- What's new
- Install
- Using MagiC
- MagicTools procedures reference:
- Reading MagiC data files
- Visualization and inspection of the data
- OnePlot(DFs_list)
- MultPlot(input, coinciding=True, atonce=False, show_sameasbond=False, *args, **kwargs)
- HeatMap(refDFset, otherDFsets, hardcopy=False, outfile=None, force=False, **kwargs)
- Deviation(filename, hardcopy=False, returnarrays=False, testpoints=False, outfile='deviation.eps')
- AnalyzeIMCOuput(filename, DFType='RDF', iters=None, hardcopy=True, mcmfile=None, PairNamesList=None)
- Analysis, processing and saving the data
- TotalPots(pots, eps, mcmfile)
- GetOptEpsilon(pots, eps_old, r1, eps_min=0, eps_max=0, npoints=100, mcmfile=None)
- PotsEpsCorrection(pots, eps_old, eps_new, mcmfile=None)
- PotsPressCorr(pots,Ucorr0)
- PotsExtendTailRange(pots, RcutNB)
- Average(listofDFset, **kwargs)
- SaveDFsAsText(DFs)
- DFset.Write(ofile, Split=False)
- Exporting topologies and potentials
- GromacsTopology(inpMagiC=None, system=None, topfile='topol.top', geometry=None, **kwargs)
- LAMMPSTopology(inpMagiC=None, system=None, outfile="LAMMPS.data", hybrid=False, **kwargs)
- GALAMOSTTopology(eps, inpMagiC=None, system=None, outfile="topology.xml", pyfile='tables.inc.py', **kwargs)
- PotsExport(pots, MDEngine, ...):
- Potential export procedure details
- xmol2gro
- gro2xmol(ifilename, ofilename='output.xmol')
- tpr2mmol(tprfile)
- dcd2xtc(trj, top)
- GetStartConfs(ifilename, Nconfs, ofilename='start.xmol', Begin=0, End=0, Random=False)
- MagicTools object-classes reference
- File formats