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.
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.
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.
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:
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.
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:
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.
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
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)
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.
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
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Copyright (C) 1989, 1991 Free Software Foundation, Inc.
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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.
