// Open Jimp 2
// Press "CTRL L"
// Copy and paste each "Section" of this log file in the bottom section of the "Script Dialog" window and press enter

// Begin Section 1
// open the molecule, the 111-trifluoroethane.msi file must exist in C:\Program Files\Jimp2
showScriptDialog();
//setWorkarea(load("C:/Documents and Settings/cewebstr/My Documents/parkin/111-trifluoroethane.msi"));
setWorkarea(load("C:/Program Files/Jimp2/111-trifluoroethane.msi"));
centerViewOrCamera();
refreshAll();
refreshView();
setSelection(getInPrism(0.000000, 0.000000, -1.000000, -1.423926, 0.925237, -0.128890, -1.423926, 1.301270, -0.128890, -1.631733, 1.301270, -0.128890, -1.631733, 0.925237, -0.128890));
setSelection(idsAdd(getSelection(), getAttachedBonds(getSelection())));
refreshView();
// set the zoom of the view
setViewZoom(2.5);
refreshView();
// End Section 1


// Begin Section 2a
// Create the fragments
// make the selection and set fragment 1
// 1) use left mouse button to select atoms for fragment 1
// 2) right click, select "Properties"
// 3) enter "1" into the text box next to "Fenske-Hall fragment", click "Apply"
setSelection(getInPrism(0.000000, 0.000000, -1.000000, 1.677855, -1.344487, -0.128890, 1.677855, 1.326236, -0.128890, 0.382037, 1.326236, -0.128890, 0.382037, -1.344487, -0.128890));
setSelection(idsAdd(getSelection(), getAttachedBonds(getSelection())));
refreshView();
showPropertiesDialog(getSelection());
tmp_props = 0;
tmp_props.fenhall_frag = 1;
setProperties(tmp_props, arrayFromVars(3,6,7,8,5,9,10));
refreshView();
// End Section 2a

// Begin Section 2b
// Create the fragments
// make the selection and set fragment 2
// 1) use left mouse button to select atoms for fragment 2
// 2) right click, select "Properties"
// 3) enter "2" into the text box next to "Fenske-Hall fragment", click "Apply"
setSelection(getInPrism(0.000000, 0.000000, -1.000000, -0.402754, -1.265399, -0.128890, -0.402754, 1.210646, -0.128890, -1.728990, 1.210646, -0.128890, -1.728990, -1.265399, -0.128890));
setSelection(idsAdd(getSelection(), getAttachedBonds(getSelection())));
refreshView();
tmp_props = 0;
tmp_props.fenhall_frag = 2;
setProperties(tmp_props, arrayFromVars(2,12,13,14,15,16,11));
refreshView();
// End Section 2b


// Begin Section 3
// run the Fenske-Hall calculations
// FH on fragment 1 (must set number of unpaired electrons to 1)
// 1) left click Dialog-->Fenske-Hall
// 2) enter "1" into text box next to "Unpaired electrons"
// 3) enter "1" into text box next to "Fragment number"
// 4) click "Run fragment"
// 5) click "OK" on dialog box "The calculation has completed successfully"
showFenhallDialog();
calcFenhallFragment("fenhall_calc",15,.001,.65,.2,.001,0,0,1,1,0,0);
// Sum of the Pop Dev and Largest Dev for cycle   1 are    4.0079  and    1.1466
// Sum of the Pop Dev and Largest Dev for cycle   2 are    2.4376  and    0.6829
// Sum of the Pop Dev and Largest Dev for cycle   3 are    1.5086  and    0.4109
// Sum of the Pop Dev and Largest Dev for cycle   4 are    0.0231  and    0.0055
// Sum of the Pop Dev and Largest Dev for cycle   5 are    0.0124  and    0.0030
// Sum of the Pop Dev and Largest Dev for cycle   6 are    0.0067  and    0.0017
// Sum of the Pop Dev and Largest Dev for cycle   7 are    0.0038  and    0.0010
//                     * SCF IS CONVERGED *
// 
// FH on fragment 2 (must keep number of unpaired electrons to 1)
// 1) left click Dialog-->Fenske-Hall
// 2) enter "1" into text box next to "Unpaired electrons"
// 3) enter "2" into text box next to "Fragment number"
// 4) click "Run fragment"
// 5) click "OK" on dialog box "The calculation has completed successfully"
calcFenhallFragment("fenhall_calc",15,.001,.65,.2,.001,0,0,1,2,0,0);
// Sum of the Pop Dev and Largest Dev for cycle   1 are    1.9375  and    0.8626
// Sum of the Pop Dev and Largest Dev for cycle   2 are    1.2449  and    0.5407
// Sum of the Pop Dev and Largest Dev for cycle   3 are    0.8011  and    0.3396
// Sum of the Pop Dev and Largest Dev for cycle   4 are    0.0031  and    0.0014
// Sum of the Pop Dev and Largest Dev for cycle   5 are    0.0020  and    0.0009
//                     * SCF IS CONVERGED *
// 
// Run FH fragment analysis on whole molecule (must set number of unpaired electrons to 0)
// 1) left click Dialog-->Fenske-Hall
// 2) enter "0" into text box next to "Unpaired electrons"
// 3) click "Run fragment analysis" (the value in "Fragment number" does not matter)
// 4) click "OK" on dialog box "The calculation has completed successfully"
calcFenhallFragmentAnalysis("fenhall_calc",15,.001,.65,.2,.001,0,0,0,2,0,0);
// Sum of the Pop Dev and Largest Dev for cycle   1 are    6.1863  and    1.2356
// Sum of the Pop Dev and Largest Dev for cycle   2 are    3.9664  and    0.7367
// Sum of the Pop Dev and Largest Dev for cycle   3 are    2.5599  and    0.4440
// Sum of the Pop Dev and Largest Dev for cycle   4 are    0.0400  and    0.0101
// Sum of the Pop Dev and Largest Dev for cycle   5 are    0.0265  and    0.0067
// Sum of the Pop Dev and Largest Dev for cycle   6 are    0.0177  and    0.0044
// Sum of the Pop Dev and Largest Dev for cycle   7 are    0.0018  and    0.0003
//                     * SCF IS CONVERGED *
// 
// End Section 3


// Begin Section 4a
// run the MO Plot calculations
// 1) left click Dialog-->Moplot
// 2) set the directory to fragment 1 (left click Set Dir, navigate to C:\Program Files\Jimp2\fenhall_calc\frag_1, click OK)
// 3) select orbital 13, click Calc Orbitals
// MOPlot on fragment 1, orbital 13
showMoplotDialog();
tmp_field = calcMoplot("C:/Program Files/Jimp2/fenhall_calc/frag_1/", 13, 2);
calcIsoSurface(tmp_field, -.05);
calcIsoSurface(tmp_field, .05);
refreshAll();
setPropHidden(arrayFromVars(17), 1);
setPropHidden(17, 0);
refreshAll();
// End Section 4a


// Begin Section 4b
// 1) left click Dialog-->Moplot
// 2) set the directory to fragment 2 (left click Set Dir, navigate to C:\Program Files\Jimp2\fenhall_calc\frag_2, click OK)
// 3) select orbital 4, click Calc Orbitals
// MOPlot on fragment 2, orbital 4
tmp_field = calcMoplot("C:/Program Files/Jimp2/fenhall_calc/frag_2/", 4, 2);
calcIsoSurface(tmp_field, -.05);
calcIsoSurface(tmp_field, .05);
refreshAll();
setPropHidden(arrayFromVars(20,17), 1);
setPropHidden(20, 0);
refreshAll();
// End Section 4b


// Begin Section 5
// Adjust the visibility ("Hidden"/"Shown")
// 1) left click "+" next to 111-trifluoroethane" node
// 2) right click "Field Moplot 13 medium", left clicking "Hidden" to uncheck it
setSelection(1);
refreshView();
setSelection(17);
refreshView();
setPropShown(arrayFromVars(17), 1);
refreshAll();
setSelection(17);
refreshView();
setPropHidden(arrayFromVars(17), 0);
refreshAll();
// End Section 5


// Begin Section 6
// Adjust the colors
// 1) right click "Surface Iso 0.050000" node, left click "Properties" from the menu
// 2) from "Properties Dialog", left click "Change Color", select yellow, left click "Apply"
showPropertiesDialog(arrayFromVars(19));
tmp_props = 0;
tmp_props.v_color.r = 0.000000;
tmp_props.v_color.g = 1.000000;
tmp_props.v_color.b = 1.000000;
setProperties(tmp_props, arrayFromVars(19));
refreshView();
// 1) right click "Surface Iso -0.050000" node, left click "Properties" from the menu
// 2) from "Properties Dialog", left click "Change Color", select blue, left click "Apply"
setSelection(18);
refreshView();
showPropertiesDialog(arrayFromVars(18));
tmp_props = 0;
tmp_props.v_color.r = 1.000000;
tmp_props.v_color.g = 1.000000;
tmp_props.v_color.b = 0.000000;
setProperties(tmp_props, arrayFromVars(18));
refreshView();
// End Section 6


// Begin Section 7
// Adjust the visibility ("Hidden"/"Shown")
// right click node, then left click "Hidden" and/or "Shown" from menu
// if an object has both "Hidden" and "Shown" checked in the menu, then "Hidden" takes precedence
setSelection(0,1);
refreshView();
setSelection(1);
refreshView();
setSelection(17);
refreshView();
setPropShown(arrayFromVars(17), 0);
refreshAll();
setSelection(17);
refreshView();
setPropHidden(arrayFromVars(17), 1);
refreshAll();
setSelection(0);
refreshView();
setSelection(17);
refreshView();
setPropHidden(arrayFromVars(17), 0);
refreshAll();
setSelection(20);
refreshView();
setPropHidden(arrayFromVars(20), 1);
refreshAll();
setSelection(0);
refreshView();
// End Section 7