#############################################################################
BETA PUBLIC RELEASE VERSION 0.3.0       02-01-04
#############################################################################
APBS is now supported by the NIH via NIGMS grant GM69702-01.

  CHANGES THAT AFFECT USERS:
  - NEW FEATURES
    * New version of the documentation
    * New directory structure in tools/
    * Finished fe-manual mode for ELEC calculations -- this is the adaptive
      finite element solver
    * Added documetnation for fe-manual
    * New apbs/tools/manip/inputgen.py script to automatically generate input
      APBS files from PQR data
    * Added new asynchronous mode in mg-para parallel calculations to enable
      running on-demand and/or limited resources
    * Added new script (tools/manip/async.sh) to convert mg-para calculations
      in mg-async calculations
    * Added following aliases for some of the more obscure parameters in the
      input files:
        chgm 0 ==> chgm spl0
        chgm 1 ==> chgm spl2
        srfm 0 ==> srfm mol
        srfm 1 ==> srfm smol
        srfm 2 ==> srfm spl2
        bcfl 0 ==> bcfl zero
        bcfl 1 ==> bcfl sdh
        bcfl 2 ==> bcfl mdh
        bcfl 4 ==> bcfl focus
        calcenergy 0 ==> calcenergy no
        calcenergy 1 ==> calcenergy total
        calcenergy 2 ==> calcenergy comps
        calcforce 0 ==> calcforce no
        calcforce 1 ==> calcforce total
        calcforce 2 ==> calcforce comps
      Example input files have been updated to reflect this change.  NOTE:
      the code is backward-compliant; i.e., old input files WILL still work.
    * Added new READ options "PARM" and "MOL PDB", see documentation for more
      information.  These options allow users to use unparameterized PDB files
      together with a parameter database.
    * Updated the documentation
    * Now include support for chain IDs and other optional fields in PQR/PDB
      files
    * Added support for parsing PDB files
    * Renamed:
        amber2charmm -> amber2charmm.sh
        pdb2pqr -> pdb2pqr.awk
        qcd2pqr -> qcd2pqr.awk
    * Added a new Python-based pdb2pqr (tools/conversion/pdb2pqr) script that 
      allows users to choose parameters from different forcefields.
    * Updated Python wrappers (tools/python) and added the python directory to 
      autoconf/automake.
    * Reformatted examples/README.html for readability.

  - BUG FIXES
    * Fixed bug in PQR parsing that can cause PDB/PQR files to be mis-read when
      they contain residues with numbers in their names (Thanks to Robert
      Konecny and Joanna Trylska)
    * Fixed bug when writing out number/charge density:  unrealistic densities
      reported inside iVdW surface.
    * Fixed bug in VMD read_dx utility
    * Invalid map IDs now result in an error message instead of a core dump 
      (thanks to Marco Berrera)
    * Modified mechanism for cubic-spline output, fixing a bug associated with
      zero-radius atoms
    * Fixed omission of srfm in sections of  documentation (thanks to Sameer 
      Varma)
    * Made autoconf/automake configure setup more robust on Solaris 8 platforms
      (thanks to Ben Carrington)

  CHANGES THAT AFFECT DEVELOPERS:
  * New docuemtnation setup
  * New tools/ directory structure
  * Changed Vgreen interface and improved efficiency
  * Changed Vopot interface to support multiple grids
  * Added several norm and seminorm functions to Vgrid class
  * Altered --with-blas syntax in configure scripts and removed --disable-blas
  * Documented high-level frontend routines
  * Cool new class and header-file dependency graphs courtesy of Doxygen and
    Graphviz
  * Added substantial mypde.c-based functionality to Vfetk
  * Moved chgm from PBEparm to MGparm
  * Minor changes to Vfetk: removed genIcos and added genCube
  * FEM solution of RPBE working again (see test/reg-fem) and is probably
    more up-to-date than test/fem
  * Updated API documentation
  * Changed many NOsh, FEMparm, MGparm variables to enums
  * Changes to Valist and Vatom classes
  * Fixed minor bugs in documentation formatting
  * Made Vopot more robust
  * Created Vparam class for parameter file parsing
  * Added vparam* parameter database flat files to tools/conversion/param
 
#############################################################################
BETA PUBLIC RELEASE VERSION 0.2.6       01-17-03
#############################################################################
 
  * Changed license to GPL 
  * Made a few routines compliant with ANSI X3.159-1989 by 
	removing snprintf (compliant with ISO/IEC 9899:1999).  This is basically
    for the sake of OSF support.


#############################################################################
BETA PUBLIC RELEASE VERSION 0.2.5       11-21-02
#############################################################################

  * Improved consistency between energies evaluated with "chgm 0" and "chgm 1"
  * Made charge-field energy evaluation consistent for user-supplied charge
    maps
  * Added new psize.py script courtesy of Todd Dolinsky.
  * Updated list of APBS-related tools in User Guide.
  * Added RPM capabilities courtesy of Steve Bond.
  * Removed annoying excess verbosity from Vgrid.
  * Updated Blue Horizon compilation instructions (thanks to Robert Konecny and
    Giri Chukkapalli)
  * Updated autoconf/automake/libtool setup and added --disable-tools option

#############################################################################
BETA PUBLIC RELEASE VERSION 0.2.4       10-21-02
#############################################################################

  * Fixed bug which set one of the  z-boundaries to zero for "bcfl 1".  This
	can perturb results for systems where the grid boundaries are particularly
	close to the biomolecule.  While this is an embarassing bug, most systems
    using settings suggested by the psize script appear largely unaffected
	(see examples/README.html).  Thanks to Michael Grabe for finding this bug
    (Michael, you can stop finding bugs now...)
  * Updated VMD scripts to agree with the current OpenDX output format
  * A COMMENT:  As far as I can tell, the current version of OpenDX-formatted
    output (same as version 0.2.3) is fully compliant with the OpenDX
    standards (see, for example, 
    http://opendx.npaci.edu/docs/html/pages/usrgu065.htm#HDRXMPLES).  
    However, I realize this is different than the format for previous versions
    and would encourage all users to update their APBS-based applications to
    accomodate these changes.  The best solution would be for all downstream
    applications to use the APBS Vgrid class (see
	http://agave.wustl.edu/apbs/doc/api/html/group__Vgrid.html) to manipulate
    the data since this class should remain internally consistent between
    releases.  Finally, I would love to have some OpenDX guru who uses APBS to
	contact me so I can solidfy the data ouput format of APBS.  I'm about ready
    to permanently switch to another format if I can't reach a consensus with
    OpenDX...
#############################################################################
BETA PUBLIC RELEASE VERSION 0.2.3       10-09-02
#############################################################################

  * Fixed bugs in salt-dependent Helmholtz/nonlinear term of PBE affecting
	both LPBE and NPBE calculations.  While this bug fix only changes most 
    energies by < 2 kJ/mol, it is recommended that all users upgrade.  Many
    thanks to Michael Grabe for finding and carefully documenting this bug!
  * A parameter (chgm) has been added which controls the charge discretization
    method used.  Therefore, this version contains substantial changes in both
	the API and input file syntax.  Specifically:
    - PBEparm has two new members (chgm, setchgm)
    - Vpmg_fillco requires another argument
    - Vpmg_*Force functions require additional arguments
    - Input files must now contain the keyword "chgm #" where # is an integer
    Please see the documentation for more information.
  * Fixed problems with "slicing" off chunks of the mesh during I/O of focused
    calculations
  * Updated authors list
  * New CHARMM parameters -- Robert Konecny
  * Created enumerations for common surface and charge discretization methods
  * Added Vmgrid class to support easy manipulation of nested grid data
  * Added more verbosity to error with NPBE forces
  * Added working Python wrappers -- Todd Dolinksy
  * Modified VMD scripts read_dx and loadstuff.vmd


#############################################################################
BETA PUBLIC RELEASE VERSION 0.2.2       08-14-02
#############################################################################

  * There were several other changes along the way... I lost track.
  * Changed coordinate indexing in some energy calculations
  * Updated documentation to reflect recent changes on Blue Horizon
  * Improved speed of problem setup BUT NOW RESTRICT use of input coefficient
    maps (see documentation)
  * Updated documentation, placing particular emphasis on use of Intel
    compilers and vendor BLAS on Intel Linux systems
  * Fixed bug for nonpolar force evaluation in Vpmg_dbnpForce
  * Removed MG test scripts -- use bin/*.c for templates/testing
  * Made main driver code completely memory-leak free (i.e., if you wanted to
    wrap it and call it repeatedly -- Thanks to Robert Konecny)
  * Fixed main driver code for compatibility with SGI compilers (Thanks to
    Fabrice Leclerc)
  * Made focused evaluation of forces more sensible.
  * Added 'print force' statement
  * Fixed bug in OpenDX input/output (OpenDX documentation is lousy!)

#############################################################################
BETA PUBLIC RELEASE VERSION 0.2.1       04-23-02
#############################################################################
This version requires the latest version of MALOC to work properly!
  * Syntax changes
    - The writepot and writeacc keywords have been generalized and new I/O
      features have been added.  The syntax is
      now:  write pot dx potential
            write smol dx potential
            etc.
      Please see the User's Manual for more information
    - The read keywords has been generalized and new I/O features have been
      added which support the use of pre-calculated coefficient grids, etc..
      The correct syntax for reading in a molecule is now 
      "read mol pqr mol.pqr end"; please see the User's Manual for more
      information.
    - The "mg" keyword is no longer supported; all input files should use
      "mg-manual" or one of the other alternatives instead.
  * A change in the behavior of the "calcenergy" keyword; passing an argument
    of 2 to this keyword now prints out per-atom energies in addition to the
    energy component information
  * A new option has been added to tools/manip/acc to give per-atom solvent-
    accessible surface area contributions
  * A new option has been added to tools/manip/coulomb to give per-atom 
    electrostatic energies
  * Added tools/mesh/dxmath for performing arithmetic on grid-based data (i.e.,
    adding potential results from two calculations, etc.)
  * Added tools/mesh/uhbd_asc2bin for converting UHBD-format grid files from
    ASCII to binary (contributed by Dave Sept)
  * Improvement of VMD visualization scripts (contributed by Dave Sept)
  * The API has changed significantly; please see the Programmer's Manual.
  * Working (but still experimental) Python wrappers for major APBS functions.
  * More flexible installation capabilities (pointed out by Steve Bond)
  * Added ability to use vendor-supplied BLAS
  * Brought up-to-date with new MALOC

#############################################################################
BETA PUBLIC RELEASE VERSION 0.2.0       03-20-02
#############################################################################
This version is a public (beta) release candidate and includes:
  * Slight modification of the user and programmer's guides
  * Scripts for visualization of potential results in VMD (Contributed by Dave
    Sept)
  * Corrections to some of the example input files
  * A few additional API features
This release requires a new version of MALOC.

#############################################################################
PRE-BETA (NOT FOR PUBLIC RELEASE) VERSION 0.1.8       01-29-02
#############################################################################
This version is a public (beta) release candidate and includes the following
bug-fixes:
  * Added warning to parallel focusing 
  * Added several test cases and validated the current version of the code for
    all but one (see examples/README.html)
  * Fixed atom partitioning bug and external energy evaluation during focusing
  * Added new program for converting OpenDX format files to MOLMOL (by
    Jung-Hsin Lin)
You should definitely upgrade, the previous versions may produce unreliable
results.

#############################################################################
PRE-BETA (NOT FOR PUBLIC RELEASE) VERSION 0.1.7       12-13-01
#############################################################################
This version is a public (beta) release candidate and includes the following
bug-fixes:
  * Fixed I/O for potential in UHBD format (thanks, Richard!)
  * Re-arranged garbage collection routines in driver code
  * Improved FORTRAN/C interfaces
  * Re-configured autoconf/libtool setup for more accurate library version
    number reporting

#############################################################################
PRE-BETA (NOT FOR PUBLIC RELEASE) VERSION 0.1.6       11-17-01
#############################################################################
This version is a public (beta) release candidate and includes the following
bug-fixes and features:
  * Fixed printf formatting in UHBD potential output
  * Added input file support for parallel focusing
  * Fixed small bug in parsing writeacc syntax (thanks, Dave)
  * Added output file support for parallel focusing
  * Changed some documentation
You need to download a new version of MALOC for this release.

#############################################################################
PRE-BETA (NOT FOR PUBLIC RELEASE) VERSION 0.1.5       10-25-01
#############################################################################
This version features minor bug fixes and several new features:
  * Fixed shift in center of geometry for OpenDX I/O
  * Made energy evaluation more robust when using NPBE
  * Rearrangments of files and modified compilation behavior
  * Input file support for ion species of varying valency and concentration
  * Input file support incorrect nlev/dime combinations; APBS now finds 
    acceptable settings near to the user's requested values
  * "Automatic focusing".  Users now simply specify the physical parameters
    (temperature, dielectric, etc.), the coarse and fine grid lengths and
    centers, and APBS calculates the rest

#############################################################################
PRE-BETA (NOT FOR PUBLIC RELEASE) VERSION 0.1.4       09-18-01
#############################################################################
This version features major bug fixes introduced in the 0.1.3 release:
  * Chain ID support has been **removed** from the PDB/PQR parser (if anyone
    has a nice, flexible PDB parser they'd like to contribute to the code, I'd
    appreciate it)
  * Configure script has been made compatible with OSF
  * Bug fix in disabling FEtk-specific header files

#############################################################################
PRE-BETA (NOT FOR PUBLIC RELEASE) VERSION 0.1.3       09-13-01
#############################################################################
This version features a few improvements in scripts, PDB parsing flexibility,
and portability, including:
  * Dave Sept upgraded the psize and shift scripts to allow more flexibility in
    PDB formats.
  * Chain ID support has been added to the PDB/PQR parser
  * Removed -g from compiler flags during linking of C and FORTAN under OSF
    (thanks to Dagmar Floeck and Julie Mitchell for help debugging this
     problem)

#############################################################################
PRE-BETA (NOT FOR PUBLIC RELEASE) VERSION 0.1.2       09-02-01
#############################################################################
This version is mainly designed to increase portability by switching to libtool
for library creation and linking.  Of course, it also contains a few bug fixes.
Highlights include:
  * Changes to the User Manual
  * Addition of a Programmer's Manual
  * Various FEtk-related things (no particular impact to the user)
  * Improvements to the test systems
  * Change in the format for printing energies
  * Change in directory structure
  * Fixed centering bug in main driver (only impacted I/o)
  * Fixed error message bug in VPMG class
  * Fixed grid length bug (popped up during sanity checks) in VPMG class
  * Switched to libtool for linking
Note that Compaq Tru64 Alpha users may still experience problems while
compiling due to some strangess with linking C and FORTRAN objects.

#############################################################################
PRE-BETA (NOT FOR PUBLIC RELEASE) VERSION 0.1.1       08-29-01
#############################################################################
I am slightly less pleased to announce the first bug-fix for APBS, version
0.1.1.  This fixes compilation problems that popped up for several folks,
including:
  * Syntax errors with non-GNU compilers
  * Errors in the installation instructions
  * Installation of binary in machine-specific directory

#############################################################################
PRE-BETA (NOT FOR PUBLIC RELEASE) VERSION 0.1.0       08-29-01
#############################################################################
I am pleased to announce the availability of a pre-beta version of the
Adaptive Poisson-Boltzmann Solver (APBS) code to selected research
groups.  APBS is new software designed to solve the Poisson-Boltzmann
equation for very large biomolecular systems.  For more information,
please visit the APBS web site at http://mccammon.ucsd.edu/apbs.

This release is designed to allow interested users to get familiar
with the code.  It is not currently fully functional; it only provides
for the sequential multigrid (Cartesian mesh) solution of the
linearized and nonlinear Poisson-Boltzmann equation.  User-friendly
parallel support will be incorporated into the next release.  Other
limitations that may impact its immediate usefulness are:
    * No finite element support.  This is awaiting the public release
      of the Holst group's FEtk library.
    * Somewhat inefficient coefficient evaluation (i.e., problem
      setup).  This should be fixed in the next release or two.
Rather than serving as a production code, this release represents a
request for help in breaking the software and finding its deficiencies
before a public beta.

If you are interested in testing this early release, please go to
http://wasabi.ucsd.edu/~nbaker/apbs/download/.  Since this is not a
public release of APBS, you will need to enter the user-name
"apbs-beta" and the password "q94p$fa!" for access to this site.  Once
there, please follow the instructions to download and install APBS.

If you are not interested in trying out this early release, but would
like to stay informed about subsequent versions of APBS, please
consider subscribing to the APBS announcements mailing list by sending
the message "subscribe apbs-announce" to majordomo@mccammon.ucsd.edu.

Thank you for your time and interest in the APBS software.

