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TOPAS-Academic

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<menu name="TOPAS_Durham_Tutorials">
<item name="Run TOPAS-Academic" type="macro"> do_ta(v) { runInSystemShell(v, jEdit.getProperty("ta.main.dir")); waitForConsole(v); runInSystemShell(v, "ta&"); } do_ta(view); </item>
<item name="Save this file and send to TA" type="macro"> 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(); } } </item>
<item name="Open XInsert file" type="macro"> jEdit.openFile(view, jEdit.getProperty("xinsert.inserts-directory") + File.separator + "foo.insert.xml"); </item>
<menu name="Simple Lab Rietveld">
<item name="File Header" type="macro"> textArea.goToBufferStart(false); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'Input File for simple Rietveld Refinement"); buffer.insert(textArea.getCaretPosition(), "\n'Use save/set current button then run with F6 in topas"); buffer.insert(textArea.getCaretPosition(), "\n'Replace $ and # symbols with text/numbers as needed"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.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"); buffer.insert(textArea.getCaretPosition(), "\n\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'General information about refinement here\n'Remove comments as required"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n\niters 100000"); buffer.insert(textArea.getCaretPosition(), "\nchi2_convergence_criteria 0.001"); buffer.insert(textArea.getCaretPosition(), "\n'do_errors"); buffer.insert(textArea.getCaretPosition(), "\n\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'Information on datafile here"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); </item>
<item name="Background" type="xinsert_script">{@textArea.goToEndOfLine(false) }\n\tbkg @ 0 0 0 0 0 0</item>
<menu name="Instrument/Corrections">
<item name="Durham_d5000" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 26.6)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2(0.001)"); </item>
<item name="Durham_d8" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 27.26)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa1(0.001)"); </item>
<item name="Variable Slits used" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tVariable_Divergence_Intensity"); </item>
<item name="Refine zero point" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tZero_Error(zero,0)"); </item>
<item name="Refine sample height" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tSpecimen_Displacement(height,0)"); </item>
</menu>
<menu name="Structure - cif">
<item name="Read a CIF file" type="macro"> 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\tPV_Peak_Type(@, 0.02,@, 0.02,@, 0.02,@, 0.02,@, 0.02,@, 0.02)"); 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); </item>
</menu>
<menu name="Structure - nocif">
<item name="Structural Information" type="macro"> 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\tPV_Peak_Type(@, 0.02,@, 0.02,@, 0.02,@, 0.02,@, 0.02,@, 0.02)"); 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)"); </item>
<item name="Space group" type="xinsert_script">{%sgrp "Enter Space Group:"}{@ textArea.goToEndOfLine(false) }\n\t\tspace_group {$$sgrp}</item>
<item name="Phase Name" type="xinsert_script">{%phname "Enter Phase Name:"}{@ textArea.goToEndOfLine(false) }\n\t\t\phase_name {$$phname}</item>
<menu name="Lattice parameters">
<item name="Cubic" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tCubic(@ #)"); </item>
<item name="Tetragonal" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tTetragonal(@ #, @ #)"); </item>
<item name="Hexagonal" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tHexagonal(@ #, @ #)"); </item>
<item name="Rhombohedral" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tRhombohedral(@ #, @ #)"); </item>
<item name="Triclinic" type="macro"> 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 @ #"); </item>
</menu>
<item name="site with beq" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tsite $site x # y # z # occ $atom # beq #"); </item>
<item name="site with adps" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tsite $site x # y # z # occ $atom # adps"); </item>
</menu>
<item name="view structure" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tview_structure"); </item>
<menu name="Preferred orientation">
<item name="PO-March Dollase - 1 Dir" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPreferred_Orientation(@, 1,, #h #k #l)"); </item>
<item name="PO-March Dollase - 2 Dirs" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPO_Two_Directions(@, 1,, 1 1 1,@, 1,, ,@, 0.5)"); </item>
<item name="PO_Spherical_Harmonics" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPO_Spherical_Harmonics(sh, 4)"); </item>
</menu>
</menu>
<menu name="Lab Pawley Refinement">
<item name="File Header" type="macro"> textArea.goToBufferStart(false); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'Input File for simple Pawley Fit"); buffer.insert(textArea.getCaretPosition(), "\n'Use save/set current button then run with F6 in TOPAS-Academic"); buffer.insert(textArea.getCaretPosition(), "\n'Introduce @ symbols or parameter names to refine variables as needed"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.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"); buffer.insert(textArea.getCaretPosition(), "\n\niters 100000"); buffer.insert(textArea.getCaretPosition(), "\nchi2_convergence_criteria 0.001"); buffer.insert(textArea.getCaretPosition(), "\n'do_errors\n"); </item>
<item name="Background" type="xinsert_script">{@textArea.goToEndOfLine(false) }\n\tbkg @ 0 0 0 0 0 0</item>
<menu name="Instrument/Corrections">
<item name="Durham_d5000" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 26.6)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa2(0.001)"); </item>
<item name="Durham_d8" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tLP_Factor(!th2_monochromator, 27.26)"); buffer.insert(textArea.getCaretPosition(), "\n\tCuKa1(0.001)"); </item>
<item name="Variable Slits used" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tVariable_Divergence_Intensity"); </item>
<item name="Refine zero point" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tZero_Error(zero,0)"); </item>
<item name="Refine sample height" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\tSpecimen_Displacement(height,0)"); </item>
</menu>
<menu name="Pawley fit phase">
<item name="Structural Information" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\n\thkl_Is"); buffer.insert(textArea.getCaretPosition(), "\n\t\tPV_Peak_Type(@, 0.02,@, 0.02,@, 0.02,@, 0.02,@, 0.02,@, 0.02)"); buffer.insert(textArea.getCaretPosition(), "\n\t\tSimple_Axial_Model(axial,10)"); </item>
<item name="Phase Name" type="xinsert_script">{%phname "Enter Phase Name:"}{@ textArea.goToEndOfLine(false) }\n\t\t\phase_name {$$phname}</item>
</menu>
<menu name="Lattice parameters">
<item name="Cubic" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tCubic(@ #)"); </item>
<item name="Tetragonal" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tTetragonal(@ #, @ #)"); </item>
<item name="Hexagonal" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tHexagonal(@ #, @ #)"); </item>
<item name="Rhombohedral" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tRhombohedral(@ #, @ #)"); </item>
<item name="Triclinic" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\ta @ #\n\t\tb @ #\n\t\tc @ #\n\t\tal @ #\n\t\tbe @ #\n\t\tga @ #"); </item>
</menu>
<item name="Space group" type="xinsert_script">{%sgrp "Enter Space Group:"}{@ textArea.goToEndOfLine(false) }\n\t\tspace_group {$$sgrp}</item>
</menu>
<menu name="Simple tof Rietveld">
<item name="File Header" type="macro"> textArea.goToBufferStart(false); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'Input File for simple Rietveld Refinement of tof data"); buffer.insert(textArea.getCaretPosition(), "\n'Use save/set current button then run with F6 in TOPAS-Academic"); buffer.insert(textArea.getCaretPosition(), "\n'Introduce @ signs to refine parameters as needed"); buffer.insert(textArea.getCaretPosition(), "\n'Red numbers are refined, blue are fixed"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.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"); buffer.insert(textArea.getCaretPosition(), "\n\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'General information about refinement here\n'Remove comments as required"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n\niters 100000"); buffer.insert(textArea.getCaretPosition(), "\nchi2_convergence_criteria 0.001"); buffer.insert(textArea.getCaretPosition(), "\n'do_errors"); buffer.insert(textArea.getCaretPosition(), "\n\n'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n'Information on datafile here"); buffer.insert(textArea.getCaretPosition(), "\n'--------------------------------------------------------------"); </item>
<item name="Background" type="xinsert_script">{@textArea.goToEndOfLine(false) }\n\tbkg @ 0 0 0 0 0 0</item>
<!-- 
		<item name="xye File" type="xinsert_script">{%xyefile "Enter xye file name with extension, calculation step (e.g. zx0002.xye,5): "}{@
			textArea.goToEndOfLine(false)
			}\nTOF_XYE({$$xyefile})
\tbkg @ 0 0 0 0 0 0
\tstart_X 40000
\tfinish_X 120000
\tscale_pks = D_spacing^4;</item>
 -->
<menu name="Instrument/Corrections">
<item name="hrpd_bs" type="macro"> 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'--------------------------------------------------------------"); buffer.insert(textArea.getCaretPosition(), "\n\tTOF_LAM(0.001)"); buffer.insert(textArea.getCaretPosition(), "\n\tTOF_x_axis_calibration(!t0_hrpd_bs,-11,!difc_hrpd_bs,48295,!difa_hrpd_bs,-5)"); buffer.insert(textArea.getCaretPosition(), "\n\tTOF_Exponential(!a1_bs, 193.26670,!a2_bs, 34.66409, 4, difc_hrpd_bs, +)"); </item>
</menu>
<menu name="Structure - cif">
<item name="Read a .CIF file" type="macro"> 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); </item>
<item name="Space group" type="xinsert_script">{%sgrp "Enter Space Group:"}{@ textArea.goToEndOfLine(false) }\n\t\tspace_group {$$sgrp}</item>
</menu>
<item name="view structure" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tview_structure"); </item>
<menu name="Preferred orientation">
<item name="PO-March Dollase - 1 Dir" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPreferred_Orientation(@, 1,, #h #k #l)"); </item>
<item name="PO-March Dollase - 2 Dirs" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPO_Two_Directions(@, 1,, 1 1 1,@, 1,, ,@, 0.5)"); </item>
<item name="PO_Spherical_Harmonics" type="macro"> textArea.goToEndOfLine(false); buffer.insert(textArea.getCaretPosition(), "\n\t\tPO_Spherical_Harmonics(sh, 4)"); </item>
</menu>
</menu>
</menu>