cosmo
Type |
Status |
|---|---|
CML extraction template |
|
HTML5 representation |
|
Attribute |
Value |
|---|---|
source |
Turbomole log |
id |
cosmo |
name |
Cosmo results |
pattern |
\s*=+\s*$\s*COSMO\sRESULTS\s*$\s*=+\s* |
endPattern |
\s*=+\s*$\s* |
endOffset |
1 |
repeat |
* |
xml:base |
cosmo.xml |
Input
==============================================================================
COSMO RESULTS
==============================================================================
PARAMETER:
nppa: 1082
nspa: 92
nsph: 32
nps: 712
npspher: 224
disex: 10.0000
disex2: 4128.15
rsolv [A]: 3.5400
routf: 0.8500
phsran: 0.00
ampran: 0.10E-04
cavity: closed
epsilon: 9.800
fepsi: 0.8543689
CAVITY VOLUME/AREA [a.u.]:
surface: V1.0, A matrix: V1.0
area: 654.69
volume: 1389.84
SCREENING CHARGE:
cosmo : -0.024349
correction : 0.024631
total : 0.000282
ENERGIES [a.u.]:
Total energy = -1650.4710944278
Total energy + OC corr. = -1650.4709392488
Dielectric energy = -0.0050408508
Diel. energy + OC corr. = -0.0048856718
The following value is included for downward compatibility
Total energy corrected = -1650.4710168383
RADII [Angstroem]:
atom 1 2 3 4 5 6 7 8 9 10 11
radius 2.00 2.00 2.00 2.00 2.00 1.06 2.00 2.00 2.00 2.00 2.00
atom 12 13 14 15 16 17 18 19 20 21
radius 1.30 1.30 1.30 1.30 1.30 1.30 1.30 1.30 1.30 1.30
==============================================================================
Input
.. container:: formalpara-title
Output text
1<comment class="example.output" id="cosmo">
2 <module cmlx:lineCount="39" cmlx:templateRef="cosmo">
3 <list cmlx:templateRef="parameters">
4 <list>
5 <scalar dataType="xsd:string" dictRef="t:parameter">nppa</scalar>
6 <scalar dataType="xsd:string" dictRef="t:value">1082</scalar>
7 </list>
8 <list>
9 <scalar dataType="xsd:string" dictRef="t:parameter">nspa</scalar>
10 <scalar dataType="xsd:string" dictRef="t:value">92</scalar>
11 </list>
12 <list>
13 <scalar dataType="xsd:string" dictRef="t:parameter">nsph</scalar>
14 <scalar dataType="xsd:string" dictRef="t:value">32</scalar>
15 </list>
16 <list>
17 <scalar dataType="xsd:string" dictRef="t:parameter">nps</scalar>
18 <scalar dataType="xsd:string" dictRef="t:value">712</scalar>
19 </list>
20 <list>
21 <scalar dataType="xsd:string" dictRef="t:parameter">npspher</scalar>
22 <scalar dataType="xsd:string" dictRef="t:value">224</scalar>
23 </list>
24 <list>
25 <scalar dataType="xsd:string" dictRef="t:parameter">disex</scalar>
26 <scalar dataType="xsd:string" dictRef="t:value">10.0000</scalar>
27 </list>
28 <list>
29 <scalar dataType="xsd:string" dictRef="t:parameter">disex2</scalar>
30 <scalar dataType="xsd:string" dictRef="t:value">4128.15</scalar>
31 </list>
32 <list>
33 <scalar dataType="xsd:string" dictRef="t:parameter">rsolv [A]</scalar>
34 <scalar dataType="xsd:string" dictRef="t:value">3.5400</scalar>
35 </list>
36 <list>
37 <scalar dataType="xsd:string" dictRef="t:parameter">routf</scalar>
38 <scalar dataType="xsd:string" dictRef="t:value">0.8500</scalar>
39 </list>
40 <list>
41 <scalar dataType="xsd:string" dictRef="t:parameter">phsran</scalar>
42 <scalar dataType="xsd:string" dictRef="t:value">0.00</scalar>
43 </list>
44 <list>
45 <scalar dataType="xsd:string" dictRef="t:parameter">ampran</scalar>
46 <scalar dataType="xsd:string" dictRef="t:value">0.10E-04</scalar>
47 </list>
48 <list>
49 <scalar dataType="xsd:string" dictRef="t:parameter">cavity</scalar>
50 <scalar dataType="xsd:string" dictRef="t:value">closed</scalar>
51 </list>
52 <list>
53 <scalar dataType="xsd:string" dictRef="t:parameter">epsilon</scalar>
54 <scalar dataType="xsd:string" dictRef="t:value">9.800</scalar>
55 </list>
56 <list>
57 <scalar dataType="xsd:string" dictRef="t:parameter">fepsi</scalar>
58 <scalar dataType="xsd:string" dictRef="t:value">0.8543689</scalar>
59 </list>
60 </list>
61 <list cmlx:templateRef="cavityVolumeArea">
62 <list>
63 <scalar dataType="xsd:string" dictRef="t:surface">V1.0</scalar>
64 <scalar dataType="xsd:string" dictRef="t:matrix">V1.0</scalar>
65 </list>
66 <list>
67 <scalar dataType="xsd:string" dictRef="t:parameter">area</scalar>
68 <scalar dataType="xsd:string" dictRef="t:value">654.69</scalar>
69 </list>
70 <list>
71 <scalar dataType="xsd:string" dictRef="t:parameter">volume</scalar>
72 <scalar dataType="xsd:string" dictRef="t:value">1389.84</scalar>
73 </list>
74 </list>
75 <list cmlx:templateRef="screeningCharge">
76 <list>
77 <scalar dataType="xsd:string" dictRef="t:parameter">cosmo</scalar>
78 <scalar dataType="xsd:string" dictRef="t:value">-0.024349</scalar>
79 </list>
80 <list>
81 <scalar dataType="xsd:string" dictRef="t:parameter">correction</scalar>
82 <scalar dataType="xsd:string" dictRef="t:value">0.024631</scalar>
83 </list>
84 <list>
85 <scalar dataType="xsd:string" dictRef="t:parameter">total</scalar>
86 <scalar dataType="xsd:string" dictRef="t:value">0.000282</scalar>
87 </list>
88 </list>
89 <list id="energies" cmlx:templateRef="energies">
90 <scalar dataType="xsd:double" dictRef="cc:energy">-1650.4710944278</scalar>
91 <scalar dataType="xsd:double" dictRef="t:energyOcCorr">-1650.4709392488</scalar>
92 <scalar dataType="xsd:double" dictRef="t:dielectricEnergy">-0.0050408508</scalar>
93 <scalar dataType="xsd:double" dictRef="t:dielectricEnergyOcCorr">-0.0048856718</scalar>
94 <scalar dataType="xsd:double" dictRef="t:energyCorrected">-1650.4710168383</scalar>
95 </list>
96 <list id="radii" cmlx:templateRef="radii">
97 <array dataType="xsd:integer" size="21" dictRef="cc:serial">1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21</array>
98 <array dataType="xsd:double" size="21" dictRef="t:radius">2.0 2.0 2.0 2.0 2.0 1.06 2.0 2.0 2.0 2.0 2.0 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3</array>
99 </list>
100 </module>
101 </comment>
Output text
1<comment class="example.output" id="cosmo2">
2 <module cmlx:templateRef="cosmo">
3 <list cmlx:templateRef="parameters">
4 <list>
5 <scalar dataType="xsd:string" dictRef="t:parameter">nppa</scalar>
6 <scalar dataType="xsd:string" dictRef="t:value">1082</scalar>
7 </list>
8 <list>
9 <scalar dataType="xsd:string" dictRef="t:parameter">nspa</scalar>
10 <scalar dataType="xsd:string" dictRef="t:value">92</scalar>
11 </list>
12 <list>
13 <scalar dataType="xsd:string" dictRef="t:parameter">nsph</scalar>
14 <scalar dataType="xsd:string" dictRef="t:value">32</scalar>
15 </list>
16 <list>
17 <scalar dataType="xsd:string" dictRef="t:parameter">nps</scalar>
18 <scalar dataType="xsd:string" dictRef="t:value">351</scalar>
19 </list>
20 <list>
21 <scalar dataType="xsd:string" dictRef="t:parameter">npspher</scalar>
22 <scalar dataType="xsd:string" dictRef="t:value">197</scalar>
23 </list>
24 <list>
25 <scalar dataType="xsd:string" dictRef="t:parameter">disex</scalar>
26 <scalar dataType="xsd:string" dictRef="t:value">10.0000</scalar>
27 </list>
28 <list>
29 <scalar dataType="xsd:string" dictRef="t:parameter">disex2</scalar>
30 <scalar dataType="xsd:string" dictRef="t:value">4473.83</scalar>
31 </list>
32 <list>
33 <scalar dataType="xsd:string" dictRef="t:parameter">rsolv [A]</scalar>
34 <scalar dataType="xsd:string" dictRef="t:value">1.3000</scalar>
35 </list>
36 <list>
37 <scalar dataType="xsd:string" dictRef="t:parameter">routf</scalar>
38 <scalar dataType="xsd:string" dictRef="t:value">0.8500</scalar>
39 </list>
40 <list>
41 <scalar dataType="xsd:string" dictRef="t:parameter">phsran</scalar>
42 <scalar dataType="xsd:string" dictRef="t:value">0.0</scalar>
43 </list>
44 <list>
45 <scalar dataType="xsd:string" dictRef="t:parameter">ampran</scalar>
46 <scalar dataType="xsd:string" dictRef="t:value">0.10E-04</scalar>
47 </list>
48 <list>
49 <scalar dataType="xsd:string" dictRef="t:parameter">cavity</scalar>
50 <scalar dataType="xsd:string" dictRef="t:value">closed</scalar>
51 </list>
52 <list>
53 <scalar dataType="xsd:string" dictRef="t:parameter">epsilon</scalar>
54 <scalar dataType="xsd:string" dictRef="t:value">infinity</scalar>
55 </list>
56 <list>
57 <scalar dataType="xsd:string" dictRef="t:parameter">refind</scalar>
58 <scalar dataType="xsd:string" dictRef="t:value">1.300</scalar>
59 </list>
60 <list>
61 <scalar dataType="xsd:string" dictRef="t:parameter">fepsi</scalar>
62 <scalar dataType="xsd:string" dictRef="t:value">1.0000000</scalar>
63 </list>
64 </list>
65 <list cmlx:templateRef="cavityVolumeArea">
66 <list>
67 <scalar dataType="xsd:string" dictRef="t:surface">V1.0</scalar>
68 <scalar dataType="xsd:string" dictRef="t:matrix">V1.0</scalar>
69 </list>
70 <list>
71 <scalar dataType="xsd:string" dictRef="t:parameter">area</scalar>
72 <scalar dataType="xsd:string" dictRef="t:value">349.52</scalar>
73 </list>
74 <list>
75 <scalar dataType="xsd:string" dictRef="t:parameter">volume</scalar>
76 <scalar dataType="xsd:string" dictRef="t:value">542.84</scalar>
77 </list>
78 </list>
79 <list cmlx:templateRef="screeningCharge">
80 <list>
81 <scalar dataType="xsd:string" dictRef="t:parameter">cosmo</scalar>
82 <scalar dataType="xsd:string" dictRef="t:value">-0.019014</scalar>
83 </list>
84 <list>
85 <scalar dataType="xsd:string" dictRef="t:parameter">correction</scalar>
86 <scalar dataType="xsd:string" dictRef="t:value">0.018692</scalar>
87 </list>
88 <list>
89 <scalar dataType="xsd:string" dictRef="t:parameter">total</scalar>
90 <scalar dataType="xsd:string" dictRef="t:value">-0.000323</scalar>
91 </list>
92 </list>
93 <list cmlx:templateRef="energies" id="energies">
94 <scalar dataType="xsd:double" dictRef="cc:energy">-190.8500889093</scalar>
95 <scalar dataType="xsd:double" dictRef="t:energyOcCorr">-190.8501078686</scalar>
96 <scalar dataType="xsd:double" dictRef="t:dielectricEnergy">-0.0158822461</scalar>
97 <scalar dataType="xsd:double" dictRef="t:dielectricEnergyOcCorr">-0.0159012054</scalar>
98 </list>
99 <list cmlx:templateRef="radii" id="radii">
100 <array dataType="xsd:string" dictRef="cc:elementType" size="3">o c h</array>
101 <array dataType="xsd:double" dictRef="t:atomicradii" size="3">1.72 2.00 1.30</array>
102 <array dataType="xsd:string" dictRef="t:atomrange" size="3">1 2-4 5-8</array>
103 </list>
104 </module>
105 </comment>
Template definition
1<templateList> <template pattern="\s*PARAMETER:.*" endPattern="\s*[A-Z]+.*" endOffset="0"> <record repeat="1" /> <record id="parameters" repeat="*">{X,t:parameter}\:{A,t:value}</record>
2 </template> <template pattern="\s*CAVITY\sVOLUME/AREA\s\[a\.u\.\].*" endPattern="\s*[A-Z]+.*" endOffset="0"> <record repeat="1" /> <record id="tmp">\s*surface:{A,t:surface},.*:{A,t:matrix}</record> <record id="cavityVolumeArea" repeat="*">{X,t:parameter}\:{A,t:value}</record> <transform process="move" xpath=".//cml:list[@cmlx:templateRef='tmp']/cml:list" to=".//cml:list[@cmlx:templateRef='cavityVolumeArea']" position="1" />
3 </template> <template pattern="\s*SCREENING\sCHARGE:.*" endPattern="\s*[A-Z]{2,}.*" endOffset="0"> <record repeat="1" /> <record id="screeningCharge" repeat="*">{X,t:parameter}\:{A,t:value}</record>
4 </template> <template pattern="\s*ENERGIES.*:.*" endPattern="\s*[A-Z]{2,}.*" endPattern2="~" endOffset="0"> <record repeat="1" /> <record>\s*Total\senergy\s*={F,cc:energy}</record> <record>\s*Total\senergy\s\+\sOC\scorr\.\s*={F,t:energyOcCorr}</record> <record>\s*Dielectric\senergy\s*={F,t:dielectricEnergy}</record> <record>\s*Diel\.\senergy\s\+\sOC\scorr\.\s*={F,t:dielectricEnergyOcCorr}</record> <record repeat="1" /> <record>\s*Total\senergy\scorrected\s*={F,t:energyCorrected}</record> <transform process="addChild" xpath="." elementName="cml:list" id="energies" /> <transform process="addAttribute" xpath=".//cml:list[@id='energies']" name="cmlx:templateRef" value="energies" /> <transform process="move" xpath=".//cml:scalar" to=".//cml:list[@id='energies']" />
5 </template> <template pattern="\s*RADII.*" endPattern="\s*=+\s*" endPattern2="\s*[A-Z]{2,}.*" endPattern3="~" endOffset="0"> <record repeat="1" /> <templateList> <template id="atom" pattern="\s*atom.*" endPattern=".*" endPattern2="~" endOffset="0" repeat="*"> <record>\s*atom{1_11I,cc:serial}</record>
6 </template> <template id="radius" pattern="\s*radius.*" endPattern=".*" endPattern2="~" endOffset="0" repeat="*"> <record>\s*radius{1_11F,t:radius}</record>
7 </template>
8 </templateList> <transform process="joinArrays" xpath=".//cml:array[@dictRef='cc:serial']" /> <transform process="joinArrays" xpath=".//cml:array[@dictRef='t:radius']" /> <transform process="addChild" xpath="." elementName="cml:list" id="radii" /> <transform process="addAttribute" xpath=".//cml:list[@id='radii']" name="cmlx:templateRef" value="radii" /> <transform process="move" xpath=".//cml:array" to=".//cml:list[@id='radii']" />
9 </template> <template id="" pattern="\s*ELEMENT\sRADIUS\s\[A\]:\sATOM\sLIST\s*" endPattern2="\s*[A-Z]{2,}.*" endPattern3="~" endOffset="0"> <record repeat="1" /> <record repeat="*" makeArray="true">{A,cc:elementType}{F,t:atomicradii}:{A,t:atomrange}</record> <transform process="addChild" xpath="." elementName="cml:list" id="radii" /> <transform process="addAttribute" xpath=".//cml:list[@id='radii']" name="cmlx:templateRef" value="radii" /> <transform process="move" xpath=".//cml:array" to=".//cml:list[@id='radii']" />
10 </template>
11 </templateList>
12<transform process="move" xpath=".//cml:module/cml:list" to="." />
13<transform process="move" xpath=".//cml:module/cml:list" to="." />
14<transform process="delete" xpath=".//cml:list[count(*)=0]" />
15<transform process="delete" xpath=".//cml:list[count(*)=0]" />
16<transform process="delete" xpath=".//cml:module[count(*)=0]" />
17<transform process="delete" xpath=".//cml:module[count(*)=0]" />