From: Miguel <mig...@us...> - 2004-10-05 08:52:38
|
Update of /cvsroot/jmol/Jmol-web/source/doc/v9 In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv27684 Added Files: JmolApplet.jar SN1_reaction.cml aspirina.mol bulk_si.in caffeine.xyz conformeren.cml dna.xyz estron.cml index.xml jmol.mol methanol1.cml move.txt testscript.txt Log Message: saving v9 stuff in preparation for v10 release --- NEW FILE: JmolApplet.jar --- PK rRósJKRt<óõ4y¹x¹ [...3041 lines suppressed...] §ê¦ñ --- NEW FILE: SN1_reaction.cml --- <?xml version="1.0" encoding="ISO-8859-1"?> <!DOCTYPE molecule SYSTEM "cml.dtd" [ <!ATTLIST list convention CDATA #IMPLIED> ]> <list convention="JMOL-ANIMATION"> <molecule id="FRAME1"> <string title="COMMENT">HEAT OF FORMATION = 38.45792 KCAL = 160.90796 KJ; FOR REACTION COORDINATE = 3.00000 ANGSTROMS</string> <atomArray> <stringArray builtin="id"> a0 a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24 </stringArray> <stringArray builtin="elementType"> C C C C C H C H H H H H H O H H O H H H H H H H H </stringArray> <floatArray builtin="x3"> 0.5960000157356262 2.118499994277954 0.10859999805688858 0.05649999901652336 0.10239999741315842 -0.08990000188350677 0.9193000197410583 2.5188000202178955 2.5081000328063965 2.4958999156951904 -1.0038000345230103 0.4049000144004822 0.5580999851226807 -1.231600046157837 -1.0858999490737915 -1.9053000211715698 -1.9467999935150146 -1.9093999862670898 -1.8866000175476074 0.3912999927997589 [...1055 lines suppressed...] -2.8705999851226807 1.1761000156402588 0.6617000102996826 1.9256999492645264 1.299399971961975 1.1593999862670898 -0.08049999922513962 -1.8664000034332275 -1.9068000316619873 -0.6725000143051147 </floatArray> <floatArray builtin="y3"> 1.4402999877929688 1.4402999877929688 2.7118000984191895 0.17839999496936798 0.14000000059604645 0.17080000042915344 -1.0677000284194946 0.8363999724388123 0.9049999713897705 2.466399908065796 2.6177000999450684 3.114799976348877 3.483299970626831 -2.8457000255584717 -3.440999984741211 -3.336400032043457 -0.8353999853134155 -1.5296000242233276 -0.7134000062942505 -1.0736000537872314 -1.152400016784668 -1.9651000499725342 1.061900019645691 -0.7534999847412109 0.030400000512599945 </floatArray> <floatArray builtin="z3"> -0.7109000086784363 -0.7109000086784363 -0.7109000086784363 -0.6725000143051147 0.5090000033378601 -1.6203999519348145 -0.6689000129699707 0.16979999840259552 -1.6259000301361084 -0.6786999702453613 -1.035599946975708 0.3479999899864197 -1.3449000120162964 -0.4090000092983246 0.2800999879837036 -0.8400999903678894 2.615999937057495 3.0392000675201416 3.2070000171661377 -1.52839994430542 0.2903999984264374 -0.7569000124931335 0.5468000173568726 0.3849000036716461 1.4673000574111938 </floatArray> </atomArray> </molecule> </list> --- NEW FILE: aspirina.mol --- aspirina.mol 1 2 2 7 9 2 11 13 2 21 21 0 0 0 -2.2240 -1.4442 -0.4577 C 0 0 0 0 0 -2.1657 -0.0545 -0.5349 C 0 0 0 0 0 -0.9916 0.6085 -0.1694 C 0 0 0 0 0 0.1471 -0.0738 0.2764 C 0 0 0 0 0 0.0751 -1.4832 0.3390 C 0 0 0 0 0 -1.1052 -2.1532 -0.0188 C 0 0 0 0 0 1.2412 -2.2934 0.7925 C 0 0 0 0 0 2.4223 -1.7619 1.1727 O 0 0 0 0 0 1.1650 -3.5162 0.8364 O 0 0 0 0 0 1.2795 0.6233 0.5954 O 0 0 0 0 0 1.1005 1.7577 1.3258 C 0 0 0 0 0 2.4429 2.3635 1.6825 C 0 0 0 0 0 0.0255 2.2041 1.6578 O 0 0 0 0 0 -3.1430 -1.9775 -0.7500 H 0 0 0 0 0 -3.0382 0.5167 -0.8915 H 0 0 0 0 0 -0.9608 1.7083 -0.2479 H 0 0 0 0 0 -1.1740 -3.2520 0.0315 H 0 0 0 0 0 2.9869 -2.5132 1.4166 H 0 0 0 0 0 2.3142 3.3967 2.0773 H 0 0 0 0 0 3.1051 2.4141 0.7884 H 0 0 0 0 0 2.9391 1.7459 2.4657 H 0 0 0 0 0 1 2 1 0 0 0 1 6 2 0 0 0 1 14 1 0 0 0 2 3 2 0 0 0 2 15 1 0 0 0 3 4 1 0 0 0 3 16 1 0 0 0 4 5 2 0 0 0 4 10 1 0 0 0 5 6 1 0 0 0 5 7 1 0 0 0 6 17 1 0 0 0 7 8 1 0 0 0 7 9 2 0 0 0 8 18 1 0 0 0 10 11 1 1 0 0 11 12 1 0 0 0 11 13 2 0 0 0 12 19 1 0 0 0 12 20 1 6 0 0 12 21 1 1 0 0 --- NEW FILE: bulk_si.in --- # Crystalline silicon : computation of the total energy # Convergence with respect to the number of k points. #Definition of the k-point grids kptopt 1 # Option for the automatic generation of k points, taking # into account the symmetry nshiftk 4 shiftk 0.5 0.5 0.5 # These shifts will be the same for all grids 0.5 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.5 ngkpt 8 8 8 # Definition of the different grids #Definition of the unit cell acell 3*10.18 # This is equivalent to 10.18 10.18 10.18 rprim 0.0 0.5 0.5 # FCC primitive vectors (to be scaled by acell) 0.5 0.0 0.5 0.5 0.5 0.0 #Definition of the atom types ntype 1 # There is only one type of atom zatnum 14 # The keyword "zatnum" refers to the atomic number of the # possible type(s) of atom. The pseudopotential(s) # mentioned in the "files" file must correspond # to the type(s) of atom. Here, the only type is Silicon. #Definition of the atoms natom 2 # There are two atoms type 1 1 # They both are of type 1, that is, Silicon. xred # This keyword indicate that the location of the atoms # will follow, one triplet of number for each atom 0.0 0.0 0.0 # Triplet giving the REDUCED coordinate of atom 1. 0.25 0.25 0.25 # Triplet giving the REDUCED coordinate of atom 2. #Definition of the planewave basis set ecut 8.0 # Maximal kinetic energy cut-off, in Hartree #Definition of the SCF procedure nstep 10 # Maximal number of SCF cycles toldfe 1.0d-6 # Will stop when, twice in a row, the difference # between two consecutive evaluations of total energy # differ by less than toldfe (in Hartree) diemac 12.0 # Although this is not mandatory, it is worth to # precondition the SCF cycle. The model dielectric # function used as the standard preconditioner # is described in the "dielng" input variable section. # Here, we follow the prescription for bulk silicon. --- NEW FILE: caffeine.xyz --- 24 Caffeine H -3.3804130 -1.1272367 0.5733036 N 0.9668296 -1.0737425 -0.8198227 C 0.0567293 0.8527195 0.3923156 N -1.3751742 -1.0212243 -0.0570552 C -1.2615018 0.2590713 0.5234135 C -0.3068337 -1.6836331 -0.7169344 C 1.1394235 0.1874122 -0.2700900 N 0.5602627 2.0839095 0.8251589 O -0.4926797 -2.8180554 -1.2094732 C -2.6328073 -1.7303959 -0.0060953 O -2.2301338 0.7988624 1.0899730 H 2.5496990 2.9734977 0.6229590 C 2.0527432 -1.7360887 -1.4931279 H -2.4807715 -2.7269528 0.4882631 H -3.0089039 -1.9025254 -1.0498023 H 2.9176101 -1.8481516 -0.7857866 H 2.3787863 -1.1211917 -2.3743655 H 1.7189877 -2.7489920 -1.8439205 C -0.1518450 3.0970046 1.5348347 C 1.8934096 2.1181245 0.4193193 N 2.2861252 0.9968439 -0.2440298 H -0.1687028 4.0436553 0.9301094 H 0.3535322 3.2979060 2.5177747 H 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