Author: bugman
Date: Fri Oct 2 10:40:33 2015
New Revision: 27935
URL: http://svn.gna.org/viewcvs/relax?rev=27935&view=rev
Log:
Merged revisions 23935-23936,23943,23947-23948,23969-23983 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r23935 | bugman | 2014-06-13 14:03:44 +0200 (Fri, 13 Jun 2014) | 12 lines
Added a script for timing different ways to calculate PCSs and RDCs for
multiple vectors.
This uses the timeit module rather than profile to demonstrate the speed of
7 different ways to
calculate the RDCs or PCSs for an array of vectors using numpy. In the
frame order analysis, this
is the bottleneck for the quasi-random numerical integration of the PCS.
The log file shows a potential 1 order of magnitude speed up between the
1st technique, which is
currently used in the frame order analysis, and the 7th and last technique.
The first technique
loops over each vector, calculating the PCS. The last expands the PCS/RDC
equation of the
projection of the vector into the alignment tensor, and calculates all PCSs
simultaneously.
........
r23936 | bugman | 2014-06-13 15:25:28 +0200 (Fri, 13 Jun 2014) | 8 lines
Added another timing script for RDC and PCS calculation timings.
This time, the calculation for multiple alignments is now being timed. An
addition set of methods
for calculating the values via tensor projections have been added. For 5
alignments and 200
vectors, this demonstrates a potential 20x speed up for this part of the
RDC/PCS calculation. Most
of this speed up should be obtainable for the numerical PCS integration in
the frame order models.
........
r23943 | bugman | 2014-06-13 17:43:50 +0200 (Fri, 13 Jun 2014) | 8 lines
Small speed up for all of the frame order models.
The PCS averaging in the quasi-random numerical integration functions now
uses the multiply() and
divide() numpy methods to eliminate a loop over the alignments. For this,
a new dimension over the
spins was added to the PCS constant calculated in the target function
__init__() method. In one
test of the pseudo-ellipse, the time dropped from 191 seconds to 172.
........
r23947 | bugman | 2014-06-13 19:51:26 +0200 (Fri, 13 Jun 2014) | 6 lines
Added another timing script for helping with speeding up the frame order
analysis.
This is for the part where the rotation matrix for each Sobol' integration
point is shifted into the
eigenframe.
........
r23948 | bugman | 2014-06-13 19:54:40 +0200 (Fri, 13 Jun 2014) | 3 lines
Python 3 fix for the CaM frame order system test base script.
........
r23969 | bugman | 2014-06-16 09:02:19 +0200 (Mon, 16 Jun 2014) | 5 lines
Added the full optimisation results for the torsionless isotropic cone
frame order model.
This is for the CaM test data using the new frame_order.py optimisation
script.
........
r23970 | bugman | 2014-06-16 11:05:28 +0200 (Mon, 16 Jun 2014) | 12 lines
Small speed ups for all of the frame order models in the quasi-random
numerical PCS integration.
These changes result in an ~10% speed up. Testing via the
func_pseudo_ellipse() target function
using the relax profiling flag, the time for one optimisation decreased
from 158 to 146 seconds.
The changes consist of pre-calculating all rotations of the rotation matrix
into the motional
eigenframe in one mathematical operation rather than one operation per
Sobol' point rotation,
unpacking the Sobol' points into the respective angles prior to looping
over the points, and taking
the absolute value of the torsion angle and testing if it is out of the
bounds rather than checking
both the negative and positive values.
........
r23971 | bugman | 2014-06-16 11:07:44 +0200 (Mon, 16 Jun 2014) | 8 lines
Attempt at speeding up the torsionless pseudo-ellipse frame order model.
The check if the Sobol' point is outside of an isotropic cone defined by
the largest angle theta_y
is now performed to avoid many unnecessary calls to the
tmax_pseudo_ellipse() function.
This however reveals a problem with the test suite data for this model.
........
r23972 | bugman | 2014-06-16 11:11:13 +0200 (Mon, 16 Jun 2014) | 7 lines
Updated all of the CaM frame order system tests for the recent speed up
(r23970).
The speed up switched to the use of numpy.tensordot() for shifting each
Sobol' rotation into the
eigenframe rather than the previous numpy.dot(). Strangely this affects
the precision and hence the
chi-squared value calculated for each system test - both increasing and
decreasing it randomly.
........
r23973 | bugman | 2014-06-16 11:40:37 +0200 (Mon, 16 Jun 2014) | 5 lines
The frame order target function calc_vectors() method arguments have all
been converted to keywords.
This is in preparation for handling a second pivot argument for the double
rotor model.
........
r23974 | bugman | 2014-06-16 11:49:10 +0200 (Mon, 16 Jun 2014) | 7 lines
Updated the double rotor frame order model to be in a pseudo-functional
state.
Bugs in the target function method have been removed, the calc_vectors()
target function now accepts
the pivot2 argument (but does nothing with it yet), and the
lib.frame_order.double_rotor module has
been updated to match the logic used in all other lib.frame_order modules.
........
r23975 | bugman | 2014-06-16 12:05:39 +0200 (Mon, 16 Jun 2014) | 3 lines
The frame_order.pdb_model user function no longer tries to create a cone
object for the double rotor.
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r23976 | bugman | 2014-06-16 16:03:55 +0200 (Mon, 16 Jun 2014) | 3 lines
Added a timeit script and log file for different ways of checking a binary
numpy array.
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r23977 | bugman | 2014-06-16 17:08:10 +0200 (Mon, 16 Jun 2014) | 8 lines
Modified the rigid_test.py system test script to really be the rigid case.
This is used in all of the Frame_order.test_rigid_data_to_*_model system
tests. Previously the
parameters of the dynamics were set to being close to zero, to catch the
cases were a few Sobol'
PCS integration points were accepted. But now the case were no Sobol'
points can be used is being
tested. This checks a code path currently untested in the test suite,
demonstrating many failures.
........
r23978 | bugman | 2014-06-16 17:30:30 +0200 (Mon, 16 Jun 2014) | 7 lines
Fix for the frame order matrix calculation for a pseudo-elliptic cone with
angles of zero degrees.
The
lib.frame_order.pseudo_ellipse_torsionless.compile_2nd_matrix_pseudo_ellipse_torsionless()
function has been changed to prevent a divide by zero failure. The surface
area normalisation
factor now defaults to 0.0.
........
r23979 | bugman | 2014-06-16 17:39:25 +0200 (Mon, 16 Jun 2014) | 7 lines
Fixes for all PCS numeric integration for all frame order models in the
rigid case.
The exact PCS values for the rigid state are now correctly calculated when
no Sobol' points lie
within the motional model. The identity matrix is used to set the rotation
to zero, and the PCS
values are now multiplied by the constant.
........
r23980 | bugman | 2014-06-16 17:40:42 +0200 (Mon, 16 Jun 2014) | 5 lines
Updates for the chi-squared value in all the
Frame_order.test_rigid_data_to_*_model system tests.
This is now much reduced as the true rigid state is now being tested for.
........
r23981 | bugman | 2014-06-16 17:53:11 +0200 (Mon, 16 Jun 2014) | 3 lines
Fix for the fix of r23978, the theta_x angle should be checked for zero as
it is the smallest.
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r23982 | bugman | 2014-06-16 18:10:07 +0200 (Mon, 16 Jun 2014) | 10 lines
The rigid frame order matrix for the pseudo-ellipse models is now correctly
handled.
This allows the rigid case RDCs to be correctly calculated for both the
pseudo-ellipse and
torsionless pseudo-ellipse models. The previous catch of the theta_x cone
angle of zero was
incorrectly recreating the frame order matrix, which really should be the
identity matrix. However
truncation artifacts due to the quadratic SciPy integration still cause the
model to be
ill-conditioned near the rigid case. The rigid case is correctly handled,
but a tiny shift of the
parameters off zero cause a discontinuity.
........
r23983 | bugman | 2014-06-16 18:28:49 +0200 (Mon, 16 Jun 2014) | 3 lines
Fix for the rigid frame order model broken at r23973.
........
Added:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/ave_pos.pdb.gz
- copied unchanged from r23983,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/ave_pos_fixed_piv.pdb.gz
- copied unchanged from r23983,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/ave_pos_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/ave_pos_true.pdb.gz
- copied unchanged from r23983,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/ave_pos_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.pdb.gz
- copied unchanged from r23983,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order_fixed_piv.pdb.gz
- copied unchanged from r23983,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order_true.pdb.gz
- copied unchanged from r23983,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order_true.pdb.gz
trunk/test_suite/shared_data/frame_order/timings/
- copied from r23983,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/
Removed:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/ave_pos.pdb
Modified:
trunk/ (props changed)
trunk/lib/frame_order/double_rotor.py
trunk/lib/frame_order/iso_cone.py
trunk/lib/frame_order/iso_cone_torsionless.py
trunk/lib/frame_order/matrix_ops.py
trunk/lib/frame_order/pseudo_ellipse.py
trunk/lib/frame_order/pseudo_ellipse_torsionless.py
trunk/lib/frame_order/rotor.py
trunk/specific_analyses/frame_order/uf.py
trunk/target_functions/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.bz2
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.log.bz2
trunk/test_suite/system_tests/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
trunk/test_suite/system_tests/scripts/frame_order/rigid_test.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/lib/frame_order/double_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/double_rotor.py?rev=27935&r1=27934&r2=27935&view=diff
Modified: trunk/lib/frame_order/iso_cone.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/iso_cone.py?rev=27935&r1=27934&r2=27935&view=diff
Modified: trunk/lib/frame_order/iso_cone_torsionless.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/iso_cone_torsionless.py?rev=27935&r1=27934&r2=27935&view=diff
Modified: trunk/lib/frame_order/matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/matrix_ops.py?rev=27935&r1=27934&r2=27935&view=diff
Modified: trunk/lib/frame_order/pseudo_ellipse.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/pseudo_ellipse.py?rev=27935&r1=27934&r2=27935&view=diff
Modified: trunk/lib/frame_order/pseudo_ellipse_torsionless.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/pseudo_ellipse_torsionless.py?rev=27935&r1=27934&r2=27935&view=diff
Modified: trunk/lib/frame_order/rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/rotor.py?rev=27935&r1=27934&r2=27935&view=diff
Modified: trunk/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/uf.py?rev=27935&r1=27934&r2=27935&view=diff
Modified: trunk/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/frame_order.py?rev=27935&r1=27934&r2=27935&view=diff
Removed:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/ave_pos.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/ave_pos.pdb?rev=27934&view=auto
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.bz2?rev=27935&r1=27934&r2=27935&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.log.bz2?rev=27935&r1=27934&r2=27935&view=diff
Modified: trunk/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/frame_order.py?rev=27935&r1=27934&r2=27935&view=diff
Modified: trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=27935&r1=27934&r2=27935&view=diff
Modified: trunk/test_suite/system_tests/scripts/frame_order/rigid_test.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/rigid_test.py?rev=27935&r1=27934&r2=27935&view=diff
r27935 - in /trunk: ./ lib/frame_order/ specific_analyses/frame_order/ target_functions/ test_suite/shared_data/frame_order/...