l103¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation |  |
| Attribute | Value |
|---|---|
| source | Gaussian log |
| id | l103 |
| name | Berny optimizations to minima and TS, STQN transition state searches |
| repeat | * |
| pattern | \s*\(Enter.*l103\..* |
| pattern2 | \s*(Grad){2,} |
| endPattern | \s*Leave\sLink\s+103\s.* |
| endOffset | 1 |
| endPattern2 | \s*(Grad){2,} |
| xml:base | l103.xml |
Input
(Enter /opt/G09/g09/l103.exe)
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Initialization pass.
----------------------------
! Initial Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.113 estimate D2E/DX2 !
! R2 R(1,3) 1.113 estimate D2E/DX2 !
! R3 R(1,4) 1.113 estimate D2E/DX2 !
! R4 R(1,5) 1.113 estimate D2E/DX2 !
! A1 A(2,1,3) 109.4712 estimate D2E/DX2 !
! A2 A(2,1,4) 109.4712 estimate D2E/DX2 !
! A3 A(2,1,5) 109.4712 estimate D2E/DX2 !
! A4 A(3,1,4) 109.4712 estimate D2E/DX2 !
! A5 A(3,1,5) 109.4712 estimate D2E/DX2 !
! A6 A(4,1,5) 109.4712 estimate D2E/DX2 !
--------------------------------------------------------------------------------
Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-06
Number of steps in this run= 20 maximum allowed number of steps= 100.
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Leave Link 103 at Fri Sep 13 17:06:50 2013, MaxMem= 419430400 cpu: 0.0
Input
(Enter /opt/G09/g09/l103.exe)
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Internal Forces: Max 0.002386724 RMS 0.000538609
Search for a saddle point.
Step number 1 out of a maximum of 137
All quantities printed in internal units (Hartrees-Bohrs-Radians)
Swaping is turned off.
Second derivative matrix not updated -- analytic derivatives used.
Eigenvalues --- -0.03403 0.00144 0.00463 0.00759 0.00906
Eigenvalues --- 0.01177 0.01317 0.01431 0.01623 0.01839
Eigenvalues --- 0.40148 0.40211 0.40329 0.46257 0.48142
Eigenvalues --- 0.51910 1.01166 1.025821000.000001000.00000
Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000
Eigenvalues --- 1000.000001000.00000
Eigenvectors required to have negative eigenvalues:
R25 R14 R27 R16 D47
1 0.36641 0.36640 0.22975 0.22974 -0.19160
D48 D8 D11 D6 D9
1 0.19153 0.16306 -0.16304 0.15371 -0.15366
RFO step: Lambda0=9.155600927D-04 Lambda=-1.51225227D-04.
Linear search not attempted -- option 19 set.
Iteration 1 RMS(Cart)= 0.01149217 RMS(Int)= 0.00020982
Iteration 2 RMS(Cart)= 0.00019717 RMS(Int)= 0.00012443
Iteration 3 RMS(Cart)= 0.00000003 RMS(Int)= 0.00012443
Variable Old X -DE/DX Delta X Delta X Delta X New X
(Linear) (Quad) (Total)
R1 2.63420 0.00003 0.00000 0.00038 0.00026 2.63446
R2 2.63420 0.00004 0.00000 0.00037 0.00026 2.63446
R41 2.01442 0.00057 0.00000 -0.00167 -0.00165 2.01277
A1 1.93497 0.00006 0.00000 -0.00261 -0.00267 1.93230
A2 2.13721 -0.00006 0.00000 0.00116 0.00111 2.13833
A37 2.20391 -0.00012 0.00000 0.01113 0.01057 2.21448
D1 3.00181 -0.00035 0.00000 0.00163 0.00163 3.00344
D2 -0.15405 -0.00021 0.00000 0.00583 0.00583 -0.14822
D49 0.00020 0.00000 0.00000 -0.00022 -0.00022 -0.00002
Item Value Threshold Converged?
Maximum Force 0.002387 0.000450 NO
RMS Force 0.000539 0.000300 NO
Maximum Displacement 0.044296 0.001800 NO
RMS Displacement 0.011477 0.001200 NO
Predicted change in Energy= 3.932148D-04
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Leave Link 103 at Fri Sep 13 17:06:50 2013, MaxMem= 419430400 cpu: 0.0
Output text
<comment class="example.output" id="l103">
<module cmlx:templateRef="l103">
<list cmlx:templateRef="berny">
<scalar dataType="xsd:string" dictRef="g:optimization">Berny optimization.</scalar>
</list>
<module cmlx:templateRef="l103.init">
<list cmlx:templateRef="length">
<array dataType="xsd:string" dictRef="g:symbol" size="4">R1 R2 R3 R4</array>
<array dataType="xsd:integer" dictRef="g:atom1" size="4">1 1 1 1</array>
<array dataType="xsd:integer" dictRef="g:atom2" size="4">2 3 4 5</array>
<array dataType="xsd:double" dictRef="cc:distance" size="4">1.113 1.113 1.113 1.113</array>
<array dataType="xsd:string" delimiter="|" dictRef="g:deriv" size="4">estimate D2E/DX2|estimate D2E/DX2|estimate D2E/DX2|estimate D2E/DX2</array>
</list>
<list cmlx:templateRef="angle">
<array dataType="xsd:string" dictRef="g:symbol" size="6">A1 A2 A3 A4 A5 A6</array>
<array dataType="xsd:integer" dictRef="g:atom1" size="6">2 2 2 3 3 4</array>
<array dataType="xsd:integer" dictRef="g:atom2" size="6">1 1 1 1 1 1</array>
<array dataType="xsd:integer" dictRef="g:atom3" size="6">3 4 5 4 5 5</array>
<array dataType="xsd:double" dictRef="cc:angle" size="6">109.4712 109.4712 109.4712 109.4712 109.4712 109.4712</array>
<array dataType="xsd:string" delimiter="|" dictRef="g:deriv" size="6">estimate D2E/DX2|estimate D2E/DX2|estimate D2E/DX2|estimate D2E/DX2|estimate D2E/DX2|estimate D2E/DX2</array>
</list>
</module>
<module cmlx:templateRef="l103.trust">
<scalar dataType="xsd:double" dictRef="g:trustrad">3.00e-01</scalar>
<scalar dataType="xsd:double" dictRef="g:fncerr">1.00e-07</scalar>
<scalar dataType="xsd:double" dictRef="g:grderr">1.00e-06</scalar>
<scalar dataType="xsd:integer" dictRef="g:nstep">20</scalar>
<scalar dataType="xsd:integer" dictRef="g:allowedstep">100</scalar>
</module>
<module cmlx:templateRef="l103.catchall">
<list cmlx:templateRef="l103.discard">
<scalar dataType="xsd:string" dictRef="x:discard" />
</list>
</module>
</module>
</comment>
Output text
<comment class="example.output" id="l103.1">
<module cmlx:templateRef="l103">
<list cmlx:templateRef="berny">
<scalar dataType="xsd:string" dictRef="g:optimization">Berny optimization.</scalar>
</list>
<module cmlx:templateRef="l103.localminsaddle">
<scalar cmlx:templateRef="r" dataType="xsd:string" dictRef="cc:minmaxts">saddle point</scalar>
<array cmlx:templateRef="junk" dataType="xsd:string" dictRef="x:junk1" size="9">Step number 1 out of a maximum of 137</array>
<array cmlx:templateRef="junk" dataType="xsd:string" dictRef="x:junk1" size="7">All quantities printed in internal units (Hartrees-Bohrs-Radians)</array>
<array cmlx:templateRef="junk" dataType="xsd:string" dictRef="x:junk1" size="4">Swaping is turned off.</array>
<array cmlx:templateRef="eigenvaluelist" dataType="xsd:double" dictRef="" size="27">-0.03403 0.00144 0.00463 0.00759 0.00906 0.01177 0.01317 0.01431 0.01623 0.01839 0.40148 0.40211 0.40329 0.46257 0.48142 0.51910 1.01166 1.02582 1000.00000 1000.00000 1000.00000 1000.00000 1000.00000 1000.00000 1000.00000 1000.00000 1000.00000</array>
</module>
<module cmlx:templateRef="rfo">
<list cmlx:templateRef="rfo">
<scalar dataType="xsd:double" dictRef="g:lambda0">9.155600927e-04</scalar>
<scalar dataType="xsd:double" dictRef="g:lambda">-1.51225227e-04</scalar>
</list>
<list cmlx:templateRef="nolinear">
<scalar dataType="xsd:string" dictRef="g:linear">Linear search</scalar>
</list>
<list cmlx:templateRef="iteration">
<array dataType="xsd:integer" dictRef="cc:serial" size="3">1 2 3</array>
<array dataType="xsd:double" dictRef="g:rmscart" size="3">0.01149217 0.00019717 0.00000003</array>
<array dataType="xsd:double" dictRef="g:rmsint" size="3">0.00020982 0.00012443 0.00012443</array>
</list>
</module>
<module cmlx:templateRef="l103.deltas">
<list cmlx:templateRef="delta">
<array dataType="xsd:string" dictRef="cc:variable" size="9">R1 R2 R41 A1 A2 A37 D1 D2 D49</array>
<array dataType="xsd:double" dictRef="g:lastval" size="9">2.63420 2.63420 2.01442 1.93497 2.13721 2.20391 3.00181 -0.15405 0.00020</array>
<array dataType="xsd:double" dictRef="cc:deriv" size="9">0.00003 0.00004 0.00057 0.00006 -0.00006 -0.00012 -0.00035 -0.00021 0.00000</array>
<array dataType="xsd:double" dictRef="cc:delta.linear" size="9">0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000</array>
<array dataType="xsd:double" dictRef="cc:delta.quad" size="9">0.00038 0.00037 -0.00167 -0.00261 0.00116 0.01113 0.00163 0.00583 -0.00022</array>
<array dataType="xsd:double" dictRef="cc:delta.total" size="9">0.00026 0.00026 -0.00165 -0.00267 0.00111 0.01057 0.00163 0.00583 -0.00022</array>
<array dataType="xsd:double" dictRef="cc:newval" size="9">2.63446 2.63446 2.01277 1.93230 2.13833 2.21448 3.00344 -0.14822 -0.00002</array>
</list>
</module>
<module cmlx:templateRef="l103.itemconverge">
<list cmlx:templateRef="row">
<array dataType="xsd:string" delimiter="|" dictRef="g:item" size="4">|Maximum Force|RMS Force|Maximum Displacement|RMS Displacement|</array>
<array dataType="xsd:double" dictRef="g:value" size="4">0.002387 0.000539 0.044296 0.011477</array>
<array dataType="xsd:double" dictRef="g:threshold" size="4">0.000450 0.000300 0.001800 0.001200</array>
<array dataType="xsd:string" dictRef="g:converged" size="4">NO NO NO NO</array>
</list>
</module>
<module cmlx:templateRef="preddelta">
<list cmlx:templateRef="predicted">
<scalar dataType="xsd:double" dictRef="g:predchange">3.932148e-04</scalar>
</list>
</module>
<module cmlx:templateRef="l103.catchall">
<list cmlx:templateRef="l103.discard">
<scalar dataType="xsd:string" dictRef="x:discard" />
</list>
</module>
</module>
</comment>
Template definition
<record id="tmp" repeat="*">(\s+\(Enter.*|\s*GradGradGrad.*|\s+)</record>
<record id="berny">{X,g:optimization}</record>
<templateList> <xi:include href="l103/l103.catchall.xml" /> <xi:include href="l103/l103.trust.xml" /> <xi:include href="l103/l103.init.xml" /> <xi:include href="l103/l103.rfo.xml" /> <xi:include href="l103/l103.localmin.xml" /> <xi:include href="l103/l103.deltas.xml" /> <xi:include href="l103/l103.itemconverge.xml" /> <xi:include href="l103/l103.optimizedparam.xml" /> <xi:include href="l103/l103.preddelta.xml" />
</templateList>
<transform process="delete" xpath=".//cml:scalar[empty(text())]" />
<transform process="delete" xpath="./text()[starts-with(normalize-space(.),'GradGrad')]" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />