control ​
Implementation level ​
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation |  |
Template attributes ​
| Attribute | Value |
|---|---|
| source | Amber log |
| id | control |
| name | Control data |
| pattern | \s*-{20,}.*$\s*2\.\s+CONTROL\s+DATA\s+FOR\s+THE\s+RUN.* |
| endPattern | \s*$\s*-{20,}. |
| endOffset | 0 |
| xml:base | job/control.xml |
Input ​
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 100000, ntrx = 1, ntwr =50000000
iwrap = 0, ntwx = 100000, ntwv = 0, ntwe = 0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 50000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 847044
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 1.00000
Monte-Carlo Barostat:
mcbarint = 100
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 100000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 46.578 Box Y = 46.578 Box Z = 46.578
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 48 NFFT2 = 48 NFFT3 = 48
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
| MONTE CARLO BAROSTAT IMPORTANT NOTE:
| The Monte-Carlo barostat does not require the virial to adjust the system volume.
| Since it is an expensive calculation, it is skipped for efficiency. A side-effect
| is that the reported pressure is always 0 because it is not calculated.
--------------------------------------------------------------------------------
Output text ​
xml
<comment class="example.output" id="">
<module cmlx:templateRef="control">
<list cmlx:templateRef="section">
<scalar dataType="xsd:string" dictRef="am:section.name">General flags</scalar>
<scalar dataType="xsd:string" dictRef="am:imin">0</scalar>
<scalar dataType="xsd:string" dictRef="am:nmropt">0</scalar>
</list>
<list cmlx:templateRef="section">
<scalar dataType="xsd:string" dictRef="am:section.name">Nature and format of input</scalar>
<scalar dataType="xsd:string" dictRef="am:ntx">5</scalar>
<scalar dataType="xsd:string" dictRef="am:irest">1</scalar>
<scalar dataType="xsd:string" dictRef="am:ntrx">1</scalar>
</list>
<list cmlx:templateRef="section">
<scalar dataType="xsd:string" dictRef="am:section.name">Nature and format of output</scalar>
<scalar dataType="xsd:string" dictRef="am:ntxo">2</scalar>
<scalar dataType="xsd:string" dictRef="am:ntpr">100000</scalar>
<scalar dataType="xsd:string" dictRef="am:ntrx">1</scalar>
<scalar dataType="xsd:string" dictRef="am:ntwr">50000000</scalar>
<scalar dataType="xsd:string" dictRef="am:iwrap">0</scalar>
<scalar dataType="xsd:string" dictRef="am:ntwx">100000</scalar>
<scalar dataType="xsd:string" dictRef="am:ntwv">0</scalar>
<scalar dataType="xsd:string" dictRef="am:ntwe">0</scalar>
<scalar dataType="xsd:string" dictRef="am:ioutfm">1</scalar>
<scalar dataType="xsd:string" dictRef="am:ntwprt">0</scalar>
<scalar dataType="xsd:string" dictRef="am:idecomp">0</scalar>
<scalar dataType="xsd:string" dictRef="am:rbornstat">0</scalar>
</list>
<list cmlx:templateRef="section">
<scalar dataType="xsd:string" dictRef="am:section.name">Potential function</scalar>
<scalar dataType="xsd:string" dictRef="am:ntf">2</scalar>
<scalar dataType="xsd:string" dictRef="am:ntb">2</scalar>
<scalar dataType="xsd:string" dictRef="am:igb">0</scalar>
<scalar dataType="xsd:string" dictRef="am:nsnb">25</scalar>
<scalar dataType="xsd:string" dictRef="am:ipol">0</scalar>
<scalar dataType="xsd:string" dictRef="am:gbsa">0</scalar>
<scalar dataType="xsd:string" dictRef="am:iesp">0</scalar>
<scalar dataType="xsd:string" dictRef="am:dielc">1.00000</scalar>
<scalar dataType="xsd:string" dictRef="am:cut">10.00000</scalar>
<scalar dataType="xsd:string" dictRef="am:intdiel">1.00000</scalar>
</list>
<list cmlx:templateRef="section">
<scalar dataType="xsd:string" dictRef="am:section.name">Frozen or restrained atoms</scalar>
<scalar dataType="xsd:string" dictRef="am:ibelly">0</scalar>
<scalar dataType="xsd:string" dictRef="am:ntr">0</scalar>
</list>
<list cmlx:templateRef="section">
<scalar dataType="xsd:string" dictRef="am:section.name">Molecular dynamics</scalar>
<scalar dataType="xsd:string" dictRef="am:nstlim">50000000</scalar>
<scalar dataType="xsd:string" dictRef="am:nscm">1000</scalar>
<scalar dataType="xsd:string" dictRef="am:nrespa">1</scalar>
<scalar dataType="xsd:string" dictRef="am:t">0.00000</scalar>
<scalar dataType="xsd:string" dictRef="am:dt">0.00200</scalar>
<scalar dataType="xsd:string" dictRef="am:vlimit">-1.00000</scalar>
</list>
<list cmlx:templateRef="section">
<scalar dataType="xsd:string" dictRef="am:section.name">Langevin dynamics temperature regulation</scalar>
<scalar dataType="xsd:string" dictRef="am:temp0">300.00000</scalar>
<scalar dataType="xsd:string" dictRef="am:tempi">0.00000</scalar>
<scalar dataType="xsd:string" dictRef="am:gamma.ln">2.00000</scalar>
<scalar dataType="xsd:string" dictRef="am:ig">847044</scalar>
</list>
<list cmlx:templateRef="section">
<scalar dataType="xsd:string" dictRef="am:section.name">Pressure regulation</scalar>
<scalar dataType="xsd:string" dictRef="am:pres0">1.00000</scalar>
<scalar dataType="xsd:string" dictRef="am:comp">44.60000</scalar>
<scalar dataType="xsd:string" dictRef="am:taup">1.00000</scalar>
<scalar dataType="xsd:string" dictRef="am:ntp">1</scalar>
<scalar dataType="xsd:string" dictRef="am:mcbarint">100</scalar>
</list>
<list cmlx:templateRef="section">
<scalar dataType="xsd:string" dictRef="am:section.name">SHAKE</scalar>
<scalar dataType="xsd:string" dictRef="am:ntc">2</scalar>
<scalar dataType="xsd:string" dictRef="am:jfastw">0</scalar>
<scalar dataType="xsd:string" dictRef="am:tol">0.00001</scalar>
</list>
</module>
</comment>Template definition ​
xml
<templateList> <template id="section" pattern="\s*[a-zA-Z0-9](?!wald\sparameters).*:" endPattern="\s*" endPattern2="~" endOffset="0" repeat="*"> <record id="section">{X,am:section.name}:</record> <templateList> <template id="section" pattern=".+,.+,.+,.+" endPattern=".*" endPattern2="~" endOffset="0" repeat="*"> <record>{X,am:name}={A,am:value},{X,am:name}={A,am:value},{X,am:name}={A,am:value},{X,am:name}={A,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=".+,.+,.+" endPattern=".*" endPattern2="~" endOffset="0" repeat="*"> <record>{X,am:name}={A,am:value},{X,am:name}={A,am:value},{X,am:name}={A,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=".+,.+" endPattern=".*" endPattern2="~" endOffset="0" repeat="*"> <record>{X,am:name}={A,am:value},{X,am:name}={A,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="pullup" xpath=".//cml:scalar" repeat="3" />
</template> <template id="section" pattern=".+" endPattern=".*" endPattern2="~" endOffset="0" repeat="*"> <record>{X,am:name}={A,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="pullup" xpath=".//cml:scalar" repeat="3" />
</template>
</templateList> <transform process="moveRelative" xpath="./cml:scalar" to="parent::cml:module/cml:list" /> <transform process="delete" xpath="./cml:module" /> <transform process="pullup" xpath="./cml:list" />
</template>
</templateList>
<transform process="delete" xpath=".//cml:module" />