| FETK | |
| The Finite Element ToolKit | |
|
Developed by the MCP Research Group at the UCSD Center for Computational Mathematics |
|
|
GAMer User's Guide
Version 0.1 Table of Contents
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 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: 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.
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:
This version of GAMer is distributed under the following guidelines:
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
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies
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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.
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