msi2lmp issue with non-orthogonal PBC

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1

Dear Users and Axel

I am having some issues with my CNT system visualization where box is not orthogonal, one of the angles is 120. I am not sure if it is VMD or msi2lmp or topotools.

I have a periodic (non-orthogonal system) (9,5) CNT in .mdf and .car format (attached) that I generated using Material Studio (PCFF forcefield). Then, I used new version (after Axel modified it back in August) to convert to lammps data file. Older version could not handle non-orthogonal boxes if I remember correctly, so Axel’s version is only choice (Thanks)

msi2lmp.exe runs fine and output a data file (attached).

When I visualize .car and .data (using topotools) file of the same system in VMD, I see differences.

.car file look as it should be in VMD.

For .data file, the CNT appears to be breaking in almost half followed by some shifting (1/2 the box length) in non-orthogonal direction (see the screenshot). Bond connectivity seems fine but due to this shifting, some of the bonds look to be extremely streched.

For your reference, I am attaching the appropriate files as well. Please have a look at them when you get a chance if you get same issue in VMD visualization. If so, what might be causing it.

Thanks in advance.

Best Regards,
Vikas

09-05-10.data (294 KB)

09-05-10.car (48.5 KB)

09-05-10.mdf (61.1 KB)

Screenshot.png

2

Dear Users and Axel

I am having some issues with my CNT system visualization where box is not
orthogonal, one of the angles is 120. I am not sure if it is VMD or msi2lmp
or topotools.

made some experiments and it most likely is due to msi2lmp.
will have a closer look at msi2lmp now.

axel.

3

Thanks. Please let me know when you get to the cause.

Best Regards,
Vikas

4

Thanks. Please let me know when you get to the cause.

please try this change and let us know. thanks.

diff --git a/tools/msi2lmp/src/ReadCarFile.c b/tools/msi2lmp/src/ReadCarFile.c
index 9a4f0e9..73209bc 100644
--- a/tools/msi2lmp/src/ReadCarFile.c
+++ b/tools/msi2lmp/src/ReadCarFile.c
@@ -25,9 +25,9 @@ void set_box(double box[3][3], double *h, double *h_inv)
   h_inv[1] = 1.0/h[1];
   h_inv[2] = 1.0/h[2];

- h[3] = box[2][0];
+ h[3] = box[2][2];
   h[4] = box[2][1];
- h[5] = box[2][2];
+ h[5] = box[2][0];
   h_inv[3] = -h[3] / (h[1]*h[2]);
   h_inv[4] = (h[3]*h[5] - h[1]*h[4]) / (h[0]*h[1]*h[2]);
   h_inv[5] = -h[5] / (h[0]*h[1]);

5

Dear Axel,
Many thanks for your quick response. It works now.

Best regards,
Vikas