irc
Type |
Status |
|---|---|
CML extraction template |
|
HTML5 representation |
|
Attribute |
Value |
|---|---|
source |
GRRM log |
id |
irc |
pattern |
IRCIRCIRCIRC.* |
endPattern |
IRCIRCIRCIRC.* |
endOffset |
1 |
xml:base |
irc.xml |
Input
IRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCI
INITIAL STRUCTURE
C -0.064198235583 -0.007930187832 -0.000000000000
O 1.233143761809 0.016481892179 0.000000000000
H 0.644724226899 1.031280651044 0.000000000000
H -0.513669753124 -1.039832355389 0.000000000000
ENERGY = -114.276451735641
Spin(**2) = 0.000000000000
(...)
FREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQF
Geometry (Origin = Center of Mass, Axes = Principal Axis), SYMMETRY = Cs
C 0.695923922878 -0.078083657444 0.000000000000
O -0.593539542416 0.066747898232 0.000000000000
H -0.142357946467 -1.016067523497 0.000000000000
H 1.276014279045 0.886458672976 0.000000000000
0 1 2
Freq. : -2057.48289608 764.48753053 1327.25146103
Red. M : 1.11011042 1.13331104 1.48466979
(...)
FREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQF
IRC FOLLOWING (FORWARD) STARTING FROM FIRST-ORDER SADDLE
=========================================================================
# STEP 1
C -0.071150053068 -0.011562155761 -0.000000000000
O 1.231437348088 0.020978168998 0.000000000000
H 0.741327492878 1.014741115267 0.000000000000
H -0.500416895204 -1.051406775680 0.000000000000
ENERGY = -114.279418458276
Spin(**2) = 0.000000000000
# STEP 2
C -0.074800472155 -0.013609448325 0.000000000000
O 1.230332553586 0.023373404369 -0.000000000000
H 0.794622143506 1.007287090514 0.000000000000
H -0.492712740670 -1.057590112617 0.000000000000
ENERGY = -114.283167686397
Spin(**2) = 0.000000000000
(...)
EQ EXIST WITHIN STEPSIZE, OPTIMIZATION CARRIED OUT
OPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTO
# ITR. 0
C -0.105850351028 -0.031433719366 0.000000000000
O 1.198842252895 0.043662456033 0.000000000000
H 1.454397774356 0.983359563995 0.000000000000
H -0.283008859220 -1.143434017688 -0.000000000000
Item Value Threshold
ENERGY -114.329482198186 ( 0.000000000000 : 0.000000000000)
Spin(**2) 0.000000000000
LAMDA 0.000000036186
TRUST RADII 0.100000000000
STEP RADII 0.000068764539
Maximum Force 0.000073967330 0.000060000000
RMS Force 0.000040582806 0.000040000000
Maximum Displacement 0.000038660074 0.000300000000
RMS Displacement 0.000019850613 0.000200000000
NORMAL MODE EIGENVALUE : N_MODE = 6
0.094521103 0.107577985 0.165587813 0.593325375 0.875514194
1.134713490
(...)
=========================================================================
Optimized structure, SYMMETRY = Cs
C -0.105863255395 -0.031402444471 0.000001934131
O 1.198838617361 0.043660566367 0.000002749597
H 1.454375505562 0.983319983770 -0.000002542309
H -0.282970050525 -1.143423822692 -0.000002141419
ENERGY = -114.329482200635
Spin(**2) = 0.000000000000
(...)
Minimum point was found
OPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTO
FREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQF
Geometry (Origin = Center of Mass, Axes = Principal Axis), SYMMETRY = Cs
C 0.732099863660 0.125228037218 -0.000000305817
O -0.557768432533 -0.084822458724 -0.000000327663
H -1.011259054252 0.776922966538 0.000004806572
H 1.146461185184 -0.921797777996 0.000004034985
0 1 2
Freq. : 1104.21793079 1214.80606311 1376.76812203
(...)
FREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQF
IRC FOLLOWING (BACKWARD) STARTING FROM FIRST-ORDER SADDLE
=========================================================================
# STEP 1
C -0.057246418098 -0.004298219903 0.000000000000
O 1.234850175530 0.011985615360 0.000000000000
H 0.548120960920 1.047820186821 0.000000000000
H -0.526922611044 -1.028257935098 0.000000000000
ENERGY = -114.279689146250
Spin(**2) = 0.000000000000
# STEP 2
C -0.049927090418 -0.000749373503 0.000000000000
O 1.236267436601 0.007489612335 -0.000000000000
H 0.451627531415 1.064724546798 0.000000000000
H -0.540072123984 -1.016062970509 0.000000000000
ENERGY = -114.289141566899
Spin(**2) = 0.000000000000
(...)
IRC following along both forward and backward directions were finished
IRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCIRCI
Output text
1<comment class="example.output" id="irc">
2 <module cmlx:templateRef="irc">
3 <module cmlx:templateRef="irc-path">
4 <scalar cmlx:templateRef="direction" dataType="xsd:string" dictRef="g:ircDirection">FORWARD</scalar>
5 <module cmlx:templateRef="irc-iteration">
6 <module cmlx:templateRef="irc-step">
7 <scalar cmlx:templateRef="step" dataType="xsd:integer" dictRef="g:ircStep">1</scalar>
8 <module cmlx:templateRef="molecule">
9 <molecule cmlx:templateRef="atom" id="molecule">
10 <atomArray>
11 <atom elementType="C" id="a1" x3="-0.07115005" y3="-0.01156216" z3="-0.0000">
12 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
13 </atom>
14 <atom elementType="O" id="a2" x3="1.23143735" y3="0.02097817" z3="0.0000">
15 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
16 </atom>
17 <atom elementType="H" id="a3" x3="0.74132749" y3="1.01474112" z3="0.0000">
18 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
19 </atom>
20 <atom elementType="H" id="a4" x3="-0.5004169" y3="-1.05140678" z3="0.0000">
21 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
22 </atom>
23 </atomArray>
24 <bondArray>
25 <bond atomRefs2="a1 a3" order="S" />
26 <bond atomRefs2="a1 a2" order="S" />
27 <bond atomRefs2="a1 a4" order="S" />
28 <bond atomRefs2="a2 a3" order="S" />
29 </bondArray>
30 <formula concise="CH2O">
31 <atomArray count="1 2 1" elementType="C H O" />
32 </formula>
33 <property dictRef="cml:molmass">
34 <scalar units="unit:dalton">28.0101</scalar>
35 </property>
36 </molecule>
37 </module>
38 <scalar cmlx:templateRef="energy" dataType="xsd:double" dictRef="cc:energy" units="nonsi:hartree">-114.279418458276</scalar>
39 <scalar cmlx:templateRef="spinsqr" dataType="xsd:double" dictRef="cc:s2">0.000000000000</scalar>
40 </module>
41 <module cmlx:templateRef="irc-step">
42 <scalar cmlx:templateRef="step" dataType="xsd:integer" dictRef="g:ircStep">2</scalar>
43 <module cmlx:templateRef="molecule">
44 <molecule cmlx:templateRef="atom" id="molecule">
45 <atomArray>
46 <atom elementType="C" id="a1" x3="-0.07480047" y3="-0.01360945" z3="0.0000">
47 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
48 </atom>
49 <atom elementType="O" id="a2" x3="1.23033255" y3="0.0233734" z3="-0.0000">
50 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
51 </atom>
52 <atom elementType="H" id="a3" x3="0.79462214" y3="1.00728709" z3="0.0000">
53 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
54 </atom>
55 <atom elementType="H" id="a4" x3="-0.49271274" y3="-1.05759011" z3="0.0000">
56 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
57 </atom>
58 </atomArray>
59 <bondArray>
60 <bond atomRefs2="a1 a3" order="S" />
61 <bond atomRefs2="a1 a2" order="S" />
62 <bond atomRefs2="a1 a4" order="S" />
63 <bond atomRefs2="a2 a3" order="S" />
64 </bondArray>
65 <formula concise="CH2O">
66 <atomArray count="1 2 1" elementType="C H O" />
67 </formula>
68 <property dictRef="cml:molmass">
69 <scalar units="unit:dalton">28.0101</scalar>
70 </property>
71 </molecule>
72 </module>
73 <scalar cmlx:templateRef="energy" dataType="xsd:double" dictRef="cc:energy" units="nonsi:hartree">-114.283167686397</scalar>
74 <scalar cmlx:templateRef="spinsqr" dataType="xsd:double" dictRef="cc:s2">0.000000000000</scalar>
75 </module>
76 </module>
77 </module>
78 <module cmlx:templateRef="irc-path">
79 <scalar cmlx:templateRef="direction" dataType="xsd:string" dictRef="g:ircDirection">BACKWARD</scalar>
80 <module cmlx:templateRef="irc-iteration">
81 <module cmlx:templateRef="irc-step">
82 <scalar cmlx:templateRef="step" dataType="xsd:integer" dictRef="g:ircStep">1</scalar>
83 <module cmlx:templateRef="molecule">
84 <molecule cmlx:templateRef="atom" id="molecule">
85 <atomArray>
86 <atom elementType="C" id="a1" x3="-0.05724642" y3="-0.00429822" z3="0.0000">
87 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
88 </atom>
89 <atom elementType="O" id="a2" x3="1.23485018" y3="0.01198562" z3="0.0000">
90 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
91 </atom>
92 <atom elementType="H" id="a3" x3="0.54812096" y3="1.04782019" z3="0.0000">
93 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
94 </atom>
95 <atom elementType="H" id="a4" x3="-0.52692261" y3="-1.02825794" z3="0.0000">
96 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
97 </atom>
98 </atomArray>
99 <bondArray>
100 <bond atomRefs2="a1 a2" order="S" />
101 <bond atomRefs2="a1 a3" order="S" />
102 <bond atomRefs2="a1 a4" order="S" />
103 <bond atomRefs2="a2 a3" order="S" />
104 </bondArray>
105 <formula concise="CH2O">
106 <atomArray count="1 2 1" elementType="C H O" />
107 </formula>
108 <property dictRef="cml:molmass">
109 <scalar units="unit:dalton">28.0101</scalar>
110 </property>
111 </molecule>
112 </module>
113 <scalar cmlx:templateRef="energy" dataType="xsd:double" dictRef="cc:energy" units="nonsi:hartree">-114.279689146250</scalar>
114 <scalar cmlx:templateRef="spinsqr" dataType="xsd:double" dictRef="cc:s2">0.000000000000</scalar>
115 </module>
116 <module cmlx:templateRef="irc-step">
117 <scalar cmlx:templateRef="step" dataType="xsd:integer" dictRef="g:ircStep">2</scalar>
118 <module cmlx:templateRef="molecule">
119 <molecule cmlx:templateRef="atom" id="molecule">
120 <atomArray>
121 <atom elementType="C" id="a1" x3="-0.04992709" y3="-0.00074937" z3="0.0000">
122 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
123 </atom>
124 <atom elementType="O" id="a2" x3="1.23626744" y3="0.00748961" z3="-0.0000">
125 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
126 </atom>
127 <atom elementType="H" id="a3" x3="0.45162753" y3="1.06472455" z3="0.0000">
128 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
129 </atom>
130 <atom elementType="H" id="a4" x3="-0.54007212" y3="-1.01606297" z3="0.0000">
131 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
132 </atom>
133 </atomArray>
134 <bondArray>
135 <bond atomRefs2="a1 a2" order="S" />
136 <bond atomRefs2="a1 a3" order="S" />
137 <bond atomRefs2="a1 a4" order="S" />
138 <bond atomRefs2="a2 a3" order="S" />
139 </bondArray>
140 <formula concise="CH2O">
141 <atomArray count="1 2 1" elementType="C H O" />
142 </formula>
143 <property dictRef="cml:molmass">
144 <scalar units="unit:dalton">28.0101</scalar>
145 </property>
146 </molecule>
147 </module>
148 <scalar cmlx:templateRef="energy" dataType="xsd:double" dictRef="cc:energy" units="nonsi:hartree">-114.289141566899</scalar>
149 <scalar cmlx:templateRef="spinsqr" dataType="xsd:double" dictRef="cc:s2">0.000000000000</scalar>
150 </module>
151 </module>
152 </module>
153 </module>
154 </comment>
Template definition
1<xi:include href="singleStruc.xml" />
2<xi:include href="freq.xml" />
3<template id="irc-path" pattern="IRC FOLLOWING.*" endPattern="IRC FOLLOWING.*" endPattern2="Energy profile along IRC.*" repeat="2"> <record id="direction">IRC FOLLOWING \({X,g:ircDirection}\).*</record> <transform process="pullupSingleton" xpath="./cml:list" /> <record id="null" repeat="2" /> <template id="irc-iteration" pattern="# STEP.*" endPattern="EQ EXIST.*" endPattern2="MAXIMUM INTER.*"> <template id="irc-step" pattern="# STEP.*" endPattern="# STEP.*" endPattern2="~" repeat="*"> <record id="step"># STEP\s*{I,g:ircStep}</record> <template id="molecule" pattern="[A-Za-z]{1,2}\s+.*" endPattern="\s*ENERGY\s*=.*" repeat="*"> <record makeArray="true" repeat="*" id="atom">\s*{A,compchem:elementType}\s*{F,compchem:x3}\s*{F,compchem:y3}\s*{F,compchem:z3}\s*
4 </record> <transform process="createMolecule" xpath="./cml:list[@cmlx:templateRef='atom']/cml:array" id="molecule" /> <transform process="pullupSingleton" xpath="./cml:list" />
5 </template> <record id="energy">\s*ENERGY\s*=\s*{F,cc:energy}\s*</record> <record id="spinsqr">\s*Spin\(\*\*2\)\s*=\s*{F,cc:s2}\s*</record> <record id="null" repeat="1">{X,cc:dummy}</record> <transform process="pullupSingleton" xpath="./cml:list" /> <transform process="delete" xpath="(//cml:list[@cmlx:templateRef='null'])" /> <transform process="delete" xpath="(//cml:scalar[@cmlx:templateRef='null'])" /> <transform process="delete" xpath=".//cml:module[count(*)=0]" /> <transform process="addUnits" xpath=".//cml:scalar[@dictRef='cc:energy']" value="nonsi:hartree" />
6 </template>
7 </template> <template id="irc-opt" pattern="EQ EXIST.*" endPattern="~"> <templateList> <xi:include href="opt.xml" /> <xi:include href="optiStruc.xml" /> <xi:include href="freq.xml" />
8 </templateList>
9 </template>
10 </template>