diff --git a/dpdata/orca/__init__.py b/dpdata/orca/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/dpdata/orca/output.py b/dpdata/orca/output.py new file mode 100644 index 00000000..13f072f3 --- /dev/null +++ b/dpdata/orca/output.py @@ -0,0 +1,64 @@ +from typing import Tuple + +import numpy as np + + +def read_orca_sp_output(fn: str) -> Tuple[np.ndarray, np.ndarray, float, np.ndarray]: + """Read from ORCA output. + + Note that both the energy and the gradient should be printed. + + Parameters + ---------- + fn : str + file name + + Returns + ------- + np.ndarray + atomic symbols + np.ndarray + atomic coordinates + float + total potential energy + np.ndarray + atomic forces + """ + coord = None + symbols = None + forces = None + energy = None + with open(fn) as f: + flag = 0 + for line in f: + if flag in (1, 3, 4): + flag += 1 + elif flag == 2: + s = line.split() + if not len(s): + flag = 0 + else: + symbols.append(s[0].capitalize()) + coord.append([float(s[1]), float(s[2]), float(s[3])]) + elif flag == 5: + s = line.split() + if not len(s): + flag = 0 + else: + forces.append([float(s[3]), float(s[4]), float(s[5])]) + elif line.startswith("CARTESIAN COORDINATES (ANGSTROEM)"): + # coord + flag = 1 + coord = [] + symbols = [] + elif line.startswith("CARTESIAN GRADIENT"): + flag = 3 + forces = [] + elif line.startswith("FINAL SINGLE POINT ENERGY"): + energy = float(line.split()[-1]) + symbols = np.array(symbols) + forces = -np.array(forces) + coord = np.array(coord) + assert coord.shape == forces.shape + + return symbols, coord, energy, forces diff --git a/dpdata/plugins/orca.py b/dpdata/plugins/orca.py new file mode 100644 index 00000000..2585743e --- /dev/null +++ b/dpdata/plugins/orca.py @@ -0,0 +1,51 @@ +import numpy as np + +from dpdata.format import Format +from dpdata.orca.output import read_orca_sp_output +from dpdata.unit import EnergyConversion, ForceConversion + +energy_convert = EnergyConversion("hartree", "eV").value() +force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value() + + +@Format.register("orca/spout") +class ORCASPOutFormat(Format): + """ORCA single point energy output. + + Note that both the energy and the gradient should be + printed into the output file. + """ + + def from_labeled_system(self, file_name: str, **kwargs) -> dict: + """Read from ORCA single point energy output. + + Parameters + ---------- + file_name : str + file name + **kwargs + keyword arguments + + Returns + ------- + dict + system data + """ + symbols, coord, energy, forces = read_orca_sp_output(file_name) + + atom_names, atom_types, atom_numbs = np.unique( + symbols, return_inverse=True, return_counts=True + ) + natoms = coord.shape[0] + + return { + "atom_types": atom_types, + "atom_names": list(atom_names), + "atom_numbs": list(atom_numbs), + "coords": coord.reshape((1, natoms, 3)), + "energies": np.array([energy * energy_convert]), + "forces": (forces * force_convert).reshape((1, natoms, 3)), + "cells": np.zeros((1, 3, 3)), + "orig": np.zeros(3), + "nopbc": True, + } diff --git a/tests/orca/orca.spout b/tests/orca/orca.spout new file mode 100644 index 00000000..7285bb69 --- /dev/null +++ b/tests/orca/orca.spout @@ -0,0 +1,1350 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.3 - 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 properties, NMR spectrum + 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 and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + 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 + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + 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, DLPNO-MP2 response + 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, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert 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) + 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, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + 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: 5.1.0 + 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 + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.19 NO_AFFINITY VORTEX SINGLE_THREADED + Core in use : VORTEX + Copyright (c) 2011-2014, The OpenBLAS Project + + +================================================================================ + +----- Orbital basis set information ----- +Your calculation utilizes the basis: def2-SVP + F. Weigend and R. Ahlrichs, Phys. Chem. Chem. Phys. 7, 3297 (2005). + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + + +INFO : the flag for use of the SHARK integral package has been found! + +================================================================================ + INPUT FILE +================================================================================ +NAME = dopamine.inp +| 1> # avogadro generated ORCA input file +| 2> # Basic Mode +| 3> # +| 4> ! RHF DEF2-SVP SP ENGRAD PAL6 +| 5> +| 6> * xyz 0 1 +| 7> C -1.74744 2.17247 0.03844 +| 8> C -3.05879 1.67227 0.03011 +| 9> C -3.27420 0.28366 -0.00786 +| 10> C -2.17997 -0.58525 -0.03679 +| 11> C -0.64257 1.30482 0.01039 +| 12> C -0.87523 -0.08541 -0.02759 +| 13> H -1.58753 3.24402 0.06795 +| 14> H -0.06231 -0.79687 -0.05066 +| 15> H -2.34094 -1.65578 -0.06624 +| 16> C 0.74327 1.92237 0.02355 +| 17> C 1.91059 0.92572 0.00406 +| 18> H 0.83621 2.54508 0.94024 +| 19> H 0.83328 2.58745 -0.86317 +| 20> N 3.18351 1.63882 0.03702 +| 21> H 1.86317 0.29904 -0.91452 +| 22> H 1.84793 0.26910 0.89940 +| 23> H 3.28398 2.20442 -0.83723 +| 24> H 3.95753 0.93591 0.05242 +| 25> O -4.10991 2.51820 0.05880 +| 26> H -3.99914 3.47933 0.08641 +| 27> O -4.52084 -0.23396 -0.01684 +| 28> H -5.31660 0.31593 0.00260 +| 29> * +| 30> +| 31> +| 32> ****END OF INPUT**** +================================================================================ + + ******************************* + * Energy+Gradient Calculation * + ******************************* + +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C -1.747440 2.172470 0.038440 + C -3.058790 1.672270 0.030110 + C -3.274200 0.283660 -0.007860 + C -2.179970 -0.585250 -0.036790 + C -0.642570 1.304820 0.010390 + C -0.875230 -0.085410 -0.027590 + H -1.587530 3.244020 0.067950 + H -0.062310 -0.796870 -0.050660 + H -2.340940 -1.655780 -0.066240 + C 0.743270 1.922370 0.023550 + C 1.910590 0.925720 0.004060 + H 0.836210 2.545080 0.940240 + H 0.833280 2.587450 -0.863170 + N 3.183510 1.638820 0.037020 + H 1.863170 0.299040 -0.914520 + H 1.847930 0.269100 0.899400 + H 3.283980 2.204420 -0.837230 + H 3.957530 0.935910 0.052420 + O -4.109910 2.518200 0.058800 + H -3.999140 3.479330 0.086410 + O -4.520840 -0.233960 -0.016840 + H -5.316600 0.315930 0.002600 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 -3.302183 4.105373 0.072641 + 1 C 6.0000 0 12.011 -5.780275 3.160132 0.056900 + 2 C 6.0000 0 12.011 -6.187341 0.536040 -0.014853 + 3 C 6.0000 0 12.011 -4.119546 -1.105962 -0.069523 + 4 C 6.0000 0 12.011 -1.214281 2.465752 0.019634 + 5 C 6.0000 0 12.011 -1.653945 -0.161402 -0.052138 + 6 H 1.0000 0 1.008 -2.999997 6.130309 0.128407 + 7 H 1.0000 0 1.008 -0.117749 -1.505866 -0.095734 + 8 H 1.0000 0 1.008 -4.423735 -3.128971 -0.125175 + 9 C 6.0000 0 12.011 1.404577 3.632753 0.044503 + 10 C 6.0000 0 12.011 3.610492 1.749357 0.007672 + 11 H 1.0000 0 1.008 1.580208 4.809504 1.776796 + 12 H 1.0000 0 1.008 1.574671 4.889572 -1.631155 + 13 N 7.0000 0 14.007 6.015962 3.096921 0.069958 + 14 H 1.0000 0 1.008 3.520881 0.565104 -1.728192 + 15 H 1.0000 0 1.008 3.492082 0.508525 1.699620 + 16 H 1.0000 0 1.008 6.205823 4.165750 -1.582135 + 17 H 1.0000 0 1.008 7.478648 1.768614 0.099059 + 18 O 8.0000 0 15.999 -7.766604 4.758708 0.111116 + 19 H 1.0000 0 1.008 -7.557279 6.574981 0.163291 + 20 O 8.0000 0 15.999 -8.543149 -0.442120 -0.031823 + 21 H 1.0000 0 1.008 -10.046918 0.597021 0.004913 + +-------------------------------- +INTERNAL COORDINATES (ANGSTROEM) +-------------------------------- + C 0 0 0 0.000000000000 0.00000000 0.00000000 + C 1 0 0 1.403534200296 0.00000000 0.00000000 + C 2 1 0 1.405731454119 119.69467915 0.00000000 + C 3 2 1 1.397562458676 119.65269208 0.00000000 + C 1 2 3 1.405112465926 120.96341667 359.95022766 + C 4 3 2 1.397236963868 120.56881911 0.03310535 + H 1 2 3 1.083817997036 119.36465349 180.01105239 + H 6 4 3 1.080530648756 117.82961357 179.98212119 + H 4 3 2 1.082964969101 119.91927013 180.00952472 + C 5 1 2 1.517265202165 117.82077675 180.08269137 + C 10 5 1 1.535033245568 115.48087070 179.48702128 + H 10 5 1 1.112081896175 108.14311161 58.28337101 + H 10 5 1 1.112072643715 108.08511067 301.12822663 + N 11 10 5 1.459425674024 110.22701775 180.75013184 + H 11 10 5 1.112998515363 110.09965629 60.06129676 + H 11 10 5 1.112074554875 109.28628075 300.06689755 + H 14 11 10 1.046093037641 109.21292686 295.47945418 + H 14 11 10 1.045670401465 108.51172994 178.29078442 + O 2 1 3 1.349545825602 120.27793928 179.97865312 + H 19 2 1 0.967885934344 122.27062215 359.94102427 + O 3 2 1 1.349860138829 121.36515946 179.99411110 + H 21 3 2 0.967466228506 122.78835998 359.96510144 + +--------------------------- +INTERNAL COORDINATES (A.U.) +--------------------------- + C 0 0 0 0.000000000000 0.00000000 0.00000000 + C 1 0 0 2.652295258151 0.00000000 0.00000000 + C 2 1 0 2.656447466124 119.69467915 0.00000000 + C 3 2 1 2.641010301947 119.65269208 0.00000000 + C 1 2 3 2.655277747958 120.96341667 359.95022766 + C 4 3 2 2.640395205903 120.56881911 0.03310535 + H 1 2 3 2.048119193414 119.36465349 180.01105239 + H 6 4 3 2.041907005456 117.82961357 179.98212119 + H 4 3 2 2.046507204231 119.91927013 180.00952472 + C 5 1 2 2.867215704620 117.82077675 180.08269137 + C 10 5 1 2.900792440588 115.48087070 179.48702128 + H 10 5 1 2.101530222262 108.14311161 58.28337101 + H 10 5 1 2.101512737648 108.08511067 301.12822663 + N 11 10 5 2.757914836719 110.22701775 180.75013184 + H 11 10 5 2.103262381497 110.09965629 60.06129676 + H 11 10 5 2.101516349216 109.28628075 300.06689755 + H 14 11 10 1.976829351742 109.21292686 295.47945418 + H 14 11 10 1.976030685116 108.51172994 178.29078442 + O 2 1 3 2.550272015565 120.27793928 179.97865312 + H 19 2 1 1.829039344784 122.27062215 359.94102427 + O 3 2 1 2.550865981484 121.36515946 179.99411110 + H 21 3 2 1.828246215694 122.78835998 359.96510144 + +--------------------- +BASIS SET INFORMATION +--------------------- +There are 4 groups of distinct atoms + + Group 1 Type C : 7s4p1d contracted to 3s2p1d pattern {511/31/1} + Group 2 Type H : 4s1p contracted to 2s1p pattern {31/1} + Group 3 Type N : 7s4p1d contracted to 3s2p1d pattern {511/31/1} + Group 4 Type O : 7s4p1d contracted to 3s2p1d pattern {511/31/1} + +Atom 0C basis set group => 1 +Atom 1C basis set group => 1 +Atom 2C basis set group => 1 +Atom 3C basis set group => 1 +Atom 4C basis set group => 1 +Atom 5C basis set group => 1 +Atom 6H basis set group => 2 +Atom 7H basis set group => 2 +Atom 8H basis set group => 2 +Atom 9C basis set group => 1 +Atom 10C basis set group => 1 +Atom 11H basis set group => 2 +Atom 12H basis set group => 2 +Atom 13N basis set group => 3 +Atom 14H basis set group => 2 +Atom 15H basis set group => 2 +Atom 16H basis set group => 2 +Atom 17H basis set group => 2 +Atom 18O basis set group => 4 +Atom 19H basis set group => 2 +Atom 20O basis set group => 4 +Atom 21H basis set group => 2 + + + ************************************************************ + * Program running with 6 parallel MPI-processes * + * working on a common directory * + ************************************************************ +------------------------------------------------------------------------------ + ORCA GTO INTEGRAL CALCULATION +------------------------------------------------------------------------------ +------------------------------------------------------------------------------ + ___ + / \ - P O W E R E D B Y - + / \ + | | | _ _ __ _____ __ __ + | | | | | | | / \ | _ \ | | / | + \ \/ | | | | / \ | | | | | | / / + / \ \ | |__| | / /\ \ | |_| | | |/ / + | | | | __ | / /__\ \ | / | \ + | | | | | | | | __ | | \ | |\ \ + \ / | | | | | | | | | |\ \ | | \ \ + \___/ |_| |_| |__| |__| |_| \__\ |__| \__/ + + - O R C A' S B I G F R I E N D - + & + - I N T E G R A L F E E D E R - + + v1 FN, 2020, v2 2021 +------------------------------------------------------------------------------ + + +Reading SHARK input file dopamine.SHARKINP.tmp ... ok +---------------------- +SHARK INTEGRAL PACKAGE +---------------------- + +Number of atoms ... 22 +Number of basis functions ... 209 +Number of shells ... 99 +Maximum angular momentum ... 2 +Integral batch strategy ... SHARK/LIBINT Hybrid +RI-J (if used) integral strategy ... SPLIT-RIJ (Revised 2003 algorithm where possible) +Printlevel ... 1 +Contraction scheme used ... SEGMENTED contraction +Coulomb Range Separation ... NOT USED +Exchange Range Separation ... NOT USED +Finite Nucleus Model ... NOT USED +Auxiliary Coulomb fitting basis ... NOT available +Auxiliary J/K fitting basis ... NOT available +Auxiliary Correlation fitting basis ... NOT available +Auxiliary 'external' fitting basis ... NOT available +Integral threshold ... 2.500000e-11 +Primitive cut-off ... 2.500000e-12 +Primitive pair pre-selection threshold ... 2.500000e-12 + +Calculating pre-screening integrals ... done ( 0.0 sec) Dimension = 99 +Organizing shell pair data ... done ( 0.0 sec) +Shell pair information +Total number of shell pairs ... 4950 +Shell pairs after pre-screening ... 4240 +Total number of primitive shell pairs ... 17754 +Primitive shell pairs kept ... 10719 + la=0 lb=0: 1342 shell pairs + la=1 lb=0: 1565 shell pairs + la=1 lb=1: 477 shell pairs + la=2 lb=0: 505 shell pairs + la=2 lb=1: 297 shell pairs + la=2 lb=2: 54 shell pairs + +Calculating one electron integrals ... done ( 0.0 sec) +Calculating Nuclear repulsion ... done ( 0.0 sec) ENN= 588.177050698793 Eh + +SHARK setup successfully completed in 0.1 seconds + +Maximum memory used throughout the entire GTOINT-calculation: 10.2 MB + + + ************************************************************ + * Program running with 6 parallel MPI-processes * + * working on a common directory * + ************************************************************ +------------------------------------------------------------------------------- + ORCA SCF +------------------------------------------------------------------------------- + +------------ +SCF SETTINGS +------------ +Hamiltonian: + Ab initio Hamiltonian Method .... Hartree-Fock(GTOs) + + +General Settings: + Integral files IntName .... dopamine + Hartree-Fock type HFTyp .... RHF + Total Charge Charge .... 0 + Multiplicity Mult .... 1 + Number of Electrons NEL .... 82 + Basis Dimension Dim .... 209 + Nuclear Repulsion ENuc .... 588.1770506988 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 + Trust-Rad. Augm. Hess. CNVTRAH .... auto + Auto Start mean grad. ratio tolernc. .... 1.125000 + Auto Start start iteration .... 20 + Auto Start num. interpolation iter. .... 10 + Max. Number of Micro iterations .... 16 + Max. Number of Macro iterations .... Maxiter - #DIIS iter + Number of Davidson start vectors .... 2 + Converg. threshold I (grad. norm) .... 1.000e-05 + Converg. threshold II (energy diff.) .... 1.000e-08 + Grad. Scal. Fac. for Micro threshold .... 0.100 + Minimum threshold for Micro iter. .... 0.010 + NR start threshold (gradient norm) .... 0.001 + Initial trust radius .... 0.400 + Minimum AH scaling param. (alpha) .... 1.000 + Maximum AH scaling param. (alpha) .... 1000.000 + Orbital update algorithm .... Taylor + White noise on init. David. guess .... on + Maximum white noise .... 0.010 + Quad. conv. algorithm .... NR + 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 .... 125 + SCF integral mode SCFMode .... Direct + Integral package .... SHARK and LIBINT hybrid scheme + 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 ... 2.145e-04 +Time for diagonalization ... 0.004 sec +Threshold for overlap eigenvalues ... 1.000e-08 +Number of eigenvalues below threshold ... 0 +Time for construction of square roots ... 0.002 sec +Total time needed ... 0.006 sec + +Time for model grid setup = 0.056 sec + +------------------------------ +INITIAL GUESS: MODEL POTENTIAL +------------------------------ +Loading Hartree-Fock densities ... done +Calculating cut-offs ... done +Initializing the effective Hamiltonian ... done +Setting up the integral package (SHARK) ... 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) +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 -512.6785606370 0.000000000000 0.06655899 0.00255672 0.2552117 0.7000 + 1 -512.8304655551 -0.151904918035 0.04952659 0.00198623 0.1569121 0.7000 + ***Turning on DIIS*** + 2 -512.9226986338 -0.092233078754 0.12575631 0.00459967 0.0869257 0.0000 + 3 -512.2705497676 0.652148866181 0.03917686 0.00093267 0.0484481 0.0000 + 4 -513.1056826882 -0.835132920524 0.00973451 0.00037032 0.0049339 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 + 5 -513.10705599 -0.0013733061 0.002188 0.002188 0.003146 0.000136 + *** Restarting incremental Fock matrix formation *** + 6 -513.11335895 -0.0063029531 0.000883 0.002078 0.001236 0.000059 + 7 -513.11338221 -0.0000232610 0.000394 0.001652 0.001273 0.000048 + 8 -513.11338799 -0.0000057864 0.000168 0.000347 0.000256 0.000010 + 9 -513.11338870 -0.0000007078 0.000087 0.000187 0.000114 0.000004 + 10 -513.11338883 -0.0000001264 0.000034 0.000200 0.000102 0.000003 + 11 -513.11338887 -0.0000000372 0.000015 0.000034 0.000020 0.000001 + 12 -513.11338887 -0.0000000026 0.000003 0.000003 0.000009 0.000000 + ***Gradient check signals convergence*** + ***Rediagonalizing the Fockian in SOSCF/NRSCF*** + + ***************************************************** + * SUCCESS * + * SCF CONVERGED AFTER 13 CYCLES * + ***************************************************** + + +---------------- +TOTAL SCF ENERGY +---------------- + +Total Energy : -513.11338887 Eh -13962.52515 eV + +Components: +Nuclear Repulsion : 588.17705070 Eh 16005.11123 eV +Electronic Energy : -1101.29043957 Eh -29967.63639 eV +One Electron Energy: -1866.28873819 Eh -50784.29839 eV +Two Electron Energy: 764.99829862 Eh 20816.66200 eV + +Virial components: +Potential Energy : -1023.69102205 Eh -27856.04888 eV +Kinetic Energy : 510.57763318 Eh 13893.52373 eV +Virial Ratio : 2.00496644 + + +--------------- +SCF CONVERGENCE +--------------- + + Last Energy change ... 1.8645e-10 Tolerance : 1.0000e-08 + Last MAX-Density change ... 3.6874e-06 Tolerance : 1.0000e-07 + Last RMS-Density change ... 1.0628e-07 Tolerance : 5.0000e-09 + Last Orbital Gradient ... 8.1082e-07 Tolerance : 1.0000e-05 + Last Orbital Rotation ... 2.5006e-06 Tolerance : 1.0000e-05 + + **** THE GBW FILE WAS UPDATED (dopamine.gbw) **** + **** DENSITY dopamine.scfp WAS UPDATED **** + **** ENERGY FILE WAS UPDATED (dopamine.en.tmp) **** + **** THE GBW FILE WAS UPDATED (dopamine.gbw) **** + **** DENSITY dopamine.scfp WAS UPDATED **** +---------------- +ORBITAL ENERGIES +---------------- + + NO OCC E(Eh) E(eV) + 0 2.0000 -20.582512 -560.0786 + 1 2.0000 -20.563086 -559.5500 + 2 2.0000 -15.541850 -422.9152 + 3 2.0000 -11.302324 -307.5519 + 4 2.0000 -11.295967 -307.3789 + 5 2.0000 -11.254656 -306.2548 + 6 2.0000 -11.239240 -305.8353 + 7 2.0000 -11.232796 -305.6599 + 8 2.0000 -11.232294 -305.6463 + 9 2.0000 -11.232251 -305.6451 + 10 2.0000 -11.228932 -305.5548 + 11 2.0000 -1.395191 -37.9651 + 12 2.0000 -1.362795 -37.0835 + 13 2.0000 -1.160468 -31.5779 + 14 2.0000 -1.129642 -30.7391 + 15 2.0000 -1.029530 -28.0149 + 16 2.0000 -0.996367 -27.1125 + 17 2.0000 -0.942362 -25.6430 + 18 2.0000 -0.857375 -23.3304 + 19 2.0000 -0.833311 -22.6756 + 20 2.0000 -0.792052 -21.5528 + 21 2.0000 -0.751668 -20.4539 + 22 2.0000 -0.716178 -19.4882 + 23 2.0000 -0.673104 -18.3161 + 24 2.0000 -0.655898 -17.8479 + 25 2.0000 -0.640195 -17.4206 + 26 2.0000 -0.611964 -16.6524 + 27 2.0000 -0.601508 -16.3679 + 28 2.0000 -0.599524 -16.3139 + 29 2.0000 -0.571109 -15.5407 + 30 2.0000 -0.564570 -15.3627 + 31 2.0000 -0.556233 -15.1359 + 32 2.0000 -0.548039 -14.9129 + 33 2.0000 -0.520950 -14.1758 + 34 2.0000 -0.509034 -13.8515 + 35 2.0000 -0.484125 -13.1737 + 36 2.0000 -0.481047 -13.0899 + 37 2.0000 -0.452177 -12.3044 + 38 2.0000 -0.386679 -10.5221 + 39 2.0000 -0.325493 -8.8571 + 40 2.0000 -0.291535 -7.9331 + 41 0.0000 0.133710 3.6384 + 42 0.0000 0.159547 4.3415 + 43 0.0000 0.168061 4.5732 + 44 0.0000 0.175208 4.7676 + 45 0.0000 0.200387 5.4528 + 46 0.0000 0.205803 5.6002 + 47 0.0000 0.220251 5.9933 + 48 0.0000 0.231073 6.2878 + 49 0.0000 0.242508 6.5990 + 50 0.0000 0.258924 7.0457 + 51 0.0000 0.288848 7.8600 + 52 0.0000 0.297917 8.1067 + 53 0.0000 0.308174 8.3858 + 54 0.0000 0.376892 10.2558 + 55 0.0000 0.380369 10.3504 + 56 0.0000 0.383648 10.4396 + 57 0.0000 0.413857 11.2616 + 58 0.0000 0.430964 11.7271 + 59 0.0000 0.460900 12.5417 + 60 0.0000 0.476127 12.9561 + 61 0.0000 0.486023 13.2254 + 62 0.0000 0.511371 13.9151 + 63 0.0000 0.529720 14.4144 + 64 0.0000 0.558811 15.2060 + 65 0.0000 0.600695 16.3458 + 66 0.0000 0.611694 16.6450 + 67 0.0000 0.644990 17.5511 + 68 0.0000 0.653368 17.7790 + 69 0.0000 0.673331 18.3223 + 70 0.0000 0.689943 18.7743 + 71 0.0000 0.700048 19.0493 + 72 0.0000 0.711892 19.3716 + 73 0.0000 0.727853 19.8059 + 74 0.0000 0.747489 20.3402 + 75 0.0000 0.751647 20.4533 + 76 0.0000 0.767100 20.8739 + 77 0.0000 0.778010 21.1707 + 78 0.0000 0.802256 21.8305 + 79 0.0000 0.834012 22.6946 + 80 0.0000 0.837310 22.7844 + 81 0.0000 0.850169 23.1343 + 82 0.0000 0.864490 23.5240 + 83 0.0000 0.870915 23.6988 + 84 0.0000 0.874517 23.7968 + 85 0.0000 0.885971 24.1085 + 86 0.0000 0.901929 24.5427 + 87 0.0000 0.912886 24.8409 + 88 0.0000 0.917862 24.9763 + 89 0.0000 0.929162 25.2838 + 90 0.0000 0.934730 25.4353 + 91 0.0000 0.943223 25.6664 + 92 0.0000 0.956377 26.0243 + 93 0.0000 0.970557 26.4102 + 94 0.0000 0.972744 26.4697 + 95 0.0000 0.998413 27.1682 + 96 0.0000 1.012153 27.5421 + 97 0.0000 1.042090 28.3567 + 98 0.0000 1.043649 28.3991 + 99 0.0000 1.064102 28.9557 + 100 0.0000 1.082027 29.4434 + 101 0.0000 1.093660 29.7600 + 102 0.0000 1.146780 31.2055 + 103 0.0000 1.151814 31.3425 + 104 0.0000 1.170701 31.8564 + 105 0.0000 1.209622 32.9155 + 106 0.0000 1.249923 34.0121 + 107 0.0000 1.277822 34.7713 + 108 0.0000 1.296574 35.2816 + 109 0.0000 1.320432 35.9308 + 110 0.0000 1.328204 36.1423 + 111 0.0000 1.349054 36.7096 + 112 0.0000 1.387070 37.7441 + 113 0.0000 1.432871 38.9904 + 114 0.0000 1.439989 39.1841 + 115 0.0000 1.472463 40.0678 + 116 0.0000 1.491236 40.5786 + 117 0.0000 1.503758 40.9193 + 118 0.0000 1.513240 41.1773 + 119 0.0000 1.522690 41.4345 + 120 0.0000 1.589442 43.2509 + 121 0.0000 1.593834 43.3704 + 122 0.0000 1.610257 43.8173 + 123 0.0000 1.615800 43.9681 + 124 0.0000 1.624293 44.1993 + 125 0.0000 1.641159 44.6582 + 126 0.0000 1.699814 46.2543 + 127 0.0000 1.769031 48.1378 + 128 0.0000 1.794704 48.8364 + 129 0.0000 1.812914 49.3319 + 130 0.0000 1.845949 50.2308 + 131 0.0000 1.858191 50.5640 + 132 0.0000 1.876424 51.0601 + 133 0.0000 1.897363 51.6299 + 134 0.0000 1.962612 53.4054 + 135 0.0000 1.973720 53.7077 + 136 0.0000 1.980529 53.8929 + 137 0.0000 1.995254 54.2936 + 138 0.0000 2.003295 54.5124 + 139 0.0000 2.016707 54.8774 + 140 0.0000 2.041239 55.5449 + 141 0.0000 2.048359 55.7387 + 142 0.0000 2.056967 55.9729 + 143 0.0000 2.073506 56.4230 + 144 0.0000 2.102070 57.2002 + 145 0.0000 2.108970 57.3880 + 146 0.0000 2.128574 57.9214 + 147 0.0000 2.129353 57.9426 + 148 0.0000 2.139431 58.2169 + 149 0.0000 2.160110 58.7796 + 150 0.0000 2.180778 59.3420 + 151 0.0000 2.194094 59.7043 + 152 0.0000 2.199474 59.8507 + 153 0.0000 2.209323 60.1187 + 154 0.0000 2.233851 60.7862 + 155 0.0000 2.264049 61.6079 + 156 0.0000 2.292949 62.3943 + 157 0.0000 2.328547 63.3630 + 158 0.0000 2.353196 64.0337 + 159 0.0000 2.386068 64.9282 + 160 0.0000 2.396850 65.2216 + 161 0.0000 2.431973 66.1774 + 162 0.0000 2.447855 66.6095 + 163 0.0000 2.464402 67.0598 + 164 0.0000 2.481870 67.5351 + 165 0.0000 2.518395 68.5290 + 166 0.0000 2.539287 69.0975 + 167 0.0000 2.550818 69.4113 + 168 0.0000 2.576999 70.1237 + 169 0.0000 2.593648 70.5768 + 170 0.0000 2.599903 70.7470 + 171 0.0000 2.644178 71.9517 + 172 0.0000 2.647941 72.0541 + 173 0.0000 2.674196 72.7686 + 174 0.0000 2.712068 73.7991 + 175 0.0000 2.730416 74.2984 + 176 0.0000 2.794514 76.0426 + 177 0.0000 2.833354 77.0995 + 178 0.0000 2.853120 77.6373 + 179 0.0000 2.890631 78.6581 + 180 0.0000 2.937856 79.9431 + 181 0.0000 2.946051 80.1661 + 182 0.0000 2.978523 81.0497 + 183 0.0000 2.990540 81.3767 + 184 0.0000 3.027876 82.3927 + 185 0.0000 3.108052 84.5744 + 186 0.0000 3.115810 84.7855 + 187 0.0000 3.171398 86.2981 + 188 0.0000 3.181488 86.5727 + 189 0.0000 3.198173 87.0267 + 190 0.0000 3.228962 87.8645 + 191 0.0000 3.231025 87.9206 + 192 0.0000 3.284378 89.3725 + 193 0.0000 3.309250 90.0493 + 194 0.0000 3.340994 90.9131 + 195 0.0000 3.360193 91.4355 + 196 0.0000 3.391735 92.2938 + 197 0.0000 3.410570 92.8063 + 198 0.0000 3.414464 92.9123 + 199 0.0000 3.463251 94.2399 + 200 0.0000 3.483717 94.7967 + 201 0.0000 3.603800 98.0644 + 202 0.0000 3.655720 99.4772 + 203 0.0000 3.748900 102.0128 + 204 0.0000 3.763301 102.4046 + 205 0.0000 3.855254 104.9068 + 206 0.0000 4.092399 111.3598 + 207 0.0000 4.198049 114.2347 + 208 0.0000 4.262423 115.9864 + + ******************************** + * MULLIKEN POPULATION ANALYSIS * + ******************************** + +----------------------- +MULLIKEN ATOMIC CHARGES +----------------------- + 0 C : -0.091167 + 1 C : 0.226660 + 2 C : 0.216986 + 3 C : -0.048539 + 4 C : -0.139953 + 5 C : -0.047398 + 6 H : 0.006831 + 7 H : 0.031351 + 8 H : 0.041188 + 9 C : 0.025565 + 10 C : 0.115109 + 11 H : 0.058329 + 12 H : 0.035990 + 13 N : -0.379821 + 14 H : 0.017916 + 15 H : 0.036933 + 16 H : 0.120814 + 17 H : 0.124192 + 18 O : -0.406863 + 19 H : 0.224684 + 20 O : -0.394688 + 21 H : 0.225879 +Sum of atomic charges: 0.0000000 + +-------------------------------- +MULLIKEN REDUCED ORBITAL CHARGES +-------------------------------- + 0 C s : 3.213707 s : 3.213707 + pz : 1.072015 p : 2.836443 + px : 0.881181 + py : 0.883248 + dz2 : 0.003641 d : 0.041017 + dxz : 0.007744 + dyz : 0.003026 + dx2y2 : 0.014439 + dxy : 0.012167 + 1 C s : 2.993719 s : 2.993719 + pz : 0.990304 p : 2.692357 + px : 0.772081 + py : 0.929972 + dz2 : 0.006833 d : 0.087263 + dxz : 0.015022 + dyz : 0.012486 + dx2y2 : 0.024888 + dxy : 0.028034 + 2 C s : 3.008961 s : 3.008961 + pz : 0.997817 p : 2.686209 + px : 0.747689 + py : 0.940703 + dz2 : 0.006759 d : 0.087844 + dxz : 0.018301 + dyz : 0.008923 + dx2y2 : 0.028942 + dxy : 0.024918 + 3 C s : 3.180509 s : 3.180509 + pz : 1.017197 p : 2.825624 + px : 0.905561 + py : 0.902867 + dz2 : 0.003671 d : 0.042405 + dxz : 0.008105 + dyz : 0.003515 + dx2y2 : 0.012342 + dxy : 0.014772 + 4 C s : 3.030892 s : 3.030892 + pz : 0.983535 p : 3.056613 + px : 1.056088 + py : 1.016990 + dz2 : 0.004269 d : 0.052448 + dxz : 0.006639 + dyz : 0.008390 + dx2y2 : 0.015539 + dxy : 0.017612 + 5 C s : 3.158469 s : 3.158469 + pz : 1.030282 p : 2.845985 + px : 0.877791 + py : 0.937913 + dz2 : 0.003636 d : 0.042944 + dxz : 0.005083 + dyz : 0.005752 + dx2y2 : 0.013822 + dxy : 0.014652 + 6 H s : 0.967290 s : 0.967290 + pz : 0.004732 p : 0.025879 + px : 0.002992 + py : 0.018155 + 7 H s : 0.942692 s : 0.942692 + pz : 0.004576 p : 0.025957 + px : 0.011664 + py : 0.009717 + 8 H s : 0.932861 s : 0.932861 + pz : 0.004152 p : 0.025951 + px : 0.002913 + py : 0.018886 + 9 C s : 3.036189 s : 3.036189 + pz : 1.018078 p : 2.893766 + px : 0.872365 + py : 1.003323 + dz2 : 0.008429 d : 0.044479 + dxz : 0.003939 + dyz : 0.012519 + dx2y2 : 0.007061 + dxy : 0.012531 + 10 C s : 3.024748 s : 3.024748 + pz : 1.003165 p : 2.797617 + px : 0.838564 + py : 0.955887 + dz2 : 0.010661 d : 0.062526 + dxz : 0.006655 + dyz : 0.015858 + dx2y2 : 0.010810 + dxy : 0.018542 + 11 H s : 0.918069 s : 0.918069 + pz : 0.013461 p : 0.023602 + px : 0.002814 + py : 0.007327 + 12 H s : 0.940278 s : 0.940278 + pz : 0.012597 p : 0.023732 + px : 0.003011 + py : 0.008123 + 13 N s : 3.492765 s : 3.492765 + pz : 1.489712 p : 3.864196 + px : 1.080987 + py : 1.293497 + dz2 : 0.006470 d : 0.022860 + dxz : 0.001564 + dyz : 0.003323 + dx2y2 : 0.002113 + dxy : 0.009389 + 14 H s : 0.960035 s : 0.960035 + pz : 0.013088 p : 0.022049 + px : 0.001964 + py : 0.006997 + 15 H s : 0.940450 s : 0.940450 + pz : 0.013059 p : 0.022617 + px : 0.001876 + py : 0.007682 + 16 H s : 0.834138 s : 0.834138 + pz : 0.021850 p : 0.045048 + px : 0.006297 + py : 0.016901 + 17 H s : 0.830821 s : 0.830821 + pz : 0.010515 p : 0.044986 + px : 0.018274 + py : 0.016198 + 18 O s : 3.690250 s : 3.690250 + pz : 1.885542 p : 4.703447 + px : 1.614868 + py : 1.203037 + dz2 : 0.002095 d : 0.013167 + dxz : 0.001925 + dyz : 0.000684 + dx2y2 : 0.004040 + dxy : 0.004423 + 19 H s : 0.703950 s : 0.703950 + pz : 0.016970 p : 0.071365 + px : 0.011604 + py : 0.042791 + 20 O s : 3.688759 s : 3.688759 + pz : 1.881570 p : 4.692571 + px : 1.164346 + py : 1.646655 + dz2 : 0.002162 d : 0.013357 + dxz : 0.001541 + dyz : 0.001128 + dx2y2 : 0.001433 + dxy : 0.007093 + 21 H s : 0.702307 s : 0.702307 + pz : 0.017015 p : 0.071814 + px : 0.034091 + py : 0.020708 + + + ******************************* + * LOEWDIN POPULATION ANALYSIS * + ******************************* + +---------------------- +LOEWDIN ATOMIC CHARGES +---------------------- + 0 C : -0.070462 + 1 C : 0.053440 + 2 C : 0.056053 + 3 C : -0.033071 + 4 C : -0.034690 + 5 C : -0.049471 + 6 H : 0.019475 + 7 H : 0.022633 + 8 H : 0.033988 + 9 C : -0.017708 + 10 C : 0.044381 + 11 H : 0.030208 + 12 H : 0.020307 + 13 N : -0.163130 + 14 H : -0.005774 + 15 H : 0.013862 + 16 H : 0.059476 + 17 H : 0.062746 + 18 O : -0.131965 + 19 H : 0.109008 + 20 O : -0.126284 + 21 H : 0.106977 + +------------------------------- +LOEWDIN REDUCED ORBITAL CHARGES +------------------------------- + 0 C s : 2.851824 s : 2.851824 + pz : 1.048519 p : 3.123260 + px : 1.039765 + py : 1.034977 + dz2 : 0.007184 d : 0.095378 + dxz : 0.015170 + dyz : 0.004711 + dx2y2 : 0.037608 + dxy : 0.030706 + 1 C s : 2.830051 s : 2.830051 + pz : 0.978773 p : 2.931448 + px : 0.960411 + py : 0.992264 + dz2 : 0.013344 d : 0.185062 + dxz : 0.029143 + dyz : 0.023808 + dx2y2 : 0.057521 + dxy : 0.061245 + 2 C s : 2.825819 s : 2.825819 + pz : 0.987819 p : 2.932734 + px : 0.897306 + py : 1.047610 + dz2 : 0.013185 d : 0.185394 + dxz : 0.034998 + dyz : 0.016949 + dx2y2 : 0.062925 + dxy : 0.057337 + 3 C s : 2.851101 s : 2.851101 + pz : 0.996979 p : 3.086047 + px : 1.051020 + py : 1.038048 + dz2 : 0.007177 d : 0.095923 + dxz : 0.016012 + dyz : 0.005223 + dx2y2 : 0.031847 + dxy : 0.035662 + 4 C s : 2.848345 s : 2.848345 + pz : 0.957786 p : 3.073516 + px : 1.041766 + py : 1.073964 + dz2 : 0.007963 d : 0.112829 + dxz : 0.011904 + dyz : 0.015755 + dx2y2 : 0.036586 + dxy : 0.040622 + 5 C s : 2.846792 s : 2.846792 + pz : 1.014750 p : 3.104886 + px : 1.044462 + py : 1.045674 + dz2 : 0.006933 d : 0.097793 + dxz : 0.009262 + dyz : 0.010951 + dx2y2 : 0.033145 + dxy : 0.037502 + 6 H s : 0.910818 s : 0.910818 + pz : 0.016350 p : 0.069706 + px : 0.010927 + py : 0.042429 + 7 H s : 0.906558 s : 0.906558 + pz : 0.015813 p : 0.070808 + px : 0.029705 + py : 0.025290 + 8 H s : 0.895943 s : 0.895943 + pz : 0.014878 p : 0.070070 + px : 0.010699 + py : 0.044493 + 9 C s : 2.839195 s : 2.839195 + pz : 1.050682 p : 3.081080 + px : 0.996586 + py : 1.033813 + dz2 : 0.018393 d : 0.097433 + dxz : 0.007697 + dyz : 0.027504 + dx2y2 : 0.016503 + dxy : 0.027337 + 10 C s : 2.837695 s : 2.837695 + pz : 1.047481 p : 2.988227 + px : 0.929671 + py : 1.011076 + dz2 : 0.022255 d : 0.129697 + dxz : 0.012761 + dyz : 0.035052 + dx2y2 : 0.021263 + dxy : 0.038365 + 11 H s : 0.905122 s : 0.905122 + pz : 0.031951 p : 0.064670 + px : 0.011442 + py : 0.021278 + 12 H s : 0.915789 s : 0.915789 + pz : 0.029712 p : 0.063904 + px : 0.011716 + py : 0.022475 + 13 N s : 3.157504 s : 3.157504 + pz : 1.499339 p : 3.960310 + px : 1.129642 + py : 1.331329 + dz2 : 0.011322 d : 0.045316 + dxz : 0.002638 + dyz : 0.007227 + dx2y2 : 0.005243 + dxy : 0.018886 + 14 H s : 0.942974 s : 0.942974 + pz : 0.031350 p : 0.062800 + px : 0.010683 + py : 0.020767 + 15 H s : 0.924488 s : 0.924488 + pz : 0.031319 p : 0.061649 + px : 0.009608 + py : 0.020722 + 16 H s : 0.825871 s : 0.825871 + pz : 0.058897 p : 0.114654 + px : 0.016698 + py : 0.039059 + 17 H s : 0.822230 s : 0.822230 + pz : 0.029180 p : 0.115025 + px : 0.043222 + py : 0.042622 + 18 O s : 3.381178 s : 3.381178 + pz : 1.837640 p : 4.726042 + px : 1.612368 + py : 1.276034 + dz2 : 0.003389 d : 0.024744 + dxz : 0.002625 + dyz : 0.001268 + dx2y2 : 0.009450 + dxy : 0.008013 + 19 H s : 0.708127 s : 0.708127 + pz : 0.050191 p : 0.182865 + px : 0.036680 + py : 0.095995 + 20 O s : 3.381833 s : 3.381833 + pz : 1.834890 p : 4.719596 + px : 1.225396 + py : 1.659309 + dz2 : 0.003467 d : 0.024856 + dxz : 0.003017 + dyz : 0.000915 + dx2y2 : 0.003613 + dxy : 0.013844 + 21 H s : 0.708693 s : 0.708693 + pz : 0.050366 p : 0.184329 + px : 0.073864 + py : 0.060099 + + + ***************************** + * 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 C 6.0912 6.0000 -0.0912 3.8703 3.8703 0.0000 + 1 C 5.7733 6.0000 0.2267 3.7989 3.7989 -0.0000 + 2 C 5.7830 6.0000 0.2170 3.8873 3.8873 0.0000 + 3 C 6.0485 6.0000 -0.0485 3.8971 3.8971 0.0000 + 4 C 6.1400 6.0000 -0.1400 3.8366 3.8366 0.0000 + 5 C 6.0474 6.0000 -0.0474 3.8924 3.8924 0.0000 + 6 H 0.9932 1.0000 0.0068 1.0051 1.0051 0.0000 + 7 H 0.9686 1.0000 0.0314 0.9973 0.9973 -0.0000 + 8 H 0.9588 1.0000 0.0412 0.9979 0.9979 0.0000 + 9 C 5.9744 6.0000 0.0256 3.8924 3.8924 0.0000 + 10 C 5.8849 6.0000 0.1151 4.0003 4.0003 -0.0000 + 11 H 0.9417 1.0000 0.0583 0.9789 0.9789 0.0000 + 12 H 0.9640 1.0000 0.0360 0.9759 0.9759 0.0000 + 13 N 7.3798 7.0000 -0.3798 2.9221 2.9221 0.0000 + 14 H 0.9821 1.0000 0.0179 0.9638 0.9638 -0.0000 + 15 H 0.9631 1.0000 0.0369 0.9712 0.9712 -0.0000 + 16 H 0.8792 1.0000 0.1208 0.9807 0.9807 -0.0000 + 17 H 0.8758 1.0000 0.1242 0.9781 0.9781 -0.0000 + 18 O 8.4069 8.0000 -0.4069 2.0022 2.0022 0.0000 + 19 H 0.7753 1.0000 0.2247 0.9804 0.9804 0.0000 + 20 O 8.3947 8.0000 -0.3947 2.0264 2.0264 -0.0000 + 21 H 0.7741 1.0000 0.2259 0.9853 0.9853 -0.0000 + + Mayer bond orders larger than 0.100000 +B( 0-C , 1-C ) : 1.3891 B( 0-C , 4-C ) : 1.4104 B( 0-C , 6-H ) : 1.0053 +B( 1-C , 2-C ) : 1.3092 B( 1-C , 18-O ) : 1.0375 B( 2-C , 3-C ) : 1.4203 +B( 2-C , 20-O ) : 1.0799 B( 3-C , 5-C ) : 1.4009 B( 3-C , 8-H ) : 1.0047 +B( 4-C , 5-C ) : 1.4303 B( 4-C , 9-C ) : 0.9678 B( 5-C , 7-H ) : 1.0022 +B( 9-C , 10-C ) : 1.0618 B( 9-C , 11-H ) : 0.9628 B( 9-C , 12-H ) : 0.9647 +B( 10-C , 13-N ) : 1.0045 B( 10-C , 14-H ) : 0.9727 B( 10-C , 15-H ) : 0.9651 +B( 13-N , 16-H ) : 0.9666 B( 13-N , 17-H ) : 0.9680 B( 18-O , 19-H ) : 0.9400 +B( 20-O , 21-H ) : 0.9381 + +------- +TIMINGS +------- + +Total SCF time: 0 days 0 hours 0 min 5 sec + +Total time .... 5.829 sec +Sum of individual times .... 5.698 sec ( 97.8%) + +Fock matrix formation .... 5.441 sec ( 93.3%) +Diagonalization .... 0.046 sec ( 0.8%) +Density matrix formation .... 0.003 sec ( 0.1%) +Population analysis .... 0.007 sec ( 0.1%) +Initial guess .... 0.050 sec ( 0.9%) +Orbital Transformation .... 0.000 sec ( 0.0%) +Orbital Orthonormalization .... 0.000 sec ( 0.0%) +DIIS solution .... 0.039 sec ( 0.7%) +SOSCF solution .... 0.056 sec ( 1.0%) + +Maximum memory used throughout the entire SCF-calculation: 229.2 MB + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -513.113388868587 +------------------------- -------------------- + + + + ************************************************************ + * Program running with 6 parallel MPI-processes * + * working on a common directory * + ************************************************************ +------------------------------------------------------------------------------ + ORCA SCF GRADIENT CALCULATION +------------------------------------------------------------------------------ + +Gradient of the Hartree-Fock SCF energy: +Hartree-Fock type ... RHF +Number of operators ... 1 +Number of atoms ... 22 +Basis set dimensions ... 209 +Integral neglect threshold ... 2.5e-11 +Integral primitive cutoff ... 2.5e-12 +SHARK Integral package ... ON + +Nuc. rep. gradient (SHARK) ... done ( 0.0 sec) +HCore & Overlap gradient (SHARK) ... done ( 0.0 sec) +Two-Electron gradient (SHARK) ... done ( 1.9 sec) + +------------------ +CARTESIAN GRADIENT +------------------ + + 1 C : 0.005778618 0.024701072 0.000628149 + 2 C : -0.032387534 -0.020888587 -0.000491316 + 3 C : 0.013022767 -0.013820567 -0.000455433 + 4 C : 0.000442791 -0.014037682 -0.000474248 + 5 C : 0.006390853 0.008424147 0.001298969 + 6 C : 0.008929845 -0.016404774 -0.000592605 + 7 H : 0.001073781 0.000156984 -0.000041875 + 8 H : -0.000468076 -0.002214979 0.000004088 + 9 H : 0.003980854 -0.002369604 -0.000108089 + 10 C : -0.005040539 -0.001038943 -0.002330039 + 11 C : -0.003126460 -0.000276820 0.003887352 + 12 H : -0.001849173 0.004741132 0.013538358 + 13 H : -0.000375276 0.004296657 -0.011656289 + 14 N : -0.020499798 0.007373483 0.020336553 + 15 H : 0.006715125 -0.001306067 -0.012263601 + 16 H : -0.001688340 -0.006585166 0.012895903 + 17 H : -0.000532610 0.020068781 -0.028391439 + 18 H : 0.022997109 -0.026866202 0.003112870 + 19 O : 0.027960063 -0.006000596 -0.000233205 + 20 H : -0.015089874 0.032118582 0.000952172 + 21 O : 0.019753810 0.011993684 0.000288137 + 22 H : -0.035987936 -0.002064536 0.000095588 + +Difference to translation invariance: + : 0.0000000000 0.0000000000 -0.0000000000 + +Difference to rotation invariance: + : -0.0000000267 0.0000000216 0.0000003064 + +Norm of the cartesian gradient ... 0.1061965748 +RMS gradient ... 0.0130718947 +MAX gradient ... 0.0359879363 + +------- +TIMINGS +------- + +Total SCF gradient time ... 2.003 sec + +One electron gradient .... 0.024 sec ( 1.2%) +Two electron gradient .... 1.944 sec ( 97.1%) + +Maximum memory used throughout the entire SCFGRAD-calculation: 19.2 MB + + *************************************** + * ORCA property calculations * + *************************************** + + --------------------- + Active property flags + --------------------- + (+) Dipole Moment + + +------------------------------------------------------------------------------ + ORCA ELECTRIC PROPERTIES CALCULATION +------------------------------------------------------------------------------ + +Dipole Moment Calculation ... on +Quadrupole Moment Calculation ... off +Polarizability Calculation ... off +GBWName ... dopamine.gbw +Electron density ... dopamine.scfp +The origin for moment calculation is the CENTER OF MASS = (-2.513873, 2.028711 0.011272) + +------------- +DIPOLE MOMENT +------------- + X Y Z +Electronic contribution: -12.88857 -0.83250 0.28654 +Nuclear contribution : 13.02291 1.52368 -0.70153 + ----------------------------------------- +Total Dipole Moment : 0.13434 0.69118 -0.41499 + ----------------------------------------- +Magnitude (a.u.) : 0.81731 +Magnitude (Debye) : 2.07744 + + + +-------------------- +Rotational spectrum +-------------------- + +Rotational constants in cm-1: 0.094926 0.017460 0.014853 +Rotational constants in MHz : 2845.800360 523.445123 445.284596 + + Dipole components along the rotational axes: +x,y,z [a.u.] : 0.195615 0.666359 -0.430923 +x,y,z [Debye]: 0.497215 1.693751 -1.095319 + + + +Timings for individual modules: + +Sum of individual times ... 8.563 sec (= 0.143 min) +GTO integral calculation ... 0.288 sec (= 0.005 min) 3.4 % +SCF iterations ... 6.050 sec (= 0.101 min) 70.7 % +SCF Gradient evaluation ... 2.225 sec (= 0.037 min) 26.0 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 0 minutes 8 seconds 825 msec diff --git a/tests/test_orca_spout.py b/tests/test_orca_spout.py new file mode 100644 index 00000000..ecb1a5ca --- /dev/null +++ b/tests/test_orca_spout.py @@ -0,0 +1,90 @@ +import unittest + +import numpy as np +from comp_sys import CompLabeledSys, IsNoPBC +from context import dpdata + + +class TestOrcaSP(unittest.TestCase, CompLabeledSys, IsNoPBC): + def setUp(self): + energy_convert = dpdata.unit.EnergyConversion("hartree", "eV").value() + force_convert = dpdata.unit.ForceConversion( + "hartree/bohr", "eV/angstrom" + ).value() + + self.system_1 = dpdata.LabeledSystem("orca/orca.spout", fmt="orca/spout") + + self.system_2 = dpdata.LabeledSystem( + data={ + "atom_types": np.array( + [0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 2, 1, 1, 1, 1, 3, 1, 3, 1] + ), + "atom_names": ["C", "H", "N", "O"], + "atom_numbs": [8, 11, 1, 2], + "coords": np.array( + [ + [ + [-1.74744e00, 2.17247e00, 3.84400e-02], + [-3.05879e00, 1.67227e00, 3.01100e-02], + [-3.27420e00, 2.83660e-01, -7.86000e-03], + [-2.17997e00, -5.85250e-01, -3.67900e-02], + [-6.42570e-01, 1.30482e00, 1.03900e-02], + [-8.75230e-01, -8.54100e-02, -2.75900e-02], + [-1.58753e00, 3.24402e00, 6.79500e-02], + [-6.23100e-02, -7.96870e-01, -5.06600e-02], + [-2.34094e00, -1.65578e00, -6.62400e-02], + [7.43270e-01, 1.92237e00, 2.35500e-02], + [1.91059e00, 9.25720e-01, 4.06000e-03], + [8.36210e-01, 2.54508e00, 9.40240e-01], + [8.33280e-01, 2.58745e00, -8.63170e-01], + [3.18351e00, 1.63882e00, 3.70200e-02], + [1.86317e00, 2.99040e-01, -9.14520e-01], + [1.84793e00, 2.69100e-01, 8.99400e-01], + [3.28398e00, 2.20442e00, -8.37230e-01], + [3.95753e00, 9.35910e-01, 5.24200e-02], + [-4.10991e00, 2.51820e00, 5.88000e-02], + [-3.99914e00, 3.47933e00, 8.64100e-02], + [-4.52084e00, -2.33960e-01, -1.68400e-02], + [-5.31660e00, 3.15930e-01, 2.60000e-03], + ] + ] + ), + "energies": np.array([-513.113388868587]) * energy_convert, + "forces": np.array( + [ + [ + [-5.7786180e-03, -2.4701072e-02, -6.2814900e-04], + [3.2387534e-02, 2.0888587e-02, 4.9131600e-04], + [-1.3022767e-02, 1.3820567e-02, 4.5543300e-04], + [-4.4279100e-04, 1.4037682e-02, 4.7424800e-04], + [-6.3908530e-03, -8.4241470e-03, -1.2989690e-03], + [-8.9298450e-03, 1.6404774e-02, 5.9260500e-04], + [-1.0737810e-03, -1.5698400e-04, 4.1875000e-05], + [4.6807600e-04, 2.2149790e-03, -4.0880000e-06], + [-3.9808540e-03, 2.3696040e-03, 1.0808900e-04], + [5.0405390e-03, 1.0389430e-03, 2.3300390e-03], + [3.1264600e-03, 2.7682000e-04, -3.8873520e-03], + [1.8491730e-03, -4.7411320e-03, -1.3538358e-02], + [3.7527600e-04, -4.2966570e-03, 1.1656289e-02], + [2.0499798e-02, -7.3734830e-03, -2.0336553e-02], + [-6.7151250e-03, 1.3060670e-03, 1.2263601e-02], + [1.6883400e-03, 6.5851660e-03, -1.2895903e-02], + [5.3261000e-04, -2.0068781e-02, 2.8391439e-02], + [-2.2997109e-02, 2.6866202e-02, -3.1128700e-03], + [-2.7960063e-02, 6.0005960e-03, 2.3320500e-04], + [1.5089874e-02, -3.2118582e-02, -9.5217200e-04], + [-1.9753810e-02, -1.1993684e-02, -2.8813700e-04], + [3.5987936e-02, 2.0645360e-03, -9.5588000e-05], + ] + ] + ) + * force_convert, + "cells": np.zeros((1, 3, 3)), + "orig": np.zeros(3), + "nopbc": True, + } + ) + self.places = 6 + self.e_places = 9 + self.f_places = 9 + self.v_places = 6