Invalid QChem input file format

[ericyuan00000]

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.

[cmartia]

Hi,
Yeah, I think the problem is a missing newline character ('\n') that needs to be added after ADDSEC. I'll try to fix it asap.