Deneb 1 26 Help

DENEb -1.
26 help documents
DENEb
help 1.26
2012 Atelgraphics
DENEb -1.26 help documents
Index
DENEb's General Introduction The philosophy behind DENEb Installation of DENEb and plugins Atoms, molecules and samples in DENEb DENEb's NanoExplorer NE: Loading new samples Note about DENEb's XY fo!mat NE: "a#ing samples NE: $!gani%ing you! samples DENEb's Sample Manipulator "&: The coo!dinates of you! ob'ects( Absolute, local, and scaled coo!dinates "&: T!anslating and !otating ob'ects( "&: The )lane( "&: "imple building "&: *uilding pe!iodic samples "&: Nanotube *uilde!s "&: +sing the atom ,)!ope!ties. )!ope!ty tags fo! "IE"TA simulations "&: Animation of samples DENEb's Project Browser )*: )*: )*: )*: )*: )*: /ene!al Idea( The concept of p!o'ect and simulation( 0uic1 !efe!ence guide( 2efining engine configu!ations( 3ob &anage! )a!amete!s Edito! )*: "IE"TA )a!amete!s Edito!
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DENEb 1.26 #ideo.demos Deneb4s YouTube #ideos DENEb's olde! #ideo.tuto!ials NanoE5plo!e! )!o'ect *!owse! "ample &anipulato!: In#o1ing &ouse d!ag mode "lide!s and buttons mode "imple building *uilding pe!iodic samples 6unning simulations DENEb's 78EAT."8EET" "ample &anipulato! &ouse Actions "ample &anipulato! 9ey na#igation DENEb's 9nown issues
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DENEb4s General Introduction
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The philosophy behind DENEb

DENEb is a softwa!e pac1age whose aim is to facilitate and e5pedite the wo!1 of !esea!che!s in the fields of Quantum Atomistic Simulations( :ith DENEb you can c!eate, e5ecute, !et!ie#e, o!gani%e and cent!ali%e you! thousands of simulations belonging to you! hund!eds of !esea!ch p!o'ects( You! simulations might apply to #e!y many diffe!ent physical systems, they could also belong to diffe!ent calculation engines ;e(g( SIESTA, uantumESP!ESS", #PM$, %ASP, etc<, and could be launched fo! e5ecution into se#e!al diffe!ent !emote hosts = Ne#e!theless, DENEb can 1eep t!ac1 of each of them and p!esent them to you neatly o!gani%ed and !eadily accessible f!om you! )7( +sing DENEb>s Project Browser the use! can choose any 1ind of classification fo! his simulations, based on 1ind of sample, type of calculation engine, etc( +se customa!y labels and o!gani%e them, in g!oups and p!o'ects, into t!ee st!uctu!es of any depth( 0uic1ly sea!ch and .with a single clic1. sto!e?!et!ie#e all of it: "imulations, p!o'ects, thei! o!gani%ation, and thei! !esulting data( In a simila! way, the g!oup of all the physical systems of you! inte!est can be easily o!gani%ed using DENEb4s NanoExplorer( This tool p!o#ides with t!ee.o!gani%ation of thousands o& samples, fully customi%able, and with quick-search abilities( It is seamlessly integ!ated with Project Browser and acts both as an independent database and as a sou!ce?!eposito!y of all you! samples( NanoExplorer p!o#ides #isuali%ation and impo!t?e5po!t abilities to?f!om diffe!ent fo!mats( You can mass import your older samples, that may be sto!ed in diffe!ent fo!mats( Also, its whole database can be sto!ed?!et!ie#ed with a single clic1( To edit you! samples use DENEb4s Sample Manipulator( This tool p!o#ides with e5tensi#e abilities to build samples f!om sc!atch, combine them into new ones, and modify e5isting ones( :ith Sample Manipulator you ha#e complete f!eedom to edit you! samples in almost any imaginable way( It int!oduces new concepts and au5ilia!y g!aphical tools that enable accu!ate manipulation and na#igation( You can open se#e!al instances of Sample Manipulator concu!!ently, this facilitates the simultaneous #isuali%ation?manipulation?combination of se#e!al samples( $f cou!se, Sample Manipulator is also fully integ!ated with the !est of DENEb>s tools by simple copy.and.paste ope!ations( @!om DENEb4s Project Browser, you can define simulations by coupling a gi#en sample to a gi#en set of computational parameters( The Parameter Editor enables g!aphical setting of all the computational parameters that define the simulation( The!e is one Parameter Editor tool fo! each calculation' en(ine plu(in ;e(g( the SIESTA plugin, the E plugin, the %ASP plugin, etc< that you include in DENEb( 2o not wo!!y about what Parameter Editor to use on what simulation: DENEb 1eeps t!ac1 of the calculation types and calls the co!!ect edito! in each case( You can use DENEb with any gi#en numbe! of plugins( )!o'ect *!owse!4s )ob Mana(er is an impo!tant tool since it holds the list of simulations that ha#e been launched, it lists thei! status and allows you to !et!ie#e and access the outputs of those that ha#e successfully finished( This tool allows you to: Launch simulations fo! e5ecution into !emote hosts whe!e the calculation engine is installedA monitor automatically the !emote computationsB state ;pending, !unning, success, fail<A and retrieve automatically the computationsB output.log and output files(
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Installation o& DENEb and plu(ins

Deneb TRIAL installation inst!uctions To install Deneb T!ial in you! )7 is #e!y easy, you only ha#e to follow these steps: *or +indows ;C, Dista<: 1. 2ownload and e5ecute the latest Deneb installe! fo! :indows, t!ial #e!sion, fo! e5ample: Edeneb_TRIAL_1.26.0-setup.exeE( F( @ollow the inst!uctions f!om the installation wi%a!d( *or ,inux ;most !ecent dist!ibutions<: 1. 2ownload and e5ecute the latest Deneb installe! fo! Linu5, t!ial #e!sion, fo! e5ample: Edeneb_TRIAL_linux_1.26.0-setup.binE( You might need to set e5ecution pe!mission to the file( 2. The installation will p!oceed automatically( E5ecute ./run.sh f!om the installation di!ecto!y, to launch Deneb( You can optionally e5ecute the shell called createShortCut.sh so that Deneb4s icon will appea! in the launche! when e5ecuting it( 8a!dwa!e minimum !eGui!ements to successfully !un Deneb T!ial: Intel iH 7)+ F(I /8% o! bette!( $! A&2 eGui#alent 7)+s( H /b 6A&( JKL &b a#ailable ha!d dis1 space( /!aphics ca!d ATI &obility 6adeon 82 KJIK, o! bette!, with J /* /!aphics &emo!y, with the latest d!i#e!s( Note: Deneb can !un in less powe!ful ha!dwa!e configu!ations, but good !eal.time !esponse might not be obtained unde! those ci!cumstances( 8a!dwa!e suggested !eGui!ements fo! a #e!y good pe!fo!mance: Intel iC MFL F(N /8% o! bette!( $! A&2 eGui#alent 7)+s( I /b 6A& o! g!eate!( JKL &b a#ailable ha!d dis1 space( /!aphics ca!d N#idia /TFFL, ATI KKCL o! bette! with F /* /!aphics &emo!y, with the latest d!i#e!s( "uppo!ted $pe!ating "ystems: :indows #ista? windowsC with (NET f!amewo!1 H(K o! bette! with latest se!#ice pac1s and the latest d!i#e!s ;2i!ectX JL o! newe!<( Linu5 9e!nel F(I o! newe!( Installing a plugin in DENEb In o!de! to c!eate simulations and !un them in you! Engine, you need to install the plu(in co!!esponding to the calculation engine ;e(g(, SIESTA o! #PM$ o! %ASP<( This is how to install a plugin in DENEb:
J(. 2ownload a plugin file ;with e5tension .bin< fo! you! Engine f!om the Atelgraphics website( F(. $btain f!om Atelgraphics you! plugin license file( H(. 6un DENEb application( I(. "elect Plugins->Install plugin f!om the Main menu( K(. *!owse and select you! downloaded -bin file and p!ess the Apply button( N(. )ut in DENEb4s !oot di!ecto!y you! plugin license file(
Notes: Deneb TRIAL version comes with the "IE"TA plugin already installed( "o, out of the bo5, you can p!oduce and launch siesta calculations f!om Deneb4s )!o'ect *!owse! with a single clic1( 2o not hesitate contacting us at: in o!atel"raphics.co# !epo!ting non e5pected beha#io!s of Deneb(
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&a1e su!e that you ha#e installed the latest d!i#e!s fo! you! g!aphics ca!d( This is !ele#ant specially in Linu5 since Deneb might not wo!1 p!ope!ly unless you ma1e su!e that you ha#e installed some !ecent d!i#e!s( To achie#e this, it sometimes !eGui!es fo! you to access the manufactu!e! web.page, download the d!i#e!s, and manually install them(
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Atoms. molecules and samples in DENEb

@o! DENEb, the sample is the basic unit that specifies a physical system( A sample is pa!t of a simulation- In othe! wo!ds, we only need to couple a sample with a set of computational parameters in o!de! to completely define a gi#en simulation( *!iefly defined: A sample is a set o& molecules( In tu!n, a molecule is simply de&ined as a set o& atoms ( And an atom is defined as a gi#en nucleus placed at a gi#en point of space( As fo! the elect!ons: To define a gi#en sample, elect!ons need not to be specified since the elect!onic density is, instead, usually a !esult of the simulation once computed( Atoms are represented as spheres in DENEb( *y default thei! si%e is gi#en by the co#alent !adius of the co!!esponding chemical specie( Thei! default colo! is gi#en by some common standa!d ;3&ol<( The !adii and colo!s of any g!oup of atoms can be customa!ily changed at will, when using Sample Manipulator&olecules and samples do not ha#e any pa!ticula! !ep!esentation on thei! own, othe! than thei! g!oup of atoms ;sphe!es<( You can, ne#e!theless, select?unselect, t!anslate, !otate, !eplace, eliminate, etc, in sho!t, t!eat them as units by using the Sample Mana(er of Sample Manipulator- "amples and molecules can also be add!essed by mouse actions if choosing the pic1 mode acco!dingly ;pic1 mode options a!e: 4atom4, 4molecule4 and 4sample4<( You can also clone them ;o! pa!ts of them< and t!ansfe! molecules f!om sample to sample, o! atoms f!om molecule to molecule, etc((( the #e!y many possibilities will be disco#e!ed in this document and #ideo.tuto!ials(
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DENEb4s NanoExplorer
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DENEb4s NanoExplorer/ ,oadin( new samples

As we ha#e said in p!e#ious sections, fo! DENEb, the sample is the basic unit that specifies a physical system( DENEb4s NanoExplorer is a database of samples, that may contain any numbe! of samples o!gani%ed in g!oups in an a!bit!a!y t!ee st!uctu!e( The samples in NanoExplorer can be used as the sta!ting point, o! building bloc1s to compose new samples using Sample Manipulator( In addition, any new sample built in Sample Manipulator can be sto!ed fo! late! use in NanoExplorer( The connection point among these tools and the Project Browser is, as you al!eady 1now, DENEb4s #lipboard( $ut of the bo5 NanoExplorer comes filled out with some samples in some default t!ee st!uctu!e, impo!tantly, note that these a!e 'ust some e5amples on how you can o!gani%e you! NanoExplorer database, they a!e not meant to be accu!ate o! useful fo! any pa!ticula! pu!pose( NanoExplorer is instead intended to be you! p!i#ate set of own tested samples( :e show ne5t how to load samples into NanoExplorer( The!e a!e se#e!al ways:
1)
+sing NanoExplorer4s Load Sample from file menu item( This is used to load into NanoExplorer samples that ha#e been sto!ed in files using DENEb4s nati#e fo!mat ;e5tension .dns). This is the p!ocedu!e:
(a) (b)
@!om DENEb4s main menu ba! choose: odules !ano"#plorer( This will !aise o! show NanoExplorer if hidden( "elect one of the g!oups in NanoExplorer, the loaded sample will be added to the selected g!oup(
(c)
"elect $ile f!om NanoExplorer4s main menu(
(d) (e)
"elect Load Sample from file A new dialog fo! the selection of the file appea!s( 7hoose o! type the name of the file that you want to load into NanoExplorer( It should be a file with e5tension (dns ;a sample in nati#e DENEb4s fo!mat<(
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(f)
7hec1 that it has been loaded into the selected g!oup( Note that the name of the new sample in NanoExplorer need not to coincide with the name of the file( Li1ewise you can sa#e any sample labeled ,5- in a file named ,y-, these names could, but need not, be the same(
2)
+sing NanoExplorer4s Import %Y& files menu item( This is used to load into NanoExplorer files that ha#e been sto!ed in the $%& simple fo!mat ;e5tension .XYZ) [1]. This is the p!ocedu!e:
(a) (b) (c)
@ollow steps a, b and c of the p!e#ious case ;called: using NanoExplorer4s Load Sample from file menu item<( "elect Import %Y& files' A new dialog fo! the selection of files appea!s( "elect one or se0eral files to be loaded( You can eithe! select them with mouse actions o! type thei! file names subseGuently between double Guotes and sepa!ated by white spaces( 7lic1 'pen.
(d)
7hec1 that the files ha#e been loaded( In this case the name of the samples in NanoExplorer is di!ectly ta1en f!om the name of the file( This is because the simple XYZ fo!mat does not include any label fo! the sample it contains( You can late! on !ename the sample as you wish using its conte5t menu ;t!igge!ed by Ri"ht-Clic( on the highlighted item<(
(e)
$ptionally, #isuali%e the samples contained in the 'ust loaded files by using thei! context) #enus( "elect, fo! this pu!pose, (isuali)e Sample( To pop out the conte5t menu of a gi#en sample you ha#e to highlight it fi!st and then Ri"ht-Clic( on it( ;f< If the file to be loaded holds mo!e than one set of atoms, i(e( it consists of the
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concatenation of ,single configu!ations- in the $%& fo!mat, a choice menu will appea! in which the use! can choose between two options, load each f!ame as:
as different molecule o! as a time step of ms
:hen the button Load %Y& $ile is p!essed, the file will be loaded using the cu!!ently selected choice( This way, one can use the $%& fo!mat files eithe! to desc!ibe a single sample composed of se#e!al molecules o! a single sample that e#ol#es in time( In the latte! choice Deneb will fi!stly chec1 that all f!ames a!e consistent ;they ha#e the same chemical species in the same o!de!<, and then, Deneb will p!oduce an animation whe!e f!om f!ame to f!ame a pause of the chosen numbe! of mili.seconds ;the default is IL< will be ta1en when it is played in the automatic mode ;automatic animation can be played using Sample Manipulator<( Note: If a sample contains an animation, we usually say that it contains a t!a'ecto!y( Notes:
The icon !ep!esenting the sample in the NanoExplorer t!ee denotes if it contains a t!a'ecto!y, in such case this is how it loo1s: If Deneb detects that the f!ames do not belong to the same sample, it will not be loaded, in this case an e!!o! message will be w!itten in Deneb's ,o( +indow, such as: ,*RR'R+,...-+,...-+the) ra#es)do)not)belon")to)the)e.olution) o )the)sa#e)sa#ple/
3)
+sing the following NanoExplorer4s menu items: Import *I$ files+ Import $,$ $iles+ is analogous to the p!e#iously e5plained section about the menu item called Import %Y& files, the!efo!e we will not !epeat the details he!e(
123 Note about the XYZ &ormat( In this simple fo!mat the list of atoms is gi#en as the chemical species symbol followed by the coo!dinates of the atom in Angst!oms( The!e is a heade! consisting of two lines: the fi!st line contains only the numbe! of atoms, while the second line is an a!bit!a!y comment that can be left blan1 e#entually ;but can not be !emo#ed<( In this fo!mat one can subseGuently attach one set of atoms afte! anothe! in the same file( DENEb can load these ,multi.f!ame files- doing the inte!p!etation of each set either as a new molecule of the same sample, or as a new f!ame ;instantaneous photo o! time step< of the dynamics of a gi#en sample( +se Sample Manipulator to open multi.f!ame $%&)files selecting one of these options, note that when you select to load a multi.f!ame $%&)file as the dynamics of the same set of atoms, one !eGuisite, that DENEb chec1s fo!, is that all f!ames !efe! to the same set of atoms at diffe!ent times, i(e( The numbe! of atoms should coincide fo! all f!ames, and the chemical species should also coincide f!om one f!ame to the ne5t( These conditions need not to be met when the file is loaded using the othe! modality: that of conside!ing each f!ame as a diffe!ent molecule of the same sample( A last note about the $%& fo!mat as unde!stood by DENEb is that one can use the comment line to instruct DENEb with useful information( In pa!ticula! one can define the 0nit)Cell of the sample in such comment line ;o! the comment line co!!esponding to the fi!st f!ame in the case of multi.f!ame files<( To achie#e this, simply w!ite the unit cell lattice
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#ecto!s in the comment line as follows: lattice1ectors+2)ax)a3)a45bx)b3)b45cx)c3)c4)6 being ;a5,ay,a%< the coo!dinates of the fi!st lattice #ecto! ins Angs ;!eplace a5 by the co!!esponding numbe!, etc<, ;b5,by,b%< the coo!dinates of the second, and so on and so fo!th( This way, the so called ,DENEb4s ) XYZ ))fo!mat) is compatible but e5tends the capabilities of the standa!d XYZ fo!mat( 8e!e is a #e!batim e5ample of a multi.f!ame file in DENEb4s XYZ fo!mat: 7 lattice1ectors+2)8.0)0.0)0.0)5)0.0)9.0)0.0)5)0.0)0.0)6.0)6 ')))0.0))0.0))0.0 :)))0.;))0.0))0.0 :))-0.2))0.9))0.0 7 ')))0.0))0.0))1.0 :)))0.;))0.0))1.0 :))-0.2))0.9))1.0 7 ')))0.0))0.0))2.0 :)))0.;))0.0))2.0 :))-0.2))0.9))2.0 7 ')))0.0))0.0))7.0 :)))0.;))0.0))7.0 :))-0.2))0.9))7.0 It contains fou! f!ames that !ep!esent the same set of atoms with the only diffe!ence that a!e displaced by one Ang along the a5is f!om one f!ame to the ne5t( The!efo!e in this case you could optionally load ;using Sample Manipulator< this file as a time se!ies o! as a se!ies of molecules that belong to the same sample(
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DENEb4s NanoExplorer/ Sa0in( samples

As we ha#e said in p!e#ious sections, fo! DENEb, the sample is the basic unit that specifies a physical system( DENEb4s NanoExplorer is a database of samples, that may contain any numbe! of samples o!gani%ed in g!oups, in an a!bit!a!y t!ee st!uctu!e( The samples in NanoExplorer can be used as the sta!ting point, o! building bloc1s to compose new samples, when using Sample Manipulator( Also, any new sample built using Sample Manipulator can be sto!ed fo! late! use in NanoExplorer( The connection point among these utilities and the Project Browser is, as you al!eady 1now, DENEb4s #lipboard( $ut of the bo5 NanoExplorer comes filled out with some samples in some default t!ee st!uctu!e, impo!tantly, note that these a!e 'ust some e5amples on how you can o!gani%e you! NanoExplorer database, they a!e not meant to be accu!ate o! useful fo! any pa!ticula! pu!pose( NanoExplorer is instead intended to be you! p!i#ate set of own tested samples( :e show ne5t how to sa0e in dis5 the samples sto!ed in NanoExplorer( The!e a!e se#e!al ways:
1)
2)
2oing nothing at all: NanoExplorer has file persistence built in, this means that, e#e!y time you add a new sample to NanoExplorer, it will c!eate a !elated file and will sto!e the info!mation in the!e( It acts as a pe!sistence database in this sense( You can close DENEb at anytime being su!e that all samples in NanoExplorer will !emain the!e ne5t time when you open DENEb( NanoExplorer is, in fact, the standa!d place whe!e you will gi#e pe!sistence and o!gani%ation to all you! samples when using DENEb( It can hold hund!eds of thousands of samples, and it implements la%y loading algo!ithmsA this means that you do not need to wo!!y about the si%e of the whole database in NanoExplorer( E#en though the data base might be too la!ge in te!ms of memo!y, DENEb only loads in 6A& the samples that a!e being used at each time, while the !est !emain sto!ed in dis1( +sing the Save Sample to file''' menu item f!om NanoExplorer4s $ile menu( ;a< 8ighlight the sample that you intend to sa#e(
(b)
$ptionally( +se its conte5t menu ;t!igge! the conte5t menu by Ri"ht-Clic( on the highlighted sample< to #isuali%e it( "o you can be su!e that it is, in fact, the one that you want to e5po!t( The co!!esponding 0iew window lets you 1now the number o& molecules and the number o& atoms that the sample contains, it can be seen in the title ba! of the same(
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(c)
"elect $ile f!om the NanoExplorer menu ba!, choose Save Sample to file
(d)
A new dialog appea!s to let you choose the file name whe!e the sample is going to be sa#ed in DENEb4s nati#e fo!mat( 7hoose the file name by mouse actions o! type a new name( 7lic1 ,Sa.e-(
(e)
This completes the p!ocess, you can 0eri&y that the sample has been co!!ectly sa#ed in that pa!ticula! file by !eloading it into NanoExplorer. into a diffe!ent g!oup to a#oid confusion( *ut note that the!e would not be name collisions as NanoExplorer admits name redundancy(
3)
+sing the "#port as ,"!"- %Y& file' menu item f!om NanoExplorer4s $ile menu(
(a) (b)
@ollow steps ;a< and ;b< f!om the p!e#ious case entitled: +sing the Save Sample to file''' menu item ((( "elect $ile f!om the NanoExplorer menu ba!, choose "#port as ,"!"- %Y& file
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(c)
A new dialog appea!s to let you choose the file name whe!e the sample is going to be sa#ed in DENEb4s XYZ fo!mat( 7hoose the file name by mouse actions o! type a new name( 7lic1 ,Sa.e-(
(d)
This completes the p!ocess, you can 0eri&y that the sample has been co!!ectly sa#ed in that pa!ticula! file by !eloading into NanoExplorer into a diffe!ent g!oup to a#oid confusion( *ut note that the!e would not be name collisions as NanoExplorer admits name redundancy, it is up to the use! to choose wisely the labels fo! the samples( Note/ If you a!e using Deneb Trial #e!sion, a ma5imum of FL atoms will be e5po!ted using the XY fo!mat, o! any fo!mat othe! than Deneb4s nati#e(
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DENEb4s NanoExplorer/ "r(ani6in( your samples

As we ha#e said in p!e#ious sections, fo! DENEb, the sample is the basic unit that specifies a physical system( DENEb4s NanoExplorer is a database of samples, that may contain any numbe! of samples o!gani%ed in g!oups in an a!bit!a!y t!ee st!uctu!e( The samples in NanoExplorer can be used as the sta!ting point, o! building bloc1s to compose new samples using Sample Manipulator( Li1ewise, any new sample built in Sample Manipulator can be sto!ed fo! late! use in NanoExplorer( The connection point among these utilities and the Project Browser is, as you al!eady 1now, DENEb4s #lipboard( $ut of the bo5 NanoExplorer comes filled out with some samples in some default t!ee st!uctu!e, impo!tantly, note that these a!e 'ust some e5amples on how you can o!gani%e you! NanoExplorer database, they a!e not meant to be accu!ate o! useful fo! any pa!ticula! pu!pose( NanoExplorer is instead intended to be you! p!i#ate set of own tested samples( :e show ne5t how to or(ani6e the samples sto!ed in NanoExplorer in a t!ee st!uctu!e with a!bit!a!y depth( The main ope!ations that you need to 1now a!e the following(
1)
8ow to c!eate (roups ;in NanoExplorer, (roups a!e to samples as folde!s a!e to files in you! ope!ating system<( To c!eate a new g!oup in NanoExplorer highlight the ta!get g!oup, whe!e the new g!oup is going to be c!eated and t!igge! its conte5t menu ;using Ri"ht<Clic(<, select then the !e. /roup menu item( As a conseGuence a new g!oup is c!eated with a default name, !ename it if you wish using its conte5t menu(
2)
8ow to eliminate (roups f!om the NanoExplorer( "elect the g!oup that is going to be eliminated and use its conte5t menu item called ,elete /roup( A confi!mation dialog will appea!, p!ess ,Yes- to p!oceed with the deletion(
Notes: The deletion of a gi#en g!oup will eliminate all its contents ;descendants<(
The!e is no undo afte! deletion, use the!efo!e with ca!e(
H< 8ow to mo#e a (roup ;sou!ce g!oup< into anothe! (roup ;ta!get g!oup< of the NanoExplorer( 8ighlight the g!oup that you want to mo#e, Le t-Clic( and d!ag it, you will see that the cu!so! changes to the following:
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This means that a d!ag.and.d!op ope!ation is being ca!!ied out( 2u!ing the d!ag, the sou!ce g!oup !emains highlighted, while the possible ta!gets will be highlighted as the cu!so! touches them(
Note that only (roups ;and not samples< a!e highlighted as possible ta!gets du!ing the d!ag ope!ation( :hen you !each the desi!ed ta!get g!oup, !elease the Le t-Clic(, this will complete the d!ag.and.d!op ope!ation( As a !esult the sou!ce g!oup will be mo#ed to become a new child of the ta!get( Notes: *efo!e sta!ting the d!ag.and.d!op ope!ation, ma1e su!e that the ta!get g!oup is !eachable, in othe! wo!ds, that its ascendants a!e not collapsed(
If the ta!get g!oup is !eachable but not #isible ;out of the cu!!ent window limits<, wo!!y not, NanoExplorer will automatically sc!oll p!ope!ly while you d!ag( If the d!op action is done o#e! a sample ;instead of a (roup<, the ope!ation will ha#e no effect( If, du!ing the d!ag, the cu!so! is ta1en beyond the limits of the NanoExplorer window, it !eco#e!s its default shape, but note that the d!op action can still occu!( :hen you ,d!op- out of NanoE5plo!e!, it will still set the ta!get at the ,cu!!ent !ow- which is deduced by e5t!apolation beyond its cu!!ent #iewpo!t(
I< 8ow to add samples to a (roup( The!e a!e two possibilities to do this: (a) Pastin( the sample sto!ed in DENEb4s #lipboard( To do this simply highlight the (roup whe!e you want the sample to be pasted and t!igge! its conte5t menu ;Ri"ht-Clic(<( 7hoose the menu item called 0aste Sample(
Note:
An e5act copy of the sample in DENEb4s #lipboard is added to the highlighted g!oup( The #lipboard the!efo!e maintains its contents intact(
;b< Importin( some sample sto!ed in files( 6efe! to the p!e#ious section about Loading samples into NanoExplorer-
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K< 8ow to mo0e a sample &rom one (roup to another( You can simply use the d!ag.and.d!op techniGue as e5plained in point ;H< abo#e, only that the sou!ce is a sample instead of a g!oup in this case( This ends this section about Deneb's NanoExplorer(
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DENEb4s Sample Manipulator
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DENEb Sample Manipulator/ The coordinates o& your objects- Absolute. local. and scaled coordinates
DENEb4s Sample Manipulator defines a fi5ed, absolute 7a!tesian system of coo!dinates( "amples a!e placed at points with absolute coo!dinates( Meanin( o& 7placin( a sample at a point8/ Note that a sample is an e5tended ob'ect, so placing it at a gi#en point in space has to be p!ope!ly defined( :e p!ope!ly define placing of a sample by !efe!!ing to an specific point !elated to the sample, we call it the sample4s re&erence point( Thus, when you place sample at a gi#en point of space ;e(g( by mouse selecting it<, what you a!e placing the!e is the sample4s re&erence point( +hat is the sample4s re&erence point9 In DENEb4s con#entions, the !efe!ence point of a sample is an a!bit!a!y point( It does not need to be its geomet!ical cente!, o! the position of any of its atoms( It is the point whe!e the sample4s local re&erence system is placed( $f cou!se, the sample4s local !efe!ence system is a 7a!tesian coo!dinate system that the sample ca!!ies with it, such that all molecules that belong to that sample a!e placed at local points defined with !espect to the sample4s local !efe!ence system( As a conseGuence, if you mo#e the sample4s !efe!ence point, f!om an absolute point to anothe!, all its molecules ;p!ese!#ing thei! local coo!dinates< mo#e along( Note that a molecule is to its atoms, li1e a sample is to its molecules( The!efo!e the position of an atom with !espect to the moleculeBs local !efe!ence system is also to be p!ope!ly defined( And DENEb defines it in a completely analogous way: Meanin( o& 7placin( a molecule at a point8/ :e p!ope!ly define placing of a molecule by !efe!!ing to an specific point !elated to the molecule, we call it the molecule4s re&erence point( Thus, when you place a molecule at a gi#en point, what you a!e placing the!e is the molecule4s re&erence point( +hat is the molecule4s re&erence point9 In DENEb4s con#entions, the !efe!ence point of a molecule is an a!bit!a!y point( It does not need to be its geomet!ical cente!, o! the position of any of its atoms( It is the point whe!e the molecule4s local re&erence system is placed( The molecule4s local !efe!ence system is a 7a!tesian coo!dinate system that the molecule ca!!ies with it, such that all atoms that belong to that molecule a!e placed at local points defined with !espect to the molecule4s local !efe!ence system( As a conseGuence, if you mo#e the molecule4s !efe!ence point, f!om a point to anothe!, all its atoms ;p!ese!#ing thei! local coo!dinates< mo#e along( $f cou!se, at a gi#en time, each atom is ultimately placed at a gi#en point of space that has its absolute coo!dinates #alues( DENEb4s Sample Manipulator does present to you both the local and absolute coordinates o& atoms and allows you to edit one or another at your will. 5eepin( their synchroni6ation at all times ;use fo! this the Atom Editor t!igge!ed by: Selection Selection operation "dit current selection<( In DENEb, all reference systems have the same orientation at all times , this is: All local o! absolute, X a5es a!e pa!allel to each othe!, and li1ewise about the Y and a5es( In @igu!e J you can see some schematic !ep!esentation of the coo!dinate systems conside!ed by Sample Manipulator(
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*i(ure2/ DENEb4s Sample Manipulator coordinate systems ( A sample, consisting of two wate! molecules, is !ep!esented along with an s1ematic #iew of the coo!dinate systems conside!ed by Sample Manipulator- The!e is an absolute re&erence system ;thic1e! a5es labeled ,Absolute-<, with !espect to which the sample has been placed at a gi#en point in space ;the sample4s re&erence point<, whe!e the a5es labeled as ,sample- a!e found( A solid blac1 line !ep!esents the #ecto! f!om the absolute o!igin to the sample4s position( *oth molecules ha#e positions defined in local coo!dinates with !espect to the sample4s !efe!ence system( The positions of the molecules in the sample4s !efe!ence system a!e !ep!esented by the solid o!ange #ecto!s( The molecule4s local re&erence systems ;labeled as ,mol.J- and ,mol.F-< a!e the ones with !espect to which the atom;s local coordinates a!e defined( )u!ple thin lines !ep!esent the positions of the atoms in thei! molecule local systems(
Scaled coordinates/ All samples posses a so called unit cell ;a bo5 intended fo! pe!iodic !epetitions<( *y default the unit cell is not shown, which means that the sample is 4non.pe!iodic4 ;also called 4isolated4<, but the use! can choose to show the unit cell ;using the molecule4s Sample Mana(er conte5t menu<, which automatically means that the sample becomes 4pe!iodic4( The pe!iodic o! isolated cha!acte! is mostly !ele#ant when a simulation is launched to a gi#en engine( The unit cell bo5 is, in tu!n, defined by : lattice 0ectors, that fo!m as well a !efe!ence system( It is usual to gi#e the atomic coo!dinates with !espect to the unit cell lattice #ecto!s, in some cases it is simple! to do it this way( Sample Manipulator p!esents, as well, the scaled coordinates of the atoms at use!4s will, and allows to di!ectly edit them, 1eeping pe!fect synch!oni%ation with !espect to thei! local and absolute ones( To #isuali%e?modify the scaled coo!dinates of any gi#en g!oup of atoms use the "ample &anipulato!4s Atom Editor that can be t!igge!ed f!om the Selection menu: Selection Selection 1perations "dit current selection.
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DENEb4s Sample Manipulator/ Translatin( and rotatin( objects

Meanin( o& translatin( samples. molecules and atoms/ in Sample Manipulator you will lea!n that you can t!anslate atoms, molecules and samples( :hat is the diffe!ence between 4mo#ing all atoms in a molecule4 and 4mo#ing the molecule itself4O If you select all atoms in a molecule and shift thei! position by a #ecto! ;using the main menu option: Selection Selection 1perations Translate , that applies to atoms< you a!e changing thei! local coo!dinates with !espect to thei! local !efe!ence system ;with !espect to thei! molecule4s !efe!ence system<( 8owe#e!, if you choose to shift the position of the molecule itself ;using its Sample Mana(er conte5t menu< you a!e 1eeping fi5ed the local coo!dinates of the atoms but you a!e changing the coo!dinates of the molecule with !espect to its sample4s local !efe!ence system( Disually, howe#e!, you will see the atoms displacing 'ust in the same way( Li1ewise, it is not the same to t!anslate all molecules in a sample than to t!anslate the sample itself( A bit of p!actice will su!ely let you lea!n these simple concepts !eadily( Meanin( o& rotatin( samples. molecules and atoms/ in Sample Manipulator you will lea!n that you can !otate atoms, molecules and samples with !espect to a!bit!a!y a5es( :hat is the diffe!ence between 4!otating all atoms in a molecule4 and 4!otating the molecule itself4O If you select all atoms in a molecule and !otate thei! position by an angle with !espect to a gi#en a5is ;using the main menu option: Selection Selection operations Rotation , that applies to all selected atoms<, you a!e changing thei! local coo!dinates with !espect to thei! local !efe!ence system ;molecule4s !efe!ence system<( 8owe#e!, if you choose to !otate the position of the molecule itself ;using the Sample Mana(er conte5t menu of that molecule< ,you a!e 1eeping fi5ed the local coo!dinates of the atoms and you a!e 'ust displacing ;a!ound the !otation a5is< the molecule4s !efe!ence point, whose local coo!dinates ;with !espect to its sample4s local !efe!ence system< will change( In fact, unli1e in the t!anslation case, these two cases !esult in !eally diffe!ent atomic motions: @o! e5ample if the molecule4s !efe!ence point lays on the !otation a5is, the ,!otations of the molecule- lea#e e#e!ything unchangedA while it is not so if one chooses to !otate the atoms indi#idually( Li1ewise, it is not the same to 4!otate all molecules in a sample4 than 4to !otate the sample itself4 ;which 'ust displaces its !efe!ence point<( A bit of p!actice with Sample Manipulator will su!ely help you lea!n these concepts bette!, as well(
DENEb4s Sample Manipulator/ The planeTo edit you! samples use DENEb4s Sample Manipulator( This tool p!o#ides with e5tensi#e abilities to build samples f!om sc!atch, combine them into new ones, and modify e5isting ones( :ith Sample Manipulator you ha#e complete f!eedom to edit you! samples in almost any imaginable way( It int!oduces new concepts and au5ilia!y g!aphical tools that enable accu!ate manipulation and na#igation( The Plane of the Sample Manipulator is one of such tools( It is an au5ilia!y ob'ect that helps in se#e!al ways: Enables accu!ate mouse.pic1ing of points in the th!ee dimensional space, fo! se#e!al uses: fo! placement of new ob'ects, placement of cente! of !otation of the main #iew came!a, displaying the coo!dinates of an specific mouse.pic1ed point( )!o#ides a geomet!ical !efe!ence to select?un.select atoms acco!ding to thei! position( The Plane is 'ust that: An infinite plane that can be placed pe!pendicula! eithe! to X, Y, o! the a5is and at any height within( Its o!ientation can be cont!olled with 0lane 0lane settings 0erpendicular to+ and its position can be controlled .ith the plane control2panel placed at the bottom2left corner of the Sample anipulator main .indo.' The plane control'panel is a combined slide!, te5t, and spinne!.buttons synch!oni%ed input system, you can specify the plane4s position by eithe! of them( The plane4s motion !ange can be modified by 0lane 0lane settings Set motion range, that has the 1ey sho!t.cut Ctrl<R( E#en though the plane is infinite, its #isual !ep!esentation is !athe! not, so we can actually see it bette!( It is a !ectangula! a!ea of a use! chosen si%e, position and colo!( To choose these 0isual settin(s o& the plane use: 0lane (isual Select color, and 0lane (isual Select visible si)e, !especti#ely( <int/ the plane can be also used as a location template by simply playing with its #a!iable #isual shape and si%e, e(g, if you wish to place I atoms in an sGua!e configu!ation of a gi#en si%e you
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can simply choose the plane to ha#e that shape and si%e, and then Clic(-place the atoms at its #e!tices(
DENEb4s Sample Manipulator/ Simple buildin(

The!e a!e many diffe!ent ways to const!uct new samples using "ample &anipulato!( In gene!al you will p!obably sta!t with some al!eady made samples, modify them and?o! combine them into new ones( Ne#e!theless, fo! the sa1e of simplicity, we desc!ibe he!e the case in which you sta!t with a clean slate: 2= <ow to build a simple molecule &rom scratch/ a) @!om DENEb4s main menu ba! choose: 3indo. (ie. Sample anipulator !e. ( This will c!eate and show a new Sample Manipulator( A toolba! sho!t.cut button fo! this menu item can be also found 'ust below the main menu ba!( This is how it loo1s:
b) c)
d)
The main la!ge! button c!eates a new Sample Manipulator when p!essed, while the smalle! button at its !ight gi#es sho!t.cut access to the al!eady c!eated "ample &anipulato!s ;if any<( @!om the newly c!eated Sample Manipulator, choose the tab ,sample- in the Palette window, placed by default at the bottom !ight( "elect the sample called ,Empty-, it is a sample with one empty molecule, whe!e we can add atoms to fill it up at will( To place the Empty sample in space Le t-Clic( at some point of the Main4s %iew Plane( *y default the plane is seen as a yellow sGua!e of K Angs of si%e( "ince it is empty, in this case, you will notice that a new sample has been c!eated not because of the appea!ance of atoms ;sphe!es< at the scene, but because of the appea!ance of a new b!anch in the Sample Mana(er window ;placed at the uppe! left co!ne! of the Sample Manipulator by default<( 6ename the sample( To do it, highlight its name in the Sample Mana(er and Ri"ht-Clic() on it to t!igge! its conte5t menu( 7hoose Rename this sample( Li1ewise do the same with its molecule that has no name by default( :e ha#e chosen ,8F- as names fo! this e5ample(
e)
Now set the molecule and sample that a!e going to be edited, in this case, the only molecule and sample that the!e a!e in the scene( To this aim, highlight the sample ,8F- in the Sample Mana(er and Ri"ht-Clic( on it to t!igge! its conte5t menu( "elect Set as sample being edited( Its icon changes afte! this selection, a pencil is added as symbol of being edited( This setting is necessa!y so the "ample &anipulato! 1nows what sample is the one that is !ecei#ing the new molecules that we may add by clic1ing on the scene( Li1ewise select the molecule and t!igge! its conte5t menu, select Set as molecule being edited' This settings is necessa!y so the "ample &anipulato! 1nows what molecule is the one that is !ecei#ing the new atoms that we may add by clic1ing on the scene(
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f)
Now lets add a couple of atoms to the molecule being edited( To this aim, select the Atom tab in the Palette and highlight the 8yd!ogen atom on the list( Le t-Clic( on the plane at couple of positions to p!oduce a couple of new atoms( Hint: if you wish to delete some atom use Shi t)<)Le t-Clic( on it( Now lets select them, to do this, simply Ctrl)<)Le tClic( on them( $nce selected we can t!igge! the Atom Editor to accu!ately edit thei! positions( +se Selection Selection operations "dit current selection
g)
Lets use the Atom Editor to set thei! local.coo!dinates to ;L,L,L< and ;J,L,L< !especti#ely( These a!e the coo!dinates at thei! molecule4s !efe!ence system( To do this, you will ha#e to display thei! local.coo!dinates by selecting Local f!om the conte5t menu *oordinates Local(
h< You can simply type.in the new local coo!dinates(
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i)
@inally place the sample4s !efe!ence point at the o!igin ;L,L,L< by using ove 0lace this sample at a point, f!om its conte5t menu at the Sample Mana(er t!ee( Li1ewise place the molecule4s !efe!ence point at the o!igin using its conte5t menu(
j)
To gi#e pe!sistence to you! newly c!eated sample the!e a!e se#e!al ways, fo! e5ample you can select Save all to !ano"#plorer f!om the $ile menu in the Sample Manipulator,
choose a name fo! the folde! that will hold the sample in NanoExplorer, o! accept the default name ,S= ) Session-, in such case the !esulting path fo! ou! sample in the NanoE5plo!e! database will be: S=)Sa.e)>)S=)Session)>):2
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>= <ow to modi&y an already built sample/ a) Let us modify a sample by simply st!etching one of its bonds( Let us choose the sample called ?utane, find it in NanoExplorer. unde! the folde! g!oup called =olecules:
b) c)
7hoose "dit *op4 to clipboard f!om the samples #isuali%ation window menu o! *op4 Sample f!om its conte5t menu in the t!ee !ep!esentation( This places an identical copy of the sample in Deneb4s #lipboard( $pen a new "ample &anipulato! and paste the 7lipboa!d contents ;in this case the copy of the sample called *utane< in it( To do this, choose Add sample from clipboard f!om the conte5t menu at the !oot of the Samples Mana(er:
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The !esult is that a copy of the sample called *utane is placed in the sample manipulato!, its !efe!ence point at ;L,L,L<:
d)
)!ess Ctrl)<)Le t-Clic( on the 7 atom at the lowe! e5t!eme ;along Y<, and on its th!ee 8yd!ogen neighbo!s( The !esult should be that they a!e selected, and the!eby ,glowingwith !espect to the !est( $n the Sample Mana(er, the selected atoms appea! in !ed in1 and in italics(
e)
:e a!e going to displace the fou! selected atoms L(F Ang along Y, this will st!etch the 7.7 bond( To this aim, choose Selection Selection operations Translation f!om the Sample Manipulator main menu(
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"et the t!anslation #ecto! as ;L(L , .L(F , L(L< and p!ess ente! o! the button to apply the t!anslation(
f)
Note: to monito! how the distance between two atoms changes in !eal time, you can use the Selection Selection operations onitor distance tool(
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You can also measu!e the distances between atoms by using the $istances tab of the Atom Editor, which is filled out when /enerate distances table is chosen f!om the conte5t menu in the same Atom Edito!, at the option: 5ighlighted /enerate distances table ( This fills the $istances tab with a table of distances fo! the cu!!ently highlighted atoms in the Atom Edito!4s list(
Note: 2o not confuse the highlighted atoms in the Atom Editor with the ;glowing< selected atoms in space, they might !efe! to the same atoms, but they need not( :e !ese!#e the wo!d , selected- fo! the glowing atoms, the ,Selection- menu applies to them( 8owe#e! the wo!d ,highlighted- is used fo! those !ows highlighted at the Atom Editor o! those b!anches highlighted at the Sample Mana(er, whose co!!esponding atom might o! might be not selected ;glowing<( Incidentally, note that ope!ations on the selected ;glowing< atoms a!e g!ouped unde! the menu called Selection, while ope!ations on molecules and samples as a whole a!e g!ouped at the Sample Mana(er t!ee conte5t menus(
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g< To #isually compa!e the new st!etched sample with the o!iginal one is simple, we can 'ust paste again a second copy of the o!iginal one and see the supe!imposed !ep!esentations(
Note: To obtain the p!e#ious snapshot, we ha#e: pasted again the same sample ;-utane< and !enamed it as -utane6original, then !educed all atoms !adii as follows: "elected all atoms, then t!igge!ed the Atom Editor fo! them by Selection Selection operations "dit current selection A then highlighted all !owsA then used the Atom Edito!4s conte5t menu 5ighlighted Radius "dit radius( Then we ha#e clea!ed the selection ; Selection *lear<, and !e.selected only the atoms of -utane6original ;using its conte5t menu in the t!ee of Sample Mana(er<( @inally, we used 0references -onds Re2calculate bonds -et.een selected atoms to show bonds between the atoms of -utane6original( :he!e we had chosen L.02)An" fo! the bond !adii at the bonds settings menu(
DENEb4s Sample Manipulator/ Buildin( Periodic samples

$i&&erence between periodic and non'periodic samples All samples in Deneb ha#e a so.called ?nit'#ell( E#en though you might ha#e not defined any, all samples ha#e a unit cell which is set as a cube of one Ang si%e by default( "o what is the diffe!ence between a pe!iodic sample and a non.pe!iodic oneO )e!iodic samples a!e those whose +nit.cell is being shown( To ma1e the +nit.cell show, simply select the chec1.bo5 Sho. f!om the sample4s conte5t menu: 7nit cell Sho., so you ma1e it pe!iodic( 7on#e!sely un.select the chec1.bo5 Sho. to !ende! the sample non.pe!iodic( If a unit cell of a sample is ,hidden-, that fact does not e!ase in any way its pa!amete!s, you can e#en modify and edit the unit cell pa!amete!s while it is being hidden( You can modify a sample4s unit cell by using its conte5t menu options: 7nit cell "dit 7nit cell Set as 8 7nit cell Scale vectors8 7nit cell Scale vectors and atoms
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The!efo!e, if you want the unit cell to be ta1en into account when its sample4s co!!esponding )ob is launched, ma1e su!e that the +nit.cell is ,showing- when you copy.paste the sample into a simulation ;simulations a!e found at the Project Browser<( Note that some calculation engines ha#e the option of specifying o! not a unit cell, so this would co!!espond to showing o! not the unit cell in Deneb( The unit cell as a buildin( tool Note that a pe!iodic sample usually !ep!esents an infinitely e5tended system that co#e!s the whole H2 space( 8owe#e!, in Deneb the only atoms that a!e shown, a!e those of the unit cell( The!efo!e, sometimes you might need to plot not only the unit cell but some !epetitions of it, in o!de! to #isuali%e bette! the e5tended system( To do so you can simply c!eate a supercell sample f!om the o!iginal one( This new sample is simply made by intege! !epetitions of the unit cell along its lattice #ecto!s( To this aim, use: 7nit cell Related operations *op4 supercell sample to clipboard ( You will be as1ed the numbe! of !epetitions of the unit cell along each #ecto!, and a new sample will be made using those pa!amete!s, its co!!esponding unit cell will be as well !esi%ed e5actly along(
The new sample is placed in Deneb4s #lipboard, so you can paste it bac1 whe!e you wish ;"ample &anipulato!4s Sample Mana(er, "ample &anipulato!4s Palette, NanoExplorer, Project Browser<( You can use the *op4 supercell sample to clipboard , menu item to Guic1ly p!oduce pa!ts of samples that 1eep some pe!iodicity, it is simple to p!oduce fo! e5ample, su!face slabs, nanowi!es, etc(
DENEb4s Sample Manipulator/ Nanotube Builders

@!om Deneb J(FN, Sample Manipulator includes nanotube builde!sA find them unde! the menu Samples -uilders( The diffe!ent 1ind of nanotube builde!s a!e labeled acco!ding to the co!!esponding two.dimensional lattice( Thus, out of the bo5, Deneb J(FN comes with honey'comb and trian(ular nanotube builde!s( Its use is #e!y simple: 3ust p!ess the button , *reate nanotube '''-( $f cou!se, if you want to build nanotubes diffe!ent f!om the default you ha#e to modify thei! pa!amete!s, which a!e:
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The chemical species of the atom?s of the F2 unit.cell basis( The nanotube chi!al #ecto! indices, typically called ,n@#-( The fi!st.neighbo!s bond.length in the F2 lattice( ;Note: inte!atomic distances might slightly change once the F2 sheet is w!apped a!ound to p!oduce the nanotube<
+pon p!essing the ,c!eate- button, a nanotube is p!oduced ;as a new sample< and added to the Sample Manipulator at the o!igin( The builde!s algo!ithm also p!oduces its unit.cellA it is accu!ately computed such that supe!cell !epetitions along the tube4s a5is do pe!fectly match( In tu!n, the pe!pendicula! lattice #ecto!s a!e chosen a bit a!bit!a!ily to fo!m a sufficiently la!ge sGua!eA you can easily modify these lattice #ecto!s .as you 1now. using the samples conte5t menu at the Sample Mana(er(
DENEb4s Sample Manipulator/ ?sin( the atom 7Properties8

"ometimes the!e a!e computational pa!amete!s that a!e attached to an specific atom( You can set these pa!amete!s in the 0roperties column of the Atom Editor in the Sample Manipulator( The p!ope!ty.tags can be multiple fo! any gi#en atom, the gene!al fo!mat that you can use to w!ite them is the following: ALabel1BCA1alue1BDALabel2BCA1alue2BD... This is, a semicolon.sepa!ated se!ies of label and .alue pai!s sepa!ated by the cha!acte! ,P-( A synta5 e5ception is that fo! boolean labels you need not to assign a #alue, Deneb unde!stands that a boolean label is ,t!ue- when it appea!s, and does not pa!se fu!the! in sea!ch fo! its #alue( To modify the p!ope!ty tags of some atom, you can di!ectly type in the co!!esponding cell using the "ample &anipulato!4s Atom Editor( You can also massively change the property tags of many atoms using the Atom Edito!4s conte5t menu: 5ighlighted 0roperties Set propert4 tags' :ith this option, you can eithe! add a p!ope!ty.tag to a gi#en list of atoms ;those highlighted<, o! you can enti!ely o0erwrite thei! p!ope!ties st!ing(
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Each simulation type has its set of )!ope!ty tags in Deneb, we list them he!e g!ouped as a function of the calculation.engine: Property'ta(s &or the simulations o& the type SIESTA/ J( FDF_ !D"!. 2efines the o!de! in which the atom will be w!itten in the co!!esponding . d )file( E5ample of use: EFE_'RF*RC1. Note: Deneb automatically sets this p!ope!ty on atoms f!om samples that a!e loaded f!om . d files, !emembe!ing, this way, thei! o!de! in such file( 2. FDF_#$"%&. )2efines the chemical species label that this atom will be assigned to in the . d ) file( E5ample of use: EFE_C:*=LC:_GGAH?*( Note: you do not need to specify it when the chemical species label desi!ed is the default which is eGual to the chemical species symbol( 7. FDF_'$ ().)2efines whethe! this atom will be conside!ed as a ghost atom in the co!!esponding "IE"TA simulation when e5ecuted( 2o not specify a #alue fo! this #a!iable, its p!esence gi#es the #alue of true automatically, its absence defaults to alse( E5ample of use: EFE_G:'ST. "ee the following figu!e as an e5ample whe!e some p!ope!ty.tags a!e al!eady defined fo! se#e!al atoms:
DENEb4s Sample Manipulator/ Animation o& samples
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You can inst!uct fo! Sample Manipulator to load a file with the animation of a sample( This file should be in the XYZ &ormat( In this simple fo!mat the list of atoms is gi#en as the chemical species symbol followed by the coo!dinates of the atom in Angst!oms( The!e is a heade! consisting of two lines: the fi!st line contains only the numbe! of atoms, while the second line is an a!bit!a!y comment that can be left blan1 e#entually ;but can not be !emo#ed<( In this fo!mat one can subseGuently attach one set of atoms afte! anothe! in the same file( DENEb can load these ,multi.f!ame files- doing the inte!p!etation of each set either as a new molecule of the same sample, or as a new f!ame ;instantaneous photo o! time step< of the dynamics of a gi#en sample( +se Sample Manipulator to open multi.f!ame $%&) files selecting one of these options, note that when you select to load a multi.f!ame $%& )file as the dynamics of the same set of atoms, one !eGuisite, that DENEb chec1s fo!, is that all f!ames !efe! to the same set of atoms at diffe!ent times, i(e( The numbe! of atoms should coincide fo! all f!ames, and the chemical species should also coincide f!om one f!ame to the ne5t( These conditions need not to be met when the file is loaded using the othe! modality: that of conside!ing each f!ame as a diffe!ent molecule of the same sample( A last note about the $%& fo!mat as unde!stood by DENEb is that one can use the comment line to inst!uct DENEb with useful info!mation( In pa!ticula! one can define the 0nit)Cell of the sample in such comment line ;o! the comment line co!!esponding to the fi!st f!ame in the case of multi.f!ame files<( To achie#e this, simply w!ite the unit cell lattice #ecto!s in the comment line as follows: lattice1ectors+2)ax)a3)a45bx)b3)b45cx)c3)c4)6 being ;a5,ay,a%< the coo!dinates of the fi!st lattice #ecto! ins Angs, ;b5,by,b%< the coo!dinates of the second, and so on and so fo!th( This way, the so called DENEb4s XYZ fo!mat is compatible but e5tends the capabilities of the standa!d XYZ fo!mat( 8e!e is a #e!batim e5ample of a multi.f!ame file in DENEb4s XYZ fo!mat: 7 lattice1ectors+2)8.0)0.0)0.0)5)0.0)9.0)0.0)5)0.0)0.0)6.0)6 ')))0.0))0.0))0.0 :)))0.;))0.0))0.0 :))-0.2))0.9))0.0 7 ')))0.0))0.0))1.0 :)))0.;))0.0))1.0 :))-0.2))0.9))1.0 7 ')))0.0))0.0))2.0 :)))0.;))0.0))2.0 :))-0.2))0.9))2.0 7 ')))0.0))0.0))I.0 :)))0.;))0.0))I.0 :))-0.2))0.9))I.0 It contains fou! f!ames that !ep!esent the same set of atoms only that a!e displaced by one Ang along the a5is f!om one f!ame to the ne5t( The!efo!e in this case you could optionally load ;using Sample Manipulator. see below< this file as a time se!ies o! as a se!ies of molecules that belong to the same sample( In the following we gi#e specific inst!uctions on how to load an animation &ile and how to cont!ol the animation with the sample4s Animation *ontrol 0anel : ;a< Load the sample with the animation f!om a file( 7hoose $ile Import from %Y& file
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;b< $nce chosen the file to be loaded, Sample Manipulator will t!y to load it( :ait fo! a little while if necessa!y, big files !eGui!e some seconds to p!ocess( Sample Manipulator will detect if the!e is mo!e than J f!ame( In that case it lets you choose the type of loading: ;a< each f!ame conside!ed as a new molecule, or ;b< each f!ame conside!ed as a time step in the e#olution of the same sample(
(c)
"elect the !adial button labeled , a time step of ms- and input the real time that each f!ame will be displayed in milliseconds ;o! simply accept the suggested #alue of IL ms fo! a smooth display<( )!ess Load %Y& $ile( The sample will be then loaded and displayed in Sample Manipulator( Notice that its co!!esponding icon in the "ample &anipulato!4s Sample Mana(er, indicates that the sample contains a t!a'ecto!y:
8e!e is an e5ample of how the icons fo! sample, molecule, and atom with trajectories loo1:
:hile the co!!esponding icons fo! sample, molecule and atom with no trajectory a!e, as you may al!eady 1now, slightly diffe!ent, he!e is an e5ample:
;d< To access the Animation *ontrol 0anel of the 'ust loaded sample use its conte5t menu called Animation'
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(e)
The Sample animation control dialog will appea!( This panel p!o#ides cont!ols to the animation of the sample, find in it the buttons fo!: )lay )ause 6eset to initial positions Ad#ance one f!ame 6etu!n one f!ame
Notes about the animation o& samples/ 2epending on the pe!fo!mance of you! ha!dwa!e, and the numbe! of atoms in motion, the
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animation display could be mo!e o! less smooth(
If bonds a!e showing ;Hre erences)>)?onds)>)ShoJ< you will notice that they do not follow the dynamics of the animation( This is a featu!e aimed not to hinde! pe!fo!mance( The!efo!e, you will p!obably want to obse!#e the dynamics while not showing bonds, and to !ecalculate bonds when wanted at specific f!ames ;Hre erences)>)?onds)>)Re-calculate)bonds)>)K)<(
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DENEb4s Project Browser
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Deneb4s Project Browser/ General ideaAs we ha#e mentioned ea!lie!, DENEb4s aim is to facilitate and e5pedite the wo!1 of !esea!che!s in the fields of Atomistic Simulations( :ith DENEb you can c!eate, e5ecute, !et!ie#e, o!gani%e and cent!ali%e you! thousands of simulations belonging to you! hund!eds of !esea!ch projects( Deneb4s Project Browser is the place whe!e you can c!eate, modify, o!gani%e, classify and cent!ali%e all you! projects( @!om DENEb4s Project Browser, you can c!eate simulations by coupling a gi#en sample to a gi#en set of computational parameters( You! simulations might apply to #e!y many diffe!ent physical systems, they could also belong to diffe!ent calculation engines ;e(g( SIESTA, uantumEspresso, #PM$, %ASP, etc<, and could be launched fo! e5ecution into se#e!al diffe!ent !emote hosts = In spite of this, Project Browser can 1eep t!ac1 of each of them and p!esent them to you neatly o!gani%ed and !eadily accessible( +sing DENEb>s Project Browser you can choose any 1ind of classification fo! you! simulations, based on 1ind of sample, type of calculation engine, etc( +se customa!y labels and o!gani%e them, in g!oups and p!o'ects, into t!ee st!uctu!es of any depth( 0uic1ly sea!ch and .with a single clic1. sto!e?!et!ie#e all of it: "imulations, p!o'ects, thei! o!gani%ation, and thei! !esulting data(
Deneb4s Project Browser/ The concept o& project and simulation:e ha#e al!eady used these wo!ds ; project and simulation<, but let us p!ope!ly define them with !ega!d to Deneb4s unde!standing befo!e continuing( $e&inition o& project/ A project in Deneb4s te!ms, is loosely defined as the set of simulations co!!esponding to a gi#en !eal. life !esea!ch p!o'ect( These can be 'ust a few o! #e!y manyA a project can, the!eby, ha#e an inte!nal classification st!uctu!e of any comple5ity, customa!ily defined into a t!ee.o!gani%ation( *ut a p!o'ect can not contain anothe! p!o'ect within( $e&inition o& simulation/ A simulation in Deneb4s te!ms, is loosely defined as a !ep!esentation of a !eady.to.use input.file fo! some calculation engine( Deneb conside!s that all simulations a!e composed of two distinct pa!ts:
1. 2.
The sample, whe!e the physical system is defined( :hich is the ob'ect that NanoExplorer and Sample Manipulator a!e dedicated to( The parameters, which a!e the !est of computational pa!amete!s ;!elated to the scientific model, the nume!ical p!ecision, etc< that a calculation.engine needs to completely define a single e5ecution !un( This is the ob'ect to which the Parameters Editor is dedicated to( Note: "ome little mi5ing is una#oidable, fo! e5ample the p!ope!ty.tags, that you can edit using the Atom Editor of Sample Manipulator, !eflect p!ope!ties of the atoms that a!e not st!ictly !elated to the definition of the physical system itself, but !athe! to the calculation acco!ding to some calculation.engine(
The Project Browser tree, p!esents diffe!ent icons fo! diffe!ent 1ind of ob'ects, this facilitates that you Guic1ly 1now what a!e you loo1ing at, he!e is an e5ample:
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Project Browser shows all you! projects and simulations in a t!ee st!uctu!e with a!bit!a!y depth, and lets you o!gani%e them in (roups as you wish( Deneb !ep!esents these 1ind of ob'ects with diffe!ent icons: Icon fo! the root of this t!ee st!uctu!e, labeled ,)!o'ects-( Icon fo! a (roup of ob'ects( Project Browser can hold as many g!oups as you wish, nested a!bit!a!ily( Icon fo! a project ob'ect( Projects may contain any numbe! of (roups and simulations. but can not contain anothe! project( Icon fo! a simulation ob'ect( A simulation must always belong to a project( They a!e lea#es of this t!ee, i(e( they ha#e no ,descendant- b!anches( Each simulation necessa!ily belongs to a gi#en type dete!mined by the 1ind of parameters it contains( You can add the same sample to two simulations of diffe!ent type ;e(g( 0E and "IE"TA<, and of cou!se the !esulting calculations ;o! )obs< will belong to diffe!ent calculation engines(
Deneb4s Project Browser/
uic5 re&erence (uide
In Project Browser you cont!ol the actions by the use of its ob'ect4s context)#enus( To show the *+nte,t menu o& a (i0en object, fi!st highlight it and then Ri"ht-Clic(( 8e!e is a @uic5 re&erence (uide to all diffe!ent context)#enus@ )acco!ding to the ob'ect that they belong to: ) Context)#enu )) fo! )) !oot )) ) : Load all pro9ects''' : Loads a file that has been sa#ed using Save all pro9ects''' ( Save all pro9ects''' : "a#es the whole Project Browser tree in Deneb4s efficient nati#e fo!mat( *reate group''' : 7!eates a new (roup unde! the root( *reate pro9ect''' : 7!eates a new project unde! the root( 0aste group : )astes unde! the root a copy of the (roup found in deneb4s #lipboard( 0aste pro9ect : )astes unde! the root a copy of the project found in deneb4s #lipboard(
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) Context)#enu )) fo! )) Group )) ) : *reate group'''+ 7!eates a new (roup unde! the highlighted (roup( "dit group'''+)Edits the highlighted (roup4s label and desc!iption( ,elete group'''+)2eletes the highlighted (roup( *reate pro9ect'''+)7!eates a new project unde! the highlighted (roup( *reate simulation'''+)7!eates a new simulation unde! the highlighted (roup( *reate simulation from file''' : Loads a #alid input.file fo! some calculation engine, and c!eates a new simulation of the co!!esponding type( @o! e5ample, f!om a "IE"TA input file ;with e5tension . d < , it c!eates a new "IE"TA simulation unde! the highlighted (roup( *op4 group+ 7!eates a copy of the highlighted (roup and places it into deneb4s #lipboard( 0aste group+ )astes a copy of the (roup found in deneb4s #lipboard( 0aste pro9ect+ )astes a copy of the project found in deneb4s #lipboard( 0aste simulation+ )astes a copy of the simulation found in deneb4s #lipboard( ) Context)#enu )) fo! )) Project )) : ) *reate simulation'''+)7!eates a new simulation unde! the highlighted project( *reate simulation from file''' : Loads a #alid input.file fo! some calculation engine, and c!eates a new simulation of the co!!esponding type( @o! e5ample, f!om a "IE"TA input file ;with e5tension . d < , it c!eates a new "IE"TA simulation unde! the highlighted project( *reate group'''+ 7!eates a new (roup unde! the highlighted project( "dit pro9ect description'''+ Edits the label and desc!iption of the highlighted project( ,elete pro9ect+ 2eletes the highlighted project( *op4 pro9ect+ )laces a copy of the highlighted project into deneb4s #lipboard( 0aste group+ )astes a copy of the (roup found in deneb4s #lipboard( 0aste simulation+ )astes a copy of the simulation found in deneb4s #lipboard( ) Context)#enu )) fo! )) Simulation )) ) : "dit simulation'''+ Edits the label and desc!iption of the highlighted simulation( ,elete simulation+)2eletes the highlighted simulation( *op4 simulation+ )laces a copy of the highlighted simulation into deneb4s #lipboard( Import % 1L Sample'''+ )6eads a file in X&ol fo!mat ;e5tension .$%&< and c!eates a sample which is placed in the highlighted simulation( Deneb will detect if the!e is mo!e than J f!ame in the file( In that case it lets you choose the type of loading: each f!ame conside!ed as a new molecule, or each f!ame conside!ed as a time step in the e#olution of the same sample( *op4 sample+ )laces a copy of the sample in the highlighted simulation into deneb4s #lipboard( Haste ) sa#ple+ )astes a copy of the sample found in deneb4s #lipboard into the highlighted simulation( "dit parameters'''+ Launches a new Parameters Editor that displays and allows to modify the parameters of the highlighted simulation( /enerate engine input file'''+ 7!eates a co!!esponding engine input.file using the data f!om the highlighted simulation ;sample and parameters<( The type of engine input.file obtained matches the type of simulation( @o! e5ample, if the highlighted simulation is of the "IE"TA type, deneb will gene!ate a !eady.to.use . d file ;"IE"TA input file<(
Run into engine'''+ 7!eates a job and launches it fo! e5ecution into a gi#en calculation engine( deneb will show you a list with all the engine configu!ations cu!!ently defined fo! the gi#en simulation type( Afte! you choose one, deneb will c!eate and submit a new job to that specified machine ;see )ob Mana(er<( You will notice that the icon co!!esponding to the simulation 'ust launched to ,!un into engine- changes( 8e!e is a list of possible icons fo! simulations that ha#e been submitted and thei! meaning: P "ubmitted and waiting to be sent to the !emote engine machine(
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P "imulation cu!!ently !unning in the !emote machine( P E5ecution finished co!!ectly ;without any detected e!!o!s<( P E5ecution finished with some detected e!!o!(
;ill simulation 9ob+ 8alts and eliminates the associated job that is cu!!ently !unning in the !emote machine ;see )ob Mana(er<( (ie. engine output'''+ 6et!ie#es and displays the cu!!ent output file of the co!!esponding !emote job ;see )ob Mana(er<(
$ra( and $rop/ In Project Browser, you can d!ag.and.d!op ob'ects to easily !ea!!ange the t!ee( It is safe to e5pe!iment with d!ag and d!op because when you attempt a non.#alid motion ;e(g(, to mo#e a project into anothe! project< Project Browser will not complete such ope!ation and will !epo!t about it(
Deneb4s Project Browser/ $e&inin( en(ine con&i(urations

Deneb4s Project Browser can di!ectly launch simulations fo! !emote e5ecution( *ut of cou!se, Deneb needs to 1now some info!mation about the remote calculation engines so it can connect and launch jobs on them( The set of data that defines a gi#en e5ecutable in a gi#en machine is called, in Deneb 4s te!ms, an en(ine con&i(uration( Deneb can sto!e and use multiple en(ine con&i(urations( This is how you can define them: 1. @!om Deneb4s main window use "dit 0references, you can also use the main toolbar sho!t.cut button that loo1s li1e the following:
2. @ill abcd-
e"h-
out the !eGuested info!mation such as: I0 : the I) add!ess of the !emote machine SS5 port: po!t to use fo! the ssh connection( 7ser name and 7ser pass.ord: login info!mation on the !emote machine, the passwo!d field is not displayed and not susceptible to be copy.pasted( 0arallel options: "elect whethe! the e5ecutable is supposed to be launched fo! e5ecution in pa!allel( $ptions a!e: 1. 7se 0I: chec1 this bo5 if you want the 'obs to be submitted using #piexec o! #pirun. 2. !0+ Input he!e the numbe! of p!ocesso!s to be used( 7. 7se 0-S: chec1 this bo5 if the 'obs a!e to be launched to a H?S type Gueue( I. Args( : set he!e the pa!ticula! a!guments to be passed when launching to the H?S Gueue( "#ecutable $ile: Name of the e5ecutable file( -in ,irector4: absolute path whe!e to find the e5ecutable file( ,ata ,irector4: absolute path whe!e to find w!ite the data gene!ated f!om simulations e5ecutions( 0seudos ,ir: absolute path whe!e to find the pseudo.potential files(
@o! e5ample, he!e is a possible engine configu!ation fo! "IE"TA type simulations:
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#hec5in( an en(ine con&i(uration/ The button *hec< *onfiguration t!igge!s the #e!ification of the data when p!essed( +se it to #e!ify the connection a#ailability( If e#e!ything goes fine, an 'L in a g!een bac1g!ound will appea!, while a !ed bac1g!ound and an e!!o! message will be displayed if the!e is some connection t!ouble( Note, ma1e su!e that you! host can !ecei#e ssh connections: @o! e5ample use ,sudo ) apt-"et) install)openssh-client- in an 0buntu)Linux, to install the ssh se!#e!(
Project Browser4s )ob Mana(er

As we mentioned in p!e#ious sections, a simulation is composed of two pa!ts: A sample. and a set computational parameters, the so.called parameters( The parameters is a set of pai!s ;label, #alue< that defines the needed input fo! a gi#en pa!ticula! computational en(ine( Note then that, while samples do not ha#e pa!ticula! association to any engine, simulations do since thei! pa!amete!s half belong to a pa!ticula! engine( This way we tal1 of, fo! instance, "IE"TA simulation, DA") simulation, etc ((( A simulation, becomes a )ob, when it is launched to a ;!emote< machine fo! e5ecution( Deneb automatically monito!s all launched 'obs, and lets you get the output.log ;du!ing and afte! the calculation with a single cloc1( The Project Browser4s )ob Mana(er is in cha!ge of facilitating all these tas1s( It also facilitates the !et!ie#al of all output files once the 'ob has finished( The following diag!am summa!i%es these p!ocesses:
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3obs can be in following status ;!ep!esented in Deneb using diffe!ent icons<: "ubmitted and awaiting to be sent to the !emote engine machine( 6unning in the !emote machine( @inished co!!ectly ;without any detected e!!o!< @inished with some detected e!!o! )ob Mana(er allows you to Guic1ly #iew the status of all you! 'obs by p!esenting them in a neat list, each !ow belongs to one 'ob:
)ob Mana(er shows in each !ow, the 'ob4s I2, the name of the associated simulation, the type of 'ob, the T7)?I) add!ess of the machine whe!e it is being ;o! was< e5ecuted, its status ;submitted, !unning, finished $9, finished with e!!o!<, its sta!ting time and date, and its ending time and date( +sing the menu called ,3obs- o! the conte5t menu of a gi#en highlighted 'ob, you can 5ill the selected jobs, 0iew the content o& the associated output'lo(. and retrie0e the remote data &iles to you! local file system(
In the following we e5plain the actions fo! each of these menu items:
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;ill selected 9obs: T!ies to 1ill all highlighted 'obs in thei! !emote machines( (ie. outputs''': 6et!ie#es the output.logs f!om !emote machine and shows them in a new window( 8e!e is an e5ample:
These windows show the status of the output log at the !et!ie#al moment, to !ef!esh the contents !epeat the ope!ation ;t!igge! again the menu item called (ie. outputs<(
/et remote data''': "hows the !emote file system ;files and di!ecto!ies< at the path whe!e the associated 'ob was e5ecuted( It lets you na#igate in the !emote file system ;within the na#igation pe!missions of the p!o#ided use!<: 2ouble.7lic1 to ente! a di!ecto!y, )!ess to go up one le#el to the pa!ent di!ecto!y( +se the chec1 bo5es at the left to select any numbe! of items( )!ess to !et!ie#e of the selected items f!om the !emote file system to you! local one(
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Deneb4s Parameters Editor

As we mentioned in p!e#ious sections, a simulation is composed of two pa!ts: A sample. and a set computational parameters, the so.called parameters( The parameters is a set of pai!s ;label, #alue< that defines the needed input fo! a gi#en pa!ticula! computational en(ine( Note then that, while samples do not ha#e pa!ticula! association to any engine, simulations do since thei! pa!amete!s half belong to a pa!ticula! engine( This way we tal1 of, fo! instance, "IE"TA simulation, DA") simulation, etc = As we ha#e seen, using Project Browser you can c!eate a new simulation, p!o#ide it with a new sample ;fo! e5ample by pasting it f!om the #lipboard<, and it will be di!ectly !eady to be clic1 to launched fo! !emote e5ecution( This sends a default calculation fo! that sample and is sometimes all we need( The typical default calculation consist of computing the co!!esponding elect!onic density( *ut fo! the most pa!t we do !eGui!e to change the default pa!amete!s so we can pe!fo!m, fo! e5ample, band st!uctu!e calculations, mechanical !ela5ations, molecula! dynamics, etc( To specify these computational parameters you can t!igge! the Parameters Editor f!om the conte5t menu of any gi#en simulation( :hen doing so, Deneb will sta!t the edito! co!!esponding to the type of simulation called fo!( Each plugin p!o#ides a new )a!amete!s Edito! so the!e a!e as many types of )a!amete! Edito!s as plugins you ha#e in you! system ;not to confuse with ,add.on-s( 6emembe! each plugin enables the compatibility with a calculation engine, while add-ons a!e featu!es that you can add to Deneb not specifically lin1ed a calculation engine<( In the following we desc!ibe the wo!1ings of the diffe!ent Parameter Editors:
Deneb4s SIESTA'Parameters Editor

To t!igge! its appea!ance use the conte5t menu of a simulation of the type "IE"TA, within the Project Browser t!ee( 7hoose "dit parameters'''
This will p!oduce the siesta.)a!amete!s Edito!( That loo1s li1e this fo! a newly c!eated simulation:
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It mainly consists of two panels, on the left you can find in a t!ee.o!gani%ation all the a#ailable siesta. fdf labels ;2eneb J(FN comes with all labels fo! its contempo!a!y siesta H(J<( The t!ee o!gani%ation !eflects the o!gani%ation of the siesta use!s manual, this way you can Guic1ly find the documentation of any gi#en label in the same( @o! Guic1.sea!ch of fdf.labels you can type any ;case sensiti#e< te5t in the co!!esponding bo5 ;labeled Search< and p!ess the button labeled MextA this will find and highlight the fi!st appea!ance, as you !epeatedly p!ess Mext the following appea!ances of the te5t will be highlighted( The icons in the t!ee gi#e you Guic1 #isual clues as to what 1ind of item each b!anch?leaf co!!esponds( In the following figu!e we specify the item type fo! all diffe!ent icons:
Note: The fdf.labels that specify the sample ;such as: numbe! of atoms, atomic coo!dinates, chemical species, lattice #ecto!s etc< a!e not p!esent in the Parameters Editor t!ee( $b#iously this is because they a!e not necessa!y he!e since they a!e al!eady dete!mined by the sample included in the co!!esponding simulation( :hen submitting a simulation fo! e5ecution, Deneb c!eates a co!!esponding en(ine input'&ile ;a siesta fdf file in this case<( This engine input.file includes both labels that define the sample and labels that dete!mine the computational pa!amete!s( The siesta engine can ta1e default #alues fo! all computational pa!amete!s but those of the sample, so a pe!fectly #alid set of computational pa!amete!s is an empty one( Ne#e!theless in most occasions one needs to specify some diffe!ent ;f!om the default< #alues( The way to do so is to ,Add- the co!!esponding pa!amete!s to the !ight hand side panel( +se the conte5t menu of the highlighted set of computational pa!amete!s to add them:
2012 Atelgraphics
You can add one o! se#e!al with one clic1, if you highlight a b!anch all of the pa!amete!s unde! such b!anch will be added( $b#iously you can add all pa!amete!s by using the conte5t menu of the t!ee !oot b!anch ;labeled ,Cate"ories-<( The added labels appea! in the !ight hand side panel and a!e w!itten with bold face cha!acte!s in the t!ee(
In o!de! to #iew the cu!!ent status of ou! added set of pa!amete!s we can use the button labeled previe.( *y p!essing it an o#e!#iew of all the added labels and thei! cu!!ent #alues is shown(
2012 Atelgraphics
You can #iew and modify specific labels f!om those that ha#e been added by using its conte5t menu ;t!igge!ed by 6ight.7lic1<( You can type in new #alues and o! units it and p!ess $9 to ma1e it count o! cancel to dis!ega!d it( Note: once you p!ess $9 the!e is no undo, so use with ca!e( If you input not a numbe!, whe!e a numbe! is e5pected, Deneb detects so and does not !egiste! the $9 p!ess( If you input units not !ecogni%ed by siesta, they will be dis!ega!ded upon p!essing $9, and the units field will not be changed( Note howe#e!, that the pa!amete!s chec1ing p!o#ided by Deneb is not foolp!oof and it does not chec1 fo! un!easonable sets of pa!amete!s f!om the )hysics #iewpoint(
@inally, when you a!e done #iewing?editing the pa!amete!s p!ess the button 1; in the pa!amete!s edito! window to actually !egiste! the changes and modify the!eby the co!!esponding simulation4s pa!amete!s( If you !eg!et of all the changes done you can still p!ess , *ancel- and the simulation pa!amete!s will !emain unchanged( The Parameters Editor window disappea!s upon p!essing 1; o! *ancel, you can obtain a new one again by the simulations conte5t menu item "dit parameters''' as e5plained abo#e(
2012 Atelgraphics
DENEb4s video-demos
2012 Atelgraphics
Deneb4s AouTube 0ideos

$ne pictu!e is wo!th a thousand wo!ds( And a #ideo is about FI pictu!es pe! second( In Atelgraphics %ouTube channel you can find some #ideo demonst!ations and tuto!ials about Deneb( "ometimes the faste! way to lea!n is to see it done, chec1 the atel"raphicschannel !egula!ly( 8e!e you ha#e a !elati#ely sho!t list of lin1s ;the one as of 2ecembe! FLJF<, the numbe! of these will steadily g!ow( J( F( H( A sho!t #ideo of the #isuali%ation of the !esults of a molecula! dynamics ;&2< simulation with Deneb, wate! o#e! a )t su!face( :ate! dissociation o#e! )t( $ne minute( A complete demo( Lea!n it all in only JK minutes: 7!eate a sample, modify it, include it in a simulation, e5ecute it !emotely, !et!ie#e the !esults and #isuali%e the &2 animation( /old dime! into 7NL complete( Anothe! demo on how to #isuali%e an animation !esulting f!om a &2 simulation( I!on atoms inside a 7a!bon nanotube("i5 minutes(
Note: if this document is al!eady old ;date of w!iting is 2ecembe! FLJF< it could be that the lin1s abo#e a!e al!eady dead(
2012 Atelgraphics
DENEb4s older video-tutorials

;Note: the following #ideo tuto!ials a!e fo! #e!sion J(F of Deneb, but still useful to lea!n many concepts(<
2012 Atelgraphics
!ano"#plorer
To see a demonst!ation of NanoExplorer4s basic use, the!e is a tuto!ial in the ,FoJnloads/)section of the Atelgraphics web site( It is entitled , ano!"plorer !ssentialsIn that tuto!ial you may lea!n the following:
8ow to in0o5e NanoExplorer 8ow to rename, delete, 0isuali6e and copy samples in NanoExplorer( 8ow to count the number o& molecules and atoms in a gi#en sample( 8ow to sa0e the loo5s o& a sample in an jpg file( 8ow to copy a gi#en sample f!om NanoExplorer into DENEb4s #lipboard( 8ow to @uic5 search fo! samples by ;pa!ts of< thei! name( 8ow to tell periodic &rom molecular sample types( 8ow to import and export samples in diffe!ent fo!mats( 8ow to @uic5ly arran(e se0eral simultaneous 0iews of se#e!al samples( 8ow to Guic1ly create a new simulation using a sample f!om NanoExplorer(
2012 Atelgraphics
0ro9ect -ro.ser
To see a demonst!ation of Project Browser4s basic use the!e is a tuto!ial in the , FoJnloads/ section of the Atelgraphics web site( It is entitled ,#ro$ect %rowser !ssentialsIn that tuto!ial you may lea!n the following:
8ow to in0o5e or show Project Browser8ow to create a new project. set its description and Bre=name it8ow to create (roups and mo0e projects into them8ow to load or sa0e all (roups and projects at once8ow to edit projects and (roups( 8ow to create simulations under projects8ow to copyCpaste. eliminate (roups. projects. simulations8ow to edit. delete. copy simulations8ow to import an XYZ &ile into a (i0en simulation8ow to directly edit the sample o& a simulation8ow to directly edit the computational parameters o& a simulation8ow to (enerate an 7en(ine input &ile8 ready to be &ed to a calculation en(ine8ow to send a simulation &or remote execution into a (i0en en(ine8ow to 5ill a remote runnin( job belon(in( to a particular simulation ( 8ow to 0isuali6e the output a&ter a (i0en simulation has success&ully run-
2012 Atelgraphics
Sample
anipulator: invo<ing
To see a demonst!ation of Sample Manipulator4s se#e!al simultaneous instances management, the!e is a tuto!ial in the ,FoJnloads/ a!ea of the Atelgraphics web site( It is entitled ,Invoking Sample &anipulatorIn that tuto!ial you may lea!n the following:
8ow to in0o5e or show se0eral instances o& Sample Manipulator8ow to eliminate some o& the instances created8ow to 0iew the list o& the currently acti0e Sample Manipulator instances:hat is the meaning of the order in which the di&&erent instances may appear in the list (
2012 Atelgraphics
Sample
anipulator:
ouse ,rag
ode
To see a demonst!ation of Sample Manipulator4s came!a cont!ol in the &ouse 'rag mode the!e is a tuto!ial in the ,FoJnloads/ a!ea of the Atelgraphics web site( It is entitled ,&ouse 'rag &ode in Sample &anipulatorIn that tuto!ial you may lea!n the following:
8ow to @uic5ly show all windows o& Sample Manipulator8ow to resi6e 4main 0iew4 and 4side 0iew4 usin( the split panel8ow to 6oom inCout o& the detached 0iew panel8ow to add a new sample chosen &rom the Sample Manipulator4s Palette8ow to set the Mouse Drag mode &or camera control8ow to control rotation. 6oom and shi&t o& the camera in the Mouse $ra( mode8ow to chan(e the 4center o& camera rotation4 by mouse pic5in( a point in space8ow to control the position o& the auxiliary plane in this Band all= mode-
2012 Atelgraphics
Sample
anipulator: Sliders and buttons mode
To see a demonst!ation of Sample Manipulator4s came!a cont!ol in the Sliders and %uttons mode the!e is a tuto!ial in the ,FoJnloads/ a!ea of the Atelgraphics web site( It is entitled (Sliders and %uttons &ode in Sample &anipulatorIn that tuto!ial you may lea!n the following:
8ow to set the Sliders and buttons mode8ow to 6oom in and out in this mode( 8ow to reset the 0iew to a default position( 8ow shi&t step by step the came!a( 8ow to create new samples pic5in( them &rom the Palette( 8ow to display the coordinate axes( 8ow to rotate the camera usin( the pro(ress bars. spinners. and typin( an(le 0alues ( 8ow to rotate around each di&&erent axis( 8ow to shi&t the camera position by mouse'dra(( A tip to bette! compa!e samples: 8ow to accurately speci&y the same 0iew point( 8ow to control the side 0iew panel camera( 8ow to doc5Cundoc5. and resi6e the detached 0iew panel( 8ow to control the detached'0iew camera/ shi&ts and 6ooms ( 8ow to reset to de&ault the 0iew o& the detached'0iew panel ( 8ow to doc5 all Sample Manipulator4s side windows ( 8ow to exit a Sample Manipulator instance destroyin( its memory content (
2012 Atelgraphics
Sample
anipulator: Simple building
To see a demonst!ation of Sample Manipulator4s abilities to build f!om sc!atch the!e is a tuto!ial in the ,FoJnloads/ a!ea of the Atelgraphics web site( It is entitled (Sample &anipulator) %uilding simple samplesIn that tuto!ial you may lea!n the following:
A sho!t.cut to show all Sample Manipulator4s windows( 8ow to choose a sample &rom the Palette( The use o& the Empty Sample of the )alette( 8ow the Sample Mana(er o&&ers a tree 0iew of the samples( 8ow to rename the samples and molecules using the "ample &anage!( 8ow to set a moleculeCsample as 4the one bein( edited4( 8ow to choose an speci&ic atom &rom the Palette( 8ow to add atoms by mouse actions usin( the plane( 8ow to select all atoms usin( the Selection menu( 8ow to edit the current selection( 8ow to type new coordinates &or a (i0en atom in the Atom Editor ( 8ow to add a just built sample to the Palette ;that has pe!sistence functions<( 8ow to place clone copies o& a (i0en sample by mouse actions( 8ow to @uic5ly 0isuali6e coordinates in the Sample Mana(er tooltips (
2012 Atelgraphics
Sample
anipulator: -uilding periodic samples
To see a demonst!ation of Sample Manipulator4s abilities to build f!om sc!atch pe!iodic samples the!e is a tuto!ial in the ,FoJnloads/ a!ea of the Atelgraphics web site( It is entitled (Sample &anipulator) %uilding simple periodic samplesIn that tuto!ial you may lea!n the following:
8ow to use the Empty sample &rom the Palette( 8ow to place a sample at an speci&ic point( 8ow to ma5e a sample periodic( 8ow to &ind an atom in the Palette( 8ow to place an atom by mouse pic5in(( 8ow to rename a sampleCmolecule( 8ow to set a sampleCmolecule as the one bein( edited( 8ow to display the coordinate axes( 8ow to select an atom by mouse ctrl'clic5in(( 8ow to edit the atom4s scaled coordinates by usin( the Atom Editor8ow to ta( an atom with a customary label( 8ow to obtain in&ormation &rom an atom 0iewin( the Atom Editor tool tips ( 8ow to edit a sample4s unit cell parameters ;to set them as an @77 lattice, in this case<( 8ow to add to the Palette a just created sample(
8ow to create a supercell sample &rom a (i0en sample, by !epetitions along the lattice #ecto!s( 8ow to choose a new center o& camera rotation by mouse pic5in( (
2012 Atelgraphics
Running simulations
To see a demonst!ation on how to launch &or execution a just created simulation the!e is a tuto!ial in the ,FoJnloads/ a!ea of the Atelgraphics web site( It is entitled (*unning simulationsIn that tuto!ial you may lea!n the following:
8ow to set the parameters relati0e to the remote host whe!e the simulations will be !un( +hat parameters are needed in o!de! to inst!uct DENEb about said !emote host( 8ow to create a new project in Project Browser( 8ow to create a new simulation under a project(
8ow to brin( a sample &rom the NanoExplorer database into the just created simulation( 8ow to short'cut 0isuali6e. as a tooltip. the sample contained in a simulation ( 8ow to edit the computational parameters o& the simulation( 8ow to select speci&ic parameters and edit them usin( Parameter Editor ( 8ow to pre0iew the parameters section ;not containing the sample< o& the en(ine input 8ow to (enerate an en(ine input'&ile that can be di!ectly sent to the calculation engine(
&ile( 8ow to instruct DENEb to/ (enerate the input &ile. deli0er it to the remote host. and start the simulation in the remote host- :ith a single clic1( 8ow to 0iew a summary o& the jobs that ha0e been launched fo! e5ecution using the )ob Mana(er+hat icons uses DENEb to indicate di&&erent statuses o& the launched simulations ( 8ow the main panel status bar shows in&ormation about the latest submitted job (
8ow DENEb detects when the remote job has &inished and. i& success&ul. retrie0es the output( 8ow the status o& a job is shown both in the Project Browser and in the )ob Mana(er ( 8ow to 0iew the output &ile o& a &inished simulation (
2012 Atelgraphics
DENEb4s cheat-sheets
2012 Atelgraphics
Sample
anipulator:
ouse actions cheat2sheet
)ic1 &ode: Atoms( ,e&t'#lic5 A new atom, whose type is the one highlighted in the Palette, is c!eated( Its cente! ;nucleus< is placed on the spot of the plane touched by the mouse cu!so!( The newly c!eated atom belongs to the molecule being edited+ that should ha#e been set using the Samples Mana(er( ;$nly i& )lane: %isible$the!wise, nothing done<
)ic1 &ode: Molecules( A new molecule, of the type highlighted in the Palette, is c!eated( Its !efe!ence point ;the point with !espect to what its atom4s local.coo!dinates a!e defined< is placed on the spot of the plane touched by the mouse cu!so!( The newly c!eated molecule belongs to the sample being edited+ that has been set using the Samples Mana(er;$nly i& )lane: %isible$the!wise, nothing done<
)ic1 &ode: Samples( A new sample, of the type highlighted in the Palette, is c!eated( Its !efe!ence point ;the point with !espect to what its molecule4s local.coo!dinates a!e defined< is placed on the spot of the plane touched by the mouse cu!so!( ;$nly i& )lane: %isible$the!wise, nothing done<
#trl D ,e&t'#lic5
If the mouse cu!so! is touching a If the mouse cu!so! is touching a gi#en atom( Its selection state is gi#en atom( The selection state of toggled( $the!wise, nothing done( all atoms in its molecule a!e toggled( $the!wise, nothing done( If the mouse cu!so! is touching a gi#en atom( It is eliminated( Note/ there is no warnin( or undo- $the!wise, nothing done( If the mouse cu!so! is touching a gi#en atom( Its whole molecule is eliminated( Note/ there is no warnin( or undo- $the!wise, nothing done(
If the mouse cu!so! is touching a gi#en atom( The selection state of all atoms in its sample a!e toggled( $the!wise, nothing done( If the mouse cu!so! is touching a gi#en atom( Its whole sample is eliminated( Note/ there is no warnin( or undo$the!wise, nothing done(
Shi&t D ,e&t'#lic5
Shi&t D !i(ht'#lic5 ,e&t'#lic5 E $ra( !i(ht'#lic5 E $ra( #enter'#lic5 E $ra( #trl D Shi&t E Mo0e #ursor
)lace the came!a !otation cente! at the point of the plane touched by the mouse cu!so!( ;$nly i& )lane: %isible- $the!wise, nothing done(< 7ame!a !otation depending on the d!ag di!ection( ;I& 0references *amera *ontrol Setting)P ouse ,rag- < 7ame!a shifts late!ally with the mouse motion( ;I& 0references *amera *ontrol Setting = > ouse ,rag? or >Sliders and buttons?(< 7ame!a %oom in and out depending on the 0ertical d!ag di!ection( ;I& 0references *amera *ontrol Setting = ouse ,rag-< Tooltip with the coo!dinates of the point at the plane touched by the mouse cu!so!( ;I& 0references /raphical tooltip options = See coords on the plane < Tooltip with the coo!dinates of the point at the plane touched by the mouse cu!so! or info!mation about the atom touched by the mouse cu!so!( ;I& 0references /raphical tooltip options = *oords on plane and atoms info< 7ame!a %oom in?out step by step( ;I& 0references *amera *ontrol Setting = > ouse ,rag? or >Sliders and buttons?(<
Mouse' +heel !otation
2012 Atelgraphics
Sample
anipulator: ;e4 navigation camera controls'
This is a !eminde! of the 1eys that cont!ol the motion of the came!a in the 9ey.Na#igation mode: 0references *amera control setting !avigation ;e4s( This mode is pa!ticula!ly useful when: You want to na#igate inside hollow samples( You want to Guic1ly 4o#e!fly4, su!faces o! elongated samples( You want to %oom.in beyond the cente! of !otation( You p!efe! to Guic1e! %oom in o! out with p!essing 1eys !athe! than using mouse wheel !epeated actions( In gene!al, when you need came!a t!a#eling in long ;but still nanomet!icQ< distances(
Action per&ormed when came!a cont!ol mode P Na0i(ation Feys B0references *amera *ontrol Setting)P ,Na0i(ation Feys8 = The came!a mo#es fo!wa!d( A ?p ' Arrow $own ' Arrow !i(ht ' Arrow ,e&t ' Arrow #trl D ?p ' Arrow #trl D $own ' Arrow #trl D !i(ht ' Arrow #trl D ,e&t ' Arrow The came!a mo#es bac1wa!ds( The came!a !otates upwa!d( The came!a !otates downwa!d( The came!a !otates to the !ight( The came!a !otates to the left( The came!a shifts upwa!d( The came!a shifts downwa!d( The came!a shifts to the !ight( The came!a shifts to the left(
2012 Atelgraphics
DENEb-1.26- Fnown issues 1.

- ut +. mem+/y0 issue/ This #e!sion can add!ess F/b of 6A& ma5imum( This means that when the use! has opened ;#isuali%ed< samples that togethe! add up to about FL9 atoms 2ENE* might e5it une5pectedly with an out of memo!y uncaught e5ception( *ewa!e the!efo!e when #isuali%ing bul1y o! nume!ous samples with NE o! "&, sa#e you! wo!1 f!eGuently 'ust in case(
2012 Atelgraphics
2012 Atelgraphics

Deneb 1 26 Help

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Deneb 1 26 Help

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DENEb -1.

DENEb -1.26 help documents

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DENEb4s General Introduction

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The philosophy behind DENEb

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Installation o& DENEb and plu(ins

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Atoms. molecules and samples in DENEb

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DENEb4s NanoExplorer/ ,oadin( new samples

"elect $ile f!om NanoExplorer4s main menu(

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(a) (b) (c)

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as different molecule o! as a time step of ms

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DENEb4s NanoExplorer/ Sa0in( samples

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DENEb4s NanoExplorer/ "r(ani6in( your samples

The!e is no undo afte! deletion, use the!efo!e with ca!e(

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DENEb4s Sample Manipulator

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DENEb4s Sample Manipulator/ Translatin( and rotatin( objects

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DENEb4s Sample Manipulator/ Simple buildin(

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h< You can simply type.in the new local coo!dinates(

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DENEb4s Sample Manipulator/ Buildin( Periodic samples

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DENEb4s Sample Manipulator/ Nanotube Builders

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DENEb4s Sample Manipulator/ ?sin( the atom 7Properties8

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DENEb4s Sample Manipulator/ Animation o& samples

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animation display could be mo!e o! less smooth(

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DENEb4s Project Browser

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