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
1<comment class="example.output" id="setup">
2 <module cmlx:templateRef="setup">
3 <parameter>
4 <scalar dataType="xsd:string" dictRef="x:label">units</scalar>
5 <scalar dataType="xsd:string" dictRef="x:value">metal</scalar>
6 </parameter>
7 <parameter>
8 <scalar dataType="xsd:string" dictRef="x:label">boundary</scalar>
9 <scalar dataType="xsd:string" dictRef="x:value">p p p</scalar>
10 </parameter>
11 <parameter>
12 <scalar dataType="xsd:string" dictRef="x:label">atom_style</scalar>
13 <scalar dataType="xsd:string" dictRef="x:value">atomic</scalar>
14 </parameter>
15 <parameter>
16 <scalar dataType="xsd:string" dictRef="x:label">pair_style</scalar>
17 <scalar dataType="xsd:string" dictRef="x:value">eam</scalar>
18 </parameter>
19 <parameter>
20 <list cmlx:templateRef="datafile">
21 <scalar dataType="xsd:string" dictRef="l:line">read_data .lammps.dat</scalar>
22 <scalar dataType="xsd:string" dictRef="l:line">orthogonal box = (-0.0167608 -0.0167608 -0.0167608) to (18.1231 18.1231 18.1231)</scalar>
23 <scalar dataType="xsd:string" dictRef="l:line">3 by 3 by 4 MPI processor grid</scalar>
24 <scalar dataType="xsd:string" dictRef="l:line">reading atoms ...</scalar>
25 <scalar dataType="xsd:string" dictRef="l:line">500 atoms</scalar>
26 <scalar dataType="xsd:string" dictRef="l:line">reading velocities ...</scalar>
27 <scalar dataType="xsd:string" dictRef="l:line">500 velocities</scalar>
28 <scalar dataType="xsd:string" dictRef="l:line">read_data CPU = 0.00427604 secs</scalar>
29 </list>
30 </parameter>
31 <parameter>
32 <scalar dataType="xsd:string" dictRef="x:label">pair_coeff</scalar>
33 <scalar dataType="xsd:string" dictRef="x:value">* * Cu_u3.eam</scalar>
34 </parameter>
35 <parameter>
36 <scalar dataType="xsd:string" dictRef="x:label">dump</scalar>
37 <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>
38 </parameter>
39 <parameter>
40 <scalar dataType="xsd:string" dictRef="x:label">thermo_style</scalar>
41 <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>
42 </parameter>
43 <parameter>
44 <scalar dataType="xsd:string" dictRef="x:label">thermo</scalar>
45 <scalar dataType="xsd:string" dictRef="x:value">100</scalar>
46 </parameter>
47 <parameter>
48 <scalar dataType="xsd:string" dictRef="x:label">fix</scalar>
49 <scalar dataType="xsd:string" dictRef="x:value">ensemble1 all nve</scalar>
50 </parameter>
51 <parameter>
52 <scalar dataType="xsd:string" dictRef="x:label">timestep</scalar>
53 <scalar dataType="xsd:string" dictRef="x:value">5.0e-4</scalar>
54 </parameter>
55 <parameter>
56 <scalar dataType="xsd:string" dictRef="x:label">run</scalar>
57 <scalar dataType="xsd:string" dictRef="x:value">200000</scalar>
58 </parameter>
59 </module>
60 </comment>
Template definition
1<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" />
2 </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" />
3 </template>
4 </templateList>
5<transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:label" value="units" />
6<transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:value" value="lj" />
7<transform process="addAttribute" xpath="./cml:scalar" name="dataType" value="xsd:string" />
8<transform process="addChild" xpath="." elementName="cml:parameter" />
9<transform process="move" xpath="./cml:scalar" to="./cml:parameter[count(*)=0]" />
10<transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:label" value="atom_style" />
11<transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:value" value="atomic" />
12<transform process="addAttribute" xpath="./cml:scalar" name="dataType" value="xsd:string" />
13<transform process="addChild" xpath="." elementName="cml:parameter" />
14<transform process="move" xpath="./cml:scalar" to="./cml:parameter[count(*)=0]" />
15<transform process="pullup" xpath="./cml:module/cml:parameter" />
16<transform process="delete" xpath=".//cml:module" />
17<transform process="delete" xpath="//cml:parameter[child::cml:scalar[@dictRef='x:label' and text()='units']][position() >1]" />
18<transform process="delete" xpath="//cml:parameter[child::cml:scalar[@dictRef='x:label' and text()='atom_style']][position() >1]" />