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