Here, we explain how to visualize VeloxChem results in Jupyter notebooks.
The underlying calculation can be obtained either directly in a notebook or imported from a VeloxChem .h5 file.
import veloxchem as vlxMolecular structure¶
In Jupyter notebook, a molecule object can be visualized using the show function.
The atom_indices and atom_labels options can be used.
From a notebook cell
molecule = vlx.Molecule.read_smiles('C1=CC=C(C=C1)C(=O)O')
molecule.show(atom_indices=True, atom_labels=True)Loading...
From an h5 file
molecule, basis = vlx.read_molecule_and_basis("../output_files/biphenyl-scf.h5")
molecule.show()Loading...
Structure optimization¶
From notebook cell
molecule = vlx.Molecule.read_smiles('CCO')
basis = vlx.MolecularBasis.read(molecule, 'def2-svp')
scf_drv = vlx.ScfRestrictedDriver()
scf_drv.xcfun = 'b3lyp'
results = scf_drv.compute(molecule, basis)
opt_drv = vlx.OptimizationDriver(scf_drv)
opt_results = opt_drv.compute(molecule, basis, results)
Self Consistent Field Driver Setup
====================================
Wave Function Model : Spin-Restricted Kohn-Sham
Initial Guess Model : Superposition of Atomic Densities
Convergence Accelerator : Two Level Direct Inversion of Iterative Subspace
Max. Number of Iterations : 50
Max. Number of Error Vectors : 10
Convergence Threshold : 1.0e-06
ERI Screening Threshold : 1.0e-12
Linear Dependence Threshold : 1.0e-06
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
* Info * Using the B3LYP functional.
P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch., J. Phys. Chem. 98, 11623 (1994)
* Info * Using the Libxc library (v7.0.0).
S. Lehtola, C. Steigemann, M. J.T. Oliveira, and M. A.L. Marques., SoftwareX 7, 1–5 (2018)
* Info * Using the following algorithm for XC numerical integration.
J. Kussmann, H. Laqua and C. Ochsenfeld, J. Chem. Theory Comput. 2021, 17, 1512-1521
* Info * Starting Reduced Basis SCF calculation...
* Info * ...done. SCF energy in reduced basis set: -153.878486404490 a.u. Time: 0.05 sec.
Iter. | Kohn-Sham Energy | Energy Change | Gradient Norm | Max. Gradient | Density Change
--------------------------------------------------------------------------------------------
1 -154.914060945813 0.0000000000 0.25700125 0.02179054 0.00000000
2 -154.917224574041 -0.0031636282 0.18477547 0.01179452 0.14535707
3 -154.921415881688 -0.0041913076 0.03153167 0.00159959 0.06527683
4 -154.921518619958 -0.0001027383 0.00963348 0.00077446 0.01040178
5 -154.921526981436 -0.0000083615 0.00173177 0.00010434 0.00336274
6 -154.921527275829 -0.0000002944 0.00029568 0.00002451 0.00063149
7 -154.921527287243 -0.0000000114 0.00003878 0.00000229 0.00013434
8 -154.921527287402 -0.0000000002 0.00001670 0.00000085 0.00001563
9 -154.921527287436 -0.0000000000 0.00000165 0.00000009 0.00000567
10 -154.921527287437 -0.0000000000 0.00000015 0.00000001 0.00000083
*** SCF converged in 10 iterations. Time: 0.83 sec.
Spin-Restricted Kohn-Sham:
--------------------------
Total Energy : -154.9215272874 a.u.
Electronic Energy : -236.6490934207 a.u.
Nuclear Repulsion Energy : 81.7275661332 a.u.
------------------------------------
Gradient Norm : 0.0000001479 a.u.
Ground State Information
------------------------
Charge of Molecule : 0.0
Multiplicity (2S+1) : 1
Magnetic Quantum Number (M_S) : 0.0
Optimization Driver Setup
===========================
Coordinate System : TRIC
Constraints : No
Max. Number of Steps : 300
Transition State : No
IRC : No
Hessian : never
* Info * Using geomeTRIC for geometry optimization.
L.-P. Wang and C.C. Song, J. Chem. Phys. 2016, 144, 214108
Optimization Step 0
=====================
* Info * Computing energy and gradient...
SCF Gradient Driver Setup
===========================
Gradient Type : Analytical
Molecular Geometry (Angstroms)
--------------------------------
Atom Coordinate X Coordinate Y Coordinate Z
C -0.683626000000 0.475176000000 0.337329000000
C -1.457381000000 -0.648173000000 -0.341829000000
O -1.185839000000 -0.665473000000 -1.716658000000
H -0.929143000000 0.497294000000 1.420011000000
H 0.408573000000 0.311445000000 0.220074000000
H -0.957201000000 1.452258000000 -0.114346000000
H -1.193374000000 -1.625922000000 0.121373000000
H -2.545134000000 -0.480187000000 -0.194651000000
H -0.287681000000 -1.075075000000 -1.823493000000
Analytical Gradient (Hartree/Bohr)
------------------------------------
Atom Gradient X Gradient Y Gradient Z
C 0.002113023944 -0.000684915057 -0.007208334459
C -0.003633598309 -0.002840387162 -0.007313108037
O -0.018683642337 0.014926588145 0.013434484347
H -0.003680469201 -0.002431888138 0.003614317624
H 0.004353491875 -0.002817336936 -0.001595869545
H -0.003067288354 0.005219576382 -0.002641140599
H 0.004244693467 -0.002635098980 -0.001427594751
H -0.003890923062 0.002992763168 0.003609717787
H 0.022272330629 -0.011744923642 -0.000484548418
*** Time spent in gradient calculation: 0.50 sec ***
* Info * Energy : -154.9215272874 a.u.
* Info * Gradient : 1.369494e-02 a.u. (RMS)
* Info * 2.742931e-02 a.u. (Max)
* Info * Time : 1.51 sec
Optimization Step 1
=====================
* Info * Computing energy and gradient...
SCF Gradient Driver Setup
===========================
Gradient Type : Analytical
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
Molecular Geometry (Angstroms)
--------------------------------
Atom Coordinate X Coordinate Y Coordinate Z
C -0.681669578272 0.479177929504 0.358773981835
C -1.438144772457 -0.650710066366 -0.345043447923
O -1.204786093360 -0.701728126536 -1.740293029630
H -0.928743412883 0.526936359984 1.433112382511
H 0.407967784599 0.334980742938 0.270211937024
H -0.936989338197 1.446308864600 -0.099392317811
H -1.201226033327 -1.617955733961 0.143431129401
H -2.523960521386 -0.499096136486 -0.226608234922
H -0.325884763944 -1.075082787538 -1.885232133855
Analytical Gradient (Hartree/Bohr)
------------------------------------
Atom Gradient X Gradient Y Gradient Z
C 0.001178554720 0.002266510210 0.002613516475
C 0.000003360565 -0.001443541867 -0.001705814035
O -0.000366301817 0.000674808485 -0.001655254575
H 0.000314776865 0.000825311677 0.000708457676
H -0.000674669428 -0.000406420516 -0.000143937881
H -0.000470624921 -0.000894699221 0.000208925703
H 0.000352018190 0.000347060066 0.000412251284
H 0.000057483894 -0.000118311857 -0.000345001866
H -0.000394371631 -0.001264229140 -0.000098612210
*** Time spent in gradient calculation: 0.52 sec ***
* Info * Energy : -154.9234098494 a.u.
* Info * Gradient : 1.731492e-03 a.u. (RMS)
* Info * 3.654658e-03 a.u. (Max)
* Info * Time : 1.41 sec
Optimization Step 2
=====================
* Info * Computing energy and gradient...
SCF Gradient Driver Setup
===========================
Gradient Type : Analytical
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
Molecular Geometry (Angstroms)
--------------------------------
Atom Coordinate X Coordinate Y Coordinate Z
C -0.681746870052 0.475093314856 0.351338830188
C -1.442493271845 -0.652966026808 -0.340428621247
O -1.205326120697 -0.703553788530 -1.733817653200
H -0.929871765907 0.522674494519 1.424145974389
H 0.408515760560 0.329762936967 0.264819796284
H -0.931078661885 1.444109775706 -0.107939805890
H -1.207223250099 -1.620346546111 0.148343715176
H -2.527951383365 -0.500516942921 -0.221037064838
H -0.316383407555 -1.050170508872 -1.875935359528
Analytical Gradient (Hartree/Bohr)
------------------------------------
Atom Gradient X Gradient Y Gradient Z
C 0.000503746686 0.000800096561 0.000567404909
C -0.000682537227 -0.000986326917 -0.000033169141
O 0.001628515279 0.000960788694 -0.000233940796
H -0.000005850554 -0.000022381898 -0.000362187713
H -0.000273643111 0.000053775432 -0.000079888785
H -0.000053128859 -0.000221786414 0.000123958636
H 0.000186869261 0.000376319754 0.000087704232
H 0.000098508854 -0.000307077310 -0.000045399857
H -0.001402879381 -0.000665648791 -0.000031061352
*** Time spent in gradient calculation: 0.53 sec ***
* Info * Energy : -154.9235334881 a.u.
* Info * Gradient : 1.014956e-03 a.u. (RMS)
* Info * 1.905231e-03 a.u. (Max)
* Info * Time : 1.28 sec
Optimization Step 3
=====================
* Info * Computing energy and gradient...
SCF Gradient Driver Setup
===========================
Gradient Type : Analytical
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
Molecular Geometry (Angstroms)
--------------------------------
Atom Coordinate X Coordinate Y Coordinate Z
C -0.681941877663 0.469906880769 0.344468816178
C -1.447242672102 -0.656354010577 -0.336152829979
O -1.210749732907 -0.714360423698 -1.728570954790
H -0.929358247358 0.523419598238 1.417254666921
H 0.408706255062 0.319836145560 0.260625030449
H -0.923366073187 1.439449242764 -0.119618023916
H -1.214710425717 -1.623445159068 0.155609863679
H -2.532376737479 -0.501270829303 -0.216239706722
H -0.302589957839 -1.010542766910 -1.866580005432
Analytical Gradient (Hartree/Bohr)
------------------------------------
Atom Gradient X Gradient Y Gradient Z
C -0.000518817309 -0.000766260081 -0.001038434246
C -0.000340955742 0.000314062355 0.000966490411
O 0.001546441078 0.001067028300 0.000557396311
H -0.000171995326 -0.000389849847 -0.000396046726
H 0.000128323238 0.000266877032 -0.000046224079
H 0.000213171935 0.000276978884 -0.000032735783
H 0.000111757099 0.000146441913 -0.000163022207
H -0.000011607191 -0.000375690694 0.000150320464
H -0.000955100862 -0.000549390494 -0.000006365617
*** Time spent in gradient calculation: 0.52 sec ***
* Info * Energy : -154.9236369616 a.u.
* Info * Gradient : 9.952293e-04 a.u. (RMS)
* Info * 1.959776e-03 a.u. (Max)
* Info * Time : 1.29 sec
Optimization Step 4
=====================
* Info * Computing energy and gradient...
SCF Gradient Driver Setup
===========================
Gradient Type : Analytical
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
Molecular Geometry (Angstroms)
--------------------------------
Atom Coordinate X Coordinate Y Coordinate Z
C -0.681090563072 0.463089312417 0.337361512645
C -1.452848105931 -0.663559083788 -0.331087247889
O -1.219940612153 -0.737087888106 -1.722986316004
H -0.928190018505 0.530374165566 1.409606212038
H 0.409391205146 0.303919930751 0.259361304867
H -0.911687976772 1.430668367081 -0.137059835034
H -1.225880465961 -1.628363347297 0.169463057274
H -2.537250182397 -0.502135489460 -0.212797184018
H -0.286519164137 -0.945770537053 -1.858165084852
Analytical Gradient (Hartree/Bohr)
------------------------------------
Atom Gradient X Gradient Y Gradient Z
C -0.001209906886 -0.001576885784 -0.001600129673
C 0.000310873204 0.001227314504 0.001328741068
O 0.000647570222 0.000585811879 0.000575440605
H -0.000110950727 -0.000406069358 -0.000231102731
H 0.000376143627 0.000353700752 0.000050161933
H 0.000391865641 0.000475035916 -0.000104838858
H -0.000055642755 -0.000144079884 -0.000197805140
H -0.000070960179 -0.000343743224 0.000088219978
H -0.000271122345 -0.000179709311 0.000077912870
*** Time spent in gradient calculation: 0.52 sec ***
* Info * Energy : -154.9237279095 a.u.
* Info * Gradient : 1.162792e-03 a.u. (RMS)
* Info * 2.551638e-03 a.u. (Max)
* Info * Time : 1.40 sec
Optimization Step 5
=====================
* Info * Computing energy and gradient...
SCF Gradient Driver Setup
===========================
Gradient Type : Analytical
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
Molecular Geometry (Angstroms)
--------------------------------
Atom Coordinate X Coordinate Y Coordinate Z
C -0.680247444555 0.461757645210 0.337062475524
C -1.454249794950 -0.666680777224 -0.330308663460
O -1.222941268760 -0.746862592791 -1.722285034872
H -0.927676308295 0.535232486035 1.408970190501
H 0.409494731079 0.298071872341 0.260617066432
H -0.909402514598 1.427077640204 -0.141985525189
H -1.229082959722 -1.629595721067 0.174921181590
H -2.538077823749 -0.501055643649 -0.212576146597
H -0.282861622207 -0.924525405131 -1.858426551867
Analytical Gradient (Hartree/Bohr)
------------------------------------
Atom Gradient X Gradient Y Gradient Z
C -0.000705263285 -0.000805907981 -0.000740572007
C 0.000238144263 0.000702468247 0.000644696596
O 0.000119549212 0.000130973256 0.000108321208
H -0.000005842559 -0.000142750535 -0.000034025460
H 0.000210332420 0.000148940946 0.000051162015
H 0.000205049433 0.000219182016 -0.000058884996
H -0.000040628093 -0.000108168531 -0.000074731967
H -0.000064753812 -0.000134650115 0.000082230926
H 0.000052158954 -0.000020327001 0.000007327807
*** Time spent in gradient calculation: 0.52 sec ***
* Info * Energy : -154.9237495146 a.u.
* Info * Gradient : 5.715176e-04 a.u. (RMS)
* Info * 1.302049e-03 a.u. (Max)
* Info * Time : 1.30 sec
Optimization Step 6
=====================
* Info * Computing energy and gradient...
SCF Gradient Driver Setup
===========================
Gradient Type : Analytical
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
Molecular Geometry (Angstroms)
--------------------------------
Atom Coordinate X Coordinate Y Coordinate Z
C -0.679758417595 0.462392520814 0.338271481124
C -1.454222964549 -0.667182434484 -0.330627777326
O -1.223567717187 -0.748299577733 -1.722595854914
H -0.927483086011 0.536811177987 1.410052297549
H 0.409487996186 0.297695545223 0.261260703344
H -0.910534551570 1.426664182035 -0.141527930055
H -1.229193609979 -1.629443990596 0.175671532497
H -2.537773671601 -0.500033436924 -0.213221798922
H -0.283169114349 -0.923723236312 -1.859326829879
Analytical Gradient (Hartree/Bohr)
------------------------------------
Atom Gradient X Gradient Y Gradient Z
C -0.000122813739 -0.000106269211 -0.000084199748
C 0.000060086078 0.000108156075 0.000101294658
O -0.000012186531 -0.000012121569 -0.000065940499
H 0.000014751391 0.000005269404 0.000013209871
H 0.000030363270 0.000006944010 0.000021472723
H 0.000036392458 0.000019819755 -0.000010784947
H -0.000001077783 -0.000015967847 -0.000021085798
H -0.000017343200 -0.000022684835 0.000021831988
H 0.000020500281 0.000006380830 0.000009825244
*** Time spent in gradient calculation: 0.51 sec ***
* Info * Energy : -154.9237532192 a.u.
* Info * Gradient : 8.813699e-05 a.u. (RMS)
* Info * 1.829370e-04 a.u. (Max)
* Info * Time : 1.23 sec
Optimization Step 7
=====================
* Info * Computing energy and gradient...
SCF Gradient Driver Setup
===========================
Gradient Type : Analytical
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
Molecular Geometry (Angstroms)
--------------------------------
Atom Coordinate X Coordinate Y Coordinate Z
C -0.679757047152 0.462729832172 0.338639193167
C -1.454225038782 -0.666996205367 -0.330572850124
O -1.223533991688 -0.747965296312 -1.722472311771
H -0.927517263515 0.536810970770 1.410417719722
H 0.409428895427 0.298197254225 0.261254574668
H -0.911146648647 1.426915538820 -0.140962951377
H -1.229215906917 -1.629201911933 0.175806290999
H -2.537727681178 -0.499635937701 -0.213290456415
H -0.283452796049 -0.924899120763 -1.859344846083
Analytical Gradient (Hartree/Bohr)
------------------------------------
Atom Gradient X Gradient Y Gradient Z
C -0.000007444877 -0.000001299181 -0.000000099882
C 0.000000090923 0.000005050234 0.000017640257
O -0.000010057265 0.000000589040 -0.000032613345
H 0.000001014395 0.000009369265 0.000002166492
H 0.000001513120 -0.000007861281 0.000009908905
H 0.000007551507 -0.000005501540 -0.000006067537
H 0.000008134585 -0.000001898909 -0.000009558055
H -0.000000026758 -0.000007526908 0.000006189765
H 0.000007845517 -0.000001361128 -0.000001869945
*** Time spent in gradient calculation: 0.52 sec ***
* Info * Energy : -154.9237533630 a.u.
* Info * Gradient : 1.585291e-05 a.u. (RMS)
* Info * 3.413394e-05 a.u. (Max)
* Info * Time : 1.16 sec
* Info * Geometry optimization completed.
Final Geometry (Angstroms)
============================
Atom Coordinate X Coordinate Y Coordinate Z
C -0.679757047152 0.462729832172 0.338639193167
C -1.454225038782 -0.666996205367 -0.330572850124
O -1.223533991688 -0.747965296312 -1.722472311771
H -0.927517263515 0.536810970770 1.410417719722
H 0.409428895427 0.298197254225 0.261254574668
H -0.911146648647 1.426915538820 -0.140962951377
H -1.229215906917 -1.629201911933 0.175806290999
H -2.537727681178 -0.499635937701 -0.213290456415
H -0.283452796049 -0.924899120763 -1.859344846083
Summary of Geometry Optimization
==================================
Opt.Step Energy (a.u.) Energy Change (a.u.) Displacement (RMS, Max)
-------------------------------------------------------------------------------------
0 -154.921527287436 0.000000000000 0.000e+00 0.000e+00
1 -154.923409849444 -0.001882562008 4.162e-02 7.222e-02
2 -154.923533488117 -0.000123638672 1.222e-02 2.811e-02
3 -154.923636961571 -0.000103473454 1.729e-02 4.265e-02
4 -154.923727909535 -0.000090947964 2.712e-02 6.669e-02
5 -154.923749514555 -0.000021605021 9.002e-03 2.140e-02
6 -154.923753219180 -0.000003704624 1.236e-03 1.684e-03
7 -154.923753362985 -0.000000143806 5.523e-04 1.243e-03
Statistical Deviation between
Optimized Geometry and Initial Geometry
=========================================
Internal Coord. RMS deviation Max. deviation
-----------------------------------------------------------
Bonds 0.012 Angstrom 0.027 Angstrom
Angles 1.504 degree 2.870 degree
Dihedrals 7.998 degree 17.618 degree
*** Time spent in Optimization Driver: 10.69 sec
* Info * Optimization results written to file: vlx_20260416_368ae0b4.h5
opt_drv.show_convergence(opt_results)Loading...
From an h5 file
opt_results = vlx.read_results("../output_files/bithio-S0-opt.h5", label="opt")
opt_drv.show_convergence(opt_results)Loading...
Spectrum plotting¶
From a notebook cell
molecule = vlx.Molecule.read_smiles('CCO')
basis = vlx.MolecularBasis.read(molecule, 'def2-svp')
scf_drv = vlx.ScfRestrictedDriver()
scf_drv.xcfun = 'b3lyp'
scf_results = scf_drv.compute(molecule, basis)
rsp_drv = vlx.lreigensolver.LinearResponseEigenSolver()
rsp_drv.nstates = 10
rsp_results = rsp_drv.compute(molecule, basis, scf_results)
Self Consistent Field Driver Setup
====================================
Wave Function Model : Spin-Restricted Kohn-Sham
Initial Guess Model : Superposition of Atomic Densities
Convergence Accelerator : Two Level Direct Inversion of Iterative Subspace
Max. Number of Iterations : 50
Max. Number of Error Vectors : 10
Convergence Threshold : 1.0e-06
ERI Screening Threshold : 1.0e-12
Linear Dependence Threshold : 1.0e-06
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
* Info * Using the B3LYP functional.
P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch., J. Phys. Chem. 98, 11623 (1994)
* Info * Using the Libxc library (v7.0.0).
S. Lehtola, C. Steigemann, M. J.T. Oliveira, and M. A.L. Marques., SoftwareX 7, 1–5 (2018)
* Info * Using the following algorithm for XC numerical integration.
J. Kussmann, H. Laqua and C. Ochsenfeld, J. Chem. Theory Comput. 2021, 17, 1512-1521
* Info * Starting Reduced Basis SCF calculation...
* Info * ...done. SCF energy in reduced basis set: -153.878486387939 a.u. Time: 0.08 sec.
Iter. | Kohn-Sham Energy | Energy Change | Gradient Norm | Max. Gradient | Density Change
--------------------------------------------------------------------------------------------
1 -154.914063830212 0.0000000000 0.25700144 0.02179029 0.00000000
2 -154.917227497348 -0.0031636671 0.18477457 0.01179485 0.14535722
3 -154.921418775684 -0.0041912783 0.03153093 0.00159943 0.06527707
4 -154.921521512189 -0.0001027365 0.00963264 0.00077439 0.01040169
5 -154.921529872168 -0.0000083600 0.00173187 0.00010435 0.00336251
6 -154.921530166587 -0.0000002944 0.00029568 0.00002451 0.00063151
7 -154.921530178001 -0.0000000114 0.00003878 0.00000229 0.00013434
8 -154.921530178159 -0.0000000002 0.00001670 0.00000085 0.00001563
9 -154.921530178194 -0.0000000000 0.00000165 0.00000009 0.00000567
10 -154.921530178194 -0.0000000000 0.00000015 0.00000001 0.00000083
*** SCF converged in 10 iterations. Time: 1.02 sec.
Spin-Restricted Kohn-Sham:
--------------------------
Total Energy : -154.9215301782 a.u.
Electronic Energy : -236.6491039117 a.u.
Nuclear Repulsion Energy : 81.7275737335 a.u.
------------------------------------
Gradient Norm : 0.0000001479 a.u.
Ground State Information
------------------------
Charge of Molecule : 0.0
Multiplicity (2S+1) : 1
Magnetic Quantum Number (M_S) : 0.0
Linear Response EigenSolver Setup
===================================
Number of States : 10
Max. Number of Iterations : 150
Convergence Threshold : 1.0e-04
ERI Screening Threshold : 1.0e-12
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
* Info * Using the B3LYP functional.
P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch., J. Phys. Chem. 98, 11623 (1994)
* Info * Using the Libxc library (v7.0.0).
S. Lehtola, C. Steigemann, M. J.T. Oliveira, and M. A.L. Marques., SoftwareX 7, 1–5 (2018)
* Info * Using the following algorithm for XC numerical integration.
J. Kussmann, H. Laqua and C. Ochsenfeld, J. Chem. Theory Comput. 2021, 17, 1512-1521
* Info * 30 gerade trial vectors in reduced space
* Info * 30 ungerade trial vectors in reduced space
*** Iteration: 1 * Residuals (Max,Min): 1.85e-01 and 6.38e-02
* Info * 40 gerade trial vectors in reduced space
* Info * 40 ungerade trial vectors in reduced space
*** Iteration: 2 * Residuals (Max,Min): 3.03e-02 and 1.21e-02
* Info * 50 gerade trial vectors in reduced space
* Info * 50 ungerade trial vectors in reduced space
*** Iteration: 3 * Residuals (Max,Min): 4.74e-03 and 1.81e-03
* Info * 60 gerade trial vectors in reduced space
* Info * 60 ungerade trial vectors in reduced space
*** Iteration: 4 * Residuals (Max,Min): 5.42e-04 and 2.22e-04
* Info * 70 gerade trial vectors in reduced space
* Info * 70 ungerade trial vectors in reduced space
*** Iteration: 5 * Residuals (Max,Min): 5.22e-05 and 1.71e-05
*** Linear response converged in 5 iterations. Time: 4.47 sec
Electric Transition Dipole Moments (dipole length, a.u.)
--------------------------------------------------------
X Y Z
Excited State S1: 0.038675 0.172852 -0.063894
Excited State S2: 0.209058 -0.284502 0.049483
Excited State S3: 0.186336 0.074107 0.043571
Excited State S4: -0.241528 -0.218187 -0.288472
Excited State S5: 0.002000 -0.003570 -0.450679
Excited State S6: 0.211384 -0.156252 -0.012145
Excited State S7: 0.103751 0.298124 -0.021213
Excited State S8: 0.428566 -0.302429 0.078009
Excited State S9: -0.020283 0.095738 0.019925
Excited State S10: 0.068754 0.389059 -0.128821
Electric Transition Dipole Moments (dipole velocity, a.u.)
----------------------------------------------------------
X Y Z
Excited State S1: 0.122734 0.306629 0.080870
Excited State S2: 0.247567 -0.183319 0.113684
Excited State S3: 0.242857 0.124809 -0.027114
Excited State S4: -0.245444 -0.161112 -0.291666
Excited State S5: -0.042124 -0.027530 -0.511560
Excited State S6: 0.231723 -0.126975 -0.090882
Excited State S7: 0.143900 0.284670 -0.034367
Excited State S8: 0.449522 -0.307280 0.092029
Excited State S9: -0.031443 0.098292 0.017025
Excited State S10: 0.064136 0.395428 -0.130420
Magnetic Transition Dipole Moments (a.u.)
-----------------------------------------
X Y Z
Excited State S1: 0.188550 0.167035 -0.189194
Excited State S2: -0.008989 -0.065601 0.039611
Excited State S3: -0.030016 -0.430202 -0.187731
Excited State S4: 0.180223 0.035431 -0.132931
Excited State S5: 0.176390 -0.086661 0.131822
Excited State S6: -0.322260 0.167964 -0.148474
Excited State S7: -0.146003 0.045431 -0.177119
Excited State S8: -0.102333 -0.163366 0.494310
Excited State S9: 0.124544 -0.009282 0.076257
Excited State S10: 0.321072 -0.022776 0.049317
One-Photon Absorption
---------------------
Excited State S1: 0.25657908 a.u. 6.98187 eV Osc.Str. 0.0061
Excited State S2: 0.30999800 a.u. 8.43548 eV Osc.Str. 0.0263
Excited State S3: 0.31641055 a.u. 8.60997 eV Osc.Str. 0.0089
Excited State S4: 0.33276732 a.u. 9.05506 eV Osc.Str. 0.0420
Excited State S5: 0.34369072 a.u. 9.35230 eV Osc.Str. 0.0465
Excited State S6: 0.36134981 a.u. 9.83283 eV Osc.Str. 0.0167
Excited State S7: 0.36299282 a.u. 9.87754 eV Osc.Str. 0.0242
Excited State S8: 0.37099920 a.u. 10.09540 eV Osc.Str. 0.0696
Excited State S9: 0.37686911 a.u. 10.25513 eV Osc.Str. 0.0025
Excited State S10: 0.38367767 a.u. 10.44040 eV Osc.Str. 0.0442
Electronic Circular Dichroism
-----------------------------
Excited State S1: Rot.Str. 0.059059 a.u. 27.8431 [10**(-40) cgs]
Excited State S2: Rot.Str. 0.014304 a.u. 6.7433 [10**(-40) cgs]
Excited State S3: Rot.Str. -0.055893 a.u. -26.3502 [10**(-40) cgs]
Excited State S4: Rot.Str. -0.011172 a.u. -5.2669 [10**(-40) cgs]
Excited State S5: Rot.Str. -0.072479 a.u. -34.1700 [10**(-40) cgs]
Excited State S6: Rot.Str. -0.082508 a.u. -38.8981 [10**(-40) cgs]
Excited State S7: Rot.Str. -0.001990 a.u. -0.9381 [10**(-40) cgs]
Excited State S8: Rot.Str. 0.049689 a.u. 23.4254 [10**(-40) cgs]
Excited State S9: Rot.Str. -0.003530 a.u. -1.6643 [10**(-40) cgs]
Excited State S10: Rot.Str. 0.005154 a.u. 2.4297 [10**(-40) cgs]
Character of excitations:
Excited state 1
---------------
HOMO -> LUMO -0.9824
Excited state 2
---------------
HOMO -> LUMO+1 -0.9670
Excited state 3
---------------
HOMO-1 -> LUMO 0.9828
Excited state 4
---------------
HOMO -> LUMO+2 0.9881
Excited state 5
---------------
HOMO -> LUMO+3 -0.9808
Excited state 6
---------------
HOMO-1 -> LUMO+1 0.7326
HOMO -> LUMO+4 -0.5321
HOMO-2 -> LUMO -0.3830
Excited state 7
---------------
HOMO -> LUMO+4 0.8200
HOMO-1 -> LUMO+1 0.5163
Excited state 8
---------------
HOMO-2 -> LUMO 0.8857
HOMO-1 -> LUMO+1 0.4213
Excited state 9
---------------
HOMO -> LUMO+5 0.9887
Excited state 10
----------------
HOMO-3 -> LUMO 0.8995
HOMO-1 -> LUMO+2 0.3820
rsp_drv.plot(rsp_results)
From an h5 file
rsp_results = vlx.read_results("../output_files/alanine-ecd.h5", label="rsp")
rsp_drv.plot_ecd(rsp_results)
Normal modes¶
From a notebook cell
molecule = vlx.Molecule.read_smiles('CCO')
basis = vlx.MolecularBasis.read(molecule, 'def2-svp')
scf_drv = vlx.ScfRestrictedDriver()
scf_drv.xcfun = 'b3lyp'
scf_results = scf_drv.compute(molecule, basis)
vib_drv = vlx.VibrationalAnalysis(scf_drv)
vib_results = vib_drv.compute(molecule, basis)
Self Consistent Field Driver Setup
====================================
Wave Function Model : Spin-Restricted Kohn-Sham
Initial Guess Model : Superposition of Atomic Densities
Convergence Accelerator : Two Level Direct Inversion of Iterative Subspace
Max. Number of Iterations : 50
Max. Number of Error Vectors : 10
Convergence Threshold : 1.0e-06
ERI Screening Threshold : 1.0e-12
Linear Dependence Threshold : 1.0e-06
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
* Info * Using the B3LYP functional.
P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch., J. Phys. Chem. 98, 11623 (1994)
* Info * Using the Libxc library (v7.0.0).
S. Lehtola, C. Steigemann, M. J.T. Oliveira, and M. A.L. Marques., SoftwareX 7, 1–5 (2018)
* Info * Using the following algorithm for XC numerical integration.
J. Kussmann, H. Laqua and C. Ochsenfeld, J. Chem. Theory Comput. 2021, 17, 1512-1521
* Info * Starting Reduced Basis SCF calculation...
* Info * ...done. SCF energy in reduced basis set: -153.878486418599 a.u. Time: 0.05 sec.
Iter. | Kohn-Sham Energy | Energy Change | Gradient Norm | Max. Gradient | Density Change
--------------------------------------------------------------------------------------------
1 -154.914063450764 0.0000000000 0.25700134 0.02179016 0.00000000
2 -154.917227185661 -0.0031637349 0.18477246 0.01179468 0.14535670
3 -154.921418377273 -0.0041911916 0.03153012 0.00159921 0.06527710
4 -154.921521113018 -0.0001027357 0.00963139 0.00077429 0.01040149
5 -154.921529470762 -0.0000083577 0.00173202 0.00010437 0.00336214
6 -154.921529765223 -0.0000002945 0.00029569 0.00002451 0.00063153
7 -154.921529776638 -0.0000000114 0.00003877 0.00000229 0.00013434
8 -154.921529776796 -0.0000000002 0.00001670 0.00000085 0.00001563
9 -154.921529776830 -0.0000000000 0.00000165 0.00000009 0.00000567
10 -154.921529776831 -0.0000000000 0.00000015 0.00000001 0.00000083
*** SCF converged in 10 iterations. Time: 0.85 sec.
Spin-Restricted Kohn-Sham:
--------------------------
Total Energy : -154.9215297768 a.u.
Electronic Energy : -236.6490971631 a.u.
Nuclear Repulsion Energy : 81.7275673863 a.u.
------------------------------------
Gradient Norm : 0.0000001479 a.u.
Ground State Information
------------------------
Charge of Molecule : 0.0
Multiplicity (2S+1) : 1
Magnetic Quantum Number (M_S) : 0.0
Vibrational Analysis Driver
=============================
The following will be computed:
- Vibrational frequencies and normal modes
- Force constants
- IR intensities
SCF Hessian Driver Setup
==========================
Hessian Type : Analytical
* Info * Computing analytical Hessian...
Reference: P. Deglmann, F. Furche, R. Ahlrichs, Chem. Phys. Lett. 2002, 362, 511-518.
* Info * Using the B3LYP functional.
P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch., J. Phys. Chem. 98, 11623 (1994)
* Info * Using the Libxc library (v7.0.0).
S. Lehtola, C. Steigemann, M. J.T. Oliveira, and M. A.L. Marques., SoftwareX 7, 1–5 (2018)
* Info * Using the following algorithm for XC numerical integration.
J. Kussmann, H. Laqua and C. Ochsenfeld, J. Chem. Theory Comput. 2021, 17, 1512-1521
* Info * CPHF/CPKS integral derivatives computed in 1.27 sec.
* Info * CPHF/CPKS right-hand side computed in 1.79 sec.
Coupled-Perturbed Kohn-Sham Solver Setup
------------------------------------------
Solver Type : Iterative Subspace Algorithm
Max. Number of Iterations : 150
Convergence Threshold : 1.0e-04
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
* Info * 24 trial vectors in reduced space
*** Iteration: 1 * Residuals (Max,Min): 3.97e-01 and 1.88e-01
* Info * 48 trial vectors in reduced space
*** Iteration: 2 * Residuals (Max,Min): 3.39e-02 and 1.78e-02
* Info * 72 trial vectors in reduced space
*** Iteration: 3 * Residuals (Max,Min): 2.16e-03 and 1.06e-03
* Info * 90 trial vectors in reduced space
*** Iteration: 4 * Residuals (Max,Min): 1.38e-04 and 3.80e-05
* Info * 108 trial vectors in reduced space
*** Iteration: 5 * Residuals (Max,Min): 9.49e-05 and 4.21e-06
*** Coupled-Perturbed Kohn-Sham converged in 5 iterations. Time: 9.42 sec
* Info * First order derivative contributions to the Hessian computed in 0.00 sec.
* Info * Second order derivative contributions to the Hessian computed in 9.98 sec.
*** Time spent in Hessian calculation: 19.41 sec ***
Free Energy Analysis
======================
Note: Rotational symmetry is set to 1 regardless of true symmetry
No Imaginary Frequencies
Free energy contributions calculated at @ 298.15 K:
Zero-point vibrational energy: 50.1144 kcal/mol
H (Trans + Rot + Vib = Tot): 1.4812 + 0.8887 + 0.6064 = 2.9763 kcal/mol
S (Trans + Rot + Vib = Tot): 37.4322 + 22.3320 + 2.8170 = 62.5813 cal/mol/K
TS (Trans + Rot + Vib = Tot): 11.1604 + 6.6583 + 0.8399 = 18.6586 kcal/mol
Ground State Electronic Energy : E0 = -154.92152978 au ( -97214.7277 kcal/mol)
Free Energy Correction (Harmonic) : ZPVE + [H-TS]_T,R,V = 0.05487118 au ( 34.4322 kcal/mol)
Gibbs Free Energy (Harmonic) : E0 + ZPVE + [H-TS]_T,R,V = -154.86665860 au ( -97180.2955 kcal/mol)
Vibrational Analysis
======================
* Info * The 5 dominant normal modes are printed below.
Vibrational Mode 3
----------------------------------------------------
Harmonic frequency: 645.86 cm**-1
Reduced mass: 1.1162 amu
Force constant: 0.2743 mdyne/A
IR intensity: 123.0871 km/mol
Normal mode:
X Y Z
1 C 0.0145 0.0173 0.0100
2 C -0.0138 -0.0256 0.0108
3 O 0.0325 -0.0051 -0.0707
4 H 0.0080 0.0764 0.0780
5 H 0.0234 0.0828 -0.0463
6 H 0.0278 0.0060 -0.0274
7 H -0.0834 -0.0060 -0.0423
8 H -0.0226 -0.0788 0.0692
9 H -0.4777 0.1000 0.8431
Vibrational Mode 7
----------------------------------------------------
Harmonic frequency: 1132.52 cm**-1
Reduced mass: 1.6310 amu
Force constant: 1.2325 mdyne/A
IR intensity: 82.0999 km/mol
Normal mode:
X Y Z
1 C -0.0824 -0.0357 -0.0174
2 C 0.1509 0.0019 0.0636
3 O -0.0876 0.0735 -0.0519
4 H 0.0155 0.1034 0.2475
5 H 0.2310 -0.1352 -0.2396
6 H 0.0297 0.1665 0.1394
7 H -0.1651 0.0001 -0.2467
8 H 0.2769 -0.4625 0.3009
9 H 0.1871 -0.4362 0.0722
Vibrational Mode 12
----------------------------------------------------
Harmonic frequency: 1443.61 cm**-1
Reduced mass: 1.1421 amu
Force constant: 1.4024 mdyne/A
IR intensity: 46.2919 km/mol
Normal mode:
X Y Z
1 C -0.0130 -0.0198 -0.0104
2 C 0.0314 0.0520 0.0276
3 O -0.0223 -0.0685 -0.0038
4 H 0.1968 -0.1259 0.0419
5 H -0.1680 0.1716 0.0070
6 H 0.2492 0.2690 0.0389
7 H -0.1266 0.1280 -0.0341
8 H 0.2941 -0.3228 0.0727
9 H -0.3102 0.5840 -0.2700
Vibrational Mode 16
----------------------------------------------------
Harmonic frequency: 2931.04 cm**-1
Reduced mass: 1.0652 amu
Force constant: 5.3916 mdyne/A
IR intensity: 72.4286 km/mol
Normal mode:
X Y Z
1 C -0.0018 0.0081 -0.0013
2 C -0.0230 -0.0359 0.0577
3 O 0.0014 -0.0013 0.0009
4 H -0.0045 -0.0049 0.0024
5 H -0.0430 -0.0316 -0.0420
6 H 0.0649 -0.0634 0.0484
7 H 0.4764 0.6241 -0.4931
8 H -0.2247 -0.1721 -0.1993
9 H 0.0024 -0.0020 -0.0027
Vibrational Mode 19
----------------------------------------------------
Harmonic frequency: 3037.43 cm**-1
Reduced mass: 1.1032 amu
Force constant: 5.9967 mdyne/A
IR intensity: 42.2126 km/mol
Normal mode:
X Y Z
1 C -0.0602 0.0300 -0.0611
2 C -0.0137 -0.0098 -0.0113
3 O 0.0007 0.0003 0.0007
4 H -0.1143 -0.1347 0.0989
5 H 0.3341 0.2804 0.3241
6 H 0.5004 -0.5082 0.3145
7 H 0.0151 0.0171 -0.0142
8 H 0.1344 0.1067 0.1313
9 H -0.0012 -0.0073 -0.0040
vib_drv.plot(vib_results)
vib_drv.animate(vib_results, mode=14)Loading...
From an h5 file
vib_results = vlx.read_results("../output_files/acro-raman.h5", label="vib")
vib_drv.plot_raman(vib_results)
vib_drv.animate(vib_results, mode=14)Loading...
