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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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Error when Running crest for some metal complexes #171

Closed Msafy2021 closed 1 year ago

Msafy2021 commented 1 year ago

Hi all,

I am trying to do a conformational search for some metal companies and got this error. Please note: I can not find the mentioned file "/home/conda/feedstock_root/build_artifacts/crest_1653057505696/work/src/confscript2_misc.f90"

Now appending opt.xyz file with new structures At line 1068 of file /home/conda/feedstock_root/build_artifacts/crest_1653057505696/work/src/confscript2_misc.f90 Fortran runtime error: End of file

Error termination. Backtrace:

0 0x2ba5b96488e5 in list_formatted_read_scalar

    at ../../../libgfortran/io/list_read.c:2308

1 0x5624d0c77b22 in ???

2 0x5624d0c7e02d in ???

3 0x5624d0c74bc0 in ???

4 0x5624d0d6dc3e in ???

5 0x5624d0c06340 in ???

6 0x2ba5bbca0554 in ???

7 0x5624d0c06370 in ???

running RMSDs... done. E lowest : 0.00000

pprcht commented 1 year ago

Hi, I see you are running the conda version, but this hasn't been updated for a while now. Could you build the program from source, or try running the continuous release build?

Msafy2021 commented 1 year ago

Thank you, Philipp, for your response. I will give your suggestion a try. However, I'm wondering if this error could be related to the molecule I'm working with. I have run multiple calculations, and all of them completed successfully except for one or two files that gave me this error. Specifically, I used various organic ligands with the same metal, and all of them terminated normally except for the one that has Isopropyl groups.

Msafy2021 commented 1 year ago

Also, Below you will find more details about the error, it is showing that the error happened in the Structure Crossing (GC). Can I optimize the structures in "crest_conformers.xyz" manually and then select the best conformer? 

 ========================================
 |        Structure Crossing (GC)       |
 ========================================

=============================

threads = 20

============================= input file name : crest_rotamers_3.xyz number of atoms : 68 number of points on xyz files : 23 conformer energy window /kcal : 6.00 CN per atom difference cut-off : 0.3000 RMSD threshold : 0.2500 max. # of generated structures : 350 reading xyz file ...

in E window 23

generating pairs ... 275 generated pairs : 3 number of clash discarded : 250 average rmsd w.r.t input : 1.02990 sd of ensemble : 0.92263 number of new structures : 3 removed identical structures : 0 writing 3 TMPCONF* dirs ...

GC: loose pre-optimization

Starting optimization of generated structures 3 jobs to do. 1 2 3 done. Now appending opt.xyz file with new structures At line 1068 of file /home/conda/feedstock_root/build_artifacts/crest_1653057505696/work/src/confscript2_misc.f90 Fortran runtime error: End of file

Error termination. Backtrace:

0 0x2ba5b96488e5 in list_formatted_read_scalar

    at ../../../libgfortran/io/list_read.c:2308

1 0x5624d0c77b22 in ???

2 0x5624d0c7e02d in ???

3 0x5624d0c74bc0 in ???

4 0x5624d0d6dc3e in ???

5 0x5624d0c06340 in ???

6 0x2ba5bbca0554 in ???

7 0x5624d0c06370 in ???

running RMSDs... done. E lowest : 0.00000

pprcht commented 1 year ago

Yes, the crest_conformers.xyz should contain all conformers up to the crash. You could try starting an optimization of all the points in there with crest coord --mdopt crest_conformers.xyz If the error keeps reoccurring in the GC step, it might be best to turn it off (--nocross)

Msafy2021 commented 1 year ago

Thank you, Philipp, I tried using crest coord --mdopt crest_conformers.xyz and it worked as I want.