair:
+ continue
+
+ # The surrounding spins.
+ if spin_id != interatoms[i].spin_id1:
+ spin_id2 = interatoms[i].spin_id1
+ else:
+ spin_id2 = interatoms[i].spin_id2
+ spin2 = return_spin(spin_id2)
+
+ # The data.
+ data_store.r = [interatoms[i].r]
+ data_store.gh = [return_gyromagnetic_ratio(spin2.isotope)]
+ if data_store.model_type != 'local_tm' and
cdp.diff_tensor.type != 'sphere':
+ data_store.xh_unit_vectors = [interatoms[i].vectors]
+ else:
+ data_store.xh_unit_vectors = [None]
# Count the number of model-free parameters for the spin index.
data_store.num_params = [len(spin.params)]
@@ -1084,18 +1102,36 @@
data_store.frq.append(data[5])
data_store.remap_table.append(data[6])
data_store.noe_r1_table.append(data[7])
-
- # Repackage the data.
+ if sim_index == None or data_store.model_type == 'diff':
+ data_store.csa.append(spin.csa)
+ else:
+ data_store.csa.append(spin.csa_sim[sim_index])
+
+ # Repackage the spin data.
data_store.equations.append(spin.equation)
data_store.param_types.append(spin.params)
-
data_store.gx.append(return_gyromagnetic_ratio(spin.heteronuc_type))
- data_store.gh.append(return_gyromagnetic_ratio(spin.proton_type))
- if sim_index == None or data_store.model_type == 'diff':
- data_store.r.append(spin.r)
- data_store.csa.append(spin.csa)
- else:
- data_store.r.append(spin.r_sim[sim_index])
- data_store.csa.append(spin.csa_sim[sim_index])
+ data_store.gx.append(return_gyromagnetic_ratio(spin.isotope))
+
+ # Repackage the interatomic data.
+ interatoms = return_interatom(spin_id)
+ for i in range(len(interatoms)):
+ # No relaxation mechanism.
+ if not interatoms[i].dipole_pair:
+ continue
+
+ # The surrounding spins.
+ if spin_id != interatoms[i].spin_id1:
+ spin_id2 = interatoms[i].spin_id1
+ else:
+ spin_id2 = interatoms[i].spin_id2
+ spin2 = return_spin(spin_id2)
+
+ # The data.
+
data_store.gh.append(return_gyromagnetic_ratio(spin2.isotope))
+ if sim_index == None or data_store.model_type == 'diff':
+ data_store.r.append(interatoms[i].r)
+ else:
+ data_store.r.append(interatoms[i].r_sim[sim_index])
# Model-free parameter values.
if data_store.model_type == 'local_tm':
@@ -1550,6 +1586,11 @@
# Unit vectors.
for i in range(len(interatoms)):
+ # No relaxation mechanism.
+ if not interatoms[i].dipole_pair:
+ continue
+
+ # Check for the vectors.
if not hasattr(interatoms[i], 'vector'):
raise RelaxNoVectorsError
@@ -1586,10 +1627,22 @@
interatoms = return_interatom(spin_id)
# Interatomic distances.
+ count = 0
for i in range(len(interatoms)):
# No relaxation mechanism.
+ if not interatoms[i].dipole_pair:
+ continue
+
+ # Check for the distances.
if not hasattr(interatoms[i], 'r') or interatoms[i].r ==
None:
raise RelaxNoValueError("interatomic distance",
spin_id=interatoms[i].spin_id1, spin_id2=interatoms[i].spin_id2)
+
+ # Count the number of interactions.
+ count += 1
+
+ # Too many interactions.
+ if count > 1:
+ raise RelaxError("The spin '%s' has %s dipolar relaxation
interactions defined, but only a maximum of one is currently supported." %
(spin_id, count))
# Number of spins, minimisation instances, and data sets for each
model type.
if data_store.model_type == 'mf' or data_store.model_type ==
'local_tm':
@@ -1672,7 +1725,7 @@
opt_params.A, opt_params.b = None, None
# Get the data for minimisation.
- self._minimise_data_setup(data_store, min_algor, num_data_sets,
opt_params.min_options, spin=spin, sim_index=sim_index)
+ self._minimise_data_setup(data_store, min_algor, num_data_sets,
opt_params.min_options, spin=spin, spin_id=data_store.spin_id,
sim_index=sim_index)
# Setup the minimisation algorithm when constraints are present.
if constraints and not match('^[Gg]rid', min_algor):
r16953 - /branches/interatomic/specific_fns/model_free/mf_minimise.py