setup¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
| Attribute | Value |
|---|---|
| source | LAMMPS log |
| id | setup |
| pattern | \s*units\s+\S+.* |
| endPattern | \s*Neighbor\slist\sinfo.* |
| endPattern2 | \s*Reading\srestart\sfile.* |
| endOffset | 0 |
| xml:base | job/setup.xml |
Input
units metal
boundary p p p
atom_style atomic
pair_style eam
read_data .lammps.dat
orthogonal box = (-0.0167608 -0.0167608 -0.0167608) to (18.1231 18.1231 18.1231)
3 by 3 by 4 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.00427604 secs
pair_coeff * * Cu_u3.eam
Reading potential file Cu_u3.eam with DATE: 2007-06-11
dump Dump all custom 1000 tmpdir/lammps.dmp.* id type x y z ix iy iz vx vy vz
thermo_style custom step time cpu pe ke etotal enthalpy temp press vol density cella cellb cellc cellalpha cellbeta cellgamma
thermo 100
fix ensemble1 all nve
timestep 5.0e-4
run 200000
Neighbor list info ...
Output text
<comment class="example.output" id="setup">
<module cmlx:templateRef="setup">
<parameter>
<scalar dataType="xsd:string" dictRef="x:label">units</scalar>
<scalar dataType="xsd:string" dictRef="x:value">metal</scalar>
</parameter>
<parameter>
<scalar dataType="xsd:string" dictRef="x:label">boundary</scalar>
<scalar dataType="xsd:string" dictRef="x:value">p p p</scalar>
</parameter>
<parameter>
<scalar dataType="xsd:string" dictRef="x:label">atom_style</scalar>
<scalar dataType="xsd:string" dictRef="x:value">atomic</scalar>
</parameter>
<parameter>
<scalar dataType="xsd:string" dictRef="x:label">pair_style</scalar>
<scalar dataType="xsd:string" dictRef="x:value">eam</scalar>
</parameter>
<parameter>
<list cmlx:templateRef="datafile">
<scalar dataType="xsd:string" dictRef="l:line">read_data .lammps.dat</scalar>
<scalar dataType="xsd:string" dictRef="l:line">orthogonal box = (-0.0167608 -0.0167608 -0.0167608) to (18.1231 18.1231 18.1231)</scalar>
<scalar dataType="xsd:string" dictRef="l:line">3 by 3 by 4 MPI processor grid</scalar>
<scalar dataType="xsd:string" dictRef="l:line">reading atoms ...</scalar>
<scalar dataType="xsd:string" dictRef="l:line">500 atoms</scalar>
<scalar dataType="xsd:string" dictRef="l:line">reading velocities ...</scalar>
<scalar dataType="xsd:string" dictRef="l:line">500 velocities</scalar>
<scalar dataType="xsd:string" dictRef="l:line">read_data CPU = 0.00427604 secs</scalar>
</list>
</parameter>
<parameter>
<scalar dataType="xsd:string" dictRef="x:label">pair_coeff</scalar>
<scalar dataType="xsd:string" dictRef="x:value">* * Cu_u3.eam</scalar>
</parameter>
<parameter>
<scalar dataType="xsd:string" dictRef="x:label">dump</scalar>
<scalar dataType="xsd:string" dictRef="x:value">Dump all custom 1000 tmpdir/lammps.dmp.* id type x y z ix iy iz vx vy vz</scalar>
</parameter>
<parameter>
<scalar dataType="xsd:string" dictRef="x:label">thermo_style</scalar>
<scalar dataType="xsd:string" dictRef="x:value">custom step time cpu pe ke etotal enthalpy temp press vol density cella cellb cellc cellalpha cellbeta cellgamma</scalar>
</parameter>
<parameter>
<scalar dataType="xsd:string" dictRef="x:label">thermo</scalar>
<scalar dataType="xsd:string" dictRef="x:value">100</scalar>
</parameter>
<parameter>
<scalar dataType="xsd:string" dictRef="x:label">fix</scalar>
<scalar dataType="xsd:string" dictRef="x:value">ensemble1 all nve</scalar>
</parameter>
<parameter>
<scalar dataType="xsd:string" dictRef="x:label">timestep</scalar>
<scalar dataType="xsd:string" dictRef="x:value">5.0e-4</scalar>
</parameter>
<parameter>
<scalar dataType="xsd:string" dictRef="x:label">run</scalar>
<scalar dataType="xsd:string" dictRef="x:value">200000</scalar>
</parameter>
</module>
</comment>
Template definition
<templateList> <template id="datafile" pattern="read_data\s+\S.*$Reading\sdata.*" pattern2="read_data\s+\S.*$\s\s.*" endPattern="\s+\S+.*$\S+.*" endPattern2="\s+\S+.*$\s*" endOffset="1"> <record id="datafile" repeat="*">{X,l:line}</record> <transform process="addChild" xpath="." elementName="cml:parameter" /> <transform process="move" xpath=".//cml:list" to=".//cml:parameter" />
</template> <template id="parameter" pattern="((?!#|WARNING|Reading\spotential\sfile).*)" endPattern=".*" endPattern2="~" repeat="*"> <record id="parameter">{A,x:label}{X,x:value}</record> <transform process="addChild" xpath="." elementName="cml:parameter" /> <transform process="move" xpath=".//cml:scalar" to=".//cml:parameter" />
</template>
</templateList>
<transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:label" value="units" />
<transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:value" value="lj" />
<transform process="addAttribute" xpath="./cml:scalar" name="dataType" value="xsd:string" />
<transform process="addChild" xpath="." elementName="cml:parameter" />
<transform process="move" xpath="./cml:scalar" to="./cml:parameter[count(*)=0]" />
<transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:label" value="atom_style" />
<transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:value" value="atomic" />
<transform process="addAttribute" xpath="./cml:scalar" name="dataType" value="xsd:string" />
<transform process="addChild" xpath="." elementName="cml:parameter" />
<transform process="move" xpath="./cml:scalar" to="./cml:parameter[count(*)=0]" />
<transform process="pullup" xpath="./cml:module/cml:parameter" />
<transform process="delete" xpath=".//cml:module" />
<transform process="delete" xpath="//cml:parameter[child::cml:scalar[@dictRef='x:label' and text()='units']][position() >1]" />
<transform process="delete" xpath="//cml:parameter[child::cml:scalar[@dictRef='x:label' and text()='atom_style']][position() >1]" />