API Reference

• ppafm.atomicUtils
  • ZsToElems()
  • countTypeBonds()
  • findBonds()
  • findBonds_()
  • findCOG()
  • findNearest()
  • findPairs()
  • findPairs_one()
  • findTypeNeigh()
  • getAllNeighsOfSelected()
  • getAtomColors()
  • groupToPair()
  • histR()
  • loadCoefs()
  • makeRotMat()
  • neighs()
  • pairsNotShareNeigh()
  • replace()
  • replacePairs()
• ppafm.chemistry
  • FIRE
    • FIRE.falpha
    • FIRE.kickStart
    • FIRE.minLastNeg
    • FIRE.move()
    • FIRE.t_dec
    • FIRE.t_inc
    • FIRE.v
  • assignAtomBOFF()
  • bonds2neighs()
  • bonds2neighsZs()
  • estimateBondOrder()
  • findBonds()
  • findTris()
  • findTris_()
  • getForceIvnR24()
  • getRingNatom()
  • group_definition
  • groups2atoms()
  • makeGroupLevels()
  • makeTetrahedron()
  • makeTetrahedronFork()
  • makeTriFork()
  • neighs2str()
  • normalize()
  • relaxAtoms()
  • relaxBondOrder()
  • removeAtoms()
  • removeBorderAtoms()
  • ringsToMolecule()
  • selectRandomElements()
  • selectRandomGroups()
  • simpleAOEnergies()
  • speciesToPLevels()
  • tris2num_()
  • trisToPoints()
  • validBonds()
• ppafm.common
  • CLIParser
    • CLIParser.add_arguments()
    • CLIParser.cli_args
  • Fz2df()
  • Fz2df_tilt()
  • PBCAtoms()
  • PBCAtoms3D()
  • PBCAtoms3D_np()
  • PpafmParameters
    • PpafmParameters.Amplitude
    • PpafmParameters.Apauli
    • PpafmParameters.Bpauli
    • PpafmParameters.Config
      • PpafmParameters.Config.arbitrary_types_allowed
      • PpafmParameters.Config.validate_assignment
    • PpafmParameters.FFgrid0
    • PpafmParameters.FFgridA
    • PpafmParameters.FFgridB
    • PpafmParameters.FFgridC
    • PpafmParameters.PBC
    • PpafmParameters.Rcore
    • PpafmParameters.Rtip
    • PpafmParameters.Vbias
    • PpafmParameters.aMorse
    • PpafmParameters.apply_options()
    • PpafmParameters.charge
    • PpafmParameters.colorscale
    • PpafmParameters.colorscale_kpfm
    • PpafmParameters.ddisp
    • PpafmParameters.f0Cantilever
    • PpafmParameters.ffModel
    • PpafmParameters.from_file()
    • PpafmParameters.gridA
    • PpafmParameters.gridB
    • PpafmParameters.gridC
    • PpafmParameters.gridN
    • PpafmParameters.gridO
    • PpafmParameters.imageInterpolation
    • PpafmParameters.kCantilever
    • PpafmParameters.klat
    • PpafmParameters.krad
    • PpafmParameters.load_ini()
    • PpafmParameters.model_config
    • PpafmParameters.moleculeShift
    • PpafmParameters.nPBC
    • PpafmParameters.permit
    • PpafmParameters.plotSliceBy
    • PpafmParameters.plotSliceFrom
    • PpafmParameters.plotSliceTo
    • PpafmParameters.probeType
    • PpafmParameters.r0Probe
    • PpafmParameters.scanMax
    • PpafmParameters.scanMin
    • PpafmParameters.scanStep
    • PpafmParameters.scanTilt
    • PpafmParameters.sigma
    • PpafmParameters.stiffness
    • PpafmParameters.tiltedScan
    • PpafmParameters.tip
    • PpafmParameters.to_file()
    • PpafmParameters.vdWDampKind
  • REA2LJ()
  • atom2iZ()
  • atoms2iZs()
  • autoGeom()
  • autoGridN()
  • findPBCAtoms3D_cutoff()
  • genFFSampling()
  • genRotations()
  • getAtomsLJ()
  • getAtomsLJ_fast()
  • getAtomsRE()
  • getAtomsREA()
  • getFFdict()
  • getPos()
  • getPos_Vec3d()
  • getSampleAtomsREA()
  • get_C612()
  • get_df_weight()
  • get_simple_df_weight()
  • loadSpecies()
  • loadSpeciesLines()
  • lvec2params()
  • makeRotJitter()
  • maxAlongDir()
  • maxAlongDirEntropy()
  • multRot()
  • params2lvec()
  • parseAtoms()
  • prepareScanGrids()
  • rotation_matrix()
  • sphereTangentSpace()
  • wrapAtomsCell()
• ppafm.core
  • SplineParameters
    • SplineParameters.from_file()
    • SplineParameters.rff_n
    • SplineParameters.rff_xs
    • SplineParameters.rff_ydys
  • computeD3Coeffs()
  • deleteFF_Epointer()
  • deleteFF_Fpointer()
  • evalRadialFF()
  • getCoulombFF()
  • getDFTD3FF()
  • getDensityR4spline()
  • getGaussDensity()
  • getInPoints_LJ()
  • getLennardJonesFF()
  • getMorseFF()
  • getSlaterDensity()
  • getVdWFF()
  • getVdWFF_RE()
  • relaxTipStroke()
  • relaxTipStrokes_omp()
  • setFF()
  • setFF_Epointer()
  • setFF_Fpointer()
  • setFF_shape()
  • setFIRE()
  • setGridCell()
  • setGridN()
  • setRelax()
  • setTip()
  • stiffnessMatrix()
  • subsample_nonuniform_spline()
  • subsample_uniform_spline()
  • test_eigen3x3()
  • test_force()
• ppafm.cpp_utils
  • cpp_modules
  • get_cdll()
• ppafm.data
  • download_dataset()
• ppafm.defaults
  • ppafm.defaults.valelec_dict
  • ppafm.defaults.d3
    • DF_DEFAULT_PARAMS
    • K1
    • K2
    • K3
    • R4R2
    • REF_CN
    • R_COV
    • get_df_params()
    • load_R0()
    • load_ref_c6()
• ppafm.elements
  • elementDict()
• ppafm.fieldFFT
  • Average_surf()
  • Average_tip()
  • addCoreDensities()
  • addCoreDensity()
  • conv3DFFT()
  • exportPotential()
  • fieldInfo()
  • getForceTransform()
  • getForces()
  • getMGrid()
  • getNormalizedBasisMatrix()
  • getProbeDensity()
  • getSampleDimensions()
  • getSize()
  • getSkewNormalBasis()
  • getSphericalHarmonic()
  • potential2forces()
  • potential2forces_mem()
  • printMetadata()
  • rotZX()
• ppafm.fitSpline
  • BsplineCubic()
  • c_int_p
  • conv1D()
  • convolve1D()
  • convolve2D_tensorProduct()
  • convolve3D_tensorProduct()
  • fit_tensorProd_2D()
  • fit_tensorProd_3D()
  • genSplineBasis()
  • setup_fit_tensorProd()
  • solveCG()
  • step_fit_tensorProd()
  • upSwizzle()
• ppafm.fitting
  • debugGeomPBC_xsf()
  • getProjections()
  • project()
  • setPBC()
  • setSplines()
• ppafm.GridUtils
  • cog()
  • dens2Q_CHGCARxsf()
  • interpolateLine()
  • interpolateQuad()
  • interpolate_cartesian()
  • readNumsUpTo()
  • renorSlice()
  • sphericalHist()
  • verticalCut()
• ppafm.GUIWidgets
  • FFViewer
    • FFViewer.saveFF()
    • FFViewer.updateFF()
    • FFViewer.updateView()
  • FigCanvas
    • FigCanvas.clear()
    • FigCanvas.set_labels()
  • FigImshow
    • FigImshow.cbar
    • FigImshow.onclick()
    • FigImshow.onscroll()
    • FigImshow.plotSlice()
    • FigImshow.plotSlice2()
  • FigPlot
    • FigPlot.clear()
    • FigPlot.defaultPlotAxis()
    • FigPlot.plotDatalines()
  • FileOpen
    • FileOpen.closeEvent()
    • FileOpen.keyPressEvent()
  • GeomEditor
    • GeomEditor.updateParent()
    • GeomEditor.updateValues()
  • LJParamEditor
    • LJParamEditor.updateParent()
  • PlotWindow
    • PlotWindow.clearFig()
    • PlotWindow.save_dat()
    • PlotWindow.save_png()
    • PlotWindow.setRange()
  • SlaveWindow
  • correct_ext()
  • set_widget_value()
  • show_warning()
• ppafm.HighLevel
  • Gauss()
  • computeDFTD3()
  • computeELFF_pointCharge()
  • computeElFF()
  • computeLJ()
  • getAtomsWhichTouchPBCcell()
  • loadValenceElectronDict()
  • meshgrid3d()
  • perform_relaxation()
  • prepareArrays()
  • relaxedScan3D()
  • relaxedScan3D_omp()
  • shift_positions()
  • subtractCoreDensities()
  • symGauss()
  • trjByDir()
• ppafm.io
  • getFromHead_PRIMCOORD()
  • limit_vec_field()
  • loadAtomsCUBE()
  • loadCUBE()
  • loadCellCUBE()
  • loadGeometry()
  • loadGeometryIN()
  • loadNCUBE()
  • loadNPYGeom()
  • loadNpy()
  • loadPOSCAR()
  • loadVecFieldNpy()
  • loadVecFieldXsf()
  • loadXSF()
  • loadXSFGeom()
  • loadXYZ()
  • load_scal_field()
  • load_vec_field()
  • makePovCam()
  • packVecGrid()
  • parseLvecASE()
  • primcoords2Xsf()
  • saveGeomXSF()
  • saveNpy()
  • saveVecFieldNpy()
  • saveVecFieldXsf()
  • saveWSxM_2D()
  • saveWSxM_3D()
  • saveXSF()
  • saveXYZ()
  • save_scal_field()
  • save_vec_field()
  • unpackVecGrid()
  • writeMatrix()
  • writePov()
• ppafm.ml
  • ppafm.ml.AuxMap
    • AtomRfunc
      • AtomRfunc.eval()
    • AtomicDisks
      • AtomicDisks.eval()
    • AuxMapBase
      • AuxMapBase.prepare_projector()
    • AuxMapFactory
    • Bonds
      • Bonds.eval()
    • ESMap
      • ESMap.eval()
    • ESMapConstant
      • ESMapConstant.eval()
    • HeightMap
      • HeightMap.eval()
    • MultiMapSpheres
      • MultiMapSpheres.eval()
    • MultiMapSpheresElements
      • MultiMapSpheresElements.convert_elements()
      • MultiMapSpheresElements.eval()
      • MultiMapSpheresElements.get_elem_channels()
    • vdwSpheres
      • vdwSpheres.eval()
  • ppafm.ml.Generator
    • GeneratorAFMtrainer
      • GeneratorAFMtrainer.bRuntime
      • GeneratorAFMtrainer.handle_distance()
      • GeneratorAFMtrainer.handle_positions()
      • GeneratorAFMtrainer.on_afm_start()
      • GeneratorAFMtrainer.on_batch_start()
      • GeneratorAFMtrainer.on_sample_start()
      • GeneratorAFMtrainer.randomize_df_steps()
      • GeneratorAFMtrainer.randomize_distance()
      • GeneratorAFMtrainer.randomize_tip()
      • GeneratorAFMtrainer.set_fdbm_parameters()
    • InverseAFMtrainer
      • InverseAFMtrainer.augment_with_rotations()
      • InverseAFMtrainer.augment_with_rotations_entropy()
      • InverseAFMtrainer.bRuntime
      • InverseAFMtrainer.handle_distance()
      • InverseAFMtrainer.handle_positions()
      • InverseAFMtrainer.on_afm_end()
      • InverseAFMtrainer.on_afm_start()
      • InverseAFMtrainer.on_batch_start()
      • InverseAFMtrainer.on_sample_start()
      • InverseAFMtrainer.randomize_distance()
      • InverseAFMtrainer.randomize_mol_parameters()
      • InverseAFMtrainer.randomize_tip()
      • InverseAFMtrainer.read_xyzs()
      • InverseAFMtrainer.shuffle_molecules()
    • getRandomUniformDisk()
    • rotate()
    • sortRotationsByEntropy()
• ppafm.ocl
  • ppafm.ocl.AFMulator
    • AFMulator
      • AFMulator.bMergeConv
      • AFMulator.bRuntime
      • AFMulator.bSaveFF
      • AFMulator.check_scan_window()
      • AFMulator.eval()
      • AFMulator.evalAFM()
      • AFMulator.eval_()
      • AFMulator.from_params()
      • AFMulator.load_params()
      • AFMulator.plot_images()
      • AFMulator.prepareFF()
      • AFMulator.prepareScanner()
      • AFMulator.relaxParams
      • AFMulator.saveDebugXSF_FF()
      • AFMulator.saveFF()
      • AFMulator.save_params()
      • AFMulator.setBPauli()
      • AFMulator.setLvec()
      • AFMulator.setQs()
      • AFMulator.setRho()
      • AFMulator.setRhoDelta()
      • AFMulator.setScanWindow()
      • AFMulator.setStiffness()
      • AFMulator.verbose
    • get_lvec()
    • quick_afm()
  • ppafm.ocl.field
    • AtomProcjetion
      • AtomProcjetion.Rfunc
      • AtomProcjetion.Rmax
      • AtomProcjetion.Rpp
      • AtomProcjetion.drStep
      • AtomProcjetion.dzmax
      • AtomProcjetion.dzmax_s
      • AtomProcjetion.elipticity
      • AtomProcjetion.makeCoefsZR()
      • AtomProcjetion.prepareBuffers()
      • AtomProcjetion.releaseBuffers()
      • AtomProcjetion.run_evalAtomRfunc()
      • AtomProcjetion.run_evalBondEllipses()
      • AtomProcjetion.run_evalCoulomb()
      • AtomProcjetion.run_evalHartreeGradient()
      • AtomProcjetion.run_evalLorenz()
      • AtomProcjetion.run_evalMultiMapSpheres()
      • AtomProcjetion.run_evalMultiMapSpheresElements()
      • AtomProcjetion.run_evalQdisks()
      • AtomProcjetion.run_evalSphereCaps()
      • AtomProcjetion.run_evalSpheres()
      • AtomProcjetion.run_evalSpheresType()
      • AtomProcjetion.run_evaldisks()
      • AtomProcjetion.run_evaldisks_occlusion()
      • AtomProcjetion.setAtomTypes()
      • AtomProcjetion.tgMax
      • AtomProcjetion.tgWidth
      • AtomProcjetion.tryReleaseBuffers()
      • AtomProcjetion.updateBuffers()
      • AtomProcjetion.zmargin
      • AtomProcjetion.zmin
    • D3Params
      • D3Params.cl_r4r2
      • D3Params.cl_rcov
      • D3Params.cl_rcut
      • D3Params.cl_ref_c6
      • D3Params.cl_ref_cn
      • D3Params.release()
    • DataGrid
      • DataGrid.add_mult()
      • DataGrid.array
      • DataGrid.cell_vol
      • DataGrid.cl_array
      • DataGrid.clamp()
      • DataGrid.from_file()
      • DataGrid.grad()
      • DataGrid.interp_at()
      • DataGrid.power_positive()
      • DataGrid.release()
      • DataGrid.step
      • DataGrid.to_file()
      • DataGrid.update_array()
    • ElectronDensity
    • FFTCrossCorrelation
      • FFTCrossCorrelation.correlate()
    • ForceField_LJC
      • ForceField_LJC.addLJ()
      • ForceField_LJC.add_dftd3()
      • ForceField_LJC.addvdW()
      • ForceField_LJC.calc_force_fdbm()
      • ForceField_LJC.calc_force_hartree()
      • ForceField_LJC.downloadFF()
      • ForceField_LJC.initPoss()
      • ForceField_LJC.initSampling()
      • ForceField_LJC.initialize()
      • ForceField_LJC.makeFF()
      • ForceField_LJC.prepareBuffers()
      • ForceField_LJC.run_evalLJC_Hartree()
      • ForceField_LJC.run_evalLJC_QZs_noPos()
      • ForceField_LJC.run_evalLJ_noPos()
      • ForceField_LJC.run_gradPotentialGrid()
      • ForceField_LJC.setLvec()
      • ForceField_LJC.setPP()
      • ForceField_LJC.setQs()
      • ForceField_LJC.tryReleaseBuffers()
      • ForceField_LJC.updateBuffers()
      • ForceField_LJC.verbose
    • HartreePotential
    • MultipoleTipDensity
    • TipDensity
      • TipDensity.interp_at()
      • TipDensity.subCores()
    • init()
    • makeDivisibleUp()
  • ppafm.ocl.oclUtils
    • OCLEnvironment
      • OCLEnvironment.loadProgram()
      • OCLEnvironment.printInfo()
      • OCLEnvironment.printPlatformInfo()
      • OCLEnvironment.updateBuffer()
    • get_platforms()
    • init_env()
    • print_platforms()
  • ppafm.ocl.relax
    • RelaxedScanner
      • RelaxedScanner.downloadPaths()
      • RelaxedScanner.prepareAuxMapBuffers()
      • RelaxedScanner.prepareBuffers()
      • RelaxedScanner.prepareFEConv()
      • RelaxedScanner.preparePosBasis()
      • RelaxedScanner.preparePossRot()
      • RelaxedScanner.releaseBuffers()
      • RelaxedScanner.run()
      • RelaxedScanner.run_convolveZ()
      • RelaxedScanner.run_getFEinStrokes()
      • RelaxedScanner.run_getFEinStrokesTilted()
      • RelaxedScanner.run_getZisoFETilted()
      • RelaxedScanner.run_getZisoTilted()
      • RelaxedScanner.run_izoZ()
      • RelaxedScanner.run_relaxStrokesTilted()
      • RelaxedScanner.run_relaxStrokesTilted_convZ()
      • RelaxedScanner.setScanRot()
      • RelaxedScanner.tryReleaseBuffers()
      • RelaxedScanner.updateAtoms()
      • RelaxedScanner.updateBuffers()
      • RelaxedScanner.updateFEin()
      • RelaxedScanner.verbose
    • getInvCell()
    • init()
    • mat3x3to4f()
    • preparePoss()
    • preparePossRot()
    • rotTip()
• ppafm.PPPlot
  • checkField()
  • checkVecField()
  • colorize_XY2RG()
  • makeCmap_Blue1()
  • makeCmap_Blue2()
  • plotArrows()
  • plotAtoms()
  • plotBonds()
  • plotDistortions()
  • plotGeom()
  • plotImages()
  • plotVecFieldRG()
  • write_plotting_slice()