Version 0.1
Table of Contents

1. Overview
2. Information and Resources
3. Obtaining GAMer
4. Frequently Asked Questions
5. Installation Instructions
6. Author Information
7. Copyright and Terms of Use
8. GNU GPL

NOTE: This documentation provides information about installation, configuration, and general usage of the GAMer libraries. Information about the programming interface provided by the GAMer software can be found in the Programmer's Guide.

Overview
GAMer (Geometry-preserving Adaptive MeshER) is mesh generation tool that produces high-quality simplex meshes of surfaces and volumes (see figures below). It is built on top of two state-of-the-art mesh generators: Triangle (for 2D constrained Delaunay meshes in the plane) and Tetgen (for 3D constrained Delaunay meshes in space), combined with a collection of algorithms for generating, improving, refining, and decimating surface triangulations of imbedded interior or exterior domain surfaces. GAMer can be used as a small stand-alone adaptive mesh generator.
GAMer can take as input a number of formats, including PDB, PQR, OFF, RawIV, and XYZR. The PDB is a standard format used in the Protein Data Bank for bio-molecules. A PQR format may be generated from PDB using PDB2PQR. The OFF is a format used in Geomview for mesh representation. More details on this format may be found at here. GAMer can also generate meshes from a 3D volume represented RawIV as used internally in CVC at UT-Austin. The XYZR format is a simplified version of the PDB/PQR format, which contains only the center (xyz) and radius (r) of each atom in a molecule. A brief structure of GAMer is shown in the following figure.
GAMer was designed primarily to generate high-quality and adaptive meshes for biomedical simulation, although it can also be used for general problems that require "good" surface and tetrahedral meshes. The outputs of GAMer can be used directly in FETK or, with slight modifications, in other finite element based numerical solvers. Ongoing projects include efficient algorithms for tetrahedral mesh smoothing and localized mesh deformation for simulation of molecular/cellular dynamics.

Information and Resources
Detailed information about GAMer can be found in the User's Guide and Programmers's Guide.
While GAMer is itself a self-contained software package, it is one of several components of FETK (the Finite Element ToolKit). FETK consists of the following components written in Clean OO C:

- MALOC - Minimal Abstraction Layer for Object-oriented C programs.
- PUNC - Portable Understructure for Numerical Computing.
- GAMer - Geometry-preserving Adaptive MeshER (uses MALOC).
- SG - Socket Graphics mesh display tool (uses MALOC).
- MC - Manifold Code finite element package (uses MALOC and PUNC).
- MCX - MC eXtension libraries (uses MALOC, PUNC, and MC).

MALOC is self-contained, and requires only an ANSI-C compiler on a UNIX or Win32 platform. PUNC, GAMer, SG, and MC are also self-contained, but rely on MALOC having been previously installed on the platform. Additional features of MC are enabled if PUNC is available, but PUNC is not required to build MC. The MC eXtension libraries MCX are constructed on top of MALOC and MC, and in order install and use MCX one must first correctly configure and install both MALOC and MC. MCX is made up of a number of individual libraries developed by members of our group, or contributed by one of a number of colleagues. More information about FETK can be found on the FETK website:

- http://www.fetk.org/

Obtaining GAMer
GAMer is copyrighted, but is redistributable in source and binary form under the following license. The GAMer source can be downloaded from the FETK Download Page.
GAMer uses the low-level FETK abstraction library MALOC, which must be installed before installing GAMer.

Frequently Asked Questions
Why did you develop GAMer, given many other mesh generation packages?
The existing mesh generation tools for biomedical applications, especially bio-molecular surface and volumetric mesh generation, are suffering from either being slow or having poorly-shaped angles (too small or too large). GAMer was developed in the hope that it could provide a fast tool of finite element mesh generation with the following properties: (1) feature-preservation, (2) local adaptivity, (3) high quality (measured by angles), and (4) smoothness (for surface meshes).
What is in all of these subdirectories? Where exactly is "GAMer"?
GAMer consists of several (class) libraries from which you will call routines to handle your application. You will need to write a main driver program (and any supporting routines you need to define your problem) and then link to the libraries. As described in the file "INSTALL", you will build all of the libraries in one shot for your particular architecture, along with a test program to verify that the various pieces are functioning correctly. After the build, you will be ready to work with your particular application main driver, and you just need to link to the libraries. Sample main drivers and makefiles are in the "gamer/tools/*" subdirectories. Things are setup for you to work completely in one of those directories. Of course, all you really have to do is link to the GAMer libraries, so you can use it how you like; the makefiles and drivers in "gamer/tools/*" just provide an example of how to get GAMer working correctly.
The following directory tree is created when you unpack the GAMer "GAMer.tgz" distribution file by following the instructions in the INSTALL document:

                                       GAMer
                                         |
                             ------------------------
                            /    |      |       |    \
                         config  doc  examples  src tools

The src directory has the additional subdirectory structure for each library forming GAMer:

                                        src
                                         |
                          ------------------------------
                         /    |      |    |     |       \
                    aaa_inc aaa_lib base biom tetgen triangle

Within each library source directory is an additional subdirectory, "GAMer". The "GAMer" subdirectory contains public headers for the library, representing the library API; these headers will be installed in the specified header install directory during the install procedure after building GAMer.
The following is a brief description of each subdirectory of the package.

        gamer              - The entire GAMer package
        gamer/config       - GNU Autoconf scripts and non-unix config files
        gamer/doc          - GAMer documentation
        gamer/examples     - Complex examples and data files for using GAMer
        gamer/src          - GAMer source code (all source and headers)
        gamer/src/aaa_inc  - Header installation tools
        gamer/src/aaa_lib  - Library installation tools
        gamer/src/*/gamer  - The GAMer headers (API)
        gamer/src/base     - Source for M. Holst's BASE (GAMer foundation)
        gamer/src/biom     - Source code for GAMer mesh generation/processing
        gamer/src/tetgen   - Source code for tetrahedral generation (TetGen)
        gamer/src/triangle - Source code for triangle generation (Triangle)
        gamer/tools        - Some examples for use with gamer

Okay, I seem to have installed GAMer correctly; how do I actually use it now?
GAMer can be called as a subroutine or used as a stand-alone program. There are examples in "/tools/MeshGen.C" for both cases. When GAMer is called as a subroutine, it returns the tetrahedral meshes into a data structure called GemMesh defined as follows (similar to the mcsf format used in FETK):

        typedef struct {
          int dim;
          int dimii;
          int vertices;
          int simplices;
          FETK_VX *vv;
          FETK_SS *ss;
        } GemMesh;

where FETK_VX and FETK_SS are defined as:

        typedef struct {
          int id;
          int chrt;
          float x;
          float y;
          float z;
        } FETK_VX;

        typedef struct {
          int id;
          int grp;
          int mat;
          int fa;
          int fb;
          int fc;
          int fd;
          int na;
          int nb;
          int nc;
          int nd;
        } FETK_SS;

When GAMer is used as a stand-alone program, it writes the results into a file named "abc.pdb.output.out.m", assuming that the input be named "abc.pdb". This format can be used directly in FETK. The output tetrahedra may be given in three forms in case of the molecular mesh generation, where a large bounding sphere is used around the molecule:
(1) The tetrahedral mesh is generated both inside and outside the molecule:

            Usage: GAMer abd.pdb 1

(2) The tetrahedral mesh is generated only inside the molecule:

            Usage: GAMer abd.pdb 2

(3) The tetrahedral mesh is generated only outside the molecule:

            Usage: GAMer abd.pdb 3

How do I specify the active sites of a molecule?
one or more active sites may be specified for a molecule, such that the mesh generated may be made denser near the active site than the mesh elsewhere and indexed differently. To generate the mesh with active sites, one can use the following sample command:

            Usage: GAMer abd.pdb 1(2 or 3) active_site.dat,

where the active_site.dat is defined by a list of spheres as follows:

        # First Line:
        #     # of active sites, and # of spheres in each active site
        #
        # The remaining lines are grouped by active sites.
        # For each line of an active site:
        #     (x,y,z): coordinates of sphere centers
        #     (r): radius of the sphere
        #     (index): the index used to represent the active site
        #
        # Note that 2,4,5 have been reserved for other purposes
        # So, don't use these numbers for index
        #
        n m
        x11 y11 z11 r11 1
        x12 y12 z12 r12 1
        ...
        x1m y1m z1m r1m 1
        x21 y21 z21 r21 2
        x22 y22 z22 r22 2
        ...
        x2m y2m z2m r2m 2
        ....
        ....

How do I modify the "hidden" parameters in GAMer?
All the "hidden" parameters may be modified in the header "gamer/src/biom/gamer/biom.h". We plan to expose some of these parameters in a later version using a graphical user interface.

Installation Instructions
Available distribution formats
GAMer is distributed in both binary format (as a binary RPM file GAMer-VERSION.i386.rpm for i386-based versions of Linux) and in source format (as a source RPM file GAMer-VERSION.src.rpm and as a gzipped tar file "GAMer-VERSION.tar.gz").
Installation using the binary RPM file
The following rpm command will install all of the GAMer headers and libraries into /usr/local/include and /usr/local/lib, and will install the GAMer documentation into /usr/share/doc/packages/GAMer:

        rpm -Uvh GAMer-VERSION.i386.rpm

Installation and rebuilding from sources using the source RPM file
The following rpm command will unpack the source rpm file "GAMer-VERSON.src.rpm" into the GAMer gzipped tar file containing the sources called "GAMer-VERSION.tar.tar.gz" and into a small RPM spec file called "GAMer-VERSON.spec":

        rpm -Uvh GAMer-VERSION.src.rpm

The sources can then be unpacked and built using the directions for the gzipped tar file below. Alternatively, the following rpm command will do these steps for you:

        rpm -bp GAMer-VERSION.spec

Rebuilding binary and source RPM files from the gzipped tar file
The GAMer sources contain the RPM spec file "GAMer-VERSON.spec" in the root source directory; as a result, rebuilding the RPM files from sources can be done using the rpm command:

        rpm -ta GAMer-VERSION.tar.gz

The result will be the corresponding source and binary rpm files, named "GAMer-VERSON.src.rpm" and "GAMer-VERSION.i386.rpm". Normally, these files are written to /usr/src/redhat/SRPMS and /usr/src/redhat/RPMS respectively, but you must be logged in as root for these to work. The destination directories can be overriden using arguments to the rpm program (see the rpm manpage).
Installation and building from sources using the gzipped tar file
The following command will unpack GAMer into a number of subdirectories and files on any UNIX machine (and on any WinNT machine with the GNU-Win32 tools gzip and tar).

        gzip -dc GAMer.tgz | tar xvf -

GAMer is essentially a multilevel adaptive finite element "kernel". It is designed to be easily extended through the use of extension packages which are constructed on top of GAMer. The extension packages that I have written such such as GAMergp (GAMer for Geometric PDEs) are also distributed as gzipped tar files (e.g. "GAMergp.tgz"). The installation instructions for such extension packages are identical to the instructions below for the GAMer kernel (e.g., substitute "GAMergp" for every occurance of "GAMer" below).
Building the package using the GNU "configure" shell script and "make"
The "configure" shell script in the "GAMer" directory (the toplevel directory created when you unpacked the GAMer tgz file) will build the entire package. This is a standard GNU autoconf-generated configuration script. For a list of the possible configuration options, type:

        ./configure --help

You should be able to build GAMer by simply typing:

        ./configure
        make
        make install

However, it is often advantageous to keep the original source directory pristine; the configure script can actually be run outside the source tree, which will keep all files created by the build outside the source tree. (This idea is related to the section below describing how to build binaries for multiple architectures at the same time using the same source tree, and requires that your version of make has the VPATH facility, such as GNU make.) For example, I build GAMer in a separate directory from the source tree as follows:

        gzip -dc GAMer.tgz | tar xvf -
        mkdir GAMer_build
        cd GAMer_build
        ../GAMer/configure
        make
        make install

Building binaries for multiple architectures in the same source directory
If you have a version of "make" that supports the VPATH facility (such as any recent version of GNU make), then you can build the package for multiple architectures in the same source directory (in fact, you can do the compiles at the same time without collisions). This is very useful if you have your home directory on an NFS volume that you share among multiple architectures, such as SGI, Linux, etc. To build GAMer for all the systems at the same time, you simply make an additional subdirectory in the main GAMer directory for each architecture, copy "configure" into it, "cd" into the subdirectory, and then install as above. For example, on a linux machine you would do the following:

        mkdir linux
        cp configure linux/.
        cd linux
        ./configure
        make
        make install

If you mount the same NFS home directory on for example an OpenStep box, you could at the same time do the following:

        mkdir next
        cp configure next/.
        cd next
        ./configure
        make
        make install

Again, both builds can actually be done outside the source tree rather than in a subdirectory of the source tree, as described in the previous section.
Rebuilding the configure script and the Makefile.in files
If for some reason you actually need to rebuild the configure script or the Makefile.in files using the GNU autoconf suite, you should read the block of documentation at the top of the configure.in file. The commentary I put there explains exactly how the GNU autoconf suite must be used and in what order, and exactly what files are produced at each step of the process. A script called "bootstrap" which automates this process is located in the config subdirectory of the GAMer source tree.
Platform-specific information
Below is some platform-specific build/usage information for GAMer.

- Linux (Source: M. Holst, UCSD)
  Things should work as described above.
- FreeBSD/NetBSD/OpenBSD (Source: M. Holst, UCSD)
  Things should work as described above.
- OpenStep (Source: M. Holst, UCSD)
  Things should just work, but you may have to set the CC environment variable as follows before typing ./configure:

          export CC="/bin/cc"

  or you might need to use:

          export CC="/bin/cc -ObjC"

- IRIX (Source: M. Holst, UCSD)
  If you are on a 64-bit IRIX box such as an Onyx, Octane, or Origin, set the CC environment variable as follows before typing ./configure:

          export CC="/bin/cc -64"

  If you are on a 32-bit IRIX box such as an O2 or Indy, set the CC environment variable as follows before typing ./configure:

          export CC="/bin/cc -32"

- Win32 (Source: M. Holst, UCSD)
  Unless you have the Cygwin environment, you need to use one of the included project file collections for one of the commercially available ANSI C or C++ compilers for the Win32 environment.

Debugging using the ElectricFence malloc debug library
To allow ElectricFence to intercept all calls to malloc, free, and related dynamic memory allocation system calls, simply run the configure script as follows:

        ./configure --enable-efence
        make clean; make; make install

Author Information
GAMer was developed primarily by Zeyun Yu in the Holst Research Group at UC San Diego. Below is a credits list for the people that have contributed to GAMer in one way or another. The fields below follow the credits file format used in the Linux kernel CREDITS file to allow for easy manipulation via shell scripts. The fields are as follows:

              N: name of contributor
              E: email address
              W: web address
              P: PGP key ID and fingerprint
              D: description of primary contributions
              S: snail-mail address

    N: Zeyun Yu
    E: zeyu@math.ucsd.edu
    D: GAMer/doc/*             -- Package documentation (with M. Holst)
    D: GAMer/examples/*        -- Package examples (in progress)
    D: GAMer/src/biom/*        -- Main source code of GAMer
    D: GAMer/tools/*           -- Tools built on the libraries
    S: Department of Mathematics
    S: UC San Diego
    S: La Jolla, CA 92093 USA

    N: Michael Holst
    E: mholst@ccom.ucsd.edu
    W: http://ccom.ucsd.edu/~mholst
    P: 1024/0xB5212DCD
    D: Makefile*               -- Makefiles for GAMer
    D: GAMer/acconfig.h        -- Platform abstraction information
    D: GAMer/configure.in      -- GNU autoconf/automake structure
    D: GAMer/config/*          -- GNU autoconf/automake shell scripts
    D: GAMer/doc/*             -- Package documentation (with Z. Yu)
    D: GAMer/src/aaa_inc/*     -- Library header build structure
    D: GAMer/src/aaa_lib/*     -- Static/shared library build structure
    D: GAMer/src/base/*        -- Foundation headers
    S: Department of Mathematics
    S: UC San Diego, AP&M 5739
    S: La Jolla, CA 92093 USA

Software included in the GAMer source code package
A complete roadmap to the source code forming the GAMer package can be found above. While the core GAMer functions were developed by Zeyun Yu, the following libraries are currently also included with GAMer:

        GAMer/src/tetgen/     -- Quality Tetrahedral Mesh Generator and
                                 3D Delaunay Triangulator
                                 (provided by Hang Si)
        GAMer/src/triangle/   -- Two-Dimensional Quality Mesh Generator
                                 and Delaunay Triangulator
                                 (provided by Jonathan Richard Shewchuk)

Contacting the Author
If you have questions or comments about GAMer, please feel free to contact us at zeyu@math.ucsd.edu or mholst@math.ucsd.edu.

Copyright and Terms of Use
Please acknowledge your use of GAMer by citing:

- Z. Yu, M. Holst, Y. Cheng, and J.A. McCammon, Feature-Preserving Adaptive Mesh Generation for Molecular Shape Modeling and Simulation. Journal of Molecular Graphics and Modeling, 26(8) (2008), pp. 1370-1380.

This version of GAMer is distributed under the following guidelines:

- GAMer (Geometry-preserving Adaptive MeshER)
  Copyright (C) 2007-- Zeyun Yu and Michael Holst
  This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
  You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.

GNU GPL
The GPL (GNU General Public License) below is copyrighted by the Free Software Foundation. However, the instance of software that it refers to, my package in this case, is copyrighted by myself as the author of the package. Any additional software that I distribute with my software is copyrighted by the authors of those pieces of software (see the individual source files for author information). ---Zeyun Yu and Michael Holst

    		    GNU GENERAL PUBLIC LICENSE
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    distribute so as to satisfy simultaneously your obligations under this
    License and any other pertinent obligations, then as a consequence you
    may not distribute the Program at all.  For example, if a patent
    license would not permit royalty-free redistribution of the Program by
    all those who receive copies directly or indirectly through you, then
    the only way you could satisfy both it and this License would be to
    refrain entirely from distribution of the Program.

    If any portion of this section is held invalid or unenforceable under
    any particular circumstance, the balance of the section is intended to
    apply and the section as a whole is intended to apply in other
    circumstances.

    It is not the purpose of this section to induce you to infringe any
    patents or other property right claims or to contest validity of any
    such claims; this section has the sole purpose of protecting the
    integrity of the free software distribution system, which is
    implemented by public license practices.  Many people have made
    generous contributions to the wide range of software distributed
    through that system in reliance on consistent application of that
    system; it is up to the author/donor to decide if he or she is willing
    to distribute software through any other system and a licensee cannot
    impose that choice.

    This section is intended to make thoroughly clear what is believed to
    be a consequence of the rest of this License.

      8. If the distribution and/or use of the Program is restricted in
    certain countries either by patents or by copyrighted interfaces, the
    original copyright holder who places the Program under this License
    may add an explicit geographical distribution limitation excluding
    those countries, so that distribution is permitted only in or among
    countries not thus excluded.  In such case, this License incorporates
    the limitation as if written in the body of this License.

      9. The Free Software Foundation may publish revised and/or new versions
    of the General Public License from time to time.  Such new versions will
    be similar in spirit to the present version, but may differ in detail to
    address new problems or concerns.

    Each version is given a distinguishing version number.  If the Program
    specifies a version number of this License which applies to it and "any
    later version", you have the option of following the terms and conditions
    either of that version or of any later version published by the Free
    Software Foundation.  If the Program does not specify a version number of
    this License, you may choose any version ever published by the Free Software
    Foundation.

      10. If you wish to incorporate parts of the Program into other free
    programs whose distribution conditions are different, write to the author
    to ask for permission.  For software which is copyrighted by the Free
    Software Foundation, write to the Free Software Foundation; we sometimes
    make exceptions for this.  Our decision will be guided by the two goals
    of preserving the free status of all derivatives of our free software and
    of promoting the sharing and reuse of software generally.

    			    NO WARRANTY

      11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
    FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
    OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
    PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
    OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
    MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
    TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
    PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
    REPAIR OR CORRECTION.

      12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
    WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
    REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
    INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
    OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
    TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
    YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
    PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
    POSSIBILITY OF SUCH DAMAGES.

    		     END OF TERMS AND CONDITIONS

    	    How to Apply These Terms to Your New Programs

      If you develop a new program, and you want it to be of the greatest
    possible use to the public, the best way to achieve this is to make it
    free software which everyone can redistribute and change under these terms.

      To do so, attach the following notices to the program.  It is safest
    to attach them to the start of each source file to most effectively
    convey the exclusion of warranty; and each file should have at least
    the "copyright" line and a pointer to where the full notice is found.

        (one line to give the program's name and a brief idea of what it does.)
        Copyright (C) 19yy  < name of author >

        This program is free software; you can redistribute it and/or modify
        it under the terms of the GNU General Public License as published by
        the Free Software Foundation; either version 2 of the License, or
        (at your option) any later version.

        This program is distributed in the hope that it will be useful,
        but WITHOUT ANY WARRANTY; without even the implied warranty of
        MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
        GNU General Public License for more details.

        You should have received a copy of the GNU General Public License
        along with this program; if not, write to the Free Software
        Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

    Also add information on how to contact you by electronic and paper mail.

    If the program is interactive, make it output a short notice like this
    when it starts in an interactive mode:

        Gnomovision version 69, Copyright (C) 19yy name of author
        Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
        This is free software, and you are welcome to redistribute it
        under certain conditions; type `show c' for details.

    The hypothetical commands `show w' and `show c' should show the appropriate
    parts of the General Public License.  Of course, the commands you use may
    be called something other than `show w' and `show c'; they could even be
    mouse-clicks or menu items--whatever suits your program.

    You should also get your employer (if you work as a programmer) or your
    school, if any, to sign a "copyright disclaimer" for the program, if
    necessary.  Here is a sample; alter the names:

      Yoyodyne, Inc., hereby disclaims all copyright interest in the program
      `Gnomovision' (which makes passes at compilers) written by James Hacker.

      < signature of Ty Coon >, 1 April 1989
      Ty Coon, President of Vice

    This General Public License does not permit incorporating your program into
    proprietary programs.  If your program is a subroutine library, you may
    consider it more useful to permit linking proprietary applications with the
    library.  If this is what you want to do, use the GNU Library General
    Public License instead of this License.