Skip to content

Instantly share code, notes, and snippets.

@conradhuebler

conradhuebler/Results for input_large.xyz Secret

Created May 10, 2023 20:36
Show Gist options
  • Save conradhuebler/445e6cd16c1f91230a9386c5abc320eb to your computer and use it in GitHub Desktop.
Save conradhuebler/445e6cd16c1f91230a9386c5abc320eb to your computer and use it in GitHub Desktop.
Download ZIP
Sample files for the failed geometry optimisation with curcuma.
Raw
input_large.xyz
231
input_2 ** Energy = -4944.36361546 Eh **
C 2.537435 -0.186203 -1.548461
C 2.179756 -1.418095 -0.983172
C 1.078574 -1.487251 -0.118265
C 0.318636 -0.340748 0.154223
C 0.627471 0.870297 -0.482146
C 1.73411 0.947177 -1.342196
C 2.082326 2.239208 -2.039142
C 2.981488 3.150846 -1.208381
C -0.779853 -0.402164 1.183171
C -0.267141 -0.075753 2.584475
C 2.982996 -2.657804 -1.297976
C 4.073063 -2.953164 -0.272198
C -0.247971 2.084123 -0.223079
N -1.512234 2.042404 -0.938095
C 0.681976 -2.793438 0.523191
N -0.580809 -3.287057 -0.008936
C 3.767082 -0.098657 -2.421651
C -2.726003 2.182811 -0.359315
N -3.785919 2.148632 -1.201435
C -4.992198 2.156351 -0.640708
C -5.160412 2.232451 0.741501
C -4.016538 2.346131 1.518237
N -2.796273 2.315636 0.975903
C -4.088132 2.553759 2.995413
C -6.170934 2.052824 -1.55568
N 3.434688 -0.300778 -3.82694
C -0.997848 -4.552326 0.576586
C -2.39607 -4.858599 0.13456
C -2.61867 -5.384054 -1.130266
C -3.90411 -5.507615 -1.64173
C -4.984472 -5.169823 -0.833598
C -4.789917 -4.691098 0.458328
C -3.490328 -4.517145 0.918962
C 4.578785 -0.303496 -4.734991
C 4.069575 -0.3723 -6.145988
C 3.920652 0.781342 -6.902718
C 3.311639 0.749927 -8.153736
C 2.81854 -0.457399 -8.625648
C 2.948489 -1.629181 -7.884456
C 3.601374 -1.579161 -6.660066
C -5.953814 -4.294732 1.317818
C 3.138522 2.011654 -8.948944
C 2.216476 -2.863324 -8.31782
N 0.914255 -2.896772 -7.631803
C -0.156497 -3.530262 -8.400388
C -1.49484 -3.317158 -7.736545
C -4.096579 -5.903832 -3.072207
N -3.49171 -4.905406 -3.961363
C -3.842534 -5.137892 -5.365566
C -3.264852 -4.084596 -6.271726
C -2.18759 -2.113382 -7.945303
C -3.405941 -1.89159 -7.285643
C -3.956704 -2.883446 -6.462907
C -2.009161 -4.282735 -6.862885
C -1.209248 -5.519969 -6.545589
C -1.481509 -6.681286 -7.49768
C -5.300674 -2.660522 -5.814977
C -6.467749 -3.090832 -6.700043
C -4.134293 -0.582772 -7.451017
N -3.776181 0.364688 -6.404058
C -4.365093 1.576003 -6.306099
C -1.648498 -1.074792 -8.899295
C -2.197053 -1.230971 -10.314237
N -5.248795 1.904485 -7.263547
C -5.833225 3.100788 -7.161147
C -5.549596 3.957545 -6.108134
C -4.606853 3.549366 -5.168053
N -4.010106 2.358605 -5.261254
C -4.200802 4.428543 -4.033971
C -6.790222 3.470307 -8.245415
N -6.058031 -2.836481 1.439674
N 2.352791 2.995061 -8.2083
C -6.150193 -2.122551 0.191665
C -7.026876 -2.419417 2.440271
C -7.426573 -2.317164 -0.609249
O -7.449411 -1.458621 -1.650615
O -8.289391 -3.134149 -0.379067
C -8.609121 -1.501151 -2.52049
C -9.719605 -0.633238 -1.987332
C -6.987496 -0.914492 2.665419
O -7.919782 -0.200071 2.375483
O -5.873498 -0.348169 3.168786
C -4.740193 -1.121681 3.632188
C -4.824425 -1.354448 5.118965
C 2.470602 4.369951 -8.650763
C 1.032134 2.591821 -7.789912
C 1.712298 4.699465 -9.927569
O 2.367138 4.257277 -11.014875
O 0.629484 5.246501 -9.956922
C 1.646433 4.336719 -12.2684
C 2.500713 3.698244 -13.328247
C -0.017151 2.413861 -8.877578
O 0.214067 2.064455 -10.016494
O -1.24417 2.663021 -8.385926
C -2.366173 2.62499 -9.304743
C -2.796544 4.029417 -9.638948
H 2.559322 2.014685 -2.990359
H 1.172631 2.778133 -2.297216
H 3.916939 2.656985 -0.949113
H 3.223342 4.063745 -1.752528
H 2.502674 3.434814 -0.272492
H -1.573207 0.294502 0.941509
H -1.23403 -1.387859 1.165816
H 0.129917 0.936726 2.639315
H -1.070629 -0.151731 3.317681
H 0.530173 -0.752548 2.890266
H 3.435891 -2.571757 -2.282359
H 2.316131 -3.513489 -1.384337
H 4.626538 -3.85389 -0.537637
H 4.783354 -2.130263 -0.204827
H 3.655194 -3.096646 0.722857
H -0.485274 2.165346 0.830864
H 0.279749 2.999053 -0.481011
H -1.500272 2.140261 -1.950699
H 1.484581 -3.531534 0.439216
H 0.545001 -2.643101 1.595903
H -0.54521 -3.364965 -1.020381
H 4.223253 0.885142 -2.330565
H 4.529423 -0.801954 -2.065283
H -6.142892 2.216813 1.190418
H -5.026421 2.192203 3.405119
H -3.254265 2.059763 3.488801
H -4.005196 3.618109 3.221341
H -6.622072 1.063836 -1.476439
H -6.94066 2.777309 -1.294139
H -5.867158 2.202951 -2.586708
H 2.938398 -1.177555 -3.939052
H -0.966826 -4.444626 1.662415
H -0.324324 -5.387886 0.32447
H -1.771654 -5.656418 -1.746384
H -5.99427 -5.267615 -1.215645
H -3.328912 -4.091722 1.902295
H 5.27794 -1.130429 -4.532962
H 5.133979 0.622685 -4.582092
H 4.249945 1.732917 -6.503238
H 2.295824 -0.478765 -9.57499
H 3.683585 -2.480025 -6.065699
H -6.876141 -4.740117 0.934647
H -5.805289 -4.680119 2.328405
H 4.113806 2.46809 -9.129468
H 2.714291 1.777642 -9.926854
H 2.083175 -2.845157 -9.40714
H 2.776799 -3.76911 -8.07793
H 0.641923 -1.940489 -7.421971
H 0.064127 -4.589514 -8.496794
H -0.186977 -3.145428 -9.427399
H -5.167102 -6.035951 -3.28035
H -3.617342 -6.863882 -3.278613
H -3.808322 -3.979742 -3.688393
H -3.472465 -6.122571 -5.636136
H -4.92916 -5.191396 -5.496266
H -0.150196 -5.274296 -6.554775
H -1.410089 -5.82661 -5.522076
H -2.529876 -6.976871 -7.479785
H -0.883935 -7.552335 -7.230468
H -1.245534 -6.417286 -8.527586
H -5.359372 -3.197265 -4.872025
H -5.408189 -1.613474 -5.543737
H -7.419994 -2.912543 -6.200483
H -6.478525 -2.546869 -7.642807
H -6.410091 -4.150856 -6.942594
H -3.924949 -0.13762 -8.418521
H -5.211275 -0.732809 -7.44738
H -3.195099 0.068761 -5.629905
H -1.87189 -0.078462 -8.528094
H -0.564469 -1.113507 -8.939041
H -1.769316 -0.478369 -10.974664
H -1.957883 -2.212803 -10.72031
H -3.2809 -1.1281 -10.338015
H -6.031663 4.920224 -6.024372
H -4.093812 3.852841 -3.117191
H -3.225646 4.870216 -4.240517
H -4.914492 5.23352 -3.880183
H -6.245299 3.670196 -9.168436
H -7.468396 2.6446 -8.449784
H -7.366635 4.356322 -7.992964
H -6.010455 -1.055211 0.360144
H -5.319139 -2.426881 -0.440671
H -8.058618 -2.662502 2.177115
H -6.793155 -2.938197 3.371948
H -8.237772 -1.139413 -3.476601
H -8.927646 -2.535305 -2.629365
H -10.080032 -1.005869 -1.03222
H -9.383672 0.393094 -1.854829
H -10.55335 -0.630687 -2.689111
H -4.666699 -2.040167 3.058512
H -3.878837 -0.507169 3.382016
H -5.680316 -1.974822 5.381415
H -3.923825 -1.861823 5.464505
H -4.911347 -0.412611 5.656947
H 2.075203 5.022942 -7.87429
H 3.528035 4.593412 -8.789891
H 1.101432 1.631838 -7.276329
H 0.654169 3.309525 -7.064822
H 0.696154 3.822002 -12.143462
H 1.437363 5.383815 -12.484653
H 2.690304 2.651945 -13.097938
H 1.990305 3.747577 -14.289315
H 3.457566 4.207702 -13.426292
H -2.074224 2.06963 -10.191379
H -3.150811 2.086072 -8.783066
H -3.650069 3.996598 -10.316419
H -3.096528 4.567413 -8.741633
H -1.991944 4.579938 -10.119396
C -1.935264 -1.414376 -3.386845
C -1.02805 -2.452329 -4.039261
C 0.380081 -1.871128 -4.1702
C 0.353556 -0.494506 -4.845154
C -0.592202 0.402225 -4.08276
O -1.896448 -0.192842 -4.128086
O -0.973013 -3.637752 -3.277151
O 1.301462 -2.763295 -4.752857
O -0.024467 -0.544139 -6.224206
C -0.703134 1.80148 -4.63596
O -1.552334 2.608236 -3.844192
H -1.768765 -4.170888 -3.503134
H 1.076717 -2.910372 -5.700404
H -2.46725 2.41135 -4.149241
H -1.430107 -2.657908 -5.033337
H 0.743254 -1.702732 -3.153708
H 1.356527 -0.078557 -4.825796
H -0.263802 0.455162 -3.041797
H -0.970082 -0.747157 -6.25245
H 0.29078 2.248158 -4.63754
H -1.054296 1.77271 -5.667613
O -3.250238 -1.857336 -3.387189
H -1.598305 -1.207797 -2.361094
C -4.109697 -1.023252 -2.606797
H -4.141016 -0.008877 -2.995068
H -5.099301 -1.462845 -2.65121
H -3.76569 -0.985238 -1.571872
Raw
input_small.xyz
66
5287993
O -0.68370 -1.20720 -1.07150
O 2.54930 -0.55250 0.69880
O -2.76690 -0.12180 -1.13570
O 4.51990 -0.11880 1.94100
O -3.33140 1.47180 -3.42390
O 0.65150 1.69270 1.64720
O -1.65350 2.13680 0.23540
O -5.63430 -1.34200 -3.02180
O 1.10260 -0.47110 3.40890
O 2.72590 -0.54940 5.68630
O 5.21100 0.91970 5.44650
O -5.15180 1.44360 -0.73000
O 0.71240 -3.31320 -2.18300
O -5.44940 1.86730 -4.31140
O -2.77710 0.14520 -6.05100
O 7.10970 1.11960 1.58880
C 1.12440 -0.49490 0.43220
C 0.47680 0.93200 0.45350
C -1.05850 0.83890 0.26710
C 0.75200 -1.21150 -0.90560
C -1.34800 0.06840 -1.03630
C -3.37090 -0.68770 -2.31800
C 3.08010 -0.00260 1.92770
C -4.90140 -0.58150 -2.06370
C -2.98860 0.08420 -3.61870
C 2.51350 -0.60920 3.25040
C 3.15500 0.08180 4.47990
C 4.70210 0.09350 4.39940
C -5.37960 0.90160 -2.03190
C 5.19040 0.60140 3.00930
C 1.18200 -2.69690 -0.98610
C -4.69840 1.80460 -3.10460
C -3.42200 -0.52730 -4.97390
C 6.72070 0.51980 2.82070
H 0.62530 -1.11480 1.17680
H 0.92810 1.52480 -0.34880
H -1.49160 0.30130 1.11650
H 1.21650 -0.68780 -1.74780
H -0.97860 0.71080 -1.83850
H -3.07900 -1.73980 -2.39050
H 2.90550 1.07170 1.88080
H -5.13850 -1.06290 -1.10960
H -1.90230 0.05170 -3.70960
H 2.73940 -1.67900 3.25280
H 2.79770 1.11670 4.51860
H 5.06930 -0.92380 4.55980
H -6.46430 0.94100 -2.16410
H 4.94070 1.66620 2.93090
H 2.26980 -2.78530 -0.96680
H 0.77540 -3.25960 -0.14270
H -4.67630 2.83330 -2.73610
H -4.49610 -0.45800 -5.13400
H -3.13580 -1.58080 -5.01440
H 0.36760 2.60420 1.42270
H -2.62100 1.98100 0.23710
H 7.05940 -0.51780 2.83110
H 7.23110 1.05960 3.62200
H -6.57370 -1.27420 -2.74920
H 0.85650 -1.04160 4.16630
H 1.74830 -0.46540 5.68930
H 4.81400 0.56850 6.27150
H -5.69920 0.89820 -0.12460
H 0.97330 -4.25560 -2.10970
H -4.97950 2.53780 -4.85260
H -3.03530 -0.35230 -6.85440
H 8.08960 1.09660 1.59110
Raw
Results for input_large.xyz
./curcuma-nightly-0.0.105-20_04-x86_64-Linux.AppImage -opt input_large.xyz -method gfnff
Step Current Energy Energy Change RMSD Change Gradient Norm time
[Eh] [kJ/mol] [A] [A] [s]
0 -39.583775 -30.497453 0.003126 0.055495 0.152000
20 -39.624708 -107.471318 0.079386 0.014595 0.931000
40 -39.634368 -25.361800 0.099848 0.013151 1.859000
60 -39.639387 -13.178218 0.094710 0.014604 4.155000
80 -39.642087 -7.086327 0.022150 0.008188 11.133000
91 -39.642087 -0.000007 0.000000 0.008188 9.366000
92 -39.642087 0.000000 0.000000 0.008188 0.000000
*** Geometry Optimisation converged ***
~/src/curcuma/release/curcuma -opt input.xyz -method gfnff [LBFGSSolver<double, LineSearchMoreThuente> solver(param);]
Step Current Energy Energy Change RMSD Change Gradient Norm time
[Eh] [kJ/mol] [A] [A] [s]
0 -39.577906 -15.089358 0.001382 0.070321 0.128000
20 -39.624545 -122.449385 0.077657 0.017403 0.771000
40 -39.633499 -23.510665 0.085080 0.011947 0.830000
60 -39.639462 -15.655750 0.095817 0.009378 0.903000
LBFGS interface signalled some runtime error!
-- the line search routine reached the maximum number of iterations --
*** Geometry Optimisation Not Really converged ***
71 -39.642037 -6.760606 0.095817 0.007523 1.292000
*** Geometry Optimisation Not Really converged ***
~/src/curcuma/release/curcuma -opt input.xyz -method gfnff [LBFGSSolver<double, LineSearchNocedalWright> solver(param);]
Step Current Energy Energy Change RMSD Change Gradient Norm time
[Eh] [kJ/mol] [A] [A] [s]
0 -39.583775 -30.497453 0.003126 0.055495 0.126000
20 -39.624708 -107.471318 0.079386 0.014595 0.790000
LBFGS interface signalled some runtime error!
-- the line search routine reached the maximum number of iterations --
*** Geometry Optimisation Not Really converged ***
33 -39.631042 -16.629026 0.079386 0.009788 1.209000
*** Geometry Optimisation Not Really converged ***
Raw
Results for input_small.xyz
./curcuma-nightly-0.0.105-20_04-x86_64-Linux.AppImage -opt input_small.xyz -method gfnff
Step Current Energy Energy Change RMSD Change Gradient Norm time
[Eh] [kJ/mol] [A] [A] [s]
0 -9.850788 -10.188329 0.003142 0.036970 0.019000
20 -9.891525 -106.955470 0.188208 0.007015 0.097000
40 -9.895651 -10.832928 0.137648 0.003334 0.099000
60 -9.896829 -3.092256 0.064002 0.001808 0.095000
80 -9.898167 -3.513409 0.087380 0.001966 0.092000
100 -9.899023 -2.247129 0.170741 0.002013 0.097000
120 -9.899469 -1.171130 0.135140 0.001721 0.094000
140 -9.900092 -1.635517 0.169274 0.002242 0.094000
160 -9.900682 -1.548617 0.169189 0.001793 0.094000
180 -9.901317 -1.666820 0.206170 0.001890 0.093000
200 -9.901715 -1.045829 0.162777 0.001741 0.096000
220 -9.902172 -1.198773 0.131913 0.001427 0.096000
240 -9.903345 -3.080516 0.169517 0.002170 0.141000
260 -9.903617 -0.712528 0.060563 0.000550 0.095000
280 -9.903693 -0.200770 0.064696 0.000532 0.095000
300 -9.903770 -0.202396 0.080745 0.000569 0.096000
320 -9.903824 -0.142514 0.058276 0.000186 0.095000
340 -9.903828 -0.008063 0.010217 0.000016 0.393000
360 -9.903828 -0.000191 0.001803 0.000012 0.097000
361 -9.903828 0.000000 0.001803 0.000012 0.000000
*** Geometry Optimisation converged ***
~/src/curcuma/release/curcuma -opt input.xyz -method gfnff [LBFGSSolver<double, LineSearchMoreThuente> solver(param);]
Step Current Energy Energy Change RMSD Change Gradient Norm time
[Eh] [kJ/mol] [A] [A] [s]
0 -9.848661 -4.603804 0.001303 0.043824 0.013000
20 -9.891477 -112.411786 0.187694 0.006514 0.089000
40 -9.895666 -10.998303 0.140166 0.002994 0.089000
60 -9.896752 -2.851811 0.054333 0.001930 0.110000
80 -9.898173 -3.730591 0.101672 0.001558 0.096000
100 -9.898914 -1.945725 0.143093 0.002675 0.083000
120 -9.899459 -1.430528 0.150258 0.001208 0.083000
140 -9.900018 -1.469265 0.143842 0.002018 0.083000
160 -9.900617 -1.570775 0.180290 0.001919 0.089000
180 -9.901290 -1.767921 0.225732 0.001584 0.085000
200 -9.901674 -1.008704 0.141522 0.001267 0.089000
220 -9.902168 -1.297412 0.152915 0.001409 0.086000
240 -9.903355 -3.115935 0.168883 0.001479 0.155000
260 -9.903616 -0.685555 0.056588 0.000597 0.089000
280 -9.903699 -0.217834 0.076048 0.000648 0.097000
300 -9.903780 -0.211101 0.072369 0.000541 0.088000
320 -9.903826 -0.121456 0.051821 0.000126 0.086000
340 -9.903827 -0.004044 0.006348 0.000018 0.088000
341 -9.903827 0.000000 0.006348 0.000018 0.000000
*** Geometry Optimisation converged ***
~/src/curcuma/release/curcuma -opt input.xyz -method gfnff [LBFGSSolver<double, LineSearchNocedalWright> solver(param);]
0 -9.850788 -10.188329 0.003142 0.036970 0.014000
20 -9.891525 -106.955470 0.188208 0.007015 0.084000
40 -9.895651 -10.832928 0.137648 0.003334 0.081000
60 -9.896829 -3.092256 0.064002 0.001808 0.082000
80 -9.898167 -3.513409 0.087380 0.001966 0.078000
100 -9.899023 -2.247130 0.170741 0.002013 0.076000
120 -9.899469 -1.171100 0.135136 0.001721 0.079000
140 -9.900092 -1.635396 0.169419 0.002259 0.080000
160 -9.900682 -1.548027 0.168800 0.001794 0.079000
180 -9.901315 -1.661598 0.204640 0.001746 0.079000
200 -9.901708 -1.031507 0.159724 0.001476 0.079000
220 -9.902148 -1.157426 0.129696 0.001450 0.078000
240 -9.903320 -3.075657 0.166196 0.001878 0.113000
260 -9.903611 -0.765092 0.067920 0.000498 0.080000
280 -9.903690 -0.206854 0.064614 0.000499 0.078000
300 -9.903767 -0.201360 0.081992 0.000716 0.080000
320 -9.903825 -0.152557 0.060138 0.000176 0.089000
LBFGS interface signalled some runtime error!
-- the line search routine reached the maximum number of iterations --
*** Geometry Optimisation Not Really converged ***
330 -9.903827 -0.005241 0.060138 0.000074 0.125000
*** Geometry Optimisation Not Really converged ***
@conradhuebler
Copy link
Author

conradhuebler commented May 10, 2023 •
edited
Loading

LineSearchNocedalWright gives the worst performance, either because signalling an error or not reaching the minimum. LineSearchMoreThuente performs better.

But using an other method (-method uff), both methods fail to reach the minimum, which can be reached used the older LBFGS method provided in the AppImage.

LBFGS interface signalled some runtime error!
 --      the line search routine reached the maximum number of iterations       --
            *** Geometry Optimisation Not Really converged ***       
      43           3.429389        -0.137370       0.151839        0.057729        0.165000    
            *** Geometry Optimisation Not Really converged ***

vs


      239          3.394504        0.000000        0.001527        0.091404        0.000000    
                  *** Geometry Optimisation converged ***

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment