Speciation*Tool*User’s*Guide,*September*20 1 6*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
Acknowledgements*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
Table*of*Contents*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
Table*of*Contents*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
1.*Background*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
2.*Introduction*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
2.*Introduction*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
3.*Initialize*the*Speciation*Tool*database*
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setenv SPTOOL_DB sptoolv4_0 # Speciation Tool Database name
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&;-'$6!67#!/.6.!6'!67#!%7.$#/!!%@7#;.!;#@7.(&%;!6.B3#!X6B3d;#@7.(&%;!0'$!"]?!-$'@#%%&(:M!!
6B3d-;d;#@7.(&%;!0'$!,<
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(#G!;'/#3!%-#@&#%!(.;#%*!Z7#!3.%6!%6#-!&%!6'!N-/.6#!67#!;#@7.(&%;!/#%@$&-6&'(!6.B3#!
X6B3d;#@7.(&%;d/#%@$&-6&'(Y!.3%'!&(!67#!shared!%@7#;.*!!!
U'$!#\.;-3#%!'0!67#!6.B3#%!N%#/!6'!/#0&(#!(#G!@7#;&@.3!;#@7.(&%;%!3''9!N(/#$!67#!
&;-'$6d/.6.!/&$#@6'$5!&(!67#!>-#@&.6&'(!Z''3!/&%6$&BN6&'(!-.@9.:#!0'$!67#!0'33'G&(:!0&3#%1!
6B3d;#@7.(&%;1!;#@7.(&%;dP);.5O+PKd0'$&;-'$6*6\6!
6B3d@.$B'(%1!@.$B'(%dP);.5O+PK*@%I!!
6B3d;#@7.(&%;d/#%@$&-6&'(1!;#@7.(&%;d/#%@$&-6&'(*P);.5O+PK*6\6!
H#0#$!6'!2--#(/&\!a!0'$!67#!0&3#!0'$;.6%*!!!
Z7#!(#G!;#@7.(&%;!/.6.!@.(!B#!&;-'$6#/!G&67!67#!import_rawdata.pl!,#$3!-$':$.;*!
perl $SPTOOL_SRC_HOME/import_rawdata.pl $SPTOOL_DB table_type input_file
6.B3#d65-#!!!!!!!!!!!S!&%!67#!9#5G'$/!0$';!Z.B3#!P!X&(!67&%!#\.;-3#!&6!G&33!B#!#&67#$!;#@7.(&%;M!
@.$B'(%M!'$!;#@7.(&%;d/#%@$&-6&'(Y!
!!!!!&(-N6d0&3#!!!!!!!!!!!!!S!@'(6.&(%!67#!%-#@&0&#/!(#G!$#@'$/%!
Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
6.*FAQ*
!
=A?S4<2WX)S+OYSPR!
VSO!
!
!
236#$(.6&I#35M!$.67#$!67.(!.--#(/&(:!$#@'$/%!6'!67$##!%#-.$.6#!%7.$#/!%@7#;.!!6.B3#%!
X6B3d;#@7.(&%;M!6B3d@.$B'(%M!6B3d;#@7.(&%;d/#%@$&-6&'(Y!.!(#G!I#$%&'(!'0!67#!>-#@&.6&'(!Z''3!
@.(!B#!:#(#$.6#/!X$#0#$!6'!67#!_N#%6&'(!.B'I#Y*!!Z7#!(#G!;#@7.(&%;!/#0&(&6&'(!/.6.!@'N3/!B#!
&;-'$6#/!.%!-.$6!'0!67#!&(&6&.3&D.6&'(!-$'@#%%*!!Z7#%#!/.6.!@'N3/!B#!.--#(/#/!6'!#\&%6&(:!0&3#%!'$!
('6!p!/#-#(/&(:!'(!5'N$!-$'@#%%&(:!-$#0#$#(@#%*!
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=-/.6#!67#!;#@7.(&%;!6.B3#1!
4\6$.@6!67#!>2,H?RR!#(6$&#%!0$';!67#!&;-'$6!0&3#!
grep ^SAPRC99 mechanism_mar2013_forimport.txt > mechanism_saprc99_wexpl_benz.txt
4/&6!67#!(#G!0&3#1!
! ?7.(:#!>2,H?RR!6'!>2,H?RRda4Aw!X'(!.33!$#@'$/%Y!
! L#3#6#!#\&%6&(:!B#(D#(#!X%-#@&#d&/!k!K+OY!.%%&:(;#(6%!'0!n2H]Po!.(/!nAH]Eo!
! 2//!#\-3&@&6!B#(D#(#!#(6$5!n>2,H?RRda4AwM!K+OM!a4AwM!P*o!
!
^;-'$6!67#!(#G!;#@7.(&%;!0&3#!6'!67#!%7.$#/!!;#@7.(&%;!6.B3#!
perl import_rawdata.pl database_name mechanism mechanism_saprc99_wexpl_benz.txt
!
=-/.6#!67#!@.$B'(!6.B3#1!
?$#.6#!.!0&3#!G&67!67#!$#@'$/!n>2,H?RRda4AwMa4AwMVo!!
^;-'$6!67#!0&3#!6'!67#!%7.$#/!!@.$B'(!6.B3#!
! perl import_rawdata.pl database_name carbons <new_carbon_file.txt>
!
=-/.6#!67#!;#@7.(&%;!/#%@$&-6&'(!6.B3#1!
?$#.6#!.!0&3#!G&67!67#!$#@'$/!n>2,H?RRda4AwM!>2,H?RR!G&67!#\-3&@&6!B#(D#(#M!FM!
u/#%@$&-6&'(qMMo!
^;-'$6!67#!0&3#!6'!67#!%7.$#/!!;#@7.(&%;!/#%@$&-6&'(!6.B3#!
! perl import_rawdata.pl database_name mechanism_description <new_file.txt>
!
Z7#!;#@7.(&%;!/#%@$&-6&'(!6.B3#!@.$$&#%!67#!0/!nA]A>]2!U3.:o!G7&@7!/#0&(#%!G7#67#$!67#!
;#@7.(&%;!6$#.6%!>]2!#\-3&@&635*!!Z7#!?a^"M!?a+Q!.(/!>2,H?RR!.33!7.I#!A]A>]2!U3.:!%#6!6'!nFo*!!
](35!67#!>]2d?2<j)Q!;#@7.(&%;!7.%!67#!03.:!%#6!6'!nAo*!
!
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Z7#!><]c4!^A"Z2ab4!/.6.!&%!&;-'$6#/!.%!-.$6!'0!67#!>-#@&.6&'(!Z''3!&(&6&.3&D.6&'(*!!?N$$#(635!
67#$#!&%!('6!.(!'-6&'(.3!&(-N6!'0!67&%!/.6.!0'$!.!%&(:3#!$N(*!!^0!5'N!'(35!(##/!5'N$!I#$%&'(!'0!67#!
^A"Z2ab4!67#(!$#-3.@#!67#!^A"Z2ab4!0&3#(.;#!67.6!&%!$#0#$#(@#/!&(!67#!2%%&:(%*%-6''3!B#0'$#!
5'N!&(&6&.3&D#!67#!/.6.B.%#*!
^0!5'N!(##/!;N36&-3#!I#$%&'(%!0'$!5'N$!-$'@#%%&(:!.--3&@.6&'(%!67#(!5'N!G&33!(##/!;N36&-3#!
I#$%&'(%!'0!67#!>-#@&.6&'(!Z''3!/.6.B.%#f!#.@7!&;-'$6&(:!.!/&00#$#(6!^A"Z2ab4!/N$&(:!
&(&6&.3&D.6&'(*!XH#0#$!6'!V*O!.B'I#Y*!
Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
6.*FAQ*
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shared!%@7#;.!tbl_species!@.$$&#%!.3;'%6!6G#(65!0/%!X#\-'$6#/!0$';!67#!>,4?^2Z4!/.6.B.%#Y*!!
Z7#!>-#@&.6&'(!Z''3!$#0#$#(@#%!'(35!.!0#G!'0!67#%#!0/%*!!Z7#!$#_N&$#/!0/%!.$#!%-#@&#d&/M!
%-#@&#d(.;#M!I'3.6&3#d;GM!.(/!('(dI'@6':*!![#$#!&%!.(!#\.;-3#!6'!.//!.!%&(:3#!$#@'$/!6'!67#!
6.B3#!G&67!'(35!67#!$#_N&$#/!0/%1!
!
psql –d $SPTOOL_DB –c “INSERT INTO shared.tbl_species
(specie_id,specie_name,volatile_mw,non_voctog)
VALUES (‘EG1’, ‘Example Name’, 70.273,FALSE)”
!
Z7#!%-#@&#d&/!;N%6!B#!N(&_N#!&(!67#!6.B3#f!5'N!G&33!:#6!.(!#$$'$!&0!5'N!.66#;-6!6'!.//!.(!
.3$#./5!#\&%6&(:!specie_id*!!Z7#!non_voctog!0/!&%!65-#!a''3#.(!.(/!%7'N3/!B#!%#6!6$N#!&0!.!Z]E!
%-#@&#%!&%!('6!$#:.$/#/!.%!.!"]?*!
!
Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*A*
!
!
!
!
!
!
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6JJ>:4AP*6*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*A*
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B#!3'::#/!&(!.%!root*!!!
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sptool_reqd_checks.sh!G7&@7!&%!-$'I&/#/!&(!67#!>-#@&.6&'(!Z''3!-.@9.:#*!Z7#!%@$&-6!@7#@9%!0'$!
67#!$#_N&$#/!%'06G.$#!.(/!N%#$!,'%6:$#>Wb!.N67'$&D.6&'(%*!
> ./sptool_reqd_checks.sh
U'33'G&(:!&%!.(!#\.;-3#!'0!.!%N@@#%%0N3!@7#@9!0'$!67#!$#_N&$#/!%'06G.$#1!
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.(/!$#./5!6'!B#!N%#/!.$#!;.$9#/!G&67![x]*!!A'6#!67.6!&0!,'%6:$#>Wb!&%!#$$'(#'N%35!%7'G(!.%!
('6!&(%6.33#/M!$#%6.$6&(:!67#!-'%6:$#%_3!%#$I&@#!@.(!0&\!;.(5!'0!67#!$#.%'(%!67.6!;&:[email protected]%#!67&%!
6'!'@@N$*!
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&%!&(%6.33#/M!#(6#$!67#!0'33'G&(:!.6!67#!b&(N\!@';;.(/!3&(#1!
# perl –v
kkkkk!>-#@&.6&'(!Z''3!H#_N&$#;#(6%!?7#@9!kkkkk!
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*A*
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2SO!
^0!,#$3!&%!&(%6.33#/M!&(0'$;.6&'(!.B'N6!67#!I#$%&'(!G&33!B#!/&%-3.5#/*!!2//&6&'(.3!&(6#$0.@#%!.(/!
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G&67!67#!/.6.B.%#*!!^(%6$N@6&'(%!0'$!67#!&(%6.33.6&'(!'0!67#%#!;'/N3#%!0'33'G!67#!,'%6:$#>Wb!
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%'06G.$#!-.@9.:#%!'(!H,<SB.%#/!%5%6#;%*!Z7&%!N6&3&65!&%!0'N(/!'(!H#/[.6M!?#(6]>M!U#/'$.M!.(/!
'67#$!H,<SB.%#/!b&(N\!/&%6$&BN6&'(%*!!F'N!@.(!N%#!5N;!6'!&(%6.33!,'%6:$#>Wb!.(/!67#!$#_N&$#/!
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.(/!&(%6.33!,'%6:$#>WbM!#\#@N6#!67#!0'33'G&(:!@';;.(/1!
# yum install postgresql
^0!-$';-6#/M!#(6#$!e5g!6'!@'(0&$;!67#!&(%6.33.6&'(*!!Z7#!-.@9.:#!G&33!/'G(3'./!.(/!&(%6.33f!
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A).'&,,*J#/,*3&'&S&.#*%)'#/X&$#*U(32,#.*
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B5!67#!>-#@&.6&'(!Z''3*!!Z7#5!.$#1!
Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*A*
!
2SK!
,#$3!La^!Xperl-DBIY! Z7#!,#$3!L.6.B.%#!^(6#$0.@#!.33'G%!@';;N(&@.6&'(!
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,'%6:$#>Wb!/.6.B.%#*!
,#$3!LaLS,:!X'$!perl-DBD-PgY! Z7&%!&%!.!,'%6:$#>WbS%-#@&0&@!/.6.B.%#!/$&I#$!0'$!67#!
La^!;'/N3#!6'!.33'G!,#$3!6'!@';;N(&@.6#!G&67!67#!
,'%6:$#>Wb!/.6.B.%#!N%&(:!67#!La^*!
'$!,#$3!LaL1,:,,!
,#$3!Z#\6S?>"!Xperl-Text-CSVY! Z7&%!;'/N3#!.33'G%!0'$!,#$3!%@$&-6%!6'!-.$%#!.(/!
@$#.6#!?>"!X?';;.!>#-.$.6#/!".3N#%Y!0&3#%*!
=%#!FN;!6'!/'G(3'./!.(/!&(%6.33!X&0!(##/#/Y!.33!67$##!;'/N3#%*!!4(6#$!67#!@';;.(/1!
# yum install perl-DBI perl-DBD-Pg perl-Text-CSV
4(6#$!e5g!G7#(!-$';-6#/!6'!@'(0&$;!67#!&(%6.33.6&'(!'0!67#%#!-.@9.:#%*!!
A'6#1!^0!#$$'$%!.B'N6!-.@9.:#%!('6!B#&(:!0'N(/!.$#!/&%-3.5#/M!@7#@9!67#!%-#33&(:!'0!67#!-.@9.:#!
(.;#%!&(!5'N$!@';;.(/f!67#5!.$#!@.%#S%#(%&6&I#*!!
!'&/'*'R#*J(.'[/#!O=*!#/]%$#*&)3*J/#"&/#*A'*X(/*'R#*!"#$%&'%()*+((,*
Z'!%6.$6!67#!,'%6:$#>Wb!/.6.B.%#!%#$I&@#M!#\#@N6#!67#!0'33'G&(:!@';;.(/1!
# /etc/init.d/postgresql start
?7.(:#!6'!67#!N%#$!G7'!G&33!B#!$N((&(:!67#!>-#@&.6&'(!Z''31!
# su <user name here>
>6.$6!67#!6#$;&(.3SB.%#/!0$'(6S#(/!6'!,'%6:$#>Wb!X-%_3Y!G&67!67#!/#0.N36!-'%6:$#%!N%#$1!
> psql –U postgres
?$#.6#!,'%6:$#>Wb!N%#$X%Y!G&67!/.6.B.%#!@$#.6#!'-6&'(!0'$!#.@7!'0!67#!N%#$%!67.6!G&33!B#!$N((&(:!
67#!>-#@&.6&'(!Z''3*!!Z7#!N%#$!(.;#!%7'N3/!@'$$#%-'(/!6'!67#!b&(N\!N%#$!.@@'N(6!(.;#*!!Z7#!
@';;.(/!&%1!
=# CREATE USER <user name here> WITH CREATEDB;
4\&6!-%_3!B5!#(6#$&(:!n|_o1!
=# \q
26!67&%!-'&(6!5'N!%7'N3/!B#!$#./5!6'!0'33'G!67#!>-#@&.6&'(!Z''3!%#6!N-!-$'@#/N$#%!X$#0#$!6'!
?7.-6#$!KY*!!HN(!67#!%@$&-6!sptool_reqd_checks.sh!6'!@7#@9!67.6!.33!'0!67#!-.@9.:#%!.$#!.I.&3.B3#!
6'!67#!>-#@&.6&'(!Z''3*!!!
! !
Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*A*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*A*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
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* *
Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*B*
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* *
Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*B*
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APPENDIX*B*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*C!
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*C!
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*C!
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*D*
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Speciation*Tool*User’s*Guide,*V@4.0,*September*2016*
APPENDIX*D*
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