Changeset 4433
 Timestamp:
 May 25, 2020 3:08:15 PM (2 years ago)
 Location:
 trunk
 Files:

 3 edited
Legend:
 Unmodified
 Added
 Removed

trunk/GSASIIphsGUI.py
r4432 r4433 3719 3719 event.StopPropagation() 3720 3720 3721 def GetSelectedAtoms( ):3722 '''Get all atoms that are selected by row or by having any cell selected.3723 produce an error message if no atoms are selected.3721 def GetSelectedAtoms(action='action'): 3722 '''Get all atoms that are selected by row or by having any cell 3723 selected. If no atoms are selected ask user. 3724 3724 ''' 3725 3725 indx = list(set([row for row,col in Atoms.GetSelectedCells()]+Atoms.GetSelectedRows())) 3726 if indx: 3727 return indx 3728 else: 3729 G2G.G2MessageBox(G2frame,'Warning: no atoms were selected','Nothing selected') 3726 # if indx: 3727 # return indx 3728 # else: 3729 # G2G.G2MessageBox(G2frame,'Warning: no atoms were selected','Nothing selected') 3730 if indx: return indx 3731 choices = [] 3732 for i in range(Atoms.GetNumberRows()): 3733 val = Atoms.GetCellValue(i,0) 3734 if val in choices: 3735 val += '_' + Atoms.GetCellValue(i,5) 3736 choices.append(val) 3737 if not choices: return 3738 dlg = G2G.G2MultiChoiceDialog(Atoms.GetTopLevelParent(), 3739 'Select atoms','Select atoms for '+action,choices) 3740 if dlg.ShowModal() == wx.ID_OK: 3741 indx = dlg.GetSelections() 3742 dlg.Destroy() 3743 return indx 3730 3744 3731 3745 def AtomRefine(event): … … 7056 7070 #### Structure drawing GUI stuff 7057 7071 ################################################################################ 7072 def getAtomSelections(drawAtoms,action='action'): 7073 '''get selected atoms from table or ask user if none selected''' 7074 #indx = drawAtoms.GetSelectedRows() 7075 indx = list(set([row for row,col in drawAtoms.GetSelectedCells()]+ 7076 drawAtoms.GetSelectedRows())) 7077 if indx: return indx 7078 choices = [] 7079 for i in range(drawAtoms.GetNumberRows()): 7080 val = drawAtoms.GetCellValue(i,0) 7081 if val in choices: 7082 val += '_' + drawAtoms.GetCellValue(i,5) 7083 choices.append(val) 7084 if not choices: return 7085 dlg = G2G.G2MultiChoiceDialog(drawAtoms.GetTopLevelParent(), 7086 'Select atoms','Select atoms for '+action,choices) 7087 if dlg.ShowModal() == wx.ID_OK: 7088 indx = dlg.GetSelections() 7089 dlg.Destroy() 7090 return indx 7058 7091 7059 7092 def SetupDrawingData(): … … 7117 7150 7118 7151 def OnRestraint(event): 7152 indx = getAtomSelections(drawAtoms) 7153 if not indx: return 7119 7154 indx = drawAtoms.GetSelectedRows() 7120 7155 restData = G2frame.GPXtree.GetItemPyData( … … 7171 7206 7172 7207 def OnDefineRB(event): 7173 indx = drawAtoms.GetSelectedRows() 7208 indx = getAtomSelections(drawAtoms) 7209 if not indx: return 7174 7210 indx.sort() 7175 7211 RBData = G2frame.GPXtree.GetItemPyData( … … 7209 7245 ##### Draw Atom routines 7210 7246 ################################################################################ 7211 7212 7247 def UpdateDrawAtoms(atomStyle=''): 7213 7248 def RefreshDrawAtomGrid(event): … … 7416 7451 7417 7452 def DrawAtomStyle(event): 7418 indx = drawAtoms.GetSelectedRows() 7419 if indx: 7420 generalData = data['General'] 7421 atomData = data['Drawing']['Atoms'] 7422 cx,ct,cs,ci = data['Drawing']['atomPtrs'] 7423 styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra'] 7424 if generalData['Type'] == 'macromolecular': 7425 styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids', 7426 'backbone','ribbons','schematic'] 7427 dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice) 7428 if dlg.ShowModal() == wx.ID_OK: 7429 sel = dlg.GetSelection() 7430 parms = styleChoice[sel] 7431 for r in indx: 7432 atomData[r][cs] = parms 7433 drawAtoms.SetCellValue(r,cs,parms) 7434 dlg.Destroy() 7435 FindBondsDraw(data) 7436 drawAtoms.ClearSelection() 7437 G2plt.PlotStructure(G2frame,data) 7453 indx = getAtomSelections(drawAtoms) 7454 if not indx: return 7455 generalData = data['General'] 7456 atomData = data['Drawing']['Atoms'] 7457 cx,ct,cs,ci = data['Drawing']['atomPtrs'] 7458 styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra'] 7459 if generalData['Type'] == 'macromolecular': 7460 styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids', 7461 'backbone','ribbons','schematic'] 7462 dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice) 7463 if dlg.ShowModal() == wx.ID_OK: 7464 sel = dlg.GetSelection() 7465 parms = styleChoice[sel] 7466 for r in indx: 7467 atomData[r][cs] = parms 7468 drawAtoms.SetCellValue(r,cs,parms) 7469 dlg.Destroy() 7470 FindBondsDraw(data) 7471 drawAtoms.ClearSelection() 7472 G2plt.PlotStructure(G2frame,data) 7473 7474 def DrawAtomLabel(event): 7475 indx = getAtomSelections(drawAtoms) 7476 if not indx: return 7477 generalData = data['General'] 7478 atomData = data['Drawing']['Atoms'] 7479 cx,ct,cs,ci = data['Drawing']['atomPtrs'] 7480 styleChoice = [' ','type','name','number'] 7481 if generalData['Type'] == 'macromolecular': 7482 styleChoice = [' ','type','name','number','residue','1letter','chain'] 7483 dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom label style',styleChoice) 7484 if dlg.ShowModal() == wx.ID_OK: 7485 sel = dlg.GetSelection() 7486 parms = styleChoice[sel] 7487 for r in indx: 7488 atomData[r][cs+1] = parms 7489 drawAtoms.SetCellValue(r,cs+1,parms) 7490 dlg.Destroy() 7491 drawAtoms.ClearSelection() 7492 G2plt.PlotStructure(G2frame,data) 7493 7494 def DrawAtomColor(event): 7495 indx = getAtomSelections(drawAtoms) 7496 if not indx: return 7497 if len(indx) > 1: 7498 G2frame.GetStatusBar().SetStatusText('Select Custom Color, change color, Add to Custom Colors, then OK',1) 7438 7499 else: 7439 G2G.G2MessageBox(G2frame,'Select atoms first') 7440 7441 def DrawAtomLabel(event): 7442 indx = drawAtoms.GetSelectedRows() 7443 if indx: 7444 generalData = data['General'] 7445 atomData = data['Drawing']['Atoms'] 7446 cx,ct,cs,ci = data['Drawing']['atomPtrs'] 7447 styleChoice = [' ','type','name','number'] 7448 if generalData['Type'] == 'macromolecular': 7449 styleChoice = [' ','type','name','number','residue','1letter','chain'] 7450 dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom label style',styleChoice) 7451 if dlg.ShowModal() == wx.ID_OK: 7452 sel = dlg.GetSelection() 7453 parms = styleChoice[sel] 7454 for r in indx: 7455 atomData[r][cs+1] = parms 7456 drawAtoms.SetCellValue(r,cs+1,parms) 7457 dlg.Destroy() 7458 drawAtoms.ClearSelection() 7459 G2plt.PlotStructure(G2frame,data) 7460 else: 7461 G2G.G2MessageBox(G2frame,'Select atoms first') 7462 7463 def DrawAtomColor(event): 7464 7465 indx = drawAtoms.GetSelectedRows() 7466 if indx: 7467 if len(indx) > 1: 7468 G2frame.GetStatusBar().SetStatusText('Select Custom Color, change color, Add to Custom Colors, then OK',1) 7469 else: 7470 G2frame.GetStatusBar().SetStatusText('Change color, Add to Custom Colors, then OK',1) 7471 atomData = data['Drawing']['Atoms'] 7472 cx,ct,cs,ci = data['Drawing']['atomPtrs'] 7473 atmColors = [] 7474 atmTypes = [] 7500 G2frame.GetStatusBar().SetStatusText('Change color, Add to Custom Colors, then OK',1) 7501 atomData = data['Drawing']['Atoms'] 7502 cx,ct,cs,ci = data['Drawing']['atomPtrs'] 7503 atmColors = [] 7504 atmTypes = [] 7505 for r in indx: 7506 if atomData[r][cs+2] not in atmColors: 7507 atmColors.append(atomData[r][cs+2]) 7508 atmTypes.append(atomData[r][ct]) 7509 if len(atmColors) > 16: 7510 break 7511 colors = wx.ColourData() 7512 colors.SetChooseFull(True) 7513 dlg = wx.ColourDialog(None,colors) 7514 if dlg.ShowModal() == wx.ID_OK: 7515 for i in range(len(atmColors)): 7516 atmColors[i] = dlg.GetColourData().GetColour()[:3] 7517 colorDict = dict(zip(atmTypes,atmColors)) 7475 7518 for r in indx: 7476 if atomData[r][cs+2] not in atmColors: 7477 atmColors.append(atomData[r][cs+2]) 7478 atmTypes.append(atomData[r][ct]) 7479 if len(atmColors) > 16: 7480 break 7481 colors = wx.ColourData() 7482 colors.SetChooseFull(True) 7483 dlg = wx.ColourDialog(None,colors) 7484 if dlg.ShowModal() == wx.ID_OK: 7485 for i in range(len(atmColors)): 7486 atmColors[i] = dlg.GetColourData().GetColour()[:3] 7487 colorDict = dict(zip(atmTypes,atmColors)) 7488 for r in indx: 7489 color = colorDict[atomData[r][ct]] 7490 atomData[r][cs+2] = color 7491 attr = wg.GridCellAttr() #needs to be here  gets lost if outside loop! 7492 attr.SetBackgroundColour(color) 7493 drawAtoms.SetAttr(r,cs+2,attr) 7494 data['Drawing']['Atoms'][r][cs+2] = color 7495 drawAtoms.ClearSelection() 7496 dlg.Destroy() 7497 G2frame.GetStatusBar().SetStatusText('',1) 7498 G2plt.PlotStructure(G2frame,data) 7499 else: 7500 G2G.G2MessageBox(G2frame,'Select atoms first') 7519 color = colorDict[atomData[r][ct]] 7520 atomData[r][cs+2] = color 7521 attr = wg.GridCellAttr() #needs to be here  gets lost if outside loop! 7522 attr.SetBackgroundColour(color) 7523 drawAtoms.SetAttr(r,cs+2,attr) 7524 data['Drawing']['Atoms'][r][cs+2] = color 7525 drawAtoms.ClearSelection() 7526 dlg.Destroy() 7527 G2frame.GetStatusBar().SetStatusText('',1) 7528 G2plt.PlotStructure(G2frame,data) 7501 7529 7502 7530 def ResetAtomColors(event): … … 7525 7553 7526 7554 def SetViewPoint(event): 7527 indx = drawAtoms.GetSelectedRows()7528 if indx:7529 7530 7531 7555 indx = getAtomSelections(drawAtoms) 7556 if not indx: return 7557 atomData = data['Drawing']['Atoms'] 7558 cx = data['Drawing']['atomPtrs'][0] 7559 data['Drawing']['viewPoint'] = [atomData[indx[0]][cx:cx+3],[indx[0],0]] 7532 7560 # drawAtoms.ClearSelection() #do I really want to do this? 7533 G2plt.PlotStructure(G2frame,data) 7534 else: 7535 G2G.G2MessageBox(G2frame,'Select atoms first') 7561 G2plt.PlotStructure(G2frame,data) 7536 7562 7537 7563 def noDuplicate(xyz,atomData): #be careful where this is used  it's slow … … 7543 7569 7544 7570 def AddSymEquiv(event): 7545 indx = drawAtoms.GetSelectedRows() 7571 indx = getAtomSelections(drawAtoms) 7572 if not indx: return 7546 7573 indx.sort() 7547 if indx: 7548 colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] 7549 cx,ct,cs,cui = data['Drawing']['atomPtrs'] 7550 cuij = cui+2 7551 cmx = 0 7552 if 'Mx' in colLabels: 7553 cmx = colLabels.index('Mx') 7554 atomData = data['Drawing']['Atoms'] 7555 generalData = data['General'] 7556 SGData = generalData['SGData'] 7557 SpnFlp = SGData.get('SpnFlp',[]) 7558 dlg = SymOpDialog(G2frame,SGData,False,True) 7559 try: 7560 if dlg.ShowModal() == wx.ID_OK: 7561 Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection() 7562 Cell = np.array(Cell) 7563 cent = SGData['SGCen'][Cent] 7564 M,T = SGData['SGOps'][Opr] 7565 for ind in indx: 7566 XYZ = np.array(atomData[ind][cx:cx+3]) 7567 XYZ = np.inner(M,XYZ)+T 7568 if Inv and not SGData['SGFixed']: 7569 XYZ = XYZ 7570 XYZ = XYZ+cent+Cell 7571 if Force: 7572 XYZ %= 1. #G2spc.MoveToUnitCell(XYZ) 7573 if noDuplicate(XYZ,atomData): 7574 atom = copy.copy(atomData[ind]) 7575 atom[cx:cx+3] = XYZ 7576 atomOp = atom[cs1] 7577 OprNum = ((Opr+1)+100*Cent)*(12*Inv) 7578 newOp = str(OprNum)+'+'+ \ 7579 str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2])) 7580 atom[cs1] = G2spc.StringOpsProd(atomOp,newOp,SGData) 7581 if cmx: #magnetic moment 7582 opNum = G2spc.GetOpNum(OprNum,SGData) 7583 mom = np.array(atom[cmx:cmx+3]) 7584 if SGData['SGGray']: 7585 atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M) 7586 else: 7587 atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum1] 7588 if atom[cui] == 'A': 7589 Uij = atom[cuij:cuij+6] 7590 Uij = G2spc.U2Uij(np.inner(np.inner(M,G2spc.Uij2U(Uij)),M)) 7591 atom[cuij:cuij+6] = Uij 7592 atomData.append(atom[:cuij+9]) #not SS stuff 7593 finally: 7594 dlg.Destroy() 7595 UpdateDrawAtoms() 7596 drawAtoms.ClearSelection() 7597 G2plt.PlotStructure(G2frame,data) 7598 else: 7599 G2G.G2MessageBox(G2frame,'Select atoms first') 7574 colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] 7575 cx,ct,cs,cui = data['Drawing']['atomPtrs'] 7576 cuij = cui+2 7577 cmx = 0 7578 if 'Mx' in colLabels: 7579 cmx = colLabels.index('Mx') 7580 atomData = data['Drawing']['Atoms'] 7581 generalData = data['General'] 7582 SGData = generalData['SGData'] 7583 SpnFlp = SGData.get('SpnFlp',[]) 7584 dlg = SymOpDialog(G2frame,SGData,False,True) 7585 try: 7586 if dlg.ShowModal() == wx.ID_OK: 7587 Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection() 7588 Cell = np.array(Cell) 7589 cent = SGData['SGCen'][Cent] 7590 M,T = SGData['SGOps'][Opr] 7591 for ind in indx: 7592 XYZ = np.array(atomData[ind][cx:cx+3]) 7593 XYZ = np.inner(M,XYZ)+T 7594 if Inv and not SGData['SGFixed']: 7595 XYZ = XYZ 7596 XYZ = XYZ+cent+Cell 7597 if Force: 7598 XYZ %= 1. #G2spc.MoveToUnitCell(XYZ) 7599 if noDuplicate(XYZ,atomData): 7600 atom = copy.copy(atomData[ind]) 7601 atom[cx:cx+3] = XYZ 7602 atomOp = atom[cs1] 7603 OprNum = ((Opr+1)+100*Cent)*(12*Inv) 7604 newOp = str(OprNum)+'+'+ \ 7605 str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2])) 7606 atom[cs1] = G2spc.StringOpsProd(atomOp,newOp,SGData) 7607 if cmx: #magnetic moment 7608 opNum = G2spc.GetOpNum(OprNum,SGData) 7609 mom = np.array(atom[cmx:cmx+3]) 7610 if SGData['SGGray']: 7611 atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M) 7612 else: 7613 atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum1] 7614 if atom[cui] == 'A': 7615 Uij = atom[cuij:cuij+6] 7616 Uij = G2spc.U2Uij(np.inner(np.inner(M,G2spc.Uij2U(Uij)),M)) 7617 atom[cuij:cuij+6] = Uij 7618 atomData.append(atom[:cuij+9]) #not SS stuff 7619 finally: 7620 dlg.Destroy() 7621 UpdateDrawAtoms() 7622 drawAtoms.ClearSelection() 7623 G2plt.PlotStructure(G2frame,data) 7600 7624 7601 7625 def AddSphere(event): 7626 indx = getAtomSelections(drawAtoms) 7627 if not indx: return 7602 7628 generalData = data['General'] 7603 7629 Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) … … 7614 7640 SpnFlp = SGData.get('SpnFlp',[]) 7615 7641 cellArray = G2lat.CellBlock(1) 7616 indx = drawAtoms.GetSelectedRows()7617 7642 indx.sort() 7618 7643 dlg = SphereEnclosure(G2frame,data['General'],data['Drawing'],indx) … … 7670 7695 7671 7696 def TransformSymEquiv(event): 7672 indx = drawAtoms.GetSelectedRows() 7697 indx = getAtomSelections(drawAtoms) 7698 if not indx: return 7673 7699 indx.sort() 7674 if indx: 7675 atomData = data['Drawing']['Atoms'] 7676 colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] 7677 cx,ct,cs,ci = data['Drawing']['atomPtrs'] 7678 cuij = ci+2 7679 cmx = 0 7680 if 'Mx' in colLabels: 7681 cmx = colLabels.index('Mx') 7682 atomData = data['Drawing']['Atoms'] 7683 generalData = data['General'] 7684 SGData = generalData['SGData'] 7685 SpnFlp = SGData.get('SpnFlp',[]) 7686 dlg = SymOpDialog(G2frame,SGData,False,True) 7687 try: 7688 if dlg.ShowModal() == wx.ID_OK: 7689 Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection() 7690 Cell = np.array(Cell) 7691 cent = SGData['SGCen'][Cent] 7692 M,T = SGData['SGOps'][Opr] 7693 for ind in indx: 7694 XYZ = np.array(atomData[ind][cx:cx+3]) 7695 XYZ = np.inner(M,XYZ)+T 7696 if Inv and not SGData['SGFixed']: 7697 XYZ = XYZ 7698 XYZ = XYZ+cent+Cell 7699 if Force: 7700 XYZ,cell = G2spc.MoveToUnitCell(XYZ) 7701 Cell += cell 7702 atom = atomData[ind] 7703 atom[cx:cx+3] = XYZ 7704 OprNum = ((Opr+1)+100*Cent)*(12*Inv) 7705 if cmx: 7706 opNum = G2spc.GetOpNum(OprNum,SGData) 7707 mom = np.array(atom[cmx:cmx+3]) 7708 atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum1] 7709 atomOp = atom[cs1] 7710 newOp = str(((Opr+1)+100*Cent)*(12*Inv))+'+'+ \ 7711 str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2])) 7712 atom[cs1] = G2spc.StringOpsProd(atomOp,newOp,SGData) 7713 if atom[ci] == 'A': 7714 Uij = atom[cuij:cuij+6] 7715 U = G2spc.Uij2U(Uij) 7716 U = np.inner(np.inner(M,U),M) 7717 Uij = G2spc.U2Uij(U) 7718 atom[cuij:cuij+6] = Uij 7719 data['Drawing']['Atoms'] = atomData 7720 finally: 7721 dlg.Destroy() 7722 UpdateDrawAtoms() 7723 drawAtoms.ClearSelection() 7724 G2plt.PlotStructure(G2frame,data) 7725 else: 7726 G2G.G2MessageBox(G2frame,'Select atoms first') 7700 atomData = data['Drawing']['Atoms'] 7701 colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] 7702 cx,ct,cs,ci = data['Drawing']['atomPtrs'] 7703 cuij = ci+2 7704 cmx = 0 7705 if 'Mx' in colLabels: 7706 cmx = colLabels.index('Mx') 7707 atomData = data['Drawing']['Atoms'] 7708 generalData = data['General'] 7709 SGData = generalData['SGData'] 7710 SpnFlp = SGData.get('SpnFlp',[]) 7711 dlg = SymOpDialog(G2frame,SGData,False,True) 7712 try: 7713 if dlg.ShowModal() == wx.ID_OK: 7714 Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection() 7715 Cell = np.array(Cell) 7716 cent = SGData['SGCen'][Cent] 7717 M,T = SGData['SGOps'][Opr] 7718 for ind in indx: 7719 XYZ = np.array(atomData[ind][cx:cx+3]) 7720 XYZ = np.inner(M,XYZ)+T 7721 if Inv and not SGData['SGFixed']: 7722 XYZ = XYZ 7723 XYZ = XYZ+cent+Cell 7724 if Force: 7725 XYZ,cell = G2spc.MoveToUnitCell(XYZ) 7726 Cell += cell 7727 atom = atomData[ind] 7728 atom[cx:cx+3] = XYZ 7729 OprNum = ((Opr+1)+100*Cent)*(12*Inv) 7730 if cmx: 7731 opNum = G2spc.GetOpNum(OprNum,SGData) 7732 mom = np.array(atom[cmx:cmx+3]) 7733 atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum1] 7734 atomOp = atom[cs1] 7735 newOp = str(((Opr+1)+100*Cent)*(12*Inv))+'+'+ \ 7736 str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2])) 7737 atom[cs1] = G2spc.StringOpsProd(atomOp,newOp,SGData) 7738 if atom[ci] == 'A': 7739 Uij = atom[cuij:cuij+6] 7740 U = G2spc.Uij2U(Uij) 7741 U = np.inner(np.inner(M,U),M) 7742 Uij = G2spc.U2Uij(U) 7743 atom[cuij:cuij+6] = Uij 7744 data['Drawing']['Atoms'] = atomData 7745 finally: 7746 dlg.Destroy() 7747 UpdateDrawAtoms() 7748 drawAtoms.ClearSelection() 7749 G2plt.PlotStructure(G2frame,data) 7727 7750 7728 7751 def FillCoordSphere(event): 7752 indx = getAtomSelections(drawAtoms) 7753 if not indx: return 7729 7754 generalData = data['General'] 7730 7755 Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) … … 7736 7761 except: 7737 7762 pass 7738 indx = drawAtoms.GetSelectedRows() 7739 if indx: 7740 indx.sort() 7741 atomData = data['Drawing']['Atoms'] 7742 numAtoms = len(atomData) 7743 cx,ct,cs,ci = data['Drawing']['atomPtrs'] 7744 cij = ci+2 7745 SGData = generalData['SGData'] 7746 cellArray = G2lat.CellBlock(1) 7747 nind = len(indx) 7748 pgbar = wx.ProgressDialog('Fill CN sphere for %d atoms'%nind,'Atoms done=',nind+1, 7749 style = wx.PD_ELAPSED_TIMEwx.PD_AUTO_HIDEwx.PD_CAN_ABORT) 7750 screenSize = wx.ClientDisplayRect() 7751 Size = pgbar.GetSize() 7752 if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 7753 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x 7754 pgbar.SetPosition(wx.Point(screenSize[2]Size[0]305,screenSize[1]+5)) 7755 for Ind,ind in enumerate(indx): 7756 atomA = atomData[ind] 7757 xyzA = np.array(atomA[cx:cx+3]) 7758 indA = atomTypes.index(atomA[ct]) 7759 for atomB in atomData[:numAtoms]: 7760 indB = atomTypes.index(atomB[ct]) 7761 sumR = radii[indA]+radii[indB] 7762 xyzB = np.array(atomB[cx:cx+3]) 7763 for xyz in cellArray+xyzB: 7764 dist = np.sqrt(np.sum(np.inner(Amat,xyzxyzA)**2)) 7765 if 0 < dist <= data['Drawing']['radiusFactor']*sumR: 7766 if noDuplicate(xyz,atomData): 7767 oprB = atomB[cs1] 7768 C = xyzxyzB 7769 newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2]))) 7770 newAtom = atomB[:] 7771 newAtom[cx:cx+3] = xyz 7772 newAtom[cs1] = G2spc.StringOpsProd(oprB,newOp,SGData) 7773 atomData.append(newAtom[:cij+9]) #not SS stuff 7774 GoOn = pgbar.Update(Ind,newmsg='Atoms done=%d'%(Ind)) 7775 if not GoOn[0]: 7776 break 7777 pgbar.Destroy() 7763 indx.sort() 7764 atomData = data['Drawing']['Atoms'] 7765 numAtoms = len(atomData) 7766 cx,ct,cs,ci = data['Drawing']['atomPtrs'] 7767 cij = ci+2 7768 SGData = generalData['SGData'] 7769 cellArray = G2lat.CellBlock(1) 7770 nind = len(indx) 7771 pgbar = wx.ProgressDialog('Fill CN sphere for %d atoms'%nind,'Atoms done=',nind+1, 7772 style = wx.PD_ELAPSED_TIMEwx.PD_AUTO_HIDEwx.PD_CAN_ABORT) 7773 screenSize = wx.ClientDisplayRect() 7774 Size = pgbar.GetSize() 7775 if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 7776 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x 7777 pgbar.SetPosition(wx.Point(screenSize[2]Size[0]305,screenSize[1]+5)) 7778 for Ind,ind in enumerate(indx): 7779 atomA = atomData[ind] 7780 xyzA = np.array(atomA[cx:cx+3]) 7781 indA = atomTypes.index(atomA[ct]) 7782 for atomB in atomData[:numAtoms]: 7783 indB = atomTypes.index(atomB[ct]) 7784 sumR = radii[indA]+radii[indB] 7785 xyzB = np.array(atomB[cx:cx+3]) 7786 for xyz in cellArray+xyzB: 7787 dist = np.sqrt(np.sum(np.inner(Amat,xyzxyzA)**2)) 7788 if 0 < dist <= data['Drawing']['radiusFactor']*sumR: 7789 if noDuplicate(xyz,atomData): 7790 oprB = atomB[cs1] 7791 C = xyzxyzB 7792 newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2]))) 7793 newAtom = atomB[:] 7794 newAtom[cx:cx+3] = xyz 7795 newAtom[cs1] = G2spc.StringOpsProd(oprB,newOp,SGData) 7796 atomData.append(newAtom[:cij+9]) #not SS stuff 7797 GoOn = pgbar.Update(Ind,newmsg='Atoms done=%d'%(Ind)) 7798 if not GoOn[0]: 7799 break 7800 pgbar.Destroy() 7801 data['Drawing']['Atoms'] = atomData 7802 UpdateDrawAtoms() 7803 drawAtoms.ClearSelection() 7804 G2plt.PlotStructure(G2frame,data) 7805 7806 def FillUnitCell(event): 7807 indx = getAtomSelections(drawAtoms) 7808 if not indx: return 7809 indx.sort() 7810 atomData = data['Drawing']['Atoms'] 7811 colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] 7812 cx,ct,cs,ci = data['Drawing']['atomPtrs'] 7813 cmx = 0 7814 if 'Mx' in colLabels: 7815 cmx = colLabels.index('Mx') 7816 cuij = cs+5 7817 generalData = data['General'] 7818 SGData = generalData['SGData'] 7819 SpnFlp = SGData.get('SpnFlp',[]) 7820 nind = len(indx) 7821 pgbar = wx.ProgressDialog('Fill unit cell for %d atoms'%nind,'Atoms done=',nind+1, 7822 style = wx.PD_ELAPSED_TIMEwx.PD_AUTO_HIDEwx.PD_CAN_ABORT) 7823 screenSize = wx.ClientDisplayRect() 7824 Size = pgbar.GetSize() 7825 if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 7826 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x 7827 pgbar.SetPosition(wx.Point(screenSize[2]Size[0]305,screenSize[1]+5)) 7828 for Ind,ind in enumerate(indx): 7829 atom = atomData[ind] 7830 XYZ = np.array(atom[cx:cx+3]) 7831 Uij = atom[cuij:cuij+6] 7832 result = G2spc.GenAtom(XYZ,SGData,False,Uij,True) 7833 for item in result: 7834 atom = copy.copy(atomData[ind]) 7835 atom[cx:cx+3] = item[0] 7836 if cmx: 7837 Opr = abs(item[2])%100 7838 M = SGData['SGOps'][Opr1][0] 7839 opNum = G2spc.GetOpNum(item[2],SGData) 7840 mom = np.array(atom[cmx:cmx+3]) 7841 if SGData['SGGray']: 7842 atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M) 7843 else: 7844 atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum1] 7845 atom[cs1] = str(item[2])+'+' \ 7846 +str(item[3][0])+','+str(item[3][1])+','+str(item[3][2]) 7847 atom[cuij:cuij+6] = item[1] 7848 Opp = G2spc.Opposite(item[0]) 7849 for key in Opp: 7850 if noDuplicate(Opp[key],atomData): 7851 unit = item[3]+np.array(eval(key))*1. 7852 cell = '%d+%d,%d,%d'%(item[2],unit[0],unit[1],unit[2]) 7853 atom[cx:cx+3] = Opp[key] 7854 atom[cs1] = cell 7855 atomData.append(atom[:cuij+9]) #not SS stuff 7778 7856 data['Drawing']['Atoms'] = atomData 7779 UpdateDrawAtoms() 7780 drawAtoms.ClearSelection() 7781 G2plt.PlotStructure(G2frame,data) 7782 else: 7783 G2G.G2MessageBox(G2frame,'Select atoms first') 7784 7785 def FillUnitCell(event): 7786 indx = drawAtoms.GetSelectedRows() 7857 GoOn = pgbar.Update(Ind,newmsg='Atoms done=%d'%(Ind)) 7858 if not GoOn[0]: 7859 break 7860 pgbar.Destroy() 7861 UpdateDrawAtoms() 7862 drawAtoms.ClearSelection() 7863 G2plt.PlotStructure(G2frame,data) 7864 7865 def DrawAtomsDelete(event): 7866 indx = getAtomSelections(drawAtoms) 7867 if not indx: return 7787 7868 indx.sort() 7788 if indx: 7789 atomData = data['Drawing']['Atoms'] 7790 colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] 7791 cx,ct,cs,ci = data['Drawing']['atomPtrs'] 7792 cmx = 0 7793 if 'Mx' in colLabels: 7794 cmx = colLabels.index('Mx') 7795 cuij = cs+5 7796 generalData = data['General'] 7797 SGData = generalData['SGData'] 7798 SpnFlp = SGData.get('SpnFlp',[]) 7799 nind = len(indx) 7800 pgbar = wx.ProgressDialog('Fill unit cell for %d atoms'%nind,'Atoms done=',nind+1, 7801 style = wx.PD_ELAPSED_TIMEwx.PD_AUTO_HIDEwx.PD_CAN_ABORT) 7802 screenSize = wx.ClientDisplayRect() 7803 Size = pgbar.GetSize() 7804 if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 7805 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x 7806 pgbar.SetPosition(wx.Point(screenSize[2]Size[0]305,screenSize[1]+5)) 7807 for Ind,ind in enumerate(indx): 7808 atom = atomData[ind] 7809 XYZ = np.array(atom[cx:cx+3]) 7810 Uij = atom[cuij:cuij+6] 7811 result = G2spc.GenAtom(XYZ,SGData,False,Uij,True) 7812 for item in result: 7813 atom = copy.copy(atomData[ind]) 7814 atom[cx:cx+3] = item[0] 7815 if cmx: 7816 Opr = abs(item[2])%100 7817 M = SGData['SGOps'][Opr1][0] 7818 opNum = G2spc.GetOpNum(item[2],SGData) 7819 mom = np.array(atom[cmx:cmx+3]) 7820 if SGData['SGGray']: 7821 atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M) 7822 else: 7823 atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum1] 7824 atom[cs1] = str(item[2])+'+' \ 7825 +str(item[3][0])+','+str(item[3][1])+','+str(item[3][2]) 7826 atom[cuij:cuij+6] = item[1] 7827 Opp = G2spc.Opposite(item[0]) 7828 for key in Opp: 7829 if noDuplicate(Opp[key],atomData): 7830 unit = item[3]+np.array(eval(key))*1. 7831 cell = '%d+%d,%d,%d'%(item[2],unit[0],unit[1],unit[2]) 7832 atom[cx:cx+3] = Opp[key] 7833 atom[cs1] = cell 7834 atomData.append(atom[:cuij+9]) #not SS stuff 7835 data['Drawing']['Atoms'] = atomData 7836 GoOn = pgbar.Update(Ind,newmsg='Atoms done=%d'%(Ind)) 7837 if not GoOn[0]: 7838 break 7839 pgbar.Destroy() 7840 UpdateDrawAtoms() 7841 drawAtoms.ClearSelection() 7842 G2plt.PlotStructure(G2frame,data) 7843 else: 7844 G2G.G2MessageBox(G2frame,'Select atoms first') 7845 7846 def DrawAtomsDelete(event): 7847 indx = drawAtoms.GetSelectedRows() 7848 indx.sort() 7849 if indx: 7850 atomData = data['Drawing']['Atoms'] 7851 indx.reverse() 7852 for ind in indx: 7853 del atomData[ind] 7854 UpdateDrawAtoms() 7855 drawAtoms.ClearSelection() 7856 G2plt.PlotStructure(G2frame,data) 7857 else: 7858 G2G.G2MessageBox(G2frame,'Select atoms first') 7869 atomData = data['Drawing']['Atoms'] 7870 indx.reverse() 7871 for ind in indx: 7872 del atomData[ind] 7873 UpdateDrawAtoms() 7874 drawAtoms.ClearSelection() 7875 G2plt.PlotStructure(G2frame,data) 7859 7876 event.StopPropagation() 7860 7877 … … 7893 7910 7894 7911 def OnDrawPlane(event): 7895 indx = drawAtoms.GetSelectedRows()7912 indx = getAtomSelections(drawAtoms) 7896 7913 if len(indx) < 4: 7897 7914 G2G.G2MessageBox(G2frame,'Select four or more atoms first') … … 7916 7933 def OnDrawDistVP(event): 7917 7934 # distance to view point 7918 indx = drawAtoms.GetSelectedRows() 7919 if not indx: 7920 G2G.G2MessageBox(G2frame,'Select atoms first') 7921 print ('***** ERROR  no atoms selected') 7922 return 7935 indx = getAtomSelections(drawAtoms,'distance calc') 7936 if not indx: return 7923 7937 generalData = data['General'] 7924 7938 Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) … … 7938 7952 7939 7953 def OnDrawDAT(event): 7940 # distance, angle, torsion7941 indx = drawAtoms.GetSelectedRows()7954 #compute distance, angle, or torsion depending on number of selections 7955 indx = getAtomSelections(drawAtoms) 7942 7956 if len(indx) not in [2,3,4]: 7943 7957 G2G.G2MessageBox(G2frame,'Select 2, 3 or 4 atoms first') 
trunk/GSASIIpwdGUI.py
r4416 r4433 4732 4732 if General.get('Modulated',False): 4733 4733 Super = 1 4734 Histograms = G2frame.GPXtree.GetItemPyData(phaseId)['Histograms'] 4735 histName = G2frame.GPXtree.GetItemText(G2frame.PatternId) 4736 histData = Histograms[histName] 4737 muStrData = histData['Mustrain'] 4738 sizeData = histData['Size'] 4734 try: 4735 Histograms = G2frame.GPXtree.GetItemPyData(phaseId)['Histograms'] 4736 histName = G2frame.GPXtree.GetItemText(G2frame.PatternId) 4737 histData = Histograms[histName] 4738 muStrData = histData['Mustrain'] 4739 sizeData = histData['Size'] 4740 except: 4741 return 4739 4742 rowLabels = [] 4740 4743 if HKLF: … … 4827 4830 if G2frame.refTable[phaseName].GetTable() is None: 4828 4831 PeakTable = MakeReflectionTable(phaseName) 4832 if not PeakTable: return 4829 4833 G2frame.refTable[phaseName].SetTable(PeakTable, True) 4830 4834 G2frame.refTable[phaseName].EnableEditing(False) 
trunk/exports/G2export_CIF.py
r4411 r4433 1338 1338 # compute maximum intensity reflection 1339 1339 Imax = 0 1340 phaselist = [] 1340 1341 for phasenam in histblk['Reflection Lists']: 1341 scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0] 1342 try: 1343 scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0] 1344 except KeyError: # reflection table from removed phase? 1345 continue 1346 phaselist.append(phasenam) 1342 1347 refList = np.asarray(histblk['Reflection Lists'][phasenam]['RefList']) 1343 1348 I100 = scale*refList.T[8]*refList.T[11] … … 1348 1353 1349 1354 WriteCIFitem(self.fp, 'loop_') 1350 if len( histblk['Reflection Lists'].keys()) > 1:1355 if len(phaselist) > 1: 1351 1356 WriteCIFitem(self.fp, ' _pd_refln_phase_id') 1352 1357 WriteCIFitem(self.fp, ' ' + refprx + 'index_h' + … … 1365 1370 dmax = None 1366 1371 dmin = None 1367 for phasenam in histblk['Reflection Lists']:1372 for phasenam in phaselist: 1368 1373 scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0] 1369 1374 phaseid = self.Phases[phasenam]['pId'] … … 1380 1385 if dmin is None: 1381 1386 dmax = dmin = ref[4] 1382 if len( histblk['Reflection Lists'].keys()) > 1:1387 if len(phaselist) > 1: 1383 1388 s = PutInCol(phaseid,2) 1384 1389 else: … … 1398 1403 WriteCIFitem(self.fp, " "+s) 1399 1404 1400 WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,len( histblk['Reflection Lists']))1405 WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,len(phaselist)) 1401 1406 WriteCIFitem(self.fp, '\n# POWDER DATA TABLE') 1402 1407 # is data fixed step? If the step varies by <0.01% treat as fixed step
Note: See TracChangeset
for help on using the changeset viewer.