From 21040b0014678ccac88e65a8b90fbfc28a64a886 Mon Sep 17 00:00:00 2001 From: Tom Date: Fri, 10 Jul 2020 13:11:15 +0100 Subject: [PATCH] Updated other wrappers and added tests --- .gitignore | 6 + autode/smiles/smiles.py | 18 +- autode/wrappers/G09.py | 11 +- autode/wrappers/MOPAC.py | 2 +- autode/wrappers/NWChem.py | 6 +- doc/examples/molecules.rst | 3 +- tests/data/orca/h2_disp_orca.out | 734 ++++++++++++++++++++++++++++ tests/data/orca/h2_disp_orca.xyz | 4 + tests/data/orca/h2_grad_orca.out | 734 ++++++++++++++++++++++++++++ tests/data/orca/h2_grad_orca.xyz | 4 + tests/data/xtb/gradient | 13 + tests/data/xtb/h2_disp_sp_xtb.out | 225 +++++++++ tests/data/xtb/h2_disp_sp_xtb.xyz | 4 + tests/data/xtb/h2_grad_xtb.out | 225 +++++++++ tests/data/xtb/h2_grad_xtb.xyz | 4 + tests/data/xtb/h2_grad_xtb_xtb.grad | 2 + tests/data/xtb/h2_sp_xtb.out | 225 +++++++++ tests/data/xtb/h2_sp_xtb.xyz | 4 + tests/data/xtb/methane_xtb_xtb.grad | 5 + tests/data/xtbopt.xyz | 8 - tests/test_1d_pes.py | 5 + tests/test_orca_calc.py | 40 ++ tests/test_ts.py | 11 +- tests/test_xtb_calc.py | 57 ++- 24 files changed, 2327 insertions(+), 23 deletions(-) create mode 100644 tests/data/orca/h2_disp_orca.out create mode 100644 tests/data/orca/h2_disp_orca.xyz create mode 100644 tests/data/orca/h2_grad_orca.out create mode 100644 tests/data/orca/h2_grad_orca.xyz create mode 100644 tests/data/xtb/gradient create mode 100644 tests/data/xtb/h2_disp_sp_xtb.out create mode 100644 tests/data/xtb/h2_disp_sp_xtb.xyz create mode 100644 tests/data/xtb/h2_grad_xtb.out create mode 100644 tests/data/xtb/h2_grad_xtb.xyz create mode 100644 tests/data/xtb/h2_grad_xtb_xtb.grad create mode 100644 tests/data/xtb/h2_sp_xtb.out create mode 100644 tests/data/xtb/h2_sp_xtb.xyz create mode 100644 tests/data/xtb/methane_xtb_xtb.grad delete mode 100644 tests/data/xtbopt.xyz diff --git a/.gitignore b/.gitignore index 3fbf7b2ce..82f48e460 100755 --- a/.gitignore +++ b/.gitignore @@ -46,3 +46,9 @@ tests/.autode_calculations tests/data/complex_conf*.xyz tests/data/*.com + +tests/data/conformers/.autode_calculations + +tests/data/orca/.autode_calculations + +tests/data/xtb/.autode_calculations diff --git a/autode/smiles/smiles.py b/autode/smiles/smiles.py index bec1663f5..b45080c59 100644 --- a/autode/smiles/smiles.py +++ b/autode/smiles/smiles.py @@ -12,7 +12,9 @@ def calc_multiplicity(molecule, n_radical_electrons): - """Calculate the spin multiplicity 2S + 1 where S is the number of unpaired electrons + """Calculate the spin multiplicity 2S + 1 where S is the number of + unpaired electrons + Arguments: molecule (autode.molecule.Molecule): n_radical_electrons (int): @@ -24,11 +26,13 @@ def calc_multiplicity(molecule, n_radical_electrons): return 1 if molecule.mult == 1 and n_radical_electrons == 1: - # Cannot have multiplicity = 1 and 1 radical electrons – override default multiplicity + # Cannot have multiplicity = 1 and 1 radical electrons – override + # default multiplicity return 2 if molecule.mult == 1 and n_radical_electrons > 1: - logger.warning('Diradicals by default singlets. Set mol.mult if it\'s any different') + logger.warning('Diradicals by default singlets. Set mol.mult if it\'s ' + 'any different') return 1 return molecule.mult @@ -36,8 +40,9 @@ def calc_multiplicity(molecule, n_radical_electrons): def init_organic_smiles(molecule, smiles): """ - Initialise a molecule from a SMILES string, set the charge, multiplicity (if it's not already specified) and the 3D - geometry using RDKit + Initialise a molecule from a SMILES string, set the charge, multiplicity ( + if it's not already specified) and the 3D geometry using RDKit + Arguments: molecule (autode.molecule.Molecule): smiles (str): SMILES string @@ -114,7 +119,8 @@ def init_smiles(molecule, smiles): def check_bonds(molecule, bonds): """ - Ensure the SMILES string and the 3D structure have the same bonds, but don't override + Ensure the SMILES string and the 3D structure have the same bonds, + but don't override Arguments: molecule (autode.molecule.Molecule): diff --git a/autode/wrappers/G09.py b/autode/wrappers/G09.py index e0f1e34b2..cb3e017fa 100644 --- a/autode/wrappers/G09.py +++ b/autode/wrappers/G09.py @@ -1,5 +1,6 @@ from copy import deepcopy import numpy as np +from autode.constants import Constants from autode.wrappers.base import ElectronicStructureMethod from autode.utils import run_external from autode.atoms import Atom @@ -440,16 +441,20 @@ def get_gradients(self, calc): gradients_section = False if gradients_section and len(line.split()) == 5: - _, _, x, y, z = line.split() + _, _, fx, fy, fz = line.split() try: - gradients.append([float(x), float(y), float(z)]) + # Ha / a0 + force = np.array([float(fx), float(fy), float(fz)]) + + grad = -force / Constants.a02ang + gradients.append(grad) except ValueError: pass for line in gradients: for i in range(3): line[i] *= -1 - return gradients + return np.array(gradients) def __init__(self): super().__init__(name='g09', path=Config.G09.path, diff --git a/autode/wrappers/MOPAC.py b/autode/wrappers/MOPAC.py index 91e304b55..867aa97a9 100644 --- a/autode/wrappers/MOPAC.py +++ b/autode/wrappers/MOPAC.py @@ -293,7 +293,7 @@ def get_gradients(self, calc): _, _, _, _, _, _, value, _ = line.split() gradients.append(value) grad_array = np.asarray(gradients) - grad_array *= Constants.a02ang/Constants.ha2kcalmol + grad_array /= Constants.ha2kcalmol # From kcal mol-1 Å^-1 to Ha Å^-1 grad_array.reshape((calc.molecule.n_atoms, 3)) return grad_array.tolist() diff --git a/autode/wrappers/NWChem.py b/autode/wrappers/NWChem.py index 34c56edac..d50f5d087 100644 --- a/autode/wrappers/NWChem.py +++ b/autode/wrappers/NWChem.py @@ -356,9 +356,11 @@ def get_gradients(self, calc): if gradients_section and len(line.split()) == 8: x, y, z = line.split()[5:] - gradients.append([float(x), float(y), float(z)]) + gradients.append(np.array([float(x), float(y), float(z)])) - return gradients + # Convert from Ha a0^-1 to Ha A-1 + gradients = [grad / Constants.a02ang for grad in gradients] + return np.array(gradients) def __init__(self): super().__init__('nwchem', path=Config.NWChem.path, diff --git a/doc/examples/molecules.rst b/doc/examples/molecules.rst index 7edbd3597..44116403c 100644 --- a/doc/examples/molecules.rst +++ b/doc/examples/molecules.rst @@ -104,7 +104,8 @@ Calculations **autodE** provides wrappers around common electronic structure theory packages (ORCA, XTB, NWChem, MOPAC, Gaussian09) so geometries may be optimised and -energies calculated. +energies calculated. Energies are in atomic Hartrees and gradients in +Ha / Å. For example, to optimise the geometry at the XTB level and then perform a single point energy evaluation with ORCA diff --git a/tests/data/orca/h2_disp_orca.out b/tests/data/orca/h2_disp_orca.out new file mode 100644 index 000000000..3d00ca524 --- /dev/null +++ b/tests/data/orca/h2_disp_orca.out @@ -0,0 +1,734 @@ + + ***************** + * O R C A * + ***************** + + --- An Ab Initio, DFT and Semiempirical electronic structure package --- + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship: Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 4.2.1 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM Hessian, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : CASSCF linear response (MC-RPA) + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : AUTO-CI + Lucas Lang : DCDCAS + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, : VdW corrections, initial TS optimization, + C. Bannwarth DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Andreas Klamt, Michael Diedenhofen : otool_cosmo (COSMO solvation model) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, Multilevel, MM, QM/MM, CI optimization + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 4.2.3 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + + +Your calculation utilizes the atom-pairwise dispersion correction +with the Becke-Johnson damping scheme (D3BJ) +Cite in your paper: +S.Grimme, S.Ehrlich, L.Goerigk, J Comput Chem, (2011), 32, 1456–1465 +S.Grimme, J.Antony, S.Ehrlich and H.Krieg, J.Chem.Phys., 132, (2010), 154104 + + +----- Orbital basis set information ----- +Your calculation utilizes the basis: def2-SVP + F. Weigend and R. Ahlrichs, Phys. Chem. Chem. Phys. 7, 3297 (2005). + +----- AuxJ basis set information ----- +Your calculation utilizes the auxiliary basis: def2/J + F. Weigend, Phys. Chem. Chem. Phys. 8, 1057 (2006). + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + + +INFO : the flag for use of LIBINT has been found! + +================================================================================ + INPUT FILE +================================================================================ +NAME = h2_disp_orca.inp +| 1> ! EnGrad PBE D3BJ def2-SVP +| 2> %geom MaxIter 100 end +| 3> %output +| 4> xyzfile=True +| 5> end +| 6> %scf +| 7> maxiter 250 +| 8> end +| 9> %output +| 10> Print[P_Hirshfeld] = 1 +| 11> end +| 12> % maxcore +| 13> 4000 +| 14> *xyz 0 1 +| 15> H 0.00000000 0.00000000 0.00000000 +| 16> H 1.00000001 0.00000000 0.00000000 +| 17> * +| 18> +| 19> ****END OF INPUT**** +================================================================================ + + ******************************* + * Energy+Gradient Calculation * + ******************************* + +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + H 0.000000 0.000000 0.000000 + H 1.000000 0.000000 0.000000 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 H 1.0000 0 1.008 0.000000 0.000000 0.000000 + 1 H 1.0000 0 1.008 1.889726 0.000000 0.000000 + +-------------------------------- +INTERNAL COORDINATES (ANGSTROEM) +-------------------------------- + H 0 0 0 0.000000000000 0.00000000 0.00000000 + H 1 0 0 1.000000010000 0.00000000 0.00000000 + +--------------------------- +INTERNAL COORDINATES (A.U.) +--------------------------- + H 0 0 0 0.000000000000 0.00000000 0.00000000 + H 1 0 0 1.889726152819 0.00000000 0.00000000 + +--------------------- +BASIS SET INFORMATION +--------------------- +There are 1 groups of distinct atoms + + Group 1 Type H : 4s1p contracted to 2s1p pattern {31/1} + +Atom 0H basis set group => 1 +Atom 1H basis set group => 1 +--------------------------------- +AUXILIARY/J BASIS SET INFORMATION +--------------------------------- +There are 1 groups of distinct atoms + + Group 1 Type H : 5s2p1d contracted to 3s1p1d pattern {311/2/1} + +Atom 0H basis set group => 1 +Atom 1H basis set group => 1 +------------------------------------------------------------------------------ + ORCA GTO INTEGRAL CALCULATION + -- RI-GTO INTEGRALS CHOSEN -- +------------------------------------------------------------------------------ + + BASIS SET STATISTICS AND STARTUP INFO + +Gaussian basis set: + # of primitive gaussian shells ... 10 + # of primitive gaussian functions ... 14 + # of contracted shells ... 6 + # of contracted basis functions ... 10 + Highest angular momentum ... 1 + Maximum contraction depth ... 3 +Auxiliary gaussian basis set: + # of primitive gaussian shells ... 16 + # of primitive gaussian functions ... 32 + # of contracted shells ... 10 + # of contracted aux-basis functions ... 22 + Highest angular momentum ... 2 + Maximum contraction depth ... 3 +Ratio of auxiliary to basis functions ... 2.20 +Integral package used ... LIBINT + One Electron integrals ... done + Ordering auxiliary basis shells ... done + Integral threshhold Thresh ... 2.500e-11 + Primitive cut-off TCut ... 2.500e-12 + Pre-screening matrix ... done + Shell pair data ... + Ordering of the shell pairs ... done ( 0.000 sec) 21 of 21 pairs + Determination of significant pairs ... done ( 0.000 sec) + Creation of shell pair data ... done ( 0.000 sec) + Storage of shell pair data ... done ( 0.000 sec) + Shell pair data done in ( 0.000 sec) + Computing two index integrals ... done + Cholesky decomposition of the V-matrix ... done + + +Timings: + Total evaluation time ... 0.061 sec ( 0.001 min) + One electron matrix time ... 0.002 sec ( 0.000 min) = 3.1% + Schwartz matrix evaluation time ... 0.052 sec ( 0.001 min) = 85.2% + Two index repulsion integral time ... 0.000 sec ( 0.000 min) = 0.1% + Cholesky decomposition of V ... 0.000 sec ( 0.000 min) = 0.3% + Three index repulsion integral time ... 0.000 sec ( 0.000 min) = 0.0% + +------------------------------------------------------------------------------- + ORCA SCF +------------------------------------------------------------------------------- + +------------ +SCF SETTINGS +------------ +Hamiltonian: + Density Functional Method .... DFT(GTOs) + Exchange Functional Exchange .... PBE + PBE kappa parameter XKappa .... 0.804000 + PBE mue parameter XMuePBE .... 0.219520 + Correlation Functional Correlation .... PBE + PBE beta parameter CBetaPBE .... 0.066725 + LDA part of GGA corr. LDAOpt .... PW91-LDA + Gradients option PostSCFGGA .... off + Density functional embedding theory .... OFF + NL short-range parameter .... 6.400000 + RI-approximation to the Coulomb term is turned on + Number of auxiliary basis functions .... 22 + + +General Settings: + Integral files IntName .... h2_disp_orca + Hartree-Fock type HFTyp .... RHF + Total Charge Charge .... 0 + Multiplicity Mult .... 1 + Number of Electrons NEL .... 2 + Basis Dimension Dim .... 10 + Nuclear Repulsion ENuc .... 0.5291772030 Eh + +Convergence Acceleration: + DIIS CNVDIIS .... on + Start iteration DIISMaxIt .... 12 + Startup error DIISStart .... 0.200000 + # of expansion vecs DIISMaxEq .... 5 + Bias factor DIISBfac .... 1.050 + Max. coefficient DIISMaxC .... 10.000 + Newton-Raphson CNVNR .... off + SOSCF CNVSOSCF .... on + Start iteration SOSCFMaxIt .... 150 + Startup grad/error SOSCFStart .... 0.003300 + Level Shifting CNVShift .... on + Level shift para. LevelShift .... 0.2500 + Turn off err/grad. ShiftErr .... 0.0010 + Zerner damping CNVZerner .... off + Static damping CNVDamp .... on + Fraction old density DampFac .... 0.7000 + Max. Damping (<1) DampMax .... 0.9800 + Min. Damping (>=0) DampMin .... 0.0000 + Turn off err/grad. DampErr .... 0.1000 + Fernandez-Rico CNVRico .... off + +SCF Procedure: + Maximum # iterations MaxIter .... 250 + SCF integral mode SCFMode .... Direct + Integral package .... LIBINT + Reset frequency DirectResetFreq .... 20 + Integral Threshold Thresh .... 2.500e-11 Eh + Primitive CutOff TCut .... 2.500e-12 Eh + +Convergence Tolerance: + Convergence Check Mode ConvCheckMode .... Total+1el-Energy + Convergence forced ConvForced .... 0 + Energy Change TolE .... 1.000e-08 Eh + 1-El. energy change .... 1.000e-05 Eh + Orbital Gradient TolG .... 1.000e-05 + Orbital Rotation angle TolX .... 1.000e-05 + DIIS Error TolErr .... 5.000e-07 + + +Diagonalization of the overlap matrix: +Smallest eigenvalue ... 1.144e-01 +Time for diagonalization ... 0.000 sec +Threshold for overlap eigenvalues ... 1.000e-08 +Number of eigenvalues below threshold ... 0 +Time for construction of square roots ... 0.000 sec +Total time needed ... 0.000 sec + +------------------- +DFT GRID GENERATION +------------------- + +General Integration Accuracy IntAcc ... 4.340 +Radial Grid Type RadialGrid ... Gauss-Chebyshev +Angular Grid (max. acc.) AngularGrid ... Lebedev-110 +Angular grid pruning method GridPruning ... 3 (G Style) +Weight generation scheme WeightScheme... Becke +Basis function cutoff BFCut ... 1.0000e-11 +Integration weight cutoff WCut ... 1.0000e-14 +Grids for H and He will be reduced by one unit + +# of grid points (after initial pruning) ... 1588 ( 0.0 sec) +# of grid points (after weights+screening) ... 1566 ( 0.0 sec) +nearest neighbour list constructed ... 0.0 sec +Grid point re-assignment to atoms done ... 0.0 sec +Grid point division into batches done ... 0.0 sec +Reduced shell lists constructed in 0.0 sec + +Total number of grid points ... 1566 +Total number of batches ... 26 +Average number of points per batch ... 60 +Average number of grid points per atom ... 783 +Average number of shells per batch ... 5.78 (96.30%) +Average number of basis functions per batch ... 9.63 (96.30%) +Average number of large shells per batch ... 5.74 (99.36%) +Average number of large basis fcns per batch ... 9.52 (98.85%) +Maximum spatial batch extension ... 15.26, 21.59, 21.59 au +Average spatial batch extension ... 5.01, 8.34, 8.47 au + +Time for grid setup = 0.002 sec + +------------------------------ +INITIAL GUESS: MODEL POTENTIAL +------------------------------ +Loading Hartree-Fock densities ... done +Calculating cut-offs ... done +Setting up the integral package ... done +Initializing the effective Hamiltonian ... done +Starting the Coulomb interaction ... done ( 0.0 sec) +Reading the grid ... done +Mapping shells ... done +Starting the XC term evaluation ... done ( 0.0 sec) + promolecular density results + # of electrons = 1.995342477 + EX = -0.539655112 + EC = -0.039204154 + EX+EC = -0.578859265 +Transforming the Hamiltonian ... done ( 0.0 sec) +Diagonalizing the Hamiltonian ... done ( 0.0 sec) +Back transforming the eigenvectors ... done ( 0.0 sec) +Now organizing SCF variables ... done + ------------------ + INITIAL GUESS DONE ( 0.1 sec) + ------------------ +-------------- +SCF ITERATIONS +-------------- +ITER Energy Delta-E Max-DP RMS-DP [F,P] Damp + *** Starting incremental Fock matrix formation *** + 0 -1.1371803689 0.000000000000 0.00800248 0.00156073 0.0277451 0.7000 + 1 -1.1376074620 -0.000427093036 0.00733753 0.00142548 0.0194169 0.7000 + ***Turning on DIIS*** + 2 -1.1378921888 -0.000284726801 0.01726758 0.00334735 0.0123998 0.0000 + 3 -1.1384268915 -0.000534702786 0.00253904 0.00049918 0.0034195 0.0000 + *** Initiating the SOSCF procedure *** + *** Shutting down DIIS *** + *** Re-Reading the Fockian *** + *** Removing any level shift *** +ITER Energy Delta-E Grad Rot Max-DP RMS-DP + 4 -1.13844475 -0.0000178584 0.000599 0.000599 0.000999 0.000193 + *** Restarting incremental Fock matrix formation *** + 5 -1.13844598 -0.0000012260 0.000027 0.000038 0.000043 0.000008 + **** Energy Check signals convergence **** + ***Rediagonalizing the Fockian in SOSCF/NRSCF*** + + ***************************************************** + * SUCCESS * + * SCF CONVERGED AFTER 6 CYCLES * + ***************************************************** + +Setting up the final grid: + +General Integration Accuracy IntAcc ... 4.670 +Radial Grid Type RadialGrid ... Gauss-Chebyshev +Angular Grid (max. acc.) AngularGrid ... Lebedev-302 +Angular grid pruning method GridPruning ... 3 (G Style) +Weight generation scheme WeightScheme... Becke +Basis function cutoff BFCut ... 1.0000e-11 +Integration weight cutoff WCut ... 1.0000e-14 +Grids for H and He will be reduced by one unit + +# of grid points (after initial pruning) ... 6788 ( 0.0 sec) +# of grid points (after weights+screening) ... 6762 ( 0.0 sec) +nearest neighbour list constructed ... 0.0 sec +Grid point re-assignment to atoms done ... 0.0 sec +Grid point division into batches done ... 0.0 sec +Reduced shell lists constructed in 0.0 sec + +Total number of grid points ... 6762 +Total number of batches ... 106 +Average number of points per batch ... 63 +Average number of grid points per atom ... 3381 +Average number of shells per batch ... 5.62 (93.61%) +Average number of basis functions per batch ... 9.13 (91.31%) +Average number of large shells per batch ... 5.35 (95.17%) +Average number of large basis fcns per batch ... 8.58 (93.96%) +Maximum spatial batch extension ... 13.36, 15.43, 15.43 au +Average spatial batch extension ... 3.44, 3.75, 3.68 au + +Final grid set up in 0.0 sec +Final integration ... done ( 0.0 sec) +Change in XC energy ... -0.000519751 +Integrated number of electrons ... 2.000001506 +Previous integrated no of electrons ... 1.996305491 + +---------------- +TOTAL SCF ENERGY +---------------- + +Total Energy : -1.13896573 Eh -30.99283 eV + +Components: +Nuclear Repulsion : 0.52917720 Eh 14.39964 eV +Electronic Energy : -1.66814293 Eh -45.39248 eV +One Electron Energy: -2.21299244 Eh -60.21859 eV +Two Electron Energy: 0.54484951 Eh 14.82611 eV + +Virial components: +Potential Energy : -2.07822304 Eh -56.55132 eV +Kinetic Energy : 0.93925731 Eh 25.55849 eV +Virial Ratio : 2.21262375 + + +DFT components: +N(Alpha) : 1.000000753145 electrons +N(Beta) : 1.000000753145 electrons +N(Total) : 2.000001506290 electrons +E(X) : -0.581529949948 Eh +E(C) : -0.042684508029 Eh +E(XC) : -0.624214457977 Eh +DFET-embed. en. : 0.000000000000 Eh + +--------------- +SCF CONVERGENCE +--------------- + + Last Energy change ... -1.6201e-09 Tolerance : 1.0000e-08 + Last MAX-Density change ... 8.9368e-06 Tolerance : 1.0000e-07 + Last RMS-Density change ... 1.7428e-06 Tolerance : 5.0000e-09 + Last Orbital Gradient ... 7.0603e-06 Tolerance : 1.0000e-05 + Last Orbital Rotation ... 8.0205e-06 Tolerance : 1.0000e-05 + + **** THE GBW FILE WAS UPDATED (h2_disp_orca.gbw) **** + **** DENSITY FILE WAS UPDATED (h2_disp_orca.scfp) **** + **** ENERGY FILE WAS UPDATED (h2_disp_orca.en.tmp) **** + **** THE GBW FILE WAS UPDATED (h2_disp_orca.gbw) **** + **** DENSITY FILE WAS UPDATED (h2_disp_orca.scfp) **** +---------------- +ORBITAL ENERGIES +---------------- + + NO OCC E(Eh) E(eV) + 0 2.0000 -0.337975 -9.1968 + 1 0.0000 -0.009271 -0.2523 + 2 0.0000 0.358351 9.7512 + 3 0.0000 0.549625 14.9561 + 4 0.0000 1.125742 30.6330 + 5 0.0000 1.125742 30.6330 + 6 0.0000 1.451556 39.4988 + 7 0.0000 1.700412 46.2706 + 8 0.0000 1.700412 46.2706 + 9 0.0000 2.578536 70.1655 + + ******************************** + * MULLIKEN POPULATION ANALYSIS * + ******************************** + +----------------------- +MULLIKEN ATOMIC CHARGES +----------------------- + 0 H : -0.000000 + 1 H : 0.000000 +Sum of atomic charges: -0.0000000 + +-------------------------------- +MULLIKEN REDUCED ORBITAL CHARGES +-------------------------------- + 0 H s : 0.994220 s : 0.994220 + pz : 0.000000 p : 0.005780 + px : 0.005780 + py : 0.000000 + 1 H s : 0.994220 s : 0.994220 + pz : 0.000000 p : 0.005780 + px : 0.005780 + py : 0.000000 + + + ******************************* + * LOEWDIN POPULATION ANALYSIS * + ******************************* + +---------------------- +LOEWDIN ATOMIC CHARGES +---------------------- + 0 H : -0.000000 + 1 H : 0.000000 + +------------------------------- +LOEWDIN REDUCED ORBITAL CHARGES +------------------------------- + 0 H s : 0.983646 s : 0.983646 + pz : 0.000000 p : 0.016354 + px : 0.016354 + py : 0.000000 + 1 H s : 0.983646 s : 0.983646 + pz : 0.000000 p : 0.016354 + px : 0.016354 + py : 0.000000 + + + ***************************** + * MAYER POPULATION ANALYSIS * + ***************************** + + NA - Mulliken gross atomic population + ZA - Total nuclear charge + QA - Mulliken gross atomic charge + VA - Mayer's total valence + BVA - Mayer's bonded valence + FA - Mayer's free valence + + ATOM NA ZA QA VA BVA FA + 0 H 1.0000 1.0000 -0.0000 1.0000 1.0000 -0.0000 + 1 H 1.0000 1.0000 0.0000 1.0000 1.0000 -0.0000 + + Mayer bond orders larger than 0.100000 +B( 0-H , 1-H ) : 1.0000 + + +------------------ +HIRSHFELD ANALYSIS +------------------ + +Total integrated alpha density = 0.998152745 +Total integrated beta density = 0.998152745 + + ATOM CHARGE SPIN + 0 H 0.001847 0.000000 + 1 H 0.001847 0.000000 + + TOTAL 0.003695 0.000000 + +------- +TIMINGS +------- + +Total SCF time: 0 days 0 hours 0 min 0 sec + +Total time .... 0.478 sec +Sum of individual times .... 0.424 sec ( 88.7%) + +Fock matrix formation .... 0.349 sec ( 73.1%) + Split-RI-J .... 0.332 sec ( 95.0% of F) + XC integration .... 0.016 sec ( 4.5% of F) + Basis function eval. .... 0.003 sec ( 20.7% of XC) + Density eval. .... 0.003 sec ( 17.7% of XC) + XC-Functional eval. .... 0.007 sec ( 43.3% of XC) + XC-Potential eval. .... 0.001 sec ( 6.5% of XC) +Diagonalization .... 0.000 sec ( 0.0%) +Density matrix formation .... 0.000 sec ( 0.0%) +Population analysis .... 0.001 sec ( 0.2%) +Initial guess .... 0.056 sec ( 11.7%) +Orbital Transformation .... 0.000 sec ( 0.0%) +Orbital Orthonormalization .... 0.000 sec ( 0.0%) +DIIS solution .... 0.000 sec ( 0.0%) +SOSCF solution .... 0.000 sec ( 0.0%) +Grid generation .... 0.018 sec ( 3.7%) + + +------------------------------------------------------------------------------- + DFT DISPERSION CORRECTION + + DFTD3 V3.1 Rev 1 + USING Becke-Johnson damping +------------------------------------------------------------------------------- +The PBE functional is recognized +Active option DFTDOPT ... 4 + +molecular C6(AA) [au] = 28.931678 + + + DFT-D V3 + parameters + s6 scaling factor : 1.0000 + a1 scaling factor : 0.4289 + s8 scaling factor : 0.7875 + a2 scaling factor : 4.4407 + ad hoc parameters k1-k3 : 16.0000 1.3333 -4.0000 + + Edisp/kcal,au: -0.132247128154 -0.000210749191 + E6 /kcal : -0.104066703 + E8 /kcal : -0.028180425 + % E8 : 21.308912950 + +------------------------- ---------------- +Dispersion correction -0.000210749 +------------------------- ---------------- + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -1.139176477697 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA SCF GRADIENT CALCULATION +------------------------------------------------------------------------------ + +Gradient of the Kohn-Sham DFT energy: +Kohn-Sham wavefunction type ... RKS +Hartree-Fock exchange scaling ... 0.000 +Number of operators ... 1 +Number of atoms ... 2 +Basis set dimensions ... 10 +Integral neglect threshold ... 2.5e-11 +Integral primitive cutoff ... 2.5e-12 + +Nuclear repulsion gradient ... done +One Electron Gradient ... done +Pre-screening matrix ... done +RI-J gradient ... done +Exchange-correlation gradient ... done +Dispersion correction ... done + +------------------ +CARTESIAN GRADIENT +------------------ + + 1 H : -0.079873920 0.000000000 -0.000000000 + 2 H : 0.079873920 -0.000000000 0.000000000 + +Difference to translation invariance: + : -0.0000000000 -0.0000000000 -0.0000000000 + +Norm of the cartesian gradient ... 0.1129587816 +RMS gradient ... 0.0461152295 +MAX gradient ... 0.0798739205 + +------- +TIMINGS +------- + +Total SCF gradient time ... 0.139 sec + +One electron gradient .... 0.000 sec ( 0.1%) +Prescreening matrices .... 0.000 sec ( 0.0%) +RI-J Coulomb gradient .... 0.042 sec ( 30.0%) +XC gradient .... 0.016 sec ( 11.3%) + + *************************************** + * ORCA property calculations * + *************************************** + + --------------------- + Active property flags + --------------------- + (+) Dipole Moment + + +------------------------------------------------------------------------------ + ORCA ELECTRIC PROPERTIES CALCULATION +------------------------------------------------------------------------------ + +Dipole Moment Calculation ... on +Quadrupole Moment Calculation ... off +Polarizability Calculation ... off +GBWName ... h2_disp_orca.gbw +Electron density file ... h2_disp_orca.scfp +The origin for moment calculation is the CENTER OF MASS = ( 0.944863, 0.000000 0.000000) + +------------- +DIPOLE MOMENT +------------- + X Y Z +Electronic contribution: 0.00000 0.00000 -0.00000 +Nuclear contribution : 0.00000 0.00000 0.00000 + ----------------------------------------- +Total Dipole Moment : 0.00000 0.00000 -0.00000 + ----------------------------------------- +Magnitude (a.u.) : 0.00000 +Magnitude (Debye) : 0.00000 + + + +-------------------- +Rotational spectrum +-------------------- + +Rotational constants in cm-1: 0.000000 33.447707 33.447707 +Rotational constants in MHz : 0.000000 1002737.042819 1002737.042819 + + Dipole components along the rotational axes: +x,y,z [a.u.] : 0.000000 0.000000 -0.000000 +x,y,z [Debye]: 0.000000 0.000000 -0.000000 + + + +Timings for individual modules: + +Sum of individual times ... 0.738 sec (= 0.012 min) +GTO integral calculation ... 0.082 sec (= 0.001 min) 11.1 % +SCF iterations ... 0.494 sec (= 0.008 min) 67.0 % +SCF Gradient evaluation ... 0.161 sec (= 0.003 min) 21.9 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 0 minutes 0 seconds 866 msec diff --git a/tests/data/orca/h2_disp_orca.xyz b/tests/data/orca/h2_disp_orca.xyz new file mode 100644 index 000000000..baea2195e --- /dev/null +++ b/tests/data/orca/h2_disp_orca.xyz @@ -0,0 +1,4 @@ +2 +Coordinates from ORCA-job h2_disp_orca + H 0.00000000000000 0.00000000000000 0.00000000000000 + H 1.00000001000000 0.00000000000000 0.00000000000000 diff --git a/tests/data/orca/h2_grad_orca.out b/tests/data/orca/h2_grad_orca.out new file mode 100644 index 000000000..df6836400 --- /dev/null +++ b/tests/data/orca/h2_grad_orca.out @@ -0,0 +1,734 @@ + + ***************** + * O R C A * + ***************** + + --- An Ab Initio, DFT and Semiempirical electronic structure package --- + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship: Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 4.2.1 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM Hessian, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : CASSCF linear response (MC-RPA) + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : AUTO-CI + Lucas Lang : DCDCAS + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, : VdW corrections, initial TS optimization, + C. Bannwarth DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Andreas Klamt, Michael Diedenhofen : otool_cosmo (COSMO solvation model) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, Multilevel, MM, QM/MM, CI optimization + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 4.2.3 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + + +Your calculation utilizes the atom-pairwise dispersion correction +with the Becke-Johnson damping scheme (D3BJ) +Cite in your paper: +S.Grimme, S.Ehrlich, L.Goerigk, J Comput Chem, (2011), 32, 1456–1465 +S.Grimme, J.Antony, S.Ehrlich and H.Krieg, J.Chem.Phys., 132, (2010), 154104 + + +----- Orbital basis set information ----- +Your calculation utilizes the basis: def2-SVP + F. Weigend and R. Ahlrichs, Phys. Chem. Chem. Phys. 7, 3297 (2005). + +----- AuxJ basis set information ----- +Your calculation utilizes the auxiliary basis: def2/J + F. Weigend, Phys. Chem. Chem. Phys. 8, 1057 (2006). + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + + +INFO : the flag for use of LIBINT has been found! + +================================================================================ + INPUT FILE +================================================================================ +NAME = h2_grad_orca.inp +| 1> ! EnGrad PBE D3BJ def2-SVP +| 2> %geom MaxIter 100 end +| 3> %output +| 4> xyzfile=True +| 5> end +| 6> %scf +| 7> maxiter 250 +| 8> end +| 9> %output +| 10> Print[P_Hirshfeld] = 1 +| 11> end +| 12> % maxcore +| 13> 4000 +| 14> *xyz 0 1 +| 15> H 0.00000000 0.00000000 0.00000000 +| 16> H 1.00000000 0.00000000 0.00000000 +| 17> * +| 18> +| 19> ****END OF INPUT**** +================================================================================ + + ******************************* + * Energy+Gradient Calculation * + ******************************* + +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + H 0.000000 0.000000 0.000000 + H 1.000000 0.000000 0.000000 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 H 1.0000 0 1.008 0.000000 0.000000 0.000000 + 1 H 1.0000 0 1.008 1.889726 0.000000 0.000000 + +-------------------------------- +INTERNAL COORDINATES (ANGSTROEM) +-------------------------------- + H 0 0 0 0.000000000000 0.00000000 0.00000000 + H 1 0 0 1.000000000000 0.00000000 0.00000000 + +--------------------------- +INTERNAL COORDINATES (A.U.) +--------------------------- + H 0 0 0 0.000000000000 0.00000000 0.00000000 + H 1 0 0 1.889726133921 0.00000000 0.00000000 + +--------------------- +BASIS SET INFORMATION +--------------------- +There are 1 groups of distinct atoms + + Group 1 Type H : 4s1p contracted to 2s1p pattern {31/1} + +Atom 0H basis set group => 1 +Atom 1H basis set group => 1 +--------------------------------- +AUXILIARY/J BASIS SET INFORMATION +--------------------------------- +There are 1 groups of distinct atoms + + Group 1 Type H : 5s2p1d contracted to 3s1p1d pattern {311/2/1} + +Atom 0H basis set group => 1 +Atom 1H basis set group => 1 +------------------------------------------------------------------------------ + ORCA GTO INTEGRAL CALCULATION + -- RI-GTO INTEGRALS CHOSEN -- +------------------------------------------------------------------------------ + + BASIS SET STATISTICS AND STARTUP INFO + +Gaussian basis set: + # of primitive gaussian shells ... 10 + # of primitive gaussian functions ... 14 + # of contracted shells ... 6 + # of contracted basis functions ... 10 + Highest angular momentum ... 1 + Maximum contraction depth ... 3 +Auxiliary gaussian basis set: + # of primitive gaussian shells ... 16 + # of primitive gaussian functions ... 32 + # of contracted shells ... 10 + # of contracted aux-basis functions ... 22 + Highest angular momentum ... 2 + Maximum contraction depth ... 3 +Ratio of auxiliary to basis functions ... 2.20 +Integral package used ... LIBINT + One Electron integrals ... done + Ordering auxiliary basis shells ... done + Integral threshhold Thresh ... 2.500e-11 + Primitive cut-off TCut ... 2.500e-12 + Pre-screening matrix ... done + Shell pair data ... + Ordering of the shell pairs ... done ( 0.000 sec) 21 of 21 pairs + Determination of significant pairs ... done ( 0.000 sec) + Creation of shell pair data ... done ( 0.000 sec) + Storage of shell pair data ... done ( 0.000 sec) + Shell pair data done in ( 0.000 sec) + Computing two index integrals ... done + Cholesky decomposition of the V-matrix ... done + + +Timings: + Total evaluation time ... 0.060 sec ( 0.001 min) + One electron matrix time ... 0.002 sec ( 0.000 min) = 3.1% + Schwartz matrix evaluation time ... 0.052 sec ( 0.001 min) = 85.5% + Two index repulsion integral time ... 0.000 sec ( 0.000 min) = 0.1% + Cholesky decomposition of V ... 0.000 sec ( 0.000 min) = 0.3% + Three index repulsion integral time ... 0.000 sec ( 0.000 min) = 0.0% + +------------------------------------------------------------------------------- + ORCA SCF +------------------------------------------------------------------------------- + +------------ +SCF SETTINGS +------------ +Hamiltonian: + Density Functional Method .... DFT(GTOs) + Exchange Functional Exchange .... PBE + PBE kappa parameter XKappa .... 0.804000 + PBE mue parameter XMuePBE .... 0.219520 + Correlation Functional Correlation .... PBE + PBE beta parameter CBetaPBE .... 0.066725 + LDA part of GGA corr. LDAOpt .... PW91-LDA + Gradients option PostSCFGGA .... off + Density functional embedding theory .... OFF + NL short-range parameter .... 6.400000 + RI-approximation to the Coulomb term is turned on + Number of auxiliary basis functions .... 22 + + +General Settings: + Integral files IntName .... h2_grad_orca + Hartree-Fock type HFTyp .... RHF + Total Charge Charge .... 0 + Multiplicity Mult .... 1 + Number of Electrons NEL .... 2 + Basis Dimension Dim .... 10 + Nuclear Repulsion ENuc .... 0.5291772083 Eh + +Convergence Acceleration: + DIIS CNVDIIS .... on + Start iteration DIISMaxIt .... 12 + Startup error DIISStart .... 0.200000 + # of expansion vecs DIISMaxEq .... 5 + Bias factor DIISBfac .... 1.050 + Max. coefficient DIISMaxC .... 10.000 + Newton-Raphson CNVNR .... off + SOSCF CNVSOSCF .... on + Start iteration SOSCFMaxIt .... 150 + Startup grad/error SOSCFStart .... 0.003300 + Level Shifting CNVShift .... on + Level shift para. LevelShift .... 0.2500 + Turn off err/grad. ShiftErr .... 0.0010 + Zerner damping CNVZerner .... off + Static damping CNVDamp .... on + Fraction old density DampFac .... 0.7000 + Max. Damping (<1) DampMax .... 0.9800 + Min. Damping (>=0) DampMin .... 0.0000 + Turn off err/grad. DampErr .... 0.1000 + Fernandez-Rico CNVRico .... off + +SCF Procedure: + Maximum # iterations MaxIter .... 250 + SCF integral mode SCFMode .... Direct + Integral package .... LIBINT + Reset frequency DirectResetFreq .... 20 + Integral Threshold Thresh .... 2.500e-11 Eh + Primitive CutOff TCut .... 2.500e-12 Eh + +Convergence Tolerance: + Convergence Check Mode ConvCheckMode .... Total+1el-Energy + Convergence forced ConvForced .... 0 + Energy Change TolE .... 1.000e-08 Eh + 1-El. energy change .... 1.000e-05 Eh + Orbital Gradient TolG .... 1.000e-05 + Orbital Rotation angle TolX .... 1.000e-05 + DIIS Error TolErr .... 5.000e-07 + + +Diagonalization of the overlap matrix: +Smallest eigenvalue ... 1.144e-01 +Time for diagonalization ... 0.000 sec +Threshold for overlap eigenvalues ... 1.000e-08 +Number of eigenvalues below threshold ... 0 +Time for construction of square roots ... 0.000 sec +Total time needed ... 0.000 sec + +------------------- +DFT GRID GENERATION +------------------- + +General Integration Accuracy IntAcc ... 4.340 +Radial Grid Type RadialGrid ... Gauss-Chebyshev +Angular Grid (max. acc.) AngularGrid ... Lebedev-110 +Angular grid pruning method GridPruning ... 3 (G Style) +Weight generation scheme WeightScheme... Becke +Basis function cutoff BFCut ... 1.0000e-11 +Integration weight cutoff WCut ... 1.0000e-14 +Grids for H and He will be reduced by one unit + +# of grid points (after initial pruning) ... 1588 ( 0.0 sec) +# of grid points (after weights+screening) ... 1566 ( 0.0 sec) +nearest neighbour list constructed ... 0.0 sec +Grid point re-assignment to atoms done ... 0.0 sec +Grid point division into batches done ... 0.0 sec +Reduced shell lists constructed in 0.0 sec + +Total number of grid points ... 1566 +Total number of batches ... 26 +Average number of points per batch ... 60 +Average number of grid points per atom ... 783 +Average number of shells per batch ... 5.78 (96.30%) +Average number of basis functions per batch ... 9.63 (96.30%) +Average number of large shells per batch ... 5.74 (99.36%) +Average number of large basis fcns per batch ... 9.52 (98.85%) +Maximum spatial batch extension ... 15.26, 21.59, 21.59 au +Average spatial batch extension ... 4.63, 8.28, 8.44 au + +Time for grid setup = 0.002 sec + +------------------------------ +INITIAL GUESS: MODEL POTENTIAL +------------------------------ +Loading Hartree-Fock densities ... done +Calculating cut-offs ... done +Setting up the integral package ... done +Initializing the effective Hamiltonian ... done +Starting the Coulomb interaction ... done ( 0.0 sec) +Reading the grid ... done +Mapping shells ... done +Starting the XC term evaluation ... done ( 0.0 sec) + promolecular density results + # of electrons = 1.995342477 + EX = -0.539655113 + EC = -0.039204154 + EX+EC = -0.578859266 +Transforming the Hamiltonian ... done ( 0.0 sec) +Diagonalizing the Hamiltonian ... done ( 0.0 sec) +Back transforming the eigenvectors ... done ( 0.0 sec) +Now organizing SCF variables ... done + ------------------ + INITIAL GUESS DONE ( 0.1 sec) + ------------------ +-------------- +SCF ITERATIONS +-------------- +ITER Energy Delta-E Max-DP RMS-DP [F,P] Damp + *** Starting incremental Fock matrix formation *** + 0 -1.1371803703 0.000000000000 0.00800249 0.00156073 0.0277451 0.7000 + 1 -1.1376074634 -0.000427093056 0.00733753 0.00142548 0.0194169 0.7000 + ***Turning on DIIS*** + 2 -1.1378921902 -0.000284726814 0.01726758 0.00334735 0.0123998 0.0000 + 3 -1.1384268930 -0.000534702810 0.00253904 0.00049918 0.0034195 0.0000 + *** Initiating the SOSCF procedure *** + *** Shutting down DIIS *** + *** Re-Reading the Fockian *** + *** Removing any level shift *** +ITER Energy Delta-E Grad Rot Max-DP RMS-DP + 4 -1.13844475 -0.0000178584 0.000599 0.000599 0.000999 0.000193 + *** Restarting incremental Fock matrix formation *** + 5 -1.13844598 -0.0000012260 0.000027 0.000038 0.000043 0.000008 + **** Energy Check signals convergence **** + ***Rediagonalizing the Fockian in SOSCF/NRSCF*** + + ***************************************************** + * SUCCESS * + * SCF CONVERGED AFTER 6 CYCLES * + ***************************************************** + +Setting up the final grid: + +General Integration Accuracy IntAcc ... 4.670 +Radial Grid Type RadialGrid ... Gauss-Chebyshev +Angular Grid (max. acc.) AngularGrid ... Lebedev-302 +Angular grid pruning method GridPruning ... 3 (G Style) +Weight generation scheme WeightScheme... Becke +Basis function cutoff BFCut ... 1.0000e-11 +Integration weight cutoff WCut ... 1.0000e-14 +Grids for H and He will be reduced by one unit + +# of grid points (after initial pruning) ... 6788 ( 0.0 sec) +# of grid points (after weights+screening) ... 6762 ( 0.0 sec) +nearest neighbour list constructed ... 0.0 sec +Grid point re-assignment to atoms done ... 0.0 sec +Grid point division into batches done ... 0.0 sec +Reduced shell lists constructed in 0.0 sec + +Total number of grid points ... 6762 +Total number of batches ... 106 +Average number of points per batch ... 63 +Average number of grid points per atom ... 3381 +Average number of shells per batch ... 5.62 (93.61%) +Average number of basis functions per batch ... 9.13 (91.31%) +Average number of large shells per batch ... 5.35 (95.17%) +Average number of large basis fcns per batch ... 8.58 (93.96%) +Maximum spatial batch extension ... 13.36, 15.43, 15.43 au +Average spatial batch extension ... 3.44, 3.76, 3.67 au + +Final grid set up in 0.0 sec +Final integration ... done ( 0.0 sec) +Change in XC energy ... -0.000519751 +Integrated number of electrons ... 2.000001506 +Previous integrated no of electrons ... 1.996305491 + +---------------- +TOTAL SCF ENERGY +---------------- + +Total Energy : -1.13896573 Eh -30.99283 eV + +Components: +Nuclear Repulsion : 0.52917721 Eh 14.39964 eV +Electronic Energy : -1.66814294 Eh -45.39248 eV +One Electron Energy: -2.21299245 Eh -60.21859 eV +Two Electron Energy: 0.54484951 Eh 14.82611 eV + +Virial components: +Potential Energy : -2.07822305 Eh -56.55132 eV +Kinetic Energy : 0.93925732 Eh 25.55849 eV +Virial Ratio : 2.21262375 + + +DFT components: +N(Alpha) : 1.000000753145 electrons +N(Beta) : 1.000000753145 electrons +N(Total) : 2.000001506290 electrons +E(X) : -0.581529952006 Eh +E(C) : -0.042684508121 Eh +E(XC) : -0.624214460127 Eh +DFET-embed. en. : 0.000000000000 Eh + +--------------- +SCF CONVERGENCE +--------------- + + Last Energy change ... -1.6201e-09 Tolerance : 1.0000e-08 + Last MAX-Density change ... 8.9368e-06 Tolerance : 1.0000e-07 + Last RMS-Density change ... 1.7428e-06 Tolerance : 5.0000e-09 + Last Orbital Gradient ... 7.0603e-06 Tolerance : 1.0000e-05 + Last Orbital Rotation ... 8.0205e-06 Tolerance : 1.0000e-05 + + **** THE GBW FILE WAS UPDATED (h2_grad_orca.gbw) **** + **** DENSITY FILE WAS UPDATED (h2_grad_orca.scfp) **** + **** ENERGY FILE WAS UPDATED (h2_grad_orca.en.tmp) **** + **** THE GBW FILE WAS UPDATED (h2_grad_orca.gbw) **** + **** DENSITY FILE WAS UPDATED (h2_grad_orca.scfp) **** +---------------- +ORBITAL ENERGIES +---------------- + + NO OCC E(Eh) E(eV) + 0 2.0000 -0.337975 -9.1968 + 1 0.0000 -0.009271 -0.2523 + 2 0.0000 0.358351 9.7512 + 3 0.0000 0.549625 14.9561 + 4 0.0000 1.125742 30.6330 + 5 0.0000 1.125742 30.6330 + 6 0.0000 1.451556 39.4988 + 7 0.0000 1.700412 46.2706 + 8 0.0000 1.700412 46.2706 + 9 0.0000 2.578536 70.1655 + + ******************************** + * MULLIKEN POPULATION ANALYSIS * + ******************************** + +----------------------- +MULLIKEN ATOMIC CHARGES +----------------------- + 0 H : -0.000000 + 1 H : 0.000000 +Sum of atomic charges: 0.0000000 + +-------------------------------- +MULLIKEN REDUCED ORBITAL CHARGES +-------------------------------- + 0 H s : 0.994220 s : 0.994220 + pz : 0.000000 p : 0.005780 + px : 0.005780 + py : 0.000000 + 1 H s : 0.994220 s : 0.994220 + pz : 0.000000 p : 0.005780 + px : 0.005780 + py : 0.000000 + + + ******************************* + * LOEWDIN POPULATION ANALYSIS * + ******************************* + +---------------------- +LOEWDIN ATOMIC CHARGES +---------------------- + 0 H : -0.000000 + 1 H : 0.000000 + +------------------------------- +LOEWDIN REDUCED ORBITAL CHARGES +------------------------------- + 0 H s : 0.983646 s : 0.983646 + pz : 0.000000 p : 0.016354 + px : 0.016354 + py : 0.000000 + 1 H s : 0.983646 s : 0.983646 + pz : 0.000000 p : 0.016354 + px : 0.016354 + py : 0.000000 + + + ***************************** + * MAYER POPULATION ANALYSIS * + ***************************** + + NA - Mulliken gross atomic population + ZA - Total nuclear charge + QA - Mulliken gross atomic charge + VA - Mayer's total valence + BVA - Mayer's bonded valence + FA - Mayer's free valence + + ATOM NA ZA QA VA BVA FA + 0 H 1.0000 1.0000 -0.0000 1.0000 1.0000 0.0000 + 1 H 1.0000 1.0000 0.0000 1.0000 1.0000 0.0000 + + Mayer bond orders larger than 0.100000 +B( 0-H , 1-H ) : 1.0000 + + +------------------ +HIRSHFELD ANALYSIS +------------------ + +Total integrated alpha density = 0.998152745 +Total integrated beta density = 0.998152745 + + ATOM CHARGE SPIN + 0 H 0.001847 0.000000 + 1 H 0.001847 0.000000 + + TOTAL 0.003695 0.000000 + +------- +TIMINGS +------- + +Total SCF time: 0 days 0 hours 0 min 0 sec + +Total time .... 0.482 sec +Sum of individual times .... 0.432 sec ( 89.6%) + +Fock matrix formation .... 0.357 sec ( 74.1%) + Split-RI-J .... 0.338 sec ( 94.7% of F) + XC integration .... 0.017 sec ( 4.8% of F) + Basis function eval. .... 0.004 sec ( 21.0% of XC) + Density eval. .... 0.003 sec ( 16.9% of XC) + XC-Functional eval. .... 0.007 sec ( 43.1% of XC) + XC-Potential eval. .... 0.001 sec ( 6.4% of XC) +Diagonalization .... 0.000 sec ( 0.0%) +Density matrix formation .... 0.000 sec ( 0.0%) +Population analysis .... 0.001 sec ( 0.2%) +Initial guess .... 0.055 sec ( 11.4%) +Orbital Transformation .... 0.000 sec ( 0.0%) +Orbital Orthonormalization .... 0.000 sec ( 0.0%) +DIIS solution .... 0.000 sec ( 0.0%) +SOSCF solution .... 0.000 sec ( 0.0%) +Grid generation .... 0.019 sec ( 3.8%) + + +------------------------------------------------------------------------------- + DFT DISPERSION CORRECTION + + DFTD3 V3.1 Rev 1 + USING Becke-Johnson damping +------------------------------------------------------------------------------- +The PBE functional is recognized +Active option DFTDOPT ... 4 + +molecular C6(AA) [au] = 28.931678 + + + DFT-D V3 + parameters + s6 scaling factor : 1.0000 + a1 scaling factor : 0.4289 + s8 scaling factor : 0.7875 + a2 scaling factor : 4.4407 + ad hoc parameters k1-k3 : 16.0000 1.3333 -4.0000 + + Edisp/kcal,au: -0.132247127680 -0.000210749190 + E6 /kcal : -0.104066702 + E8 /kcal : -0.028180425 + % E8 : 21.308912949 + +------------------------- ---------------- +Dispersion correction -0.000210749 +------------------------- ---------------- + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -1.139176479197 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA SCF GRADIENT CALCULATION +------------------------------------------------------------------------------ + +Gradient of the Kohn-Sham DFT energy: +Kohn-Sham wavefunction type ... RKS +Hartree-Fock exchange scaling ... 0.000 +Number of operators ... 1 +Number of atoms ... 2 +Basis set dimensions ... 10 +Integral neglect threshold ... 2.5e-11 +Integral primitive cutoff ... 2.5e-12 + +Nuclear repulsion gradient ... done +One Electron Gradient ... done +Pre-screening matrix ... done +RI-J gradient ... done +Exchange-correlation gradient ... done +Dispersion correction ... done + +------------------ +CARTESIAN GRADIENT +------------------ + + 1 H : -0.079873919 0.000000000 -0.000000000 + 2 H : 0.079873919 -0.000000000 0.000000000 + +Difference to translation invariance: + : -0.0000000000 -0.0000000000 0.0000000000 + +Norm of the cartesian gradient ... 0.1129587797 +RMS gradient ... 0.0461152287 +MAX gradient ... 0.0798739191 + +------- +TIMINGS +------- + +Total SCF gradient time ... 0.141 sec + +One electron gradient .... 0.000 sec ( 0.1%) +Prescreening matrices .... 0.000 sec ( 0.0%) +RI-J Coulomb gradient .... 0.043 sec ( 30.5%) +XC gradient .... 0.016 sec ( 11.4%) + + *************************************** + * ORCA property calculations * + *************************************** + + --------------------- + Active property flags + --------------------- + (+) Dipole Moment + + +------------------------------------------------------------------------------ + ORCA ELECTRIC PROPERTIES CALCULATION +------------------------------------------------------------------------------ + +Dipole Moment Calculation ... on +Quadrupole Moment Calculation ... off +Polarizability Calculation ... off +GBWName ... h2_grad_orca.gbw +Electron density file ... h2_grad_orca.scfp +The origin for moment calculation is the CENTER OF MASS = ( 0.944863, 0.000000 0.000000) + +------------- +DIPOLE MOMENT +------------- + X Y Z +Electronic contribution: 0.00000 -0.00000 -0.00000 +Nuclear contribution : 0.00000 0.00000 0.00000 + ----------------------------------------- +Total Dipole Moment : 0.00000 -0.00000 -0.00000 + ----------------------------------------- +Magnitude (a.u.) : 0.00000 +Magnitude (Debye) : 0.00000 + + + +-------------------- +Rotational spectrum +-------------------- + +Rotational constants in cm-1: 0.000000 33.447708 33.447708 +Rotational constants in MHz : 0.000000 1002737.062874 1002737.062874 + + Dipole components along the rotational axes: +x,y,z [a.u.] : 0.000000 -0.000000 -0.000000 +x,y,z [Debye]: 0.000000 -0.000000 -0.000000 + + + +Timings for individual modules: + +Sum of individual times ... 0.742 sec (= 0.012 min) +GTO integral calculation ... 0.078 sec (= 0.001 min) 10.5 % +SCF iterations ... 0.499 sec (= 0.008 min) 67.2 % +SCF Gradient evaluation ... 0.165 sec (= 0.003 min) 22.3 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 0 minutes 0 seconds 907 msec diff --git a/tests/data/orca/h2_grad_orca.xyz b/tests/data/orca/h2_grad_orca.xyz new file mode 100644 index 000000000..497170bda --- /dev/null +++ b/tests/data/orca/h2_grad_orca.xyz @@ -0,0 +1,4 @@ +2 +Coordinates from ORCA-job h2_grad_orca + H 0.00000000000000 0.00000000000000 0.00000000000000 + H 1.00000000000000 0.00000000000000 0.00000000000000 diff --git a/tests/data/xtb/gradient b/tests/data/xtb/gradient new file mode 100644 index 000000000..95b0b7337 --- /dev/null +++ b/tests/data/xtb/gradient @@ -0,0 +1,13 @@ +$gradient +cycle = 1 SCF energy = -4.17404780397 |dE/dxyz| = 0.027866 +3.63797523123375 -1.13138130908142 -0.00032759661848 C +5.72449332438353 -1.13197561185651 0.00028950521969 H + 2.94133258016711 0.22776472016180 -1.42078243039077 H + 2.94175598539510 -0.58111835182372 1.88747566982948 H +2.94180792167968 -3.04156357656436 -0.46665514803992 H +-1.7221823521705E-05 7.9930724499610E-05 -1.1737079840097E-04 + 1.4116296505865E-02 -4.0359524399270E-05 3.9719638516747E-05 +-4.7199424681741E-03 9.0086220034949E-03 -9.4114548523723E-03 +-4.6956970257351E-03 3.6356853660431E-03 1.2558467871909E-02 + -4.6834351884340E-03 -1.2683878569638E-02 -3.0693618596526E-03 +$end diff --git a/tests/data/xtb/h2_disp_sp_xtb.out b/tests/data/xtb/h2_disp_sp_xtb.out new file mode 100644 index 000000000..a04ebb5b2 --- /dev/null +++ b/tests/data/xtb/h2_disp_sp_xtb.out @@ -0,0 +1,225 @@ + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + ----------------------------------------------------------- + + * xtb version 6.2.3 (830e466) compiled by 'ehlert@majestix' on 2020-03-16 + + 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: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + + 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 + + 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 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + with help from (in alphabetical order) + C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher, M. Checinski, + S. Dohm, S. Ehlert, S. Ehrlich, F. März, H. Neugebauer, J. Pisarek, + P. Pracht, P. Shushkov, and S. Spicher. + + * started run on 2020/07/10 at 11:58:33.648 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/tom/.local/bin/xtb h2_disp_sp_xtb.xyz --chrg 0 + coordinate file : h2_disp_sp_xtb.xyz + omp threads : 4 + number of atoms : 2 + number of electrons : 2 + charge : 0 + spin : 0.0 + first test random number : 0.67842890260110 + + +molecular fragmentation (1/2 indicates fragments): +12 +# atoms in fragment 1/2: 1 1 + fragment masses (1/2) : 1.01 1.01 +CMA distance (Bohr) : 1.890 +constraining FC (au) : 0.0500 +######################################################################## +[WARNING] Please study the warnings concerning your input carefully +-2- prog_main: XTBPATH is not set, using XTBHOME instead +-1- prog_main: XTBHOME is not set, using HOME instead +######################################################################## + ------------------------------------------------- + | G F N 2 - x T B | + | Geometry, Frequencies, Noncovalent interactions | + | JCTC 2019 parametrisation | + ------------------------------------------------- + k(s) : 1.8500 + k(p) : 2.2300 + k(d) : 2.2300 + k(f) : 2.0000 + kEN (H0ij) : -2.0000 + D4 a1 : 0.5200 + D4 a2 : 5.0000 + D4 s6 : 1.0000 + D4 s8 : 2.7000 + D4 s9 : 5.0000 + alphaj : 2.0000 + + Z AO/shell Hii/eV exponent + 1 Wed Apr 25 08:07:45 CEST 2018 EN: 2.200 GM2: 0.406 GM3: 0.0800 RAES: 1.40 + 1s -10.707211 1.230000 + + ------------------------------------------------- + | Self-Consistent Charge Iterations | + ------------------------------------------------- + + ................................................... + : SETUP : + :.................................................: + : # basis functions 2 : + : # atomic orbitals 2 : + : # shells 2 : + : # electrons 2 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : 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 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -0.9763805 -0.976380E+00 0.539E+00 11.55 0.0 T + 2 -0.9763805 0.111022E-15 0.323E+00 10.60 1.0 T + 3 -0.9763805 -0.333067E-15 0.194E-04 9.18 364.7 T + 4 -0.9763805 0.333067E-15 0.838E-14 9.18 100000.0 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.4332513 -11.7894 (HOMO) + 2 -0.0957936 -2.6067 (LUMO) + ------------------------------------------------------------- + HL-Gap 0.3374576 Eh 9.1827 eV + Fermi-level -0.2645225 Eh -7.1980 eV + + SCC (total) 0 d, 0 h, 0 min, 0.001 sec + SCC setup ... 0 min, 0.000 sec ( 10.575%) + Dispersion ... 0 min, 0.000 sec ( 2.965%) + integral evaluation ... 0 min, 0.000 sec ( 4.425%) + zeroth order Hamiltonian ... 0 min, 0.000 sec ( 2.035%) + iterations ... 0 min, 0.000 sec ( 58.628%) + molecular gradient ... 0 min, 0.000 sec ( 11.504%) + printout ... 0 min, 0.000 sec ( 5.752%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -0.966521858391 Eh :: + :: gradient norm 0.089193551151 Eh/a0 :: + :: HOMO-LUMO gap 9.182689883989 eV :: + ::.................................................:: + :: SCC energy -0.976380476204 Eh :: + :: -> isotropic ES 0.000000000000 Eh :: + :: -> anisotropic ES 0.010484358440 Eh :: + :: -> anisotropic XC 0.011179676128 Eh :: + :: -> dispersion -0.000130282514 Eh :: + :: repulsion energy 0.009858617812 Eh :: + :: add. restraining 0.000000000000 Eh :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ------------------------------------------------- + | Property Printout | + ------------------------------------------------- + + * Orbital Energies and Occupations + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.4332513 -11.7894 (HOMO) + 2 -0.0957936 -2.6067 (LUMO) + ------------------------------------------------------------- + HL-Gap 0.3374576 Eh 9.1827 eV + Fermi-level -0.2645225 Eh -7.1980 eV + + # Z covCN q C6AA α(0) + 1 1 H 0.033 -0.000 7.614 5.045 + 2 1 H 0.033 -0.000 7.614 5.045 + + Mol. C6AA /au·bohr⁶ : 30.454152 + Mol. C8AA /au·bohr⁸ : 368.140452 + Mol. α(0) /au : 10.089605 + + +Wiberg/Mayer (AO) data. +largest (>0.10) Wiberg bond orders for each atom + total WBO WBO to atom ... + 1 H 1.000 H 2 1.000 + 2 H 1.000 H 1 1.000 + +molecular dipole: + x y z tot (Debye) + q only: -0.000 0.000 0.000 + full: -0.000 0.000 0.000 0.000 +molecular quadrupole (traceless): + xx xy yy xz yz zz + q only: -0.000 0.000 0.000 0.000 0.000 0.000 + q+dip: 1.192 0.000 -0.596 0.000 0.000 -0.596 + full: 0.480 0.000 -0.240 0.000 0.000 -0.240 + + + ------------------------------------------------- + | TOTAL ENERGY -0.966521858391 Eh | + | GRADIENT NORM 0.089193551151 Eh/α | + | HOMO-LUMO GAP 9.182689883989 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2020/07/10 at 11:58:33.672 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.023 sec + * cpu-time: 0 d, 0 h, 0 min, 0.073 sec + * ratio c/w: 3.118 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.001 sec + * cpu-time: 0 d, 0 h, 0 min, 0.002 sec + * ratio c/w: 4.010 speedup + diff --git a/tests/data/xtb/h2_disp_sp_xtb.xyz b/tests/data/xtb/h2_disp_sp_xtb.xyz new file mode 100644 index 000000000..1491b13f1 --- /dev/null +++ b/tests/data/xtb/h2_disp_sp_xtb.xyz @@ -0,0 +1,4 @@ +2 + +H 0.00000 0.00000 0.00000 +H 1.00001 0.00000 0.00000 diff --git a/tests/data/xtb/h2_grad_xtb.out b/tests/data/xtb/h2_grad_xtb.out new file mode 100644 index 000000000..1324856b1 --- /dev/null +++ b/tests/data/xtb/h2_grad_xtb.out @@ -0,0 +1,225 @@ + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + ----------------------------------------------------------- + + * xtb version 6.2.3 (830e466) compiled by 'ehlert@majestix' on 2020-03-16 + + 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: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + + 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 + + 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 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + with help from (in alphabetical order) + C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher, M. Checinski, + S. Dohm, S. Ehlert, S. Ehrlich, F. März, H. Neugebauer, J. Pisarek, + P. Pracht, P. Shushkov, and S. Spicher. + + * started run on 2020/07/10 at 11:57:51.850 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/tom/.local/bin/xtb h2_grad_xtb.xyz --chrg 0 --grad + coordinate file : h2_grad_xtb.xyz + omp threads : 1 + number of atoms : 2 + number of electrons : 2 + charge : 0 + spin : 0.0 + first test random number : 0.28874914839104 + + +molecular fragmentation (1/2 indicates fragments): +12 +# atoms in fragment 1/2: 1 1 + fragment masses (1/2) : 1.01 1.01 +CMA distance (Bohr) : 1.890 +constraining FC (au) : 0.0500 +######################################################################## +[WARNING] Please study the warnings concerning your input carefully +-2- prog_main: XTBPATH is not set, using XTBHOME instead +-1- prog_main: XTBHOME is not set, using HOME instead +######################################################################## + ------------------------------------------------- + | G F N 2 - x T B | + | Geometry, Frequencies, Noncovalent interactions | + | JCTC 2019 parametrisation | + ------------------------------------------------- + k(s) : 1.8500 + k(p) : 2.2300 + k(d) : 2.2300 + k(f) : 2.0000 + kEN (H0ij) : -2.0000 + D4 a1 : 0.5200 + D4 a2 : 5.0000 + D4 s6 : 1.0000 + D4 s8 : 2.7000 + D4 s9 : 5.0000 + alphaj : 2.0000 + + Z AO/shell Hii/eV exponent + 1 Wed Apr 25 08:07:45 CEST 2018 EN: 2.200 GM2: 0.406 GM3: 0.0800 RAES: 1.40 + 1s -10.707211 1.230000 + + ------------------------------------------------- + | Self-Consistent Charge Iterations | + ------------------------------------------------- + + ................................................... + : SETUP : + :.................................................: + : # basis functions 2 : + : # atomic orbitals 2 : + : # shells 2 : + : # electrons 2 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : 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 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -0.9763822 -0.976382E+00 0.539E+00 11.55 0.0 T + 2 -0.9763822 0.000000E+00 0.323E+00 10.60 1.0 T + 3 -0.9763822 -0.111022E-15 0.194E-04 9.18 364.7 T + 4 -0.9763822 0.111022E-15 0.883E-14 9.18 100000.0 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.4332524 -11.7894 (HOMO) + 2 -0.0957872 -2.6065 (LUMO) + ------------------------------------------------------------- + HL-Gap 0.3374652 Eh 9.1829 eV + Fermi-level -0.2645198 Eh -7.1979 eV + + SCC (total) 0 d, 0 h, 0 min, 0.000 sec + SCC setup ... 0 min, 0.000 sec ( 11.106%) + Dispersion ... 0 min, 0.000 sec ( 2.404%) + integral evaluation ... 0 min, 0.000 sec ( 5.625%) + zeroth order Hamiltonian ... 0 min, 0.000 sec ( 2.019%) + iterations ... 0 min, 0.000 sec ( 58.894%) + molecular gradient ... 0 min, 0.000 sec ( 9.904%) + printout ... 0 min, 0.000 sec ( 6.058%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -0.966523050218 Eh :: + :: gradient norm 0.089191857169 Eh/a0 :: + :: HOMO-LUMO gap 9.182896506924 eV :: + ::.................................................:: + :: SCC energy -0.976382179047 Eh :: + :: -> isotropic ES 0.000000000000 Eh :: + :: -> anisotropic ES 0.010484355527 Eh :: + :: -> anisotropic XC 0.011179625009 Eh :: + :: -> dispersion -0.000130282477 Eh :: + :: repulsion energy 0.009859128829 Eh :: + :: add. restraining 0.000000000000 Eh :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ------------------------------------------------- + | Property Printout | + ------------------------------------------------- + + * Orbital Energies and Occupations + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.4332524 -11.7894 (HOMO) + 2 -0.0957872 -2.6065 (LUMO) + ------------------------------------------------------------- + HL-Gap 0.3374652 Eh 9.1829 eV + Fermi-level -0.2645198 Eh -7.1979 eV + + # Z covCN q C6AA α(0) + 1 1 H 0.033 -0.000 7.614 5.045 + 2 1 H 0.033 0.000 7.614 5.045 + + Mol. C6AA /au·bohr⁶ : 30.454143 + Mol. C8AA /au·bohr⁸ : 368.140340 + Mol. α(0) /au : 10.089603 + + +Wiberg/Mayer (AO) data. +largest (>0.10) Wiberg bond orders for each atom + total WBO WBO to atom ... + 1 H 1.000 H 2 1.000 + 2 H 1.000 H 1 1.000 + +molecular dipole: + x y z tot (Debye) + q only: 0.000 0.000 0.000 + full: 0.000 0.000 0.000 0.000 +molecular quadrupole (traceless): + xx xy yy xz yz zz + q only: 0.000 0.000 -0.000 0.000 0.000 -0.000 + q+dip: 1.192 0.000 -0.596 0.000 0.000 -0.596 + full: 0.480 0.000 -0.240 0.000 0.000 -0.240 + + + ------------------------------------------------- + | TOTAL ENERGY -0.966523050218 Eh | + | GRADIENT NORM 0.089191857169 Eh/α | + | HOMO-LUMO GAP 9.182896506924 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2020/07/10 at 11:57:51.857 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.007 sec + * cpu-time: 0 d, 0 h, 0 min, 0.007 sec + * ratio c/w: 0.980 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.001 sec + * cpu-time: 0 d, 0 h, 0 min, 0.001 sec + * ratio c/w: 0.998 speedup + diff --git a/tests/data/xtb/h2_grad_xtb.xyz b/tests/data/xtb/h2_grad_xtb.xyz new file mode 100644 index 000000000..228ed4e0e --- /dev/null +++ b/tests/data/xtb/h2_grad_xtb.xyz @@ -0,0 +1,4 @@ +2 + +H 0.00000 0.00000 0.00000 +H 1.00000 0.00000 0.00000 diff --git a/tests/data/xtb/h2_grad_xtb_xtb.grad b/tests/data/xtb/h2_grad_xtb_xtb.grad new file mode 100644 index 000000000..19b6fd689 --- /dev/null +++ b/tests/data/xtb/h2_grad_xtb_xtb.grad @@ -0,0 +1,2 @@ +-0.06306817 0.00000000 0.00000000 + 0.06306817 0.00000000 0.00000000 diff --git a/tests/data/xtb/h2_sp_xtb.out b/tests/data/xtb/h2_sp_xtb.out new file mode 100644 index 000000000..bd98639b9 --- /dev/null +++ b/tests/data/xtb/h2_sp_xtb.out @@ -0,0 +1,225 @@ + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + ----------------------------------------------------------- + + * xtb version 6.2.3 (830e466) compiled by 'ehlert@majestix' on 2020-03-16 + + 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: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + + 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 + + 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 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + with help from (in alphabetical order) + C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher, M. Checinski, + S. Dohm, S. Ehlert, S. Ehrlich, F. März, H. Neugebauer, J. Pisarek, + P. Pracht, P. Shushkov, and S. Spicher. + + * started run on 2020/07/10 at 11:57:51.789 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/tom/.local/bin/xtb h2_sp_xtb.xyz --chrg 0 + coordinate file : h2_sp_xtb.xyz + omp threads : 4 + number of atoms : 2 + number of electrons : 2 + charge : 0 + spin : 0.0 + first test random number : 0.61746211279383 + + +molecular fragmentation (1/2 indicates fragments): +12 +# atoms in fragment 1/2: 1 1 + fragment masses (1/2) : 1.01 1.01 +CMA distance (Bohr) : 1.890 +constraining FC (au) : 0.0500 +######################################################################## +[WARNING] Please study the warnings concerning your input carefully +-2- prog_main: XTBPATH is not set, using XTBHOME instead +-1- prog_main: XTBHOME is not set, using HOME instead +######################################################################## + ------------------------------------------------- + | G F N 2 - x T B | + | Geometry, Frequencies, Noncovalent interactions | + | JCTC 2019 parametrisation | + ------------------------------------------------- + k(s) : 1.8500 + k(p) : 2.2300 + k(d) : 2.2300 + k(f) : 2.0000 + kEN (H0ij) : -2.0000 + D4 a1 : 0.5200 + D4 a2 : 5.0000 + D4 s6 : 1.0000 + D4 s8 : 2.7000 + D4 s9 : 5.0000 + alphaj : 2.0000 + + Z AO/shell Hii/eV exponent + 1 Wed Apr 25 08:07:45 CEST 2018 EN: 2.200 GM2: 0.406 GM3: 0.0800 RAES: 1.40 + 1s -10.707211 1.230000 + + ------------------------------------------------- + | Self-Consistent Charge Iterations | + ------------------------------------------------- + + ................................................... + : SETUP : + :.................................................: + : # basis functions 2 : + : # atomic orbitals 2 : + : # shells 2 : + : # electrons 2 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : 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 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -0.9763822 -0.976382E+00 0.539E+00 11.55 0.0 T + 2 -0.9763822 0.000000E+00 0.323E+00 10.60 1.0 T + 3 -0.9763822 -0.111022E-15 0.194E-04 9.18 364.7 T + 4 -0.9763822 0.111022E-15 0.883E-14 9.18 100000.0 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.4332524 -11.7894 (HOMO) + 2 -0.0957872 -2.6065 (LUMO) + ------------------------------------------------------------- + HL-Gap 0.3374652 Eh 9.1829 eV + Fermi-level -0.2645198 Eh -7.1979 eV + + SCC (total) 0 d, 0 h, 0 min, 0.008 sec + SCC setup ... 0 min, 0.001 sec ( 6.535%) + Dispersion ... 0 min, 0.000 sec ( 3.215%) + integral evaluation ... 0 min, 0.002 sec ( 19.261%) + zeroth order Hamiltonian ... 0 min, 0.000 sec ( 0.181%) + iterations ... 0 min, 0.005 sec ( 62.261%) + molecular gradient ... 0 min, 0.000 sec ( 4.710%) + printout ... 0 min, 0.000 sec ( 3.395%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -0.966523050218 Eh :: + :: gradient norm 0.089191857169 Eh/a0 :: + :: HOMO-LUMO gap 9.182896506924 eV :: + ::.................................................:: + :: SCC energy -0.976382179047 Eh :: + :: -> isotropic ES 0.000000000000 Eh :: + :: -> anisotropic ES 0.010484355527 Eh :: + :: -> anisotropic XC 0.011179625009 Eh :: + :: -> dispersion -0.000130282477 Eh :: + :: repulsion energy 0.009859128829 Eh :: + :: add. restraining 0.000000000000 Eh :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ------------------------------------------------- + | Property Printout | + ------------------------------------------------- + + * Orbital Energies and Occupations + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.4332524 -11.7894 (HOMO) + 2 -0.0957872 -2.6065 (LUMO) + ------------------------------------------------------------- + HL-Gap 0.3374652 Eh 9.1829 eV + Fermi-level -0.2645198 Eh -7.1979 eV + + # Z covCN q C6AA α(0) + 1 1 H 0.033 -0.000 7.614 5.045 + 2 1 H 0.033 0.000 7.614 5.045 + + Mol. C6AA /au·bohr⁶ : 30.454143 + Mol. C8AA /au·bohr⁸ : 368.140340 + Mol. α(0) /au : 10.089603 + + +Wiberg/Mayer (AO) data. +largest (>0.10) Wiberg bond orders for each atom + total WBO WBO to atom ... + 1 H 1.000 H 2 1.000 + 2 H 1.000 H 1 1.000 + +molecular dipole: + x y z tot (Debye) + q only: 0.000 0.000 0.000 + full: 0.000 0.000 0.000 0.000 +molecular quadrupole (traceless): + xx xy yy xz yz zz + q only: 0.000 0.000 -0.000 0.000 0.000 -0.000 + q+dip: 1.192 0.000 -0.596 0.000 0.000 -0.596 + full: 0.480 0.000 -0.240 0.000 0.000 -0.240 + + + ------------------------------------------------- + | TOTAL ENERGY -0.966523050218 Eh | + | GRADIENT NORM 0.089191857169 Eh/α | + | HOMO-LUMO GAP 9.182896506924 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2020/07/10 at 11:57:51.842 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.051 sec + * cpu-time: 0 d, 0 h, 0 min, 0.138 sec + * ratio c/w: 2.708 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.009 sec + * cpu-time: 0 d, 0 h, 0 min, 0.027 sec + * ratio c/w: 2.916 speedup + diff --git a/tests/data/xtb/h2_sp_xtb.xyz b/tests/data/xtb/h2_sp_xtb.xyz new file mode 100644 index 000000000..228ed4e0e --- /dev/null +++ b/tests/data/xtb/h2_sp_xtb.xyz @@ -0,0 +1,4 @@ +2 + +H 0.00000 0.00000 0.00000 +H 1.00000 0.00000 0.00000 diff --git a/tests/data/xtb/methane_xtb_xtb.grad b/tests/data/xtb/methane_xtb_xtb.grad new file mode 100644 index 000000000..e30e27b19 --- /dev/null +++ b/tests/data/xtb/methane_xtb_xtb.grad @@ -0,0 +1,5 @@ +-0.00001722 0.00007993 -0.00011737 + 0.01411630 -0.00004036 0.00003972 +-0.00471994 0.00900862 -0.00941145 +-0.00469570 0.00363569 0.01255847 +-0.00468344 -0.01268388 -0.00306936 diff --git a/tests/data/xtbopt.xyz b/tests/data/xtbopt.xyz deleted file mode 100644 index 48cbcbed5..000000000 --- a/tests/data/xtbopt.xyz +++ /dev/null @@ -1,8 +0,0 @@ -6 - energy: -13.191605770476 gnorm: 0.000387392520 xtb: 6.2.3 (830e466) -C -0.00574967262589 -0.01085571761125 -0.02597769822345 -F 0.58591477377632 -1.09061806899196 0.59503434605500 -H -0.46261868045701 0.60478393745781 0.74798789369103 -H 0.77787505033051 0.54155220814803 -0.54405213169454 -H -0.76278974746505 -0.35174309896199 -0.73487361835079 -Cl -2.39536172355888 0.30689073995933 -2.30085879147730 diff --git a/tests/test_1d_pes.py b/tests/test_1d_pes.py index 82497a640..1122ae02e 100644 --- a/tests/test_1d_pes.py +++ b/tests/test_1d_pes.py @@ -97,4 +97,9 @@ def test_1d_pes(): if filename.endswith(('.inp', '.png')): os.remove(filename) + for filename in os.listdir(os.path.join(here, 'data', 'pes1d')): + if filename.endswith('.xyz') and 'optimised' in filename: + xyz_path = os.path.join(here, 'data', 'pes1d', filename) + os.remove(xyz_path) + os.chdir(here) diff --git a/tests/test_orca_calc.py b/tests/test_orca_calc.py index 3cf23b14a..ff620a5b2 100644 --- a/tests/test_orca_calc.py +++ b/tests/test_orca_calc.py @@ -1,4 +1,5 @@ from autode.wrappers.ORCA import ORCA +from autode.atoms import Atom from autode.calculation import Calculation from autode.calculation import execute_calc from autode.species.molecule import Molecule @@ -10,6 +11,7 @@ from autode.exceptions import UnsuppportedCalculationInput from autode.wrappers.keywords import SinglePointKeywords, OptKeywords from autode.solvent.solvents import Solvent +import numpy as np import pytest import os @@ -182,3 +184,41 @@ def test_solvation(): assert any('smd' in line.lower() for line in open('methane_smd_orca.inp', 'r')) os.remove('methane_smd_orca.inp') + + +def test_gradients(): + os.chdir(os.path.join(here, 'data', 'orca')) + + h2 = Molecule(name='h2', atoms=[Atom('H'), Atom('H', x=1.0)]) + calc = Calculation(name='h2_grad', molecule=h2, + method=method, + keywords=method.keywords.grad) + calc.run() + h2.energy = calc.get_energy() + + delta_r = 1E-8 + + # Energy of a finite difference approximation + h2_disp = Molecule(name='h2_disp', + atoms=[Atom('H'), Atom('H', x=1.0 + delta_r)]) + calc = Calculation(name='h2_disp', molecule=h2_disp, + method=method, + keywords=method.keywords.grad) + calc.run() + h2_disp.energy = calc.get_energy() + + delta_energy = h2_disp.energy - h2.energy # Ha + grad = delta_energy / delta_r # Ha A^-1 + + calc = Calculation(name='h2_grad', molecule=h2, + method=method, + keywords=method.keywords.grad) + + calc.run() + + diff = calc.get_gradients()[1, 0] - grad # Ha A^-1 + + # Difference between the absolute and finite difference approximation + assert np.abs(diff) < 1E-3 + + os.chdir(here) diff --git a/tests/test_ts.py b/tests/test_ts.py index 61ce93d35..8d505ca32 100644 --- a/tests/test_ts.py +++ b/tests/test_ts.py @@ -152,7 +152,8 @@ def test_isomorphic_reactant_product(): p_water = Product(name='h2o', smiles='O') p_methane = Product(name='methane', smiles='C') - # Reaction where the reactant and product complexes are isomorphic should return no TS + # Reaction where the reactant and product complexes are isomorphic + # should return no TS reaction = Reaction(r_water, r_methane, p_water, p_methane) reaction.locate_transition_state() @@ -206,6 +207,14 @@ def test_find_tss(): # Truncated graph has 7 atoms in assert template.graph.number_of_nodes() == 7 + # Tidy the generated files + pes_path = os.path.join(here, 'data', 'locate_ts', + 'transition_states', 'pes1d') + + for filename in os.listdir(pes_path): + if 'optimised' in filename and filename.endswith('.xyz'): + os.remove(os.path.join(pes_path, filename)) + os.remove('template0.obj') os.chdir(here) diff --git a/tests/test_xtb_calc.py b/tests/test_xtb_calc.py index a2d2d4051..dd7e89f01 100644 --- a/tests/test_xtb_calc.py +++ b/tests/test_xtb_calc.py @@ -1,9 +1,11 @@ import pytest +from autode.atoms import Atom from autode.wrappers.XTB import XTB from autode.calculation import Calculation from autode.species.molecule import Molecule from autode.point_charges import PointCharge from autode.config import Config +import numpy as np import os here = os.path.dirname(os.path.abspath(__file__)) @@ -72,4 +74,57 @@ def test_point_charge(): calc.run() assert -4.178 < calc.get_energy() < -4.175 - os.chdir(here) \ No newline at end of file + os.chdir(here) + + +def test_gradients(): + os.chdir(os.path.join(here, 'data', 'xtb')) + + h2 = Molecule(name='h2', atoms=[Atom('H'), Atom('H', x=1.0)]) + h2.single_point(method) + + delta_r = 1E-5 + h2_disp = Molecule(name='h2_disp', + atoms=[Atom('H'), Atom('H', x=1.0 + delta_r)]) + h2_disp.single_point(method) + + delta_energy = h2_disp.energy - h2.energy # Ha + grad = delta_energy / delta_r # Ha A^-1 + + calc = Calculation(name='h2_grad', molecule=h2, + method=method, + keywords=method.keywords.grad) + + calc.run() + + diff = calc.get_gradients()[1, 0] - grad # Ha A^-1 + + # Difference between the absolute and finite difference approximation + assert np.abs(diff) < 1E-5 + + # Older xtb version + with open('gradient', 'w') as gradient_file: + print('$gradient\n' + 'cycle = 1 SCF energy = -4.17404780397 |dE/dxyz| = 0.027866\n' + '3.63797523123375 -1.13138130908142 -0.00032759661848 C \n' + '5.72449332438353 -1.13197561185651 0.00028950521969 H \n' + ' 2.94133258016711 0.22776472016180 -1.42078243039077 H \n' + ' 2.94175598539510 -0.58111835182372 1.88747566982948 H \n' + '2.94180792167968 -3.04156357656436 -0.46665514803992 H \n' + '-1.7221823521705E-05 7.9930724499610E-05 -1.1737079840097E-04\n' + ' 1.4116296505865E-02 -4.0359524399270E-05 3.9719638516747E-05\n' + '-4.7199424681741E-03 9.0086220034949E-03 -9.4114548523723E-03\n' + '-4.6956970257351E-03 3.6356853660431E-03 1.2558467871909E-02\n' + ' -4.6834351884340E-03 -1.2683878569638E-02 -3.0693618596526E-03\n' + '$end', file=gradient_file) + + calc = Calculation(name='methane', + molecule=Molecule(name='methane', smiles='C'), + method=method, + keywords=method.keywords.grad) + gradients = method.get_gradients(calc) + + assert gradients.shape == (5, 3) + assert np.abs(gradients[0, 0]) < 1E-3 + + os.chdir(here)