Changeset 4417
- Timestamp:
- May 12, 2020 5:03:59 PM (3 years ago)
- Location:
- trunk
- Files:
-
- 2 edited
-
GSASIIphsGUI.py (modified) (4 diffs)
-
GSASIIpwd.py (modified) (5 diffs)
Legend:
- Unmodified
- Added
- Removed
-
trunk/GSASIIphsGUI.py
r4415 r4417 4427 4427 4428 4428 Indx = {} 4429 atChoice = RMCPdict['atSeq'] 4429 atChoice = atNames 4430 if G2frame.RMCchoice == 'RMCProfile': 4431 atChoice = RMCPdict['atSeq'] 4430 4432 swapSizer = wx.FlexGridSizer(4,5,5) 4431 4433 swapLabels = [' ','Atom-A','Atom-B',' Swap prob.'] … … 4649 4651 def OnByMolec(event): 4650 4652 RMCPdict['byMolec'] = bymolec.GetValue() 4653 wx.CallAfter(UpdateRMC) 4651 4654 4652 4655 def OnReStart(event): … … 4854 4857 restart.Bind(wx.EVT_CHECKBOX,OnReStart) 4855 4858 resLine.Add(restart,0,WACV) 4856 resLine.Add(wx.StaticText(G2frame.FRMC,label=' Computation cycles: '),0,WACV)4859 resLine.Add(wx.StaticText(G2frame.FRMC,label=' 10,000X Computation cycles: '),0,WACV) 4857 4860 resLine.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'Cycles',min=1,size=[60,25]),0,WACV) 4858 4861 mainSizer.Add(resLine,0,WACV) … … 4879 4882 distBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'min Contact',min=0.,max=4.,size=(50,25)),0,WACV) 4880 4883 mainSizer.Add(distBox,0,WACV) 4881 mainSizer.Add(GetPairSizer(RMCPdict),0,WACV) 4882 4883 angBox = wx.BoxSizer(wx.HORIZONTAL) 4884 angAdd = wx.Button(G2frame.FRMC,label='Add') 4885 angAdd.Bind(wx.EVT_BUTTON,OnAddAngle) 4886 angBox.Add(angAdd,0,WACV) 4887 angBox.Add(wx.StaticText(G2frame.FRMC,label=' A-B-C angle restraints, weight: '),0,WACV) 4888 angBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'Angle Weight',min=0.,max=100.,size=(50,25)),0,WACV) 4889 mainSizer.Add(angBox,0,WACV) 4890 if len(RMCPdict['Angles']): 4891 mainSizer.Add(GetAngleSizer(),0,WACV) 4892 4893 torBox = wx.BoxSizer(wx.HORIZONTAL) 4894 torAdd = wx.Button(G2frame.FRMC,label='Add') 4895 torAdd.Bind(wx.EVT_BUTTON,OnAddTorsion) 4896 torBox.Add(torAdd,0,WACV) 4897 torBox.Add(wx.StaticText(G2frame.FRMC,label=' A-B-C-D torsion angle restraints, weight: '),0,WACV) 4898 torBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'Torsion Weight',min=0.,max=100.,size=(50,25)),0,WACV) 4899 mainSizer.Add(torBox,0,WACV) 4900 if len(RMCPdict['Torsions']): 4901 mainSizer.Add(GetTorsionSizer(),0,WACV) 4902 4884 if RMCPdict['byMolec']: 4885 mainSizer.Add(GetPairSizer(RMCPdict),0,WACV) 4886 4887 angBox = wx.BoxSizer(wx.HORIZONTAL) 4888 angAdd = wx.Button(G2frame.FRMC,label='Add') 4889 angAdd.Bind(wx.EVT_BUTTON,OnAddAngle) 4890 angBox.Add(angAdd,0,WACV) 4891 angBox.Add(wx.StaticText(G2frame.FRMC,label=' A-B-C angle restraints, weight: '),0,WACV) 4892 angBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'Angle Weight',min=0.,max=100.,size=(50,25)),0,WACV) 4893 mainSizer.Add(angBox,0,WACV) 4894 if len(RMCPdict['Angles']): 4895 mainSizer.Add(GetAngleSizer(),0,WACV) 4896 4897 torBox = wx.BoxSizer(wx.HORIZONTAL) 4898 torAdd = wx.Button(G2frame.FRMC,label='Add') 4899 torAdd.Bind(wx.EVT_BUTTON,OnAddTorsion) 4900 torBox.Add(torAdd,0,WACV) 4901 torBox.Add(wx.StaticText(G2frame.FRMC,label=' A-B-C-D torsion angle restraints, weight: '),0,WACV) 4902 torBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'Torsion Weight',min=0.,max=100.,size=(50,25)),0,WACV) 4903 mainSizer.Add(torBox,0,WACV) 4904 if len(RMCPdict['Torsions']): 4905 mainSizer.Add(GetTorsionSizer(),0,WACV) 4906 4903 4907 G2G.HorizontalLine(mainSizer,G2frame.FRMC) 4904 4908 mainSizer.Add(FileSizer(RMCPdict),0,WACV) -
trunk/GSASIIpwd.py
r4416 r4417 2625 2625 from fullrmc.Constraints.DihedralAngleConstraints import DihedralAngleConstraint 2626 2626 from fullrmc.Core.MoveGenerator import MoveGeneratorCollector 2627 from fullrmc.Generators.Swaps import SwapPositionsGenerator 2627 2628 from fullrmc.Core.GroupSelector import RecursiveGroupSelector 2628 2629 from fullrmc.Selectors.RandomSelectors import RandomSelector … … 2632 2633 from fullrmc.Generators.Rotations import RotationGenerator, RotationAboutAxisGenerator 2633 2634 from fullrmc.Core.Collection import get_principal_axis 2635 from fullrmc.debugStuff import * 2636 InvokeDebugOpts() 2637 SwapGen = {} 2634 2638 # engine setup\n''' 2635 2639 rundata += 'LOGGER.set_log_file_basename("%s")\n'%pName … … 2662 2666 wtDict['Struct'] = filDat[1] 2663 2667 rundata += ' ENGINE.add_constraints(InterMolecularDistanceConstraint())\n' 2664 if len(BondList): 2665 rundata += ' B_CONSTRAINT = BondConstraint()\n' 2666 rundata += ' ENGINE.add_constraints(B_CONSTRAINT)\n' 2667 if len(AngleList): 2668 rundata += ' A_CONSTRAINT = BondsAngleConstraint()\n' 2669 rundata += ' ENGINE.add_constraints(A_CONSTRAINT)\n' 2670 if len(RMCPdict['Torsions']): 2671 rundata += ' T_CONSTRAINT = DihedralAngleConstraint()\n' 2672 rundata += ' ENGINE.add_constraints(T_CONSTRAINT)\n' 2668 if RMCPdict['byMolec']: 2669 if len(BondList): 2670 rundata += ' B_CONSTRAINT = BondConstraint()\n' 2671 rundata += ' ENGINE.add_constraints(B_CONSTRAINT)\n' 2672 if len(AngleList): 2673 rundata += ' A_CONSTRAINT = BondsAngleConstraint()\n' 2674 rundata += ' ENGINE.add_constraints(A_CONSTRAINT)\n' 2675 if len(RMCPdict['Torsions']): 2676 rundata += ' T_CONSTRAINT = DihedralAngleConstraint()\n' 2677 rundata += ' ENGINE.add_constraints(T_CONSTRAINT)\n' 2673 2678 rundata += ' ENGINE.save()\n' 2674 2679 rundata += 'else:\n' … … 2678 2683 rundata += 'for constraint in Constraints:\n' 2679 2684 rundata += ' strcons = str(type(constraint))\n' 2680 if len(BondList): 2681 rundata += ' if "BondConstraint" in strcons:\n' 2682 rundata += ' constraint.set_variance_squared(%f)\n'%RMCPdict['Bond Weight'] 2683 rundata += ' constraint.create_bonds_by_definition(bondsDefinition={"%s":[\n'%Res 2684 for bond in BondList: 2685 rundata += ' %s'%bond 2686 rundata += ' ]})\n' 2687 if len(AngleList): 2688 rundata += ' elif "BondsAngleConstraint" in strcons:\n' 2689 rundata += ' constraint.set_variance_squared(%f)\n'%RMCPdict['Angle Weight'] 2690 rundata += ' constraint.create_angles_by_definition(anglesDefinition={"%s":[\n'%Res 2691 for angle in AngleList: 2692 rundata += ' %s'%angle 2693 rundata += ' ]})\n' 2694 if len(RMCPdict['Torsions']): 2695 rundata += ' elif "DihedralAngleConstraint" in strcons:\n' 2696 rundata += ' constraint.set_variance_squared(%f)\n'%RMCPdict['Torsion Weight'] 2697 rundata += ' constraint.create_angles_by_definition(anglesDefinition={"%s":[\n'%Res 2698 for torsion in RMCPdict['Torsions']: 2699 rundata += ' %s\n'%str(tuple(torsion)) 2700 rundata += ' ]})\n' 2701 rundata += ' elif "InterMolecular" in strcons:\n' 2685 rundata += ' if "InterMolecular" in strcons:\n' 2702 2686 rundata += ' constraint.set_default_distance(%f)\n'%RMCPdict['min Contact'] 2703 2687 rundata += ' elif "PairDistribution" in strcons:\n' … … 2710 2694 if RMCPdict['FitScale']: 2711 2695 rundata += ' constraint.set_adjust_scale_factor((10, 0.01, 100.))\n' 2712 rundata += 'ENGINE.set_groups_as_atoms()\n' 2696 if RMCPdict['byMolec']: 2697 if len(BondList): 2698 rundata += ' elif "BondConstraint" in strcons:\n' 2699 rundata += ' constraint.set_variance_squared(%f)\n'%RMCPdict['Bond Weight'] 2700 rundata += ' constraint.create_bonds_by_definition(bondsDefinition={"%s":[\n'%Res 2701 for bond in BondList: 2702 rundata += ' %s'%bond 2703 rundata += ' ]})\n' 2704 if len(AngleList): 2705 rundata += ' elif "BondsAngleConstraint" in strcons:\n' 2706 rundata += ' constraint.set_variance_squared(%f)\n'%RMCPdict['Angle Weight'] 2707 rundata += ' constraint.create_angles_by_definition(anglesDefinition={"%s":[\n'%Res 2708 for angle in AngleList: 2709 rundata += ' %s'%angle 2710 rundata += ' ]})\n' 2711 if len(RMCPdict['Torsions']): 2712 rundata += ' elif "DihedralAngleConstraint" in strcons:\n' 2713 rundata += ' constraint.set_variance_squared(%f)\n'%RMCPdict['Torsion Weight'] 2714 rundata += ' constraint.create_angles_by_definition(anglesDefinition={"%s":[\n'%Res 2715 for torsion in RMCPdict['Torsions']: 2716 rundata += ' %s\n'%str(tuple(torsion)) 2717 rundata += ' ]})\n' 2713 2718 if len(RMCPdict['Swaps']): 2714 print(RMCPdict['Swaps']) 2715 2716 # allElements = ENGINE.allElements 2717 # niSwapList = [[idx] for idx in range(len(allElements)) if allElements[idx]=='ni'] 2718 # tiSwapList = [[idx] for idx in range(len(allElements)) if allElements[idx]=='ti'] 2719 # # create swap generator 2720 # toNiSG = SwapPositionsGenerator(swapList=niSwapList) 2721 # toTiSG = SwapPositionsGenerator(swapList=tiSwapList) 2722 2723 2724 rundata += 'ENGINE.run(restartPdb="%s",numberOfSteps=%d, saveFrequency=1000)\n'%(restart,RMCPdict['Cycles']) 2719 rundata += ' allNames = ENGINE.allNames\n' 2720 for swap in RMCPdict['Swaps']: 2721 rundata += ' SwapA = [[idx] for idx in range(len(allNames)) if allNames[idx]=="%s"]\n'%swap[0] 2722 rundata += ' SwapB = [[idx] for idx in range(len(allNames)) if allNames[idx]=="%s"]\n'%swap[1] 2723 rundata += ' SwapGen["%s-%s"] = [SwapPositionsGenerator(swapList=SwapA),SwapPositionsGenerator(swapList=SwapB),%.2f]\n'%(swap[0],swap[1],swap[2]) 2725 2724 rundata += 'ENGINE.save()\n' 2726 2725 rundata += '#setup runs for fullrmc\n' 2727 2728 2729 2730 2731 2732 2733 2734 2726 2727 rundata += 'for _ in range(%d):\n'%RMCPdict['Cycles'] 2728 rundata += ' ENGINE.set_groups_as_atoms()\n' 2729 rundata += ' ENGINE.run(restartPdb="%s",numberOfSteps=10000, saveFrequency=1000)\n'%restart 2730 rundata += ' for swaps in SwapGen:\n' 2731 rundata += ' AB = swaps.split("-")\n' 2732 rundata += ' ENGINE.set_groups_as_atoms()\n' 2733 rundata += ' for g in ENGINE.groups:\n' 2734 rundata += ' if allNames[g.indexes[0]]==AB[0]:\n' 2735 rundata += ' g.set_move_generator(SwapGen[swaps][0])\n' 2736 rundata += ' elif allNames[g.indexes[0]]==AB[1]:\n' 2737 rundata += ' g.set_move_generator(SwapGen[swaps][1])\n' 2738 rundata += ' sProb = SwapGen[swaps][2]\n' 2739 rundata += ' ENGINE.run(restartPdb="%s",numberOfSteps=10000*sProb, saveFrequency=1000)\n'%restart 2740 rundata += ' ENGINE.set_groups_as_atoms()\n' 2741 rundata += ' ENGINE.run(restartPdb="%s",numberOfSteps=10000*(1.-sProb), saveFrequency=1000)\n'%restart 2742 rundata += 'ENGINE.close()\n' 2735 2743 rfile = open(rname,'w') 2736 2744 rfile.writelines(rundata)
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