The fate of chemical and radioactive wastes in the environment is linked to the ability of natural phases to attenuate and immobilize contaminants through chemical adsorption and precipitation processes. Our ability to understand the molecular control of these processes is provided by a few experimental and analytical methods such as X-ray absorption, vibrational, and NMR spectroscopies. However, due to complexities in the structure and composition of clay and other hydrated minerals, and the inherent uncertainties of the experimental methods, it is important to apply theoretical molecular models for a fundamental understanding and interpretation of these phenomena. In this effort, we have developed a general force field suitable for the simulation of hydrated and multicomponent mineral systems. Interatomic potentials were derived from parameterizations incorporating structural and spectroscopic data from a variety of simple hydrated compounds. A flexible water model is used to describe the water and hydroxyl behavior. Bulk structures, interfacial behavior, and intercalation processes are evaluated and compared to experimental and spectroscopic findings. Classical molecular dynamics methods and ab initio molecular dynamics using quantum approaches provide additional insights into the structure, dynamics, and reactivity of these complex materials.
Friday, February 29, 2008
Molecular Simulations And Applications In Environmental Chemistry
The fate of chemical and radioactive wastes in the environment is linked to the ability of natural phases to attenuate and immobilize contaminants through chemical adsorption and precipitation processes. Our ability to understand the molecular control of these processes is provided by a few experimental and analytical methods such as X-ray absorption, vibrational, and NMR spectroscopies. However, due to complexities in the structure and composition of clay and other hydrated minerals, and the inherent uncertainties of the experimental methods, it is important to apply theoretical molecular models for a fundamental understanding and interpretation of these phenomena. In this effort, we have developed a general force field suitable for the simulation of hydrated and multicomponent mineral systems. Interatomic potentials were derived from parameterizations incorporating structural and spectroscopic data from a variety of simple hydrated compounds. A flexible water model is used to describe the water and hydroxyl behavior. Bulk structures, interfacial behavior, and intercalation processes are evaluated and compared to experimental and spectroscopic findings. Classical molecular dynamics methods and ab initio molecular dynamics using quantum approaches provide additional insights into the structure, dynamics, and reactivity of these complex materials.
Thursday, February 28, 2008
SUN OpenxVM
By combining virtualization software and data center automation tools, OpenxVM technology provides the technologies to operate data centers at radically reduced costs.
Friday, February 22, 2008
Challenges For The Message-Passing Interface In The PetaFLOPS Era
OSG All Hands Consortium Meeting
from Monday 03 March 2008 (08:00)
to Thursday 06 March 2008 (18:00)
at RENCI
Fermilab
>>>> Timetable:
Tuesday 04 March 2008 | top |
09:00->17:00 US ATLAS Transparent Distributed Facility workshop (Convener: Michael Ernst (Brookhaven National Laboratory) , Robert Gardner (University of Chicago) ) agenda |
09:00->17:00 US CMS Tier-3 workshop (Convener: Burt Holzman (Fermilab) , Brian Bockelman (University of Nebraska–Lincoln) ) agenda |
09:00->12:30 Biology Applications workshop (Convener: Maxim Potekhin (Brookhaven National Laboratory) , Mats Rynge (Renaissance Computing Institute) ) Description:
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Friday, February 15, 2008
WideShark: network protocol analyzer
Wireshark is the world's foremost network protocol analyzer, and is the de facto (and often de jure) standard across many industries and educational institutions.
Wireshark development thrives thanks to the contributions of networking experts across the globe. It is the continuation of a project that started in 1998.
Features
Wireshark has a rich feature set which includes the following:
- Deep inspection of hundreds of protocols, with more being added all the time
- Live capture and offline analysis
- Standard three-pane packet browser
- Multi-platform: Runs on Windows, Linux, OS X, Solaris, FreeBSD, NetBSD, and many others
- Captured network data can be browsed via a GUI, or via the TTY-mode TShark utility
- The most powerful display filters in the industry
- Rich VoIP analysis
- Read/write many different capture file formats: tcpdump (libpcap), Catapult DCT2000, Cisco Secure IDS iplog, Microsoft Network Monitor, Network General Sniffer® (compressed and uncompressed), Sniffer® Pro, and NetXray®, Network Instruments Observer, Novell LANalyzer, RADCOM WAN/LAN Analyzer, Shomiti/Finisar Surveyor, Tektronix K12xx, Visual Networks Visual UpTime, WildPackets EtherPeek/TokenPeek/AiroPeek, and many others
- Capture files compressed with gzip can be decompressed on the fly
- Live data can be read from Ethernet, IEEE 802.11, PPP/HDLC, ATM, Bluetooth, USB, Token Ring, Frame Relay, FDDI, and others (depending on your platfrom)
- Decryption support for many protocols, including IPsec, ISAKMP, Kerberos, SNMPv3, SSL/TLS, WEP, and WPA/WPA2
- Coloring rules can be applied to the packet list for quick, intuitive analysis
- Output can be exported to XML, PostScript®, CSV, or plain text
http://www.wireshark.org/
Friday, February 8, 2008
GNOME Glib
_____________________________________________________
GNOME Glib Reference Manual:
http://library.gnome.org/devel/glib/stable/
String: http://library.gnome.org/devel/glib/stable/glib-String-Utility-Functions.html
Error Reporting:http://library.gnome.org/devel/glib/stable/glib-Error-Reporting.html
Glob-style pattern matching: http://library.gnome.org/devel/glib/stable/glib-Glob-style-pattern-matching.html
String Chunks: http://library.gnome.org/devel/glib/stable/glib-String-Chunks.html
_____________________________________________________
GNOME GLIB - GNU C library - C++ tutorial
GNOME Glib Library Reference:
http://library.gnome.org/devel/glib/stable/
GNU C library:
http://www.cs.utah.edu/dept/old/texinfo/glibc-manual-0.02/library_toc.html
GNU C Library Pattern Matching
http://www.gnu.org/software/libc/manual/html_node/Pattern-Matching.html#Pattern-Matching
GNU C Library Wildcard Matching
http://www.gnu.org/software/libc/manual/html_node/Wildcard-Matching.html#Wildcard-Matching
C++ tutorial:
http://www.cplusplus.com/doc/tutorial/inheritance.html
C++ reference:
C++ String:
http://www.cppreference.com/cppstring/index.html
C++ standard Components
http://uw713doc.sco.com/en/SDK_c++/CONTENTS.html
C++ string parse:
http://www.cprogramming.com/faq/cgi-bin/smartfaq.cgi?answer=1057105750&id=1044780608
Regular expression in C - regexex regcomp fnmatch
Parsing URL with regex: how it is done in apache
http://www.divms.uiowa.edu/~luke/xls/projects/regexp/regexp.html#NWcite-welch97:_pract_progr_tcl_tk
http://www.divms.uiowa.edu/~luke/xls/projects/regexp/regexp.html
Unix Programming Examples: Parsing Command Line - Regular expressions
http://mij.oltrelinux.com/devel/unixprg/#regex_notes
Regexex / regcomp
http://www.opengroup.org/onlinepubs/000095399/functions/regcomp.html
Fnmatch:
http://docs.hp.com/en/36430-90007/ch04s20.html
C++ string parse:
http://www.cprogramming.com/faq/cgi-bin/smartfaq.cgi?answer=1057105750&id=1044780608
#include
#include
#include
#include
#include
/* max error message length */
#define MAX_ERR_LENGTH 80
bool match( char * pattern, char * string );bool match( char * pattern, char * string ){
regex_t myre;
int err;
char err_msg[MAX_ERR_LENGTH];
/* compiles the RE. If this step fails, reveals what's wrong with the RE */
if ( (err = regcomp(&myre, pattern, REG_EXTENDED)) != 0 ) {
regerror(err, &myre, err_msg, MAX_ERR_LENGTH);
printf("Error analyzing regular expression '%s': %s - %s:%d\n", pattern, err_msg, __FILE__,__LINE__);
regfree(&myre);
return false;
}
if ( (err = regexec(&myre, string, 0, NULL, 0)) == 0 ) {
regfree(&myre);
return true;
}
if ( err != REG_NOMATCH ) {
/* this is when errors have been encountered */
regerror(err, &myre, err_msg, MAX_ERR_LENGTH);
printf("Error analyzing regular expression '%s' over '%s': %s - %s:%d\n", pattern, string, err_msg, __FILE__,__LINE__);
}
regfree(&myre);
return false;
}//match
regex_t re;
int error;
char *buffer="gsiftp://alo:90/lls/lsld/l";
regmatch_t pm[8];
(void) regcomp (&re, "^(([^:]+)://)?([^:/]+)(:([0-9]+))?(/.*)", REG_EXTENDED);
error = regexec (&re, &buffer[0], 6, &pm[0], 0);
printf("%d %d\n",pm[3].rm_so, pm[3].rm_eo);
}
GNU C Library Pattern Matching
http://www.gnu.org/software/libc/manual/html_node/Pattern-Matching.html#Pattern-Matching
GNU C Library Wildcard Matching
http://www.gnu.org/software/libc/manual/html_node/Wildcard-Matching.html#Wildcard-Matching
Thursday, February 7, 2008
Migol: A Fault Tolerant Grid Service Framework for Computational Applications in the Grid
http://www.cct.lsu.edu/events/talks/314
Andre Luckow, University of Potsdam, Germany
February 07 2008 3:00 pm
Johnston Hall Room 338 CCT
Wednesday, February 6, 2008
High Performance SSH/SCP - HPN-SSH
HPN-SSH
- from Pitsburg SuperComputing Center - PSC
- presented in Mardi Gras Conference 2008