Naming input files

Submitted ⁨⁨1⁩ ⁨day⁩ ago⁩ by ⁨Helium5793@discuss.avogadro.cc⁩ to ⁨Avogadro General Discussion@discuss.avogadro.cc⁩

https://discuss.avogadro.cc/t/naming-input-files/7527/1

I have bee working with the input files and have found that the default name is job whatever. If I am running through several molecules I have to take the time to rename them to a unique name. It seems to me it would be better to have the default name to be the same as the filename you are studying. So if I were using MOPAC on benzene the default would be benzene.mop. I might even suggest “benzene-Eq_Geo” so that the calculation type would included in the default. Also the input generator defaults to 1 core. My computer has 10 cores and 10 threads. For things like this it would be good to have a settings file that the user could fill out and have it default to what the computer has available.

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Thomas@discuss.avogadro.cc ⁨1⁩ ⁨day⁩ ago
@Helium5793 Are these i) large batches of input files to generate and ii) are the instructions to deliver to MOPAC per batch the same? Do you feel comfortable with the command line?

Let’s assume you have two structure files, benzene.xyz and pyridine.xyz in one folder, and you have openbabel at hand, you can convert the two into .mop

$ obabel *.xyz -O .mop -m 2 molecules converted 2 files output. The first is benzene.mop

where flag -m just tells that there multiple input files (for openbabel) to convert from .xyz to .mop. File pyridine.mop for instance reads

PUT KEYWORDS HERE pyridine.xyz C 1.43303 1 0.05159 1 0.00100 1 C 0.68800 1 1.22595 1 0.00151 1 C -0.69424 1 1.12563 1 0.00218 1 N -1.36237 1 -0.04853 1 0.00552 1 C -0.61197 1 -1.17189 1 0.00692 1 C 0.77379 1 -1.17331 1 0.00332 1 H 2.51852 1 0.09036 1 -0.00113 1 H 1.17153 1 2.19630 1 0.00127 1 H -1.31976 1 2.01344 1 0.00006 1 H -1.17257 1 -2.10232 1 0.01145 1 H 1.32543 1 -2.10632 1 0.00270 1

which a UNIX like operating system (for instance Linux Debian) can adjust further by

sed -i 's/PUT KEYWORDS HERE/pm3 charge=0 cycles=200/g' *.mop

to instruct MOPAC about the level of theory, the charge, the maximal number of iterations to improve the geometry, etc. by substitution of the placeholder PUT KEYWORDS HERE openbabel added. (Openbabel has an optional -k flag to write the instructions for MOPAC into the .mop, too).
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- Helium5793@discuss.avogadro.cc ⁨1⁩ ⁨day⁩ ago
  Instead, let us assume this. One wants to compare the properties of benzene, toluene, all the Xylenes, and mesitylenes in mopac(or any of the outputs) So one loads the structures in and calls mopac to write the mop file. All the files are named job.mop. So one has to rename them all before mopac can be run on them. Why not have the name of the file (benzene..etc) be the default name that avogadro assigns in this situation? and not have to manually do that. Avogadro knows the file name from the structure it is working with. It just has to use it. Having to call openbabel doesn’t seem necessary.
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ghutchis@discuss.avogadro.cc ⁨1⁩ ⁨day⁩ ago

Image Helium5793:

For things like this it would be good to have a settings file that the user could fill out and have it default to what the computer has available.

The nightly builds remember settings in the input generators, yes.

Image Helium5793:

default name to be the same as the filename you are studying

I’ll take a look at the default filenames later this afternoon.
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