Appendix

Appendix

program SpinSim (input, output, resultdata);

{Isotropic Spectral Simulation}

{Pascal port of BASIC code}

{From U.M. Oehler, and E.G. Janzen, Can. J. Chem., 60, 1542-1548 (1982)}

{Macintosh Version by John Boswell, August 30, 1991 }

label

450, 550, 570, 770, 830;

const

tsinit = 2;

xcinit = 0.146;

phinit = 1;

lwinit = 1;

yminit = 100;

dginit = 0;

lrinit = 0.3;

var

{GLOBALS}

done: boolean;

WindowRect: rect;

sp: array[1..3000] of real;

mk: array[1..3000] of real;

ln: array[1..100] of real;

nu: array[1..20] of integer;

cc: array[1..20] of real;

sn: array[1..20] of real;

ar: array[1..20] of real;

xc, ph, lw, ym, dg, lr, ma, mx, tt1, t2, t3, ta, mn: real;

fi, t6, tl, sr, st, q, t4, count, mt, ts, t1, J, k, l, x, N: integer;

nc, i1, i2, i3, i4, i5, i6, i7, i8, b: integer;

answer, goagain: char;

filename, prompt, name: string;

resultdata: text;

procedure SaveData;

var

n: integer;

begin

writeln('I need a drink. >'); {for some weird reason an extra return char was generated}

readln;

{writeln('Filename??? >');}

{readln(filename);}

{filename := 'Calvin:ResultFile';}

Prompt := 'Save Data as .. . ';

name := 't1';

filename := NewFileName(prompt, name);

rewrite(resultdata, filename);

for n := 1 to 1500 do

begin

writeln(resultdata, n, ' ', sp[n]);

end;

{sysbeep(25);}

close(resultdata);

end; {SaveData}

{*********************************}

procedure READData;

var

n: integer;

begin

writeln('I need a drink. >'); {for some weird reason an extra return char was generated}

readln;

writeln('Data Filename??? >');

readln(filename);

{filename := 'Calvin:ResultFile';}

reset(resultdata, filename);

{readln(resultdata, n, ' ', sp[n]);}

close(resultdata);

sysbeep(125);

end; {READData}

begin {MAIN}

SetRect(WindowRect, 0, 38, 511, 314);

SetTextRect(WindowRect);

ShowText;

done := false;

repeat

writeln(' Isotropic EPR simulation program.');

{sysbeep(25);}

writeln;

writeln(' Enter number of spectra, X increment (0.05 or so), and Phase (1 or -1) ');

writeln(' --separate with space: ');

writeln('Use default values? (y/n)', tsinit, ', ', xcinit : 4 : 3, ', ', phinit);

readln(answer);

if answer = 'n' then

begin

writeln(' enter values--separate with space: ');

read(ts, xc, ph);

answer := 'y';

writeln;

end

else

begin

ts := tsinit;

xc := xcinit;

ph := phinit;

answer := 'y';

end; {if}

for i1 := 1 to ts do

begin {i1}

if i1 <> 1 then

for J := 1 to 3000 do

begin

mk[J] := 0

end;

write('Number of coupling constants for spectrum ', i1, ' -->');

readln(nc);

writeln;

writeln(' Line width, Maximum Y, Delta G, Fraction Lorenztian(typical=.3-.5)');

writeln('( sep . by space ); the defaults are: ', lwinit, ', ', yminit, ', ', dginit, ', ', lrinit);

writeln('Use default values? (y/n) ');

readln(answer);

if answer = 'n' then

begin

writeln(' enter values--separate with space: ');

read(lw, ym, dg, lr);

answer := 'y';

writeln;

end

else

begin

lw := lwinit;

ym := yminit;

dg := dginit;

lr := lrinit;

answer := 'y';

writeln;

end; {if}

{convert fraction lorenztian (lr) from height contribution to area contribution}

{Now lr = 0.5 means 50% of the area is due to lorentzian lineshape}

lr := 0.275664 * lr / (0.275664 * lr + 0.967883 * (1 - lr));

dg := dg / xc;

lw := lw / xc;

for k := 1 to nc do

begin

writeln(' coupling number ', k, ' : ');

writeln('Number of nuclei , coupling constant , Spin ( 0.5 , 1.0 , 1.5 etc .) : ');

write('( sep . by space ) : ');

read(nu[k], cc[k], sn[k]);

cc[k] := cc[k] / xc;

end;

{calculate stick spectrum}

N := 1;

mk[1] := 1;

{start L4 repeat once for each DIFFERENT coupling constant}

for i2 := 1 to nc do

{start L3. repeat once for each equivalent nucleus}

begin {i2}

for i3 := 1 to nu[i2] do

{start l2. Repeat until all peaks in spectrum have been located.}

begin {i3}

i4 := N;

450:

if mk[i4] = 0 then

begin

i4 := i4 - 1;

goto 450;

end;

{start l1. Repeat 2*S times where S + Spin of the nucleus.}

count := round(2 * sn[i2]); {transfer function---need an integer for the loop}

for i5 := 1 to count do

begin {i5}

t1 := i4 + round(i5 * cc[i2]);

mk[t1] := mk[t1] + mk[i4];

{add up the number of unit lineshapes used in the simulation.}

{This times the area of the lineshape is the total area}

mt := mt + 1;

if ma < mk[t1] then

ma := mk[t1];

end; {i5}

if t1 > N then

N := t1;

i4 := i4 - 1;

{end l2 Done splitting each peak in the stick diagram}

if i4 > 1 then

goto 450;

{end l3. no more equivalent nuclei}

end; {i3}

{end l4. no more different coupling constants}

end; { i2}

{center stick diagram with respect to first spectrum. Include G shift}

if i1 = 1 then

begin

fi := N + 2 * round(8 * lw);

goto 550;

end;

t6 := round((fi - N - 2 * round(8 * lw)) / 2 + dg);

if t6 = 0 then

goto 550;

for l := N downto 1 do

begin

mk[l + t6] := mk[l];

mk[l] := 0;

end;

N := N + t6;

550:

if tl < (N + round(16 * lw)) then

tl := N + round(16 * lw);

sr := -1 * round(8 * lw);

570:

st := sr + 99;

if st > 0 then

st := 0;

t4 := 1;

{calculate 100 points of lineshape from sr(start) to st(stop) }

for i6 := sr to st do

begin

tt1 := -1 * ph * ym / ma * (1 - lr); {tt1 is t1 in basic code ???}

t2 := lr * 16 * ym / ma * (-1 * ph);

t3 := i6 * 2 / lw;

ln[t4] := t3 * tt1 * exp(-1 * 0.5 * (t3 * t3 - 1)); {tt1 is t1 in basic code ???}

ln[t4] := ln[t4] + t3 * t2 / ((3 + t3 * t3) * (3 + t3 * t3));

t4 := t4 + 1;

end; {i6}

{locate each stick in the stick diagram}

for i7 := 1 to N do

begin

if mk[i7] = 0 then

goto 770;

t4 := 1;

{copy LINESHAPE*INTENSITY into sp[] at location of stick}

for i8 := (sr + round(8 * lw)) to (st + round(8 * lw)) do

begin

sp[i7 + i8] := sp[i7 + i8] + ln[t4] * mk[i7];

sp[i7 + 2 * round(8 * lw) - i8] := -1 * mk[i7] * ln[t4] + sp[i7 + 2 * round(8 * lw) - i8];

t4 := t4 + 1;

end; {i8}

770:

end; {i7}

{if LINESHAPE calculation is incomplete go back and calculate up to 100 more points}

if st <> 0 then

begin

sr := sr + 100;

goto 570;

end;

{calculate AREA from line width, height, % Lorentzian,}

{number of unit lineshapes and relative height of the largest peak}

ar[i1] := lr * 2 * 3.14159 / sqrt(3) * (ym * (lw * lw));

ar[i1] := ar[i1] + (1 - lr) * sqrt(2 * 3.14159 * exp(1)) * ((0.5 * lw) * (0.5 * lw)) * ym;

ar[i1] := ar[i1] * mt / ma;

mt := 1;

ma := 0;

end; {i1}

{find minimum and maximum values in sp[] for scaling}

for x := 1 to tl do

begin

if mn > sp[x] then

begin

mn := sp[x];

goto 830;

end;

if mx < sp[x] then

mx := sp[x];

830:

end; {for}

{sum total area of all components in mixture}

for q := 1 to ts do

begin

ta := ta + ar[q]

end;

writeln('Areas of component spectra: ');

writeln;

{print component spectra areas as percentages of total area}

for b := 1 to ts do

begin

writeln('area of component ', b, ' is ', ar[b] / ta * 100);

end;

{the points of the spectra are now contained in the array sp[]. }

SaveData;

writeln('Run again? y/n ');

readln(goagain);

if goagain = 'n' then

done := true

else

done := false;

until done;

end. {SpinSim}

program EPRSim (input, output);

{Anisotropic simulation of esr spectra - Joseph Warden 1986}

{Pascal port of FORTRAN code for Macintosh Pascal with }

{modifications to run in THINK Pascal by John Boswell December, 1989}

const

pi2 = 1.570796;

bm = 9.27408E-21;

var

{GLOBALS}

done: boolean;

WindowRect: rect;

intensity: array[1..1500] of real;

g: array[1..3] of real;

hg: array[1..3] of real;

hmin, hmax, hinc, hx, hy, hz, frequency, gx, gy, gz: real;

bi, ci, hi, e, ee, h, cc, cd, ce, intenmin, intenmax, intennorm: real;

naintx, nainty: integer;

i, j, n, nh, nth, yamp: integer;

filename, thestring: string;

resultdata: text;

x: string;

answer, answer2: char;

function fxy (t1, p1: real): real;

var

a, a1, g4, g6, d, d1, d2, z1, z2, z3, x, chi: real;

aho, gls1, gls2, gls3, gls4, s, ai: real;

begin

a1 := cos(p1) * cos(p1);

a := sin(t1) * sin(t1);

g4 := (gx * gx * a * a1) + (gy * gy * a * (1.0 - a1)) + (gz * gz * (1.0 - a));

g6 := sqrt(g4);

d := hx * hx * gx * gx * a * a1 + hy * hy * gy * gy * a * (1.0 - a1) + hz * hz * gz * gz * (1.0 - a);

d2 := sqrt(d);

d1 := 1.178 * d2 / g6;

z1 := gx * gx * gy * gy * a;

z2 := gy * gy * gz * gz * (1.0 - a1 + (1.0 - a) * a1);

z3 := gx * gx * gz * gz * (a1 + (1.0 - a) * (1.0 - a1));

x := (z1 + z2 + z3) / (2.0 * g6 * g6 * g6);

chi := 1.0;

aho := 714.431 * frequency / g6;

gls1 := -2.77256 * chi / (d1 * d1);

gls2 := (h - aho) / (0.5 * d1);

gls3 := gls1 * gls2;

gls4 := exp(-0.69314 * gls2 * gls2);

s := gls3 * gls4;

ai := x * s * sqrt(a);

fxy := ai;

end; {Function fxy}

function fy (y, a, b: real; nx: integer): real;

var

hx, hx2, hx3, xo, xe, xi: real;

nx2, j: integer;

begin

hx := (b - a) / nx;

hx2 := 2.0 * hx;

hx3 := hx / 3.0;

nx2 := (nx div 2) - 1;

xi := hx3 * fxy(a, y);

for j := 1 to nx2 do

begin

xo := a + hx + hx2 * (j - 1);

xe := a + hx2 * j;

xi := xi + hx3 * (4.0 * fxy(xo, y) + 2.0 * fxy(xe, y));

end;

xi := xi + hx3 * (4.0 * fxy((b - hx), y) + fxy(b, y));

fy := xi;

end; {Function fy}

function fxyint (a, b, c, d: real; nx, ny: integer): real;

var

hy, hy2, hy3, yi, yo, ye: real;

ny2, j: integer;

begin

hy := (d - c) / ny;

hy2 := 2.0 * hy;

hy3 := hy / 3.0;

ny2 := (ny div 2) - 1;

yi := hy3 * fy(c, a, b, nx);

for j := 1 to ny2 do

begin

yo := c + hy + hy2 * (j - 1);

ye := c + hy2 * j;

yi := yi + hy3 * (4.0 * fy(yo, a, b, nx) + 2.0 * (fy(ye, a, b, nx)));

end;

yi := yi + hy3 * (4.0 * fy((d - hy), a, b, nx) + fy(d, a, b, nx));

fxyint := yi;

end; {Function fxyint}

{*********************************}

procedure PlotData;

var

n, firstpoint: integer;

begin

{Graphics output to Mac Screen - primitive compared to 4010 orig.}

SetRect(WindowRect, 0, 38, 511, 370);

SetdrawingRect(WindowRect);

ShowDrawing;

EraseRect(0, 0, 512, 512);

pen(1, 1);

{firstpoint := 270 - (trunc(intensity[2] / intennorm * 250.0));}

firstpoint := 71;

MoveTo(0, firstpoint);

for n := 2 to nth do

begin

i := n;

{if (nth = 1024) then}

{********i := n div 2;***********}

intensity[i] := intensity[i] + abs(intenmin);

yamp := 270 - (trunc(intensity[i] / intennorm * 250.0));

if nth <= 20 then

LineTo(n * 10, yamp)

else if (20 < nth) and (nth <= 100) then

LineTo(n * 5, yamp)

else if (100 < nth) then

LineTo(n div 2, yamp)

end;

while not button do

begin

end;

sysbeep(25);

end; {PlotData}

procedure SaveData;

var

n: integer;

begin

SetRect(WindowRect, 0, 38, 511, 370);

SetTextRect(WindowRect);

showtext;

write('Filename??? >');

readln(filename);

{filename := 'Calvin:ResultFile';}

rewrite(resultdata, filename);

for n := 2 to nth do

begin

i := n;

if (nth = 1024) then

i := n div 2;

intensity[i] := intensity[i] + abs(intenmin);

{yamp := 270 - (trunc(intensity[i] / intennorm * 250.0));}

yamp := (trunc(intensity[i] / intennorm * 250.0));

writeln(resultdata, n, ' ', yamp);

end;

sysbeep(25);

close(resultdata);

end; {SaveData}

{*********************************}

procedure Setup;

{READ SETUP PARAMETERS}

begin

SetRect(WindowRect, 0, 38, 511, 314);

SetTextRect(WindowRect);

ShowText;

write(' enter microwave frequency (GHz): ');

readln(frequency);

write(' enter hmin (in Gauss) : ');

readln(hmin);

write(' enter hmax : ');

readln(hmax);

write(' enter field increment (in Gauss) : ');

readln(hinc);

write(' enter g(x), g(y), g(z) --(separate with space: ');

read(gx, gy, gz);

writeln;

write(' Peak-to-peak linewidth (in Gauss) - ');

write(' enter hx= ');

readln(hx);

write(' enter hy= ');

readln(hy);

write(' enter hz= ');

readln(hz);

{naintx and nainty should be in multiples of 2 ; 32 is a good number to try}

write(' enter number of iterations in x (multiple of 2; 32 is good): ');

readln(naintx);

write(' enter number of iterations in y (usually same as x): ');

readln(nainty);

end; {Setup}

{*********************************}

procedure Iterate;

label

100, 105; {110, 115;}

var

i, j: integer;

begin

for i := 1 to 1500 do

begin

intensity[i] := 0.0;

end;

bi := 0.0;

ci := 0.0;

ee := hinc / 2.0;

nth := trunc(((hmax - hmin) / hinc) + 0.01);

nh := 0;

h := hmin;

g[1] := gx;

g[2] := gy;

g[3] := gz;

cc := (gx * gx + gy * gy + gz * gz) / 3.0;

cd := sqrt(cc);

ce := 0.666666 * cd + (gx + gy + gz) / 9.0;

100:

nh := nh + 1;

h := h + hinc;

105:

hi := fxyint(0.0, pi2, 0.0, pi2, naintx, nainty);

hi := hi / 0.000225;

bi := bi + hi * hinc;

ci := ci + (bi * hinc / ce);

intensity[nh] := hi;

e := hmax - h;

if (e > ee) then

goto 100;

intenmin := intensity[1];

intenmax := intensity[1];

intennorm := 0.0;

for i := 2 to nth do

begin

if (intensity[i] < intenmin) then

intenmin := intensity[i];

if (intensity[i] > intenmax) then

intenmax := intensity[i];

end;

intennorm := intenmax - intenmin;

for j := 1 to 3 do

begin

hg[j] := (6.62618e-27 * frequency * 1.0e09) / (bm * g[j]);

end;

sysbeep(25);

end; {Iterate}

{writeln(' H(gx) = ', hg[1] : 6 : 1);}

{writeln(' H(gy) = ', hg[2] : 6 : 1);}

{writeln(' H(gz) = ', hg[3] : 6 : 1);}

{******************************}

procedure Main;

begin

done := false;

repeat

Setup;

Iterate;

write('Plot data (y/n)? ');

readln(answer);

if answer = 'y' then

begin

writeln('Click the Mouse button to plot the simulation, and');

writeln('also after viewing the simulation.');

while not button do

begin

end;

plotdata;

SetRect(WindowRect, 0, 38, 511, 370);

SetTextRect(WindowRect);

showtext;

write('Save data (y/n)? ');

readln(answer);

if answer = 'y' then

saveData;

end

else

begin

write('Save data (y/n)? ');

readln(answer);

if answer = 'y' then

saveData;

end;

SetRect(WindowRect, 0, 38, 511, 370);

SetTextRect(WindowRect);

showtext;

write('Run again, or Quit (r/q)? ');

readln(answer);

if answer = 'q' then

done := true;

until done;

end; {Main}

begin

Main;

end.

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