2011-10-04 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * src/virtual_sites_com.h: More warnings fixed.

 * src/particle_data.c: Some more fix.

 * src/communication.c: Alternative fix for warning.

 * src/communication.c, src/mpifake/mpi.h, src/p3m-magnetostatics.c: Fixed
 wsome warnings.

2011-10-04 Stefan Kesselheim <stefan@kesselheim-online.de>

 * src/particle_data.c: Bugfix 33489 ( setting dip and quat simultanously)
 part dip and part quat can not be set in the same command also: part dip and
 part dipm can not be set in the same command  Both cases could lead to
 ambigous results.

 * testsuite/lb.tcl: changed the necessary precision in the lb testcase

 * testsuite/lb.tcl: enables the particle temperature check in lb testcase

2011-09-27 Olaf Lenz <olaf@lenz.name>

 * testsuite/comforce.tcl, testsuite/dh.tcl, testsuite/layered.tcl,
 testsuite/nsquare.tcl: ADRESS without MPI.

2011-09-27 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * src/dihedral.h, testsuite/configs/myconfig-adress.h,
 testsuite/constraints.tcl, testsuite/el2d.tcl, testsuite/el2d_die.tcl,
 testsuite/el2d_nonneutral.tcl, testsuite/fene.tcl, testsuite/harm.tcl,
 testsuite/kinetic.tcl, testsuite/lj-cos.tcl, testsuite/lj-generic.tcl,
 testsuite/lj.tcl, testsuite/maggs.tcl, testsuite/mmm1d.tcl,
 testsuite/p3m.tcl, testsuite/tabulated.tcl: testsuite now also runs with
 ADRESS.

 * NEWS, src/virtual_sites_com.c, src/virtual_sites_com.h,
 testsuite/configs/myconfig-restcompile2.h: Fixed features ADRESS and
 VIRTUAL_SITES_COM that were broken since a while.

2011-09-23 Peter Košovan <kosovan@icp.uni-stuttgart.de>

 * scripts/vtf.tcl: Bugfix in VTF generation.

2011-09-19 Stefan Kesselheim <kessel@icp.uni-stuttgart.de>

 * src/lb-boundaries.c, src/lb-boundaries.h, src/lb.c: fixed bug in
 lb-boundaries  lb boundaries at the boundary of the local box now behave
 correctly.

2011-09-07 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * NEWS: Updated NEWS.

2011-09-06 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * src/config.h: Corrected mathematical constants definitions for non-gcc
 compilers

2011-08-24 Peter Košovan <kosovan@icp.uni-stuttgart.de>

 * doc/ug/mbtools.tex: Removed reference to Espresso_bin from the mbtools
 section of the user guide

2011-08-17 Peter Košovan <kosovan@icp.uni-stuttgart.de>

 * doc/ug/aux.tex: Fixed documentation of LinRegression command in the User
 Guide

2011-08-15 Peter Košovan <kosovan@icp.uni-stuttgart.de>

 * doc/ug/analysis.tex, doc/ug/inter.tex, doc/ug/setup.tex: Two fixes to user
 guide: 1. what happens when temperature is set to zero; 2. analyze set chains
 (see also bug bug #33980)

2011-07-28 Olaf Lenz <olaf@lenz.name>

 * src/communication.c: Completed patch

 * src/communication.c: Allowed DIPOLES without ROTATION.

2011-07-28 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/p3m_wall.tcl, testsuite/p3m_wall_system.data: Fixed accuracy of
 p3m_wall test.

 * testsuite/p3m_wall.tcl: Fixed p3m_wall.tcl: now it really computes the rms
 error.  Conflicts:  testsuite/p3m_wall.tcl

2011-06-16 Dominic <dominic@icp.uni-stuttgart.de>

 * src/communication.c: fix fixed :p

 * src/communication.c: maybe final bugfix for lb boundaries

2011-06-15 Dominic <dominic@icp.uni-stuttgart.de>

 * src/communication.c: bugfix for lg_gpu boundaries

2011-06-10 Dominic <dominic@icp.uni-stuttgart.de>

 * src/communication.c, src/communication.h, src/initialize.c,
 src/lb_boundaries_gpu.c, src/lbgpu.cu, src/lbgpu.h, src/lbgpu_cfile.c: bugfix
 boundary conditions and lbfluid cmd

2011-06-09 Dominic <dominic@icp.uni-stuttgart.de>

 * src/initialize.c: bugfix in initialize.c for lbgpu params change

2011-06-08 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lb.c, src/lb_boundaries_gpu.c, src/lbgpu.cu, src/lbgpu_cfile.c:
 bugfixes, extern force strength ...

2011-06-06 Dominic <dominic@icp.uni-stuttgart.de>

 * src/initialize.c, src/lbgpu.cu, src/lbgpu.h, src/lbgpu_cfile.c,
 src/thermostat.c: parameterchange on the fly added

2011-05-06 Dominic <dominic@icp.uni-stuttgart.de>

 * src/cuda_init.cu: cuda cmd show number of available cuda devices added

2011-05-05 Dominic <dominic@icp.uni-stuttgart.de>

 * configure.ac: configure.ac nvcc flag

 * configure.ac, src/initialize.c, src/lbgpu.cu: small fix for lbnode cmd

2011-06-02 Peter Košovan <kosovan@icp.uni-stuttgart.de>

 * scripts/statistics.tcl: Fixed warnings about deprecated tcl functions in
 scripts/statistics.tcl which were printing a misleading warning with a wrong
 function name

2011-05-31 Peter Košovan <kosovan@icp.uni-stuttgart.de>

 * testsuite/analysis.tcl, testsuite/intpbc.tcl, testsuite/intppbc.tcl,
 testsuite/layered.tcl, testsuite/nsquare.tcl: And finally fixed also
 testcases which were relying on rotational contribution to ideal gas pressure

 * src/pressure.c: One more line where rotational virials had to be discarded.

2011-05-25 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * configure.ac: Bumped version number.

 * NEWS, src/tab.h: Updated NEWS and copyright notice.

2011-05-25 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/ug/Makefile.am: added missing figure files to UGs Makefile.

2011-05-24 Marcello Sega <sega@icp.uni-stuttgart.de>

 * src/fene.h, src/harmonic.h: fixed undefined forces in harmonic and fene
 bonds

2011-05-25 kosovan <kosovan@icp.uni-stuttgart.de>

 * doc/ug/analysis.tex, doc/ug/bibliography.bib: Small fix to documentation of
 pressure tensor.

2011-05-24 kosovan <kosovan@icp.uni-stuttgart.de>

 * doc/ug/analysis.tex, src/pressure.h: Added rotational inertia to kinetic
 virials. Updated documentation on usability of pressure and stress tensor
 analysis routines.

2011-05-24 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * NEWS: Updated NEWS.

2011-05-23 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * src/statistics.c: Fixed analyze rdf parser

2011-05-19 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * src/p3m.c: removed wrong checks for alpha>1 from tuning

2011-05-18 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * src/communication.c, src/config.h, src/elc.c, src/elc.h, src/energy.c,
 src/energy.h, src/fft.c, src/fft.h, src/forces.c, src/forces.h, src/iccp3m.c,
 src/iccp3m.h, src/initialize.c, src/interaction_data.c,
 src/mdlc_correction.c, src/p3m-common.c, src/p3m-common.h,
 src/p3m-magnetostatics.c, src/p3m-magnetostatics.h, src/p3m.c, src/p3m.h,
 src/pressure.c, src/pressure.h: Fixed problem with feature MAGNETOSTATICS
 without ELECTROSTATICS.

2011-05-17 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * src/mmm2d.c: Fixed a bug in MMM2D which caused a segfault when particle
 coordinates were NaNs.

2011-05-10 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * configure.ac: Reintroduced CJ's CFLAGS handling, with correct quoting.

2011-05-10 Stefan Kesselheim <stefan@kesselheim-online.de>

 * src/lb.c: corrected an error in the initialization of the lb fluid

2011-05-09 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * NEWS: Updated NEWS.

 * configure.ac: Removed bashism.

2011-05-06 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * src/fft.c, src/p3m.c: fixed FFT to use fftw_malloc for alignment

2011-05-03 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/configs/myconfig-tunableslip.h, testsuite/tunable_slip.tcl:
 Testcase tunable_slip.tcl should not use VIRTUAL_SITES_RELATIVE.

2011-04-19 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * src/statistics_fluid.c, src/thermostat.h: Fixed two warnings

2011-05-02 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * src/Makefile.am: [FIX] added DEFAULT_INCLUDES to NVCC flags

2011-04-28 Florian Weik <fweik@icq.uni-stuttgart.de>

 * src/p3m.c: p3m-charges: Reenabled tcl-output for tuning.

2011-05-02 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * src/Makefile.am: [FIX] added DEFAULT_INCLUDES to NVCC flags

2011-04-28 Florian Weik <fweik@icq.uni-stuttgart.de>

 * src/p3m.c: p3m-charges: Reenabled tcl-output for tuning.

2011-04-20 Christoph Junghans <junghans@mpip-mainz.mpg.de>

 * configure.ac: configure: never overwrite users CFLAGS

 * configure.ac: configure: never overwrite users CFLAGS

2011-04-19 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * NEWS, doc/ug/ug.tex: And back into developer mode again.
2011-04-19 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/comforce.tcl, testsuite/mdlc.tcl: Fixed mdlc test for 3 procs.

 * NEWS, doc/ug/analysis.tex, doc/ug/io.tex, doc/ug/plotting.tex,
 doc/ug/ug.tex, scripts/auxiliary.tcl, scripts/init.tcl,
 scripts/statistics.tcl, testsuite/analysis.tcl: Deprecated various functions.

 * doc/ug/io.tex: Updated blockfile docs.

2011-04-19 Stefan Kesselheim <kessel@icp.uni-stuttgart.de>

 * src/lb.c: two small fixes to the lb module

2011-04-18 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * src/initialize.c, src/lb.c, src/lb.h: Fixed bug for LB that crashes when
 system is changed.

 * myconfig-sample.h.in, src/dpd.h, src/forces.c, src/interaction_data.c,
 testsuite/configs/myconfig-LB.h, testsuite/configs/myconfig-LBGPU.h,
 testsuite/configs/myconfig-maxset.h, testsuite/configs/myconfig-nofftw.h,
 testsuite/configs/myconfig-restcompile1.h,
 testsuite/configs/myconfig-restcompile2.h,
 testsuite/configs/myconfig-tunableslip.h, testsuite/constraints.tcl,
 testsuite/mass.tcl, testsuite/tunable_slip.tcl: Added config files for
 testcase tunable_slip.tcl and to compile all features that are not
 compatible.

 * src/lbgpu.h, src/p3m-magnetostatics.c, src/p3m-magnetostatics.h, src/p3m.c,
 src/p3m.h: Removed all doxygen warnings again.

2011-04-18 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * src/config.c, src/config.h, src/p3m-magnetostatics.c: Fix compilation
 without FFTW.

2011-04-17 Stefan Kesselheim <kessel@icp.uni-stuttgart.de>

 * src/constraint.h, testsuite/Makefile.am,
 testsuite/constraints_reflecting.tcl: fixed the reflecting constraints that
 were broken  and added a simple testcase for it

 * src/lb.c, src/statistics_fluid.c: small bugfix in the LB module

2011-04-15 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/Makefile.am, testsuite/p3m_wall_system.data,
 testsuite/p3m_wall_system.tcl: Repaired p3m_wall.tcl.

 * testsuite/Makefile.am, testsuite/p3m_noncubic.tcl,
 testsuite/p3m_noncubic_system.data: Removed test case p3m_noncubic.tcl, which
 was identical to p3m.tcl.

 * testsuite/Makefile.am, testsuite/p3m-wall.dat, testsuite/p3m-wall.tcl,
 testsuite/p3m.tcl, testsuite/p3m_noncubic.tcl,
 testsuite/p3m_noncubic_system.data, testsuite/p3m_simple_noncubic.tcl,
 testsuite/p3m_system_noncubic.data, testsuite/p3m_wall.tcl,
 testsuite/p3m_wall_system.tcl: Fixed P3M Testcases.

 * testsuite/Makefile.am: Added missing \ that left a number of tests out.

 * testsuite/Makefile.am: Put testcases in alphabetic roder again.

 * samples/lj_benchmark.tcl: Fixed lj_benchmark.tcl script.

2011-04-14 Stefan Kesselheim <stefan@kesselheim-online.de>

 * src/p3m-charges.c, testsuite/Makefile.am, testsuite/p3m-wall.dat,
 testsuite/p3m-wall.tcl, testsuite/p3m_simple_noncubic.tcl: Added two new
 testcases for p3m (fweik did the work!)  also removed alpha>1 warning.

2011-04-14 Florian Weik <fweik@icq.uni-stuttgart.de>

 * src/p3m-charges.c: p3m-charges: fixed p3m.

2011-04-13 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * src/maggs.c: Removed debug lines for Maggs algorithm.

2011-04-13 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/Makefile.am, testsuite/tests_common.tcl: Fixed distcheck.

2011-04-13 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * src/adresso.h, src/lbgpu.cu, src/lbgpu.h, src/lbgpu_cfile.c: Fixed doxygen
 warnings from lbgpu

 * testsuite/mdlc.tcl: Testcase mdlc required P3M and therefore FFTW. Should
 work now.

 * doc/ug/features.tex, doc/ug/inter.tex, src/communication.c,
 src/communication.h, src/config.c, src/energy.c, src/forces.c, src/forces.h,
 src/interaction_data.c, src/magnetic_non_p3m_methods.c,
 src/magnetic_non_p3m_methods.h, src/mdlc_correction.c, src/mdlc_correction.h,
 src/pressure.c, src/pressure.h, testsuite/configs/myconfig-maxset.h,
 testsuite/el2d_nonneutral.tcl, testsuite/mdlc.tcl, testsuite/nve_pe.tcl,
 testsuite/p3m_magnetostatics.tcl, testsuite/p3m_magnetostatics2.tcl: With
 Axel: Removed the features MDLC and DAWAANR, since they are obsolete. Made
 compilation without fftw possible without error.

 * testsuite/configs/myconfig-nofftw.h: Added new myconfig for build without
 fftw.

2011-04-12 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * configure.ac: [BUG] fixed without-fftw configure-switch

2011-04-11 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * src/lb.c, src/lb_boundaries_gpu.c, src/lbgpu.cu, src/lbgpu_cfile.c,
 src/maggs.c, src/metadynamics.h: Some doxygen bugs. Added another sanity
 check to maggs.

2011-04-11 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * src/Makefile.am, src/communication.c, src/energy.h, src/fft.c,
 src/forces.h, src/iccp3m.h, src/interaction_data.c, src/mdlc_correction.c,
 src/mdlc_correction.h, src/p3m-common.c, src/p3m-common.h, src/p3m-dipoles.c,
 src/p3m-dipoles.h, src/p3m-magnetostatics.c, src/p3m-magnetostatics.h,
 src/p3m.c, src/p3m.h, testsuite/configs/myconfig-maxset.h: Got magnetostatics
 running again, renamed p3m-dipoles to p3m-magnetostatics.

 * testsuite/configs/myconfig-maxset.h: Added MDLC to myconfig-maxset.h.

 * src/Makefile.am, src/iccp3m.c, src/p3m.c, src/p3m.h: Deinlined two
 functions from p3m.h, made electrostatics P3M compile.

 * src/p3m-charges.c, src/p3m-charges.h, src/p3m-dipoles.c, src/p3m-dipoles.h,
 src/p3m.c, src/p3m.h: Moved functions for charge P3M into p3m.[hc], removed
 p3m-charges.[ch]. Doesn't compile in this state

 * src/p3m-assignment.c, src/p3m-common.c, src/p3m-common.h, src/p3m.c,
 src/p3m.h: Moved common P3M functions from p3m.[hc]/p3m-assignment.c into
 p3m-common.[hc] This state does not compile!

 * configure.ac: small fix.

2011-02-23 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * src/p3m-charges.h, src/p3m-dipoles.h, src/p3m.c, src/p3m.h: Updated
 copyright headers.

 * src/p3m-charges.c: Removed completely obsolete test.

2011-04-11 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.h: bugfix in lbgpu.h for electrohydrodyn

2011-04-08 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * src/adresso.c, src/adresso.h, src/communication.c, src/communication.h,
 src/forces.c, src/initialize.c, src/interaction_data.c,
 src/interaction_data.h: Removed first bunch of Doxygen warnings.

 * doc/dg/Doxyfile, doc/dg/Makefile.am, src/myconfig-sample.h,
 src/p3m-charges.h: t DG up.

2011-04-08 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * src/maggs.c: Fixed warnings in unused helper functions.

 * src/maggs.c: Added check for fixed particles and periodicity.

2011-04-07 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * AUTHORS, doc/ug/todonotes.sty: Added GPL-version of todonotes.sty (thanks
 to Henrik Skov Midtiby!)

 * doc/latexit.sh.in: Small fix.

 * doc/latexit.sh.in, doc/tutorials/tut2/Makefile.am, doc/ug/Makefile.am: MOre
 fixes to latex.

 * doc/latexit.sh.in, doc/ug/Makefile.am: Made compilation of the ug
 error-safe.

2011-04-07 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * src/maggs.c: More doxygen formatting (headings).

 * src/maggs.c, src/maggs.h: Commented parameters in maggs.c functions for
 doxygen.

 * .gitignore, src/maggs.c, src/maggs.h: Added some functions for self
 influence. Extended maggs structure.

2011-04-06 Mingyang Hu <mingyang@cmu.edu>

 * doc/ug/mbtools.tex: mbtools: update user's guide about two handy math tools
  1. distance_min pos1 pos2 calculate the minimum image distance between
 position 1 and 2 2. min_vec pos1 pos2 calculate the minimum image vector

 * packages/mbtools/analysis/cylinder_radius.tcl,
 packages/mbtools/utils/math.tcl: mbtools: fix a bug in analyze
 cylinder_radius

2011-04-05 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * src/maggs.c: Added some sanity checks to avoid occuring segfault.

 * src/maggs.c: formatted for emacs, switching from XCode.

2011-04-05 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * .gitignore, configure.ac: Updated .gitignore.

2011-04-04 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * baseversion.txt, doc/ug/Makefile.am: Added forgoten files.

2011-04-04 Stefan Kesselheim <stefan@kesselheim-online.de>

 * src/lb.c: small fix to increase the stability of LB.

 * src/lb.c: small fix to increase the stability of LB.

2011-04-04 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.cu, testsuite/lb_gpu.tcl: fix in testcase

2011-04-02 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * configure.ac, src/cuda_init.cu, src/cuda_init.h: [BUG] nvcc configure now
 also works with older toolkits doxified cuda_init

2011-04-01 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.cu, src/lbgpu_cfile.c, testsuite/lb.tcl, testsuite/lb_gpu.tcl:
 doxygen stuff tried to add and testcase modified

2011-04-01 Stefan Kesselheim <stefan@kesselheim-online.de>

 * src/debug.h: added a NANCHECK macro to check for nans in the code

2011-04-01 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * src/ewald.c: Fixed realloc on uninitialized memory in Ewald

2011-04-01 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * config/ax_mpi_only.m4: Repair autoconf w3arning.

2011-04-01 Dominic <dominic@icp.uni-stuttgart.de>

 * testsuite/lb_gpu.tcl: bug in lb_gpu.tcl fixed

2011-04-01 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/lb_gpu.tcl: Fixed lb gpu testcase.

 * configure.ac, doc/dg/Doxyfile, doc/dg/Makefile.am: Some more improvement to
 DG.

2011-04-01 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * src/maggs.c: Added some additional constants

 * src/modes.h: removed the last doxygen warning

2011-04-01 Dominic <dominic@icp.uni-stuttgart.de>

 * myconfig-sample.h, src/lbgpu.cu, src/lbgpu_cfile.c: tidy up for the release
 version

2011-04-01 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * doc/dg/Doxyfile, myconfig-sample.h, myconfig-sample.h.in, src/config.h:
 Improved doxygen docs. myconfig-samples.h.in now contains everything
 uncommented.

2011-04-01 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * src/global.c: Fixed the fix for the warning

2011-04-01 Stefan Kesselheim <stefan@kesselheim-online.de>

 * src/lb-boundaries.c, src/lb-boundaries.h: added the lbboundary pore

 * src/constraint.h: micro change in pore constraint >= istead of > everywhere

 * src/global.c: fixed type-punned warings in global.c  Indeed Olaf told me
 how to do it :-)

2011-04-01 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/ug/contributing.tex, doc/ug/introduction.tex: Minor grammar
 corrections. Added something to "get involved".

2011-03-31 kosovan <kosovan@icp.uni-stuttgart.de>

 * doc/ug/contributing.tex, doc/ug/introduction.tex, doc/ug/io.tex: Some more
 minor changes to ug

2011-03-31 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * src/angle.h, src/communication.h, src/halo.c, src/halo.h, src/lattice.h,
 src/lb-boundaries.c, src/lb.c, src/lb.h, src/mmm2d.h, src/modes.h,
 src/overlap.h, src/p3m-charges.c, src/polymer.h, src/statistics.h,
 src/subt_lj.h, src/utils.h: Commented all parameters for partly commented
 functions. Removed some discrepancies.

2011-03-31 kosovan <kosovan@icp.uni-stuttgart.de>

 * doc/ug/introduction.tex: Changes to introduction

2011-03-31 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * myconfig-sample.h, src/angledist.h, src/debye_hueckel.h, src/p3m-charges.h,
 src/p3m-dipoles.c, src/reaction_field.h, src/subt_lj.h: Corrected the newly
 occuring errors from doxygen.

 * doc/dg/Doxyfile, src/maggs.h: Added all includes from myconfig-maxset.h to
 PREDEFINED tags of doxygen. Lots of new documentation now!

2011-03-31 Stefan Kesselheim <stefan@kesselheim-online.de>

 * src/constraint.c, src/constraint.h: corrected a bug in the pore constraint

2011-03-31 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * myconfig-sample.h, src/adresso.h, src/blockfile.c, src/blockfile.h,
 src/blockfile_tcl.h, src/cells.h, src/communication.c, src/communication.h,
 src/config.c, src/config.h, src/domain_decomposition.h, src/elc.h,
 src/errorhandling.h, src/fene.h, src/forces.h, src/global.h, src/grid.h,
 src/harmonic.h, src/iccp3m.h, src/integrate.h, src/interaction_data.h,
 src/lb.c, src/lb.h, src/lbgpu_cfile.c, src/mmm1d.h, src/mmm2d.h,
 src/molforces.c, src/molforces.h, src/mpifake/mpi.c, src/myconfig-sample.h,
 src/nemd.h, src/p3m-charges.h, src/p3m-dipoles.c, src/particle_data.h,
 src/pressure.c, src/random.c, src/random.h, src/statistics.c,
 src/statistics.h, src/statistics_chain.c, src/thermostat.h, src/uwerr.h,
 src/verlet.h: Repaired all broken doxygen references.

2011-03-30 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/dg/pages/new_files.doc, doc/dg/pages/progguide.doc: Corrected all
 references in the Related Pages section of the Developer's Guide.

2011-03-30 Dominic <dominic@icp.uni-stuttgart.de>

 * testsuite/lb_gpu.tcl: and again the testcase

 * testsuite/lb_gpu.tcl: changes in testcase script for lbgpu

2011-03-30 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * src/lj.h, src/ljcos.h, testsuite/Makefile.am, testsuite/command_syntax.tcl,
 testsuite/lj.tcl, testsuite/tests_common.tcl: Fixed bug that prevented
 blockfiles with several interactions from loading.

2011-03-30 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/ug/inter.tex: Minor corrections in P3M tuning description warning.

2011-03-30 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.cu, src/lbgpu_cfile.c, testsuite/lb_gpu.tcl: lbgpu testcase
 updated and buxfixes in lbgpu.cu + random seed for latticenodes couple to
 irandom

2011-03-30 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/ug/io.tex: Warning about deprecated checkpoints in user's guide.

 * doc/ug/bibliography.bib, doc/ug/setup.tex: Added warning comment to NPT
 thermostat.

 * doc/ug/inter.tex: added comment on P3M tuning in symmetric systems

2011-03-30 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * doc/ug/introduction.tex: Some improvements on the intro.

2011-03-30 kosovan <kosovan@icp.uni-stuttgart.de>

 * doc/ug/contributing.tex, doc/ug/introduction.tex: Minor corrections to
 Introduction and Getting involved

2011-03-30 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * AUTHORS, src/angle.h: Thanks to Muhammed Anwar: Added 3-body force for
 cossquare angle potential.

2011-03-29 kosovan <kosovan@icp.uni-stuttgart.de>

 * doc/dg/pages/ug.doc, doc/ug/contributing.tex: Added documentation to make
 ug, dg and doc into the User guide.

 * doc/ug/analysis.tex, doc/ug/contributing.tex, doc/ug/installation.tex,
 doc/ug/inter.tex, doc/ug/introduction.tex: Turned list in the Introduction
 and Getting involved sections to text. Some minor fixes and a spellchecks.

2011-03-29 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/ug/bibliography.bib, doc/ug/features.tex, doc/ug/lb.tex: Added all
 features, partly without documentation. Added documentation and reference for
 LB electrohydrodynamics (Owen Hickey).

 * doc/ug/Makefile.am, doc/ug/analysis.tex, doc/ug/bibliography.bib,
 doc/ug/figures/elc-errordist.pdf, doc/ug/inter.tex, doc/ug/io.tex,
 doc/ug/mmm.tex, doc/ug/part.tex, doc/ug/run.tex, doc/ug/setup.tex,
 doc/ug/ug.tex: Lots of small changes. Added some references and pictures.
 Mainly bugfixes and improvements.

 * doc/ug/ug.tex: enabled boxes.

2011-03-29 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * NEWS: Updated NEWS.

 * configure.ac: Removed maggs_doc from configure.ac.

 * README, doc/Makefile.am: Removed maggs_doc from Makefile.am. Added new
 figures to README.

 * doc/ug/installation.tex, doc/ug/maggs.tex, doc/ug/ug.tex: Header fix,
 \todo.

2011-03-29 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/maggs_doc/Makefile.am, doc/maggs_doc/figs/cell.eps,
 doc/maggs_doc/figs/charge_assig_cube.eps,
 doc/maggs_doc/figs/initializationE.eps,
 doc/maggs_doc/figs/initializationE.pdf, doc/maggs_doc/memd.tex,
 doc/ug/figures/maggs-charge-assignment.pdf,
 doc/ug/figures/maggs-initial-scheme.pdf, doc/ug/figures/maggs-rotation.pdf,
 doc/ug/inter.tex, doc/ug/maggs.tex, doc/ug/ug.tex: Included the more detailed
 description of the Maggs algorithm in the User's Guide. Adapted the figures
 and reformulated most of the descriptions.

 * doc/ug/bibliography.bib: Added the papers of Maggs/Rottler and
 Pasichnyk/Dünweg to the bibliography for citation.

2011-03-29 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * configure.ac: Default CUDA compute models are now 1.1 and 2.0

2011-03-29 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/lb.tcl: Reduced lb.tcl runtime and output.

 * NEWS: Updated NEWS.

 * doc/ug/setup.tex: Made comments into \todo s

 * src/angle.h, src/virtual_sites_com.c, src/virtual_sites_relative.c: Fixed
 virtual_sites_relative error messages.

 * src/cells.h, src/communication.c, src/communication.h, src/energy.h,
 src/ghosts.h, src/particle_data.c, src/particle_data.h,
 src/statistics_fluid.c, src/thermostat.h, src/utils.h, src/virtual_sites.h,
 src/virtual_sites_com.h, src/virtual_sites_relative.h: Removed warnings.

 * configure.ac, myconfig-sample.h.in, src/myconfig-sample.h.in: Moves
 myconfig-sample.h.in into top level source dir.

 * src/communication.c, src/communication.h, src/lb-boundaries.c, src/lb.c,
 src/particle_data.c, src/statistics_fluid.c, src/virtual_sites_relative.c,
 src/virtual_sites_relative.h: Removed warnings.

 * doc/ug/ug.tex: Use package todonotes.

 * doc/ug/introduction.tex: Removed test.

 * src/mol_cut.h, testsuite/p3m.tcl: Feature-fixes.

2011-03-28 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/ug/aux.tex, doc/ug/features.tex, doc/ug/firststeps.tex,
 doc/ug/inter.tex, doc/ug/io.tex, doc/ug/part.tex, doc/ug/run.tex,
 doc/ug/setup.tex: Fixed all LaTeX issues with undefined references. Added
 labels where necessary.

2011-03-28 Dominic <dominic@icp.uni-stuttgart.de>

 * doc/ug/installation.tex, doc/ug/lb.tex, doc/ug/setup.tex,
 src/communication.c, src/config.c, src/cuda_init.cu, src/cuda_init.h,
 src/initialize.c, src/lbgpu.cu, src/lbgpu.h, src/lbgpu_cfile.c,
 testsuite/configs/myconfig-LB.h, testsuite/configs/myconfig-maxset.h,
 testsuite/lb.tcl, testsuite/lb_gpu.tcl, testsuite/virtual-sites.tcl: changes
 for merge to lbgpu

2011-03-28 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * src/maggs.c, src/maggs.h, testsuite/Makefile.am: Fixed featuyres.

 * src/config.h, src/maggs.c, src/maggs.h, testsuite/Makefile.am,
 testsuite/configs/myconfig-LBGPU.h, testsuite/lb_gpu.tcl,
 testsuite/runtest.sh.in: Fixed features for maggs and lbgpu.

2011-03-28 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.cu, src/lbgpu.h: fixes for use of arch 1.1

2011-03-28 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * configure.ac, testsuite/Makefile.am, testsuite/configs/Makefile.am,
 testsuite/configs/myconfig-LBGPU.h, testsuite/runtest.sh.in: Added lb_gpu
 test and config. Added configs to Makefile.am.

2011-03-28 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.cu, src/lbgpu.h, testsuite/lb_gpu.tcl: memory aligment of nodes
 structes changed

2011-03-25 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.cu: tiny fixes in lbgpu.cu

 * src/lb.c, src/lbgpu.cu, src/statistics_fluid.c: temperatur calc of lb gpu
 fixed Please enter the commit message for your changes. Lines starting

2011-03-25 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/virtual-sites.tcl: Removed extensive testcase output.

 * testsuite/configs/myconfig-LB.h, testsuite/configs/myconfig-maxset.h: Added
 example configs to testsuite.

 * src/communication.c: Fixed forgotten REQ_ of virtual sites.

2011-03-25 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * testsuite/Makefile.am, testsuite/maggs.tcl,
 testsuite/maggs_correct_rdf.dat, testsuite/maggs_correct_rdf.data: Added
 testcase for Maggs algorithm to testsuite.

2011-03-25 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lb.c, src/lbgpu.cu, src/lbgpu.h, src/lbgpu_cfile.c,
 src/statistics_fluid.c: analyze fluid temperature cmd added

2011-03-24 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lb.c, src/lbgpu.cu: bug in thermal of modes in lbgpu.cu and lb.c fixed

2011-03-24 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/ug/inter.tex, doc/ug/part.tex: Corrected some double used figure tags
 in user's guide

 * doc/ug/inter.tex: Adapted and improved the documentation for the Maggs
 (MEMD) algorithm.

 * .gitignore, testsuite/maggs.tcl, testsuite/maggs_correct_rdf.dat: Added
 maggs Testcase TCL file. Test itself has to be included yet.

 * src/initialize.c, src/maggs.c, src/maggs.h: changed function names for
 Maggs_init() and Maggs_exit() to lower case letters.

 * .gitignore: added all build files to .gitignore for convenience

 * src/maggs.c: formatted function comments to fit doxygen

2011-03-24 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.cu: calc of node velocity renormalizied

 * src/lbgpu.cu, src/lbgpu.h, src/statistics_fluid.c: GAUSSRANDOM buxfixes and
 analyze fluid momentum added

2011-03-23 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * doc/dg/Makefile.am: Small fix.

 * doc/Makefile.am, doc/dg/Doxyfile, doc/dg/Makefile.am, doc/latexit.sh.in,
 doc/ug/Makefile.am: Some work on the doc generation output.

2011-03-23 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lb.c, src/lbgpu.cu, src/lbgpu_cfile.c: index calc of lbgpu changed +
 GAUSSRANDOM in lb.c added

2011-03-23 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * README, doc/dg/Doxyfile, doc/dg/Makefile.am, doc/dg/figs/logo.gif,
 doc/dg/figs/logo.png, src/communication.h, src/p3m-assignment.c: Fixed some
 more wanringns, fixed some of the DG.

 * doc/dg/Makefile.am: Fixed.

 * doc/dg/Doxyfile, doc/dg/Makefile.am, doc/dg/background_errors.sh,
 doc/dg/header.html, doc/dg/pages/build.doc, doc/dg/pages/cvs.doc,
 doc/dg/pages/header.doc, doc/dg/pages/testsuite.doc, doc/dg/pages/ug.doc,
 src/constraint.c, src/initialize.c, src/integrate.c, src/p3m-charges.c: Some
 work on the DG, cleaned up warnings.

 * src/communication.c: Removed unnecessary status requests that were
 igrnored.

 * src/mpifake/mpi.h: Added MPI_STATUS_IGNORE

 * src/communication.c, src/communication.h: Radically simplified adding new
 callback functions.

 * src/communication.c, src/communication.h, src/particle_data.c: Removed
 "REQ_*" definitions. slaves can be called via mpi_call directly, no need for
 error-prone constants.

 * src/maggs.c, src/maggs.h: Some fixes.

2011-03-22 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * src/maggs.c, src/maggs.h: Thoroughly commented the new maggs code and
 changed the order of functions.

2011-03-22 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * configure.ac: Require at least automake 1.10.

2011-03-21 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * old/maggs_old.c, old/maggs_old.h, src/forces.c, src/forces.h, src/iccp3m.h,
 src/integrate.c, src/interaction_data.c, src/maggs.c, src/maggs.h: Merged new
 version of Maggs algorithm into current ESPResSo release. Replaced maggs.c
 and maggs.h file. Some minor modifications in other files.

2011-03-21 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.cu, src/lbgpu_cfile.c, testsuite/lb_gpu.tcl: bugfixes

 * src/lbgpu.cu, src/myconfig-sample.h, testsuite/lb_gpu.tcl: index
 calculation changed

 * src/lbgpu_cfile.c: fluidupdate counter changed to int counter

2011-03-20 Olaf Lenz <olaf@lenz.name>

 * src/config.c: Fixed FFTW feature output.

2011-03-18 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/thermostat.tcl: Let test spam less

 * testsuite/tests_common.tcl: require_feature now hits better.

 * configure.ac: Fixed usage of CPU_COUNT.

2011-03-17 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * doc/dg/Doxyfile: Included .c and .h files into DG again.

 * doc/dg/Doxyfile, doc/dg/Makefile.am, doc/dg/doxygen.cfg: Changed name of
 doxygen file.

 * README: Updated URL.

 * testsuite/Makefile.am, testsuite/p3m_magnetostatics.data,
 testsuite/p3m_magnetostatics.tcl, testsuite/p3m_magnetostatics_expected.data:
 Repaired distcheck.

 * doc/dg/Makefile.am, doc/ug/Makefile.am, scripts/Makefile.am,
 testsuite/runtest.sh.in: Revert "Build system couldn't handle spaces in
 directories."  This reverts commit df8cabd61bdd13af92c2390d6db777a6e55604b4.

 * Makefile.am: Removed obsolete darwinlink.sh.

2011-03-15 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * doc/dg/Makefile.am, doc/ug/Makefile.am, scripts/Makefile.am,
 testsuite/runtest.sh.in: Build system couldn't handle spaces in directories.

 * src/statistics.c: Made RDF counter long int.

 * Makefile.am, configure.ac, darwinlink.sh, src/Makefile.am,
 src/initialize.c: Removed some specifities of the build system, simplify
 compilation with condor.

2011-03-14 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/el2d.tcl, testsuite/mdlc.tcl: Retuned P3M for elc and mdlc test
 cases.

 * testsuite/gen_harm.tcl, testsuite/gen_mdlc.tcl: Added mdlc test system
 generation script.

 * testsuite/Makefile.am, testsuite/mdlc.tcl,
 testsuite/mdlc_expected_energy.data,
 testsuite/mdlc_expected_force_torque.data, testsuite/mdlc_system.data: Added
 MDLC test (provided by Marco Klinkigt).

 * Makefile.am: Small bugfix for build system with automake 1.9.

2011-03-10 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * src/debug.c, src/domain_decomposition.c, src/lattice.c, src/lattice.h:
 [Bug] added scaling to ROUND_ERROR_PREC in some places, since this should
 always be relative accuracy with floating point.

2011-03-10 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/Makefile.am, testsuite/p3m-magnetostatics-t1.data,
 testsuite/p3m-magnetostatics.tcl, testsuite/p3m_magnetostatics.tcl,
 testsuite/p3m_magnetostatics2.tcl,
 testsuite/p3m_magnetostatics2_expected.data,
 testsuite/p3m_magnetostatics2_system.data,
 testsuite/p3m_magnetostatics_expected.data: Added test case for
 magnetostatics P3M.

 * src/Makefile.am: Added generation of ESPResSo blockfile lib.

 * src/blockfile.c: Removed unnecessary include.

 * src/Makefile.am, testsuite/Makefile.am: make distcheck runs.

 * testsuite/Makefile.am, testsuite/lb_gpu.tcl: Updated lb_gpu testcase.

2011-03-10 Dominic <dominic@icp.uni-stuttgart.de>

 * myconfig-sample.h: my-config-sample.h flags for lbgpu added

 * src/lbgpu.cu, testsuite/lb_gpu.tcl: safe calls for cuda kernel rewritten in
 macro

2011-03-10 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: fix energy influence function.

2011-03-10 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * doc/ug/lb.tex, src/myconfig-sample.h.in, testsuite/runtest.sh.in: Added
 LBGPU features to myconfig-sample.h, improved docs.

 * NEWS: Updated NEWS.

 * testsuite/Makefile.am, testsuite/runtest.sh.in: Fixed runtest.sh script.

2011-03-10 Florian Weik <fweik@icq.uni-stuttgart.de>

 * testsuite/p3m_noncubic.tcl, testsuite/p3m_system_noncubic.data: bla

2011-03-04 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c: p3m-chages: index notation cleanup.

2011-02-23 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: removed unused variables.

2011-02-18 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: fixed small error in d_op calculation.

2011-02-10 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: fixed prefactors.

2011-02-22 Florian Weik <fweik@icp.uni-stuttgart.de>

 * p3m-charges.c, p3m-charges.h: p3m-charges: made internal functions static
 where appropriate.

2011-02-18 Florian Weik <fweik@icq.uni-stuttgart.de>

 * pressure.c: p3m-charges: added calculation of kspace pressure tensor for
 p3m-charges.

 * fft.c: fft: reenable reality check.

 * p3m-charges.c: p3m-charges: fixed small error in d_op calculation.

2011-02-16 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: fixed bug in tuning.

2011-02-10 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c, testsuite/p3m.tcl: p3m-charges: fixed prefactors.

2011-03-10 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * configure.ac: Removed silent-rules option, which works only after Automake
 1.9.

 * doc/ug/bibliography.bib, doc/ug/inter.tex, doc/ug/part.tex: Added rattle
 shake docs (from Marco Klinkigt).

 * INSTALL: Updated INSTALL.

2011-03-10 Stefan Kesselheim <kessel@icp.uni-stuttgart.de>

 * doc/ug/lb.tex: added more LB documentation

2011-03-09 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.cu: temp threads_per_block size added

 * src/lbgpu.cu: bla

 * src/lbgpu.cu, testsuite/lb_gpu.tcl: kernel safe calls added

 * src/lbgpu.cu, src/lbgpu.h: safe routine for mem allocation on gpu added

 * src/lbgpu.cu, src/lbgpu_cfile.c: tidy up again

 * src/lb.c, src/lb_boundaries_gpu.c, src/lb_boundaries_gpu.h, src/lbgpu.cu,
 src/lbgpu.h, src/lbgpu_cfile.c: code tidy up action

2011-03-09 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * doc/ug/installation.tex: Updated docs: sautogen.sh -> bootsrap.sh

 * src/Makefile.am: Fix to myconfig logic.

2011-03-08 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.h, testsuite/lb_gpu.tcl: ka

2011-03-04 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.cu: node force struct rewritten

 * src/lbgpu.cu, src/lbgpu.h: node structs of lbgpu code rewritten

 * src/myconfig-default.h: ka

 * configure.ac, src/communication.c, src/lb-boundaries.c, src/lbgpu_cfile.c:
 little fixes

2011-03-03 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * configure.ac, src/Makefile.am, src/myconfig-default.h,
 src/myconfig-default.h.in, src/myconfig-sample.h, src/myconfig-sample.h.in:
 Myconfig logic.

 * configure.ac: Removed subdir-obj which made make clean fail.

2011-03-03 Dominic <dominic@icp.uni-stuttgart.de>

 * src/lbgpu.cu: changes in lbgpu.cu for release version

2011-03-02 Dominic <dominic@icp.uni-stuttgart.de>

 * src/forces.c, src/lb.c, src/lbgpu.cu, src/lbgpu_cfile.c,
 testsuite/lb_gpu.tcl: asyncMemCpy for particle data communcation between cpu
 and gpu added

2011-03-01 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * configure.ac, src/config.c: Removed --enable-debug and --enable-profiling,
 as it wasn't used anywhere.

2011-02-28 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * NEWS, src/particle_data.h: Updated NEWS.

2011-02-28 Stefan Kesselheim <kessel@icp.uni-stuttgart.de>

 * src/constraint.c: fixed bug. compiling without CONSTRAINTS works again

 * src/communication.c: fixed bug in last merge

2011-02-25 Sela Samin <samins@bgu.ac.il>

 * src/mdlc_correction.c, src/p3m.c: Fixed blockfile support for dipolar
 interactions.

 * scripts/blockfile_support.tcl: Added blockfile support for constraints.

2011-02-25 Dominic <dominic@icp.uni-stuttgart.de>

 * lb.c_old, lb.h_old, src/cuda_init.cu, src/forces.c, src/lbgpu.cu: changes
 due to pmalloc/malloc problem with cuda

2011-02-24 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * Makefile.am: Removed files from Makefile.am.

 * configure.ac: Readded -Wall as default flags.

 * src/config.h: Added mathematical constants fro strcit C99 compilers.

 * NEWS, config/ax_mpi_only.m4, configure.ac, src/config.c, src/config.h,
 src/fft.c, src/fft.h, src/modes.c, src/modes.h: Fixed FFTW recognition.
 Removed FFTW2 support.

 * src/Makefile.am, src/forces.c, src/integrate.c, src/p3m.c, src/p3m.h,
 src/pressure.c: Some small fixes.

2011-02-24 Stefan Kesselheim <kessel@icp.uni-stuttgart.de>

 * src/constraint.c, src/constraint.h: fixed a bug of the pore constraint

 * doc/ug/part.tex, src/constraint.c: added a command to check the distance
 from constraints  See users guide: constraint mindist_position

2011-02-23 Dominic <dominic@icp.uni-stuttgart.de>

 * testsuite/lb_gpu.tcl: just for chekcout Please enter the commit message for
 your changes. Lines starting

 * forces.c, lbgpu_cfile.c: small mod on executionorder in forces.c

2011-02-23 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: removed unused variables.

2011-02-22 Florian Weik <fweik@icp.uni-stuttgart.de>

 * p3m-charges.c, p3m-charges.h: p3m-charges: made internal functions static
 where appropriate.

2011-02-18 Florian Weik <fweik@icq.uni-stuttgart.de>

 * pressure.c: p3m-charges: added calculation of kspace pressure tensor for
 p3m-charges.

 * fft.c: fft: reenable reality check.

 * p3m-charges.c: p3m-charges: fixed small error in d_op calculation.

2011-02-16 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: fixed bug in tuning.

2011-02-10 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c, testsuite/p3m.tcl: p3m-charges: fixed prefactors.

2011-02-18 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-dipoles.c: p3m-dipolar: debug messages.

 * mpifake/mpi.c, mpifake/mpi.h: mpifake: fixed inplace.

2011-02-16 Florian Weik <fweik@icq.uni-stuttgart.de>

 * mdlc_correction.c: mdlc-corrections: still bugfix.

 * mdlc_correction.c: mdlc-corrections: fixed energy calculation.

2011-02-14 Florian Weik <fweik@icq.uni-stuttgart.de>

 * communication.c, debug.h, mdlc_correction.c, mdlc_correction.h:
 mdlc-correction: fixed deadlock in tuning.

 * mdlc_correction.c: mdlc-correction: fixed missing communication.

2011-02-11 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-dipoles.c: p3m-dipolar: small optimazion

 * mdlc_correction.c: mdlc-correction: finished paralallization.

2011-02-11 Florian Weik <fweik@icp.uni-stuttgart.de>

 * mdlc_correction.c: mdlc-correction: paralellized slab_dip_count_mu().

2011-02-09 Florian Weik <fweik@icq.uni-stuttgart.de>

 * mdlc_correction.c: mdlc-corection: parallized slab_dip_count_mu().

2011-02-09 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * mdlc_correction.c: mdlc-correction: paralellized get_mu_max()

2011-02-09 Florian Weik <fweik@icp.uni-stuttgart.de>

 * mpifake/mpi.c, mpifake/mpi.h: fakempi: support for MPI_IN_PLACE in
 MPI_Allreduce().

2011-02-04 Florian Weik <fweik@icp.uni-stuttgart.de>

 * testsuite/p3m-magnetostatics.tcl: testsuit: removed contraint for number of
 nodes for p3m-dipol testcase.

 * p3m-dipoles.c: p3m-dipolar: put surface torque correction in right place.

 * p3m-dipoles.c: p3m-dipolar: cleanup

2011-02-03 Florian Weik <fweik@icp.uni-stuttgart.de>

 * p3m-dipoles.c: p3m-dipolar: cleanup

 * p3m-dipoles.c: p3m-dipolar: add surface term only on master.

 * p3m-dipoles.c: p3m-dipolar: fixed segfault.

 * p3m-dipoles.c: p3m-dipolar: do energy correction only on one node

 * p3m-dipoles.c: p3m-dipolar: parallelization of surface correction
 calculation.

 * p3m-dipoles.c: p3m-dipolar: fixed index-error in energy calculation.

 * p3m-dipoles.c: p3m-dipolar: fixed index-error in force calculation.

2011-02-03 Florian Weik <florian@earth.(none)>

 * p3m-dipoles.c: p3m-diplolar: fixed index-error for torques calculation.

2011-02-22 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * configure.ac, src/Makefile.am: Even more elaborated myconfig logic.

2011-02-22 Florian Weik <fweik@icp.uni-stuttgart.de>

 * p3m-charges.c, p3m-charges.h: p3m-charges: made internal functions static
 where appropriate.

2011-02-18 Florian Weik <fweik@icq.uni-stuttgart.de>

 * pressure.c: p3m-charges: added calculation of kspace pressure tensor for
 p3m-charges.

 * fft.c: fft: reenable reality check.

 * p3m-charges.c: p3m-charges: fixed small error in d_op calculation.

2011-02-16 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: fixed bug in tuning.

2011-02-10 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c, testsuite/p3m.tcl: p3m-charges: fixed prefactors.

2011-02-22 Florian Weik <fweik@icp.uni-stuttgart.de>

 * p3m-charges.c, p3m-charges.h: p3m-charges: made internal functions static
 where appropriate.

2011-02-22 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * src/communication.c: Fixed misleading comment.

 * Makefile.am, NEWS, bootstrap.sh, configure.ac, src/Makefile.am,
 src/config.h, src/config/myconfig-default.h.in, src/myconfig-default.h.in,
 src/myconfig-sample.h, src/myconfig-sample.h.in: Updated handling of
 myconfig.h.

2011-02-21 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * NEWS: Fixed NEWS.

 * NEWS: Updated NEWS.

 * doc/ug/part.tex, doc/ug/ug.tex, doc/ug/virtual.tex: Integrated and fixed
 virtual sites documentation in the UG.

 * NEWS, autogen.sh, bootstrap.sh: Updated NEWS, renamed autogen.sh.

 * doc/ug/inter.tex, main.c, mdlc_correction.c, random.c: Small fixes.

2011-02-21 Rudolf Weeber <weeber@icp.uni-stuttgart.de>

 * virtual_sites_relative.c: Virtual_sites_relative: Significant performance
 improvement

2011-02-18 Florian Weik <fweik@icq.uni-stuttgart.de>

 * pressure.c: p3m-charges: added calculation of kspace pressure tensor for
 p3m-charges.

 * fft.c: fft: reenable reality check.

 * p3m-charges.c: p3m-charges: fixed small error in d_op calculation.

2011-01-31 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * utils.h: utils: small fix

 * utils.h: utils: dont segfault when out of memory.

2011-02-18 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-dipoles.c: p3m-dipolar: debug messages.

 * mpifake/mpi.c, mpifake/mpi.h: mpifake: fixed inplace.

2011-02-17 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * config.h: [NEW] Changed P3M Brillouin Zone to 0 for faster tuning. Accuracy
 is ensured by the tuning procedure, but it doesn't seem to affect it too
 much.

2011-02-16 Florian Weik <fweik@icq.uni-stuttgart.de>

 * mdlc_correction.c: mdlc-corrections: still bugfix.

 * mdlc_correction.c: mdlc-corrections: fixed energy calculation.

2011-02-16 Dominic <dominic@icp.uni-stuttgart.de>

 * lbgpu.cu, lbgpu.h, lbgpu_cfile.c: new tcl cmds added

2011-02-16 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: fixed bug in tuning.

2011-02-15 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * config.h, myconfig-sample.h: [NEW] a couple of constants are now
 configurable via myconfig.h

2011-02-15 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * INSTALL, NEWS, README: Added GNU All-Permissive License to README, NEWS and
 INSTALL file.

2011-02-14 Florian Weik <fweik@icq.uni-stuttgart.de>

 * communication.c, debug.h, mdlc_correction.c, mdlc_correction.h:
 mdlc-correction: fixed deadlock in tuning.

 * mdlc_correction.c: mdlc-correction: fixed missing communication.

2011-02-11 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-dipoles.c: p3m-dipolar: small optimazion

 * mdlc_correction.c: mdlc-correction: finished paralallization.

2011-02-11 Florian Weik <fweik@icp.uni-stuttgart.de>

 * mdlc_correction.c: mdlc-correction: paralellized slab_dip_count_mu().

2011-02-10 Florian Weik <fweik@icq.uni-stuttgart.de>

 * p3m-charges.c, testsuite/p3m.tcl: p3m-charges: fixed prefactors.

2011-02-10 Dominic <dominic@icp.uni-stuttgart.de>

 * lb.c, lbgpu.cu, lbgpu.h, lbgpu_cfile.c: included electrohydrodynamics in lb
 gpu code

 * initialize.c, lb.c, lbgpu.cu, lbgpu.h, lbgpu_cfile.c: modfication of
 lb_pref for gaussian randomnr

2011-02-09 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * NEWS: Updated NEWS.

2011-02-09 Stefan Kesselheim <kessel@tahr.ica1.uni-stuttgart.de>

 * doc/ug/part.tex: added documentation for the reflecting contraint  and the
 conical pore.

 * doc/ug/part.tex: added documentation for the reflecting contraint  and the
 conical pore.

2011-01-26 Stefan Kesselheim <kessel@tahr.ica1.uni-stuttgart.de>

 * statistics.c: analyze momentum can now be called also without LB

2011-02-09 Florian Weik <fweik@icq.uni-stuttgart.de>

 * mdlc_correction.c: mdlc-corection: parallized slab_dip_count_mu().

2011-01-26 Stefan Kesselheim <kessel@tahr.ica1.uni-stuttgart.de>

 * constraint.c, constraint.h, interaction_data.h: conical pores and
 reflecting walls added  Both are extensions to the constraint concept: Pores
 can have two different radii, given by its args radii ( replacing the arg
 radius ) that corresponds to both pore openings. Additionally the constraint
 sphere cylinder and pore can have the property of being reflecting, i.e.
 penetrating particles are reflected a) in a elastic fashion or b) in a
 "bounce back" fashion.

2011-02-09 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * mdlc_correction.c: mdlc-correction: paralellized get_mu_max()

2011-02-09 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * CMakeLists.txt, XCodeEspresso/README,
 XCodeEspresso/XCodeGen/project.pbxproj, XCodeEspresso/XCodeGen/user.mode1,
 XCodeEspresso/XCodeGen/user.pbxuser, XCodeEspresso/gen.sh,
 acconfig.h.cmakein, cmake/EspGenerateVersionInfo.cmake,
 cmake/EspSignalType.cmake, cmake/EspTestInline.cmake, cmake/Espresso.cmakein,
 cmake/FindFFTW3.cmake, cmake/FindMPI.cmake, cmake/FindTCL.cmake,
 cmake/TestInline.c, cmake/TestRetSigType.c, cmake/myconfig-default.h.cmakein,
 old/CMakeLists.txt, old/XCodeEspresso/README,
 old/XCodeEspresso/XCodeGen/project.pbxproj,
 old/XCodeEspresso/XCodeGen/user.mode1,
 old/XCodeEspresso/XCodeGen/user.pbxuser, old/XCodeEspresso/gen.sh,
 old/acconfig.h.cmakein, old/cmake/EspGenerateVersionInfo.cmake,
 old/cmake/EspSignalType.cmake, old/cmake/EspTestInline.cmake,
 old/cmake/Espresso.cmakein, old/cmake/FindFFTW3.cmake,
 old/cmake/FindMPI.cmake, old/cmake/FindTCL.cmake, old/cmake/TestInline.c,
 old/cmake/TestRetSigType.c, old/cmake/myconfig-default.h.cmakein: Moved
 obsolete files for xcode and cmake into old/ subdir.

 * Makefile.am, adresso.c, adresso.h, angle.h, angledist.h, bin.c, bin.h,
 binary_file.c, binary_file.h, blockfile.c, blockfile.h, blockfile_tcl.c,
 blockfile_tcl.h, blockfile_test.c, bmhtf-nacl.h, buckingham.h, cells.c,
 cells.h, comfixed.h, comforce.h, communication.c, communication.h, config.c,
 config.h, config/myconfig-default.h.in, configure.ac, constraint.c,
 constraint.h, cuda_init.cu, cuda_init.h, debug.c, debug.h, debye_hueckel.h,
 dihedral.h, domain_decomposition.c, domain_decomposition.h, dpd.c, dpd.h,
 elc.c, elc.h, endangledist.h, energy.c, energy.h, errorhandling.c,
 errorhandling.h, ewald.c, ewald.h, fene.h, fft.c, fft.h, forces.c, forces.h,
 gb.h, ghosts.c, ghosts.h, global.c, global.h, grid.c, grid.h, halo.c, halo.h,
 harmonic.h, hertzian.h, iccp3m.c, iccp3m.h, imd.c, imd.h, initialize.c,
 initialize.h, integrate.c, integrate.h, interaction_data.c,
 interaction_data.h, lattice.c, lattice.h, layered.c, layered.h,
 lb-boundaries.c, lb-boundaries.h, lb-d3q18.h, lb-d3q19.h, lb.c, lb.h, lj.h,
 ljangle.h, ljcos.h, ljcos2.h, ljgen.c, ljgen.h, maggs.c, maggs.h,
 magnetic_non_p3m_methods.c, magnetic_non_p3m_methods.h, main.c,
 mdlc_correction.c, mdlc_correction.h, metadynamics.c, metadynamics.h,
 mmm-common.c, mmm-common.h, mmm1d.c, mmm1d.h, mmm2d.c, mmm2d.h, modes.c,
 modes.h, mol_cut.h, molforces.c, molforces.h, morse.h, mpifake/mpi.c,
 mpifake/mpi.h, myconfig-sample.h, nemd.c, nemd.h, npt.h, nsquare.c,
 nsquare.h, overlap.h, p3m-assignment.c, p3m-charges.c, p3m-charges.h,
 p3m-dipoles.c, p3m-dipoles.h, p3m.c, p3m.h, parser.c, parser.h,
 particle_data.c, particle_data.h, polymer.c, polymer.h, polynom.h,
 pressure.c, pressure.h, pwdist.h, random.c, random.h, rattle.c, rattle.h,
 reaction_field.h, rotation.c, rotation.h, scriptsdir.c, soft_sphere.h,
 specfunc.c, specfunc.h, src/Makefile.am, src/adresso.c, src/adresso.h,
 src/angle.h, src/angledist.h, src/bin.c, src/bin.h, src/binary_file.c,
 src/binary_file.h, src/blockfile.c, src/blockfile.h, src/blockfile_tcl.c,
 src/blockfile_tcl.h, src/blockfile_test.c, src/bmhtf-nacl.h,
 src/buckingham.h, src/cells.c, src/cells.h, src/comfixed.h, src/comforce.h,
 src/communication.c, src/communication.h, src/config.c, src/config.h,
 src/config/myconfig-default.h.in, src/constraint.c, src/constraint.h,
 src/cuda_init.cu, src/cuda_init.h, src/debug.c, src/debug.h,
 src/debye_hueckel.h, src/dihedral.h, src/domain_decomposition.c,
 src/domain_decomposition.h, src/dpd.c, src/dpd.h, src/elc.c, src/elc.h,
 src/endangledist.h, src/energy.c, src/energy.h, src/errorhandling.c,
 src/errorhandling.h, src/ewald.c, src/ewald.h, src/fene.h, src/fft.c,
 src/fft.h, src/forces.c, src/forces.h, src/gb.h, src/ghosts.c, src/ghosts.h,
 src/global.c, src/global.h, src/grid.c, src/grid.h, src/halo.c, src/halo.h,
 src/harmonic.h, src/hertzian.h, src/iccp3m.c, src/iccp3m.h, src/imd.c,
 src/imd.h, src/initialize.c, src/initialize.h, src/integrate.c,
 src/integrate.h, src/interaction_data.c, src/interaction_data.h,
 src/lattice.c, src/lattice.h, src/layered.c, src/layered.h,
 src/lb-boundaries.c, src/lb-boundaries.h, src/lb-d3q18.h, src/lb-d3q19.h,
 src/lb.c, src/lb.h, src/lj.h, src/ljangle.h, src/ljcos.h, src/ljcos2.h,
 src/ljgen.c, src/ljgen.h, src/maggs.c, src/maggs.h,
 src/magnetic_non_p3m_methods.c, src/magnetic_non_p3m_methods.h, src/main.c,
 src/mdlc_correction.c, src/mdlc_correction.h, src/metadynamics.c,
 src/metadynamics.h, src/mmm-common.c, src/mmm-common.h, src/mmm1d.c,
 src/mmm1d.h, src/mmm2d.c, src/mmm2d.h, src/modes.c, src/modes.h,
 src/mol_cut.h, src/molforces.c, src/molforces.h, src/morse.h,
 src/mpifake/mpi.c, src/mpifake/mpi.h, src/myconfig-sample.h, src/nemd.c,
 src/nemd.h, src/npt.h, src/nsquare.c, src/nsquare.h, src/overlap.h,
 src/p3m-assignment.c, src/p3m-charges.c, src/p3m-charges.h,
 src/p3m-dipoles.c, src/p3m-dipoles.h, src/p3m.c, src/p3m.h, src/parser.c,
 src/parser.h, src/particle_data.c, src/particle_data.h, src/polymer.c,
 src/polymer.h, src/polynom.h, src/pressure.c, src/pressure.h, src/pwdist.h,
 src/random.c, src/random.h, src/rattle.c, src/rattle.h, src/reaction_field.h,
 src/rotation.c, src/rotation.h, src/scriptsdir.c, src/soft_sphere.h,
 src/specfunc.c, src/specfunc.h, src/statistics.c, src/statistics.h,
 src/statistics_chain.c, src/statistics_chain.h, src/statistics_cluster.c,
 src/statistics_cluster.h, src/statistics_fluid.c, src/statistics_fluid.h,
 src/statistics_molecule.c, src/statistics_molecule.h, src/steppot.h,
 src/subt_lj.h, src/tab.h, src/thermostat.c, src/thermostat.h, src/topology.c,
 src/topology.h, src/tunable_slip.h, src/tuning.c, src/tuning.h, src/utils.c,
 src/utils.h, src/uwerr.c, src/uwerr.h, src/verlet.c, src/verlet.h,
 src/virtual_sites.c, src/virtual_sites.h, src/virtual_sites_com.c,
 src/virtual_sites_com.h, src/virtual_sites_relative.c,
 src/virtual_sites_relative.h, src/vmdsock.c, src/vmdsock.h, statistics.c,
 statistics.h, statistics_chain.c, statistics_chain.h, statistics_cluster.c,
 statistics_cluster.h, statistics_fluid.c, statistics_fluid.h,
 statistics_molecule.c, statistics_molecule.h, steppot.h, subt_lj.h, tab.h,
 thermostat.c, thermostat.h, topology.c, topology.h, tunable_slip.h, tuning.c,
 tuning.h, utils.c, utils.h, uwerr.c, uwerr.h, verlet.c, verlet.h,
 virtual_sites.c, virtual_sites.h, virtual_sites_com.c, virtual_sites_com.h,
 virtual_sites_relative.c, virtual_sites_relative.h, vmdsock.c, vmdsock.h:
 Moved all source files to src/ subdir.

2011-02-09 Florian Weik <fweik@icp.uni-stuttgart.de>

 * mpifake/mpi.c, mpifake/mpi.h: fakempi: support for MPI_IN_PLACE in
 MPI_Allreduce().

2011-02-09 Dominic <dominic@icp.uni-stuttgart.de>

 * initialize.c, lb.c: problem with cpu code in initialize.c fixed

2011-02-09 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * NEWS, doc/ug/ug.tex: Updated NEWS, put virtual sites docs more central.

 * config.c, config.h, debug.c, global.c, testsuite/virtual-sites.tcl: Added
 some config logics and code_info output for virtual_sites.

2011-02-09 Rudolf Weeber <weeber@icp.uni-stuttgart.de>

 * particle_data.c: virtual_sites: Corrected ifdef

 * virtual_sites_com.c, virtual_sites_com.h: Virtual_sites_com: Renamed
 functions to match new names in statistics.c

2011-02-08 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * config.h: VIRTUAL_SITES_RELATIVE implies ROTATION

 * doc/ug/plotting.tex: Updated copyright notice.

 * lb.c, lb.h: Added correct copyright headers.

 * doc/ug/lb.tex, doc/ug/ug.tex, lb.c_old, lb.h_old: Removed obsolete files,
 added lb docs.

 * config.h, myconfig-sample.h: Added feature logic for virtual sites.

 * doc/ug/inter.tex, doc/ug/ug.tex: Updated P3M documentation.

2011-02-08 Dominic <dominic@icp.uni-stuttgart.de>

 * initialize.c, integrate.c, lb-boundaries.c, lb.c, lb_boundaries_gpu.c,
 lb_boundaries_gpu.h, lbgpu.cu, lbgpu.h, lbgpu_cfile.c, statistics_fluid.c,
 thermostat.c: fixes for lb and lb gpu code (tcl stuff)

2011-02-08 Rudolf Weeber <weeber@icp.uni-stuttgart.de>

 * particle_data.c, testsuite/virtual-sites.tcl: Virtual sites: Small tcl
 interface change  part vs_relate_to -> vs_auto_relate_to to make it more
 distinguishable from vs_relative

 * doc/ug/features.tex, doc/ug/part.tex, doc/ug/ug.tex, doc/ug/virtual.tex:
 Virtual sites: Work on documentation

2011-02-08 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * magnetic_non_p3m_methods.c, magnetic_non_p3m_methods.h: Removed
 autogenerated file quickref.inp.

 * configure.ac: Compile using C99 by default.

 * NEWS: Updated NEWS.

 * Makefile.am: Added virtual_site-files.

 * virtual_sites.c, virtual_sites.h, virtual_sites_com.c, virtual_sites_com.h,
 virtual_sites_relative.c, virtual_sites_relative.h: Uopdated copyright
 notices.

 * magnetic_non_p3m_methods.c: Updated copyright.

 * NEWS: Updated NEWS.

2011-02-07 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * magnetic_non_p3m_methods.c, magnetic_non_p3m_methods.h, overlap.h,
 p3m-dipoles.c, p3m-dipoles.h, tab.h, utils.h: [BUG] Fixed several warnings
 [BUG] Fixed several incorrect uses of fscanf

2011-02-07 Dominic <dominic@icp.uni-stuttgart.de>

 * lb.c, lb.h: changes for lb gpu tcl cmds

 * lb.c: changes for lb gpu code

2011-02-04 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/ug/plotting.tex: minor changes

 * doc/ug/analysis.tex: Included all missing analyze commands, partly not
 documented.

 * doc/ug/analysis.tex, doc/ug/plotting.tex, doc/ug/ug.tex: Made the plotting
 chapter an appendix. Wrote an introduction for the analysis chapter.

 * doc/ug/run.tex: corrected the paragraph on invalidate_system

2011-02-04 Florian Weik <fweik@icp.uni-stuttgart.de>

 * testsuite/p3m-magnetostatics.tcl: testsuit: removed contraint for number of
 nodes for p3m-dipol testcase.

 * p3m-dipoles.c: p3m-dipolar: put surface torque correction in right place.

2011-02-04 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/ug/run.tex: Documented integrate command.

2011-02-04 Florian Weik <fweik@icp.uni-stuttgart.de>

 * p3m-dipoles.c: p3m-dipolar: cleanup

2011-02-04 Dominic <dominic@icp.uni-stuttgart.de>

 * initialize.c, integrate.c, lb.c, lb.h, lb_boundaries_gpu.c, lbgpu.cu,
 lbgpu.h, lbgpu_cfile.c, statistics_fluid.c, statistics_fluid.h: changes for
 simultaneous compiling of lb cpu and gpu codes

2011-02-04 Rudolf Weeber <weeber@icp.uni-stuttgart.de>

 * integrate.c, rotation.c, rotation.h: Removed typo in function name

 * integrate.c: Bugfix: Ghost communication at the wrong place in
 integrate_vv()  When using "integrate 0" ghost communication has to happen
 before torques are converted to body-fixed reference frame.

2011-02-03 Florian Weik <fweik@icp.uni-stuttgart.de>

 * p3m-dipoles.c: p3m-dipolar: cleanup

 * p3m-dipoles.c: p3m-dipolar: add surface term only on master.

 * p3m-dipoles.c: p3m-dipolar: fixed segfault.

 * p3m-dipoles.c: p3m-dipolar: do energy correction only on one node

2011-02-03 Mingyang Hu <mingyang@cmu.edu>

 * doc/ug/inter.tex, ljcos2.h: LJ-cos2: fix the wrong pair energy in presence
 of r_offset  User's guide updated.

2011-02-03 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/ug/inter.tex: Split up documentation on electrostatic and dipolar P3M.
 Spelled out the strange acronyms of the other electrostatic interactions.

 * doc/ug/figures/fullerene.png, doc/ug/part.tex: All my corrections in
 part.tex are done. A picture for the icosaeder is added.

2011-02-03 Florian Weik <fweik@icp.uni-stuttgart.de>

 * p3m-dipoles.c: p3m-dipolar: parallelization of surface correction
 calculation.

2011-02-03 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/ug/firststeps.tex, doc/ug/part.tex: Some minor changes in formulation
 etc.

2011-02-03 Florian Weik <fweik@icp.uni-stuttgart.de>

 * p3m-dipoles.c: p3m-dipolar: fixed index-error in energy calculation.

 * p3m-dipoles.c: p3m-dipolar: fixed index-error in force calculation.

2011-02-03 Florian Weik <florian@earth.(none)>

 * p3m-dipoles.c: p3m-diplolar: fixed index-error for torques calculation.

2011-02-02 Stefan Kesselheim <kessel@tahr.ica1.uni-stuttgart.de>

 * lb-boundaries.c: fixed the lbboundary command if LB_BOUNDARIES is not
 compiled in

2011-02-02 Dominic <dominic@icp.uni-stuttgart.de>

 * initialize.c, integrate.c, lb_boundaries_gpu.c, lbgpu.cu, lbgpu.h,
 lbgpu_cfile.c, statistics.c, thermostat.c, thermostat.h: changed name of
 lbpar struct and several #ifdef  changes to reduce codesize

2011-02-02 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * hertzian.h: [BUG] fixed output of Hertzian potential missing a trailing
 space

2011-02-01 Marcello Sega <marcello.sega@gmail.com>

 * config.c, testsuite/virtual-sites.tcl: Virtual particles: Callback for
 compilation status added; Test fails in parallel

 * testsuite/Makefile.am, testsuite/virtual-sites.tcl: virtual sites test
 added

2011-02-01 Dominic <dominic@icp.uni-stuttgart.de>

 * initialize.c, integrate.c, lb_boundaries_gpu.c, lbgpu.cu, lbgpu.h,
 lbgpu_cfile.c: changed name of host parameter struct to lb_para for better
 identification

2011-02-01 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * scripts/vtf.tcl: Fixed using userdata .

2011-01-31 Dominic <dominic@icp.uni-stuttgart.de>

 * configure.ac, lbgpu.cu, lbgpu_cfile.c, testsuite/lb_gpu.tcl: tidy up
 changes in lbgpu code

2011-01-31 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: fixed debugging message

 * p3m-charges.c: p3m-charges: cleanup

2011-01-28 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * initialize.c: [BUG] fixed missing forward declaration

 * CMakeLists.txt, Makefile.am, doc/ug/inter.tex, energy.c, forces.c,
 interaction_data.c, magnetic_non_p3m__methods.c, magnetic_non_p3m__methods.h,
 magnetic_non_p3m_methods.c, magnetic_non_p3m_methods.h: [BUG] DAWAANR fixed
 to use minimum image convention

2011-01-28 Rudolf Weeber <weeber@icp.uni-stuttgart.de>

 * virtual_sites.c: Virtual sites update -- correction to part 1 
 UpdatePartCfg() was broken resulting in "analyze mindist" alwasy returning 0

2011-01-28 Axel Arnold <arnolda@icp.uni-stuttgart.de>

 * ghosts.c: [BUG] fixed ghost particle tagging with GHOST_FLAG - currently
 only used by user-specific extensions

2011-01-27 Mingyang Hu <mingyang@cmu.edu>

 * scripts/init.tcl: Correct the wrong indent of the ESPResSo startup page

 * statistics.c: fix segmentation fault with "analyze gyration_tensor"

2011-01-27 kosovan <kosovan@icp.uni-stuttgart.de>

 * doc/ug/analysis.tex: Commented out the documentation to analyze set trapmol

 * doc/ug/analysis.tex, doc/ug/bibliography.bib, doc/ug/inter.tex: Fixed
 incomplete docs to som analyze commands.

2011-01-27 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * p3m-charges.c, p3m-charges.h: p3m-charges: added funtion for p3m kspace
 stress tensor calculation.

2011-01-20 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * p3m-charges.c: p3m-chages: small optimization.

 * p3m-charges.c: p3m-charges: small bugfixes in tuning routine. skip odd
 meshsizes, they produce problems with the fft-code. TODO: this should be
 investigated.

 * fft.c: p3m-charges: removed error-checking for zero imaginary part of
 backtransformed force/potential. the numerical errors that lead to non-zero
 imaginary part are system dependend.

 * p3m-charges.c, samples/espresso_logo.tcl, testsuite/p3m.tcl: p3m-charges:
 cleanup

2011-01-17 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: include energy+force calculation from florian
 hauessermann.

 * p3m-charges.c: p3m-charges: include calc_influence_function_energy() from
 florian hauessermann.

 * p3m-charges.c: p3m-charges: include calc_influence_function_force() from
 florian hauessermann.

 * p3m-charges.c: p3m-charges: include calc_differential_operator() from
 florian hauessermann.

2011-01-11 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: applied patch from Florian Haeussermann for
 non-cubic influence functions calculation.

2011-01-10 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: typo

2010-12-20 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: tuning bugfix/debugging messages

2010-12-16 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * p3m-charges.c, samples/espresso_logo.tcl: p3m-charges: adapted adaptive
 tuning for non-equal-sided boxes.

2010-12-09 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: adjusted tuning helper functions for
 non-equqal-sided boxes

2010-12-08 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: removed
 tclcommand_inter_coulomb_print_p3m_tune_parameteres() which contained the
 older tuning algorith (tune v1). p3m with support for non-equal-sided boxes
 will only make use of tunev2.

 * p3m-charges.c: p3m-charges: adjusted error-formulas for non-equal-sided
 boxes.

2011-01-27 Francesca Lugli <lugli@icp.uni-stuttgart.de>

 * p3m-charges.c: Fixed a wrog return value which prevented tuning to succeed

 * p3m-charges.c: Proper charge initialization of p3m tune v2 back.

2011-01-27 Dominic <dominic@icp.uni-stuttgart.de>

 * lbgpu.cu, statistics.c, statistics_fluid.c, statistics_fluid.h: dummy tcl
 cmd for analyze fluid redefined to new syntax

2011-01-27 Rudolf Weeber <weeber@icp.uni-stuttgart.de>

 * statistics.c: Virtual sites update -- Small correction to part 4

 * integrate.c: Virtual sites update -- part 9  Exclude virtual sites from
 Velocity Verlet interation

 * communication.c: Virtual sites update -- part 8  mpi communication for
 vs_relative particle attributes

 * adresso.h: Virtual sites update -- part 7  Make sure that Adres only
 compiles with the "center of mass" implementation for virtual sites

 * particle_data.c, particle_data.h: Virtual sites update -- part 6 
 Additional attributes for the particle data structure and functions to set
 and print them.

2011-01-27 Stefan Kesselheim <stefankesselheim@kessels-mac-2.fritz.box>

 * doc/ug/lb.tex, test/doc/ug/lb.tex: moved LB doc to the right place and
 added some text

2011-01-26 Stefan Kesselheim <kessel@tahr.ica1.uni-stuttgart.de>

 * test/doc/ug/lb.tex: Added first version of LB documentation

 * communication.c, communication.h, initialize.c, initialize.h,
 lb-boundaries.c, lb-boundaries.h, lb.c: Cleaned up lb-boundaries!  Removed
 all other boundary conditions than bounce back from the file and changed to a
 consistent naming.

2011-01-26 Rudolf Weeber <weeber@icp.uni-stuttgart.de>

 * rotation.c, rotation.h: Virtual sites update -- part 5  some support
 functions in rotation.c/.h

 * statistics.c: Virtual sites update -- part 4  Some analysis routines only
 exist in the "center of mass" implementation

 * myconfig-sample.h: Virtual sites update -- part 3  Add virtual sites
 related switches to myconfig-sample.h

 * thermostat.h: Virtual sites update -- part 2  Make the thermostating of
 virtual and non-virtual particles switchable from myconfig.h

 * virtual_sites.c, virtual_sites.h, virtual_sites_com.c, virtual_sites_com.h,
 virtual_sites_relative.c, virtual_sites_relative.h: Virtual sites update --
 part 1  * Split virtual sites code into an implementation independet part and
 implementations * Convert the existing code into an implementation called
 VIRTUAL_SITES_COM, i.e., center of mass. * Add a new implementation
 VIRTUAL_SITES_RELATIVE for rigid-body like objects

2011-01-26 Dominic <dominic@icp.uni-stuttgart.de>

 * lb_boundaries_gpu.c, lbgpu.cu, lbgpu_cfile.c: lbgpu code clean up for
 release

2011-01-26 kosovan <kosovan@icp.uni-stuttgart.de>

 * doc/ug/inter.tex: Update to Debye-Hueckel documentation

2011-01-26 Stefan Kesselheim <kessel@tahr.ica1.uni-stuttgart.de>

 * statistics.c: analyze momentum can now be called also without LB

 * constraint.c, constraint.h, interaction_data.h: conical pores and
 reflecting walls added  Both are extensions to the constraint concept: Pores
 can have two different radii, given by its args radii ( replacing the arg
 radius ) that corresponds to both pore openings. Additionally the constraint
 sphere cylinder and pore can have the property of being reflecting, i.e.
 penetrating particles are reflected a) in a elastic fashion or b) in a
 "bounce back" fashion.

2011-01-25 Stefan Kesselheim <kessel@tahr.ica1.uni-stuttgart.de>

 * lb.c: Some changes to lb.c were not included in last comit  now I added
 them

2011-01-25 kosovan <kosovan@icp.uni-stuttgart.de>

 * doc/ug/figures/diamond.png, doc/ug/part.tex: Fix to documentation of the
 diamond command.

2011-01-25 Dominic <dominic@icp.uni-stuttgart.de>

 * initialize.c, lbgpu.h, lbgpu_cfile.c: lbprint fluid 'filename' command
 added to lb gpu code

2011-01-24 Dominic <dominic@icp.uni-stuttgart.de>

 * initialize.c, lb.c, lb.h, lb_boundaries_gpu.c, lb_boundaries_gpu.h,
 lbgpu.h, lbgpu_cfile.c, thermostat.c: lb gpu tcl commands updatet to new
 convetion

 * Makefile-am.am: missing lbgpu fiels in Makefiel-am.am added

 * Makefile-am.am, config.c, config.h, config/cuda.m4, forces.c, initialize.c,
 integrate.c, lattice.h, lb_boundaries_gpu.c, lb_boundaries_gpu.h, lbgpu.cu,
 lbgpu.h, lbgpu_cfile.c, p3m-dipoles.c, statistics.c, statistics_fluid.c,
 testsuite/lb_gpu.tcl, testsuite/lb_system.data, thermostat.c, thermostat.h:
 Included lbgpu

2011-01-24 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/runtest.sh.in: Only run testsuite on one number of processors by
 default.

2011-01-18 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * config/ax_count_cpus.m4, configure.ac, testsuite/Makefile.am,
 testsuite/runtest.sh.in: Added guessing of number of CPUs for the testsuite.

 * scripts/Makefile.am, testsuite/Makefile.am: Some fixes to the build system.

 * .gitignore: Small build system fixes.

 * scripts/Makefile.am: Fixed building in src dir.

2011-01-17 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * NEWS: Extended NEWS.

 * NEWS: Updated NEWS.

 * doc/ug/inter.tex: Improved P3M docs.

2011-01-14 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * doc/ug/firststeps.tex, doc/ug/installation.tex: Adapted UG to build system
 modifications.

 * doc/ug/Makefile.am, doc/ug/deserno.tex, doc/ug/ug.tex: Removed deserno
 conversion documenation.

2011-01-10 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * INSTALL, admin/espresso-2.1.2j.ebuild, doc/dg/header.html,
 doc/maggs_doc/memd.tex, doc/ug/installation.tex, doc/ug/io.tex, energy.h,
 fene.h, halo.c, halo.h, lattice.c, lattice.h, lb-boundaries.c,
 lb-boundaries.h, lb-d3q18.h, lb-d3q19.h, lb.c, lb.h,
 packages/mbtools/doc/index.html, packages/mbtools/doc/install.html, pwdist.h,
 reaction_field.h, statistics_fluid.c, statistics_fluid.h,
 testsuite/analysis.tcl, testsuite/lb.tcl, testsuite/tunable_slip.tcl: Changed
 forgotten copyright headers, changed URL from espresso.mpg.de to
 espressomd.org.

 * doc/ug/mbtools.tex: Standardized wrapping of doc/ug/mbtools.tex.

2011-01-06 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * config/Espresso.m4, config/compiler.m4, config/cuda.m4, config/fftw.m4,
 config/mpi.m4, configure.ac: Incorporated sub-m4 files into configure.ac: no
 code reuse, and it was hard to find the functions.

2011-01-05 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * testsuite/analysis.tcl, testsuite/comfixed.tcl, testsuite/comforce.tcl,
 testsuite/constraints.tcl, testsuite/dh.tcl, testsuite/el2d.tcl,
 testsuite/el2d_die.tcl, testsuite/el2d_nonneutral.tcl, testsuite/fene.tcl,
 testsuite/gb.tcl, testsuite/harm.tcl, testsuite/intpbc.tcl,
 testsuite/intppbc.tcl, testsuite/kinetic.tcl, testsuite/layered.tcl,
 testsuite/lb.tcl, testsuite/lj-cos.tcl, testsuite/lj-generic.tcl,
 testsuite/lj.tcl, testsuite/madelung.tcl, testsuite/madelung_ewald.tcl,
 testsuite/mass.tcl, testsuite/mmm1d.tcl, testsuite/npt.tcl,
 testsuite/nsquare.tcl, testsuite/nve_pe.tcl,
 testsuite/p3m-magnetostatics.tcl, testsuite/p3m.tcl,
 testsuite/pe_micelle.tcl, testsuite/rotation.tcl, testsuite/runtest.sh.in,
 testsuite/tabulated.tcl, testsuite/tests_common.tcl,
 testsuite/thermostat.tcl, testsuite/tunable_slip.tcl,
 testsuite/uwerr_test.tcl: Removed errf argument from testcases.

 * config/mpi.m4, configure.ac, testsuite/Makefile.am,
 testsuite/constraints.tcl, testsuite/runtest.sh.in, testsuite/test.sh.in:
 Testsuite works with new MPI handling.

 * scripts/init.tcl: Updated copyright notice.

2011-01-04 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * config/ax_mpi_only.m4: Added comments.

2010-12-29 Rudolf Weeber <weeber@icp.uni-stuttgart.de>

 * interaction_data.c: Bugfix: Call of p3m-charges function, where dipoles
 were ment. Made Espesso uncompilable with magnetostatics

2010-12-28 Rudolf Weeber <weeber@icp.uni-stuttgart.de>

 * communication.c: A string name for debugging of mpi commnuncation for mu_e
 was missing.

2010-12-22 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * config/ax_mpi_only.m4, config/mpi.m4: Using factorized macro AX_MPI_ONLY
 now.

 * config/mpi.m4, configure.ac: Small imrpovements to MPI recognition.

2010-12-21 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * Makefile.am, config.c, config/compiler.m4, config/mpi.m4, configure.ac,
 tools/Makefile.am, tools/es_mpiexec.in: Reworked MPI recognition.

2010-12-14 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * doc/ug/.gitignore: To make compilation with ./latexmk easier: The file
 .gitignore lets git ignore the automatically produced LaTeX-helpfiles. The
 empty dummy file quickred.inp inhibits the LaTeX-error.

2010-12-14 Peter Kosovan <kosovan@linux-q0mq.(none)>

 * doc/ug/introduction.tex: Another testing change

2010-12-12 Peter Kosovan <kosovan@pudu.ica1.uni-stuttgart.de>

 * doc/ug/introduction.tex: Test modification.

2010-12-07 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * p3m-charges.c: p3m-charges: changed debug messages to reflect new function
 names

 * p3m-charges.c: p3m-charges: seperated tcl and actual code for tunev2 -
 part3

2010-12-01 Florian Weik <fweik@eldi.ica1.uni-stuttgart.de>

 * p3m-charges.c, p3m-charges.h: p3m-charges: seperated tcl and actual code
 for tunev2 - part2

2010-11-30 Florian Weik <f.weik@web.de>

 * p3m-charges.c: p3m-charges: seperated tcl and actual code for tunev2 -
 part1

2010-11-26 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * Makefile.am, doc/latexit.sh.in: Some fixes.

 * config/compiler.m4, config/config.guess, config/config.sub, configure.ac:
 Removed selfmade compiler flag optimization. Now we just use -O5 and let the
 compiler decide.

 * Espresso.in, Espresso.install_reloc: Removed obsolete files.

 * Makefile.am, initialize.c, scriptsdir.c: Compiled script directory into
 binary.  Two binaries are produced, one for the build dir, one for the
 installation dir.

 * Makefile.am, configure.ac, scripts/Makefile.am: Copy init scripts into
 build dir upon build.

2010-11-24 Olaf Lenz <olaf@lenz.name>

 * configure.ac, doc/latexit.sh.in, doc/tutorials/common/common.tex,
 doc/tutorials/tut2/Makefile.am, doc/tutorials/tut2/figures/Makefile.am,
 doc/ug/Makefile.am, doc/ug/figures/logo.png, doc/ug/latexit.sh.in,
 doc/ug/ug.tex: Improved LaTeX build process.

 * configure.ac, doc/ug/Makefile.am, doc/ug/figures/Makefile.am,
 doc/ug/latexit.sh.in: Overhauled build system for UG.

 * NEWS: Added NEWS.

 * Makefile.am, configure.ac, initialize.c: Compile scripts directory into
 binary.

2010-11-23 Olaf Lenz <olaf@lenz.name>

 * Espresso, Makefile.am, chooser/Espresso.in, config/Espresso.m4,
 configure.ac, mpiwrap/Espresso.in: Removed wrapper scripts for MPI, chooser
 and Espresso.

 * Makefile, Makefile-am.am, Makefile.am, autogen.sh, config/Espresso.m4,
 configure, configure.ac: Got rid of Makefile-am.am, configure-ac, etc.

 * doc/ug/Makefile.am, doc/ug/underscore.sty: Removed underscore.sty. 
 underscore.sty is usually part of modern LaTeX environments and there are
 problems with the license if including it.

2010-11-22 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * AUTHORS, NEWS: Updated AUTHORS and NEWS.

2010-11-21 Marcello Sega <sega@icp.uni-stuttgart.de>

 * adresso.c, adresso.h, angle.h, angledist.h, bin.c, bin.h, binary_file.c,
 binary_file.h, blockfile_tcl.c, blockfile_tcl.h, bmhtf-nacl.h, buckingham.h,
 cells.c, cells.h, comfixed.h, comforce.h, communication.c, communication.h,
 config.c, config.h, constraint.c, debug.c, debug.h, debye_hueckel.h,
 dihedral.h, domain_decomposition.c, domain_decomposition.h, dpd.c, dpd.h,
 elc.c, elc.h, endangledist.h, energy.c, energy.h, ewald.c, ewald.h, fene.h,
 forces.h, gb.h, ghosts.h, global.c, global.h, grid.c, grid.h, harmonic.h,
 hertzian.h, iccp3m.c, iccp3m.h, imd.c, imd.h, initialize.c, integrate.c,
 integrate.h, interaction_data.c, interaction_data.h, lb.c, lb.h, lj.h,
 ljangle.h, ljcos.h, ljcos2.h, ljgen.c, ljgen.h, maggs.c, maggs.h,
 magnetic_non_p3m__methods.c, magnetic_non_p3m__methods.h, mdlc_correction.c,
 mdlc_correction.h, metadynamics.c, metadynamics.h, mmm1d.c, mmm1d.h, mmm2d.c,
 mmm2d.h, modes.c, mol_cut.h, morse.h, myconfig-sample.h, nemd.c, nemd.h,
 overlap.h, p3m-charges.c, p3m-charges.h, p3m-dipoles.c, p3m-dipoles.h, p3m.c,
 p3m.h, particle_data.c, particle_data.h, polymer.c, polymer.h, pressure.c,
 pressure.h, random.c, random.h, rattle.h, reaction_field.h, soft_sphere.h,
 statistics.c, statistics.h, statistics_chain.c, statistics_chain.h,
 statistics_cluster.c, statistics_cluster.h, statistics_fluid.c,
 statistics_fluid.h, statistics_molecule.c, steppot.h, subt_lj.h, tab.h,
 thermostat.c, thermostat.h, topology.c, topology.h, tunable_slip.h, tuning.c,
 tuning.h, utils.c, utils.h, uwerr.c, uwerr.h, verlet.c, verlet.h,
 virtual_sites.c, virtual_sites.h: This is a small guide to the new naming
 convention in ESPResSo.  Tcl commands parsing functions in ESPResSo were
 somehow heterogeneous both in logical structure and in naming convention: I
 tried to make some order as explained below. Summarizing, now every function
 involving the Tcl interpreter(*) has one of the following forms 
 tclcommand_SOMETHING tclcallback_SOMETHING tclprint_SOMETHING  Please notice
 that this is still a test version: the naming convention can still (will) be
 changed, and not every combination of #defines in myconfig.h has been tried,
 so some problems might still pop out. Feel free to contact me
 (sega@icp.uni-stuttgart.de) (a) about problematic as well as successful
 merges -good news are always welcome- with your actual branch (b) if some
 code got broken (c) to suggest improvements, or changes in the naming scheme.
  (*) besides very few exceptions like: functions commented out, not used
 anywhere in the code, or marked as experimental (hence, which are supposed
 anyway to be cleaned/checked),  the mpi_gather_runtime_errors(),
 on_program_start() appinit(), parse_*_list(), and init_tcl() functions. Some
 UWerr functions using the interpreter were also not changed, because new tcl
 commands are created within the module, and need probably a different
 treatment.  The details of the naming convention follows. 
 ********************************************************************* TCL
 COMMANDS AND RELATED
 ********************************************************************* All C
 functions associated to an ESPResSo tcl command have now the form 
 tclcommand_COMMAND()  where COMMAND corresponds without any exception to the
 name of the corresponding tcl command.  This should make rather easy to spot
 them in the code.  For example,  grep "tclcommand_part\>" *.[ch]  searches
 for the references to the "part" command. 
 ----------------------------------------------------------------------  When
 the first argument of a command needs to be parsed, as in the case of 'inter
 coulomb', the name of the parsing function is always 
 tclcommand_COMMAND_parse_SUBCOMMAND()  again, with strict correspondence to
 the tcl interface (this was not always the case before).  Suppose you want to
 search for all possible ways of calling the 'inter' command, then just  grep
 "tclcommand_inter_parse_[a-z]\+" *.[ch] 
 ----------------------------------------------------------------------  The
 functions parsing one level deeper are called 
 tclcommand_COMMAND_SUBCOMMAND_parse_ARGUMENT()  so, for example, the function
 which parses 'inter coulomb p3m' is  tclcommand_inter_coulomb_parse_p3m() 
 After this level, the way parsing functions are organized is too
 heterogeneous to find a unifiying naming convention without rewriting code,
 hence, all subsequent options are just appended after an underscore: 
 tclcommand_COMMAND_SUBCOMMAND_parse_ARGUMENT_OPTION()  Thus, the function
 that parses 'inter coulomb p3m tune' is 
 tclcommand_inter_coulomb_parse_p3m_tune()  The strict correspondence to the
 tcl command is also lost at this level, as for example the
 tclcommand_inter_coulomb_parse_p3m_tune() function is used to parse both the
 'tune' and the 'tunev2' options. 
 ---------------------------------------------------------------------- In
 ESPResSo, some functions involving the tcl interpreter are used just to print
 out some information, and do not parse anything (the opposite often happens).
 Even though in many cases they are also performing some operation but jut
 I/O, they have been called  tclcommand_COMMAND_print_SOMETHING  like in 
 tclcommand_inter_print_all or tclcommand_inter_print_bonded  Not in all cases
 it was possible to relate SOMETHING to a tcl command option. 
 **********************************************************************
 CALLBACKS
 **********************************************************************  All
 callbacks have now either the form  tclcallback_NAME  where NAME is the tcl
 name of the variable addressed, or they point to some default read-only
 message, like  tclcallback_ro() or tclcallback_thermo_ro(). 
 **********************************************************************
 printXYZToResult() FUNCTIONS
 **********************************************************************  All
 functions printXYZToResult() have been renamed to tclprint_to_result_XYZ() 
 ********************************************************************** MISC
 **********************************************************************  In
 addition, going through the code, all functions (not just parsers) which are
 not called anywhere have been marked with a comment like  /* TODO: this
 function is not used anywhere. To be removed? */ 
 ----------------------------------------------------------------------  This
 patch includes also some minor changes to clean the code. 
 ********************************************************************** EOF

2010-11-19 Mingyang Hu <mingyang@cmu.edu>

 * constraint.c, constraint.h, doc/ug/analysis.tex, doc/ug/part.tex,
 interaction_data.h, statistics.c, statistics.h: Add penetrable option to
 constraints; Add analyze gyration_tensor command  Add option "penetrable" to
 wall, sphere, cylinder, and maze constraint, so allow particles to pass
 throught the constraint surface. Add command "analyze gyration_tensor", which
 calculate the gyration tensor of a type of particles and returns the squared
 radius of gyration, asphericity, acylindricity, relative shape anisotropy,
 eigenvalues in descending order and their corresponding eigenvectors.

2010-11-19 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * doc/logo/logo_on_transparent.png: Added logo with transparent background.

2010-11-16 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * constraint.h: Small fixes to Rudolf's commits.

2010-11-16 Rudolf Weeber <weeber@icp.uni-stuttgart.de>

 * constraint.c, constraint.h, energy.c: Correction to external magnetic filed
 energy  * Prevent segfault in 'analyze energy' when a magnetic filed
 constraint is set * Add missing sign in energy = -<dipole_moment, field> *
 Energy of dipoles interacting with field now is still considered, when no
 dipole-dipole interaction is active

2010-11-12 Mingyang Hu <mingyang@cmu.edu>

 * packages/mbtools/examples/scripts/main.tcl: mbtools: Adjust when the
 analysis is set up in main.tcl

2010-11-11 Mingyang Hu <mingyang@cmu.edu>

 * packages/mbtools/examples/scripts/analysis.tcl,
 packages/mbtools/examples/scripts/main.tcl: mbtools: Bad comments again...

 * packages/mbtools/examples/3-4bilayer.tcl,
 packages/mbtools/examples/3-4sphere.tcl,
 packages/mbtools/examples/colloid.tcl,
 packages/mbtools/examples/cylinder.tcl,
 packages/mbtools/examples/januscolloid.tcl,
 packages/mbtools/examples/mixedbilayer.tcl,
 packages/mbtools/examples/protein.tcl,
 packages/mbtools/examples/random_DPD.tcl,
 packages/mbtools/examples/readfromfile.tcl,
 packages/mbtools/examples/simplebilayer.tcl,
 packages/mbtools/examples/sphere-bilayer.tcl,
 packages/mbtools/examples/sphere.tcl, packages/mbtools/examples/sticky2.tcl,
 packages/mbtools/examples/torus.tcl,
 packages/mbtools/examples/trappedlipids.tcl: mbtools: Correct the bad comment
 at the beginning of each file.

2010-11-10 Stefan Kesselheim <kessel@tahr.ica1.uni-stuttgart.de>

 * testsuite/lb.tcl: Reduced number of timesteps and the necessary accuracy
 for mass conservation. Now it should be a valid test for the testsuite.

2010-11-10 Mingyang Hu <mingyang@cmu.edu>

 * doc/ug/mbtools.tex, packages/mbtools/system_generation/random.tcl,
 packages/mbtools/system_generation/sphere_cap.tcl,
 packages/mbtools/utils/misc.tcl: mbtools: add new options for random
 geometry, fix bug in misc.tcl, update User's Guide  For the random geometry,
 new option -inside is added; New geometry sphere_cap is updated to the User's
 Guide; A bug in ::mbtools::utils::isoutside is fixed.

2010-11-10 Stefan Kesselheim <kessel@tahr.ica1.uni-stuttgart.de>

 * testsuite/lb.tcl: Reduced number of timesteps and the necessary accuracy
 for mass conservation. Now it should be a valid test for the testsuite.

 * lb.c, lb.h: Now I put in quite new versions of lb.c and lb.h. I hope that
 this will work now

2010-11-03 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * README, doc/dg/figs/README, doc/maggs_doc/figs/README,
 doc/tutorials/tut2/figures/README, doc/tutorials/tut2/figures/data/README,
 doc/ug/figures/README, doc/ug/ug.tex, packages/mbtools/doc/README,
 packages/mbtools/examples/forcetables/README, samples/README,
 samples/adress/README, testsuite/README: Put all license and copyright
 information for binary files into main README.

 * doc/ug/underscore.sty: Updated underscore.sty.

2010-11-03 Axel Arnold <arnolda@nana.ica1.uni-stuttgart.de>

 * scripts/init.tcl: Fixed the initial output and moved it to stderr

 * polymer.c: Fixed the polymer command

2010-10-29 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * Makefile-am.am, configure.ac: Set version to 2.9.0.

 * Makefile-am.am, config.c, packages/mbtools/doc/README: Removed RELASE_NOTES
 dependency.

 * XCodeEspresso/README, packages/mbtools/README,
 packages/mbtools/analysis/analysis.tcl, packages/mbtools/analysis/boxl.tcl,
 packages/mbtools/analysis/clusters.tcl,
 packages/mbtools/analysis/cylinder_radius.tcl,
 packages/mbtools/analysis/density_profile.tcl,
 packages/mbtools/analysis/distance.tcl, packages/mbtools/analysis/energy.tcl,
 packages/mbtools/analysis/flipflop.tcl,
 packages/mbtools/analysis/fluctuations.tcl,
 packages/mbtools/analysis/localheights.tcl,
 packages/mbtools/analysis/localorients.tcl,
 packages/mbtools/analysis/molcom.tcl, packages/mbtools/analysis/molforce.tcl,
 packages/mbtools/analysis/oop.tcl, packages/mbtools/analysis/pressure.tcl,
 .../mbtools/analysis/radial_density_profile.tcl,
 packages/mbtools/analysis/stray.tcl,
 packages/mbtools/analysis/stress_profile.tcl,
 packages/mbtools/analysis/stress_tensor.tcl,
 packages/mbtools/analysis/tiltangle.tcl, packages/mbtools/doc/analysis.html,
 packages/mbtools/doc/index.html, packages/mbtools/doc/install.html,
 packages/mbtools/doc/maintcl.html, packages/mbtools/doc/manual.html,
 packages/mbtools/doc/mmsg.html, packages/mbtools/doc/overview.html,
 packages/mbtools/doc/system_generation.html, packages/mbtools/doc/utils.html,
 packages/mbtools/examples/3-4bilayer.tcl,
 packages/mbtools/examples/3-4sphere.tcl,
 packages/mbtools/examples/colloid.tcl,
 packages/mbtools/examples/cylinder.tcl,
 packages/mbtools/examples/forcetables/README,
 packages/mbtools/examples/januscolloid.tcl,
 packages/mbtools/examples/mixedbilayer.tcl,
 packages/mbtools/examples/protein.tcl,
 packages/mbtools/examples/random_DPD.tcl,
 packages/mbtools/examples/readfromfile.tcl,
 packages/mbtools/examples/scripts/analysis.tcl,
 packages/mbtools/examples/scripts/main.tcl,
 packages/mbtools/examples/simplebilayer.tcl,
 packages/mbtools/examples/sphere-bilayer.tcl,
 packages/mbtools/examples/sphere.tcl, packages/mbtools/examples/sticky2.tcl,
 packages/mbtools/examples/torus.tcl,
 packages/mbtools/examples/trappedlipids.tcl, packages/mbtools/mbtools.tcl,
 packages/mbtools/registerpkgs.tcl,
 packages/mbtools/system_generation/constraint.tcl,
 packages/mbtools/system_generation/cylinder.tcl,
 packages/mbtools/system_generation/flat.tcl,
 packages/mbtools/system_generation/place.tcl,
 packages/mbtools/system_generation/random.tcl,
 packages/mbtools/system_generation/readfile.tcl,
 packages/mbtools/system_generation/singlemol.tcl,
 packages/mbtools/system_generation/sphere.tcl,
 packages/mbtools/system_generation/sphere_cap.tcl,
 .../system_generation/system_generation.tcl,
 packages/mbtools/system_generation/topologies.tcl,
 packages/mbtools/system_generation/torus.tcl,
 packages/mbtools/utils/math.tcl, packages/mbtools/utils/misc.tcl,
 packages/mbtools/utils/setup.tcl, packages/mbtools/utils/topo.tcl,
 packages/mbtools/utils/utils.tcl, packages/mbtools/utils/warmup.tcl,
 packages/mmsg/mmsg.tcl: Copyrighted and licensed packages/

 * samples/README: Added forgotten README.

 * .cvsignore, doc/dg/.cvsignore, doc/tutorials/tut2/scripts/analyze.tcl,
 doc/tutorials/tut2/scripts/analyze_rho.tcl,
 doc/tutorials/tut2/scripts/analzye_rho.tcl,
 doc/tutorials/tut2/scripts/replay.tcl, doc/tutorials/tut2/scripts/sim.tcl,
 doc/tutorials/tut2/scripts/sim_charged_walls.tcl,
 doc/tutorials/tut2/scripts/sim_walls.tcl, samples/.cvsignore,
 .../CECAM_Tutorial_2006/harmonic-oscillator.tcl,
 samples/CECAM_Tutorial_2006/lj_binary_liquid.tcl,
 samples/CECAM_Tutorial_2006/lj_simple_liquid.tcl,
 samples/CECAM_Tutorial_2006/single_chain.tcl,
 .../tutorial_single_chain_charged.tcl, samples/HMC+PT/README,
 samples/HMC+PT/acceptanceratio.tcl, samples/HMC+PT/aggregate-03.tcl,
 samples/HMC+PT/ave_agg_size-05.tcl, samples/HMC+PT/coulomb.txt,
 samples/HMC+PT/energy-v3.tcl, samples/HMC+PT/equilibrized.gz,
 samples/HMC+PT/hex_input.txt, samples/HMC+PT/hmc-initialize.tcl,
 samples/HMC+PT/hmc-master3.tcl, samples/HMC+PT/hmc-prepare.tcl,
 samples/HMC+PT/hmc-setup.tcl, samples/HMC+PT/hmc-watch.tcl,
 samples/HMC+PT/input.txt, samples/HMC+PT/rdf.tcl,
 samples/adress/Adress_t.tcl, samples/adress/README,
 samples/adress/tetrahedral.tcl, samples/bundle_sim2.tcl,
 samples/cell_model.tcl, samples/check_potential.tcl,
 samples/create_analysis.tcl, samples/create_bonded.tcl, samples/diamond.tcl,
 samples/espresso_logo.tcl, samples/harmonic-oscillator.tcl,
 samples/kremerGrest.tcl, samples/lj_benchmark.tcl,
 samples/lj_grandcanonical.tcl, samples/lj_liquid.tcl, samples/maggs.tcl,
 samples/pe_analyze.tcl, samples/pe_network.tcl, samples/pe_solution.tcl,
 samples/polymer_RW_sphere.tcl, samples/pong.tcl, samples/pressure.tcl,
 samples/series.tcl, samples/starwars.tcl, samples/tk_pe_solution.tcl,
 samples/tutorial.tcl, samples/watch.tcl, testsuite/.cvsignore,
 tools/series.tcl, tools/watch.tcl: Added copyright and license headers to
 some mor3e files.

 * config/cuda.m4, config/mpi.m4, cuda_init.cu, cuda_init.h: Added gpl and
 copyright headers to new files.

2010-10-29 Axel Arnold <arnolda@nana.ica1.uni-stuttgart.de>

 * polymer.c: fixed angle move

2010-10-29 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * doc/logo/logo_on_white.png, doc/logo/powered_by.gif, internal/.cvsignore,
 .../CECAM_Tutorial_2006/harmonic-oscillator.tcl,
 internal/CECAM_Tutorial_2006/lj_binary_liquid.tcl,
 internal/CECAM_Tutorial_2006/lj_simple_liquid.tcl,
 internal/CECAM_Tutorial_2006/single_chain.tcl,
 .../tutorial_single_chain_charged.tcl, internal/HMC+PT/README,
 internal/HMC+PT/acceptanceratio.tcl, internal/HMC+PT/aggregate-03.tcl,
 internal/HMC+PT/ave_agg_size-05.tcl, internal/HMC+PT/coulomb.txt,
 internal/HMC+PT/energy-v3.tcl, internal/HMC+PT/equilibrized.gz,
 internal/HMC+PT/hex_input.txt, internal/HMC+PT/hmc-initialize.tcl,
 internal/HMC+PT/hmc-master3.tcl, internal/HMC+PT/hmc-prepare.tcl,
 internal/HMC+PT/hmc-setup.tcl, internal/HMC+PT/hmc-watch.tcl,
 internal/HMC+PT/input.txt, internal/HMC+PT/rdf.tcl, internal/bundle_sim2.tcl,
 internal/cell_model.tcl, internal/create_analysis.tcl,
 internal/create_bonded.tcl, internal/cup_icon.gif, internal/diamond.tcl,
 internal/espresso_users.txt, internal/lj_benchmark.tcl, internal/logo.gif,
 internal/mpicc.modf, internal/pong.tcl, internal/starwars.tcl,
 .../CECAM_Tutorial_2006/harmonic-oscillator.tcl,
 samples/CECAM_Tutorial_2006/lj_binary_liquid.tcl,
 samples/CECAM_Tutorial_2006/lj_simple_liquid.tcl,
 samples/CECAM_Tutorial_2006/single_chain.tcl,
 .../tutorial_single_chain_charged.tcl, samples/HMC+PT/README,
 samples/HMC+PT/acceptanceratio.tcl, samples/HMC+PT/aggregate-03.tcl,
 samples/HMC+PT/ave_agg_size-05.tcl, samples/HMC+PT/coulomb.txt,
 samples/HMC+PT/energy-v3.tcl, samples/HMC+PT/equilibrized.gz,
 samples/HMC+PT/hex_input.txt, samples/HMC+PT/hmc-initialize.tcl,
 samples/HMC+PT/hmc-master3.tcl, samples/HMC+PT/hmc-prepare.tcl,
 samples/HMC+PT/hmc-setup.tcl, samples/HMC+PT/hmc-watch.tcl,
 samples/HMC+PT/input.txt, samples/HMC+PT/rdf.tcl, samples/bundle_sim2.tcl,
 samples/cell_model.tcl, samples/create_analysis.tcl,
 samples/create_bonded.tcl, samples/diamond.tcl, samples/lj_benchmark.tcl,
 samples/pong.tcl, samples/starwars.tcl: Removed internal directory,
 distributed contents on other dirs.

 * Makefile-am.am, admin/Espresso.spec, admin/espresso-2.1.2j.ebuild,
 chooser/Espresso.in, cmake/EspGenerateVersionInfo.cmake,
 cmake/EspSignalType.cmake, cmake/EspTestInline.cmake, cmake/Espresso.cmakein,
 cmake/FindFFTW3.cmake, cmake/FindMPI.cmake, cmake/FindTCL.cmake,
 cmake/TestInline.c, cmake/TestRetSigType.c, cmake/myconfig-default.h.cmakein,
 doc/Makefile.am, doc/dg/Makefile.am, doc/dg/background_errors.awk,
 doc/dg/background_errors.sh, doc/dg/figs/README, doc/dg/header.html,
 doc/dg/pages/build.doc, doc/dg/pages/cvs.doc, doc/dg/pages/doxygen.doc,
 doc/dg/pages/header.doc, doc/dg/pages/new_files.doc,
 doc/dg/pages/progguide.doc, doc/dg/pages/testsuite.doc, doc/dg/pages/ug.doc,
 doc/maggs_doc/figs/README, doc/maggs_doc/memd.tex,
 doc/tutorials/common/common.tex, doc/tutorials/tut2/figures/README,
 doc/tutorials/tut2/figures/data/README, doc/tutorials/tut2/tut2.tex,
 doc/ug/Makefile.am, doc/ug/analysis.tex, doc/ug/aux.tex,
 doc/ug/bibliography.bib, doc/ug/check_consistency.sh,
 doc/ug/contributing.tex, doc/ug/deserno.tex, doc/ug/examples.tex,
 doc/ug/features.tex, doc/ug/figures/Makefile.am, doc/ug/figures/README,
 doc/ug/firststeps.tex, doc/ug/installation.tex, doc/ug/inter.tex,
 doc/ug/internal.tex, doc/ug/introduction.tex, doc/ug/io.tex, doc/ug/latexmk,
 doc/ug/mbtools.tex, doc/ug/mmm.tex, doc/ug/part.tex, doc/ug/quickref.tex,
 doc/ug/run.tex, doc/ug/setup.tex, doc/ug/ug.tex, mpifake/mpi.c,
 mpifake/mpi.h, mpiwrap/Espresso.in, scripts/ABHmath.tcl, scripts/Makefile.am,
 scripts/auxiliary.tcl, scripts/blockfile_support.tcl, scripts/bundle.tcl,
 scripts/countBonds.tcl, scripts/init.tcl,
 scripts/obsolete/convertDeserno.tcl, scripts/obsolete/pov.tcl,
 scripts/parallel_tempering.tcl, scripts/pdb.tcl, scripts/polymer.tcl,
 scripts/statistics.tcl, scripts/tclline.tcl, scripts/vtf.tcl,
 testsuite/Makefile.am, testsuite/README, testsuite/analysis.tcl,
 testsuite/comfixed.tcl, testsuite/comforce.tcl, testsuite/constraints.tcl,
 testsuite/dh.tcl, testsuite/el2d.tcl, testsuite/el2d_die.tcl,
 testsuite/el2d_nonneutral.tcl, testsuite/fene.tcl, testsuite/gb.tcl,
 testsuite/gen_fene.tcl, testsuite/gen_harm.tcl, testsuite/harm.tcl,
 testsuite/intpbc.tcl, testsuite/intppbc.tcl, testsuite/kinetic.tcl,
 testsuite/layered.tcl, testsuite/lj-cos.tcl, testsuite/lj-generic.tcl,
 testsuite/lj.tcl, testsuite/madelung.tcl, testsuite/madelung_ewald.tcl,
 testsuite/mass.tcl, testsuite/mmm1d.tcl, testsuite/npt.tcl,
 testsuite/nsquare.tcl, testsuite/nve_pe.tcl,
 testsuite/p3m-magnetostatics-t1.dat, testsuite/p3m-magnetostatics-t1.data,
 testsuite/p3m-magnetostatics.tcl, testsuite/p3m.tcl,
 testsuite/pe_micelle.data, testsuite/pe_micelle.tcl,
 testsuite/pe_micelle_input.txt, testsuite/rotation.tcl,
 testsuite/tabulated.tcl, testsuite/test.sh.in, testsuite/tests_common.tcl,
 testsuite/thermostat.tcl, testsuite/uwerr_test.tcl, tools/Makefile.am,
 tools/set_features, tools/trace_memory.py, tools/trace_memory.tcl,
 tools/uwerr.tcl, tools/vmd_plg.tcl: Updated copyright/license header in
 subdirs.

2010-10-28 Axel Arnold <arnolda@nana.ica1.uni-stuttgart.de>

 * Makefile-am.am, config/cuda.m4, configure.ac, cuda_init.cu, cuda_init.h,
 initialize.c, utils.h: [NEW] Added support for CUDA

2010-10-28 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * binary_file.h, elc.c, elc.h, endangledist.h, energy.c, errorhandling.c,
 errorhandling.h, ewald.c, ewald.h, fft.c, fft.h, forces.c, forces.h, gb.h,
 ghosts.c, ghosts.h, global.c, global.h, grid.c, grid.h, harmonic.h,
 hertzian.h, iccp3m.c, iccp3m.h, imd.c, imd.h, initialize.c, initialize.h,
 integrate.c, integrate.h, interaction_data.c, interaction_data.h, layered.c,
 layered.h, lj.h, ljangle.h, ljcos.h, ljcos2.h, ljgen.c, ljgen.h, maggs.c,
 maggs.h, magnetic_non_p3m__methods.c, magnetic_non_p3m__methods.h, main.c,
 mdlc_correction.c, mdlc_correction.h, metadynamics.c, metadynamics.h,
 mmm-common.c, mmm-common.h, mmm1d.c, mmm1d.h, mmm2d.c, mmm2d.h, modes.c,
 modes.h, mol_cut.h, molforces.c, molforces.h, morse.h, nemd.c, nemd.h, npt.h,
 nsquare.c, nsquare.h, overlap.h, p3m-assignment.c, p3m-charges.c,
 p3m-charges.h, p3m-dipoles.c, p3m-dipoles.h, p3m.c, p3m.h, parser.c,
 parser.h, particle_data.c, particle_data.h, polymer.c, polymer.h, polynom.h,
 pressure.c, pressure.h, random.c, random.h, rattle.c, rattle.h, rotation.c,
 rotation.h, soft_sphere.h, specfunc.c, specfunc.h, statistics.c,
 statistics.h, statistics_chain.c, statistics_chain.h, statistics_cluster.c,
 statistics_cluster.h, statistics_molecule.c, statistics_molecule.h,
 steppot.h, subt_lj.h, tab.h, thermostat.c, thermostat.h, topology.c,
 topology.h, tuning.c, tuning.h, utils.c, utils.h, uwerr.c, uwerr.h, verlet.c,
 verlet.h, virtual_sites.c, virtual_sites.h, vmdsock.c, vmdsock.h: Replaced
 headers in all files.

2010-10-19 Tristan Bereau <tbereau@harry.phys.cmu.edu>

 * packages/mbtools/system_generation/sphere_cap.tcl: mbtools: added
 sphere_cap.tcl

 * packages/mbtools/system_generation/cylinder.tcl,
 packages/mbtools/system_generation/flat.tcl,
 packages/mbtools/system_generation/random.tcl,
 .../system_generation/system_generation.tcl,
 packages/mbtools/system_generation/torus.tcl: mbtools: updated shuffle
 topology

2010-10-15 Tristan Bereau <tbereau@harry.phys.cmu.edu>

 * packages/mbtools/analysis/analysis.tcl: mbtools: register
 cylinder_radius.tcl in analysis.tcl

 * packages/mbtools/analysis/cylinder_radius.tcl: [NEW] mbtools: added
 cylinder_radius analysis routine

2010-10-15 Rudolf Weeber <weeber@okapi.ica1.uni-stuttgart.de>

 * rotation.c: Fix for bug in the setting of dipole moments  Setting a dipole
 moment to (0,0,-1) resulted in a dipole of (0,0,1) being set

2010-10-14 Olaf Lenz <olenz@icp.uni-stuttgart.de>

 * AUTHORS, debug.c, debug.h, debye_hueckel.h, dihedral.h, doc/Makefile.am,
 doc/dg/Makefile.am, doc/dg/background_errors.awk,
 doc/dg/background_errors.sh, doc/maggs_doc/Makefile.am,
 doc/tutorials/Makefile.am, doc/tutorials/tut2/Makefile.am,
 doc/ug/Makefile.am, domain_decomposition.c, domain_decomposition.h, dpd.c,
 dpd.h: Added license/copyright header C-D.

 * AUTHORS, CMakeLists.txt, ChangeLog, Espresso, Espresso.in, Makefile-am.am,
 NEWS, RELEASE_NOTES, adresso.c, adresso.h, angle.h, angledist.h, bin.c,
 bin.h, binary_file.c, blockfile.c, blockfile.h, blockfile_tcl.c,
 blockfile_tcl.h, blockfile_test.c, bmhtf-nacl.h, buckingham.h, cells.c,
 cells.h, comfixed.h, comforce.h, communication.c, communication.h, config.c,
 config.h, config/Espresso.m4, config/compiler.m4, config/fftw.m4,
 config/header.txt, config/mpi.m4, config/myconfig-default.h.in, configure.ac,
 constraint.c, constraint.h, copyright.sh, internal/naming_convention.txt,
 old/RELEASE_NOTES, tools/copyright.sh: Added files required for GNU
 compliance. Added copyright headers for files from A to C.

2010-10-14 Olaf Lenz <olaf@lenz.name>

 * COPYING, GPL.TXT, LICENSE.TXT, README, configure.ac: Updated license to
 GPLv3. Removed "ESPResSo license" in LICENSE.TXT (which just contained
 additional clauses to the GPL that didn't change the license as such).
 Updated README. Made licensing to follow GNU standards.

2010-10-13 Olaf Lenz <olaf@lenz.name>

 * testsuite/lb.tcl: Added "require_feature LENNARD_JONES", adapted precision
 requirements, made test quicker.

 * .gitignore, Makefile-am.am, Makefile-am.in, acconfig.h.in, configure.ac,
 doc/Makefile.in, doc/dg/Makefile.in, doc/maggs_doc/Makefile.in,
 doc/tutorials/Makefile.in, doc/tutorials/tut2/Makefile.in,
 doc/tutorials/tut2/figures/Makefile.in, doc/ug/Makefile.in,
 doc/ug/figures/Makefile.in, scripts/Makefile.am, scripts/Makefile.in,
 scripts/bundle.tcl, scripts/obsolete/bundle.tcl, testsuite/Makefile.in,
 tools/Makefile.am: Removed generated files from repo, resurrected bundle.tcl
 (required by some tests)

2010-10-12 Olaf Lenz <olaf@lenz.name>

 * scripts/bundle.tcl, scripts/convertDeserno.tcl, scripts/init.tcl,
 scripts/obsolete/bundle.tcl, scripts/obsolete/convertDeserno.tcl,
 scripts/obsolete/pov.tcl, scripts/pov.tcl, scripts/set_features,
 scripts/vmd_plg.tcl, tools/set_features, tools/trace_memory.py,
 tools/trace_memory.tcl, tools/uwerr.tcl, tools/vmd_plg.tcl, trace_memory.py,
 trace_memory.tcl: Moved some obsolete tcl scripts to scripts/obsolete. Moved
 tools into tools subdirectory.

 * doc/ug/inter.tex, energy.h, fene.h, forces.h, harmonic.h,
 interaction_data.c: Fixed harmonic r_cut.

 * doc/ug/inter.tex, lj.h, scripts/ABHmath.tcl, testsuite/lj.tcl: Made
 parameters shift and offset optional. shift can also be "auto", then it will
 be autocomputed.

 * .gitignore: Added gitignore

2010-10-08 Rudolf Weeber <weeber@okapi.ica1.uni-stuttgart.de>

 * rotation.c, thermostat.h: When fixing any spacial coordinate of a particle,
 rotation was frozen entirely

2010-10-04 Stefan Kesselheim <kessel@tahr.ica1.uni-stuttgart.de>

 * communication.c, communication.h, lb.c, lb.h: added lbnode set command

2010-10-01 Stefan Kesselheim <Stefan.Kesselheim@icp.uni-stuttgart.de>

 * communication.c, lb-boundaries.h: Replaced MPI_INTEGER with MPI_INT since
 some implementations of MPI lack the definition of MPI_INTEGER.

2010-09-30 Florian Ruehle <floh@kuri.ica1.uni-stuttgart.de>

 * communication.c: Updated some MPI issues for LB_ELECTROHYDRODYNAMICS method

2010-09-30 Florian Fahrenberger <Florian.Fahrenberger@icp.uni-stuttgart.de>

 * communication.c: Fixed some MPI issues for the LB_ELECTROHYDRODYNAMICS
 method

2010-09-30 Stefan Kesselheim <kessel@tahr.ica1.uni-stuttgart.de>

 * lb.c: removed the fftw include in lb

 * communication.c, communication.h, config.h, lattice.c, lattice.h,
 lb-boundaries.h, lb.c, lb.h, myconfig-sample.h, particle_data.c,
 particle_data.h: added the Hickey coupling method. See publication Hickey et
 al 2010

2010-09-29 Stefan Kesselheim <Stefan.Kesselheim@icp.uni-stuttgart.de>

 * lb-boundaries.h: some changes :-)

2010-09-21 Stefan Kesselheim <Stefan.Kesselheim@icp.uni-stuttgart.de>

 * lb-boundaries.h: removed minor problems

2010-09-03 Stefan Kesselheim <Stefan.Kesselheim@icp.uni-stuttgart.de>

 * lb-boundaries.h, lb.c, lb.h: additions and correction

2010-08-26 Stefan Kesselheim <Stefan.Kesselheim@icp.uni-stuttgart.de>

 * lb-boundaries.c, lb-boundaries.h, lb.c: We realized that we have a slip,
 depending on the orientation of the LB wall and the LB cell length.

2010-08-25 Stefan Kesselheim <Stefan.Kesselheim@icp.uni-stuttgart.de>

 * lb.c, lb.h: fixed conversion factor for external forces in LB

2010-08-18 Stefan Kesselheim <Stefan.Kesselheim@icp.uni-stuttgart.de>

 * lb-boundaries.c, lb.h: lb_boundary wall, sphere, cylinder work

 * lb.c, lb.h: changes work in progress

 * communication.c, lb-boundaries.h: added some functionality for
 lb-boundaries

 * lb-boundaries.c: Implemented "lb_boundary sphere" command

2010-08-17 Stefan Kesselheim <Stefan.Kesselheim@icp.uni-stuttgart.de>

 * communication.c, communication.h, lb-boundaries.c, lb.c, lb.h: TCL command
 "lbnode x y z print boundary" works.

2010-08-16 Stefan Kesselheim <Stefan.Kesselheim@icp.uni-stuttgart.de>

 * initialize.c, lb-boundaries.c, lb.c, lb.h: Couldn't make up a test routine
 for the placement of the wall that quickly. Discovered that the bounce-back
 part at the walls doesn't work as intended.

2010-08-04 Stefan Kesselheim <Stefan.Kesselheim@icp.uni-stuttgart.de>

 * initialize.c, lb-boundaries.c, lb.c: added a few functionalities, mainly
 lbnode command

 * communication.c, communication.h, initialize.c, lattice.h, lb-boundaries.c,
 lb-boundaries.h, lb.c, lb.h: Lattice-Boltzmann arbitrary wall boundary works
 and marks fluid nodes correctly.

2010-07-19 Stefan Kesselheim <Stefan.Kesselheim@icp.uni-stuttgart.de>

 * communication.c, communication.h, initialize.c, initialize.h,
 lb-boundaries.c, lb-boundaries.h, lb.h: Half merged version (version before
 branching + Ulis LB version + 2 new lb-boundary.c/.h from Stefan). Not
 functional, only for Stefan.

 * lattice.h: *** empty log message ***

 * communication.c, config.c, halo.c, halo.h, initialize.c, integrate.c,
 lattice.c, lattice.h, lb-boundaries.c, lb-boundaries.h, lb-d3q19.h, random.h,
 statistics_fluid.c, statistics_fluid.h, thermostat.c: some more added
 features, homogenized stuff and so on.

2010-10-14  Olaf Lenz  <olenz@icp.uni-stuttgart.de>

 * Started ChangeLog. For older changes, see ./old/RELEASE_NOTES.
