van der Walt, S, Colbert, SC, Varoquaux, G. The NumPy array: a structure for efficient numerical computation. Comput Sci Eng 2011, 13:22.
Jones, E, Oliphant, T, Peterson, P, et al. SciPy: Open source scientific tools for Python, 2001. Available at: http://www.scipy.org/. (Accessed September 6, 2017).
Dalcin, LD, Paz, RR, Kler, PA, Cosimo, A. Parallel distributed computing using Python. Adv Water Resour 2011, 34:1124–1139.
Turney, JM, Simmonett, AC, Parrish, RM, Hohenstein, EG, Evangelista, FA, Fermann, JT, Mintz, BJ, Burns, LA, Wilke, JJ, Abrams, ML, et al. Psi4: an open‐source ab initio electronic structure program. WIREs Comput Mol Sci 2012, 2:556–565. https://doi.org/10.1002/wcms.93.
Bahn, SR, Jacobsen, KW. An object‐oriented scripting interface to a legacy electronic structure code. Comput Sci Eng 2002, 4:56.
Ong, SP, Richards, WD, Jain, A, Hautier, G, Kocher, M, Cholia, S, Gunter, D, Chevrier, VL, Persson, KA, Ceder, G. Python Materials Genomics (pymatgen): a robust, open‐source python library for materials analysis. Comput Mater Sci 2013, 68:314–319.
Jacob, CR, Beyhan, SM, Bulo, RE, Gomes, ASP, Götz, AW, Kiewisch, K, Sikkema, J, Visscher, L. PyADF—a scripting framework for multiscale quantum chemistry. J Comput Chem 2011, 32:2328–2338. https://doi.org/10.1002/jcc.21810.
Hirata, S. Tensor contraction engine: abstraction and automated parallel implementation of configuration‐interaction, coupled‐cluster, and many‐body perturbation theories. J Phys Chem A 2003, 107:9887–9897. https://doi.org/10.1021/jp034596z.
Neuscamman, E, Yanai, T, Chan, GK‐L. Quadratic canonical transformation theory and higher order density matrices. J Chem Phys 2009, 130:124102.
Saitow, M, Kurashige, Y, Yanai, T. Multireference configuration interaction theory using cumulant reconstruction with internal contraction of density matrix renormalization group wave function. J Chem Phys 2013, 139:044118.
Muller, RP. PyQuante, Version 1.6.3. Available at: http://pyquante.sourceforge.net/. (Accessed September 6, 2017).
Enkovaara, J, Rostgaard, C, Mortensen, JJ, Chen, J, Dułak, M, Ferrighi, L, Gavnholt, J, Glinsvad, C, Haikola, V, Hansen, HA, et al. Electronic structure calculations with GPAW: a real‐space implementation of the projector augmented‐wave method. J Phys Condens Matter 2010, 22:253202.
Sun, Q, Chan, GK‐L. Exact and optimal quantum mechanics/molecular mechanics boundaries. J Chem Theory Comput 2014, 10:3784–3790. https://doi.org/10.1021/ct500512f.
Marques, MA, Oliveira, MJ, Burnus, T. Libxc: a library of exchange and correlation functionals for density functional theory. Comput Phys Commun 2012, 183:2272–2281.
Ekström, U, Visscher, L, Bast, R, Thorvaldsen, AJ, Ruud, K. Arbitrary‐order density functional response theory from automatic differentiation. J Chem Theory Comput 2010, 6:1971–1980.
Sun, Q. Libcint: an efficient general integral library for Gaussian basis functions. J Comput Chem 2015, 36:1664–1671. https://doi.org/10.1002/jcc.23981.
Sun, Q. Co‐iterative augmented Hessian method for orbital optimization. arXiv:1610.08423v1 [physics.chem‐ph], 2016.
Scuseria, GE, Janssen, CL, Schaefer, III HF. An efficient reformulation of the closed‐shell coupled cluster single and double excitation (CCSD) equations. J Chem Phys 1988, 89:7382.
Stanton, JF, Gauss, J, Watts JD, Bartlett, RJ. A direct product decomposition approach for symmetry exploitation in many‐body methods. I. Energy calculations. J Chem Phys 1991, 94:4334.
Koch, H, de Merás, AS, Helgaker, T, Christiansen, O. The integral‐direct coupled cluster singles and doubles model. J Chem Phys 1996, 104:4157. https://doi.org/10.1063/1.471227.
Hirata, S, Podeszwa, R, Tobita, M, Bartlett, RJ. Coupled‐cluster singles and doubles for extended systems. J Chem Phys 2004, 120:2581. https://doi.org/10.1063/1.1637577.
Raghavachari, K, Trucks, GW, Pople, JA, Head‐Gordon, M. A fifth‐order perturbation comparison of electron correlation theories. Chem Phys Lett 1989, 157:479–483.
Scuseria, GE. Analytic evaluation of energy gradients for the singles and doubles coupled cluster method including perturbative triple excitations: theory and applications to FOOF and Cr2. J Chem Phys 1991, 94:442. https://doi.org/10.1063/1.460359.
Scheiner, AC, Scuseria, GE, Rice, JE, Lee, TJ, Schaefer III, HFS. Analytic evaluation of energy gradients for the single and double excitation coupled cluster (CCSD) wave function: theory and application. J Chem Phys 1987, 87:5361. https://doi.org/10.1063/1.453655.
Salter, EA, Trucks, GW, Bartlett, RJ. Analytic energy derivatives in many‐body methods. I. First derivatives. J Chem Phys 1989, 90:1752. https://doi.org/10.1063/1.456069.
Sekino, H, Bartlett, RJ. A linear response, coupled‐cluster theory for excitation energy. Int J Quantum Chem 1984, 26:255–265. https://doi.org/10.1002/qua.560260826.
Nooijen, M, Bartlett, RJ. Equation of motion coupled cluster method for electron attachment. J Chem Phys 1995, 102:3629. https://doi.org/10.1063/1.468592.
Musiał, M, Kucharski, SA, Bartlett, RJ. Equation‐of‐motion coupled cluster method with full inclusion of the connected triple excitations for ionized states: IP‐EOM‐CCSDT. J Chem Phys 2003, 118:1128. https://doi.org/10.1063/1.1527013.
Gauss, J, Stanton, JF. Coupled‐cluster calculations of nuclear magnetic resonance chemical shifts. J Chem Phys 1995, 103:3561. https://doi.org/10.1063/1.470240.
Wang, Z, Tu, Z, Wang, F. Equation‐of‐motion coupled‐cluster theory for excitation energies of closed‐shell systems with spin–orbit coupling. J Chem Theory Comput 2014, 10:5567–5576. https://doi.org/10.1021/ct500854m.
Knowles, PJ, Handy, NC. A new determinant‐based full configuration interaction method. Chem Phys Lett 1984, 111:315–321.
Jensen, HJA, Jørgensen, P, Ågren, H. Efficient optimization of large scale MCSCF wave functions with a restricted step algorithm. J Chem Phys 1987, 87:451. https://doi.org/10.1063/1.453590.
Werner, H‐J, Knowles, PJ. A second order multiconfiguration SCF procedure with optimum convergence. J Chem Phys 1985, 82:5053.
Angeli, C, Cimiraglia, R, Evangelisti, S, Leininger, T, Malrieu, J‐P. Introduction of n‐electron valence states for multireference perturbation theory. J Chem Phys 2001, 114:10252. https://doi.org/10.1063/1.1361246.
Guo, S, Watson, MA, Hu, W, Sun, Q, Chan, GK‐L. N‐Electron valence state perturbation theory based on a density matrix renormalization group reference function, with applications to the chromium dimer and a trimer model of poly(p‐phenylenevinylene). J Chem Theory Comput 2016, 12:1583–1591. https://doi.org/10.1021/acs.jctc.5b01225.
Sharma, S, Chan, GK‐L. Spin‐adapted density matrix renormalization group algorithms for quantum chemistry. J Chem Phys 2012, 136:124121.
Wouters, S, Poelmans, W, Ayers, PW, Van Neck, D. CheMPS2: a free open‐source spin‐adapted implementation of the density matrix renormalization group for ab initio quantum chemistry. Comput Phys Comm 2014, 185:1501–1514.
Sun, Q, Yang, J, Chan, GK‐L. A general second order complete active space self‐consistent‐field solver for large‐scale systems. Chem Phys Lett 2017, 683:291–299. http://dx.doi.org/10.1016/j.cplett.2017.03.004
Booth, GH, Thom, AJW, Alavi, A. Fermion Monte Carlo without fixed nodes: a game of life, death, and annihilation in Slater determinant space. J Chem Phys 2009, 131:054106.
Thomas, RE, Sun, Q, Alavi, A, Booth, GH. Stochastic multiconfigurational self‐consistent field theory. J Chem Theory Comput 2015, 11:5316–5325. https://doi.org/10.1021/acs.jctc.5b00917.
Sharma, S, Jeanmairet, G, Alavi, A. Quasi‐degenerate perturbation theory using matrix product states. J Chem Phys 2016, 144:034103.
Chan, GK‐L, Head‐Gordon, M. Highly correlated calculations with a polynomial cost algorithm: a study of the density matrix renormalization group. J Chem Phys 2002, 116:4462. https://doi.org/10.1063/1.1449459.
Chan, GK‐L. An algorithm for large scale density matrix renormalization group calculations. J Chem Phys 2004, 120:3172. https://doi.org/10.1063/1.1638734.
Ghosh, D, Hachmann, J, Yanai, T, Chan, GK‐L. Orbital optimization in the density matrix renormalization group, with applications to polyenes and β‐carotene. J Chem Phys 2008, 128:144117. https://doi.org/10.1063/1.2883976.
Furche, F, Ahlrichs, R. Adiabatic time‐dependent density functional methods for excited state properties. J Chem Phys 2002, 117:7433. https://doi.org/10.1063/1.1508368.
Flores‐Moreno, R, Alvarez‐Mendez, RJ, Vela, A, Köster, AM. Half‐numerical evaluation of pseudopotential integrals. J Comput Chem 2006, 27:1009–1019. https://doi.org/10.1002/jcc.20410.
Liu, W, Peng, D. Exact two‐component Hamiltonians revisited. J Chem Phys 2009, 131:031104.
Cheng, L, Xiao, Y, Liu, W. Four‐component relativistic theory for NMR parameters: unified formulation and numerical assessment of different approaches. J Chem Phys 2009, 130:144102. https://doi.org/10.1063/1.3110602.
Knizia, G. Intrinsic atomic orbitals: an unbiased bridge between quantum theory and chemical concepts. J Chem Theory Comput 2013, 9:4834–4843.
Reed, AE, Curtiss, LA, Weinhold, F. Intermolecular interactions from a natural bond orbital, donor‐acceptor viewpoint. Chem Rev 1988, 88:899–926.
Schaftenaar, G, Noordik, J. Molden: a pre‐ and post‐processing program for molecular and electronic structures. J Comput Aided Mol Des 2000, 14:123–134. https://doi.org/10.1023/A:1008193805436.
Jmol: an open‐source Java viewer for chemical structures in 3d. Available at: http://www.jmol.org/. (Accessed September 6, 2017).
Gonze, X, Jollet, F, Araujo, FA, Adams, D, Amadon, B, Applencourt, T, Audouze, C, Beuken, J‐M, Bieder, J, Bokhanchuk, A, et al. Recent developments in the ABINIT software package. Comput Phys Commun 2016, 205:106–131.
van Dam, HJJ, de Jong, W, Bylaska, E, Govind, N, Kowalski, K, Straatsma, T, Valiev, M. NWChem: scalable parallel computational chemistry. WIREs Comput Mol Sci 2011, 1:888–894. https://doi.org/10.1002/wcms.62.
Giannozzi, P, Baroni, S, Bonini, N, Calandra, M, Car, R, Cavazzoni, C, Ceresoli, D, Chiarotti, GL, Cococcioni, M, Dabo, I, et al. QUANTUM ESPRESSO: a modular and open‐source software project for quantum simulations of materials. J Phys Condens Matter 2009, 21:395502.
Schwarz, K, Blaha, P. Solid state calculations using WIEN2k. Comput Mater Sci 2003, 28:259–273.
Dovesi, R, Orlando, R, Erba, A, Zicovich‐Wilson, CM, Civalleri, B, Casassa, S, Maschio, L, Ferrabone, M, De La Pierre, M, D`Arco, P, et al. CRYSTAL14: a program for the ab initio investigation of crystalline solids. Int J Quantum Chem 2014, 114:1287–1317. https://doi.org/10.1002/qua.24658.
Pisani, C, Schutz, M, Casassa, S, Usvyat, D, Maschio, L, Lorenz, M, Erba, A. Cryscor: a program for the post‐Hartree–Fock treatment of periodic systems. Phys Chem Chem Phys 2012, 14:7615–7628. https://doi.org/10.1039/C2CP23927B.
Blum, V, Gehrke, R, Hanke, F, Havu, P, Havu, V, Ren, X, Reuter, K, Scheffler, M. Ab initio molecular simulations with numeric atom‐centered orbitals. Comput Phys Comm 2009, 180:2175–2196.
Artacho, E, Anglada, E, Diéguez, O, Gale, JD, García, A, Junquera, J, Martin, RM, Ordejón, P, Pruneda, JM, Sánchez‐Portal, D, et al. The SIESTA method: developments and applicability. J Phys Condens Matter 2008, 20:064208.
Hutter, J, Iannuzzi, M, Schiffmann, F, VandeVondele, J. cp2k: atomistic simulations of condensed matter systems. WIREs Comput Mol Sci 2014, 4:15–25. https://doi.org/10.1002/wcms.1159.
Booth, GH, Tsatsoulis, T, Chan, GK‐L, Grüneis, A. From plane waves to local Gaussians for the simulation of correlated periodic systems. J Chem Phys 2016, 145:084111.
Goedecker, S, Teter, M, Hutter, J. Separable dual‐space Gaussian pseudopotentials. Phys Rev B 1996, 54:1703.
Hartwigsen, C, Goedecker, S, Hutter, J. Relativistic separable dual‐space Gaussian pseudopotentials from H to Rn. Phys Rev B 1998, 58:3641.
Burkatzki, M, Filippi, C, Dolg, M. Energy‐consistent pseudopotentials for quantum Monte Carlo calculations. J Chem Phys 2007, 126:234105. https://doi.org/10.1063/1.2741534.
McClain, J, Sun, Q, Chan, GK‐L, Berkelbach, TC. Gaussian‐based coupled‐cluster theory for the ground‐state and band structure of solids. J Chem Theory Comput 2017, 13:1209–1218. http://dx.doi.org/10.1021/acs.jctc.7b00049
Wouters, S, Van Speybroeck, V, Van Neck, D. DMRG‐CASPT2 study of the longitudinal static second hyperpolarizability of all‐trans polyenes. J Chem Phys 2016, 145:054120.
Booth, GH, Smart, SD, Alavi, A. Linear‐scaling and parallelisable algorithms for stochastic quantum chemistry. Mol Phys 2014, 112:1855. https://doi.org/10.1080/00268976.2013.877165.
Booth, GH. Standalone NECI codebase designed for FCIQMC and other stochastic quantum chemistry methods. Available at: https://github.com/ghb24/NECI_STABLE.git. (Accessed September 6, 2017).
Werner, H‐J, Knowles, PJ, Knizia, G, Manby, FR, Schütz, M, Celani, P, Györffy, W, Kats, D, Korona, T, Lindh, R, et al., MOLPRO, version 2015.1: a package of ab initio programs, 2015. Available at: http://www.molpro.net. (Accessed September 6, 2017).
Schmidt, MW, Baldridge, KK, Boatz, JA, Elbert, ST, Gordon, MS, Jensen, JH, Koseki, S, Matsunaga, N, Nguyen, KA, Su, S, et al. General atomic and molecular electronic structure system. J Comput Chem 1993, 14:1347–1363. https://doi.org/10.1002/jcc.540141112.
Frisch, MJ, Trucks, GW, Schlegel, HB, Scuseria, GE, Robb, MA, Cheeseman, JR, Scalmani, G, Barone, V, Petersson, GA, Nakatsuji, H, et al. Gaussian 09 Revision A.02. Wallingford, CT: Gaussian Inc.; 2016.
Pulay, P. Convergence acceleration of iterative sequences. the case of SCF iteration. Chem Phys Lett 1980, 73:393–398.
Pulay, P. Improved SCF convergence acceleration. J Comput Chem 1982, 3:556–560. https://doi.org/10.1002/jcc.540030413.