From 31b22cf35821c3cbc62a1225df59f0ae7f8d1e3c Mon Sep 17 00:00:00 2001 From: kfir4444 Date: Fri, 30 Oct 2026 02:55:10 +0200 Subject: [PATCH 1/3] Add an Arkane adapter for the YAML outputs ARC writes for ASE calculators --- arkane/data/arc_yaml/C3H8_scan_uma.yml | 2295 +++++++++++++++++ arkane/data/arc_yaml/CH3_freq_uma.yml | 269 ++ arkane/data/arc_yaml/H2O_freq_uma.yml | 146 ++ .../data/arc_yaml/H2O_freq_uma_ev_hessian.out | 146 ++ arkane/data/arc_yaml/TS_OHCH4_freq_uma.yml | 854 ++++++ arkane/ess/__init__.py | 1 + arkane/ess/arc_yaml.py | 302 +++ arkane/ess/arc_yaml_test.py | 134 + arkane/ess/factory.py | 11 +- 9 files changed, 4156 insertions(+), 2 deletions(-) create mode 100644 arkane/data/arc_yaml/C3H8_scan_uma.yml create mode 100644 arkane/data/arc_yaml/CH3_freq_uma.yml create mode 100644 arkane/data/arc_yaml/H2O_freq_uma.yml create mode 100644 arkane/data/arc_yaml/H2O_freq_uma_ev_hessian.out create mode 100644 arkane/data/arc_yaml/TS_OHCH4_freq_uma.yml create mode 100644 arkane/ess/arc_yaml.py create mode 100644 arkane/ess/arc_yaml_test.py diff --git a/arkane/data/arc_yaml/C3H8_scan_uma.yml b/arkane/data/arc_yaml/C3H8_scan_uma.yml new file mode 100644 index 00000000000..6eccdea1f87 --- /dev/null +++ b/arkane/data/arc_yaml/C3H8_scan_uma.yml @@ -0,0 +1,2295 @@ +angles: +- 0.0 +- 8.0 +- 16.0 +- 24.0 +- 32.0 +- 40.0 +- 48.0 +- 56.0 +- 64.0 +- 72.0 +- 80.0 +- 88.0 +- 96.0 +- 104.0 +- 112.0 +- 120.0 +- 128.0 +- 136.0 +- 144.0 +- 152.0 +- 160.0 +- 168.0 +- 176.0 +- 184.0 +- 192.0 +- 200.0 +- 208.0 +- 216.0 +- 224.0 +- 232.0 +- 240.0 +- 248.0 +- 256.0 +- 264.0 +- 272.0 +- 280.0 +- 288.0 +- 296.0 +- 304.0 +- 312.0 +- 320.0 +- 328.0 +- 336.0 +- 344.0 +- 352.0 +- 360.0 +branch_gap_max: 5.71824466533144e-05 +converged: true +energies: +- -119.09651518907732 +- -119.09632197416079 +- -119.09578033678865 +- -119.09496800658023 +- -119.09401044752849 +- -119.0930662855105 +- -119.09230850687719 +- -119.09188666897046 +- -119.09188974338026 +- -119.09231695038898 +- -119.09307753078811 +- -119.09402051918771 +- -119.09497450079787 +- -119.0957816639989 +- -119.09632022732869 +- -119.09651478452072 +- -119.09634010682186 +- -119.09581880163476 +- -119.09502355870725 +- -119.09407365389605 +- -119.09312561202948 +- -119.09235088905126 +- -119.09190260431221 +- -119.0918755482566 +- -119.09227574256815 +- -119.09301849969467 +- -119.0939564592461 +- -119.09491799956119 +- -119.09574196159903 +- -119.09630091517012 +- -119.0965138045457 +- -119.09635011822016 +- -119.09583185547518 +- -119.09503152895026 +- -119.09407248431957 +- -119.09311652034526 +- -119.09233837241497 +- -119.09189593188393 +- -119.09188408215977 +- -119.09230438414764 +- -119.093068451597 +- -119.09401967112535 +- -119.09498240747293 +- -119.09579465868073 +- -119.09633028575992 +- -119.09651518907732 +fmax_worst: 0.004984728526324034 +opt_xyz: + coords: !!python/tuple + - !!python/tuple + - -1.2586322810840838 + - -0.023906163696375576 + - 0.2672015616889118 + - !!python/tuple + - 0.04666883668411464 + - 0.5605609555826064 + - -0.2581280265629718 + - !!python/tuple + - 1.2210020478918608 + - -0.393203480910381 + - -0.07753839896164381 + - !!python/tuple + - -1.1823227404845902 + - -0.25156620114394906 + - 1.332555469543582 + - !!python/tuple + - -1.5056864468032174 + - -0.9531226883963032 + - -0.25066560426480194 + - !!python/tuple + - -2.0927573731290074 + - 0.6655973470750921 + - 0.13206243006643167 + - !!python/tuple + - 0.2580877250535657 + - 1.5022085738718503 + - 0.2551417161969452 + - !!python/tuple + - -0.06360653515459037 + - 0.808105386245578 + - -1.3170806905103434 + - !!python/tuple + - 1.0456880259067831 + - -1.3315047764510255 + - -0.6080690629987441 + - !!python/tuple + - 1.3679397251420937 + - -0.6345746017399848 + - 0.977333596988847 + - !!python/tuple + - 2.150469779944395 + - 0.03494593525664683 + - -0.4546407570172308 + isotopes: &id001 !!python/tuple + - 12 + - 12 + - 12 + - 1 + - 1 + - 1 + - 1 + - 1 + - 1 + - 1 + - 1 + symbols: &id002 !!python/tuple + - C + - C + - C + - H + - H + - H + - H + - H + - H + - H + - H +scan_coords: +- coords: &id003 !!python/tuple + - !!python/tuple + - -1.2586322810840838 + - -0.023906163696375576 + - 0.2672015616889118 + - !!python/tuple + - 0.04666883668411464 + - 0.5605609555826064 + - -0.2581280265629718 + - !!python/tuple + - 1.2210020478918608 + - -0.393203480910381 + - -0.07753839896164381 + - !!python/tuple + - -1.1823227404845902 + - -0.25156620114394906 + - 1.332555469543582 + - !!python/tuple + - -1.5056864468032174 + - -0.9531226883963032 + - -0.25066560426480194 + - !!python/tuple + - -2.0927573731290074 + - 0.6655973470750921 + - 0.13206243006643167 + - !!python/tuple + - 0.2580877250535657 + - 1.5022085738718503 + - 0.2551417161969452 + - !!python/tuple + - -0.06360653515459037 + - 0.808105386245578 + - -1.3170806905103434 + - !!python/tuple + - 1.0456880259067831 + - -1.3315047764510255 + - -0.6080690629987441 + - !!python/tuple + - 1.3679397251420937 + - -0.6345746017399848 + - 0.977333596988847 + - !!python/tuple + - 2.150469779944395 + - 0.03494593525664683 + - -0.4546407570172308 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2586987226728201 + - -0.026286753595555393 + - 0.26829679497457354 + - !!python/tuple + - 0.047904183687811096 + - 0.5560752024443025 + - -0.2582993454030624 + - !!python/tuple + - 1.1802889622287989 + - -0.4634285436009353 + - -0.25833587846117406 + - !!python/tuple + - -1.18509812918689 + - -0.25378619142302183 + - 1.3335843681145414 + - !!python/tuple + - -1.516697275524976 + - -0.9488350787159515 + - -0.2555235087127864 + - !!python/tuple + - -2.087197706822927 + - 0.6721103527915662 + - 0.14169885562947032 + - !!python/tuple + - 0.3310928241487357 + - 1.4239620539790698 + - 0.34245547657512837 + - !!python/tuple + - -0.10259658881577274 + - 0.9257835264111589 + - -1.2758759883643123 + - !!python/tuple + - 0.9338928445188106 + - -1.3170694975161308 + - -0.8930758447201155 + - !!python/tuple + - 1.3641157575610412 + - -0.8443052579408814 + - 0.7486189450955012 + - !!python/tuple + - 2.111606190121397 + - -0.031258957967222535 + - -0.6262047545445651 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2594308930400713 + - -0.028573114699513593 + - 0.2691401425748924 + - !!python/tuple + - 0.04849314823693057 + - 0.5548416994558865 + - -0.25747476144308884 + - !!python/tuple + - 1.1278189456628351 + - -0.5051231700333567 + - -0.44119192986020744 + - !!python/tuple + - -1.1896889946925489 + - -0.2568824683003296 + - 1.334264755771301 + - !!python/tuple + - -1.5252927079090097 + - -0.9448566241355618 + - -0.26112013145689955 + - !!python/tuple + - -2.084279704208172 + - 0.6756553290605347 + - 0.15001719029185073 + - !!python/tuple + - 0.40273142940188505 + - 1.3358411614716326 + - 0.4194922654571545 + - !!python/tuple + - -0.13346736149003652 + - 1.04420910423895 + - -1.2178136639598915 + - !!python/tuple + - 0.8067322428005457 + - -1.2628488615430742 + - -1.1586427741283105 + - !!python/tuple + - 1.343296726922214 + - -1.0143572525529736 + - 0.5007547526854619 + - !!python/tuple + - 2.0598732935403268 + - -0.07208382635327779 + - -0.8061903646600018 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2599499870322364 + - -0.03047773721145723 + - 0.27101347896777533 + - !!python/tuple + - 0.04800437857116315 + - 0.5570600203834459 + - -0.25669438283847024 + - !!python/tuple + - 1.0641110851049946 + - -0.5181326033171736 + - -0.6236741597824627 + - !!python/tuple + - -1.1930537817612001 + - -0.2589996916153703 + - 1.3360764298457442 + - !!python/tuple + - -1.5288831172056219 + - -0.9424673729194069 + - -0.2645478607091315 + - !!python/tuple + - -2.084789363099479 + - 0.6748120257862711 + - 0.15788843838029493 + - !!python/tuple + - 0.472890337260685 + - 1.2408058765226513 + - 0.4814879387308073 + - !!python/tuple + - -0.15776043426018352 + - 1.1597596525179852 + - -1.1450508694805925 + - !!python/tuple + - 0.6676513102004955 + - -1.1695736901430787 + - -1.4048226890201456 + - !!python/tuple + - 1.302868945416111 + - -1.145868439608035 + - 0.23793077934292106 + - !!python/tuple + - 1.9963418559983541 + - -0.08524606138292513 + - -0.9887875514051119 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2621271926934245 + - -0.030877691302792887 + - 0.27305603054844574 + - !!python/tuple + - 0.048718974215968935 + - 0.556245438586203 + - -0.2572320539097211 + - !!python/tuple + - 0.9899800957318917 + - -0.5105191453459195 + - -0.8053515811735646 + - !!python/tuple + - -1.198358508204036 + - -0.25938346431782583 + - 1.337975911977561 + - !!python/tuple + - -1.534690307367372 + - -0.9417391898745854 + - -0.26232824189604176 + - !!python/tuple + - -2.0867725621938384 + - 0.6748181632090998 + - 0.16126009399541788 + - !!python/tuple + - 0.5466281882766804 + - 1.1282990909807646 + - 0.5284775677667618 + - !!python/tuple + - -0.16938820091966164 + - 1.268500747711132 + - -1.056797844967323 + - !!python/tuple + - 0.5231645792359142 + - -1.0433111467897322 + - -1.6360197965960817 + - !!python/tuple + - 1.2391274749737864 + - -1.2486264045917048 + - -0.03948113893624236 + - !!python/tuple + - 1.9236997328715038 + - -0.0774960871615072 + - -1.1666491910586312 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2637943989310478 + - -0.03062209381600533 + - 0.27423823728986096 + - !!python/tuple + - 0.049529185222768994 + - 0.5568110775847728 + - -0.25783472700205196 + - !!python/tuple + - 0.9058536481702254 + - -0.47739768205920186 + - -0.9802200149525594 + - !!python/tuple + - -1.2025550969096412 + - -0.2596939390202474 + - 1.3386772943544538 + - !!python/tuple + - -1.5367173399688294 + - -0.9427310877580453 + - -0.2584758669347002 + - !!python/tuple + - -2.089999891432146 + - 0.6724615950211844 + - 0.16094247392663147 + - !!python/tuple + - 0.6178638794870857 + - 1.005664637499959 + - 0.5591486731088734 + - !!python/tuple + - -0.1691248939462798 + - 1.3702545010357994 + - -0.9534745516558355 + - !!python/tuple + - 0.37124706353884174 + - -0.8848078493228756 + - -1.8404191110639223 + - !!python/tuple + - 1.1546276581801584 + - -1.3123934059376474 + - -0.32130240165736335 + - !!python/tuple + - 1.8414202497323904 + - -0.04713012789340784 + - -1.3399470567431335 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.266251083713357 + - -0.02838387297072328 + - 0.2758496870328585 + - !!python/tuple + - 0.04992422187581176 + - 0.5573321478328147 + - -0.25904312757780806 + - !!python/tuple + - 0.8141350932165988 + - -0.4198418934906915 + - -1.1458076880913075 + - !!python/tuple + - -1.2065801775276668 + - -0.2574498892727809 + - 1.3401603936173945 + - !!python/tuple + - -1.5349813955103435 + - -0.9454247138523002 + - -0.2508811700554482 + - !!python/tuple + - -2.095652379464866 + - 0.6692021625745772 + - 0.15505102906582674 + - !!python/tuple + - 0.6849069805321362 + - 0.8717419822136889 + - 0.5714378882918142 + - !!python/tuple + - -0.1569893097462536 + - 1.4615310174943508 + - -0.8354439795887697 + - !!python/tuple + - 0.21718934727229855 + - -0.6978558348819615 + - -2.016630049715504 + - !!python/tuple + - 1.052799661560115 + - -1.3374421328551758 + - -0.6036198204382235 + - !!python/tuple + - 1.750803003217571 + - 0.009141130223136682 + - -1.504374974218575 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2681142633053348 + - -0.024942247454661417 + - 0.276603397928147 + - !!python/tuple + - 0.04989970927550457 + - 0.5585151796659608 + - -0.2599463025614986 + - !!python/tuple + - 0.7160850764317175 + - -0.3383971181101679 + - -1.2977250994049305 + - !!python/tuple + - -1.2091646132225993 + - -0.25430562748715896 + - 1.340602342768161 + - !!python/tuple + - -1.5294810694318042 + - -0.9486916461074423 + - -0.24241618026848596 + - !!python/tuple + - -2.1017422733235236 + - 0.665091534049014 + - 0.1453705404165389 + - !!python/tuple + - 0.7442759785559264 + - 0.7310791300487366 + - 0.5645204898294897 + - !!python/tuple + - -0.13240665884540345 + - 1.5384649862731092 + - -0.7053161066966871 + - !!python/tuple + - 0.06266823454523748 + - -0.48560011599686775 + - -2.1600605075184007 + - !!python/tuple + - 0.9351451809862832 + - -1.3229429628819418 + - -0.8792159417477918 + - !!python/tuple + - 1.6535846253818887 + - 0.08868046970906492 + - -1.6565829072977334 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2692957045353812 + - -0.021436138432638117 + - 0.27260117427047625 + - !!python/tuple + - 0.05306354229521057 + - 0.5582941512425685 + - -0.2574710055898314 + - !!python/tuple + - 0.6162949164070901 + - -0.23522651785722817 + - -1.4314421990038406 + - !!python/tuple + - -1.216119264489619 + - -0.25684221997264317 + - 1.3354567340516832 + - !!python/tuple + - -1.522722774240497 + - -0.9483232843568494 + - -0.24565031993800895 + - !!python/tuple + - -2.103801386622863 + - 0.6648780636195208 + - 0.12982543047695433 + - !!python/tuple + - 0.7956481494375515 + - 0.5813115134776556 + - 0.5426216101278524 + - !!python/tuple + - -0.08970747333732404 + - 1.5973287869726076 + - -0.5608088083075375 + - !!python/tuple + - -0.09350856989716265 + - -0.2593199909282127 + - -2.2609566857863417 + - !!python/tuple + - 0.8167052549310202 + - -1.2683783424719253 + - -1.140309737518675 + - !!python/tuple + - 1.547758888601664 + - 0.19616150318919356 + - -1.800571199888391 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2692406372046001 + - -0.017740844442885106 + - 0.27229719725871854 + - !!python/tuple + - 0.052438291798569125 + - 0.559728122528813 + - -0.2575695232705743 + - !!python/tuple + - 0.5136299774994975 + - -0.11079633626794018 + - -1.5469353724930373 + - !!python/tuple + - -1.2161303052462529 + - -0.2536925425291077 + - 1.3350188643339702 + - !!python/tuple + - -1.513117329995429 + - -0.9508341832147558 + - -0.24020973570600232 + - !!python/tuple + - -2.1070833440901877 + - 0.6619207671760127 + - 0.11811157889359991 + - !!python/tuple + - 0.8341105273528278 + - 0.4418526108141732 + - 0.49592368477445614 + - !!python/tuple + - -0.04589592845958261 + - 1.6350072905456077 + - -0.4187796352995399 + - !!python/tuple + - -0.23731166209530768 + - -0.005859260332573895 + - -2.3330414227570855 + - !!python/tuple + - 0.6766556074568094 + - -1.1786585246798635 + - -1.388696335301084 + - !!python/tuple + - 1.4454094857763526 + - 0.3205388477022135 + - -1.9153809076208799 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.268250714770859 + - -0.01515744700567932 + - 0.2717297544990896 + - !!python/tuple + - 0.05154075462846038 + - 0.5609278505949242 + - -0.2573636751847028 + - !!python/tuple + - 0.41187481610477206 + - 0.03069735248165294 + - -1.6406005207007182 + - !!python/tuple + - -1.214635017599737 + - -0.25126058928478895 + - 1.3345637887530253 + - !!python/tuple + - -1.5045752569974105 + - -0.952400451425947 + - -0.237627488494633 + - !!python/tuple + - -2.10788112957308 + - 0.6605221553852771 + - 0.10890190268814003 + - !!python/tuple + - 0.861367615125745 + - 0.3101805502989847 + - 0.4316622448499713 + - !!python/tuple + - 0.004012485103194978 + - 1.651607673425421 + - -0.27829489068723595 + - !!python/tuple + - -0.37057115952230085 + - 0.26209962757780003 + - -2.3668644657765237 + - !!python/tuple + - 0.5284522985147223 + - -1.0544581277702707 + - -1.6171779715235675 + - !!python/tuple + - 1.3446728744025795 + - 0.46112700281266306 + - -2.007251547943558 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2664766131827017 + - -0.013999064505580723 + - 0.2707443296032158 + - !!python/tuple + - 0.050394876210879805 + - 0.5615786514974 + - -0.2568393102426071 + - !!python/tuple + - 0.3133551085348649 + - 0.1863844291118879 + - -1.7107496804158213 + - !!python/tuple + - -1.2117318309644867 + - -0.24980621778356757 + - 1.333744529371172 + - !!python/tuple + - -1.4982430259507014 + - -0.9530030593609999 + - -0.2379960462819364 + - !!python/tuple + - -2.1062709444018486 + - 0.6608138045595757 + - 0.10324493718064354 + - !!python/tuple + - 0.8779964612627105 + - 0.18951737419962342 + - 0.35208290543024967 + - !!python/tuple + - 0.05815738903527969 + - 1.647692310543825 + - -0.14273682049813852 + - !!python/tuple + - -0.4906256122188249 + - 0.5388475017707424 + - -2.3610364419564633 + - !!python/tuple + - 0.374572398170619 + - -0.8978641467305727 + - -1.8217515059958074 + - !!python/tuple + - 1.247999204754439 + - 0.6149088981872435 + - -2.0750054656637396 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2647428040079716 + - -0.012871982654583973 + - 0.27133431296785776 + - !!python/tuple + - 0.048649118202685776 + - 0.5621022962209963 + - -0.25694087018342493 + - !!python/tuple + - 0.2171770265603103 + - 0.3500716156542896 + - -1.7566620551070915 + - !!python/tuple + - -1.2069949323545448 + - -0.24563840401422102 + - 1.334884878561882 + - !!python/tuple + - -1.4994340618680988 + - -0.9506985974643527 + - -0.2383114613377175 + - !!python/tuple + - -2.1021119766807534 + - 0.6657844104196788 + - 0.10533180282069407 + - !!python/tuple + - 0.8853472206259332 + - 0.0850003387571763 + - 0.2595570748564699 + - !!python/tuple + - 0.11351637477108925 + - 1.6262274077018801 + - -0.018498136177598965 + - !!python/tuple + - -0.6000086034587812 + - 0.8128917068308898 + - -2.314563520711211 + - !!python/tuple + - 0.21719889653759686 + - -0.7149377318934317 + - -1.9965298595404177 + - !!python/tuple + - 1.1523974042807852 + - 0.7764047205096956 + - -2.1216645549357738 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2625226913628906 + - -0.014798323161941867 + - 0.2696505293327275 + - !!python/tuple + - 0.04865971396088927 + - 0.561046921445726 + - -0.25617761345090506 + - !!python/tuple + - 0.13110000960137733 + - 0.5239578944892416 + - -1.77726041449188 + - !!python/tuple + - -1.2041867104530426 + - -0.24730643470804278 + - 1.3333973880677543 + - !!python/tuple + - -1.5014970671465322 + - -0.9483611932282654 + - -0.24552838382240966 + - !!python/tuple + - -2.09613161473815 + - 0.6704079742951248 + - 0.10815305197224699 + - !!python/tuple + - 0.8849460206108006 + - -0.00837048429093613 + - 0.15756672434991226 + - !!python/tuple + - 0.17348961789444245 + - 1.5864323665644844 + - 0.10016289750350814 + - !!python/tuple + - -0.6884678305864277 + - 1.0870755080827166 + - -2.2292453030538963 + - !!python/tuple + - 0.06457799990210987 + - -0.5028751522607859 + - -2.142208437738496 + - !!python/tuple + - 1.0673245652292205 + - 0.9491515095633802 + - -2.1409968462998132 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.260281090988421 + - -0.01820999200440415 + - 0.2680204241802771 + - !!python/tuple + - 0.04912147581415835 + - 0.5596503526350632 + - -0.25578403699636015 + - !!python/tuple + - 0.05338015996100257 + - 0.7023515896680055 + - -1.7727210514209524 + - !!python/tuple + - -1.2019015774760065 + - -0.2504371782595652 + - 1.3319737709283275 + - !!python/tuple + - -1.5069817512824188 + - -0.9455339879173067 + - -0.2541507195228439 + - !!python/tuple + - -2.089024228476852 + - 0.6754797225562642 + - 0.11415504911173714 + - !!python/tuple + - 0.8775268638237759 + - -0.08610682735374238 + - 0.04701216554641426 + - !!python/tuple + - 0.23487689833726624 + - 1.5315893276422723 + - 0.20827255644115486 + - !!python/tuple + - -0.7577490187090307 + - 1.3530079915460427 + - -2.1067467465878904 + - !!python/tuple + - -0.08466042982379716 + - -0.2681540899137728 + - -2.2537713263977905 + - !!python/tuple + - 0.9908589177552211 + - 1.125506357948848 + - -2.1355157198611763 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2583558190953499 + - -0.022581262268633853 + - 0.2666358973267384 + - !!python/tuple + - 0.04971911185966381 + - 0.5581568289545267 + - -0.2558658257312861 + - !!python/tuple + - -0.01471918712735949 + - 0.882130702273665 + - -1.743209840395598 + - !!python/tuple + - -1.200252116474859 + - -0.25449672367160303 + - 1.33072384763015 + - !!python/tuple + - -1.5148104539804688 + - -0.9427222453969892 + - -0.2626139566912383 + - !!python/tuple + - -2.0819078073999404 + - 0.6800506454180444 + - 0.12231027803258872 + - !!python/tuple + - 0.8630527142115045 + - -0.14825273533055508 + - -0.07074484174329265 + - !!python/tuple + - 0.2977583106124556 + - 1.462994815681801 + - 0.30501299358191514 + - !!python/tuple + - -0.8064263657944524 + - 1.605314714900169 + - -1.9499205900448293 + - !!python/tuple + - -0.22788570362332652 + - -0.014803346495461108 + - -2.328677002633767 + - !!python/tuple + - 0.9241587774880078 + - 1.3023613446855258 + - -2.105694293797641 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2558524940368863 + - -0.030903449264605386 + - 0.26424663953194616 + - !!python/tuple + - 0.05039508428988773 + - 0.5573323277688106 + - -0.25565250602658113 + - !!python/tuple + - -0.07161238151151761 + - 1.0627399440777276 + - -1.6878051415362614 + - !!python/tuple + - -1.198265898328157 + - -0.2640492410295947 + - 1.3280339874007219 + - !!python/tuple + - -1.5196336998151494 + - -0.9444327569209874 + - -0.27203170842252605 + - !!python/tuple + - -2.0766581788404093 + - 0.6773768256821295 + - 0.13001317767566856 + - !!python/tuple + - 0.8426308234308125 + - -0.19304599344689025 + - -0.19405204651696123 + - !!python/tuple + - 0.36030225582577535 + - 1.381767169376164 + - 0.3917836873350838 + - !!python/tuple + - -0.8281271487771926 + - 1.846900477586687 + - -1.7591627616295749 + - !!python/tuple + - -0.36866098715176465 + - 0.2572306356893399 + - -2.3628907975019966 + - !!python/tuple + - 0.870877938926303 + - 1.4727635864671351 + - -2.0526495200440613 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.255326181529356 + - -0.03529884363745777 + - 0.2639929136117423 + - !!python/tuple + - 0.05083711311550116 + - 0.5562237444874254 + - -0.2566328917643766 + - !!python/tuple + - -0.11766321822551815 + - 1.235249254179374 + - -1.6103155254676733 + - !!python/tuple + - -1.1979343532751312 + - -0.2681941991557321 + - 1.327730763326736 + - !!python/tuple + - -1.5291542577755264 + - -0.942734006181289 + - -0.27653955269234615 + - !!python/tuple + - -2.0727291003297466 + - 0.6792078130775491 + - 0.1397995818219575 + - !!python/tuple + - 0.8120540137897889 + - -0.22499649367754826 + - -0.32240096141946306 + - !!python/tuple + - 0.4278133199301832 + - 1.2882429984764545 + - 0.46232908276692486 + - !!python/tuple + - -0.8352709313859599 + - 2.0554152969794766 + - -1.5438950535596057 + - !!python/tuple + - -0.4902101018961587 + - 0.5324555266869239 + - -2.358914746477498 + - !!python/tuple + - 0.8250302984472488 + - 1.6433481059739306 + - -1.9769378738172576 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2556326401998381 + - -0.03881313825542578 + - 0.2643417206359621 + - !!python/tuple + - 0.05117307501980113 + - 0.5557270296339066 + - -0.2577647880563233 + - !!python/tuple + - -0.15083939936821839 + - 1.3995370553945288 + - -1.5105787326012272 + - !!python/tuple + - -1.1986790017121254 + - -0.2716849724616337 + - 1.3279134119861247 + - !!python/tuple + - -1.5372735610968 + - -0.941964018695862 + - -0.27826749457917244 + - !!python/tuple + - -2.0711915045525573 + - 0.6792601920258939 + - 0.14792089865013036 + - !!python/tuple + - 0.7721117050805079 + - -0.24120347770179387 + - -0.4540199979734455 + - !!python/tuple + - 0.49766716394195537 + - 1.1831004009827124 + - 0.5177961165139436 + - !!python/tuple + - -0.821341246705158 + - 2.2364430242874946 + - -1.3062791396962736 + - !!python/tuple + - -0.5964775341214125 + - 0.8103416406575629 + - -2.3152110407124895 + - !!python/tuple + - 0.7916426775556067 + - 1.8065858162308497 + - -1.879000302195247 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2574914569511266 + - -0.038999375458749895 + - 0.26543463723293403 + - !!python/tuple + - 0.051459605764463005 + - 0.5569901998369893 + - -0.25859524182284577 + - !!python/tuple + - -0.16998505240229114 + - 1.5518769311331313 + - -1.3920971747805986 + - !!python/tuple + - -1.2029194153867266 + - -0.27070049365745535 + - 1.329350331664597 + - !!python/tuple + - -1.5444067797125824 + - -0.9405241540608021 + - -0.27644029232241085 + - !!python/tuple + - -2.0716700600029925 + - 0.6810568316615797 + - 0.15180001131970783 + - !!python/tuple + - 0.722911464265402 + - -0.24008365730452189 + - -0.5850320681733826 + - !!python/tuple + - 0.5677084298474384 + - 1.0698207848750227 + - 0.5566773257588873 + - !!python/tuple + - -0.7858769853779745 + - 2.387311665080063 + - -1.0539250434105107 + - !!python/tuple + - -0.684871344319508 + - 1.083155373822324 + - -2.2339218772996414 + - !!python/tuple + - 0.7724633947123507 + - 1.9574256543219686 + - -1.7624549519309485 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2594286791963627 + - -0.03978470431081407 + - 0.2665400070776594 + - !!python/tuple + - 0.05187919076747472 + - 0.5583171549073638 + - -0.25866605747995264 + - !!python/tuple + - -0.17545816070827086 + - 1.6914168421039966 + - -1.2530195348513 + - !!python/tuple + - -1.2059454764070714 + - -0.27187227998231384 + - 1.3302863061824595 + - !!python/tuple + - -1.545226100471918 + - -0.9435525123585949 + - -0.27158951817535193 + - !!python/tuple + - -2.0762014666772663 + - 0.6767155576910813 + - 0.1512322032918047 + - !!python/tuple + - 0.6636734993104634 + - -0.22144363894209818 + - -0.71693550389377 + - !!python/tuple + - 0.6377259152100695 + - 0.9445254623336373 + - 0.5786829843151106 + - !!python/tuple + - -0.7291162506089435 + - 2.5074424729528144 + - -0.7847540845202226 + - !!python/tuple + - -0.7565163388399042 + - 1.3501201244201224 + - -2.112756388961289 + - !!python/tuple + - 0.7664275782217096 + - 2.095318518959264 + - -1.6265585452484295 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2616541902796747 + - -0.0389053609393318 + - 0.26790820036922497 + - !!python/tuple + - 0.05186489016466682 + - 0.559790327234603 + - -0.2582559051930134 + - !!python/tuple + - -0.16655435143841574 + - 1.8136667114820162 + - -1.0977702363848933 + - !!python/tuple + - -1.2085626575911639 + - -0.27133290328268134 + - 1.3314143745509994 + - !!python/tuple + - -1.5426202780333258 + - -0.9477123924171715 + - -0.26388342464820946 + - !!python/tuple + - -2.082333803281248 + - 0.6715639993050618 + - 0.1472174647345387 + - !!python/tuple + - 0.5948364129309448 + - -0.184068322690048 + - -0.8445434822581495 + - !!python/tuple + - 0.7038874786333281 + - 0.8112868294607801 + - 0.5809789116317965 + - !!python/tuple + - -0.6540760388479906 + - 2.5920094683115615 + - -0.5075056434949808 + - !!python/tuple + - -0.8070073726248637 + - 1.6031221781282858 + - -1.9570624816112483 + - !!python/tuple + - 0.7747997966507193 + - 2.2169140831765155 + - -1.473587955403239 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2638678805773862 + - -0.0365770722491414 + - 0.2696286655589508 + - !!python/tuple + - 0.05159236457132359 + - 0.5611151016752223 + - -0.2574705067591429 + - !!python/tuple + - -0.1437027686433467 + - 1.9159507493933934 + - -0.929365603045299 + - !!python/tuple + - -1.2104863713576441 + - -0.2693666489054122 + - 1.333062891368935 + - !!python/tuple + - -1.5367946391259357 + - -0.9525221070684777 + - -0.254166328330969 + - !!python/tuple + - -2.0891958045609025 + - 0.666302623777131 + - 0.1399636472334184 + - !!python/tuple + - 0.5180507594504579 + - -0.1277823747480183 + - -0.9644606752991977 + - !!python/tuple + - 0.7635342866785249 + - 0.6728525510743975 + - 0.5628009246579793 + - !!python/tuple + - -0.5620124093541923 + - 2.6398205855698373 + - -0.22697816417560665 + - !!python/tuple + - -0.8351934301988848 + - 1.8370766785872374 + - -1.7708951575403744 + - !!python/tuple + - 0.7972965743561672 + - 2.319169871403739 + - -1.3061146661369198 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.264727711405182 + - -0.03491118471473368 + - 0.2733984256936037 + - !!python/tuple + - 0.04986283556962586 + - 0.5602326835691936 + - -0.2589021007822061 + - !!python/tuple + - -0.10569059374146521 + - 1.9950446061996885 + - -0.7512729637527021 + - !!python/tuple + - -1.205114178908602 + - -0.269601777816383 + - 1.3362080612702683 + - !!python/tuple + - -1.5323081350952268 + - -0.9572354284011021 + - -0.24236175464110934 + - !!python/tuple + - -2.094238651365141 + - 0.6615556606797147 + - 0.13952251452010792 + - !!python/tuple + - 0.4311593533055293 + - -0.05451576602981329 + - -1.0765800765220885 + - !!python/tuple + - 0.8152835912150888 + - 0.5287365879312457 + - 0.5188439503089959 + - !!python/tuple + - -0.46290231936745657 + - 2.6454248624654744 + - 0.04989897005659557 + - !!python/tuple + - -0.8300233468488905 + - 2.049348353952297 + - -1.5665564848571047 + - !!python/tuple + - 0.8395018824397762 + - 2.400568332529673 + - -1.114951777855769 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2654437429454273 + - -0.03108751035958361 + - 0.27439075185215095 + - !!python/tuple + - 0.049319510677903265 + - 0.5607343940925016 + - -0.2576078963556867 + - !!python/tuple + - -0.05591085458512081 + - 2.0500889185353657 + - -0.5673471167392728 + - !!python/tuple + - -1.2050983458342552 + - -0.2657029200986182 + - 1.3374061937704902 + - !!python/tuple + - -1.52372362794203 + - -0.9603543419431313 + - -0.2342761289805324 + - !!python/tuple + - -2.097860779039694 + - 0.6593550063085462 + - 0.12971279591167784 + - !!python/tuple + - 0.3476657540039202 + - 0.03604747080667046 + - -1.1676599467213442 + - !!python/tuple + - 0.8536901453556208 + - 0.39250955490304307 + - 0.4609747121941825 + - !!python/tuple + - -0.3404637227163582 + - 2.6163662392661475 + - 0.32217322192452175 + - !!python/tuple + - -0.8151836225744856 + - 2.2324674504101942 + - -1.3303730071608175 + - !!python/tuple + - 0.8896914026290444 + - 2.4538903147381816 + - -0.9316879145180147 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2650653095373272 + - -0.02772881284277865 + - 0.2741846607623576 + - !!python/tuple + - 0.048984750927344306 + - 0.5604488210713165 + - -0.2564476255251798 + - !!python/tuple + - 0.0048869746834147125 + - 2.07938742685375 + - -0.38142687953350013 + - !!python/tuple + - -1.2034578571800951 + - -0.2615420548416411 + - 1.337610918241912 + - !!python/tuple + - -1.5170191243170474 + - -0.9616127803137294 + - -0.22996966316129774 + - !!python/tuple + - -2.0983515483496897 + - 0.6599108815993268 + - 0.12189061759715632 + - !!python/tuple + - 0.2674367015029759 + - 0.13883757567148916 + - -1.240239232617654 + - !!python/tuple + - 0.8793765913659753 + - 0.26446428441784336 + - 0.3876825226092509 + - !!python/tuple + - -0.2058820070410256 + - 2.547806599323842 + - 0.5825821631673055 + - !!python/tuple + - -0.781204701345691 + - 2.3847935812228043 + - -1.0746547308787466 + - !!python/tuple + - 0.9501601642967366 + - 2.4819073542772307 + - -0.7476657814261314 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.264581787021358 + - -0.025076597567551328 + - 0.27341483925685667 + - !!python/tuple + - 0.04672443959236883 + - 0.5624952328864101 + - -0.2551932589493507 + - !!python/tuple + - 0.07289216438079442 + - 2.0856252190128117 + - -0.19884218820839702 + - !!python/tuple + - -1.2009760078325862 + - -0.25692219502807956 + - 1.3374548893514748 + - !!python/tuple + - -1.5092805522589003 + - -0.9623447011051114 + - -0.22844519851871228 + - !!python/tuple + - -2.100014955653359 + - 0.6587903272022702 + - 0.11639776246150955 + - !!python/tuple + - 0.19149952741183007 + - 0.2531167989942793 + - -1.293140163337696 + - !!python/tuple + - 0.89100450706365 + - 0.15181884271668963 + - 0.3022877098296462 + - !!python/tuple + - -0.06435935900323929 + - 2.4455060193622766 + - 0.823340460331423 + - !!python/tuple + - -0.7314525889890995 + - 2.5055973067981383 + - -0.8056571071742044 + - !!python/tuple + - 1.0172641346466829 + - 2.486841587133223 + - -0.5689571300033656 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.262568733272681 + - -0.02397777138935315 + - 0.27199581782130033 + - !!python/tuple + - 0.04756585723953576 + - 0.5592107514985408 + - -0.2554171725996792 + - !!python/tuple + - 0.15538348935108698 + - 2.0610516371185548 + - -0.019495583191192354 + - !!python/tuple + - -1.196558135188184 + - -0.25541504519742025 + - 1.336356737673425 + - !!python/tuple + - -1.5098653109172469 + - -0.9594715659278 + - -0.23208989566495827 + - !!python/tuple + - -2.094540975715234 + - 0.6648225159955194 + - 0.11707710162838583 + - !!python/tuple + - 0.1220964239455323 + - 0.3694543917045233 + - -1.3292111518953391 + - !!python/tuple + - 0.8947065991898422 + - 0.04421308066890078 + - 0.20284335315817148 + - !!python/tuple + - 0.08826262937055707 + - 2.2991837471934553 + - 1.0444333192186457 + - !!python/tuple + - -0.6556402433473788 + - 2.5882393527832996 + - -0.5253914924577188 + - !!python/tuple + - 1.099384495691664 + - 2.4614897126773103 + - -0.39119422478135935 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2610126073462602 + - -0.024137355096424496 + - 0.2709916029095804 + - !!python/tuple + - 0.04590685953010763 + - 0.5609187750457216 + - -0.25661858788660546 + - !!python/tuple + - 0.2380834699078042 + - 2.0176373302643316 + - 0.14749585968057569 + - !!python/tuple + - -1.1901509248075202 + - -0.2530868725073267 + - 1.3358923037352486 + - !!python/tuple + - -1.5113874508812741 + - -0.9569524661013362 + - -0.23663570627136915 + - !!python/tuple + - -2.0920177724304523 + - 0.6679981216888952 + - 0.12348465240539738 + - !!python/tuple + - 0.05957804115724337 + - 0.49221183833192916 + - -1.3474514312010264 + - !!python/tuple + - 0.8877518514463972 + - -0.03939389022467631 + - 0.09638792518012589 + - !!python/tuple + - 0.23612797463371393 + - 2.127901251743076 + - 1.234169864672667 + - !!python/tuple + - -0.5692888312466735 + - 2.637490829412 + - -0.2473610837611505 + - !!python/tuple + - 1.1811943316877591 + - 2.4183618344533544 + - -0.22592101187966074 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.259176843785881 + - -0.02492557105828067 + - 0.269431151299137 + - !!python/tuple + - 0.046020035272051174 + - 0.5600478244372502 + - -0.2579227902404606 + - !!python/tuple + - 0.3301517982963559 + - 1.947513069604829 + - 0.30414814784181643 + - !!python/tuple + - -1.1847369633472187 + - -0.2522300944160669 + - 1.3346974299922385 + - !!python/tuple + - -1.5168244474596055 + - -0.9529110763047679 + - -0.2430956751595449 + - !!python/tuple + - -2.086803999078886 + - 0.6735954666365347 + - 0.13124091499161156 + - !!python/tuple + - 0.004789532128380867 + - 0.6162535023452658 + - -1.3487693544844532 + - !!python/tuple + - 0.8729767985245531 + - -0.113110383897559 + - -0.018553267354659432 + - !!python/tuple + - 0.3890079422875442 + - 1.9237559053321762 + - 1.3944676415060873 + - !!python/tuple + - -0.4638986965403006 + - 2.646145774525911 + - 0.032671624116151744 + - !!python/tuple + - 1.2718340180093126 + - 2.349426655827199 + - -0.07155422488265413 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2574051313330008 + - -0.025654688886499043 + - 0.2677147107534066 + - !!python/tuple + - 0.047109623544074365 + - 0.5586830419133172 + - -0.25981936628036884 + - !!python/tuple + - 0.4263363758538521 + - 1.8545936991882237 + - 0.4460243197924055 + - !!python/tuple + - -1.179650873962854 + - -0.2507149243829446 + - 1.333548227897399 + - !!python/tuple + - -1.5251517947790714 + - -0.9478502278212627 + - -0.24936204444646914 + - !!python/tuple + - -2.08070343599016 + - 0.680332772219846 + - 0.13948256947057133 + - !!python/tuple + - -0.04128859572079454 + - 0.7405236692740969 + - -1.3340986717820273 + - !!python/tuple + - 0.8506744119706439 + - -0.1724375110384664 + - -0.13885317466259312 + - !!python/tuple + - 0.541264817196863 + - 1.6943234063696202 + - 1.5201898508622456 + - !!python/tuple + - -0.3465400427003879 + - 2.613605808837022 + - 0.3077823232145135 + - !!python/tuple + - 1.3646706183765307 + - 2.261000254106939 + - 0.0669206458069117 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2569531003881966 + - -0.026678352172938975 + - 0.2657072999822503 + - !!python/tuple + - 0.04860890326755787 + - 0.5576301335398754 + - -0.2604239664994222 + - !!python/tuple + - 0.5260564607801056 + - 1.7418747096745493 + - 0.5705630216114065 + - !!python/tuple + - -1.1798419411091001 + - -0.24976093783520445 + - 1.3320643119386135 + - !!python/tuple + - -1.5339031962782057 + - -0.9429261119354772 + - -0.2561182059135824 + - !!python/tuple + - -2.076291942077547 + - 0.68573833494335 + - 0.14671268133810847 + - !!python/tuple + - -0.07799043262422183 + - 0.8628350719461911 + - -1.302136410839797 + - !!python/tuple + - 0.8204896066610634 + - -0.2164608580342351 + - -0.26148284343933575 + - !!python/tuple + - 0.6947315894221274 + - 1.444762276298464 + - 1.607659979960053 + - !!python/tuple + - -0.21819096058484708 + - 2.5411978435170868 + - 0.5744332537140632 + - !!python/tuple + - 1.4583649122410511 + - 2.1560524250490967 + - 0.1851190354532019 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.258367615510036 + - -0.029742631619641937 + - 0.2619684027682646 + - !!python/tuple + - 0.05052473037341509 + - 0.5554457582568657 + - -0.25876612034592494 + - !!python/tuple + - 0.6284866726777357 + - 1.6080462897459498 + - 0.6791339083531387 + - !!python/tuple + - -1.1857384493201304 + - -0.25382444081631617 + - 1.3283747194954374 + - !!python/tuple + - -1.5409450329889904 + - -0.9399527391091063 + - -0.26694418674042847 + - !!python/tuple + - -2.0746319232762844 + - 0.6874247320612291 + - 0.14968914141180356 + - !!python/tuple + - -0.10543246810757284 + - 0.9837695041965929 + - -1.2516854615290371 + - !!python/tuple + - 0.7827691411114833 + - -0.2465141041154578 + - -0.38492453869757837 + - !!python/tuple + - 0.8428905763043011 + - 1.175874801566587 + - 1.6585020771570107 + - !!python/tuple + - -0.07562146826435917 + - 2.4294950904899952 + - 0.8298442665344223 + - !!python/tuple + - 1.5550330018630567 + - 2.03070059242179 + - 0.2885924858859891 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.259434535914066 + - -0.031774907732554716 + - 0.2615782990939364 + - !!python/tuple + - 0.05095629133733544 + - 0.5562845391985225 + - -0.25923249032109325 + - !!python/tuple + - 0.7283820484143321 + - 1.4618302892894965 + - 0.7620331233530749 + - !!python/tuple + - -1.1880100318050537 + - -0.2569167410378776 + - 1.3277419788062008 + - !!python/tuple + - -1.546155091759426 + - -0.9385437238440607 + - -0.27004697258720983 + - !!python/tuple + - -2.076016181482211 + - 0.6856568910657346 + - 0.1556514593462727 + - !!python/tuple + - -0.13021594923316912 + - 1.1044613927406546 + - -1.1864815851348935 + - !!python/tuple + - 0.7372440339182692 + - -0.25480638033144176 + - -0.5161608215179317 + - !!python/tuple + - 0.9699777437583419 + - 0.9047277567437116 + - 1.6691579919725255 + - !!python/tuple + - 0.0761121423539471 + - 2.289791311600174 + - 1.048767742982737 + - !!python/tuple + - 1.6541297534087336 + - 1.8871150187165526 + - 0.37272115423271956 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2617134361721978 + - -0.0320229525976696 + - 0.262897075530221 + - !!python/tuple + - 0.049901287374796315 + - 0.5587589319372627 + - -0.2599557112536226 + - !!python/tuple + - 0.8256722243802551 + - 1.3067373260593322 + - 0.8180753884829388 + - !!python/tuple + - -1.189293814823807 + - -0.25616129598973214 + - 1.3290532117235756 + - !!python/tuple + - -1.551128290785078 + - -0.9383488119017774 + - -0.26777752484787193 + - !!python/tuple + - -2.080220985327441 + - 0.6836034524611074 + - 0.16114040258598855 + - !!python/tuple + - -0.14816673008120182 + - 1.218925544824371 + - -1.1069152150557677 + - !!python/tuple + - 0.6827337261725609 + - -0.24441988556644684 + - -0.6458348774551939 + - !!python/tuple + - 1.0853001419223538 + - 0.6358191509909014 + - 1.6390912367101171 + - !!python/tuple + - 0.23324999829320747 + - 2.123845634995721 + - 1.2362668297516242 + - !!python/tuple + - 1.7503954541066242 + - 1.7328233181675272 + - 0.4265533546677139 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2642924054552598 + - -0.03154367995540892 + - 0.26310587901395993 + - !!python/tuple + - 0.05116241554015007 + - 0.5590773033081068 + - -0.26009926676818307 + - !!python/tuple + - 0.9183409719611468 + - 1.1362265148748965 + - 0.8529926071963716 + - !!python/tuple + - -1.1936380477871147 + - -0.2557715461010884 + - 1.3292452292080679 + - !!python/tuple + - -1.5522129613503104 + - -0.9406160273596039 + - -0.2636042172069854 + - !!python/tuple + - -2.085142359208353 + - 0.6801477345350871 + - 0.15854034046931173 + - !!python/tuple + - -0.15375732692632577 + - 1.3267411104686593 + - -1.008931413516798 + - !!python/tuple + - 0.6218081224002149 + - -0.2171342251212138 + - -0.7754402522117098 + - !!python/tuple + - 1.1857794819590914 + - 0.3601876290263845 + - 1.5726131404198913 + - !!python/tuple + - 0.38927588343388286 + - 1.9219103460372742 + - 1.3971115242293952 + - !!python/tuple + - 1.8421517104986171 + - 1.5655819156922677 + - 0.4633188564454237 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2673486114175623 + - -0.029737798306194954 + - 0.2635576345124126 + - !!python/tuple + - 0.051935777130457265 + - 0.559290686169637 + - -0.2595501999855471 + - !!python/tuple + - 1.0043487834272185 + - 0.9580604690855746 + - 0.8624004945342121 + - !!python/tuple + - -1.1986537534975767 + - -0.2542414051508847 + - 1.329623790119046 + - !!python/tuple + - -1.5492557818894586 + - -0.9443382446450842 + - -0.25698329004664694 + - !!python/tuple + - -2.092088262284192 + - 0.6753066006735177 + - 0.1510610120086319 + - !!python/tuple + - -0.14934187987193132 + - 1.423944276389485 + - -0.8947959738771919 + - !!python/tuple + - 0.553483422457406 + - -0.17018159952513576 + - -0.8992309584874566 + - !!python/tuple + - 1.268007434890381 + - 0.09037508719046822 + - 1.4702801403078456 + - !!python/tuple + - 0.5437907289243348 + - 1.6955361055594707 + - 1.5235214824581715 + - !!python/tuple + - 1.9279602209741193 + - 1.3890638341132024 + - 0.47367993506947087 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2691691627141866 + - -0.031072014396655842 + - 0.262362605540056 + - !!python/tuple + - 0.05231627822066339 + - 0.5598470693587249 + - -0.2575476125823711 + - !!python/tuple + - 1.0807418059270257 + - 0.7727253629329903 + - 0.8479743715481408 + - !!python/tuple + - -1.2030122469732438 + - -0.2612652139303026 + - 1.327301938628362 + - !!python/tuple + - -1.5410119906259494 + - -0.9508783361366836 + - -0.25478116706911624 + - !!python/tuple + - -2.0995566167061996 + - 0.665027110166769 + - 0.1413446410388081 + - !!python/tuple + - -0.13578539859116787 + - 1.5099401466587936 + - -0.7611170792985098 + - !!python/tuple + - 0.4806528059050748 + - -0.0987334380446526 + - -1.0158007488150804 + - !!python/tuple + - 1.3213128555126639 + - -0.17130049424022856 + - 1.3410203859371865 + - !!python/tuple + - 0.6969764145799572 + - 1.4535577436217775 + - 1.6106139993298705 + - !!python/tuple + - 2.008805430631913 + - 1.1949956818298593 + - 0.45996020885927485 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2707827322175964 + - -0.025116898546917187 + - 0.26444768080363645 + - !!python/tuple + - 0.051413073950797 + - 0.5620743992521573 + - -0.25798992228098905 + - !!python/tuple + - 1.1451695808657985 + - 0.5933886777702184 + - 0.8041390081277527 + - !!python/tuple + - -1.203687881162642 + - -0.2539376793235793 + - 1.32965845535559 + - !!python/tuple + - -1.530445003328777 + - -0.9545859429333508 + - -0.24263376636236914 + - !!python/tuple + - -2.1070095271990406 + - 0.6606182625147634 + - 0.12964894620274275 + - !!python/tuple + - -0.11243384403849385 + - 1.576878922235758 + - -0.6262131412113637 + - !!python/tuple + - 0.40130211089635603 + - -0.013336178816997777 + - -1.1172560588511604 + - !!python/tuple + - 1.3580902905797765 + - -0.41181416561519874 + - 1.1740497483982182 + - !!python/tuple + - 0.8386781529116917 + - 1.2001193639546435 + - 1.6586475151070321 + - !!python/tuple + - 2.074696756609438 + - 1.0097945230330465 + - 0.41340104017785284 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2693576313881816 + - -0.02532274495645584 + - 0.26395439621219996 + - !!python/tuple + - 0.050842679294156076 + - 0.5629079463887461 + - -0.25776588019523894 + - !!python/tuple + - 1.1965511514148441 + - 0.41188180247752054 + - 0.7368860531197718 + - !!python/tuple + - -1.1993240074311329 + - -0.25789201674369716 + - 1.3281840910920482 + - !!python/tuple + - -1.516835756647908 + - -0.9608737937222921 + - -0.23944055195511657 + - !!python/tuple + - -2.110756219734579 + - 0.6518712226212664 + - 0.12139247119468473 + - !!python/tuple + - -0.08031126356616965 + - 1.6241985233206448 + - -0.4796387622818829 + - !!python/tuple + - 0.32272344014796245 + - 0.09205836059932489 + - -1.2043346841666593 + - !!python/tuple + - 1.3667375041410634 + - -0.638957796357455 + - 0.9812389040713041 + - !!python/tuple + - 0.9691035681655877 + - 0.9333450154771074 + - 1.668676977117435 + - !!python/tuple + - 2.1291687676053668 + - 0.8182735384187575 + - 0.3431087687747221 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.26818046819604 + - -0.02216666888315449 + - 0.26470475037649505 + - !!python/tuple + - 0.050052336078165505 + - 0.5629969151327162 + - -0.25836476584865287 + - !!python/tuple + - 1.2343866771388328 + - 0.24012382030003881 + - 0.6457409712011599 + - !!python/tuple + - -1.1960117322458506 + - -0.2538700931039025 + - 1.3291338229204768 + - !!python/tuple + - -1.5071787114186965 + - -0.9633408627354568 + - -0.23357425953477645 + - !!python/tuple + - -2.112039116208713 + - 0.6499947587864014 + - 0.11357111193211188 + - !!python/tuple + - -0.03747102513385333 + - 1.6490438240040528 + - -0.33892617361154714 + - !!python/tuple + - 0.2451487412181349 + - 0.2027087812558572 + - -1.2703588844786164 + - !!python/tuple + - 1.3625453163594496 + - -0.839145366404447 + - 0.7556806786710442 + - !!python/tuple + - 1.0805074634812295 + - 0.6564839341352988 + - 1.6430822435496422 + - !!python/tuple + - 2.1661282626471383 + - 0.6476532088760889 + - 0.251301849149635 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.266242430449481 + - -0.02008137888445315 + - 0.2651636166406973 + - !!python/tuple + - 0.04906680134992209 + - 0.5628621363318762 + - -0.25868222104186983 + - !!python/tuple + - 1.2583620771166366 + - 0.07957266113105375 + - 0.5334442632475251 + - !!python/tuple + - -1.1918445200570398 + - -0.2507955286566265 + - 1.3297909179076413 + - !!python/tuple + - -1.4998299236932087 + - -0.9640902922363974 + - -0.23138631102423013 + - !!python/tuple + - -2.110958904438692 + - 0.6501437509490136 + - 0.10950878013089486 + - !!python/tuple + - 0.01234001581570773 + - 1.6536404635109085 + - -0.20233719687262422 + - !!python/tuple + - 0.17121686126481964 + - 0.32051917152923864 + - -1.3164200365415755 + - !!python/tuple + - 1.33723850910599 + - -1.0097365222755263 + - 0.5075769545514753 + - !!python/tuple + - 1.1754969629891339 + - 0.3788365096180812 + - 1.5799597627906659 + - !!python/tuple + - 2.1888998115294838 + - 0.4898430951361638 + - 0.139223720261248 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2639786223087188 + - -0.018027878925087913 + - 0.2654784952578324 + - !!python/tuple + - 0.04785914938793647 + - 0.5643220172271027 + - -0.2581513867050187 + - !!python/tuple + - 1.2683858882313197 + - -0.06333677888232846 + - 0.4040356147175046 + - !!python/tuple + - -1.1899193997099156 + - -0.24759942894292816 + - 1.330525608270331 + - !!python/tuple + - -1.4967692023236743 + - -0.9611354303152407 + - -0.2337366590526 + - !!python/tuple + - -2.1068654240580873 + - 0.6544210285068188 + - 0.10922751946302885 + - !!python/tuple + - 0.06688616825748317 + - 1.6417370541406109 + - -0.07450579518996064 + - !!python/tuple + - 0.10311968586089967 + - 0.4412500822449483 + - -1.3420704530074394 + - !!python/tuple + - 1.2904981758585894 + - -1.1440510106589505 + - 0.2463969003261188 + - !!python/tuple + - 1.2534248208105494 + - 0.11118000761699914 + - 1.4815269627124488 + - !!python/tuple + - 2.1979232873691337 + - 0.3493096150388201 + - 0.009967582214499676 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2618577740467787 + - -0.018958435314208058 + - 0.265199084657193 + - !!python/tuple + - 0.04716681960514609 + - 0.5645094255219474 + - -0.25749099464262465 + - !!python/tuple + - 1.2655585395556137 + - -0.1921944021666377 + - 0.25697654751991894 + - !!python/tuple + - -1.1861073979850378 + - -0.2486417828394163 + - 1.3301924794169298 + - !!python/tuple + - -1.4952660077617592 + - -0.9591703260499637 + - -0.2395460211774329 + - !!python/tuple + - -2.1031419711989914 + - 0.6572135776427034 + - 0.11323399956189731 + - !!python/tuple + - 0.12626083970643007 + - 1.6113416493697352 + - 0.04767220779463248 + - !!python/tuple + - 0.041017546139288236 + - 0.5659709598765466 + - -1.3500175437103243 + - !!python/tuple + - 1.2236870284774364 + - -1.2457101604079865 + - -0.028725918542109683 + - !!python/tuple + - 1.3140717061868221 + - -0.14947985590363339 + - 1.3468112402584946 + - !!python/tuple + - 2.1939328877968074 + - 0.22325551404253607 + - -0.1369826991569815 + isotopes: *id001 + symbols: *id002 +- coords: !!python/tuple + - !!python/tuple + - -1.2598686864583883 + - -0.020961997019708394 + - 0.26507135879394544 + - !!python/tuple + - 0.04680413642996734 + - 0.5646343327782501 + - -0.25672097724609283 + - !!python/tuple + - 1.2494454717999341 + - -0.3016228954424144 + - 0.09636233494804346 + - !!python/tuple + - -1.183486789757009 + - -0.25097266781498884 + - 1.3299704420998322 + - !!python/tuple + - -1.4965280124716525 + - -0.9559639509570372 + - -0.24763224494960986 + - !!python/tuple + - -2.09861325442495 + - 0.6606528734372178 + - 0.12092773180544213 + - !!python/tuple + - 0.1892973914526296 + - 1.5655389400381678 + - 0.15925548153985897 + - !!python/tuple + - -0.014060315906668156 + - 0.6906156293450457 + - -1.3405197514763416 + - !!python/tuple + - 1.1386812428683335 + - -1.3091652897035613 + - -0.3107611155567355 + - !!python/tuple + - 1.35530849790175 + - -0.3946174485173543 + - 1.179160199241403 + - !!python/tuple + - 2.1769489128325974 + - 0.11684513172213187 + - -0.2962280861403898 + isotopes: *id001 + symbols: *id002 +- coords: *id003 + isotopes: *id001 + symbols: *id002 +schema_version: 2 +top: +- 1 +- 2 +- 6 +- 7 +- 8 +- 9 +- 10 diff --git a/arkane/data/arc_yaml/CH3_freq_uma.yml b/arkane/data/arc_yaml/CH3_freq_uma.yml new file mode 100644 index 00000000000..86b550e15ac --- /dev/null +++ b/arkane/data/arc_yaml/CH3_freq_uma.yml @@ -0,0 +1,269 @@ +force_constants: +- 0.2293311393364642 +- 1.2511657654129484 +- 1.251166161965859 +- 5.848443589668234 +- 7.250020167049637 +- 7.250023212854017 +freqs: +- 561.2474384489253 +- 1388.1071346136007 +- 1388.107338399838 +- 3138.0855973627195 +- 3316.706855838608 +- 3316.707597842139 +hessian: +- - 2.218711266303615 + - 2.8303765828275255e-08 + - 4.351923242600923e-09 + - -0.18866877901536222 + - -7.229493912204099e-09 + - 8.841638019334112e-10 + - -1.0150211209800246 + - 0.4770949099615459 + - 3.2323651672987663e-09 + - -1.0150212611675697 + - -0.47709512024286355 + - -1.8257408954083953e-09 +- - 8.369290901624887e-08 + - 2.2187105653658903 + - -8.066971478970714e-09 + - 1.933751994485844e-09 + - -1.2904714927545724 + - 4.636931424661307e-09 + - 0.4770949800553185 + - -0.4641196414463177 + - 1.3913486417583735e-09 + - -0.47709505014909104 + - -0.4641197465869764 + - 4.541812847222772e-09 +- - -2.686939485173038e-09 + - -6.838051010398185e-09 + - 0.10283845512841075 + - 1.6598165651059395e-08 + - 2.085645034240255e-09 + - -0.03427954564471108 + - 2.6065608509028705e-09 + - 6.016907000028809e-09 + - -0.034279458027495414 + - -2.9969707633701947e-09 + - 1.0552552201099535e-08 + - -0.03427945145620424 +- - -0.18866876149191908 + - 1.468721919407585e-09 + - 2.663974011884618e-09 + - 0.15766698683751698 + - 5.405065534720482e-09 + - -2.1817029896225668e-10 + - 0.015500901564998589 + - 0.08207939583729848 + - -2.0553938004550364e-09 + - 0.015500898279353002 + - -0.08207941336074162 + - 2.147254910249763e-09 +- - -2.9986150338113225e-09 + - -1.2904713525670273 + - 1.64143650955747e-09 + - 6.237362487615098e-09 + - 1.3393565719708598 + - 1.5656592278539434e-10 + - -0.012895174332740194 + - -0.024442660081815202 + - -1.2563089170661324e-09 + - 0.012895173237524997 + - -0.024442660081815202 + - -5.738477727570493e-10 +- - 6.0628374243663475e-09 + - -4.085215892386955e-09 + - -0.03427956973944539 + - -5.879115204776895e-09 + - -6.995477044993356e-11 + - 0.011426777701478968 + - 2.5261823145525717e-10 + - 4.501197774497048e-09 + - 0.011426402042666789 + - 9.071290793820927e-10 + - 3.720377688442748e-09 + - 0.01142639656659081 +- - -1.015021050886252 + - 0.4770949450084322 + - -2.7558353827989947e-09 + - 0.015500901564998589 + - -0.012895174332740194 + - -2.2735640994172933e-09 + - 1.0439347320568435 + - -0.5116869927858376 + - 7.635960463678983e-10 + - -0.044414441452829696 + - 0.047487291108702916 + - -9.989902544567316e-10 +- - 0.4770949800553185 + - -0.4641196414463177 + - -4.593058753731949e-10 + - 0.08207940459902005 + - -0.024442653510524028 + - -4.42081887910723e-09 + - -0.5116871329733826 + - 0.4530895802595879 + - -3.4103461491259393e-09 + - -0.047487299870424486 + - 0.03547268184079789 + - 1.5386746988201812e-09 +- - -1.929084611287506e-09 + - 8.956464602417258e-09 + - -0.03427945364663463 + - -9.140187344246011e-09 + - -1.1884539729281146e-09 + - 0.011426383424008459 + - -1.0104729258210287e-09 + - -7.968957084604736e-09 + - 0.011426651751731444 + - -1.1827126046060096e-09 + - -6.372868963683155e-09 + - 0.011426416280464334 +- - -1.0150212611675697 + - -0.4770949800553185 + - -4.225614183993219e-09 + - 0.015500910326720154 + - 0.012895176523170586 + - 1.6018292281240335e-09 + - -0.044414441452829696 + - -0.0474872954895637 + - -1.9520499540161005e-09 + - 1.043934802150616 + - 0.5116872381140415 + - 6.717348712932595e-10 +- - -0.47709508519597726 + - -0.46411971154009013 + - 6.8436577715402985e-09 + - -0.08207941336074162 + - -0.02444265570095442 + - -3.904099777472375e-10 + - 0.047487291108702916 + - 0.035472679650367496 + - 3.272554353874025e-09 + - 0.5116872030671552 + - 0.45308972044713297 + - -5.500187767834129e-09 +- - -1.4468134584656296e-09 + - 2.0209458516420574e-09 + - -0.034279427361469925 + - -1.5846052537175444e-09 + - -8.095266012652615e-10 + - 0.011426383424008459 + - -1.8429648698148844e-09 + - -2.537664953276913e-09 + - 0.011426399852236396 + - 3.2610716172298147e-09 + - -7.923026138027896e-09 + - 0.011426635323503506 +hessian_method: analytic +modes: +- - - -5.336181813399536e-10 + - 1.844013724670874e-09 + - -0.14384727368356123 + - - -1.6950748366273965e-09 + - 5.737818056072887e-09 + - 0.5713458357571031 + - - -4.007700192269693e-09 + - -1.715873914773742e-08 + - 0.571345735005007 + - - 1.2061195676133995e-08 + - -1.0551746402993637e-08 + - 0.571345735005007 +- - - 0.030953008684532338 + - 0.08714119672983488 + - 2.839630873949293e-09 + - - -0.27096550343841946 + - 0.07061134734550369 + - -1.1278707179039689e-08 + - - -0.40982628998415394 + - -0.682670867440476 + - -1.1278705130006789e-08 + - - 0.31196581394844836 + - -0.4262866246689631 + - -1.1278705110601787e-08 +- - - 0.08714121118098837 + - -0.0309530057469899 + - -7.424984018555035e-10 + - - -0.7628421837590486 + - -0.025081510682798697 + - 2.9491236166181422e-09 + - - -0.009559902949555645 + - -0.16394222300132727 + - 2.9491230125407827e-09 + - - -0.26594423025057345 + - 0.557849678155451 + - 2.949123145748259e-09 +- - - 5.1399087014881946e-08 + - 2.9371634615442283e-07 + - -3.846073018111192e-10 + - - -4.019387777452889e-09 + - -0.5773527475898186 + - 1.5276188575238686e-09 + - - -0.49999916816882295 + - 0.28867479720032396 + - 1.5276185767248423e-09 + - - 0.4999985597334149 + - 0.2886744505610881 + - 1.527618556232693e-09 +- - - 0.008448720183083654 + - -0.09990209220898184 + - 2.6327305812405756e-10 + - - 0.0013310824494902282 + - 0.8093380154359234 + - -1.0456924086129632e-09 + - - -0.4082731205143891 + - 0.22074572263268308 + - -1.0456922823485663e-09 + - - 0.3062698375500002 + - 0.1603170848699659 + - -1.0456922505480167e-09 +- - - 0.09990207811447789 + - 0.008448722448542584 + - -9.5344832672782e-10 + - - 0.01573944679160186 + - -0.06844540097007455 + - 3.7869938202804105e-09 + - - -0.5728553274973974 + - 0.34115649521519154 + - 3.7869931332892805e-09 + - - -0.6332847742872539 + - -0.37338332175448685 + - 3.7869931238609526e-09 +opt_xyz: + coords: !!python/tuple + - !!python/tuple + - -0.0 + - 5.0e-08 + - -0.0 + - !!python/tuple + - -0.0 + - 1.07745346 + - -0.0 + - !!python/tuple + - 0.93310198 + - -0.53872675 + - 0.0 + - !!python/tuple + - -0.93310198 + - -0.53872675 + - 0.0 + isotopes: !!python/tuple + - null + - null + - null + - null + symbols: + - C + - H + - H + - H +reduced_masses: +- 1.2356744957225634 +- 1.1020941010862004 +- 1.102094126797244 +- 1.008000000000979 +- 1.118600053331805 +- 1.1186000227670083 +schema_version: 2 diff --git a/arkane/data/arc_yaml/H2O_freq_uma.yml b/arkane/data/arc_yaml/H2O_freq_uma.yml new file mode 100644 index 00000000000..ee782b91d53 --- /dev/null +++ b/arkane/data/arc_yaml/H2O_freq_uma.yml @@ -0,0 +1,146 @@ +force_constants: +- 1.681037496426943 +- 8.991561117710436 +- 9.80446140374819 +freqs: +- 1622.8806456626505 +- 3821.6458861947726 +- 3920.7853750367576 +hessian: +- - 2.2054031011144793e-06 + - -1.8372235014927796e-10 + - -2.0209458516420574e-09 + - -1.0979247571807348e-06 + - 4.593058623172124e-09 + - -4.593058623172124e-09 + - -1.1023340946287962e-06 + - 5.0523644332654065e-09 + - -1.929084611287506e-09 +- - 5.195259828412309e-11 + - 2.4412486202231656 + - -1.2346141512240038e-07 + - 2.0094632047577277e-11 + - -1.2206243101115828 + - 0.9372478046325761 + - 9.186117507463898e-10 + - -1.2206243101115828 + - -0.9372475943512585 +- - -6.952742594621864e-09 + - -5.2912036842992053e-08 + - 1.6133388296796665 + - 4.6583662145567e-09 + - 0.7264155499761519 + - -0.8066695550273784 + - 3.9751487371790565e-09 + - -0.7264154798823794 + - -0.8066694148398332 +- - -1.0971898453238478e-06 + - 1.2860564510449457e-09 + - -1.8372235014927796e-10 + - 1.421276080909721e-06 + - -1.6994317062408648e-09 + - 5.511670504478339e-10 + - -3.255559924530166e-07 + - -3.9500305934893884e-09 + - 6.889588456997487e-10 +- - 4.4364855359163105e-09 + - -1.2206243101115828 + - 0.7264154097886069 + - -3.401734161922695e-09 + - 1.330307185561531 + - -0.8318316072105915 + - -1.9427202794526146e-09 + - -0.10968277030928962 + - 0.10541611856649054 +- - 3.459147322904442e-09 + - 0.9372475943512585 + - -0.8066693447460609 + - -2.1214189486400286e-09 + - -0.8318316773043639 + - 0.7631655046348126 + - -3.4476648473798834e-09 + - -0.10541613608993367 + - 0.04350409858203441 +- - -1.108213188944001e-06 + - -1.1023341008956678e-09 + - 2.2046682017913356e-09 + - -3.2298390122385775e-07 + - -2.893626916931259e-09 + - 4.041891703284115e-09 + - 1.4278901539284433e-06 + - -1.1023341008956678e-09 + - 1.2860564510449457e-09 +- - -4.488438423880046e-09 + - -1.2206244502991277 + - -0.7264152696010617 + - 3.3816394380752404e-09 + - -0.10968275278584648 + - -0.10541613608993367 + - 1.0248262160664656e-09 + - 1.330307045373986 + - 0.8318313969292738 +- - 3.493595271717421e-09 + - -0.9372475943512585 + - -0.8066694148398332 + - -2.537664953276913e-09 + - 0.10541611856649054 + - 0.043504116105477546 + - -5.282017729991524e-10 + - 0.8318316072105915 + - 0.7631653644472676 +hessian_method: analytic +modes: +- - - -7.72819960479696e-19 + - -2.512646223737874e-09 + - -0.07087943746873238 + - - 8.017436283728623e-17 + - 0.42553701677266353 + - 0.5625000442435872 + - - -6.790814602407724e-17 + - -0.4255369768918831 + - 0.5625000748657881 +- - - 4.1755965198854864e-19 + - 5.420713789432629e-08 + - 0.04962828729447997 + - - -8.262889595739319e-17 + - 0.5862163892331456 + - -0.39385034846446854 + - - 7.600137921913446e-17 + - -0.5862172496101287 + - -0.39385100909940524 +- - - -4.089198578037246e-18 + - 0.07049513823508612 + - -4.205837406679078e-08 + - - 8.815894740500481e-17 + - -0.5594507080862843 + - 0.4295706173281188 + - - -2.3255090212526718e-17 + - -0.559449804436675 + - -0.42956994977660434 +opt_xyz: + coords: !!python/tuple + - !!python/tuple + - 0.0 + - 0.0 + - 0.1121557 + - !!python/tuple + - -0.0 + - 0.76271987 + - -0.47349385 + - !!python/tuple + - -0.0 + - -0.76271987 + - -0.47349385 + isotopes: !!python/tuple + - null + - null + - null + symbols: + - O + - H + - H +reduced_masses: +- 1.0833132047863558 +- 1.0449223367946978 +- 1.082498741641152 +schema_version: 2 diff --git a/arkane/data/arc_yaml/H2O_freq_uma_ev_hessian.out b/arkane/data/arc_yaml/H2O_freq_uma_ev_hessian.out new file mode 100644 index 00000000000..ef48e5315fb --- /dev/null +++ b/arkane/data/arc_yaml/H2O_freq_uma_ev_hessian.out @@ -0,0 +1,146 @@ +force_constants: +- 1.6809958789822612 +- 8.991750141424617 +- 9.804724347938532 +freqs: +- 1622.860036861635 +- 3821.6872367553538 +- 3920.83583296181 +hessian: +- - 52.34270095825195 + - 6.660839062533341e-07 + - -10.905820846557617 + - -4.258204460144043 + - -3.144116078601655e-08 + - 2.647361993789673 + - -48.08449935913086 + - -6.749498879798921e-07 + - 8.258461952209473 +- - 1.1698455182340695e-06 + - -0.00047857678146101534 + - 1.094855406336137e-06 + - -8.373893933821819e-07 + - 0.00024718735949136317 + - -1.3498217299456883e-07 + - -3.299564070857741e-07 + - 0.00023077952209860086 + - -6.911586751812138e-07 +- - -10.905820846557617 + - 5.297737857290485e-07 + - 57.990604400634766 + - -3.0897159576416016 + - -5.135258902555506e-07 + - -50.90849685668945 + - 13.995539665222168 + - -1.5015716448019134e-09 + - -7.082123756408691 +- - -4.258204460144043 + - -2.667225658115058e-07 + - -3.0897159576416016 + - 4.63610315322876 + - 9.59150625590155e-08 + - -1.79643976688385 + - -0.3778989911079407 + - 1.8614728958255e-07 + - 4.886155605316162 +- - -7.499009768707765e-08 + - 0.0002473273198120296 + - -6.099194251873996e-07 + - 1.8497556197871745e-07 + - -0.00015251984586939216 + - 2.9746070140390657e-07 + - -8.030189491137207e-08 + - -9.467749623581767e-05 + - 3.5245344065515383e-07 +- - 2.647362470626831 + - -2.81369068488857e-07 + - -50.908485412597656 + - -1.7964401245117188 + - 3.297611215202778e-07 + - 52.33126449584961 + - -0.8509224653244019 + - -6.33627550428173e-08 + - -1.4227629899978638 +- - -48.08449172973633 + - -3.9936131202011893e-07 + - 13.995535850524902 + - -0.3778991997241974 + - -6.44641389158096e-08 + - -0.8509219884872437 + - 48.46239471435547 + - 4.887635896011489e-07 + - -13.144618034362793 +- - -1.094855406336137e-06 + - 0.00023122945276554674 + - -4.830611715078703e-07 + - 6.52413802981755e-07 + - -9.465749462833628e-05 + - -1.5997886748664314e-07 + - 4.099458408290957e-07 + - -0.0001361020258627832 + - 3.3870526294776937e-07 +- - 8.258458137512207 + - -2.484046888184821e-07 + - -7.082122325897217 + - 4.88615608215332 + - 1.8376478294612753e-07 + - -1.4227629899978638 + - -13.14461612701416 + - 6.486432369001705e-08 + - 8.50488567352295 +hessian_method: analytic +modes: +- - - -0.05605036225148609 + - -1.0321075044024505e-09 + - -0.04338545659562618 + - - 0.705285257631109 + - 9.242548462144512e-09 + - 0.00780379903532377 + - - 0.1843474265569132 + - 7.139086775239507e-09 + - 0.6808112010375169 +- - - -0.03924553921056583 + - -7.22653480553637e-10 + - -0.030376166303507566 + - - -0.04737759412566988 + - 4.285998715229871e-09 + - 0.7046316328873977 + - - 0.670283726893371 + - 7.183974177259727e-09 + - -0.2225003980760696 +- - - -0.04314962972578372 + - -1.7422023096274286e-10 + - 0.05574721475325248 + - - 0.0027513863326259673 + - -4.872412763193857e-09 + - -0.7053555317371467 + - - 0.6821205640471498 + - 7.637641129482936e-09 + - -0.17946558814111513 +opt_xyz: + coords: !!python/tuple + - !!python/tuple + - 4.598794733005291e-05 + - -5.68515377200173e-09 + - 3.573568792391168e-05 + - !!python/tuple + - -0.0037039321114414386 + - 9.574549937374164e-10 + - 0.9616519298811632 + - !!python/tuple + - 0.9300209933965768 + - 4.727682990408997e-09 + - -0.24464133593728785 + isotopes: !!python/tuple + - 16 + - 1 + - 1 + symbols: !!python/tuple + - O + - H + - H +reduced_masses: +- 1.0833138988194335 +- 1.0449216910939507 +- 1.082499910690778 +schema_version: 2 diff --git a/arkane/data/arc_yaml/TS_OHCH4_freq_uma.yml b/arkane/data/arc_yaml/TS_OHCH4_freq_uma.yml new file mode 100644 index 00000000000..eda29545780 --- /dev/null +++ b/arkane/data/arc_yaml/TS_OHCH4_freq_uma.yml @@ -0,0 +1,854 @@ +force_constants: +- -0.785272453920216 +- 0.00014027505306821026 +- 0.06693539988740117 +- 0.06876749533184671 +- 0.642509923990138 +- 0.7646789196879674 +- 0.9027611374008552 +- 1.012842249198268 +- 1.1678554674116302 +- 1.2742071761121727 +- 1.277498753349335 +- 5.723474850117076 +- 6.694847664921766 +- 6.724986901164005 +- 8.812871601301259 +freqs: +- -1058.1653158279487 +- 15.08949635199117 +- 323.96031556868127 +- 329.1875198738176 +- 764.078762314154 +- 897.1095090527634 +- 1177.495874986306 +- 1261.3484432643074 +- 1338.878516499239 +- 1432.18350344967 +- 1447.7436047372871 +- 3081.3994721982913 +- 3203.0771118231164 +- 3209.550145819104 +- 3744.1125622618188 +hessian: +- - 2.025924653386267 + - -0.002688062225037242 + - -0.014821923999543022 + - -1.1021509746480491 + - 0.06326372581745969 + - 0.30155658707380406 + - -0.3391889171880187 + - 0.3684535929245779 + - -0.09057427917382606 + - -0.48232579792449803 + - -0.42600191195729975 + - -0.20679742930456227 + - -0.10575554765999012 + - -0.0013789872328266479 + - 0.002698194608421701 + - -0.0006275778841969615 + - -0.005092763803311513 + - 0.0165616612907927 + - 0.004123792967866874 + - 0.0034442179625219682 + - -0.008622743139352561 +- - -0.002687907525890827 + - 2.017777794392096 + - 0.08061157967009107 + - 0.06406068324945842 + - -0.1759564322409118 + - -0.027460724883161328 + - 0.3679607986567722 + - -0.9901837431511927 + - 0.1973258681032568 + - -0.4261019357707068 + - -0.7528887762684003 + - -0.2913736792219295 + - -0.005788331140946304 + - -0.0997290340467175 + - -0.006553434786581171 + - -0.0034499221170657835 + - 0.001435278008248045 + - 0.0534189415625713 + - 0.0060067104797087625 + - -0.00045508624819069033 + - -0.005968554825107942 +- - -0.014821888952656754 + - 0.08061153586148323 + - 0.9947702590632327 + - 0.27900123467394333 + - -0.024855021745637237 + - -0.18861711990500407 + - -0.08140921175465043 + - 0.17488909684308176 + - -0.14032502524263932 + - -0.19349809975546256 + - -0.27017378267190295 + - -0.22035060345089658 + - 0.04861050876668629 + - 0.02374798698738783 + - -0.015639004915550408 + - -0.01837327317448561 + - 0.02857594527978456 + - -0.43107112863390035 + - -0.019509258851222268 + - -0.012795867885286366 + - 0.0012325936508497974 +- - -1.102150694272959 + - 0.06406069639204078 + - 0.27900123467394333 + - 1.1736042159011277 + - -0.07042860172444398 + - -0.30552788994430635 + - -0.02869218046852073 + - -0.005624699967001881 + - 0.012187939120016353 + - -0.043736630291557714 + - 0.01125538309461872 + - 0.019906561306101286 + - -0.003628770210941427 + - 0.0010525260348535686 + - -0.010340599126204239 + - 0.004366057307228151 + - -0.0007022235079876044 + - 0.0025409447058159307 + - 0.00023842393305153496 + - 0.0003869310750035378 + - 0.0022318005029121246 +- - 0.06326368200885185 + - -0.1759564322409118 + - -0.02485500860305489 + - -0.07042860172444398 + - 0.16120029124689267 + - 0.025090547773506014 + - 0.09133788949354138 + - 0.004276975788842834 + - -0.032503481160630066 + - -0.07718232070432168 + - 0.012583419136809467 + - 0.029117634334794022 + - -0.0061628109539664825 + - -0.0016753773809709152 + - 0.005841451268375699 + - -0.0007809739298813647 + - -0.0009093398590287315 + - -0.001570969558036692 + - -4.690477691472916e-05 + - 0.00048047518460626925 + - -0.0011201674152119653 +- - 0.30155648193314527 + - -0.027460753358756414 + - -0.18861710238156093 + - -0.30552788994430635 + - 0.02509056748737954 + - 0.2056881603073133 + - -0.025979818703933035 + - 0.0008422608032224569 + - 0.009967123077911063 + - -0.04015871995768524 + - 0.004268225019427946 + - 0.014966334694407774 + - 0.06650642144590622 + - -0.0027706083205450895 + - -0.059380399393210104 + - 0.00034288394983493595 + - 0.0007534409728179988 + - 0.016938689121966038 + - 0.0032605859686708266 + - -0.0007231427342869965 + - 0.000437209358578011 +- - -0.3391888120473599 + - 0.3679607986567722 + - -0.08140920299292888 + - -0.028692178278090338 + - 0.09133787197009825 + - -0.0259798011804899 + - 0.3387902238098409 + - -0.40196062415003136 + - 0.0891158292869736 + - 0.03047760904252631 + - -0.056011530593340214 + - 0.016287289075142118 + - -0.00047936823007253295 + - -0.00026774731026906357 + - 0.004233685765403843 + - -1.7821802641329165e-05 + - -0.002206632868417058 + - -0.0014775178572161106 + - -0.0008895356987006198 + - 0.0011478618480657704 + - -0.000770283534354617 +- - 0.36845352283080535 + - -0.9901838132449652 + - 0.17488907931963862 + - -0.005624699967001881 + - 0.004276976336450432 + - 0.0008422664846512854 + - -0.40196065919691765 + - 1.0487536088248361 + - -0.19441282348704128 + - 0.036985250691338366 + - -0.055946295195414254 + - 0.02111688799990224 + - 0.003420142942086667 + - -0.009928459791066964 + - -0.006008139187931756 + - -0.001681986046364608 + - 0.002572281824411152 + - 0.0035696187334284544 + - 0.00040832733597167485 + - 0.0004557853035149202 + - 3.1302154064002674e-06 +- - -0.09057427917382606 + - 0.1973258681032568 + - -0.14032499895747463 + - 0.012187941310446744 + - -0.03250347020847811 + - 0.009967119792265475 + - 0.08911584681041673 + - -0.19441285853392756 + - 0.15503119813856273 + - 0.01846758872629192 + - -0.03621552688039978 + - 0.011803145117889203 + - -0.03198674986950376 + - 0.06570820670686264 + - -0.05794768268259946 + - 0.0013379489718303354 + - -0.004102515948453185 + - 0.020828020611134507 + - 0.001451724170334713 + - 0.0042002964873353865 + - 0.0006432281670909912 +- - -0.48232579792449803 + - -0.42610179558316175 + - -0.19349808223201942 + - -0.043736639053279285 + - -0.07718232946604325 + - -0.04015873310026759 + - 0.030477622185108664 + - 0.036985250691338366 + - 0.018467586535861526 + - 0.49621519437423844 + - 0.4667992913234355 + - 0.21205945642596286 + - -0.0009319327110492907 + - -0.003164276029992861 + - 0.006493113071631427 + - 0.0015062942257815216 + - 0.002333472341385201 + - -0.005249710331308031 + - -0.0012046731929599478 + - 0.00033057530540536153 + - 0.0018863766121360993 +- - -0.4260017717697547 + - -0.7528886360808552 + - -0.27017373010157353 + - 0.011255380904188329 + - 0.01258342132723986 + - 0.004268225840839343 + - -0.05601154373592256 + - -0.05594629957627504 + - -0.03621552688039978 + - 0.466799221229663 + - 0.7928605911816216 + - 0.294276893186547 + - 0.0015864710970169343 + - 0.0008798314760067905 + - 0.0164996896341504 + - 0.003357089760438459 + - 0.003987139956038165 + - -0.011293910574778535 + - -0.0009848578901738231 + - -0.0014759152835807745 + - 0.00263832932440483 +- - -0.20679748187489166 + - -0.2913736266516001 + - -0.22035058592745344 + - 0.019906563496531676 + - 0.029117640906085197 + - 0.014966345646559734 + - 0.016287290170357314 + - 0.02111689019033263 + - 0.011803149498749986 + - 0.212059473949406 + - 0.29427692823343327 + - 0.24234867531221968 + - -0.045026872647769875 + - -0.053430853123041425 + - -0.07520580774466476 + - -0.0013963795239406358 + - -0.0021415562766945065 + - 0.027889376777806518 + - 0.004967387948550731 + - 0.002434645856944163 + - -0.001451125909033977 +- - -0.10575552137482543 + - -0.005788353592857819 + - 0.048610513147547066 + - -0.003628768841922432 + - -0.0061627906924853594 + - 0.06650640830332387 + - -0.0004793629251239281 + - 0.0034201407516562757 + - -0.031986752059934155 + - -0.0009319319580888435 + - 0.0015864672637637487 + - -0.045026872647769875 + - 0.16109092743829528 + - 0.027789449343336638 + - -0.017292359298657356 + - -0.045541400365922115 + - -0.01795250573403538 + - 0.029006831413429295 + - -0.004753926673625264 + - -0.002892410214317994 + - -0.0498177820005212 +- - -0.001378982167456367 + - -0.0997290340467175 + - 0.023748024224704487 + - 0.0010525271300687643 + - -0.0016753653336037606 + - -0.002770612701405873 + - -0.00026774511983867187 + - -0.009928461981497357 + - 0.0657081891834195 + - -0.0031642839703030314 + - 0.0008798320236143882 + - -0.053430853123041425 + - 0.027789444962475852 + - 0.138086247671322 + - 0.00820809740423957 + - -0.014620820585279993 + - -0.030444432783813452 + - -0.012207414236629058 + - -0.009410141533121866 + - 0.0028112147929504356 + - -0.02925542335858463 +- - 0.0026981918703837117 + - -0.006553389335150543 + - -0.015638953440436202 + - -0.010340599126204239 + - 0.005841422245173008 + - -0.059380425678374794 + - 0.004233687682030435 + - -0.006008150687691312 + - -0.0579477002060426 + - 0.006493111428808634 + - 0.016499701681517553 + - -0.07520581650638633 + - -0.017292350536935792 + - 0.008208109999214324 + - -0.06600257864720474 + - -0.01393279325666107 + - -0.03860120566593723 + - 0.29422621538900434 + - 0.028140754950420104 + - 0.02061353585760851 + - -0.02005072010147099 +- - -0.0006275793901178557 + - -0.0034499218432619844 + - -0.01837328850749835 + - 0.004366058128639549 + - -0.0007809742036851637 + - 0.0003428865167455512 + - -1.7821572688919878e-05 + - -0.001681986046364608 + - 0.0013379488349284361 + - 0.0015062942257815216 + - 0.003357090034242258 + - -0.0013963791132349374 + - -0.045541400365922115 + - -0.014620820585279993 + - -0.013932781209293914 + - 1.3042338442415935 + - 0.823951805489778 + - 0.13067107128347683 + - -1.2639194109682224 + - -0.8067752564363609 + - -0.09864947604730173 +- - -0.005092761612881121 + - 0.0014352749964062564 + - 0.0285759343276326 + - -0.0007022235079876044 + - -0.0009093404066363293 + - 0.0007534413835236972 + - -0.0022066332791227565 + - 0.0025722826458225486 + - -0.0041025145794341905 + - 0.002333471246170005 + - 0.003987140229841964 + - -0.002141554223166014 + - -0.017952504638820185 + - -0.030444428402952667 + - -0.038601196904215665 + - 0.8239518755835504 + - 0.5374040474599809 + - 0.07139991303476216 + - -0.800331185458377 + - -0.5140450173876797 + - -0.055884025640238685 +- - 0.016561664576438286 + - 0.05341892841998895 + - -0.43107119872767286 + - 0.0025409529199298996 + - -0.001570974760308872 + - 0.01693870116933319 + - -0.001477518267921809 + - 0.003569619554839851 + - 0.0208280228015649 + - -0.005249710878915629 + - -0.011293910574778535 + - 0.027889376777806518 + - 0.029006829222998905 + - -0.012207409855768275 + - 0.29422621538900434 + - 0.1306710800451984 + - 0.07139989551131903 + - 0.1610504307612133 + - -0.17205327804075643 + - -0.10331617047339986 + - -0.08986161826502195 +- - 0.004123793241670673 + - 0.006006708836885969 + - -0.019509247899070308 + - 0.00023842283783633914 + - -4.690357046673997e-05 + - 0.0032605851472594298 + - -0.0008895356987006198 + - 0.00040832668568765236 + - 0.0014517238965309142 + - -0.0012046727822542492 + - -0.0009848579586247729 + - 0.0049673863057279385 + - -0.004753928864055656 + - -0.009410141533121866 + - 0.028140746188698544 + - -1.2639194109682224 + - -0.8003311153646044 + - -0.17205327804075643 + - 1.2664052165173953 + - 0.8043580726904993 + - 0.15374210356787582 +- - 0.0034442179625219682 + - -0.0004550849818481202 + - -0.01279586350442558 + - 0.0003869306642978393 + - 0.00048047532150816873 + - -0.0007231428027379462 + - 0.0011478617111638709 + - 0.00045578482435827195 + - 0.004200295939727788 + - 0.000330575442307261 + - -0.0014759158311883726 + - 0.0024346453093365646 + - -0.002892411583336989 + - 0.0028112153405580338 + - 0.020613531476747726 + - -0.8067751863425884 + - -0.5140450173876797 + - -0.10331617047339986 + - 0.8043580726904993 + - 0.5122285022255549 + - 0.0895867104891406 +- - -0.008622745877390552 + - -0.005968554825107942 + - 0.0012325978948086814 + - 0.002231799818402627 + - -0.0011201668676043674 + - 0.000437208845195888 + - -0.0007702837397074661 + - 3.1303359977218812e-06 + - 0.0006432286462476393 + - 0.0018863757907247028 + - 0.0026383290506010308 + - -0.0014511263197396753 + - -0.049817777619660414 + - -0.029255436501166982 + - -0.020050713530179818 + - -0.09864945852385859 + - -0.05588399935507398 + - -0.08986161826502195 + - 0.1537420860444327 + - 0.08958670172741903 + - 0.10905042810208879 +hessian_method: analytic +modes: +- - - -0.004020020161887209 + - -0.0017340259850885085 + - -0.012042582741398076 + - - -0.03557578420702775 + - 0.02104614182571696 + - -0.15225964541813944 + - - 0.02363108163595405 + - -0.020372352372105714 + - -0.197242191157068 + - - 0.034226813355928705 + - 0.06742186084427283 + - -0.2564356440655624 + - - -0.09766038614371234 + - 0.02878683922504391 + - -0.9134554555280145 + - - 0.0059750972411606665 + - -0.0063460706649674644 + - 0.10938631164287181 + - - 0.02844264183018441 + - 0.024504584560120127 + - -0.07329370933456227 +- - - 0.0016977527438827742 + - -0.0009544883496977355 + - -0.0006226547333961897 + - - -0.03398350158759761 + - -0.25521466704455 + - -0.059202704717495516 + - - 0.23299699386917821 + - 0.11807546597735644 + - 0.06764583232251681 + - - -0.2366241377115112 + - 0.17460666222615948 + - -0.005386441707846189 + - - 0.05992311521815946 + - -0.0873378096724612 + - -0.00907425279303263 + - - 0.026998414771476142 + - -0.04203597612415668 + - -0.0034062365027940494 + - - -0.4710618211132518 + - 0.7284397350002042 + - 0.06750078496234892 +- - - -0.004210193445638161 + - -0.03649253514326523 + - 0.05163515213176643 + - - 0.052052475775274415 + - 0.11020030987585776 + - 0.20349346756066744 + - - 0.05910854625878817 + - 0.0796213603160266 + - 0.46025553150401477 + - - 0.04703289061519943 + - 0.16479266924858615 + - -0.4841600520998831 + - - -0.1797387641125663 + - -0.5193635299887662 + - -0.007026496112606453 + - - 0.0008719298489176474 + - 0.037011979562700185 + - -0.025508154758138845 + - - 0.057872855255691774 + - 0.012127343903571801 + - -0.38296408208154076 +- - - 0.03095407079628207 + - -0.01982341282204401 + - -0.03979789403594232 + - - -0.11623736056011566 + - 0.11180079350457281 + - -0.5696949300649282 + - - -0.1278479751147654 + - 0.008697066409766892 + - 0.42839167618552526 + - - -0.13000656489400086 + - 0.0557868515910365 + - 0.0534736205853891 + - - 0.5204481852176646 + - -0.2721328660375689 + - -0.05344079188651627 + - - -0.03403139382073352 + - 0.027575713262411965 + - 0.023131267198230474 + - - 0.0249521730930548 + - -0.10562488622153639 + - 0.24834915668967075 +- - - 0.06486648565715618 + - 0.021338420655484705 + - 0.2248311288630533 + - - -0.10135263455789331 + - -0.03467565735858266 + - -0.3233373697366866 + - - -0.08657612820063482 + - -0.09189509317959975 + - 0.007121529015163675 + - - -0.05037272778612069 + - -0.046254850019545136 + - 0.5436385917755817 + - - 0.07029244481566403 + - 0.065771089666236 + - -0.3347670091560726 + - - -0.03752319890139531 + - -0.01232106735113792 + - -0.1236003205272051 + - - -0.009349783640736254 + - 0.04835310817108513 + - -0.609883083821972 +- - - -0.043512895930811604 + - -0.042489158599962086 + - 0.14856574468497147 + - - -0.020831296254021615 + - 0.021684210313888973 + - 0.19443451448177734 + - - 0.06869629216462678 + - -0.01498968620001792 + - 0.022312124962734617 + - - 0.052206139332617967 + - 0.06603691983373694 + - -0.25819901720729493 + - - 0.07257863940019384 + - 0.0815080229163308 + - -0.3207080137648341 + - - 0.022862332559704664 + - 0.02760088058954018 + - -0.14189546640049852 + - - -0.017035752418949685 + - -0.08603431270511781 + - 0.8440675418553789 +- - - 0.0480455294378892 + - -0.07965196117003655 + - -0.010469908673972714 + - - -0.008612450709978667 + - 0.19811332412316474 + - -0.22913031213297702 + - - -0.03240962421793617 + - 0.0036603230052197787 + - 0.4514787918267384 + - - -0.14746034914311554 + - 0.12769034403233961 + - -0.12928712979305634 + - - -0.4092614522952011 + - 0.6841382386422237 + - 0.05138473841634302 + - - 0.002901873150827857 + - -0.006096826884113965 + - -0.0007902226577574542 + - - -0.020809618295060228 + - 0.03227360247110803 + - -0.007147630594282145 +- - - -0.01638691463678054 + - 0.0019055758101178572 + - -0.07841174418599875 + - - 0.15799862160417844 + - -0.04936308694161516 + - 0.5554988691620024 + - - -0.02348193236744768 + - 0.11054061819835348 + - 0.5021373637893083 + - - -0.060722890394706464 + - -0.17498676098190732 + - 0.4337260799401242 + - - 0.15827550165340437 + - 0.09500368747072405 + - -0.36847110656273485 + - - -0.0024661553219989946 + - -0.0002800644328951064 + - -0.010816626881701989 + - - 0.002334718055199219 + - 0.0005445103165109785 + - -0.01688061813586194 +- - - 0.07250208856434222 + - 0.046805690429711805 + - -0.02803191794076575 + - - 0.013913129707691404 + - -0.21452846865166889 + - -0.09961609034354184 + - - -0.34113099520929385 + - -0.12500489435197626 + - 0.06422094703883609 + - - -0.12802310812426845 + - 0.030396636081132588 + - 0.2800064223250994 + - - -0.6675424216087105 + - -0.3990661772510849 + - -0.07325345846444244 + - - 0.016401225238889663 + - 0.01139322665372125 + - -0.008877861971647277 + - - -0.0014485376456863364 + - -0.03035203727893718 + - 0.30357102872075703 +- - - 0.04227175012464306 + - -0.04913556589443966 + - -0.0032844888848329004 + - - 0.14518115511703736 + - 0.4692087878772956 + - 0.2623134942615899 + - - -0.15443586643592544 + - -0.18338427572178245 + - -0.28341983709078344 + - - -0.6051099063900632 + - 0.39017666181190463 + - 0.08326346111026385 + - - 0.12338422348370923 + - -0.08232076020128981 + - -0.008513591713351249 + - - -0.0011960781839852332 + - -7.733137828101942e-05 + - 0.0004183584484236094 + - - 0.006268156247555704 + - -0.006969593647841557 + - -0.021146821032600616 +- - - 0.033217462100023555 + - 0.03352126320001297 + - 0.01076211900803781 + - - 0.03112389853129887 + - -0.5310648574346144 + - 0.15855592305108582 + - - -0.5933500187283552 + - -0.24233376668462117 + - 0.05862925015370508 + - - -0.022855448371369467 + - 0.2110417341023295 + - -0.319004676037633 + - - 0.26858584461740914 + - 0.21507286301559567 + - 0.028393718233039347 + - - -0.005224857168131265 + - -0.003687438729794433 + - 0.0025779208662708776 + - - 0.003616311797791657 + - 0.006382677738042296 + - -0.09572894490913623 +- - - 0.0006356781832393787 + - -0.0004287957438660664 + - 0.03701560353196842 + - - 0.5525839806541698 + - -0.039229897449752096 + - -0.14968130173330663 + - - -0.22659996509929953 + - 0.5006439088963873 + - -0.0953564575607713 + - - -0.3346747512799122 + - -0.45778670937898003 + - -0.19138122304962793 + - - 0.0026671028340346787 + - 0.0015803285652117394 + - 0.006184855576203528 + - - -0.000148278409293798 + - -4.338506321481953e-05 + - -0.0006695814383500774 + - - 0.0008025769499391378 + - 0.0005903686785908716 + - -0.00020414762764618975 +- - - 0.07926412948462418 + - 0.05244743280722879 + - 0.003466645183886492 + - - -0.6165681764357289 + - 0.05299357455147622 + - 0.18516767742379167 + - - 0.07019683434885117 + - -0.11637421229613697 + - 0.027605440565788973 + - - -0.4071872727890393 + - -0.5680865647275358 + - -0.25628041768602305 + - - 0.012832090889406603 + - 0.00906679880613228 + - 0.0014831577525607964 + - - -0.00020994600138880644 + - -0.0001313859791203156 + - 0.0003052270134350381 + - - -0.000426782723411583 + - -0.0004607780479031283 + - -0.004127844456522719 +- - - -0.052720816772585305 + - 0.07919834184718277 + - 0.006288535568665579 + - - 0.4761176956165686 + - -0.020429542528060066 + - -0.14101290034592104 + - - 0.32606740634855413 + - -0.7300790209381913 + - 0.15998928853552316 + - - -0.16809915681682056 + - -0.20340484573944342 + - -0.09559399554173642 + - - -0.0071362874704545025 + - 0.012807159369231245 + - 0.0013981271891451736 + - - 9.28570065651754e-05 + - -0.0002097864250888285 + - 1.1564244131790538e-05 + - - -0.00021938882121489968 + - 0.0007343144083721189 + - 0.00010378863808164281 +- - - 0.00028178890880238425 + - 0.00021164208711617235 + - -0.0009878203783845424 + - - -0.0007277911890488043 + - 0.00025872195858152265 + - 0.0008844501882041927 + - - 0.00016279260334741753 + - -6.0572750383433845e-05 + - 0.0014753078073826687 + - - -0.00030691097849890725 + - -0.0006848398811004625 + - 0.0026001092076628537 + - - -0.00481097753334175 + - -0.004289058090302462 + - 0.0162856214822438 + - - -0.05263998038543227 + - -0.03339375738546158 + - -0.007042784794522939 + - - 0.8378282041639169 + - 0.5322804028322998 + - 0.10230830545374188 +opt_xyz: + coords: !!python/tuple + - !!python/tuple + - 0.00556673 + - -0.0071973 + - 0.0120571 + - !!python/tuple + - 1.04383567 + - -0.07979111 + - -0.29593001 + - !!python/tuple + - -0.43230487 + - 0.96316545 + - -0.19869735 + - !!python/tuple + - -0.59714046 + - -0.83200429 + - -0.35691858 + - !!python/tuple + - -0.02348879 + - -0.13569658 + - 1.21415916 + - !!python/tuple + - 0.08906227 + - -0.1829257 + - 2.52508864 + - !!python/tuple + - 0.90405617 + - 0.33526221 + - 2.62112084 + isotopes: !!python/tuple + - null + - null + - null + - null + - null + - null + - null + symbols: + - C + - H + - H + - H + - H + - O + - H +reduced_masses: +- 1.1903183174191376 +- 1.0456365389464217 +- 1.0824853654660649 +- 1.0770758314342508 +- 1.867898962692433 +- 1.6126421089962724 +- 1.105105815449419 +- 1.0804917518668131 +- 1.1057489874718125 +- 1.054368713755175 +- 1.0344916098929933 +- 1.0230893625306565 +- 1.1075305364739862 +- 1.1080335483184616 +- 1.0670123525229729 +schema_version: 2 diff --git a/arkane/ess/__init__.py b/arkane/ess/__init__.py index 9582e4ca5a2..4d0d41a9dc5 100644 --- a/arkane/ess/__init__.py +++ b/arkane/ess/__init__.py @@ -40,3 +40,4 @@ from arkane.ess.qchem import QChemLog from arkane.ess.terachem import TeraChemLog from arkane.ess.xtb import XTBLog +from arkane.ess.arc_yaml import ARCYAMLLog diff --git a/arkane/ess/arc_yaml.py b/arkane/ess/arc_yaml.py new file mode 100644 index 00000000000..eff91be3d0c --- /dev/null +++ b/arkane/ess/arc_yaml.py @@ -0,0 +1,302 @@ +#!/usr/bin/env python3 + +############################################################################### +# # +# RMG - Reaction Mechanism Generator # +# # +# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), # +# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) # +# # +# Permission is hereby granted, free of charge, to any person obtaining a # +# copy of this software and associated documentation files (the 'Software'), # +# to deal in the Software without restriction, including without limitation # +# the rights to use, copy, modify, merge, publish, distribute, sublicense, # +# and/or sell copies of the Software, and to permit persons to whom the # +# Software is furnished to do so, subject to the following conditions: # +# # +# The above copyright notice and this permission notice shall be included in # +# all copies or substantial portions of the Software. # +# # +# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # +# DEALINGS IN THE SOFTWARE. # +# # +############################################################################### + +""" +Arkane ESS adapter for the YAML output files that ARC writes for programs without a log of their own, +e.g., ARC's ASE adapter (machine-learned interatomic potentials such as UMA, TorchANI, or xTB through ASE). + +The file is a YAML mapping. The keys read here are: + +- ``opt_xyz`` or ``xyz``: the geometry, ``{'symbols': [...], 'coords': [[x, y, z], ...], 'isotopes': [...]}`` in Angstrom +- ``freqs``: the vibrational frequencies in cm^-1, imaginary ones as negative numbers +- ``hessian``: the Cartesian Hessian, (3N x 3N) or (N, N, 3, 3). ARC writes it in Hartree/Angstrom^2, but older + ARC versions wrote eV/Angstrom^2 for some calculators, so the units are taken from ``hessian_units`` if given, + and are otherwise the ones that reproduce ``freqs``. +- ``sp`` (kJ/mol) or ``energy`` (Hartree): the electronic energy; ``zpe`` (kJ/mol), optional +- ``energies`` (Hartree) and ``angles`` (degrees): a 1D rotor scan +- ``error``: set by ARC when the job failed +""" + +import logging +import math +import os + +import numpy as np +import yaml + +import rmgpy.constants as constants +from rmgpy.statmech import Conformer, HarmonicOscillator, IdealGasTranslation, LinearRotor, NonlinearRotor + +from arkane.common import check_conformer_energy, get_element_mass, get_principal_moments_of_inertia +from arkane.exceptions import LogError +from arkane.ess.adapter import ESSAdapter +from arkane.ess.factory import register_ess_adapter + +logger = logging.getLogger(__name__) + +# Keys that identify a YAML output written by ARC. +ARC_YAML_KEYS = ('freqs', 'frequencies', 'hessian', 'opt_xyz', 'xyz', 'sp', 'energies') + +# Hessian units ARC has written, as factors to Hartree/Bohr^2. +HESSIAN_UNITS_TO_HARTREE_PER_BOHR2 = { + 'hartree/angstrom^2': (constants.a0 * 1e10) ** 2, + 'ev/angstrom^2': (constants.a0 * 1e10) ** 2 / (constants.E_h / constants.e), + 'hartree/bohr^2': 1.0, +} +INERTIA_ZERO_TOL = 1e-4 # amu*angstrom^2 + + +def is_arc_yaml(path: str) -> bool: + """ + Whether a file is a YAML output written by ARC, as recognized by its content rather than its extension + (ARC copies these files to names such as ``freq.out``). + + Args: + path (str): The path to the file. + + Returns: + bool: Whether the file holds a YAML mapping with any of ARC's output keys. + """ + try: + content = load_arc_yaml(path) + except Exception: + return False + return isinstance(content, dict) and any(key in content for key in ARC_YAML_KEYS) + + +def load_arc_yaml(path: str) -> dict: + """ + Load an ARC YAML output. ARC writes coordinates as tuples, which the safe loader cannot construct. + """ + with open(path, 'r') as f: + return yaml.load(f, Loader=yaml.FullLoader) + + +class ARCYAMLLog(ESSAdapter): + """ + A class for parsing the YAML output files written by ARC (e.g., by its ASE adapter). + """ + + def __init__(self, path, check_for_errors=True, scratch_directory=None): + self.data = load_arc_yaml(path) + if not isinstance(self.data, dict): + raise LogError(f'The file {path} is not an ARC YAML output.') + super().__init__(path, check_for_errors=check_for_errors, scratch_directory=scratch_directory) + + def check_for_errors(self): + """ + Raise an error if ARC recorded that the job failed. + """ + if self.data.get('error'): + raise LogError(f'The job of {self.path} failed: {self.data["error"]}') + + def _xyz(self) -> dict: + xyz = self.data.get('opt_xyz') or self.data.get('xyz') + if not xyz or not xyz.get('symbols'): + raise LogError(f'No geometry found in {self.path}.') + return xyz + + def get_number_of_atoms(self): + """ + Return the number of atoms in the molecule. + """ + return len(self._xyz()['symbols']) + + def load_geometry(self): + """ + Return the geometry as Cartesian coordinates (Angstrom), atomic numbers, and atomic masses (amu). + """ + xyz = self._xyz() + isotopes = xyz.get('isotopes') or [None] * len(xyz['symbols']) + number, mass = list(), list() + for symbol, isotope in zip(xyz['symbols'], isotopes): + m, z = get_element_mass(symbol, isotope) + number.append(z) + mass.append(m) + coord = np.array(xyz['coords'], dtype=np.float64).reshape(-1, 3) + return coord, np.array(number, int), np.array(mass, np.float64) + + def _all_frequencies(self) -> list: + freqs = self.data.get('freqs') + if freqs is None: + freqs = self.data.get('frequencies') + return [float(f) for f in freqs] if freqs is not None else list() + + def load_conformer(self, symmetry=None, spin_multiplicity=0, optical_isomers=None, label=''): + """ + Load the molecular degrees of freedom. + + ARC's YAML output has no spin multiplicity; if none is given, it is taken from ARC's job input. + The frequencies are the real ones; translations and rotations are not among them. + + Returns: + tuple: The Conformer (E0 not set) and the unscaled real frequencies in cm^-1. + """ + if optical_isomers is None or symmetry is None: + _optical_isomers, _symmetry, _ = self.get_symmetry_properties() + optical_isomers = _optical_isomers if optical_isomers is None else optical_isomers + symmetry = _symmetry if symmetry is None else symmetry + if not spin_multiplicity: + spin_multiplicity = self._load_spin_multiplicity() + coord, number, mass = self.load_geometry() + modes = [IdealGasTranslation(mass=(float(sum(mass)), 'amu'))] + if len(number) > 1: + inertia = list(get_principal_moments_of_inertia(coord, numbers=number)[0]) + nonzero = [i for i in inertia if abs(i) >= INERTIA_ZERO_TOL] + if len(nonzero) < len(inertia): + modes.append(LinearRotor(inertia=(max(nonzero), 'amu*angstrom^2'), symmetry=symmetry)) + else: + modes.append(NonlinearRotor(inertia=(nonzero, 'amu*angstrom^2'), symmetry=symmetry)) + unscaled_frequencies = [f for f in self._all_frequencies() if f > 0] + if unscaled_frequencies: + modes.append(HarmonicOscillator(frequencies=(unscaled_frequencies, 'cm^-1'))) + return Conformer(E0=(0.0, 'kJ/mol'), modes=modes, spin_multiplicity=spin_multiplicity, + optical_isomers=optical_isomers), unscaled_frequencies + + def _load_spin_multiplicity(self) -> int: + """ + The spin multiplicity: ``multiplicity`` in the output if present, otherwise in the ``input.yml`` that ARC + writes next to the output in the job directory. + """ + if self.data.get('multiplicity'): + return int(self.data['multiplicity']) + input_path = os.path.join(os.path.dirname(self.path), 'input.yml') + if os.path.isfile(input_path): + multiplicity = (load_arc_yaml(input_path) or dict()).get('multiplicity') + if multiplicity: + return int(multiplicity) + raise LogError(f'No spin multiplicity found for {self.path}: set spin_multiplicity in the species file.') + + def _hessian_units(self, hessian: np.ndarray) -> str: + """ + The units of the stored Hessian: ``hessian_units`` if given, otherwise the units under which the Hessian + reproduces the stored frequencies (Hartree/Angstrom^2 if there are none). + """ + units = self.data.get('hessian_units') + if units: + units = str(units).lower().replace(' ', '') + if units not in HESSIAN_UNITS_TO_HARTREE_PER_BOHR2: + raise LogError(f'Unknown hessian_units {units} in {self.path}.') + return units + freqs = [f for f in self._all_frequencies() if f > 0] + if not freqs: + return 'hartree/angstrom^2' + _, _, mass = self.load_geometry() + best, best_error = 'hartree/angstrom^2', None + for units, factor in HESSIAN_UNITS_TO_HARTREE_PER_BOHR2.items(): + computed = self._frequencies_from_hessian(hessian * factor, mass) + if len(computed) < len(freqs): + continue + error = abs(computed[-1] - max(freqs)) / max(freqs) + if best_error is None or error < best_error: + best, best_error = units, error + return best + + @staticmethod + def _frequencies_from_hessian(hessian_hartree_bohr2: np.ndarray, mass: np.ndarray) -> np.ndarray: + """ + The sorted positive vibrational wavenumbers (cm^-1) of a Hessian in Hartree/Bohr^2, without projection. + """ + to_si = constants.E_h / constants.a0 ** 2 # Hartree/Bohr^2 to J/m^2 + weights = np.repeat(np.sqrt(mass * constants.amu), 3) + eigenvalues = np.linalg.eigvalsh(hessian_hartree_bohr2 * to_si / np.outer(weights, weights)) + return np.sort(np.sqrt(eigenvalues[eigenvalues > 0]) / (2 * math.pi * constants.c * 100)) + + def load_force_constant_matrix(self): + """ + Return the Cartesian force constant matrix in J/m^2, or ``None`` if the file has no Hessian. + """ + hessian = self.data.get('hessian') + if hessian is None: + return None + n_coords = 3 * self.get_number_of_atoms() + hessian = np.array(hessian, dtype=np.float64).reshape(n_coords, n_coords) + hessian = hessian * HESSIAN_UNITS_TO_HARTREE_PER_BOHR2[self._hessian_units(hessian)] + return hessian * constants.E_h / constants.a0 ** 2 + + def load_energy(self, zpe_scale_factor=1.): + """ + Return the electronic energy in J/mol, without the zero-point energy. + """ + if self.data.get('sp') is not None: + return float(self.data['sp']) * 1000.0 + if self.data.get('energy') is not None: + return float(self.data['energy']) * constants.E_h * constants.Na + raise LogError(f'No electronic energy found in {self.path}.') + + def load_zero_point_energy(self): + """ + Return the zero-point energy in J/mol: ``zpe`` if stored, otherwise the harmonic ZPE of the real frequencies. + """ + if self.data.get('zpe') is not None: + return float(self.data['zpe']) * 1000.0 + freqs = [f for f in self._all_frequencies() if f > 0] + if not freqs: + raise LogError(f'No zero-point energy or frequencies found in {self.path}.') + return 0.5 * constants.h * constants.c * 100.0 * sum(freqs) * constants.Na + + def load_scan_energies(self): + """ + Return the energies of a 1D rotor scan in J/mol, relative to the lowest one, and the scan angles in radians + from 0 to 2*pi, as the other adapters do. + """ + energies, angles = self.data.get('energies'), self.data.get('angles') + if not energies or not angles or len(energies) != len(angles): + raise LogError(f'No rotor scan found in {self.path}.') + vlist = np.array(energies, dtype=np.float64) + check_conformer_energy(vlist, self.path) + vlist = (vlist - np.min(vlist)) * constants.E_h * constants.Na + angle = np.radians(np.array(angles, dtype=np.float64)) + angle = angle - angle[0] + angle[1:] = np.where(angle[1:] <= 0, angle[1:] + 2 * math.pi, angle[1:]) + return vlist, angle + + def load_negative_frequency(self): + """ + Return the imaginary frequency of a transition state in cm^-1 (a negative number). + """ + negative = [f for f in self._all_frequencies() if f < 0] + if not negative: + raise LogError(f'No imaginary frequency found in {self.path}.') + return min(negative) + + def load_scan_pivot_atoms(self): + """ + ARC's YAML scan output does not record the pivots; ARC gives them in the species file. + """ + raise NotImplementedError('ARC YAML scan outputs do not record the scan pivots; give them in the species file.') + + def load_scan_frozen_atoms(self): + """ + ARC's YAML scan output does not record frozen atoms. + """ + return dict() + + +register_ess_adapter('ARCYAMLLog', ARCYAMLLog) diff --git a/arkane/ess/arc_yaml_test.py b/arkane/ess/arc_yaml_test.py new file mode 100644 index 00000000000..000239585a8 --- /dev/null +++ b/arkane/ess/arc_yaml_test.py @@ -0,0 +1,134 @@ +#!/usr/bin/env python3 + +############################################################################### +# # +# RMG - Reaction Mechanism Generator # +# # +# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), # +# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) # +# # +# Permission is hereby granted, free of charge, to any person obtaining a # +# copy of this software and associated documentation files (the 'Software'), # +# to deal in the Software without restriction, including without limitation # +# the rights to use, copy, modify, merge, publish, distribute, sublicense, # +# and/or sell copies of the Software, and to permit persons to whom the # +# Software is furnished to do so, subject to the following conditions: # +# # +# The above copyright notice and this permission notice shall be included in # +# all copies or substantial portions of the Software. # +# # +# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # +# DEALINGS IN THE SOFTWARE. # +# # +############################################################################### + +""" +Tests for the Arkane adapter of ARC's YAML outputs (arkane/ess/arc_yaml.py). +The fixtures are outputs of ARC's ASE adapter with the UMA-S 1.2 potential. +""" + +import math +import os +import shutil +import tempfile + +import numpy as np +import pytest + +import rmgpy.constants as constants +from rmgpy.statmech import HarmonicOscillator, NonlinearRotor + +from arkane.exceptions import LogError +from arkane.ess.arc_yaml import ARCYAMLLog +from arkane.ess.factory import ess_factory + +DATA = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'data', 'arc_yaml') + + +def wavenumbers(force_si, mass_amu): + """Positive wavenumbers (cm^-1) of a force constant matrix in J/m^2.""" + weights = np.repeat(np.sqrt(np.asarray(mass_amu) * constants.amu), 3) + eig = np.linalg.eigvalsh(force_si / np.outer(weights, weights)) + return np.sort(np.sqrt(eig[eig > 0]) / (2 * math.pi * constants.c * 100)) + + +class TestARCYAMLLog: + def test_factory_recognizes_yaml_by_extension_and_by_content(self): + assert isinstance(ess_factory(os.path.join(DATA, 'H2O_freq_uma.yml')), ARCYAMLLog) + with tempfile.TemporaryDirectory() as tmp: + freq_out = os.path.join(tmp, 'freq.out') # ARC copies its outputs to this name + shutil.copyfile(os.path.join(DATA, 'H2O_freq_uma.yml'), freq_out) + assert isinstance(ess_factory(freq_out), ARCYAMLLog) + + def test_load_geometry(self): + coord, number, mass = ARCYAMLLog(os.path.join(DATA, 'H2O_freq_uma.yml')).load_geometry() + assert coord.shape == (3, 3) + assert sorted(number.tolist()) == [1, 1, 8] + assert sum(mass) == pytest.approx(18.0106, abs=1e-3) + + def test_load_conformer(self): + log = ARCYAMLLog(os.path.join(DATA, 'H2O_freq_uma.yml')) + conformer, frequencies = log.load_conformer(symmetry=2, spin_multiplicity=1, optical_isomers=1) + assert len(frequencies) == 3 + assert any(isinstance(mode, NonlinearRotor) for mode in conformer.modes) + oscillator = [mode for mode in conformer.modes if isinstance(mode, HarmonicOscillator)][0] + assert oscillator.frequencies.value_si.tolist() == pytest.approx(frequencies) + with pytest.raises(LogError): + log.load_conformer(symmetry=2, optical_isomers=1) # no multiplicity given, and no job input next to it + + def test_spin_multiplicity_from_the_job_input(self): + with tempfile.TemporaryDirectory() as tmp: + shutil.copyfile(os.path.join(DATA, 'CH3_freq_uma.yml'), os.path.join(tmp, 'output.yml')) + with open(os.path.join(tmp, 'input.yml'), 'w') as f: + f.write('job_type: freq\ncharge: 0\nmultiplicity: 2\n') + conformer, _ = ARCYAMLLog(os.path.join(tmp, 'output.yml')).load_conformer(symmetry=6, optical_isomers=1) + assert conformer.spin_multiplicity == 2 + + def test_force_constant_matrix_reproduces_the_frequencies(self): + for name in ('H2O_freq_uma.yml', 'CH3_freq_uma.yml', 'H2O_freq_uma_ev_hessian.out'): + log = ARCYAMLLog(os.path.join(DATA, name)) + force = log.load_force_constant_matrix() + _, _, mass = log.load_geometry() + stored = sorted(f for f in log.data['freqs'] if f > 0) + # the unprojected Hessian has near-zero rotations too; the highest modes are the vibrations + assert wavenumbers(force, mass)[-len(stored):].tolist() == pytest.approx(stored, abs=2.0), name + + def test_hessian_units_are_detected(self): + assert ARCYAMLLog(os.path.join(DATA, 'H2O_freq_uma.yml'))._hessian_units( + np.array(ARCYAMLLog(os.path.join(DATA, 'H2O_freq_uma.yml')).data['hessian'])) == 'hartree/angstrom^2' + old = ARCYAMLLog(os.path.join(DATA, 'H2O_freq_uma_ev_hessian.out')) + assert old._hessian_units(np.array(old.data['hessian'])) == 'ev/angstrom^2' + + def test_transition_state(self): + log = ARCYAMLLog(os.path.join(DATA, 'TS_OHCH4_freq_uma.yml')) + assert log.load_negative_frequency() == pytest.approx(-1058.2, abs=0.1) + _, frequencies = log.load_conformer(symmetry=1, spin_multiplicity=2, optical_isomers=1) + assert all(f > 0 for f in frequencies) + assert len(frequencies) == 3 * log.get_number_of_atoms() - 7 # 3N-6 minus the reaction coordinate + + def test_zero_point_energy(self): + log = ARCYAMLLog(os.path.join(DATA, 'H2O_freq_uma.yml')) + expected = 0.5 * constants.h * constants.c * 100 * sum(log.data['freqs']) * constants.Na + assert log.load_zero_point_energy() == pytest.approx(expected) + assert log.load_zero_point_energy() / 1000 == pytest.approx(56.0, abs=0.5) # kJ/mol + + def test_load_scan_energies(self): + vlist, angle = ARCYAMLLog(os.path.join(DATA, 'C3H8_scan_uma.yml')).load_scan_energies() + assert len(vlist) == len(angle) == 46 + assert min(vlist) == 0.0 + assert angle[0] == 0.0 and angle[-1] == pytest.approx(2 * math.pi) + assert np.all(np.diff(angle) > 0) + assert 5e3 < max(vlist) < 2e4 # a methyl rotor barrier, J/mol + + def test_a_failed_job_raises(self): + with tempfile.TemporaryDirectory() as tmp: + path = os.path.join(tmp, 'output.yml') + with open(path, 'w') as f: + f.write("error: 'Optimization failed: SCF did not converge'\nopt_xyz: {symbols: [H], coords: [[0, 0, 0]]}\n") + with pytest.raises(LogError): + ARCYAMLLog(path) diff --git a/arkane/ess/factory.py b/arkane/ess/factory.py index d40d95625c9..defaf613be4 100644 --- a/arkane/ess/factory.py +++ b/arkane/ess/factory.py @@ -80,7 +80,9 @@ def ess_factory(fullpath: str, ess_name = None if os.path.splitext(fullpath)[-1] in ['.xyz', '.dat', '.geometry']: ess_name = 'TeraChemLog' - else: + elif os.path.splitext(fullpath)[-1] in ['.yml', '.yaml']: + ess_name = 'ARCYAMLLog' + if ess_name is None: with open(fullpath, 'r') as f: line = f.readline().lower() while ess_name is None and line != '': @@ -106,8 +108,13 @@ def ess_factory(fullpath: str, ess_name = 'XTBLog' break line = f.readline().lower() + if ess_name is None: + # ARC copies the YAML output of e.g. its ASE adapter to names such as freq.out, so recognize it by content. + from arkane.ess.arc_yaml import is_arc_yaml + if is_arc_yaml(fullpath): + ess_name = 'ARCYAMLLog' if ess_name is None: raise InputError(f'The file at {fullpath} could not be identified as a ' - f'Gaussian, Molpro, Orca, Psi4, QChem, TeraChem, or xTB log file.') + f'Gaussian, Molpro, Orca, Psi4, QChem, TeraChem, or xTB log file, or an ARC YAML output.') return _registered_ess_adapters[ess_name](path=fullpath, check_for_errors=check_for_errors, scratch_directory=scratch_directory) From 8244a43ab497198250bbf0f6e30c5a1c4b906d9c Mon Sep 17 00:00:00 2001 From: kfir4444 Date: Fri, 30 Oct 2026 08:08:54 +0200 Subject: [PATCH 2/3] Accept ARC YAML scans as hindered rotor scan logs in Arkane --- arkane/data/arc_yaml/C3H8_freq_uma.yml | 2138 ++++++++++++++++++++++++ arkane/ess/arc_yaml_test.py | 24 + arkane/statmech.py | 4 +- 3 files changed, 2164 insertions(+), 2 deletions(-) create mode 100644 arkane/data/arc_yaml/C3H8_freq_uma.yml diff --git a/arkane/data/arc_yaml/C3H8_freq_uma.yml b/arkane/data/arc_yaml/C3H8_freq_uma.yml new file mode 100644 index 00000000000..8efdb266609 --- /dev/null +++ b/arkane/data/arc_yaml/C3H8_freq_uma.yml @@ -0,0 +1,2138 @@ +force_constants: +- 0.028596021342427554 +- 0.0483619465029334 +- 0.1607346966104671 +- 0.3551892177982383 +- 1.1396752324389752 +- 0.5327900755150246 +- 0.6000289558252493 +- 1.5501905640100284 +- 1.483140052437128 +- 1.435973436082666 +- 1.1411804333730615 +- 1.5158696197775545 +- 1.5848350937747084 +- 1.4735591565646249 +- 1.337973901368334 +- 1.3493028269122425 +- 1.3755871756621099 +- 1.3749064915131146 +- 1.4489694627385192 +- 5.6573515508338446 +- 5.794855316997849 +- 5.670529071494483 +- 6.110905654036055 +- 6.254759483854245 +- 6.30389599299654 +- 6.301946615571084 +- 6.307208633686358 +freqs: +- 217.22943715459039 +- 269.10004029072485 +- 365.7975891405594 +- 747.4445544007566 +- 889.022967602015 +- 905.9982282749173 +- 928.0938884059123 +- 1075.4520604324198 +- 1175.9298629493146 +- 1208.4618749542678 +- 1311.511139093294 +- 1362.5017998707133 +- 1402.3452491155908 +- 1414.404692710797 +- 1480.0369788827315 +- 1482.8980584267224 +- 1487.6850311951473 +- 1497.8446721101811 +- 1504.1082958646186 +- 3044.4351511407463 +- 3045.5001451738985 +- 3047.097625602972 +- 3068.4442019813328 +- 3103.3589424475767 +- 3114.1769730360706 +- 3115.6674635366917 +- 3118.7607810465984 +hessian: +- - 1.8208930789697297 + - -0.1242382941645927 + - 0.09432987722107418 + - -0.6004119704354358 + - -0.14883702898310852 + - 0.131359882786176 + - -0.10871127062195775 + - -0.0314127125384695 + - 0.03622189665197888 + - -0.17226757222683836 + - 0.017040891318397706 + - -0.07548578855733333 + - -0.20918936176886804 + - -0.1708144056580907 + - -0.10005679252709007 + - -0.7114641277318509 + - 0.4656887255913947 + - -0.09512479317194783 + - -0.026923237073643167 + - -0.011451528469690112 + - 0.010731746471682548 + - 0.00550035197170241 + - 0.002540100294899926 + - -0.0014172359807191155 + - 0.007531969588723621 + - -0.004063943564470342 + - 0.00028262781089504363 + - 0.0061172198834009974 + - -0.0043720673006154105 + - 0.0009636256376812654 + - -0.011075232242267606 + - 0.009920274152693137 + - -0.0018050931628471741 +- - -0.12423832921147897 + - 1.9813799207528775 + - 0.03930205139320845 + - -0.1610581761230784 + - -0.35405237174778853 + - 0.06549350948158865 + - 0.07009961660305206 + - 0.03384329076617626 + - -0.028831474317990446 + - 0.018120714359890884 + - -0.2048680982155428 + - 0.1838774140530894 + - -0.16757393550692215 + - -0.8417734275318326 + - -0.38719274244911267 + - 0.46003685443059883 + - -0.5595736212592535 + - 0.08011646354607017 + - -0.09208547462451093 + - -0.03867166743077781 + - 0.04017871420630078 + - -0.02338252243825234 + - -0.01133943209917908 + - 0.0077684013595593696 + - 0.0027691201968977203 + - 0.003400285595370607 + - -0.00046758816387685844 + - -0.0008571552507294467 + - 0.0016750752384787583 + - -0.0015278816018013354 + - 0.018169328772004528 + - -0.010019856594376321 + - 0.001283258442711983 +- - 0.09432995607656827 + - 0.03930213901042412 + - 1.9763012063700982 + - 0.136646863290599 + - 0.06318384082107398 + - -0.3362674087487696 + - -0.008585085260058257 + - -0.008108950310596741 + - 0.006259880971990372 + - -0.07969947569326083 + - 0.1825947155391463 + - -1.0613889926370434 + - -0.09784232873312075 + - -0.3850962026657115 + - -0.38735301186001336 + - -0.09257257377329817 + - 0.07895507982894161 + - -0.18274599542371944 + - -0.050966137037679854 + - -0.021022583400247884 + - 0.02080227429231033 + - 0.10745646942948349 + - 0.04696949964926702 + - -0.038940590950829 + - 0.0017719014342196704 + - 0.0009413146666717395 + - -0.0005297169154488148 + - -0.005086050681768516 + - -0.0007527796681925512 + - 0.0027010243706839933 + - -0.005453540283801144 + - 0.003033955278622791 + - 0.0011609760232718965 +- - -0.6004119003416633 + - -0.161058123552749 + - 0.13664688957576368 + - 1.6714289034803096 + - 0.05288745115146565 + - 0.067030262874084 + - -0.5359103141203787 + - 0.22544254803324162 + - -0.047259985766094234 + - 0.0057711373575865645 + - 0.0035703336351475493 + - -0.0030246481398884095 + - -0.02610071950940355 + - -0.010693733742664788 + - 0.011063765339166996 + - -0.06913977438626487 + - -0.04178835197964995 + - 0.03161465050671178 + - -0.1996226307479035 + - -0.15263374578966982 + - -0.08783776572373936 + - -0.17498857742975174 + - 0.017837329618393603 + - -0.0931971443334692 + - 0.013445777344228726 + - -0.01277842439286197 + - 0.0028923852981722884 + - -0.01518839395622831 + - 0.011235331894812994 + - -0.0011247160492732034 + - -0.06928333957499842 + - 0.0679793982671165 + - -0.01680373999117828 +- - -0.14883702898310852 + - -0.3540524067946748 + - 0.06318387586796025 + - 0.0528874380088833 + - 1.9554246173458882 + - 0.05919441432951066 + - 0.21331269803199823 + - -0.46716304295600464 + - 0.0385955324512227 + - -0.019990481075268535 + - -0.012524483416690078 + - 0.008890902199197056 + - -0.08922711191259411 + - -0.04339488372270368 + - 0.0397224957451759 + - 0.06880165078927872 + - 0.03411946022996325 + - -0.03153653537808256 + - -0.1535550408124237 + - -0.8415517209293051 + - -0.37972463650128213 + - 0.018726968541126435 + - -0.21681335626681583 + - 0.19027438201592983 + - 0.08172962791235 + - -0.06943372576397178 + - 0.01639678430956299 + - 0.01902706188565169 + - -0.01913547066659827 + - 0.003747772734673724 + - -0.04287581305191902 + - 0.03452534260068659 + - -0.008745020630324268 +- - 0.13135982145412503 + - 0.06549350071986708 + - -0.3362674437956559 + - 0.06703028477838793 + - 0.059194458138118494 + - 2.074299309750956 + - -0.04172199508136344 + - 0.03626645657743746 + - -0.2877465017276866 + - 0.10549449216590595 + - 0.05038839349842282 + - -0.04126252164067648 + - -0.05212985137274519 + - -0.022464554679263504 + - 0.021656246436974922 + - -0.017537508982452116 + - -0.008859310716872596 + - 0.002264542645701729 + - -0.08696884827251211 + - -0.37395490266196907 + - -0.3899937246464882 + - -0.09414944708884812 + - 0.18450405237955023 + - -1.0394234267627334 + - 0.049062985972702124 + - -0.03830434101580936 + - 0.007997346239316248 + - -0.09220524735832972 + - 0.07906918372890664 + - -0.013560839557490132 + - 0.03176526231001547 + - -0.031332996205223944 + - 0.0020366316490897382 +- - -0.10871127062195775 + - 0.07009961222219127 + - -0.00858509018852664 + - -0.5359103141203787 + - 0.21331271555544137 + - -0.04172199946222423 + - 1.870433254584127 + - 0.1619491205423247 + - -0.042174936658622326 + - 0.007725723013807263 + - 0.002081164878677926 + - -0.00268413834279429 + - 0.006496670878195165 + - 0.0031396202716999573 + - -0.0022196258169911933 + - -0.01538996174173438 + - -0.006809717880449403 + - 0.006461488732851094 + - 0.014092956431687816 + - -0.01050144023943722 + - 0.0031010536375968927 + - -0.015359124862679867 + - 0.011792568624742825 + - -0.002423267666274418 + - -0.19448072682918435 + - -0.13857201503843106 + - -0.0783999546739094 + - -0.18102288021349727 + - 0.022695121572725446 + - -0.11443271861371594 + - -0.8478743193994862 + - -0.32918674612862503 + - 0.28307913264902784 +- - -0.03141271910976068 + - 0.03384328638531548 + - -0.008108955786672721 + - 0.22544254803324162 + - -0.46716304295600464 + - 0.03626648067217177 + - 0.16194919063609722 + - 1.8952055152982743 + - 0.018950379298498653 + - -0.0013652792456315184 + - 0.0006883016800254842 + - -0.0008700685223980831 + - -0.0037510622135144777 + - 0.0034083879973895474 + - 0.0008411397820185487 + - -0.015067543530656802 + - -0.0024880403357801194 + - 0.004816920166045298 + - 0.08598583568304141 + - -0.06621116457168585 + - 0.015674740692175986 + - 0.021979764244109138 + - -0.018996058533887403 + - 0.0019485386993205798 + - -0.14236428089043643 + - -0.8484452331767819 + - -0.395806811484114 + - 0.022102456821640075 + - -0.20714521708043662 + - 0.19194198295830447 + - -0.3234988818156326 + - -0.32269676372963096 + - 0.13434574607033356 +- - 0.03622189227111809 + - -0.02883149184143358 + - 0.006259880424382774 + - -0.047259985766094234 + - 0.03859555435552661 + - -0.2877464666808004 + - -0.04217494542034389 + - 0.018950405583663354 + - 2.0132253440535077 + - 0.0032415316884971276 + - -0.0029105059073915207 + - 0.0019941164904018144 + - -0.0035593713524484302 + - 0.0006993057178039452 + - 0.0005813545322087194 + - 0.01009388985597058 + - 0.003065782232214359 + - -0.0020597939445611926 + - 0.04801464160636824 + - -0.03661811703424439 + - 0.007347081930650431 + - -0.09426107142160974 + - 0.07621632337813379 + - -0.010413803309895237 + - -0.08011221411111025 + - -0.3940233455357394 + - -0.3956684814240166 + - -0.11084651969124122 + - 0.18935503209536383 + - -1.0502547370574407 + - 0.2806421474124253 + - 0.1355011630550751 + - -0.283264618294598 +- - -0.17226757222683836 + - 0.018120699026878143 + - -0.07969944064637456 + - 0.0057711406432321526 + - -0.01999047669440775 + - 0.10549449216590595 + - 0.007725721918592067 + - -0.0013652804777486139 + - 0.0032415327837123234 + - 0.18502772295415745 + - -0.009734145615803044 + - 0.07683161527516555 + - -0.006064465557847018 + - 0.006568725633538112 + - -0.021962518985635192 + - -0.006851319629663983 + - 0.012271455849991527 + - -0.08569076718583474 + - 0.004595438082632981 + - 0.0015485752822213311 + - -0.002521918353629726 + - -0.017857657907643883 + - -0.008326976442458537 + - 0.008546497543062673 + - -0.00030129356347801295 + - 0.00030083980213217997 + - -0.00016020662426709475 + - -0.0007299364910487891 + - 0.0009478418069842911 + - -0.0027584076232632566 + - 0.000952205760383128 + - -0.0003412615254241752 + - -0.0013208514305059322 +- - 0.017040891318397706 + - -0.20486806316865655 + - 0.18259468049226002 + - 0.003570328706679168 + - -0.012524482321474881 + - 0.05038839349842282 + - 0.0020811659738931214 + - 0.000688301474672635 + - -0.0029105070026067166 + - -0.009734148901448633 + - 0.2090770540218242 + - -0.20823943344003376 + - -0.008076049498505636 + - 0.023458002479120322 + - -0.09716648457834053 + - 0.003172263708220036 + - -0.015627761436349752 + - 0.07340648746111494 + - 0.0023358957788098306 + - 1.6054577733213953e-05 + - 0.00014984036110010792 + - -0.009781662622290441 + - -0.0012289998390864962 + - 0.0029930585741905435 + - -0.00023900665598667996 + - 5.9595386200226964e-05 + - -0.0004178404436138276 + - -0.0005226562684339821 + - 0.0015173015492055699 + - -0.0005459814087148705 + - 0.0001529766809408152 + - -0.0005669460864448906 + - -0.00025228637981475485 +- - -0.07548578855733333 + - 0.18387744909997567 + - -1.0613887122619532 + - -0.003024643485223827 + - 0.008890903842019848 + - -0.04126253040239805 + - -0.002684138068990491 + - -0.0008700684539471333 + - 0.001994116901107513 + - 0.07683163279860868 + - -0.20823941591659062 + - 1.1551998342342193 + - -0.005126889613599182 + - 0.011060596881605387 + - -0.05222433777812205 + - -0.0024855454355639604 + - 0.0018513442374700612 + - -0.010609070322379552 + - 0.0006699854379918923 + - 0.0012303401086824247 + - 0.0027835126935902596 + - 0.008252292075430339 + - 0.00413479577352824 + - 0.0033794748638265545 + - 0.00012002126210455515 + - -4.0170563922842494e-05 + - -0.0003357504025586291 + - 0.0028583219151507833 + - -0.0015850499183984118 + - 0.0009223501941441006 + - 7.477187301107141e-05 + - -0.000310706664282594 + - 0.0015412240609248477 +- - -0.20918936176886804 + - -0.1675739705538084 + - -0.09784233749484231 + - -0.02610072827112512 + - -0.08922712067431568 + - -0.05212985137274519 + - 0.006496668687764773 + - -0.0037510633087296727 + - -0.0035593713524484302 + - -0.006064455153302658 + - -0.00807605387936642 + - -0.005126890708814377 + - 0.22646968465252296 + - 0.19780122654514445 + - 0.10188680950214933 + - 0.021232363109292485 + - 0.07223695096206845 + - 0.04624037108477803 + - -0.01753548940563096 + - -0.008101129926490733 + - 0.00840058859380999 + - 0.004331955044067194 + - 0.0024989193821243535 + - 6.3846446870203566e-06 + - -0.0007132045462469525 + - 0.002972587633161005 + - 0.0013887335528545682 + - -0.0003608932578098892 + - 0.00022719833666149985 + - -0.00010994177419150815 + - 0.0014334414692664943 + - 0.0009923781853161666 + - 0.0008455090061405157 +- - -0.17081444070497695 + - -0.8417734976256052 + - -0.3850960975250527 + - -0.01069374359960155 + - -0.0433948793418429 + - -0.022464545917541937 + - 0.003139621366915153 + - 0.0034083869021743515 + - 0.0006993054440001462 + - 0.006568723443107719 + - 0.023458011240841892 + - 0.011060596881605387 + - 0.1978012615920307 + - 0.9147432877412462 + - 0.42256833346279793 + - -0.016505851314842283 + - -0.060439222778537936 + - -0.03500527466123214 + - -0.008346950429592956 + - 0.0008132301393787581 + - 0.006146803288663855 + - 0.001025262774532182 + - 0.00023176647924341414 + - 0.0014901756699403138 + - -0.00228501824139585 + - 0.0021917119303925185 + - -0.00029699836905819083 + - -0.0001772290577868948 + - 6.25896360947468e-05 + - 8.343082403324991e-05 + - 0.0002883607148377505 + - 0.0006983805347672461 + - 0.0008144168050434679 +- - -0.10005680128881164 + - -0.3871928826366577 + - -0.38735304690689965 + - 0.011063771910458172 + - 0.03972248260259355 + - 0.021656242056114137 + - -0.0022196275967158864 + - 0.000841139165960001 + - 0.0005813545322087194 + - -0.02196251460477441 + - -0.09716648457834053 + - -0.05222433777812205 + - 0.10188682702559246 + - 0.42256833346279793 + - 0.40779940035529116 + - 0.006394691558055852 + - 0.016568781284780957 + - 0.006096743192491681 + - 0.00945873513614679 + - 0.0046590876089553325 + - 0.000988943864265762 + - -0.0028728217429325165 + - 0.0003635607228703456 + - 0.002688074820011994 + - -0.0012544894668491443 + - -0.0006322220757840379 + - 0.0002270413444082689 + - 2.5486744266390064e-05 + - -0.0005125689257744524 + - -0.0003124509998348435 + - -0.00046324806563400624 + - 0.0007807860320243257 + - -0.00014803214369901269 +- - -0.7114641978256234 + - 0.46003681938371255 + - -0.09257255624985503 + - -0.06913977000540408 + - 0.06880163326583559 + - -0.017537512268097705 + - -0.015389962836949576 + - -0.015067543530656802 + - 0.010093888760755386 + - -0.006851322915309571 + - 0.00317226261300484 + - -0.002485545983171558 + - 0.021232360918862096 + - -0.016505856790918264 + - 0.006394686629587471 + - 0.7783125585982582 + - -0.5037079032362287 + - 0.09741426606425092 + - 0.0027463991362482966 + - -0.0008436522741287916 + - -0.0028434450595378772 + - 0.0038584121951704678 + - 0.0006582371330368977 + - 0.0016579033594229366 + - 0.0008759680359524596 + - -0.0001000703001583553 + - 0.00036154867565365916 + - 0.001247376865563458 + - -0.0007761735332269793 + - -0.00010923791018805906 + - -0.005427887058268615 + - 0.004332258144872647 + - -0.000373992510708972 +- - 0.46568886577893975 + - -0.5595735862123672 + - 0.07895509735238475 + - -0.04178834321792838 + - 0.03411945365867207 + - -0.008859315645340978 + - -0.006809721713702589 + - -0.002488041157191516 + - 0.0030657800417839675 + - 0.012271454754776331 + - -0.015627758150704163 + - 0.0018513436898624632 + - 0.07223695972379 + - -0.060439222778537936 + - 0.01656877799913537 + - -0.5037078681893424 + - 0.597204759779335 + - -0.08970708778174749 + - 0.002477409081873948 + - 0.002542179834753057 + - -0.0014087423130714554 + - 0.0027741691389506153 + - 0.0015696748767732905 + - -0.001481145346846684 + - -0.0008338136137696707 + - 0.0010457309090727812 + - 0.0009396141397273244 + - -0.0002512348534375713 + - -0.00046582811883164336 + - -0.0002783318806275118 + - -0.0020577482194772336 + - 0.002112707760828068 + - 0.00035399846744627896 +- - -0.09512475812506156 + - 0.08011643726090546 + - -0.18274601294716258 + - 0.03161466583972452 + - -0.03153653318765217 + - 0.0022645518181289943 + - 0.006461488732851094 + - 0.0048169190708301024 + - -0.0020597929862478962 + - -0.08569077594755631 + - 0.07340649622283651 + - -0.01060906813194916 + - 0.04624035356133489 + - -0.03500526808994097 + - 0.006096737168808104 + - 0.09741426606425092 + - -0.0897070614965828 + - 0.1823901643874467 + - -0.002170802629480839 + - 0.00026894650245757587 + - 0.000804654809748057 + - -0.0015268764680553388 + - -0.0019772557893635153 + - 0.0007607363381394933 + - -0.0009167602842354027 + - 0.0011087433624058936 + - 2.6717277363968917e-06 + - 0.0012537348635791995 + - -0.0005393024441957934 + - 0.0012053474348148964 + - 0.002445475070996985 + - -0.0009521087653873449 + - 0.0018900098516464513 +- - -0.02692325240665591 + - -0.09208547462451093 + - -0.05096611951423672 + - -0.19962261322446037 + - -0.15355507585930994 + - -0.08696887455767682 + - 0.014092942193890269 + - 0.08598581815959828 + - 0.04801464160636824 + - 0.004595435892202589 + - 0.0023358955050060315 + - 0.0006699845481295458 + - -0.01753548392955498 + - -0.008346948786770161 + - 0.00945873513614679 + - 0.0027464013266786883 + - 0.002477408808070149 + - -0.002170804683009331 + - 0.2344811750484861 + - 0.1650180361852144 + - 0.09042712606011089 + - -0.004818335184078344 + - -0.009630760586959851 + - -0.006113188396265052 + - -0.013941771830836695 + - 0.014074252346572991 + - -0.0029385757252537053 + - 0.0035570473058028247 + - -0.0032872804700508156 + - -0.000714260675950506 + - 0.003368449606253674 + - -0.0029858914859488637 + - 0.0013013338743043863 +- - -0.01145152627925972 + - -0.038671649907334675 + - -0.02102258778110867 + - -0.1526337107427836 + - -0.8415518611168502 + - -0.37395483256819656 + - -0.010501434763361241 + - -0.06621116019082507 + - -0.03661811703424439 + - 0.0015485756929270295 + - 1.6054577733213953e-05 + - 0.0012303395610748268 + - -0.008101128283667939 + - 0.0008132319191034513 + - 0.004659087061347734 + - -0.0008436530955401884 + - 0.0025421781919302633 + - 0.00026894660513400047 + - 0.16501800113832812 + - 0.921552266899046 + - 0.41204301753209105 + - 0.004937029678536807 + - 0.022739727497222258 + - 0.00858369762240511 + - 0.013415110223529569 + - -0.00578050199511873 + - 0.0034207477746785783 + - -0.002153971909958526 + - 0.0014246868665984216 + - 0.0019186935376259132 + - 0.0007667181297354583 + - 0.003127007225896885 + - -0.0005289291134682459 +- - 0.010731751947758527 + - 0.04017870106371843 + - 0.020802267721019153 + - -0.08783776572373936 + - -0.37972463650128213 + - -0.3899937246464882 + - 0.0031010561018310835 + - 0.015674749453897553 + - 0.007347086859118813 + - -0.002521918079825927 + - 0.00014983965947787308 + - 0.002783512145982662 + - 0.008400586950987195 + - 0.006146804383879051 + - 0.0009889455070885558 + - -0.002843445880949274 + - -0.0014087414916600586 + - 0.0008046557680613533 + - 0.09042712606011089 + - 0.41204294743831854 + - 0.4069010084727131 + - -0.021737956061876933 + - -0.09644592059668312 + - -0.05561575924930501 + - -0.0014902827272257086 + - 0.004407446310890937 + - 0.004017834457117218 + - 0.0020880333838768357 + - 0.00030800401543397074 + - 0.002261935896633693 + - 0.001682826487125528 + - -0.0013292320171846203 + - -0.00029769122957146903 +- - 0.005500348138449225 + - -0.02338251367653077 + - 0.10745647819120506 + - -0.17498857742975174 + - 0.018726946636822516 + - -0.09414939451851871 + - -0.015359131433971043 + - 0.02197976643453953 + - -0.0942610801833313 + - -0.017857661193289468 + - -0.009781662622290441 + - 0.008252292075430339 + - 0.00433195613928239 + - 0.0010252635274926292 + - -0.0028728209215211197 + - 0.0038584121951704678 + - 0.002774169960362012 + - -0.0015268755097420424 + - -0.004818341207761922 + - 0.004937029678536807 + - -0.02173796044273772 + - 0.207096764760172 + - -0.02535181573933818 + - 0.09738112047156355 + - 0.0038347900462186533 + - -0.0015671044067086172 + - 0.002450784400462695 + - -0.013795948308369286 + - 0.013902717552167675 + - -0.0012800230401215258 + - 0.0021973976031799043 + - -0.003262807065088022 + - 0.0002875587435105851 +- - 0.002540093449804952 + - -0.011339418956596731 + - 0.04696949526840624 + - 0.01783733290403919 + - -0.21681337379025897 + - 0.18450403485610709 + - 0.01179257738646439 + - -0.018996049772165836 + - 0.07621632337813379 + - -0.008326975894850938 + - -0.0012289999759883957 + - 0.00413479577352824 + - 0.002498922120162343 + - 0.00023176735199302332 + - 0.0003635605175174964 + - 0.0006582356955669531 + - 0.0015696748767732905 + - -0.001977255241755917 + - -0.009630761682175047 + - 0.02273972968765265 + - -0.09644591183496155 + - -0.025351820120198962 + - 0.2275338483071458 + - -0.21476985994578038 + - -0.0033866767251507024 + - 0.0015552875823529318 + - 0.0003976236609606773 + - 0.01285455608677149 + - -0.008035095569079404 + - 0.00254382813362282 + - -0.0014854791133766853 + - 0.0027826496640159255 + - -0.0019366907982337118 +- - -0.001417236391424814 + - 0.007768396978698586 + - -0.03894059533168979 + - -0.09319710928658294 + - 0.19027438201592983 + - -1.0394230762938708 + - -0.002423256987926258 + - 0.0019485371933996853 + - -0.010413803309895237 + - 0.008546496995455075 + - 0.0029930583003867444 + - 0.0033794748638265545 + - 6.384397621873636e-06 + - 0.00149017662825361 + - 0.002688075093815793 + - 0.0016579036332267354 + - -0.0014811460313561816 + - 0.0007607362696885436 + - -0.006113190586695444 + - 0.008583699265227902 + - -0.05561575924930501 + - 0.09738110294812041 + - -0.21476984242233724 + - 1.128358054885983 + - -4.3488137600279506e-05 + - 0.0019626903855719303 + - 0.0020126735428765952 + - -0.00198240781854672 + - 0.0011992830913735437 + - 0.006093803634906004 + - -0.0024151608833946937 + - 3.0760002220678384e-05 + - 0.001100719473626306 +- - 0.007531971231546415 + - 0.0027691193754863235 + - 0.0017719011604158715 + - 0.013445780629874313 + - 0.08172964543579313 + - 0.04906299911528447 + - -0.19448074435262747 + - -0.14236427212871486 + - -0.08011223163455339 + - -0.00030129366615443755 + - -0.00023900674155036714 + - 0.00012002121932271156 + - -0.0007132045462469525 + - -0.0022850183782977497 + - -0.0012544894668491443 + - 0.0008759682413053087 + - -0.0008338136137696707 + - -0.0009167605580392016 + - -0.01394177840212787 + - 0.013415112413959962 + - -0.0014902830010295077 + - 0.0038347903200224524 + - -0.0033866761775431043 + - -4.348820605122925e-05 + - 0.20556476022076584 + - 0.14188266657935003 + - 0.08991521371584635 + - -0.006402360802464832 + - -0.01039255503988044 + - -0.004865242703309247 + - -0.01541394476409323 + - -0.08029517638086911 + - -0.052187634926478536 +- - -0.004063944659685539 + - 0.003400285595370607 + - 0.0009413141190641416 + - -0.01277842439286197 + - -0.06943372576397178 + - -0.03830434101580936 + - -0.13857202380015263 + - -0.8484453032705545 + - -0.3940233455357394 + - 0.00030083980213217997 + - 5.9595373365673896e-05 + - -4.0170683712004543e-05 + - 0.0029725870855534073 + - 0.0021917124780001167 + - -0.0006322222126859374 + - -0.00010007062530036659 + - 0.001045730977523731 + - 0.0011087430886020948 + - 0.014074254537003384 + - -0.005780502542726327 + - 0.00440744548947954 + - -0.0015671037221991198 + - 0.0015552860764320377 + - 0.001962689564160533 + - 0.14188264029418535 + - 0.9294511341259889 + - 0.43421956566173076 + - 0.004889215321123736 + - 0.024315928350641954 + - 0.011483289710369927 + - -0.007037994131329211 + - -0.03836015756305095 + - -0.021122962063378454 +- - 0.0002826297446343738 + - -0.0004675882665532831 + - -0.0005297173261545133 + - 0.002892387214798881 + - 0.016396778833487013 + - 0.007997341310847866 + - -0.0783999546739094 + - -0.3958068815778865 + - -0.3956685515177892 + - -0.0001602066071543573 + - -0.00041784047783930247 + - -0.0003357502314312548 + - 0.001388733279050769 + - -0.00029699836905819083 + - 0.0002270413444082689 + - 0.0003615486072027094 + - 0.0009396143450801736 + - 2.6715900323378423e-06 + - -0.002938575177646107 + - 0.0034207469532671815 + - 0.004017834457117218 + - 0.0024507822100323035 + - 0.00039762444814659927 + - 0.002012673269072796 + - 0.08991520495412479 + - 0.434219600708617 + - 0.4143432848653644 + - -0.02021450296272004 + - -0.0968866527149386 + - -0.052753436239239955 + - 0.004421957364628427 + - 0.038501650604633945 + - 0.020686507855677987 +- - 0.006117220978616194 + - -0.0008571581256693357 + - -0.005086050681768516 + - -0.0151883961466587 + - 0.01902707721866443 + - -0.09220522107316502 + - -0.18102288021349727 + - 0.022102437107766545 + - -0.11084649340607652 + - -0.000729936011892141 + - -0.0005226557208263843 + - 0.0028583213675431856 + - -0.00036089363429011277 + - -0.0001772290064486825 + - 2.5486665119979427e-05 + - 0.0012473767286615585 + - -0.00025123473364840925 + - 0.0012537348635791995 + - 0.003557046210587629 + - -0.0021539709516452295 + - 0.0020880335207787352 + - -0.013795949403584482 + - 0.01285455061069551 + - -0.001982408776860016 + - -0.006402356969211647 + - 0.0048892169639465285 + - -0.02021450515315043 + - 0.1912472835787124 + - -0.038023571648199785 + - 0.12825571873742286 + - 0.015331478345490882 + - -0.01688746700247106 + - 0.0958534266991683 +- - -0.004372068395830606 + - 0.0016750761967920548 + - -0.0007527789836830537 + - 0.011235336275673776 + - -0.01913547066659827 + - 0.07906917496718507 + - 0.02269510404928231 + - -0.20714516451010723 + - 0.1893549620015913 + - 0.0009478416016314419 + - 0.0015173014123036706 + - -0.0015850500553003114 + - 0.00022719794306853884 + - 6.258939223823836e-05 + - -0.0005125689942254021 + - -0.0007761732594231804 + - -0.0004658279134787942 + - -0.0005393026837741175 + - -0.003287280743854614 + - 0.001424686729696522 + - 0.0003080041865613451 + - 0.013902718647382871 + - -0.008035093378649015 + - 0.00119928404968684 + - -0.010392548468589264 + - 0.024315930541072346 + - -0.09688668776182487 + - -0.038023571648199785 + - 0.2184754022777171 + - -0.21500879209290827 + - 0.007843437290665436 + - -0.012689352731413415 + - 0.04535369362393479 +- - 0.0009636258430341146 + - -0.0015278818756051344 + - 0.002701023823076395 + - -0.0011247197456244894 + - 0.003747771091850931 + - -0.013560845033566112 + - -0.11443270985199437 + - 0.19194198295830447 + - -1.0502545267761232 + - -0.0027584076232632566 + - -0.0005459816140677196 + - 0.0009223508786535981 + - -0.00010994164584597739 + - 8.343082403324991e-05 + - -0.0003124511025112681 + - -0.00010923795296990265 + - -0.0002783320517548862 + - 0.0012053472979129968 + - -0.0007142608813033553 + - 0.001918694085233511 + - 0.002261936170437492 + - -0.001280023724631023 + - 0.002543828955034217 + - 0.006093803087298406 + - -0.0048652432509168455 + - 0.011483289710369927 + - -0.05275343185837917 + - 0.12825574502258755 + - -0.21500887971012395 + - 1.1394560719851852 + - -0.003824810445354016 + - 0.0056419769867165044 + - -0.0357591507082867 +- - -0.011075230051837215 + - 0.018169326581574136 + - -0.005453542474231536 + - -0.06928333957499842 + - -0.042875799909336675 + - 0.031765260119585075 + - -0.8478744595870313 + - -0.3234988467687463 + - 0.2806421123655391 + - 0.0009522056919321782 + - 0.00015297635579880392 + - 7.477210403302679e-05 + - 0.001433440784756997 + - 0.0002883602356811023 + - -0.00046324758647735807 + - -0.005427888153483811 + - -0.0020577484932810326 + - 0.0024454756186045833 + - 0.003368450153861271 + - 0.0007667175136769107 + - 0.0016828263502236284 + - 0.002197395412749512 + - -0.0014854796609842832 + - -0.0024151617048060905 + - -0.01541393928801725 + - -0.007037994678936809 + - 0.004421952162356247 + - 0.015331477250275685 + - 0.007843439481095827 + - -0.003824808802531222 + - 0.9257918186370389 + - 0.34973508601605463 + - -0.3088756736612256 +- - 0.009920269771832356 + - -0.010019856594376321 + - 0.0030339561000341884 + - 0.0679793982671165 + - 0.03452533821982581 + - -0.03133300277651512 + - -0.3291867811755113 + - -0.3226967286827447 + - 0.1355011280081888 + - -0.00034126159387512495 + - -0.0005669460864448906 + - -0.0003107065958316442 + - 0.0009923781168652169 + - 0.0006983807401200953 + - 0.0007807860320243257 + - 0.004332259787695441 + - 0.002112707760828068 + - -0.0009521089022892444 + - -0.002985892581164059 + - 0.003127008868719679 + - -0.0013292316064789217 + - -0.003262806517480424 + - 0.0027826493902121264 + - 3.0760002220678384e-05 + - -0.08029517638086911 + - -0.03836014880132938 + - 0.038501650604633945 + - -0.016887470288116647 + - -0.012689356017059004 + - 0.0056419780819317 + - 0.34973508601605463 + - 0.34108702150137393 + - -0.14956525070941534 +- - -0.0018050939842585707 + - 0.0012832567998891894 + - 0.0011609762970756956 + - -0.01680374327682387 + - -0.008745017892286277 + - 0.0020366283634441506 + - 0.2830791676959141 + - 0.13434569350000417 + - -0.283264618294598 + - -0.0013208510198002338 + - -0.0002522863284765425 + - 0.0015412236502191493 + - 0.0008455092114933649 + - 0.0008144172157491662 + - -0.00014803197257163832 + - -0.00037399210000327353 + - 0.00035399846744627896 + - 0.0018900102623521497 + - 0.0013013353802252805 + - -0.0005289284631842234 + - -0.00029769167450264237 + - 0.000287557990550138 + - -0.0019366907982337118 + - 0.0011007203634886525 + - -0.05218763054561776 + - -0.021122964253808846 + - 0.020686507855677987 + - 0.09585341793744673 + - 0.04535369362393479 + - -0.035759148517856304 + - -0.3088756736612256 + - -0.14956525070941534 + - 0.29105340325177503 +hessian_method: analytic +modes: +- - - 0.005631214560918017 + - 0.012150752894011846 + - 0.027555822898613944 + - - -3.7800909822784024e-05 + - -4.031045139227224e-05 + - -0.00020780009168760096 + - - -0.005593772669826713 + - -0.012105753554959102 + - -0.027377536203532574 + - - -0.10630702607788275 + - 0.3967786905404905 + - 0.11715050880872656 + - - 0.19588864016216115 + - -0.2027445791097142 + - 0.3211138679560063 + - - -0.06670910369374566 + - -0.14472642762580065 + - -0.32630391619094307 + - - 0.0077625735830650884 + - -0.001057664559470316 + - -0.0015749408083042616 + - - -0.007927127323633208 + - 0.0008643859531801062 + - 0.0008348924113107298 + - - 0.15428437855913973 + - 0.15232272445286998 + - -0.36976976307429743 + - - -0.2438565686115664 + - -0.3457994387149727 + - -0.06991803289692304 + - - 0.06686851135284312 + - 0.14430643780380428 + - 0.3288190558248184 +- - - 0.007104787623765609 + - 0.015350679161216414 + - 0.03472806666575176 + - - -0.016928098570945984 + - -0.036408987866509965 + - -0.08245186914665859 + - - 0.007181988962629373 + - 0.015385213961209458 + - 0.03487292714743741 + - - 0.22231117980935278 + - -0.2731102348952077 + - -0.04176988165219262 + - - -0.2607498633388042 + - 0.18896581180389868 + - -0.1478408536494534 + - - 0.08404010457686559 + - 0.18235728486077815 + - 0.41192449247528834 + - - -0.0227411808590234 + - 0.02093524868566458 + - -0.1852229771125306 + - - -0.03724998222176729 + - -0.14987579374729398 + - -0.10683896213091003 + - - 0.25457957223241945 + - 0.1121343302447901 + - -0.21686812576088094 + - - -0.2921770566970914 + - -0.19456855442571788 + - 0.029101271681989147 + - - 0.08346035978816993 + - 0.18076065843657457 + - 0.4106418849882745 +- - - -0.16328135218050524 + - 0.0753512968109333 + - 0.0001891044694761836 + - - -0.013136432767668982 + - -0.15433472667154519 + - 0.07084376675850919 + - - 0.1718490390350976 + - 0.025411882150438433 + - -0.046451628147527985 + - - -0.37176878012327574 + - 0.13000860337781617 + - 0.026018534684150916 + - - -0.37452670321269255 + - 0.12441495355903595 + - 0.014600471407928849 + - - 0.05024408116247686 + - 0.3084702020845817 + - -0.14667862581612143 + - - -0.013939467784802654 + - -0.13993076806436622 + - 0.049133993807090395 + - - -0.008894702648102376 + - -0.12873871369197498 + - 0.07425996307748091 + - - 0.3837137121239087 + - 0.011941266102277057 + - -0.09106185111460362 + - - 0.3867299262184881 + - 0.016519246897984133 + - -0.07923864833791944 + - - 0.002881623908804694 + - 0.3156563402375164 + - -0.13993593159627501 +- - - 0.0032113067888271747 + - 0.006940132653728242 + - 0.015594301001863533 + - - 0.014025966129370735 + - 0.030388941973155937 + - 0.06881360227443845 + - - 0.003213584875271284 + - 0.006849474626079832 + - 0.015657799427741512 + - - -0.2415665023849816 + - -0.19492026759245998 + - -0.01261648788062069 + - - 0.1923898710536964 + - 0.08888957268720703 + - -0.22712497446886637 + - - -0.02171795319411242 + - -0.0473032093615463 + - -0.10744124449765928 + - - -0.015453314691672078 + - 0.30815487913687317 + - -0.44071561012138255 + - - -0.08653555795848908 + - -0.5279065138021827 + - -0.05707811693361854 + - - -0.21234678710809782 + - 0.14953604982652421 + - -0.17069842230228183 + - - 0.16317857011098458 + - -0.2551968731340247 + - -0.06925227222362776 + - - -0.021634092650104422 + - -0.04767085509903223 + - -0.10742322393133417 +- - - 0.21117521820164714 + - 0.020616458630460032 + - -0.052538966468509245 + - - -0.014525095853779311 + - -0.17014044811141937 + - 0.07807762441967799 + - - -0.20246908190934806 + - 0.08222602925939394 + - 0.005365976340871249 + - - 0.008751211562400092 + - 0.11194248025152624 + - -0.021146682082383586 + - - -0.003417542543867757 + - 0.08916402253208092 + - -0.06773506649912987 + - - 0.4767183469758315 + - 0.30463138771613935 + - -0.23146487242177033 + - - -0.015341192076242328 + - -0.16882609149891598 + - 0.07763818523453747 + - - -0.01301327319695154 + - -0.16914991313874225 + - 0.07735848746852834 + - - 0.00888148200889443 + - 0.08906940924230722 + - -0.07129937743267728 + - - 0.020882939775247893 + - 0.10755173896080839 + - -0.022619583676851244 + - - -0.41412514384168264 + - 0.437517561392357 + - -0.108980656544314 +- - - -0.012348239234429945 + - -0.025871559469686046 + - -0.058600954322049134 + - - 2.3459223576805378e-05 + - 0.0001953994566194519 + - -0.00011349545672916557 + - - 0.012299104659783414 + - 0.025795765668592322 + - 0.05865522235143968 + - - 0.3375538455418812 + - 0.22263041897742894 + - -0.02526674263106448 + - - -0.28958546880136266 + - -0.12116919296822277 + - 0.2555252862139187 + - - 0.035358944203946224 + - 0.07863426962475412 + - 0.1800817612740658 + - - -0.35037620187268276 + - 0.052213389595338146 + - 0.04880774516673313 + - - 0.35063017482542524 + - -0.052074648047319434 + - -0.048846188783378805 + - - -0.3006256849962714 + - 0.20922110419717801 + - -0.17296476114512227 + - - 0.2528574926300033 + - -0.31078857820815037 + - -0.05721198721808185 + - - -0.03550716240227034 + - -0.08009194524295024 + - -0.17941937812532036 +- - - 0.021460209900851426 + - -0.07746141029727176 + - 0.02977990962101216 + - - 0.03320895475258708 + - -0.005010981677863945 + - -0.004522925513839806 + - - 0.03377890123348844 + - 0.06930288908080913 + - -0.0374669229101303 + - - -0.30837963382298933 + - 0.055964830804868734 + - 0.07933917510286437 + - - -0.32310765543056225 + - 0.026114827532432945 + - 0.01359221653822011 + - - 0.3453525689214714 + - 0.27938573769055347 + - -0.19404657085362365 + - - -0.21383687871321153 + - 0.03186498943279984 + - 0.029520133327029824 + - - -0.21371108812964806 + - 0.0314541997952603 + - 0.029680807124908292 + - - -0.30759250450489756 + - 0.06707578915910213 + - 0.07410234812734805 + - - -0.321925966901961 + - 0.03868495464600644 + - 0.00766686189820563 + - - 0.2892827861930283 + - -0.3736218178866618 + - 0.10563468643576972 +- - - 0.13375842446435793 + - 0.07559500526720798 + - -0.06066030254322449 + - - -0.24119610129305402 + - 0.035812494389278984 + - 0.033361663297846435 + - - 0.11772827539318408 + - -0.11291606086863831 + - 0.025886562307953317 + - - 0.18116859380392902 + - 0.1036029448032912 + - -0.06273745904210636 + - - 0.1749106825833568 + - 0.0893448142434929 + - -0.09537646825375085 + - - 0.15658987592632836 + - 0.09926558895613129 + - -0.076254083704548 + - - -0.5430097521607271 + - 0.08036480894272909 + - 0.07600840425973876 + - - -0.5428658653370219 + - 0.08154241509346852 + - 0.07548794102327988 + - - 0.16029380684876585 + - -0.13905356912475836 + - 0.048661271984380555 + - - 0.1542528371868238 + - -0.1537974370650743 + - 0.016147738250621588 + - - 0.13604039718221025 + - -0.1432940413263152 + - 0.034888504783384296 +- - - 0.024806558938812638 + - -0.12445380850804083 + - 0.04975248951815866 + - - 0.014766788773082707 + - 0.17354336113171862 + - -0.07960558942700548 + - - -0.045085924162330974 + - -0.11399886760730887 + - 0.059623558694423186 + - - -0.34637783996157273 + - 0.0737205766659756 + - 0.11300295581459605 + - - -0.37205019175621756 + - 0.019279191487715105 + - -0.006973044780074547 + - - 0.3054451695749148 + - 0.1967821245299298 + - -0.1487145268088218 + - - 0.01619461883249772 + - 0.16655025418297945 + - -0.06290302718827837 + - - 0.011054471123778487 + - 0.1566107652811501 + - -0.08533866222163511 + - - 0.3453659977536052 + - -0.08618896913310269 + - -0.10718191429409071 + - - 0.3707349852054372 + - -0.03445035803816438 + - 0.014075690225496587 + - - -0.26468114356392897 + - 0.2811346910834302 + - -0.07070257042334027 +- - - 0.021518037698776627 + - 0.04660991880777255 + - 0.10578536831022944 + - - -0.032796056496685246 + - -0.0714863120099784 + - -0.1619375569436366 + - - 0.02153208163943067 + - 0.046742695034381936 + - 0.10574128454906383 + - - -0.2753247126858785 + - -0.2406385872697566 + - 0.055027146152701954 + - - 0.2385606544205003 + - 0.163520608591999 + - -0.22942724089651706 + - - -0.042613623880777135 + - -0.09275526659242993 + - -0.20983075653544106 + - - -0.009816517146242586 + - -0.29080722019800204 + - 0.24042739486936301 + - - 0.04617122471047407 + - 0.36944526276078243 + - -0.06250283944491525 + - - -0.23480551095442592 + - 0.23454723645414663 + - -0.16304886231140625 + - - 0.19808596747141174 + - -0.3112528896863902 + - -0.011523918781591607 + - - -0.04244155811514257 + - -0.09261088146736024 + - -0.21000845384877334 +- - - -0.01350636487326524 + - -0.029004821079466905 + - -0.06589727526949377 + - - 5.821818119291491e-05 + - -3.0355683191815884e-05 + - 1.7330553814637577e-05 + - - 0.013480492562756562 + - 0.029114674501432014 + - 0.06583258930433884 + - - 0.13773790417709855 + - 0.12543910387525198 + - -0.04235690602719027 + - - -0.12340280083163184 + - -0.09599395519392578 + - 0.10940740240719178 + - - 0.019295348229642774 + - 0.042487619294217134 + - 0.09655604881426012 + - - 0.6275177551211105 + - -0.09366699176527028 + - -0.08674615099175635 + - - -0.6278540675939449 + - 0.09291549724596194 + - 0.0871671866234368 + - - -0.11577561733313534 + - 0.13174776897328933 + - -0.07570430182502115 + - - 0.10142842642021867 + - -0.16121676845620042 + - 0.008710503317481924 + - - -0.019332371059188048 + - -0.04265954316023448 + - -0.0964695106461724 +- - - 0.0020907875262319423 + - -0.051119912753511 + - 0.022179072875926766 + - - -0.16435957047339134 + - 0.024427183297236307 + - 0.02273865220192205 + - - 0.010616920068187147 + - 0.04928026288297325 + - -0.023837038522862633 + - - 0.10953282839973096 + - 0.1538919126397414 + - 0.046652134786982324 + - - 0.06449241256040242 + - 0.055499219623808986 + - -0.17494472662101807 + - - 0.21356753477471144 + - 0.17096441811067467 + - -0.11909911123224527 + - - 0.552816950149839 + - -0.08237803368836501 + - -0.076712049448493 + - - 0.552425289803532 + - -0.08196179335832965 + - -0.07676203456773557 + - - 0.08971734793375943 + - -0.07901895896217549 + - 0.15354808736472153 + - - 0.04501041860239215 + - -0.17661863677005618 + - -0.06855743238914085 + - - 0.1794714688067197 + - -0.22952382599616797 + - 0.06468453070619593 +- - - 0.1040922018762606 + - 0.0208031159960534 + - -0.030538475909204093 + - - -0.08929736730667734 + - 0.013256062247688221 + - 0.012341170403934405 + - - 0.09797578102939013 + - -0.05092068246350521 + - 0.0024076675820948394 + - - -0.39032770497662544 + - -0.039263495586421004 + - 0.0014613603441266318 + - - -0.35767039164106607 + - 0.028871135014223087 + - 0.1560191766194048 + - - -0.17883252950225625 + - -0.26513569030516926 + - 0.15492111968926428 + - - 0.22010759534376023 + - -0.03282563961533227 + - -0.030598314990878284 + - - 0.22003853375644686 + - -0.032620383442443626 + - -0.03061407003724337 + - - -0.3799752480418119 + - 0.08089557654898485 + - -0.05386595752051528 + - - -0.34748055410525763 + - 0.14901511268158946 + - 0.10075357714140092 + - - -0.12959766111024357 + - 0.3119795823073276 + - -0.10993270365106295 +- - - 0.08736452775578199 + - 0.04371153120771786 + - -0.03724826419593405 + - - -0.0008970759622471437 + - -0.010962068704001305 + - 0.005016187473728927 + - - -0.07783461934868116 + - 0.06836223026194115 + - -0.01418609668235257 + - - -0.3750592146486679 + - -0.1457891151800137 + - -0.0342672015035242 + - - -0.3162470064427792 + - -0.020395710164413414 + - 0.24918550596587608 + - - -0.22932230200630765 + - -0.2832283086806548 + - 0.17302137027387515 + - - -0.0013853272071562394 + - -0.021261518361810054 + - 0.014123954143035078 + - - -0.0026875061483390005 + - -0.02443551321734515 + - 0.00689357732710196 + - - 0.35232259716837827 + - -0.12027873136136125 + - 0.15649681356707923 + - - 0.29374720495131723 + - -0.24509525464532983 + - -0.12729597052867145 + - - 0.17576553201694944 + - -0.3443298779608126 + - 0.11494580071767091 +- - - 0.006448913131883795 + - 0.014764124895346658 + - 0.03229904672961332 + - - -8.372260940764336e-05 + - -0.0011388289721784722 + - 0.0005035123488834809 + - - -0.006349222655679019 + - -0.013947716356364898 + - -0.03269560690180354 + - - 0.31343622616602856 + - -0.15798819540892814 + - -0.04049098916843087 + - - -0.326201381106414 + - 0.11676239286205746 + - -0.021300504707579365 + - - -0.08908932482326243 + - -0.1960182292529093 + - -0.4513712647454032 + - - 0.05022953091122556 + - -0.0006431648662637617 + - -0.020059102725239294 + - - -0.04852267084429394 + - 0.02178612417481785 + - 0.01038450005827757 + - - -0.32953728601411725 + - -0.027282466140896376 + - 0.1255725306776829 + - - 0.340173002794671 + - 0.04523251017847735 + - -0.05304411488141678 + - - 0.0893216350113009 + - 0.20199288542103147 + - 0.4490345381565307 +- - - 0.011085957550192259 + - -0.013963663688946814 + - 0.005079496362976523 + - - 0.0037087600369323103 + - 0.043945969081724566 + - -0.020154836612279476 + - - -0.013240655034463495 + - -0.011270312777705613 + - 0.006515441239040051 + - - 0.0044510342511978294 + - 0.27859987925891183 + - 0.0623724228040898 + - - -0.0750136432000822 + - 0.15163843662496534 + - -0.24093551621317452 + - - -0.10956573915191409 + - -0.13021168749296527 + - 0.06466731758900372 + - - 0.030162925970273903 + - -0.2549493352859977 + - 0.4805177237274908 + - - -0.09609409163993649 + - -0.5217014607717274 + - -0.12416045252078274 + - - 0.03092839386524745 + - 0.1328490886587292 + - -0.2515037582596043 + - - 0.11066650063908899 + - 0.26889206951474653 + - 0.04841190503481249 + - - 0.08594691557563633 + - -0.14808300568486824 + - 0.06262732908049366 +- - - -0.007392875120595542 + - 0.03247905855636397 + - -0.013036974290650538 + - - -0.040506451027851845 + - 0.005875342778614686 + - 0.0054227875512517665 + - - -0.012707402023024322 + - -0.02965447064236363 + - 0.01544106724028122 + - - -0.014529446687599824 + - -0.4447289229164924 + - -0.10614972894619724 + - - 0.0902597792616559 + - -0.22671258787847545 + - 0.38850890716046865 + - - 0.15119932033506808 + - 0.18380502332916482 + - -0.10946608801290728 + - - 0.09570740468095232 + - -0.01440190908124986 + - -0.013560946396712226 + - - 0.0958178195058926 + - -0.01344222948545278 + - -0.013352880055456921 + - - 0.041037224268917184 + - 0.20772215435129437 + - -0.40533626660111355 + - - 0.14598553733207303 + - 0.4257081193162248 + - 0.08922366681185717 + - - 0.11669241295735298 + - -0.2216151908383858 + - 0.07687077483361351 +- - - 0.005944586844190587 + - 0.013005731842936094 + - 0.028715684764152784 + - - 0.004997992881924332 + - 0.011746467734638664 + - 0.02647826384362582 + - - 0.00591468953901961 + - 0.012476152668882308 + - 0.02892622616961917 + - - 0.3223173551433123 + - -0.14495487880382846 + - -0.038004823513068685 + - - -0.3338362695178204 + - 0.11614355784527418 + - -0.01565767518715063 + - - -0.09018502508517104 + - -0.19644351045197908 + - -0.44574421065916475 + - - 0.004448059197051981 + - 0.039493327189351356 + - -0.018474068326498044 + - - -0.002349977726528282 + - -0.040091946535623056 + - 0.01790263720429451 + - - 0.3360523498983407 + - 0.01909800770482661 + - -0.1125843304201753 + - - -0.3471751589212418 + - -0.040310752629402105 + - 0.055550725132914903 + - - -0.0901370682493828 + - -0.196534735699766 + - -0.44533688444079994 +- - - -0.020157947251733865 + - 0.021647347845472634 + - -0.005439726712673829 + - - 0.0056180977143099825 + - 0.06644220707312662 + - -0.030501016718854093 + - - 0.023298072719409115 + - 0.01514038666812895 + - -0.011475399426605274 + - - 0.010417702215283691 + - -0.3472691282322664 + - -0.07951128255081666 + - - 0.08744754023849098 + - -0.1817528624019756 + - 0.2938688932568374 + - - 0.12966702389647924 + - 0.1699704501612586 + - -0.10151243708947086 + - - 0.0272976275816222 + - -0.18056950448931086 + - 0.3915304300565744 + - - -0.07716274927056162 + - -0.4071854050488059 + - -0.12184087507330747 + - - -0.054343345650523796 + - -0.16160028481550381 + - 0.31282707119014214 + - - -0.13008987686902618 + - -0.32557544420284457 + - -0.06103221872066619 + - - -0.09759405968028098 + - 0.20392778577727325 + - -0.06933425183413608 +- - - 0.027298404495297062 + - 0.019970795275790758 + - -0.014266536243589928 + - - -0.0018116809577393294 + - -0.00044626714130063984 + - 0.000557261631103206 + - - 0.022010559076006873 + - -0.025675786432716098 + - 0.006889630572131288 + - - 0.04092226544052224 + - -0.08740522012111272 + - 0.43724110574467984 + - - -0.09385529761444054 + - -0.38055287594930265 + - -0.2210283123516556 + - - -0.2640517258089777 + - 0.23137661713975377 + - -0.048558635745324666 + - - 0.0040357760617523684 + - 0.006387397340014941 + - 0.0035286304305351002 + - - 0.0016916919646346599 + - 0.0012397324680743596 + - -0.007872474411983616 + - - 0.07603434544210658 + - 0.35745757189395355 + - 0.209737672325085 + - - -0.05005697221502151 + - 0.08547665090099002 + - -0.41068128367453965 + - - -0.28068224742883474 + - -0.1406834813906328 + - 0.11889395697755809 +- - - 0.00047204454715478586 + - 0.011349539568770255 + - -0.004920825698816616 + - - -0.005134215667032698 + - -0.06042110872394099 + - 0.027532140602584763 + - - 0.0006513062959880139 + - 0.012010087426473822 + - -0.005526007156908907 + - - 0.007549206687257286 + - -0.02020272197944237 + - 0.11145211175923699 + - - -0.027335234241503407 + - -0.09714302895145255 + - -0.057944293984877195 + - - 0.016092327729779348 + - -0.017208320767825025 + - 0.0044208211907153265 + - - 0.13325195334786571 + - 0.5809110028896791 + - 0.3372255763379764 + - - -0.07196091230437873 + - 0.13699130216085692 + - -0.6643829796900568 + - - -0.020235814044270307 + - -0.1092327852628478 + - -0.06600023208465246 + - - 0.01880639199846955 + - -0.0254856055653333 + - 0.1269124456927531 + - - -0.008375759054428214 + - -0.007017285932981623 + - 0.004733583172231175 +- - - 0.026819255514212836 + - 0.01640499976459086 + - -0.012598607352763429 + - - 0.0010488411469574059 + - 0.011751985924304934 + - -0.0053954798170477054 + - - -0.024640294225541606 + - 0.02522625330629914 + - -0.00616846845032139 + - - 0.03528144931721875 + - -0.0798086289212777 + - 0.3948018806724835 + - - -0.08608550590297369 + - -0.3440028565342337 + - -0.19843112837942312 + - - -0.26465626265587683 + - 0.22859563431462426 + - -0.04717461121578515 + - - -0.027038695119624492 + - -0.11607208908985243 + - -0.06956793292513072 + - - 0.014816614971261098 + - -0.025861862663551925 + - 0.13463936262143159 + - - -0.07556477816417943 + - -0.36412579579386256 + - -0.2124000366710274 + - - 0.052251085576421934 + - -0.08821711820401756 + - 0.4170390001611304 + - - 0.3125346484714674 + - 0.15339541176192703 + - -0.13099338391307191 +- - - -0.0052359998278439235 + - -0.011107644060665901 + - -0.025469946113212648 + - - 0.015285487724454925 + - 0.03288693505176805 + - 0.07482519133870459 + - - -0.005226673402710758 + - -0.011219901029449262 + - -0.02527631101096706 + - - 0.01779201610613765 + - -0.04858636924691761 + - 0.2146177351865585 + - - 0.046583294763720764 + - 0.18742523883297052 + - 0.1019211196404029 + - - -0.0006522919988919131 + - -0.003642095653904286 + - -0.006682500376951768 + - - -0.12175803520284062 + - -0.5459737772409997 + - -0.2916177792783652 + - - -0.0630279225879889 + - 0.14848150375755953 + - -0.6127251113374775 + - - 0.0378244749953272 + - 0.18906451566884566 + - 0.10420462931222756 + - - 0.026231939400662433 + - -0.050033473114890335 + - 0.21053037839462319 + - - -0.00046056365691627055 + - -0.0025577977937474594 + - -0.007165216432544128 +- - - 0.011732224821545366 + - 0.026564063334563882 + - 0.059064902154751936 + - - 8.337773933107027e-05 + - 0.00034198541548019213 + - 0.00023422500959848318 + - - -0.011623788065919018 + - -0.025570083297302863 + - -0.05872413871051584 + - - -0.0396456105869023 + - 0.10995173856249447 + - -0.48584393441033097 + - - -0.1077698096956651 + - -0.4298029216114105 + - -0.23413525838255167 + - - 0.007250572071169075 + - 0.0026983228247216325 + - 0.01499214526135963 + - - -0.004125396279848839 + - -0.0036091541910615167 + - -0.0018502788492882883 + - - 0.0031513214903699893 + - -0.00026313110299081314 + - -0.0009819465302677124 + - - 0.08470024357921806 + - 0.4264674467502156 + - 0.2350908986260151 + - - 0.06045575108369794 + - -0.11353806326874882 + - 0.47864961983065374 + - - -0.006302670768123745 + - -0.007823167579167135 + - -0.012772620862064979 +- - - 0.007333998760449023 + - 0.027941016562640853 + - 0.05068070101486932 + - - 0.007671969337148403 + - 0.016647583945309005 + - 0.0376475586842533 + - - 0.0070699801592810614 + - 0.019837267890747613 + - 0.055285438644365456 + - - -0.030105968588596252 + - 0.09430322235362633 + - -0.4091441777252064 + - - -0.10390498245654878 + - -0.39691586399041834 + - -0.21617230601613888 + - - 0.04607992931286842 + - -0.032227470965838986 + - 0.017366243784559348 + - - -0.059468854151437545 + - -0.2652186142342823 + - -0.14331400015077644 + - - -0.03090621778206529 + - 0.07057545342067013 + - -0.29709953247474974 + - - -0.07040619183892728 + - -0.37164258961398416 + - -0.20259574582862006 + - - -0.06138909978383263 + - 0.10795155530022596 + - -0.45223990487228627 + - - 0.04705156930305552 + - 0.02549662386417224 + - -0.008054674736261563 +- - - 0.03655263834341021 + - -0.050990094457106803 + - 0.020901269447615275 + - - 0.0010652598569538406 + - 0.0013422136702799206 + - 0.0035486781135461195 + - - 0.04338704687534521 + - 0.04227178473585287 + - -0.021717245016552374 + - - -0.016312581277085316 + - 0.047493382106102634 + - -0.2777412513367192 + - - 0.05183635819103236 + - 0.16577514372530794 + - 0.10562113320670276 + - - -0.47438425521207117 + - 0.3955588785530697 + - -0.07726845427033648 + - - -0.004004038509450581 + - -0.023657998724085492 + - -0.012827221645006055 + - - -0.001796024342133061 + - 0.006766667641280253 + - -0.029545418632706755 + - - -0.039564246705383666 + - -0.23158438858980865 + - -0.14332928106327203 + - - 0.03367741291177756 + - -0.03313723038818268 + - 0.19163717382521187 + - - -0.5146811918268692 + - -0.23932329393851628 + - 0.2108913256072975 +- - - 0.03457560972864757 + - -0.05061987565943405 + - 0.01604453467718648 + - - -0.0009189144074847038 + - -0.010922521337376158 + - 0.00512138126113282 + - - -0.04343556430815513 + - -0.04083220803955589 + - 0.026434697890075645 + - - -0.011717297660573254 + - 0.03930614647937071 + - -0.24045587206449362 + - - 0.06067942733405656 + - 0.19270915428628285 + - 0.11938245947402604 + - - -0.455215047940437 + - 0.37838828908741207 + - -0.07451912029910807 + - - 0.020592266357885705 + - 0.09091382992479627 + - 0.05091868081284865 + - - -0.011091786003945147 + - 0.02323577154094458 + - -0.10454950359983131 + - - 0.03307107886834924 + - 0.20873342245716683 + - 0.13113408327529621 + - - -0.04202191130728089 + - 0.04415263493959166 + - -0.23630159593391115 + - - 0.5222250911880205 + - 0.2424232325262936 + - -0.21280255695535408 +opt_xyz: + coords: !!python/tuple + - !!python/tuple + - -1.2586322810840838 + - -0.023906163696375576 + - 0.2672015616889118 + - !!python/tuple + - 0.04666883668411464 + - 0.5605609555826064 + - -0.2581280265629718 + - !!python/tuple + - 1.2210020478918608 + - -0.393203480910381 + - -0.07753839896164381 + - !!python/tuple + - -1.1823227404845902 + - -0.25156620114394906 + - 1.332555469543582 + - !!python/tuple + - -1.5056864468032174 + - -0.9531226883963032 + - -0.25066560426480194 + - !!python/tuple + - -2.0927573731290074 + - 0.6655973470750921 + - 0.13206243006643167 + - !!python/tuple + - 0.2580877250535657 + - 1.5022085738718503 + - 0.2551417161969452 + - !!python/tuple + - -0.06360653515459037 + - 0.808105386245578 + - -1.3170806905103434 + - !!python/tuple + - 1.0456880259067831 + - -1.3315047764510255 + - -0.6080690629987441 + - !!python/tuple + - 1.3679397251420937 + - -0.6345746017399848 + - 0.977333596988847 + - !!python/tuple + - 2.150469779944395 + - 0.03494593525664683 + - -0.4546407570172308 + isotopes: !!python/tuple + - 12 + - 12 + - 12 + - 1 + - 1 + - 1 + - 1 + - 1 + - 1 + - 1 + - 1 + symbols: !!python/tuple + - C + - C + - C + - H + - H + - H + - H + - H + - H + - H + - H +reduced_masses: +- 1.0285325886446797 +- 1.1335117979821507 +- 2.038814695050416 +- 1.0790749419146202 +- 2.447399947319763 +- 1.1016692505915027 +- 1.1823285622402133 +- 2.274850051844449 +- 1.8204096217987564 +- 1.6688999311147013 +- 1.126056411253335 +- 1.3859178167119286 +- 1.3678043557849346 +- 1.2501726578343484 +- 1.0366981113069915 +- 1.0414457096259102 +- 1.054911264655581 +- 1.0401342627810815 +- 1.0870532469405032 +- 1.0359755590409918 +- 1.060413251207966 +- 1.0365747887183323 +- 1.1015872894263457 +- 1.1022913315762943 +- 1.1032457396332378 +- 1.1018496038399699 +- 1.100583168174747 +schema_version: 2 diff --git a/arkane/ess/arc_yaml_test.py b/arkane/ess/arc_yaml_test.py index 000239585a8..107aac16dfd 100644 --- a/arkane/ess/arc_yaml_test.py +++ b/arkane/ess/arc_yaml_test.py @@ -125,6 +125,30 @@ def test_load_scan_energies(self): assert np.all(np.diff(angle) > 0) assert 5e3 < max(vlist) < 2e4 # a methyl rotor barrier, J/mol + def test_a_yaml_scan_is_a_hindered_rotor_scan_log(self): + """StatMechJob fits a hindered rotor to an ARC YAML scan, as it does to a Gaussian one""" + from rmgpy.species import Species + from rmgpy.statmech import HinderedRotor + from arkane.statmech import StatMechJob + freq, scan = os.path.join(DATA, 'C3H8_freq_uma.yml'), os.path.join(DATA, 'C3H8_scan_uma.yml') + with tempfile.TemporaryDirectory() as tmp: + path = os.path.join(tmp, 'C3H8.py') + with open(path, 'w') as f: + f.write(f"spin_multiplicity = 1\noptical_isomers = 1\nexternal_symmetry = 2\nenergy = -119.0\n" + f"geometry = Log('{freq}')\nfrequencies = Log('{freq}')\n" + f"rotors = [HinderedRotor(scanLog=Log('{scan}'), pivots=[1, 2], top=[1, 4, 5, 6], " + f"symmetry=3, fit='fourier')]\n") + species = Species(label='C3H8', smiles='CCC') + job = StatMechJob(species=species, path=path) + job.applyAtomEnergyCorrections = job.applyBondEnergyCorrections = False + job.load(pdep=False, plot=False) + rotors = [mode for mode in species.conformer.modes if isinstance(mode, HinderedRotor)] + assert len(rotors) == 1 + assert rotors[0].symmetry == 3 + # The methyl torsion leaves the harmonic modes, which keep 3N - 6 - 1 = 26 of propane's 27 frequencies. + oscillator = [mode for mode in species.conformer.modes if isinstance(mode, HarmonicOscillator)][0] + assert len(oscillator.frequencies.value_si) == 26 + def test_a_failed_job_raises(self): with tempfile.TemporaryDirectory() as tmp: path = os.path.join(tmp, 'output.yml') diff --git a/arkane/statmech.py b/arkane/statmech.py index f212e7cc1dc..f35eae7ebc9 100644 --- a/arkane/statmech.py +++ b/arkane/statmech.py @@ -57,7 +57,7 @@ from arkane.common import ArkaneSpecies, symbol_by_number, get_principal_moments_of_inertia from arkane.encorr.corr import get_atom_correction, get_bac -from arkane.ess import ESSAdapter, ess_factory, _registered_ess_adapters, GaussianLog, QChemLog, XTBLog +from arkane.ess import ESSAdapter, ess_factory, _registered_ess_adapters, ARCYAMLLog, GaussianLog, QChemLog, XTBLog from arkane.encorr.isodesmic import ErrorCancelingSpecies, IsodesmicRingScheme from arkane.modelchem import LevelOfTheory, CompositeLevelOfTheory, standardize_name from arkane.output import prettify @@ -801,7 +801,7 @@ def _fit_rotors(self, rotors, conformer, hessian, is_ts, linear, directory, plot 'in the specified path {1}'.format(self.species.label, scan_log.path)) else: scan_log.path = modified_scan_path - if isinstance(scan_log, (GaussianLog, QChemLog)): + if isinstance(scan_log, (GaussianLog, QChemLog, ARCYAMLLog)): v_list, angle = scan_log.load_scan_energies() try: pivot_atoms = scan_log.load_scan_pivot_atoms() From 25b714e29f88515eff8b0a5316ed7b5d6565a276 Mon Sep 17 00:00:00 2001 From: kfir4444 Date: Fri, 30 Oct 2026 08:09:32 +0200 Subject: [PATCH 3/3] Move the ARC YAML adapter tests to test/arkane/ess, where pytest collects them --- arkane/ess/arc_yaml_test.py => test/arkane/ess/arcYamlTest.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename arkane/ess/arc_yaml_test.py => test/arkane/ess/arcYamlTest.py (99%) diff --git a/arkane/ess/arc_yaml_test.py b/test/arkane/ess/arcYamlTest.py similarity index 99% rename from arkane/ess/arc_yaml_test.py rename to test/arkane/ess/arcYamlTest.py index 107aac16dfd..21912eddb93 100644 --- a/arkane/ess/arc_yaml_test.py +++ b/test/arkane/ess/arcYamlTest.py @@ -47,7 +47,7 @@ from arkane.ess.arc_yaml import ARCYAMLLog from arkane.ess.factory import ess_factory -DATA = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'data', 'arc_yaml') +DATA = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), '..', '..', 'arkane', 'data', 'arc_yaml') def wavenumbers(force_si, mass_amu):