Filtern
Erscheinungsjahr
Dokumenttyp
- Sonstiges (31) (entfernen)
Sprache
- Englisch (31) (entfernen)
Volltext vorhanden
- nein (31) (entfernen)
From https://github.com/zielesny/MFsim:
MFsim - An open Java all-in-one rich-client simulation environment for mesoscopic simulation
MFsim is an open Java all-in-one rich-client computing environment for mesoscopic simulation with Jdpd as its default simulation kernel for Molecular Fragment Dissipative Particle Dynamics (DPD). The environment integrates and supports the complete preparation-simulation-evaluation triad of a mesoscopic simulation task. Productive highlights are a SPICES molecular structure editor, a PDB-to-SPICES parser for particle-based peptide/protein representations, a support of polymer definitions, a compartment editor for complex simulation box start configurations, interactive and flexible simulation box views including analytics, simulation movie generation or animated diagrams. As an open project, MFsim enables customized extensions for different fields of research.
MFsim uses several open libraries (see MFSimVersionHistory.txt for details and references below) and is published as open source under the GNU General Public License version 3 (see LICENSE).
MFsim has been described in the scientific literature and used for DPD studies (see references below).
From https://github.com/zielesny/Jdpd:
Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics (DPD)
Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics (DPD) with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated “all-in-one” simulation systems like MFsim.
Since Jdpd version 1.6.1.0 Jdpd is available in a (basic) double-precision version and a (derived) single-precision version (= JdpdSP) for all numerical calculations, where the single precision version needs about half the memory of the double precision version.
Jdpd uses the Apache Commons Math and Apache Commons RNG libraries and is published as open source under the GNU General Public License version 3. This repository comprises the Java bytecode libraries (including the Apache Commons Math and RNG libraries), the Javadoc HTML documentation and the Netbeans source code packages including Unit tests.
Jdpd has been described in the scientific literature (the final manuscript 2018 - van den Broek - Jdpd - Final Manucsript.pdf is added to the repository) and used for DPD studies (see references below).
See text file JdpdVersionHistory.txt for a version history with more detailed information.
MFsim - An open Java all-in-one rich-client simulation environment for mesoscopic simulation
MFsim is an open Java all-in-one rich-client computing environment for mesoscopic simulation with Jdpd as its default simulation kernel for Molecular Fragment Dissipative Particle Dynamics (DPD). The environment integrates and supports the complete preparation-simulation-evaluation triad of a mesoscopic simulation task. Productive highlights are a SPICES molecular structure editor, a PDB-to-SPICES parser for particle-based peptide/protein representations, a support of polymer definitions, a compartment editor for complex simulation box start configurations, interactive and flexible simulation box views including analytics, simulation movie generation or animated diagrams. As an open project, MFsim enables customized extensions for different fields of research.
MFsim uses several open libraries (see MFSimVersionHistory.txt for details and references below) and is published as open source under the GNU General Public License version 3 (see LICENSE).
MFsim has been described in the scientific literature and used for DPD studies.
Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics (DPD)
Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics (DPD) with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated “all-in-one” simulation systems like MFsim.
Since Jdpd version 1.6.1.0 Jdpd is available in a (basic) double-precision version and a (derived) single-precision version (= JdpdSP) for all numerical calculations, where the single precision version needs about half the memory of the double precision version.
Jdpd uses the Apache Commons Math and Apache Commons RNG libraries and is published as open source under the GNU General Public License version 3. This repository comprises the Java bytecode libraries (including the Apache Commons Math and RNG libraries), the Javadoc HTML documentation and the Netbeans source code packages including Unit tests.
Jdpd has been described in the scientific literature (the final manuscript 2018 - van den Broek - Jdpd - Final Manucsript.pdf is added to the repository) and used for DPD studies (see references below).
See text file JdpdVersionHistory.txt for a version history with more detailed information.
The algorithm for automated functional groups detection and extraction of organic molecules developed by Peter Ertl is implemented on the basis of the Chemistry Development Kit (CDK).
Folder Basic contains the basic ErtlFunctionalGroupsFinder code and test code for integration in Java projects.
Folder CDK contains CDK library jar file cdk-2.2.jar that ErtlFunctionalGroupsFinder works with.
Folder Evaluation contains sample code for evaluation of functional groups with ErtlFunctionalGroupsFinder.
Folder JUnit 4 contains library jar files for unit testing.
Folder Performance contains a jar library for performance tests.
ErtlFunctionalGroupsFinder is described in the scientific literature
CIP is an open-source high-level function library for (non-linear) curve fitting and data smoothing (with cubic splines), clustering (k-medoids, ART-2a) and machine learning (multiple linear/polynomial regression, feed-forward perceptron-type shallow and deep neural networks and support vector machines). In addition it provides several heuristics for the selection of training and test data or methods to estimate the relevance of data input components. CIP is built on top of the computing platform Mathematica to exploit its algorithmic and graphical capabilities.
CIP is an open-source high-level function library for (non-linear) curve fitting and data smoothing (with cubic splines), clustering (k-medoids, ART-2a) and machine learning (multiple linear/polynomial regression, feed-forward perceptron-type shallow and deep neural networks and support vector machines). In addition it provides several heuristics for the selection of training and test data or methods to estimate the relevance of data input components. CIP is built on top of the computing platform Mathematica to exploit its algorithmic and graphical capabilities.
Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The new kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated “all-in-one” simulation systems.
SPICES (Simplified Particle Input ConnEction Specification) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims at supporting tedious and error-prone molecular structure definitions for particle-based mesoscopic simulation techniques like Dissipative Particle Dynamics by allowing for an interplay of different molecular encoding levels that range from topological line notations and corresponding particle-graph visualizations to 3D structures with support of their spatial mapping into a simulation box. An open Java library for SPICES structure handling and mesoscopic simulation support in combination with an open Java Graphical User Interface viewer application for visual topological inspection of SPICES definitions are provided.