Error in reading box dimension from topology.xml file

[Sanjeet Singh]

Hello Christoph,

I am trying to use a manually made topology.xml file in VOTCA. But, whenever I run it with the following command:

csg_dump --top topology.xml

It always shows Boundary Condition: Open, inspite  of box dimension specified in the topology.xml file.

Here are the first few lines of my topology.xml file, where I have specified the box dimension.

<topology name="">
  <molecules>
  <clear/>
    <box xx="100.0" yy="100.0" zz="100.0" />
    <!-- define molecule, number of beads, number of mols -->
    <molecule name="PEOAA" nmols="1" nbeads="75">
      <!-- composition of molecule, bead definition -->
      <bead name="C1" type="C" mass="12.0112" q="0.054" />
      <bead name="C2" type="C" mass="12.0112" q="-0.159" />

Can you please help me with the reason as why the box dimension is not read by the csg_dump command?

I am also attaching my topology.xml file for your reference. 

Thank you.

Sanjeet

[Christoph Junghans]

On Sat, Nov 5, 2022 at 7:57 PM Sanjeet Singh <sanje...@gmail.com> wrote:
>
> Hello Christoph,
>
> I am trying to use a manually made topology.xml file in VOTCA. But, whenever I run it with the following command:
>
> csg_dump --top topology.xml
>
> It always shows Boundary Condition: Open, inspite of box dimension specified in the topology.xml file.
>
> Here are the first few lines of my topology.xml file, where I have specified the box dimension.
>
> <topology name="">

Just move the box line here! That should fix the problem.
VOTCA looks for the <box> property directly under <topology> and not
in the <molecules> section.

Christoph

> <molecules>
> <clear/>
> <box xx="100.0" yy="100.0" zz="100.0" />
> <!-- define molecule, number of beads, number of mols -->
> <molecule name="PEOAA" nmols="1" nbeads="75">
> <!-- composition of molecule, bead definition -->
> <bead name="C1" type="C" mass="12.0112" q="0.054" />
> <bead name="C2" type="C" mass="12.0112" q="-0.159" />
>
> Can you please help me with the reason as why the box dimension is not read by the csg_dump command?
>
> I am also attaching my topology.xml file for your reference.
>
> Thank you.
>
> Sanjeet
>

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--
Christoph Junghans
Web: http://www.compphys.de

[Sanjeet Singh]

Dear Christoph,

Thank you for your suggestion. Now, it works.

Cheers,

Sanjeet

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e7QkTvgfv%2ByoseafS41CwtAzwEd4XCf%2BL%3Di0yw62uS%2BbA%40mail.gmail.com.

--

Sanjeet Kumar Singh

Postdoctoral Fellow

LPCM Lab.

University De Sherbrooke

Sherbrooke, Canada.