1@Article{porezag-PRB-51-12947,
2 author = {D. Porezag and T. Frauenheim and T. K\"ohler and G. Seifert and
3 R. Kaschner},
4 title = {Construction of tight-binding-like potentials on the basis of
5 density-functional theory: Application to carbon},
6 journal = prb,
7 year = {1995},
8 volume = {51},
9 pages = {12947}
10}
11
12@Article{seifert-ijqc-58-185,
13 author = {G. Seifert and D. Porezag and T. Frauenheim},
14 title = {Calculations of molecules, clusters, and solids with a
15                  simplified \mbox{LCAO-DFT-LDA} scheme},
16 journal = ijqc,
17 year = {1996},
18 volume = {58},
19 pages = {185}
20}
21
22@Article{elstner-prb-58-7260,
23 author = {M. Elstner and D. Porezag and G. Jungnickel and J. Elsner and
24 M. Haugk and T. Frauenheim and S. Suhai and G. Seifert},
25 title = {Self-consistent-charge density-functional tight-binding method for
26 simulations of complex materials properties},
27 journal = prb,
28 year = {1998},
29 volume = {58},
30 pages = {7260}
31}
32
33@Article{koehler-cp-309-23,
34 author = {C. K\"ohler and G. Seifert and T. Frauenheim},
35 title = {Density-Functional based calculations for {F}e(n), (n$\le$32)},
36 journal = cp,
37 year = {2005},
38 volume = {309},
39 pages = {23}
40}
41
42@Article{han-ijqc-78-459,
43 author = {W. Han and M. Elstner and K. J. Jalkanen and T. Frauenheim and
44 S. Suhai},
45 title = {Hybrid \mbox{SCC-DFTB}/Molecular Mechanical Studies of
46                  {H}-Bonded Systems and of
47                  {N}-acetyl-({L}-{A}la)$_\mathrm{n}$-{N}'-{M}ethylamide
48                  Helices in Water Solution},
49 journal = ijqc,
50 year = {2000},
51 volume = {78},
52 pages = {459}
53}
54
55@Article{cui-jpcb-105-569,
56 author = {Q. Cui and M. Elstner and T. Frauenheim and E. Kaxiras and
57 M. Karplus},
58 title = {Combined self-consistent charge density functional
59                  tight-binding (\mbox{SCC-DFTB}) and \mbox{CHARMM}},
60 journal = jpcb,
61 year = {2001},
62 volume = {105},
63 pages = {569}
64}
65
66@Article{elstner-jcp-114-5149,
67 author = {M. Elstner and P. Hobza and T. Frauenheim and S. Suhai and
68 E. Kaxiras},
69 title = {Hydrogen bonding and stacking interactions of nucleic acid base
70 pairs: a density-functional-theory based treatment},
71 journal = jcp,
72 year = {2001},
73 volume = {114},
74 pages = {5149}
75}
76
77@Article{frauenheim-JPCM-14-3015,
78 author = {Frauenheim, T. and Seifert, G. and Elstner, M. and Niehaus, T. and
79 Kohler, C. and Amkreutz, M. and Sternberg, M. and Hajnal, Z. and Di~Carlo, A.
80 and Suhai, S.},
81 title = {Atomistic simulations of complex materials: ground-state and
82 excited-state properties},
83 journal = jpcm,
84 year = 2002,
85 volume = 14,
86 number = 11,
87 pages = {3015-3047},
88 month = {Mar}
89}
90
91@Article{petukhov-PRB-67-153106,
92 author = {Petukhov, A. G. and Mazin, I. I. and Chioncel, L. and
93 Lichtenstein, A. I.},
94 title = {Correlated metals and the \mbox{LDA+U} method},
95 journal = prb,
96 year = 2003,
97 volume = 67,
98 pages = {153106-4}
99}
100
101@Article{han-PRB-73-045110,
102 author = {Han, M. J. and Ozaki, T. and Yu, J.},
103 title = {\mbox{O($N$) LDA+$U$} electronic structure calculation method based
104 on the nonorthogonal pseudoatomic orbital basis},
105 journal = prb,
106 year = 2006,
107 volume = 73,
108 pages = {045110}
109}
110
111@Article{johnson-PRB-38-12807,
112 author = {Johnson, D. D.},
113 title = {Modified {B}royden's method for accelerating convergence in
114                  self consistent calculations},
115 journal = prb,
116 year = {2003},
117 volume = {38},
118 pages = {12807}
119}
120
121@Article{eyert-JCP-124-271,
122 author = {Eyert, V.},
123 title = {A Comparative Study on Methods for Convergence Acceleration
124of Iterative Vector Sequences},
125 journal = jcop,
126 year = {1996},
127 volume = {124},
128 pages = {271}
129}
130
131@Article{monkhorst-prb-13-5188,
132 author = {Monkhorst, H. J. and Pack, J. D.},
133 title = {Special points for {B}rillouin-zone integrations},
134 journal = prb,
135 year = {1976},
136 volume = {13},
137 pages = {5188},
138 annote = {Monkhorst-Pack original paper}
139}
140
141@Article{monkhorst-prb-16-1748,
142 author = {Monkhorst, H. J. and Pack, J. D.},
143 title = {"Special points for {B}rillouin-zone integrations"--a reply},
144 journal = prb,
145 year = {1977},
146 volume = {16},
147 pages = {1748},
148 annote = {Monkhorst-Pack erratum}
149}
150
151
152@PhdThesis{KoehlerThesis,
153 author = {Christof K\"ohler},
154 title = {Ber\"ucksichtigung von Spinpolarisationseffekten in einem
155 dichtefunktionalbasierten Ansatz},
156 school = {Department Physik der Fakult\"at fur Naturwissenschaften an der
157 Universit\"at Paderborn},
158 year = 2004,
159 note = {http://ubdata.uni-paderborn.de/ediss/06/2004/koehler/}
160}
161
162
163@PhdThesis{garcia14Thesis,
164  author = 	 {Adriel Dominguez Garcia},
165  title = 	 {Density functional approaches for the interaction of
166                  metal oxides with small molecules},
167  school = 	 {Universit\"at Bremen},
168  year = 	 2014,
169  note = 	 {http://elib.suub.uni-bremen.de/edocs/00103868-1.pdf}
170}
171
172@Article{andersen-JCP-72-2384,
173 author = {Andersen, H. C.},
174 title = {Molecular dynamics at constant pressure and/or temperature},
175 journal = jcp,
176 year = 1980,
177 volume = 72,
178 pages = 2384
179}
180
181@BOOK{lapack3,
182      AUTHOR = {Anderson, E. and Bai, Z. and Bischof, C. and
183                Blackford, S. and Demmel, J. and Dongarra, J. and
184                Du Croz, J. and Greenbaum, A. and Hammarling, S. and
185                McKenney, A. and Sorensen, D.},
186      TITLE = {{LAPACK} Users' Guide},
187      EDITION = {Third},
188      PUBLISHER = {Society for Industrial and Applied Mathematics},
189      YEAR = {1999},
190      ADDRESS = {Philadelphia, PA},
191      ISBN = {0-89871-447-8 (paperback)}
192}
193
194@MISC{Lehoucq97arpackusers,
195    author = {R. B. Lehoucq and D. C. Sorensen and C. Yang},
196    title = {ARPACK Users Guide: Solution of Large Scale Eigenvalue
197                  Problems by Implicitly Restarted Arnoldi Methods.},
198    year = {1997}
199}
200
201@MISC{ARPACK-ng,
202 howpublished = {https://github.com/opencollab/arpack-ng}
203}
204
205@Article{methfessel-PRB-40-3616,
206 author = {Methfessel, M. and Paxton, A. T.},
207 title = {High-precision sampling for {B}rillouin-zone integration in metals},
208 journal = prb,
209 year = 1989,
210 volume = 40,
211 pages = 3616
212}
213
214@Article{miller-JAmChemSoc-112-8533,
215 author = {K. J. Miller},
216 title = {Additivity methods in molecular polarizability},
217 journal = jacs,
218 year = 1990,
219 volume = 112,
220 pages = 8533,
221 annote = {Dispersion values (cited in Marcus paper)}
222}
223
224@Article{kang-TheorChimActa-61-41,
225 author = {Y. K. Kang and M. S. Jhon},
226 title = {Additivity of atomic static polarizabilities and dispersion
227 coefficients},
228 journal = tca,
229 year = 1982,
230 volume = 61,
231 pages = 41,
232 annote = {Dispersion values (cited in Marcus paper)}
233}
234
235
236@Article{dftbp-paper,
237 author = {B. Aradi and B. Hourahine and Th. Frauenheim},
238 title = {{DFTB+}, a Sparse Matrix-Based Implementation of the {DFTB} Method},
239 journal = jpca,
240 year = {2007},
241 volume = {111},
242 number = {26},
243 pages = {5678}
244}
245
246
247
248@Article{hourahine07,
249 author = {Hourahine, B. and Sanna, S. and Aradi, B. and K\"ohler, C.
250 and Niehaus, T. and Frauenheim, Th.},
251 title = {Self-Interaction and Strong Correlation in {DFTB}},
252 journal = jpca,
253 year = {2007},
254 volume = {111},
255 number = {26},
256 pages = {5671}
257}
258
259@Article{koehler-JPCA-111-5622,
260 author = {K\"ohler, C. and  Frauenheim, T. and Hourahine, B. and Seifert, G.
261 and Sternberg, M.},
262 title = {Treatment of Collinear and Noncollinear Electron Spin within an
263 Approximate Density Functional Based Method},
264 journal = jpca,
265 year = 2007,
266 volume = 111,
267 number = 26,
268 pages = 5622,
269 doi = {10.1021/jp068802p}
270}
271
272@Article{harvey-JCC-19-726,
273 author = {Harvey, S. C. and Tan, R. K. Z. and Cheatham, T. E.},
274 title = {The flying ice cube: Velocity rescaling in molecular dynamics leads
275 to violation of energy equipartition},
276 journal = jcc,
277 year = 1998,
278 volume = 19,
279 number = 7,
280 pages = {726-740}
281}
282
283@Article{berendsen-JCP-81-3684,
284 author = {Berendsen, H. J. C. and Postma, J. P. M. and Van~Gunsteren, W. F.
285 and Dinola, A. and Haak, J. R.},
286 title = {Molecular-Dynamics with Coupling to an External Bath},
287 journal = jcp,
288 year = 1984,
289 volume = 81,
290 number = 8,
291 pages = {3684-3690}
292}
293
294@Article{yang-JPCA-111-10861,
295  author = 	 {Yang, Y. and Yu, H. and York, D. and Cui, Q. and Elstner, M.},
296  title = 	 {Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method: Third-Order Expansion of the Density Functional Theory Total Energy and Introduction of a Modified Effective Coulomb Interaction},
297  journal = 	 jpca,
298  year = 	 {2007},
299  volume =	 {111},
300  pages =        {10861},
301  annote =	 {3rd order on-site paper}
302}
303
304@Article{zhechkov-JCTC-1-841,
305  author = 	 {Zhechkov, L. and Heine, Th. and Patchkovskii, S. and
306                  Seifert, G. and Duarte, H. A.},
307  title = 	 {An Efficient a Posteriori Treatment for Dispersion
308                  Interaction in Density-Functional-Based Tight
309                  Binding},
310  journal = 	 jctc,
311  year = 	 2005,
312  volume =	 1,
313  pages =	 {841-847},
314  annote =	 {Thomas Heines \mbox{UFF} dispersion paper.}
315}
316
317@Article{rappe-JACS-114-10024,
318  author = 	 {Rappe, A. K. and Casewit, C. J. and Colwell, K. S. and {Goddard III}, W. A. and Skiff, W. M.},
319  title = 	 {\mbox{UFF}, a full periodic table force field for
320                  molecular mechanics and molecular dynamics
321                  simulations},
322  journal = 	 jacs,
323  year = 	 1992,
324  volume =	 {114},
325  pages =	 {10024-10035},
326  annote =	 {UFF paper}
327}
328
329@Article{gauss-jctc-7-931,
330  author = 	 {Gaus, M. and Cui, Q. and Elstner, M.},
331  title = 	 {\mbox{DFTB}3: {E}xtension of the {S}elf-{C}onsistent-{C}harge
332     {D}ensity-{F}unctional {T}ight-{B}inding {M}ethod (\mbox{SCC-DFTB})},
333  journal = 	 jctc,
334  year = 	 {2011},
335  volume =	 {7},
336  pages =	 {931-948},
337  annote =	 {DFTB3 paper}
338}
339
340@Article{martyna-mp-87-1117,
341 author = {Martyna, G. J. and Tuckerman, M. E. and Tobias, D. J. and
342 Klein, M. L.},
343 title = {Explicit reversible integrators for extended systems dynamics},
344 journal = mp,
345 year = 1996,
346 volume = 87,
347 pages = {1117-1157}
348}
349
350@Article{pipek-JCP-90-4916,
351  author = 	 {Pipek, J. and Mezey, P. G.},
352  title = 	 {A fast intrinsic localization procedure applicable
353                  for {\it ab initio} and semiempirical linear
354                  combination of atomic orbital wave functions},
355  journal = 	 jcp,
356  year = 	 1989,
357  volume = 	 90,
358  pages = 	 4916
359}
360
361@Article{niehaus-prb-63-085108,
362 author = {Niehaus, T. A. and Suhai, S. and Della Sala, F. and
363 Lugli, P and Elstner, M. and Seifert, G. and Frauenheim, Th.},
364 title = {Tight-binding approach to time-dependent density-functional
365                  response theory},
366 journal = prb,
367 year = 2001,
368 volume = 63,
369 pages = {085108}
370}
371
372@Article{heringer2007aes,
373  author = {Heringer, D. and Niehaus, T. A. and Wanko, M. and Frauenheim, T.},
374  title = {Analytical excited state forces for the time-dependent
375                  density-functional tight-binding method.},
376  journal = jcc,
377  year = {2007},
378  volume = {28},
379  pages = {2589},
380  number = {16}
381}
382
383@article{Ceriotti20141019,
384title = "i-PI: A Python interface for ab initio path integral
385                  molecular dynamics simulations ",
386journal = cpc,
387volume = "185",
388pages = "1019-1026",
389year = "2014",
390doi = "http://dx.doi.org/10.1016/j.cpc.2013.10.027",
391author = "Ceriotti, M.  and More, J. and Manolopoulos, D. E."
392}
393
394@Article{grimme-jcp-132-154104,
395 author = {Grimme, S. and Antony, J. and Ehrlich, S. and Krieg, H.},
396 title = {A consistent and accurate ab initio parametrization of
397                  density functional dispersion correction
398                  (\mbox{DFT-D}) for the 94 elements {H}-{P}u},
399 journal = jcp,
400 year = 2010,
401 volume = 132,
402 pages = {154104}
403}
404
405@Article{grimme-jcp-32-1456-1465,
406 author = {Grimme, S. and Ehrlich, S. and Goerigk, L.},
407 title = {Effect of the Damping Function in Dispersion Corrected
408Density Functional Theory},
409 journal = jcp,
410 year = 2011,
411 volume = 32,
412 pages = {1456-1465}
413}
414
415@Misc{grimme-param,
416 howpublished = {http://toc.uni-muenster.de/DFTD3/}
417}
418
419@Article{kovalenko-JCC-20-928,
420 author = {Kovalenko, A. and Ten-no, S. and Hirata, F.},
421 title = {Solution of three-dimensional reference interaction site
422                  model and hypernetted chain equations for simple
423                  point charge water by modified method of direct
424                  inversion in iterative subspace },
425 journal = jcc,
426 year = 1999,
427 volume = 20,
428 pages = {928-936}
429}
430
431@Article{aradi-jctc-11-3357,
432  author =       {Aradi, B. and Niklasson, A. M. N. and Frauenheim, T.},
433  title =        {Extended Lagrangian Density Functional Tight-Binding
434                  Molecular Dynamics for Molecules and Solids},
435  journal =      jctc,
436  year =         {2015},
437  volume =       {11},
438  pages =        {3357-3363},
439}
440
441@Book{NoceWrig06,
442  Title                    = {Numerical Optimization},
443  Author                   = {Jorge Nocedal and Stephen J. Wright},
444  Publisher                = {Springer},
445  Year                     = {2006},
446  Address                  = {New York, NY, USA},
447  Edition                  = {second}
448}
449
450@article{YU2018267,
451  title = "\mbox{ELSI}: {A} unified software interface for
452                  {K}ohn-{S}ham electronic structure solvers",
453  journal = cpc,
454  volume = "222",
455  pages = "267-285",
456  year = "2018",
457  doi = "https://doi.org/10.1016/j.cpc.2017.09.007",
458  author = "Yu, V. W.-z. and Corsetti, F. and Garc\'ia, A. and Huhn,
459                  W. P. and Jacquelin, M. and Jia, W. and Lange,
460                  B. and Lin, L. and Lu, J. and Mi, W. and
461                  Seifitokaldani, A.  and V\'azquez-Mayagoitia, {\'A}
462                  and Yang, C. and Yang, H. and Blum, V."
463}
464
465@Article{Pecchia_RPP,
466 author = {Pecchia, A. and Di~Carlo, A.},
467 title = {Atomistic theory of transport in organic and inorganic
468                  nanostructures},
469 journal = rpp,
470 year = 2004,
471 volume = 67,
472 pages = 1497
473}
474
475@Article{Pecchia_NJP,
476 author = {Pecchia, A. and G Penazzi, G. and Salvucci, L. and Di~Carlo, A.},
477 title = {Non-equilibrium {G}reen's functions in density functional
478                  tight binding: method and applications},
479 journal = njp,
480 year = 2008,
481 volume = 10,
482 number = 6,
483 pages = 065022
484}
485
486@InBook{Pecchia_spring,
487  ALTauthor = 	 {Di~Carlo, A. and Pecchia, A.  and Latessa, L. and
488                  Frauenheim, Th.  and Seifert, G. },
489  ALTeditor = 	 {Cuniberti, G. and Fagas, G. and Richter, K.},
490  title = 	 {Introducing Molecular Electronics},
491  chapter = 	 {Tight-Binding DFT for Molecular Electronics (\mbox{gDFTB})},
492  publisher = 	 {Springer},
493  year = 	 {2005},
494  series = 	 {Lecture Notes in Physics},
495  pages = 	 {153-184}
496}
497
498@article{rezac-jctc-13-2017,
499  author = {{\v R}ez{\'a}{\v c}, Jan},
500  title = {Empirical {Self}-{Consistent} {Correction} for the
501                  {Description} of {Hydrogen} {Bonds} in {DFTB}3},
502  journal = jctc,
503  volume = {13},
504  year = {2017},
505  pages = {4804--4817},
506  doi = {10.1021/acs.jctc.7b00629},
507  number = {10}
508}
509
510@article{rezac-jctc-8-2012,
511  author = {{\v R}ez{\'a}{\v c}, Jan and Hobza, Pavel},
512  title = {Advanced Corrections of Hydrogen Bonding and Dispersion for
513                  Semiempirical Quantum Mechanical Methods},
514  journal = jctc,
515  volume = {8},
516  year = {2012},
517  pages = {141--151},
518  doi = {10.1021/ct200751e}
519}
520
521@article{tdb10,
522    title     = {{Towards dense linear algebra for hybrid GPU accelerated manycore systems}},
523    author    = {Stanimire Tomov and Jack Dongarra and Marc Baboulin},
524    booktitle = {Parallel Matrix Algorithms and Applications},
525    doi       = {10.1016/j.parco.2009.12.005},
526    issn      = {0167-8191},
527    journal   = {Parallel Computing},
528    month     = jun,
529    number    = {5-6},
530    pages     = {232--240},
531    posted-at = {2010-12-17 09:48:58},
532    priority  = {2},
533    volume    = {36},
534    year      = {2010}
535}
536
537@inproceedings{tnld10,
538    title     = {Dense Linear Algebra Solvers for Multicore with {GPU} Accelerators},
539    author    = {Stanimire Tomov and Rajib Nath and Hatem Ltaief and Jack Dongarra},
540    address   = {Atlanta, GA},
541    booktitle = {Proc. of the IEEE IPDPS'10},
542    month     = {April 19-23},
543    note      = {{DOI:~10.1109/IPDPSW.2010.5470941}},
544    pages     = {1-8},
545    publisher = {IEEE Computer Society},
546    year      = {2010}
547}
548
549@article{dghklty14,
550    title     = {Accelerating Numerical Dense Linear Algebra Calculations with GPUs},
551    author    = {Jack Dongarra and Mark Gates and Azzam Haidar and Jakub Kurzak and
552                 Piotr Luszczek and Stanimire Tomov and Ichitaro Yamazaki},
553    journal   = {Numerical Computations with GPUs},
554    pages     = {1-26},
555    year      = {2014},
556    publisher = {Springer}
557}
558
559@Article{niehaus-PSSB-249-237,
560  author =       {Niehaus, T. A. and Della~Sala, F.},
561  title =        {Range separated functionalsin the density functional
562                  based tight-binding method: Formalism},
563  journal =      pssb,
564  year =         2012,
565  volume =    249,
566  number =    2,
567  pages =     {237-244},
568  DOI = {10.1002/pssb.201100694}
569}
570
571@Article{lutsker-JCP-143-184107,
572  author =       {Lutsker, V. and Aradi, B. and Niehaus, T. A.},
573  title =        {Implementation and benchmark of a long-range
574                  corrected functional in the densityfunctional based
575                  tight-binding method},
576  journal =      jcp,
577  year =         2015,
578  volume =    143,
579  pages =     184107,
580  DOI = {10.1063/1.4935095}
581}
582
583@article{garcia13,
584author = {Dom\'inguez, A. and Aradi, B. and Frauenheim, T. and
585                  Lutsker, V. and Niehaus, T. A.},
586title = {Extensions of the Time-Dependent Density Functional Based
587                  Tight-Binding Approach},
588journal = {Journal of Chemical Theory and Computation},
589volume = 9,
590number = 11,
591pages = {4901-4914},
592year = 2013,
593doi = {10.1021/ct400123t}
594}
595
596@article{dominguez15,
597author = {Dom\'inguez, A. and Niehaus, T. A. and Frauenheim, T.},
598title = {Accurate Hydrogen Bond Energies within the Density Functional
599                  Tight Binding Method},
600journal = {The Journal of Physical Chemistry A},
601volume = 119,
602number = 14,
603pages = {3535-3544},
604year = 2015,
605doi = {10.1021/acs.jpca.5b01732}
606}
607
608@article{Lany_2009,
609doi = {10.1088/0965-0393/17/8/084002},
610url = {https://doi.org/10.1088%2F0965-0393%2F17%2F8%2F084002},
611year = 2009,
612month = {{N}ov},
613publisher = {{IOP} Publishing},
614volume = 17,
615number = 8,
616pages = 084002,
617author = {Stephan Lany and Alex Zunger},
618title = {Accurate prediction of defect properties in density functional supercell calculations},
619journal = {Modelling and Simulation in Materials Science and Engineering}
620}
621