command line utility (voro++: File import error)

[49n3r]

I used the command line utility for my file but ut does not work. I am probably doing something wrong and need help

here are some of the outputs i get:

$ which voro++

/usr/local/bin/voro++

$ voro++ 1.7 -1 11.42 -1 11.42 -1 11.42 file.txt

voro++: Unrecognized command-line options; type "voro++ -h" for more
information.

$ voro++ -c 1.7 -1 11.42 -1 11.42 -1 11.42 file.txt

voro++: File import error

This is the format of file.txt

1 2.2022195764 0.0882639228 0.2652000719
2 0.061581751 0.9691128644 0.2866639925
3 5.4166190508 5.3541257598 2.620338246
4 1.6310048028 1.6326451092 4.3502133366
5 2.7096653697 0.6759740358 4.4542436774
6 0.3643502753 0.9240571118 4.5976255654
7 4.5862121436 1.9835610692 3.7784469093
8 4.0829712416 0.7441541825 4.2161691391
9 5.2724841356 4.028051288 2.9595762809
10 1.7034971813 2.9943995924 4.0509491695
11 0.4745472907 3.7241880652 4.0212346382
12 0.7596018007 5.1113110828 3.7226285345
13 2.2467716391 5.2040868219 3.5679059473
14 2.8257309397 3.8742132526 3.7674502882
15 4.1257520881 3.3557331052 3.5621434363
16 1.3031302888 1.5258780961 8.3183619035
17 2.6838537043 1.4291649176 8.0343168416
18 3.5019432891 2.5179376873 7.5111683185
19 5.3897838719 0.7850666458 7.5980058469
20 4.8528646713 2.1281372622 7.2049581742
21 0.746083309 2.8157883653 8.1837581849
22 0.7571463583 5.1937767629 7.6461557258
23 1.4673383034 3.9351736932 7.7037156419
24 4.8279491076 5.0031735687 6.0510078664
25 3.4626047744 4.9470427667 6.5944297033
26 2.8540016376 3.8118939667 7.2787048482
27 3.2001550244 0.1631769742 8.3226402782
28 0.5028964084 0.4017329886 8.7934080307
29 1.9439231676 2.3926837946 10.849739634
30 0.615337097 2.1788986379 11.2476402333
31 2.6863251027 1.2400779118 11.0496817175
32 4.7735738509 5.0292918775 9.9451946222
33 4.0117160924 1.3723532215 10.8056962156 ...

[chr1shr]

There is small issue with your command-line arguments. You don't need the 1.7 entry. Furthermore the -c option expects the next entry to be a custom output string. Hence, currently you are specifying 1.7 as the custom output string.

You could run Voro++ by omitting the -c and the 1.7 options like this:

voro++ -1 11.42 -1 11.42 -1 11.42 file.txt

Alternatively if you wanted to specify a custom output string (e.g. %i %q %v) you could write

voro++ -c "%i %q %v" -1 11.42 -1 11.42 -1 11.42

This small issue doesn't explain why you are getting the "File import error", though. From the text you included, it looks like your input file has the correct format with four entries per line, so I am not sure what is going on. But here are two options you could try.

Option 1. The main thing that Voro++ looks for is that the number of entries in the file is divisible by four. It might be that there is some problem later in the file. You could test this by making a small input data file with just the first 32 lines in, to see if it works with that.

Option 2. There is a troublesome and pervasive issue where newline characters on Linux/Mac operating systems are different from those on Windows/DOS systems. This is due to some fateful historical decisions that were made as these systems were developed. This has caused huge problems ever since, and it means that if you open text files created on one system in programs on another system, the newlines can be interpreted incorrectly. This is a broad issue that affects many programs, and not just Voro++.

This might have happened if you are running the program on a different operating system from where the input file was originally generated. Indeed, it can happen even on the same operating system: suppose you have a Mac and you output a CSV file using the Mac version of Excel, then because Excel is a Microsoft program, it will use the Windows newlines.

There are two small utilities called dos2unix and unix2dos that can convert files between the two newline formats. So you could try running those on your data file. You can read more about this problem online, and some text editors (e.g. Vim) will tell you what format a text file is using.