cmmde-gui modification

Aditya Wibawa Sakti 2 years ago
parent 29116e3053
commit 87d2e62c1a
  1. 10
      cmmde_gui/gui.py
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  101. Some files were not shown because too many files have changed in this diff Show More

@ -12,6 +12,7 @@ from panel_chemistry.pane.ngl_viewer import EXTENSIONS
import py3Dmol
from panel_chemistry.pane import Py3DMol
import subprocess
import uuid
# from iodata import IOData
@ -54,8 +55,13 @@ def cmmde_gui():
def run(event):
# RunMessage.value = " "
# terminal.clear()
os.makedirs(Name_input.value)
os.chdir(Name_input.value)
unik = str(uuid.uuid4().hex)
Folder = Name_input.value + "_" + unik
os.makedirs(Folder)
os.chdir(Folder)
job_list = [job[i] for i in job_btn.value]
jobs = ",".join(job_list)
cmd = subprocess.run(["cmmde.py","-i","{}".format(editor.value),"-s","{}".format(software[software_btn.value]),"-j","{}".format(jobs),"-m","{}".format(method[method_btn.value])],capture_output=True,text=True)

@ -1,298 +0,0 @@
#
# Number of atoms
#
71
#
# The current total energy in Eh
#
-106.584609849900
#
# The current gradient in Eh/bohr
#
0.000012434938
0.000003391057
-0.000003321356
-0.000008112395
-0.000019366935
-0.000007027411
0.000007702114
0.000028151841
-0.000027730849
0.000020687858
0.000008675811
-0.000005742211
-0.000003903790
-0.000048421805
0.000047709565
0.000048246564
-0.000061127583
-0.000026271659
-0.000053925571
0.000001575583
-0.000028196995
0.000031648291
0.000032801706
0.000033036343
0.000004141107
-0.000007283302
-0.000038075314
-0.000021083590
-0.000005497721
0.000049420434
-0.000017643399
-0.000038472445
-0.000054995889
0.000018370442
0.000096795823
0.000120899036
0.000044028453
-0.000126763553
-0.000194650689
0.000053839849
0.000205225883
0.000002118298
0.000018980627
-0.000128205259
-0.000007485304
-0.000021195777
0.000034682283
0.000015893514
-0.000023781656
-0.000012719725
-0.000011931615
0.000033871956
0.000011669556
0.000000386219
-0.000002368742
-0.000015009876
-0.000017593337
-0.000005979656
-0.000000847897
-0.000009767010
0.000008394600
0.000005492788
0.000014347190
-0.000014986012
-0.000011121906
-0.000020725502
0.000028144657
0.000005693398
0.000007215545
-0.000001836192
-0.000004941521
0.000004275985
-0.000012167056
-0.000002000396
0.000003681707
0.000028555709
0.000004748171
0.000002822717
-0.000014198526
-0.000000946476
-0.000012165884
-0.000009099833
-0.000011377097
0.000013512852
0.000017045835
0.000008970975
0.000028257524
-0.000004051596
0.000008277547
-0.000026984700
-0.000009038531
0.000010110245
0.000000197894
0.000020728949
0.000016549328
-0.000025451848
-0.000025549662
0.000004278239
0.000057828924
0.000004777463
-0.000006121602
-0.000044295569
-0.000055432087
-0.000030842844
0.000040500942
0.000104267579
0.000029917255
-0.000020155499
0.000004952904
0.000003744939
-0.000009932713
-0.000045941580
0.000017547022
-0.000042417750
0.000013701618
0.000028931679
0.000006626910
-0.000004777434
-0.000018973001
0.000006815630
-0.000012566777
0.000003961274
-0.000000290495
0.000023762434
-0.000000680331
0.000012167392
-0.000021489741
-0.000005129746
-0.000003186058
-0.000001420915
-0.000000183604
-0.000000379390
0.000001455137
-0.000006116840
0.000000234290
-0.000007236940
-0.000008772200
0.000030181576
0.000000661606
0.000021309682
0.000010348427
-0.000017662625
-0.000006468910
0.000000526887
0.000007442540
0.000009541652
-0.000020497364
-0.000006940906
0.000007347513
-0.000012573760
-0.000009734241
0.000014933254
0.000038977278
-0.000026645418
0.000000488223
-0.000012232614
0.000011965820
-0.000004627710
-0.000002394198
-0.000010603484
0.000007846102
-0.000009920215
-0.000016237820
-0.000014228781
0.000004245497
-0.000001564989
-0.000012650798
-0.000041025624
-0.000025167468
0.000006722300
0.000046596824
-0.000019310143
0.000029395265
0.000045374628
-0.000025632836
-0.000033267220
0.000011713308
-0.000002140626
-0.000025639450
0.000059997407
0.000009319352
-0.000017151742
0.000000217840
0.000007257631
0.000003887648
-0.000004172665
-0.000000782613
0.000005493576
0.000001443301
-0.000003562666
-0.000002247086
0.000006128976
-0.000007962565
-0.000008306052
0.000009109571
0.000007573836
0.000011780771
0.000003616352
0.000003652743
0.000002111423
0.000002437966
-0.000005402791
0.000000266564
-0.000000670810
-0.000008506876
-0.000000943392
0.000000110232
0.000001979165
0.000002851888
0.000004688478
-0.000013946253
0.000001286540
-0.000001401167
#
# The atomic numbers and current coordinates in Bohr
#
6 11.2976954 -5.0017672 8.4371308
6 11.0509311 -4.0792889 6.1090126
6 13.1540058 -2.6430107 4.8625477
6 13.1597995 -2.8777150 1.9936868
6 15.1546219 -1.1263409 0.8637619
6 17.6203873 -1.0170415 2.3000566
6 19.6564325 0.2491804 1.2241563
6 19.3913950 1.5060812 -1.3092213
6 21.2541549 3.6794332 -1.5635075
6 23.9337083 2.7129031 -1.1910463
6 24.2045614 1.4245254 1.3293362
6 26.5115020 1.2866485 2.5048470
6 28.8489214 2.3977280 1.3144035
6 31.2520199 1.0766343 2.1982040
6 31.3449754 0.9087994 5.0205233
6 33.5472880 1.1850790 6.3640989
6 33.5637083 0.9112333 8.9901628
6 31.4207001 0.1818695 10.2586412
6 31.3458939 -0.0462455 13.0844216
6 29.6808842 -2.2555045 13.8892542
6 27.1271596 -2.1300246 12.6595943
6 25.0168125 -2.9903880 13.8426831
6 22.6404610 -3.1071390 12.5965218
6 20.4742185 -3.9238279 13.8245708
6 18.1716319 -4.1394626 12.5523201
6 15.9418606 -4.9688687 13.7721626
6 13.7360138 -5.2207298 12.4684839
6 13.6244071 -4.6908479 9.8573353
6 15.7769574 -3.8755586 8.6190088
6 18.0646532 -3.5590489 9.9264230
6 20.2407107 -2.6461696 8.6668692
6 20.0799929 -1.8191309 6.0801622
6 17.8425748 -2.0751015 4.7116232
6 15.7113081 -3.6024583 5.7981547
6 22.2124751 -0.6888503 4.9315975
6 22.0130884 0.3363498 2.4696658
6 24.5556623 -0.6063741 6.2267317
6 26.7219958 0.2671703 4.9788244
6 29.0871413 0.3008503 6.2918244
6 29.1697686 -0.2476772 8.8963453
6 26.9775884 -1.2326491 10.1232524
6 24.7063874 -1.4311708 8.7885134
6 22.5113334 -2.3977291 9.9982805
1 9.7544856 -5.9693088 9.3617779
1 9.2937198 -4.2368022 5.0804643
1 12.9540855 -0.6329911 5.3637331
1 11.3092812 -2.3929766 1.2167501
1 13.5614090 -4.8376943 1.4810634
1 14.3795316 0.7942325 0.8073748
1 15.5208897 -1.6953762 -1.0872227
1 17.4763398 2.2249853 -1.5583675
1 19.7377362 0.1183421 -2.8070845
1 21.0684044 4.5652009 -3.4182204
1 20.8372925 5.1036746 -0.1277104
1 24.3986179 1.3752891 -2.7023864
1 25.2451783 4.2975782 -1.3228111
1 28.9498742 4.4037633 1.8249291
1 28.7473058 2.2707274 -0.7395327
1 31.2780246 -0.8490839 1.4348896
1 32.9135704 2.0609555 1.4716791
1 35.2831294 1.6431850 5.3896627
1 35.2927237 1.2488418 10.0242375
1 30.5604894 1.7082233 13.8570036
1 33.2523021 -0.2666997 13.8417996
1 30.5846345 -4.0249842 13.3013778
1 29.4863693 -2.3052609 15.9426435
1 25.1198110 -3.6551926 15.7728153
1 20.5674127 -4.4160414 15.8055454
1 16.0297784 -5.4105727 15.7642288
1 12.0384136 -5.8504567 13.4144756
1 15.9384454 -5.5454457 5.0555804

File diff suppressed because it is too large Load Diff

File diff suppressed because it is too large Load Diff

@ -1,73 +0,0 @@
71
Coordinates from ORCA-job cmmd
C 5.97848292227904 -2.64682122276911 4.46473733913830
C 5.84790084724943 -2.15866672146033 3.23275021415626
C 6.96080005815379 -1.39862102621101 2.57314942053880
C 6.96386594614745 -1.52282120155028 1.05501363093393
C 8.01948053588850 -0.59603395259741 0.45708310508559
C 9.32430737085525 -0.53819516247474 1.21713753339898
C 10.40173605767687 0.13186057020019 0.64779562191024
C 10.26148427591736 0.79698386697550 -0.69281006629740
C 11.24721433432398 1.94707216289516 -0.82737253044232
C 12.66517295020455 1.43560651499299 -0.63027453120388
C 12.80850223257784 0.75382639523883 0.70345443684858
C 14.02928262082641 0.68086508196686 1.32550791795183
C 15.26619168199529 1.26882298316129 0.69555237740619
C 16.53785665556502 0.56973034535385 1.16323947693111
C 16.58704658600130 0.48091595264054 2.65674651101873
C 17.75246023074004 0.62711680775512 3.36773608410543
C 17.76114946247022 0.48220387222681 4.75738922945350
C 16.62711838321354 0.09624117050565 5.42863910220794
C 16.58753261377575 -0.02447208294616 6.92397771989722
C 15.70644744063530 -1.19356156918612 7.34987676603452
C 14.35507456107774 -1.12716046730315 6.69916874499826
C 13.23832700657148 -1.58244519711857 7.32523241601003
C 11.98081595795971 -1.64422714244578 6.66579222406349
C 10.83448978337768 -2.07640029731820 7.31564776809629
C 9.61601342462801 -2.19050924838847 6.64240169897696
C 8.43606928602578 -2.62941209208893 7.28791457516977
C 7.26878545045833 -2.76269121637430 6.59803747846171
C 7.20972573453389 -2.48228979441454 5.21627717090888
C 8.34880625528048 -2.05085726538503 4.56098301260707
C 9.55940277123032 -1.88336758566790 5.25283679344501
C 10.71092279368064 -1.40029264276640 4.58630964227842
C 10.62587457726097 -0.96264262550886 3.21748328506328
C 9.44188394504274 -1.09809639581324 2.49328362980176
C 8.31406613942317 -1.90633885016553 3.06825129746761
C 11.75433555668981 -0.36452388611557 2.60968898332605
C 11.64882464129668 0.17798865470172 1.30689085634491
C 12.99429682216915 -0.32087933760251 3.29504450611523
C 14.14067115232695 0.14138044646240 2.63468040283324
C 15.39225224524583 0.15920311616137 3.32949007692182
C 15.43597673333186 -0.13106510802484 4.70774317896792
C 14.27592490742450 -0.65228980512658 5.35699445263271
C 13.07405711851004 -0.75734295262974 4.65068097814951
C 11.91248454724954 -1.26882361302687 5.29086217556897
H 5.16185143514081 -3.15882215729037 4.95403949008511
H 4.91802467599078 -2.24201913845910 2.68846591450517
H 6.85500679826839 -0.33496448330993 2.83836530526916
H 5.98461386444324 -1.26630869356802 0.64387641820013
H 7.17638852989058 -2.55999758194727 0.78374501060828
H 7.60932040336028 0.42028974688182 0.42724433109965
H 8.21330108761868 -0.89715441920766 -0.57533346212512
H 9.24808071143430 1.17741152364752 -0.82465256537855
H 10.44476012626449 0.06262393035398 -1.48544516274204
H 11.14891940878957 2.41580026352334 -1.80884434866177
H 11.02662027705112 2.70074828394699 -0.06758141173515
H 12.91119250845211 0.72777163749630 -1.43004131122708
H 13.35917297596527 2.27418042402556 -0.70000147983408
H 15.31961363016889 2.33037115147470 0.96571086165418
H 15.21241904613515 1.20161717795566 -0.39134387501925
H 16.55161773026214 -0.44931583271431 0.75931087110127
H 17.41711129166774 1.09061065318135 0.77877902014267
H 18.67102790036752 0.86953605388811 2.85208666734182
H 18.67610500266945 0.66085864065976 5.30459803675925
H 16.17191446950705 0.90395283201875 7.33281050670623
H 17.59636041899511 -0.14113141823571 7.32476486198412
H 16.18469147913577 -2.12992990498067 7.03878599101778
H 15.60351461488460 -1.21989151110030 8.43648360238666
H 13.29283143296124 -1.93424461794932 8.34661439239236
H 10.88380604831301 -2.33686848565543 8.36393437140590
H 8.48259336596857 -2.86315175237683 8.34207056876517
H 6.37045410726021 -3.09592833661734 7.09863476621227
H 8.43426204174167 -2.93452346439970 2.67529792180339

File diff suppressed because it is too large Load Diff

@ -1,71 +0,0 @@
-0.04217847
-0.04290674
-0.00833544
-0.04834424
-0.04824291
-0.01567417
-0.00886872
-0.04859533
-0.04058975
-0.04807889
-0.01102690
-0.01236832
-0.04508654
-0.04405994
-0.00031105
-0.04300191
-0.04183275
-0.00125066
-0.04430427
-0.04436281
0.00681281
-0.05585292
0.01188300
-0.05195054
0.00909741
-0.04259012
-0.03244423
-0.00845218
-0.00331346
-0.00741485
-0.00122354
-0.00910097
-0.00726897
-0.01358112
-0.00457262
-0.01109382
-0.00504026
-0.00548182
-0.00845894
-0.00669753
-0.01186227
-0.00085888
-0.00847907
0.03163018
0.03081475
0.03480601
0.02872946
0.02700014
0.03474261
0.03314557
0.03165048
0.03540163
0.02609424
0.02874119
0.03456874
0.03199368
0.03664342
0.03070310
0.03684641
0.02999382
0.02819675
0.02831425
0.03724966
0.03047089
0.03798862
0.03151872
0.03049641
0.03187238
0.03052359
0.02980316
0.04742482

@ -1,298 +0,0 @@
#
# Number of atoms
#
71
#
# The current total energy in Eh
#
-106.196831730670
#
# The current gradient in Eh/bohr
#
0.000674227956
0.000680444598
-0.000621186098
0.001616919200
0.000452590030
0.001106420163
-0.000331875650
-0.003766368988
-0.000920006064
0.000552182022
0.001510645235
0.001497012134
0.001155354300
-0.001532226013
0.000984783012
-0.000568179895
-0.000046601034
-0.000517010439
-0.000061055401
0.000795138662
-0.001331170225
0.000264848844
0.001060222727
0.002361365830
0.000692250217
-0.002344109916
-0.000208407174
-0.000841845562
0.000888569825
0.002135620281
-0.000492952695
0.000622951310
-0.000916780243
0.000890703542
0.000543161148
-0.000353464846
-0.000629810546
-0.002423559792
0.000239437400
-0.001383784608
0.001029843702
0.002088063072
0.001297200269
0.000232855919
-0.001369415920
-0.001538861413
-0.000406800302
0.001953764316
-0.001423170738
-0.000299736581
-0.002010535112
0.001221807696
0.000320479951
0.001462345388
-0.000573103651
-0.001567618653
-0.001919534563
-0.001275903593
0.001911570932
-0.001203076478
0.000852740021
-0.000809414147
0.002033476622
-0.000840225924
0.000711748649
-0.002846580877
0.000327778682
-0.000483676034
0.001697544033
-0.000329215074
0.000453413512
-0.002234600124
0.000039347681
-0.000373354707
0.001630186534
-0.000554000242
0.000240485021
-0.001568734425
0.001591999708
0.000304688525
-0.000271873765
-0.001147353652
-0.000114076198
0.000329494468
0.000666711916
0.000260413582
-0.001310991848
-0.000272557884
-0.000201021748
0.000219282328
-0.000185675804
0.000201365226
-0.000355359878
0.000469259216
0.000236371437
-0.000094750991
-0.000670098056
-0.000382643905
0.000653453990
-0.000106180509
0.002808074660
0.001252724466
0.000241209149
-0.000002837353
0.000305548635
0.000267522340
-0.000010442664
0.000150849711
-0.000487198141
-0.000251280421
0.000280259036
0.000258960633
0.000378830486
-0.000158373267
0.000176347289
0.000140295005
-0.000116005045
0.000215869330
0.000011474622
0.000098099163
0.000110930373
-0.000185380719
0.000283172717
-0.000435356264
0.000093839187
-0.000370892491
0.000168091211
0.000138285114
-0.000185785903
0.002481785016
0.001203829079
-0.001062727571
0.002480644873
0.000269609705
0.001509367765
0.000394551009
-0.001109718451
-0.000040711253
0.000774378703
-0.000617269228
0.000317011161
-0.000120474272
0.001477502339
0.000894005337
0.000654745008
-0.000639647752
0.000706281819
0.000319539640
0.000553662910
0.001229862639
0.001511780954
-0.000871744005
0.000565687802
0.000300550028
0.000524559535
0.001041233511
-0.000005920964
-0.000019088603
0.001079955000
0.000489413086
-0.001626088079
-0.000745379269
-0.000667113572
0.000127697979
0.000996572235
-0.000910573302
-0.001313144674
0.000644173881
-0.000338135533
-0.000904375066
0.000659953845
-0.000348241768
-0.000150943133
0.001548975949
-0.000457891780
0.000640386799
0.000764492375
-0.000608245787
-0.000863288259
0.000964407254
-0.002625852378
-0.000664439863
0.000984196489
-0.002623847741
-0.000550082411
-0.001080096568
-0.000183001346
-0.000726152499
-0.000721430853
-0.000907216317
0.000545642701
-0.000946654513
-0.000531366740
0.000807431985
-0.000409195783
-0.000478822589
-0.000326310394
-0.001325318294
-0.000182611548
0.001001948384
-0.002754299389
-0.000115345797
0.000694234257
-0.002772804129
0.000229660758
0.000697944269
-0.002825157839
0.002164757283
0.000898137312
-0.001549300120
-0.000301001215
0.000113095273
0.000448530991
#
# The atomic numbers and current coordinates in Bohr
#
6 11.2976954 -5.0017672 8.4371308
6 11.0509311 -4.0792889 6.1090126
6 13.1540058 -2.6430107 4.8625477
6 13.1597995 -2.8777150 1.9936868
6 15.1546219 -1.1263409 0.8637619
6 17.6203873 -1.0170415 2.3000566
6 19.6564325 0.2491804 1.2241563
6 19.3913950 1.5060812 -1.3092213
6 21.2541549 3.6794332 -1.5635075
6 23.9337083 2.7129031 -1.1910463
6 24.2045614 1.4245254 1.3293362
6 26.5115020 1.2866485 2.5048470
6 28.8489214 2.3977280 1.3144035
6 31.2520199 1.0766343 2.1982040
6 31.3449754 0.9087994 5.0205233
6 33.5472880 1.1850790 6.3640989
6 33.5637083 0.9112333 8.9901628
6 31.4207001 0.1818695 10.2586412
6 31.3458939 -0.0462455 13.0844216
6 29.6808842 -2.2555045 13.8892542
6 27.1271596 -2.1300246 12.6595943
6 25.0168125 -2.9903880 13.8426831
6 22.6404610 -3.1071390 12.5965218
6 20.4742185 -3.9238279 13.8245708
6 18.1716319 -4.1394626 12.5523201
6 15.9418606 -4.9688687 13.7721626
6 13.7360138 -5.2207298 12.4684839
6 13.6244071 -4.6908479 9.8573353
6 15.7769574 -3.8755586 8.6190088
6 18.0646532 -3.5590489 9.9264230
6 20.2407107 -2.6461696 8.6668692
6 20.0799929 -1.8191309 6.0801622
6 17.8425748 -2.0751015 4.7116232
6 15.7113081 -3.6024583 5.7981547
6 22.2124751 -0.6888503 4.9315975
6 22.0130884 0.3363498 2.4696658
6 24.5556623 -0.6063741 6.2267317
6 26.7219958 0.2671703 4.9788244
6 29.0871413 0.3008503 6.2918244
6 29.1697686 -0.2476772 8.8963453
6 26.9775884 -1.2326491 10.1232524
6 24.7063874 -1.4311708 8.7885134
6 22.5113334 -2.3977291 9.9982805
1 9.7544856 -5.9693088 9.3617779
1 9.2937198 -4.2368022 5.0804643
1 12.9540855 -0.6329911 5.3637331
1 11.3092812 -2.3929766 1.2167501
1 13.5614090 -4.8376943 1.4810634
1 14.3795316 0.7942325 0.8073748
1 15.5208897 -1.6953762 -1.0872227
1 17.4763398 2.2249853 -1.5583675
1 19.7377362 0.1183421 -2.8070845
1 21.0684044 4.5652009 -3.4182204
1 20.8372925 5.1036746 -0.1277104
1 24.3986179 1.3752891 -2.7023864
1 25.2451783 4.2975782 -1.3228111
1 28.9498742 4.4037633 1.8249291
1 28.7473058 2.2707274 -0.7395327
1 31.2780246 -0.8490839 1.4348896
1 32.9135704 2.0609555 1.4716791
1 35.2831294 1.6431850 5.3896627
1 35.2927237 1.2488418 10.0242375
1 30.5604894 1.7082233 13.8570036
1 33.2523021 -0.2666997 13.8417996
1 30.5846345 -4.0249842 13.3013778
1 29.4863693 -2.3052609 15.9426435
1 25.1198110 -3.6551926 15.7728153
1 20.5674127 -4.4160414 15.8055454
1 16.0297784 -5.4105727 15.7642288
1 12.0384136 -5.8504567 13.4144756
1 15.9384454 -5.5454457 5.0555804

@ -1,223 +0,0 @@
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
| Aditya W. Sakti |
| Departemen Kimia |
| Universitas Pertamina |
-----------------------------------------------------------
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
* started run on 2022/08/04 at 09:43:13.535
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --gfn 1 --acc 1.000000
hostname : compute
calculation namespace : cmmd
coordinate file : cmmd_XTB.xyz
number of atoms : 71
number of electrons : 200
charge : 0
spin : 0.0
first test random number : 0.11018891849212
ID Z sym. atoms
1 6 C 1-43
2 1 H 44-71
-------------------------------------------------
| G F N 1 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.7b00118
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.250000 2.000000
zeta-weighting 0.000000
* Dispersion:
s8 2.400000
a1 0.630000
a2 5.000000
s9 0.000000
* Repulsion:
kExp 1.500000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order atomic
anisotropic false
* Halogen bond correction:
rad-scale 1.300000
damping 0.440000
q/qsh data taken from xtbrestart
...................................................
: SETUP :
:.................................................:
: # basis functions 228 :
: # atomic orbitals 228 :
: # shells 142 :
: # electrons 200 :
: # halogen bonds 0 :
: max. iterations 250 :
: Hamiltonian GFN1-xTB :
: restarted? true :
: GBSA solvation false :
: PC potential false :
: electronic temp. 300.0000000 K :
: accuracy 1.0000000 :
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.2000000E-04 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -107.9721901 -0.107972E+03 0.178E-05 1.49 0.0 T
2 -107.9721901 -0.515854E-11 0.840E-06 1.49 1412.6 T
3 -107.9721901 -0.626699E-11 0.690E-06 1.49 1720.5 T
*** convergence criteria satisfied after 3 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.6780197 -18.4499
... ... ... ...
94 2.0000 -0.4299532 -11.6996
95 2.0000 -0.4242112 -11.5434
96 2.0000 -0.4217085 -11.4753
97 2.0000 -0.4141609 -11.2699
98 2.0000 -0.4065524 -11.0629
99 2.0000 -0.4025241 -10.9532
100 2.0000 -0.3741491 -10.1811 (HOMO)
101 -0.3193036 -8.6887 (LUMO)
102 -0.2855655 -7.7706
103 -0.2802990 -7.6273
104 -0.2694395 -7.3318
105 -0.2598321 -7.0704
... ... ...
228 0.6943959 18.8955
-------------------------------------------------------------
HL-Gap 0.0548455 Eh 1.4924 eV
Fermi-level -0.3467264 Eh -9.4349 eV
SCC (total) 0 d, 0 h, 0 min, 0.284 sec
SCC setup ... 0 min, 0.001 sec ( 0.327%)
Dispersion ... 0 min, 0.002 sec ( 0.752%)
classical contributions ... 0 min, 0.000 sec ( 0.124%)
integral evaluation ... 0 min, 0.058 sec ( 20.367%)
iterations ... 0 min, 0.034 sec ( 12.056%)
molecular gradient ... 0 min, 0.187 sec ( 65.718%)
printout ... 0 min, 0.002 sec ( 0.644%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -106.196831730824 Eh ::
:: gradient norm 0.015896246397 Eh/a0 ::
:: HOMO-LUMO gap 1.492421979466 eV ::
::.................................................::
:: SCC energy -107.972190143497 Eh ::
:: -> electrostatic 0.004053563662 Eh ::
:: repulsion energy 1.841954650940 Eh ::
:: dispersion energy -0.066596238268 Eh ::
:: halogen bond corr. 0.000000000000 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge -0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -106.196831730824 Eh |
| GRADIENT NORM 0.015896246397 Eh/α |
| HOMO-LUMO GAP 1.492421979466 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/08/04 at 09:43:13.869
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.334 sec
* cpu-time: 0 d, 0 h, 0 min, 0.333 sec
* ratio c/w: 0.997 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.284 sec
* cpu-time: 0 d, 0 h, 0 min, 0.284 sec
* ratio c/w: 0.997 speedup

File diff suppressed because it is too large Load Diff

@ -1,7 +0,0 @@
cmmd # BaseName
cmmd # GBWName
426 # number of calculations
1 # number of CPUs
1 # program flag
0 # printing flag
1 # free_end

@ -1,2 +0,0 @@
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
normal termination of xtb

@ -1,160 +0,0 @@
xtb 08042209433D
xtb: 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54)
71 84 0 0 0 999 V2000
5.9785 -2.6468 4.4647 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8479 -2.1587 3.2328 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9608 -1.3986 2.5731 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9639 -1.5228 1.0550 C 0 0 0 0 0 0 0 0 0 0 0 0
8.0195 -0.5960 0.4571 C 0 0 0 0 0 0 0 0 0 0 0 0
9.3243 -0.5382 1.2171 C 0 0 0 0 0 0 0 0 0 0 0 0
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M END

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