Author: bugman
Date: Wed Sep 17 17:11:14 2014
New Revision: 25864
URL: http://svn.gna.org/viewcvs/relax?rev=25864&view=rev
Log:
Renamed the frame_order.num_int_pts user function to frame_order.sobol_setup.
The user function no longer specifies the number of integration points.
Instead it now specifies
the maximum number of points N and oversampling factor Ov used to generate
the oversampled Sobol'
sequence.
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
branches/frame_order_cleanup/user_functions/frame_order.py
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=25864&r1=25863&r2=25864&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/uf.py Wed
Sep 17 17:11:14 2014
@@ -41,27 +41,6 @@
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
-
-
-def num_int_pts(num=200000):
- """Set the number of integration points to use in the quasi-random
Sobol' sequence.
-
- @keyword num: The number of integration points.
- @type num: int
- """
-
- # Test if the current data pipe exists.
- pipes.test()
-
- # Throw a warning to the user if not enough points are being used.
- if num < 1000:
- warn(RelaxWarning("To obtain reliable results in a frame order
analysis, the number of integration points should be greater than 1000."))
-
- # 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):
@@ -386,3 +365,27 @@
# Update the model.
update_model()
+
+
+def sobol_setup(max_num=200, oversample=100):
+ """Oversampling setup for the quasi-random Sobol' sequence used for
numerical PCS integration.
+
+ @keyword max_num: The maximum number of integration points N.
+ @type max_num: int
+ @keyword oversample: The oversampling factor Ov used for the N * Ov *
10**M, where M is the number of dimensions or torsion-tilt angles for the
system.
+ @type oversample: int
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Throw a warning to the user if not enough points are being used.
+ if num < 200:
+ warn(RelaxWarning("To obtain reliable results in a frame order
analysis, the maximum number of integration points should be greater than
200."))
+
+ # Store the values.
+ cdp.sobol_max_points = max_num
+ cdp.sobol_oversample_factor = oversample
+
+ # Count the number of Sobol' points for the current model.
+ count_sobol_points()
Modified: branches/frame_order_cleanup/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/frame_order.py?rev=25864&r1=25863&r2=25864&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/frame_order.py (original)
+++ branches/frame_order_cleanup/user_functions/frame_order.py Wed Sep 17
17:11:14 2014
@@ -25,7 +25,7 @@
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from specific_analyses.frame_order.optimisation import count_sobol_points
-from specific_analyses.frame_order.uf import num_int_pts, pdb_model,
permute_axes, pivot, ref_domain, select_model
+from specific_analyses.frame_order.uf import sobol_setup, pdb_model,
permute_axes, pivot, ref_domain, select_model
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_PSEUDO_ELLIPSE,
MODEL_PSEUDO_ELLIPSE_FREE_ROTOR, MODEL_PSEUDO_ELLIPSE_TORSIONLESS,
MODEL_RIGID, MODEL_ROTOR
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
@@ -241,50 +241,6 @@
uf.backend = pivot
uf.menu_text = "&pivot"
uf.wizard_size = (900, 600)
-uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
-
-
-# The frame_order.num_int_pts user function.
-uf = uf_info.add_uf('frame_order.num_int_pts')
-uf.title = "Set the maximum number of integration points used in the
quasi-random Sobol' sequence during optimisation."
-uf.title_short = "Maximum number of integration points."
-uf.add_keyarg(
- name = "num",
- default = 200,
- min = 3,
- max = 10000000,
- py_type = "int",
- desc_short = "number of points",
- desc = "The maximum number of integration points to use in the Sobol'
sequence during optimisation.",
- wiz_element_type = "spin"
-)
-uf.add_keyarg(
- name = "oversample",
- default = 100,
- min = 1,
- max = 10000000,
- py_type = "int",
- desc_short = "oversampling factor",
- desc = "The generation of the Sobol' sequence oversamples as N * Ov *
10**M, where N is the maximum number of points, Ov is the oversamling value,
and M is the number of dimensions or torsion-tilt angles used in the system.",
- wiz_element_type = "spin"
-)
-# Description.
-uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This allows the maximum number of integration
points N used during the Frame Order target function optimisation to be
specified. This is used in the quasi-random Sobol' sequence for the
numerical integration of the PCS. The symbols used to describe the algorithm
are:")
-uf.desc[-1].add_list_element("N, the maximum number of Sobol' integration
points.")
-uf.desc[-1].add_list_element("Ov, the oversampling factor.")
-uf.desc[-1].add_list_element("M, the number of dimensions or torsion-tilt
angles used in the system.")
-uf.desc[-1].add_paragraph("The algorithm used for uniformly sampling the
motional space is:")
-uf.desc[-1].add_list_element("Generate the Sobol' sequence. The number of
points is oversampled as N * Ov * 10**M.")
-uf.desc[-1].add_list_element("Convert all points to the torsion-tilt angle
system.")
-uf.desc[-1].add_list_element("Skip all Sobol' points with angles greater
than the current parameter values.")
-uf.desc[-1].add_list_element("Terminate the loop over the Sobol' points for
calculating the PCS once the maximum number of points has been reached.")
-uf.desc[-1].add_paragraph("The aim of the oversampling is to try to reach
the maximum number of points. However if the system is not very dynamic, the
maximum number of points may not be reached. In this case, simply increase
the oversampling factor.")
-uf.backend = num_int_pts
-uf.menu_text = "&num_int_pts"
-uf.gui_icon = "oxygen.actions.edit-rename"
-uf.wizard_height_desc = 500
-uf.wizard_size = (1000, 700)
uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
@@ -375,3 +331,47 @@
uf.wizard_size = (1000, 750)
uf.wizard_apply_button = False
uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
+
+
+# The frame_order.sobol_setup user function.
+uf = uf_info.add_uf('frame_order.sobol_setup')
+uf.title = "Set up the quasi-random Sobol' sequence points for numerical PCS
integration."
+uf.title_short = "Set up the quasi-random Sobol' sequence."
+uf.add_keyarg(
+ name = "max_num",
+ default = 200,
+ min = 3,
+ max = 10000000,
+ py_type = "int",
+ desc_short = "maximum number of Sobol' points",
+ desc = "The maximum number of integration points to use in the Sobol'
sequence during optimisation. This can be considered as the number of
molecular structures in an ensemble used form a uniform distribution of the
dynamics.",
+ wiz_element_type = "spin"
+)
+uf.add_keyarg(
+ name = "oversample",
+ default = 100,
+ min = 1,
+ max = 10000000,
+ py_type = "int",
+ desc_short = "oversampling factor",
+ desc = "The generation of the Sobol' sequence oversamples as N * Ov *
10**M, where N is the maximum number of points, Ov is the oversamling value,
and M is the number of dimensions or torsion-tilt angles used in the system.",
+ wiz_element_type = "spin"
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This allows the maximum number of integration
points N used during the Frame Order target function optimisation to be
specified. This is used in the quasi-random Sobol' sequence for the
numerical integration of the PCS. The symbols used to describe the algorithm
are:")
+uf.desc[-1].add_list_element("N, the maximum number of Sobol' integration
points.")
+uf.desc[-1].add_list_element("Ov, the oversampling factor.")
+uf.desc[-1].add_list_element("M, the number of dimensions or torsion-tilt
angles used in the system.")
+uf.desc[-1].add_paragraph("The algorithm used for uniformly sampling the
motional space is:")
+uf.desc[-1].add_list_element("Generate the Sobol' sequence. The number of
points is oversampled as N * Ov * 10**M.")
+uf.desc[-1].add_list_element("Convert all points to the torsion-tilt angle
system.")
+uf.desc[-1].add_list_element("Skip all Sobol' points with angles greater
than the current parameter values.")
+uf.desc[-1].add_list_element("Terminate the loop over the Sobol' points for
calculating the PCS once the maximum number of points has been reached.")
+uf.desc[-1].add_paragraph("The aim of the oversampling is to try to reach
the maximum number of points. However if the system is not very dynamic, the
maximum number of points may not be reached. In this case, simply increase
the oversampling factor.")
+uf.backend = sobol_setup
+uf.menu_text = "&sobol_setup"
+uf.gui_icon = "oxygen.actions.edit-rename"
+uf.wizard_height_desc = 500
+uf.wizard_size = (1000, 700)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
r25864 - in /branches/frame_order_cleanup: specific_analyses/frame_order/uf.py user_functions/frame_order.py