Author: bugman
Date: Fri Oct 28 12:34:05 2016
New Revision: 28267
URL: http://svn.gna.org/viewcvs/relax?rev=28267&view=rev
Log:
Backported the relax 4.0.3 CHANGES file changes to trunk.
The command used was:
svn merge -r28265:28266 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/4.0.3 .
Modified:
trunk/docs/CHANGES
Modified: trunk/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/CHANGES?rev=28267&r1=28266&r2=28267&view=diff
==============================================================================
--- trunk/docs/CHANGES (original)
+++ trunk/docs/CHANGES Fri Oct 28 12:34:05 2016
@@ -1,10 +1,64 @@
+Version 4.0.3
+(28 October 2016, from /trunk)
+http://svn.gna.org/svn/relax/tags/4.0.3
+
+ Features:
+ * Per-atom RMSD calculation by the structure.rmsd user function.
+ * Much faster superimposition of structures.
+ * More relax deployment scripts for Google Cloud for different
GNU/Linux distributions.
+ * Addition of OpenMPI testing scripts.
+ * Improved relax information printout.
+
+
+ Changes:
+ * Addition of the atomic boolean argument to the structure.rmsd user
function front end. This will be used to enable the calculation of per-atom
RMSDs.
+ * Created the Structure.test_rmsd_spins system test for checking the
per-atom RMSD calculation. This is for the new option in the structure.rmsd
user function.
+ * Implemented the per-atom RMSD calculation for the structure.rmsd
user function.
+ * Fixes for the Relax_fit.test_inversion_recovery system test. The
wrong equation was used in the calc.py Python script used to calculate the
peak intensities in the
test_suite/shared_data/curve_fitting/inversion_recovery/*.list files. The
script and Sparky files have been updated. And the I0 value in the script
and system test has been changed from 30 to -30, so that the curves start as
negative.
+ * Huge speed up for the superimposition of a large number of
structures. The internal structural object validate_models() method was
being called once for each structure via the selection() method prior
performing the translations, and once prior to performing the rotations, for
creating the atomic selection object. This resulted in the _translate()
internal structural object method, which converts all input data to formatted
strings, being called hundreds of millions of times. Therefore selection()
method no longer calls validate_models(). This may speed up quite a number
of internal structure object methods when large numbers of structures are
present.
+ * Copying deployment script of Ubuntu to a Fedora version. This is
a response to bug #25084 (https://gna.org/bugs/?25084).
+ * Moving fedora to redhat. Google Cloud does not offer fedora
images.
+ * Adding deploy script for RHEL 6.
+ * Added initial script for testing OpenMPI.
+ * Making a redhat 6 deploy script, which will upgrade Python from
2.6 to 2.7 The normal installation through yum will have Python 2.6 and only
numpy 2.4. This is not good.
+ * Moved deploy scripts. There would probably have to be a deploy
script for each system.
+ * Renamed the Ubuntu deploy script.
+ * Adding scripts to test OpenMPI installation and deploy in redhat.
+ * Change to pip install command, to source Python first.
+ * Adding installation of matplotlib to Redhat 6, Python 2.7.
+ * More changing to deploy scripts.
+ * Small change to deploy script to build wxPython.
+ * More changing to deployment scripts.
+ * Moving test script of OpenMPI to bash version.
+ * Made a copy of OpenMPI test script for tcsh shell.
+ * Again small changes to deployment scripts.
+ * Changed more to OpenMPI script.
+ * Altering test OpenMPI script to an alias function.
+ * Change to bash OpenMPI test script.
+ * Last changes to testing of OpenMPI.
+ * Small change to test OpenMPI script for bash
+ * Back to function in bash script for OpenMPI.
+ * Made a deployment script for CentOS 6.
+ * Scons on CentOS finds python2.6 instead of python2.7
+ * Try to make the script for tcsh and OpenMPI working on all
versions of tcsh.
+ * Added the MPI version information to the mpi4py information
printout.
+ * Windows scons C module compilation now defaults to 32-bit. This
is because the default Python downloads are 32-bit. And many libraries (e.g.
numpy and scipy) are only pre-compiled as 32-bit. Hence a 64-bit relax build
on Windows will require a lot of custom compilation that most users will
never do.
+ * Added support in the information printout for Windows versions of
the 'file' program. This enables the C modules to be identified as 32 or
64-bit, if the 'file' program is installed.
+
+
+ Bugfixes:
+ * Fix for bug #24723 (https://gna.org/bugs/?24723). This is the bug
that the mean RMSD from the structure.rmsd user function is incorrectly
calculated - it should be a quadratic mean. The quadratic mean and quadratic
standard deviation are now correctly calculated, and the structure.test_rmsd,
structure.test_rmsd_molecules, and structure.test_rmsd_ubi system tests have
been updated for the fix.
+ * Bug fix for the inversion recovery equations (sr #3345). The
inversion recovery experiment was incorrectly implemented as I(t) = Iinf - I0
* exp(-R1 * t) whereas it should be I(t) = Iinf - (Iinf - I0) * exp(-R1 * t).
+
+
+
Version 4.0.2
(13 May 2016, from /trunk)
http://svn.gna.org/svn/relax/tags/4.0.2
Features:
* Addition of the new user functions system.cd and system.pwd to
allow the working directory to be changed and displayed.
- * Addition of the structure.delete_ss user function to remove the
helix and sheet information from the internal structural object.
+ * Addition of the structure.delete_ss user function to remove the
helix and sheet information from the internal structural object.
Changes:
r28267 - /trunk/docs/CHANGES