averages ​
Implementation level ​
Type | Status |
---|---|
CML extraction template | |
HTML5 representation |
Template attributes ​
Attribute | Value |
---|---|
source | Amber log |
id | averages |
name | Averages |
pattern | \s*A\sV\sE\sR\sA\sG\sE\sS\s*O\sV\sE\sR\s*.*S\sT\sE\sP\sS |
endPattern | \s*-{20,}.* |
endOffset | 0 |
xml:base | job/averages.xml |
Input ​
A V E R A G E S O V E R 500 S T E P S
NSTEP = 50000000 TIME(PS) = 101030.000 TEMP(K) = 300.00 PRESS = 0.0
Etot = -19416.4470 EKtot = 4561.4534 EPtot = -23977.9004
BOND = 19.5282 ANGLE = 98.7153 DIHED = 27.7291
1-4 NB = 9.2337 1-4 EEL = -54.1394 VDWAALS = 3532.6281
EELEC = -27611.5955 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 77394.8592
Density = 0.9869
------------------------------------------------------------------------------
Output text ​
xml
<comment class="example.output" id="averages">
<module cmlx:templateRef="averages">
<scalar dataType="xsd:integer" dictRef="am:nstep">50000000</scalar>
<scalar dataType="xsd:double" dictRef="am:time" units="nonsi:picoseconds">101030.000</scalar>
<scalar dataType="xsd:double" dictRef="am:temp" units="nonsi:k">300.00</scalar>
<scalar dataType="xsd:double" dictRef="am:press" units="nonsi2:bar">0.0</scalar>
<scalar dataType="xsd:double" dictRef="am:etot" units="nonsi2:kcal.mol-1">-19416.4470</scalar>
<scalar dataType="xsd:double" dictRef="am:ektot" units="nonsi2:kcal.mol-1">4561.4534</scalar>
<scalar dataType="xsd:double" dictRef="am:eptot" units="nonsi2:kcal.mol-1">-23977.9004</scalar>
<scalar dataType="xsd:double" dictRef="am:bond" units="nonsi2:kcal.mol-1">19.5282</scalar>
<scalar dataType="xsd:double" dictRef="am:angle" units="nonsi2:kcal.mol-1">98.7153</scalar>
<scalar dataType="xsd:double" dictRef="am:dihed" units="nonsi2:kcal.mol-1">27.7291</scalar>
<scalar dataType="xsd:double" dictRef="am:nb14" units="nonsi2:kcal.mol-1">9.2337</scalar>
<scalar dataType="xsd:double" dictRef="am:eel14" units="nonsi2:kcal.mol-1">-54.1394</scalar>
<scalar dataType="xsd:double" dictRef="am:vdwaals" units="nonsi2:kcal.mol-1">3532.6281</scalar>
<scalar dataType="xsd:double" dictRef="am:eelec" units="nonsi2:kcal.mol-1">-27611.5955</scalar>
<scalar dataType="xsd:double" dictRef="am:ehbond" units="nonsi2:kcal.mol-1">0.0000</scalar>
<scalar dataType="xsd:double" dictRef="am:restraint" units="nonsi2:kcal.mol-1">0.0000</scalar>
<scalar dataType="xsd:double" dictRef="am:ekcmt" units="nonsi2:kcal.mol-1">0.0000</scalar>
<scalar dataType="xsd:double" dictRef="am:virial" units="nonsi2:kcal.mol-1">0.0000</scalar>
<scalar dataType="xsd:double" dictRef="am:volume">77394.8592</scalar>
<scalar dataType="xsd:double" dictRef="am:density">0.9869</scalar>
</module>
</comment>
Template definition ​
xml
<record repeat="3" />
<templateList> <template id="section" pattern="(.+=){4}.+" endPattern=".*" endPattern2="~" endOffset="0" repeat="*"> <record>{X,am:name}={F,am:value}{X,am:name}={F,am:value}{X,am:name}={F,am:value}{X,am:name}={F,am:value}</record> <transform process="setValue" xpath=".//cml:scalar[@dictRef='am:name']" value="$string(lower-case(./text()))" /> <transform process="setValue" xpath=".//cml:scalar[@dictRef='am:name']" value="$string(replace(./text(), '[-_ ]', '.'))" /> <transform process="createNameValue" xpath="./cml:list/cml:list" name="./cml:scalar[@dictRef='am:name'][position() = 1]" value="./cml:scalar[@dictRef='am:value'][position()= 1]" /> <transform process="createNameValue" xpath="./cml:list/cml:list" name="./cml:scalar[@dictRef='am:name'][position() = 1]" value="./cml:scalar[@dictRef='am:value'][position()= 1]" /> <transform process="createNameValue" xpath="./cml:list/cml:list" name="./cml:scalar[@dictRef='am:name'][position() = 1]" value="./cml:scalar[@dictRef='am:value'][position()= 1]" /> <transform process="createNameValue" xpath="./cml:list/cml:list" name="./cml:scalar[@dictRef='am:name'][position() = 1]" value="./cml:scalar[@dictRef='am:value'][position()= 1]" /> <transform process="pullup" xpath=".//cml:scalar" repeat="3" />
</template> <template id="section" pattern="(.+=){3}.+" endPattern=".*" endPattern2="~" endOffset="0" repeat="*"> <record>{X,am:name}={F,am:value}{X,am:name}={F,am:value}{X,am:name}={F,am:value}</record> <transform process="setValue" xpath=".//cml:scalar[@dictRef='am:name']" value="$string(lower-case(./text()))" /> <transform process="setValue" xpath=".//cml:scalar[@dictRef='am:name']" value="$string(replace(./text(), '[-_ ]', '.'))" /> <transform process="createNameValue" xpath="./cml:list/cml:list" name="./cml:scalar[@dictRef='am:name'][position() = 1]" value="./cml:scalar[@dictRef='am:value'][position()= 1]" /> <transform process="createNameValue" xpath="./cml:list/cml:list" name="./cml:scalar[@dictRef='am:name'][position() = 1]" value="./cml:scalar[@dictRef='am:value'][position()= 1]" /> <transform process="createNameValue" xpath="./cml:list/cml:list" name="./cml:scalar[@dictRef='am:name'][position() = 1]" value="./cml:scalar[@dictRef='am:value'][position()= 1]" /> <transform process="pullup" xpath=".//cml:scalar" repeat="3" />
</template> <template id="section" pattern="\s*Density\s*=.+" endPattern=".*" endPattern2="~" endOffset="0"> <record>\s*Density\s*={F,am:density}</record> <transform process="pullup" xpath=".//cml:scalar" repeat="2" />
</template>
</templateList>
<transform process="delete" xpath=".//cml:module" />
<transform process="delete" xpath=".//cml:list" />
<transform process="addAttribute" xpath="./cml:scalar[@dictRef='am:time(ps)']" name="dictRef" value="am:time" />
<transform process="addAttribute" xpath="./cml:scalar[@dictRef='am:temp(k)']" name="dictRef" value="am:temp" />
<transform process="addAttribute" xpath="./cml:scalar[@dictRef='am:1.4.nb']" name="dictRef" value="am:nb14" />
<transform process="addAttribute" xpath="./cml:scalar[@dictRef='am:1.4.eel']" name="dictRef" value="am:eel14" />
<transform process="addAttribute" xpath="./cml:scalar[@dictRef='am:1.4.vdw']" name="dictRef" value="am:vdw14" />
<transform process="addUnits" xpath="./cml:scalar[@dictRef='am:time']" value="nonsi:picoseconds" />
<transform process="addUnits" xpath="./cml:scalar[@dictRef='am:temp']" value="si:k" />
<transform process="addUnits" xpath="./cml:scalar[@dictRef='am:temp']" value="nonsi:k" />
<transform process="addUnits" xpath="./cml:scalar[matches(@dictRef, 'am:e.*') ]" value="nonsi2:kcal.mol-1" />
<transform process="addUnits" xpath="./cml:scalar[matches(@dictRef, 'am:(bond|angle|dihed|nb14|eel14|vdwaals|vdw14|restraint|virial)') ]" value="nonsi2:kcal.mol-1" />
<transform process="addUnits" xpath="./cml:scalar[matches(@dictRef, 'am:press') ]" value="nonsi2:bar" />
<transform process="addAttribute" xpath="./cml:scalar" name="dataType" value="xsd:double" />
<transform process="addAttribute" xpath="./cml:scalar[@dictRef='am:nstep']" name="dataType" value="xsd:integer" />