GALAMOST
GPU-Accelerated Large-Scale Molecular Simulation Toolkit
Station: News
New Features
1. Fix a bug of polymerization object, in which particle groups may have directional migration.
2. The particle type can be changed in polymerization.
3. Add a module of depolymerization.
4. Fix a bug of MdScfForce object, in which the simulation may jump out in some conditions.
5. The DPDThermoLJforce object supports DPDVV integration, with the command setDPDVV(True)
6. The compile system adds the commands "--boost=/boost/path" and "--python=/python/path" to set boost and python paths.
7. The galaTackle plugin can recognize rigid bodies. A type of rigid bodies is given a name of "Mol + type index".
8. The command "comp_info.setNdof(app.getNdof())" is not needed anymore.
9. The galaTackle plugin can deal with DCD file, along with a XML file, such as "galaTackle a.xml b.dcd".
10. The "10 msd" in galaTackle plugin outputs the MSD by molecule types.
11. The ParticleSet object supports new usages, such as "group=galamost.ParticleSet(all_info, ["A", "B", "G"])" and "group=galamost.ParticleSet(all_info, ["A", 1, 2])"
12. The XmlDump object can output the xml file of a group of particle, such as "xml = galamost.XmlDump(all_info, group_out, 'particles')"
13. The XmlDump object supports new usages, such as "xml.setOutput(['bond','image','velocity'])"

Notes

1. For correct MSD calculation with DCD file, the command "dcd.unpbc(True)" should be called in script for the particle position before the implementation of PBC.
2. The command "dcd.removePbc(bool)" is abandoned.
3. The command "dcd.unwrap(bool)" is used for unfolding the molecules.