diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index ef6479bcf..503c0d349 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -9,8 +9,6 @@ on: jobs: build: runs-on: ubuntu-latest - strategy: - max-parallel: 1 steps: - uses: actions/checkout@v4 with: diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index ea797b8e7..41072db62 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -14,30 +14,36 @@ on: jobs: build: strategy: - max-parallel: 1 matrix: - os: [ubuntu-latest] - python-version: ["3.10"] + os: [ubuntu-latest, windows-latest, macos-14] + # not testing on 3.9 because tests use glob("*", root_dir=TEST_FILES) + # and root_dir only added in 3.10 + python-version: ["3.10", "3.12"] runs-on: ${{ matrix.os }} + defaults: + run: + shell: bash -l {0} steps: - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + cache: pip + cache-dependency-path: pyproject.toml + - uses: conda-incubator/setup-miniconda@v3 with: python-version: ${{ matrix.python-version }} + activate-environment: qchem - name: Install OpenBabel - shell: bash -l {0} run: conda install -c conda-forge openbabel - - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: pip install -e '.[dev]' + run: pip install '.[dev]' - name: pytest env: diff --git a/custodian/qchem/handlers.py b/custodian/qchem/handlers.py index 2927fea57..0f4b5edaf 100644 --- a/custodian/qchem/handlers.py +++ b/custodian/qchem/handlers.py @@ -380,6 +380,6 @@ def correct(self): ) and str(self.qcinp.geom_opt["initial_hessian"]).lower() == "read": del self.qcinp.geom_opt["initial_hessian"] actions.append({"initial_hessian": "deleted"}) - os.rename(self.input_file, self.input_file + ".last") + os.replace(self.input_file, f"{self.input_file}.last") self.qcinp.write_file(self.input_file) return {"errors": self.errors, "warnings": self.warnings, "actions": actions} diff --git a/custodian/qchem/jobs.py b/custodian/qchem/jobs.py index bbd43435d..7f0bea23a 100644 --- a/custodian/qchem/jobs.py +++ b/custodian/qchem/jobs.py @@ -590,7 +590,7 @@ def opt_with_frequency_flattener( else: good_child = copy.deepcopy(history[-1]) if good_child["num_neg_freqs"] > 1: - raise Exception( + raise ValueError( "ERROR: Child with lower energy has more negative frequencies! Exiting..." ) if good_child["energy"] < parent_hist["energy"] or ( @@ -602,7 +602,7 @@ def opt_with_frequency_flattener( ): make_good_child_next_parent = True else: - raise Exception("ERROR: Good child not good enough! Exiting...") + raise ValueError("ERROR: Good child not good enough! Exiting...") if make_good_child_next_parent: good_child["index"] = len(history) history.append(good_child) @@ -610,9 +610,9 @@ def opt_with_frequency_flattener( geom_to_perturb = history[-1]["geometry"] negative_freq_vecs = history[-1]["frequency_mode_vectors"][perturb_index] else: - raise Exception("ERROR: Can't deal with multiple neg frequencies yet! Exiting...") + raise ValueError("ERROR: Can't deal with multiple neg frequencies yet! Exiting...") else: - raise AssertionError("ERROR: Parent cannot have more than two children! Exiting...") + raise ValueError("ERROR: Parent cannot have more than two children! Exiting...") # Implicitly, if the number of negative frequencies decreased from parent to child, # continue normally. if standard: diff --git a/tests/files/qchem/new_test_files/FF_working/test_cust.py b/tests/files/qchem/new_test_files/FF_working/test_cust.py deleted file mode 100644 index 04073991a..000000000 --- a/tests/files/qchem/new_test_files/FF_working/test_cust.py +++ /dev/null @@ -1,24 +0,0 @@ -import pytest - -from custodian import Custodian -from custodian.qchem.handlers import QChemErrorHandler -from custodian.qchem.jobs import QCJob - -pytest.importorskip("openbabel") -my_input = "test.qin" -my_output = "test.qout" - -job = QCJob.opt_with_frequency_flattener( - qchem_command="qchem -slurm", - multimode="openmp", - input_file=my_input, - output_file=my_output, - max_iterations=10, - max_molecule_perturb_scale=0.3, - max_cores=12, -) -myhandler = QChemErrorHandler(input_file=my_input, output_file=my_output) - -cust = Custodian([myhandler], job, max_errors_per_job=10, max_errors=10) - -cust.run() diff --git a/tests/files/qchem/new_test_files/fileman_cpscf.qin b/tests/files/qchem/new_test_files/fileman_cpscf.qin new file mode 100644 index 000000000..e1512a7c4 --- /dev/null +++ b/tests/files/qchem/new_test_files/fileman_cpscf.qin @@ -0,0 +1,98 @@ +$molecule + 0 2 + O 0.2914152612 -4.5445442042 3.0161751692 + O -1.5304339813 -3.2367784149 2.9281824830 + C 0.8295530097 -3.9366715322 4.2435768817 + C -0.1230659566 -4.2007068432 5.3950468933 + C 2.1314679452 -4.6891692104 4.4343334880 + C 1.0891180123 -2.4551760936 4.0360799358 + C -0.8605961838 -4.1422775145 2.4861350017 + C -1.2116960079 -4.9374875952 1.2364985602 + C -2.6517342220 -4.6163181541 0.8175486720 + H -0.3280027986 -5.2718477365 5.4811047398 + H 0.3385752508 -3.8702900027 6.3302131252 + H -1.0648795958 -3.6651308672 5.2679406205 + H 2.8060542012 -4.5134182893 3.5911657969 + H 1.9470806743 -5.7639090000 4.5122126635 + H 2.6262968839 -4.3565250871 5.3502869188 + H 1.6558832285 -2.2928927340 3.1137215346 + H 0.1610759990 -1.8839982580 3.9934806758 + H 1.6896565513 -2.0812658626 4.8711834869 + C -1.0164727255 -6.4347242690 1.4797433050 + H -1.5581303737 -6.7836873265 2.3638647772 + H 0.0398286180 -6.6745120675 1.6184484158 + H -1.3829909813 -6.9970496209 0.6140214151 + C -0.2642252347 -4.4709101412 0.1263230216 + H -0.3925640144 -3.4049115606 -0.0773598657 + H -0.4789826082 -5.0237708051 -0.7947386622 + H 0.7815646456 -4.6470496024 0.3929852586 + C -3.7386359783 -5.1159593031 1.7522230896 + H -2.8000270794 -5.0438393410 -0.1827625673 + H -2.7338896931 -3.5296566953 0.7024878530 + H -3.7691013071 -6.2090022139 1.7949719714 + H -4.7241345868 -4.7791401993 1.4163909720 + H -3.5933064317 -4.7432620029 2.7707341718 + S -3.1095688405 -0.8338328120 1.9223394071 + C -1.4763090285 -0.6530852521 0.5550909541 + C -1.7891128457 -0.8441888555 -0.7833876727 + H -2.8272949027 -0.8142864366 -1.1170758647 + C -0.7598974121 -1.0500002977 -1.7040885688 + H -0.9909069977 -1.1779594339 -2.7596192371 + C 0.5668601276 -1.0856329376 -1.2708524494 + H 1.3694627147 -1.2422432626 -1.9871957374 + C 0.8611607361 -0.9378379065 0.0855095498 + H 1.8948169178 -0.9779391480 0.4236494734 + C -0.1682729563 -0.7392449587 1.0085213741 + H 0.0565492183 -0.6401064636 2.0671273707 + C -2.3463554075 -0.1413857476 3.3511116054 + C -1.6861008228 1.0969952276 3.3571269080 + C -1.1464262498 1.5804639094 4.5468959620 + H -0.6384784857 2.5416032340 4.5463233852 + C -1.2451485056 0.8426672145 5.7244777657 + H -0.8196610583 1.2241103280 6.6487441345 + C -1.9004041859 -0.3950415761 5.7114055631 + H -1.9807860619 -0.9794453631 6.6245370395 + C -2.4557420740 -0.8829375023 4.5380818681 + H -2.9596492827 -1.8437276305 4.5221216535 + C -4.1249281175 0.4004756787 1.1655216406 + C -3.6353302924 1.6229046114 0.6843711827 + H -1.5667550440 1.6629973908 2.4414322262 + C -4.5234891084 2.5509004307 0.1444384244 + H -4.1442520184 3.5017916858 -0.2216525594 + C -5.8845872809 2.2671234587 0.0644736389 + H -6.5705578262 2.9985074190 -0.3548381451 + C -6.3661310487 1.0371574340 0.5275291796 + H -7.4256662542 0.8058548518 0.4619447035 + C -5.4944582701 0.1113707308 1.0849708426 + H -5.8630706203 -0.8369243514 1.4678940842 + H -2.5707192368 1.8246188792 0.6894404950 +$end + +$rem + job_type = freq + basis = def2-svpd + max_scf_cycles = 100 + gen_scfman = true + xc_grid = 3 + thresh = 14 + s2thresh = 16 + scf_algorithm = diis + resp_charges = true + symmetry = false + sym_ignore = true + method = b97mv + solvent_method = pcm + mem_total = 170000 +$end + +$pcm + heavypoints 194 + hpoints 194 + radii uff + theory cpcm + vdwscale 1.1 +$end + +$solvent + dielectric 78.39 +$end diff --git a/tests/files/qchem/new_test_files/fileman_cpscf.qin.gz b/tests/files/qchem/new_test_files/fileman_cpscf.qin.gz deleted file mode 100644 index 65256078e..000000000 Binary files a/tests/files/qchem/new_test_files/fileman_cpscf.qin.gz and /dev/null differ diff --git a/tests/files/qchem/new_test_files/fileman_cpscf.qout b/tests/files/qchem/new_test_files/fileman_cpscf.qout new file mode 100644 index 000000000..479ae5bbf --- /dev/null +++ b/tests/files/qchem/new_test_files/fileman_cpscf.qout @@ -0,0 +1,814 @@ + +Running Job 1 of 1 mol.qin +qchem mol.qin_10791.0 /tmp/scratch/ 0 +/clusterfs/mp/software/qchem6.0/exe/qcprog.exe_s mol.qin_10791.0 /tmp/scratch/ + Welcome to Q-Chem + A Quantum Leap Into The Future Of Chemistry + + + Q-Chem 6.0, Q-Chem, Inc., Pleasanton, CA (2022) + + E. Epifanovsky, A. T. B. Gilbert, Xintian Feng, Joonho Lee, Yuezhi Mao, + N. Mardirossian, P. Pokhilko, A. White, M. Wormit, M. P. Coons, + A. L. Dempwolff, Zhengting Gan, D. Hait, P. R. Horn, L. D. Jacobson, + I. Kaliman, J. Kussmann, A. W. Lange, Ka Un Lao, D. S. Levine, Jie Liu, + S. C. McKenzie, A. F. Morrison, K. Nanda, F. Plasser, D. R. Rehn, + M. L. Vidal, Zhi-Qiang You, Ying Zhu, B. Alam, B. Albrecht, + A. Aldossary, E. Alguire, J. H. Andersen, V. Athavale, D. Barton, + K. Begam, A. Behn, N. Bellonzi, Y. A. Bernard, E. J. Berquist, + H. Burton, A. Carreras, K. Carter-Fenk, Romit Chakraborty, + Chandrima Chakravarty, Junhan Chen, A. D. Chien, K. D. Closser, + V. Cofer-Shabica, L. Cunha, S. Dasgupta, Jia Deng, M. de Wergifosse, + M. Diedenhofen, Hainam Do, S. Ehlert, Po-Tung Fang, S. Fatehi, + Qingguo Feng, T. Friedhoff, B. Ganoe, J. Gayvert, Qinghui Ge, + G. Gidofalvi, M. Goldey, J. Gomes, C. Gonzalez-Espinoza, S. Gulania, + A. Gunina, J. A. Gyamfi, M. W. D. Hanson-Heine, P. H. P. Harbach, + A. W. Hauser, M. F. Herbst, M. Hernandez Vera, M. Hodecker, + Z. C. Holden, S. Houck, Xunkun Huang, Kerwin Hui, B. C. Huynh, + K. Ikeda, M. Ivanov, Hyunjun Ji, Zuxin Jin, Hanjie Jiang, B. Kaduk, + S. Kaehler, R. Kang, K. Khistyaev, Jaehoon Kim, Yongbin Kim, + P. Klunzinger, Z. Koczor-Benda, Joong Hoon Koh, D. Kosenkov, + Saikiran Kotaru, L. Koulias, T. Kowalczyk, C. M. Krauter, K. Kue, + A. Kunitsa, T. Kus, A. Landau, K. V. Lawler, D. Lefrancois, S. Lehtola, + Rain Li, Shaozhi Li, Yi-Pei Li, Jiashu Liang, M. Liebenthal, + Hung-Hsuan Lin, You-Sheng Lin, Fenglai Liu, Kuan-Yu Liu, + M. Loipersberger, A. Luenser, C. Malbon, A. Manjanath, P. Manohar, + E. Mansoor, S. F. Manzer, Shan-Ping Mao, A. V. Marenich, T. Markovich, + S. Mason, F. Matz, S. A. Maurer, P. F. McLaughlin, M. F. S. J. Menger, + J.-M. Mewes, S. A. Mewes, P. Morgante, Mohammad Mostafanejad, + J. W. Mullinax, K. J. Oosterbaan, G. Paran, V. Parravicini, + Alexander C. Paul, Suranjan K. Paul, F. Pavosevic, Zheng Pei, S. Prager, + E. I. Proynov, E. Ramos, B. Rana, A. E. Rask, A. Rettig, R. M. Richard, + F. Rob, E. Rossomme, T. Scheele, M. Scheurer, M. Schneider, + P. E. Schneider, N. Sergueev, S. M. Sharada, Hengyuan Shen, + W. Skomorowski, D. W. Small, C. J. Stein, Yingli Su, Yu-Chuan Su, + E. J. Sundstrom, 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 6.0.2 for Intel X86 EM64T Linux + + Parts of Q-Chem use Armadillo 9.900.5 (Nocturnal Misbehaviour). + http://arma.sourceforge.net/ + + Q-Chem begins on Fri Jun 30 11:40:02 2023 + + Host: +0 + + Scratch files written to /tmp/scratch// + Dec722 |scratch|qcdevops|jenkins|workspace|build_RNUM -1 + Processing $rem in /clusterfs/mp/software/qchem6.0/config/preferences: + Processing $rem in /global/home/users/smblau/.qchemrc: + Symmetry turned off for PCM/SM12/SMD calculation + + Checking the input file for inconsistencies... ...done. + +-------------------------------------------------------------- +User input: +-------------------------------------------------------------- +$molecule +0 2 +O 0.2914152612 -4.5445442042 3.0161751692 +O -1.5304339813 -3.2367784149 2.9281824830 +C 0.8295530097 -3.9366715322 4.2435768817 +C -0.1230659566 -4.2007068432 5.3950468933 +C 2.1314679452 -4.6891692104 4.4343334880 +C 1.0891180123 -2.4551760936 4.0360799358 +C -0.8605961838 -4.1422775145 2.4861350017 +C -1.2116960079 -4.9374875952 1.2364985602 +C -2.6517342220 -4.6163181541 0.8175486720 +H -0.3280027986 -5.2718477365 5.4811047398 +H 0.3385752508 -3.8702900027 6.3302131252 +H -1.0648795958 -3.6651308672 5.2679406205 +H 2.8060542012 -4.5134182893 3.5911657969 +H 1.9470806743 -5.7639090000 4.5122126635 +H 2.6262968839 -4.3565250871 5.3502869188 +H 1.6558832285 -2.2928927340 3.1137215346 +H 0.1610759990 -1.8839982580 3.9934806758 +H 1.6896565513 -2.0812658626 4.8711834869 +C -1.0164727255 -6.4347242690 1.4797433050 +H -1.5581303737 -6.7836873265 2.3638647772 +H 0.0398286180 -6.6745120675 1.6184484158 +H -1.3829909813 -6.9970496209 0.6140214151 +C -0.2642252347 -4.4709101412 0.1263230216 +H -0.3925640144 -3.4049115606 -0.0773598657 +H -0.4789826082 -5.0237708051 -0.7947386622 +H 0.7815646456 -4.6470496024 0.3929852586 +C -3.7386359783 -5.1159593031 1.7522230896 +H -2.8000270794 -5.0438393410 -0.1827625673 +H -2.7338896931 -3.5296566953 0.7024878530 +H -3.7691013071 -6.2090022139 1.7949719714 +H -4.7241345868 -4.7791401993 1.4163909720 +H -3.5933064317 -4.7432620029 2.7707341718 +S -3.1095688405 -0.8338328120 1.9223394071 +C -1.4763090285 -0.6530852521 0.5550909541 +C -1.7891128457 -0.8441888555 -0.7833876727 +H -2.8272949027 -0.8142864366 -1.1170758647 +C -0.7598974121 -1.0500002977 -1.7040885688 +H -0.9909069977 -1.1779594339 -2.7596192371 +C 0.5668601276 -1.0856329376 -1.2708524494 +H 1.3694627147 -1.2422432626 -1.9871957374 +C 0.8611607361 -0.9378379065 0.0855095498 +H 1.8948169178 -0.9779391480 0.4236494734 +C -0.1682729563 -0.7392449587 1.0085213741 +H 0.0565492183 -0.6401064636 2.0671273707 +C -2.3463554075 -0.1413857476 3.3511116054 +C -1.6861008228 1.0969952276 3.3571269080 +C -1.1464262498 1.5804639094 4.5468959620 +H -0.6384784857 2.5416032340 4.5463233852 +C -1.2451485056 0.8426672145 5.7244777657 +H -0.8196610583 1.2241103280 6.6487441345 +C -1.9004041859 -0.3950415761 5.7114055631 +H -1.9807860619 -0.9794453631 6.6245370395 +C -2.4557420740 -0.8829375023 4.5380818681 +H -2.9596492827 -1.8437276305 4.5221216535 +C -4.1249281175 0.4004756787 1.1655216406 +C -3.6353302924 1.6229046114 0.6843711827 +H -1.5667550440 1.6629973908 2.4414322262 +C -4.5234891084 2.5509004307 0.1444384244 +H -4.1442520184 3.5017916858 -0.2216525594 +C -5.8845872809 2.2671234587 0.0644736389 +H -6.5705578262 2.9985074190 -0.3548381451 +C -6.3661310487 1.0371574340 0.5275291796 +H -7.4256662542 0.8058548518 0.4619447035 +C -5.4944582701 0.1113707308 1.0849708426 +H -5.8630706203 -0.8369243514 1.4678940842 +H -2.5707192368 1.8246188792 0.6894404950 +$end + +$rem +job_type = freq +basis = def2-svpd +max_scf_cycles = 100 +gen_scfman = true +xc_grid = 3 +thresh = 14 +s2thresh = 16 +scf_algorithm = diis +resp_charges = true +symmetry = false +sym_ignore = true +method = b97mv +solvent_method = pcm +mem_total = 170000 +$end + +$pcm +heavypoints 194 +hpoints 194 +radii uff +theory cpcm +vdwscale 1.1 +$end + +$solvent +dielectric 78.39 +$end +-------------------------------------------------------------- + ---------------------------------------------------------------- + Standard Nuclear Orientation (Angstroms) + I Atom X Y Z + ---------------------------------------------------------------- + 1 O 0.2914152612 -4.5445442042 3.0161751692 + 2 O -1.5304339813 -3.2367784149 2.9281824830 + 3 C 0.8295530097 -3.9366715322 4.2435768817 + 4 C -0.1230659566 -4.2007068432 5.3950468933 + 5 C 2.1314679452 -4.6891692104 4.4343334880 + 6 C 1.0891180123 -2.4551760936 4.0360799358 + 7 C -0.8605961838 -4.1422775145 2.4861350017 + 8 C -1.2116960079 -4.9374875952 1.2364985602 + 9 C -2.6517342220 -4.6163181541 0.8175486720 + 10 H -0.3280027986 -5.2718477365 5.4811047398 + 11 H 0.3385752508 -3.8702900027 6.3302131252 + 12 H -1.0648795958 -3.6651308672 5.2679406205 + 13 H 2.8060542012 -4.5134182893 3.5911657969 + 14 H 1.9470806743 -5.7639090000 4.5122126635 + 15 H 2.6262968839 -4.3565250871 5.3502869188 + 16 H 1.6558832285 -2.2928927340 3.1137215346 + 17 H 0.1610759990 -1.8839982580 3.9934806758 + 18 H 1.6896565513 -2.0812658626 4.8711834869 + 19 C -1.0164727255 -6.4347242690 1.4797433050 + 20 H -1.5581303737 -6.7836873265 2.3638647772 + 21 H 0.0398286180 -6.6745120675 1.6184484158 + 22 H -1.3829909813 -6.9970496209 0.6140214151 + 23 C -0.2642252347 -4.4709101412 0.1263230216 + 24 H -0.3925640144 -3.4049115606 -0.0773598657 + 25 H -0.4789826082 -5.0237708051 -0.7947386622 + 26 H 0.7815646456 -4.6470496024 0.3929852586 + 27 C -3.7386359783 -5.1159593031 1.7522230896 + 28 H -2.8000270794 -5.0438393410 -0.1827625673 + 29 H -2.7338896931 -3.5296566953 0.7024878530 + 30 H -3.7691013071 -6.2090022139 1.7949719714 + 31 H -4.7241345868 -4.7791401993 1.4163909720 + 32 H -3.5933064317 -4.7432620029 2.7707341718 + 33 S -3.1095688405 -0.8338328120 1.9223394071 + 34 C -1.4763090285 -0.6530852521 0.5550909541 + 35 C -1.7891128457 -0.8441888555 -0.7833876727 + 36 H -2.8272949027 -0.8142864366 -1.1170758647 + 37 C -0.7598974121 -1.0500002977 -1.7040885688 + 38 H -0.9909069977 -1.1779594339 -2.7596192371 + 39 C 0.5668601276 -1.0856329376 -1.2708524494 + 40 H 1.3694627147 -1.2422432626 -1.9871957374 + 41 C 0.8611607361 -0.9378379065 0.0855095498 + 42 H 1.8948169178 -0.9779391480 0.4236494734 + 43 C -0.1682729563 -0.7392449587 1.0085213741 + 44 H 0.0565492183 -0.6401064636 2.0671273707 + 45 C -2.3463554075 -0.1413857476 3.3511116054 + 46 C -1.6861008228 1.0969952276 3.3571269080 + 47 C -1.1464262498 1.5804639094 4.5468959620 + 48 H -0.6384784857 2.5416032340 4.5463233852 + 49 C -1.2451485056 0.8426672145 5.7244777657 + 50 H -0.8196610583 1.2241103280 6.6487441345 + 51 C -1.9004041859 -0.3950415761 5.7114055631 + 52 H -1.9807860619 -0.9794453631 6.6245370395 + 53 C -2.4557420740 -0.8829375023 4.5380818681 + 54 H -2.9596492827 -1.8437276305 4.5221216535 + 55 C -4.1249281175 0.4004756787 1.1655216406 + 56 C -3.6353302924 1.6229046114 0.6843711827 + 57 H -1.5667550440 1.6629973908 2.4414322262 + 58 C -4.5234891084 2.5509004307 0.1444384244 + 59 H -4.1442520184 3.5017916858 -0.2216525594 + 60 C -5.8845872809 2.2671234587 0.0644736389 + 61 H -6.5705578262 2.9985074190 -0.3548381451 + 62 C -6.3661310487 1.0371574340 0.5275291796 + 63 H -7.4256662542 0.8058548518 0.4619447035 + 64 C -5.4944582701 0.1113707308 1.0849708426 + 65 H -5.8630706203 -0.8369243514 1.4678940842 + 66 H -2.5707192368 1.8246188792 0.6894404950 + ---------------------------------------------------------------- + Nuclear Repulsion Energy = 3446.26455428 hartrees + There are 118 alpha and 117 beta electrons + Requested basis set is def2-SVPD + There are 393 shells and 913 basis functions + + Total QAlloc Memory Limit 170000 MB + Mega-Array Size 188 MB + MEM_STATIC part 192 MB + + Using C-PCM dielectric factor f(eps) = (eps-1)/eps = 0.987243 + Discretize the solute cavity surface with Lebedev spheres + Using 194 Lebedev grid points for each H atom + Using 194 Lebedev grid points for other atoms + Atomic van der Waals radii (UFF set) will be scaled by 1.10 + Using smooth SwiG surface discretization + Remove points where switching function is < 1.0e-08 + Keep 4608 surface tesserae and discard 8196 interior tesserae + Molecular Surface Area = 532.774 Angst**2 + + A cutoff of 1.0D-16 yielded 66530 shell pairs + There are 358784 function pairs ( 409471 Cartesian) + Smallest overlap matrix eigenvalue = 1.70E-06 + Guess from superposition of atomic densities + Warning: Energy on first SCF cycle will be non-variational + SAD guess density has 235.000000 electrons + + ----------------------------------------------------------------------- + General SCF calculation program by + Eric Jon Sundstrom, Paul Horn, Yuezhi Mao, Dmitri Zuev, Alec White, + David Stuck, Shaama M.S., Shane Yost, Joonho Lee, David Small, + Daniel Levine, Susi Lehtola, Hugh Burton, Evgeny Epifanovsky, + Bang C. Huynh + ----------------------------------------------------------------------- + Exchange: B97M-V Correlation: B97M-V + Using SG-3 standard quadrature grid + Nonlocal Correlation: VV10 with C = 0.0100 and b = 6.00 and scale = 1.00000 + Grid used for NLC: SG-1 standard quadrature + using 40 threads for integral computing + ------------------------------------------------------- + OpenMP Integral computing Module + Release: version 1.0, May 2013, Q-Chem Inc. Pittsburgh + ------------------------------------------------------- + C-PCM solvent model [f = (eps-1)/eps], solve by matrix inversion + A unrestricted SCF calculation will be + performed using DIIS + SCF converges when DIIS error is below 1.0e-08 + --------------------------------------- + Cycle Energy DIIS error + --------------------------------------- + 1 -1641.0290347638 1.03e-02 + 2 -1634.7843761788 1.27e-03 + 3 -1634.0613181571 1.83e-03 + 4 -1635.4711581448 3.81e-04 + 5 -1635.5247517298 1.76e-04 + 6 -1635.5367056813 7.94e-05 + 7 -1635.5392603182 3.24e-05 + 8 -1635.5396909643 1.11e-05 + 9 -1635.5397442115 4.57e-06 + 10 -1635.5397553829 3.01e-06 + 11 -1635.5397612249 1.20e-06 + 12 -1635.5397622936 7.29e-07 + 13 -1635.5397628627 3.09e-07 + 14 -1635.5397629836 2.36e-07 + 15 -1635.5397630408 9.17e-08 + 16 -1635.5397630488 4.32e-08 + 17 -1635.5397630500 1.81e-08 + 18 -1635.5397630502 7.29e-09 Convergence criterion met + --------------------------------------- + SCF time: CPU 25465.89s wall 1193.00s + = 0.758919214 + +************** Final PCM Free Energy Summary ************** + G_electrostatic = -0.00822432 hartree = -5.16083699 kcal/mol + G_cavitation = 0.00000000 hartree = 0.00000000 kcal/mol + G_dispersion = 0.00000000 hartree = 0.00000000 kcal/mol + G_repulsion = 0.00000000 hartree = 0.00000000 kcal/mol + -------------------------------------------------- + Non-electrostatic Free Energy = 0.00000000 hartree = 0.00000000 kcal/mol + Total = -0.00822432 hartree = -5.16083699 kcal/mol + -------------------------------------------------- + SCF Energy (H0 + V/2) = -1635.53976305 + Solute Internal Energy (H0) = -1635.53153873 + Total Free Energy (H0 + V/2 + non-elec) = -1635.53976305 hartree + = -1026316.69151108 kcal/mol +*********************************************************** + + SCF energy in the final basis set = -1635.5397630502 + Total energy in the final basis set = -1635.5397630502 + + -------------------------------------------------------------- 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Spin (a.u.) + -------------------------------------------------------- + 1 O -0.495426 0.000268 + 2 O -1.096590 0.014642 + 3 C -4.651302 0.001426 + 4 C 1.557182 -0.000809 + 5 C 1.381552 -0.000089 + 6 C 1.714709 0.001866 + 7 C 2.047289 0.004245 + 8 C -5.155258 -0.000422 + 9 C 0.260921 0.000990 + 10 H 0.137651 -0.000099 + 11 H 0.108343 0.000028 + 12 H -0.284699 -0.000355 + 13 H 0.063653 0.000005 + 14 H 0.068625 -0.000054 + 15 H 0.116352 0.000003 + 16 H 0.129736 -0.000166 + 17 H -0.235193 -0.003741 + 18 H 0.010049 -0.000058 + 19 C 1.474138 0.000157 + 20 H 0.115388 0.000001 + 21 H 0.072072 -0.000016 + 22 H 0.012793 0.000007 + 23 C 1.705384 -0.000814 + 24 H -0.249996 0.000359 + 25 H 0.162251 -0.000068 + 26 H 0.081701 -0.000371 + 27 C 1.238188 -0.000613 + 28 H -0.129436 0.000247 + 29 H -0.100849 -0.000624 + 30 H 0.113691 -0.000004 + 31 H 0.033994 -0.000190 + 32 H -0.158098 -0.000506 + 33 S -1.402607 0.224553 + 34 C -0.789694 0.383562 + 35 C 0.169611 0.002480 + 36 H -0.052802 0.033744 + 37 C -0.186324 0.018883 + 38 H 0.168359 -0.000906 + 39 C -0.068720 -0.006438 + 40 H 0.496168 0.000244 + 41 C -0.278766 0.017857 + 42 H 0.196040 -0.000543 + 43 C 0.363860 -0.054308 + 44 H -0.075384 0.045145 + 45 C -1.566818 -0.089707 + 46 C 0.490152 0.202521 + 47 C -0.391308 -0.094475 + 48 H 0.495360 0.005706 + 49 C -0.226317 0.153506 + 50 H 0.505168 -0.018583 + 51 C -0.388757 -0.066411 + 52 H 0.227424 0.003712 + 53 C 0.820051 0.096629 + 54 H 0.488605 0.003717 + 55 C -1.312113 -0.083691 + 56 C 0.523947 0.149583 + 57 H 0.252216 -0.014585 + 58 C -0.449003 -0.063227 + 59 H 0.292159 0.003913 + 60 C -0.154574 0.106560 + 61 H 0.530136 -0.012652 + 62 C -0.400102 -0.028382 + 63 H 0.276953 -0.001148 + 64 C 0.560732 0.069081 + 65 H 0.472377 0.014391 + 66 H 0.365153 -0.015976 + -------------------------------------------------------- + Sum of atomic charges = 0.000000 + Sum of spin charges = 1.000000 + + Building new vdw surfaces + Merz-Kollman RESP Net Atomic Charges + + Atom Charge (a.u.) + ---------------------------------------- + 1 O -0.438388 + 2 O -0.356904 + 3 C 0.874819 + 4 C -0.693138 + 5 C -0.638565 + 6 C -0.644113 + 7 C 0.395311 + 8 C 0.415456 + 9 C 0.240133 + 10 H 0.170403 + 11 H 0.170403 + 12 H 0.170403 + 13 H 0.157585 + 14 H 0.157585 + 15 H 0.157585 + 16 H 0.154679 + 17 H 0.180732 + 18 H 0.154679 + 19 C -0.558214 + 20 H 0.133792 + 21 H 0.133792 + 22 H 0.133792 + 23 C -0.552699 + 24 H 0.134683 + 25 H 0.134683 + 26 H 0.134683 + 27 C -0.458392 + 28 H -0.033229 + 29 H -0.033229 + 30 H 0.099444 + 31 H 0.099444 + 32 H 0.099444 + 33 S -0.336949 + 34 C 0.424800 + 35 C -0.395062 + 36 H 0.182240 + 37 C -0.114710 + 38 H 0.147156 + 39 C -0.190893 + 40 H 0.139216 + 41 C -0.047740 + 42 H 0.125753 + 43 C -0.448827 + 44 H 0.216054 + 45 C 0.089435 + 46 C -0.147875 + 47 C -0.148610 + 48 H 0.142601 + 49 C -0.173389 + 50 H 0.140878 + 51 C -0.120128 + 52 H 0.134787 + 53 C -0.159413 + 54 H 0.139386 + 55 C 0.455761 + 56 C -0.313370 + 57 H 0.115575 + 58 C -0.127728 + 59 H 0.148539 + 60 C -0.169163 + 61 H 0.142208 + 62 C -0.113462 + 63 H 0.145824 + 64 C -0.325295 + 65 H 0.180129 + 66 H 0.165615 + ---------------------------------------- + Sum of atomic charges = 0.000000 + + Related Dipole Moment = 2.0381 (X 1.6904 Y -0.9561 Z 0.6186) + + ----------------------------------------------------------------- + Cartesian Multipole Moments + ----------------------------------------------------------------- + Charge (ESU x 10^10) + 0.0000 + Dipole Moment (Debye) + X 1.6858 Y -0.9090 Z 0.6002 + Tot 2.0071 + Quadrupole Moments (Debye-Ang) + XX -190.5703 XY -3.2582 YY -185.3894 + XZ 12.3126 YZ -7.0716 ZZ -182.9046 + Octopole Moments (Debye-Ang^2) + XXX 958.4000 XXY 327.6180 XYY 329.9563 + YYY 952.9876 XXZ -433.1765 XYZ 2.7569 + YYZ -372.8059 XZZ 395.1172 YZZ 269.9143 + ZZZ -1094.1070 + Hexadecapole Moments (Debye-Ang^3) + XXXX -8333.9064 XXXY -243.7942 XXYY -3278.1288 + XYYY -151.0287 YYYY -10686.7498 XXXZ 1500.6375 + XXYZ 686.8212 XYYZ 550.5794 YYYZ 2252.7041 + XXZZ -3367.9578 XYZZ -42.6974 YYZZ -3322.9076 + XZZZ 1528.6240 YZZZ 2088.1881 ZZZZ -9326.2798 + ----------------------------------------------------------------- + Calculating MO derivatives via CPSCF + CPSCF will be done in 2 segments to save memory. + Computing fast CPCM-SWIG hessian. + Computing fast CPCM-SWIG hessian. + 1 0 99 0.251587 0.013107 + 2 0 99 0.048418 0.001982 + 3 0 99 0.004366 0.000332 + 4 0 99 0.000474 0.000060 + 5 35 64 0.000070 0.000016 + 6 84 15 0.000012 0.000004 + 7 96 3 0.000002 0.000001 + 8 99 0 0.000000 0.000000 Roots Converged + 1 0 102 0.618701 0.036403 + 2 0 102 0.083578 0.006111 + 3 0 102 0.010124 0.001624 + 4 0 102 0.001592 0.000361 + 5 0 102 0.000198 0.000048 + 6 70 29 0.000018 0.000005 Collapsing Subspace + + Q-Chem fatal error occurred in module libmdc/newfileman.C, line 376: + + FileMan error: End of file reached prematurely reading (1495536) bytes in file FILE_SET_TMP_A + Path: /tmp/scratch/78.0 + + + Please submit a crash report at q-chem.com/reporter + + diff --git a/tests/files/qchem/new_test_files/fileman_cpscf.qout.gz b/tests/files/qchem/new_test_files/fileman_cpscf.qout.gz deleted file mode 100644 index 0d05d38b3..000000000 Binary files a/tests/files/qchem/new_test_files/fileman_cpscf.qout.gz and /dev/null differ diff --git a/tests/files/qchem/new_test_files/gdm_neg_precon_error.qin b/tests/files/qchem/new_test_files/gdm_neg_precon_error.qin new file mode 100644 index 000000000..978a91cb8 --- /dev/null +++ b/tests/files/qchem/new_test_files/gdm_neg_precon_error.qin @@ -0,0 +1,173 @@ +$molecule +2 4 +Co 3.9649000000 2.0123000000 40.9150000000 +C 5.1562000000 -1.1009000000 41.1795000000 +H 5.4039000000 -1.8436000000 41.9527000000 +H 6.0838000000 -0.8168000000 40.6705000000 +N 4.6095000000 0.0865000000 41.7792000000 +C 4.5447000000 0.1908000000 43.0569000000 +H 4.8480000000 -0.6139000000 43.7260000000 +C 4.1436000000 1.4472000000 43.6236000000 +N 3.9167000000 2.4208000000 42.7114000000 +C 3.6254000000 3.6692000000 43.1371000000 +C 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+symmetry = false +sym_ignore = true +method = wb97mv +geom_opt_max_cycles = 200 +ecp = def2-ecp +scf_convergence = 6 +mem_total = 450000 +$end + +$geom_opt +maxiter = 200 +coordinates = redundant +max_displacement = 0.1 +optimization_restart = false +$end + diff --git a/tests/files/qchem/new_test_files/gdm_neg_precon_error.qin.gz b/tests/files/qchem/new_test_files/gdm_neg_precon_error.qin.gz deleted file mode 100644 index e62d5f8ce..000000000 Binary files a/tests/files/qchem/new_test_files/gdm_neg_precon_error.qin.gz and /dev/null differ diff --git a/tests/files/qchem/new_test_files/gdm_neg_precon_error.qout b/tests/files/qchem/new_test_files/gdm_neg_precon_error.qout new file mode 100644 index 000000000..fa5c9a15b --- /dev/null +++ b/tests/files/qchem/new_test_files/gdm_neg_precon_error.qout @@ -0,0 +1,1936 @@ + +Running Job 1 of 1 mol.qin +qchem mol.qin_90679.0 /tmp/scratch/ 0 +/global/common/software/m4119/qchem/exe/qcprog.exe_s mol.qin_90679.0 /tmp/scratch/ + Welcome to Q-Chem + A Quantum Leap Into The Future Of Chemistry + + + Q-Chem 6.0, Q-Chem, Inc., Pleasanton, CA (2022) + + License issued to: National Energy Research Scientific Computing Center (site) + + E. Epifanovsky, A. T. B. Gilbert, Xintian Feng, Joonho Lee, Yuezhi Mao, + N. Mardirossian, P. Pokhilko, A. White, M. Wormit, M. P. Coons, + A. L. Dempwolff, Zhengting Gan, D. Hait, P. R. Horn, L. D. Jacobson, + I. Kaliman, J. Kussmann, A. W. Lange, Ka Un Lao, D. S. Levine, Jie Liu, + S. C. McKenzie, A. F. Morrison, K. Nanda, F. Plasser, D. R. Rehn, + M. L. Vidal, Zhi-Qiang You, Ying Zhu, B. Alam, B. Albrecht, + A. Aldossary, E. Alguire, J. H. Andersen, V. Athavale, D. Barton, + K. Begam, A. Behn, N. Bellonzi, Y. A. Bernard, E. J. Berquist, + H. Burton, A. Carreras, K. Carter-Fenk, Romit Chakraborty, + Chandrima Chakravarty, Junhan Chen, A. D. Chien, K. D. Closser, + V. Cofer-Shabica, L. Cunha, S. Dasgupta, Jia Deng, M. de Wergifosse, + M. Diedenhofen, Hainam Do, S. Ehlert, Po-Tung Fang, S. Fatehi, + Qingguo Feng, T. Friedhoff, B. Ganoe, J. Gayvert, Qinghui Ge, + G. Gidofalvi, M. Goldey, J. Gomes, C. Gonzalez-Espinoza, S. Gulania, + A. Gunina, J. A. Gyamfi, M. W. D. Hanson-Heine, P. H. P. Harbach, + A. W. Hauser, M. F. Herbst, M. Hernandez Vera, M. Hodecker, + Z. C. Holden, S. Houck, Xunkun Huang, Kerwin Hui, B. C. Huynh, + K. Ikeda, M. Ivanov, Hyunjun Ji, Zuxin Jin, Hanjie Jiang, B. Kaduk, + S. Kaehler, R. Kang, K. Khistyaev, Jaehoon Kim, Yongbin Kim, + P. Klunzinger, Z. Koczor-Benda, Joong Hoon Koh, D. Kosenkov, + Saikiran Kotaru, L. Koulias, T. Kowalczyk, C. M. Krauter, K. Kue, + A. Kunitsa, T. Kus, A. Landau, K. V. Lawler, D. Lefrancois, S. Lehtola, + Rain Li, Shaozhi Li, Yi-Pei Li, Jiashu Liang, M. Liebenthal, + Hung-Hsuan Lin, You-Sheng Lin, Fenglai Liu, Kuan-Yu Liu, + M. Loipersberger, A. Luenser, C. Malbon, A. Manjanath, P. Manohar, + E. Mansoor, S. F. Manzer, Shan-Ping Mao, A. V. Marenich, T. Markovich, + S. Mason, F. Matz, S. A. Maurer, P. F. McLaughlin, M. F. S. J. Menger, + J.-M. Mewes, S. A. Mewes, P. Morgante, Mohammad Mostafanejad, + J. W. Mullinax, K. J. Oosterbaan, G. Paran, V. Parravicini, + Alexander C. Paul, Suranjan K. Paul, F. Pavosevic, Zheng Pei, S. Prager, + E. I. Proynov, E. Ramos, B. Rana, A. E. Rask, A. Rettig, R. M. Richard, + F. Rob, E. Rossomme, T. Scheele, M. Scheurer, M. Schneider, + P. E. Schneider, N. Sergueev, S. M. Sharada, Hengyuan Shen, + W. Skomorowski, D. W. Small, C. J. Stein, Yingli Su, Yu-Chuan Su, + E. J. Sundstrom, 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 6.0.1 for Intel X86 EM64T Linux + + Parts of Q-Chem use Armadillo 9.900.5 (Nocturnal Misbehaviour). + http://arma.sourceforge.net/ + + Q-Chem begins on Mon Apr 3 11:33:57 2023 + + Host: login23 +0 + + Scratch files written to /tmp/scratch// + Aug2322 |scratch|qcdevops|jenkins|workspace|build_RNUM -1 + Processing $rem in /global/common/software/m4119/qchem/config/preferences: + Processing $rem in /global/homes/s/sblau/.qchemrc: + + Checking the input file for inconsistencies... ...done. + Reading auxiliary files from /global/common/software/m4119/qchem/qcaux (QCAUX) + +-------------------------------------------------------------- +User input: +-------------------------------------------------------------- +$molecule +2 4 +Co 3.9649000000 2.0123000000 40.9150000000 +C 5.1562000000 -1.1009000000 41.1795000000 +H 5.4039000000 -1.8436000000 41.9527000000 +H 6.0838000000 -0.8168000000 40.6705000000 +N 4.6095000000 0.0865000000 41.7792000000 +C 4.5447000000 0.1908000000 43.0569000000 +H 4.8480000000 -0.6139000000 43.7260000000 +C 4.1436000000 1.4472000000 43.6236000000 +N 3.9167000000 2.4208000000 42.7114000000 +C 3.6254000000 3.6692000000 43.1371000000 +C 3.5522000000 3.9809000000 44.4917000000 +H 3.3254000000 4.9892000000 44.7989000000 +C 3.7790000000 2.9836000000 45.4289000000 +H 3.7290000000 3.2031000000 46.4829000000 +C 4.0778000000 1.7025000000 44.9894000000 +H 4.2712000000 0.9091000000 45.6935000000 +C 3.4200000000 4.6189000000 42.0745000000 +H 3.1325000000 5.6421000000 42.3193000000 +N 3.6025000000 4.2238000000 40.8694000000 +C 3.4469000000 5.1379000000 39.7714000000 +H 2.9852000000 6.0784000000 40.1036000000 +H 4.4465000000 5.3623000000 39.3836000000 +C 2.6269000000 4.5116000000 38.6753000000 +C 3.2082000000 4.1194000000 37.4743000000 +H 4.2626000000 4.2848000000 37.3081000000 +C 2.4468000000 3.5431000000 36.4830000000 +H 2.8838000000 3.2572000000 35.5395000000 +C 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44.0469000000 +C 0.9762000000 1.4711000000 45.3464000000 +H 0.8686000000 2.0456000000 46.2526000000 +$end + +$rem +job_type = opt +basis = def2-svpd +max_scf_cycles = 500 +gen_scfman = true +xc_grid = 3 +thresh = 14 +s2thresh = 16 +scf_algorithm = gdm +resp_charges = false +symmetry = false +sym_ignore = true +method = wb97mv +geom_opt_max_cycles = 200 +ecp = def2-ecp +scf_convergence = 6 +mem_total = 450000 +$end + +$geom_opt +maxiter = 200 +coordinates = redundant +max_displacement = 0.1 +optimization_restart = false +$end +-------------------------------------------------------------- + ---------------------------------------------------------------- + Standard Nuclear Orientation (Angstroms) + I Atom X Y Z + ---------------------------------------------------------------- + 1 Co 3.9649000000 2.0123000000 40.9150000000 + 2 C 5.1562000000 -1.1009000000 41.1795000000 + 3 H 5.4039000000 -1.8436000000 41.9527000000 + 4 H 6.0838000000 -0.8168000000 40.6705000000 + 5 N 4.6095000000 0.0865000000 41.7792000000 + 6 C 4.5447000000 0.1908000000 43.0569000000 + 7 H 4.8480000000 -0.6139000000 43.7260000000 + 8 C 4.1436000000 1.4472000000 43.6236000000 + 9 N 3.9167000000 2.4208000000 42.7114000000 + 10 C 3.6254000000 3.6692000000 43.1371000000 + 11 C 3.5522000000 3.9809000000 44.4917000000 + 12 H 3.3254000000 4.9892000000 44.7989000000 + 13 C 3.7790000000 2.9836000000 45.4289000000 + 14 H 3.7290000000 3.2031000000 46.4829000000 + 15 C 4.0778000000 1.7025000000 44.9894000000 + 16 H 4.2712000000 0.9091000000 45.6935000000 + 17 C 3.4200000000 4.6189000000 42.0745000000 + 18 H 3.1325000000 5.6421000000 42.3193000000 + 19 N 3.6025000000 4.2238000000 40.8694000000 + 20 C 3.4469000000 5.1379000000 39.7714000000 + 21 H 2.9852000000 6.0784000000 40.1036000000 + 22 H 4.4465000000 5.3623000000 39.3836000000 + 23 C 2.6269000000 4.5116000000 38.6753000000 + 24 C 3.2082000000 4.1194000000 37.4743000000 + 25 H 4.2626000000 4.2848000000 37.3081000000 + 26 C 2.4468000000 3.5431000000 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110 H 8.5710000000 -0.6051000000 48.3121000000 + 111 C 6.6176000000 -1.5064000000 48.1906000000 + 112 H 6.1197000000 -0.5351000000 48.1606000000 + 113 H 6.0793000000 -2.1852000000 47.5244000000 + 114 C 6.5586000000 -2.0718000000 49.6204000000 + 115 H 7.0377000000 -3.0526000000 49.6273000000 + 116 H 7.1087000000 -1.4080000000 50.2875000000 + 117 C 5.1374000000 -2.1873000000 50.0584000000 + 118 H 4.6881000000 -1.2977000000 50.4805000000 + 119 C 4.4026000000 -3.2921000000 49.8981000000 + 120 H 4.8626000000 -4.1724000000 49.4667000000 + 121 C 2.9505000000 -3.4125000000 50.2047000000 + 122 H 2.6344000000 -2.6368000000 50.9029000000 + 123 H 2.7600000000 -4.3886000000 50.6528000000 + 124 C 2.1197000000 -3.2977000000 48.9128000000 + 125 H 2.5554000000 -3.9469000000 48.1502000000 + 126 H 1.1036000000 -3.6420000000 49.1039000000 + 127 C 2.0863000000 -1.8533000000 48.4196000000 + 128 H 3.0940000000 -1.4326000000 48.4486000000 + 129 H 1.4533000000 -1.2540000000 49.0757000000 + 130 C 1.5576000000 -1.7341000000 46.9930000000 + 131 H 2.2701000000 -2.1939000000 46.2969000000 + 132 H 0.5886000000 -2.2400000000 46.8915000000 + 133 O 1.4036000000 -0.3514000000 46.7186000000 + 134 C 1.2250000000 0.0972000000 45.4628000000 + 135 C 1.2903000000 -0.6719000000 44.3006000000 + 136 H 1.4132000000 -1.7420000000 44.3491000000 + 137 C 1.1750000000 -0.0601000000 43.0658000000 + 138 H 1.2154000000 -0.6560000000 42.1684000000 + 139 C 0.9941000000 1.3112000000 42.9498000000 + 140 C 0.8626000000 2.0649000000 44.1105000000 + 141 H 0.6610000000 3.1247000000 44.0469000000 + 142 C 0.9762000000 1.4711000000 45.3464000000 + 143 H 0.8686000000 2.0456000000 46.2526000000 + ---------------------------------------------------------------- + Nuclear Repulsion Energy = 13828.20107576 hartrees + There are 272 alpha and 269 beta electrons + Requested basis set is def2-SVPD + There are 872 shells and 2046 basis functions + + Total QAlloc Memory Limit 450000 MB + Mega-Array Size 188 MB + MEM_STATIC part 192 MB + + ----------------------------------------------------------------------- + STARTING GEOMETRY OPTIMIZER USING LIBOPT3 + by Peter F. McLaughlin, Yu Zhang, Evgeny Epifanovsky + ----------------------------------------------------------------------- + + Initial Energy and Gradient Calculation + -- Checking Topology for Ill-Behaving Coordinates -- + + ------------------------------------------- + Coordinate | Removed | Additions + ------------------------------------------- + Bonds 0 0 + Angles 1 0 + Torsions 4 4 + Co-Linear Type5s 0 4 + Co-Linear Type6s 0 4 + ------------------------------------------- + + ** Ill-Behaving Topology Definitions (No action needed.) ** + + Ill-Defined Angles Removed: + 9 1 80 + + Ill-Defined Torsions Removed: + 8 9 1 80, 9 1 80 79, 9 1 80 81, 10 9 1 80 + + Done Checking Topology + ---------------------------------------------------------------- + Standard Nuclear Orientation (Angstroms) + I Atom X Y Z + ---------------------------------------------------------------- + 1 Co 3.9649000000 2.0123000000 40.9150000000 + 2 C 5.1562000000 -1.1009000000 41.1795000000 + 3 H 5.4039000000 -1.8436000000 41.9527000000 + 4 H 6.0838000000 -0.8168000000 40.6705000000 + 5 N 4.6095000000 0.0865000000 41.7792000000 + 6 C 4.5447000000 0.1908000000 43.0569000000 + 7 H 4.8480000000 -0.6139000000 43.7260000000 + 8 C 4.1436000000 1.4472000000 43.6236000000 + 9 N 3.9167000000 2.4208000000 42.7114000000 + 10 C 3.6254000000 3.6692000000 43.1371000000 + 11 C 3.5522000000 3.9809000000 44.4917000000 + 12 H 3.3254000000 4.9892000000 44.7989000000 + 13 C 3.7790000000 2.9836000000 45.4289000000 + 14 H 3.7290000000 3.2031000000 46.4829000000 + 15 C 4.0778000000 1.7025000000 44.9894000000 + 16 H 4.2712000000 0.9091000000 45.6935000000 + 17 C 3.4200000000 4.6189000000 42.0745000000 + 18 H 3.1325000000 5.6421000000 42.3193000000 + 19 N 3.6025000000 4.2238000000 40.8694000000 + 20 C 3.4469000000 5.1379000000 39.7714000000 + 21 H 2.9852000000 6.0784000000 40.1036000000 + 22 H 4.4465000000 5.3623000000 39.3836000000 + 23 C 2.6269000000 4.5116000000 38.6753000000 + 24 C 3.2082000000 4.1194000000 37.4743000000 + 25 H 4.2626000000 4.2848000000 37.3081000000 + 26 C 2.4468000000 3.5431000000 36.4830000000 + 27 H 2.8838000000 3.2572000000 35.5395000000 + 28 C 1.0746000000 3.3349000000 36.6690000000 + 29 C 0.4874000000 3.7376000000 37.8679000000 + 30 H -0.5711000000 3.6221000000 38.0358000000 + 31 C 1.2633000000 4.3219000000 38.8508000000 + 32 H 0.7908000000 4.6533000000 39.7637000000 + 33 O 0.4295000000 2.7371000000 35.6493000000 + 34 C -0.9720000000 2.5275000000 35.7277000000 + 35 H -1.4914000000 3.4871000000 35.8456000000 + 36 H -1.2041000000 1.8917000000 36.5943000000 + 37 C -1.4248000000 1.8415000000 34.4420000000 + 38 H -1.2006000000 2.4925000000 33.5971000000 + 39 H -2.5051000000 1.7037000000 34.4931000000 + 40 C -0.7260000000 0.4978000000 34.2495000000 + 41 H 0.3445000000 0.6856000000 34.1572000000 + 42 H -0.8940000000 -0.1247000000 35.1330000000 + 43 C -1.2338000000 -0.2379000000 33.0139000000 + 44 H -2.3137000000 -0.3986000000 33.1000000000 + 45 H -1.0958000000 0.3930000000 32.1281000000 + 46 C -0.5816000000 -1.5512000000 32.7513000000 + 47 H -1.0431000000 -2.1502000000 31.9780000000 + 48 C 0.5006000000 -2.0194000000 33.3778000000 + 49 H 0.9760000000 -1.4185000000 34.1400000000 + 50 C 1.1083000000 -3.3578000000 33.1395000000 + 51 H 2.1871000000 -3.3017000000 33.2946000000 + 52 H 0.9228000000 -3.6778000000 32.1133000000 + 53 C 0.5123000000 -4.4282000000 34.0797000000 + 54 H -0.4871000000 -4.6793000000 33.7223000000 + 55 H 1.1259000000 -5.3282000000 34.0185000000 + 56 C 0.3882000000 -3.9836000000 35.5352000000 + 57 H -0.2941000000 -3.1341000000 35.6035000000 + 58 H -0.0441000000 -4.7994000000 36.1160000000 + 59 C 1.7159000000 -3.5985000000 36.1823000000 + 60 H 2.4350000000 -4.4241000000 36.1079000000 + 61 H 2.1441000000 -2.7125000000 35.6980000000 + 62 O 1.4439000000 -3.3195000000 37.5470000000 + 63 C 2.4072000000 -2.8279000000 38.3478000000 + 64 C 2.0577000000 -2.6747000000 39.6961000000 + 65 H 1.0837000000 -3.0114000000 40.0107000000 + 66 C 2.9526000000 -2.1374000000 40.5902000000 + 67 H 2.6911000000 -2.0586000000 41.6342000000 + 68 C 4.2121000000 -1.7106000000 40.1749000000 + 69 C 4.5721000000 -1.9001000000 38.8501000000 + 70 H 5.5607000000 -1.6202000000 38.5145000000 + 71 C 3.6902000000 -2.4616000000 37.9421000000 + 72 H 4.0144000000 -2.6211000000 36.9260000000 + 73 C 0.8867000000 1.9441000000 41.5862000000 + 74 H -0.0550000000 1.6310000000 41.1138000000 + 75 H 0.8585000000 3.0334000000 41.7051000000 + 76 N 1.9928000000 1.6194000000 40.7177000000 + 77 C 1.7334000000 1.1048000000 39.5523000000 + 78 H 0.7239000000 0.8417000000 39.2508000000 + 79 C 2.8286000000 0.9876000000 38.6494000000 + 80 N 3.9677000000 1.4835000000 39.1902000000 + 81 C 5.1082000000 1.5330000000 38.4646000000 + 82 C 5.1351000000 1.0868000000 37.1487000000 + 83 H 6.0481000000 1.1419000000 36.5774000000 + 84 C 3.9706000000 0.5779000000 36.5841000000 + 85 H 3.9746000000 0.2343000000 35.5622000000 + 86 C 2.8060000000 0.5240000000 37.3370000000 + 87 H 1.8855000000 0.1457000000 36.9205000000 + 88 C 6.1833000000 2.1011000000 39.2202000000 + 89 H 7.1654000000 2.2504000000 38.7760000000 + 90 N 5.9143000000 2.4541000000 40.4365000000 + 91 C 6.9372000000 3.1023000000 41.2218000000 + 92 H 6.6073000000 4.1268000000 41.4256000000 + 93 H 7.8774000000 3.1473000000 40.6544000000 + 94 C 7.1682000000 2.3924000000 42.5322000000 + 95 C 6.9081000000 3.0101000000 43.7507000000 + 96 H 6.5694000000 4.0355000000 43.7718000000 + 97 C 7.0880000000 2.3329000000 44.9362000000 + 98 H 6.8977000000 2.8102000000 45.8837000000 + 99 C 7.5347000000 1.0062000000 44.9383000000 + 100 C 7.8498000000 0.4027000000 43.7208000000 + 101 H 8.2516000000 -0.5973000000 43.6854000000 + 102 C 7.6671000000 1.0970000000 42.5397000000 + 103 H 7.9310000000 0.6206000000 41.6073000000 + 104 O 7.6074000000 0.4080000000 46.1444000000 + 105 C 8.1173000000 -0.9125000000 46.2429000000 + 106 H 9.1550000000 -0.9372000000 45.8881000000 + 107 H 7.5156000000 -1.5941000000 45.6248000000 + 108 C 8.0553000000 -1.3474000000 47.7035000000 + 109 H 8.5845000000 -2.2961000000 47.7970000000 + 110 H 8.5710000000 -0.6051000000 48.3121000000 + 111 C 6.6176000000 -1.5064000000 48.1906000000 + 112 H 6.1197000000 -0.5351000000 48.1606000000 + 113 H 6.0793000000 -2.1852000000 47.5244000000 + 114 C 6.5586000000 -2.0718000000 49.6204000000 + 115 H 7.0377000000 -3.0526000000 49.6273000000 + 116 H 7.1087000000 -1.4080000000 50.2875000000 + 117 C 5.1374000000 -2.1873000000 50.0584000000 + 118 H 4.6881000000 -1.2977000000 50.4805000000 + 119 C 4.4026000000 -3.2921000000 49.8981000000 + 120 H 4.8626000000 -4.1724000000 49.4667000000 + 121 C 2.9505000000 -3.4125000000 50.2047000000 + 122 H 2.6344000000 -2.6368000000 50.9029000000 + 123 H 2.7600000000 -4.3886000000 50.6528000000 + 124 C 2.1197000000 -3.2977000000 48.9128000000 + 125 H 2.5554000000 -3.9469000000 48.1502000000 + 126 H 1.1036000000 -3.6420000000 49.1039000000 + 127 C 2.0863000000 -1.8533000000 48.4196000000 + 128 H 3.0940000000 -1.4326000000 48.4486000000 + 129 H 1.4533000000 -1.2540000000 49.0757000000 + 130 C 1.5576000000 -1.7341000000 46.9930000000 + 131 H 2.2701000000 -2.1939000000 46.2969000000 + 132 H 0.5886000000 -2.2400000000 46.8915000000 + 133 O 1.4036000000 -0.3514000000 46.7186000000 + 134 C 1.2250000000 0.0972000000 45.4628000000 + 135 C 1.2903000000 -0.6719000000 44.3006000000 + 136 H 1.4132000000 -1.7420000000 44.3491000000 + 137 C 1.1750000000 -0.0601000000 43.0658000000 + 138 H 1.2154000000 -0.6560000000 42.1684000000 + 139 C 0.9941000000 1.3112000000 42.9498000000 + 140 C 0.8626000000 2.0649000000 44.1105000000 + 141 H 0.6610000000 3.1247000000 44.0469000000 + 142 C 0.9762000000 1.4711000000 45.3464000000 + 143 H 0.8686000000 2.0456000000 46.2526000000 + ---------------------------------------------------------------- + Nuclear Repulsion Energy = 13828.20107576 hartrees + There are 272 alpha and 269 beta electrons + Requested basis set is def2-SVPD + There are 872 shells and 2046 basis functions + A cutoff of 1.0D-16 yielded 244926 shell pairs + There are 1333752 function pairs ( 1539617 Cartesian) + Smallest overlap matrix eigenvalue = 9.55E-07 + Linear dependence detected in AO basis + Number of orthogonalized atomic orbitals = 2045 + Maximum deviation from orthogonality = 1.265E-10 + + Scale SEOQF with 1.000000e-02/1.000000e-02/1.000000e-03 + + Standard Electronic Orientation quadrupole field applied + Nucleus-field energy = -0.0000009420 hartrees + Guess from superposition of atomic densities + Warning: Energy on first SCF cycle will be non-variational + SAD guess density has 543.000000 electrons + + ----------------------------------------------------------------------- + General SCF calculation program by + Eric Jon Sundstrom, Paul Horn, Yuezhi Mao, Dmitri Zuev, Alec White, + David Stuck, Shaama M.S., Shane Yost, Joonho Lee, David Small, + Daniel Levine, Susi Lehtola, Hugh Burton, Evgeny Epifanovsky, + Bang C. Huynh + ----------------------------------------------------------------------- + Exchange: 0.1500 Hartree-Fock + 1.0000 wB97M-V + LR-HF + Correlation: 1.0000 wB97M-V + Using SG-3 standard quadrature grid + Nonlocal Correlation: VV10 with C = 0.0100 and b = 6.00 and scale = 1.00000 + Grid used for NLC: SG-1 standard quadrature + using 128 threads for integral computing + ------------------------------------------------------- + OpenMP Integral computing Module + Release: version 1.0, May 2013, Q-Chem Inc. Pittsburgh + ------------------------------------------------------- + A unrestricted SCF calculation will be + performed using Roothaan-Hall, GDM + SCF converges when RMS gradient is below 1.0e-06 + --------------------------------------- + Cycle Energy DIIS error + --------------------------------------- + 1 -4440.7997320748 7.43e-03 Roothaan Step + --------------------------------------- + Cycle Energy RMS Gradient + --------------------------------------- + 1 -4411.7037773801 2.00e-01 Descent step + 2 -4412.3368023021 2.35e-01 Descent step + 3 -4412.6071996904 6.29e-02 Descent step + 4 -4412.7602121579 2.34e-01 Descent step + 5 -4412.7317363203 5.02e-01 Line search: overstep + 6 -4412.8213041294 3.90e-02 Descent step + 7 -4412.8758238423 4.46e-01 Descent step + 8 -4412.7853566681 6.57e-01 Line search: overstep + 9 -4412.9247805260 8.92e-02 Dog-leg BFGS step + 10 -4412.9845663167 1.13e-01 Dog-leg BFGS step + 11 -4413.0118392123 1.89e-02 Normal BFGS step + 12 -4413.0157530247 1.14e-02 Normal BFGS step + 13 -4413.0174626774 6.15e-03 Normal BFGS step + 14 -4413.0179838742 3.47e-03 Normal BFGS step + 15 -4413.0182275010 2.27e-03 Normal BFGS step + 16 -4413.0183265116 1.46e-03 Normal BFGS step + 17 -4413.0183745276 1.07e-03 Normal BFGS step + 18 -4413.0183998335 5.50e-04 Normal BFGS step + 19 -4413.0184107250 4.89e-04 Normal BFGS step + 20 -4413.0184169588 5.05e-04 Normal BFGS step + 21 -4413.0184219482 4.93e-04 Normal BFGS step + 22 -4413.0184260232 4.93e-04 Normal BFGS step + 23 -4413.0184300260 4.70e-04 Normal BFGS step + 24 -4413.0184371416 4.64e-04 Normal BFGS step + 25 -4413.0184472386 4.97e-04 Normal BFGS step + 26 -4413.0184587913 5.96e-04 Normal BFGS step + 27 -4413.0184697219 4.55e-04 Normal BFGS step + 28 -4413.0184767860 5.19e-04 Normal BFGS step + 29 -4413.0184811519 5.18e-04 Normal BFGS step + 30 -4413.0184857183 5.65e-04 Normal BFGS step + 31 -4413.0184925062 5.64e-04 Normal BFGS step + 32 -4413.0184990551 5.48e-04 Normal BFGS step + 33 -4413.0185048120 3.89e-04 Normal BFGS step + 34 -4413.0185085666 2.29e-04 Normal BFGS step + 35 -4413.0185111574 1.77e-04 Normal BFGS step + 36 -4413.0185128300 1.53e-04 Normal BFGS step + 37 -4413.0185138902 1.09e-04 Normal BFGS step + 38 -4413.0185144924 9.10e-05 Normal BFGS step + 39 -4413.0185147714 6.75e-05 Normal BFGS step + 40 -4413.0185148920 5.11e-05 Normal BFGS step + 41 -4413.0185149455 3.43e-05 Normal BFGS step + 42 -4413.0185149727 1.82e-05 Normal BFGS step + 43 -4413.0185149842 6.35e-06 Normal BFGS step + 44 -4413.0185149870 5.94e-06 Normal BFGS step + 45 -4413.0185149874 3.78e-06 Normal BFGS step + 46 -4413.0185149878 2.59e-06 Normal BFGS step + 47 -4413.0185149880 1.30e-06 Normal BFGS step + 48 -4413.0185149879 1.04e-06 Normal BFGS step + 49 -4413.0185149881 8.86e-07 Convergence criterion met + --------------------------------------- + SCF time: CPU 1151815.98s wall 27852.00s + = 3.768671364 + SCF energy in the final basis set = -4413.0185149881 + Total energy in the 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Spin (a.u.) + -------------------------------------------------------- + 1 Co -0.910869 2.967319 + 2 C 2.368998 -0.004067 + 3 H 0.010886 0.000748 + 4 H 0.153234 0.000614 + 5 N -0.864699 0.008206 + 6 C 0.032326 -0.000792 + 7 H -0.097164 0.006134 + 8 C -0.223472 -0.012824 + 9 N -0.260821 0.008590 + 10 C 0.890306 -0.005451 + 11 C 0.305208 0.001500 + 12 H -0.457917 0.000821 + 13 C 0.494124 -0.004249 + 14 H 0.279583 -0.000226 + 15 C 1.198148 0.004915 + 16 H -1.060115 0.000904 + 17 C -0.547101 -0.025515 + 18 H 0.009017 0.005573 + 19 N -0.433239 0.029174 + 20 C 2.044518 -0.004365 + 21 H 0.072193 0.001030 + 22 H 0.201890 0.001586 + 23 C -1.669254 0.001215 + 24 C 0.055145 -0.000088 + 25 H 0.034913 0.000076 + 26 C 0.049934 0.000322 + 27 H -0.081858 -0.000584 + 28 C -0.242758 -0.000213 + 29 C 0.381906 0.000438 + 30 H 0.860834 -0.000295 + 31 C -0.432224 0.000762 + 32 H -0.278311 0.000309 + 33 O -0.996004 -0.000170 + 34 C 0.655385 0.000023 + 35 H -0.141021 -0.000002 + 36 H 0.259195 0.000019 + 37 C 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----------------------------------------------------------------- + Cartesian Multipole Moments + ----------------------------------------------------------------- + Charge (ESU x 10^10) + 9.6064 + Dipole Moment (Debye) + X 34.6321 Y 10.9846 Z 393.3090 + Tot 394.9836 + Quadrupole Moments (Debye-Ang) + XX -229.3813 XY 37.8551 YY -337.6179 + XZ 1457.3304 YZ 453.1959 ZZ 15857.5508 + Octopole Moments (Debye-Ang^2) + XXX -2971.5007 XXY -26.2866 XYY -1110.1998 + YYY -343.4418 XXZ -9359.1547 XYZ 1516.6579 + YYZ -13853.9755 XZZ 60381.3083 YZZ 18360.5041 + ZZZ 628861.3269 + Hexadecapole Moments (Debye-Ang^3) + XXXX -35990.1295 XXXY -2077.6330 XXYY -8939.0486 + XYYY -1606.3624 YYYY -15510.9735 XXXZ -129094.3386 + XXYZ -1392.8259 XYYZ -47943.2497 YYYZ -12256.1063 + XXZZ -395309.6600 XYZZ 59610.3513 YYZZ -579200.1139 + XZZZ 2458037.6679 YZZZ 731224.2091 ZZZZ ************ + ----------------------------------------------------------------- + Calculating analytic gradient of the SCF energy + Gradient 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33.5433923774 + 39 H -2.4640210441 1.7813609576 34.4073196350 + 40 C -0.6699846482 0.5783312123 34.2167175626 + 41 H 0.4085125076 0.7644713765 34.1572853655 + 42 H -0.8634942701 -0.0414018182 35.1041936648 + 43 C -1.1263348610 -0.1760504744 32.9720168928 + 44 H -2.2124313119 -0.3392070039 33.0172979531 + 45 H -0.9584171075 0.4543371119 32.0858257196 + 46 C -0.4592780452 -1.5008176996 32.7462574748 + 47 H -0.8892264797 -2.1132983576 31.9532992734 + 48 C 0.5926072660 -1.9778588343 33.4164224165 + 49 H 1.0362922508 -1.3685349774 34.2036850597 + 50 C 1.2024118460 -3.3325495175 33.2040616930 + 51 H 2.2811623371 -3.2829241700 33.3979228645 + 52 H 1.0610507921 -3.6439018112 32.1638092135 + 53 C 0.5708242294 -4.4131847044 34.1122145169 + 54 H -0.4177555871 -4.6620010419 33.7120746543 + 55 H 1.1852517538 -5.3202994227 34.0648519481 + 56 C 0.3889346606 -3.9910715896 35.5694780872 + 57 H -0.2958831528 -3.1369178053 35.6264389797 + 58 H -0.0678857370 -4.8129885486 36.1313912550 + 59 C 1.6907398301 -3.6204819088 36.2622942539 + 60 H 2.4145292929 -4.4474776987 36.2044063554 + 61 H 2.1402797232 -2.7283675949 35.8008763595 + 62 O 1.3812104866 -3.3468853011 37.6240052592 + 63 C 2.3403040787 -2.8703785422 38.4344796864 + 64 C 1.9813594820 -2.6914309724 39.7818004510 + 65 H 0.9895665529 -3.0030782651 40.0964996625 + 66 C 2.8936296569 -2.1574113512 40.6760630661 + 67 H 2.6248499272 -2.0547315408 41.7241994203 + 68 C 4.1722424830 -1.7613696858 40.2582428334 + 69 C 4.5314951969 -1.9831278095 38.9324953009 + 70 H 5.5341450667 -1.7282326539 38.5952016708 + 71 C 3.6347221316 -2.5434697930 38.0208908893 + 72 H 3.9554363078 -2.7283623827 37.0001869988 + 73 C 0.7800317329 1.8903075782 41.5569467320 + 74 H -0.1434138168 1.5637612335 41.0541023703 + 75 H 0.7291497044 2.9821932671 41.6663173009 + 76 N 1.9279088754 1.5782535099 40.7202422697 + 77 C 1.6857549961 1.0632644720 39.5763045446 + 78 H 0.6697873816 0.7962046018 39.2774249562 + 79 C 2.7922322599 0.9220980040 38.6398545127 + 80 N 3.9298125903 1.4098984003 39.1478785337 + 81 C 5.0573226794 1.4568937206 38.4336606247 + 82 C 5.0835464090 0.9960838043 37.1167065022 + 83 H 5.9991291067 1.0464904488 36.5345784983 + 84 C 3.9085082397 0.4823608924 36.5700840194 + 85 H 3.8999676412 0.1242285181 35.5449793833 + 86 C 2.7429945168 0.4398383215 37.3357592583 + 87 H 1.8098505872 0.0589654178 36.9303175999 + 88 C 6.1469172415 2.0507711140 39.1987250557 + 89 H 7.1298801614 2.1985446559 38.7424754330 + 90 N 5.9050093068 2.4175315686 40.4002226767 + 91 C 6.9736795422 3.0764659274 41.1390346609 + 92 H 6.6630698364 4.1119021885 41.3316924304 + 93 H 7.8903164359 3.1028727268 40.5305282523 + 94 C 7.2450326692 2.3899501155 42.4570781966 + 95 C 7.0399347927 3.0470758543 43.6750013113 + 96 H 6.7219083914 4.0874218043 43.6805586863 + 97 C 7.2387614847 2.3922542330 44.8797223331 + 98 H 7.0840632418 2.8973151234 45.8288284917 + 99 C 7.6475771701 1.0506510063 44.8963512257 + 100 C 7.9201263903 0.4008095938 43.6855826125 + 101 H 8.2942709841 -0.6180625746 43.6701546529 + 102 C 7.7195270622 1.0780811667 42.4838528142 + 103 H 7.9419737333 0.5665814439 41.5493111045 + 104 O 7.7267286547 0.4670695921 46.1051452263 + 105 C 8.2135946554 -0.8668289930 46.1920375278 + 106 H 9.2482455743 -0.9032503524 45.8216001815 + 107 H 7.5946513333 -1.5333796770 45.5697761924 + 108 C 8.1363396780 -1.3093896630 47.6446653857 + 109 H 8.6529370885 -2.2720172869 47.7293330051 + 110 H 8.6723324707 -0.5796979113 48.2614296619 + 111 C 6.6945571345 -1.4530122347 48.1341226098 + 112 H 6.2051159992 -0.4708723822 48.1106504408 + 113 H 6.1469938932 -2.1200599844 47.4544168888 + 114 C 6.6028965668 -2.0338856603 49.5563858123 + 115 H 7.0736351809 -3.0240895234 49.5572333398 + 116 H 7.1634716842 -1.3829219218 50.2366843676 + 117 C 5.1771107043 -2.1541312856 50.0115588059 + 118 H 4.7224940733 -1.2666999940 50.4543325392 + 119 C 4.4410968488 -3.2571483674 49.8487074499 + 120 H 4.9168437734 -4.1318851105 49.4006280543 + 121 C 2.9835805957 -3.4103033106 50.1636219047 + 122 H 2.6594881184 -2.6485525570 50.8818172410 + 123 H 2.8173136378 -4.3975392708 50.6086257476 + 124 C 2.1241235154 -3.3007111749 48.8872661444 + 125 H 2.5662669945 -3.9383155429 48.1098174046 + 126 H 1.1152333355 -3.6766233048 49.0909533618 + 127 C 2.0318193793 -1.8566112405 48.3983974033 + 128 H 3.0273881073 -1.3970956849 48.4124225375 + 129 H 1.3873367390 -1.2807594705 49.0722411030 + 130 C 1.4815518421 -1.7414087433 46.9854003459 + 131 H 2.2056378456 -2.1684633149 46.2755026566 + 132 H 0.5268507288 -2.2775156395 46.8771729709 + 133 O 1.2782133985 -0.3577026039 46.7229532075 + 134 C 1.0893775775 0.0803997089 45.4675738388 + 135 C 1.2001691704 -0.7094156198 44.3168032501 + 136 H 1.3618126686 -1.7807951396 44.3870715482 + 137 C 1.0860190421 -0.1083133885 43.0632034253 + 138 H 1.1668684623 -0.7180223275 42.1680371807 + 139 C 0.8671007689 1.2623735109 42.9271555617 + 140 C 0.6847922181 2.0245000429 44.0847801369 + 141 H 0.4528732438 3.0846378604 44.0049951860 + 142 C 0.7921718933 1.4454119016 45.3383414554 + 143 H 0.6527451217 2.0279246364 46.2448368929 + ---------------------------------------------------------------- + Nuclear Repulsion Energy = 13747.92976385 hartrees + There are 272 alpha and 269 beta electrons + Nucleus-field energy =-9.4192353652e-07 hartrees + Requested basis set is def2-SVPD + There are 872 shells and 2046 basis functions + A cutoff of 1.0D-16 yielded 244660 shell pairs + There are 1332806 function pairs ( 1538610 Cartesian) + Smallest overlap matrix eigenvalue = 1.13E-06 + Guess MOs from SCF MO coefficient file + + ----------------------------------------------------------------------- + General SCF calculation program by + Eric Jon Sundstrom, Paul Horn, Yuezhi Mao, Dmitri Zuev, Alec White, + David Stuck, Shaama M.S., Shane Yost, Joonho Lee, David Small, + Daniel Levine, Susi Lehtola, Hugh Burton, Evgeny Epifanovsky, + Bang C. Huynh + ----------------------------------------------------------------------- + Exchange: 0.1500 Hartree-Fock + 1.0000 wB97M-V + LR-HF + Correlation: 1.0000 wB97M-V + Using SG-3 standard quadrature grid + Nonlocal Correlation: VV10 with C = 0.0100 and b = 6.00 and scale = 1.00000 + Grid used for NLC: SG-1 standard quadrature + Size of previous SCF MO coefficient file: 8376324 (expected); 8372230 (actual). + + Q-Chem warning in module libgscf/gen_scfman/uhf.C, line 793: + + Inconsistent size for SCF MO coefficient file. Please check basis and PURECART setting. + + A unrestricted SCF calculation will be + performed using GDM + SCF converges when RMS gradient is below 1.0e-06 + --------------------------------------- + Cycle Energy RMS Gradient + --------------------------------------- + GDM::project_to_ew_ss: zero or negative preconditioner scaling factor +gen_scfman_exception: GDM:: Zero or negative preconditioner scaling factor + + Q-Chem fatal error occurred in module libgscf/gen_scfman/gen_scfman_main.C, line 246: + + Error in gen_scfman + + + Please submit a crash report at q-chem.com/reporter + + diff --git a/tests/files/qchem/new_test_files/gdm_neg_precon_error.qout.gz b/tests/files/qchem/new_test_files/gdm_neg_precon_error.qout.gz deleted file mode 100644 index 687ed5bcd..000000000 Binary files a/tests/files/qchem/new_test_files/gdm_neg_precon_error.qout.gz and /dev/null differ diff --git a/tests/qchem/test_handlers.py b/tests/qchem/test_handlers.py index cbf7a5e53..ae0b86b87 100644 --- a/tests/qchem/test_handlers.py +++ b/tests/qchem/test_handlers.py @@ -37,8 +37,8 @@ def setUp(self): def _check_equivalent_inputs(self, input1, input2): QCinput1 = QCInput.from_file(input1) QCinput2 = QCInput.from_file(input2) - sections1 = QCInput.find_sections(QCinput1.get_string()) - sections2 = QCInput.find_sections(QCinput2.get_string()) + sections1 = QCInput.find_sections(QCinput1.get_str()) + sections2 = QCInput.find_sections(QCinput2.get_str()) assert sections1 == sections2 for key in sections1: assert QCinput1.as_dict().get(key) == QCinput2.as_dict().get(key) @@ -285,8 +285,8 @@ def test_OOS_read_hess(self): self._check_equivalent_inputs(f"{TEST_DIR}/OOS_read_hess_next.qin", "mol.qin") def test_gdm_neg_precon_error(self): - shutil.copyfile(f"{TEST_DIR}/gdm_neg_precon_error.qin.gz", f"{SCR_DIR}/mol.qin.gz") - shutil.copyfile(f"{TEST_DIR}/gdm_neg_precon_error.qout.gz", f"{SCR_DIR}/mol.qout.gz") + shutil.copyfile(f"{TEST_DIR}/gdm_neg_precon_error.qin", f"{SCR_DIR}/mol.qin") + shutil.copyfile(f"{TEST_DIR}/gdm_neg_precon_error.qout", f"{SCR_DIR}/mol.qout") handler = QChemErrorHandler(input_file="mol.qin", output_file="mol.qout") handler.check() dct = handler.correct() @@ -294,8 +294,8 @@ def test_gdm_neg_precon_error(self): assert dct["actions"] == [{"molecule": "molecule_from_last_geometry"}] def test_fileman_cpscf_nseg_error(self): - shutil.copyfile(f"{TEST_DIR}/fileman_cpscf.qin.gz", f"{SCR_DIR}/mol.qin.gz") - shutil.copyfile(f"{TEST_DIR}/fileman_cpscf.qout.gz", f"{SCR_DIR}/mol.qout.gz") + shutil.copyfile(f"{TEST_DIR}/fileman_cpscf.qin", f"{SCR_DIR}/mol.qin") + shutil.copyfile(f"{TEST_DIR}/fileman_cpscf.qout", f"{SCR_DIR}/mol.qout") handler = QChemErrorHandler(input_file="mol.qin", output_file="mol.qout") handler.check() dct = handler.correct() diff --git a/tests/qchem/test_job_handler_interaction.py b/tests/qchem/test_job_handler_interaction.py index 4e7edc46a..d54bbd611 100644 --- a/tests/qchem/test_job_handler_interaction.py +++ b/tests/qchem/test_job_handler_interaction.py @@ -32,8 +32,8 @@ class FFOptJobHandlerInteraction(TestCase): def _check_equivalent_inputs(self, input1, input2): QCinput1 = QCInput.from_file(input1) QCinput2 = QCInput.from_file(input2) - sections1 = QCInput.find_sections(QCinput1.get_string()) - sections2 = QCInput.find_sections(QCinput2.get_string()) + sections1 = QCInput.find_sections(QCinput1.get_str()) + sections2 = QCInput.find_sections(QCinput2.get_str()) assert sections1 == sections2 for key in sections1: assert QCinput1.as_dict().get(key) == QCinput2.as_dict().get(key) diff --git a/tests/qchem/test_jobs.py b/tests/qchem/test_jobs.py index 82507eb2d..43491746a 100644 --- a/tests/qchem/test_jobs.py +++ b/tests/qchem/test_jobs.py @@ -626,6 +626,7 @@ def setUp(self): shutil.copyfile(f"{TEST_DIR}/5952_frag16/mol.qin.orig", f"{SCR_DIR}/mol.qin") shutil.copyfile(f"{TEST_DIR}/5952_frag16/mol.qout.opt_0", f"{SCR_DIR}/mol.qout.opt_0") shutil.copyfile(f"{TEST_DIR}/5952_frag16/mol.qout.freq_0", f"{SCR_DIR}/mol.qout.freq_0") + shutil.copyfile(f"{TEST_DIR}/5952_frag16/mol.qin.freq_0", f"{SCR_DIR}/mol.qin.freq_0") os.chdir(SCR_DIR) def tearDown(self): @@ -661,7 +662,7 @@ def test_OptFF(self): ).as_dict() assert next(job).as_dict() == expected_next assert ( - QCInput.from_file(f"{TEST_DIR}/5952_frag16/mol.qin.freq_0").as_dict() + QCInput.from_file(f"{SCR_DIR}/mol.qin.freq_0").as_dict() == QCInput.from_file(os.path.join(SCR_DIR, "mol.qin")).as_dict() ) with pytest.raises(StopIteration): @@ -776,8 +777,8 @@ def test_OptFF(self): QCInput.from_file(f"{TEST_DIR}/5690_frag18/mol.qin.freq_2").as_dict() == QCInput.from_file(os.path.join(SCR_DIR, "mol.qin")).as_dict() ) - with pytest.raises(StopIteration): - job.__next__() + with pytest.raises(ValueError, match="ERROR: Can't deal with multiple neg frequencies yet! Exiting..."): + next(job) @unittest.skipIf(ob is None, "openbabel not installed")