runInSystemShell(view, "start \"http:\\\\www.dur.ac.uk\\john.evans\\topas_workshop\\pcg_workshop_menu.htm\"&"); runInSystemShell(view, "start \"http:\\\\www.dur.ac.uk\\john.evans\\topas_workshop\\tutorial_menu.htm\"&"); runInSystemShell(view, "start \"http:\\\\topas.dur.ac.uk\\topaswiki\\doku.php\"&"); runInSystemShell(view, "start /D\""+ jEdit.getProperty("ta.main.dir") +"\" Technical_Reference.pdf&"); waitForConsole(view); runInSystemShell(view, "start /D\""+ jEdit.getProperty("ta.main.dir") +"\" Users_Manual.pdf&"); waitForConsole(view); runInSystemShell(view, "start \"http:\\\\www.dur.ac.uk\\john.evans\\topas_academic\\topas_main.htm\"&"); jEdit.openFile(editPane.getView(), jEdit.getProperty("ta.main.dir") + "local.inc"); jEdit.openFile(editPane.getView(), jEdit.getProperty("ta.main.dir") + "topas.inc"); runInSystemShell(view, "start \"http:\\\\www.dur.ac.uk\\john.evans\\topas_academic\\topas_macros.htm\"&"); jEdit.openFile(editPane.getView(), jEdit.getProperty("ta.main.dir") + "topas.log"); runInSystemShell(view, "start \"http:\\\\img.chem.ucl.ac.uk\\sgp\\mainmenu.htm\"&"); do_ta(v) { runInSystemShell(v, jEdit.getProperty("ta.main.dir")); waitForConsole(v); runInSystemShell(v, "ta&"); } do_ta(view); Buffer b = jEdit.openTemporary(view,null,jEdit.getProperty("ta.main.dir") + "launch_file.txt",false); try { if (buffer.isDirty()) { buffer.save(view,null,true); } if (b != null) { while(!b.isLoaded()) VFSManager.waitForRequests(); b.remove(0,b.getLength()); b.insert(0, '"'+buffer.getPath()+'"'); b.save(view, b.getPath()); } } finally { if(b != null) { //b.close(); } } TAnewINP(v) { String w_ext = jEdit.getProperty("ta.last_xdd_type"); if (w_ext == null) w_ext = "*.raw"; jEdit.setProperty("vfs.browser.last-filter", w_ext); String w_path = jEdit.getProperty("ta.last_new_inp_dir"); if (w_path == null) { w_path = jEdit.getProperty("ta.main.dir") +"test_examples\\"; } jEdit.setProperty("vfs.browser.last-path", w_path); VFSFileChooserDialog chooser = new VFSFileChooserDialog(v, w_path, VFSBrowser.OPEN_DIALOG, true); String[] files = chooser.getSelectedFiles(); if (files != null) { String w_dir = MiscUtilities.getParentOfPath(files[0]); String w_fn_no_ext = MiscUtilities.getFileNameNoExtension(files[0]); jEdit.setProperty("ta.last_new_inp_dir", w_dir); String w_path_inp = w_dir + w_fn_no_ext + "_riet_01.inp"; b = jEdit.openFile(v, w_path_inp); if (b != null) { if (b.isNewFile()) { t = v.getTextArea(); int i = 0; while(true) { t.goToEndOfLine(false); String w_path = MiscUtilities.getFileName(files[i]); if (w_path.indexOf(' ') != -1) { w_path = "\"" + w_path + "\""; } b.insert(t.getCaretPosition(), "'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Input File for simple Rietveld Refinement"); b.insert(t.getCaretPosition(), "\n'Replace any $, # or text after ---> as needed"); b.insert(t.getCaretPosition(), "\n'Use Ta-> button to save/send to topas; Ta button to launch topas; run in topas with red arrow"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\nr_wp 0 r_exp 0 r_p 0 r_wp_dash 0 r_p_dash 0 r_exp_dash 0 weighted_Durbin_Watson 0 gof 0"); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'General information about refinement here\n'Remove commented lines as required"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\niters 100000"); b.insert(t.getCaretPosition(), "\nchi2_convergence_criteria 0.001"); b.insert(t.getCaretPosition(), "\n'do_errors"); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Information on datafile etc here"); b.insert(t.getCaretPosition(), "\n'Check that default weighting is appropriate for your data"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\nxdd " + w_path); b.insert(t.getCaretPosition(), "\n\tx_calculation_step = Yobs_dx_at(Xo); convolution_step 4"); b.insert(t.getCaretPosition(), "\n\tbkg @ 0 0 0 0 0 0"); b.insert(t.getCaretPosition(), "\n\tSimple_Axial_Model(axial,10)"); i++; if (i == files.length) break; } jEdit.setProperty("ta.last_xdd_type", "*" + MiscUtilities.getFileExtension(files[0])); } else { String wmes = "INP file " + w_path_inp + " already exists"; Macros.message(v, wmes); } } } } TAnewINP(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd5000 Bragg Brentano graphite diffracted beam monochromator Cu Ka1/a2 2 line emission"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 26.6)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2_analyt(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd5000 Bragg Brentano Sol-X Cu Ka1/a2 2 line emission"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 0)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2_analyt(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd5000 Ge(111) monochromator Capillary Braun PSD Cu Ka1"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 27.26)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa1(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd8 Ge(111) monochromator capillary Lynxeye Mo Ka1"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 12.46)"); buffer.insert(textArea.getCaretPosition(), "\n\tla 1.0 lo 0.70930 lh 0.2695"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd8 Ge(111) monochromator Vantec Cu Ka1"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 27.26)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa1(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd8 Lynx Eye Cu Ka1/a2 2 line emission"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 0)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2_analyt(0.0001)"); {%wavelength "Enter Wavelength:"}{@ textArea.goToEndOfLine(false); }\n\tlam ymin_on_ymax 0.0001 la 1.0 lo {$$wavelength} lh 0.1\n\tLP_Factor( 90) 'change the LP correction or lh value if required {%wavelength "Enter Wavelength:"}{@ textArea.goToEndOfLine(false); }\n\tlam ymin_on_ymax 0.0001 la 1.0 lo {$$wavelength} lh 0.5\n\tneutron_data\n\tLP_Factor( 90) {%mono "Enter Monochromator angle (e.g. 26.6 graphite/Cu; 27.26 Ge/Cu; 0 for energy dispersive): "}{@ textArea.goToEndOfLine(false); }\n\tLP_Factor(!th2_monochromator, {$$mono}) Macros.getMacro("TAInsertLAM").invoke(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tVariable_Divergence_Intensity"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tZero_Error(zero,0)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tSpecimen_Displacement(height,0)"); do_cif(v) { t = v.getTextArea(); b = t.getBuffer(); t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Information on structure"); b.insert(t.getCaretPosition(), "\n'Change recurring numbers in coordinates as required e.g. 0.3333 to =1/3;"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); jEdit.setProperty("vfs.browser.last-filter", "*.cif"); w_path = jEdit.getProperty("ta.last_cif_path"); if (w_path == null) { w_path = jEdit.getProperty("ta.main.dir") +"cif\\"; } jEdit.setProperty("vfs.browser.last-path", w_path); waitForConsole(v); VFSFileChooserDialog chooser = new VFSFileChooserDialog(v, w_path, VFSBrowser.OPEN_DIALOG, true); String[] files = chooser.getSelectedFiles(); if (files != null) { int i = 0; b.beginCompoundEdit(); while(true) { runInSystemShell(v, jEdit.getProperty("ta.main.dir")); waitForConsole(v); runInSystemShell(v, "cif1 " + "\"" + files[i] + "\" cif1.tmp"); waitForConsole(v); t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n"); b.insertFile(v, jEdit.getProperty("ta.main.dir") + "cif1.tmp"); VFSManager.waitForRequests(); i++; if (i == files.length) break; b.insert(t.getCaretPosition(), "\n"); } b.endCompoundEdit(); jEdit.setProperty("ta.last_cif_path", files[0]); } t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n\t\tscale @ 0.0001"); b.insert(t.getCaretPosition(), "\n\t\tr_bragg 0"); b.insert(t.getCaretPosition(), "\n\t\tTCHZ_Peak_Type(pku, 0.00039,pkv, -0.00221,pkw, -0.00146,!pkz, 0.0000,pkx, 0.00957, pky, 0.0001)"); b.insert(t.getCaretPosition(), "\n\t\tPhase_Density_g_on_cm3(0)"); } do_cif(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'Information on structure"); buffer.insert(textArea.getCaretPosition(), "\n'Type in phase/space group/cell etc"); buffer.insert(textArea.getCaretPosition(), "\n'Comment in/out sections as needed"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n\n\tstr"); buffer.insert(textArea.getCaretPosition(), "\n\t\tscale @ 0.0001"); buffer.insert(textArea.getCaretPosition(), "\n\t\tr_bragg 0"); buffer.insert(textArea.getCaretPosition(), "\n\t\tTCHZ_Peak_Type(pku, 0.00039,pkv, -0.00221,pkw, -0.00146,!pkz, 0.0000,pkx, 0.00957,!pky, 0.0000)"); buffer.insert(textArea.getCaretPosition(), "\n\t\tSimple_Axial_Model(axial,10)"); buffer.insert(textArea.getCaretPosition(), "\n\t\tPhase_Density_g_on_cm3(0)"); buffer.insert(textArea.getCaretPosition(), "\n\t\t'append_bond_lengths"); buffer.insert(textArea.getCaretPosition(), "\n\t\t\t'consider_lattice_parameters"); buffer.insert(textArea.getCaretPosition(), "\n\t\t'Out_FCF(" + buffer.getPath() + ".cif)"); {%sgrp "Enter Space Group:"}{@ textArea.goToEndOfLine(false) }\n\t\tspace_group {$$sgrp} {%phname "Enter Phase Name:"}{@ textArea.goToEndOfLine(false) }\n\t\tphase_name {$$phname} textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tCubic(@ #)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tTetragonal(@ #, @ #)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tHexagonal(@ #, @ #)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tRhombohedral(@ #, @ #)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\ta @ #\n\t\tb @ #\n\t\tc @ #\n\t\tal @ #\n\t\tbe @ #\n\t\tga @ #"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tsite $site x # y # z # occ $atom # beq #"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tsite $site x # y # z # occ $atom # adps"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tview_structure"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPreferred_Orientation(@, 1,, #h #k #l)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPO_Two_Directions(@, 1,, 1 1 1,@, 1,, ,@, 0.5)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPO_Spherical_Harmonics(sh, 4)"); TAnewINP(v) { String w_ext = jEdit.getProperty("ta.last_xdd_type"); if (w_ext == null) w_ext = "*.raw"; jEdit.setProperty("vfs.browser.last-filter", w_ext); String w_path = jEdit.getProperty("ta.last_new_inp_dir"); if (w_path == null) { w_path = jEdit.getProperty("ta.main.dir") +"test_examples\\"; } jEdit.setProperty("vfs.browser.last-path", w_path); VFSFileChooserDialog chooser = new VFSFileChooserDialog(v, w_path, VFSBrowser.OPEN_DIALOG, true); String[] files = chooser.getSelectedFiles(); if (files != null) { String w_dir = MiscUtilities.getParentOfPath(files[0]); String w_fn_no_ext = MiscUtilities.getFileNameNoExtension(files[0]); jEdit.setProperty("ta.last_new_inp_dir", w_dir); String w_path_inp = w_dir + w_fn_no_ext + "_pawley_01.inp"; b = jEdit.openFile(v, w_path_inp); if (b != null) { if (b.isNewFile()) { t = v.getTextArea(); int i = 0; while(true) { t.goToEndOfLine(false); String w_path = MiscUtilities.getFileName(files[i]); if (w_path.indexOf(' ') != -1) { w_path = "\"" + w_path + "\""; } b.insert(t.getCaretPosition(), "'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Input File for simple Pawley Refinement"); b.insert(t.getCaretPosition(), "\n'Replace any $, # or text after ---> as needed"); b.insert(t.getCaretPosition(), "\n'Use Ta-> button to save/send to topas; Ta button to launch topas; run in topas with red arrow"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\nr_wp 0 r_exp 0 r_p 0 r_wp_dash 0 r_p_dash 0 r_exp_dash 0 weighted_Durbin_Watson 0 gof 0"); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'General information about refinement here\n'Remove commented lines as required"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\niters 100000"); b.insert(t.getCaretPosition(), "\nchi2_convergence_criteria 0.001"); b.insert(t.getCaretPosition(), "\n'do_errors"); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Information on datafile etc here"); b.insert(t.getCaretPosition(), "\n'Check that default weighting is appropriate for your data"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\nxdd " + w_path); b.insert(t.getCaretPosition(), "\n\tx_calculation_step = Yobs_dx_at(Xo); convolution_step 4"); b.insert(t.getCaretPosition(), "\n\tbkg @ 0 0 0 0 0 0"); b.insert(t.getCaretPosition(), "\n\tSimple_Axial_Model(axial,10)"); i++; if (i == files.length) break; } jEdit.setProperty("ta.last_xdd_type", "*" + MiscUtilities.getFileExtension(files[0])); } else { String wmes = "INP file " + w_path_inp + " already exists"; Macros.message(v, wmes); } } } } TAnewINP(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd5000 Bragg Brentano graphite diffracted beam monochromator Cu Ka1/a2 2 line emission"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 26.6)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2_analyt(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd5000 Bragg Brentano Sol-X Cu Ka1/a2 2 line emission"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 0)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2_analyt(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd5000 Ge(111) monochromator Capillary Braun PSD Cu Ka1"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 27.26)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa1(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd8 Ge(111) monochromator capillary Lynxeye Mo Ka1"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 12.46)"); buffer.insert(textArea.getCaretPosition(), "\n\tla 1.0 lo 0.70930 lh 0.2695"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd8 Ge(111) monochromator Vantec Cu Ka1"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 27.26)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa1(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd8 Lynx Eye Cu Ka1/a2 2 line emission"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 0)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2_analyt(0.0001)"); {%wavelength "Enter Wavelength:"}{@ textArea.goToEndOfLine(false); }\n\tlam ymin_on_ymax 0.0001 la 1.0 lo {$$wavelength} lh 0.1\n\tLP_Factor( 90) 'change the LP correction or lh value if required {%wavelength "Enter Wavelength:"}{@ textArea.goToEndOfLine(false); }\n\tlam ymin_on_ymax 0.0001 la 1.0 lo {$$wavelength} lh 0.5 \tneutron_data \tLP_Factor( 90) {%mono "Enter Monochromator angle (e.g. 26.6 graphite/Cu; 27.26 Ge/Cu; 0 for energy dispersive): "}{@ textArea.goToEndOfLine(false); }\n\tLP_Factor(!th2_monochromator, {$$mono}) Macros.getMacro("TAInsertLAM").invoke(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tVariable_Divergence_Intensity"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tZero_Error(zero,0)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tSpecimen_Displacement(height,0)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\n\thkl_Is"); buffer.insert(textArea.getCaretPosition(), "\n\t\tTCHZ_Peak_Type(pku, 0.00039,pkv, -0.00221,pkw, -0.00146,!pkz, 0.0000,pkx, 0.00957,!pky, 0.0000)"); {%phname "Enter Phase Name:"}{@ textArea.goToEndOfLine(false) }\n\t\tphase_name {$$phname} textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tCubic(@ #)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tTetragonal(@ #, @ #)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tHexagonal(@ #, @ #)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tRhombohedral(@ #, @ #)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\ta @ #\n\t\tb @ #\n\t\tc @ #\n\t\tal @ #\n\t\tbe @ #\n\t\tga @ #"); {%sgrp "Enter Space Group:"}{@ textArea.goToEndOfLine(false) }\n\t\tspace_group {$$sgrp} TAnewINP(v) { String w_ext = jEdit.getProperty("ta.last_xdd_type"); if (w_ext == null) w_ext = "*.raw"; jEdit.setProperty("vfs.browser.last-filter", w_ext); String w_path = jEdit.getProperty("ta.last_new_inp_dir"); if (w_path == null) { w_path = jEdit.getProperty("ta.main.dir") +"test_examples\\"; } jEdit.setProperty("vfs.browser.last-path", w_path); VFSFileChooserDialog chooser = new VFSFileChooserDialog(v, w_path, VFSBrowser.OPEN_DIALOG, true); String[] files = chooser.getSelectedFiles(); if (files != null) { String w_dir = MiscUtilities.getParentOfPath(files[0]); String w_fn_no_ext = MiscUtilities.getFileNameNoExtension(files[0]); jEdit.setProperty("ta.last_new_inp_dir", w_dir); String w_path_inp = w_dir + w_fn_no_ext + "_riet_01.inp"; b = jEdit.openFile(v, w_path_inp); if (b != null) { if (b.isNewFile()) { t = v.getTextArea(); int i = 0; while(true) { t.goToEndOfLine(false); String w_path = MiscUtilities.getFileName(files[i]); if (w_path.indexOf(' ') != -1) { w_path = "\"" + w_path + "\""; } b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Input File for simple tof Rietveld Refinement"); b.insert(t.getCaretPosition(), "\n'Use Ta-> button to save/send to topas; Ta button to launch topas; run in topas with red arrow"); b.insert(t.getCaretPosition(), "\n'Replace $ and # symbols with text/numbers as needed"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n\nr_wp 0 r_exp 0 r_p 0 r_wp_dash 0 r_p_dash 0 r_exp_dash 0 weighted_Durbin_Watson 0 gof 0"); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'General information about refinement here\n'Remove comments as required"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n\niters 100000"); b.insert(t.getCaretPosition(), "\nchi2_convergence_criteria 0.001"); b.insert(t.getCaretPosition(), "\n'do_errors"); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Information on datafile etc here"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\nTOF_XYE( " + w_path + ", 3)"); b.insert(t.getCaretPosition(), "\n\tx_calculation_step = Yobs_dx_at(Xo); convolution_step 4"); b.insert(t.getCaretPosition(), "\n\tTOF_LAM(0.001)"); b.insert(t.getCaretPosition(), "\n\tscale_pks = D_spacing^4;"); b.insert(t.getCaretPosition(), "\n\tbkg @ 0 0 0 0 0 0"); b.insert(t.getCaretPosition(), "\n\tstart_X ->#"); b.insert(t.getCaretPosition(), "\n\tfinish_X ->#"); b.insert(t.getCaretPosition(), "\n"); b.insert(t.getCaretPosition(), "\n\tbkg @ 0 0 0 0 0 0"); i++; if (i == files.length) break; } jEdit.setProperty("ta.last_xdd_type", "*" + MiscUtilities.getFileExtension(files[0])); } else { String wmes = "INP file " + w_path_inp + " already exists"; Macros.message(v, wmes); } } } } TAnewINP(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'Change instrument/peak shape constants from a recent silicon calibration"); buffer.insert(textArea.getCaretPosition(), "\n'Only refine these parameters if you're sure what you're doing"); buffer.insert(textArea.getCaretPosition(), "\n'Peak shape macro courtesy of Bill David"); buffer.insert(textArea.getCaretPosition(), "\n'Get macros you need from http://www.dur.ac.uk/john.evans/topas_academic/topas_macros.htm"); buffer.insert(textArea.getCaretPosition(), "\n'or use the alternate peak shape description currently commented out"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n\tTOF_LAM(0.001)"); buffer.insert(textArea.getCaretPosition(), "\n\tTOF_x_axis_calibration(!t0_bs, 0.27394, !difc_bs, 48213.48769, !difa_bs, -5.50739)"); buffer.insert(textArea.getCaretPosition(), "\n\twifd_pkshape(!two_theta, 168.657, !aprm, 2.50000, !tauf_2, 9.80744, !tauf_1, 0.43977, !tauf_0, 0.000, !taus_0, 25.27420, !taus_1, 2.66797, !t_eff, 144.41296, !hhh, 3.58595, !hhh_0, 11.61348)"); buffer.insert(textArea.getCaretPosition(), "\n\t'TOF_Exponential(!a1_bs, 230.98670,!a2_bs, 27.018, 4, difc_hrpd_bs, +)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'Change instrument/peak shape constants from a recent silicon calibration"); buffer.insert(textArea.getCaretPosition(), "\n'Only refine these parameters if you're sure what you're doing"); buffer.insert(textArea.getCaretPosition(), "\n'Peak shape macro courtesy of Bill David"); buffer.insert(textArea.getCaretPosition(), "\n'Get macros you need from http://www.dur.ac.uk/john.evans/topas_academic/topas_macros.htm"); buffer.insert(textArea.getCaretPosition(), "\n'or use the alternate peak shape description currently commented out"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n\tTOF_LAM(0.001)"); buffer.insert(textArea.getCaretPosition(), "\n\tTOF_x_axis_calibration(!t0_90, 7.60, !difc_90, 34729.97, !difa_90, 0.296)"); buffer.insert(textArea.getCaretPosition(), "\n\twifd_pkshape(!two_theta, 90.2481, !aprm, 2.50000, !tauf_2, 9.80744, !tauf_1, 0.43977, !tauf_0, 0.000, !taus_0, 25.27420, !taus_1, 2.66797, !t_eff, 144.41296, !hhh, 3.58595, !hhh_0, 11.61348)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'Change instrument/peak shape constants from a recent silicon calibration"); buffer.insert(textArea.getCaretPosition(), "\n'Only refine these parameters if you're sure what you're doing"); buffer.insert(textArea.getCaretPosition(), "\n'Peak shape macro courtesy of Bill David"); buffer.insert(textArea.getCaretPosition(), "\n'Get macros you need from http://www.dur.ac.uk/john.evans/topas_academic/topas_macros.htm"); buffer.insert(textArea.getCaretPosition(), "\n'or use the alternate peak shape description currently commented out"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n\tTOF_LAM(0.001)"); buffer.insert(textArea.getCaretPosition(), "\n\tTOF_x_axis_calibration(!t0_30, 12.09, !difc_30, 12897.29, !difa_30, 1.44)"); buffer.insert(textArea.getCaretPosition(), "\n\twifd_pkshape(!two_theta, 29.93, !aprm, 2.50000, !tauf_2, 9.80744, !tauf_1, 0.43977, !tauf_0, 0.000, !taus_0, 25.27420, !taus_1, 2.66797, !t_eff, 144.41296, !hhh, 3.58595, !hhh_0, 11.61348)"); do_cif(v) { t = v.getTextArea(); b = t.getBuffer(); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Information on structure"); b.insert(t.getCaretPosition(), "\n'Type in phase/space group/cell etc"); b.insert(t.getCaretPosition(), "\n'Comment in/out sections as needed"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); jEdit.setProperty("vfs.browser.last-filter", "*.cif"); w_path = jEdit.getProperty("ta.last_cif_path"); if (w_path == null) { w_path = jEdit.getProperty("ta.main.dir") +"cif\\"; } jEdit.setProperty("vfs.browser.last-path", w_path); VFSFileChooserDialog chooser = new VFSFileChooserDialog(v, w_path, VFSBrowser.OPEN_DIALOG, true); String[] files = chooser.getSelectedFiles(); if (files != null) { int i = 0; b.beginCompoundEdit(); while(true) { runInSystemShell(v, jEdit.getProperty("ta.main.dir")); waitForConsole(v); runInSystemShell(v, "cif1 " + "\"" + files[i] + "\" cif1.tmp"); waitForConsole(v); t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n"); b.insertFile(v, jEdit.getProperty("ta.main.dir") + "cif1.tmp"); VFSManager.waitForRequests(); i++; if (i == files.length) break; b.insert(t.getCaretPosition(), "\n"); } b.endCompoundEdit(); jEdit.setProperty("ta.last_cif_path", files[0]); } t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n\t\tscale @ 0.0001"); b.insert(t.getCaretPosition(), "\n\t\tr_bragg 0"); b.insert(t.getCaretPosition(), "\n\t\ttof_sample_peakshape(lor,0.2,dsp,30,dspsq,1)"); b.insert(t.getCaretPosition(), "\n\t\tPhase_Density_g_on_cm3(0)"); } do_cif(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tview_structure"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPreferred_Orientation(@, 1,, #h #k #l)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPO_Two_Directions(@, 1,, 1 1 1,@, 1,, ,@, 0.5)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPO_Spherical_Harmonics(sh, 4)"); TAnewINP(v) { String w_ext = jEdit.getProperty("ta.last_xdd_type"); if (w_ext == null) w_ext = "*.raw"; jEdit.setProperty("vfs.browser.last-filter", w_ext); String w_path = jEdit.getProperty("ta.last_new_inp_dir"); if (w_path == null) { w_path = jEdit.getProperty("ta.main.dir") +"test_examples\\"; } jEdit.setProperty("vfs.browser.last-path", w_path); VFSFileChooserDialog chooser = new VFSFileChooserDialog(v, w_path, VFSBrowser.OPEN_DIALOG, true); String[] files = chooser.getSelectedFiles(); if (files != null) { String w_dir = MiscUtilities.getParentOfPath(files[0]); String w_fn_no_ext = MiscUtilities.getFileNameNoExtension(files[0]); jEdit.setProperty("ta.last_new_inp_dir", w_dir); String w_path_inp = w_dir + w_fn_no_ext + "_pkfit_01.inp"; b = jEdit.openFile(v, w_path_inp); if (b != null) { if (b.isNewFile()) { t = v.getTextArea(); int i = 0; while(true) { t.goToEndOfLine(false); String w_path = MiscUtilities.getFileName(files[i]); if (w_path.indexOf(' ') != -1) { w_path = "\"" + w_path + "\""; } b.insert(t.getCaretPosition(), "'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Input File for Peak Fitting with overall TCHz peak shape"); b.insert(t.getCaretPosition(), "\n'To find peaks load experimental data into topas"); b.insert(t.getCaretPosition(), "\n'Use View/search peaks then insert peaks"); b.insert(t.getCaretPosition(), "\n'Click on plus sign by file name"); b.insert(t.getCaretPosition(), "\n'Click on peaks phase"); b.insert(t.getCaretPosition(), "\n'Highlight Position and Area columns, right click to copy then paste below"); b.insert(t.getCaretPosition(), "\n'Use Ta-> button to save/send to topas; Ta button to launch topas; run in topas with red arrow"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\nr_wp 0 r_exp 0 r_p 0 r_wp_dash 0 r_p_dash 0 r_exp_dash 0 weighted_Durbin_Watson 0 gof 0"); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'General information about refinement here\n'Remove comments as required"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\niters 100000"); b.insert(t.getCaretPosition(), "\nchi2_convergence_criteria 0.001"); b.insert(t.getCaretPosition(), "\n'do_errors"); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Information on datafile etc here"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\nxdd " + w_path); b.insert(t.getCaretPosition(), "\n\tx_calculation_step = Yobs_dx_at(Xo); convolution_step 4"); i++; if (i == files.length) break; } jEdit.setProperty("ta.last_xdd_type", "*" + MiscUtilities.getFileExtension(files[0])); } else { String wmes = "INP file " + w_path_inp + " already exists"; Macros.message(v, wmes); } } } } TAnewINP(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd5000 Bragg Brentano graphite diffracted beam monochromator Cu Ka1/a2 2 line emission"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 26.6)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2_analyt(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd5000 Bragg Brentano Sol-X Cu Ka1/a2 2 line emission"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 0)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2_analyt(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd5000 Ge(111) monochromator Capillary Braun PSD Cu Ka1"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 27.26)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa1(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd8 Ge(111) monochromator capillary Lynxeye Mo Ka1"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 12.46)"); buffer.insert(textArea.getCaretPosition(), "\n\tla 1.0 lo 0.70930 lh 0.2695"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd8 Ge(111) monochromator Vantec Cu Ka1"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 27.26)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa1(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd8 Lynx Eye Cu Ka1/a2 2 line emission"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 0)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2_analyt(0.0001)"); {%wavelength "Enter Wavelength:"}{@ textArea.goToEndOfLine(false); }\n\tlam ymin_on_ymax 0.0001 la 1.0 lo {$$wavelength} lh 0.1\n\tLP_Factor( 90) 'change the LP correction or lh value if required {%wavelength "Enter Wavelength:"}{@ textArea.goToEndOfLine(false); }\n\tlam ymin_on_ymax 0.0001 la 1.0 lo {$$wavelength} lh 0.5 {%mono "Enter Monochromator angle (e.g. 26.6 graphite/Cu; 27.26 Ge/Cu; 0 for energy dispersive): "}{@ textArea.goToEndOfLine(false); }\n\tLP_Factor(!th2_monochromator, {$$mono}) Macros.getMacro("TAInsertLAM").invoke(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tSimple_Axial_Model(axial,10)"); buffer.insert(textArea.getCaretPosition(), "\n\tbkg @ 0 0 0 0 0 0"); buffer.insert(textArea.getCaretPosition(), "\n\n\txo_Is"); buffer.insert(textArea.getCaretPosition(), "\n\tTCHZ_Peak_Type(pku, 0.00039,pkv, -0.00221,pkw, -0.00146,!pkz, 0.0000,pkx, 0.00957,!pky, 0.0000)"); buffer.insert(textArea.getCaretPosition(), "\n\tload xo I {"); buffer.insert(textArea.getCaretPosition(), "\n'copy peak position and intensity here"); buffer.insert(textArea.getCaretPosition(), "\n'insert @'s before 2th and area to refine"); buffer.insert(textArea.getCaretPosition(), "\n"); buffer.insert(textArea.getCaretPosition(), "\n\t}"); buffer.insert(textArea.getCaretPosition(), "\n"); textArea.goToBufferStart(false); buffer.insert(textArea.getCaretPosition(), "'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'Input File for Indexing powder data"); buffer.insert(textArea.getCaretPosition(), "\n\n'Paste 2theta/Area values from peak fitting"); buffer.insert(textArea.getCaretPosition(), "\n'Comment out header line and any peaks you don't want to include"); buffer.insert(textArea.getCaretPosition(), "\n'e.g. exclude high angle and weak/broad peaks"); buffer.insert(textArea.getCaretPosition(), "\n'Change wavelength as needed"); buffer.insert(textArea.getCaretPosition(), "\n'Comment out any crystal systems not to be checked"); buffer.insert(textArea.getCaretPosition(), "\n'Load filename.ndx after running"); buffer.insert(textArea.getCaretPosition(), "\n\n'Use Ta-> button to save/send to topas; Ta button to launch topas; run in topas with red arrow"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\nseed "); buffer.insert(textArea.getCaretPosition(), "\nindex_zero_error "); buffer.insert(textArea.getCaretPosition(), "\nindex_lam 1.5406"); buffer.insert(textArea.getCaretPosition(), "\nindex_min_lp 1 "); buffer.insert(textArea.getCaretPosition(), "\nindex_max_lp 40 "); buffer.insert(textArea.getCaretPosition(), "\n"); buffer.insert(textArea.getCaretPosition(), "\nBravais_Cubic_sgs "); buffer.insert(textArea.getCaretPosition(), "\nBravais_Trigonal_Hexagonal_sgs "); buffer.insert(textArea.getCaretPosition(), "\nBravais_Tetragonal_sgs "); buffer.insert(textArea.getCaretPosition(), "\nBravais_Orthorhombic_sgs "); buffer.insert(textArea.getCaretPosition(), "\nBravais_Monoclinic_sgs "); buffer.insert(textArea.getCaretPosition(), "\nBravais_Triclinic_sgs "); buffer.insert(textArea.getCaretPosition(), "\n"); buffer.insert(textArea.getCaretPosition(), "\nload index_th2 index_I {"); buffer.insert(textArea.getCaretPosition(), "\n'Paste position and area values below here"); buffer.insert(textArea.getCaretPosition(), "\n"); buffer.insert(textArea.getCaretPosition(), "\n"); buffer.insert(textArea.getCaretPosition(), "\n}"); TAnewINP(v) { String w_ext = jEdit.getProperty("ta.last_xdd_type"); if (w_ext == null) w_ext = "*.raw"; jEdit.setProperty("vfs.browser.last-filter", w_ext); String w_path = jEdit.getProperty("ta.last_new_inp_dir"); if (w_path == null) { w_path = jEdit.getProperty("ta.main.dir") +"test_examples\\"; } jEdit.setProperty("vfs.browser.last-path", w_path); VFSFileChooserDialog chooser = new VFSFileChooserDialog(v, w_path, VFSBrowser.OPEN_DIALOG, true); String[] files = chooser.getSelectedFiles(); if (files != null) { String w_dir = MiscUtilities.getParentOfPath(files[0]); String w_fn_no_ext = MiscUtilities.getFileNameNoExtension(files[0]); jEdit.setProperty("ta.last_new_inp_dir", w_dir); String w_path_inp = w_dir + w_fn_no_ext + "_xtal_01.inp"; b = jEdit.openFile(v, w_path_inp); if (b != null) { if (b.isNewFile()) { t = v.getTextArea(); int i = 0; while(true) { t.goToEndOfLine(false); String w_path = MiscUtilities.getFileName(files[i]); if (w_path.indexOf(' ') != -1) { w_path = "\"" + w_path + "\""; } b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Input File for simple single crystal refinement"); b.insert(t.getCaretPosition(), "\n'Use Ta-> button to save/send to topas; Ta button to launch topas; run in topas with red arrow"); b.insert(t.getCaretPosition(), "\n'Replace $ and # symbols with text/numbers as needed"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n\nr_wp 0 "); b.insert(t.getCaretPosition(), "\nr_p 0 "); b.insert(t.getCaretPosition(), "\ngof 0 "); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'General information about refinement here\n'Remove comments as required"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n\niters 100000"); b.insert(t.getCaretPosition(), "\nchi2_convergence_criteria 0.001"); b.insert(t.getCaretPosition(), "\n'do_errors"); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Information on datafile etc here"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\nxdd_scr " + w_path ); b.insert(t.getCaretPosition(), "\n\tweighting = If(Yobs<1,1,(1/Yobs));"); b.insert(t.getCaretPosition(), "\n\tfinish_X 180"); b.insert(t.getCaretPosition(), "\n\tfinish_X 180"); b.insert(t.getCaretPosition(), "\n"); i++; if (i == files.length) break; } jEdit.setProperty("ta.last_xdd_type", "*" + MiscUtilities.getFileExtension(files[0])); } else { String wmes = "INP file " + w_path_inp + " already exists"; Macros.message(v, wmes); } } } } TAnewINP(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\tlam la 1 lo 0.71073 lh 0.5 ymin_on_ymax 0.0001"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\tlam la 1 lo 1.5406 lh 0.5 ymin_on_ymax 0.0001"); do_cif(v) { t = v.getTextArea(); b = t.getBuffer(); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Information on structure"); b.insert(t.getCaretPosition(), "\n'Type in phase/space group/cell etc"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); jEdit.setProperty("vfs.browser.last-filter", "*.cif"); w_path = jEdit.getProperty("ta.last_cif_path"); if (w_path == null) { w_path = jEdit.getProperty("ta.main.dir") +"cif\\"; } jEdit.setProperty("vfs.browser.last-path", w_path); VFSFileChooserDialog chooser = new VFSFileChooserDialog(v, w_path, VFSBrowser.OPEN_DIALOG, true); String[] files = chooser.getSelectedFiles(); if (files != null) { int i = 0; b.beginCompoundEdit(); while(true) { runInSystemShell(v, jEdit.getProperty("ta.main.dir")); waitForConsole(v); runInSystemShell(v, "cif1 " + "\"" + files[i] + "\" cif1.tmp"); waitForConsole(v); t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n"); b.insertFile(v, jEdit.getProperty("ta.main.dir") + "cif1.tmp"); VFSManager.waitForRequests(); i++; if (i == files.length) break; b.insert(t.getCaretPosition(), "\n"); } b.endCompoundEdit(); jEdit.setProperty("ta.last_cif_path", files[0]); } t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n\t\tscale @ 0.0001"); b.insert(t.getCaretPosition(), "\n\t\tr_bragg 0"); b.insert(t.getCaretPosition(), "\n\t\tPhase_Density_g_on_cm3(0)"); } do_cif(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'Information on structure"); buffer.insert(textArea.getCaretPosition(), "\n'Type in phase/space group/cell etc"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n\n\tstr"); buffer.insert(textArea.getCaretPosition(), "\n\t\tscale @ 0.0001"); buffer.insert(textArea.getCaretPosition(), "\n\t\tPhase_Density_g_on_cm3(0)"); buffer.insert(textArea.getCaretPosition(), "\n\t\t'append_bond_lengths"); buffer.insert(textArea.getCaretPosition(), "\n\t\t'Out_FCF(" + buffer.getPath() + ".cif)"); {%sgrp "Enter Space Group:"}{@ textArea.goToEndOfLine(false) }\n\t\tspace_group {$$sgrp} {%phname "Enter Phase Name:"}{@ textArea.goToEndOfLine(false) }\n\t\tphase_name {$$phname} textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tCubic(@ #)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tTetragonal(@ #, @ #)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tHexagonal(@ #, @ #)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tRhombohedral(@ #, @ #)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\ta @ #\n\t\tb @ #\n\t\tc @ #\n\t\tal @ #\n\t\tbe @ #\n\t\tga @ #"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tsite $site x # y # z # occ $atom # beq #"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\ttweightingsite $site x # y # z # occ $atom # adps"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tview_structure"); {%dummy "Symmetry mode refinements use the matrices produced by ISODISTORT (Campbell et al J. Appl. Cryst., 2006, 39, 607). Go to the isodistort web page for more info. Hit ok to cancel this window!"} runInSystemShell(view, "start \"http:\\\\stokes.byu.edu\\isodistort.html\"&"); runInSystemShell(view, "start \"http:\\\\www.dur.ac.uk\\john.evans\\topas_workshop\\tutorial_isoriet.htm\"&"); TAnewINP(v) { String w_ext = jEdit.getProperty("ta.last_xdd_type"); if (w_ext == null) w_ext = "*.raw"; jEdit.setProperty("vfs.browser.last-filter", w_ext); String w_path = jEdit.getProperty("ta.last_new_inp_dir"); if (w_path == null) { w_path = jEdit.getProperty("ta.main.dir") +"test_examples\\"; } jEdit.setProperty("vfs.browser.last-path", w_path); VFSFileChooserDialog chooser = new VFSFileChooserDialog(v, w_path, VFSBrowser.OPEN_DIALOG, true); String[] files = chooser.getSelectedFiles(); if (files != null) { String w_dir = MiscUtilities.getParentOfPath(files[0]); String w_fn_no_ext = MiscUtilities.getFileNameNoExtension(files[0]); jEdit.setProperty("ta.last_new_inp_dir", w_dir); String w_path_inp = w_dir + w_fn_no_ext + "_riet_01.inp"; b = jEdit.openFile(v, w_path_inp); if (b != null) { if (b.isNewFile()) { t = v.getTextArea(); int i = 0; while(true) { t.goToEndOfLine(false); String w_path = MiscUtilities.getFileName(files[i]); if (w_path.indexOf(' ') != -1) { w_path = "\"" + w_path + "\""; } b.insert(t.getCaretPosition(), "'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Input File for Isodistort Distortion Mode Rietveld Refinement"); b.insert(t.getCaretPosition(), "\n'Use isodistort to produce _distortion.str files"); b.insert(t.getCaretPosition(), "\n'These are automatically read into topas via jedit menus"); b.insert(t.getCaretPosition(), "\n'Modes 1-3 will produce matrices to convert high to low symmetry structures"); b.insert(t.getCaretPosition(), "\n'Mode 4 will produce mode amplitudes from two cif files"); b.insert(t.getCaretPosition(), "\n'Refine on distortion mode amplitudes instead of fractional coordinates"); b.insert(t.getCaretPosition(), "\n'Values of an are summed rms displacements of atom in superstructure"); b.insert(t.getCaretPosition(), "\n'http://stokes.byu.edu/isodistort.html"); b.insert(t.getCaretPosition(), "\n'http://iucrcomputing.ccp14.ac.uk/iucr-top/comm/ccom/newsletters/2007nov/"); b.insert(t.getCaretPosition(), "\n'Branton J. Campbell, Harold T. Stokes, David E. Tanner, Dorian M. Hatch, J. Appl. Cryst., 2006, 39, 607-614"); b.insert(t.getCaretPosition(), "\n'UUse Ta-> button to save/send to topas; Ta button to launch topas; run in topas with red arrow"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\nr_wp 0 r_exp 0 r_p 0 r_wp_dash 0 r_p_dash 0 r_exp_dash 0 weighted_Durbin_Watson 0 gof 0"); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'General information about refinement here\n'Remove comments as required"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\niters 100000"); b.insert(t.getCaretPosition(), "\nchi2_convergence_criteria 0.001"); b.insert(t.getCaretPosition(), "\n'randomize_on_errors"); b.insert(t.getCaretPosition(), "\n'continue_after_convergence"); b.insert(t.getCaretPosition(), "\n'do_errors"); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Information on datafile etc here"); b.insert(t.getCaretPosition(), "\n'Check that default weighting is appropriate for your data"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\nxdd " + w_path); b.insert(t.getCaretPosition(), "\n\tx_calculation_step = Yobs_dx_at(Xo); convolution_step 4"); b.insert(t.getCaretPosition(), "\n\tbkg @ 0 0 0 0 0 0"); b.insert(textArea.getCaretPosition(), "\n\t\tSimple_Axial_Model(axial,10)"); i++; if (i == files.length) break; } jEdit.setProperty("ta.last_xdd_type", "*" + MiscUtilities.getFileExtension(files[0])); } else { String wmes = "INP file " + w_path_inp + " already exists"; Macros.message(v, wmes); } } } } TAnewINP(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd5000 Bragg Brentano graphite diffracted beam monochromator Cu Ka1/a2 2 line emission"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 26.6)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2_analyt(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd5000 Bragg Brentano Sol-X Cu Ka1/a2 2 line emission"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 0)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2_analyt(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd5000 Ge(111) monochromator Capillary Braun PSD Cu Ka1"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 27.26)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa1(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd8 Ge(111) monochromator capillary Lynxeye Mo Ka1"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 12.46)"); buffer.insert(textArea.getCaretPosition(), "\n\tla 1.0 lo 0.70930 lh 0.2695"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd8 Ge(111) monochromator Vantec Cu Ka1"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 27.26)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa1(0.0001)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t'd8 Lynx Eye Cu Ka1/a2 2 line emission"); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 0)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2_analyt(0.0001)"); {%wavelength "Enter Wavelength:"}{@ textArea.goToEndOfLine(false); }\n\tlam ymin_on_ymax 0.0001 la 1.0 lo {$$wavelength} lh 0.1\n\tLP_Factor( 90) 'change the LP correction or lh value if required {%wavelength "Enter Wavelength:"}{@ textArea.goToEndOfLine(false); }\n\tlam ymin_on_ymax 0.0001 la 1.0 lo {$$wavelength} lh 0.5\n\tneutron_data\n\tLP_Factor( 90) {%mono "Enter Monochromator angle (e.g. 26.6 graphite/Cu; 27.26 Ge/Cu; 0 for energy dispersive): "}{@ textArea.goToEndOfLine(false); }\n\tLP_Factor(!th2_monochromator, {$$mono}) Macros.getMacro("TAInsertLAM").invoke(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tVariable_Divergence_Intensity"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tZero_Error(zero,0)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tSpecimen_Displacement(height,0)"); Macros.getMacro("TAInsertSTR").invoke(view); buffer.insert(textArea.getCaretPosition(), "\n\t\tscale @ 0.0001"); buffer.insert(textArea.getCaretPosition(), "\n\t\tr_bragg 0"); buffer.insert(textArea.getCaretPosition(), "\n\t\tTCHZ_Peak_Type(pku, 0.00039,pkv, -0.00221,pkw, -0.00146,!pkz, 0.0000,pkx, 0.00957,!pky, 0.0000)"); buffer.insert(textArea.getCaretPosition(), "\n\t\tPhase_Density_g_on_cm3(0)"); do_cif(v) { t = v.getTextArea(); b = t.getBuffer(); t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'str file as generated by isotropy and isocif2topas.exe"); b.insert(t.getCaretPosition(), "\n'refine coordinates using mode amplitudes a1....an"); b.insert(t.getCaretPosition(), "\n'refine occupancies using mode amplitudes b1....bn"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); jEdit.setProperty("vfs.browser.last-filter", "*.cif"); w_path = jEdit.getProperty("ta.last_cif_path"); if (w_path == null) { w_path = jEdit.getProperty("ta.main.dir") +"cif\\"; } jEdit.setProperty("vfs.browser.last-path", w_path); waitForConsole(v); VFSFileChooserDialog chooser = new VFSFileChooserDialog(v, w_path, VFSBrowser.OPEN_DIALOG, true); String[] files = chooser.getSelectedFiles(); if (files != null) { int i = 0; b.beginCompoundEdit(); while(true) { runInSystemShell(v, jEdit.getProperty("ta.main.dir")); waitForConsole(v); runInSystemShell(v, "isocif2topas " + "\"" + files[i] + "\" > isocif2topas.str"); waitForConsole(v); t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n"); b.insertFile(v, jEdit.getProperty("ta.main.dir") + "isocif2topas.str"); runInSystemShell(v, "del isocif2topas.str"); waitForConsole(v); runInSystemShell(v, "del cifscratch.dat"); waitForConsole(v); runInSystemShell(v, "del ciftbx_error.dat"); waitForConsole(v); VFSManager.waitForRequests(); i++; if (i == files.length) break; b.insert(t.getCaretPosition(), "\n"); } b.endCompoundEdit(); jEdit.setProperty("ta.last_cif_path", files[0]); } t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n\t\tscale @ 0.0001"); b.insert(t.getCaretPosition(), "\n\t\tr_bragg 0"); b.insert(t.getCaretPosition(), "\n\t\tTCHZ_Peak_Type(pku, 0.00039,pkv, -0.00221,pkw, -0.00146,!pkz, 0.0000,pkx, 0.00957,!pky, 0.0000)"); b.insert(t.getCaretPosition(), "\n\t\tPhase_Density_g_on_cm3(0)"); } do_cif(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tview_structure"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPreferred_Orientation(@, 1,, #h #k #l)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPO_Two_Directions(@, 1,, 1 1 1,@, 1,, ,@, 0.5)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPO_Spherical_Harmonics(sh, 4)"); {%wavelength "Enter Wavelength:"}{@ textArea.goToEndOfLine(false) }\n\tlam ymin_on_ymax 0.0001 la 1.0 lo {$$wavelength} lh 0.5 textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tstart_X #"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tfinish_X #"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n'Approximate method - better to add second phase"); buffer.insert(textArea.getCaretPosition(), "\n\tla @ 0.0010 lo 1.39222 lh 0.5 'CU KB"); buffer.insert(textArea.getCaretPosition(), "\n\tla @ 0.0010 lo 1.47639 lh 0.5 'W LA"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tappend_bond_lengths min_r 0 max_r 3.5"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tDistance_Restrain($site1 $site2, #ideal_dist, 0.000, #tolerance, #weight)"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tdo_errors"); {%phname "Enter Phase Name:"}{@ textArea.goToEndOfLine(false) }\n\t\tphase_name {$$phname} textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tcalc_pattern(10,90,0.02,calc.xy)"); do_cif(v) { t = v.getTextArea(); b = t.getBuffer(); t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Calculated Pattern"); b.insert(t.getCaretPosition(), "\n'Assumes Cu Ka2, no monochromator"); b.insert(t.getCaretPosition(), "\n'Change as appropriate"); b.insert(t.getCaretPosition(), "\n'Youll need Durham calc_pattern macro:"); b.insert(t.getCaretPosition(), "\n'macro calc_pattern(start,stop,step,filename) {yobs_eqn !aac.xy = 1; min start max stop del step xdd_out filename load out_record out_fmt out_eqn { \" %11.5f \" = X; \" %11.5f\\n\" = Ycalc;}}"); b.insert(t.getCaretPosition(), "\n'is similar"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\niters 0"); b.insert(t.getCaretPosition(), "\ncalc_pattern(10,90,0.02,calc.xy)"); b.insert(t.getCaretPosition(), "\nLP_Factor(!th2_monochromator, 0)"); b.insert(t.getCaretPosition(), "\nCuKa2_analyt(0.0001)"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Information on structure - add beq values as needed"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); jEdit.setProperty("vfs.browser.last-filter", "*.cif"); w_path = jEdit.getProperty("ta.last_cif_path"); if (w_path == null) { w_path = jEdit.getProperty("ta.main.dir") +"cif\\"; } jEdit.setProperty("vfs.browser.last-path", w_path); waitForConsole(v); VFSFileChooserDialog chooser = new VFSFileChooserDialog(v, w_path, VFSBrowser.OPEN_DIALOG, true); String[] files = chooser.getSelectedFiles(); if (files != null) { int i = 0; b.beginCompoundEdit(); while(true) { runInSystemShell(v, jEdit.getProperty("ta.main.dir")); waitForConsole(v); runInSystemShell(v, "cif1 " + "\"" + files[i] + "\" cif1.tmp"); waitForConsole(v); t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n"); b.insertFile(v, jEdit.getProperty("ta.main.dir") + "cif1.tmp"); VFSManager.waitForRequests(); i++; if (i == files.length) break; b.insert(t.getCaretPosition(), "\n"); } b.endCompoundEdit(); jEdit.setProperty("ta.last_cif_path", files[0]); } t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n\t\tscale 0.001"); b.insert(t.getCaretPosition(), "\n\t\tr_bragg 0"); b.insert(t.getCaretPosition(), "\n\t\tTCHZ_Peak_Type(!pku, 0.00039,!pkv, -0.00221,!pkw, -0.00146,!pkz, 0.0000,!pkx, 0.00957,!pky, 0.0000)"); b.insert(t.getCaretPosition(), "\n\t\tSimple_Axial_Model(!axial,0)"); b.insert(t.getCaretPosition(), "\n\t\tPhase_Density_g_on_cm3(0)"); } do_cif(view); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\nno_LIMIT_warnings"); Macros.getMacro("TAInsertSTR").invoke(view); {%alphaval "Enter Incident Beam Angle in degrees:"}{@ textArea.goToEndOfLine(false) }\n\tFIXEDTHETA(alpha, {$$alphaval})\n\tSDINEL(!delta,0,!alpha,{$$alphaval}) textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n'Robust refinement for xye file; Stone et al J. Appl. Cryst. (2009). 42, 385 to 391"); buffer.insert(textArea.getCaretPosition(), "\n'Get macro from http://www.dur.ac.uk/john.evans/topas_academic/topas_macros.htm"); buffer.insert(textArea.getCaretPosition(), "\nRobust_refinement_xye"); textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n'Robust refinement; Stone et al J. Appl. Cryst. (2009). 42, 385 to 391"); buffer.insert(textArea.getCaretPosition(), "\n'Use with raw files or xy files with no esd"); buffer.insert(textArea.getCaretPosition(), "\n'Get macro from http://www.dur.ac.uk/john.evans/topas_academic/topas_macros.htm"); buffer.insert(textArea.getCaretPosition(), "\nRobust_refinement_poisson"); Macros.getMacro("TAtemplate").invoke(view); do_cif(v) { t = v.getTextArea(); b = t.getBuffer(); t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n\n'--------------------------------------------------------------"); b.insert(t.getCaretPosition(), "\n'Information on structure"); b.insert(t.getCaretPosition(), "\n'Type in phase/space group/cell etc"); b.insert(t.getCaretPosition(), "\n'Comment in/out sections as needed"); b.insert(t.getCaretPosition(), "\n'--------------------------------------------------------------"); jEdit.setProperty("vfs.browser.last-filter", "*.cif"); w_path = jEdit.getProperty("ta.last_cif_path"); if (w_path == null) { w_path = jEdit.getProperty("ta.main.dir") +"cif\\"; } jEdit.setProperty("vfs.browser.last-path", w_path); waitForConsole(v); VFSFileChooserDialog chooser = new VFSFileChooserDialog(v, w_path, VFSBrowser.OPEN_DIALOG, true); String[] files = chooser.getSelectedFiles(); if (files != null) { int i = 0; b.beginCompoundEdit(); while(true) { runInSystemShell(v, jEdit.getProperty("ta.main.dir")); waitForConsole(v); runInSystemShell(v, "cif1 " + "\"" + files[i] + "\" cif1.tmp"); waitForConsole(v); t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n"); b.insertFile(v, jEdit.getProperty("ta.main.dir") + "cif1.tmp"); VFSManager.waitForRequests(); i++; if (i == files.length) break; b.insert(t.getCaretPosition(), "\n"); } b.endCompoundEdit(); jEdit.setProperty("ta.last_cif_path", files[0]); } t.goToEndOfLine(false); b.insert(t.getCaretPosition(), "\n\t\tscale @ 0.0001"); b.insert(t.getCaretPosition(), "\n\t\tr_bragg 0"); b.insert(t.getCaretPosition(), "\n\t\tTCHZ_Peak_Type(pku, 0.00039,pkv, -0.00221,pkw, -0.00146,!pkz, 0.0000,pkx, 0.00957,!pky, 0.0000)"); b.insert(t.getCaretPosition(), "\n\t\tSimple_Axial_Model(axial,10)"); b.insert(t.getCaretPosition(), "\n\t\tPhase_Density_g_on_cm3(0)"); } do_cif(view);