geometry
Type |
Status |
|---|---|
CML extraction template |
|
HTML5 representation |
|
Attribute |
Value |
|---|---|
source |
ADF log |
id |
geometry |
pattern |
\sG\sE\s O\sM\sE\sT\sR\sY.*(3D\s*Molecule|Planar\s*Molecule|Linear\s*Molecule|Single\s*Atom).* |
endPattern |
\s+[0-9]+.*$\s*$\s* |
offset |
-1 |
endOffset |
1 |
xml:base |
runtype/geometry.xml |
Input
===============
G E O M E T R Y *** 3D Molecule ***
===============
ATOMS
===== X Y Z CHARGE
(Angstrom) Nucl +Core At.Mass
-------------------------- ---------------- -------
1 Lu 0.5510 -0.8582 1.7445 71.00 17.00 174.9408
2 Lu -1.3822 1.4940 -0.0964 71.00 17.00 174.9408
3 Lu 0.5842 -0.9156 -1.8136 71.00 17.00 174.9408
4 N 0.1194 0.0590 -0.0694 7.00 5.00 14.0031
5 N 1.2612 -3.1890 -5.7161 7.00 5.00 14.0031
6 H 0.1199 -1.5550 -6.4368 1.00 1.00 1.0078
7 H 1.8649 -1.1924 -6.2222 1.00 1.00 1.0078
8 H 2.3966 -4.3625 -4.3698 1.00 1.00 1.0078
9 H 3.2480 -2.9007 -4.9668 1.00 1.00 1.0078
10 H 2.6474 -3.3171 -7.3537 1.00 1.00 1.0078
11 H 0.9297 -3.6743 -7.7381 1.00 1.00 1.0078
12 H 1.8943 -4.8586 -6.8242 1.00 1.00 1.0078
13 C 0.9985 -1.7560 -5.8088 6.00 4.00 12.0000
14 C 2.2587 -3.3131 -4.6649 6.00 4.00 12.0000
15 C 1.7107 -3.7836 -6.9715 6.00 4.00 12.0000
16 C -2.8978 3.2168 -0.7460 6.00 4.00 12.0000
17 C -3.3899 2.0349 -1.4821 6.00 4.00 12.0000
18 C -2.6810 1.6122 -2.6756 6.00 4.00 12.0000
19 C 3.9518 -0.8543 -0.7169 6.00 4.00 12.0000
20 C -2.8553 3.1643 0.7715 6.00 4.00 12.0000
21 C -2.6687 1.5849 2.7059 6.00 4.00 12.0000
22 C -3.3582 2.0001 1.5019 6.00 4.00 12.0000
23 C -3.9599 0.9360 0.7401 6.00 4.00 12.0000
24 C -3.8899 -0.4381 -1.1609 6.00 4.00 12.0000
Output text
1<comment class="example.output" id="geometry">
2 <module cmlx:lineCount="33" cmlx:templateRef="geometry">
3 <molecule id="coordinates">
4 <atomArray>
5 <atom id="a1" elementType="Lu" x3="0.551" y3="-0.8582" z3="1.7445">
6 <scalar dataType="xsd:integer" dictRef="cc:serial">1</scalar>
7 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">71</scalar>
8 </atom>
9 <atom id="a2" elementType="Lu" x3="-1.3822" y3="1.494" z3="-0.0964">
10 <scalar dataType="xsd:integer" dictRef="cc:serial">2</scalar>
11 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">71</scalar>
12 </atom>
13 <atom id="a3" elementType="Lu" x3="0.5842" y3="-0.9156" z3="-1.8136">
14 <scalar dataType="xsd:integer" dictRef="cc:serial">3</scalar>
15 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">71</scalar>
16 </atom>
17 <atom id="a4" elementType="N" x3="0.1194" y3="0.059" z3="-0.0694">
18 <scalar dataType="xsd:integer" dictRef="cc:serial">4</scalar>
19 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">7</scalar>
20 </atom>
21 <atom id="a5" elementType="N" x3="1.2612" y3="-3.189" z3="-5.7161">
22 <scalar dataType="xsd:integer" dictRef="cc:serial">5</scalar>
23 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">7</scalar>
24 </atom>
25 <atom id="a6" elementType="H" x3="0.1199" y3="-1.555" z3="-6.4368">
26 <scalar dataType="xsd:integer" dictRef="cc:serial">6</scalar>
27 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
28 </atom>
29 <atom id="a7" elementType="H" x3="1.8649" y3="-1.1924" z3="-6.2222">
30 <scalar dataType="xsd:integer" dictRef="cc:serial">7</scalar>
31 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
32 </atom>
33 <atom id="a8" elementType="H" x3="2.3966" y3="-4.3625" z3="-4.3698">
34 <scalar dataType="xsd:integer" dictRef="cc:serial">8</scalar>
35 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
36 </atom>
37 <atom id="a9" elementType="H" x3="3.248" y3="-2.9007" z3="-4.9668">
38 <scalar dataType="xsd:integer" dictRef="cc:serial">9</scalar>
39 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
40 </atom>
41 <atom id="a10" elementType="H" x3="2.6474" y3="-3.3171" z3="-7.3537">
42 <scalar dataType="xsd:integer" dictRef="cc:serial">10</scalar>
43 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
44 </atom>
45 <atom id="a11" elementType="H" x3="0.9297" y3="-3.6743" z3="-7.7381">
46 <scalar dataType="xsd:integer" dictRef="cc:serial">11</scalar>
47 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
48 </atom>
49 <atom id="a12" elementType="H" x3="1.8943" y3="-4.8586" z3="-6.8242">
50 <scalar dataType="xsd:integer" dictRef="cc:serial">12</scalar>
51 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
52 </atom>
53 <atom id="a13" elementType="C" x3="0.9985" y3="-1.756" z3="-5.8088">
54 <scalar dataType="xsd:integer" dictRef="cc:serial">13</scalar>
55 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
56 </atom>
57 <atom id="a14" elementType="C" x3="2.2587" y3="-3.3131" z3="-4.6649">
58 <scalar dataType="xsd:integer" dictRef="cc:serial">14</scalar>
59 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
60 </atom>
61 <atom id="a15" elementType="C" x3="1.7107" y3="-3.7836" z3="-6.9715">
62 <scalar dataType="xsd:integer" dictRef="cc:serial">15</scalar>
63 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
64 </atom>
65 <atom id="a16" elementType="C" x3="-2.8978" y3="3.2168" z3="-0.746">
66 <scalar dataType="xsd:integer" dictRef="cc:serial">16</scalar>
67 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
68 </atom>
69 <atom id="a17" elementType="C" x3="-3.3899" y3="2.0349" z3="-1.4821">
70 <scalar dataType="xsd:integer" dictRef="cc:serial">17</scalar>
71 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
72 </atom>
73 <atom id="a18" elementType="C" x3="-2.681" y3="1.6122" z3="-2.6756">
74 <scalar dataType="xsd:integer" dictRef="cc:serial">18</scalar>
75 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
76 </atom>
77 <atom id="a19" elementType="C" x3="3.9518" y3="-0.8543" z3="-0.7169">
78 <scalar dataType="xsd:integer" dictRef="cc:serial">19</scalar>
79 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
80 </atom>
81 <atom id="a20" elementType="C" x3="-2.8553" y3="3.1643" z3="0.7715">
82 <scalar dataType="xsd:integer" dictRef="cc:serial">20</scalar>
83 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
84 </atom>
85 <atom id="a21" elementType="C" x3="-2.6687" y3="1.5849" z3="2.7059">
86 <scalar dataType="xsd:integer" dictRef="cc:serial">21</scalar>
87 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
88 </atom>
89 <atom id="a22" elementType="C" x3="-3.3582" y3="2.0001" z3="1.5019">
90 <scalar dataType="xsd:integer" dictRef="cc:serial">22</scalar>
91 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
92 </atom>
93 <atom id="a23" elementType="C" x3="-3.9599" y3="0.936" z3="0.7401">
94 <scalar dataType="xsd:integer" dictRef="cc:serial">23</scalar>
95 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
96 </atom>
97 <atom id="a24" elementType="C" x3="-3.8899" y3="-0.4381" z3="-1.1609">
98 <scalar dataType="xsd:integer" dictRef="cc:serial">24</scalar>
99 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
100 </atom>
101 </atomArray>
102 <formula formalCharge="0" concise="C 12 H 7 Lu 3 N 2">
103 <atomArray elementType="C H Lu N" count="12.0 7.0 3.0 2.0" />
104 </formula>
105 <bondArray>
106 <bond atomRefs2="a1 a2" id="a1_a2" order="S" />
107 <bond atomRefs2="a1 a3" id="a1_a3" order="S" />
108 <bond atomRefs2="a1 a4" id="a1_a4" order="S" />
109 <bond atomRefs2="a2 a3" id="a2_a3" order="S" />
110 <bond atomRefs2="a2 a4" id="a2_a4" order="S" />
111 <bond atomRefs2="a2 a16" id="a2_a16" order="S" />
112 <bond atomRefs2="a2 a17" id="a2_a17" order="S" />
113 <bond atomRefs2="a2 a18" id="a2_a18" order="S" />
114 <bond atomRefs2="a2 a20" id="a2_a20" order="S" />
115 <bond atomRefs2="a2 a22" id="a2_a22" order="S" />
116 <bond atomRefs2="a2 a23" id="a2_a23" order="S" />
117 <bond atomRefs2="a3 a4" id="a3_a4" order="S" />
118 <bond atomRefs2="a5 a13" id="a5_a13" order="S" />
119 <bond atomRefs2="a5 a14" id="a5_a14" order="S" />
120 <bond atomRefs2="a5 a15" id="a5_a15" order="S" />
121 <bond atomRefs2="a6 a13" id="a6_a13" order="S" />
122 <bond atomRefs2="a7 a13" id="a7_a13" order="S" />
123 <bond atomRefs2="a8 a14" id="a8_a14" order="S" />
124 <bond atomRefs2="a9 a14" id="a9_a14" order="S" />
125 <bond atomRefs2="a10 a15" id="a10_a15" order="S" />
126 <bond atomRefs2="a11 a15" id="a11_a15" order="S" />
127 <bond atomRefs2="a12 a15" id="a12_a15" order="S" />
128 <bond atomRefs2="a16 a17" id="a16_a17" order="S" />
129 <bond atomRefs2="a16 a20" id="a16_a20" order="S" />
130 <bond atomRefs2="a17 a18" id="a17_a18" order="S" />
131 <bond atomRefs2="a20 a22" id="a20_a22" order="S" />
132 <bond atomRefs2="a21 a22" id="a21_a22" order="S" />
133 <bond atomRefs2="a22 a23" id="a22_a23" order="S" />
134 </bondArray>
135 <property dictRef="cml:molmass">
136 <scalar dataType="xsd:double" units="unit:dalton">704.0983800000001</scalar>
137 </property>
138 </molecule>
139 </module>
140 </comment>
Template definition
1<templateList> <template id="coordinates" name="coordinates" pattern="\s*ATOMS.*" endPattern="\s+[0-9]+.*$\s*$\s*" endPattern2="~" endOffset="1"> <record repeat="4" /> <record id="atom" repeat="*" makeArray="true">{I,cc:serial}{A,cc:elementType}{F,cc:x3,unit:angstrom}{F,cc:y3,unit:angstrom}{F,cc:z3,unit:angstrom}.*</record> <transform process="createMolecule" xpath=".//cml:list[@cmlx:templateRef='atom']/cml:array" id="coordinates" /> <transform process="pullup" repeat="2" xpath=".//cml:molecule" /> <transform process="delete" xpath=".//cml:list[count(*)=0]" /> <transform process="delete" xpath=".//cml:list[count(*)=0]" /> <transform process="delete" xpath=".//cml:module[count(*)=0]" />
2 </template>
3 </templateList>