diff --git a/ChangeLog.txt b/ChangeLog.txt index da75fcb..8c33688 100644 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -41,7 +41,7 @@ IMPROVEMENTS the list of atoms inside the group. BUG FIXES - * Correct EstimateCellVolume estimation for orthorombic F + * Correct EstimateCellVolume estimation for orthorhombic F * Correct calculation of integrated figures of merit (Rwp, etc..) with multiple crystalline phases (https://github.com/vincefn/objcryst/pull/53) * + several minor issues diff --git a/Fox/src/Fox.cpp b/Fox/src/Fox.cpp index dcb60e1..693913c 100644 --- a/Fox/src/Fox.cpp +++ b/Fox/src/Fox.cpp @@ -1018,7 +1018,7 @@ int main (int argc, char *argv[]) } else { wxMessageDialog d(NULL,_T("Failed loading file:\n")+name,_T("Error"),wxOK|wxICON_ERROR); d.ShowModal(); - } + } }; } else @@ -1047,7 +1047,7 @@ int main (int argc, char *argv[]) } else { wxMessageDialog d(NULL,_T("Failed loading file:\n")+name,_T("Error"),wxOK|wxICON_ERROR); d.ShowModal(); - } + } }; } } diff --git a/Fox/src/foxgrid/FoxGridSlave.cpp b/Fox/src/foxgrid/FoxGridSlave.cpp index eff7f7d..7bf0abb 100644 --- a/Fox/src/foxgrid/FoxGridSlave.cpp +++ b/Fox/src/foxgrid/FoxGridSlave.cpp @@ -347,7 +347,7 @@ void FoxGridSlave::CheckJobsAndStartCalculation() WriteLogMessage("ERROR: Can't write a file " + proc->dir + _T("\\input.xml")); return; } - + wxString cmd_content; wxString appname = wxApp::GetInstance()->argv[0]; if(rand) { diff --git a/ObjCryst/ObjCryst/Crystal.h b/ObjCryst/ObjCryst/Crystal.h index 1551870..cfb3c18 100644 --- a/ObjCryst/ObjCryst/Crystal.h +++ b/ObjCryst/ObjCryst/Crystal.h @@ -99,7 +99,7 @@ class Crystal:public UnitCell public: /// Default Constructor Crystal(); - /** \brief Crystal Constructor (orthorombic) + /** \brief Crystal Constructor (orthorhombic) * \param a,b,c : unit cell dimension, in angstroems * \param SpaceGroupId: space group symbol or number */ diff --git a/ObjCryst/ObjCryst/Indexing.cpp b/ObjCryst/ObjCryst/Indexing.cpp index 2de0c88..931ea24 100644 --- a/ObjCryst/ObjCryst/Indexing.cpp +++ b/ObjCryst/ObjCryst/Indexing.cpp @@ -63,7 +63,7 @@ float EstimateCellVolume(const float dmin, const float dmax, const float nbrefl, } // "*.85" means using D0_min rather than D0 if(system==MONOCLINIC) {C0=1.047;D0=0.786*.85;} - if(system==ORTHOROMBIC){C0=0.524;D0=1.36 *.85;} + if(system==ORTHORHOMBIC){C0=0.524;D0=1.36 *.85;} if(system==HEXAGONAL) {C0=0.150;D0=1.04 *.85;} if(system==RHOMBOEDRAL){C0=0.230;D0=1.04 *.85;} if(system==TETRAGONAL) {C0=0.214;D0=1.25 *.85;} @@ -121,7 +121,7 @@ float RecUnitCell::hkl2d(const float h,const float k,const float l,REAL *derivpa return par[0]+par[1]*par[1]*h*h + par[2]*par[2]*k*k + par[3]*par[3]*l*l + 2*par[1]*par[3]*par[4]*h*l; break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: { return par[0]+par[1]*par[1]*h*h + par[2]*par[2]*k*k + par[3]*par[3]*l*l; break; @@ -162,7 +162,7 @@ float RecUnitCell::hkl2d(const float h,const float k,const float l,REAL *derivpa return 2*par[1]*par[1]*h + 2*par[1]*par[3]*par[4]*l; break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: { return 2*par[1]*par[1]*h; break; @@ -203,7 +203,7 @@ float RecUnitCell::hkl2d(const float h,const float k,const float l,REAL *derivpa return 2*par[2]*par[2]*k; break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: { return 2*par[2]*par[2]*k; break; @@ -244,7 +244,7 @@ float RecUnitCell::hkl2d(const float h,const float k,const float l,REAL *derivpa return 2*par[3]*par[3]*l + 2*par[1]*par[3]*par[4]*h; break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: { return 2*par[3]*par[3]*l; break; @@ -287,7 +287,7 @@ float RecUnitCell::hkl2d(const float h,const float k,const float l,REAL *derivpa return 2*par[1]*h*h + 2*par[3]*par[4]*h*l; break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: { return 2*par[1]*h*h; break; @@ -328,7 +328,7 @@ float RecUnitCell::hkl2d(const float h,const float k,const float l,REAL *derivpa return 2*par[2]*k*k; break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: { return 2*par[2]*k*k; break; @@ -369,7 +369,7 @@ float RecUnitCell::hkl2d(const float h,const float k,const float l,REAL *derivpa return 2*par[3]*l*l + 2*par[1]*par[4]*h*l; break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: { return 2*par[3]*l*l; break; @@ -520,7 +520,7 @@ void RecUnitCell::hkl2d_delta(const float h,const float k,const float l, } } } - case ORTHOROMBIC: //OK + case ORTHORHOMBIC: //OK { dmin= p0m + p1m*p1m*h*h + p2m*p2m*k*k + p3m*p3m*l*l; dmax= p0p + p1p*p1p*h*h + p2p*p2p*k*k + p3p*p3p*l*l; @@ -593,7 +593,7 @@ vector RecUnitCell::DirectUnitCell(const bool equiv)const sgammaa=1; break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: { aa=par[1]; bb=par[2]; @@ -962,7 +962,7 @@ float Score(const PeakList &dhkl, const RecUnitCell &rpar, const unsigned int nb case MONOCLINIC: sk0=1;sl0=-1; break; - case ORTHOROMBIC: + case ORTHORHOMBIC: sk0=1;sl0=1; break; case HEXAGONAL: @@ -1274,7 +1274,7 @@ void CellExplorer::Evolution(unsigned int ng,const bool randomize,const float f, } break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: break; case HEXAGONAL: break; @@ -1622,7 +1622,7 @@ bool DichoIndexed(const PeakList &dhkl, const RecUnitCell &par,const RecUnitCell sk0=1;sl0=-1; break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: sk0=1;sl0=1; break; case HEXAGONAL: @@ -1894,7 +1894,7 @@ unsigned int CellExplorer::RDicVol(RecUnitCell par0,RecUnitCell dpar, unsigned i if(vq0[2].first>0) {par0.par[3]=vq0[2].second/vq0[2].first ; vdepth[2]=mDicVolDepthReport;dpar.par[3]*=.0625;} break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: { if(vq0[0].first>0) {par0.par[1]=vq0[0].second/vq0[0].first ; vdepth[0]=mDicVolDepthReport;dpar.par[1]*=.0625;}//pow((float)0.5,(int)(mDicVolDepthReport-depth));} if(vq0[1].first>0) {par0.par[2]=vq0[1].second/vq0[1].first ; vdepth[1]=mDicVolDepthReport;dpar.par[2]*=.0625;}//pow((float)0.5,(int)(mDicVolDepthReport-depth));} @@ -2410,7 +2410,7 @@ void CellExplorer::DicVol(const float minScore,const unsigned int minDepth,const }//x4 break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: { if(false) { @@ -2730,7 +2730,7 @@ void CellExplorer::Init() mMin[4]=0;mAmp[4]=amp_crossp; mnpar=5; break; - case ORTHOROMBIC: + case ORTHORHOMBIC: mMin[1]=min_latt;mAmp[1]=max_latt-min_latt; mMin[2]=min_latt;mAmp[2]=max_latt-min_latt; mMin[3]=min_latt;mAmp[3]=max_latt-min_latt; @@ -2773,7 +2773,7 @@ void CellExplorer::Init() nb2=1; break; } - case ORTHOROMBIC: + case ORTHORHOMBIC: { nb1=3; break; diff --git a/ObjCryst/ObjCryst/Indexing.h b/ObjCryst/ObjCryst/Indexing.h index a683f4f..fda3633 100644 --- a/ObjCryst/ObjCryst/Indexing.h +++ b/ObjCryst/ObjCryst/Indexing.h @@ -37,7 +37,9 @@ namespace ObjCryst * */ enum CrystalSystem -{ TRICLINIC, MONOCLINIC, ORTHOROMBIC, HEXAGONAL, RHOMBOEDRAL, TETRAGONAL, CUBIC}; +{ TRICLINIC, MONOCLINIC, ORTHORHOMBIC, HEXAGONAL, RHOMBOEDRAL, TETRAGONAL, CUBIC, +ORTHOROMBIC=ORTHORHOMBIC // Fix historical typo for backwards compatibility +}; enum CrystalCentering { LATTICE_P,LATTICE_I,LATTICE_A,LATTICE_B,LATTICE_C,LATTICE_F}; @@ -91,7 +93,7 @@ class RecUnitCell * d*_hkl^2 = par[0] + par[1] h^2 + par[1] k^2 + par[2]^2 l^2 + par[3] hk + par[4] kl + par[5] hl * for monoclinic: * d*_hkl^2 = zero + par[0]^2 h^2 + par[1]^2 k^2 + par[2]^2 l^2 + par[0]*par[2]*par[3] hl - * for orthorombic: + * for orthorhombic: * d*_hkl^2 = zero + par[0]^2 h^2 + par[1]^2 k^2 + par[2]^2 l^2 * for hexagonal: * d*_hkl^2 = zero + par[0]^2 h^2 + par[0]^2 k^2 + par[2]^2 l^2 + sqrt(3)/2*par[0]^2 hk diff --git a/ObjCryst/ObjCryst/UnitCell.h b/ObjCryst/ObjCryst/UnitCell.h index 7f2720a..d5d8cc5 100644 --- a/ObjCryst/ObjCryst/UnitCell.h +++ b/ObjCryst/ObjCryst/UnitCell.h @@ -73,7 +73,7 @@ class UnitCell:public RefinableObj public: /// Default Constructor UnitCell(); - /** \brief UnitCell Constructor (orthorombic) + /** \brief UnitCell Constructor (orthorhombic) * \param a,b,c : unit cell dimension, in angstroems * \param SpaceGroupId: space group symbol or number */ @@ -251,7 +251,7 @@ class UnitCell:public RefinableObj * \warning EXPERIMENTAL * * Normally lattice parameters are constrained by the space group choice - * (e.g. a=b=c and angles =90° for cubic spacegroups). Using this option + * (e.g. a=b=c and angles =90� for cubic spacegroups). Using this option * allows you to override this, and choose any lattice parameter. THis works * as long as symmetry operations are applied to fractionnal coordinates. * diff --git a/ObjCryst/wxCryst/wxPowderPattern.cpp b/ObjCryst/wxCryst/wxPowderPattern.cpp index 5d734fb..745e08f 100644 --- a/ObjCryst/wxCryst/wxPowderPattern.cpp +++ b/ObjCryst/wxCryst/wxPowderPattern.cpp @@ -2313,9 +2313,9 @@ wxWindow(parent,-1),mpGraph(graph),mpPeakList(&peaklist),mpCellExplorer(0),mpCry mpLog->AppendText(wxString::Format(_T(" Cubic F v=%6.0f -> %6.0f A\n"),EstimateCellVolume(dmin,dmax,nb,CUBIC ,LATTICE_F,1.2),EstimateCellVolume(dmin,dmax,nb,CUBIC ,LATTICE_F,0.3))); mpLog->AppendText(wxString::Format(_T(" Tetragonal P v=%6.0f -> %6.0f A\n"),EstimateCellVolume(dmin,dmax,nb,TETRAGONAL ,LATTICE_P,1.2),EstimateCellVolume(dmin,dmax,nb,TETRAGONAL ,LATTICE_P,0.3))); mpLog->AppendText(wxString::Format(_T(" Tetragonal I v=%6.0f -> %6.0f A\n"),EstimateCellVolume(dmin,dmax,nb,TETRAGONAL ,LATTICE_I,1.2),EstimateCellVolume(dmin,dmax,nb,TETRAGONAL ,LATTICE_I,0.3))); - mpLog->AppendText(wxString::Format(_T(" Orthorombic P v=%6.0f -> %6.0f A\n"),EstimateCellVolume(dmin,dmax,nb,ORTHOROMBIC,LATTICE_P,1.2),EstimateCellVolume(dmin,dmax,nb,ORTHOROMBIC,LATTICE_P,0.3))); - mpLog->AppendText(wxString::Format(_T(" Orthorombic I,C v=%6.0f -> %6.0f A\n"),EstimateCellVolume(dmin,dmax,nb,ORTHOROMBIC,LATTICE_I,1.2),EstimateCellVolume(dmin,dmax,nb,ORTHOROMBIC,LATTICE_I,0.3))); - mpLog->AppendText(wxString::Format(_T(" Orthorombic F v=%6.0f -> %6.0f A\n"),EstimateCellVolume(dmin,dmax,nb,ORTHOROMBIC,LATTICE_F,1.2),EstimateCellVolume(dmin,dmax,nb,ORTHOROMBIC,LATTICE_F,0.3))); + mpLog->AppendText(wxString::Format(_T(" Orthorombic P v=%6.0f -> %6.0f A\n"),EstimateCellVolume(dmin,dmax,nb,ORTHORHOMBIC,LATTICE_P,1.2),EstimateCellVolume(dmin,dmax,nb,ORTHORHOMBIC,LATTICE_P,0.3))); + mpLog->AppendText(wxString::Format(_T(" Orthorombic I,C v=%6.0f -> %6.0f A\n"),EstimateCellVolume(dmin,dmax,nb,ORTHORHOMBIC,LATTICE_I,1.2),EstimateCellVolume(dmin,dmax,nb,ORTHORHOMBIC,LATTICE_I,0.3))); + mpLog->AppendText(wxString::Format(_T(" Orthorombic F v=%6.0f -> %6.0f A\n"),EstimateCellVolume(dmin,dmax,nb,ORTHORHOMBIC,LATTICE_F,1.2),EstimateCellVolume(dmin,dmax,nb,ORTHORHOMBIC,LATTICE_F,0.3))); mpLog->AppendText(wxString::Format(_T(" Hexagonal v=%6.0f -> %6.0f A\n"),EstimateCellVolume(dmin,dmax,nb,HEXAGONAL ,LATTICE_P,1.2),EstimateCellVolume(dmin,dmax,nb,HEXAGONAL ,LATTICE_P,0.3))); mpLog->AppendText(wxString::Format(_T(" Monoclinic P v=%6.0f -> %6.0f A\n"),EstimateCellVolume(dmin,dmax,nb,MONOCLINIC ,LATTICE_P,1.2),EstimateCellVolume(dmin,dmax,nb,MONOCLINIC ,LATTICE_P,0.3))); mpLog->AppendText(wxString::Format(_T(" Monoclinic C v=%6.0f -> %6.0f A\n"),EstimateCellVolume(dmin,dmax,nb,MONOCLINIC ,LATTICE_C,1.2),EstimateCellVolume(dmin,dmax,nb,MONOCLINIC ,LATTICE_C,0.3))); @@ -2486,17 +2486,17 @@ void WXCellExplorer::OnIndex(wxCommandEvent &event) case 4:cent=LATTICE_C;centc='C';break; case 5:cent=LATTICE_F;centc='F';break; } - minv=EstimateCellVolume(dmin,dmax,nb,ORTHOROMBIC,cent,1.5); - maxv=EstimateCellVolume(dmin,dmax,nb,ORTHOROMBIC,cent,0.4*weak_f); + minv=EstimateCellVolume(dmin,dmax,nb,ORTHORHOMBIC,cent,1.5); + maxv=EstimateCellVolume(dmin,dmax,nb,ORTHORHOMBIC,cent,0.4*weak_f); mpCellExplorer->SetVolumeMinMax(minv,maxv); lengthmax=pow(maxv,(float)(1/3.0))*3; if(lengthmax<25)lengthmax=25; mpCellExplorer->SetLengthMinMax(3,lengthmax); - mpCellExplorer->SetCrystalSystem(ORTHOROMBIC); + mpCellExplorer->SetCrystalSystem(ORTHORHOMBIC); mpCellExplorer->SetCrystalCentering(cent); - mpLog->AppendText(wxString::Format(_T("ORTHOROMBIC %c: V= %6.0f -> %6.0f A^3, max length=%6.2fA"),centc,minv,maxv,lengthmax)); + mpLog->AppendText(wxString::Format(_T("ORTHORHOMBIC %c: V= %6.0f -> %6.0f A^3, max length=%6.2fA"),centc,minv,maxv,lengthmax)); t0=chrono.seconds(); - if(dlgProgress.Update(4,wxString::Format(_T("ORTHOROMBIC %c (%u spurious), V=%6.0f-%6.0f, l<%6.2fA\n") + if(dlgProgress.Update(4,wxString::Format(_T("ORTHORHOMBIC %c (%u spurious), V=%6.0f-%6.0f, l<%6.2fA\n") _T("Best Score=%6.1f"),centc, nbSpurious,minv,maxv,lengthmax,mpCellExplorer->GetBestScore()))==false) break; mpCellExplorer->DicVol(reportOnScore,reportOnDepth,stopOnScore,stopOnDepth); @@ -2612,7 +2612,7 @@ void WXCellExplorer::OnIndex(wxCommandEvent &event) { case TRICLINIC:sys="TRICLINIC"; break; case MONOCLINIC:sys="MONOCLINIC"; break; - case ORTHOROMBIC:sys="ORTHOROMBIC"; break; + case ORTHORHOMBIC:sys="ORTHORHOMBIC"; break; case HEXAGONAL:sys="HEXAGONAL"; break; case RHOMBOEDRAL:sys="RHOMBOEDRAL"; break; case TETRAGONAL:sys="TETRAGONAL"; break; @@ -2678,7 +2678,7 @@ void WXCellExplorer::OnSelectCell(wxCommandEvent &event) { case TRICLINIC:mpCrystal->ChangeSpaceGroup("P-1");break; case MONOCLINIC:mpCrystal->ChangeSpaceGroup("P2/m");break; - case ORTHOROMBIC:mpCrystal->ChangeSpaceGroup("Pmmm");break; + case ORTHORHOMBIC:mpCrystal->ChangeSpaceGroup("Pmmm");break; case HEXAGONAL:mpCrystal->ChangeSpaceGroup("P6/mmm");break; case RHOMBOEDRAL:mpCrystal->ChangeSpaceGroup("R-3m");break; case TETRAGONAL:mpCrystal->ChangeSpaceGroup("P4/mmm");break; @@ -2691,7 +2691,7 @@ void WXCellExplorer::OnSelectCell(wxCommandEvent &event) switch(pos->first.mlattice) { case MONOCLINIC:mpCrystal->ChangeSpaceGroup("I2/m");break; - case ORTHOROMBIC:mpCrystal->ChangeSpaceGroup("I222");break; + case ORTHORHOMBIC:mpCrystal->ChangeSpaceGroup("I222");break; case TETRAGONAL:mpCrystal->ChangeSpaceGroup("I4/mmm");break; case CUBIC:mpCrystal->ChangeSpaceGroup("Im-3m");break; } @@ -2702,7 +2702,7 @@ void WXCellExplorer::OnSelectCell(wxCommandEvent &event) switch(pos->first.mlattice) { case MONOCLINIC:mpCrystal->ChangeSpaceGroup("A2/m");break; - case ORTHOROMBIC:mpCrystal->ChangeSpaceGroup("Amm2");break; + case ORTHORHOMBIC:mpCrystal->ChangeSpaceGroup("Amm2");break; } break; } @@ -2711,7 +2711,7 @@ void WXCellExplorer::OnSelectCell(wxCommandEvent &event) switch(pos->first.mlattice) { case MONOCLINIC:mpCrystal->ChangeSpaceGroup("C2/m");break; - case ORTHOROMBIC:mpCrystal->ChangeSpaceGroup("Cmmm");break; + case ORTHORHOMBIC:mpCrystal->ChangeSpaceGroup("Cmmm");break; } break; } @@ -2719,7 +2719,7 @@ void WXCellExplorer::OnSelectCell(wxCommandEvent &event) { switch(pos->first.mlattice) { - case ORTHOROMBIC:mpCrystal->ChangeSpaceGroup("Fmmm");break; + case ORTHORHOMBIC:mpCrystal->ChangeSpaceGroup("Fmmm");break; case CUBIC:mpCrystal->ChangeSpaceGroup("Fm-3m");break; } break; @@ -3209,7 +3209,7 @@ void WXCellExplorer::OnExportIndexingResults(wxCommandEvent &event) { case TRICLINIC:sys="TRICLINIC"; break; case MONOCLINIC:sys="MONOCLINIC"; break; - case ORTHOROMBIC:sys="ORTHOROMBIC"; break; + case ORTHORHOMBIC:sys="ORTHORHOMBIC"; break; case HEXAGONAL:sys="HEXAGONAL"; break; case RHOMBOEDRAL:sys="RHOMBOEDRAL"; break; case TETRAGONAL:sys="TETRAGONAL"; break;