Invalid QChem input file format

Hi,

I'm using "qc": "qchem", but the generated QChem input file is formatted in a way that's not accepted by QChem. An ADDSEC argument is added under $rem with value $OPT and CONSTRAINT. The QChem calculation stops at Illegal rem input in read_rem error according to the output file.

Example Kinbot arguments

``` { "title": "005", "structure": [ "C", -2.577633181322523, -0.14899699736569763, -0.07009320293759329, "C", -1.4710364844720145, 0.03988258853136189, -0.75032448258031, "C", -0.1604917635492785, -0.5703266103263727, -0.3919795546490268, "C", 0.8018278972888587, 0.5767209791158451, -0.14215601731303748, "C", 2.178991157385679, 0.059339271574617665, 0.23352777583103357, "H", -2.556372304909696, -0.7801537606225438, 0.8028529167299286, "H", -3.4881061869665815, 0.32354520244998, -0.38688528578309284, "H", -1.4917649457035762, 0.6733445897635278, -1.6267160667606906, "H", 0.22447548582474966, -1.2334174456304299, -1.1935419248390915, "H", -0.26597759790880043, -1.204604573308268, 0.511917577388464, "H", 0.40977650064470755, 1.147928280817434, 0.7396010636033121, "H", 0.8408829942731407, 1.2127708839806202, -1.027043850430413, "H", 2.68398201445469, 0.8544480216185247, 0.821403187037373, "H", 2.7918195957522594, -0.13837106750946224, -0.6468712969708699, "H", 2.0796268192086607, -0.8121093630892011, 0.9106049588215894 ], "charge": 0, "mult": 1, "qc": "qchem", "qc_command": "qchem", "families": "intra_H_migration", "queuing": "slurm", "queue_template": "queue.tmp", "scratch": "/global/scratch/users/ericyuan/KinBot" } ```

Example QChem input file by KinBot

``` $comment ASE generated input file $end $rem METHOD B3LYP BASIS STO-3G JOBTYPE OPT UNRESTRICTED TRUE SCF_ALGORITHM DIIS_GDM MAX_SCF_CYCLES 100 GEOM_OPT_MAX_CYCLES 500 SCF_CONVERGENCE 4 GEOM_OPT_TOL_GRADIENT 1500 GEOM_OPT_TOL_DISPLACEMENT 6000 GEOM_OPT_TOL_ENERGY 500 ADDSEC $OPT CONSTRAINT STRE 1 2 1.3382760256394144 STRE 1 6 1.0878758922264666 STRE 1 7 1.0860760178902613 STRE 2 3 1.5075948774964534 STRE 2 8 1.0918265854457123 STRE 3 4 1.5475057900669216 STRE 3 9 1.1018713063126104 STRE 3 10 1.098991334510338 STRE 4 5 1.536430012149745 STRE 4 11 1.0983972829511321 STRE 4 12 1.1000496422646011 STRE 5 13 1.096071787627103 STRE 5 14 1.0975509909543386 STRE 5 15 1.0972339650058218 BEND 2 1 6 121.71005680089769 ENDCONSTRAINT $END SYM_IGNORE TRUE $end $molecule 0 1 C -2.669788 -0.208572 -0.122289 C -1.528213 0.036435 -0.776323 C -0.172945 -0.504076 -0.396932 C 0.840984 0.607505 -0.034841 C 2.245720 0.059142 0.259493 H -2.699273 -0.849669 0.756119 H -3.617675 0.217208 -0.438173 H -1.546496 0.687539 -1.652574 H 0.240305 -1.087054 -1.235671 H -0.272641 -1.198574 0.448950 H 0.464268 1.161686 0.835472 H 0.893597 1.330531 -0.862230 H 2.948325 0.867855 0.491232 H 2.641531 -0.492269 -0.603003 H 2.232302 -0.627689 1.115066 $end ```

Example QChem output file

``` M. Scheurer, M. Schneider, P. E. Schneider, Tim K. Schramm, N. Sergueev, S. M. Sharada, M. Sharma, Hengyuan Shen, W. Skomorowski, D. W. Small, C. J. Stein, Alistair J. Sterling, Yingli Su, Yu-Chuan Su, E. J. Sundstrom, J. Talbot, Zhen Tao, J. Thirman, Hung-Yi Tsai, T. Tsuchimochi, N. M. Tubman, C. Utku, S. P. Veccham, O. Vydrov, J. Wenzel, Jonathan Wong, J. Witte, A. Yamada, Chou-Hsun Yang, Kun Yao, S. Yeganeh, S. R. Yost, A. Zech, F. Zeller, Igor Ying Zhang, Xing Zhang, Yu Zhang, D. Zuev, A. Aspuru-Guzik, A. T. Bell, N. A. Besley, K. B. Bravaya, B. R. Brooks, D. Casanova, Jeng-Da Chai, Hsing-Ta Chen, S. Coriani, C. J. Cramer, A. E. DePrince, III, R. A. DiStasio Jr., A. Dreuw, B. D. Dunietz, T. R. Furlani, W. A. Goddard III, S. Grimme, S. Hammes-Schiffer, T. Head-Gordon, W. J. Hehre, Chao-Ping Hsu, T.-C. Jagau, Yousung Jung, A. Klamt, Jing Kong, D. S. Lambrecht, Xiangyuan Li, WanZhen Liang, N. J. Mayhall, C. W. McCurdy, J. B. Neaton, T. Neudecker, C. Ochsenfeld, J. A. Parkhill, R. Peverati, V. A. Rassolov, Haisheng Ren, Yihan Shao, L. V. Slipchenko, R. P. Steele, J. E. Subotnik, A. J. W. Thom, A. Tkatchenko, D. G. Truhlar, T. Van Voorhis, Fan Wang, T. A. Wesolowski, K. B. Whaley, H. L. Woodcock III, P. M. Zimmerman, S. Faraji, P. M. W. Gill, M. Head-Gordon, J. M. Herbert, A. I. Krylov Contributors to earlier versions of Q-Chem not listed above: R. D. Adamson, B. Austin, R. Baer, J. Baker, G. J. O. Beran, K. Brandhorst, S. T. Brown, E. F. C. Byrd, Arup K. Chakraborty, G. K. L. Chan, Chun-Min Chang, Yunqing Chen, C.-L. Cheng, Siu Hung Chien, D. M. Chipman, D. L. Crittenden, H. Dachsel, R. J. Doerksen, A. D. Dutoi, R. G. Edgar, J. Fosso-Tande, L. Fusti-Molnar, D. Ghosh, A. Ghysels, A. Golubeva-Zadorozhnaya, J. Gonthier, M. S. Gordon, S. R. Gwaltney, G. Hawkins, J. E. Herr, A. Heyden, S. Hirata, E. G. Hohenstein, G. Kedziora, F. J. Keil, C. Kelley, Jihan Kim, R. A. King, R. Z. Khaliullin, P. P. Korambath, W. Kurlancheek, A. Laurent, A. M. Lee, M. S. Lee, S. V. Levchenko, Ching Yeh Lin, D. Liotard, E. Livshits, R. C. Lochan, I. Lotan, L. A. Martinez-Martinez, P. E. Maslen, N. Nair, D. P. O'Neill, D. Neuhauser, E. Neuscamman, C. M. Oana, R. Olivares-Amaya, R. Olson, T. M. Perrine, B. Peters, P. A. Pieniazek, A. Prociuk, Y. M. Rhee, J. Ritchie, M. A. Rohrdanz, E. Rosta, N. J. Russ, H. F. Schaefer III, M. W. Schmidt, N. E. Schultz, S. Sharma, N. Shenvi, C. D. Sherrill, A. C. Simmonett, A. Sodt, T. Stein, D. Stuck, K. S. Thanthiriwatte, V. Vanovschi, L. Vogt, Tao Wang, A. Warshel, M. A. Watson, C. F. Williams, Q. Wu, X. Xu, Jun Yang, W. Zhang, Yan Zhao Please cite Q-Chem as follows: "Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package" J. Chem. Phys. 155, 084801 (2021) https://doi.org/10.1063/5.0055522 (open access) Q-Chem 6.1.0 for Intel X86 EM64T Linux Parts of Q-Chem use Armadillo 9.900.5 (Nocturnal Misbehaviour). http://arma.sourceforge.net/ Q-Chem begins on Wed Nov 8 14:01:03 2023 Host: 0 Scratch files written to /tmp/702262792321520790121_intra_H_migration_2_6.sv// Jul923 |scratch|qcdevops|jenkins|workspace|build_RNUM -1 Processing $rem in /clusterfs/mp/software/qchem6.1/config/preferences: Processing $rem in /global/home/users/ericyuan/.qchemrc: Problem with processed rem input line: ADDSEC $OPT ADDSEC (rem variable) is not correct. Please make sure the variable is legal and the spelling is correct. Q-Chem fatal error occurred in module qparser/new_read_rem.C, line 429: Illegal rem input in read_rem Please submit a crash report at q-chem.com/reporter ```

Thanks.

zadorlab / KinBot

Invalid QChem input file format #67