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Fixed GFN1-xTB selection issue in qcxms_neutral_run tool #513

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merged 2 commits into from
Apr 16, 2024
Merged

Fixed GFN1-xTB selection issue in qcxms_neutral_run tool #513

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c3120c7
fixed GFN1-xTB selection issue
zargham-ahmad Mar 28, 2024
d576327
Merge branch 'master' into issue511
hechth Apr 16, 2024
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45 changes: 36 additions & 9 deletions tools/qcxms/qcxms_neutral_run.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy1" profile="22.09">
<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy2" profile="22.09">
<description>required as first step to prepare for the production runs</description>

<macros>
Expand All @@ -24,13 +24,13 @@

<configfiles>
<configfile filename="qcxms.in"><![CDATA[
${QC_Level}
#if $keywords.ntraj
ntraj ${keywords.ntraj}
#end if
tmax ${keywords.tmax}
tinit ${keywords.tinit}
ieeatm ${keywords.ieeatm}]]>
${QC_Level}
#if $keywords.ntraj
ntraj ${keywords.ntraj}
#end if
tmax ${keywords.tmax}
tinit ${keywords.tinit}
ieeatm ${keywords.ieeatm}]]>
</configfile>
<configfile filename="rename.py">
import os
Expand Down Expand Up @@ -59,7 +59,7 @@ rename_files_with_folder_name(path)
<param type="data" name="mol" label="Molecule 3D structure [.xzy]" format="xyz" />
<param name="QC_Level" type="select" display="radio" label="QC Method">
<option value="xtb2" selected="true">GFN2-xTB</option>
<option value="xtb1">GFN1-xTB</option>
<option value="xtb">GFN1-xTB</option>
</param>
<section name="keywords" title="Advanced method parameters" expanded="false"
help="List of advanced keywords to specify the method - for more information see [1].">
Expand Down Expand Up @@ -121,6 +121,33 @@ rename_files_with_folder_name(path)
</assert_contents>
</output>
</test>
<!-- test 2-->
<test expect_num_outputs="6">
<param name="mol" value="mol.xyz" ftype="xyz"/>
<param name="QC_Level" value="xtb"/>
<section name="keywords">
<param name="ntraj" value="2"/>
</section>
<param name="store_extended_output" value="true"/>
<output_collection name="coords1" type="list" count="2"/>
<output_collection name="coords2" type="list" count="2"/>
<output_collection name="coords3" type="list" count="2"/>
<output name="qcxms_out">
<assert_contents>
<has_size value="174613" delta="300"/>
</assert_contents>
</output>
<output name="trajectory">
<assert_contents>
<has_size value="22150" delta="300"/>
</assert_contents>
</output>
<output name="log">
<assert_contents>
<has_text text="initializing GFN1-xTB"/>
</assert_contents>
</output>
</test>
</tests>

<help><![CDATA[
Expand Down