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Commit 17564899 authored by Lauri Himanen's avatar Lauri Himanen
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Added parsing of cell periodicity from the the input file.

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...@@ -54,7 +54,6 @@ lib/ ...@@ -54,7 +54,6 @@ lib/
env/ env/
# CP2K files # CP2K files
*.inp
*.wfn *.wfn
*.cube *.cube
parser/parser-cp2k/cp2kparser/versions/**/input_data/*.xml parser/parser-cp2k/cp2kparser/versions/**/input_data/*.xml
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parser/parser-cp2k/cp2kparser/versions/cp2k262/input_data/cp2k_input.xml deleted 100644 → 0
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parser/parser-cp2k/cp2kparser/versions/cp2k262/input_data/references.html deleted 100644 → 0
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<HTML><BODY><HEAD><TITLE>The cp2k literature list</TITLE>
<H1>CP2K references</H1>
<TABLE border="1">
<TR><TD>[Merlot2014]</TD><TD>
<A NAME="reference_139">Merlot, P; Izsak, R; Borgo, A; Kjaergaard, T; Helgaker, T; Reine, S.<br>
<A HREF="http://dx.doi.org/10.1063/1.4894267">JOURNAL OF CHEMICAL PHYSICS, 141 (9), 094104 (2014).</A></A><br>
Charge-constrained auxiliary-density-matrix methods for the
Hartree-Fock exchange contribution.
</TD></TR>
<TR><TD>[Borstnik2014]</TD><TD>
<A NAME="reference_138">Borstnik, U; VandeVondele, J; Weber, V; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1016/j.parco.2014.03.012">PARALLEL COMPUTING, 40 (5-6), 47-58 (2014).</A></A><br>
Sparse matrix multiplication: The distributed block-compressed sparse
row library.
</TD></TR>
<TR><TD>[Rubensson2014]</TD><TD>
<A NAME="reference_137">Rubensson, E.; Niklasson, A..<br>
<A HREF="http://dx.doi.org/10.1137/130911585">SIAM Journal on Scientific Computing, 36 (2), B147-B170 (2014).</A></A><br>
Interior Eigenvalues from Density Matrix Expansions in Quantum
Mechanical Molecular Dynamics.
</TD></TR>
<TR><TD>[Hutter2014]</TD><TD>
<A NAME="reference_134">Hutter, J; Iannuzzi, M; Schiffmann, F; VandeVondele, J.<br>
<A HREF="http://dx.doi.org/10.1002/wcms.1159">WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 4 (1), 15-25 (2014).</A></A><br>
CP2K: atomistic simulations of condensed matter systems.
</TD></TR>
<TR><TD>[QUIP2014]</TD><TD>
<A NAME="reference_5">QUIP.<br>
web site, (2014).</A><br>
libAtoms/QUIP libraries from http://www.libatoms.org, please cite
web site and references for appropriate potential invoked.
</TD></TR>
<TR><TD>[Golze2013]</TD><TD>
<A NAME="reference_126">Golze, D; Iannuzzi, M; Nguyen, M-T; Passerone, D; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1021/ct400698y">Journal of Chemical Theory and Computation, 9 (11), 5086-5097 (2013).</A></A><br>
Simulation of Adsorption Processes at Metallic Interfaces:
An Image Charge Augmented QM/MM Approach.
</TD></TR>
<TR><TD>[Khaliullin2013]</TD><TD>
<A NAME="reference_133">Khaliullin, RZ; VandeVondele, J; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1021/ct400595k">JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9 (10), 4421-4427 (2013).</A></A><br>
Efficient Linear-Scaling Density Functional Theory for Molecular Systems.
</TD></TR>
<TR><TD>[DelBen2013]</TD><TD>
<A NAME="reference_119">Del Ben, M; Hutter, J; VandeVondele, J.<br>
<A HREF="http://dx.doi.org/10.1021/ct4002202">JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9 (6), 2654-2671 (2013).</A></A><br>
Electron Correlation in the Condensed Phase from a Resolution of
Identity Approach Based on the Gaussian and Plane Waves Scheme.
</TD></TR>
<TR><TD>[Tran2013]</TD><TD>
<A NAME="reference_122">Tran, F; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1063/1.4807332">JOURNAL OF CHEMICAL PHYSICS, 138 (20), 204103 (2013).</A></A><br>
Nonlocal van der Waals functionals: The case of rare-gas dimers and
solids.
</TD></TR>
<TR><TD>[Sabatini2013]</TD><TD>
<A NAME="reference_118">Sabatini, R; Gorni, T; de Gironcoli, S.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevB.87.041108">Phys. Rev. B, 87 (4), 041108(R) (2013).</A></A><br>
Nonlocal van der Waals density functional made simple and efficient.
</TD></TR>
<TR><TD>[DelBen2012]</TD><TD>
<A NAME="reference_117">Del Ben, M; Hutter, J; VandeVondele, J.<br>
<A HREF="http://dx.doi.org/10.1021/ct300531w">JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8 (11), 4177-4188 (2012).</A></A><br>
Second-Order Moller-Plesset Perturbation Theory in the Condensed Phase:
An Efficient and Massively Parallel Gaussian and Plane Waves Approach.
</TD></TR>
<TR><TD>[Marques2012]</TD><TD>
<A NAME="reference_104">Marques, MAL; Oliveira, MJT; Burnus, T.<br>
<A HREF="http://dx.doi.org/10.1016/j.cpc.2012.05.007">COMPUTER PHYSICS COMMUNICATIONS, 183 (10), 2272-2281 (2012).</A></A><br>
LIBXC: A library of exchange and correlation functionals for density
functional theory.
</TD></TR>
<TR><TD>[VandeVondele2012]</TD><TD>
<A NAME="reference_111">VandeVondele, J; Borstnik, U; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1021/ct200897x">JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8 (10), 3565-3573 (2012).</A></A><br>
Linear Scaling Self-Consistent Field Calculations with Millions of Atoms
in the Condensed Phase.
</TD></TR>
<TR><TD>[Devynck2012]</TD><TD>
<A NAME="reference_110">Devynck, F; Iannuzzi, M; Krack, M.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevB.85.184103">Phys. Rev. B, 85 (18), (2012).</A></A><br>
Frenkel pair recombinations in UO2: Importance of explicit description of
polarizability in core-shell molecular dynamics simulations.
</TD></TR>
<TR><TD>[Andreussi2012]</TD><TD>
<A NAME="reference_128">Andreussi, O; Dabo, I; Marzari, N.<br>
<A HREF="http://dx.doi.org/10.1063/1.3676407">J. Chem. Phys., 136 (6), 064102 (2012).</A></A><br>
Revised self-consistent continuum solvation in electronic-structure calculations.
</TD></TR>
<TR><TD>[Wellendorff2012]</TD><TD>
<A NAME="reference_1">Wellendorff, J; Lundgaard, K; Mogelhoj, A; Petzold, V; Landis, D; Norskov, J; Bligaard, T; Jacobsen, K.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevB.85.235149">PHYSICAL REVIEW B, 85 (23), 235149 (2012).</A></A><br>
Density functionals for surface science: Exchange-correlation model development with Bayesian error estimation.
</TD></TR>
<TR><TD>[Bernstein2012]</TD><TD>
<A NAME="reference_106">Bernstein, Noam; Varnai, Csilla; Solt, Ivan; Winfield, Steven A; Payne, Mike C; Simon, Istvan; Fuxreiter, Monika; Csanyi, Gabor.<br>
<A HREF="http://dx.doi.org/10.1039/c1cp22600b">PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14 (2), 646-656 (2012).</A></A><br>
QM/MM simulation of liquid water with an adaptive quantum region.
</TD></TR>
<TR><TD>[Jones2011]</TD><TD>
<A NAME="reference_105">Jones, Andrew; Leimkuhler, Ben.<br>
<A HREF="http://dx.doi.org/10.1063/1.3626941">JOURNAL OF CHEMICAL PHYSICS, 135 (8), 084125 (2011).</A></A><br>
Adaptive stochastic methods for sampling driven molecular systems.
</TD></TR>
<TR><TD>[Grimme2011]</TD><TD>
<A NAME="reference_89">Grimme, S; Ehrlich, S; Goerigk, L.<br>
<A HREF="http://dx.doi.org/10.1002/jcc.21759">JOURNAL OF COMPUTATIONAL CHEMISTRY, 32, 1456 (2011).</A></A><br>
Effect of the damping function in dispersion corrected density functional theory.
</TD></TR>
<TR><TD>[Guidon2010]</TD><TD>
<A NAME="reference_103">Guidon, M; Hutter, J; VandeVondele, J.<br>
<A HREF="http://dx.doi.org/10.1021/ct1002225">JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6 (8), 2348-2364 (2010).</A></A><br>
Auxiliary Density Matrix Methods for Hartree-Fock Exchange Calculations.
</TD></TR>
<TR><TD>[Grimme2010]</TD><TD>
<A NAME="reference_88">Grimme, S; Antony, J; Ehrlich, S; Krieg, H.<br>
<A HREF="http://dx.doi.org/10.1063/1.3382344">JOURNAL OF CHEMICAL PHYSICS, 132 (15), 154104 (2010).</A></A><br>
A consistent and accurate ab initio parametrization of density
functional dispersion correction (DFT-D) for the 94 elements H-Pu.
</TD></TR>
<TR><TD>[Guidon2009]</TD><TD>
<A NAME="reference_101">Guidon, M; Hutter, J; VandeVondele, J.<br>
<A HREF="http://dx.doi.org/10.1021/ct900494g">JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5 (11), 3010-3021 (2009).</A></A><br>
Robust Periodic Hartree-Fock Exchange for Large-Scale Simulations Using
Gaussian Basis Sets.
</TD></TR>
<TR><TD>[Kikuchi2009]</TD><TD>
<A NAME="reference_120">Kikuchi, Y; Imamura, Y; Nakai, H.<br>
<A HREF="http://dx.doi.org/10.1002/qua.22017">INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 109 (11), 2464-2473 (2009).</A></A><br>
One-Body Energy Decomposition Schemes Revisited: Assessment of
Mulliken-, Grid-, and Conventional Energy Density Analyses.
</TD></TR>
<TR><TD>[RomanPerez2009]</TD><TD>
<A NAME="reference_116">Roman-Perez, G; Soler, JM.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevLett.103.096102">Phys. Rev. Lett., 103 (9), 096102 (2009).</A></A><br>
Efficient Implementation of a van der Waals Density Functional:
Application to Double-Wall Carbon Nanotubes.
</TD></TR>
<TR><TD>[Ceriotti2009b]</TD><TD>
<A NAME="reference_100">Ceriotti, M; Bussi, G; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevLett.103.030603">PHYSICAL REVIEW LETTERS, 103 (3), 030603 (2009).</A></A><br>
Nuclear Quantum Effects in Solids Using a Colored-Noise Thermostat.
</TD></TR>
<TR><TD>[Weber2009]</TD><TD>
<A NAME="reference_125">Weber, V; Iannuzzi, M; Giani, S; Hutter, S; Declerck, R; Waroduier, M.<br>
<A HREF="http://dx.doi.org/10.1063/1.3156803">THE JOURNAL OF CHEMICAL PHYSICS, 131 (1), 014106 (2009).</A></A><br>
Magnetic Linear Response Properties Calculations with the
Gaussian and Augmanted-Plane-Wave Method.
</TD></TR>
<TR><TD>[Bernstein2009]</TD><TD>
<A NAME="reference_107">Bernstein, N; Kermode, J R; Csanyi, G.<br>
<A HREF="http://dx.doi.org/10.1088/0034-4885/72/2/026501">REPORTS ON PROGRESS IN PHYSICS, 72 (2), 026501 (2009).</A></A><br>
Hybrid atomistic simulation methods for materials systems.
</TD></TR>
<TR><TD>[Ceriotti2009]</TD><TD>
<A NAME="reference_99">Ceriotti, M; Bussi, G; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevLett.102.020601">PHYSICAL REVIEW LETTERS, 102 (2), 020601 (2009).</A></A><br>
Langevin equation with colored noise for constant-temperature molecular dynamics simulations.
</TD></TR>
<TR><TD>[Kantorovich2008]</TD><TD>
<A NAME="reference_135">Kantorovich, L.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevB.78.094304">PHYSICAL REVIEW B, 78 (9), 094304 (2008).</A></A><br>
Generalized Langevin equation for solids. I.
Rigorous derivation and main properties.
</TD></TR>
<TR><TD>[Kantorovich2008b]</TD><TD>
<A NAME="reference_136">Kantorovich, L; Rompotis, N.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevB.78.094305">PHYSICAL REVIEW B, 78 (9), 094305 (2008).</A></A><br>
Generalized Langevin equation for solids. II.
Stochastic boundary conditions for nonequilibrium molecular dynamics simulations.
</TD></TR>
<TR><TD>[Laino2008]</TD><TD>
<A NAME="reference_11">Laino, T; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1063/1.2970887">JOURNAL OF CHEMICAL PHYSICS, 129 (7), 074102 (2008).</A></A><br>
Notes on "Ewald summation of electrostatic multipole interactions up to
quadrupolar level" [J. Chem. Phys. 119, 7471 (2003)].
</TD></TR>
<TR><TD>[Guidon2008]</TD><TD>
<A NAME="reference_83">Guidon, M; Schiffmann, F; Hutter, J; VandeVondele, J.<br>
<A HREF="http://dx.doi.org/10.1063/1.2931945">JOURNAL OF CHEMICAL PHYSICS, 128 (21), 214104 (2008).</A></A><br>
Ab initio molecular dynamics using hybrid density functionals.
</TD></TR>
<TR><TD>[Chang2008]</TD><TD>
<A NAME="reference_91">Chang, DT; Schenter, GK; Garrett, BC.<br>
<A HREF="http://dx.doi.org/10.1063/1.2905230">JOURNAL OF CHEMICAL PHYSICS, 128 (16), 164111 (2008).</A></A><br>
Self-consistent polarization neglect of diatomic differential overlap: Applications to water clusters.
</TD></TR>
<TR><TD>[Perdew2008]</TD><TD>
<A NAME="reference_70">Perdew, JP; Ruzsinszky, A; Csonka, GI; Vydrov, OA; Scuseria, GE; Constantin, LA; Zhou, X; Burke, K.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevLett.100.136406">PHYSICAL REVIEW LETTERS, 100 (13), 136406-136409 (2008).</A></A><br>
Restoring the Density-Gradient Expansion for Exchange in Solids and Surfaces.
</TD></TR>
<TR><TD>[Proynov2008]</TD><TD>
<A NAME="reference_92">Proynov, E; Gan, Z; Kong, J.<br>
<A HREF="http://dx.doi.org/10.1016/j.cplett.2008.02.039">CHEMICAL PHYSICS LETTERS, 455 (1-3), 103-109 (2008).</A></A><br>
Analytical representation of the Becke-Roussel exchange functional.
</TD></TR>
<TR><TD>[Weber2008]</TD><TD>
<A NAME="reference_18">Weber, V; VandeVondele, J; Hutter, J; Niklasson, AMN.<br>
<A HREF="http://dx.doi.org/10.1063/1.2841077">JOURNAL OF CHEMICAL PHYSICS, 128 (8), 084113 (2008).</A></A><br>
Direct energy functional minimization under orthogonality constraints.
</TD></TR>
<TR><TD>[Barducci2008]</TD><TD>
<A NAME="reference_102">Barducci, A; Bussi, G; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevLett.100.020603">PHYSICAL REVIEW LETTERS, 100 (2), 020603 (2008).</A></A><br>
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method.
</TD></TR>
<TR><TD>[Stewart2007]</TD><TD>
<A NAME="reference_19">Stewart, JJP.<br>
<A HREF="http://dx.doi.org/10.1007/s00894-007-0233-4">JOURNAL OF MOLECULAR MODELING, 13 (12), 1173-1213 (2007).</A></A><br>
Optimization of parameters for semiempirical methods V: Modification of
NDDO approximations and application to 70 elements.
</TD></TR>
<TR><TD>[Khaliullin2008]</TD><TD>
<A NAME="reference_132">Khaliullin, RZ; Bell, AT; Head-Gordon, M.<br>
<A HREF="http://dx.doi.org/10.1063/1.2912041">Journal of Chemical Physics, 128 (18), 184112 (2008).</A></A><br>
Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals.
</TD></TR>
<TR><TD>[VandeVondele2007]</TD><TD>
<A NAME="reference_65">VandeVondele, J; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1063/1.2770708">JOURNAL OF CHEMICAL PHYSICS, 127 (11), 114105 (2007).</A></A><br>
Gaussian basis sets for accurate calculations on molecular systems in
gas and condensed phases.
</TD></TR>
<TR><TD>[Genovese2007]</TD><TD>
<A NAME="reference_61">Genovese, L; Deutsch, T; Goedecker, S.<br>
<A HREF="http://dx.doi.org/10.1063/1.2754685">JOURNAL OF CHEMICAL PHYSICS, 127 (5), 054704 (2007).</A></A><br>
Efficient and accurate three-dimensional Poisson solver for surface
problems.
</TD></TR>
<TR><TD>[Hu2007]</TD><TD>
<A NAME="reference_7">Hu, H; Lu, ZY; Elstner, M; Hermans, J; Yang, WT.<br>
<A HREF="http://dx.doi.org/10.1021/jp070308d">JOURNAL OF PHYSICAL CHEMISTRY A, 111 (26), 5685-5691 (2007).</A></A><br>
Simulating water with the self-consistent-charge density functional
tight binding method: From molecular clusters to the liquid state.
</TD></TR>
<TR><TD>[Kuhne2007]</TD><TD>
<A NAME="reference_97">Kuhne, TD; Krack, M; Mohamed, FR; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevLett.98.066401">PHYSICAL REVIEW LETTERS, 98 (6), 066401 (2007).</A></A><br>
Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics.
</TD></TR>
<TR><TD>[Branduardi2007]</TD><TD>
<A NAME="reference_90">Branduardi, D; Gervasio, FL; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1063/1.2432340">JOURNAL OF CHEMICAL PHYSICS, 126 (5), 054103 (2007).</A></A><br>
From A to B in free energy space.
</TD></TR>
<TR><TD>[Bussi2007]</TD><TD>
<A NAME="reference_33">Bussi, G; Donadio, D; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1063/1.2408420">JOURNAL OF CHEMICAL PHYSICS, 126 (1), 014101 (2007).</A></A><br>
Canonical sampling through velocity rescaling.
</TD></TR>
<TR><TD>[Iannuzzi2007]</TD><TD>
<A NAME="reference_47">Iannuzzi, M; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1039/b615522g">PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 9 (13), 1599-1610 (2007).</A></A><br>
Inner-shell spectroscopy by the Gaussian and augmented plane wave method.
</TD></TR>
<TR><TD>[Khaliullin2007]</TD><TD>
<A NAME="reference_131">Khaliullin, RZ; Cobar, EA; Lochan, RC; Bell, AT; Head-Gordon, M.<br>
<A HREF="http://dx.doi.org/10.1021/jp073685z">Journal of Physical Chemistry A, 111 (36), 8753-8765 (2007).</A></A><br>
Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals.
</TD></TR>
<TR><TD>[Grimme2006]</TD><TD>
<A NAME="reference_87">Grimme, S.<br>
<A HREF="http://dx.doi.org/10.1002/jcc.20495">JOURNAL OF COMPUTATIONAL CHEMISTRY, 27 (15), 1787-1799 (2006).</A></A><br>
Semiempirical GGA-type density functional constructed with a long-range
dispersion correction.
</TD></TR>
<TR><TD>[VandenEijnden2006]</TD><TD>
<A NAME="reference_6">Vanden-Eijnden, E; Ciccotti, G.<br>
<A HREF="http://dx.doi.org/10.1016/j.cplett.2006.07.086">CHEMICAL PHYSICS LETTERS, 429 (1-3), 310-316 (2006).</A></A><br>
Second-order integrators for Langevin equations with holonomic
constraints.
</TD></TR>
<TR><TD>[Laino2006]</TD><TD>
<A NAME="reference_39">Laino, T; Mohamed, F; Laio, A; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1021/ct6001169">JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2 (5), 1370-1378 (2006).</A></A><br>
An efficient linear-scaling electrostatic coupling for treating
periodic boundary conditions in QM/MM simulations.
</TD></TR>
<TR><TD>[Genovese2006]</TD><TD>
<A NAME="reference_60">Genovese, L; Deutsch, T; Neelov, A; Goedecker, S; Beylkin, G.<br>
<A HREF="http://dx.doi.org/10.1063/1.2335442">JOURNAL OF CHEMICAL PHYSICS, 125 (7), 074105 (2006).</A></A><br>
Efficient solution of Poisson's equation with free boundary conditions.
</TD></TR>
<TR><TD>[Vydrov2006]</TD><TD>
<A NAME="reference_75">Vydrov, OA; Heyd, J; Krukau, AV; Scuseria, GE.<br>
<A HREF="http://dx.doi.org/10.1063/1.2244560">JOURNAL OF CHEMICAL PHYSICS, 125 (7), 074106 (2006).</A></A><br>
Importance of short-range versus long-range Hartree-Fock exchange for
the performance of hybrid density functionals.
</TD></TR>
<TR><TD>[Rocha2006]</TD><TD>
<A NAME="reference_23">Rocha, GB; Freire, RO; Simas, AM; Stewart, JJP.<br>
<A HREF="http://dx.doi.org/10.1002/jcc.20425">JOURNAL OF COMPUTATIONAL CHEMISTRY, 27 (10), 1101-1111 (2006).</A></A><br>
RMI: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I.
</TD></TR>
<TR><TD>[Heyd2006]</TD><TD>
<A NAME="reference_74">Heyd, J; Scuseria, GE; Ernzerhof, M.<br>
<A HREF="http://dx.doi.org/10.1063/1.2204597">JOURNAL OF CHEMICAL PHYSICS, 124 (21), 219906 (2006).</A></A><br>
Hybrid functionals based on a screened Coulomb potential (vol 118, pg
8207, 2003).
</TD></TR>
<TR><TD>[Iannuzzi2006]</TD><TD>
<A NAME="reference_48">Iannuzzi, M; Kirchner, B; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1016/j.cplett.2005.08.155">CHEMICAL PHYSICS LETTERS, 421 (1-3), 16-20 (2006).</A></A><br>
Density functional embedding for molecular systems.
</TD></TR>
<TR><TD>[VandeVondele2006]</TD><TD>
<A NAME="reference_86">VandeVondele, J; Iannuzzi, M; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1007/3-540-35273-2_8">Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology, Vol 1, 703, 287-314 (2006).</A></A><br>
Large scale condensed matter calculations using the gaussian and
augmented plane waves method.
</TD></TR>
<TR><TD>[Laino2005]</TD><TD>
<A NAME="reference_38">Laino, T; Mohamed, F; Laio, A; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1021/ct050123f">JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 1 (6), 1176-1184 (2005).</A></A><br>
An efficient real space multigrid OM/MM electrostatic coupling.
</TD></TR>
<TR><TD>[Krack2005]</TD><TD>
<A NAME="reference_42">Krack, M.<br>
<A HREF="http://dx.doi.org/10.1007/s00214-005-0655-y">THEORETICAL CHEMISTRY ACCOUNTS, 114 (1-3), 145-152 (2005).</A></A><br>
Pseudopotentials for H to Kr optimized for gradient-corrected
exchange-correlation functionals.
</TD></TR>
<TR><TD>[Zhechkov2005]</TD><TD>
<A NAME="reference_55">Zhechkov, L; Heine, T; Patchkovskii, S; Seifert, G; Duarte, HA.<br>
<A HREF="http://dx.doi.org/10.1021/ct050065y">JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 1 (5), 841-847 (2005).</A></A><br>
An efficient a Posteriori treatment for dispersion interaction in
density-functional-based tight binding.
</TD></TR>
<TR><TD>[dAvezac2005]</TD><TD>
<A NAME="reference_54">d'Avezac, M; Calandra, M; Mauri, F.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevB.71.205210">PHYSICAL REVIEW B, 71 (20), 205210 (2005).</A></A><br>
Density functional theory description of hole-trapping in SiO2: A
self-interaction-corrected approach.
</TD></TR>
<TR><TD>[VandeVondele2005]</TD><TD>
<A NAME="reference_36">VandeVondele, J; Krack, M; Mohamed, F; Parrinello, M; Chassaing, T; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1016/j.cpc.2004.12.014">COMPUTER PHYSICS COMMUNICATIONS, 167 (2), 103-128 (2005).</A></A><br>
QUICKSTEP: Fast and accurate density functional calculations using a
mixed Gaussian and plane waves approach.
</TD></TR>
<TR><TD>[Frigo2005]</TD><TD>
<A NAME="reference_59">Frigo, M; Johnson, SG.<br>
<A HREF="http://dx.doi.org/10.1109/JPROC.2004.840301">PROCEEDINGS OF THE IEEE, 93 (2), 216-231 (2005).</A></A><br>
The design and implementation of FFTW3.
</TD></TR>
<TR><TD>[Iannuzzi2005]</TD><TD>
<A NAME="reference_49">Iannuzzi, M; Chassaing, T; Wallman, T; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.2533/000942905777676164">CHIMIA, 59 (7-8), 499-503 (2005).</A></A><br>
Ground and excited state density functional calculations with the
Gaussian and augmented-plane-wave method.
</TD></TR>
<TR><TD>[VandeVondele2005b]</TD><TD>
<A NAME="reference_52">VandeVondele, J; Sprik, M.<br>
<A HREF="http://dx.doi.org/10.1039/b501603g">PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 7 (7), 1363-1367 (2005).</A></A><br>
A molecular dynamics study of the hydroxyl radical in solution applying
self-interaction-corrected density functional methods.
</TD></TR>
<TR><TD>[Dion2004]</TD><TD>
<A NAME="reference_115">Dion, M; Rydberg, H; Schroder, E; Langreth, DC; Lundqvist, BI.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevLett.92.246401">Phys. Rev. Lett., 92 (24), 246401 (2004).</A></A><br>
Van der Waals density functional for general geometries.
</TD></TR>
<TR><TD>[Heyd2004]</TD><TD>
<A NAME="reference_72">Heyd, J; Scuseria, GE.<br>
<A HREF="http://dx.doi.org/10.1063/1.1668634">JOURNAL OF CHEMICAL PHYSICS, 120 (16), 7274-7280 (2004).</A></A><br>
Assessment and validation of a screened Coulomb hybrid density
functional.
</TD></TR>
<TR><TD>[Trygubenko2004]</TD><TD>
<A NAME="reference_13">Trygubenko, SA; Wales, DJ.<br>
<A HREF="http://dx.doi.org/10.1063/1.1636455">JOURNAL OF CHEMICAL PHYSICS, 120 (5), 2082-2094 (2004).</A></A><br>
A doubly nudged elastic band method for finding transition states.
</TD></TR>
<TR><TD>[Kolafa2004]</TD><TD>
<A NAME="reference_96">Kolafa, J.<br>
<A HREF="http://dx.doi.org/10.1002/jcc.10385">JOURNAL OF COMPUTATIONAL CHEMISTRY, 25 (3), 335-342 (2004).</A></A><br>
Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules.
</TD></TR>
<TR><TD>[Goedecker2004]</TD><TD>
<A NAME="reference_130">Goedecker, S.<br>
<A HREF="http://dx.doi.org/10.1063/1.1724816">Journal of Chemical Physics, 120 (21), 9911-9917 (2004).</A></A><br>
Minima hopping: An efficient search method for the global minimum
of the potential energy surface of complex molecular systems.
</TD></TR>
<TR><TD>[Aguado2003]</TD><TD>
<A NAME="reference_27">Aguado, A; Madden, PA.<br>
<A HREF="http://dx.doi.org/10.1063/1.1605941">JOURNAL OF CHEMICAL PHYSICS, 119 (14), 7471-7483 (2003).</A></A><br>
Ewald summation of electrostatic multipole interactions up to the
quadrupolar level.
</TD></TR>
<TR><TD>[Tao2003]</TD><TD>
<A NAME="reference_85">Tao, JM; Perdew, JP; Staroverov, VN; Scuseria, GE.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevLett.91.146401">PHYSICAL REVIEW LETTERS, 91 (14), 146401 (2003).</A></A><br>
Climbing the density functional ladder: Nonempirical meta-generalized
gradient approximation designed for molecules and solids.
</TD></TR>
<TR><TD>[Hunt2003]</TD><TD>
<A NAME="reference_82">Hunt, P; Sprik, M; Vuilleumier, R.<br>
<A HREF="http://dx.doi.org/10.1016/S0009-2614(03)00954-0">CHEMICAL PHYSICS LETTERS, 376 (1-2), 68-74 (2003).</A></A><br>
Thermal versus electronic broadening in the density of states of liquid
water.
</TD></TR>
<TR><TD>[Kunert2003]</TD><TD>
<A NAME="reference_98">Kunert, T; Schmidt, R.<br>
<A HREF="http://dx.doi.org/10.1140/epjd/e2003-00086-8">EUROPEAN PHYSICAL JOURNAL D, 25 (1), (2003).</A></A><br>
Non-adiabatic quantum molecular dynamics: General formalism and case
study H-2(+) in strong laser fields.
</TD></TR>
<TR><TD>[Ricci2003]</TD><TD>
<A NAME="reference_95">Ricci, A; Ciccotti, G.<br>
<A HREF="http://dx.doi.org/10.1080/0026897031000108113">MOLECULAR PHYSICS, 101 (12), 1927-1931 (2003).</A></A><br>
Algorithms for Brownian dynamics.
</TD></TR>
<TR><TD>[Niklasson2003]</TD><TD>
<A NAME="reference_112">Niklasson, AMN; Tymczak, CJ; Challacombe, M.<br>
<A HREF="http://dx.doi.org/10.1063/1.1559913">JOURNAL OF CHEMICAL PHYSICS, 118 (19), 8611-8620 (2003).</A></A><br>
Trace resetting density matrix purification in O(N)
self-consistent-field theory.
</TD></TR>
<TR><TD>[Heyd2003]</TD><TD>
<A NAME="reference_73">Heyd, J; Scuseria, GE; Ernzerhof, M.<br>
<A HREF="http://dx.doi.org/10.1063/1.1564060">JOURNAL OF CHEMICAL PHYSICS, 118 (18), 8207-8215 (2003).</A></A><br>
Hybrid functionals based on a screened Coulomb potential.
</TD></TR>
<TR><TD>[Shao2003]</TD><TD>
<A NAME="reference_113">Shao, Y; Saravanan, C; Head-Gordon, M; White, CA.<br>
<A HREF="http://dx.doi.org/10.1063/1.1558476">JOURNAL OF CHEMICAL PHYSICS, 118 (14), 6144-6151 (2003).</A></A><br>
Curvy steps for density matrix-based energy minimization: Application to
large-scale self-consistent-field calculations.
</TD></TR>
<TR><TD>[VandeVondele2003]</TD><TD>
<A NAME="reference_37">VandeVondele, J; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1063/1.1543154">JOURNAL OF CHEMICAL PHYSICS, 118 (10), 4365-4369 (2003).</A></A><br>
An efficient orbital transformation method for electronic structure
calculations.
</TD></TR>
<TR><TD>[Minary2003]</TD><TD>
<A NAME="reference_62">Minary, P; Martyna, GJ; Tuckerman, ME.<br>
<A HREF="http://dx.doi.org/10.1063/1.1534582">JOURNAL OF CHEMICAL PHYSICS, 118 (6), 2510-2526 (2003).</A></A><br>
Algorithms and novel applications based on the isokinetic ensemble. I.
Biophysical and path integral molecular dynamics.
</TD></TR>
<TR><TD>[Repasky2002]</TD><TD>
<A NAME="reference_20">Repasky, MP; Chandrasekhar, J; Jorgensen, WL.<br>
<A HREF="http://dx.doi.org/10.1002/jcc.10162">JOURNAL OF COMPUTATIONAL CHEMISTRY, 23 (16), 1601-1622 (2002).</A></A><br>
PDDG/PM3 and PDDG/MNDO: Improved semiempirical methods.
</TD></TR>
<TR><TD>[Krack2002]</TD><TD>
<A NAME="reference_45">Krack, M; Gambirasio, A; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1063/1.1517040">JOURNAL OF CHEMICAL PHYSICS, 117 (20), 9409-9412 (2002).</A></A><br>
Ab initio x-ray scattering of liquid water.
</TD></TR>
<TR><TD>[E2002]</TD><TD>
<A NAME="reference_12">E, WN; Ren, WQ; Vanden-Eijnden, E.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevB.66.052301">PHYSICAL REVIEW B, 66 (5), 052301 (2002).</A></A><br>
String method for the study of rare events.
</TD></TR>
<TR><TD>[Putrino2002]</TD><TD>
<A NAME="reference_123">Putrino, A; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevLett.88.176401">PHYSICAL REVIEW LETTERS, 88 (17), 176401 (2002).</A></A><br>
Anharmonic Raman Spectra in High-Pressure Ice from Ab Initio Simulations.
</TD></TR>
<TR><TD>[Fattebert2002]</TD><TD>
<A NAME="reference_127">Fattebert, JL; Gygi, F.<br>
<A HREF="http://dx.doi.org/10.1002/jcc.10069">J. Comput. Chem., 23 (6), (2002).</A></A><br>
Density functional theory for efficient ab initio molecular dynamics
simulations in solution.
</TD></TR>
<TR><TD>[VandeVondele2002]</TD><TD>
<A NAME="reference_114">VandeVondele, J; Rothlisberger, U.<br>
<A HREF="http://dx.doi.org/10.1021/jp013346k">JOURNAL OF PHYSICAL CHEMISTRY B, 106 (1), 203-208 (2002).</A></A><br>
Canonical adiabatic free energy sampling (CAFES): A novel method for the
exploration of free energy surfaces.
</TD></TR>
<TR><TD>[Sebastiani2001]</TD><TD>
<A NAME="reference_124">Sebastiani, D; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1021/jp002807j">THE JOURNAL OF PHYSICAL CHEMISTRY A, 105 (10), 1951-1958 (2001).</A></A><br>
A New Ab Initio Approach for NMR Chemical Shifts in Periodic Systems.
</TD></TR>
<TR><TD>[Henkelman2000]</TD><TD>
<A NAME="reference_14">Henkelman, G; Uberuaga, BP; Jonsson, H.<br>
<A HREF="http://dx.doi.org/10.1063/1.1329672">JOURNAL OF CHEMICAL PHYSICS, 113 (22), 9901-9904 (2000).</A></A><br>
A climbing image nudged elastic band method for finding saddle points
and minimum energy paths.
</TD></TR>
<TR><TD>[Henkelman2000b]</TD><TD>
<A NAME="reference_15">Henkelman, G; Jonsson, H.<br>
<A HREF="http://dx.doi.org/10.1063/1.1323224">JOURNAL OF CHEMICAL PHYSICS, 113 (22), 9978-9985 (2000).</A></A><br>
Improved tangent estimate in the nudged elastic band method for finding
minimum energy paths and saddle points.
</TD></TR>
<TR><TD>[Putrino2000]</TD><TD>
<A NAME="reference_121">Putrino, A; Sebastiani, D; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1063/1.1312830">JOURNAL OF CHEMICAL PHYSICS, 113 (17), 7102-7109 (2000).</A></A><br>
Generalized Variational Density Functional Perturbation Theory.
</TD></TR>
<TR><TD>[Yamada2000]</TD><TD>
<A NAME="reference_28">Yamada, K; Kurosaki, K; Uno, M; Yamanaka, S.<br>
<A HREF="http://dx.doi.org/10.1016/S0925-8388(00)00806-9">JOURNAL OF ALLOYS AND COMPOUNDS, 307, 10-16 (2000).</A></A><br>
Evaluation of thermal properties of uranium dioxide by molecular
dynamics.
</TD></TR>
<TR><TD>[Lippert1999]</TD><TD>
<A NAME="reference_44">Lippert, G; Hutter, J; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1007/s002140050523">THEORETICAL CHEMISTRY ACCOUNTS, 103 (2), 124-140 (1999).</A></A><br>
The Gaussian and augmented-plane-wave density functional method for ab
initio molecular dynamics simulations.
</TD></TR>
<TR><TD>[Krack2000]</TD><TD>
<A NAME="reference_46">Krack, M; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1039/b001167n">PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2 (10), 2105-2112 (2000).</A></A><br>
All-electron ab-initio molecular dynamics.
</TD></TR>
<TR><TD>[Henkelman1999]</TD><TD>
<A NAME="reference_26">Henkelman, G; Jonsson, H.<br>
<A HREF="http://dx.doi.org/10.1063/1.480097">JOURNAL OF CHEMICAL PHYSICS, 111 (15), 7010-7022 (1999).</A></A><br>
A dimer method for finding saddle points on high dimensional potential
surfaces using only first derivatives.
</TD></TR>
<TR><TD>[Martyna1999]</TD><TD>
<A NAME="reference_51">Martyna, GJ; Tuckerman, ME.<br>
<A HREF="http://dx.doi.org/10.1063/1.477923">JOURNAL OF CHEMICAL PHYSICS, 110 (6), 2810-2821 (1999).</A></A><br>
A reciprocal space based method for treating long range interactions in
ab initio and force-field-based calculations in clusters.
</TD></TR>
<TR><TD>[BENGTSSON1999]</TD><TD>
<A NAME="reference_3">BENGTSSON, L.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevB.59.12301">PHYSICAL REVIEW B, 59 (19), 12301-12304 (1999).</A></A><br>
DIPOLE CORRECTION FOR SURFACE SUPERCELL CALCULATIONE.
</TD></TR>
<TR><TD>[Elstner1998]</TD><TD>
<A NAME="reference_56">Elstner, M; Porezag, D; Jungnickel, G; Elsner, J; Haugk, M; Frauenheim, T; Suhai, S; Seifert, G.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevB.58.7260">PHYSICAL REVIEW B, 58 (11), 7260-7268 (1998).</A></A><br>
Self-consistent-charge density-functional tight-binding method for
simulations of complex materials properties.
</TD></TR>
<TR><TD>[Hartwigsen1998]</TD><TD>
<A NAME="reference_41">Hartwigsen, C; Goedecker, S; Hutter, J.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevB.58.3641">PHYSICAL REVIEW B, 58 (7), 3641-3662 (1998).</A></A><br>
Relativistic separable dual-space Gaussian pseudopotentials from H to Rn.
</TD></TR>
<TR><TD>[Zhang1998]</TD><TD>
<A NAME="reference_69">Zhang, YK; Yang, WT.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevLett.80.890">PHYSICAL REVIEW LETTERS, 80 (4), 890-890 (1998).</A></A><br>
Comment on Generalized gradient approximation made simple.
</TD></TR>
<TR><TD>[Dudarev1998]</TD><TD>
<A NAME="reference_81">Dudarev, SL; Botton, GA; Savrasov, SY; Humphreys, CJ; Sutton, AP.<br>
<A HREF="http://dx.doi.org/10.1103/PhysRevB.57.1505">PHYSICAL REVIEW B, 57 (3), 1505-1509 (1998).</A></A><br>
Electron-energy-loss spectra and the structural stability of
nickel oxide: An LSDA+U study.
</TD></TR>
<TR><TD>[JONSSON1998]</TD><TD>
<A NAME="reference_16">JONSSON, H; MILLS, G; JACOBSEN, K W.<br>
Classical and Quantum Dynamics in Condensed Phase Simulations, 385-404 (1998).</A><br>
Nudged elastic band method for finding minimum energy paths
of transitions.
</TD></TR>
<TR><TD>[Lippert1997]</TD><TD>
<A NAME="reference_43">Lippert, G; Hutter, J; Parrinello, M.<br>
<A HREF="http://dx.doi.org/10.1080/002689797170220">MOLECULAR PHYSICS, 92 (3), 477-487 (1997).</A></A><br>
A hybrid Gaussian and plane wave density functional scheme.
</TD></TR>
<TR><TD>[Dudarev1997]</TD><TD>
<A NAME="reference_80">Dudarev, SL; Manh, DN; Sutton, AP.<br>
<A HREF="http://dx.doi.org/10.1080/13642819708202343">PHILOSOPHICAL MAGAZINE B, 75 (5), 613-628 (1997).</A></A><br>
Effect of Mott-Hubbard correlations on the electronic
structure and structural stability of uranium dioxide.
</TD></TR>
<TR><TD>[Becke1997]</TD><TD>
<A NAME="reference_94">Becke, AD.<br>