Author: bugman
Date: Tue Aug 26 21:51:35 2014
New Revision: 25320
URL: http://svn.gna.org/viewcvs/relax?rev=25320&view=rev
Log:
Merged revisions 25289-25298,25302-25316 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r25289 | tlinnet | 2014-08-26 14:37:28 +0200 (Tue, 26 Aug 2014) | 3 lines
Added initial documentation for multifit_covar.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25290 | tlinnet | 2014-08-26 14:37:30 +0200 (Tue, 26 Aug 2014) | 3 lines
Modified profiling script to use the new estimate R2eff module.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25291 | tlinnet | 2014-08-26 14:46:04 +0200 (Tue, 26 Aug 2014) | 3 lines
Modified verify error script, to use new estimate R2eff module.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25292 | tlinnet | 2014-08-26 15:56:22 +0200 (Tue, 26 Aug 2014) | 3 lines
Removed all unnessary code from estimate R2eff module.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25293 | tlinnet | 2014-08-26 15:56:24 +0200 (Tue, 26 Aug 2014) | 3 lines
More removal of code.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25294 | bugman | 2014-08-26 16:56:24 +0200 (Tue, 26 Aug 2014) | 6 lines
Changed the array declarations in the target_functions/exponential C file
and header.
Instead of using the pointer format of *xyz, the array format of xyz[] is
now being used. These are
equivalent and the later is more obvious that this is an array.
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r25295 | bugman | 2014-08-26 16:57:57 +0200 (Tue, 26 Aug 2014) | 6 lines
Changed the array declarations in the target_functions/c_chi2 C file and
header.
Instead of using the pointer format of *xyz, the array format of xyz[] is
now being used. These are
equivalent and the later is more obvious that this is an array.
........
r25296 | bugman | 2014-08-26 17:13:48 +0200 (Tue, 26 Aug 2014) | 5 lines
Shifted all of the parameter Python lists to C arrays into the new
param_to_c() function.
This is for the target_functions.relax_fit C module to avoid much
duplicated code.
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r25297 | bugman | 2014-08-26 17:17:33 +0200 (Tue, 26 Aug 2014) | 3 lines
Removed the comment and docstring saying that the exponential curve-fitting
gradient is unimplemented.
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r25298 | bugman | 2014-08-26 17:22:58 +0200 (Tue, 26 Aug 2014) | 3 lines
Comment fix for the target_functions/relax_fit.c file.
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r25302 | bugman | 2014-08-26 17:56:45 +0200 (Tue, 26 Aug 2014) | 3 lines
Updated the copyright notices in the C files of the target_functions
directory.
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r25303 | bugman | 2014-08-26 18:08:15 +0200 (Tue, 26 Aug 2014) | 5 lines
Implemented the C version of the chi-squared Hessian.
This is a direct translation of the Python code.
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r25304 | bugman | 2014-08-26 18:09:39 +0200 (Tue, 26 Aug 2014) | 3 lines
Changed the internal variables of the chi-squared gradient C code to match
the Python code.
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r25305 | bugman | 2014-08-26 18:25:19 +0200 (Tue, 26 Aug 2014) | 13 lines
Standardisation of the array dimensionality in the target function C code.
The new target_functions/dimensions.h header file defines MAX_PARAMS and
MAX_DATA which is then
included in the header files of all the other C files. All array
declarations now explicitly
specify the length of each dimension.
The values of MAX_PARAMS and MAX_DATA have increased from 3 and 50 to 20
and 5000. This is to allow
for models with more parameters and to allow a much larger number of input
data points to be
supported before memory corruptions happen. The data structures now take
up more memory, but as the
functions do not loop up to maximum but only the number of parameters and
points specified, this
will not make the code slower.
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r25306 | bugman | 2014-08-26 18:29:25 +0200 (Tue, 26 Aug 2014) | 3 lines
Better commenting in the C header files.
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r25307 | bugman | 2014-08-26 18:31:30 +0200 (Tue, 26 Aug 2014) | 3 lines
All of the C code chi-squared functions now have the array argument
dimensions explicitly declared.
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r25308 | bugman | 2014-08-26 18:45:52 +0200 (Tue, 26 Aug 2014) | 6 lines
The target_functions/exponential.c file no longer includes exponential.h.
This is not needed as exponential.h only contains the function definitions
of the exponential.c
file.
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r25309 | bugman | 2014-08-26 18:48:30 +0200 (Tue, 26 Aug 2014) | 6 lines
Clean up of the header and includes of the target_functions/c_chi2.c file.
The square() function macro has been shifted to the header file and the
stdio.h and math.h standard
library headers are no longer included as they are not used.
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r25310 | bugman | 2014-08-26 18:49:12 +0200 (Tue, 26 Aug 2014) | 3 lines
Comment fix in the target_functions/c_chi2.c file.
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r25311 | bugman | 2014-08-26 18:54:25 +0200 (Tue, 26 Aug 2014) | 3 lines
Comment fixes and formatting changes in all of the target_functions C files
and headers.
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r25312 | bugman | 2014-08-26 19:04:09 +0200 (Tue, 26 Aug 2014) | 6 lines
Partly implemented the front end target_functions.relax_fit.d2func() C
module Python function.
This is not fully implemented as the exponential curve double partial
derivatives are not
implemented.
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r25313 | bugman | 2014-08-26 19:13:59 +0200 (Tue, 26 Aug 2014) | 6 lines
Implemented the exponential curve second partial derivative C functions.
These are declared in the exponential.h header file and are now used by the
Python function
target_functions.relax_fit.d2func().
........
r25314 | bugman | 2014-08-26 19:18:24 +0200 (Tue, 26 Aug 2014) | 5 lines
The square() function macro is now defined for the
target_functions/exponential.c file.
This is defined in the header, and now the exponential.h is included in the
C file to access it.
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r25315 | bugman | 2014-08-26 19:20:48 +0200 (Tue, 26 Aug 2014) | 8 lines
Implemented the specific_analyses.relax_fit.optimisation.d2func_wrapper()
function.
This converts the numpy parameter array into a Python list, calls the
target_functions.relax_fit.d2func() function with this list, converts the
Hessian output list of
lists into a numpy rank-2 array, and returns it. This will allow Newton
optimisation to be used for
the relaxation curve-fitting analysis.
........
r25316 | bugman | 2014-08-26 19:22:26 +0200 (Tue, 26 Aug 2014) | 7 lines
Switched the optimisation algorithm in
test_suite/system_tests/scripts/relax_fit.py.
This script, used by the Relax_fit.test_curve_fitting_height and
Relax_fit.test_curve_fitting_volume
system tests, now uses Newton optimisation. This is to demonstrate that
the exponential curve
gradient function dfunc() and Hessian function d2func() are implemented
correctly.
........
Added:
branches/frame_order_cleanup/target_functions/dimensions.h
- copied unchanged from r25316, trunk/target_functions/dimensions.h
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py
branches/frame_order_cleanup/specific_analyses/relax_fit/optimisation.py
branches/frame_order_cleanup/target_functions/c_chi2.c
branches/frame_order_cleanup/target_functions/c_chi2.h
branches/frame_order_cleanup/target_functions/exponential.c
branches/frame_order_cleanup/target_functions/exponential.h
branches/frame_order_cleanup/target_functions/relax_fit.c
branches/frame_order_cleanup/target_functions/relax_fit.h
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/profiling/verify_error.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/relax_fit.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py?rev=25320&r1=25319&r2=25320&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_fit/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_fit/optimisation.py?rev=25320&r1=25319&r2=25320&view=diff
Modified: branches/frame_order_cleanup/target_functions/c_chi2.c
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/c_chi2.c?rev=25320&r1=25319&r2=25320&view=diff
Modified: branches/frame_order_cleanup/target_functions/c_chi2.h
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/c_chi2.h?rev=25320&r1=25319&r2=25320&view=diff
Modified: branches/frame_order_cleanup/target_functions/exponential.c
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/exponential.c?rev=25320&r1=25319&r2=25320&view=diff
Modified: branches/frame_order_cleanup/target_functions/exponential.h
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/exponential.h?rev=25320&r1=25319&r2=25320&view=diff
Modified: branches/frame_order_cleanup/target_functions/relax_fit.c
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/relax_fit.c?rev=25320&r1=25319&r2=25320&view=diff
Modified: branches/frame_order_cleanup/target_functions/relax_fit.h
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/relax_fit.h?rev=25320&r1=25319&r2=25320&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py?rev=25320&r1=25319&r2=25320&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/profiling/verify_error.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/profiling/verify_error.py?rev=25320&r1=25319&r2=25320&view=diff
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/relax_fit.py?rev=25320&r1=25319&r2=25320&view=diff
r25320 - in /branches/frame_order_cleanup: ./ specific_analyses/relax_disp/ specific_analyses/relax_fit/ target_functions/ t...