6.3.3. RADII AND NUCLEAR CHARGE OPTION, [R]

next, previous Section / Table of Contents / Index [R] This option allows you to redefine or scale atom radii and nuclear charges of all cluster atoms. Nuclear charges together with atom radii are used by BALSAC to identify atoms. Since BALSAC can display atoms of equal charge with the same color reassigning charges to different atoms becomes useful if structural details in complex clusters need to be visualized. This is also true for modifications of atomic radii. If a cluster is built from scratch default values are used for both radii (defined by touching spheres) and nuclear charges (from an internal table) unless structural information is read in from an input file and meaningful (non-zero) values are provided for all radii and charges. Default values of atomic radii and nuclear charges are given in Sec. 5.3. The radii option menu R of the BALSAC/CLUSTER session reads ========== RADII/CHARGES OPTIONS ================================== nct atoms nel elements Nuc Rmin Rmax | Nuc Rmin Rmax 1) nc/el rmin rmax | 2) ... Modify radii : [A]ll [Z]select [S]elect [R]escale charges: a[L]l s[E]lect [T]abl [D]ispla [X]plot [?,]esc ============================================================= 10 == where for each of the nel different elements (described by their nuclear charge nc and element name el) which appear in the cluster (of nct atoms) smallest and largest atom radii, rmin and rmax respectively, are given. Here rmin and rmax differ only if different cluster atoms of the same element been assigned different radii, see below. > [A] selected from submenu R allows you to change all atom radii globally. The prompt ============================================================== Change all nct radii: [A]bs [R]el [?,]esc ======================================================== 11 == gives the total number nct of radii (= atoms) defined in the cluster and option > > [A] asks Input nct radii ("/"=esc) : for nct numbers defining radii (absolute values) of all cluster atoms. The order of the radii is identical to that of the atoms shown in the graphics or full analysis, see Sec. 6.3.12. If the option was selected erroneously it can be cancelled by the dummy input "/". After complete input BALSAC returns to submenu R. > > [R] asks Global stretch factor Q : for a value of Q > 0.0 to scale all atom radii of the cluster after which BALSAC returns to submenu R. > > [,] returns immediately to submenu R. > [Z] selected from submenu R allows you to change radii of all atoms of a given nuclear (element) charge. The prompt Change radii of selected elements Nuc (0=esc) : asks for the nuclear charge nuc defining the element. If a charge nuc appearing in the list of menu R is chosen the prompt ============================================================== nel atoms(s) R= rmin/rmax: change radii [A]bs [R]el [?,]esc ======================================================== 12 == gives the number nel of different cluster atoms of charge nuc and lists the smallest and largest radii assigned to them and option > > [A] asks Radius : for a new radius to be assigned to all atoms of charge nuc after which BALSAC returns to submenu R. > > [R] asks Factor : asks for a factor q to scale the radii assigned to all atoms of charge nuc after which BALSAC returns to submenu R. > > [,] returns immediately to submenu R. > [S] selected from submenu R allows you to change radii of selected cluster atoms. The prompt Change radius of selected atom N (1- nct, 0=esc) : asks for the number n of any of the nct cluster atoms where the numbering is identical to that of the atoms shown in the graphics or full analysis, see Sec. 6.3.12. For a valid atom number n the prompt =============================================== Xyz,R,Id,V( n)= x y z , rad , nuc , V Change radius [A]bs [R]el [?,]esc ========================================= 59 == lists coordinates (x,y,z), the atom radius rad, the nuclear charge / element name, and the visibility ("T" for visible or "F" for invisible) of the respective atom and option > > [A] asks Radius : for a new radius to be assigned to atom n after which BALSAC returns to submenu R. > > [R] asks Factor : asks for a factor q to scale the radius assigned to atom n after which BALSAC returns to submenu R. > > [,] returns immediately to submenu R. > [R] selected from submenu R rescales all atom radii of the cluster using a scaling factor such that highest packing without overlapping atom spheres is achieved. If (at least) one of the original radii was chosen to be zero then internal radii (derived from atom radii according to respective nuclear charges, see Sec. 5.3) will be used. Rescaling may take some time during which the message ... Rescaling ... shows. After all radii are rescaled BALSAC shows Radii rescaled: factor = qr / min ( n1 - n2 ) = dmin ** Press [C], L-click to continue ** the value of the computed rescaling factor qr. Further, n1, n2 denote the two atoms of smallest distance dmin in the cluster. For qr < 1.D-5 no renormalization is performed which is indicated by "NO rescaling" added to the above line. This may occur if duplicate atoms or atoms very close to each other have been generated which can be checked by dmin in the above message line. Coinciding atoms can be identified in the atom listing of the analysis option, see Sec. 6.3.12. Removing coinciding atoms is possible with the reduction option (option [R] of the symmetry submenu, see Sec. 6.3.2.3). Selecting [C] in the above prompt (or L-click (DOS)) returns to submenu R. > [L] selected from submenu R allows you to assign new nuclear charges to all atoms of the cluster in one step (where atom radii and positions are kept fixed). The prompt Input nct nuclear charges ("/"=esc) : asks for nct nuclear charges to be assigned to each of the cluster atoms. The order of the radii is identical to that of the atoms shown in the graphics or full analysis, see Sec. 6.3.12. If the option was selected erroneously it can be cancelled by the dummy input "/". After complete input BALSAC returns to submenu R. > [E] selected from submenu R allows you to change the nuclear charge of selected cluster atoms. The prompt Change charge of selected atom N (1- nct, 0=esc) : asks for the number n of any of the nct cluster atoms where the numbering is identical to that of the atoms shown in the graphics or full analysis, see Sec. 6.3.12. For a valid atom number n the prompt Xyz,R,Id,V( n)= x y z , rad , nuc , V New charge : lists coordinates (x,y,z), the atom radius rad, the nuclear charge / element name, and the visibility ("T" for visible or "F" for invisible) of the respective atom and asks for a new nuclear charge value. After this BALSAC returns to submenu R. > [T] selected from submenu R shows a table of all elements and atom radii defined internally. The default radii are close to covalent radii (given in Angstrom) except for rare gas atoms where Van der Waals radii were chosen, see Sec. 5.3. The table reads Element/radii table: H( 1): .4350 He( 2):1.4000 Li( 3):1.5199 Be( 4):1.1430 B( 5): .9750 C( 6): .6550 N( 7): .7500 O( 8): .7300 F( 9): .7200 Ne(10):1.6000 Na(11):1.8579 Mg(12):1.6047 Al(13):1.4318 Si(14):1.1758 P(15):1.0600 S(16):1.0200 Cl(17): .9900 Ar(18):1.9000 K(19):2.2620 Ca(20):1.9758 Sc(21):1.6545 Ti(22):1.4755 V(23):1.3090 Cr(24):1.2490 Mn(25):1.3500 Fe(26):1.2411 Co(27):1.2535 Ni(28):1.2460 Cu(29):1.2780 Zn(30):1.3325 Ga(31):1.3501 Ge(32):1.2248 As(33):1.2000 Se(34):1.1600 Br(35):1.1400 Kr(36):2.0000 Rb(37):2.4700 Sr(38):2.1513 Y(39):1.8237 Zr(40):1.6156 Nb(41):1.4318 Mo(42):1.3626 Tc(43):1.3675 Ru(44):1.3529 Rh(45):1.3450 Pd(46):1.3755 Ag(47):1.4447 Cd(48):1.4894 In(49):1.6662 Sn(50):1.5375 Sb(51):1.4000 Te(52):1.3600 I(53):1.3300 Xe(54):2.2000 Cs(55):2.6325 Ba(56):2.1705 La(57):1.8725 Ce(58):1.8243 Pr(59):1.8362 Nd(60):1.8295 Pm(61):1.8090 Sm(62):1.8040 Eu(63):1.9840 Gd(64):1.8180 Tb(65):1.8005 Dy(66):1.7951 Ho(67):1.7886 Er(68):1.7794 Tm(69):1.7687 Yb(70):1.9396 Lu(71):1.7515 Hf(72):1.5973 Ta(73):1.4280 W(74):1.3705 Re(75):1.3800 Os(76):1.3676 Ir(77):1.3573 Pt(78):1.3873 Au(79):1.4419 Hg(80):1.5025 Tl(81):1.7283 Pb(82):1.7501 Bi(83):1.4600 Po(84):1.4600 At(85):1.4500 Rn(86):1.4300 Fr(87):2.5000 Ra(88):2.1400 Ac(89):1.8775 Th(90):1.7975 Pa(91):1.6086 U(92):1.5683 Np(93):1.6000 Pu(94):1.6000 Am(95):1.6000 Cm(96):1.6000 Bk(97):1.6000 Cf(98):1.6000 Es(99):1.6000 ** Press [C], L-click to continue ** and selecting [C] (or L-click (DOS)) returns to submenu R. > [D] selected from submenu R shows up to 10 lines of the most recent output generated by the graphic analysis option, see Sec. 6.3.12.2, by ============ Latest Graphics Output ================== 1: Xyz,R,Id( n1)= x y z rad nuc ... ====================================================== This allows you to look up and use numerical output from the analysis for input within submenu R. After the listing BALSAC returns to submenu R. > [X] selected from submenu R plots the lattice section (switching to graphics mode (DOS) or opening a graphics window (Unix)) or lists its atom coordinates depending on the plot/list mode defined in the graphics option, see Sec. 6.2.7. > [,] selected from submenu R returns to the BALSAC/CLUSTER main option menu, see Sec. 6.3.0. next, previous Section / Table of Contents / Index