Author: bugman
Date: Wed Jan 23 22:55:07 2013
New Revision: 18288
URL: http://svn.gna.org/viewcvs/relax?rev=18288&view=rev
Log:
Merged revisions 18279-18287 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18279 | bugman | 2013-01-23 18:51:33 +0100 (Wed, 23 Jan 2013) | 3 lines
Simplified the parameter unpacking in the func_standard() N-state model
target function.
........
r18280 | bugman | 2013-01-23 21:08:23 +0100 (Wed, 23 Jan 2013) | 3 lines
Improved the comments in the _disassemble_param_vector() N-state model
method.
........
r18281 | bugman | 2013-01-23 21:09:49 +0100 (Wed, 23 Jan 2013) | 6 lines
Modified the populations.py N-state model system test script to better test
optimisation.
The probability of the 2nd state has been slightly shifted to make sure the
original value can be
found.
........
r18282 | bugman | 2013-01-23 21:35:53 +0100 (Wed, 23 Jan 2013) | 5 lines
Bug fix for the N-state model Hessian d2func_standard() method.
An index variable name was incorrect causing the population model to fail
with Newton optimisation.
........
r18283 | bugman | 2013-01-23 21:38:05 +0100 (Wed, 23 Jan 2013) | 5 lines
Modified the metal_pos_opt.py N-state model system test script to
demonstrate some failures.
This change also caught the bug fixed in r18282.
........
r18284 | bugman | 2013-01-23 21:41:08 +0100 (Wed, 23 Jan 2013) | 3 lines
Improved the checks of the metal_pos_opt.py N-state model system test
script.
........
r18285 | bugman | 2013-01-23 22:12:42 +0100 (Wed, 23 Jan 2013) | 5 lines
Bug fixes for the _opt_uses_pcs() and _opt_uses_rdc() N-state model methods.
These now check that the populations are optimised as well.
........
r18286 | bugman | 2013-01-23 22:14:19 +0100 (Wed, 23 Jan 2013) | 3 lines
Modified the metal_pos_opt.py N-state model system test script to catch yet
another bug.
........
r18287 | bugman | 2013-01-23 22:51:13 +0100 (Wed, 23 Jan 2013) | 6 lines
Fix for a bug caught by the N_state_model.test_metal_pos_opt system test.
The problem was that uninitalised probability arrays of None from cdp.probs
was always sent into the
target function, whereas None should be sent in instead.
........
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/maths_fns/n_state_model.py
branches/frame_order_testing/specific_fns/n_state_model.py
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/populations.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Jan 23 22:55:07 2013
@@ -1,1 +1,1 @@
-/trunk:1-18277
+/trunk:1-18287
Modified: branches/frame_order_testing/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/n_state_model.py?rev=18288&r1=18287&r2=18288&view=diff
==============================================================================
--- branches/frame_order_testing/maths_fns/n_state_model.py (original)
+++ branches/frame_order_testing/maths_fns/n_state_model.py Wed Jan 23
22:55:07 2013
@@ -638,21 +638,17 @@
# Initial chi-squared (or SSE) value.
chi2_sum = 0.0
- # Unpack both the probabilities and paramagnetic centre.
+ # Unpack both the probabilities (when the paramagnetic centre is
also optimised).
if not self.probs_fixed and not self.centre_fixed:
# The probabilities.
self.probs = params[-(self.N-1)-3:-3]
- # The position (also update the paramagnetic info).
- self.paramag_centre = params[-3:]
- self.paramag_info()
-
# Unpack the probabilities (located at the end of the parameter
array).
elif not self.probs_fixed:
self.probs = params[-(self.N-1):]
# Unpack the paramagnetic centre (also update the paramagnetic info).
- elif not self.centre_fixed:
+ if not self.centre_fixed:
self.paramag_centre = params[-3:]
self.paramag_info()
@@ -1126,20 +1122,20 @@
# Calculate the RDC Hessian component.
for j in range(self.num_interatom):
if self.fixed_tensors[align_index] and
self.rdc_flag[align_index] and not self.missing_rdc[align_index, j]:
- self.d2rdc_theta[pc_index, i*5+0, align_index,
j] = self.d2rdc_theta[align_index*5+0, pc_index, align_index, j] =
rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[0],
absolute=self.absolute_rdc[align_index, j])
- self.d2rdc_theta[pc_index, i*5+1, align_index,
j] = self.d2rdc_theta[align_index*5+1, pc_index, align_index, j] =
rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[1],
absolute=self.absolute_rdc[align_index, j])
- self.d2rdc_theta[pc_index, i*5+2, align_index,
j] = self.d2rdc_theta[align_index*5+2, pc_index, align_index, j] =
rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[2],
absolute=self.absolute_rdc[align_index, j])
- self.d2rdc_theta[pc_index, i*5+3, align_index,
j] = self.d2rdc_theta[align_index*5+3, pc_index, align_index, j] =
rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[3],
absolute=self.absolute_rdc[align_index, j])
- self.d2rdc_theta[pc_index, i*5+4, align_index,
j] = self.d2rdc_theta[align_index*5+4, pc_index, align_index, j] =
rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[4],
absolute=self.absolute_rdc[align_index, j])
+ self.d2rdc_theta[pc_index, align_index*5+0,
align_index, j] = self.d2rdc_theta[align_index*5+0, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[0],
absolute=self.absolute_rdc[align_index, j])
+ self.d2rdc_theta[pc_index, align_index*5+1,
align_index, j] = self.d2rdc_theta[align_index*5+1, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[1],
absolute=self.absolute_rdc[align_index, j])
+ self.d2rdc_theta[pc_index, align_index*5+2,
align_index, j] = self.d2rdc_theta[align_index*5+2, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[2],
absolute=self.absolute_rdc[align_index, j])
+ self.d2rdc_theta[pc_index, align_index*5+3,
align_index, j] = self.d2rdc_theta[align_index*5+3, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[3],
absolute=self.absolute_rdc[align_index, j])
+ self.d2rdc_theta[pc_index, align_index*5+4,
align_index, j] = self.d2rdc_theta[align_index*5+4, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[4],
absolute=self.absolute_rdc[align_index, j])
# Calculate the PCS Hessian component.
for j in range(self.num_spins):
if self.fixed_tensors[align_index] and
self.pcs_flag[align_index] and not self.missing_deltaij[align_index, j]:
- self.d2deltaij_theta[pc_index, i*5+0,
align_index, j] = self.d2deltaij_theta[align_index*5+0, pc_index,
align_index, j] = pcs_tensor(self.pcs_const[align_index, j, c],
self.paramag_unit_vect[j, c], self.dA[0])
- self.d2deltaij_theta[pc_index, i*5+1,
align_index, j] = self.d2deltaij_theta[align_index*5+1, pc_index,
align_index, j] = pcs_tensor(self.pcs_const[align_index, j, c],
self.paramag_unit_vect[j, c], self.dA[1])
- self.d2deltaij_theta[pc_index, i*5+2,
align_index, j] = self.d2deltaij_theta[align_index*5+2, pc_index,
align_index, j] = pcs_tensor(self.pcs_const[align_index, j, c],
self.paramag_unit_vect[j, c], self.dA[2])
- self.d2deltaij_theta[pc_index, i*5+3,
align_index, j] = self.d2deltaij_theta[align_index*5+3, pc_index,
align_index, j] = pcs_tensor(self.pcs_const[align_index, j, c],
self.paramag_unit_vect[j, c], self.dA[3])
- self.d2deltaij_theta[pc_index, i*5+4,
align_index, j] = self.d2deltaij_theta[align_index*5+4, pc_index,
align_index, j] = pcs_tensor(self.pcs_const[align_index, j, c],
self.paramag_unit_vect[j, c], self.dA[4])
+ self.d2deltaij_theta[pc_index, align_index*5+0,
align_index, j] = self.d2deltaij_theta[align_index*5+0, pc_index,
align_index, j] = pcs_tensor(self.pcs_const[align_index, j, c],
self.paramag_unit_vect[j, c], self.dA[0])
+ self.d2deltaij_theta[pc_index, align_index*5+1,
align_index, j] = self.d2deltaij_theta[align_index*5+1, pc_index,
align_index, j] = pcs_tensor(self.pcs_const[align_index, j, c],
self.paramag_unit_vect[j, c], self.dA[1])
+ self.d2deltaij_theta[pc_index, align_index*5+2,
align_index, j] = self.d2deltaij_theta[align_index*5+2, pc_index,
align_index, j] = pcs_tensor(self.pcs_const[align_index, j, c],
self.paramag_unit_vect[j, c], self.dA[2])
+ self.d2deltaij_theta[pc_index, align_index*5+3,
align_index, j] = self.d2deltaij_theta[align_index*5+3, pc_index,
align_index, j] = pcs_tensor(self.pcs_const[align_index, j, c],
self.paramag_unit_vect[j, c], self.dA[3])
+ self.d2deltaij_theta[pc_index, align_index*5+4,
align_index, j] = self.d2deltaij_theta[align_index*5+4, pc_index,
align_index, j] = pcs_tensor(self.pcs_const[align_index, j, c],
self.paramag_unit_vect[j, c], self.dA[4])
# Construct the paramagnetic centre c partial derivative
components for the PCS.
if not self.centre_fixed:
Modified: branches/frame_order_testing/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/n_state_model.py?rev=18288&r1=18287&r2=18288&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/n_state_model.py (original)
+++ branches/frame_order_testing/specific_fns/n_state_model.py Wed Jan 23
22:55:07 2013
@@ -580,7 +580,7 @@
# Create a new parameter vector without the tensors.
param_vector = param_vector[5*tensor_num:]
- # Monte Carlo simulation data structures.
+ # Alias the Monte Carlo simulation data structures.
if sim_index != None:
# Populations.
if cdp.model in ['2-domain', 'population']:
@@ -592,7 +592,7 @@
beta = cdp.beta_sim[sim_index]
gamma = cdp.gamma_sim[sim_index]
- # Normal data structures.
+ # Alias the normal data structures.
else:
# Populations.
if cdp.model in ['2-domain', 'population']:
@@ -604,7 +604,7 @@
beta = cdp.beta
gamma = cdp.gamma
- # The probabilities for states 0 to N-1.
+ # Set the probabilities for states 0 to N-1 in the aliased
structures.
if cdp.model in ['2-domain', 'population']:
for i in range(cdp.N-1):
probs[i] = param_vector[i]
@@ -612,7 +612,7 @@
# The probability for state N.
probs[-1] = 1 - sum(probs[0:-1])
- # The Euler angles.
+ # Set the Euler angles in the aliased structures.
if cdp.model == '2-domain':
for i in range(cdp.N):
alpha[i] = param_vector[cdp.N-1 + 3*i]
@@ -1422,8 +1422,13 @@
if hasattr(cdp, 'paramag_centre_fixed') and not
cdp.paramag_centre_fixed:
pos_flag = True
+ # Are the populations optimised?
+ prob_flag = False
+ if cdp.model == 'population':
+ prob_flag = True
+
# Not used.
- if not tensor_flag and not pos_flag:
+ if not tensor_flag and not pos_flag and not prob_flag:
return False
# The PCS data is to be used for optimisation.
@@ -1455,8 +1460,13 @@
if hasattr(cdp, 'paramag_centre_fixed') and not
cdp.paramag_centre_fixed:
pos_flag = True
+ # Are the populations optimised?
+ prob_flag = False
+ if cdp.model == 'population':
+ prob_flag = True
+
# Not used.
- if not tensor_flag and not pos_flag:
+ if not tensor_flag and not pos_flag and not prob_flag:
return False
# The RDC data is to be used for optimisation.
@@ -1627,7 +1637,7 @@
# The probabilities.
probs = None
- if hasattr(cdp, 'probs'):
+ if hasattr(cdp, 'probs') and len(cdp.probs) and cdp.probs[0] != None:
probs = cdp.probs
# Diagonal scaling.
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py?rev=18288&r1=18287&r2=18288&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
(original)
+++
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
Wed Jan 23 22:55:07 2013
@@ -115,7 +115,20 @@
# Optimise the Ln3+ position.
x, y, z = cdp.paramagnetic_centre
-#self._execute_uf(uf_name='n_state_model.select_model', model='population')
+self._execute_uf(uf_name='n_state_model.select_model', model='population')
+self._execute_uf(uf_name='calc')
+print("Chi2: %s" % cdp.chi2)
+chi2 = cdp.chi2
+if cdp.chi2 < 1e-15:
+ raise RelaxError("The chi2 value cannot be zero here!")
+self._execute_uf(uf_name='paramag.centre', fix=True)
+self._execute_uf(uf_name='calc')
+print("Chi2: %s" % cdp.chi2)
+if abs(cdp.chi2 - chi2) > 1e-15:
+ raise RelaxError("The chi2 value must match the previous value of %s." %
chi2)
+self._execute_uf(uf_name='n_state_model.select_model', model='fixed')
+self._execute_uf(uf_name='paramag.centre', fix=False)
+self._execute_uf(uf_name='calc')
self._execute_uf('bfgs', constraints=False, max_iter=500,
uf_name='minimise', verbosity=1)
# Check that the metal moved.
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/populations.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/populations.py?rev=18288&r1=18287&r2=18288&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/populations.py
(original)
+++
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/populations.py
Wed Jan 23 22:55:07 2013
@@ -109,8 +109,11 @@
# The population model opt.
###########################
+# Change a probability
+self._execute_uf(uf_name='value.set', val=0.6005, param='p1')
+
# Minimisation.
-self._execute_uf(uf_name='minimise', min_algor='sd', func_tol=1e-2)
+self._execute_uf(uf_name='minimise', min_algor='bfgs')
# Write out a results file.
self._execute_uf(uf_name='results.write', file='devnull', force=True)
r18288 - in /branches/frame_order_testing: ./ maths_fns/ specific_fns/ test_suite/system_tests/scripts/n_state_model/