Author: bugman
Date: Wed Nov 27 08:53:09 2013
New Revision: 21659
URL: http://svn.gna.org/viewcvs/relax?rev=21659&view=rev
Log:
Merged revisions
19169-19272,19275-19280,19310-19319,19322-19325,19328-19332,19335-19348,19359-19373,19376-19388,19439,19454-19455,19458,19461,19463,19465-19473,19475-19482,19485-19487,19491-19493,19497,19501-19506,19511,19516-19517,19528,19530,19539,19546-19548,19559-19562,19565-19567,19570,19574-19576,19579-19580,19585-19589,19611,19619-19646,19657-19661,19663-19668,19676,19679,19685-19687,19690,19693-19694,19697-19700,19710-19719,19721-19722,19735,19738-19744,19747-19767,19770-19804,19807-19856,19859-19870,19873-19874,19883,19887-19894,19896-19910,19928-19933,19936-19939,19941,19943-19946,19949-19960,19963-20036,20040,20042-20043,20047-20048,20051,20054-20058,20061-20062,20068,20071-20078,20083,20086,20094,20098-20105,20108,20137-20138,20141,20166,20169-20175,20182-20183,20185-20186,20189-20191,20196,20204-20207,20210,20217-20219,20230,20238-20239,20244,20263-20264,20266,20268-20291,20293-20336,20338-20340,20342-20349,20354-20387,20389-20390,20392-20394,20402-20420,20423-20438,20449-20473,20475-20494,20500,20524,20537-20541,20586,20628-20633,20637,20641-20646,20652-20654,20673-20674,20677-20681,20686-20736,20750-20757,20761-20774,20779,20782,20784,20787,20795-20806,20813-20872,20875-20897,20900-20911,20914,20921,20924-20926,20929,20935-20943,20949,20952-20953,20956,20959-20971,20973-20999,21004-21011,21014,21017-21024,21028-21035,21055-21088,21091-21096,21101-21102,21113-21149,21152-21158,21170-21173,21175-21186,21189-21244,21247-21256,21259-21260,21263-21268,21271-21291,21294-21296,21299-21329,21335-21345,21354-21358,21362,21365-21390,21392-21406,21456-21473,21475-21491,21496-21577,21584-21612,21615-21620,21623-21628,21633-21646
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp
........
r19169 | bugman | 2013-03-27 12:12:45 +0100 (Wed, 27 Mar 2013) | 14 lines
Ported r8246 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8245:8246
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp@r18123 .
.....
r8246 | semor | 2009-01-06 22:32:20 +0100 (Tue, 06 Jan 2009) | 3 lines
Changed paths:
M /branches/relax_disp/test_suite/system_tests/__init__.py
Started to implement the framework for system tests.
.....
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r19170 | bugman | 2013-03-27 12:14:09 +0100 (Wed, 27 Mar 2013) | 19 lines
Ported r8247 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8246:8247
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp@r18123 .
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r8247 | semor | 2009-01-06 22:36:04 +0100 (Tue, 06 Jan 2009) | 8 lines
Changed paths:
A /branches/relax_disp/test_suite/system_tests/relax_disp.py (from
/branches/relax_disp/test_suite/system_tests/relax_fit.py:8240)
Copied 'test_suite/system_tests/relax_fit.py' for relaxation dispersion.
The command used was:
svn cp test_suite/system_tests/relax_fit.py
test_suite/system_tests/relax_disp.py
The code now needs to be tailored for relaxation dispersion.
.....
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r19171 | bugman | 2013-03-27 12:14:58 +0100 (Wed, 27 Mar 2013) | 14 lines
Ported r8248 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8247:8248
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp@r18123 .
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r8248 | semor | 2009-01-06 22:46:44 +0100 (Tue, 06 Jan 2009) | 3 lines
Changed paths:
M /branches/relax_disp/test_suite/system_tests/relax_disp.py
Started to implement relaxation dispersion system tests.
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r19172 | bugman | 2013-03-27 12:38:00 +0100 (Wed, 27 Mar 2013) | 18 lines
Created the user_functions.relax_disp module by copying
user_functions.relax_fit.
This is equivalent to r8321 of the old relax_disp branch which copied the
prompt.relax_fit module.
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r8321 | semor | 2009-01-07 21:18:14 +0100 (Wed, 07 Jan 2009) | 8 lines
Changed paths:
A /branches/relax_disp/prompt/relax_disp.py (from
/branches/relax_disp/prompt/relax_fit.py:8319)
Copied 'prompt/relax_fit.py' to 'prompt/relax_disp.py'.
The command used was:
svn cp prompt/relax_fit.py prompt/relax_disp.py
This file now needs to be modified to suit the needs of relaxation
dispersion.
.....
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r19173 | bugman | 2013-03-27 12:54:22 +0100 (Wed, 27 Mar 2013) | 21 lines
Manually created the relax_disp user functions.
This is equivalent to Seb's commit at r8322 for the prompt.relax_disp
module. The equivalent
changes to the user_functions.relax_disp were hand edited.
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r8322 | semor | 2009-01-07 21:53:01 +0100 (Wed, 07 Jan 2009) | 10 lines
Changed paths:
M /branches/relax_disp/prompt/relax_disp.py
Added functions to select the experiment type and mathematical model used.
These functions allow the user to select the experiment type (cpmg or
r1rho) as well as the
mathematical model to fit the data (fast or slow).
These changes follow a discussion on relaxation dispersion, and mainly
the post at:
https://mail.gna.org/public/relax-devel/2009-01/msg00020.html
(Message-id: <7f080ed10901070529s397f7f23p914c820ced4d07f@xxxxxxxxxxxxxx>)
.....
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r19174 | bugman | 2013-03-27 12:55:14 +0100 (Wed, 27 Mar 2013) | 19 lines
Ported r8323 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8322:8323
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp@r18123 .
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r8323 | semor | 2009-01-07 21:56:49 +0100 (Wed, 07 Jan 2009) | 8 lines
Changed paths:
A /branches/relax_disp/test_suite/system_tests/scripts/relax_disp.py
(from /branches/relax_disp/test_suite/system_tests/scripts/relax_fit.py:8319)
Copied the 'relax_fit.py' script to 'relax_disp.py'.
The command used was:
svn cp test_suite/system_tests/scripts/relax_fit.py
test_suite/system_tests/scripts/relax_disp.py
This file, obviously, will need to be modified to suit the needs of the
relaxation dispersion code.
.....
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r19175 | bugman | 2013-03-27 12:56:08 +0100 (Wed, 27 Mar 2013) | 17 lines
Ported r8324 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8323:8324
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp@r18123 .
.....
r8324 | semor | 2009-01-07 22:16:16 +0100 (Wed, 07 Jan 2009) | 5 lines
Changed paths:
M /branches/relax_disp/test_suite/system_tests/relax_disp.py
M /branches/relax_disp/test_suite/system_tests/scripts/relax_disp.py
Modified the script so it will test for fast-exchange curve fitting from
CPMG data.
Data and functions to treat it arestill missing.
.....
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r19176 | bugman | 2013-03-27 12:57:14 +0100 (Wed, 27 Mar 2013) | 16 lines
Ported r8325 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8324:8325
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp@r18123 .
.....
r8325 | semor | 2009-01-07 22:23:22 +0100 (Wed, 07 Jan 2009) | 3 lines
Changed paths:
M /branches/relax_disp/test_suite/system_tests/relax_disp.py
D /branches/relax_disp/test_suite/system_tests/scripts/relax_disp.py
A
/branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
(from /branches/relax_disp/test_suite/system_tests/scripts/relax_disp.py:8324)
Added a test for CPMG data in slow-exchange and changed the name of the
test for fast-exchange.
.....
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r19177 | bugman | 2013-03-27 12:59:17 +0100 (Wed, 27 Mar 2013) | 19 lines
Ported r8326 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8325:8326
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
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r8326 | semor | 2009-01-07 22:33:41 +0100 (Wed, 07 Jan 2009) | 8 lines
Changed paths:
A /branches/relax_disp/specific_fns/relax_disp.py (from
/branches/relax_disp/specific_fns/relax_fit.py:8319)
Copied the 'relax_fit.py' specific functions to 'relax_disp.py'.
The command used was:
svn cp specific_fns/relax_fit.py specific_fns/relax_disp.py
The code will now need many many many changes to suit the needs of
relaxation disperison.
.....
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r19178 | bugman | 2013-03-27 13:01:18 +0100 (Wed, 27 Mar 2013) | 16 lines
Ported r8327 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8326:8327
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
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r8327 | semor | 2009-01-07 22:53:12 +0100 (Wed, 07 Jan 2009) | 5 lines
Changed paths:
M /branches/relax_disp/specific_fns/relax_disp.py
Made a few changes towards a functional relaxation dispersion code.
This includes several modifications as well as the addition of the
exp_type() function.
.....
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r19179 | bugman | 2013-03-27 13:02:20 +0100 (Wed, 27 Mar 2013) | 16 lines
Ported r8328 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8327:8328
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
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r8328 | semor | 2009-01-08 00:16:20 +0100 (Thu, 08 Jan 2009) | 5 lines
Changed paths:
M /branches/relax_disp/specific_fns/relax_disp.py
Moved the relax_time() function to cpmg_frq() and made other small
changes.
Still much (!) work is needed for this code to be complete.
.....
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r19180 | bugman | 2013-03-27 13:03:12 +0100 (Wed, 27 Mar 2013) | 16 lines
Ported r8329 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8328:8329
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
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r8329 | semor | 2009-01-08 00:23:28 +0100 (Thu, 08 Jan 2009) | 5 lines
Changed paths:
M /branches/relax_disp/specific_fns/relax_disp.py
Renamed 'cdp.frq' to 'cdp.cpmg_frqs' so it is not confusing with the
spectrometer frequency.
Indeed, 'cdp.cpmg_frqs' points to the CPMG pulse train frequency
(nu_cpmg).
.....
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r19181 | bugman | 2013-03-27 13:03:48 +0100 (Wed, 27 Mar 2013) | 14 lines
Ported r8330 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8329:8330
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
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r8330 | semor | 2009-01-08 00:38:30 +0100 (Thu, 08 Jan 2009) | 3 lines
Changed paths:
M /branches/relax_disp/specific_fns/relax_disp.py
Changed all instances of 'relax_times' to 'cpmg_frqs' and made other
small changes.
.....
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r19182 | bugman | 2013-03-27 13:04:25 +0100 (Wed, 27 Mar 2013) | 14 lines
Ported r8331 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8330:8331
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
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r8331 | semor | 2009-01-08 00:48:34 +0100 (Thu, 08 Jan 2009) | 3 lines
Changed paths:
M /branches/relax_disp/specific_fns/relax_disp.py
Changed 'relax_time' instances to 'cpmg_frq'.
.....
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r19183 | bugman | 2013-03-27 13:05:12 +0100 (Wed, 27 Mar 2013) | 20 lines
Ported r8335 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8334:8335
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
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r8335 | semor | 2009-01-08 16:19:09 +0100 (Thu, 08 Jan 2009) | 9 lines
Changed paths:
M /branches/relax_disp/specific_fns/relax_disp.py
Changed the index name and description.
This is as proposed by Ed in a post at:
https://mail.gna.org/public/relax-devel/2009-01/msg00029.html
(Message-id:
<7f080ed10901080144u541e6ed5ve52d2d233f8d7cf7@xxxxxxxxxxxxxx>)
The description might change later to be more appropriate when the code
is more mature...
.....
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r19184 | bugman | 2013-03-27 13:06:34 +0100 (Wed, 27 Mar 2013) | 17 lines
Ported r8337 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8336:8337
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp@r18123 .
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r8337 | semor | 2009-01-08 16:51:44 +0100 (Thu, 08 Jan 2009) | 6 lines
Changed paths:
M
/branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
Included the setting of the spectrometer frequency and uncommented a few
lines of code.
Of course, this won't work until the sample data has been introduced and
the right namesfor the
different files be input in the system test script...
.....
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r19185 | bugman | 2013-03-27 13:41:12 +0100 (Wed, 27 Mar 2013) | 26 lines
Ported r8338 from the old relax_disp branch into the new branch (partly
manually).
The changes not made by hand come from the command:
svn merge -r8337:8338
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
All changes not in the specific_analyses package were hand edited.
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r8338 | semor | 2009-01-08 17:17:32 +0100 (Thu, 08 Jan 2009) | 7 lines
Changed paths:
M /branches/relax_disp/generic_fns/pipes.py
M /branches/relax_disp/prompt/__init__.py
M /branches/relax_disp/prompt/interpreter.py
M /branches/relax_disp/prompt/pipe.py
M /branches/relax_disp/specific_fns/__init__.py
M /branches/relax_disp/specific_fns/relax_disp.py
M /branches/relax_disp/specific_fns/setup.py
Fixed many formatting errors and made the 'relax_disp' code accessible
(pipes, interpreter, etc).
These changes also include a coming back to using the C code
'math_fns/relax_fit.py' since there is
still no such code associated to relaxation dispersion. This will allow
workingin the code without
relax crashing and complaining about the lack of a C module name
'relax_disp.py'.
.....
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r19186 | bugman | 2013-03-27 13:47:48 +0100 (Wed, 27 Mar 2013) | 24 lines
Ported r8339 from the old relax_disp branch into the new branch.
The commands used were:
svn merge -r8338:8339
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp@r18123 .
svn merge -r8338:8339
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
The code for the user_functions package was manually ported over.
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r8339 | semor | 2009-01-08 17:48:13 +0100 (Thu, 08 Jan 2009) | 8 lines
Changed paths:
M /branches/relax_disp/prompt/relax_disp.py
M /branches/relax_disp/specific_fns/relax_disp.py
M
/branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
Added the user function cpmg_delayT() which allows setting the CPMG
constant time delay T used for
the analysed dataset.
This follows a post at:
https://mail.gna.org/public/relax-devel/2009-01/msg00027.html
(Message-id: <496583C7.6050607@xxxxxxxxx>)
.....
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r19187 | bugman | 2013-03-27 13:49:27 +0100 (Wed, 27 Mar 2013) | 15 lines
Ported r8340 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8339:8340
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp@r18123 .
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r8340 | semor | 2009-01-08 18:07:15 +0100 (Thu, 08 Jan 2009) | 3 lines
Changed paths:
M /branches/relax_disp/prompt/relax_disp.py
M
/branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
Fixed a few typos.
.....
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r19188 | bugman | 2013-03-27 13:51:22 +0100 (Wed, 27 Mar 2013) | 14 lines
Ported r8342 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8341:8342
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
.....
r8342 | semor | 2009-01-08 19:44:36 +0100 (Thu, 08 Jan 2009) | 3 lines
Changed paths:
M /branches/relax_disp/specific_fns/relax_disp.py
Made a few changes so the cpmg_delayT() function now works.
.....
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r19189 | bugman | 2013-03-27 13:58:48 +0100 (Wed, 27 Mar 2013) | 18 lines
Ported r8343 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8342:8343
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
The user function code was ported manually from the prompt package changes
to the user_functions
package.
.....
r8343 | semor | 2009-01-08 20:13:00 +0100 (Thu, 08 Jan 2009) | 3 lines
Changed paths:
M /branches/relax_disp/prompt/relax_disp.py
M /branches/relax_disp/specific_fns/relax_disp.py
Added the user function cpmg_frq() and added examples to the user
function cpmg_delayT().
.....
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r19190 | bugman | 2013-03-27 14:03:10 +0100 (Wed, 27 Mar 2013) | 20 lines
Ported r from the old relax_disp branch into the new branch.
The commands used were:
svn merge -r8344:8345
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
svn merge -r8344:8345
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/test_suite/@r18123
test_suite
The prompt package changes were manually ported to the user_functions
package.
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r8345 | semor | 2009-01-08 20:30:41 +0100 (Thu, 08 Jan 2009) | 4 lines
Changed paths:
M /branches/relax_disp/prompt/relax_disp.py
M /branches/relax_disp/specific_fns/relax_disp.py
M
/branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
Corrected remaining frq instances to cpmg_frq when appropriate to avoid
confusion and corrected a
few related things in the system test script.
.....
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r19191 | bugman | 2013-03-27 14:06:08 +0100 (Wed, 27 Mar 2013) | 11 lines
Manually ported the prompt package changes of r8347 to the user_functions
package.
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r8347 | semor | 2009-01-08 21:18:09 +0100 (Thu, 08 Jan 2009) | 3 lines
Changed paths:
M /branches/relax_disp/prompt/relax_disp.py
Made the cpmg_frq() function accept only None for the reference spectrum
and corrected a typo.
.....
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r19192 | bugman | 2013-03-27 14:07:46 +0100 (Wed, 27 Mar 2013) | 14 lines
Ported r8351 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8350:8351
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
.....
r8351 | semor | 2009-01-09 21:09:00 +0100 (Fri, 09 Jan 2009) | 3 lines
Changed paths:
M /branches/relax_disp/specific_fns/relax_disp.py
Added the parameters for the slow- and fast-exchange regime.
.....
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r19193 | bugman | 2013-03-27 14:08:20 +0100 (Wed, 27 Mar 2013) | 14 lines
Ported r8352 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8351:8352
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
.....
r8352 | semor | 2009-01-09 21:27:59 +0100 (Fri, 09 Jan 2009) | 3 lines
Changed paths:
M /branches/relax_disp/specific_fns/relax_disp.py
Added the parameters for the slow- and fast-exchange regime in the
function data_names().
.....
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r19194 | bugman | 2013-03-27 14:08:59 +0100 (Wed, 27 Mar 2013) | 14 lines
Ported r8353 from the old relax_disp branch into the new branch.
The command used was:
[... 14311 lines stripped ...]
r21659 - in /trunk: ./ auto_analyses/ docs/latex/ graphics/analyses/ graphics/analyses/dispersion/ graphics/misc/ graphics/r...