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crest-lab / crest

CREST - A program for the automated exploration of low-energy molecular chemical space.
https://crest-lab.github.io/crest-docs/
GNU Lesser General Public License v3.0
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Crest constrained conformational search on Linux incorrectly fails due to a missing coord file #314

Open tfhughes opened 4 days ago

tfhughes commented 4 days ago

Hello,

I am running a constrained conformational search using Crest Version 3.0.1 built by my team for Mac and Linux. The attached job runs just fine on Mac but fails on CentOS 7 (Core) with an error about a missing coord file. Yet I can see that the coord file is in the cwd after the job fails. I follow the instructions here https://crest-lab.github.io/crest-docs/page/examples/example_4.html#fixing-of-entire-substructure-parts. I using toml input pointing to inp and xyz files but using the latter directly as input results in the same error.

[hughes@boltio TS_R]$ ls TS_R.inp TS_R.toml TS_R.xyz [hughes@boltio TS_R]$ crest TS_R.toml > TS_R.log coord file does not exist. [hughes@boltio TS_R]$ tail TS_R.log

file present. content of the constraining file (sorted): > $constrain > atoms: 1,61,62 > force constant=0.5 > reference=TS_R.xyz > $metadyn > atoms: 2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,4 Parsing xtb-type input file TS_R.inp to set up calculators ... [hughes@boltio TS_R]$ ls coord crest_input_copy.xyz energies.log TS_R.inp TS_R.log TS_R.toml TS_R.xyz [hughes@boltio TS_R]$ [crest_github.tar.gz](https://github.com/user-attachments/files/16034226/crest_github.tar.gz)
pprcht commented 4 days ago

Hi, The structure you provide as reference= may not be the same input file. Simply creating a differently named copy of TS_R.xyz and providing that instead should work.

tfhughes commented 1 day ago

Thanks for the reply. Yes I tried that before after reading that link I sent above but I get the same behavior.

[hughes@boltio crest_github]$ ls run TS_R.inp TS_R_ref.xyz TS_R.toml TS_R.xyz [hughes@boltio crest_github]$ cat TS_R.inp $constrain atoms: 1,61,62 force constant=0.5 reference=TS_R_ref.xyz $metadyn atoms: 2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90 $end [hughes@boltio crest_github]$ ls -all total 44 drwxr-xr-x 2 hughes psgvb 2560 Jul 1 08:24 . drwxr-xr-x 18 hughes psgvb 12800 Jul 1 08:23 .. -rwxr-xr-x 1 hughes psgvb 33 Jul 1 08:23 run -rw-r--r-- 1 hughes psgvb 350 Jul 1 08:21 TS_R.inp -rw-r--r-- 1 hughes psgvb 4430 Jul 1 08:20 TS_R_ref.xyz -rw-r--r-- 1 hughes psgvb 219 Jun 28 10:12 TS_R.toml -rw-r--r-- 1 hughes psgvb 4430 Jun 28 10:12 TS_R.xyz [hughes@boltio crest_github]$ vi run [hughes@boltio crest_github]$ ./run coord file does not exist. [hughes@boltio crest_github]$ tail TS_R.log

file present. content of the constraining file (sorted): > $constrain > atoms: 1,61,62 > force constant=0.5 > reference=TS_R_ref.xyz > $metadyn > atoms: 2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,4 Parsing xtb-type input file TS_R.inp to set up calculators ... [hughes@boltio crest_github]$ Again on Mac it is fine but not on Linux.
pprcht commented 1 day ago

for me it works perfectly fine on linux, given the change of the reference file name

pprcht commented 1 day ago

okay, sorry, I have to revise: It apparently depends on the name of the reference file (which it shouldn't). Calling it dummy.xyz or ref.xyz works fine for me, if I call it TS_R_ref.xyz like you did, it doesn't work. If it's urgent I suggest using such a simple name while I look into why exactly this is happening.

tfhughes commented 19 hours ago

Yes, using a file with a different base name works. Many thanks! Probably worth a fix but I can manage with that.