diff --git a/cmake/README.md b/cmake/README.md index 6255307ef3..9fb5dc3c16 100644 --- a/cmake/README.md +++ b/cmake/README.md @@ -1383,8 +1383,8 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP Some potentials that are also implemented in the Yet Another Force Field (YAFF) code. The expressions and their use are discussed in the following papers: diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index 480ddc3bc6..0d2e2796cb 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -41,7 +41,7 @@ coefficients. | For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005); -http://dx.doi.org/10.1063/1.1931662) these values can be used: +https://doi.org/10.1063/1.1931662) these values can be used: | O mass = 15.9994 | H mass = 1.008 @@ -57,7 +57,7 @@ http://dx.doi.org/10.1063/1.1931662) these values can be used: | For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005); -http://dx.doi.org/10.1063/1.2121687), these values can be used: +https://doi.org/10.1063/1.2121687), these values can be used: | O mass = 15.9994 | H mass = 1.008 diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 00103088a7..9832bf15de 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -2515,8 +2515,8 @@ The expressions and their use are discussed in the following papers which discuss the `QuickFF `_ methodology. -.. _vanduyfhuys2015: http://dx.doi.org/10.1002/jcc.23877 -.. _vanduyfhuys2018: http://dx.doi.org/10.1002/jcc.25173 +.. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877 +.. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173 .. _quickff: http://molmod.github.io/QuickFF .. _yaff: https://github.com/molmod/yaff diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index a23b98fbae..a6033f4828 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -205,7 +205,7 @@ Science, 117, 397-405 (2016). **(Wicaksono2)** Wicaksono, figshare, -https://dx.doi.org/10.6084/m9.figshare.1488628.v1 (2015). +https://doi.org/10.6084/m9.figshare.1488628.v1 (2015). ---------- diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst index 57579b0fce..e42d7a237f 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -218,7 +218,7 @@ the :doc:`dimension ` command, and nasr = 20. **(Campana)** C. Campana and M. H. Muser, *Practical Green's function approach to the -simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) `_ +simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) `_ .. _Kong: @@ -226,15 +226,15 @@ simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) **(Kong)** L.T. Kong, G. Bartels, C. Campana, C. Denniston, and Martin H. Muser, *Implementation of Green's -function molecular dynamics: An extension to LAMMPS*\ , `Computer Physics Communications [180](6):1004-1010 (2009). `_ +function molecular dynamics: An extension to LAMMPS*\ , `Computer Physics Communications [180](6):1004-1010 (2009). `_ L.T. Kong, C. Denniston, and Martin H. Muser, *An improved version of the Green's function molecular dynamics -method*\ , `Computer Physics Communications [182](2):540-541 (2011). `_ +method*\ , `Computer Physics Communications [182](2):540-541 (2011). `_ .. _Kong2011: **(Kong2011)** L.T. Kong, *Phonon dispersion measured directly from -molecular dynamics simulations*\ , `Computer Physics Communications [182](10):2201-2207, (2011). `_ +molecular dynamics simulations*\ , `Computer Physics Communications [182](10):2201-2207, (2011). `_ diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst index 38b4794237..fa34c7cef5 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -151,4 +151,4 @@ Related commands **(Anderson)** Anderson, Mukherjee, Critchley, Ziegler, and Lipton "POEMS: Parallelizable Open-source Efficient Multibody Software ", -Engineering With Computers (2006). (`link to paper `_) +Engineering With Computers (2006). (`link to paper `_) diff --git a/examples/HEAT/README b/examples/HEAT/README index 89ad04398f..ff6abb8dd6 100644 --- a/examples/HEAT/README +++ b/examples/HEAT/README @@ -6,7 +6,7 @@ All input scripts are part of the supplementary (open access) material supporting the publication of Wirnsberger et al. [J. Chem. Phys. 143, 124104 (2015)] and allow one to reproduce the key results reported in that paper. The full article is available for download under -http://dx.doi.org/10.1063/1.4931597 or http://arxiv.org/pdf/1507.07081 +https://doi.org/10.1063/1.4931597 or http://arxiv.org/pdf/1507.07081 and the supplementary material is available under https://www.repository.cam.ac.uk/handle/1810/250539. diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1 b/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1 index 3b5203ba6f..1003b9729e 100644 --- a/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1 +++ b/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1 @@ -101,7 +101,7 @@ colvars: Creating proxy instance colvars: ---------------------------------------------------------------------- colvars: Initializing the collective variables module, version 2018-11-16. colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: in any publication based on this calculation. colvars: SMP parallelism is available. colvars: Using LAMMPS interface, version 2018-08-29. @@ -405,7 +405,7 @@ colvars: Creating proxy instance colvars: ---------------------------------------------------------------------- colvars: Initializing the collective variables module, version 2018-11-16. colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: in any publication based on this calculation. colvars: SMP parallelism is available. colvars: Using LAMMPS interface, version 2018-08-29. diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4 b/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4 index 586ebbc5c5..91ef59b619 100644 --- a/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4 +++ b/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4 @@ -101,7 +101,7 @@ colvars: Creating proxy instance colvars: ---------------------------------------------------------------------- colvars: Initializing the collective variables module, version 2018-11-16. colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: in any publication based on this calculation. colvars: SMP parallelism is available. colvars: Using LAMMPS interface, version 2018-08-29. @@ -405,7 +405,7 @@ colvars: Creating proxy instance colvars: ---------------------------------------------------------------------- colvars: Initializing the collective variables module, version 2018-11-16. colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: in any publication based on this calculation. colvars: SMP parallelism is available. colvars: Using LAMMPS interface, version 2018-08-29. diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1 b/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1 index 8e5c990f40..df7aca475f 100644 --- a/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1 +++ b/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1 @@ -100,7 +100,7 @@ colvars: Creating proxy instance colvars: ---------------------------------------------------------------------- colvars: Initializing the collective variables module, version 2018-11-16. colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: in any publication based on this calculation. colvars: SMP parallelism is available. colvars: Using LAMMPS interface, version 2018-08-29. diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4 b/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4 index 47f1b672df..b1916fda17 100644 --- a/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4 +++ b/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4 @@ -100,7 +100,7 @@ colvars: Creating proxy instance colvars: ---------------------------------------------------------------------- colvars: Initializing the collective variables module, version 2018-11-16. colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: in any publication based on this calculation. colvars: SMP parallelism is available. colvars: Using LAMMPS interface, version 2018-08-29. diff --git a/examples/USER/misc/rhok/README.md b/examples/USER/misc/rhok/README.md index 4e011255fc..cbef8e9e14 100644 --- a/examples/USER/misc/rhok/README.md +++ b/examples/USER/misc/rhok/README.md @@ -19,7 +19,7 @@ For future reference we note that the structure factor S(k) is given by the vari It is recommended to get familiar with the interface pinning method by reading: - [Ulf R. Pedersen, JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747) + [Ulf R. Pedersen, JCP 139, 104102 (2013)](https://doi.org/10.1063/1.4818747) A detailed bibliography is provided at @@ -63,8 +63,8 @@ can be used to show this. The present directory contains the input files that we the value fluctuates around the anchor point (a) -- showing that this is indeed a coexistence state point. -The reference [JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747) gives details on using the method to find coexistence state points, -and the reference [JCP 142, 044104 (2015)](http://dx.doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations. +The reference [JCP 139, 104102 (2013)](https://doi.org/10.1063/1.4818747) gives details on using the method to find coexistence state points, +and the reference [JCP 142, 044104 (2015)](https://doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations. That method have been experienced to be most effective in the slightly super-heated regime above the melting temperature. ## Contact diff --git a/examples/USER/misc/ti/in.ti_spring b/examples/USER/misc/ti/in.ti_spring index 2e853bc5c3..383d4b688c 100644 --- a/examples/USER/misc/ti/in.ti_spring +++ b/examples/USER/misc/ti/in.ti_spring @@ -2,7 +2,7 @@ # # Description: nonequilibrium thermodynamic integration. Further details in: # R. Freitas, M. Asta, and M. de Koning, Computational Materials Science, (2016) -# http://dx.doi.org/10.1016/j.commatsci.2015.10.050 +# https://doi.org/10.1016/j.commatsci.2015.10.050 #--------------------------- System setup -------------------------------------# diff --git a/lib/colvars/README b/lib/colvars/README index 6be1b8dd58..cd6e59511a 100644 --- a/lib/colvars/README +++ b/lib/colvars/README @@ -27,7 +27,7 @@ Also available is a Doxygen-based developer documentation: The reference article is: G. Fiorin, M. L. Klein, and J. Hénin, Molecular Physics 111, 3345 (2013). - http://dx.doi.org/10.1080/00268976.2013.813594 + https://doi.org/10.1080/00268976.2013.813594 ## Requirements diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp index 83632d9458..1d5f75bbca 100644 --- a/lib/colvars/colvarmodule.cpp +++ b/lib/colvars/colvarmodule.cpp @@ -50,7 +50,7 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) cvm::log("Initializing the collective variables module, version "+ cvm::to_str(COLVARS_VERSION)+".\n"); cvm::log("Please cite Fiorin et al, Mol Phys 2013:\n " - "https://dx.doi.org/10.1080/00268976.2013.813594\n" + "https://doi.org/10.1080/00268976.2013.813594\n" "in any publication based on this calculation.\n"); if (proxy->smp_enabled() == COLVARS_OK) { diff --git a/lib/linalg/iparam2stage.F b/lib/linalg/iparam2stage.F index 60bd0b696b..7062b45aac 100644 --- a/lib/linalg/iparam2stage.F +++ b/lib/linalg/iparam2stage.F @@ -130,7 +130,7 @@ *> of 2011 International Conference for High Performance Computing, *> Networking, Storage and Analysis (SC '11), New York, NY, USA, *> Article 8 , 11 pages. -*> http://doi.acm.org/10.1145/2063384.2063394 +*> https://doi.acm.org/10.1145/2063384.2063394 *> *> A. Haidar, J. Kurzak, P. Luszczek, 2013. *> An improved parallel singular value algorithm and its implementation @@ -138,7 +138,7 @@ *> for High Performance Computing, Networking, Storage and Analysis (SC '13). *> Denver, Colorado, USA, 2013. *> Article 90, 12 pages. -*> http://doi.acm.org/10.1145/2503210.2503292 +*> https://doi.acm.org/10.1145/2503210.2503292 *> *> A. Haidar, R. Solca, S. Tomov, T. Schulthess and J. Dongarra. *> A novel hybrid CPU-GPU generalized eigensolver for electronic structure diff --git a/potentials/AlSiMgCuFe.meam b/potentials/AlSiMgCuFe.meam index 30f1c78df8..bbc8894a04 100644 --- a/potentials/AlSiMgCuFe.meam +++ b/potentials/AlSiMgCuFe.meam @@ -1,7 +1,7 @@ # DATE: 2012-06-29 CONTRIBUTOR: Greg Wagner, gjwagne@sandia.gov CITATION: Jelinek, Groh, Horstemeyer, Houze, Kim, Wagner, Moitra and Baskes, Phys Rev B, 85, 245102 (2012) # MEAM Al, Si, Mg, Cu, Fe alloy potential # use with AlS SiS MgS CuS FeS from library.meam -# http://dx.doi.org/10.1103/PhysRevB.85.245102 +# https://doi.org/10.1103/PhysRevB.85.245102 Cmin(1,1,1) = 0.8 repuls(1,1) = 0.1 diff --git a/potentials/CH.airebo-m b/potentials/CH.airebo-m index fb543dd58f..3a0299c161 100644 --- a/potentials/CH.airebo-m +++ b/potentials/CH.airebo-m @@ -1,8 +1,8 @@ # DATE: 2016-03-15 CONTRIBUTOR: T.C. O'Connor CITATION: O'Connor, Andzelm, Robbins, J. Chem. Phys. 142, 024903 (2015) # AIREBO-M of T.C. O'Connor, J.W. Andzelm, M.O. Robbins (2015) -# Citation: J. Chem. Phys. 142, 024903 (2015); http://dx.doi.org/10.1063/1.4905549 +# Citation: J. Chem. Phys. 142, 024903 (2015); https://doi.org/10.1063/1.4905549 # Based on AIREBO of S.J. Stuart, A.B. Tutein, J.A. Harrison (2000) -# Citation: J. Chem. Phys. 112, 6472 (2000); http://dx.doi.org/10.1063/1.481208 +# Citation: J. Chem. Phys. 112, 6472 (2000); https://doi.org/10.1063/1.481208 1.7 rcmin_CC 1.3 rcmin_CH diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index 1453ceb317..f93c7f8a6a 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -15,7 +15,7 @@ Contributing authors: Koenraad Janssens and David Olmsted (SNL) Modification for bcc provided by: Tegar Wicaksono (UBC) For a tutorial, please see "Order parameters of crystals in LAMMPS" - (https://dx.doi.org/10.6084/m9.figshare.1488628.v1 + (https://doi.org/10.6084/m9.figshare.1488628.v1 ------------------------------------------------------------------------- */ #include "fix_orient_bcc.h" diff --git a/src/USER-COLVARS/README b/src/USER-COLVARS/README index 9090a07ead..6627bc9ec4 100644 --- a/src/USER-COLVARS/README +++ b/src/USER-COLVARS/README @@ -27,7 +27,7 @@ and in the reference article: Using collective variables to drive molecular dynamics simulations, G. Fiorin, M. L. Klein, and J. Henin, Molecular Physics 111, 3345 (2013) -http://dx.doi.org/10.1080/00268976.2013.813594 +https://doi.org/10.1080/00268976.2013.813594 A reference manual for the package and library is included with the LAMMPS doc pages: diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp index ba97be25d4..3a1d5271c6 100644 --- a/src/USER-MISC/compute_cnp_atom.cpp +++ b/src/USER-MISC/compute_cnp_atom.cpp @@ -12,7 +12,7 @@ Common Neighbor Parameter as proposed in: Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007) - Cite: http://dx.doi.org/10.1063/1.2197987 + Cite: https://doi.org/10.1063/1.2197987 ------------------------------------------------------------------------- */ diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp index f552126f4f..d1f3e6b6f8 100644 --- a/src/USER-MISC/compute_hma.cpp +++ b/src/USER-MISC/compute_hma.cpp @@ -31,16 +31,16 @@ More information about HMA is available in these publications: A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy equation of state and coexistence properties for classical Lennard-Jones crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018) -https://dx.doi.org/10.1063/1.5053714 +https://doi.org/10.1063/1.5053714 S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for Computing the Free Energy of Classical Crystals by Molecular Simulation: A Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017) -https://dx.doi.org/10.1021/acs.jctc.6b01082 +https://doi.org/10.1021/acs.jctc.6b01082 S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015) -https://dx.doi.org/10.1103/PhysRevE.92.043303 +https://doi.org/10.1103/PhysRevE.92.043303 ------------------------------------------------------------------------- */ #include diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp index bfc5f58f93..52e979d32c 100644 --- a/src/USER-MISC/fix_filter_corotate.cpp +++ b/src/USER-MISC/fix_filter_corotate.cpp @@ -54,7 +54,7 @@ static const char cite_filter_corotate[] = " Year = {2017},\n" " Pages = {180 - 198},\n" " Volume = {333},\n\n" - " Doi = {http://dx.doi.org/10.1016/j.jcp.2016.12.024},\n" + " Doi = {https://doi.org/10.1016/j.jcp.2016.12.024},\n" " ISSN = {0021-9991},\n" " Keywords = {Mollified impulse method},\n" " Url = {http://www.sciencedirect.com/science/article/pii/S0021999116306787}\n" diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index 70be1f1e45..218ba3cfa6 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -37,7 +37,7 @@ static const char cite_flow_gauss[] = "title = {The Dynamics of Water in Porous Two-Dimensional Crystals},\n" "volume = {121},\n" "number = {1},\n" - "url = {http://dx.doi.org/10.1021/acs.jpcb.6b09387},\n" + "url = {https://doi.org/10.1021/acs.jpcb.6b09387},\n" "doi = {10.1021/acs.jpcb.6b09387},\n" "urldate = {2016-12-07},\n" "journal = {J. Phys. Chem. B},\n" diff --git a/src/USER-MISC/fix_grem.cpp b/src/USER-MISC/fix_grem.cpp index 4272740068..9600cce90e 100644 --- a/src/USER-MISC/fix_grem.cpp +++ b/src/USER-MISC/fix_grem.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. Force scaling fix for gREM. - Cite: http://dx.doi.org/10.1063/1.3432176 - Cite: http://dx.doi.org/10.1021/acs.jpcb.5b07614 + Cite: https://doi.org/10.1063/1.3432176 + Cite: https://doi.org/10.1021/acs.jpcb.5b07614 ------------------------------------------------------------------------- */ diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp index 8786394221..010aa1e5fd 100644 --- a/src/USER-MISC/pair_momb.cpp +++ b/src/USER-MISC/pair_momb.cpp @@ -37,7 +37,7 @@ static const char cite_momb[] = " solution-phase synthesis of shape-selective Ag nanoparticles.},\n" "volume = {118},\n" "number = {6},\n" - "url = {http://dx.doi.org/10.1021/jp412098n},\n" + "url = {https://doi.org/10.1021/jp412098n},\n" "doi = {10.1021/jp412098n},\n" "journal = {J. Phys. Chem. C},\n" "author = {Zhou, Ya, Wissam A. Saidi, and Kristen A. Fichthorn},\n" diff --git a/src/USER-YAFF/README b/src/USER-YAFF/README index 4fabe67390..9d095b8216 100644 --- a/src/USER-YAFF/README +++ b/src/USER-YAFF/README @@ -1,8 +1,8 @@ This package implements the styles that are needed to use typical force fields generated by QuickFF for the simulation of metal-organic frameworks. The QuickFF methodology is detailed in following papers: - Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) http://dx.doi.org/10.1002/jcc.23877 - Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) http://dx.doi.org/10.1002/jcc.25173 + Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) https://doi.org/10.1002/jcc.23877 + Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) https://doi.org/10.1002/jcc.25173 The corresponding software package can be found on http://molmod.github.io/QuickFF