Author: bugman
Date: Sun Sep 14 14:43:07 2014
New Revision: 25826
URL: http://svn.gna.org/viewcvs/relax?rev=25826&view=rev
Log:
Implementation of the
specific_analyses.frame_order.optimisation.count_sobol_points() function.
This is used by the frame_order.num_int_pts user function to provide a
printout of the number of
Sobol' integration points used for the current parameter values. This is to
provide user feedback
so that it is know if enough Sobol' points have been used.
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py?rev=25826&r1=25825&r2=25826&view=diff
==============================================================================
---
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
(original)
+++
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
Sun Sep 14 14:43:07 2014
@@ -26,7 +26,7 @@
from math import cos, pi
from minfx.generic import generic_minimise
from minfx.grid import grid_point_array
-from numpy import arccos, array, dot, float64, ones, zeros
+from numpy import arccos, array, dot, float64, ones, swapaxes, zeros
from numpy.linalg import inv, norm
from re import search
import sys
@@ -35,6 +35,7 @@
# relax module imports.
from lib.float import isNaN, isInf
from lib.errors import RelaxError, RelaxInfError, RelaxNaNError,
RelaxNoPCSError, RelaxNoRDCError
+from lib.frame_order.pseudo_ellipse import tmax_pseudo_ellipse_array
from lib.geometry.angles import wrap_angles
from lib.order import order_parameters
from lib.periodic_table import periodic_table
@@ -44,10 +45,95 @@
from pipe_control.interatomic import interatomic_loop
from pipe_control.mol_res_spin import return_spin, spin_loop
from pipe_control.structure.mass import pipe_centre_of_mass
+from specific_analyses.frame_order.checks import check_domain, check_model,
check_parameters
from specific_analyses.frame_order.data import base_data_types,
domain_moving, pivot_fixed, tensor_loop
from specific_analyses.frame_order.parameters import assemble_param_vector,
linear_constraints
-from specific_analyses.frame_order.variables import MODEL_DOUBLE_ROTOR,
MODEL_FREE_ROTOR, MODEL_RIGID, MODEL_ROTOR
+from specific_analyses.frame_order.variables import MODEL_DOUBLE_ROTOR,
MODEL_FREE_ROTOR, MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR,
MODEL_ISO_CONE_TORSIONLESS, MODEL_LIST_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE,
MODEL_PSEUDO_ELLIPSE_FREE_ROTOR, MODEL_PSEUDO_ELLIPSE_TORSIONLESS,
MODEL_RIGID, MODEL_ROTOR
from target_functions.frame_order import Frame_order
+
+
+def count_sobol_points():
+ """Count the number of Sobol' points for the current parameter values of
the model.
+
+ The count will be stored in the current data pipe and printed out.
+ """
+
+ # Printout.
+ print("Sobol' integration point counting for the current parameter
values.")
+
+ # Checks.
+ if not check_model(escalate=1):
+ return
+ if not check_parameters(escalate=1):
+ return
+ if not check_domain(escalate=1):
+ return
+
+ # Set up the data structures for the target function.
+ param_vector, full_tensors, full_in_ref_frame, rdcs, rdc_err,
rdc_weight, rdc_vect, rdc_const, pcs, pcs_err, pcs_weight, atomic_pos, temp,
frq, paramag_centre, com, ave_pos_pivot, pivot, pivot_opt =
target_fn_data_setup(verbosity=0, unset_fail=True)
+
+ # Set up the optimisation target function class.
+ target_fn = Frame_order(model=cdp.model, init_params=param_vector,
full_tensors=full_tensors, full_in_ref_frame=full_in_ref_frame, rdcs=rdcs,
rdc_errors=rdc_err, rdc_weights=rdc_weight, rdc_vect=rdc_vect,
dip_const=rdc_const, pcs=pcs, pcs_errors=pcs_err, pcs_weights=pcs_weight,
atomic_pos=atomic_pos, temp=temp, frq=frq, paramag_centre=paramag_centre,
scaling_matrix=None, com=com, ave_pos_pivot=ave_pos_pivot, pivot=pivot,
pivot_opt=pivot_opt, num_int_pts=cdp.num_int_pts)
+
+ # The Sobol' sequence dimensions.
+ if cdp.model in [MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR,
MODEL_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE_FREE_ROTOR]:
+ dims = ['theta', 'phi', 'sigma']
+ elif cdp.model in [MODEL_ISO_CONE_TORSIONLESS,
MODEL_PSEUDO_ELLIPSE_TORSIONLESS]:
+ dims = ['theta', 'phi']
+ elif cdp.model in [MODEL_ROTOR, MODEL_FREE_ROTOR]:
+ dims = ['sigma']
+ elif cdp.model in [MODEL_DOUBLE_ROTOR]:
+ dims = ['sigma', 'sigma2']
+
+ # Unpack the points.
+ theta, phi, sigma, sigma2 = None, None, None, None
+ if dims == ['theta', 'phi', 'sigma']:
+ theta, phi, sigma = swapaxes(target_fn.sobol_angles, 0, 1)
+ elif dims == ['theta', 'phi']:
+ theta, phi = swapaxes(target_fn.sobol_angles, 0, 1)
+ elif dims == ['sigma']:
+ sigma = swapaxes(target_fn.sobol_angles, 0, 1)
+ elif dims == ['sigma', 'sigma2']:
+ sigma, sigma2 = swapaxes(target_fn.sobol_angles, 0, 1)
+
+ # Pseudo-ellipse.
+ pe = False
+ if cdp.model in MODEL_LIST_PSEUDO_ELLIPSE:
+ pe = True
+
+ # Calculate theta_max.
+ theta_max = tmax_pseudo_ellipse_array(phi, cdp.cone_theta_x,
cdp.cone_theta_y)
+
+ # Loop over the Sobol' points to count them.
+ count = 0
+ for i in range(len(target_fn.sobol_angles)):
+ # Pseudo-elliptic cone opening angle.
+ if pe and theta[i] > theta_max[i]:
+ continue
+
+ # Isotropic cones.
+ if not pe and 'theta' in dims and theta[i] > cdp.cone_theta:
+ continue
+
+ # 1st torsion angle.
+ if 'sigma' in dims and sigma[i] > cdp.cone_sigma_max:
+ continue
+
+ # 2nd torsion angle.
+ if 'sigma2' in dims and sigma2[i] > cdp.cone_sigma_max_2:
+ continue
+
+ # Increment the point count.
+ count += 1
+
+ # Store the count.
+ cdp.used_sobol_points = count
+
+ # Printout.
+ print("\n%-20s %20s" % ("Total points:", cdp.num_int_pts))
+ print("%-20s %20s" % ("Used points:", count))
+ percent = "%s" % (float(count)/float(cdp.num_int_pts)*100) + '%'
+ print("%-20s %20s" % ("Percentage:", percent))
def grid_row(incs, lower, upper, dist_type=None, end_point=True):
Modified: branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/uf.py?rev=25826&r1=25825&r2=25826&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/uf.py Sun
Sep 14 14:43:07 2014
@@ -38,6 +38,7 @@
from pipe_control import pipes
from specific_analyses.frame_order.checks import check_domain
from specific_analyses.frame_order.geometric import create_ave_pos,
create_distribution, create_geometric_rep
+from specific_analyses.frame_order.optimisation import count_sobol_points
from specific_analyses.frame_order.parameters import update_model
from specific_analyses.frame_order.variables import MODEL_ISO_CONE,
MODEL_ISO_CONE_FREE_ROTOR, MODEL_ISO_CONE_TORSIONLESS, MODEL_LIST,
MODEL_LIST_FREE_ROTORS, MODEL_LIST_ISO_CONE, MODEL_LIST_PSEUDO_ELLIPSE,
MODEL_LIST_RESTRICTED_TORSION, MODEL_PSEUDO_ELLIPSE,
MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_RIGID
@@ -58,6 +59,9 @@
# Store the value.
cdp.num_int_pts = num
+
+ # Count the number of Sobol' points for the current model.
+ count_sobol_points()
def pdb_model(ave_pos="ave_pos", rep="frame_order",
dist="domain_distribution", dir=None, compress_type=0, size=30.0, inc=36,
model=1, force=False):
r25826 - in /branches/frame_order_cleanup/specific_analyses/frame_order: optimisation.py uf.py