Introduction Culgi Library Detailed Description Services and training Publications

Release version 4.0, August 2009

Scroll or jump to:

Platforms
Molecular Modelling
Mesoscopic Modelling
Analysis Tools
Graphics
Scripting Interface
Graphical Programming Environment
Manual
Examples
Movie Maker

Culgi Library

Platforms

Serial Windows 2000, XP, Vista (32 and 64 bit)
Serial Linux (32 and 64 bit)
Parallel Linux and Windows (32 and 64 bit)

Molecular Modelling

Monte Carlo (including Configurational Biased Monte Carlo sampling)
Energy minimization
MD Simulations in NVE, NVT, and NPT ensembles
Parallel MD
Parallel MC
OPLS-AA, Dreiding, and NERD force fields
automated force field assignment
.mol molecular modeling reader
.cif crystal reader
.car MD trajectories reader (on script level)
Molecule builder
Polymer chain builder
Crystal surface builders with molecule grafting
Amorphous builder
Crystal editor (on script level)
Electrostatics interaction with Ewald or charge group method
Reactions (on script level)
Mapper to mesoscopic bead models
Full control of atomic positions and velocities on script level

Mesoscopic Modelling

Parallel Dissipative Particle Dynamics (DPD)
Parallel Brownian Dynamics (BD)
Parallel Dynamic Density Field Method (DDFT) (aka Mesodyn)
Parallel Hybrid Mesoscopic Bead-Field engine (MBF)
Extensive intra-molecular force field in DPD, BD and MBF, with dihedrals, torsion and bond length control
Hoogerbrugge-Koelman intermolecular bead interactions in DPD, BD and MBF
Free tabular potential intermolecular bead interactions in DPD, BD and MBF
String topology chain buillder
Free topology chain builder (for gels, networks etc.)
Full particle-mesh Poisson Boltzman in DPD, BD, DDFT, and MBF
Electrostatics of weak charges (titrations)
Electrostatics with variable dielectrics
Interactions with external field in DPD. BD, DDFT and MBF
Stokesian Hydrodynamics with variable viscosity in DDFT
Flory-Huggins interactions in DDFT and MBF
Various diffusive modes in DDFT and MBF (density dynamics, external potential, local density) with or without noise
Gaussian particle-mesh coupling interaction in MBF
Chemical potential calculator, based on the Widom insertion technique, for particle mesoscopic model
Colloid Builder based on shape definition commands.
Colloid modification to arbitrary bulk and surface composition
Colloidal dynamics in DPD with rigid internal coordinates
Shapes builder with Boolean logic to create colloids, molecular assemblies and density fields.
Mapper from Mesoscopic bead models (DPD, BD and MBF) to molecular modelling
Mappers from DDFT to BD and DPD (on script level)
Mappers from BD and DPD to DDFT (on script level)
Reactions (on script level)
Full control of individual bead position and velocity (on script level)
Full control of individual colloid postion,, rotation and velocity (on script level)
Full control of field values on script level
Porosity calculator

Analysis tools

The Culgi Library provides a wide range of tools to analyze structures and related properties. Using script, any possible analysis can be performed. Some tools are used frequently, and are implemented in the library itself:

Storage and retrieval of human readable ascii-formated archive
Sophisticated filter and selector commands with Boolean logic
All varieties of molecular distributions (bond length, bending angles, dihedrals, inter and intranolecular pair correlation functions, mean square displacements, end-to-end chain length, radius of gyration, etc.)
Density profiles along planes and lines
Cluster size and shape distributions
Energies, Forces and Free Energies
Stress analysis

Graphics

The serial graphics windows and linux version have full graphics, plotting and printing capability. The graphics includes:

Filtered real-time 3D graphics rendering of crystals, particles and fields.
Full control of graphics view modes (on script level)
Interactive graphics rotate and zoom.
On-screen rendering
Batchmode off-screen rendering
Export to JPEG or TIFF
Export to Maya 3D format
Export to X3D format, an interactive 3D format that can be made public on the Internet using a web browser.
Plotting of 2D results (graphs)

Scripting Interface

Tcl
Python
Culgi GPE
C++ (in commercial license)
Palette for construction of physical objects (molecules, colloids, fields)
Graphics manager for control of 3D graphics and plotter
Calculator manager for pre-defined modeling (MD, MC, Energy Minimization, DPD, DDFT, MBF)
Calculator manager for analysis
Utiltymanager (archives, parameters, shapes)
Mappers manager (molecular to mesoscopic and vice versa)
Selector manager for object filters
Complete control of individual objects (position, velocity, colors, etc.)
Same script can be used on parallel and serial machines

Graphical Programming Environment

The Culgi GPE is a high-level graphical programming tool to facilitate writing scripts. It is compact and straightforward to use. It is intended to set up a simulation, which then can be exported to a scripting environment.

Linux and Windows serial platforms
Object-oriented visualization of library and script variables
Linear textual visualization of workflow
Integrated GUI for Graphical Molecular Editor
Molecukar Editor for loading, manual edting and relaxation of molecular structures
Integrated GUI for Graphical Plotter
Graphical Plotter for loading and viewing of Culgi tabular text files.
Integrated file Workspace
Procedures
File I/O
Flow control
Math environment
Sophisticated debugger
Integrated help and manual
View in GPE, tcl or python mode
Export to tcl or python
GUI Maker

Manual

The manual includes

Guide to installation
Tutorials on several levels
Full explanation of the structure of the software library
List with help to all commands
Seperate Culgi Scientific document explaining all theoretical methods

Examples

The installation includes a large number of annotated examples scripts, from simple to sophisticated, that each highlight a certain library function

Movie Maker