├── .travis.yml ├── Eigen3 ├── BSD_LICENSE ├── Eigen │ ├── CMakeLists.txt │ ├── Cholesky │ ├── CholmodSupport │ ├── Core │ ├── Dense │ ├── Eigen │ ├── Eigenvalues │ ├── Geometry │ ├── Householder │ ├── IterativeLinearSolvers │ ├── Jacobi │ ├── LU │ ├── MetisSupport │ ├── OrderingMethods │ ├── PaStiXSupport │ ├── PardisoSupport │ ├── QR │ ├── QtAlignedMalloc │ ├── SPQRSupport │ ├── SVD │ ├── Sparse │ ├── SparseCholesky │ ├── SparseCore │ ├── SparseLU │ ├── SparseQR │ ├── StdDeque │ ├── StdList │ ├── StdVector │ ├── SuperLUSupport │ ├── UmfPackSupport │ └── src │ │ ├── Cholesky │ │ ├── LDLT.h │ │ ├── LLT.h │ │ └── LLT_LAPACKE.h │ │ ├── CholmodSupport │ │ └── CholmodSupport.h │ │ ├── Core │ │ ├── ArithmeticSequence.h │ │ ├── Array.h │ │ ├── ArrayBase.h │ │ ├── ArrayWrapper.h │ │ ├── Assign.h │ │ ├── AssignEvaluator.h │ │ ├── Assign_MKL.h │ │ ├── BandMatrix.h │ │ ├── Block.h │ │ ├── BooleanRedux.h │ │ ├── CommaInitializer.h │ │ ├── ConditionEstimator.h │ │ ├── CoreEvaluators.h │ │ ├── CoreIterators.h │ │ ├── CwiseBinaryOp.h │ │ ├── CwiseNullaryOp.h │ │ ├── CwiseTernaryOp.h │ │ ├── CwiseUnaryOp.h │ │ ├── CwiseUnaryView.h │ │ ├── DenseBase.h │ │ ├── DenseCoeffsBase.h │ │ ├── DenseStorage.h │ │ ├── Diagonal.h │ │ ├── DiagonalMatrix.h │ │ ├── DiagonalProduct.h │ │ ├── Dot.h │ │ ├── EigenBase.h │ │ ├── ForceAlignedAccess.h │ │ ├── Fuzzy.h │ │ ├── GeneralProduct.h │ │ ├── GenericPacketMath.h │ │ ├── GlobalFunctions.h │ │ ├── IO.h │ │ ├── IndexedView.h │ │ ├── Inverse.h │ │ ├── Map.h │ │ ├── MapBase.h │ │ ├── MathFunctions.h │ │ ├── MathFunctionsImpl.h │ │ ├── Matrix.h │ │ ├── MatrixBase.h │ │ ├── NestByValue.h │ │ ├── NoAlias.h │ │ ├── NumTraits.h │ │ ├── PermutationMatrix.h │ │ ├── PlainObjectBase.h │ │ ├── Product.h │ │ ├── ProductEvaluators.h │ │ ├── Random.h │ │ ├── Redux.h │ │ ├── Ref.h │ │ ├── Replicate.h │ │ ├── ReturnByValue.h │ │ ├── Reverse.h │ │ ├── Select.h │ │ ├── SelfAdjointView.h │ │ ├── SelfCwiseBinaryOp.h │ │ ├── Solve.h │ │ ├── SolveTriangular.h │ │ ├── SolverBase.h │ │ ├── StableNorm.h │ │ ├── Stride.h │ │ ├── Swap.h │ │ ├── Transpose.h │ │ ├── Transpositions.h │ │ ├── TriangularMatrix.h │ │ ├── VectorBlock.h │ │ ├── VectorwiseOp.h │ │ ├── Visitor.h │ │ ├── arch │ │ │ ├── AVX │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ ├── PacketMath.h │ │ │ │ └── TypeCasting.h │ │ │ ├── AVX512 │ │ │ │ ├── MathFunctions.h │ │ │ │ └── PacketMath.h │ │ │ ├── AltiVec │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ └── PacketMath.h │ │ │ ├── CUDA │ │ │ │ ├── Complex.h │ │ │ │ ├── Half.h │ │ │ │ ├── MathFunctions.h │ │ │ │ ├── PacketMath.h │ │ │ │ ├── PacketMathHalf.h │ │ │ │ └── TypeCasting.h │ │ │ ├── Default │ │ │ │ ├── ConjHelper.h │ │ │ │ └── Settings.h │ │ │ ├── NEON │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ └── PacketMath.h │ │ │ ├── SSE │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ ├── PacketMath.h │ │ │ │ └── TypeCasting.h │ │ │ └── ZVector │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ └── PacketMath.h │ │ ├── functors │ │ │ ├── AssignmentFunctors.h │ │ │ ├── BinaryFunctors.h │ │ │ ├── NullaryFunctors.h │ │ │ ├── StlFunctors.h │ │ │ ├── TernaryFunctors.h │ │ │ └── UnaryFunctors.h │ │ ├── products │ │ │ ├── GeneralBlockPanelKernel.h │ │ │ ├── GeneralMatrixMatrix.h │ │ │ ├── GeneralMatrixMatrixTriangular.h │ │ │ ├── GeneralMatrixMatrixTriangular_BLAS.h │ │ │ ├── GeneralMatrixMatrix_BLAS.h │ │ │ ├── GeneralMatrixVector.h │ │ │ ├── GeneralMatrixVector_BLAS.h │ │ │ ├── Parallelizer.h │ │ │ ├── SelfadjointMatrixMatrix.h │ │ │ ├── SelfadjointMatrixMatrix_BLAS.h │ │ │ ├── SelfadjointMatrixVector.h │ │ │ ├── SelfadjointMatrixVector_BLAS.h │ │ │ ├── SelfadjointProduct.h │ │ │ ├── SelfadjointRank2Update.h │ │ │ ├── TriangularMatrixMatrix.h │ │ │ ├── TriangularMatrixMatrix_BLAS.h │ │ │ ├── TriangularMatrixVector.h │ │ │ ├── TriangularMatrixVector_BLAS.h │ │ │ ├── TriangularSolverMatrix.h │ │ │ ├── TriangularSolverMatrix_BLAS.h │ │ │ └── TriangularSolverVector.h │ │ └── util │ │ │ ├── BlasUtil.h │ │ │ ├── Constants.h │ │ │ ├── DisableStupidWarnings.h │ │ │ ├── ForwardDeclarations.h │ │ │ ├── IndexedViewHelper.h │ │ │ ├── IntegralConstant.h │ │ │ ├── MKL_support.h │ │ │ ├── Macros.h │ │ │ ├── Memory.h │ │ │ ├── Meta.h │ │ │ ├── NonMPL2.h │ │ │ ├── ReenableStupidWarnings.h │ │ │ ├── StaticAssert.h │ │ │ ├── SymbolicIndex.h │ │ │ └── XprHelper.h │ │ ├── Eigenvalues │ │ ├── ComplexEigenSolver.h │ │ ├── ComplexSchur.h │ │ ├── ComplexSchur_LAPACKE.h │ │ ├── EigenSolver.h │ │ ├── GeneralizedEigenSolver.h │ │ ├── GeneralizedSelfAdjointEigenSolver.h │ │ ├── HessenbergDecomposition.h │ │ ├── MatrixBaseEigenvalues.h │ │ ├── RealQZ.h │ │ ├── RealSchur.h │ │ ├── RealSchur_LAPACKE.h │ │ ├── SelfAdjointEigenSolver.h │ │ ├── SelfAdjointEigenSolver_LAPACKE.h │ │ └── Tridiagonalization.h │ │ ├── Geometry │ │ ├── AlignedBox.h │ │ ├── AngleAxis.h │ │ ├── EulerAngles.h │ │ ├── Homogeneous.h │ │ ├── Hyperplane.h │ │ ├── OrthoMethods.h │ │ ├── ParametrizedLine.h │ │ ├── Quaternion.h │ │ ├── Rotation2D.h │ │ ├── RotationBase.h │ │ ├── Scaling.h │ │ ├── Transform.h │ │ ├── Translation.h │ │ ├── Umeyama.h │ │ └── arch │ │ │ └── Geometry_SSE.h │ │ ├── Householder │ │ ├── BlockHouseholder.h │ │ ├── Householder.h │ │ └── HouseholderSequence.h │ │ ├── IterativeLinearSolvers │ │ ├── BasicPreconditioners.h │ │ ├── BiCGSTAB.h │ │ ├── ConjugateGradient.h │ │ ├── IncompleteCholesky.h │ │ ├── IncompleteLUT.h │ │ ├── IterativeSolverBase.h │ │ ├── LeastSquareConjugateGradient.h │ │ └── SolveWithGuess.h │ │ ├── Jacobi │ │ └── Jacobi.h │ │ ├── LU │ │ ├── Determinant.h │ │ ├── FullPivLU.h │ │ ├── InverseImpl.h │ │ ├── PartialPivLU.h │ │ ├── PartialPivLU_LAPACKE.h │ │ └── arch │ │ │ └── Inverse_SSE.h │ │ ├── MetisSupport │ │ └── MetisSupport.h │ │ ├── OrderingMethods │ │ ├── Amd.h │ │ ├── Eigen_Colamd.h │ │ └── Ordering.h │ │ ├── PaStiXSupport │ │ └── PaStiXSupport.h │ │ ├── PardisoSupport │ │ └── PardisoSupport.h │ │ ├── QR │ │ ├── ColPivHouseholderQR.h │ │ ├── ColPivHouseholderQR_LAPACKE.h │ │ ├── CompleteOrthogonalDecomposition.h │ │ ├── FullPivHouseholderQR.h │ │ ├── HouseholderQR.h │ │ └── HouseholderQR_LAPACKE.h │ │ ├── SPQRSupport │ │ └── SuiteSparseQRSupport.h │ │ ├── SVD │ │ ├── BDCSVD.h │ │ ├── JacobiSVD.h │ │ ├── JacobiSVD_LAPACKE.h │ │ ├── SVDBase.h │ │ └── UpperBidiagonalization.h │ │ ├── SparseCholesky │ │ ├── SimplicialCholesky.h │ │ └── SimplicialCholesky_impl.h │ │ ├── SparseCore │ │ ├── AmbiVector.h │ │ ├── CompressedStorage.h │ │ ├── ConservativeSparseSparseProduct.h │ │ ├── MappedSparseMatrix.h │ │ ├── SparseAssign.h │ │ ├── SparseBlock.h │ │ ├── SparseColEtree.h │ │ ├── SparseCompressedBase.h │ │ ├── SparseCwiseBinaryOp.h │ │ ├── SparseCwiseUnaryOp.h │ │ ├── SparseDenseProduct.h │ │ ├── SparseDiagonalProduct.h │ │ ├── SparseDot.h │ │ ├── SparseFuzzy.h │ │ ├── SparseMap.h │ │ ├── SparseMatrix.h │ │ ├── SparseMatrixBase.h │ │ ├── SparsePermutation.h │ │ ├── SparseProduct.h │ │ ├── SparseRedux.h │ │ ├── SparseRef.h │ │ ├── SparseSelfAdjointView.h │ │ ├── SparseSolverBase.h │ │ ├── SparseSparseProductWithPruning.h │ │ ├── SparseTranspose.h │ │ ├── SparseTriangularView.h │ │ ├── SparseUtil.h │ │ ├── SparseVector.h │ │ ├── SparseView.h │ │ └── TriangularSolver.h │ │ ├── SparseLU │ │ ├── SparseLU.h │ │ ├── SparseLUImpl.h │ │ ├── SparseLU_Memory.h │ │ ├── SparseLU_Structs.h │ │ ├── SparseLU_SupernodalMatrix.h │ │ ├── SparseLU_Utils.h │ │ ├── SparseLU_column_bmod.h │ │ ├── SparseLU_column_dfs.h │ │ ├── SparseLU_copy_to_ucol.h │ │ ├── SparseLU_gemm_kernel.h │ │ ├── SparseLU_heap_relax_snode.h │ │ ├── SparseLU_kernel_bmod.h │ │ ├── SparseLU_panel_bmod.h │ │ ├── SparseLU_panel_dfs.h │ │ ├── SparseLU_pivotL.h │ │ ├── SparseLU_pruneL.h │ │ └── SparseLU_relax_snode.h │ │ ├── SparseQR │ │ └── SparseQR.h │ │ ├── StlSupport │ │ ├── StdDeque.h │ │ ├── StdList.h │ │ ├── StdVector.h │ │ └── details.h │ │ ├── SuperLUSupport │ │ └── SuperLUSupport.h │ │ ├── UmfPackSupport │ │ └── UmfPackSupport.h │ │ ├── misc │ │ ├── Image.h │ │ ├── Kernel.h │ │ ├── RealSvd2x2.h │ │ ├── blas.h │ │ ├── lapack.h │ │ ├── lapacke.h │ │ └── lapacke_mangling.h │ │ └── plugins │ │ ├── ArrayCwiseBinaryOps.h │ │ ├── ArrayCwiseUnaryOps.h │ │ ├── BlockMethods.h │ │ ├── CommonCwiseBinaryOps.h │ │ ├── CommonCwiseUnaryOps.h │ │ ├── IndexedViewMethods.h │ │ ├── MatrixCwiseBinaryOps.h │ │ └── MatrixCwiseUnaryOps.h ├── GPL_LICENSE ├── LGPL_LICENSE ├── MINPACK_LICENSE ├── MPL2_LICENSE └── README ├── Makefile ├── README.md ├── doc ├── Development_checklist ├── Example_input │ ├── Gaussian_files │ │ └── BASIS │ ├── NWChem_files │ │ └── BASIS │ ├── PDB_input │ │ ├── LICHEM_files │ │ │ ├── BASIS │ │ │ ├── connect.inp │ │ │ ├── peptide.xyz │ │ │ ├── regions.inp │ │ │ ├── tinker.key │ │ │ └── xyzfile.xyz │ │ ├── Original_files │ │ │ ├── caps.xyz │ │ │ ├── peptide_orig.pdb │ │ │ └── tinker.key │ │ ├── README │ │ └── amoebapro13.prm │ ├── Region_files │ │ ├── AMOEBAQMMM_reg.inp │ │ ├── QMMMOpt_reg.inp │ │ ├── QMMMPIMC_reg.inp │ │ └── QMOpt_reg.inp │ └── TINKER_files │ │ └── tinker.key ├── KNOWNISSUES └── images │ ├── QMMM_1.png │ ├── QMMM_2.png │ ├── QMMM_3.png │ ├── dimer.png │ └── trimer.png ├── include ├── LICHEM_Hermite.h ├── LICHEM_base_classes.h ├── LICHEM_classes.h ├── LICHEM_clibs.h ├── LICHEM_constants.h ├── LICHEM_globals.h ├── LICHEM_headers.h ├── LICHEM_matrix.h └── LICHEM_options.h ├── src ├── Analysis.cpp ├── Basis.cpp ├── Basis_sets.cpp ├── Core_funcs.cpp ├── Frozen_density.cpp ├── GPL_LICENSE ├── GauExternal.cpp ├── Gaussian.cpp ├── Hermite_eng.cpp ├── Input_reader.cpp ├── LAMMPS.cpp ├── LAMMPS2LICHEM.cpp ├── LICHEM.cpp ├── LICHEM_classes.cpp ├── Multipoles.cpp ├── NWChem.cpp ├── Optimizers.cpp ├── PSI4.cpp ├── Path_integral.cpp ├── Reaction_path.cpp ├── Struct_writer.cpp ├── TINK2LICHEM.cpp ├── TINKER.cpp ├── Text_format.cpp ├── doxygen.cfg ├── manual.bib ├── manual.tex └── runtests.py └── tests ├── Code_analysis ├── RunLint.bash ├── cpplint.py └── lichem.cppcheck ├── Gau_LAMMPS ├── freqreg.inp ├── hfreg.inp ├── methflbeads.xyz ├── methflcon.inp ├── methfluor.xyz ├── nebreg.inp ├── pbereg.inp ├── pchrgreg.inp ├── pm6reg.inp ├── watercon.inp └── waterdimer.xyz ├── Gau_TINKER ├── alkcon.inp ├── alkyl.xyz ├── freqreg.inp ├── hfreg.inp ├── methflbeads.xyz ├── methflcon.inp ├── methfluor.xyz ├── mmreg.inp ├── nebreg.inp ├── pbbasis.txt ├── pbereg.inp ├── pbopt.key ├── pboptreg.inp ├── pchrg.key ├── pchrgreg.inp ├── pm6reg.inp ├── pol.key ├── polreg.inp ├── solvreg.inp ├── watercon.inp └── waterdimer.xyz ├── NWChem_LAMMPS ├── freqreg.inp ├── methflbeads.xyz ├── methflcon.inp ├── methfluor.xyz ├── nebreg.inp ├── pbereg.inp ├── pchrgreg.inp ├── watercon.inp └── waterdimer.xyz ├── NWChem_TINKER ├── alkcon.inp ├── alkyl.xyz ├── freqreg.inp ├── methflbeads.xyz ├── methflcon.inp ├── methfluor.xyz ├── mmreg.inp ├── nebreg.inp ├── pbbasis.txt ├── pbereg.inp ├── pbopt.key ├── pboptreg.inp ├── pchrg.key ├── pchrgreg.inp ├── pol.key ├── polreg.inp ├── solvreg.inp ├── watercon.inp └── 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