Gavrog 0.6.0 beta 2 has been released
by odf
Hello again!
This is just a quick announcement of the release of a second beta test version for Gavrog version 0.6.0, which includes 3dt 0.6.0 and Systre 1.2.0. The new release fixes a small number of bugs, mostly related to saving data to files. You can look at the detailed list or download the new release at https://github.com/odf/gavrog/releases.
Advertisements
Hello. I’ve been reading the “Systre Help” page, which tells the command for opening Systre on the command line. However, I also want to know the command (which I hope exists) for saving the Systre output file on the command line. Could you tell me what this command is?
Sincerely,
Rebecca Rohrlich
Hello Rebecca,
Unfortunately, there is currently no special option for that.
You can redirect the normal output to a file in the usual manner (appending a ‘>’ and a name for the output file to the usual command works on Linux and Apple, and I think also on Windows, but I haven’t tried that lately), but at the moment, there is no option to produce output on the command line that Systre can read back in.
If you have a particular application in mind that you require this kind of functionality for, please contact me and I’ll see if I can write a custom script for you.
Cheers,
Olaf
Hi again —
Thanks so much for your response Olaf! (I tried to leave a comment thank you several days ago, but somehow it didn’t get posted. My apologies.)
I have another problem. I set my options for Systre so that the “Output Complete Unit Cell Contents” box is checked and used this file as input:
_____________________________________________________
CRYSTAL
ID SiO2
GROUP P3221
CELL 4.9137 4.9137 5.40513 90.0 90.0 120.0
ATOM 1 2 0.41450 0.26620 0.78560
ATOM 2 4 0.46980 0.00000 0.66667
END
_____________________________________________________
This gave me an output file with edge information. I saved the output file and fed it into Systre as a new input, which gave me the following new output file with P1 symmetry:
______________________________________________________
Structure #1 – “SiO2”.
Input structure described as 3-periodic.
Given space group is P1.
9 nodes and 12 edges in repeat unit as given.
Given repeat unit is accurate.
Point group has 12 elements.
2 kinds of node.
Equivalences for non-unique nodes:
2 –> 1
3 –> 1
4 –> 1
5 –> 1
6 –> 1
8 –> 7
9 –> 7
Coordination sequences:
Node 1: 2 6 6 18 18 51 42 103 62 156
Node 7: 4 4 12 12 36 30 84 52 124 80
TD10 = 456
Ideal space group is P6222.
Ideal group or setting differs from given (P6222 vs P1).
Structure already seen in this run.
Name: SiO2
Coordinates below are given for a full conventional cell.
Relaxed cell parameters:
a = 3.26599, b = 3.26599, c = 3.46410
alpha = 90.0000, beta = 90.0000, gamma = 120.0000
Cell volume: 32.00000
Relaxed positions:
Node 1: 0.50000 0.25000 0.16667
Node 2: 0.25000 0.50000 0.50000
Node 3: 0.50000 0.75000 0.16667
Node 4: 0.75000 0.50000 0.50000
Node 5: 0.25000 0.75000 0.83333
Node 6: 0.75000 0.25000 0.83333
Node 7: 0.50000 0.00000 0.00000
Node 8: 0.00000 0.50000 0.66667
Node 9: 0.50000 0.50000 0.33333
Edges:
0.50000 0.00000 0.00000 0.25000 -0.25000 -0.16667
0.50000 0.00000 0.00000 0.50000 0.25000 0.16667
0.50000 0.00000 0.00000 0.50000 -0.25000 0.16667
0.50000 0.00000 0.00000 0.75000 0.25000 -0.16667
0.00000 0.50000 0.66667 0.25000 0.50000 0.50000
0.00000 0.50000 0.66667 0.25000 0.75000 0.83333
0.00000 0.50000 0.66667 -0.25000 0.50000 0.50000
0.00000 0.50000 0.66667 -0.25000 0.25000 0.83333
0.50000 0.25000 0.16667 0.50000 0.00000 0.00000
0.50000 0.25000 0.16667 0.50000 0.50000 0.33333
0.25000 0.50000 0.50000 0.00000 0.50000 0.66667
0.25000 0.50000 0.50000 0.50000 0.50000 0.33333
0.50000 0.50000 0.33333 0.50000 0.25000 0.16667
0.50000 0.50000 0.33333 0.25000 0.50000 0.50000
0.50000 0.50000 0.33333 0.50000 0.75000 0.16667
0.50000 0.50000 0.33333 0.75000 0.50000 0.50000
0.50000 0.75000 0.16667 0.50000 1.00000 0.00000
0.50000 0.75000 0.16667 0.50000 0.50000 0.33333
0.75000 0.50000 0.50000 0.50000 0.50000 0.33333
0.75000 0.50000 0.50000 1.00000 0.50000 0.66667
0.25000 0.75000 0.83333 0.00000 0.50000 0.66667
0.25000 0.75000 0.83333 0.50000 1.00000 1.00000
0.75000 0.25000 0.83333 0.50000 0.00000 1.00000
0.75000 0.25000 0.83333 1.00000 0.50000 0.66667
Edge centers:
0.37500 -0.12500 -0.08333
0.50000 0.12500 0.08333
0.50000 -0.12500 0.08333
0.62500 0.12500 -0.08333
0.12500 0.50000 0.58333
0.12500 0.62500 0.75000
-0.12500 0.50000 0.58333
-0.12500 0.37500 0.75000
0.50000 0.12500 0.08333
0.50000 0.37500 0.25000
0.12500 0.50000 0.58333
0.37500 0.50000 0.41667
0.50000 0.37500 0.25000
0.37500 0.50000 0.41667
0.50000 0.62500 0.25000
0.62500 0.50000 0.41667
0.50000 0.87500 0.08333
0.50000 0.62500 0.25000
0.62500 0.50000 0.41667
0.87500 0.50000 0.58333
0.12500 0.62500 0.75000
0.37500 0.87500 0.91667
0.62500 0.12500 0.91667
0.87500 0.37500 0.75000
Edge statistics: minimum = 1.00000, maximum = 1.00000, average = 1.00000
Angle statistics: minimum = 90.00000, maximum = 180.00000, average = 127.82038
Shortest non-bonded distance = 1.41421
Degrees of freedom: 3
Finished structure #1 – “SiO2”.
____________________________________________________
This output contains all the information I wanted — namely, the locations of all the edges — and I could write new code to parse that information out of this file easily. However, my advisor went to a conference and obtained a Systre output file for the same crystal (alpha quartz) from one of her colleagues. This output file had a very different format from the one I was able to produce, and I’ve already written code to parse it:
______________________________________________________
CRYSTAL
NAME SiO2
GROUP P1
CELL 3.26599 3.26599 3.46410 90.0000 90.0000 120.0000
NODE 1 2 0.25000 0.50000 0.00000
NODE 2 2 0.75000 0.50000 0.00000
NODE 3 2 0.25000 0.75000 0.33333
NODE 4 2 0.75000 0.25000 0.33333
NODE 5 2 0.50000 0.25000 0.66667
NODE 6 2 0.50000 0.75000 0.66667
NODE 7 4 0.00000 0.50000 0.16667
NODE 8 4 0.50000 0.00000 0.50000
NODE 9 4 0.50000 0.50000 0.83333
EDGE 0.00000 0.50000 0.16667 0.25000 0.50000 0.00000
EDGE 0.00000 0.50000 0.16667 0.25000 0.75000 0.33333
EDGE 0.00000 0.50000 0.16667 -0.25000 0.50000 0.00000
EDGE 0.00000 0.50000 0.16667 -0.25000 0.25000 0.33333
EDGE 0.25000 0.50000 0.00000 0.00000 0.50000 0.16667
EDGE 0.25000 0.50000 0.00000 0.50000 0.50000 -0.16667
EDGE 0.50000 0.00000 0.50000 0.25000 -0.25000 0.33333
EDGE 0.50000 0.00000 0.50000 0.75000 0.25000 0.33333
EDGE 0.50000 0.00000 0.50000 0.50000 0.25000 0.66667
EDGE 0.50000 0.00000 0.50000 0.50000 -0.25000 0.66667
EDGE 0.75000 0.50000 0.00000 0.50000 0.50000 -0.16667
EDGE 0.75000 0.50000 0.00000 1.00000 0.50000 0.16667
EDGE 0.25000 0.75000 0.33333 0.00000 0.50000 0.16667
EDGE 0.25000 0.75000 0.33333 0.50000 1.00000 0.50000
EDGE 0.75000 0.25000 0.33333 0.50000 0.00000 0.50000
EDGE 0.75000 0.25000 0.33333 1.00000 0.50000 0.16667
EDGE 0.50000 0.25000 0.66667 0.50000 0.00000 0.50000
EDGE 0.50000 0.25000 0.66667 0.50000 0.50000 0.83333
EDGE 0.50000 0.50000 0.83333 0.50000 0.25000 0.66667
EDGE 0.50000 0.50000 0.83333 0.50000 0.75000 0.66667
EDGE 0.50000 0.50000 0.83333 0.25000 0.50000 1.00000
EDGE 0.50000 0.50000 0.83333 0.75000 0.50000 1.00000
EDGE 0.50000 0.75000 0.66667 0.50000 0.50000 0.83333
EDGE 0.50000 0.75000 0.66667 0.50000 1.00000 0.50000
# EDGE_CENTER 0.12500 0.50000 0.08333
# EDGE_CENTER 0.12500 0.62500 0.25000
# EDGE_CENTER -0.12500 0.50000 0.08333
# EDGE_CENTER -0.12500 0.37500 0.25000
# EDGE_CENTER 0.12500 0.50000 0.08333
# EDGE_CENTER 0.37500 0.50000 -0.08333
# EDGE_CENTER 0.37500 -0.12500 0.41667
# EDGE_CENTER 0.62500 0.12500 0.41667
# EDGE_CENTER 0.50000 0.12500 0.58333
# EDGE_CENTER 0.50000 -0.12500 0.58333
# EDGE_CENTER 0.62500 0.50000 -0.08333
# EDGE_CENTER 0.87500 0.50000 0.08333
# EDGE_CENTER 0.12500 0.62500 0.25000
# EDGE_CENTER 0.37500 0.87500 0.41667
# EDGE_CENTER 0.62500 0.12500 0.41667
# EDGE_CENTER 0.87500 0.37500 0.25000
# EDGE_CENTER 0.50000 0.12500 0.58333
# EDGE_CENTER 0.50000 0.37500 0.75000
# EDGE_CENTER 0.50000 0.37500 0.75000
# EDGE_CENTER 0.50000 0.62500 0.75000
# EDGE_CENTER 0.37500 0.50000 0.91667
# EDGE_CENTER 0.62500 0.50000 0.91667
# EDGE_CENTER 0.50000 0.62500 0.75000
# EDGE_CENTER 0.50000 0.87500 0.58333
END
______________________________________________________
This file and the other one both have the information I need (i.e. edge coordinates), but I’d like to know what causes Systre to produce one format versus the other. (I’d like to make sure all output files have the same format to make parsing easier.) Do the different formats just depend on what version of Systre you’re using? I use Systre 1.2.0.
Sincerely,
Rebecca Rohrlich
Hi Rebecca,
The difference between the two files is simply due to the type of output file chosen in the file selector box (under “Files of Type”) when saving the data. Your format is the default one, “Systre Transcripts – *.out”, your supervisor’s was produced by selecting “Embedded Nets – *.cgd” instead.
Does that answer you question or have I missed something?
Cheers,
Olaf
PS: Please also feel free to email me if you have further questions: olaf dot delgado at gmail dot com.