manu_with_reference

This commit is contained in:
linjiez 2019-10-02 20:10:11 +02:00
parent b099a55761
commit 782925fba6
9 changed files with 23742 additions and 39 deletions

Binary file not shown.

816
figure/mass_spec.eps Normal file
View File

@ -0,0 +1,816 @@
%!PS-Adobe-2.0 EPSF-2.0
%%Title: mass_spec.eps
%%Creator: gnuplot 5.2 patchlevel 2
%%CreationDate: Tue Oct 1 18:10:29 2019
%%DocumentFonts: (atend)
%%BoundingBox: 50 50 900 900
%%EndComments
%%BeginProlog
/gnudict 256 dict def
gnudict begin
%
% The following true/false flags may be edited by hand if desired.
% The unit line width and grayscale image gamma correction may also be changed.
%
/Color true def
/Blacktext false def
/Solid false def
/Dashlength 1 def
/Landscape false def
/Level1 false def
/Level3 false def
/Rounded false def
/ClipToBoundingBox false def
/SuppressPDFMark false def
/TransparentPatterns false def
/gnulinewidth 15.000 def
/userlinewidth gnulinewidth def
/Gamma 1.0 def
/BackgroundColor {-1.000 -1.000 -1.000} def
%
/vshift -166 def
/dl1 {
10.0 Dashlength userlinewidth gnulinewidth div mul mul mul
Rounded { currentlinewidth 0.75 mul sub dup 0 le { pop 0.01 } if } if
} def
/dl2 {
10.0 Dashlength userlinewidth gnulinewidth div mul mul mul
Rounded { currentlinewidth 0.75 mul add } if
} def
/hpt_ 31.5 def
/vpt_ 31.5 def
/hpt hpt_ def
/vpt vpt_ def
/doclip {
ClipToBoundingBox {
newpath 50 50 moveto 900 50 lineto 900 900 lineto 50 900 lineto closepath
clip
} if
} def
%
% Gnuplot Prolog Version 5.1 (Oct 2015)
%
%/SuppressPDFMark true def
%
/M {moveto} bind def
/L {lineto} bind def
/R {rmoveto} bind def
/V {rlineto} bind def
/N {newpath moveto} bind def
/Z {closepath} bind def
/C {setrgbcolor} bind def
/f {rlineto fill} bind def
/g {setgray} bind def
/Gshow {show} def % May be redefined later in the file to support UTF-8
/vpt2 vpt 2 mul def
/hpt2 hpt 2 mul def
/Lshow {currentpoint stroke M 0 vshift R
Blacktext {gsave 0 setgray textshow grestore} {textshow} ifelse} def
/Rshow {currentpoint stroke M dup stringwidth pop neg vshift R
Blacktext {gsave 0 setgray textshow grestore} {textshow} ifelse} def
/Cshow {currentpoint stroke M dup stringwidth pop -2 div vshift R
Blacktext {gsave 0 setgray textshow grestore} {textshow} ifelse} def
/UP {dup vpt_ mul /vpt exch def hpt_ mul /hpt exch def
/hpt2 hpt 2 mul def /vpt2 vpt 2 mul def} def
/DL {Color {setrgbcolor Solid {pop []} if 0 setdash}
{pop pop pop 0 setgray Solid {pop []} if 0 setdash} ifelse} def
/BL {stroke userlinewidth 2 mul setlinewidth
Rounded {1 setlinejoin 1 setlinecap} if} def
/AL {stroke userlinewidth 2 div setlinewidth
Rounded {1 setlinejoin 1 setlinecap} if} def
/UL {dup gnulinewidth mul /userlinewidth exch def
dup 1 lt {pop 1} if 10 mul /udl exch def} def
/PL {stroke userlinewidth setlinewidth
Rounded {1 setlinejoin 1 setlinecap} if} def
3.8 setmiterlimit
% Classic Line colors (version 5.0)
/LCw {1 1 1} def
/LCb {0 0 0} def
/LCa {0 0 0} def
/LC0 {1 0 0} def
/LC1 {0 1 0} def
/LC2 {0 0 1} def
/LC3 {1 0 1} def
/LC4 {0 1 1} def
/LC5 {1 1 0} def
/LC6 {0 0 0} def
/LC7 {1 0.3 0} def
/LC8 {0.5 0.5 0.5} def
% Default dash patterns (version 5.0)
/LTB {BL [] LCb DL} def
/LTw {PL [] 1 setgray} def
/LTb {PL [] LCb DL} def
/LTa {AL [1 udl mul 2 udl mul] 0 setdash LCa setrgbcolor} def
/LT0 {PL [] LC0 DL} def
/LT1 {PL [2 dl1 3 dl2] LC1 DL} def
/LT2 {PL [1 dl1 1.5 dl2] LC2 DL} def
/LT3 {PL [6 dl1 2 dl2 1 dl1 2 dl2] LC3 DL} def
/LT4 {PL [1 dl1 2 dl2 6 dl1 2 dl2 1 dl1 2 dl2] LC4 DL} def
/LT5 {PL [4 dl1 2 dl2] LC5 DL} def
/LT6 {PL [1.5 dl1 1.5 dl2 1.5 dl1 1.5 dl2 1.5 dl1 6 dl2] LC6 DL} def
/LT7 {PL [3 dl1 3 dl2 1 dl1 3 dl2] LC7 DL} def
/LT8 {PL [2 dl1 2 dl2 2 dl1 6 dl2] LC8 DL} def
/SL {[] 0 setdash} def
/Pnt {stroke [] 0 setdash gsave 1 setlinecap M 0 0 V stroke grestore} def
/Dia {stroke [] 0 setdash 2 copy vpt add M
hpt neg vpt neg V hpt vpt neg V
hpt vpt V hpt neg vpt V closepath stroke
Pnt} def
/Pls {stroke [] 0 setdash vpt sub M 0 vpt2 V
currentpoint stroke M
hpt neg vpt neg R hpt2 0 V stroke
} def
/Box {stroke [] 0 setdash 2 copy exch hpt sub exch vpt add M
0 vpt2 neg V hpt2 0 V 0 vpt2 V
hpt2 neg 0 V closepath stroke
Pnt} def
/Crs {stroke [] 0 setdash exch hpt sub exch vpt add M
hpt2 vpt2 neg V currentpoint stroke M
hpt2 neg 0 R hpt2 vpt2 V stroke} def
/TriU {stroke [] 0 setdash 2 copy vpt 1.12 mul add M
hpt neg vpt -1.62 mul V
hpt 2 mul 0 V
hpt neg vpt 1.62 mul V closepath stroke
Pnt} def
/Star {2 copy Pls Crs} def
/BoxF {stroke [] 0 setdash exch hpt sub exch vpt add M
0 vpt2 neg V hpt2 0 V 0 vpt2 V
hpt2 neg 0 V closepath fill} def
/TriUF {stroke [] 0 setdash vpt 1.12 mul add M
hpt neg vpt -1.62 mul V
hpt 2 mul 0 V
hpt neg vpt 1.62 mul V closepath fill} def
/TriD {stroke [] 0 setdash 2 copy vpt 1.12 mul sub M
hpt neg vpt 1.62 mul V
hpt 2 mul 0 V
hpt neg vpt -1.62 mul V closepath stroke
Pnt} def
/TriDF {stroke [] 0 setdash vpt 1.12 mul sub M
hpt neg vpt 1.62 mul V
hpt 2 mul 0 V
hpt neg vpt -1.62 mul V closepath fill} def
/DiaF {stroke [] 0 setdash vpt add M
hpt neg vpt neg V hpt vpt neg V
hpt vpt V hpt neg vpt V closepath fill} def
/Pent {stroke [] 0 setdash 2 copy gsave
translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
closepath stroke grestore Pnt} def
/PentF {stroke [] 0 setdash gsave
translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
closepath fill grestore} def
/Circle {stroke [] 0 setdash 2 copy
hpt 0 360 arc stroke Pnt} def
/CircleF {stroke [] 0 setdash hpt 0 360 arc fill} def
/C0 {BL [] 0 setdash 2 copy moveto vpt 90 450 arc} bind def
/C1 {BL [] 0 setdash 2 copy moveto
2 copy vpt 0 90 arc closepath fill
vpt 0 360 arc closepath} bind def
/C2 {BL [] 0 setdash 2 copy moveto
2 copy vpt 90 180 arc closepath fill
vpt 0 360 arc closepath} bind def
/C3 {BL [] 0 setdash 2 copy moveto
2 copy vpt 0 180 arc closepath fill
vpt 0 360 arc closepath} bind def
/C4 {BL [] 0 setdash 2 copy moveto
2 copy vpt 180 270 arc closepath fill
vpt 0 360 arc closepath} bind def
/C5 {BL [] 0 setdash 2 copy moveto
2 copy vpt 0 90 arc
2 copy moveto
2 copy vpt 180 270 arc closepath fill
vpt 0 360 arc} bind def
/C6 {BL [] 0 setdash 2 copy moveto
2 copy vpt 90 270 arc closepath fill
vpt 0 360 arc closepath} bind def
/C7 {BL [] 0 setdash 2 copy moveto
2 copy vpt 0 270 arc closepath fill
vpt 0 360 arc closepath} bind def
/C8 {BL [] 0 setdash 2 copy moveto
2 copy vpt 270 360 arc closepath fill
vpt 0 360 arc closepath} bind def
/C9 {BL [] 0 setdash 2 copy moveto
2 copy vpt 270 450 arc closepath fill
vpt 0 360 arc closepath} bind def
/C10 {BL [] 0 setdash 2 copy 2 copy moveto vpt 270 360 arc closepath fill
2 copy moveto
2 copy vpt 90 180 arc closepath fill
vpt 0 360 arc closepath} bind def
/C11 {BL [] 0 setdash 2 copy moveto
2 copy vpt 0 180 arc closepath fill
2 copy moveto
2 copy vpt 270 360 arc closepath fill
vpt 0 360 arc closepath} bind def
/C12 {BL [] 0 setdash 2 copy moveto
2 copy vpt 180 360 arc closepath fill
vpt 0 360 arc closepath} bind def
/C13 {BL [] 0 setdash 2 copy moveto
2 copy vpt 0 90 arc closepath fill
2 copy moveto
2 copy vpt 180 360 arc closepath fill
vpt 0 360 arc closepath} bind def
/C14 {BL [] 0 setdash 2 copy moveto
2 copy vpt 90 360 arc closepath fill
vpt 0 360 arc} bind def
/C15 {BL [] 0 setdash 2 copy vpt 0 360 arc closepath fill
vpt 0 360 arc closepath} bind def
/Rec {newpath 4 2 roll moveto 1 index 0 rlineto 0 exch rlineto
neg 0 rlineto closepath} bind def
/Square {dup Rec} bind def
/Bsquare {vpt sub exch vpt sub exch vpt2 Square} bind def
/S0 {BL [] 0 setdash 2 copy moveto 0 vpt rlineto BL Bsquare} bind def
/S1 {BL [] 0 setdash 2 copy vpt Square fill Bsquare} bind def
/S2 {BL [] 0 setdash 2 copy exch vpt sub exch vpt Square fill Bsquare} bind def
/S3 {BL [] 0 setdash 2 copy exch vpt sub exch vpt2 vpt Rec fill Bsquare} bind def
/S4 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt Square fill Bsquare} bind def
/S5 {BL [] 0 setdash 2 copy 2 copy vpt Square fill
exch vpt sub exch vpt sub vpt Square fill Bsquare} bind def
/S6 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt vpt2 Rec fill Bsquare} bind def
/S7 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt vpt2 Rec fill
2 copy vpt Square fill Bsquare} bind def
/S8 {BL [] 0 setdash 2 copy vpt sub vpt Square fill Bsquare} bind def
/S9 {BL [] 0 setdash 2 copy vpt sub vpt vpt2 Rec fill Bsquare} bind def
/S10 {BL [] 0 setdash 2 copy vpt sub vpt Square fill 2 copy exch vpt sub exch vpt Square fill
Bsquare} bind def
/S11 {BL [] 0 setdash 2 copy vpt sub vpt Square fill 2 copy exch vpt sub exch vpt2 vpt Rec fill
Bsquare} bind def
/S12 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt2 vpt Rec fill Bsquare} bind def
/S13 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt2 vpt Rec fill
2 copy vpt Square fill Bsquare} bind def
/S14 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt2 vpt Rec fill
2 copy exch vpt sub exch vpt Square fill Bsquare} bind def
/S15 {BL [] 0 setdash 2 copy Bsquare fill Bsquare} bind def
/D0 {gsave translate 45 rotate 0 0 S0 stroke grestore} bind def
/D1 {gsave translate 45 rotate 0 0 S1 stroke grestore} bind def
/D2 {gsave translate 45 rotate 0 0 S2 stroke grestore} bind def
/D3 {gsave translate 45 rotate 0 0 S3 stroke grestore} bind def
/D4 {gsave translate 45 rotate 0 0 S4 stroke grestore} bind def
/D5 {gsave translate 45 rotate 0 0 S5 stroke grestore} bind def
/D6 {gsave translate 45 rotate 0 0 S6 stroke grestore} bind def
/D7 {gsave translate 45 rotate 0 0 S7 stroke grestore} bind def
/D8 {gsave translate 45 rotate 0 0 S8 stroke grestore} bind def
/D9 {gsave translate 45 rotate 0 0 S9 stroke grestore} bind def
/D10 {gsave translate 45 rotate 0 0 S10 stroke grestore} bind def
/D11 {gsave translate 45 rotate 0 0 S11 stroke grestore} bind def
/D12 {gsave translate 45 rotate 0 0 S12 stroke grestore} bind def
/D13 {gsave translate 45 rotate 0 0 S13 stroke grestore} bind def
/D14 {gsave translate 45 rotate 0 0 S14 stroke grestore} bind def
/D15 {gsave translate 45 rotate 0 0 S15 stroke grestore} bind def
/DiaE {stroke [] 0 setdash vpt add M
hpt neg vpt neg V hpt vpt neg V
hpt vpt V hpt neg vpt V closepath stroke} def
/BoxE {stroke [] 0 setdash exch hpt sub exch vpt add M
0 vpt2 neg V hpt2 0 V 0 vpt2 V
hpt2 neg 0 V closepath stroke} def
/TriUE {stroke [] 0 setdash vpt 1.12 mul add M
hpt neg vpt -1.62 mul V
hpt 2 mul 0 V
hpt neg vpt 1.62 mul V closepath stroke} def
/TriDE {stroke [] 0 setdash vpt 1.12 mul sub M
hpt neg vpt 1.62 mul V
hpt 2 mul 0 V
hpt neg vpt -1.62 mul V closepath stroke} def
/PentE {stroke [] 0 setdash gsave
translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
closepath stroke grestore} def
/CircE {stroke [] 0 setdash
hpt 0 360 arc stroke} def
/Opaque {gsave closepath 1 setgray fill grestore 0 setgray closepath} def
/DiaW {stroke [] 0 setdash vpt add M
hpt neg vpt neg V hpt vpt neg V
hpt vpt V hpt neg vpt V Opaque stroke} def
/BoxW {stroke [] 0 setdash exch hpt sub exch vpt add M
0 vpt2 neg V hpt2 0 V 0 vpt2 V
hpt2 neg 0 V Opaque stroke} def
/TriUW {stroke [] 0 setdash vpt 1.12 mul add M
hpt neg vpt -1.62 mul V
hpt 2 mul 0 V
hpt neg vpt 1.62 mul V Opaque stroke} def
/TriDW {stroke [] 0 setdash vpt 1.12 mul sub M
hpt neg vpt 1.62 mul V
hpt 2 mul 0 V
hpt neg vpt -1.62 mul V Opaque stroke} def
/PentW {stroke [] 0 setdash gsave
translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
Opaque stroke grestore} def
/CircW {stroke [] 0 setdash
hpt 0 360 arc Opaque stroke} def
/BoxFill {gsave Rec 1 setgray fill grestore} def
/Density {
/Fillden exch def
currentrgbcolor
/ColB exch def /ColG exch def /ColR exch def
/ColR ColR Fillden mul Fillden sub 1 add def
/ColG ColG Fillden mul Fillden sub 1 add def
/ColB ColB Fillden mul Fillden sub 1 add def
ColR ColG ColB setrgbcolor} def
/BoxColFill {gsave Rec PolyFill} def
/PolyFill {gsave Density fill grestore grestore} def
/h {rlineto rlineto rlineto gsave closepath fill grestore} bind def
%
% PostScript Level 1 Pattern Fill routine for rectangles
% Usage: x y w h s a XX PatternFill
% x,y = lower left corner of box to be filled
% w,h = width and height of box
% a = angle in degrees between lines and x-axis
% XX = 0/1 for no/yes cross-hatch
%
/PatternFill {gsave /PFa [ 9 2 roll ] def
PFa 0 get PFa 2 get 2 div add PFa 1 get PFa 3 get 2 div add translate
PFa 2 get -2 div PFa 3 get -2 div PFa 2 get PFa 3 get Rec
TransparentPatterns {} {gsave 1 setgray fill grestore} ifelse
clip
currentlinewidth 0.5 mul setlinewidth
/PFs PFa 2 get dup mul PFa 3 get dup mul add sqrt def
0 0 M PFa 5 get rotate PFs -2 div dup translate
0 1 PFs PFa 4 get div 1 add floor cvi
{PFa 4 get mul 0 M 0 PFs V} for
0 PFa 6 get ne {
0 1 PFs PFa 4 get div 1 add floor cvi
{PFa 4 get mul 0 2 1 roll M PFs 0 V} for
} if
stroke grestore} def
%
/languagelevel where
{pop languagelevel} {1} ifelse
dup 2 lt
{/InterpretLevel1 true def
/InterpretLevel3 false def}
{/InterpretLevel1 Level1 def
2 gt
{/InterpretLevel3 Level3 def}
{/InterpretLevel3 false def}
ifelse }
ifelse
%
% PostScript level 2 pattern fill definitions
%
/Level2PatternFill {
/Tile8x8 {/PaintType 2 /PatternType 1 /TilingType 1 /BBox [0 0 8 8] /XStep 8 /YStep 8}
bind def
/KeepColor {currentrgbcolor [/Pattern /DeviceRGB] setcolorspace} bind def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop 0 0 M 8 8 L 0 8 M 8 0 L stroke}
>> matrix makepattern
/Pat1 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop 0 0 M 8 8 L 0 8 M 8 0 L stroke
0 4 M 4 8 L 8 4 L 4 0 L 0 4 L stroke}
>> matrix makepattern
/Pat2 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop 0 0 M 0 8 L
8 8 L 8 0 L 0 0 L fill}
>> matrix makepattern
/Pat3 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop -4 8 M 8 -4 L
0 12 M 12 0 L stroke}
>> matrix makepattern
/Pat4 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop -4 0 M 8 12 L
0 -4 M 12 8 L stroke}
>> matrix makepattern
/Pat5 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop -2 8 M 4 -4 L
0 12 M 8 -4 L 4 12 M 10 0 L stroke}
>> matrix makepattern
/Pat6 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop -2 0 M 4 12 L
0 -4 M 8 12 L 4 -4 M 10 8 L stroke}
>> matrix makepattern
/Pat7 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop 8 -2 M -4 4 L
12 0 M -4 8 L 12 4 M 0 10 L stroke}
>> matrix makepattern
/Pat8 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop 0 -2 M 12 4 L
-4 0 M 12 8 L -4 4 M 8 10 L stroke}
>> matrix makepattern
/Pat9 exch def
/Pattern1 {PatternBgnd KeepColor Pat1 setpattern} bind def
/Pattern2 {PatternBgnd KeepColor Pat2 setpattern} bind def
/Pattern3 {PatternBgnd KeepColor Pat3 setpattern} bind def
/Pattern4 {PatternBgnd KeepColor Landscape {Pat5} {Pat4} ifelse setpattern} bind def
/Pattern5 {PatternBgnd KeepColor Landscape {Pat4} {Pat5} ifelse setpattern} bind def
/Pattern6 {PatternBgnd KeepColor Landscape {Pat9} {Pat6} ifelse setpattern} bind def
/Pattern7 {PatternBgnd KeepColor Landscape {Pat8} {Pat7} ifelse setpattern} bind def
} def
%
%
%End of PostScript Level 2 code
%
/PatternBgnd {
TransparentPatterns {} {gsave 1 setgray fill grestore} ifelse
} def
%
% Substitute for Level 2 pattern fill codes with
% grayscale if Level 2 support is not selected.
%
/Level1PatternFill {
/Pattern1 {0.250 Density} bind def
/Pattern2 {0.500 Density} bind def
/Pattern3 {0.750 Density} bind def
/Pattern4 {0.125 Density} bind def
/Pattern5 {0.375 Density} bind def
/Pattern6 {0.625 Density} bind def
/Pattern7 {0.875 Density} bind def
} def
%
% Now test for support of Level 2 code
%
Level1 {Level1PatternFill} {Level2PatternFill} ifelse
%
/Symbol-Oblique /Symbol findfont [1 0 .167 1 0 0] makefont
dup length dict begin {1 index /FID eq {pop pop} {def} ifelse} forall
currentdict end definefont pop
%
/Metrics {ExtendTextBox Gswidth} def
/Lwidth {currentpoint stroke M 0 vshift R Metrics} def
/Rwidth {currentpoint stroke M dup stringwidth pop neg vshift R Metrics} def
/Cwidth {currentpoint stroke M dup stringwidth pop -2 div vshift R Metrics} def
/GLwidth {currentpoint stroke M 0 vshift R {ExtendTextBox} forall} def
/GRwidth {currentpoint stroke M dup Gwidth vshift R {ExtendTextBox} forall} def
/GCwidth {currentpoint stroke M dup Gwidth 2 div vshift R {ExtendTextBox} forall} def
/GLwidth2 {0 Gwidth AddGlyphWidth} def
/GRwidth2 {Gwidth -1 mul 0 AddGlyphWidth} def
/GCwidth2 {Gwidth 2 div dup -1 mul AddGlyphWidth} def
/AddGlyphWidth { dup TBx2 gt {userdict /TBx2 3 -1 roll put} {pop} ifelse
dup TBx1 lt {userdict /TBx1 3 -1 roll put} {pop} ifelse } def
/MFshow {
{ dup 5 get 3 ge
{ 5 get 3 eq {gsave} {grestore} ifelse }
{dup dup 0 get findfont exch 1 get scalefont setfont
[ currentpoint ] exch dup 2 get 0 exch R dup 5 get 2 ne {dup dup 6
get exch 4 get {textshow} {Metrics pop 0 R} ifelse }if dup 5 get 0 eq
{dup 3 get {2 get neg 0 exch R pop} {pop aload pop M} ifelse} {dup 5
get 1 eq {dup 2 get exch dup 3 get exch 6 get Gswidth pop -2 div
dup 0 R} {dup 6 get Gswidth pop -2 div 0 R 6 get
textshow 2 index {aload pop M neg 3 -1 roll neg R pop pop} {pop pop pop
pop aload pop M} ifelse }ifelse }ifelse }
ifelse }
forall} def
/Gswidth {dup type /stringtype eq {stringwidth} {pop (n) stringwidth} ifelse} def
/MFwidth {0 exch { dup 5 get 3 ge { 5 get 3 eq { 0 } { pop } ifelse }
{dup 3 get{dup dup 0 get findfont exch 1 get scalefont setfont
6 get Gswidth pop add} {pop} ifelse} ifelse} forall} def
/MLshow { currentpoint stroke M
0 exch R
Blacktext {gsave 0 setgray MFshow grestore} {MFshow} ifelse } bind def
/MRshow { currentpoint stroke M
exch dup MFwidth neg 3 -1 roll R
Blacktext {gsave 0 setgray MFshow grestore} {MFshow} ifelse } bind def
/MCshow { currentpoint stroke M
exch dup MFwidth -2 div 3 -1 roll R
Blacktext {gsave 0 setgray MFshow grestore} {MFshow} ifelse } bind def
/XYsave { [( ) 1 2 true false 3 ()] } bind def
/XYrestore { [( ) 1 2 true false 4 ()] } bind def
Level1 SuppressPDFMark or
{} {
/SDict 10 dict def
systemdict /pdfmark known not {
userdict /pdfmark systemdict /cleartomark get put
} if
SDict begin [
/Title (mass_spec.eps)
/Subject (gnuplot plot)
/Creator (gnuplot 5.2 patchlevel 2)
% /Producer (gnuplot)
% /Keywords ()
/CreationDate (Tue Oct 1 18:10:29 2019)
/DOCINFO pdfmark
end
} ifelse
%
% Support for boxed text - Ethan A Merritt Sep 2016
%
/InitTextBox { userdict /TBy2 3 -1 roll put userdict /TBx2 3 -1 roll put
userdict /TBy1 3 -1 roll put userdict /TBx1 3 -1 roll put
/Boxing true def } def
/ExtendTextBox { dup type /stringtype eq
{ Boxing { gsave dup false charpath pathbbox
dup TBy2 gt {userdict /TBy2 3 -1 roll put} {pop} ifelse
dup TBx2 gt {userdict /TBx2 3 -1 roll put} {pop} ifelse
dup TBy1 lt {userdict /TBy1 3 -1 roll put} {pop} ifelse
dup TBx1 lt {userdict /TBx1 3 -1 roll put} {pop} ifelse
grestore } if }
{} ifelse} def
/PopTextBox { newpath TBx1 TBxmargin sub TBy1 TBymargin sub M
TBx1 TBxmargin sub TBy2 TBymargin add L
TBx2 TBxmargin add TBy2 TBymargin add L
TBx2 TBxmargin add TBy1 TBymargin sub L closepath } def
/DrawTextBox { PopTextBox stroke /Boxing false def} def
/FillTextBox { gsave PopTextBox fill grestore /Boxing false def} def
0 0 0 0 InitTextBox
/TBxmargin 20 def
/TBymargin 20 def
/Boxing false def
/textshow { ExtendTextBox Gshow } def
%
end
%%EndProlog
%%Page: 1 1
gnudict begin
gsave
doclip
50 50 translate
0.050 0.050 scale
0 setgray
newpath
(Times-New-Roman) findfont 500 scalefont setfont
BackgroundColor 0 lt 3 1 roll 0 lt exch 0 lt or or not {BackgroundColor C 1.000 0 0 17006.00 17006.00 BoxColFill} if
1.000 UL
LTb
LCb setrgbcolor
2150 1600 M
63 0 V
13892 0 R
-63 0 V
stroke
1850 1600 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 0)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
2150 3587 M
63 0 V
13892 0 R
-63 0 V
stroke
1850 3587 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 10)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
2150 5575 M
63 0 V
13892 0 R
-63 0 V
stroke
1850 5575 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 20)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
2150 7562 M
63 0 V
13892 0 R
-63 0 V
stroke
1850 7562 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 30)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
2150 9549 M
63 0 V
13892 0 R
-63 0 V
stroke
1850 9549 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 40)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
2150 11537 M
63 0 V
13892 0 R
-63 0 V
stroke
1850 11537 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 50)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
2150 13524 M
63 0 V
13892 0 R
-63 0 V
stroke
1850 13524 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 60)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
2150 15511 M
63 0 V
13892 0 R
-63 0 V
stroke
1850 15511 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 70)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
2150 1600 M
0 63 V
0 14842 R
0 -63 V
stroke
2150 1100 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 50)]
] -233.3 MCshow
1.000 UL
LTb
LCb setrgbcolor
5639 1600 M
0 63 V
0 14842 R
0 -63 V
stroke
5639 1100 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 100)]
] -233.3 MCshow
1.000 UL
LTb
LCb setrgbcolor
9128 1600 M
0 63 V
0 14842 R
0 -63 V
stroke
9128 1100 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 150)]
] -233.3 MCshow
1.000 UL
LTb
LCb setrgbcolor
12616 1600 M
0 63 V
0 14842 R
0 -63 V
stroke
12616 1100 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 200)]
] -233.3 MCshow
1.000 UL
LTb
LCb setrgbcolor
16105 1600 M
0 63 V
0 14842 R
0 -63 V
stroke
16105 1100 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 ( 250)]
] -233.3 MCshow
1.000 UL
LTb
LCb setrgbcolor
1.000 UL
LTB
LCb setrgbcolor
2150 16505 N
0 -14905 V
13955 0 V
0 14905 V
-13955 0 V
Z stroke
1.000 UP
1.00 0.00 0.00 C 5709 2594 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 (n=6)]
] -233.3 MLshow
1.00 0.00 0.00 C 6964 2395 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 (n=7)]
] -233.3 MLshow
0.00 0.00 1.00 C 8500 2196 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 (n=2)]
] -233.3 MLshow
0.00 0.00 1.00 C 9755 2395 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 (n=3)]
] -233.3 MLshow
0.00 0.00 1.00 C 11011 2792 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 (n=4)]
] -233.3 MLshow
0.00 0.00 1.00 C 12267 3587 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 (n=5)]
] -233.3 MLshow
0.00 0.00 1.00 C 13523 5773 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 (n=6)]
] -233.3 MLshow
0.00 0.00 1.00 C 14779 14915 M
[ [(Times-New-Roman) 700.0 0.0 true true 0 (n=7)]
] -233.3 MLshow
LCb setrgbcolor
2778 15710 M
[ [(Times-New-Roman) 900.0 0.0 true true 0 (\(a\))]
] -300.0 MLshow
1.000 UL
LTb
LCb setrgbcolor
LCb setrgbcolor
450 9052 M
currentpoint gsave translate -270 rotate 0 0 moveto
[ [(Times-New-Roman) 900.0 0.0 true true 0 (Intensity \(arbitrary units\))]
] -300.0 MCshow
grestore
LTb
LCb setrgbcolor
9127 350 M
[ [(Times-New-Roman) 900.0 0.0 true true 0 (m/z \(Da\))]
] -300.0 MCshow
LTb
% Begin plot #1
3.500 UL
LTb
1.00 0.00 0.00 C LCb setrgbcolor
9396 15942 M
[ [(Times-New-Roman) 500.0 0.0 true true 0 (\(H)]
[(Times-New-Roman) 400.0 -150.0 true true 0 (2)]
[(Times-New-Roman) 500.0 0.0 true true 0 (O\))]
[(Times-New-Roman) 400.0 -150.0 true true 0 (n)]
[(Times-New-Roman) 500.0 0.0 true true 0 (H)]
[(Times-New-Roman) 400.0 250.0 true true 0 (+)]
] -166.7 MRshow
3.500 UL
LTb
1.00 0.00 0.00 C 9696 15942 M
1263 0 V
2499 1600 M
1256 0 R
1256 0 R
1256 0 R
0 521 V
7523 1600 M
0 425 V
6546 1600 M
1256 0 R
1256 0 R
1256 0 R
1256 0 R
1256 0 R
1256 0 R
1255 0 R
% End plot #1
% Begin plot #2
stroke
LTb
0.00 0.00 1.00 C LCb setrgbcolor
9396 14942 M
[ [(Times-New-Roman) 500.0 0.0 true true 0 (U\(H)]
[(Times-New-Roman) 400.0 -150.0 true true 0 (2)]
[(Times-New-Roman) 500.0 0.0 true true 0 (O\))]
[(Times-New-Roman) 400.0 -150.0 true true 0 (n)]
[(Times-New-Roman) 500.0 0.0 true true 0 (H)]
[(Times-New-Roman) 400.0 250.0 true true 0 (+)]
] -166.7 MRshow
3.500 UL
LTb
0.00 0.00 1.00 C 9696 14942 M
1263 0 V
2499 1600 M
1256 0 R
1256 0 R
1256 0 R
1256 0 R
-977 0 R
1256 0 R
0 14 V
1256 -14 R
0 81 V
1256 -81 R
0 318 V
1256 -318 R
0 727 V
1256 -727 R
0 1502 V
14082 1600 M
0 3595 V
15337 1600 M
0 12685 V
% End plot #2
stroke
2.000 UL
LTb
LCb setrgbcolor
1.000 UL
LTB
LCb setrgbcolor
2150 16505 N
0 -14905 V
13955 0 V
0 14905 V
-13955 0 V
Z stroke
1.000 UP
1.000 UL
LTb
LCb setrgbcolor
stroke
grestore
end
showpage
%%Trailer
%%DocumentFonts: Times-New-Roman

835
figure/mass_spec.png Normal file
View File

@ -0,0 +1,835 @@
%!PS-Adobe-2.0
%%Title: mass_spec.png
%%Creator: gnuplot 5.2 patchlevel 2
%%CreationDate: Tue Oct 1 18:03:38 2019
%%DocumentFonts: (atend)
%%BoundingBox: 50 50 554 770
%%Orientation: Landscape
%%Pages: (atend)
%%EndComments
%%BeginProlog
/gnudict 256 dict def
gnudict begin
%
% The following true/false flags may be edited by hand if desired.
% The unit line width and grayscale image gamma correction may also be changed.
%
/Color false def
/Blacktext false def
/Solid false def
/Dashlength 1 def
/Landscape true def
/Level1 false def
/Level3 false def
/Rounded false def
/ClipToBoundingBox false def
/SuppressPDFMark false def
/TransparentPatterns false def
/gnulinewidth 5.000 def
/userlinewidth gnulinewidth def
/Gamma 1.0 def
/BackgroundColor {-1.000 -1.000 -1.000} def
%
/vshift -46 def
/dl1 {
10.0 Dashlength userlinewidth gnulinewidth div mul mul mul
Rounded { currentlinewidth 0.75 mul sub dup 0 le { pop 0.01 } if } if
} def
/dl2 {
10.0 Dashlength userlinewidth gnulinewidth div mul mul mul
Rounded { currentlinewidth 0.75 mul add } if
} def
/hpt_ 31.5 def
/vpt_ 31.5 def
/hpt hpt_ def
/vpt vpt_ def
/doclip {
ClipToBoundingBox {
newpath 50 50 moveto 554 50 lineto 554 770 lineto 50 770 lineto closepath
clip
} if
} def
%
% Gnuplot Prolog Version 5.1 (Oct 2015)
%
%/SuppressPDFMark true def
%
/M {moveto} bind def
/L {lineto} bind def
/R {rmoveto} bind def
/V {rlineto} bind def
/N {newpath moveto} bind def
/Z {closepath} bind def
/C {setrgbcolor} bind def
/f {rlineto fill} bind def
/g {setgray} bind def
/Gshow {show} def % May be redefined later in the file to support UTF-8
/vpt2 vpt 2 mul def
/hpt2 hpt 2 mul def
/Lshow {currentpoint stroke M 0 vshift R
Blacktext {gsave 0 setgray textshow grestore} {textshow} ifelse} def
/Rshow {currentpoint stroke M dup stringwidth pop neg vshift R
Blacktext {gsave 0 setgray textshow grestore} {textshow} ifelse} def
/Cshow {currentpoint stroke M dup stringwidth pop -2 div vshift R
Blacktext {gsave 0 setgray textshow grestore} {textshow} ifelse} def
/UP {dup vpt_ mul /vpt exch def hpt_ mul /hpt exch def
/hpt2 hpt 2 mul def /vpt2 vpt 2 mul def} def
/DL {Color {setrgbcolor Solid {pop []} if 0 setdash}
{pop pop pop 0 setgray Solid {pop []} if 0 setdash} ifelse} def
/BL {stroke userlinewidth 2 mul setlinewidth
Rounded {1 setlinejoin 1 setlinecap} if} def
/AL {stroke userlinewidth 2 div setlinewidth
Rounded {1 setlinejoin 1 setlinecap} if} def
/UL {dup gnulinewidth mul /userlinewidth exch def
dup 1 lt {pop 1} if 10 mul /udl exch def} def
/PL {stroke userlinewidth setlinewidth
Rounded {1 setlinejoin 1 setlinecap} if} def
3.8 setmiterlimit
% Classic Line colors (version 5.0)
/LCw {1 1 1} def
/LCb {0 0 0} def
/LCa {0 0 0} def
/LC0 {1 0 0} def
/LC1 {0 1 0} def
/LC2 {0 0 1} def
/LC3 {1 0 1} def
/LC4 {0 1 1} def
/LC5 {1 1 0} def
/LC6 {0 0 0} def
/LC7 {1 0.3 0} def
/LC8 {0.5 0.5 0.5} def
% Default dash patterns (version 5.0)
/LTB {BL [] LCb DL} def
/LTw {PL [] 1 setgray} def
/LTb {PL [] LCb DL} def
/LTa {AL [1 udl mul 2 udl mul] 0 setdash LCa setrgbcolor} def
/LT0 {PL [] LC0 DL} def
/LT1 {PL [2 dl1 3 dl2] LC1 DL} def
/LT2 {PL [1 dl1 1.5 dl2] LC2 DL} def
/LT3 {PL [6 dl1 2 dl2 1 dl1 2 dl2] LC3 DL} def
/LT4 {PL [1 dl1 2 dl2 6 dl1 2 dl2 1 dl1 2 dl2] LC4 DL} def
/LT5 {PL [4 dl1 2 dl2] LC5 DL} def
/LT6 {PL [1.5 dl1 1.5 dl2 1.5 dl1 1.5 dl2 1.5 dl1 6 dl2] LC6 DL} def
/LT7 {PL [3 dl1 3 dl2 1 dl1 3 dl2] LC7 DL} def
/LT8 {PL [2 dl1 2 dl2 2 dl1 6 dl2] LC8 DL} def
/SL {[] 0 setdash} def
/Pnt {stroke [] 0 setdash gsave 1 setlinecap M 0 0 V stroke grestore} def
/Dia {stroke [] 0 setdash 2 copy vpt add M
hpt neg vpt neg V hpt vpt neg V
hpt vpt V hpt neg vpt V closepath stroke
Pnt} def
/Pls {stroke [] 0 setdash vpt sub M 0 vpt2 V
currentpoint stroke M
hpt neg vpt neg R hpt2 0 V stroke
} def
/Box {stroke [] 0 setdash 2 copy exch hpt sub exch vpt add M
0 vpt2 neg V hpt2 0 V 0 vpt2 V
hpt2 neg 0 V closepath stroke
Pnt} def
/Crs {stroke [] 0 setdash exch hpt sub exch vpt add M
hpt2 vpt2 neg V currentpoint stroke M
hpt2 neg 0 R hpt2 vpt2 V stroke} def
/TriU {stroke [] 0 setdash 2 copy vpt 1.12 mul add M
hpt neg vpt -1.62 mul V
hpt 2 mul 0 V
hpt neg vpt 1.62 mul V closepath stroke
Pnt} def
/Star {2 copy Pls Crs} def
/BoxF {stroke [] 0 setdash exch hpt sub exch vpt add M
0 vpt2 neg V hpt2 0 V 0 vpt2 V
hpt2 neg 0 V closepath fill} def
/TriUF {stroke [] 0 setdash vpt 1.12 mul add M
hpt neg vpt -1.62 mul V
hpt 2 mul 0 V
hpt neg vpt 1.62 mul V closepath fill} def
/TriD {stroke [] 0 setdash 2 copy vpt 1.12 mul sub M
hpt neg vpt 1.62 mul V
hpt 2 mul 0 V
hpt neg vpt -1.62 mul V closepath stroke
Pnt} def
/TriDF {stroke [] 0 setdash vpt 1.12 mul sub M
hpt neg vpt 1.62 mul V
hpt 2 mul 0 V
hpt neg vpt -1.62 mul V closepath fill} def
/DiaF {stroke [] 0 setdash vpt add M
hpt neg vpt neg V hpt vpt neg V
hpt vpt V hpt neg vpt V closepath fill} def
/Pent {stroke [] 0 setdash 2 copy gsave
translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
closepath stroke grestore Pnt} def
/PentF {stroke [] 0 setdash gsave
translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
closepath fill grestore} def
/Circle {stroke [] 0 setdash 2 copy
hpt 0 360 arc stroke Pnt} def
/CircleF {stroke [] 0 setdash hpt 0 360 arc fill} def
/C0 {BL [] 0 setdash 2 copy moveto vpt 90 450 arc} bind def
/C1 {BL [] 0 setdash 2 copy moveto
2 copy vpt 0 90 arc closepath fill
vpt 0 360 arc closepath} bind def
/C2 {BL [] 0 setdash 2 copy moveto
2 copy vpt 90 180 arc closepath fill
vpt 0 360 arc closepath} bind def
/C3 {BL [] 0 setdash 2 copy moveto
2 copy vpt 0 180 arc closepath fill
vpt 0 360 arc closepath} bind def
/C4 {BL [] 0 setdash 2 copy moveto
2 copy vpt 180 270 arc closepath fill
vpt 0 360 arc closepath} bind def
/C5 {BL [] 0 setdash 2 copy moveto
2 copy vpt 0 90 arc
2 copy moveto
2 copy vpt 180 270 arc closepath fill
vpt 0 360 arc} bind def
/C6 {BL [] 0 setdash 2 copy moveto
2 copy vpt 90 270 arc closepath fill
vpt 0 360 arc closepath} bind def
/C7 {BL [] 0 setdash 2 copy moveto
2 copy vpt 0 270 arc closepath fill
vpt 0 360 arc closepath} bind def
/C8 {BL [] 0 setdash 2 copy moveto
2 copy vpt 270 360 arc closepath fill
vpt 0 360 arc closepath} bind def
/C9 {BL [] 0 setdash 2 copy moveto
2 copy vpt 270 450 arc closepath fill
vpt 0 360 arc closepath} bind def
/C10 {BL [] 0 setdash 2 copy 2 copy moveto vpt 270 360 arc closepath fill
2 copy moveto
2 copy vpt 90 180 arc closepath fill
vpt 0 360 arc closepath} bind def
/C11 {BL [] 0 setdash 2 copy moveto
2 copy vpt 0 180 arc closepath fill
2 copy moveto
2 copy vpt 270 360 arc closepath fill
vpt 0 360 arc closepath} bind def
/C12 {BL [] 0 setdash 2 copy moveto
2 copy vpt 180 360 arc closepath fill
vpt 0 360 arc closepath} bind def
/C13 {BL [] 0 setdash 2 copy moveto
2 copy vpt 0 90 arc closepath fill
2 copy moveto
2 copy vpt 180 360 arc closepath fill
vpt 0 360 arc closepath} bind def
/C14 {BL [] 0 setdash 2 copy moveto
2 copy vpt 90 360 arc closepath fill
vpt 0 360 arc} bind def
/C15 {BL [] 0 setdash 2 copy vpt 0 360 arc closepath fill
vpt 0 360 arc closepath} bind def
/Rec {newpath 4 2 roll moveto 1 index 0 rlineto 0 exch rlineto
neg 0 rlineto closepath} bind def
/Square {dup Rec} bind def
/Bsquare {vpt sub exch vpt sub exch vpt2 Square} bind def
/S0 {BL [] 0 setdash 2 copy moveto 0 vpt rlineto BL Bsquare} bind def
/S1 {BL [] 0 setdash 2 copy vpt Square fill Bsquare} bind def
/S2 {BL [] 0 setdash 2 copy exch vpt sub exch vpt Square fill Bsquare} bind def
/S3 {BL [] 0 setdash 2 copy exch vpt sub exch vpt2 vpt Rec fill Bsquare} bind def
/S4 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt Square fill Bsquare} bind def
/S5 {BL [] 0 setdash 2 copy 2 copy vpt Square fill
exch vpt sub exch vpt sub vpt Square fill Bsquare} bind def
/S6 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt vpt2 Rec fill Bsquare} bind def
/S7 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt vpt2 Rec fill
2 copy vpt Square fill Bsquare} bind def
/S8 {BL [] 0 setdash 2 copy vpt sub vpt Square fill Bsquare} bind def
/S9 {BL [] 0 setdash 2 copy vpt sub vpt vpt2 Rec fill Bsquare} bind def
/S10 {BL [] 0 setdash 2 copy vpt sub vpt Square fill 2 copy exch vpt sub exch vpt Square fill
Bsquare} bind def
/S11 {BL [] 0 setdash 2 copy vpt sub vpt Square fill 2 copy exch vpt sub exch vpt2 vpt Rec fill
Bsquare} bind def
/S12 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt2 vpt Rec fill Bsquare} bind def
/S13 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt2 vpt Rec fill
2 copy vpt Square fill Bsquare} bind def
/S14 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt2 vpt Rec fill
2 copy exch vpt sub exch vpt Square fill Bsquare} bind def
/S15 {BL [] 0 setdash 2 copy Bsquare fill Bsquare} bind def
/D0 {gsave translate 45 rotate 0 0 S0 stroke grestore} bind def
/D1 {gsave translate 45 rotate 0 0 S1 stroke grestore} bind def
/D2 {gsave translate 45 rotate 0 0 S2 stroke grestore} bind def
/D3 {gsave translate 45 rotate 0 0 S3 stroke grestore} bind def
/D4 {gsave translate 45 rotate 0 0 S4 stroke grestore} bind def
/D5 {gsave translate 45 rotate 0 0 S5 stroke grestore} bind def
/D6 {gsave translate 45 rotate 0 0 S6 stroke grestore} bind def
/D7 {gsave translate 45 rotate 0 0 S7 stroke grestore} bind def
/D8 {gsave translate 45 rotate 0 0 S8 stroke grestore} bind def
/D9 {gsave translate 45 rotate 0 0 S9 stroke grestore} bind def
/D10 {gsave translate 45 rotate 0 0 S10 stroke grestore} bind def
/D11 {gsave translate 45 rotate 0 0 S11 stroke grestore} bind def
/D12 {gsave translate 45 rotate 0 0 S12 stroke grestore} bind def
/D13 {gsave translate 45 rotate 0 0 S13 stroke grestore} bind def
/D14 {gsave translate 45 rotate 0 0 S14 stroke grestore} bind def
/D15 {gsave translate 45 rotate 0 0 S15 stroke grestore} bind def
/DiaE {stroke [] 0 setdash vpt add M
hpt neg vpt neg V hpt vpt neg V
hpt vpt V hpt neg vpt V closepath stroke} def
/BoxE {stroke [] 0 setdash exch hpt sub exch vpt add M
0 vpt2 neg V hpt2 0 V 0 vpt2 V
hpt2 neg 0 V closepath stroke} def
/TriUE {stroke [] 0 setdash vpt 1.12 mul add M
hpt neg vpt -1.62 mul V
hpt 2 mul 0 V
hpt neg vpt 1.62 mul V closepath stroke} def
/TriDE {stroke [] 0 setdash vpt 1.12 mul sub M
hpt neg vpt 1.62 mul V
hpt 2 mul 0 V
hpt neg vpt -1.62 mul V closepath stroke} def
/PentE {stroke [] 0 setdash gsave
translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
closepath stroke grestore} def
/CircE {stroke [] 0 setdash
hpt 0 360 arc stroke} def
/Opaque {gsave closepath 1 setgray fill grestore 0 setgray closepath} def
/DiaW {stroke [] 0 setdash vpt add M
hpt neg vpt neg V hpt vpt neg V
hpt vpt V hpt neg vpt V Opaque stroke} def
/BoxW {stroke [] 0 setdash exch hpt sub exch vpt add M
0 vpt2 neg V hpt2 0 V 0 vpt2 V
hpt2 neg 0 V Opaque stroke} def
/TriUW {stroke [] 0 setdash vpt 1.12 mul add M
hpt neg vpt -1.62 mul V
hpt 2 mul 0 V
hpt neg vpt 1.62 mul V Opaque stroke} def
/TriDW {stroke [] 0 setdash vpt 1.12 mul sub M
hpt neg vpt 1.62 mul V
hpt 2 mul 0 V
hpt neg vpt -1.62 mul V Opaque stroke} def
/PentW {stroke [] 0 setdash gsave
translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
Opaque stroke grestore} def
/CircW {stroke [] 0 setdash
hpt 0 360 arc Opaque stroke} def
/BoxFill {gsave Rec 1 setgray fill grestore} def
/Density {
/Fillden exch def
currentrgbcolor
/ColB exch def /ColG exch def /ColR exch def
/ColR ColR Fillden mul Fillden sub 1 add def
/ColG ColG Fillden mul Fillden sub 1 add def
/ColB ColB Fillden mul Fillden sub 1 add def
ColR ColG ColB setrgbcolor} def
/BoxColFill {gsave Rec PolyFill} def
/PolyFill {gsave Density fill grestore grestore} def
/h {rlineto rlineto rlineto gsave closepath fill grestore} bind def
%
% PostScript Level 1 Pattern Fill routine for rectangles
% Usage: x y w h s a XX PatternFill
% x,y = lower left corner of box to be filled
% w,h = width and height of box
% a = angle in degrees between lines and x-axis
% XX = 0/1 for no/yes cross-hatch
%
/PatternFill {gsave /PFa [ 9 2 roll ] def
PFa 0 get PFa 2 get 2 div add PFa 1 get PFa 3 get 2 div add translate
PFa 2 get -2 div PFa 3 get -2 div PFa 2 get PFa 3 get Rec
TransparentPatterns {} {gsave 1 setgray fill grestore} ifelse
clip
currentlinewidth 0.5 mul setlinewidth
/PFs PFa 2 get dup mul PFa 3 get dup mul add sqrt def
0 0 M PFa 5 get rotate PFs -2 div dup translate
0 1 PFs PFa 4 get div 1 add floor cvi
{PFa 4 get mul 0 M 0 PFs V} for
0 PFa 6 get ne {
0 1 PFs PFa 4 get div 1 add floor cvi
{PFa 4 get mul 0 2 1 roll M PFs 0 V} for
} if
stroke grestore} def
%
/languagelevel where
{pop languagelevel} {1} ifelse
dup 2 lt
{/InterpretLevel1 true def
/InterpretLevel3 false def}
{/InterpretLevel1 Level1 def
2 gt
{/InterpretLevel3 Level3 def}
{/InterpretLevel3 false def}
ifelse }
ifelse
%
% PostScript level 2 pattern fill definitions
%
/Level2PatternFill {
/Tile8x8 {/PaintType 2 /PatternType 1 /TilingType 1 /BBox [0 0 8 8] /XStep 8 /YStep 8}
bind def
/KeepColor {currentrgbcolor [/Pattern /DeviceRGB] setcolorspace} bind def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop 0 0 M 8 8 L 0 8 M 8 0 L stroke}
>> matrix makepattern
/Pat1 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop 0 0 M 8 8 L 0 8 M 8 0 L stroke
0 4 M 4 8 L 8 4 L 4 0 L 0 4 L stroke}
>> matrix makepattern
/Pat2 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop 0 0 M 0 8 L
8 8 L 8 0 L 0 0 L fill}
>> matrix makepattern
/Pat3 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop -4 8 M 8 -4 L
0 12 M 12 0 L stroke}
>> matrix makepattern
/Pat4 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop -4 0 M 8 12 L
0 -4 M 12 8 L stroke}
>> matrix makepattern
/Pat5 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop -2 8 M 4 -4 L
0 12 M 8 -4 L 4 12 M 10 0 L stroke}
>> matrix makepattern
/Pat6 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop -2 0 M 4 12 L
0 -4 M 8 12 L 4 -4 M 10 8 L stroke}
>> matrix makepattern
/Pat7 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop 8 -2 M -4 4 L
12 0 M -4 8 L 12 4 M 0 10 L stroke}
>> matrix makepattern
/Pat8 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop 0 -2 M 12 4 L
-4 0 M 12 8 L -4 4 M 8 10 L stroke}
>> matrix makepattern
/Pat9 exch def
/Pattern1 {PatternBgnd KeepColor Pat1 setpattern} bind def
/Pattern2 {PatternBgnd KeepColor Pat2 setpattern} bind def
/Pattern3 {PatternBgnd KeepColor Pat3 setpattern} bind def
/Pattern4 {PatternBgnd KeepColor Landscape {Pat5} {Pat4} ifelse setpattern} bind def
/Pattern5 {PatternBgnd KeepColor Landscape {Pat4} {Pat5} ifelse setpattern} bind def
/Pattern6 {PatternBgnd KeepColor Landscape {Pat9} {Pat6} ifelse setpattern} bind def
/Pattern7 {PatternBgnd KeepColor Landscape {Pat8} {Pat7} ifelse setpattern} bind def
} def
%
%
%End of PostScript Level 2 code
%
/PatternBgnd {
TransparentPatterns {} {gsave 1 setgray fill grestore} ifelse
} def
%
% Substitute for Level 2 pattern fill codes with
% grayscale if Level 2 support is not selected.
%
/Level1PatternFill {
/Pattern1 {0.250 Density} bind def
/Pattern2 {0.500 Density} bind def
/Pattern3 {0.750 Density} bind def
/Pattern4 {0.125 Density} bind def
/Pattern5 {0.375 Density} bind def
/Pattern6 {0.625 Density} bind def
/Pattern7 {0.875 Density} bind def
} def
%
% Now test for support of Level 2 code
%
Level1 {Level1PatternFill} {Level2PatternFill} ifelse
%
/Symbol-Oblique /Symbol findfont [1 0 .167 1 0 0] makefont
dup length dict begin {1 index /FID eq {pop pop} {def} ifelse} forall
currentdict end definefont pop
%
/Metrics {ExtendTextBox Gswidth} def
/Lwidth {currentpoint stroke M 0 vshift R Metrics} def
/Rwidth {currentpoint stroke M dup stringwidth pop neg vshift R Metrics} def
/Cwidth {currentpoint stroke M dup stringwidth pop -2 div vshift R Metrics} def
/GLwidth {currentpoint stroke M 0 vshift R {ExtendTextBox} forall} def
/GRwidth {currentpoint stroke M dup Gwidth vshift R {ExtendTextBox} forall} def
/GCwidth {currentpoint stroke M dup Gwidth 2 div vshift R {ExtendTextBox} forall} def
/GLwidth2 {0 Gwidth AddGlyphWidth} def
/GRwidth2 {Gwidth -1 mul 0 AddGlyphWidth} def
/GCwidth2 {Gwidth 2 div dup -1 mul AddGlyphWidth} def
/AddGlyphWidth { dup TBx2 gt {userdict /TBx2 3 -1 roll put} {pop} ifelse
dup TBx1 lt {userdict /TBx1 3 -1 roll put} {pop} ifelse } def
/MFshow {
{ dup 5 get 3 ge
{ 5 get 3 eq {gsave} {grestore} ifelse }
{dup dup 0 get findfont exch 1 get scalefont setfont
[ currentpoint ] exch dup 2 get 0 exch R dup 5 get 2 ne {dup dup 6
get exch 4 get {textshow} {Metrics pop 0 R} ifelse }if dup 5 get 0 eq
{dup 3 get {2 get neg 0 exch R pop} {pop aload pop M} ifelse} {dup 5
get 1 eq {dup 2 get exch dup 3 get exch 6 get Gswidth pop -2 div
dup 0 R} {dup 6 get Gswidth pop -2 div 0 R 6 get
textshow 2 index {aload pop M neg 3 -1 roll neg R pop pop} {pop pop pop
pop aload pop M} ifelse }ifelse }ifelse }
ifelse }
forall} def
/Gswidth {dup type /stringtype eq {stringwidth} {pop (n) stringwidth} ifelse} def
/MFwidth {0 exch { dup 5 get 3 ge { 5 get 3 eq { 0 } { pop } ifelse }
{dup 3 get{dup dup 0 get findfont exch 1 get scalefont setfont
6 get Gswidth pop add} {pop} ifelse} ifelse} forall} def
/MLshow { currentpoint stroke M
0 exch R
Blacktext {gsave 0 setgray MFshow grestore} {MFshow} ifelse } bind def
/MRshow { currentpoint stroke M
exch dup MFwidth neg 3 -1 roll R
Blacktext {gsave 0 setgray MFshow grestore} {MFshow} ifelse } bind def
/MCshow { currentpoint stroke M
exch dup MFwidth -2 div 3 -1 roll R
Blacktext {gsave 0 setgray MFshow grestore} {MFshow} ifelse } bind def
/XYsave { [( ) 1 2 true false 3 ()] } bind def
/XYrestore { [( ) 1 2 true false 4 ()] } bind def
Level1 SuppressPDFMark or
{} {
/SDict 10 dict def
systemdict /pdfmark known not {
userdict /pdfmark systemdict /cleartomark get put
} if
SDict begin [
/Title (mass_spec.png)
/Subject (gnuplot plot)
/Creator (gnuplot 5.2 patchlevel 2)
% /Producer (gnuplot)
% /Keywords ()
/CreationDate (Tue Oct 1 18:03:38 2019)
/DOCINFO pdfmark
end
} ifelse
%
% Support for boxed text - Ethan A Merritt Sep 2016
%
/InitTextBox { userdict /TBy2 3 -1 roll put userdict /TBx2 3 -1 roll put
userdict /TBy1 3 -1 roll put userdict /TBx1 3 -1 roll put
/Boxing true def } def
/ExtendTextBox { dup type /stringtype eq
{ Boxing { gsave dup false charpath pathbbox
dup TBy2 gt {userdict /TBy2 3 -1 roll put} {pop} ifelse
dup TBx2 gt {userdict /TBx2 3 -1 roll put} {pop} ifelse
dup TBy1 lt {userdict /TBy1 3 -1 roll put} {pop} ifelse
dup TBx1 lt {userdict /TBx1 3 -1 roll put} {pop} ifelse
grestore } if }
{} ifelse} def
/PopTextBox { newpath TBx1 TBxmargin sub TBy1 TBymargin sub M
TBx1 TBxmargin sub TBy2 TBymargin add L
TBx2 TBxmargin add TBy2 TBymargin add L
TBx2 TBxmargin add TBy1 TBymargin sub L closepath } def
/DrawTextBox { PopTextBox stroke /Boxing false def} def
/FillTextBox { gsave PopTextBox fill grestore /Boxing false def} def
0 0 0 0 InitTextBox
/TBxmargin 20 def
/TBymargin 20 def
/Boxing false def
/textshow { ExtendTextBox Gshow } def
%
end
%%EndProlog
%%Page: 1 1
gnudict begin
gsave
doclip
50 50 translate
0.100 0.100 scale
90 rotate
0 -5040 translate
0 setgray
newpath
(Helvetica) findfont 140 scalefont setfont
BackgroundColor 0 lt 3 1 roll 0 lt exch 0 lt or or not {gsave BackgroundColor C clippath fill grestore} if
1.000 UL
LTb
LCb setrgbcolor
602 448 M
63 0 V
6282 0 R
-63 0 V
stroke
518 448 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 0)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
602 1041 M
63 0 V
6282 0 R
-63 0 V
stroke
518 1041 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 10)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
602 1635 M
63 0 V
6282 0 R
-63 0 V
stroke
518 1635 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 20)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
602 2228 M
63 0 V
6282 0 R
-63 0 V
stroke
518 2228 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 30)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
602 2822 M
63 0 V
6282 0 R
-63 0 V
stroke
518 2822 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 40)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
602 3415 M
63 0 V
6282 0 R
-63 0 V
stroke
518 3415 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 50)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
602 4009 M
63 0 V
6282 0 R
-63 0 V
stroke
518 4009 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 60)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
602 4602 M
63 0 V
6282 0 R
-63 0 V
stroke
518 4602 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 70)]
] -233.3 MRshow
1.000 UL
LTb
LCb setrgbcolor
602 448 M
0 63 V
0 4388 R
0 -63 V
stroke
602 308 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 50)]
] -233.3 MCshow
1.000 UL
LTb
LCb setrgbcolor
2188 448 M
0 63 V
0 4388 R
0 -63 V
stroke
2188 308 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 100)]
] -233.3 MCshow
1.000 UL
LTb
LCb setrgbcolor
3775 448 M
0 63 V
0 4388 R
0 -63 V
stroke
3775 308 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 150)]
] -233.3 MCshow
1.000 UL
LTb
LCb setrgbcolor
5361 448 M
0 63 V
0 4388 R
0 -63 V
stroke
5361 308 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 200)]
] -233.3 MCshow
1.000 UL
LTb
LCb setrgbcolor
6947 448 M
0 63 V
0 4388 R
0 -63 V
stroke
6947 308 M
[ [(Helvetica) 700.0 0.0 true true 0 ( 250)]
] -233.3 MCshow
1.000 UL
LTb
LCb setrgbcolor
1.000 UL
LTB
LCb setrgbcolor
602 4899 N
602 448 L
6345 0 V
0 4451 V
-6345 0 V
Z stroke
1.000 UP
LCb setrgbcolor
2220 745 M
[ [(Helvetica) 700.0 0.0 true true 0 (n=6)]
] -233.3 MLshow
LCb setrgbcolor
2791 685 M
[ [(Helvetica) 700.0 0.0 true true 0 (n=7)]
] -233.3 MLshow
LCb setrgbcolor
3489 626 M
[ [(Helvetica) 700.0 0.0 true true 0 (n=2)]
] -233.3 MLshow
LCb setrgbcolor
4060 685 M
[ [(Helvetica) 700.0 0.0 true true 0 (n=3)]
] -233.3 MLshow
LCb setrgbcolor
4631 804 M
[ [(Helvetica) 700.0 0.0 true true 0 (n=4)]
] -233.3 MLshow
LCb setrgbcolor
5202 1041 M
[ [(Helvetica) 700.0 0.0 true true 0 (n=5)]
] -233.3 MLshow
LCb setrgbcolor
5773 1694 M
[ [(Helvetica) 700.0 0.0 true true 0 (n=6)]
] -233.3 MLshow
LCb setrgbcolor
6344 4424 M
[ [(Helvetica) 700.0 0.0 true true 0 (n=7)]
] -233.3 MLshow
LCb setrgbcolor
888 4662 M
[ [(Helvetica) 900.0 0.0 true true 0 (\(a\))]
] -300.0 MLshow
1.000 UL
LTb
LCb setrgbcolor
LCb setrgbcolor
42 2673 M
currentpoint gsave translate -270 rotate 0 0 moveto
[ [(Helvetica) 900.0 0.0 true true 0 (Intensity \(arbitrary units\))]
] -300.0 MCshow
grestore
LTb
LCb setrgbcolor
3774 168 M
[ [(Helvetica) 900.0 0.0 true true 0 (m/z \(Da\))]
] -300.0 MCshow
LTb
% Begin plot #1
3.500 UL
LTb
LCb setrgbcolor
LCb setrgbcolor
3827 4696 M
[ [(Helvetica) 0.0 0.0 true true 0 (\(H)]
[(Helvetica) 0.0 0.0 true true 0 (2)]
[(Helvetica) 0.0 0.0 true true 0 (O\))]
[(Helvetica) 0.0 0.0 true true 0 (n)]
[(Helvetica) 0.0 0.0 true true 0 (H)]
[(Helvetica) 0.0 0.0 true true 0 (+)]
] -0.0 MRshow
3.500 UL
LTb
LCb setrgbcolor
3911 4696 M
399 0 V
761 448 M
571 0 R
571 0 R
571 0 R
0 155 V
3045 448 M
0 127 V
2601 448 M
571 0 R
571 0 R
571 0 R
571 0 R
571 0 R
571 0 R
571 0 R
% End plot #1
% Begin plot #2
stroke
LTb
LT1
LCb setrgbcolor
LCb setrgbcolor
3827 4416 M
[ [(Helvetica) 0.0 0.0 true true 0 (U\(H)]
[(Helvetica) 0.0 0.0 true true 0 (2)]
[(Helvetica) 0.0 0.0 true true 0 (O\))]
[(Helvetica) 0.0 0.0 true true 0 (n)]
[(Helvetica) 0.0 0.0 true true 0 (H)]
[(Helvetica) 0.0 0.0 true true 0 (+)]
] -0.0 MRshow
3.500 UL
LTb
LT1
LCb setrgbcolor
3911 4416 M
399 0 V
761 448 M
571 0 R
571 0 R
571 0 R
571 0 R
-444 0 R
571 0 R
0 4 V
571 -4 R
0 24 V
571 -24 R
0 95 V
571 -95 R
0 217 V
5456 448 M
0 449 V
6027 448 M
0 1074 V
6598 448 M
0 3788 V
% End plot #2
stroke
2.000 UL
LTb
LCb setrgbcolor
1.000 UL
LTB
LCb setrgbcolor
602 4899 N
602 448 L
6345 0 V
0 4451 V
-6345 0 V
Z stroke
1.000 UP
1.000 UL
LTb
LCb setrgbcolor
stroke
grestore
end
showpage
%%Trailer
%%DocumentFonts: Helvetica
%%Pages: 1

Binary file not shown.

11016
figure/proporEachFrag_12_6.eps Normal file

File diff suppressed because it is too large Load Diff

Binary file not shown.

11020
figure/proporEachFrag_7_2.eps Normal file

File diff suppressed because it is too large Load Diff

View File

Before

Width:  |  Height:  |  Size: 110 KiB

After

Width:  |  Height:  |  Size: 110 KiB

View File

@ -29,6 +29,7 @@
\newcommand*\mycommand[1]{\texttt{\emph{#1}}}
%% Added by author
\usepackage{epstopdf}
\usepackage{graphicx}
\usepackage{tikz}
\usepackage{xcolor}
@ -165,7 +166,7 @@ QM/MM method was used to describe the collision process of uracil protonated wat
\textbf{The Distributions of the Initial Collision Models} In order to simulate the collision process of the obtained lowest-energy configuration of (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters with Ar, a reasonable construction of the collision models are needed. In our dynamics collision simulations, totally 2R+3 series were performed for every (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster. And 600 models were conducted in every series. For visualization, the distribution maps of the initial positions of Ar atom with respect to each (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster configuration were made. Here we take the collision of Ar to (H$_2$O)$_4$UH$^+$ cluster as an example, Figure \ref{fig:sphere} displays the collision models of the relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration of the first series that the collision positions are at the center of size of the cluster. As shown in Figure \ref{fig:sphere}, the sphere in picture a is composed of 200 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series. The sphere in picture b is composed of 400 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series and the sphere in picture c is composed of 600 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series. From pictures a, b, and c in Figure \ref{fig:sphere}, it indicates the more simulations are performed, the more colliding opportunities at all the possible positions of (H$_2$O)$_4$UH$^+$ cluster Ar will have. As shown in picture d of Figure \ref{fig:sphere}, the outer layer of the sphere is the 200 relative Ar positions in the first series and the inner layer is the 200 relative Ar positions to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the last series (the distance between collision positions and the center of size of the cluster is R$_{(H_2O)_4UH^+}$ Å. The collision models of Ar and (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters are displayed in Figure SX in the SI. In experiment, the collision positions are randomly, which means that Ar can reach any position of the clusters. All the collision model pictures of Ar and (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters shows our constructions for the collision simulation models are reliable and close to the collision situation in the experiment. With these reasonable models, the explicit collision simulations were conducted. To confirm the statistical convergence is reached, we compare the proportions of neutral uracil molecules loss and the total fragmentation cross sections of (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters with those in experiment. As shown in Table S1 in SI, the data of 200 simulations, 400 simulations, and 600 simulations in every series for all (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters were almost the same, which indicates 600(2R + 3) simulations are enough.
\begin{figure}
\includegraphics[width=0.4\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/sphere}
\includegraphics[width=0.4\linewidth]{figure/sphere}
\centering
\caption{Representation of initial Ar positions of the first series to perform collision simulations with the lowest-energy isomer of (H$_2$O)$_4$UH$^+$; For the first series, a: 200 representation of initial Ar positions; b: 400 representation of initial Ar positions; c: 600 representation of initial Ar positions; d: 200 representation of initial Ar positions of the first series and last series, separately.}
\label{fig:sphere}
@ -178,7 +179,7 @@ Formula of calculating the proportion of neutral uracil loss:
In this part, the proportion of neutral uracil molecule loss of each lowest-energy (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster by colliding with Ar atom will be discussed. No neutral uracil loss for (H$_2$O)$_{n=1-4}$UH$^+$, the evaporation of uracil starts at n=5, and becomes significant at n=6 were observed in experiment.\cite{Braud2019} In our calculations, the proportions of neutral uracil molecule loss extracted from 600(2R + 3) dynamics collision simulations for (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters were plotted in Figure \ref{fig:neutralUloss} as a function of number of water molecules n. As displayed in Figure \ref{fig:neutralUloss}, the overall trend of the proportion of neutral uracil molecule loss in theory is consistent with the one in experiment except the case n=5. The evaporation of neutral uracil molecule means the excess proton stayed in the water clusters. When n = 3-4, and 6-7 the neutral uracil loss increases with n. It indicates with the increase of the number of water molecules in the cluster, the excess proton is more likely to lie in the water cluster after collision.
\begin{figure}
\includegraphics[width=0.5\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/neutralUloss}
\includegraphics[width=0.5\linewidth]{figure/neutralUloss}
\centering
\caption{Proportion of neutral uracil loss after collision of clusters (H$_2$O)$_{n=3-7, 12}$UH$^+$ with Ar from both theoretical (pink line) and experiment (green line) results.}
\label{fig:neutralUloss}
@ -217,7 +218,7 @@ The neutral uracil molecule loss proportion, 0.0\%, of n = 3 in Figure \ref{fig:
\end{table}
\begin{figure}
\includegraphics[width=0.8\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/3ato5d}
\includegraphics[width=0.8\linewidth]{figure/3ato5d}
\centering
\caption{Some lowest-energy configurations of clusters (H$_2$O)$_{n=3-5}$UH$^+$ (the distances are given in Å and relative binding energies are in kcal$\cdot$mol$^{-1}$.}
\label{fig:3ato5d}
@ -230,13 +231,13 @@ As displayed in Figure \ref{fig:neutralUloss}, the neutral uracil molecule loss
For (H$_2$O)$_6$UH$^+$ cluster, the neutral uracil molecule loss proportion is 14.2\% in Figure \ref{fig:neutralUloss}, which is from the sixth lowest-energy isomer (see 6f in Figure \ref{fig:6ato7b}) that the excess proton is bounded to water cluster but close to one oxygen atom of uracil (W-H-U form). For the first, second, third, fourth, and fifth lowest-energy configurations of (H$_2$O)$_6$UH$^+$ cluster (W-H form) (see 6a, 6b, 6c, 6d, and 6e in Figure \ref{fig:6ato7b}) and was separated by one water molecule from uracil, the proportion is 36.6\%, 30.0\%, 31.2\%, 28.5\%, and 30.1\% (see Table \ref{tab:table1}), respectively. The distances between OX and HX in 6a, 6c, 6d are 1.774 Å, 1.745 Å, 1.804 Å, and the distances between OY and HY in 6b and 6e are 1.660 Å and 1.614 Å, respectively. It implies that the neutral uracil loss proportion increases with the distance between uracil and the excess proton in (H$_2$O)$_6$UH$^+$ cluster, which is in line with the observation from dynamics collision simulations that (H$_2$O)$_6$UH$^+$ cluster has a direct dissociation after collision. The relative energy of 6a and 6f calculated at MP2/Def2TZVP level is 2.7 kcal$\cdot$mol$^{-1}$. From the neutral uracil molecule loss proportion of configurations 6a, 6b, 6c, 6d, 6e, and 6f, the proportion of 6f, 14.2\% is the closest to the one, 14.3\%, in experiment, it indicates the configuration that the excess proton is close to water clusters but is still bounded to uracil is dominant.
\begin{figure}
\includegraphics[width=0.8\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/6ato7b}
\includegraphics[width=0.8\linewidth]{figure/6ato7b}
\caption{Some lowest-energy configurations of clusters (H$_2$O)$_{n=6-7}$UH$^+$ (the distances are given in Å and relative binding energies are in kcal$\cdot$mol$^{-1}$.}
\label{fig:6ato7b}
\end{figure}
\begin{figure}
\includegraphics[width=0.5\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/12ad.png}
\includegraphics[width=0.5\linewidth]{figure/12ad.png}
\centering
\caption{Some lowest-energy configurations of clusters (H$_2$O)$_{12}$UH$^+$ (the distances are given in Å and relative binding energies are in kcal$\cdot$mol$^{-1}$ ).}
\label{fig:12ad}
@ -257,7 +258,7 @@ The total fragmentation cross sections of mixed (H$_2$O)$_{n=3-7}$UH$^+$ cluster
If it needs to make a further detailed description of the total fragmentation cross sections?
\begin{figure}
\includegraphics[width=0.5\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/crosssection}
\includegraphics[width=0.5\linewidth]{figure/crosssection}
\centering
\caption{Total fragmentation cross section in both theory (pink line) and experiment (green line) of clusters (H$_2$O)$_{n=3-7}$UH$^+$ who the closest neutral uracil loss proportion compared with those in experiment.}
\label{fig:crosssection}
@ -266,36 +267,44 @@ If it needs to make a further detailed description of the total fragmentation cr
\textbf{Mass Spectrum of Fragments with Excess Proton}
Formula of calculating the fragment ratio:
To explore the collision products, the branching ratios of different fragments with the excess proton were extracted from the dynamics collision simulations and compared with the mass spectrum obtained by colliding cluster (H$_2$O)$_7$UH$^+$ with Ne at 7.2 eV center of mass collision energy in experiment.\cite{Braud2019} Table \ref{tab:massspectrum} displays the specific fragment ratio in the total fragments from the collision of the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ with Ar. Fragments (H$_2$O)$_{n=3-5}$H$^+$ were not found in our calculation, which agrees with the very low intensity of fragments (H$_2$O)$_{n=3-5}$H$^+$ in experiment. This implies when (H$_2$O)$_{n=3-5}$ leave, they dont have enough proton affinity to take away the excess proton. The intensity of fragments (H$_2$O)$_{n=6-7}$H$^+$ are higher than fragments (H$_2$O)$_{n=3-5}$H$^+$ in experiment results and we also determined the fragments (H$_2$O)$_{n=6-7}$H$^+$ in our calculation, which indicate the proton affinity of (H$_2$O)$_{n=6-7}$ is higher than (H$_2$O)$_{n=3-5}$ that in line with the previous study. \cite{Magnera1991}
To explore the collision products, the branching ratios (intensity) of different fragments with the excess proton were extracted from the dynamics collision simulations and compared with the mass spectrum obtained by colliding cluster (H$_2$O)$_7$UH$^+$ with Ne at 7.2 eV center of mass collision energy in experiment.\cite{Braud2019} Figure\ref{fig:mass_spec} displays the specific fragment ratio in the total fragments from the collision of the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ with Ar. Fragments (H$_2$O)$_{n=3-5}$H$^+$ were not found in our calculation, which agrees with the very low intensity of fragments (H$_2$O)$_{n=3-5}$H$^+$ in experiment. This implies when (H$_2$O)$_{n=3-5}$ leave, they dont have enough proton affinity to take away the excess proton. The intensity of fragments (H$_2$O)$_{n=6-7}$H$^+$ are higher than fragments (H$_2$O)$_{n=3-5}$H$^+$ in experiment results and we also determined the fragments (H$_2$O)$_{n=6-7}$H$^+$ in our calculation, which indicate the proton affinity of (H$_2$O)$_{n=6-7}$ is higher than (H$_2$O)$_{n=3-5}$ that in line with the previous study. \cite{Magnera1991}
As shown in Table \ref{tab:massspectrum}, we didnt get UH$^+$ but it was detected in experiment with time of flight 60 $\mu$s. For each dynamics collision simulation of cluster (H$_2$O)$_7$H$^+$ was performed with simulation time 15 ps, we cannot assert that the UH$^+$ will not appear in longer simulation. Modeling the complete duration of the experiment (up to $\mu$s) is out of reach with MD/SCC-DFTB simulations. Additionally, we calculated the energy of (H$_2$O)$_6$H$^+$, which is from (H$_2$O)$_7$H$^+$ cluster with the dissociation of one water after collision with Ar at SCC-DFTB level (see Table \ref{tab:fragenergy}). We also calculated the lowest energies of (H$_2$O)$_5$H$^+$ and water (see Table \ref{tab:fragenergy}). From the data in Table \ref{tab:fragenergy}, the relative energy $\Delta$E between energy of (H$_2$O)$_6$H$^+$ and lowest energy of (H$_2$O)$_5$H$^+$ plus H$_2$O can reach 1.007 eV, so it is possible for the fragment (H$_2$O)$_6$H$^+$ to lose more water molecules. From this, we suggest if the dynamics collision simulation is long enough, finally UH$^+$ can be obtained.
As shown in Figure \ref{fig:mass_spec}, we didnt get UH$^+$ but it was detected in experiment with time of flight 60 $\mu$s. For each dynamics collision simulation of cluster (H$_2$O)$_7$H$^+$ was performed with simulation time 15 ps, we cannot assert that the UH$^+$ will not appear in longer simulation. Modeling the complete duration of the experiment (up to $\mu$s) is out of reach with MD/SCC-DFTB simulations. Additionally, we calculated the energy of (H$_2$O)$_6$H$^+$, which is from (H$_2$O)$_7$H$^+$ cluster with the dissociation of one water after collision with Ar at SCC-DFTB level (see Table \ref{tab:fragenergy}). We also calculated the lowest energies of (H$_2$O)$_5$H$^+$ and water (see Table \ref{tab:fragenergy}). From the data in Table \ref{tab:fragenergy}, the relative energy $\Delta$E between energy of (H$_2$O)$_6$H$^+$ and lowest energy of (H$_2$O)$_5$H$^+$ plus H$_2$O can reach 1.007 eV, so it is possible for the fragment (H$_2$O)$_6$H$^+$ to lose more water molecules. From this, we suggest if the dynamics collision simulation is long enough, finally UH$^+$ can be obtained.
As displayed in Table \ref{tab:fragenergy}, ratios of fragments (H$_2$O)$_{n=1-4}$UH$^+$ increase with the number of n which is in line with the results in experiment. It indicates the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ has more chances to lose three water molecules than to lose six water molecules. Ratio of fragment (H$_2$O)$_5$UH$^+$ is close to it of fragment (H$_2$O)$_4$UH$^+$ in theory which agree with the one in experiment. The ratio of fragment (H$_2$O)$_6$UH$^+$ increases a lot in the calculated results but it is not so high in experiment, which indicates in our simulations, the dissociation of the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ losing one water molecule is dominant. The parent cluster (H$_2$O)$_7$UH$^+$ has the highest ratio among all fragments, which is fully consistent with it in experiment. From the analyses of the mass spectrum in theory and experiment, it implies our simulations can quantitatively describe the fragment ratios.
As displayed in Figure \ref{fig:mass_spec}, the intensity of fragments (H$_2$O)$_{n=2-4}$UH$^+$ increase with the number of n which is in line with the results in experiment. It indicates the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ has more chances to lose three water molecules than to lose six water molecules. The intensity of fragment (H$_2$O)$_5$UH$^+$ is close to it of fragment (H$_2$O)$_4$UH$^+$ in theory which agree with the one in experiment. The intensity of fragment (H$_2$O)$_6$UH$^+$ increases a lot compared with these of (H$_2$O)$_{n=2-5}$UH$^+$ in the calculated results but it is not so high in experiment, which indicates in our simulations, the dissociation of the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ losing one water molecule is dominant. The parent cluster (H$_2$O)$_7$UH$^+$ has the highest ratio among all fragments, which is fully consistent with it in experiment. From the analyses of the mass spectrum in theory and experiment, it implies our simulations can quantitatively describe the fragment ratios.
\begin{figure}[h]
\includegraphics[width=0.5\linewidth, left]{figure/mass_spec.eps}
\raggedright
\caption{(a): Mass spectrum in theory of the charged fragments from the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ with simulation time 15 ps (in red and are in blue); (b): Mass spectrum of the charged fragments of cluster (H$_2$O)$_7$UH$^+$ in experiment.}
\label{fig:mass_spec}
\end{figure}
\begin{table}
\begin{center}
\caption{Fragment ratios in the total fragments from the dissociation of the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ with simulation time 15 ps.}
\label{tab:massspectrum}
\begin{tabular}{c|c}
\textbf{Fragment} & \textbf{Ratio (\%)} \\
\hline
(H$_2$O)$_3$H$^+$ & 0.00 \\
(H$_2$O)$_4$H$^+$ & 0.00 \\
(H$_2$O)$_5$H$^+$ & 0.00 \\
(H$_2$O)$_6$H$^+$ & 2.62 \\
(H$_2$O)$_7$H$^+$ & 2.14 \\
UH$^+$ & 0.00 \\
(H$_2$O)UH$^+$ & 0.07 \\
(H$_2$O)$_2$UH$^+$ & 0.41 \\
(H$_2$O)$_3$UH$^+$ & 1.60 \\
(H$_2$O)$_4$UH$^+$ & 3.66 \\
(H$_2$O)$_5$UH$^+$ & 7.56 \\
(H$_2$O)$_6$UH$^+$ & 18.09 \\
(H$_2$O)$_7$UH$^+$ & 63.83 \\
\end{tabular}
\end{center}
\end{table}
%\begin{table}
% \begin{center}
% \caption{Fragment ratios in the total fragments from the %dissociation of the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ % with simulation time 15 ps.}
% \label{tab:massspectrum}
% \begin{tabular}{c|c}
% \textbf{Fragment} & \textbf{Ratio (\%)} \\
% \hline
% % (H$_2$O)$_3$H$^+$ & 0.00 \\
% (H$_2$O)$_4$H$^+$ & 0.00 \\
% (H$_2$O)$_5$H$^+$ & 0.00 \\
% (H$_2$O)$_6$H$^+$ & 2.62 \\
% % (H$_2$O)$_7$H$^+$ & 2.14 \\
% UH$^+$ & 0.00 \\
% (H$_2$O)UH$^+$ & 0.07 \\
% (H$_2$O)$_2$UH$^+$ & 0.41 \\
% (H$_2$O)$_3$UH$^+$ & 1.60 \\
% % (H$_2$O)$_4$UH$^+$ & 3.66 \\
% (H$_2$O)$_5$UH$^+$ & 7.56 \\
% (H$_2$O)$_6$UH$^+$ & 18.09 \\
% (H$_2$O)$_7$UH$^+$ & 63.83 \\
% \end{tabular}
% \end{center}
% \end{table}
\begin{table}
\begin{center}
@ -312,16 +321,23 @@ As displayed in Table \ref{tab:fragenergy}, ratios of fragments (H$_2$O)$_{n=1-4
\end{table}
\begin{figure}
\includegraphics[width=0.8\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/proporMainFrag}
\includegraphics[width=0.8\linewidth]{figure/proporEachFrag_7_2.eps}
\centering
\caption{The proportions of the main fragment from the second lowest-energy parent cluster (H$_2$O)$_7$UH$^+$ as a function of time (The values 200 and 1000 in horizontal axis correspond to 3 ps and 15 ps, respectively).}
\label{fig:proporEachFrag}
\caption{The proportions of the main fragment from the dissociation of the second lowest-energy parent cluster (H$_2$O)$_7$UH$^+$.}
\label{fig:proporEachFrag_7_2}
\end{figure}
\textbf{Time-Dependent Proportion of Each Fragment}
In addition, we got the time-dependent proportion of each fragment which confirm that up to 7 water molecules a direct dissociation mechanism occurs. For (H$_2$O)$_{12}$UH$^+$, the cluster undergoes structural rearrangements prior to dissociation, which is proof of a statistical dissociation mechanism.
In addition, the time-dependent proportion of each fragment was extracted from 600(2R + 3) dynamics collision simulations. Here we take the time-dependent proportion of each fragment from second lowest-energy parent cluster (H$_2$O)$_7$UH$^+$ as an example. For the sake of seeing clearly, only the main fragment proportions plotted as a function of simulation time are showed in Figure 7. The proportions of the main fragment of clusters (H$_2$O)$_{n=3-6, 12}$UH$^+$ are shown in SI Figure SX. From Figure \ref{fig:proporEachFrag}, it clear that the parent cluster (H$_2$O)$_7$UH$^+$ exists from the beginning and different fragments starts to appear after collision. It can be seen when the collision is finished, the fragment proportions almost doesnt change any more. It is worth noticing the fragment (H$_2$O)$_6$UH$^+$ increase first and then it decreases, which indicates there are water molecules dissociated form it.
\begin{figure}
\includegraphics[width=0.8\linewidth]{figure/proporEachFrag_12_6.eps}
\centering
\caption{The proportions of the main fragment from the dissociation of the sixth lowest-energy parent cluster (H$_2$O)$_{12}$UH$^+$.}
\label{fig:proporEachFrag_12_6}
\end{figure}
\textbf{Time-Dependent Proportion of Each Fragment}
In addition, the time-dependent proportion of each fragment was extracted from 600(2R + 3) dynamics collision simulations. Here we take the time-dependent proportion of each fragment from the dissociation second lowest-energy parent cluster (H$_2$O)$_7$UH$^+$ and the sixth lowest-energy parent cluster (H$_2$O)$_{12}$UH$^+$ as an example. For the sake of seeing clearly, only the main fragment proportions plotted as a function of simulation time are showed in Figure 7. The proportions of the main fragment of clusters (H$_2$O)$_{n=3-6}$UH$^+$ are shown in SI Figure SX. From Figure \ref{fig:proporEachFrag_7_2}, it is clear that the parent cluster (H$_2$O)$_7$UH$^+$ exists from the beginning and different fragments starts to appear after collision. It can be seen when the collision is finished, the fragment proportions almost doesnt change any more. It is worth noticing the fragment (H$_2$O)$_6$UH$^+$ increase first and then it decreases, which indicates there are water molecules dissociated from it. For fragment proportios of cluster (H$_2$O)$_{12}$UH$^+$, from Figure \ref{fig:proporEachFrag_12_6}, it shows fragments
(H$_2$O)$_{11}$UH$^+$ and (H$_2$O)$_{10}$UH$^+$ increase at the beginning and then decrease, and finally they tend to be steady. The second and the third or more times dissociation after collision and all the main fragment proportion do not tend to a constant so fast imply that there are more chances to rearrange prior to complete dissociation.
From the time-dependent proportion of each fragment from clusters (H$_2$O)$_{n=3-6, 12}$UH$^+$, it confirms that up to 7 water molecules a direct dissociation mechanism occurs. For cluster (H$_2$O)$_{12}$UH$^+$, it undergoes structural rearrangements prior to dissociation, which is proof of a statistical dissociation mechanism.