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/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index 9d03be99ec..6b589e3cd9 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -7,11 +7,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU SRD VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP - USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-YAFF) + USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ + USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 2ff107975a..e46157bb96 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -9,11 +9,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU SRD VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP - USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-YAFF) + USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ + USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index eed560b995..b2c53bd41d 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -2,13 +2,13 @@ # external libraries. Compared to all_on.cmake some more unusual packages # are removed. The resulting binary should be able to run most inputs. -set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE - GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI - PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI - USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD - USER-DRUDE USER-FEP USER-MEAMC USER-MESO - USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC - USER-SPH USER-SMD USER-UEF USER-YAFF) +set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL + DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI + POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI + USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION + USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESODPD + USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION + USER-REAXC USER-SPH USER-SMD USER-UEF USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index e3129ae06a..1aa5712b19 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 5e1b7fd437..4501b1b34d 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -2339,8 +2339,8 @@ 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 cf85a253f7..30e5f87ee9 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -193,7 +193,7 @@ Science, 117, 397-405 (2016). .. _Wicaksono2: **(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 43178d6958..6a6a8c6b96 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -203,19 +203,19 @@ 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: **(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 b53252668a..ec1d1335a5 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -140,4 +140,4 @@ 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/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index 9fd2f00321..560c6f0a03 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -126,9 +126,14 @@ the work of :ref:`(Afshar) ` and :ref:`(Phillips) `. .. note:: - The virial calculation for pressure when using this pair style + The virial calculation for pressure when using these pair styles includes all the components of force listed above, including the - random force. + random force. Since the random force depends on random numbers, + everything that changes the order of atoms in the neighbor list + (e.g. different number of MPI ranks or a different neighbor list + skin distance) will also change the sequence in which the random + numbers are applied and thus the individual forces and therefore + also the virial/pressure. ---------- diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index 317e417bfc..cb60a0285d 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -15,9 +15,9 @@ Syntax * distance = *min* or *mid* * zero or more keyword/value pairs may be appended * keyword = *exclude* - + .. parsed-literal:: - + *bptype* value = atom type for bond particles *exclude* value = *yes* or *no* @@ -31,7 +31,7 @@ Examples pair_coeff 1 2 none pair_coeff 2 2 srp 100.0 0.8 - pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 \* min exclude yes + pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes pair_coeff 1 1 dpd 60.0 50 1.0 pair_coeff 1 2 none pair_coeff 2 2 srp 40.0 @@ -57,7 +57,7 @@ bond-pairwise potential, such that the force on bond *i* due to bond .. math:: - F^{SRP}_{ij} & = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c + F^{\mathrm{SRP}}_{ij} = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c where *r* and :math:`\hat{r}_{ij}` are the distance and unit vector between the two bonds. Note that *btype* can be specified as an @@ -70,8 +70,8 @@ lever rule, .. math:: - F_{i1}^{SRP} & = F^{SRP}_{ij}(L) \\ - F_{i2}^{SRP} & = F^{SRP}_{ij}(1-L) + F_{i1}^{\mathrm{SRP}} & = F^{\mathrm{SRP}}_{ij}(L) \\ + F_{i2}^{\mathrm{SRP}} & = F^{\mathrm{SRP}}_{ij}(1-L) where *L* is the normalized distance from the atom to the point of closest approach of bond *i* and *j*\ . The *mid* option takes *L* as 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/python/lammps.py b/python/lammps.py index 2e597f9e18..484c30d9ac 100644 --- a/python/lammps.py +++ b/python/lammps.py @@ -486,6 +486,7 @@ class lammps(object): return None elif style == 2: self.lib.lammps_extract_compute.restype = POINTER(c_int) + ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) return ptr[0] if type == 1: self.lib.lammps_extract_compute.restype = POINTER(c_double) @@ -509,6 +510,10 @@ class lammps(object): result = ptr[0] self.lib.lammps_free(ptr) return result + elif (style == 2) and (type == 0): + self.lib.lammps_extract_fix.restype = POINTER(c_int) + ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j) + return ptr[0] elif (style == 1) or (style == 2): if type == 1: self.lib.lammps_extract_fix.restype = POINTER(c_double) diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index 2766ac3391..e53dec4d86 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -38,7 +38,7 @@ struct TagPairSNAPComputeNeigh{}; struct TagPairSNAPPreUi{}; struct TagPairSNAPComputeUi{}; struct TagPairSNAPComputeUiTot{}; // accumulate ulist into ulisttot separately -struct TagPairSNAPComputeUiCPU{}; +struct TagPairSNAPComputeUiCPU{}; struct TagPairSNAPComputeZi{}; struct TagPairSNAPComputeBi{}; struct TagPairSNAPZeroYi{}; diff --git a/src/KOKKOS/sna_kokkos.h b/src/KOKKOS/sna_kokkos.h index 7a24bfbecd..133db2139f 100644 --- a/src/KOKKOS/sna_kokkos.h +++ b/src/KOKKOS/sna_kokkos.h @@ -32,7 +32,7 @@ template struct alignas(2*sizeof(real)) SNAComplex { real re,im; - + KOKKOS_FORCEINLINE_FUNCTION SNAComplex() = default; KOKKOS_FORCEINLINE_FUNCTION SNAComplex(real re) @@ -172,7 +172,7 @@ inline static KOKKOS_FORCEINLINE_FUNCTION void caxpy(const SNAcomplex& a, const SNAcomplex& x, SNAcomplex& y); - // efficient complex FMA, conjugate of scalar + // efficient complex FMA, conjugate of scalar static KOKKOS_FORCEINLINE_FUNCTION void caconjxpy(const SNAcomplex& a, const SNAcomplex& x, SNAcomplex& y); @@ -201,7 +201,7 @@ inline void grow_rij(int, int); int twojmax, diagonalstyle; - + t_sna_2d_ll blist; t_sna_2c_ll ulisttot; t_sna_2c_ll zlist; 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 diff --git a/src/library.cpp b/src/library.cpp index ee98e47aaa..72fcbba833 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -537,35 +537,19 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type) if (style == 1) { if (!compute->peratom_flag) return NULL; - if (type == 1) { - if (compute->invoked_peratom != lmp->update->ntimestep) - compute->compute_peratom(); - return (void *) compute->vector_atom; - } - if (type == 2) { - if (compute->invoked_peratom != lmp->update->ntimestep) - compute->compute_peratom(); - return (void *) compute->array_atom; - } + if (compute->invoked_peratom != lmp->update->ntimestep) + compute->compute_peratom(); + if (type == 1) return (void *) compute->vector_atom; + if (type == 2) return (void *) compute->array_atom; } if (style == 2) { if (!compute->local_flag) return NULL; - if (type == 0) { - if (compute->invoked_local != lmp->update->ntimestep) - compute->compute_local(); - return (void *) &compute->size_local_rows; - } - if (type == 1) { - if (compute->invoked_local != lmp->update->ntimestep) - compute->compute_local(); - return (void *) compute->vector_local; - } - if (type == 2) { - if (compute->invoked_local != lmp->update->ntimestep) - compute->compute_local(); - return (void *) compute->array_local; - } + if (compute->invoked_local != lmp->update->ntimestep) + compute->compute_local(); + if (type == 0) return (void *) &compute->size_local_rows; + if (type == 1) return (void *) compute->vector_local; + if (type == 2) return (void *) compute->array_local; } } END_CAPTURE @@ -637,6 +621,7 @@ void *lammps_extract_fix(void *ptr, char *id, int style, int type, if (style == 2) { if (!fix->local_flag) return NULL; + if (type == 0) return (void *) &fix->size_local_rows; if (type == 1) return (void *) fix->vector_local; if (type == 2) return (void *) fix->array_local; } diff --git a/src/min_cg.cpp b/src/min_cg.cpp index 9db1fd9799..46da4bfa5b 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -113,7 +113,7 @@ int MinCG::iterate(int maxiter) if (update->ftol > 0.0) { if (normstyle == MAX) fdotf = fnorm_max(); // max force norm else if (normstyle == INF) fdotf = fnorm_inf(); // infinite force norm - else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm + else if (normstyle == TWO) fdotf = dotall[0]; // same as fnorm_sqr(), Euclidean force 2-norm else error->all(FLERR,"Illegal min_modify command"); if (fdotf < update->ftol*update->ftol) return FTOL; }