dlpoly topology reader reports the wrong molecule number

[GoogleCodeExporter]

What steps will reproduce the problem?
1. run spce/ibi_dlpoly
2. stop after step_001
3. go into step_001
4. $ csg_stat --options ../settings.xml --top .dlpoly --trj traj.xyz 
begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 1

 field_scan(1/2): (re)allocating memory - SUCCESS!
I have 1 beads in 1 molecules
Segmentation fault

The segfault comes from inside votca::csg::XYZReader::NextFrame, but obviously 
the number of molecules is wrong.

Same for csg_dump
$ csg_dump --top .dlpoly

 field_scan(1/2): (re)allocating memory - SUCCESS!
I have 1 beads in 1 molecules

List of molecules:
molecule: 1 CG beads: 1
0 Name 1:no:CG Type CG Mass 18.0154
(Also the residuum name is wrong!)

But NUMMOLS in FIELD is correct
$ grep NUMMOLS FIELD
NUMMOLS 2180

Original issue reported on code.google.com by christop...@gmail.com on 24 Oct 2013 at 5:47

[GoogleCodeExporter]

Hi Christoph,

From what you sent I appreciate that something goes wrong if one runs a
dev-version (1.3) of Votca with binding to dlpoly in the case of spce water
model. In particular, the field file reader seems to return a wrong number
of molecules in FIELD.

I also see that I am resposible for solving the issue, which is fine.
However, I need to be introduced into the workflow of your dev-branch and
such.

Could you please provide me with either brief instructions as to how one
should deal with such issues, or a link to where this sort of info can be
found.

Great to see the work is going on!

Original comment by abruk...@googlemail.com on 24 Oct 2013 at 6:08

[GoogleCodeExporter]

Hi Guys,

Please fix your CONFIG file here:

http://code.google.com/p/votca/source/browse/spce/ibi_dlpoly/CONFIG?spec=svn.csg
-tutorials.4c345fbf25352c3720d68cea41f9d642f99769da&repo=csg-tutorials&r=4c345fb
f25352c3720d68cea41f9d642f99769da

Note that the second line must contain at least three (int) numbers, the last 
figure
being the total number of atoms (sites or beads) in the entire system.

Hope it helps.

Andrey

Original comment by abruk...@googlemail.com on 25 Oct 2013 at 10:23

[GoogleCodeExporter]

This issue was updated by revision 35457f2d6015.

Original comment by jungh...@votca.org on 25 Oct 2013 at 4:21

[GoogleCodeExporter]

Adding the number of molecules in CONFIG didn't help, but in the meanwhile I 
fixed the segfault in xyzreader.c. This was a missing throw, now is stops with 
an error:
$ csg_stat --options ../settings.xml --top .dlpoly --trj traj.xyz 
begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 1

 field_scan(1/2): (re)allocating memory - SUCCESS!
I have 1 beads in 1 molecules
an error occurred:
number of beads in topology and trajectory differ

Original comment by christop...@gmail.com on 25 Oct 2013 at 4:23

[GoogleCodeExporter]

... please, make sure you're using the numbers from FIELD correctly,
as described below:

-------
# of molecular types = nmolt as returned to the C-side (the F-reader reads only 
"molec" as a keyword)

MOLECULES 1

...

# of molecules of the latest (current) molecular type = MolecBase[im].nrept (or 
MolecSpecsT->nrept)
NUMMOLS 2180
-------

The total number of molecules and atoms (or beads, returned as matoms) can be 
calculated by summing up,

correspondingly, MolecBase[im].nrept and MolecBase[im].nsites while doing 
for(im=0; im<nmolt; im++)

Original comment by abruk...@googlemail.com on 25 Oct 2013 at 6:40

[GoogleCodeExporter]

Guys, please remove it from bugs/issues, cause it is not... 
it is a small thing that needs to be properly coded.

Will get to it tomorrow.

Thanks

Original comment by abruk...@googlemail.com on 4 Nov 2013 at 6:55

[GoogleCodeExporter]

i think it is fixed now, please verify

Original comment by victor.r...@gmail.com on 7 Nov 2013 at 9:13

[GoogleCodeExporter]

step_001 $ csg_stat --options ../settings.xml --top .dlpoly --trj traj.xyz
begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 1

 field_scan(1/2): (re)allocating memory - SUCCESS!
I have 2180 beads in 2180 molecules
NOTE: You are using OpenBox boundary conditions. Check if this is intended.

written CG-CG.dist.new

The number of molecules is now correct, but the  boundary conditions are still 
work, which leads to the wrong rdf, which is a separate issue.

One can use the following workaround for now:
$ cat topol.xml
<topology base=".dlpoly">
  <box xx="40.3100" yy="40.3100" zz="40.3100"/>
</topology>

And the reported residuum are still work, too, which is a separate issue as 
well.

Original comment by christop...@gmail.com on 7 Nov 2013 at 5:14

• Changed state: Fixed

[GoogleCodeExporter]

Great to know!

NOTE: You are using OpenBox boundary conditions. Check if this is intended.

- I would check the CONFIG, first of all, for the second number in the
second line (i.e. after the title), the possible values are:
0 - no PBC, 1 - cubic PBC, 2 - orthorhombic PBC, 3 - parallelepiped PBC etc
(see DL_POLY manual).

One has to take care about the first number there too, it defines the level
of CONFIG data:
0 - coords only, 1 - plus velocities, 2 - plus both velocities and forces
included.

- I do not understand this remark...

Original comment by abruk...@googlemail.com on 7 Nov 2013 at 8:46

[GoogleCodeExporter]

Let's stay on topic here, these are separate issues!

See issue #141 for the boundary condition issue and issue #142 for the residuum 
naming issue.

Original comment by christop...@gmail.com on 7 Nov 2013 at 10:20