diff --git a/doc/Makefile b/doc/Makefile index a1f76d7041..2274ca5550 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -100,6 +100,7 @@ epub: $(OBJECTS) pdf: utils/txt2html/txt2html.exe @(\ + set -e; \ cd src; \ ../utils/txt2html/txt2html.exe -b *.txt; \ htmldoc --batch lammps.book; \ diff --git a/doc/src/Eqs/cnp_cutoff.jpg b/doc/src/Eqs/cnp_cutoff.jpg new file mode 100644 index 0000000000..fae5c6b636 Binary files /dev/null and b/doc/src/Eqs/cnp_cutoff.jpg differ diff --git a/doc/src/Eqs/cnp_cutoff.tex b/doc/src/Eqs/cnp_cutoff.tex new file mode 100644 index 0000000000..f74166e608 --- /dev/null +++ b/doc/src/Eqs/cnp_cutoff.tex @@ -0,0 +1,14 @@ +\documentclass[12pt,article]{article} + +\usepackage{indentfirst} +\usepackage{amsmath} + +\begin{document} + +\begin{eqnarray*} + r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\ + r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\ + r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a} +\end{eqnarray*} + +\end{document} diff --git a/doc/src/Eqs/cnp_cutoff2.jpg b/doc/src/Eqs/cnp_cutoff2.jpg new file mode 100644 index 0000000000..744b61e9b4 Binary files /dev/null and b/doc/src/Eqs/cnp_cutoff2.jpg differ diff --git a/doc/src/Eqs/cnp_cutoff2.tex b/doc/src/Eqs/cnp_cutoff2.tex new file mode 100644 index 0000000000..fcec31fd24 --- /dev/null +++ b/doc/src/Eqs/cnp_cutoff2.tex @@ -0,0 +1,12 @@ +\documentclass[12pt,article]{article} + +\usepackage{indentfirst} +\usepackage{amsmath} + +\begin{document} + +$$ + Rc + Rs > 2*{\rm cutoff} +$$ + +\end{document} diff --git a/doc/src/Eqs/cnp_eq.jpg b/doc/src/Eqs/cnp_eq.jpg new file mode 100644 index 0000000000..d421314442 Binary files /dev/null and b/doc/src/Eqs/cnp_eq.jpg differ diff --git a/doc/src/Eqs/cnp_eq.tex b/doc/src/Eqs/cnp_eq.tex new file mode 100644 index 0000000000..e5f157e6ba --- /dev/null +++ b/doc/src/Eqs/cnp_eq.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} | \sum_{k = 1}^{n_{ij}} \vec{R}_{ik} + \vec{R}_{jk} |^2 +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_lj_sf.jpg b/doc/src/Eqs/pair_lj_sf.jpg deleted file mode 100644 index a702240003..0000000000 Binary files a/doc/src/Eqs/pair_lj_sf.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_lj_sf.tex b/doc/src/Eqs/pair_lj_sf.tex deleted file mode 100644 index e78e2ca75f..0000000000 --- a/doc/src/Eqs/pair_lj_sf.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - F & = & F_{\mathrm{LJ}}(r) - F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\ - E & = & E_{\mathrm{LJ}}(r) - E_{\mathrm{LJ}}(r_{\mathrm{c}}) + (r - r_{\mathrm{c}}) F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\ - \mathrm{with} \qquad E_{\mathrm{LJ}}(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad \mathrm{and} \qquad F_{\mathrm{LJ}}(r) = - E^\prime_{\mathrm{LJ}}(r) -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index dc7ddebe58..8aa5bdec2e 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -717,7 +717,7 @@ package"_Section_start.html#start_3. "phonon"_fix_phonon.html, "pimd"_fix_pimd.html, "qbmsst"_fix_qbmsst.html, -"qeq/reax"_fix_qeq_reax.html, +"qeq/reax (ko)"_fix_qeq_reax.html, "qmmm"_fix_qmmm.html, "qtb"_fix_qtb.html, "reax/c/bonds"_fix_reax_bonds.html, @@ -831,6 +831,7 @@ package"_Section_start.html#start_3. "ackland/atom"_compute_ackland_atom.html, "basal/atom"_compute_basal_atom.html, +"cnp/atom"_compute_cnp_atom.html, "dpd"_compute_dpd.html, "dpd/atom"_compute_dpd_atom.html, "fep"_compute_fep.html, @@ -1038,7 +1039,6 @@ package"_Section_start.html#start_3. "lj/sdk (gko)"_pair_sdk.html, "lj/sdk/coul/long (go)"_pair_sdk.html, "lj/sdk/coul/msm (o)"_pair_sdk.html, -"lj/sf (o)"_pair_lj_sf.html, "meam/spline (o)"_pair_meam_spline.html, "meam/sw/spline"_pair_meam_sw_spline.html, "mgpt"_pair_mgpt.html, @@ -1057,7 +1057,7 @@ package"_Section_start.html#start_3. "oxdna2/excv"_pair_oxdna2.html, "oxdna2/stk"_pair_oxdna2.html, "quip"_pair_quip.html, -"reax/c (k)"_pair_reaxc.html, +"reax/c (ko)"_pair_reaxc.html, "smd/hertz"_pair_smd_hertz.html, "smd/tlsph"_pair_smd_tlsph.html, "smd/triangulated/surface"_pair_smd_triangulated_surface.html, diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt index 5e0574b390..23942a75e5 100644 --- a/doc/src/Section_errors.txt +++ b/doc/src/Section_errors.txt @@ -8890,6 +8890,14 @@ This is a requirement to use this potential. :dd See the newton command. This is a restriction to use this potential. :dd +{Pair style vashishta/gpu requires atom IDs} :dt + +This is a requirement to use this potential. :dd + +{Pair style vashishta/gpu requires newton pair off} :dt + +See the newton command. This is a restriction to use this potential. :dd + {Pair style tersoff/gpu requires atom IDs} :dt This is a requirement to use the tersoff/gpu potential. :dd diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index cc44c05906..14b2c0baa3 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -1502,7 +1502,7 @@ oxDNA model of Doye, Louis and Ouldridge at the University of Oxford. This includes Langevin-type rigid-body integrators with improved stability. -[Author:] Oliver Henrich (University of Edinburgh). +[Author:] Oliver Henrich (University of Strathclyde, Glasgow). [Install or un-install:] @@ -2027,8 +2027,8 @@ algorithm to formulate single-particle constraint functions g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold) n = grad(g). -[Author:] Stefan Paquay (Eindhoven University of Technology (TU/e), The -Netherlands) +[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The +Netherlands; since 2017: Brandeis University, Waltham, MA, USA) [Install or un-install:] diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt index 74240b515d..23289b0132 100644 --- a/doc/src/compute_cna_atom.txt +++ b/doc/src/compute_cna_atom.txt @@ -26,7 +26,7 @@ Define a computation that calculates the CNA (Common Neighbor Analysis) pattern for each atom in the group. In solid-state systems the CNA pattern is a useful measure of the local crystal structure around an atom. The CNA methodology is described in "(Faken)"_#Faken -and "(Tsuzuki)"_#Tsuzuki. +and "(Tsuzuki)"_#Tsuzuki1. Currently, there are five kinds of CNA patterns LAMMPS recognizes: @@ -93,5 +93,5 @@ above. :link(Faken) [(Faken)] Faken, Jonsson, Comput Mater Sci, 2, 279 (1994). -:link(Tsuzuki) +:link(Tsuzuki1) [(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007). diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt new file mode 100644 index 0000000000..9aa63c84de --- /dev/null +++ b/doc/src/compute_cnp_atom.txt @@ -0,0 +1,111 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute cnp/atom command :h3 + +[Syntax:] + +compute ID group-ID cnp/atom cutoff :pre + +ID, group-ID are documented in "compute"_compute.html command +cnp/atom = style name of this compute command +cutoff = cutoff distance for nearest neighbors (distance units) :ul + +[Examples:] + +compute 1 all cnp/atom 3.08 :pre + +[Description:] + +Define a computation that calculates the Common Neighborhood +Parameter (CNP) for each atom in the group. In solid-state systems +the CNP is a useful measure of the local crystal structure +around an atom and can be used to characterize whether the +atom is part of a perfect lattice, a local defect (e.g. a dislocation +or stacking fault), or at a surface. + +The value of the CNP parameter will be 0.0 for atoms not in the +specified compute group. Note that normally a CNP calculation should +only be performed on single component systems. + +This parameter is computed using the following formula from +"(Tsuzuki)"_#Tsuzuki2 + +:c,image(Eqs/cnp_eq.jpg) + +where the index {j} goes over the {n}i nearest neighbors of atom +{i}, and the index {k} goes over the {n}ij common nearest neighbors +between atom {i} and atom {j}. Rik and Rjk are the vectors connecting atom +{k} to atoms {i} and {j}. The quantity in the double sum is computed +for each atom. + +The CNP calculation is sensitive to the specified cutoff value. +You should ensure that the appropriate nearest neighbors of an atom are +found within the cutoff distance for the presumed crystal structure. +E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest +neighbors for perfect BCC crystals. These formulas can be used to +obtain a good cutoff distance: + +:c,image(Eqs/cnp_cutoff.jpg) + +where a is the lattice constant for the crystal structure concerned +and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a +for HCP crystals. + +Also note that since the CNP calculation in LAMMPS uses the neighbors +of an owned atom to find the nearest neighbors of a ghost atom, the +following relation should also be satisfied: + +:c,image(Eqs/cnp_cutoff2.jpg) + +where Rc is the cutoff distance of the potential, Rs is the skin +distance as specified by the "neighbor"_neighbor.html command, and +cutoff is the argument used with the compute cnp/atom command. LAMMPS +will issue a warning if this is not the case. + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (e.g. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently or to have multiple compute/dump commands, each with a +{cnp/atom} style. + +[Output info:] + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +"Section 6.15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. + +The per-atom vector values will be real positive numbers. Some typical CNP +values: + +FCC lattice = 0.0 +BCC lattice = 0.0 +HCP lattice = 4.4 :pre + +FCC (111) surface ~ 13.0 +FCC (100) surface ~ 26.5 +FCC dislocation core ~ 11 :pre + +[Restrictions:] + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"compute cna/atom"_compute_cna_atom.html +"compute centro/atom"_compute_centro_atom.html + +[Default:] none + +:line + +:link(Tsuzuki2) +[(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007). diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt index aadda49533..020f72f565 100644 --- a/doc/src/compute_saed.txt +++ b/doc/src/compute_saed.txt @@ -111,26 +111,26 @@ Coefficients parameterized by "(Fox)"_#Fox are assigned for each atom type designating the chemical symbol and charge of each atom type. Valid chemical symbols for compute saed are: - H: He: Li: Be: B: - C: N: O: F: Ne: - Na: Mg: Al: Si: P: - S: Cl: Ar: K: Ca: - Sc: Ti: V: Cr: Mn: - Fe: Co: Ni: Cu: Zn: - Ga: Ge: As: Se: Br: - Kr: Rb: Sr: Y: Zr: - Nb: Mo: Tc: Ru: Rh: - Pd: Ag: Cd: In: Sn: - Sb: Te: I: Xe: Cs: - Ba: La: Ce: Pr: Nd: - Pm: Sm: Eu: Gd: Tb: - Dy: Ho: Er: Tm: Yb: - Lu: Hf: Ta: W: Re: - Os: Ir: Pt: Au: Hg: - Tl: Pb: Bi: Po: At: - Rn: Fr: Ra: Ac: Th: - Pa: U: Np: Pu: Am: - Cm: Bk: Cf:tb(c=5,s=:) +H: He: Li: Be: B: +C: N: O: F: Ne: +Na: Mg: Al: Si: P: +S: Cl: Ar: K: Ca: +Sc: Ti: V: Cr: Mn: +Fe: Co: Ni: Cu: Zn: +Ga: Ge: As: Se: Br: +Kr: Rb: Sr: Y: Zr: +Nb: Mo: Tc: Ru: Rh: +Pd: Ag: Cd: In: Sn: +Sb: Te: I: Xe: Cs: +Ba: La: Ce: Pr: Nd: +Pm: Sm: Eu: Gd: Tb: +Dy: Ho: Er: Tm: Yb: +Lu: Hf: Ta: W: Re: +Os: Ir: Pt: Au: Hg: +Tl: Pb: Bi: Po: At: +Rn: Fr: Ra: Ac: Th: +Pa: U: Np: Pu: Am: +Cm: Bk: Cf:tb(c=5,s=:) If the {echo} keyword is specified, compute saed will provide extra diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index f82df0d816..defd98d520 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -231,11 +231,12 @@ the numbers of columns are 930, 2790, and 5580, respectively. If the {quadratic} keyword value is set to 1, then additional columns are appended to each per-atom array, corresponding to -a matrix of quantities that are products of two bispectrum components. If the -number of bispectrum components is {K}, then the number of matrix elements -is {K}^2. These are output in subblocks of {K}^2 columns, using the same -ordering of columns and sub-blocks as was used for the bispectrum -components. +the products of all distinct pairs of bispectrum components. If the +number of bispectrum components is {K}, then the number of distinct pairs +is {K}({K}+1)/2. These are output in subblocks of {K}({K}+1)/2 columns, using the same +ordering of sub-blocks as was used for the bispectrum +components. Within each sub-block, the ordering is upper-triangular, +(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}) These values can be accessed by any command that uses per-atom values from a compute as input. See "Section diff --git a/doc/src/computes.txt b/doc/src/computes.txt index 1d01798791..5a6ca66c46 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -17,6 +17,7 @@ Computes :h1 compute_chunk_atom compute_cluster_atom compute_cna_atom + compute_cnp_atom compute_com compute_com_chunk compute_contact_atom diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt index c71a319912..7c17fbf5ef 100644 --- a/doc/src/dihedral_spherical.txt +++ b/doc/src/dihedral_spherical.txt @@ -18,6 +18,7 @@ dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 dihedral_coeff 1 3 69.3 1 93.9 1 1 90 0 1 90 0 & 49.1 0 0.00 0 1 74.4 1 0 0.00 0 & 25.2 0 0.00 0 0 0.00 0 1 48.1 1 +:pre [Description:] diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index b5daa6416e..2ea1da3db3 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -16,7 +16,8 @@ dump-ID = ID of dump to modify :ulb,l one or more keyword/value pairs may be appended :l these keywords apply to various dump styles :l keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l - {append} arg = {yes} or {no} + {append} arg = {yes} or {no} or {at} N + N = index of frame written upon first dump {buffer} arg = {yes} or {no} {element} args = E1 E2 ... EN, where N = # of atom types E1,...,EN = element name, e.g. C or Fe or Ga @@ -41,6 +42,7 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o {region} arg = region-ID or "none" {scale} arg = {yes} or {no} {sfactor} arg = coordinate scaling factor (> 0.0) + {thermo} arg = {yes} or {no} {tfactor} arg = time scaling factor (> 0.0) {sort} arg = {off} or {id} or N or -N off = no sorting of per-atom lines within a snapshot @@ -139,12 +141,13 @@ and {dcd}. It also applies only to text output files, not to binary or gzipped or image/movie files. If specified as {yes}, then dump snapshots are appended to the end of an existing dump file. If specified as {no}, then a new dump file will be created which will -overwrite an existing file with the same name. This keyword can only -take effect if the dump_modify command is used after the -"dump"_dump.html command, but before the first command that causes -dump snapshots to be output, e.g. a "run"_run.html or -"minimize"_minimize.html command. Once the dump file has been opened, -this keyword has no further effect. +overwrite an existing file with the same name. If the {at} option is present +({netcdf} only), then the frame to append to can be specified. Negative values +are counted from the end of the file. This keyword can only take effect if the +dump_modify command is used after the "dump"_dump.html command, but before the +first command that causes dump snapshots to be output, e.g. a "run"_run.html or +"minimize"_minimize.html command. Once the dump file has been opened, this +keyword has no further effect. :line @@ -413,6 +416,13 @@ most effective when the typical magnitude of position data is between :line +The {thermo} keyword ({netcdf} only) triggers writing of "thermo"_thermo.html +information to the dump file alongside per-atom data. The data included in the +dump file is identical to the data specified by +"thermo_style"_thermo_style.html. + +:line + The {region} keyword only applies to the dump {custom}, {cfg}, {image}, and {movie} styles. If specified, only atoms in the region will be written to the dump file or included in the image/movie. Only diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt index 4e82656698..63568137a6 100644 --- a/doc/src/dump_netcdf.txt +++ b/doc/src/dump_netcdf.txt @@ -24,7 +24,7 @@ args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule [Examples:] dump 1 all netcdf 100 traj.nc type x y z vx vy vz -dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press +dump_modify 1 append yes at -1 thermo yes dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre [Description:] @@ -44,7 +44,7 @@ rank. NetCDF files can be directly visualized via the following tools: Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and -all of the above extensions. :ule,b +all extensions of this dump style. :ule,b VMD (http://www.ks.uiuc.edu/Research/vmd/). :l @@ -52,15 +52,9 @@ AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains a NetCDF reader that is not present in the standard distribution of AtomEye. :l,ule -In addition to per-atom data, global data can be included in the dump -file, which are the kinds of values output by the -"thermo_style"_thermo_style.html command . See "Section howto -6.15"_Section_howto.html#howto_15 for an explanation of per-atom -versus global data. The global output written into the dump file can -be from computes, fixes, or variables, by prefixing the compute/fix ID -or variable name with "c_" or "f_" or "v_" respectively, as in the -example above. These global values are specified via the "dump_modify -global"_dump_modify.html command. +In addition to per-atom data, "thermo"_thermo.html data can be included in the +dump file. The data included in the dump file is identical to the data specified +by "thermo_style"_thermo_style.html. :link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/) :link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/) diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt index d7c32bef3d..19d1009b8a 100644 --- a/doc/src/fix_adapt.txt +++ b/doc/src/fix_adapt.txt @@ -47,7 +47,7 @@ keyword = {scale} or {reset} :l fix 1 all adapt 1 pair soft a 1 1 v_prefactor fix 1 all adapt 1 pair soft a 2* 3 v_prefactor fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes -fix 1 all adapt 10 atom diameter v_size +fix 1 all adapt 10 atom diameter v_size :pre variable ramp_up equal "ramp(0.01,0.5)" fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up :pre diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index 8c3a9fa499..d3254eece6 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -565,8 +565,10 @@ more instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options +This fix will restore the initial box settings from "binary restart +files"_restart.html, which allows the fix to be properly continue +deformation, when using the start/stop options of the "run"_run.html +command. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various "output commands"_Section_howto.html#howto_15. diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt index b8d3cc9b34..6568060f0c 100644 --- a/doc/src/fix_gle.txt +++ b/doc/src/fix_gle.txt @@ -68,7 +68,7 @@ matrix that gives canonical sampling for a given A is computed automatically. However, the GLE framework also allow for non-equilibrium sampling, that can be used for instance to model inexpensively zero-point energy effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the {noneq} - keyword followed by the name of the file that contains the static covariance +keyword followed by the name of the file that contains the static covariance matrix for the non-equilibrium dynamics. Please note, that the covariance matrix is expected to be given in [temperature units]. diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt index 04437e7f36..afc9c5f257 100644 --- a/doc/src/fix_langevin_drude.txt +++ b/doc/src/fix_langevin_drude.txt @@ -67,11 +67,11 @@ The Langevin forces are computed as \(F_r'\) is a random force proportional to \(\sqrt \{ \frac \{2\, k_B \mathtt\{Tcom\}\, m'\} \{\mathrm dt\, \mathtt\{damp\_com\} \} - \} \). :b + \} \). \(f_r'\) is a random force proportional to \(\sqrt \{ \frac \{2\, k_B \mathtt\{Tdrude\}\, m'\} \{\mathrm dt\, \mathtt\{damp\_drude\} \} - \} \). :b + \} \). Then the real forces acting on the particles are computed from the inverse transform: \begin\{equation\} F = \frac M \{M'\}\, F' - f' \end\{equation\} diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt index 9d11b7289e..94c6ee84fd 100644 --- a/doc/src/fix_neb.txt +++ b/doc/src/fix_neb.txt @@ -10,68 +10,156 @@ fix neb command :h3 [Syntax:] -fix ID group-ID neb Kspring :pre +fix ID group-ID neb Kspring keyword value :pre -ID, group-ID are documented in "fix"_fix.html command -neb = style name of this fix command -Kspring = inter-replica spring constant (force/distance units) :ul +ID, group-ID are documented in "fix"_fix.html command :ulb,l +neb = style name of this fix command :l +Kspring = parallel spring constant (force/distance units or force units) :l +zero or more keyword/value pairs may be appended :l +keyword = {nudg_style} or {perp} or {freend} or {freend_k_spring} :l + {nudg_style} value = {neigh} or {idealpos} + {neigh} = the parallel nudging force is calculated from the distances to neighbouring replicas (in this case, Kspring is in force/distance units) + {idealpos} = the parallel nudging force is proportional to the distance between the replica and its interpolated ideal position (in this case Kspring is in force units) + {perp} value {none} or kspring2 + {none} = no perpendicular spring force is applied + {kspring2} = spring constant for the perpendicular nudging force (in force/distance units) + {freeend} value = {none} or {ini} or {final} or {finaleini} or {final2eini} + {none} = no nudging force is applied to the first and last replicas + {ini} = set the first replica to be a free end + {final} = set the last replica to be a free end + {finaleini} = set the last replica to be a free end and set its target energy as that of the first replica + {final2eini} = same as {finaleini} plus prevent intermediate replicas to have a lower energy than the first replica + {freeend_kspring} value = kspring3 + kspring3 = spring constant of the perpendicular spring force (per distance units) + :pre [Examples:] -fix 1 active neb 10.0 :pre +fix 1 active neb 10.0 +fix 2 all neb 1.0 perp 1.0 freeend final +fix 1 all neb 1.0 nudg_style idealpos freeend final2eini freend_kspring 1:pre [Description:] -Add inter-replica forces to atoms in the group for a multi-replica +Add a nudging force to atoms in the group for a multi-replica simulation run via the "neb"_neb.html command to perform a nudged -elastic band (NEB) calculation for transition state finding. Hi-level -explanations of NEB are given with the "neb"_neb.html command and in -"Section 6.5"_Section_howto.html#howto_5 of the manual. The fix -neb command must be used with the "neb" command to define how -inter-replica forces are computed. +elastic band (NEB) calculation for finding the transition state. +Hi-level explanations of NEB are given with the "neb"_neb.html command +and in "Section_howto 5"_Section_howto.html#howto_5 of the manual. +The fix neb command must be used with the "neb" command and defines +how nudging inter-replica forces are computed. A NEB calculation is +divided in two stages. In the first stage n replicas are relaxed +toward a MEP and in a second stage, the climbing image scheme (see +"(Henkelman2)"_#Henkelman2) is turned on so that the replica having +the highest energy relaxes toward the saddle point (i.e. the point of +highest energy along the MEP). -Only the N atoms in the fix group experience inter-replica forces. -Atoms in the two end-point replicas do not experience these forces, -but those in intermediate replicas do. During the initial stage of -NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting -on the atoms of each intermediate replica I is altered, as described -in the "(Henkelman1)"_#Henkelman1 paper, to become: +One purpose of the nudging forces is to keep the replicas equally +spaced. During the NEB, the 3N-length vector of interatomic force Fi += -Grad(V) of replicas i is altered. For all intermediate replicas +(i.e. for 1 0 +:pre + +where E is the energy of the free end replica and ETarget is the +target energy. + +When the value {ini} ({final}) is used after the keyword {freeend}, +the first (last) replica is considered as a free end. The target +energy is set to the energy of the replica at starting of the NEB +calculation. When the value {finaleini} or {final2eini} is used the +last image is considered as a free end and the target energy is equal +to the energy of the first replica (which can evolve during the NEB +relaxation). With the value {finaleini}, when the initial path is too +far from the MEP, an intermediate repilica might relax "faster" and +get a lower energy than the last replica. The benefit of the free end +is then lost since this intermediate replica will relax toward a local +minima. This behavior can be prevented by using the value {final2eini} +which remove entirely the contribution of the gradient for all +intermediate replica which have a lower energy than the initial one +thus preventing these replicae to over-relax. After converging a NEB +with the {final2eini} value it is recommended to check that all +intermediate replica have a larger energy than the initial +replica. Finally note that if the last replica converges toward a +local minimum with a larger energy than the energy of the first +replica, a free end neb calculation with the value {finaleini} or +{final2eini} cannot reach the convergence criteria. + +:line + + + +In the second stage of the NEB, the interatomic force Fi for the +climbing replica (which is the replica of highest energy) becomes: Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre -The inter-replica forces for the other replicas are unchanged from the -first equation. + [Restart, fix_modify, output, run start/stop, minimize info:] @@ -96,7 +184,11 @@ for more info on packages. "neb"_neb.html -[Default:] none +[Default:] + +The option defaults are nudg_style = neigh, perp = none, freeend = none and freend_kspring = 1. + +:line :link(Henkelman1) [(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000). @@ -104,3 +196,15 @@ for more info on packages. :link(Henkelman2) [(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, 9901-9904 (2000). + +:link(E) +[(E)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002) + +:link(Jonsson) +[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum +Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti, and Coker +World Scientific, Singapore, 1998, p. 385 + +:link(Maras1) +[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, +Comp Phys Comm, 205, 13-21 (2016) diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt index aed043f6c0..a1a19b7368 100644 --- a/doc/src/fix_qeq_reax.txt +++ b/doc/src/fix_qeq_reax.txt @@ -8,17 +8,19 @@ fix qeq/reax command :h3 fix qeq/reax/kk command :h3 +fix qeq/reax/omp command :h3 [Syntax:] -fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params :pre +fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params args :pre ID, group-ID are documented in "fix"_fix.html command qeq/reax = style name of this fix command Nevery = perform QEq every this many steps cutlo,cuthi = lo and hi cutoff for Taper radius tolerance = precision to which charges will be equilibrated -params = reax/c or a filename :ul +params = reax/c or a filename +args = {dual} (optional) :ul [Examples:] @@ -59,6 +61,10 @@ potential file, except that eta is defined here as twice the eta value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units of this fix are hard-coded to be A, eV, and electronic charge. +The optional {dual} keyword allows to perform the optimization +of the S and T matrices in parallel. This is only supported for +the {qeq/reax/omp} style. Otherwise they are processed separately. + [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index 03edf61ed8..dbadd3fa63 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -31,11 +31,12 @@ bodystyle = {single} or {molecule} or {group} :l groupID1, groupID2, ... = list of N group IDs :pre zero or more keyword/value pairs may be appended :l -keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l +keyword = {langevin} or {reinit} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l {langevin} values = Tstart Tstop Tperiod seed Tstart,Tstop = desired temperature at start/stop of run (temperature units) Tdamp = temperature damping parameter (time units) seed = random number seed to use for white noise (positive integer) + {reinit} = {yes} or {no} {temp} values = Tstart Tstop Tdamp Tstart,Tstop = desired temperature at start/stop of run (temperature units) Tdamp = temperature damping parameter (time units) @@ -68,10 +69,10 @@ keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {coup [Examples:] -fix 1 clump rigid single +fix 1 clump rigid single reinit yes fix 1 clump rigid/small molecule fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984 -fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0 +fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0 reinit no fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984 fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off @@ -87,7 +88,12 @@ means that each timestep the total force and torque on each rigid body is computed as the sum of the forces and torques on its constituent particles. The coordinates, velocities, and orientations of the atoms in each body are then updated so that the body moves and rotates as a -single entity. +single entity. This is implemented by creating internal data structures +for each rigid body and performing time integration on these data +structures. Positions, velocities, and orientations of the constituent +particles are regenerated from the rigid body data structures in every +time step. This restricts which operations and fixes can be applied to +rigid bodies. See below for a detailed discussion. Examples of large rigid bodies are a colloidal particle, or portions of a biomolecule such as a protein. @@ -148,8 +154,9 @@ differences may accumulate to produce divergent trajectories. NOTE: You should not update the atoms in rigid bodies via other time-integration fixes (e.g. "fix nve"_fix_nve.html, "fix -nvt"_fix_nh.html, "fix npt"_fix_nh.html), or you will be integrating -their motion more than once each timestep. When performing a hybrid +nvt"_fix_nh.html, "fix npt"_fix_nh.html, "fix move"_fix_move.html), +or you will have conflicting updates to positions and velocities +resulting in unphysical behavior in most cases. When performing a hybrid simulation with some atoms in rigid bodies, and some not, a separate time integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html should be used for the non-rigid particles. @@ -165,23 +172,29 @@ setting the force on them to 0.0 (via the "fix setforce"_fix_setforce.html command), and integrating them as usual (e.g. via the "fix nve"_fix_nve.html command). -NOTE: The aggregate properties of each rigid body are calculated one -time at the start of the first simulation run after these fixes are -specified. The properties include the position and velocity of the -center-of-mass of the body, its moments of inertia, and its angular -momentum. This is done using the properties of the constituent atoms -of the body at that point in time (or see the {infile} keyword -option). Thereafter, changing properties of individual atoms in the -body will have no effect on a rigid body's dynamics, unless they -affect the "pair_style"_pair_style.html interactions that individual -particles are part of. For example, you might think you could -displace the atoms in a body or add a large velocity to each atom in a -body to make it move in a desired direction before a 2nd run is +IMPORTANT NOTE: The aggregate properties of each rigid body are +calculated at the start of a simulation run and are maintained in +internal data structures. The properties include the position and +velocity of the center-of-mass of the body, its moments of inertia, and +its angular momentum. This is done using the properties of the +constituent atoms of the body at that point in time (or see the {infile} +keyword option). Thereafter, changing these properties of individual +atoms in the body will have no effect on a rigid body's dynamics, unless +they effect any computation of per-atom forces or torques. If the +keyword {reinit} is set to {yes} (the default), the rigid body data +structures will be recreated at the beginning of each {run} command; +if the keyword {reinit} is set to {no}, the rigid body data structures +will be built only at the very first {run} command and maintained for +as long as the rigid fix is defined. For example, you might think you +could displace the atoms in a body or add a large velocity to each atom +in a body to make it move in a desired direction before a 2nd run is performed, using the "set"_set.html or "displace_atoms"_displace_atoms.html or "velocity"_velocity.html -command. But these commands will not affect the internal attributes -of the body, and the position and velocity of individual atoms in the -body will be reset when time integration starts. +commands. But these commands will not affect the internal attributes +of the body unless {reinit} is set to {yes}. With {reinit} set to {no} +(or using the {infile} option, which implies {reinit} {no}) the position +and velocity of individual atoms in the body will be reset when time +integration starts again. :line @@ -401,6 +414,14 @@ couple none :pre The keyword/value option pairs are used in the following ways. +The {reinit} keyword determines, whether the rigid body properties +are reinitialized between run commands. With the option {yes} (the +default) this is done, with the option {no} this is not done. Turning +off the reinitialization can be helpful to protect rigid bodies against +unphysical manipulations between runs or when properties cannot be +easily recomputed (e.g. when read from a file). When using the {infile} +keyword, the {reinit} option is automatically set to {no}. + The {langevin} and {temp} and {tparam} keywords perform thermostatting of the rigid bodies, altering both their translational and rotational degrees of freedom. What is meant by "temperature" of a collection of @@ -778,7 +799,7 @@ exclude, "fix shake"_fix_shake.html The option defaults are force * on on on and torque * on on on, meaning all rigid bodies are acted on by center-of-mass force and -torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3. +torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3, reinit = yes. :line diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 1769f29825..d901ef3f77 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -301,6 +301,7 @@ compute_centro_atom.html compute_chunk_atom.html compute_cluster_atom.html compute_cna_atom.html +compute_cnp_atom.html compute_com.html compute_com_chunk.html compute_contact_atom.html @@ -446,7 +447,6 @@ pair_lj96.html pair_lj_cubic.html pair_lj_expand.html pair_lj_long.html -pair_lj_sf.html pair_lj_smooth.html pair_lj_smooth_linear.html pair_lj_soft.html diff --git a/doc/src/manifolds.txt b/doc/src/manifolds.txt index 9f0082d5dc..c9bb1ce57f 100644 --- a/doc/src/manifolds.txt +++ b/doc/src/manifolds.txt @@ -24,14 +24,15 @@ to the relevant fixes. {manifold} @ {parameters} @ {equation} @ {description} cylinder @ R @ x^2 + y^2 - R^2 = 0 @ Cylinder along z-axis, axis going through (0,0,0) cylinder_dent @ R l a @ x^2 + y^2 - r(z)^2 = 0, r(x) = R if | z | > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise @ A cylinder with a dent around z = 0 -dumbbell @ a A B c @ -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 @ A dumbbell @ +dumbbell @ a A B c @ -( x^2 + y^2 ) + (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 @ A dumbbell ellipsoid @ a b c @ (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 @ An ellipsoid +gaussian_bump @ A l rc1 rc2 @ if( x < rc1) -z + A * exp( -x^2 / (2 l^2) ); else if( x < rc2 ) -z + a + b*x + c*x^2 + d*x^3; else z @ A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0. plane @ a b c x0 y0 z0 @ a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 @ A plane with normal (a,b,c) going through point (x0,y0,z0) plane_wiggle @ a w @ z - a*sin(w*x) = 0 @ A plane with a sinusoidal modulation on z along x. sphere @ R @ x^2 + y^2 + z^2 - R^2 = 0 @ A sphere of radius R supersphere @ R q @ | x |^q + | y |^q + | z |^q - R^q = 0 @ A supersphere of hyperradius R -spine @ a, A, B, B2, c @ -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ An approximation to a dendtritic spine -spine_two @ a, A, B, B2, c @ -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ Another approximation to a dendtritic spine +spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ An approximation to a dendtritic spine +spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ Another approximation to a dendtritic spine thylakoid @ wB LB lB @ Various, see "(Paquay)"_#Paquay1 @ A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB torus @ R r @ (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2 @ A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=@) diff --git a/doc/src/neb.txt b/doc/src/neb.txt index 3a62a77a6e..a4afc2fe6d 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -10,28 +10,31 @@ neb command :h3 [Syntax:] -neb etol ftol N1 N2 Nevery file-style arg :pre +neb etol ftol N1 N2 Nevery file-style arg keyword :pre etol = stopping tolerance for energy (energy units) :ulb,l ftol = stopping tolerance for force (force units) :l N1 = max # of iterations (timesteps) to run initial NEB :l N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l Nevery = print replica energies and reaction coordinates every this many timesteps :l -file-style= {final} or {each} or {none} :l +file-style = {final} or {each} or {none} :l {final} arg = filename filename = file with initial coords for final replica - coords for intermediate replicas are linearly interpolated between first and last replica + coords for intermediate replicas are linearly interpolated + between first and last replica {each} arg = filename - filename = unique filename for each replica (except first) with its initial coords - {none} arg = no argument - all replicas assumed to already have their initial coords :pre + filename = unique filename for each replica (except first) + with its initial coords + {none} arg = no argument all replicas assumed to already have + their initial coords :pre +keyword = {verbose} :ule [Examples:] neb 0.1 0.0 1000 500 50 final coords.final neb 0.0 0.001 1000 500 50 each coords.initial.$i -neb 0.0 0.001 1000 500 50 none :pre +neb 0.0 0.001 1000 500 50 none verbose :pre [Description:] @@ -43,8 +46,8 @@ NEB is a method for finding both the atomic configurations and height of the energy barrier associated with a transition state, e.g. for an atom to perform a diffusive hop from one energy basin to another in a coordinated fashion with its neighbors. The implementation in LAMMPS -follows the discussion in these 3 papers: "(HenkelmanA)"_#HenkelmanA, -"(HenkelmanB)"_#HenkelmanB, and "(Nakano)"_#Nakano3. +follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA, +"(HenkelmanB)"_#HenkelmanB, "(Nakano)"_#Nakano3 and "(Maras)"_#Maras2. Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line @@ -70,18 +73,17 @@ I.e. the simulation domain, the number of atoms, the interaction potentials, and the starting configuration when the neb command is issued should be the same for every replica. -In a NEB calculation each atom in a replica is connected to the same -atom in adjacent replicas by springs, which induce inter-replica -forces. These forces are imposed by the "fix neb"_fix_neb.html -command, which must be used in conjunction with the neb command. The -group used to define the fix neb command defines the NEB atoms which -are the only ones that inter-replica springs are applied to. If the -group does not include all atoms, then non-NEB atoms have no -inter-replica springs and the forces they feel and their motion is -computed in the usual way due only to other atoms within their -replica. Conceptually, the non-NEB atoms provide a background force -field for the NEB atoms. They can be allowed to move during the NEB -minimization procedure (which will typically induce different +In a NEB calculation each replica is connected to other replicas by +inter-replica nudging forces. These forces are imposed by the "fix +neb"_fix_neb.html command, which must be used in conjunction with the +neb command. The group used to define the fix neb command defines the +NEB atoms which are the only ones that inter-replica springs are +applied to. If the group does not include all atoms, then non-NEB +atoms have no inter-replica springs and the forces they feel and their +motion is computed in the usual way due only to other atoms within +their replica. Conceptually, the non-NEB atoms provide a background +force field for the NEB atoms. They can be allowed to move during the +NEB minimization procedure (which will typically induce different coordinates for non-NEB atoms in different replicas), or held fixed using other LAMMPS commands such as "fix setforce"_fix_setforce.html. Note that the "partition"_partition.html command can be used to invoke @@ -93,33 +95,18 @@ specified in different manners via the {file-style} setting, as discussed below. Only atoms whose initial coordinates should differ from the current configuration need be specified. -Conceptually, the initial configuration for the first replica should -be a state with all the atoms (NEB and non-NEB) having coordinates on -one side of the energy barrier. A perfect energy minimum is not -required, since atoms in the first replica experience no spring forces -from the 2nd replica. Thus the damped dynamics minimization will -drive the first replica to an energy minimum if it is not already -there. However, you will typically get better convergence if the -initial state is already at a minimum. For example, for a system with -a free surface, the surface should be fully relaxed before attempting -a NEB calculation. - -Likewise, the initial configuration of the final replica should be a -state with all the atoms (NEB and non-NEB) on the other side of the -energy barrier. Again, a perfect energy minimum is not required, -since the atoms in the last replica also experience no spring forces -from the next-to-last replica, and thus the damped dynamics -minimization will drive it to an energy minimum. +Conceptually, the initial and final configurations for the first +replica should be states on either side of an energy barrier. As explained below, the initial configurations of intermediate replicas can be atomic coordinates interpolated in a linear fashion -between the first and last replicas. This is often adequate state for +between the first and last replicas. This is often adequate for simple transitions. For more complex transitions, it may lead to slow convergence or even bad results if the minimum energy path (MEP, see below) of states over the barrier cannot be correctly converged to -from such an initial configuration. In this case, you will want to -generate initial states for the intermediate replicas that are -geometrically closer to the MEP and read them in. +from such an initial path. In this case, you will want to generate +initial states for the intermediate replicas that are geometrically +closer to the MEP and read them in. :line @@ -135,10 +122,11 @@ is assigned to be a fraction of the distance. E.g. if there are 10 replicas, the 2nd replica will assign a position that is 10% of the distance along a line between the starting and final point, and the 9th replica will assign a position that is 90% of the distance along -the line. Note that this procedure to produce consistent coordinates -across all the replicas, the current coordinates need to be the same -in all replicas. LAMMPS does not check for this, but invalid initial -configurations will likely result if it is not the case. +the line. Note that for this procedure to produce consistent +coordinates across all the replicas, the current coordinates need to +be the same in all replicas. LAMMPS does not check for this, but +invalid initial configurations will likely result if it is not the +case. NOTE: The "distance" between the starting and final point is calculated in a minimum-image sense for a periodic simulation box. @@ -150,8 +138,8 @@ interpolation is outside the periodic box, the atom will be wrapped back into the box when the NEB calculation begins. For a {file-style} setting of {each}, a filename is specified which is -assumed to be unique to each replica. This can be done by -using a variable in the filename, e.g. +assumed to be unique to each replica. This can be done by using a +variable in the filename, e.g. variable i equal part neb 0.0 0.001 1000 500 50 each coords.initial.$i :pre @@ -198,11 +186,10 @@ The minimizer tolerances for energy and force are set by {etol} and A non-zero {etol} means that the NEB calculation will terminate if the energy criterion is met by every replica. The energies being compared to {etol} do not include any contribution from the inter-replica -forces, since these are non-conservative. A non-zero {ftol} means -that the NEB calculation will terminate if the force criterion is met -by every replica. The forces being compared to {ftol} include the -inter-replica forces between an atom and its images in adjacent -replicas. +nudging forces, since these are non-conservative. A non-zero {ftol} +means that the NEB calculation will terminate if the force criterion +is met by every replica. The forces being compared to {ftol} include +the inter-replica nudging forces. The maximum number of iterations in each stage is set by {N1} and {N2}. These are effectively timestep counts since each iteration of @@ -220,27 +207,27 @@ finding a good energy barrier. {N1} and {N2} must both be multiples of {Nevery}. In the first stage of NEB, the set of replicas should converge toward -the minimum energy path (MEP) of conformational states that transition -over the barrier. The MEP for a barrier is defined as a sequence of -3N-dimensional states that cross the barrier at its saddle point, each -of which has a potential energy gradient parallel to the MEP itself. -The replica states will also be roughly equally spaced along the MEP -due to the inter-replica spring force added by the "fix -neb"_fix_neb.html command. +a minimum energy path (MEP) of conformational states that transition +over a barrier. The MEP for a transition is defined as a sequence of +3N-dimensional states, each of which has a potential energy gradient +parallel to the MEP itself. The configuration of highest energy along +a MEP corresponds to a saddle point. The replica states will also be +roughly equally spaced along the MEP due to the inter-replica nugding +force added by the "fix neb"_fix_neb.html command. -In the second stage of NEB, the replica with the highest energy -is selected and the inter-replica forces on it are converted to a -force that drives its atom coordinates to the top or saddle point of -the barrier, via the barrier-climbing calculation described in +In the second stage of NEB, the replica with the highest energy is +selected and the inter-replica forces on it are converted to a force +that drives its atom coordinates to the top or saddle point of the +barrier, via the barrier-climbing calculation described in "(HenkelmanB)"_#HenkelmanB. As before, the other replicas rearrange themselves along the MEP so as to be roughly equally spaced. When both stages are complete, if the NEB calculation was successful, -one of the replicas should be an atomic configuration at the top or -saddle point of the barrier, the potential energies for the set of -replicas should represent the energy profile of the barrier along the -MEP, and the configurations of the replicas should be a sequence of -configurations along the MEP. +the configurations of the replicas should be along (close to) the MEP +and the replica with the highest energy should be an atomic +configuration at (close to) the saddle point of the transition. The +potential energies for the set of replicas represents the energy +profile of the transition along the MEP. :line @@ -284,9 +271,9 @@ ID2 x2 y2 z2 ... IDN xN yN zN :pre -The fields are the atom ID, followed by the x,y,z coordinates. -The lines can be listed in any order. Additional trailing information -on the line is OK, such as a comment. +The fields are the atom ID, followed by the x,y,z coordinates. The +lines can be listed in any order. Additional trailing information on +the line is OK, such as a comment. Note that for a typical NEB calculation you do not need to specify initial coordinates for very many atoms to produce differing starting @@ -310,38 +297,54 @@ this case), the print-out to the screen and master log.lammps file contains a line of output, printed once every {Nevery} timesteps. It contains the timestep, the maximum force per replica, the maximum force per atom (in any replica), potential gradients in the initial, -final, and climbing replicas, the forward and backward energy barriers, -the total reaction coordinate (RDT), and the normalized reaction -coordinate and potential energy of each replica. +final, and climbing replicas, the forward and backward energy +barriers, the total reaction coordinate (RDT), and the normalized +reaction coordinate and potential energy of each replica. -The "maximum force per replica" is -the two-norm of the 3N-length force vector for the atoms in each -replica, maximized across replicas, which is what the {ftol} setting -is checking against. In this case, N is all the atoms in each -replica. The "maximum force per atom" is the maximum force component -of any atom in any replica. The potential gradients are the two-norm -of the 3N-length force vector solely due to the interaction potential i.e. -without adding in inter-replica forces. Note that inter-replica forces -are zero in the initial and final replicas, and only affect -the direction in the climbing replica. For this reason, the "maximum -force per replica" is often equal to the potential gradient in the -climbing replica. In the first stage of NEB, there is no climbing -replica, and so the potential gradient in the highest energy replica -is reported, since this replica will become the climbing replica -in the second stage of NEB. +The "maximum force per replica" is the two-norm of the 3N-length force +vector for the atoms in each replica, maximized across replicas, which +is what the {ftol} setting is checking against. In this case, N is +all the atoms in each replica. The "maximum force per atom" is the +maximum force component of any atom in any replica. The potential +gradients are the two-norm of the 3N-length force vector solely due to +the interaction potential i.e. without adding in inter-replica +forces. -The "reaction coordinate" (RD) for each -replica is the two-norm of the 3N-length vector of distances between -its atoms and the preceding replica's atoms, added to the RD of the -preceding replica. The RD of the first replica RD1 = 0.0; -the RD of the final replica RDN = RDT, the total reaction coordinate. -The normalized RDs are divided by RDT, -so that they form a monotonically increasing sequence -from zero to one. When computing RD, N only includes the atoms -being operated on by the fix neb command. +The "reaction coordinate" (RD) for each replica is the two-norm of the +3N-length vector of distances between its atoms and the preceding +replica's atoms, added to the RD of the preceding replica. The RD of +the first replica RD1 = 0.0; the RD of the final replica RDN = RDT, +the total reaction coordinate. The normalized RDs are divided by RDT, +so that they form a monotonically increasing sequence from zero to +one. When computing RD, N only includes the atoms being operated on by +the fix neb command. -The forward (reverse) energy barrier is the potential energy of the highest -replica minus the energy of the first (last) replica. +The forward (reverse) energy barrier is the potential energy of the +highest replica minus the energy of the first (last) replica. + +Supplementary informations for all replicas can be printed out to the +screen and master log.lammps file by adding the verbose keyword. These +informations include the following. The "path angle" (pathangle) for +the replica i which is the angle between the 3N-length vectors (Ri-1 - +Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica +i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are +aligned. "angletangrad" is the angle between the 3N-length tangent +vector and the 3N-length force vector at image i. The tangent vector +is calculated as in "(HenkelmanA)"_#HenkelmanA for all intermediate +replicas and at R2 - R1 and RM - RM-1 for the first and last replica, +respectively. "anglegrad" is the angle between the 3N-length energy +gradient vector of replica i and that of replica i+1. It is not +defined for the final replica and reads nan. gradV is the norm of the +energy gradient of image i. ReplicaForce is the two-norm of the +3N-length force vector (including nudging forces) for replica i. +MaxAtomForce is the maximum force component of any atom in replica i. + +When a NEB calculation does not converge properly, these suplementary +informations can help understanding what is going wrong. For instance +when the path angle becomes accute the definition of tangent used in +the NEB calculation is questionable and the NEB cannot may diverge +"(Maras)"_#Maras2. + When running on multiple partitions, LAMMPS produces additional log files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a @@ -396,12 +399,16 @@ This command can only be used if LAMMPS was built with the REPLICA package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info on packages. +:line + [Related commands:] -"prd"_prd.html, "temper"_temper.html, "fix -langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html +"prd"_prd.html, "temper"_temper.html, "fix langevin"_fix_langevin.html, +"fix viscous"_fix_viscous.html -[Default:] none +[Default:] + +none :line @@ -414,3 +421,7 @@ langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html :link(Nakano3) [(Nakano)] Nakano, Comp Phys Comm, 178, 280-289 (2008). + +:link(Maras2) +[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, +Comp Phys Comm, 205, 13-21 (2016) diff --git a/doc/src/package.txt b/doc/src/package.txt index a0894b3128..18a26bd55c 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -574,9 +574,9 @@ is used. If it is not used, you must invoke the package intel command in your input script or or via the "-pk intel" "command-line switch"_Section_start.html#start_7. -For the KOKKOS package, the option defaults neigh = full, neigh/qeq - = full, newton = off, binsize = 0.0, and comm = device. These settings - are made automatically by the required "-k on" "command-line +For the KOKKOS package, the option defaults neigh = full, +neigh/qeq = full, newton = off, binsize = 0.0, and comm = device. +These settings are made automatically by the required "-k on" "command-line switch"_Section_start.html#start_7. You can change them bu using the package kokkos command in your input script or via the "-pk kokkos" "command-line switch"_Section_start.html#start_7. diff --git a/doc/src/pair_lj_sf.txt b/doc/src/pair_lj_sf.txt deleted file mode 100644 index 65e28b6f51..0000000000 --- a/doc/src/pair_lj_sf.txt +++ /dev/null @@ -1,114 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -pair_style lj/sf command :h3 -pair_style lj/sf/omp command :h3 - -[Syntax:] - -pair_style lj/sf cutoff :pre - -cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul - -[Examples:] - -pair_style lj/sf 2.5 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.0 1.0 3.0 :pre - -[Description:] - -Style {lj/sf} computes a truncated and force-shifted LJ interaction -(Shifted Force Lennard-Jones), so that both the potential and the -force go continuously to zero at the cutoff "(Toxvaerd)"_#Toxvaerd: - -:c,image(Eqs/pair_lj_sf.jpg) - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global -LJ cutoff specified in the pair_style command is used. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. - -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma -coefficients and cutoff distance for this pair style can be mixed. -Rin is a cutoff value and is mixed like the cutoff. The -default mix value is {geometric}. See the "pair_modify" command for -details. - -The "pair_modify"_pair_modify.html shift option is not relevant for -this pair style, since the pair interaction goes to 0.0 at the cutoff. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure, since the energy of the pair interaction is smoothed to 0.0 -at the cutoff. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the USER-MISC package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Toxvaerd) -[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011). diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt index 8b9b9aa5fa..5721b02eb3 100644 --- a/doc/src/pair_lj_smooth_linear.txt +++ b/doc/src/pair_lj_smooth_linear.txt @@ -11,26 +11,26 @@ pair_style lj/smooth/linear/omp command :h3 [Syntax:] -pair_style lj/smooth/linear Rc :pre +pair_style lj/smooth/linear cutoff :pre -Rc = cutoff for lj/smooth/linear interactions (distance units) :ul +cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul [Examples:] -pair_style lj/smooth/linear 5.456108274435118 -pair_coeff * * 0.7242785984051078 2.598146797350056 -pair_coeff 1 1 20.0 1.3 9.0 :pre +pair_style lj/smooth/linear 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.3 3.0 9.0 :pre [Description:] -Style {lj/smooth/linear} computes a LJ interaction that combines the -standard 12/6 Lennard-Jones function and subtracts a linear term that -includes the cutoff distance Rc, as in this formula: +Style {lj/smooth/linear} computes a truncated and force-shifted LJ +interaction (aka Shifted Force Lennard-Jones) that combines the +standard 12/6 Lennard-Jones function and subtracts a linear term based +on the cutoff distance, so that both, the potential and the force, go +continuously to zero at the cutoff Rc "(Toxvaerd)"_#Toxvaerd: :c,image(Eqs/pair_lj_smooth_linear.jpg) -At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0. - The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the @@ -41,8 +41,8 @@ epsilon (energy units) sigma (distance units) cutoff (distance units) :ul -The last coefficient is optional. If not specified, the global value -for Rc is used. +The last coefficient is optional. If not specified, the global +LJ cutoff specified in the pair_style command is used. :line @@ -76,10 +76,11 @@ and cutoff distance can be mixed. The default mix value is geometric. See the "pair_modify" command for details. This pair style does not support the "pair_modify"_pair_modify.html -shift option for the energy of the pair interaction. +shift option for the energy of the pair interaction, since it goes +to 0.0 at the cutoff by construction. -The "pair_modify"_pair_modify.html table option is not relevant for -this pair style. +The "pair_modify"_pair_modify.html table option is not relevant +for this pair style. This pair style does not support the "pair_modify"_pair_modify.html tail option for adding long-range tail corrections to energy and diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt index c5e3a3c399..5fbb6d5c0a 100644 --- a/doc/src/pair_morse.txt +++ b/doc/src/pair_morse.txt @@ -26,7 +26,7 @@ args = list of arguments for a particular style :ul {morse/smooth/linear} args = cutoff cutoff = global cutoff for Morse interactions (distance units) {morse/soft} args = n lf cutoff - n = soft-core parameter + n = soft-core parameter lf = transformation range is lf < lambda < 1 cutoff = global cutoff for Morse interactions (distance units) :pre @@ -36,7 +36,7 @@ args = list of arguments for a particular style :ul pair_style morse 2.5 pair_style morse/smooth/linear 2.5 pair_coeff * * 100.0 2.0 1.5 -pair_coeff 1 1 100.0 2.0 1.5 3.0 +pair_coeff 1 1 100.0 2.0 1.5 3.0 :pre pair_style morse/soft 4 0.9 10.0 pair_coeff * * 100.0 2.0 1.5 1.0 diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt index 557db37bbb..2f8ed7a27c 100644 --- a/doc/src/pair_python.txt +++ b/doc/src/pair_python.txt @@ -74,7 +74,7 @@ placeholders for atom types that will be used with other potentials. The python potential file has to start with the following code: from __future__ import print_function - +# class LAMMPSPairPotential(object): def __init__(self): self.pmap=dict() @@ -163,9 +163,10 @@ pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj :pre Note that it is strongly recommended to try to [delete] the potential table file before generating it. Since the {pair_write} command will -always append to a table file, which pair style table will use the -first match. Thus when changing the potential function in the python -class, the table pair style will still read the old variant. +always [append] to a table file, while pair style table will use the +[first match]. Thus when changing the potential function in the python +class, the table pair style will still read the old variant unless the +table file is first deleted. After switching the pair style to {table}, the potential tables need to be assigned to the LAMMPS atom types like this: diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt index 76a8e6fd5c..cfa88673d7 100644 --- a/doc/src/pair_reaxc.txt +++ b/doc/src/pair_reaxc.txt @@ -8,6 +8,7 @@ pair_style reax/c command :h3 pair_style reax/c/kk command :h3 +pair_style reax/c/omp command :h3 [Syntax:] diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt index ab7313832c..fa90dc34e9 100644 --- a/doc/src/pair_snap.txt +++ b/doc/src/pair_snap.txt @@ -10,7 +10,8 @@ pair_style snap command :h3 [Syntax:] -pair_style snap :pre +pair_style snap +:pre [Examples:] @@ -19,11 +20,11 @@ pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre [Description:] -Style {snap} computes interactions +Pair style {snap} computes interactions using the spectral neighbor analysis potential (SNAP) "(Thompson)"_#Thompson20142. Like the GAP framework of Bartok et al. "(Bartok2010)"_#Bartok20102, "(Bartok2013)"_#Bartok2013 -it uses bispectrum components +which uses bispectrum components to characterize the local neighborhood of each atom in a very general way. The mathematical definition of the bispectrum calculation used by SNAP is identical @@ -139,10 +140,15 @@ The default values for these keywords are {rmin0} = 0.0 {diagonalstyle} = 3 {switchflag} = 0 -{bzeroflag} = 1 :ul +{bzeroflag} = 1 +{quadraticflag} = 1 :ul -Detailed definitions of these keywords are given on the "compute +Detailed definitions for all the keywords are given on the "compute sna/atom"_compute_sna_atom.html doc page. +If {quadraticflag} is set to 1, then the SNAP energy expression includes the quadratic term, +0.5*B^t.alpha.B, where alpha is a symmetric {K} by {K} matrix. +The SNAP element file should contain {K}({K}+1)/2 additional coefficients +for each element, the upper-triangular elements of alpha. :line diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt index 902e6012f8..9c275a61d3 100644 --- a/doc/src/pair_vashishta.txt +++ b/doc/src/pair_vashishta.txt @@ -7,6 +7,7 @@ :line pair_style vashishta command :h3 +pair_style vashishta/gpu command :h3 pair_style vashishta/omp command :h3 pair_style vashishta/kk command :h3 pair_style vashishta/table command :h3 diff --git a/doc/src/pair_zero.txt b/doc/src/pair_zero.txt index ffd40a977d..e58b33c75f 100644 --- a/doc/src/pair_zero.txt +++ b/doc/src/pair_zero.txt @@ -14,7 +14,7 @@ pair_style zero cutoff {nocoeff} :pre zero = style name of this pair style cutoff = global cutoff (distance units) -nocoeff = ignore all pair_coeff parameters (optional) :l +nocoeff = ignore all pair_coeff parameters (optional) :ul [Examples:] diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt index 538e2a7268..2c1b20f4d3 100644 --- a/doc/src/pairs.txt +++ b/doc/src/pairs.txt @@ -49,7 +49,6 @@ Pair Styles :h1 pair_lj_cubic pair_lj_expand pair_lj_long - pair_lj_sf pair_lj_smooth pair_lj_smooth_linear pair_lj_soft diff --git a/doc/src/set.txt b/doc/src/set.txt index 6b59bf1332..14460c9741 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -80,6 +80,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ value can be an atom-style variable (see below) {image} nx ny nz nx,ny,nz = which periodic image of the simulation box the atom is in + any of nx,ny,nz can be an atom-style variable (see below) {bond} value = bond type for all bonds between selected atoms {angle} value = angle type for all angles between selected atoms {dihedral} value = dihedral type for all dihedrals between selected atoms @@ -363,9 +364,8 @@ A value of -1 means subtract 1 box length to get the true value. LAMMPS updates these flags as atoms cross periodic boundaries during the simulation. The flags can be output with atom snapshots via the "dump"_dump.html command. If a value of NULL is specified for any of -nx,ny,nz, then the current image value for that dimension is -unchanged. For non-periodic dimensions only a value of 0 can be -specified. This keyword does not allow use of atom-style variables. +nx,ny,nz, then the current image value for that dimension is unchanged. +For non-periodic dimensions only a value of 0 can be specified. This command can be useful after a system has been equilibrated and atoms have diffused one or more box lengths in various directions. This command can then reset the image values for atoms so that they diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt index 6924b321a0..6a661015bd 100644 --- a/doc/src/special_bonds.txt +++ b/doc/src/special_bonds.txt @@ -65,7 +65,13 @@ sense to define permanent bonds between atoms that interact via these potentials, though such bonds may exist elsewhere in your system, e.g. when using the "pair_style hybrid"_pair_hybrid.html command. Thus LAMMPS ignores special_bonds settings when manybody potentials -are calculated. +are calculated. Please note, that the existence of explicit bonds +for atoms that are described by a manybody potential will alter the +neigborlist and thus can render the computation of those interactions +invalid, since those pairs are not only used to determine direct +pairwise interactions but also neighbors of neighbors and more. +The recommended course of action is to remove such bonds, or - if +that is not possible - use a special bonds setting of 1.0 1.0 1.0. NOTE: Unlike some commands in LAMMPS, you cannot use this command multiple times in an incremental fashion: e.g. to first set the LJ diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/tutorial_pylammps.txt index a4a7a4041e..0b4fb32ed2 100644 --- a/doc/src/tutorial_pylammps.txt +++ b/doc/src/tutorial_pylammps.txt @@ -10,6 +10,7 @@ PyLammps Tutorial :h1 Overview :h2 diff --git a/examples/COUPLE/simple/simple.cpp b/examples/COUPLE/simple/simple.cpp index b279ae704c..894c708978 100644 --- a/examples/COUPLE/simple/simple.cpp +++ b/examples/COUPLE/simple/simple.cpp @@ -153,7 +153,7 @@ int main(int narg, char **arg) for (int i = 0; i < natoms; i++) type[i] = 1; lmp->input->one("delete_atoms group all"); - lammps_create_atoms(lmp,natoms,NULL,type,x,v); + lammps_create_atoms(lmp,natoms,NULL,type,x,v,NULL,0); lmp->input->one("run 10"); } diff --git a/examples/USER/cgdna/util/generate.py b/examples/USER/cgdna/util/generate.py index d5a74e9bf7..eb97f482cc 100644 --- a/examples/USER/cgdna/util/generate.py +++ b/examples/USER/cgdna/util/generate.py @@ -14,7 +14,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Oliver Henrich (EPCC, University of Edinburgh) + Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ """ diff --git a/examples/USER/misc/cnp/Cu_Mishin1.eam b/examples/USER/misc/cnp/Cu_Mishin1.eam new file mode 100644 index 0000000000..8ea788b16d --- /dev/null +++ b/examples/USER/misc/cnp/Cu_Mishin1.eam @@ -0,0 +1,30009 @@ +#-> LAMMPS Potential File in DYNAMO 86 setfl Format <-# +# Mishin Cu EAM1 PRB(2001)63:224106 +# Implemented by G. 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system +lattice fcc 3.615 origin 0.01 0.01 0.01 orient x -1 -1 2 orient y 1 1 1 orient z -1 1 0 +region mdbox block 0 3 0.0 14.0 0 84 units lattice +region system block 0 3 1.1 13.1 0 84 units lattice +create_box 2 mdbox +create_atoms 1 region system + +# Define atoms mass and force field +mass * 63.54 +pair_style eam/alloy +pair_coeff * * Cu_Mishin1.eam Cu Cu + +# Delete a plane of atoms along the z direction to generate a partial dislocation +region dislocation_atoms block 0 3 7 14 41.9 42.1 units lattice +delete_atoms region dislocation_atoms +region quarter_up block 0 3 7 11 0 84 units lattice +group middle region quarter_up + +# specify simulation parameters +timestep 0.004 + +# Relax configuration using conjugate gradient +#min_style cg +#minimize 1.0e-4 1.0e-6 100 1000 + +# Setup calculations +compute 1 all cnp/atom 3.086 +compute 2 all cna/atom 3.086 +compute 3 all centro/atom fcc +compute 4 all coord/atom cutoff 3.086 +dump 1 all custom 100 dump.lammpstrj id type xu yu zu c_1 c_2 c_3 c_4 + +### Set up thermo display +thermo 10 +thermo_style custom step atoms temp press pe ke etotal + +# Relax the system performing a langevin dynamics (freeze motion along y 111 direction) +fix 1 all nve +fix 2 all langevin 50 1 0.1 699483 +fix 3 all setforce NULL 0.0 NULL +fix 4 middle setforce 0.0 0.0 0.0 +run 100 +unfix 4 +run 200 diff --git a/examples/USER/misc/cnp/log.31May17.cnp.g++.4 b/examples/USER/misc/cnp/log.31May17.cnp.g++.4 new file mode 100644 index 0000000000..d86d0b5600 --- /dev/null +++ b/examples/USER/misc/cnp/log.31May17.cnp.g++.4 @@ -0,0 +1,185 @@ +LAMMPS (19 May 2017) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# Generation and relaxation of a partial dislocation in Cu perfect FCC crystal + +# Initialization +units metal +boundary p p p +atom_style atomic + +# create simulation box and system +lattice fcc 3.615 origin 0.01 0.01 0.01 orient x -1 -1 2 orient y 1 1 1 orient z -1 1 0 +Lattice spacing in x,y,z = 5.90327 6.26136 5.11238 +region mdbox block 0 3 0.0 14.0 0 84 units lattice +region system block 0 3 1.1 13.1 0 84 units lattice +create_box 2 mdbox +Created orthogonal box = (0 0 0) to (17.7098 87.6591 429.44) + 1 by 1 by 4 MPI processor grid +create_atoms 1 region system +Created 48384 atoms + +# Define atoms mass and force field +mass * 63.54 +pair_style eam/alloy +pair_coeff * * Cu_Mishin1.eam Cu Cu + +# Delete a plane of atoms along the z direction to generate a partial dislocation +region dislocation_atoms block 0 3 7 14 41.9 42.1 units lattice +delete_atoms region dislocation_atoms +Deleted 76 atoms, new total = 48308 +region quarter_up block 0 3 7 11 0 84 units lattice +group middle region quarter_up +16080 atoms in group middle + +# specify simulation parameters +timestep 0.004 + +# Relax configuration using conjugate gradient +#min_style cg +#minimize 1.0e-4 1.0e-6 100 1000 + +# Setup calculations +compute 1 all cnp/atom 3.086 +compute 2 all cna/atom 3.086 +compute 3 all centro/atom fcc +compute 4 all coord/atom cutoff 3.086 +dump 1 all custom 100 dump.lammpstrj id type xu yu zu c_1 c_2 c_3 c_4 + +### Set up thermo display +thermo 10 +thermo_style custom step atoms temp press pe ke etotal + +# Relax the system performing a langevin dynamics (freeze motion along y 111 direction) +fix 1 all nve +fix 2 all langevin 50 1 0.1 699483 +fix 3 all setforce NULL 0.0 NULL +fix 4 middle setforce 0.0 0.0 0.0 +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.50679 + ghost atom cutoff = 7.50679 + binsize = 3.75339, bins = 5 24 115 + 5 neighbor lists, perpetual/occasional/extra = 1 4 0 + (1) pair eam/alloy, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute cnp/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (3) compute cna/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (4) compute centro/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (5) compute coord/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 45.41 | 45.41 | 45.41 Mbytes +Step Atoms Temp Press PotEng KinEng TotEng + 0 48308 0 -3388.0911 -169746.07 0 -169746.07 + 10 48308 7.35092 -3091.0864 -169715.96 45.900393 -169670.05 + 20 48308 9.9162268 -2822.7045 -169678.51 61.918604 -169616.59 + 30 48308 12.351316 -2726.7195 -169666.35 77.123716 -169589.23 + 40 48308 13.302856 -2703.586 -169662.9 83.06529 -169579.83 + 50 48308 12.782228 -2706.8662 -169662.36 79.814401 -169582.55 + 60 48308 12.198179 -2772.4206 -169670.02 76.167503 -169593.86 + 70 48308 10.663322 -2841.3384 -169677.48 66.583595 -169610.9 + 80 48308 9.1169804 -2932.3896 -169687.85 56.927974 -169630.92 + 90 48308 7.2905076 -3029.9433 -169699.09 45.523167 -169653.56 + 100 48308 5.4063635 -3139.4496 -169711.65 33.758252 -169677.89 +Loop time of 10.9003 on 4 procs for 100 steps with 48308 atoms + +Performance: 3.171 ns/day, 7.570 hours/ns, 9.174 timesteps/s +31.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.8764 | 9.9587 | 10.021 | 1.6 | 91.36 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.1232 | 0.18385 | 0.26683 | 12.1 | 1.69 +Output | 0.45385 | 0.45451 | 0.45634 | 0.2 | 4.17 +Modify | 0.25026 | 0.2537 | 0.25744 | 0.5 | 2.33 +Other | | 0.04949 | | | 0.45 + +Nlocal: 12077 ave 12096 max 12020 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 14204 ave 14261 max 14109 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 814050 ave 818584 max 809212 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 1.6281e+06 ave 1.63296e+06 max 1.61808e+06 min +Histogram: 1 0 0 0 0 0 1 0 0 2 + +Total # of neighbors = 6512400 +Ave neighs/atom = 134.81 +Neighbor list builds = 0 +Dangerous builds = 0 +unfix 4 +run 200 +Per MPI rank memory allocation (min/avg/max) = 45.41 | 45.41 | 45.41 Mbytes +Step Atoms Temp Press PotEng KinEng TotEng + 100 48308 5.4063635 -3139.4496 -169711.65 33.758252 -169677.89 + 110 48308 15.260795 -2793.119 -169677.24 95.290993 -169581.95 + 120 48308 18.548656 -2433.1584 -169624.79 115.82096 -169508.97 + 130 48308 22.15831 -2276.626 -169604.28 138.36025 -169465.92 + 140 48308 24.393841 -2208.1771 -169596.16 152.31929 -169443.84 + 150 48308 24.797558 -2173.3145 -169591.43 154.84016 -169436.59 + 160 48308 24.73371 -2188.909 -169593.08 154.44148 -169438.64 + 170 48308 24.128467 -2220.3404 -169596.96 150.66225 -169446.29 + 180 48308 22.975708 -2275.1244 -169602.72 143.46422 -169459.26 + 190 48308 21.936324 -2348.3762 -169610.59 136.97413 -169473.61 + 200 48308 20.516249 -2432.8447 -169619.98 128.10694 -169491.87 + 210 48308 19.000566 -2510.2915 -169628.58 118.64276 -169509.93 + 220 48308 17.490407 -2597.299 -169638.24 109.21307 -169529.03 + 230 48308 16.062482 -2684.1203 -169648.31 100.29687 -169548.01 + 240 48308 14.360342 -2768.2313 -169657.7 89.668411 -169568.03 + 250 48308 12.802315 -2852.6965 -169666.99 79.939831 -169587.05 + 260 48308 11.258205 -2944.4533 -169677.52 70.298142 -169607.23 + 270 48308 9.6159129 -3038.6304 -169688.06 60.043393 -169628.02 + 280 48308 7.972425 -3129.0826 -169698.03 49.781176 -169648.25 + 290 48308 6.3752377 -3219.2054 -169708.23 39.808067 -169668.42 + 300 48308 4.7374688 -3306.1468 -169718.27 29.58156 -169688.69 +Loop time of 23.0164 on 4 procs for 200 steps with 48308 atoms + +Performance: 3.003 ns/day, 7.992 hours/ns, 8.689 timesteps/s +31.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 20.221 | 20.423 | 20.57 | 3.1 | 88.73 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.27748 | 0.42603 | 0.62832 | 21.4 | 1.85 +Output | 1.5454 | 1.5473 | 1.5529 | 0.3 | 6.72 +Modify | 0.48886 | 0.49773 | 0.50842 | 1.1 | 2.16 +Other | | 0.1221 | | | 0.53 + +Nlocal: 12077 ave 12096 max 12020 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 14204 ave 14261 max 14109 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 814094 ave 818584 max 809212 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 1.62852e+06 ave 1.63296e+06 max 1.61892e+06 min +Histogram: 1 0 0 0 0 0 0 1 0 2 + +Total # of neighbors = 6514094 +Ave neighs/atom = 134.845 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/USER/misc/grem/lj-temper/0/log.lammps.0 b/examples/USER/misc/grem/lj-temper/0/log.lammps.0 index 22998f8893..1c1aaaf042 100644 --- a/examples/USER/misc/grem/lj-temper/0/log.lammps.0 +++ b/examples/USER/misc/grem/lj-temper/0/log.lammps.0 @@ -16,10 +16,6 @@ read_data 0/lj.data #dump dump all xyz 1000 ${rep}/dump.xyz -thermo 100 -thermo_style custom step temp pe etotal press vol -timestep 1.0 - fix fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0 @@ -27,135 +23,1044 @@ fix fxnpt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso 0 0 10000.0 fix fxgREM all grem ${lambda} -.03 -30000 fxnpt fix fxgREM all grem 900 -.03 -30000 fxnpt + +thermo 10 +thermo_style custom step temp f_fxgREM pe etotal press vol thermo_modify press fxgREM_press +timestep 1.0 temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker} temper/grem 10000 100 900 fxgREM fxnpt 10294 98392 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 - binsize = 3.5 -> bins = 7 7 7 -Memory usage per processor = 5.38195 Mbytes -Step Temp PotEng TotEng Press Volume - 0 299.42262 -3416.9 -2971.5315 134.01052 11328.967 - 100 294.63941 -3417.2566 -2979.0028 164.62038 11328.996 - 200 302.86941 -3421.7405 -2971.2452 116.35909 11329.199 - 300 297.43413 -3417.6882 -2975.2774 143.60143 11329.666 - 400 300.1465 -3421.466 -2975.0208 108.02406 11330.366 - 500 300.2847 -3419.7205 -2973.0698 51.93802 11331.264 - 600 297.98642 -3416.0758 -2972.8436 102.67264 11332.303 - 700 308.88819 -3423.7386 -2964.2908 -84.991092 11333.461 - 800 300.03002 -3418.2447 -2971.9728 61.530839 11334.623 - 900 294.38296 -3416.7286 -2978.8563 59.4512 11336.02 - 1000 301.55478 -3419.3685 -2970.8287 -70.828164 11337.415 - 1100 304.76191 -3420.01 -2966.6997 -46.02246 11338.757 - 1200 300.87935 -3418.357 -2970.8218 -27.557375 11340.179 - 1300 297.90925 -3416.7586 -2973.6412 27.202549 11341.647 - 1400 304.0426 -3421.0828 -2968.8425 -150.93733 11343.177 - 1500 293.50425 -3416.0019 -2979.4366 -32.703088 11344.538 - 1600 298.70817 -3416.4247 -2972.1189 -111.16189 11345.702 - 1700 293.12426 -3415.1528 -2979.1527 -12.438698 11346.701 - 1800 289.23529 -3413.4211 -2983.2055 -27.234713 11347.494 - 1900 292.62679 -3415.5324 -2980.2722 -121.80014 11347.911 - 2000 295.3705 -3415.4594 -2976.1182 -118.35918 11347.97 - 2100 288.3131 -3411.9071 -2983.0632 11.471141 11347.887 - 2200 312.55009 -3422.4761 -2957.5815 -294.72858 11347.644 - 2300 285.92437 -3414.5956 -2989.3047 -43.986075 11346.986 - 2400 300.19294 -3419.6619 -2973.1476 -153.30034 11346.114 - 2500 295.61459 -3415.1159 -2975.4116 20.33969 11344.962 - 2600 297.71268 -3415.7827 -2972.9577 -52.926913 11343.679 - 2700 298.56462 -3417.9995 -2973.9072 -131.29953 11342.271 - 2800 286.03931 -3410.6373 -2985.1754 164.72078 11340.629 - 2900 290.70577 -3411.5311 -2979.1283 143.13209 11338.97 - 3000 303.332 -3415.7792 -2964.5958 -49.330701 11337.303 - 3100 301.73339 -3417.0188 -2968.2132 -8.5041565 11335.568 - 3200 313.04988 -3423.077 -2957.439 -122.70098 11333.927 - 3300 286.09745 -3408.4061 -2982.8579 353.68123 11332.253 - 3400 303.00349 -3413.2328 -2962.5381 231.93254 11330.816 - 3500 308.79241 -3417.4556 -2958.1503 91.741468 11329.674 - 3600 287.41302 -3407.5431 -2980.038 543.23683 11329.043 - 3700 294.17479 -3407.5416 -2969.9788 449.07447 11329.318 - 3800 289.81831 -3405.492 -2974.4092 576.60121 11330.443 - 3900 295.40157 -3408.4609 -2969.0734 451.50877 11332.572 - 4000 287.71309 -3402.6497 -2974.6982 573.42617 11335.583 - 4100 290.02657 -3403.0786 -2971.686 527.71502 11339.534 - 4200 297.74424 -3409.8018 -2966.9298 277.40905 11344.404 - 4300 292.06583 -3402.1684 -2967.7426 444.89069 11349.944 - 4400 300.74402 -3406.2366 -2958.9027 139.09782 11356.223 - 4500 295.14988 -3402.5929 -2963.5798 173.91619 11362.896 - 4600 299.82229 -3402.1676 -2956.2047 114.51482 11369.919 - 4700 299.72789 -3400.7608 -2954.9383 83.204669 11377.21 - 4800 292.34822 -3393.2268 -2958.3809 161.50646 11384.622 - 4900 298.32652 -3395.3712 -2951.6331 29.917068 11392.178 - 5000 293.0855 -3395.7079 -2959.7654 -67.018003 11399.715 - 5100 302.58088 -3398.1836 -2948.1175 -214.79018 11407.054 - 5200 302.00186 -3395.3231 -2946.1182 -305.62771 11413.967 - 5300 308.44521 -3396.6926 -2937.9037 -455.80177 11420.397 - 5400 305.55347 -3392.9576 -2938.4699 -464.74116 11426.162 - 5500 306.15731 -3393.3834 -2937.9976 -453.93342 11431.122 - 5600 300.86617 -3390.7578 -2943.2421 -413.36436 11435.339 - 5700 311.4673 -3395.9418 -2932.6578 -637.62795 11438.796 - 5800 302.31851 -3388.9636 -2939.2877 -501.87858 11441.318 - 5900 315.93456 -3400.2717 -2930.343 -753.56358 11443.043 - 6000 304.69067 -3391.9711 -2938.7668 -477.72322 11443.646 - 6100 311.80005 -3393.0048 -2929.2259 -633.56098 11443.351 - 6200 307.36579 -3391.6406 -2934.4573 -532.82298 11442.106 - 6300 302.7084 -3389.8455 -2939.5897 -490.38666 11439.901 - 6400 306.78573 -3392.1276 -2935.807 -547.43007 11436.8 - 6500 304.23179 -3388.17 -2935.6483 -348.52993 11432.753 - 6600 296.7094 -3385.8464 -2944.5136 -201.5605 11428.01 - 6700 313.3959 -3395.26 -2929.1073 -415.82786 11422.724 - 6800 316.4072 -3399.1224 -2928.4906 -496.33753 11416.786 - 6900 302.56547 -3389.7698 -2939.7266 -80.175542 11410.218 - 7000 299.36836 -3387.708 -2942.4203 128.86864 11403.334 - 7100 309.39575 -3396.2826 -2936.0798 -53.969342 11396.555 - 7200 324.25215 -3405.3158 -2923.0153 -227.25827 11389.761 - 7300 305.99737 -3393.6219 -2938.474 235.46369 11382.905 - 7400 317.73948 -3402.1318 -2929.5184 21.699572 11376.471 - 7500 315.75908 -3400.7608 -2931.0931 148.23486 11370.37 - 7600 311.46203 -3401.9952 -2938.7191 182.85745 11364.81 - 7700 309.3606 -3403.1221 -2942.9717 257.80591 11359.711 - 7800 300.78232 -3397.6295 -2950.2386 440.63834 11355.144 - 7900 306.59047 -3402.2326 -2946.2025 287.86462 11351.377 - 8000 311.28944 -3406.6966 -2943.6772 268.88617 11348.336 - 8100 299.93421 -3405.6032 -2959.4738 356.79664 11346.007 - 8200 302.26336 -3406.5846 -2956.9908 246.8694 11344.383 - 8300 294.27353 -3406.1343 -2968.4247 428.02411 11343.38 - 8400 273.01304 -3396.291 -2990.2048 712.6039 11343.239 - 8500 294.90301 -3407.461 -2968.8151 259.18716 11344.147 - 8600 295.43347 -3410.2779 -2970.8431 127.32619 11345.636 - 8700 285.2568 -3407.4342 -2983.1364 223.78377 11347.458 - 8800 296.45048 -3413.1605 -2972.2128 61.542232 11349.754 - 8900 306.82798 -3417.5232 -2961.1398 -170.00394 11352.317 - 9000 287.0527 -3408.5483 -2981.5791 46.683648 11354.612 - 9100 296.30539 -3414.6325 -2973.9007 -222.07876 11356.77 - 9200 300.16761 -3415.9641 -2969.4875 -218.94764 11358.601 - 9300 310.01596 -3418.7396 -2957.6143 -409.04518 11360.094 - 9400 293.6059 -3411.4846 -2974.768 -112.34303 11361.015 - 9500 306.2565 -3416.0499 -2960.5165 -230.75414 11361.667 - 9600 298.77172 -3410.0086 -2965.6083 -160.9185 11361.994 - 9700 287.60936 -3408.4236 -2980.6264 -50.45167 11361.936 - 9800 298.13818 -3413.9967 -2970.5387 -252.57086 11361.537 - 9900 292.93826 -3411.9851 -2976.2616 -152.45548 11360.629 - 10000 286.02579 -3405.9303 -2980.4887 67.188883 11359.503 -Loop time of 3.25987 on 1 procs for 10000 steps with 500 atoms + binsize = 3.5, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.728 | 5.728 | 5.728 Mbytes +Step Temp f_fxgREM PotEng TotEng Press Volume + 0 299.42262 102.507 -3416.9 -2971.5315 134.01052 11328.967 + 10 305.01315 102.57259 -3419.0863 -2965.4023 52.103984 11328.968 + 20 309.92197 102.64755 -3421.585 -2960.5996 -26.370593 11328.97 + 30 311.99962 102.71885 -3423.9618 -2959.886 -76.248163 11328.972 + 40 310.18839 102.69518 -3423.1727 -2961.791 -52.274449 11328.972 + 50 305.15121 102.6302 -3421.0067 -2967.1174 16.259045 11328.972 + 60 299.39836 102.5938 -3419.7932 -2974.4609 80.723613 11328.972 + 70 295.2947 102.55104 -3418.3682 -2979.1397 134.53808 11328.974 + 80 293.51832 102.50438 -3416.8126 -2980.2263 170.69406 11328.978 + 90 293.4313 102.51498 -3417.1659 -2980.7091 170.93297 11328.985 + 100 294.63941 102.5177 -3417.2566 -2979.0028 164.62038 11328.996 + 110 297.25348 102.56555 -3418.8518 -2976.7098 131.78524 11329.01 + 120 300.50388 102.60344 -3420.1147 -2973.138 98.057487 11329.026 + 130 302.95328 102.6409 -3421.3632 -2970.7432 69.182017 11329.044 + 140 304.05933 102.70523 -3423.5076 -2971.2424 38.480693 11329.064 + 150 304.21872 102.71956 -3423.9853 -2971.483 33.117628 11329.084 + 160 304.38371 102.70642 -3423.5475 -2970.7998 39.859883 11329.105 + 170 304.80117 102.70106 -3423.3687 -2970.0001 43.810288 11329.127 + 180 305.13983 102.71028 -3423.6759 -2969.8035 46.007676 11329.15 + 190 304.94578 102.68774 -3422.9246 -2969.3408 69.449779 11329.173 + 200 302.86941 102.65221 -3421.7405 -2971.2452 116.35909 11329.199 + 210 297.662 102.5571 -3418.57 -2975.8203 210.54052 11329.226 + 220 290.84972 102.4888 -3416.2934 -2983.6765 300.40584 11329.257 + 230 286.66935 102.40548 -3413.5161 -2987.1171 365.46428 11329.294 + 240 288.43119 102.42846 -3414.2821 -2985.2626 333.78695 11329.338 + 250 295.9831 102.53577 -3417.8591 -2977.6067 218.31479 11329.388 + 260 305.50936 102.66938 -3422.3128 -2967.8908 75.635176 11329.443 + 270 311.52891 102.76931 -3425.6438 -2962.2682 -26.093631 11329.498 + 280 311.04895 102.75023 -3425.0078 -2962.346 -28.116138 11329.554 + 290 305.15136 102.64834 -3421.6115 -2967.722 47.657742 11329.609 + 300 297.43413 102.53064 -3417.6882 -2975.2774 143.60143 11329.666 + 310 292.00918 102.45991 -3415.3303 -2980.9888 202.75098 11329.725 + 320 291.38867 102.45449 -3415.1495 -2981.731 200.97437 11329.788 + 330 294.86583 102.51948 -3417.316 -2978.7254 144.54327 11329.854 + 340 299.07345 102.62717 -3420.9058 -2976.0567 71.367848 11329.924 + 350 301.19767 102.64391 -3421.4636 -2973.4549 53.019075 11329.994 + 360 301.40218 102.64706 -3421.5686 -2973.2557 57.550459 11330.066 + 370 301.60343 102.63439 -3421.1465 -2972.5342 71.264067 11330.139 + 380 302.3767 102.66604 -3422.2013 -2972.4389 65.704342 11330.213 + 390 302.18634 102.66324 -3422.1079 -2972.6286 79.588346 11330.289 + 400 300.1465 102.64398 -3421.466 -2975.0208 108.02406 11330.366 + 410 297.66938 102.55498 -3418.4992 -2975.7385 159.37689 11330.446 + 420 296.70991 102.52861 -3417.6203 -2976.2868 170.02926 11330.528 + 430 297.60515 102.52266 -3417.4218 -2974.7567 154.72136 11330.614 + 440 299.48021 102.57498 -3419.166 -2973.7119 108.67344 11330.703 + 450 301.07427 102.60725 -3420.2418 -2972.4166 73.295179 11330.793 + 460 302.09454 102.59522 -3419.8407 -2970.498 61.278464 11330.886 + 470 302.70993 102.61648 -3420.5493 -2970.2912 41.512266 11330.979 + 480 302.81262 102.62998 -3420.9993 -2970.5885 29.560402 11331.073 + 490 302.14786 102.61601 -3420.5338 -2971.1117 34.608836 11331.168 + 500 300.2847 102.59162 -3419.7205 -2973.0698 51.93802 11331.264 + 510 297.96748 102.55635 -3418.545 -2975.3409 76.76076 11331.361 + 520 296.76806 102.53422 -3417.8075 -2976.3875 89.385785 11331.459 + 530 296.70055 102.51748 -3417.2493 -2975.9297 92.386458 11331.559 + 540 296.45476 102.50595 -3416.8648 -2975.9109 92.522412 11331.661 + 550 296.25617 102.49905 -3416.6349 -2975.9763 88.090319 11331.765 + 560 297.43141 102.48149 -3416.0497 -2973.643 77.975047 11331.87 + 570 299.89275 102.52306 -3417.4354 -2971.3677 40.26193 11331.977 + 580 301.71033 102.55476 -3418.492 -2969.7207 18.941485 11332.085 + 590 301.0837 102.56499 -3418.833 -2970.9938 31.38825 11332.194 + 600 297.98642 102.48227 -3416.0758 -2972.8436 102.67264 11332.303 + 610 293.64246 102.45555 -3415.1849 -2978.414 160.19415 11332.414 + 620 290.00186 102.38828 -3412.9426 -2981.5869 218.76366 11332.528 + 630 289.94928 102.41899 -3413.9664 -2982.6888 200.08217 11332.646 + 640 295.74572 102.48763 -3416.2545 -2976.3551 112.68119 11332.768 + 650 306.46178 102.65897 -3421.9655 -2966.1269 -54.544301 11332.892 + 660 317.10206 102.85711 -3428.5703 -2956.905 -227.40954 11333.015 + 670 322.23923 102.91998 -3430.6661 -2951.3597 -299.41158 11333.135 + 680 320.5723 102.93397 -3431.1325 -2954.3055 -291.13842 11333.248 + 690 314.82311 102.8303 -3427.6765 -2959.401 -196.15735 11333.357 + 700 308.88819 102.71216 -3423.7386 -2964.2908 -84.991092 11333.461 + 710 304.9868 102.66458 -3422.1526 -2968.5078 -11.177461 11333.565 + 720 303.01004 102.61889 -3420.6298 -2969.9253 49.289549 11333.668 + 730 300.99168 102.60022 -3420.0074 -2972.3051 98.740194 11333.772 + 740 296.94374 102.54664 -3418.2214 -2976.5401 171.9416 11333.877 + 750 291.19139 102.44341 -3414.7802 -2981.6551 269.15521 11333.987 + 760 285.41566 102.3714 -3412.3799 -2987.8457 343.50487 11334.101 + 770 281.59912 102.30948 -3410.3161 -2991.4588 384.62499 11334.222 + 780 282.54974 102.32011 -3410.6705 -2990.3991 347.61696 11334.35 + 790 289.63184 102.42814 -3414.2713 -2983.4659 218.95403 11334.485 + 800 300.03002 102.54734 -3418.2447 -2971.9728 61.530839 11334.623 + 810 308.28446 102.63792 -3421.2641 -2962.7143 -61.683906 11334.763 + 820 310.71517 102.67118 -3422.3726 -2960.2073 -105.82674 11334.902 + 830 307.51937 102.64604 -3421.5347 -2964.1229 -72.21706 11335.04 + 840 302.15103 102.52481 -3417.4936 -2968.0669 22.7566 11335.176 + 850 298.13259 102.46761 -3415.5869 -2972.1373 83.701724 11335.312 + 860 296.67204 102.44948 -3414.9826 -2973.7055 105.71932 11335.45 + 870 296.58815 102.49174 -3416.3914 -2975.239 86.7842 11335.59 + 880 296.07017 102.48007 -3416.0022 -2975.6203 85.129741 11335.731 + 890 294.71487 102.49894 -3416.6313 -2978.2652 73.985492 11335.875 + 900 294.38296 102.50186 -3416.7286 -2978.8563 59.4512 11336.02 + 910 297.14646 102.51252 -3417.0839 -2975.1011 20.162699 11336.166 + 920 302.00677 102.60648 -3420.216 -2971.0038 -63.001904 11336.312 + 930 305.93557 102.65476 -3421.8253 -2966.7693 -118.84051 11336.457 + 940 307.40744 102.65758 -3421.9192 -2964.6739 -136.4053 11336.601 + 950 306.77038 102.64009 -3421.3363 -2965.0386 -128.88393 11336.742 + 960 305.29301 102.60192 -3420.0641 -2965.9639 -105.70523 11336.88 + 970 304.01625 102.62204 -3420.7347 -2968.5336 -106.83536 11337.017 + 980 303.31176 102.61148 -3420.3825 -2969.2293 -99.75059 11337.151 + 990 302.52222 102.60354 -3420.1179 -2970.139 -91.350072 11337.284 + 1000 301.55478 102.58106 -3419.3685 -2970.8287 -70.828164 11337.415 + 1010 300.80872 102.57382 -3419.1273 -2971.6971 -51.456861 11337.545 + 1020 300.39394 102.57561 -3419.1869 -2972.3737 -30.06259 11337.674 + 1030 299.3407 102.56375 -3418.7917 -2973.5451 8.5095011 11337.802 + 1040 296.64408 102.51102 -3417.0339 -2975.7983 76.942673 11337.931 + 1050 292.71654 102.45136 -3415.0454 -2979.6518 150.13917 11338.061 + 1060 290.03112 102.41851 -3413.9503 -2982.551 191.32381 11338.195 + 1070 291.18322 102.40463 -3413.4876 -2980.3746 184.12677 11338.331 + 1080 295.92737 102.46916 -3415.6386 -2975.4691 109.66058 11338.472 + 1090 301.38195 102.55252 -3418.4174 -2970.1346 17.470646 11338.614 + 1100 304.76191 102.6003 -3420.01 -2966.6997 -46.02246 11338.757 + 1110 305.67145 102.63011 -3421.0035 -2966.3404 -77.688687 11338.899 + 1120 304.63891 102.59084 -3419.6947 -2966.5674 -58.912495 11339.04 + 1130 302.03115 102.55519 -3418.5064 -2969.258 -22.869742 11339.18 + 1140 298.58726 102.51077 -3417.0257 -2972.8997 25.472397 11339.319 + 1150 295.27588 102.46046 -3415.3487 -2976.1482 73.241528 11339.459 + 1160 292.9158 102.45232 -3415.0775 -2979.3875 92.346457 11339.6 + 1170 292.32496 102.4632 -3415.4399 -2980.6287 85.260271 11339.743 + 1180 294.10212 102.48255 -3416.085 -2978.6304 55.687553 11339.888 + 1190 297.62415 102.51671 -3417.2237 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296.62536 112.13628 -3404.5425 -2963.3348 414.74564 11343.516 + 8290 295.44616 112.17397 -3405.7989 -2966.3451 416.02766 11343.444 + 8300 294.27353 112.18403 -3406.1343 -2968.4247 428.02411 11343.38 + 8310 293.47291 112.17651 -3405.8838 -2969.3651 442.09035 11343.324 + 8320 293.20923 112.16604 -3405.5345 -2969.408 451.29146 11343.276 + 8330 293.37895 112.16265 -3405.4216 -2969.0426 453.54056 11343.237 + 8340 293.17434 112.17654 -3405.8848 -2969.8102 452.17679 11343.207 + 8350 291.35219 112.13175 -3404.3917 -2971.0274 486.27357 11343.185 + 8360 286.87666 112.08591 -3402.8637 -2976.1564 541.51548 11343.172 + 8370 279.90361 111.98636 -3399.5454 -2983.21 635.85067 11343.17 + 8380 273.13983 111.93354 -3397.7848 -2991.51 706.92172 11343.179 + 8390 270.55407 111.86327 -3395.4422 -2993.0136 748.69151 11343.202 + 8400 273.01304 111.88873 -3396.291 -2990.2048 712.6039 11343.239 + 8410 277.46032 111.95111 -3398.3703 -2985.6691 644.90535 11343.29 + 8420 280.98629 112.02173 -3400.7242 -2982.7784 578.18296 11343.353 + 8430 283.42861 112.07813 -3402.6045 -2981.0259 521.42184 11343.426 + 8440 286.72442 112.12112 -3404.0373 -2977.5564 459.53741 11343.51 + 8450 291.7267 112.2044 -3406.8132 -2972.8919 365.59913 11343.603 + 8460 296.5633 112.29276 -3409.7587 -2968.6432 269.22624 11343.702 + 8470 298.9194 112.3279 -3410.93 -2966.3101 213.58812 11343.807 + 8480 298.71888 112.31627 -3410.5424 -2966.2207 201.91582 11343.916 + 8490 297.17189 112.26233 -3408.7442 -2966.7235 226.26406 11344.03 + 8500 294.90301 112.22383 -3407.461 -2968.8151 259.18716 11344.147 + 8510 292.39286 112.18913 -3406.3042 -2971.392 296.96289 11344.27 + 8520 291.14853 112.17538 -3405.846 -2972.7846 317.20394 11344.398 + 8530 291.91158 112.22667 -3407.5555 -2973.3592 296.58708 11344.533 + 8540 292.91813 112.20303 -3406.7678 -2971.0743 300.20133 11344.673 + 8550 292.41103 112.21716 -3407.2388 -2972.2995 296.55479 11344.819 + 8560 290.68114 112.17923 -3405.9744 -2973.6082 315.31139 11344.971 + 8570 289.55071 112.13935 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11347.655 + 8720 282.71291 112.18784 -3406.2612 -2985.7472 244.16641 11347.857 + 8730 277.88776 112.09313 -3403.1044 -2989.7675 327.27761 11348.064 + 8740 271.06737 111.98882 -3399.6275 -2996.4353 437.0719 11348.277 + 8750 265.18763 111.90797 -3396.9322 -3002.4857 531.24712 11348.499 + 8760 263.21239 111.84863 -3394.9545 -3003.446 579.13885 11348.731 + 8770 266.98443 111.86908 -3395.6361 -2998.517 540.52799 11348.974 + 8780 276.00421 112.05186 -3401.7288 -2991.1934 388.42612 11349.227 + 8790 287.04901 112.2291 -3407.6367 -2980.6731 215.77508 11349.489 + 8800 296.45048 112.39481 -3413.1605 -2972.2128 61.542232 11349.754 + 8810 303.84332 102.5009 -3416.6966 -2964.7527 -102.60393 11350.021 + 8820 308.35593 102.54287 -3418.0955 -2959.4395 -156.26397 11350.286 + 8830 309.34553 102.56267 -3418.7555 -2958.6275 -169.44279 11350.548 + 8840 307.92936 102.57728 -3419.2427 -2961.2211 -159.36337 11350.808 + 8850 306.49168 102.51666 -3417.2219 -2961.3388 -120.8613 11351.065 + 8860 307.02003 102.50577 -3416.8591 -2960.19 -118.8501 11351.32 + 8870 308.78244 102.51765 -3417.255 -2957.9645 -139.87882 11351.573 + 8880 309.4166 102.52413 -3417.471 -2957.2372 -156.54316 11351.824 + 8890 308.17218 102.52172 -3417.3905 -2959.0077 -161.32511 11352.072 + 8900 306.82798 102.52569 -3417.5232 -2961.1398 -170.00394 11352.317 + 8910 306.92686 102.52414 -3417.4712 -2960.9407 -186.21426 11352.56 + 8920 308.0801 102.54255 -3418.0851 -2959.8393 -215.35285 11352.799 + 8930 309.07511 102.53491 -3417.8303 -2958.1045 -229.29742 11353.034 + 8940 308.83435 102.54793 -3418.2644 -2958.8967 -236.83009 11353.266 + 8950 306.20013 102.50473 -3416.8242 -2961.3747 -198.18845 11353.493 + 8960 299.78229 102.45513 -3415.1708 -2969.2674 -124.11711 11353.717 + 8970 290.40609 102.32891 -3410.9636 -2979.0066 1.3665885 11353.939 + 8980 282.5525 102.23389 -3407.7963 -2987.5209 99.179915 11354.161 + 8990 281.20504 102.18256 -3406.0854 -2987.8142 125.84255 11354.385 + 9000 287.0527 102.25645 -3408.5483 -2981.5791 46.683648 11354.612 + 9010 295.6651 102.36854 -3412.2846 -2972.5052 -70.693581 11354.84 + 9020 302.05074 102.44673 -3414.8911 -2965.6136 -159.48967 11355.067 + 9030 304.50107 102.50445 -3416.8148 -2963.8926 -211.01569 11355.291 + 9040 304.28774 102.51765 -3417.255 -2964.6501 -223.85983 11355.511 + 9050 302.28659 102.46413 -3415.471 -2965.8426 -196.35161 11355.728 + 9060 298.64342 102.41317 -3413.7725 -2969.563 -159.56094 11355.942 + 9070 294.89692 102.3567 -3411.8898 -2973.253 -123.95652 11356.152 + 9080 292.89751 102.31892 -3410.6307 -2974.9679 -113.05552 11356.36 + 9090 293.44894 102.39098 -3413.0327 -2976.5497 -164.79219 11356.567 + 9100 296.30539 102.43897 -3414.6325 -2973.9007 -222.07876 11356.77 + 9110 300.45266 102.4672 -3415.5735 -2968.6729 -273.82557 11356.97 + 9120 303.24645 102.47481 -3415.8271 -2964.771 -295.97287 11357.165 + 9130 302.0034 102.50375 -3416.7918 -2967.5846 -285.82159 11357.354 + 9140 297.22892 102.43941 -3414.6469 -2972.5414 -207.07355 11357.538 + 9150 291.80756 102.39282 -3413.0939 -2979.0523 -128.58195 11357.719 + 9160 288.25245 102.34705 -3411.5685 -2982.8148 -67.13035 11357.898 + 9170 287.47436 102.34359 -3411.4531 -2983.8568 -50.741803 11358.076 + 9180 289.65745 102.36539 -3412.1798 -2981.3363 -76.008823 11358.253 + 9190 294.40993 102.43028 -3414.3425 -2976.4301 -145.63657 11358.428 + 9200 300.16761 102.47892 -3415.9641 -2969.4875 -218.94764 11358.601 + 9210 304.03105 102.53822 -3417.9405 -2965.7174 -279.64516 11358.771 + 9220 304.45288 102.53714 -3417.9046 -2965.054 -285.20667 11358.935 + 9230 302.34912 102.45421 -3415.1404 -2965.419 -234.46962 11359.094 + 9240 299.9859 102.40287 -3413.429 -2967.2227 -191.14447 11359.249 + 9250 299.26036 102.40403 -3413.4677 -2968.3406 -182.52388 11359.401 + 9260 300.61341 102.41715 -3413.905 -2966.7654 -201.16731 11359.549 + 9270 303.15524 102.4879 -3416.2632 -2965.3428 -259.88954 11359.693 + 9280 305.7968 102.55222 -3418.4075 -2963.5579 -324.73273 11359.833 + 9290 308.13692 102.54889 -3418.2962 -2959.9659 -365.60648 11359.967 + 9300 310.01596 102.56219 -3418.7396 -2957.6143 -409.04518 11360.094 + 9310 310.51245 102.5781 -3419.27 -2957.4063 -438.84588 11360.214 + 9320 308.74264 102.52394 -3417.4648 -2958.2335 -415.60354 11360.325 + 9330 304.79422 102.4761 -3415.8701 -2962.5118 -367.20347 11360.429 + 9340 299.98192 102.39538 -3413.1793 -2966.9789 -290.51501 11360.526 + 9350 296.40204 102.34525 -3411.5082 -2970.6326 -230.13543 11360.618 + 9360 295.69416 102.34673 -3411.5575 -2971.7349 -209.91046 11360.705 + 9370 297.70643 102.38972 -3412.9908 -2970.1751 -224.99069 11360.789 + 9380 299.82096 102.43428 -3414.4761 -2968.5151 -239.37907 11360.868 + 9390 298.72337 102.42593 -3414.1978 -2969.8694 -206.21757 11360.943 + 9400 293.6059 102.34454 -3411.4846 -2974.768 -112.34303 11361.015 + 9410 287.13801 102.25842 -3408.614 -2981.5179 -5.7729342 11361.084 + 9420 282.8911 102.1548 -3405.1599 -2984.3808 87.012111 11361.153 + 9430 283.42692 102.17512 -3405.8373 -2984.2613 87.107479 11361.224 + 9440 289.72806 102.25543 -3408.5142 -2977.5657 10.6752 11361.297 + 9450 299.9244 102.41878 -3413.9592 -2967.8444 -133.86835 11361.37 + 9460 309.66009 102.532 -3417.7333 -2957.1374 -259.63954 11361.441 + 9470 315.28802 102.61817 -3420.6055 -2951.6385 -343.43136 11361.507 + 9480 315.52197 102.64969 -3421.6563 -2952.3412 -362.61942 11361.567 + 9490 311.57319 102.59769 -3419.923 -2956.4815 -315.2172 11361.62 + 9500 306.2565 102.4815 -3416.0499 -2960.5165 -230.75414 11361.667 + 9510 301.77507 102.40965 -3413.655 -2964.7874 -168.80118 11361.711 + 9520 298.06371 102.36942 -3412.3141 -2968.9669 -127.60351 11361.75 + 9530 294.76822 102.34731 -3411.5771 -2973.1317 -102.52302 11361.788 + 9540 292.90584 102.28385 -3409.4618 -2973.7865 -77.156962 11361.824 + 9550 293.16449 102.2921 -3409.7367 -2973.6767 -95.839672 11361.858 + 9560 294.55295 102.32549 -3410.8498 -2972.7246 -130.00817 11361.89 + 9570 295.8006 102.34483 -3411.4945 -2971.5135 -152.72227 11361.921 + 9580 296.56754 102.34105 -3411.3684 -2970.2466 -158.45379 11361.948 + 9590 297.31038 102.32507 -3410.8355 -2968.6089 -157.7167 11361.972 + 9600 298.77172 102.30026 -3410.0086 -2965.6083 -160.9185 11361.994 + 9610 301.97013 102.34529 -3411.5097 -2962.352 -206.50568 11362.013 + 9620 306.75609 102.42638 -3414.2128 -2957.9364 -278.49373 11362.027 + 9630 310.90991 102.52954 -3417.6512 -2955.1963 -353.7554 11362.037 + 9640 312.31799 102.61062 -3420.354 -2955.8047 -397.46392 11362.04 + 9650 310.56146 102.5724 -3419.0801 -2957.1435 -366.33137 11362.036 + 9660 306.52496 102.52312 -3417.4373 -2961.5047 -309.52269 11362.025 + 9670 301.5321 102.45538 -3415.1793 -2966.6732 -237.6061 11362.008 + 9680 296.45601 102.39829 -3413.2764 -2972.3206 -171.66047 11361.986 + 9690 291.72252 102.30306 -3410.1021 -2976.187 -97.600507 11361.962 + 9700 287.60936 102.25271 -3408.4236 -2980.6264 -50.45167 11361.936 + 9710 284.48914 102.20566 -3406.8552 -2983.6992 -17.860652 11361.908 + 9720 283.50169 102.17913 -3405.971 -2984.2837 -14.443294 11361.881 + 9730 286.7196 102.21649 -3407.2163 -2980.7426 -68.48769 11361.852 + 9740 294.47386 102.35054 -3411.6845 -2973.677 -189.93928 11361.823 + 9750 303.04659 102.46162 -3415.3875 -2964.6286 -302.19943 11361.79 + 9760 307.57479 102.51124 -3417.0413 -2959.5471 -355.30344 11361.752 + 9770 306.33697 102.48869 -3416.2898 -2960.6367 -335.18312 11361.707 + 9780 301.59673 102.4207 -3414.0233 -2965.421 -271.49738 11361.655 + 9790 297.79054 102.41425 -3413.8083 -2970.8674 -241.91326 11361.599 + 9800 298.13818 102.4199 -3413.9967 -2970.5387 -252.57086 11361.537 + 9810 302.00013 102.47911 -3415.9702 -2966.7679 -313.68954 11361.471 + 9820 306.02146 102.5605 -3418.6833 -2963.4996 -383.20843 11361.399 + 9830 306.37399 102.56224 -3418.7413 -2963.0332 -388.56733 11361.32 + 9840 301.99104 102.49174 -3416.3914 -2967.2027 -323.29197 11361.234 + 9850 296.02715 102.3854 -3412.8467 -2972.5287 -226.75584 11361.141 + 9860 292.42188 102.30722 -3410.2407 -2975.2854 -155.99935 11361.044 + 9870 291.8673 102.30306 -3410.1021 -2975.9716 -137.71183 11360.944 + 9880 292.47183 102.29279 -3409.7597 -2974.73 -129.16333 11360.842 + 9890 292.67046 102.31184 -3410.3947 -2975.0696 -133.25336 11360.737 + 9900 292.93826 102.35955 -3411.9851 -2976.2616 -152.45548 11360.629 + 9910 292.98738 112.38031 -3412.677 -2976.8805 -98.388723 11360.519 + 9920 291.50325 112.33603 -3411.2009 -2977.612 -60.193026 11360.407 + 9930 289.16 112.27732 -3409.2439 -2979.1403 -8.3725785 11360.294 + 9940 287.58579 112.26303 -3408.7678 -2981.0057 18.664629 11360.18 + 9950 287.74855 112.25799 -3408.5998 -2980.5956 25.021437 11360.067 + 9960 289.38626 112.25385 -3408.4617 -2978.0215 15.413572 11359.954 + 9970 291.31111 112.27816 -3409.2721 -2975.9689 -9.6707803 11359.842 + 9980 291.60283 112.29087 -3409.6956 -2975.9585 -17.695205 11359.729 + 9990 289.34786 112.2374 -3407.9134 -2977.5304 19.599433 11359.616 + 10000 286.02579 112.17791 -3405.9303 -2980.4887 67.188883 11359.503 +Loop time of 2.50279 on 1 procs for 10000 steps with 500 atoms -Performance: 265.041 ns/day, 0.091 hours/ns, 3067.606 timesteps/s -100.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 345.215 ns/day, 0.070 hours/ns, 3995.539 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.5777 | 2.5777 | 2.5777 | 0.0 | 79.07 -Bond | 0.0006814 | 0.0006814 | 0.0006814 | 0.0 | 0.02 -Neigh | 0.019258 | 0.019258 | 0.019258 | 0.0 | 0.59 -Comm | 0.088224 | 0.088224 | 0.088224 | 0.0 | 2.71 -Output | 0.0010309 | 0.0010309 | 0.0010309 | 0.0 | 0.03 -Modify | 0.33808 | 0.33808 | 0.33808 | 0.0 | 10.37 -Other | | 0.2349 | | | 7.20 +Pair | 2.0544 | 2.0544 | 2.0544 | 0.0 | 82.08 +Bond | 0.00075364 | 0.00075364 | 0.00075364 | 0.0 | 0.03 +Neigh | 0.015478 | 0.015478 | 0.015478 | 0.0 | 0.62 +Comm | 0.07215 | 0.07215 | 0.07215 | 0.0 | 2.88 +Output | 0.0074148 | 0.0074148 | 0.0074148 | 0.0 | 0.30 +Modify | 0.23494 | 0.23494 | 0.23494 | 0.0 | 9.39 +Other | | 0.1177 | | | 4.70 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -171,4 +1076,4 @@ Neighbor list builds = 20 Dangerous builds = 0 #write_data ${rep}/lj-out.data -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/examples/USER/misc/grem/lj-temper/1/log.lammps.1 b/examples/USER/misc/grem/lj-temper/1/log.lammps.1 index 8b12a2c318..3241f17a5c 100644 --- a/examples/USER/misc/grem/lj-temper/1/log.lammps.1 +++ b/examples/USER/misc/grem/lj-temper/1/log.lammps.1 @@ -16,10 +16,6 @@ read_data 1/lj.data #dump dump all xyz 1000 ${rep}/dump.xyz -thermo 100 -thermo_style custom step temp pe etotal press vol -timestep 1.0 - fix fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0 @@ -27,135 +23,1044 @@ fix fxnpt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso 0 0 10000.0 fix fxgREM all grem ${lambda} -.03 -30000 fxnpt fix fxgREM all grem 910 -.03 -30000 fxnpt + +thermo 10 +thermo_style custom step temp f_fxgREM pe etotal press vol thermo_modify press fxgREM_press +timestep 1.0 temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker} temper/grem 10000 100 910 fxgREM fxnpt 10294 98392 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 - binsize = 3.5 -> bins = 7 7 7 -Memory usage per processor = 5.38334 Mbytes -Step Temp PotEng TotEng Press Volume - 0 288.55656 -3406.7669 -2977.5609 178.123 11354.789 - 100 292.15244 -3406.6138 -2972.0592 101.11822 11354.9 - 200 284.76856 -3403.8146 -2980.243 229.78409 11355.232 - 300 292.70849 -3408.8867 -2973.505 148.33374 11355.918 - 400 300.34739 -3407.488 -2960.744 182.63695 11357.028 - 500 285.96923 -3401.9081 -2976.5506 276.3915 11358.563 - 600 307.70286 -3413.8121 -2956.1274 -99.74504 11360.502 - 700 282.68114 -3402.3696 -2981.9028 215.37371 11362.639 - 800 296.16373 -3406.3812 -2965.8601 17.480161 11365.099 - 900 295.1242 -3403.489 -2964.5141 139.94644 11367.775 - 1000 298.65751 -3404.9437 -2960.7133 43.569751 11370.721 - 1100 299.9828 -3403.2527 -2957.051 1.5561287 11373.784 - 1200 283.05677 -3393.2885 -2972.263 279.02297 11376.992 - 1300 301.24616 -3401.9018 -2953.821 -61.001277 11380.464 - 1400 289.04947 -3395.7975 -2965.8583 92.997624 11383.831 - 1500 274.01283 -3384.3607 -2976.7874 455.32787 11387.235 - 1600 302.26525 -3397.7531 -2948.1564 12.134543 11391.218 - 1700 293.79228 -3393.1889 -2956.1952 57.363507 11395.294 - 1800 306.98845 -3396.1039 -2939.4818 -135.9312 11399.326 - 1900 293.15719 -3386.5828 -2950.5337 132.42643 11403.179 - 2000 307.19197 -3395.5097 -2938.585 -161.2466 11406.936 - 2100 307.45189 -3392.5861 -2935.2747 -157.46524 11410.403 - 2200 300.88603 -3388.4914 -2940.9462 -28.501997 11413.598 - 2300 289.88236 -3384.6698 -2953.4918 122.58753 11416.723 - 2400 296.43305 -3388.0129 -2947.0912 -25.774318 11420.076 - 2500 317.23755 -3397.1902 -2925.3234 -459.4925 11423.59 - 2600 287.60187 -3378.3654 -2950.5794 184.57759 11426.853 - 2700 303.64909 -3386.2885 -2934.6335 -135.08152 11430.242 - 2800 302.47742 -3388.9859 -2939.0737 -323.13721 11433.517 - 2900 291.98004 -3377.25 -2942.9518 -47.677493 11436.421 - 3000 307.8161 -3390.9845 -2933.1314 -381.60025 11439.119 - 3100 279.57067 -3372.6802 -2956.8401 112.35716 11441.316 - 3200 288.77945 -3377.9064 -2948.3688 -56.270381 11443.418 - 3300 304.79453 -3385.7254 -2932.3667 -445.46244 11445.179 - 3400 292.93209 -3377.8456 -2942.1313 -194.7257 11446.284 - 3500 306.76065 -3386.1118 -2929.8286 -428.54219 11447.116 - 3600 309.27383 -3386.5092 -2926.4878 -396.29387 11447.442 - 3700 295.73613 -3380.6566 -2940.7715 -224.46949 11447.298 - 3800 286.51576 -3373.1466 -2946.9762 -38.200592 11446.876 - 3900 297.11081 -3379.8253 -2937.8955 -209.71089 11446.168 - 4000 298.6827 -3378.5589 -2934.291 -161.67235 11445.075 - 4100 296.79632 -3375.8545 -2934.3925 -3.2770185 11443.642 - 4200 293.39337 -3373.8298 -2937.4294 61.151041 11442.097 - 4300 305.32078 -3376.9036 -2922.7621 -35.097493 11440.456 - 4400 288.33476 -3367.9377 -2939.0616 323.25684 11438.693 - 4500 301.83114 -3379.5242 -2930.5732 44.950393 11437.061 - 4600 296.53718 -3370.7936 -2929.717 247.99542 11435.523 - 4700 313.14834 -3380.7524 -2914.9679 24.50122 11434.29 - 4800 316.57471 -3385.4942 -2914.6133 -89.103894 11433.295 - 4900 295.8169 -3373.4805 -2933.4753 186.45389 11432.498 - 5000 302.82001 -3376.4769 -2926.0551 126.1166 11431.848 - 5100 293.31592 -3369.1186 -2932.8334 398.18962 11431.273 - 5200 300.8404 -3371.9981 -2924.5208 325.82663 11431.294 - 5300 288.65507 -3366.8598 -2937.5072 560.98385 11432.053 - 5400 300.15414 -3370.3662 -2923.9097 331.21385 11433.792 - 5500 293.62342 -3364.1197 -2927.3771 510.06055 11436.251 - 5600 293.52337 -3365.0972 -2928.5034 443.00006 11439.517 - 5700 314.46913 -3373.0792 -2905.3302 116.1735 11443.39 - 5800 316.07035 -3371.7131 -2901.5824 59.579025 11447.527 - 5900 302.07546 -3364.3048 -2914.9904 292.07764 11452.145 - 6000 298.16549 -3363.0572 -2919.5586 322.85603 11457.452 - 6100 299.62417 -3361.8594 -2916.1912 270.01732 11463.408 - 6200 307.26123 -3366.6924 -2909.6646 33.334477 11469.872 - 6300 301.85984 -3360.01 -2911.0164 152.48267 11476.656 - 6400 304.04037 -3359.0287 -2906.7917 85.558236 11483.787 - 6500 315.39938 -3361.3137 -2892.181 -27.949849 11491.188 - 6600 312.50182 -3354.0774 -2889.2547 14.380903 11498.754 - 6700 312.24745 -3354.727 -2890.2826 -11.564949 11506.565 - 6800 299.5486 -3344.6674 -2899.1115 140.00843 11514.587 - 6900 319.34442 -3353.0254 -2878.0248 -369.57931 11522.809 - 7000 312.5114 -3351.5646 -2886.7275 -338.9529 11530.444 - 7100 301.83696 -3339.7552 -2890.7956 -59.056671 11537.499 - 7200 317.79602 -3352.0354 -2879.3379 -476.34779 11544.273 - 7300 305.24957 -3341.8025 -2887.7669 -284.85596 11550.312 - 7400 327.39994 -3353.74 -2866.7574 -694.54924 11555.826 - 7500 320.25094 -3351.0448 -2874.6958 -667.61837 11560.396 - 7600 298.07438 -3332.5105 -2889.1475 -256.85225 11564.025 - 7700 310.50497 -3344.7831 -2882.9305 -657.61332 11566.855 - 7800 314.16294 -3347.8412 -2880.5476 -688.03112 11568.446 - 7900 300.40053 -3338.4536 -2891.6306 -476.3332 11568.775 - 8000 316.35903 -3348.7364 -2878.1763 -751.21864 11567.899 - 8100 308.957 -3347.7238 -2888.1737 -689.04336 11565.712 - 8200 296.70594 -3337.3321 -2896.0045 -354.23246 11562.212 - 8300 306.40458 -3348.666 -2892.9124 -647.83868 11557.563 - 8400 314.95559 -3354.0671 -2885.5945 -672.95129 11551.603 - 8500 299.19386 -3343.5909 -2898.5628 -244.49812 11544.459 - 8600 313.97242 -3350.861 -2883.8508 -417.72283 11536.587 - 8700 308.40661 -3348.3697 -2889.6382 -234.46379 11527.955 - 8800 299.75365 -3345.1001 -2899.2392 30.349293 11518.756 - 8900 310.85222 -3354.562 -2892.1929 -112.13993 11509.361 - 9000 307.93603 -3354.4949 -2896.4634 -24.119632 11499.746 - 9100 294.88785 -3349.2164 -2910.593 357.76086 11489.968 - 9200 296.56133 -3350.8626 -2909.7501 415.59418 11480.36 - 9300 304.6863 -3357.1682 -2903.9704 367.05129 11471.041 - 9400 314.87579 -3363.7046 -2895.3507 267.77411 11462.364 - 9500 295.39002 -3353.7081 -2914.3378 677.18586 11454.261 - 9600 310.14825 -3364.8576 -2903.5356 492.49166 11447.14 - 9700 302.90439 -3360.306 -2909.7587 620.88798 11441.001 - 9800 308.43227 -3363.4547 -2904.6851 678.75194 11435.989 - 9900 297.04137 -3358.0021 -2916.1755 801.45219 11432.184 - 10000 306.41271 -3360.5568 -2904.7911 825.76031 11429.68 -Loop time of 3.25989 on 1 procs for 10000 steps with 500 atoms + binsize = 3.5, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.729 | 5.729 | 5.729 Mbytes +Step Temp f_fxgREM PotEng TotEng Press Volume + 0 288.55656 112.20301 -3406.7669 -2977.5609 178.123 11354.789 + 10 288.31142 112.19886 -3406.6287 -2977.7873 169.48583 11354.791 + 20 289.8223 112.2004 -3406.6801 -2975.5914 143.0151 11354.796 + 30 291.70551 112.20808 -3406.9361 -2973.0463 110.8113 11354.804 + 40 292.3991 112.19188 -3406.3961 -2971.4746 97.5904 11354.814 + 50 292.5823 112.21058 -3407.0192 -2971.8253 77.444998 11354.825 + 60 293.9295 112.21708 -3407.2359 -2970.038 57.79557 11354.839 + 70 296.04201 112.2877 -3409.5899 -2969.2498 13.811528 11354.853 + 80 296.75736 112.29156 -3409.7185 -2968.3144 11.76625 11354.868 + 90 295.13392 112.24842 -3408.2806 -2969.2912 48.889984 11354.884 + 100 292.15244 112.19841 -3406.6138 -2972.0592 101.11822 11354.9 + 110 289.12916 112.15164 -3405.0545 -2974.9968 152.31767 11354.918 + 120 287.27612 112.08096 -3402.6986 -2975.3971 202.34047 11354.94 + 130 287.42354 112.0831 -3402.7701 -2975.2494 207.659 11354.965 + 140 289.21301 112.14415 -3404.805 -2974.6226 176.72962 11354.993 + 150 291.22691 112.22079 -3407.3598 -2974.1819 138.20681 11355.026 + 160 291.8086 112.23001 -3407.667 -2973.6239 136.41994 11355.061 + 170 290.14945 112.24531 -3408.1771 -2976.6018 147.28873 11355.098 + 180 287.06496 112.19729 -3406.5762 -2979.5889 189.13996 11355.139 + 190 284.67717 112.11349 -3403.7829 -2980.3472 235.97079 11355.183 + 200 284.76856 112.11444 -3403.8146 -2980.243 229.78409 11355.232 + 210 287.30412 112.19165 -3406.3882 -2979.0451 178.2025 11355.285 + 220 290.24387 112.2716 -3409.0532 -2977.3375 128.2392 11355.341 + 230 291.75312 112.26846 -3408.9488 -2974.9881 127.5165 11355.4 + 240 291.56602 112.24089 -3408.0298 -2974.3475 156.54095 11355.461 + 250 289.54014 112.18263 -3406.0876 -2975.4186 212.94237 11355.526 + 260 286.70194 112.15809 -3405.2696 -2978.8222 257.79759 11355.594 + 270 285.294 112.15348 -3405.1159 -2980.7627 275.81206 11355.668 + 280 286.55908 112.15001 -3405.0003 -2978.7654 263.50914 11355.747 + 290 289.68555 112.21705 -3407.235 -2976.3497 203.07914 11355.83 + 300 292.70849 112.2666 -3408.8867 -2973.505 148.33374 11355.918 + 310 294.49815 112.29546 -3409.8488 -2971.8051 116.25484 11356.008 + 320 295.01917 112.26366 -3408.7887 -2969.97 128.97587 11356.101 + 330 293.62796 112.22757 -3407.5857 -2970.8364 172.03075 11356.196 + 340 289.75335 112.17364 -3405.7881 -2974.802 251.12304 11356.295 + 350 284.97643 112.09285 -3403.0949 -2979.214 349.19648 11356.399 + 360 281.8078 112.02317 -3400.7724 -2981.6047 424.30214 11356.509 + 370 281.86417 111.99526 -3399.842 -2980.5904 446.31739 11356.627 + 380 285.76759 112.05907 -3401.969 -2976.9114 388.90905 11356.754 + 390 292.89931 112.11358 -3403.7861 -2968.1206 299.89217 11356.888 + 400 300.34739 112.22464 -3407.488 -2960.744 182.63695 11357.028 + 410 304.41494 112.31486 -3410.4953 -2957.7011 100.39899 11357.171 + 420 303.85492 112.30406 -3410.1355 -2958.1743 95.619711 11357.317 + 430 300.81739 112.25584 -3408.528 -2961.0849 126.6436 11357.464 + 440 298.33667 112.26429 -3408.8098 -2965.0566 131.90634 11357.614 + 450 297.59531 112.2703 -3409.0098 -2966.3594 123.7656 11357.766 + 460 297.63297 112.29317 -3409.7725 -2967.066 102.31468 11357.921 + 470 297.08461 112.30627 -3410.2092 -2968.3183 91.899247 11358.078 + 480 294.93467 112.27288 -3409.096 -2970.403 117.26815 11358.237 + 490 290.85555 112.17178 -3405.726 -2973.1004 189.72375 11358.398 + 500 285.96923 112.05724 -3401.9081 -2976.5506 276.3915 11358.563 + 510 282.89047 111.98875 -3399.6252 -2978.847 332.0296 11358.733 + 520 282.00698 111.95278 -3398.4259 -2978.9619 356.61549 11358.909 + 530 281.59566 111.97984 -3399.3281 -2980.4759 347.9844 11359.092 + 540 282.13143 112.00287 -3400.0957 -2980.4466 327.18332 11359.282 + 550 285.29816 112.05396 -3401.7988 -2977.4394 270.12617 11359.477 + 560 290.61836 112.13691 -3404.5637 -2972.2909 180.78896 11359.678 + 570 296.03555 112.19783 -3406.5945 -2966.264 98.242808 11359.883 + 580 300.53871 112.26318 -3408.7725 -2961.744 23.345649 11360.089 + 590 304.57492 112.35224 -3411.7414 -2958.7093 -51.135366 11360.296 + 600 307.70286 112.41436 -3413.8121 -2956.1274 -99.74504 11360.502 + 610 307.4453 112.41196 -3413.7319 -2956.4303 -89.528722 11360.707 + 620 302.60338 112.36055 -3412.0183 -2961.9187 -20.95705 11360.909 + 630 295.45279 112.24699 -3408.2329 -2968.7692 88.92139 11361.112 + 640 288.99864 112.14528 -3404.8425 -2974.9789 184.507 11361.316 + 650 284.34769 112.06977 -3402.3256 -2979.3799 248.31274 11361.524 + 660 281.61709 111.99077 -3399.6924 -2980.8083 291.11773 11361.737 + 670 280.81464 112.02279 -3400.7596 -2983.0691 272.78278 11361.955 + 680 281.12808 112.05752 -3401.9172 -2983.7605 245.57676 11362.178 + 690 281.62922 112.06372 -3402.1239 -2983.2218 230.96812 11362.406 + 700 282.68114 112.07109 -3402.3696 -2981.9028 215.37371 11362.639 + 710 285.68075 112.10301 -3403.4336 -2978.5051 179.25783 11362.875 + 720 291.09563 112.17909 -3405.9695 -2972.9868 110.88608 11363.115 + 730 296.71165 112.25454 -3408.4848 -2967.1487 43.449083 11363.358 + 740 298.95953 112.34075 -3411.3584 -2966.6788 -0.16353109 11363.601 + 750 296.12026 112.26709 -3408.903 -2968.4466 55.376662 11363.845 + 760 290.41552 112.14957 -3404.9858 -2973.0147 143.51434 11364.089 + 770 286.15427 112.06806 -3402.2686 -2976.6358 197.31982 11364.337 + 780 286.44173 112.09388 -3403.1293 -2977.0689 166.80088 11364.588 + 790 291.05969 112.11693 -3403.8977 -2970.9685 101.12001 11364.842 + 800 296.16373 112.19144 -3406.3812 -2965.8601 17.480161 11365.099 + 810 297.57076 112.16867 -3405.6224 -2963.0084 10.893497 11365.356 + 820 295.03676 112.10776 -3403.5921 -2964.7473 62.199066 11365.613 + 830 291.33925 112.06297 -3402.0989 -2968.7538 126.16879 11365.871 + 840 288.62338 112.02665 -3400.8882 -2971.5828 181.67525 11366.132 + 850 287.67016 111.98421 -3399.4736 -2971.5861 220.14947 11366.397 + 860 288.98767 112.00317 -3400.1058 -2970.2585 209.25845 11366.666 + 870 292.17389 112.03349 -3401.1163 -2966.5298 174.42425 11366.939 + 880 295.40208 112.08024 -3402.6746 -2963.2864 133.4123 11367.215 + 890 296.65783 112.12162 -3404.0539 -2962.7979 113.59974 11367.494 + 900 295.1242 112.10467 -3403.489 -2964.5141 139.94644 11367.775 + 910 291.92281 112.00467 -3400.1557 -2965.9426 209.05038 11368.059 + 920 289.32856 111.97002 -3399.0008 -2968.6465 240.69528 11368.347 + 930 289.67692 111.96061 -3398.6872 -2967.8147 228.61897 11368.639 + 940 294.3022 112.0659 -3402.1968 -2964.4446 130.39654 11368.936 + 950 301.51105 112.13134 -3404.378 -2955.9032 25.61018 11369.235 + 960 306.83743 112.27981 -3409.327 -2952.9296 -91.059043 11369.535 + 970 307.4444 112.29416 -3409.8054 -2952.5051 -109.84508 11369.833 + 980 304.50616 112.27686 -3409.2287 -2956.2989 -78.391305 11370.13 + 990 301.06082 112.21176 -3407.0587 -2959.2536 -15.295458 11370.425 + 1000 298.65751 112.14831 -3404.9437 -2960.7133 43.569751 11370.721 + 1010 297.03945 112.14146 -3404.7155 -2962.8918 73.28153 11371.017 + 1020 295.59833 112.09804 -3403.268 -2963.5879 110.62196 11371.314 + 1030 293.93194 112.05872 -3401.9573 -2964.7558 139.816 11371.614 + 1040 292.24705 112.00732 -3400.2439 -2965.5486 164.01425 11371.917 + 1050 291.34252 111.98463 -3399.4876 -2966.1376 163.57877 11372.222 + 1060 291.75453 112.00753 -3400.2511 -2966.2883 132.24681 11372.531 + 1070 293.50063 112.03285 -3401.0949 -2964.535 90.509052 11372.842 + 1080 296.32578 112.0879 -3402.93 -2962.1679 34.42726 11373.156 + 1090 298.98455 112.08885 -3402.9618 -2958.2449 8.5704615 11373.47 + 1100 299.9828 112.09758 -3403.2527 -2957.051 1.5561287 11373.784 + 1110 298.93539 112.0604 -3402.0133 -2957.3696 34.967375 11374.099 + 1120 296.7305 112.04723 -3401.5744 -2960.2103 69.990098 11374.414 + 1130 295.27674 112.02291 -3400.7635 -2961.5617 100.03863 11374.731 + 1140 296.45601 112.02269 -3400.7563 -2959.8005 95.241061 11375.05 + 1150 299.73047 112.0732 -3402.44 -2956.6136 50.324323 11375.37 + 1160 302.03965 112.15096 -3405.0321 -2955.771 0.470984 11375.692 + 1170 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11433.963 + 9860 320.01362 131.12947 -3370.9825 -2894.9865 433.4292 11433.587 + 9870 313.81089 131.05079 -3368.3598 -2901.5899 515.78327 11433.22 + 9880 305.53941 130.90419 -3363.4731 -2909.0064 649.28439 11432.862 + 9890 299.21519 130.7995 -3359.9832 -2914.9233 753.05794 11432.516 + 9900 297.04137 130.74006 -3358.0021 -2916.1755 801.45219 11432.184 + 9910 298.82519 130.76151 -3358.7171 -2914.2373 781.78912 11431.867 + 9920 302.18487 130.79397 -3359.7989 -2910.3219 743.67238 11431.564 + 9930 304.1639 130.83896 -3361.2986 -2908.8779 716.25452 11431.276 + 9940 303.39638 130.86995 -3362.3318 -2911.0527 726.22258 11431.001 + 9950 300.5113 130.78869 -3359.623 -2912.6352 804.30803 11430.741 + 9960 297.71143 130.74853 -3358.2844 -2915.4612 867.5875 11430.495 + 9970 297.2169 130.70973 -3356.991 -2914.9034 908.28216 11430.266 + 9980 299.38293 130.71469 -3357.1564 -2911.847 904.21977 11430.054 + 9990 303.00811 130.7639 -3358.7965 -2908.0949 865.72383 11429.859 + 10000 306.41271 130.8167 -3360.5568 -2904.7911 825.76031 11429.68 +Loop time of 2.50278 on 1 procs for 10000 steps with 500 atoms -Performance: 265.040 ns/day, 0.091 hours/ns, 3067.589 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 345.216 ns/day, 0.070 hours/ns, 3995.560 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.688 | 2.688 | 2.688 | 0.0 | 82.46 -Bond | 0.00086093 | 0.00086093 | 0.00086093 | 0.0 | 0.03 -Neigh | 0.03159 | 0.03159 | 0.03159 | 0.0 | 0.97 -Comm | 0.093323 | 0.093323 | 0.093323 | 0.0 | 2.86 -Output | 0.0014281 | 0.0014281 | 0.0014281 | 0.0 | 0.04 -Modify | 0.35664 | 0.35664 | 0.35664 | 0.0 | 10.94 -Other | | 0.0881 | | | 2.70 +Pair | 2.0969 | 2.0969 | 2.0969 | 0.0 | 83.78 +Bond | 0.0007844 | 0.0007844 | 0.0007844 | 0.0 | 0.03 +Neigh | 0.026091 | 0.026091 | 0.026091 | 0.0 | 1.04 +Comm | 0.076576 | 0.076576 | 0.076576 | 0.0 | 3.06 +Output | 0.0075617 | 0.0075617 | 0.0075617 | 0.0 | 0.30 +Modify | 0.2441 | 0.2441 | 0.2441 | 0.0 | 9.75 +Other | | 0.05081 | | | 2.03 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -171,4 +1076,4 @@ Neighbor list builds = 32 Dangerous builds = 0 #write_data ${rep}/lj-out.data -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/examples/USER/misc/grem/lj-temper/2/log.lammps.2 b/examples/USER/misc/grem/lj-temper/2/log.lammps.2 index cc4fd71a24..4d3076a406 100644 --- a/examples/USER/misc/grem/lj-temper/2/log.lammps.2 +++ b/examples/USER/misc/grem/lj-temper/2/log.lammps.2 @@ -16,10 +16,6 @@ read_data 2/lj.data #dump dump all xyz 1000 ${rep}/dump.xyz -thermo 100 -thermo_style custom step temp pe etotal press vol -timestep 1.0 - fix fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0 @@ -27,135 +23,1044 @@ fix fxnpt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso 0 0 10000.0 fix fxgREM all grem ${lambda} -.03 -30000 fxnpt fix fxgREM all grem 920 -.03 -30000 fxnpt + +thermo 10 +thermo_style custom step temp f_fxgREM pe etotal press vol thermo_modify press fxgREM_press +timestep 1.0 temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker} temper/grem 10000 100 920 fxgREM fxnpt 10294 98392 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 - binsize = 3.5 -> bins = 7 7 7 -Memory usage per processor = 5.3797 Mbytes -Step Temp PotEng TotEng Press Volume - 0 303.5147 -3379.1918 -2927.7367 939.06157 11374.376 - 100 318.12855 -3389.1972 -2916.0051 732.24211 11375.313 - 200 300.55209 -3378.8051 -2931.7566 879.17024 11377.778 - 300 303.98225 -3382.1398 -2929.9893 688.68264 11381.592 - 400 315.07191 -3384.8092 -2916.1636 538.20119 11386.698 - 500 309.36576 -3382.7455 -2922.5874 478.65718 11393.035 - 600 310.56557 -3382.7619 -2920.8192 337.42905 11400.274 - 700 304.59438 -3382.4412 -2929.3802 343.41809 11408.201 - 800 307.37357 -3384.554 -2927.3591 165.57164 11416.925 - 900 316.86746 -3390.4013 -2919.085 -181.01119 11426.176 - 1000 299.18538 -3381.9504 -2936.9349 -39.701634 11435.48 - 1100 300.12698 -3382.5392 -2936.1231 -186.50374 11444.773 - 1200 296.14975 -3382.3095 -2941.8092 -328.47519 11453.747 - 1300 290.48513 -3379.3388 -2947.2642 -379.01155 11462.196 - 1400 307.12598 -3390.0083 -2933.1817 -784.07577 11469.94 - 1500 292.27399 -3382.948 -2948.2126 -757.50578 11476.37 - 1600 298.4373 -3386.9034 -2943.0005 -916.53485 11481.206 - 1700 284.99283 -3380.9051 -2956.9999 -761.53168 11484.379 - 1800 296.30929 -3387.9389 -2947.2013 -939.04947 11486.001 - 1900 274.95571 -3376.1525 -2967.1767 -557.57811 11485.93 - 2000 286.6494 -3387.2487 -2960.8795 -874.00502 11484.534 - 2100 301.45624 -3391.8264 -2943.4331 -1081.5931 11481.54 - 2200 294.31641 -3388.9801 -2951.2068 -874.50856 11476.941 - 2300 308.19066 -3397.6354 -2939.2252 -1180.813 11470.81 - 2400 294.64485 -3394.5337 -2956.2718 -968.71497 11462.705 - 2500 298.56162 -3398.2204 -2954.1326 -933.7456 11452.815 - 2600 294.06753 -3394.6475 -2957.2443 -699.18137 11441.168 - 2700 293.43299 -3392.0706 -2955.6113 -469.64296 11428.099 - 2800 294.09756 -3396.3977 -2958.9499 -245.0764 11414.04 - 2900 299.63675 -3400.8857 -2955.1988 -183.76834 11399.474 - 3000 289.06398 -3398.5529 -2968.5921 99.751425 11384.569 - 3100 307.44213 -3408.7747 -2951.4778 -8.3031637 11369.696 - 3200 302.98498 -3406.3856 -2955.7184 182.98744 11355.058 - 3300 291.9362 -3402.8973 -2968.6643 497.72457 11340.867 - 3400 295.54663 -3410.1026 -2970.4993 587.20344 11327.555 - 3500 304.27556 -3418.4127 -2965.8259 574.20245 11315.364 - 3600 303.72416 -3418.133 -2966.3663 573.08992 11304.186 - 3700 309.84914 -3426.5382 -2965.6611 418.30717 11294.016 - 3800 317.00037 -3430.4681 -2958.9541 467.30843 11284.802 - 3900 297.49383 -3424.0999 -2981.6004 779.41312 11276.818 - 4000 299.31354 -3421.8877 -2976.6815 903.93135 11270.237 - 4100 294.42695 -3423.8465 -2985.9087 1006.7998 11265.197 - 4200 300.01777 -3428.3819 -2982.1283 922.16275 11261.965 - 4300 292.77221 -3426.1312 -2990.6547 959.47941 11260.451 - 4400 300.87895 -3431.0308 -2983.4961 790.75992 11260.593 - 4500 290.78158 -3422.5048 -2989.9892 1001.9136 11262.315 - 4600 297.70252 -3430.615 -2987.8051 741.34784 11265.627 - 4700 303.5284 -3430.3888 -2978.9133 665.85341 11270.32 - 4800 291.67229 -3426.7342 -2992.8938 674.67006 11276.471 - 4900 297.00112 -3426.7467 -2984.98 532.96983 11283.928 - 5000 301.01123 -3430.4774 -2982.746 304.12386 11292.466 - 5100 302.29794 -3430.5071 -2980.8618 154.274 11301.776 - 5200 298.81333 -3428.9592 -2984.497 71.617996 11311.612 - 5300 287.74054 -3421.9947 -2994.0024 126.94546 11321.814 - 5400 299.8741 -3430.5222 -2984.4822 -283.50833 11332.317 - 5500 285.30311 -3421.1025 -2996.7357 -152.79946 11342.614 - 5600 293.4497 -3423.1142 -2986.63 -384.69324 11352.571 - 5700 292.90437 -3421.8788 -2986.2057 -385.78559 11361.964 - 5800 295.75086 -3421.8274 -2981.9204 -538.6221 11370.715 - 5900 285.54471 -3417.8008 -2993.0746 -584.6133 11378.554 - 6000 279.42138 -3415.0373 -2999.4192 -496.44729 11385.309 - 6100 292.98635 -3420.2915 -2984.4965 -807.7782 11390.881 - 6200 285.18497 -3413.9471 -2989.7561 -720.47221 11394.96 - 6300 296.76693 -3419.0502 -2977.6318 -883.05972 11397.626 - 6400 288.53322 -3415.8922 -2986.7209 -743.81572 11398.671 - 6500 301.89212 -3418.3134 -2969.2718 -760.06071 11398.197 - 6600 295.43874 -3414.401 -2974.9583 -595.49387 11396.453 - 6700 307.77134 -3414.4111 -2956.6245 -619.65168 11393.607 - 6800 307.77881 -3415.132 -2957.3343 -598.73379 11389.666 - 6900 299.95571 -3411.6113 -2965.4499 -414.64515 11384.775 - 7000 310.48581 -3418.9557 -2957.1316 -554.8734 11379.061 - 7100 297.78265 -3411.5928 -2968.6637 -204.17877 11372.511 - 7200 308.16321 -3414.8796 -2956.5102 -168.32518 11365.403 - 7300 305.49867 -3410.8638 -2956.4577 -63.088242 11357.993 - 7400 302.44796 -3410.8142 -2960.9458 62.696434 11350.522 - 7500 312.15684 -3419.0214 -2954.7118 27.395999 11343.127 - 7600 307.34561 -3414.5741 -2957.4208 257.94209 11335.847 - 7700 304.79016 -3411.896 -2958.5437 470.94979 11328.999 - 7800 311.79257 -3417.7252 -2953.9574 385.82094 11322.846 - 7900 316.24138 -3419.8749 -2949.4899 332.38484 11317.485 - 8000 315.73781 -3421.0721 -2951.436 300.24782 11312.939 - 8100 303.38025 -3416.1142 -2964.8591 623.97214 11309.099 - 8200 313.53945 -3418.4381 -2952.072 462.62665 11306.275 - 8300 312.90183 -3417.7579 -2952.3402 535.34718 11304.458 - 8400 302.89319 -3412.1607 -2961.63 754.08676 11303.725 - 8500 321.89652 -3422.325 -2943.5284 382.37676 11304.219 - 8600 308.02194 -3419.4464 -2961.2871 471.90335 11305.76 - 8700 310.12893 -3419.2625 -2957.9692 389.78683 11308.17 - 8800 306.85617 -3418.0084 -2961.5831 425.37989 11311.375 - 8900 287.92832 -3407.5424 -2979.2708 659.46236 11315.622 - 9000 278.06342 -3403.7402 -2990.142 757.54946 11321.103 - 9100 290.97422 -3412.7395 -2979.9374 406.79415 11327.735 - 9200 285.14294 -3408.7977 -2984.6692 329.51839 11335.252 - 9300 280.67249 -3406.8005 -2989.3214 234.83036 11343.32 - 9400 289.42707 -3416.0941 -2985.5933 -28.179186 11351.699 - 9500 285.62232 -3407.4208 -2982.5793 10.204022 11360.293 - 9600 285.51121 -3409.1935 -2984.5173 -102.42078 11368.884 - 9700 280.01648 -3404.052 -2987.5487 -91.259523 11377.233 - 9800 289.42587 -3410.2875 -2979.7884 -383.72706 11385.424 - 9900 291.01583 -3408.3435 -2975.4795 -514.96551 11393.129 - 10000 290.66211 -3409.5137 -2977.1759 -667.48493 11399.792 -Loop time of 3.25989 on 1 procs for 10000 steps with 500 atoms + binsize = 3.5, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.725 | 5.725 | 5.725 Mbytes +Step Temp f_fxgREM PotEng TotEng Press Volume + 0 303.5147 121.37576 -3379.1918 -2927.7367 939.06157 11374.376 + 10 302.01819 121.39208 -3379.7359 -2930.5067 955.34812 11374.385 + 20 299.66358 121.35742 -3378.5808 -2932.854 998.03963 11374.412 + 30 297.90005 121.29795 -3376.5984 -2933.4946 1044.5312 11374.459 + 40 297.80982 121.28845 -3376.2818 -2933.3122 1054.8591 11374.525 + 50 299.23154 121.29836 -3376.6121 -2931.5279 1041.3766 11374.611 + 60 302.03518 121.3687 -3378.9567 -2929.7023 989.46264 11374.717 + 70 306.89734 121.46445 -3382.1482 -2925.6616 909.21372 11374.842 + 80 312.96036 121.61757 -3387.2525 -2921.7477 798.74753 11374.984 + 90 317.17373 121.67419 -3389.1395 -2917.3676 741.54767 11375.141 + 100 318.12855 121.67592 -3389.1972 -2916.0051 732.24211 11375.313 + 110 317.40874 121.63553 -3387.8509 -2915.7295 752.10626 11375.498 + 120 317.26883 121.64121 -3388.0404 -2916.1271 747.01078 11375.698 + 130 318.44405 121.66687 -3388.8957 -2915.2343 716.45621 11375.912 + 140 320.49327 121.72022 -3390.6741 -2913.9647 662.18511 11376.14 + 150 321.57523 121.72069 -3390.6897 -2912.3709 631.6531 11376.38 + 160 319.8381 121.66628 -3388.8758 -2913.1409 645.43574 11376.633 + 170 314.72914 121.61398 -3387.1325 -2918.9968 690.12596 11376.897 + 180 307.88565 121.47522 -3382.5075 -2924.5509 787.49791 11377.175 + 190 302.4306 121.38539 -3379.5129 -2929.6703 860.06931 11377.468 + 200 300.55209 121.36415 -3378.8051 -2931.7566 879.17024 11377.778 + 210 302.1658 121.35469 -3378.4897 -2929.0409 861.25419 11378.104 + 220 306.03052 121.42929 -3380.9764 -2925.7792 784.32025 11378.447 + 230 311.24302 121.51255 -3383.7517 -2920.8013 683.50702 11378.804 + 240 317.19613 121.63306 -3387.7686 -2915.9634 557.05248 11379.175 + 250 321.84027 121.77732 -3392.5772 -2913.8642 433.86307 11379.556 + 260 322.49145 121.77838 -3392.6128 -2912.9312 405.00168 11379.945 + 270 319.15693 121.73888 -3391.296 -2916.5742 434.93244 11380.343 + 280 313.97609 121.65023 -3388.341 -2921.3254 510.85834 11380.749 + 290 308.48891 121.54438 -3384.8125 -2925.9586 605.15694 11381.164 + 300 303.98225 121.46419 -3382.1398 -2929.9893 688.68264 11381.592 + 310 301.16194 121.35538 -3378.5127 -2930.5572 772.56756 11382.032 + 320 299.57734 121.33603 -3377.8676 -2932.269 811.10407 11382.487 + 330 298.20583 121.29686 -3376.5619 -2933.0033 850.91749 11382.958 + 340 296.68231 121.27869 -3375.9562 -2934.6638 875.27503 11383.445 + 350 296.07804 121.2376 -3374.5866 -2934.193 890.91889 11383.949 + 360 297.85202 121.28674 -3376.2248 -2933.1925 843.92836 11384.469 + 370 302.07191 121.34854 -3378.2848 -2928.9758 765.82512 11385.006 + 380 307.49834 121.42425 -3380.8082 -2923.4278 672.28582 11385.557 + 390 312.23703 121.47974 -3382.6579 -2918.229 595.95834 11386.122 + 400 315.07191 121.54428 -3384.8092 -2916.1636 538.20119 11386.698 + 410 315.94513 121.55364 -3385.1213 -2915.1768 524.5897 11387.284 + 420 315.30599 121.57916 -3385.9721 -2916.9783 521.24858 11387.881 + 430 313.40144 121.54636 -3384.8785 -2918.7176 551.21708 11388.488 + 440 310.63766 121.51 -3383.6667 -2921.6167 585.62129 11389.105 + 450 308.5878 121.47864 -3382.6214 -2923.6204 604.44349 11389.733 + 460 308.95854 121.50288 -3383.4294 -2923.877 573.35315 11390.374 + 470 311.48972 121.52682 -3384.2274 -2920.91 518.66227 11391.025 + 480 313.53991 121.55393 -3385.131 -2918.7641 464.40873 11391.686 + 490 312.7438 121.56121 -3385.3737 -2920.191 442.86257 11392.356 + 500 309.36576 121.48237 -3382.7455 -2922.5874 478.65718 11393.035 + 510 306.02972 121.44378 -3381.4592 -2926.2632 503.73832 11393.723 + 520 304.91443 121.42569 -3380.8562 -2927.3191 503.69667 11394.421 + 530 306.90624 121.44801 -3381.6004 -2925.1006 461.88876 11395.128 + 540 310.95566 121.50359 -3383.453 -2920.93 389.09174 11395.845 + 550 314.97025 121.58624 -3386.2079 -2917.7136 305.58596 11396.569 + 560 317.27856 121.58689 -3386.2296 -2914.3018 271.64243 11397.299 + 570 316.65742 121.58979 -3386.3265 -2915.3226 265.5502 11398.034 + 580 313.57724 121.55613 -3385.2042 -2918.7818 296.4929 11398.775 + 590 310.76616 121.50776 -3383.592 -2921.3508 332.13482 11399.521 + 600 310.56557 121.48286 -3382.7619 -2920.8192 337.42905 11400.274 + 610 312.25189 121.52378 -3384.1259 -2919.6749 301.12723 11401.034 + 620 313.24348 121.52065 -3384.0218 -2918.0959 287.28351 11401.799 + 630 311.62555 121.50992 -3383.6639 -2920.1445 300.88185 11402.57 + 640 306.89182 121.41129 -3380.3762 -2923.8979 376.45557 11403.347 + 650 300.52127 121.30298 -3376.7659 -2929.7633 469.88722 11404.132 + 660 295.39559 121.24088 -3374.6961 -2935.3176 534.41022 11404.925 + 670 293.59119 121.20717 -3373.5724 -2936.8778 557.79376 11405.729 + 680 295.36949 121.2459 -3374.8633 -2935.5236 520.47729 11406.543 + 690 299.69654 121.34257 -3378.0857 -2932.3098 439.24953 11407.368 + 700 304.59438 121.47324 -3382.4412 -2929.3802 343.41809 11408.201 + 710 307.96318 121.55668 -3385.2225 -2927.1506 284.402 11409.041 + 720 308.35357 121.56263 -3385.4211 -2926.7686 286.21174 11409.886 + 730 305.33918 121.48732 -3382.9107 -2928.7418 350.49893 11410.738 + 740 300.03501 121.40623 -3380.2078 -2933.9285 432.74134 11411.596 + 750 295.12581 121.33235 -3377.7448 -2938.7676 498.71123 11412.463 + 760 293.47318 121.31724 -3377.2413 -2940.7222 500.40178 11413.339 + 770 296.15733 121.36068 -3378.6892 -2938.1776 430.22536 11414.225 + 780 301.50769 121.4365 -3381.2166 -2932.7467 318.64474 11415.119 + 790 306.13175 121.49937 -3383.3122 -2927.9645 219.00268 11416.02 + 800 307.37357 121.53662 -3384.554 -2927.3591 165.57164 11416.925 + 810 304.85262 121.4546 -3381.8199 -2928.3748 199.62236 11417.834 + 820 300.60164 121.32558 -3377.5193 -2930.3971 273.18602 11418.746 + 830 297.77967 121.28163 -3376.0544 -2933.1297 303.65329 11419.664 + 840 298.49364 121.32122 -3377.374 -2933.3873 268.86417 11420.588 + 850 302.57668 121.41376 -3380.4586 -2930.3987 179.21637 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+ 9850 282.1127 112.15105 -3405.0351 -2985.4139 -326.8267 11389.361 + 9860 285.987 112.19812 -3406.604 -2981.22 -392.3815 11390.131 + 9870 290.07281 112.22891 -3407.6304 -2976.1691 -455.73 11390.894 + 9880 292.98661 112.26374 -3408.7915 -2972.9961 -509.79706 11391.648 + 9890 293.4771 112.31718 -3410.5726 -2974.0477 -548.94532 11392.394 + 9900 291.01583 112.25031 -3408.3435 -2975.4795 -514.96551 11393.129 + 9910 288.3146 102.21877 -3407.2925 -2978.4464 -552.6703 11393.854 + 9920 289.81888 102.2633 -3408.7767 -2977.6931 -595.04901 11394.569 + 9930 295.20081 102.38658 -3412.8859 -2973.797 -695.95493 11395.273 + 9940 301.57118 102.49325 -3416.4418 -2967.8775 -794.95454 11395.964 + 9950 305.76964 102.57072 -3419.024 -2964.2148 -862.85164 11396.64 + 9960 306.04627 102.5489 -3418.2967 -2963.076 -860.0359 11397.301 + 9970 302.3909 102.50659 -3416.8863 -2967.1028 -818.623 11397.945 + 9980 296.77037 102.38306 -3412.7686 -2971.3451 -733.14902 11398.574 + 9990 292.19734 102.29924 -3409.9746 -2975.3532 -674.286 11399.189 + 10000 290.66211 102.28541 -3409.5137 -2977.1759 -667.48493 11399.792 +Loop time of 2.5027 on 1 procs for 10000 steps with 500 atoms -Performance: 265.040 ns/day, 0.091 hours/ns, 3067.591 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 345.227 ns/day, 0.070 hours/ns, 3995.683 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.5437 | 2.5437 | 2.5437 | 0.0 | 78.03 -Bond | 0.00067735 | 0.00067735 | 0.00067735 | 0.0 | 0.02 -Neigh | 0.017251 | 0.017251 | 0.017251 | 0.0 | 0.53 -Comm | 0.08847 | 0.08847 | 0.08847 | 0.0 | 2.71 -Output | 0.0010381 | 0.0010381 | 0.0010381 | 0.0 | 0.03 -Modify | 0.33628 | 0.33628 | 0.33628 | 0.0 | 10.32 -Other | | 0.2725 | | | 8.36 +Pair | 2.0312 | 2.0312 | 2.0312 | 0.0 | 81.16 +Bond | 0.00069571 | 0.00069571 | 0.00069571 | 0.0 | 0.03 +Neigh | 0.013799 | 0.013799 | 0.013799 | 0.0 | 0.55 +Comm | 0.073534 | 0.073534 | 0.073534 | 0.0 | 2.94 +Output | 0.0074136 | 0.0074136 | 0.0074136 | 0.0 | 0.30 +Modify | 0.23759 | 0.23759 | 0.23759 | 0.0 | 9.49 +Other | | 0.1385 | | | 5.53 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -171,4 +1076,4 @@ Neighbor list builds = 18 Dangerous builds = 0 #write_data ${rep}/lj-out.data -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/examples/USER/misc/grem/lj-temper/3/log.lammps.3 b/examples/USER/misc/grem/lj-temper/3/log.lammps.3 index 2bd265431d..4d4060558f 100644 --- a/examples/USER/misc/grem/lj-temper/3/log.lammps.3 +++ b/examples/USER/misc/grem/lj-temper/3/log.lammps.3 @@ -16,10 +16,6 @@ read_data 3/lj.data #dump dump all xyz 1000 ${rep}/dump.xyz -thermo 100 -thermo_style custom step temp pe etotal press vol -timestep 1.0 - fix fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0 @@ -27,135 +23,1044 @@ fix fxnpt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso 0 0 10000.0 fix fxgREM all grem ${lambda} -.03 -30000 fxnpt fix fxgREM all grem 930 -.03 -30000 fxnpt + +thermo 10 +thermo_style custom step temp f_fxgREM pe etotal press vol thermo_modify press fxgREM_press +timestep 1.0 temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker} temper/grem 10000 100 930 fxgREM fxnpt 10294 98392 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 - binsize = 3.5 -> bins = 7 7 7 -Memory usage per processor = 5.38075 Mbytes -Step Temp PotEng TotEng Press Volume - 0 290.839 -3356.3647 -2923.7637 13.376266 11488.157 - 100 285.69508 -3350.6878 -2925.738 167.78531 11487.986 - 200 303.33832 -3362.4442 -2911.2515 -285.77881 11487.825 - 300 296.08102 -3356.4942 -2916.0962 -14.958212 11487.267 - 400 293.47704 -3361.3097 -2924.7849 -10.620913 11486.528 - 500 299.4194 -3361.7955 -2916.4318 -50.507149 11485.642 - 600 305.29691 -3363.5524 -2909.4464 -108.7678 11484.625 - 700 303.76824 -3363.3253 -2911.493 -104.4867 11483.395 - 800 294.51417 -3359.4431 -2921.3756 69.012038 11481.959 - 900 317.06683 -3376.5605 -2904.9476 -394.53967 11480.603 - 1000 295.23442 -3359.4678 -2920.3289 140.84436 11479.118 - 1100 295.40528 -3359.5295 -2920.1365 238.50053 11477.82 - 1200 296.4057 -3358.2915 -2917.4104 187.0124 11476.739 - 1300 301.90051 -3364.4524 -2915.3982 37.401199 11475.788 - 1400 292.85338 -3358.8438 -2923.2466 166.77089 11474.892 - 1500 306.57141 -3367.7234 -2911.7217 -37.617278 11474.193 - 1600 303.60667 -3363.5842 -2911.9923 59.354855 11473.503 - 1700 309.11038 -3368.2542 -2908.4759 -77.354272 11473.036 - 1800 300.88534 -3360.8762 -2913.3321 157.35644 11472.739 - 1900 300.76857 -3362.1419 -2914.7714 64.474646 11472.846 - 2000 304.83747 -3362.6904 -2909.2678 74.697763 11473.205 - 2100 303.13383 -3361.2408 -2910.3522 23.427206 11473.697 - 2200 310.28177 -3369.0928 -2907.5722 -54.59024 11474.389 - 2300 301.49445 -3364.3099 -2915.8597 57.698577 11475.107 - 2400 302.32605 -3363.1745 -2913.4874 -101.51258 11475.951 - 2500 312.1335 -3371.5673 -2907.2924 -298.61384 11476.757 - 2600 311.48564 -3369.8118 -2906.5005 -248.29721 11477.348 - 2700 302.70772 -3366.2003 -2915.9455 -112.41764 11477.885 - 2800 296.91863 -3362.2907 -2920.6467 -11.436148 11478.398 - 2900 295.20791 -3360.1207 -2921.0213 28.151935 11478.849 - 3000 298.7181 -3363.3108 -2918.9903 -24.285938 11479.232 - 3100 299.63105 -3361.6655 -2915.987 -85.460877 11479.532 - 3200 299.2326 -3362.7204 -2917.6346 -1.4187391 11479.74 - 3300 292.01842 -3359.6831 -2925.3278 111.54019 11479.801 - 3400 300.40417 -3364.1372 -2917.3087 -35.829416 11479.821 - 3500 303.01655 -3366.1156 -2915.4014 -213.6144 11479.867 - 3600 300.80325 -3367.3344 -2919.9124 -108.94713 11479.727 - 3700 301.93871 -3365.3419 -2916.231 -108.25614 11479.485 - 3800 298.59542 -3364.1482 -2920.0102 -73.755956 11479.116 - 3900 296.82227 -3366.2208 -2924.7202 -102.3413 11478.537 - 4000 298.85366 -3363.1199 -2918.5977 -141.73373 11477.785 - 4100 285.93508 -3361.0953 -2935.7885 33.105452 11476.764 - 4200 294.13198 -3366.6662 -2929.1672 -61.017319 11475.527 - 4300 289.62881 -3360.4118 -2929.6109 72.508715 11474.117 - 4400 292.16548 -3363.2769 -2928.7029 69.460552 11472.679 - 4500 296.10391 -3364.7776 -2924.3455 -44.256514 11471.222 - 4600 298.19488 -3367.9838 -2924.4415 -79.787912 11469.536 - 4700 285.80539 -3358.8854 -2933.7716 197.88821 11467.664 - 4800 306.36811 -3371.2406 -2915.5413 -88.96311 11465.916 - 4900 292.49926 -3361.8643 -2926.7938 185.57775 11464.23 - 5000 290.88226 -3361.5861 -2928.9208 259.04414 11462.735 - 5100 307.58823 -3374.2434 -2916.7292 -29.448909 11461.464 - 5200 302.16928 -3370.5539 -2921.1 -33.25034 11460.298 - 5300 316.06674 -3376.741 -2906.6157 -242.91365 11458.915 - 5400 303.96005 -3370.8575 -2918.7399 -141.06744 11457.186 - 5500 311.74544 -3377.0044 -2913.3067 -274.23168 11455.241 - 5600 300.49781 -3366.7267 -2919.7589 112.99595 11452.946 - 5700 292.28467 -3363.6982 -2928.9469 345.58668 11450.884 - 5800 306.41131 -3375.5954 -2919.8318 44.031034 11449.306 - 5900 304.59946 -3373.6282 -2920.5596 11.550291 11447.886 - 6000 311.8961 -3377.6423 -2913.7205 -109.77328 11446.479 - 6100 291.20342 -3368.383 -2935.24 203.83576 11445.011 - 6200 297.89834 -3373.1747 -2930.0735 26.610471 11443.642 - 6300 300.56911 -3378.1564 -2931.0826 -35.208037 11442.15 - 6400 307.53502 -3382.2265 -2924.7914 -91.070456 11440.514 - 6500 303.68877 -3381.5242 -2929.8102 -47.863863 11438.647 - 6600 307.2743 -3383.4914 -2926.4441 -176.63601 11436.802 - 6700 294.30769 -3379.6274 -2941.8671 24.164729 11434.849 - 6800 303.13931 -3381.7922 -2930.8954 -111.95234 11432.875 - 6900 296.26164 -3381.8788 -2941.2121 -57.549381 11430.738 - 7000 289.01191 -3378.9354 -2949.0521 126.23987 11428.513 - 7100 302.81602 -3388.9706 -2938.5547 -237.78388 11426.322 - 7200 294.50663 -3383.9162 -2945.8599 -39.728782 11423.859 - 7300 290.35305 -3382.6487 -2950.7705 94.790713 11421.387 - 7400 282.82774 -3377.867 -2957.1822 250.1436 11419.087 - 7500 300.09907 -3388.5306 -2942.1559 -155.8278 11416.997 - 7600 297.08335 -3388.2429 -2946.354 -74.771931 11414.718 - 7700 296.10041 -3389.0183 -2948.5914 39.612836 11412.516 - 7800 302.26382 -3392.6735 -2943.079 -108.12678 11410.56 - 7900 299.45316 -3389.6586 -2944.2447 -67.016831 11408.644 - 8000 279.75796 -3383.3458 -2967.227 212.04894 11406.742 - 8100 296.1234 -3391.5243 -2951.0632 14.909942 11405.025 - 8200 283.90018 -3385.3372 -2963.0572 242.009 11403.233 - 8300 294.40491 -3390.3819 -2952.4769 144.49126 11401.685 - 8400 284.83989 -3386.3812 -2962.7034 294.44578 11400.452 - 8500 310.91803 -3399.32 -2936.853 -187.72128 11399.607 - 8600 280.73817 -3381.818 -2964.2413 368.28406 11398.828 - 8700 293.03064 -3389.802 -2953.9412 60.228584 11398.442 - 8800 284.38203 -3385.0501 -2962.0534 283.35374 11398.194 - 8900 296.26156 -3391.0805 -2950.4139 105.69366 11398.307 - 9000 293.15104 -3388.0276 -2951.9876 176.06272 11398.732 - 9100 296.37884 -3387.4524 -2946.6113 188.95802 11399.501 - 9200 299.22093 -3389.1839 -2944.1154 146.14576 11400.688 - 9300 284.90575 -3379.3036 -2955.5278 411.30367 11402.307 - 9400 300.14961 -3385.9354 -2939.4856 205.76471 11404.592 - 9500 298.23305 -3382.4734 -2938.8744 283.06153 11407.279 - 9600 282.24345 -3371.4137 -2951.598 615.47273 11410.426 - 9700 318.39873 -3390.0399 -2916.4459 -28.07165 11414.311 - 9800 311.94009 -3386.2127 -2922.2255 70.507396 11418.547 - 9900 317.20428 -3383.9541 -2912.1367 -26.751232 11423.218 - 10000 318.36799 -3382.5532 -2909.0049 -46.362454 11428.313 -Loop time of 3.25989 on 1 procs for 10000 steps with 500 atoms + binsize = 3.5, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.726 | 5.726 | 5.726 Mbytes +Step Temp f_fxgREM PotEng TotEng Press Volume + 0 290.839 130.69094 -3356.3647 -2923.7637 13.376266 11488.157 + 10 298.49016 130.86737 -3362.2456 -2918.2641 -139.01604 11488.157 + 20 305.83037 130.96693 -3365.5642 -2910.6647 -254.45224 11488.154 + 30 310.23182 131.06065 -3368.6884 -2907.2421 -332.60751 11488.147 + 40 310.27284 131.0497 -3368.3232 -2906.8159 -322.86391 11488.133 + 50 306.53667 130.92563 -3364.1878 -2908.2377 -229.32421 11488.113 + 60 301.05575 130.86235 -3362.0784 -2914.2808 -139.22921 11488.089 + 70 295.62185 130.74887 -3358.2958 -2918.5807 -30.488671 11488.062 + 80 291.00386 130.62365 -3354.1217 -2921.2755 71.019816 11488.035 + 90 287.64085 130.55052 -3351.684 -2923.84 136.24318 11488.009 + 100 285.69508 130.52063 -3350.6878 -2925.738 167.78531 11487.986 + 110 285.01446 130.47978 -3349.3259 -2925.3885 187.55076 11487.966 + 120 285.5602 130.50213 -3350.0709 -2925.3218 166.71919 11487.95 + 130 287.3227 130.55196 -3351.7321 -2924.3613 117.78775 11487.937 + 140 290.25957 130.63244 -3354.4147 -2922.6756 40.299682 11487.926 + 150 294.42021 130.70913 -3356.9709 -2919.0432 -49.667147 11487.916 + 160 299.06616 130.7992 -3359.9734 -2915.1351 -148.10202 11487.905 + 170 302.27193 130.85741 -3361.9138 -2912.3072 -219.90367 11487.892 + 180 303.13784 130.86602 -3362.2007 -2911.3062 -249.85871 11487.874 + 190 302.80628 130.87507 -3362.5024 -2912.101 -267.67656 11487.852 + 200 303.33832 130.87333 -3362.4442 -2911.2515 -285.77881 11487.825 + 210 305.5023 130.89943 -3363.3144 -2908.9029 -322.79381 11487.792 + 220 307.85065 130.92123 -3364.0411 -2906.1366 -351.67602 11487.753 + 230 308.22104 130.93218 -3364.406 -2905.9506 -348.91637 11487.707 + 240 305.74564 130.91929 -3363.9764 -2909.2029 -303.52406 11487.654 + 250 301.78413 130.84598 -3361.5326 -2912.6516 -216.19532 11487.596 + 260 298.46788 130.79715 -3359.9048 -2915.9565 -141.52764 11487.534 + 270 296.63349 130.7376 -3357.92 -2916.7002 -78.205751 11487.469 + 280 295.89932 130.72322 -3357.4406 -2917.3128 -46.177821 11487.402 + 290 295.70212 130.70344 -3356.7815 -2916.947 -22.759891 11487.335 + 300 296.08102 130.69483 -3356.4942 -2916.0962 -14.958212 11487.267 + 310 297.44455 130.7448 -3358.1599 -2915.7337 -42.692278 11487.199 + 320 299.60732 130.81428 -3360.4761 -2914.833 -85.527147 11487.13 + 330 301.41392 130.84528 -3361.5094 -2913.179 -109.23287 11487.059 + 340 301.95602 130.87141 -3362.3802 -2913.2435 -116.52949 11486.987 + 350 301.04313 130.87719 -3362.573 -2914.7942 -99.370101 11486.912 + 360 298.75171 130.86396 -3362.1319 -2917.7614 -61.477019 11486.836 + 370 295.31919 130.80085 -3360.0283 -2920.7634 2.7109805 11486.758 + 380 292.01147 130.74417 -3358.1391 -2923.7942 56.679543 11486.68 + 390 291.02267 130.76412 -3358.8039 -2925.9297 52.137334 11486.604 + 400 293.47704 130.83929 -3361.3097 -2924.7849 -10.620913 11486.528 + 410 298.04072 130.90419 -3363.4731 -2920.1601 -92.539319 11486.453 + 420 302.65763 130.9386 -3364.6201 -2914.4398 -161.34189 11486.375 + 430 305.58577 130.94802 -3364.9342 -2910.3985 -199.69054 11486.295 + 440 306.15192 130.96265 -3365.4217 -2910.0439 -210.24137 11486.211 + 450 304.70394 130.95 -3365.0002 -2911.7761 -185.30124 11486.122 + 460 302.72281 130.89534 -3363.178 -2912.9008 -135.5125 11486.031 + 470 301.565 130.87256 -3362.4188 -2913.8637 -103.42872 11485.936 + 480 301.09466 130.88295 -3362.7649 -2914.9094 -90.679055 11485.84 + 490 300.36785 130.88439 -3362.8128 -2916.0384 -75.984213 11485.742 + 500 299.4194 130.85387 -3361.7955 -2916.4318 -50.507149 11485.642 + 510 299.01319 130.85365 -3361.7883 -2917.0289 -42.892731 11485.542 + 520 299.3401 130.84795 -3361.5982 -2916.3525 -40.095555 11485.441 + 530 299.80119 130.82122 -3360.7075 -2914.7759 -29.794671 11485.339 + 540 299.83338 130.81373 -3360.4575 -2914.4781 -22.047344 11485.237 + 550 299.4037 130.80908 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310.90613 121.65292 -3388.4306 -2925.9813 83.616787 11408.486 + 9550 310.34517 121.6161 -3387.2034 -2925.5885 114.7155 11408.795 + 9560 306.11703 121.50118 -3383.3726 -2928.0467 217.12485 11409.107 + 9570 298.57301 121.39359 -3379.7864 -2935.6817 347.79888 11409.424 + 9580 290.5066 121.24927 -3374.9755 -2942.869 492.52626 11409.748 + 9590 284.8869 121.21634 -3373.8779 -2950.1302 564.58935 11410.081 + 9600 282.24345 121.14241 -3371.4137 -2951.598 615.47273 11410.426 + 9610 281.54477 121.17453 -3372.4844 -2953.7079 597.63074 11410.783 + 9620 282.37592 121.16698 -3372.2327 -2952.22 572.73408 11411.152 + 9630 285.87631 121.23507 -3374.5024 -2949.283 489.72728 11411.532 + 9640 293.23863 121.32922 -3377.6407 -2941.4704 359.22268 11411.922 + 9650 303.78977 121.52811 -3384.2703 -2932.406 160.0119 11412.32 + 9660 314.90908 121.70572 -3390.1907 -2921.7873 -31.00397 11412.721 + 9670 323.19384 121.81222 -3393.7407 -2913.0144 -159.81088 11413.122 + 9680 326.47698 121.83596 -3394.5319 -2908.9221 -197.94728 11413.521 + 9690 324.49204 121.77608 -3392.5359 -2909.8786 -140.96579 11413.917 + 9700 318.39873 121.7012 -3390.0399 -2916.4459 -28.07165 11414.311 + 9710 309.9298 121.56798 -3385.5994 -2924.6024 134.24289 11414.705 + 9720 301.40115 121.38285 -3379.4283 -2931.117 314.19572 11415.102 + 9730 295.50304 121.29689 -3376.5631 -2937.0247 424.36683 11415.506 + 9740 293.69194 121.24535 -3374.845 -2938.0005 472.17246 11415.918 + 9750 295.82738 121.28075 -3376.0249 -2936.0041 436.99987 11416.34 + 9760 300.84709 121.36028 -3378.6761 -2931.1888 346.71992 11416.77 + 9770 306.75344 121.43996 -3381.3319 -2925.0594 241.24451 11417.208 + 9780 311.02557 121.5807 -3386.0235 -2923.3965 124.30422 11417.651 + 9790 312.54333 121.58098 -3386.0327 -2921.1481 86.777327 11418.098 + 9800 311.94009 121.58638 -3386.2127 -2922.2255 70.507396 11418.547 + 9810 310.63038 121.53963 -3384.6545 -2922.6153 85.926164 11418.997 + 9820 310.24158 121.54915 -3384.9716 -2923.5107 80.534768 11419.451 + 9830 310.26239 121.57399 -3385.7997 -2924.3079 74.796432 11419.906 + 9840 308.09463 121.48045 -3382.6815 -2924.4141 137.35072 11420.364 + 9850 303.25155 121.36246 -3378.7487 -2927.685 230.41562 11420.825 + 9860 298.15768 121.24027 -3374.6756 -2931.1886 319.73318 11421.291 + 9870 296.24967 121.20328 -3373.4426 -2932.7936 338.78078 11421.764 + 9880 299.74146 121.24008 -3374.6695 -2928.8268 273.4407 11422.244 + 9890 308.03575 121.3596 -3378.6534 -2920.4736 131.9849 11422.729 + 9900 317.20428 121.51862 -3383.9541 -2912.1367 -26.751232 11423.218 + 9910 322.01402 121.62253 -3387.4177 -2908.4463 -114.41883 11423.707 + 9920 319.17778 121.54485 -3384.8285 -2910.0757 -51.898249 11424.195 + 9930 309.068 121.37161 -3379.0535 -2919.3383 121.82333 11424.683 + 9940 295.19905 121.13123 -3371.0411 -2931.9549 355.38766 11425.174 + 9950 283.24166 120.94189 -3364.7297 -2943.4292 543.86415 11425.673 + 9960 278.89942 120.87426 -3362.4754 -2947.6337 605.50591 11426.182 + 9970 284.59829 120.96752 -3365.5839 -2942.2655 505.31899 11426.703 + 9980 297.42507 121.21278 -3373.7593 -2931.3621 277.96374 11427.235 + 9990 310.57569 121.40093 -3380.0309 -2918.0731 68.495001 11427.773 + 10000 318.36799 121.47659 -3382.5532 -2909.0049 -46.362454 11428.313 +Loop time of 2.5028 on 1 procs for 10000 steps with 500 atoms -Performance: 265.040 ns/day, 0.091 hours/ns, 3067.588 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 345.213 ns/day, 0.070 hours/ns, 3995.527 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.5437 | 2.5437 | 2.5437 | 0.0 | 78.03 -Bond | 0.00088167 | 0.00088167 | 0.00088167 | 0.0 | 0.03 -Neigh | 0.027397 | 0.027397 | 0.027397 | 0.0 | 0.84 -Comm | 0.088112 | 0.088112 | 0.088112 | 0.0 | 2.70 -Output | 0.0010602 | 0.0010602 | 0.0010602 | 0.0 | 0.03 -Modify | 0.33726 | 0.33726 | 0.33726 | 0.0 | 10.35 -Other | | 0.2614 | | | 8.02 +Pair | 2.0314 | 2.0314 | 2.0314 | 0.0 | 81.16 +Bond | 0.00091743 | 0.00091743 | 0.00091743 | 0.0 | 0.04 +Neigh | 0.022412 | 0.022412 | 0.022412 | 0.0 | 0.90 +Comm | 0.074236 | 0.074236 | 0.074236 | 0.0 | 2.97 +Output | 0.0073647 | 0.0073647 | 0.0073647 | 0.0 | 0.29 +Modify | 0.23464 | 0.23464 | 0.23464 | 0.0 | 9.38 +Other | | 0.1319 | | | 5.27 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -171,4 +1076,4 @@ Neighbor list builds = 29 Dangerous builds = 0 #write_data ${rep}/lj-out.data -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/examples/USER/misc/grem/lj-temper/in.gREM-temper b/examples/USER/misc/grem/lj-temper/in.gREM-temper index 9e94edec79..8aa495d9d2 100644 --- a/examples/USER/misc/grem/lj-temper/in.gREM-temper +++ b/examples/USER/misc/grem/lj-temper/in.gREM-temper @@ -18,14 +18,14 @@ read_data ${rep}/lj.data #dump dump all xyz 1000 ${rep}/dump.xyz -thermo 10 -thermo_style custom step temp pe etotal press vol -timestep 1.0 - fix fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxgREM all grem ${lambda} -.03 -30000 fxnpt -thermo_modify press fxgREM_press -temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker} +thermo 10 +thermo_style custom step temp f_fxgREM pe etotal press vol +thermo_modify press fxgREM_press +timestep 1.0 + +temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker} #write_data ${rep}/lj-out.data diff --git a/examples/USER/tally/log.12Jun17.force.1 b/examples/USER/tally/log.12Jun17.force.1 new file mode 100644 index 0000000000..98b3bad245 --- /dev/null +++ b/examples/USER/tally/log.12Jun17.force.1 @@ -0,0 +1,177 @@ +LAMMPS (19 May 2017) + +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style lj/cut/coul/long 12.0 12.0 +kspace_style pppm 1.0e-4 + +pair_coeff 1 1 0.15535 3.166 +pair_coeff * 2 0.0000 0.0000 + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +# make certain that shake constraints are satisfied +run 0 post no +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 8000 3375 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 26.54 | 26.54 | 26.54 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.358 0 -16692.358 -1289.8319 +Loop time of 3e-06 on 1 procs for 0 steps with 4500 atoms + + +group one molecule 1 2 +6 atoms in group one + +# the following section shows equivalences between using the force/tally compute and other computes and thermo keywords + +# compute pairwise force between two molecules and everybody +compute fpa one group/group all pair yes kspace no boundary no +# tally pairwise force between two molecules and the all molecules +compute c1 one force/tally all +# tally the force of all with all (should be zero) +compute c2 all force/tally all +# collect per atom data. only reduce over the first group. +compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] +compute red all reduce sum c_c2[1] c_c2[2] c_c2[3] +# determine magnitude of force +variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3]) +variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3]) +# round to 10**-10 absolute precision. +variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10 +variable all equal round(1e10*c_c2)*1e-10 + +velocity all create 300 432567 dist uniform + +timestep 2.0 + +# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero +thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all +thermo 10 + +run 50 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 8000 3375 +WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77) +WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute group/group, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 28.47 | 28.47 | 28.47 Mbytes +Step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all + 0 22.7331 22.7331 22.7331 -17.068295 -17.068295 -8.8348335 -8.8348334 -12.141369 -12.141369 0 0 + 10 11.736901 11.736901 11.736901 -3.3897029 -3.3897029 9.1193856 9.1193856 -6.5651786 -6.5651786 0 0 + 20 5.6120339 5.6120339 5.6120339 -0.60046861 -0.60046861 -4.4481306 -4.4481306 3.3687528 3.3687528 0 0 + 30 17.29261 17.29261 17.29261 6.179302 6.179302 -10.593979 -10.593979 12.190906 12.190906 0 0 + 40 18.664433 18.664433 18.664433 5.4727782 5.4727782 -6.9329319 -6.9329319 16.442148 16.442148 0 0 + 50 12.130407 12.130407 12.130407 -1.0321196 -1.0321196 8.0035558 8.0035558 -9.0567428 -9.0567428 0 0 +Loop time of 13.9507 on 1 procs for 50 steps with 4500 atoms + +Performance: 0.619 ns/day, 38.752 hours/ns, 3.584 timesteps/s +32.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.594 | 12.594 | 12.594 | 0.0 | 90.27 +Bond | 7.3e-05 | 7.3e-05 | 7.3e-05 | 0.0 | 0.00 +Kspace | 0.56296 | 0.56296 | 0.56296 | 0.0 | 4.04 +Neigh | 0.65858 | 0.65858 | 0.65858 | 0.0 | 4.72 +Comm | 0.019093 | 0.019093 | 0.019093 | 0.0 | 0.14 +Output | 0.055025 | 0.055025 | 0.055025 | 0.0 | 0.39 +Modify | 0.057276 | 0.057276 | 0.057276 | 0.0 | 0.41 +Other | | 0.004003 | | | 0.03 + +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21131 ave 21131 max 21131 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2601983 +Ave neighs/atom = 578.218 +Ave special neighs/atom = 2 +Neighbor list builds = 4 +Dangerous builds = 1 + +Total wall time: 0:00:15 diff --git a/examples/USER/tally/log.12Jun17.force.4 b/examples/USER/tally/log.12Jun17.force.4 new file mode 100644 index 0000000000..4238173fb6 --- /dev/null +++ b/examples/USER/tally/log.12Jun17.force.4 @@ -0,0 +1,177 @@ +LAMMPS (19 May 2017) + +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style lj/cut/coul/long 12.0 12.0 +kspace_style pppm 1.0e-4 + +pair_coeff 1 1 0.15535 3.166 +pair_coeff * 2 0.0000 0.0000 + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +# make certain that shake constraints are satisfied +run 0 post no +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 3380 960 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.61 | 10.61 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.358 0 -16692.358 -1289.8319 +Loop time of 4.5e-06 on 4 procs for 0 steps with 4500 atoms + + +group one molecule 1 2 +6 atoms in group one + +# the following section shows equivalences between using the force/tally compute and other computes and thermo keywords + +# compute pairwise force between two molecules and everybody +compute fpa one group/group all pair yes kspace no boundary no +# tally pairwise force between two molecules and the all molecules +compute c1 one force/tally all +# tally the force of all with all (should be zero) +compute c2 all force/tally all +# collect per atom data. only reduce over the first group. +compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] +compute red all reduce sum c_c2[1] c_c2[2] c_c2[3] +# determine magnitude of force +variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3]) +variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3]) +# round to 10**-10 absolute precision. +variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10 +variable all equal round(1e10*c_c2)*1e-10 + +velocity all create 300 432567 dist uniform + +timestep 2.0 + +# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero +thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all +thermo 10 + +run 50 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 3380 960 +WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77) +WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute group/group, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 11.58 | 11.59 | 11.6 Mbytes +Step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all + 0 22.7331 22.7331 22.7331 -17.068295 -17.068295 -8.8348335 -8.8348334 -12.141369 -12.141369 0 0 + 10 11.736901 11.736901 11.736901 -3.3897029 -3.3897029 9.1193856 9.1193856 -6.5651786 -6.5651786 0 0 + 20 5.6120339 5.6120339 5.6120339 -0.60046861 -0.60046861 -4.4481306 -4.4481306 3.3687528 3.3687528 0 0 + 30 17.29261 17.29261 17.29261 6.179302 6.179302 -10.593979 -10.593979 12.190906 12.190906 0 0 + 40 18.664433 18.664433 18.664433 5.4727782 5.4727782 -6.9329319 -6.9329319 16.442148 16.442148 0 0 + 50 12.130407 12.130407 12.130407 -1.0321196 -1.0321196 8.0035558 8.0035558 -9.0567428 -9.0567428 0 0 +Loop time of 4.31614 on 4 procs for 50 steps with 4500 atoms + +Performance: 2.002 ns/day, 11.989 hours/ns, 11.584 timesteps/s +31.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.5075 | 3.6114 | 3.7489 | 4.7 | 83.67 +Bond | 8.6e-05 | 0.00010525 | 0.000141 | 0.0 | 0.00 +Kspace | 0.2581 | 0.39489 | 0.49723 | 14.2 | 9.15 +Neigh | 0.19826 | 0.19888 | 0.19918 | 0.1 | 4.61 +Comm | 0.034639 | 0.037137 | 0.038938 | 0.9 | 0.86 +Output | 0.025465 | 0.025997 | 0.027558 | 0.6 | 0.60 +Modify | 0.044022 | 0.044175 | 0.044407 | 0.1 | 1.02 +Other | | 0.003593 | | | 0.08 + +Nlocal: 1125 ave 1148 max 1097 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 12212.5 ave 12269 max 12162 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 650496 ave 675112 max 631353 min +Histogram: 1 0 0 1 1 0 0 0 0 1 + +Total # of neighbors = 2601983 +Ave neighs/atom = 578.218 +Ave special neighs/atom = 2 +Neighbor list builds = 4 +Dangerous builds = 1 + +Total wall time: 0:00:04 diff --git a/examples/USER/tally/log.21Aug15.pe.1 b/examples/USER/tally/log.12Jun17.pe.1 similarity index 50% rename from examples/USER/tally/log.21Aug15.pe.1 rename to examples/USER/tally/log.12Jun17.pe.1 index aea5530038..8b0f753414 100644 --- a/examples/USER/tally/log.21Aug15.pe.1 +++ b/examples/USER/tally/log.12Jun17.pe.1 @@ -1,5 +1,4 @@ -LAMMPS (21 Aug 2015-ICMS) - using 1 OpenMP thread(s) per MPI task +LAMMPS (19 May 2017) units real atom_style full @@ -50,6 +49,35 @@ fix 1 all shake 0.0001 20 0 b 1 a 1 1500 = # of frozen angles fix 2 all nvt temp 300.0 300.0 100.0 +# make certain that shake constraints are satisfied +run 0 post no +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 8000 3375 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 26.54 | 26.54 | 26.54 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.358 0 -16692.358 -1289.8319 +Loop time of 1e-06 on 1 procs for 0 steps with 4500 atoms + + group oxy type 1 1500 atoms in group oxy group hyd type 2 @@ -88,6 +116,7 @@ thermo 10 run 50 PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.218482 grid = 15 15 15 stencil order = 5 @@ -95,38 +124,49 @@ PPPM initialization ... estimated relative force accuracy = 9.61968e-05 using double precision FFTs 3d grid and FFT values/proc = 8000 3375 -WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75) -WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75) +WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77) +WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77) Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 - binsize = 7 -> bins = 6 6 6 -Memory usage per processor = 17.381 Mbytes -Step epa epa E_vdwl vdwl E_coul coul eref pe c2 pair - 0 -516632.19 -516632.19 3169.9382 3169.9382 46213.889 46213.889 49383.827 49383.827 49383.827 49383.827 - 10 -517027.36 -517027.36 3099.1322 3099.1322 45891.84 45891.84 48990.972 48990.972 48990.972 48990.972 - 20 -516828.06 -516828.06 3101.4321 3101.4321 45884.14 45884.14 48985.572 48985.572 48985.572 48985.572 - 30 -517032.1 -517032.1 3198.5939 3198.5939 45793.571 45793.571 48992.165 48992.165 48992.165 48992.165 - 40 -517095.56 -517095.56 3244.0797 3244.0797 45715.265 45715.265 48959.345 48959.345 48959.345 48959.345 - 50 -517273.54 -517273.54 3274.9142 3274.9142 45665.997 45665.997 48940.911 48940.911 48940.911 48940.911 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute group/group, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 29.08 | 29.08 | 29.08 Mbytes +Step c_epa v_epa E_vdwl v_vdwl E_coul v_coul v_eref v_pe c_c2 v_pair + 0 -516634.27 -516634.27 3169.9427 3169.9427 46212.482 46212.482 49382.425 49382.425 49382.425 49382.425 + 10 -517027.35 -517027.35 3099.1374 3099.1374 45891.866 45891.866 48991.003 48991.003 48991.003 48991.003 + 20 -516828.05 -516828.05 3101.4373 3101.4373 45884.156 45884.156 48985.594 48985.594 48985.594 48985.594 + 30 -517032.07 -517032.07 3198.5951 3198.5951 45793.595 45793.595 48992.191 48992.191 48992.191 48992.191 + 40 -517095.54 -517095.54 3244.0771 3244.0771 45715.292 45715.292 48959.369 48959.369 48959.369 48959.369 + 50 -517273.5 -517273.5 3274.9097 3274.9097 45666.025 45666.025 48940.935 48940.935 48940.935 48940.935 +Loop time of 15.3339 on 1 procs for 50 steps with 4500 atoms -Loop time of 4.31105 on 1 procs for 50 steps with 4500 atoms -100.1% CPU use with 1 MPI tasks x 1 OpenMP threads -Performance: 2.004 ns/day 11.975 hours/ns 11.598 timesteps/s +Performance: 0.563 ns/day, 42.594 hours/ns, 3.261 timesteps/s +32.0% CPU use with 1 MPI tasks x no OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.5071 | 3.5071 | 3.5071 | 0.0 | 81.35 -Bond | 0.00025034 | 0.00025034 | 0.00025034 | 0.0 | 0.01 -Kspace | 0.19991 | 0.19991 | 0.19991 | 0.0 | 4.64 -Neigh | 0.31459 | 0.31459 | 0.31459 | 0.0 | 7.30 -Comm | 0.010338 | 0.010338 | 0.010338 | 0.0 | 0.24 -Output | 0.24722 | 0.24722 | 0.24722 | 0.0 | 5.73 -Modify | 0.029466 | 0.029466 | 0.029466 | 0.0 | 0.68 -Other | | 0.002182 | | | 0.05 +Pair | 13.432 | 13.432 | 13.432 | 0.0 | 87.60 +Bond | 0.000365 | 0.000365 | 0.000365 | 0.0 | 0.00 +Kspace | 0.581 | 0.581 | 0.581 | 0.0 | 3.79 +Neigh | 0.66081 | 0.66081 | 0.66081 | 0.0 | 4.31 +Comm | 0.019908 | 0.019908 | 0.019908 | 0.0 | 0.13 +Output | 0.57731 | 0.57731 | 0.57731 | 0.0 | 3.76 +Modify | 0.058515 | 0.058515 | 0.058515 | 0.0 | 0.38 +Other | | 0.003889 | | | 0.03 Nlocal: 4500 ave 4500 max 4500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -135,10 +175,10 @@ Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 2601984 -Ave neighs/atom = 578.219 +Total # of neighbors = 2601983 +Ave neighs/atom = 578.218 Ave special neighs/atom = 2 Neighbor list builds = 4 Dangerous builds = 1 -Total wall time: 0:00:04 +Total wall time: 0:00:16 diff --git a/examples/USER/tally/log.21Aug15.pe.4 b/examples/USER/tally/log.12Jun17.pe.4 similarity index 50% rename from examples/USER/tally/log.21Aug15.pe.4 rename to examples/USER/tally/log.12Jun17.pe.4 index 303af555ff..f684fabe01 100644 --- a/examples/USER/tally/log.21Aug15.pe.4 +++ b/examples/USER/tally/log.12Jun17.pe.4 @@ -1,5 +1,4 @@ -LAMMPS (21 Aug 2015-ICMS) - using 1 OpenMP thread(s) per MPI task +LAMMPS (19 May 2017) units real atom_style full @@ -50,6 +49,35 @@ fix 1 all shake 0.0001 20 0 b 1 a 1 1500 = # of frozen angles fix 2 all nvt temp 300.0 300.0 100.0 +# make certain that shake constraints are satisfied +run 0 post no +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 3380 960 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.61 | 10.61 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.358 0 -16692.358 -1289.8319 +Loop time of 1.75e-06 on 4 procs for 0 steps with 4500 atoms + + group oxy type 1 1500 atoms in group oxy group hyd type 2 @@ -88,6 +116,7 @@ thermo 10 run 50 PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.218482 grid = 15 15 15 stencil order = 5 @@ -95,38 +124,49 @@ PPPM initialization ... estimated relative force accuracy = 9.61968e-05 using double precision FFTs 3d grid and FFT values/proc = 3380 960 -WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75) -WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75) +WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77) +WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77) Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 - binsize = 7 -> bins = 6 6 6 -Memory usage per processor = 8.44413 Mbytes -Step epa epa E_vdwl vdwl E_coul coul eref pe c2 pair - 0 -516632.19 -516632.19 3169.9382 3169.9382 46213.889 46213.889 49383.827 49383.827 49383.827 49383.827 - 10 -517027.36 -517027.36 3099.1322 3099.1322 45891.84 45891.84 48990.972 48990.972 48990.972 48990.972 - 20 -516828.06 -516828.06 3101.4321 3101.4321 45884.14 45884.14 48985.572 48985.572 48985.572 48985.572 - 30 -517032.1 -517032.1 3198.5939 3198.5939 45793.571 45793.571 48992.165 48992.165 48992.165 48992.165 - 40 -517095.56 -517095.56 3244.0797 3244.0797 45715.265 45715.265 48959.345 48959.345 48959.345 48959.345 - 50 -517273.54 -517273.54 3274.9142 3274.9142 45665.997 45665.997 48940.911 48940.911 48940.911 48940.911 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute group/group, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 11.86 | 11.87 | 11.88 Mbytes +Step c_epa v_epa E_vdwl v_vdwl E_coul v_coul v_eref v_pe c_c2 v_pair + 0 -516634.27 -516634.27 3169.9427 3169.9427 46212.482 46212.482 49382.425 49382.425 49382.425 49382.425 + 10 -517027.35 -517027.35 3099.1374 3099.1374 45891.866 45891.866 48991.003 48991.003 48991.003 48991.003 + 20 -516828.05 -516828.05 3101.4373 3101.4373 45884.156 45884.156 48985.594 48985.594 48985.594 48985.594 + 30 -517032.07 -517032.07 3198.5951 3198.5951 45793.595 45793.595 48992.191 48992.191 48992.191 48992.191 + 40 -517095.54 -517095.54 3244.0771 3244.0771 45715.292 45715.292 48959.369 48959.369 48959.369 48959.369 + 50 -517273.5 -517273.5 3274.9097 3274.9097 45666.025 45666.025 48940.935 48940.935 48940.935 48940.935 +Loop time of 2.32344 on 4 procs for 50 steps with 4500 atoms -Loop time of 1.20533 on 4 procs for 50 steps with 4500 atoms -100.0% CPU use with 4 MPI tasks x 1 OpenMP threads -Performance: 7.168 ns/day 3.348 hours/ns 41.482 timesteps/s +Performance: 3.719 ns/day, 6.454 hours/ns, 21.520 timesteps/s +64.0% CPU use with 4 MPI tasks x no OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.87053 | 0.90325 | 0.94364 | 2.8 | 74.94 -Bond | 0.00015402 | 0.00018191 | 0.00020909 | 0.2 | 0.02 -Kspace | 0.061657 | 0.10164 | 0.13394 | 8.4 | 8.43 -Neigh | 0.088292 | 0.088332 | 0.088373 | 0.0 | 7.33 -Comm | 0.017319 | 0.017806 | 0.018291 | 0.4 | 1.48 -Output | 0.07067 | 0.070706 | 0.070813 | 0.0 | 5.87 -Modify | 0.021655 | 0.021694 | 0.02173 | 0.0 | 1.80 -Other | | 0.001719 | | | 0.14 +Pair | 1.5561 | 1.8883 | 2.0327 | 14.1 | 81.27 +Bond | 8.8e-05 | 0.000116 | 0.000135 | 0.0 | 0.00 +Kspace | 0.094718 | 0.1933 | 0.26055 | 14.1 | 8.32 +Neigh | 0.085117 | 0.1073 | 0.1147 | 3.9 | 4.62 +Comm | 0.014156 | 0.017907 | 0.020005 | 1.8 | 0.77 +Output | 0.071634 | 0.090599 | 0.097665 | 3.6 | 3.90 +Modify | 0.019447 | 0.024101 | 0.026277 | 1.8 | 1.04 +Other | | 0.001804 | | | 0.08 Nlocal: 1125 ave 1148 max 1097 min Histogram: 1 0 0 1 0 0 0 0 1 1 @@ -135,10 +175,10 @@ Histogram: 1 0 0 1 0 1 0 0 0 1 Neighs: 650496 ave 675112 max 631353 min Histogram: 1 0 0 1 1 0 0 0 0 1 -Total # of neighbors = 2601984 -Ave neighs/atom = 578.219 +Total # of neighbors = 2601983 +Ave neighs/atom = 578.218 Ave special neighs/atom = 2 Neighbor list builds = 4 Dangerous builds = 1 -Total wall time: 0:00:01 +Total wall time: 0:00:02 diff --git a/examples/USER/tally/log.21Aug15.stress.1 b/examples/USER/tally/log.12Jun17.stress.1 similarity index 56% rename from examples/USER/tally/log.21Aug15.stress.1 rename to examples/USER/tally/log.12Jun17.stress.1 index c20b515596..a76012487c 100644 --- a/examples/USER/tally/log.21Aug15.stress.1 +++ b/examples/USER/tally/log.12Jun17.stress.1 @@ -1,5 +1,4 @@ -LAMMPS (21 Aug 2015-ICMS) - using 1 OpenMP thread(s) per MPI task +LAMMPS (19 May 2017) units real atom_style full @@ -50,6 +49,35 @@ fix 1 all shake 0.0001 20 0 b 1 a 1 1500 = # of frozen angles fix 2 all nvt temp 300.0 300.0 100.0 +# make certain that shake constraints are satisfied +run 0 post no +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 8000 3375 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 26.54 | 26.54 | 26.54 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.358 0 -16692.358 -1289.8319 +Loop time of 2e-06 on 1 procs for 0 steps with 4500 atoms + + group one molecule 1 2 6 atoms in group one @@ -79,6 +107,7 @@ thermo 10 run 50 PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.218482 grid = 15 15 15 stencil order = 5 @@ -86,38 +115,32 @@ PPPM initialization ... estimated relative force accuracy = 9.61968e-05 using double precision FFTs 3d grid and FFT values/proc = 8000 3375 -WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75) -WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7 -> bins = 6 6 6 -Memory usage per processor = 24.631 Mbytes -Step press spa press one ref - 0 26497.547 26497.547 26497.547 -2357033.6 -2357033.6 - 10 23665.073 23665.073 23665.073 -2096057.3 -2096057.3 - 20 23338.149 23338.149 23338.149 -2034283 -2034283 - 30 25946.4 25946.4 25946.4 -2002817 -2002817 - 40 27238.349 27238.349 27238.349 -2155411.5 -2155411.5 - 50 27783.092 27783.092 27783.092 -1862190.3 -1862190.3 +WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79) +WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79) +Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes +Step c_press v_spa v_press v_one v_ref + 0 26496.811 26496.811 26496.811 -2356992.7 -2356992.7 + 10 23665.129 23665.129 23665.129 -2096059 -2096059 + 20 23338.197 23338.197 23338.197 -2034284.1 -2034284.1 + 30 25946.434 25946.434 25946.434 -2002815.3 -2002815.3 + 40 27238.374 27238.374 27238.374 -2155408.7 -2155408.7 + 50 27783.107 27783.107 27783.107 -1862191.5 -1862191.5 +Loop time of 14.2089 on 1 procs for 50 steps with 4500 atoms -Loop time of 4.15609 on 1 procs for 50 steps with 4500 atoms -100.1% CPU use with 1 MPI tasks x 1 OpenMP threads -Performance: 2.079 ns/day 11.545 hours/ns 12.031 timesteps/s +Performance: 0.608 ns/day, 39.469 hours/ns, 3.519 timesteps/s +32.0% CPU use with 1 MPI tasks x no OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.6444 | 3.6444 | 3.6444 | 0.0 | 87.69 -Bond | 0.0016105 | 0.0016105 | 0.0016105 | 0.0 | 0.04 -Kspace | 0.22345 | 0.22345 | 0.22345 | 0.0 | 5.38 -Neigh | 0.23588 | 0.23588 | 0.23588 | 0.0 | 5.68 -Comm | 0.010035 | 0.010035 | 0.010035 | 0.0 | 0.24 -Output | 0.0084085 | 0.0084085 | 0.0084085 | 0.0 | 0.20 -Modify | 0.029978 | 0.029978 | 0.029978 | 0.0 | 0.72 -Other | | 0.002368 | | | 0.06 +Pair | 12.983 | 12.983 | 12.983 | 0.0 | 91.37 +Bond | 0.002788 | 0.002788 | 0.002788 | 0.0 | 0.02 +Kspace | 0.62745 | 0.62745 | 0.62745 | 0.0 | 4.42 +Neigh | 0.49839 | 0.49839 | 0.49839 | 0.0 | 3.51 +Comm | 0.018597 | 0.018597 | 0.018597 | 0.0 | 0.13 +Output | 0.015852 | 0.015852 | 0.015852 | 0.0 | 0.11 +Modify | 0.058415 | 0.058415 | 0.058415 | 0.0 | 0.41 +Other | | 0.004126 | | | 0.03 Nlocal: 4500 ave 4500 max 4500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -132,4 +155,4 @@ Ave special neighs/atom = 2 Neighbor list builds = 3 Dangerous builds = 0 -Total wall time: 0:00:04 +Total wall time: 0:00:15 diff --git a/examples/USER/tally/log.21Aug15.stress.4 b/examples/USER/tally/log.12Jun17.stress.4 similarity index 55% rename from examples/USER/tally/log.21Aug15.stress.4 rename to examples/USER/tally/log.12Jun17.stress.4 index c681960c99..37bb60f013 100644 --- a/examples/USER/tally/log.21Aug15.stress.4 +++ b/examples/USER/tally/log.12Jun17.stress.4 @@ -1,5 +1,4 @@ -LAMMPS (21 Aug 2015-ICMS) - using 1 OpenMP thread(s) per MPI task +LAMMPS (19 May 2017) units real atom_style full @@ -50,6 +49,35 @@ fix 1 all shake 0.0001 20 0 b 1 a 1 1500 = # of frozen angles fix 2 all nvt temp 300.0 300.0 100.0 +# make certain that shake constraints are satisfied +run 0 post no +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 3380 960 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.61 | 10.61 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.358 0 -16692.358 -1289.8319 +Loop time of 4e-06 on 4 procs for 0 steps with 4500 atoms + + group one molecule 1 2 6 atoms in group one @@ -79,6 +107,7 @@ thermo 10 run 50 PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.218482 grid = 15 15 15 stencil order = 5 @@ -86,44 +115,38 @@ PPPM initialization ... estimated relative force accuracy = 9.61968e-05 using double precision FFTs 3d grid and FFT values/proc = 3380 960 -WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75) -WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7 -> bins = 6 6 6 -Memory usage per processor = 12.0691 Mbytes -Step press spa press one ref - 0 26497.547 26497.547 26497.547 -2357033.6 -2357033.6 - 10 23665.073 23665.073 23665.073 -2096057.3 -2096057.3 - 20 23338.149 23338.149 23338.149 -2034283 -2034283 - 30 25946.4 25946.4 25946.4 -2002817 -2002817 - 40 27238.349 27238.349 27238.349 -2155411.5 -2155411.5 - 50 27783.092 27783.092 27783.092 -1862190.3 -1862190.3 +WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79) +WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79) +Per MPI rank memory allocation (min/avg/max) = 15.25 | 15.26 | 15.27 Mbytes +Step c_press v_spa v_press v_one v_ref + 0 26496.811 26496.811 26496.811 -2356992.7 -2356992.7 + 10 23665.129 23665.129 23665.129 -2096059 -2096059 + 20 23338.197 23338.197 23338.197 -2034284.1 -2034284.1 + 30 25946.434 25946.434 25946.434 -2002815.3 -2002815.3 + 40 27238.374 27238.374 27238.374 -2155408.7 -2155408.7 + 50 27783.107 27783.107 27783.107 -1862191.5 -1862191.5 +Loop time of 4.32017 on 4 procs for 50 steps with 4500 atoms -Loop time of 1.17266 on 4 procs for 50 steps with 4500 atoms -100.0% CPU use with 4 MPI tasks x 1 OpenMP threads -Performance: 7.368 ns/day 3.257 hours/ns 42.638 timesteps/s +Performance: 2.000 ns/day, 12.000 hours/ns, 11.574 timesteps/s +31.8% CPU use with 4 MPI tasks x no OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.89832 | 0.93222 | 0.98611 | 3.4 | 79.50 -Bond | 0.00081754 | 0.00096095 | 0.0011327 | 0.4 | 0.08 -Kspace | 0.068058 | 0.12154 | 0.15522 | 9.4 | 10.36 -Neigh | 0.065756 | 0.065785 | 0.065824 | 0.0 | 5.61 -Comm | 0.017489 | 0.017982 | 0.018623 | 0.4 | 1.53 -Output | 0.010985 | 0.011017 | 0.011111 | 0.1 | 0.94 -Modify | 0.021429 | 0.021491 | 0.021551 | 0.0 | 1.83 -Other | | 0.001671 | | | 0.14 +Pair | 3.5816 | 3.6917 | 3.839 | 4.9 | 85.45 +Bond | 0.001579 | 0.0016563 | 0.001709 | 0.1 | 0.04 +Kspace | 0.22505 | 0.3716 | 0.48023 | 15.3 | 8.60 +Neigh | 0.14558 | 0.14568 | 0.14575 | 0.0 | 3.37 +Comm | 0.032009 | 0.03441 | 0.036274 | 0.8 | 0.80 +Output | 0.02253 | 0.023115 | 0.024844 | 0.7 | 0.54 +Modify | 0.046954 | 0.047086 | 0.047132 | 0.0 | 1.09 +Other | | 0.004935 | | | 0.11 Nlocal: 1125 ave 1154 max 1092 min Histogram: 1 0 0 0 1 0 1 0 0 1 Nghost: 12263.5 ave 12300 max 12219 min Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 650438 ave 678786 max 626279 min +Neighs: 650438 ave 678787 max 626279 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 2601750 @@ -132,4 +155,4 @@ Ave special neighs/atom = 2 Neighbor list builds = 3 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:04 diff --git a/examples/USER/tally/log.21Aug15.force.1 b/examples/USER/tally/log.21Aug15.force.1 deleted file mode 100644 index 8e7bdb9520..0000000000 --- a/examples/USER/tally/log.21Aug15.force.1 +++ /dev/null @@ -1,136 +0,0 @@ -LAMMPS (21 Aug 2015-ICMS) - using 1 OpenMP thread(s) per MPI task - -units real -atom_style full - -read_data data.spce - orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 3000 bonds - reading angles ... - 1500 angles - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -pair_style lj/cut/coul/long 12.0 12.0 -kspace_style pppm 1.0e-4 - -pair_coeff 1 1 0.15535 3.166 -pair_coeff * 2 0.0000 0.0000 - -bond_style harmonic -angle_style harmonic -dihedral_style none -improper_style none - -bond_coeff 1 1000.00 1.000 -angle_coeff 1 100.0 109.47 - -special_bonds lj/coul 0.0 0.0 1.0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 2 = max # of special neighbors - -neighbor 2.0 bin - -fix 1 all shake 0.0001 20 0 b 1 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 1500 = # of frozen angles -fix 2 all nvt temp 300.0 300.0 100.0 - -group one molecule 1 2 -6 atoms in group one - -# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords - -# compute pairwise force between two molecules and everybody -compute fpa one group/group all pair yes kspace no boundary no -# tally pairwise force between two molecules and the all molecules -compute c1 one force/tally all -# tally the force of all with all (should be zero) -compute c2 all force/tally all -# collect per atom data. only reduce over the first group. -compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] -compute red all reduce sum c_c2[1] c_c2[2] c_c2[3] -# determine magnitude of force -variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3]) -variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3]) -# round to 10**-10 absolute precision. -variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10 - -velocity all create 300 432567 dist uniform - -timestep 2.0 - -# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero -thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref c_c2 -thermo 10 - -run 50 -PPPM initialization ... - G vector (1/distance) = 0.218482 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0319435 - estimated relative force accuracy = 9.61968e-05 - using double precision FFTs - 3d grid and FFT values/proc = 8000 3375 -WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75) -WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7 -> bins = 6 6 6 -Memory usage per processor = 16.7648 Mbytes -Step fpa for c1 fpa[1] one[1] fpa[2] one[2] fpa[3] one[3] ref c2 - 0 22.732789 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878 0 0 - 10 11.736915 11.736915 11.736915 -3.3898298 -3.3898298 9.119272 9.119272 -6.5652948 -6.5652948 0 0 - 20 5.6119761 5.6119761 5.6119761 -0.60028931 -0.60028931 -4.4479886 -4.4479886 3.368876 3.368876 0 0 - 30 17.292617 17.292617 17.292617 6.1793856 6.1793856 -10.593927 -10.593927 12.190919 12.190919 0 0 - 40 18.664226 18.664226 18.664226 5.4725079 5.4725079 -6.933046 -6.933046 16.441955 16.441955 0 0 - 50 12.130282 12.130282 12.130282 -1.0321244 -1.0321244 8.0032646 8.0032646 -9.0568326 -9.0568326 0 0 - -Loop time of 4.11825 on 1 procs for 50 steps with 4500 atoms -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads -Performance: 2.098 ns/day 11.440 hours/ns 12.141 timesteps/s - -MPI task timings breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.5286 | 3.5286 | 3.5286 | 0.0 | 85.68 -Bond | 6.1274e-05 | 6.1274e-05 | 6.1274e-05 | 0.0 | 0.00 -Kspace | 0.1937 | 0.1937 | 0.1937 | 0.0 | 4.70 -Neigh | 0.31454 | 0.31454 | 0.31454 | 0.0 | 7.64 -Comm | 0.01037 | 0.01037 | 0.01037 | 0.0 | 0.25 -Output | 0.039355 | 0.039355 | 0.039355 | 0.0 | 0.96 -Modify | 0.029273 | 0.029273 | 0.029273 | 0.0 | 0.71 -Other | | 0.002351 | | | 0.06 - -Nlocal: 4500 ave 4500 max 4500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 21131 ave 21131 max 21131 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2601984 -Ave neighs/atom = 578.219 -Ave special neighs/atom = 2 -Neighbor list builds = 4 -Dangerous builds = 1 - -Total wall time: 0:00:04 diff --git a/examples/USER/tally/log.21Aug15.force.4 b/examples/USER/tally/log.21Aug15.force.4 deleted file mode 100644 index 17cbc50f02..0000000000 --- a/examples/USER/tally/log.21Aug15.force.4 +++ /dev/null @@ -1,136 +0,0 @@ -LAMMPS (21 Aug 2015-ICMS) - using 1 OpenMP thread(s) per MPI task - -units real -atom_style full - -read_data data.spce - orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 3000 bonds - reading angles ... - 1500 angles - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -pair_style lj/cut/coul/long 12.0 12.0 -kspace_style pppm 1.0e-4 - -pair_coeff 1 1 0.15535 3.166 -pair_coeff * 2 0.0000 0.0000 - -bond_style harmonic -angle_style harmonic -dihedral_style none -improper_style none - -bond_coeff 1 1000.00 1.000 -angle_coeff 1 100.0 109.47 - -special_bonds lj/coul 0.0 0.0 1.0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 2 = max # of special neighbors - -neighbor 2.0 bin - -fix 1 all shake 0.0001 20 0 b 1 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 1500 = # of frozen angles -fix 2 all nvt temp 300.0 300.0 100.0 - -group one molecule 1 2 -6 atoms in group one - -# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords - -# compute pairwise force between two molecules and everybody -compute fpa one group/group all pair yes kspace no boundary no -# tally pairwise force between two molecules and the all molecules -compute c1 one force/tally all -# tally the force of all with all (should be zero) -compute c2 all force/tally all -# collect per atom data. only reduce over the first group. -compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] -compute red all reduce sum c_c2[1] c_c2[2] c_c2[3] -# determine magnitude of force -variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3]) -variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3]) -# round to 10**-10 absolute precision. -variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10 - -velocity all create 300 432567 dist uniform - -timestep 2.0 - -# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero -thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref c_c2 -thermo 10 - -run 50 -PPPM initialization ... - G vector (1/distance) = 0.218482 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0319435 - estimated relative force accuracy = 9.61968e-05 - using double precision FFTs - 3d grid and FFT values/proc = 3380 960 -WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75) -WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7 -> bins = 6 6 6 -Memory usage per processor = 8.16441 Mbytes -Step fpa for c1 fpa[1] one[1] fpa[2] one[2] fpa[3] one[3] ref c2 - 0 22.732789 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878 0 0 - 10 11.736915 11.736915 11.736915 -3.3898298 -3.3898298 9.119272 9.119272 -6.5652948 -6.5652948 0 0 - 20 5.6119761 5.6119761 5.6119761 -0.60028931 -0.60028931 -4.4479886 -4.4479886 3.368876 3.368876 0 0 - 30 17.292617 17.292617 17.292617 6.1793856 6.1793856 -10.593927 -10.593927 12.190919 12.190919 0 0 - 40 18.664226 18.664226 18.664226 5.4725079 5.4725079 -6.933046 -6.933046 16.441955 16.441955 0 0 - 50 12.130282 12.130282 12.130282 -1.0321244 -1.0321244 8.0032646 8.0032646 -9.0568326 -9.0568326 0 0 - -Loop time of 1.13658 on 4 procs for 50 steps with 4500 atoms -100.0% CPU use with 4 MPI tasks x 1 OpenMP threads -Performance: 7.602 ns/day 3.157 hours/ns 43.991 timesteps/s - -MPI task timings breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.85795 | 0.89088 | 0.93636 | 3.0 | 78.38 -Bond | 3.4571e-05 | 4.4644e-05 | 5.4598e-05 | 0.1 | 0.00 -Kspace | 0.059847 | 0.1051 | 0.1384 | 8.9 | 9.25 -Neigh | 0.085891 | 0.085954 | 0.086 | 0.0 | 7.56 -Comm | 0.01758 | 0.018091 | 0.019178 | 0.5 | 1.59 -Output | 0.013697 | 0.013725 | 0.013805 | 0.0 | 1.21 -Modify | 0.021068 | 0.021137 | 0.021205 | 0.0 | 1.86 -Other | | 0.001656 | | | 0.15 - -Nlocal: 1125 ave 1148 max 1097 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Nghost: 12212.5 ave 12269 max 12162 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 650496 ave 675112 max 631353 min -Histogram: 1 0 0 1 1 0 0 0 0 1 - -Total # of neighbors = 2601984 -Ave neighs/atom = 578.219 -Ave special neighs/atom = 2 -Neighbor list builds = 4 -Dangerous builds = 1 - -Total wall time: 0:00:01 diff --git a/examples/neb/README b/examples/neb/README index 130d0fd2e3..0993c5fcdb 100644 --- a/examples/neb/README +++ b/examples/neb/README @@ -2,13 +2,19 @@ Run these examples as: mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1 mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2 +mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1freeend mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1 mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2 +mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1freeend mpirun -np 6 lmp_g++ -partition 3x2 -in in.neb.sivac mpirun -np 9 lmp_g++ -partition 3x3 -in in.neb.sivac + +Note that more than 4 replicas should be used for a precise estimate +of the activation energy corresponding to a transition. + If you uncomment the dump command lines in the input scripts, you can create dump files to do visualization from via Python tools: (see lammps/tools/README and lammps/tools/python/README for more info on diff --git a/examples/neb/in.neb.hop1 b/examples/neb/in.neb.hop1 index 9a3d7579f3..b874d1ba32 100644 --- a/examples/neb/in.neb.hop1 +++ b/examples/neb/in.neb.hop1 @@ -51,7 +51,7 @@ set group nebatoms type 3 group nonneb subtract all nebatoms fix 1 lower setforce 0.0 0.0 0.0 -fix 2 nebatoms neb 1.0 +fix 2 nebatoms neb 1.0 nudg_style idealpos fix 3 all enforce2d thermo 100 diff --git a/examples/neb/in.neb.hop1freeend b/examples/neb/in.neb.hop1freeend new file mode 100644 index 0000000000..fa90e9a98c --- /dev/null +++ b/examples/neb/in.neb.hop1freeend @@ -0,0 +1,56 @@ +# 2d NEB surface simulation, hop from surface to become adatom + +dimension 2 +boundary p s p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 +atom_modify map array sort 0 0.0 + +variable u uloop 20 + +# create geometry with flat surface + +lattice hex 0.9 +region box block 0 20 0 10 -0.25 0.25 + +read_data initial.hop1freeend + +# LJ potentials + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_modify shift yes + +# define groups + +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +group mobile subtract all lower +set group lower type 2 + +timestep 0.05 + +# group of NEB atoms - either block or single atom ID 412 + +region surround block 10 18 17 20 0 0 units box +group nebatoms region surround +#group nebatoms id 412 +set group nebatoms type 3 +group nonneb subtract all nebatoms + +fix 1 lower setforce 0.0 0.0 0.0 +fix 2 nebatoms neb 1.0 nudg_style idealpos freeend ini +fix 3 all enforce2d + +thermo 100 + +#dump 1 nebatoms atom 10 dump.neb.$u +#dump 2 nonneb atom 10 dump.nonneb.$u + +# run NEB for 2000 steps or to force tolerance + +min_style quickmin + +neb 0.0 0.1 1000 1000 100 final final.hop1 diff --git a/examples/neb/in.neb.hop2 b/examples/neb/in.neb.hop2 index 3eb16248e1..242de759fa 100644 --- a/examples/neb/in.neb.hop2 +++ b/examples/neb/in.neb.hop2 @@ -53,7 +53,7 @@ set group nebatoms type 3 group nonneb subtract all nebatoms fix 1 lower setforce 0.0 0.0 0.0 -fix 2 nebatoms neb 1.0 +fix 2 nebatoms neb 1.0 fix 3 all enforce2d thermo 100 diff --git a/examples/neb/in.neb.sivac b/examples/neb/in.neb.sivac index 566a380627..941d063b90 100644 --- a/examples/neb/in.neb.sivac +++ b/examples/neb/in.neb.sivac @@ -66,7 +66,7 @@ minimize 1.0e-6 1.0e-4 1000 10000 reset_timestep 0 -fix 1 all neb 1.0 +fix 1 all neb 1.0 thermo 100 diff --git a/examples/neb/initial.hop1freeend b/examples/neb/initial.hop1freeend new file mode 100644 index 0000000000..0357431fda --- /dev/null +++ b/examples/neb/initial.hop1freeend @@ -0,0 +1,860 @@ +LAMMPS data file via write_data, version 4 May 2017, timestep = 155 + +420 atoms +3 atom types + +0.0000000000000000e+00 2.2653923264628304e+01 xlo xhi +2.1918578738841410e-01 1.9932852254455714e+01 ylo yhi +-2.8317404080785380e-01 2.8317404080785380e-01 zlo zhi + +Masses + +1 1 +2 1 +3 1 + +Atoms # atomic + +1 2 0.0000000000000000e+00 2.2114806707013038e-01 0.0000000000000000e+00 0 0 0 +2 2 5.6634808161570760e-01 1.1832938184587634e+00 0.0000000000000000e+00 0 0 0 +3 2 1.1326961632314152e+00 2.2114806707013018e-01 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7b30312f59..283629d658 100644 --- a/examples/snap/Ta06A.snapparam +++ b/examples/snap/Ta06A.snapparam @@ -8,8 +8,8 @@ twojmax 6 # optional -gamma 1 rfac0 0.99363 rmin0 0 diagonalstyle 3 bzeroflag 0 +quadraticflag 0 diff --git a/examples/snap/W_2940_2017_2.snap b/examples/snap/W_2940_2017_2.snap index 51eee41a0a..04b8d58094 100644 --- a/examples/snap/W_2940_2017_2.snap +++ b/examples/snap/W_2940_2017_2.snap @@ -5,7 +5,7 @@ variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay & zbl ${zblcutinner} ${zblcutouter} & diff --git a/examples/snap/W_2940_2017_2.snapparam b/examples/snap/W_2940_2017_2.snapparam index f17961bdd7..27ab61a266 100644 --- a/examples/snap/W_2940_2017_2.snapparam +++ b/examples/snap/W_2940_2017_2.snapparam @@ -6,8 +6,8 @@ twojmax 8 # optional -gamma 1 rfac0 0.99363 rmin0 0 diagonalstyle 3 bzeroflag 0 +quadraticflag 0 diff --git a/examples/snap/W_2940_2017_2_He_JW2013.snap b/examples/snap/W_2940_2017_2_He_JW2013.snap index 45a31955b3..cb70916ec4 100644 --- a/examples/snap/W_2940_2017_2_He_JW2013.snap +++ b/examples/snap/W_2940_2017_2_He_JW2013.snap @@ -5,7 +5,7 @@ variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000 pair_coeff 1 1 zbl ${zblz} ${zblz} diff --git a/lib/gpu/Makefile.linux.mixed b/lib/gpu/Makefile.linux.mixed index 42fc8e9740..6289163ac8 100644 --- a/lib/gpu/Makefile.linux.mixed +++ b/lib/gpu/Makefile.linux.mixed @@ -8,7 +8,6 @@ EXTRAMAKE = Makefile.lammps.standard CUDA_HOME = /usr/local/cuda -CUDA_HOME = /home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37 NVCC = nvcc # Kepler CUDA diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile index 660544cfaa..ee2eb72632 100644 --- a/lib/gpu/Nvidia.makefile +++ b/lib/gpu/Nvidia.makefile @@ -63,6 +63,7 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \ $(OBJ_DIR)/lal_lj_coul_debye.o $(OBJ_DIR)/lal_lj_coul_debye_ext.o \ $(OBJ_DIR)/lal_coul_dsf.o $(OBJ_DIR)/lal_coul_dsf_ext.o \ $(OBJ_DIR)/lal_sw.o $(OBJ_DIR)/lal_sw_ext.o \ + $(OBJ_DIR)/lal_vashishta.o $(OBJ_DIR)/lal_vashishta_ext.o \ $(OBJ_DIR)/lal_beck.o $(OBJ_DIR)/lal_beck_ext.o \ $(OBJ_DIR)/lal_mie.o $(OBJ_DIR)/lal_mie_ext.o \ $(OBJ_DIR)/lal_soft.o $(OBJ_DIR)/lal_soft_ext.o \ @@ -117,6 +118,7 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \ $(OBJ_DIR)/lj_coul_debye.cubin $(OBJ_DIR)/lj_coul_debye_cubin.h \ $(OBJ_DIR)/coul_dsf.cubin $(OBJ_DIR)/coul_dsf_cubin.h \ $(OBJ_DIR)/sw.cubin $(OBJ_DIR)/sw_cubin.h \ + $(OBJ_DIR)/vashishta.cubin $(OBJ_DIR)/vashishta_cubin.h \ $(OBJ_DIR)/beck.cubin $(OBJ_DIR)/beck_cubin.h \ $(OBJ_DIR)/mie.cubin $(OBJ_DIR)/mie_cubin.h \ $(OBJ_DIR)/soft.cubin $(OBJ_DIR)/soft_cubin.h \ @@ -613,6 +615,18 @@ $(OBJ_DIR)/lal_coul_dsf.o: $(ALL_H) lal_coul_dsf.h lal_coul_dsf.cpp $(OBJ_DIR)/c $(OBJ_DIR)/lal_coul_dsf_ext.o: $(ALL_H) lal_coul_dsf.h lal_coul_dsf_ext.cpp lal_base_charge.h $(CUDR) -o $@ -c lal_coul_dsf_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/vashishta.cubin: lal_vashishta.cu lal_precision.h lal_preprocessor.h + $(CUDA) --cubin -DNV_KERNEL -o $@ lal_vashishta.cu + +$(OBJ_DIR)/vashishta_cubin.h: $(OBJ_DIR)/vashishta.cubin $(OBJ_DIR)/vashishta.cubin + $(BIN2C) -c -n vashishta $(OBJ_DIR)/vashishta.cubin > $(OBJ_DIR)/vashishta_cubin.h + +$(OBJ_DIR)/lal_vashishta.o: $(ALL_H) lal_vashishta.h lal_vashishta.cpp $(OBJ_DIR)/vashishta_cubin.h $(OBJ_DIR)/lal_base_three.o + $(CUDR) -o $@ -c lal_vashishta.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_vashishta_ext.o: $(ALL_H) lal_vashishta.h lal_vashishta_ext.cpp lal_base_three.h + $(CUDR) -o $@ -c lal_vashishta_ext.cpp -I$(OBJ_DIR) + $(OBJ_DIR)/sw.cubin: lal_sw.cu lal_precision.h lal_preprocessor.h $(CUDA) --cubin -DNV_KERNEL -o $@ lal_sw.cu diff --git a/lib/gpu/Opencl.makefile b/lib/gpu/Opencl.makefile index 4a59595313..f116508ae5 100644 --- a/lib/gpu/Opencl.makefile +++ b/lib/gpu/Opencl.makefile @@ -52,6 +52,7 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_answer.o \ $(OBJ_DIR)/lal_lj_coul_debye.o $(OBJ_DIR)/lal_lj_coul_debye_ext.o \ $(OBJ_DIR)/lal_coul_dsf.o $(OBJ_DIR)/lal_coul_dsf_ext.o \ $(OBJ_DIR)/lal_sw.o $(OBJ_DIR)/lal_sw_ext.o \ + $(OBJ_DIR)/lal_vashishta.o $(OBJ_DIR)/lal_vashishta_ext.o \ $(OBJ_DIR)/lal_beck.o $(OBJ_DIR)/lal_beck_ext.o \ $(OBJ_DIR)/lal_mie.o $(OBJ_DIR)/lal_mie_ext.o \ $(OBJ_DIR)/lal_soft.o $(OBJ_DIR)/lal_soft_ext.o \ @@ -92,7 +93,7 @@ KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \ $(OBJ_DIR)/tersoff_cl.h $(OBJ_DIR)/tersoff_zbl_cl.h \ $(OBJ_DIR)/tersoff_mod_cl.h $(OBJ_DIR)/coul_cl.h \ $(OBJ_DIR)/coul_debye_cl.h $(OBJ_DIR)/zbl_cl.h \ - $(OBJ_DIR)/lj_cubic_cl.h + $(OBJ_DIR)/lj_cubic_cl.h $(OBJ_DIR)/vashishta_cl.h OCL_EXECS = $(BIN_DIR)/ocl_get_devices @@ -450,6 +451,15 @@ $(OBJ_DIR)/lal_sw.o: $(ALL_H) lal_sw.h lal_sw.cpp $(OBJ_DIR)/sw_cl.h $(OBJ_DIR) $(OBJ_DIR)/lal_sw_ext.o: $(ALL_H) lal_sw.h lal_sw_ext.cpp lal_base_three.h $(OCL) -o $@ -c lal_sw_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/vashishta_cl.h: lal_vashishta.cu $(PRE1_H) + $(BSH) ./geryon/file_to_cstr.sh vashishta $(PRE1_H) lal_vashishta.cu $(OBJ_DIR)/vashishta_cl.h; + +$(OBJ_DIR)/lal_vashishta.o: $(ALL_H) lal_vashishta.h lal_vashishta.cpp $(OBJ_DIR)/vashishta_cl.h $(OBJ_DIR)/vashishta_cl.h $(OBJ_DIR)/lal_base_three.o + $(OCL) -o $@ -c lal_vashishta.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_vashishta_ext.o: $(ALL_H) lal_vashishta.h lal_vashishta_ext.cpp lal_base_three.h + $(OCL) -o $@ -c lal_vashishta_ext.cpp -I$(OBJ_DIR) + $(OBJ_DIR)/beck_cl.h: lal_beck.cu $(PRE1_H) $(BSH) ./geryon/file_to_cstr.sh beck $(PRE1_H) lal_beck.cu $(OBJ_DIR)/beck_cl.h; diff --git a/lib/gpu/lal_vashishta.cpp b/lib/gpu/lal_vashishta.cpp new file mode 100644 index 0000000000..96537e65d3 --- /dev/null +++ b/lib/gpu/lal_vashishta.cpp @@ -0,0 +1,283 @@ +/*************************************************************************** + vashishta.cpp + ------------------- + Anders Hafreager (UiO) + + Class for acceleration of the vashishta pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : Mon June 12, 2017 + email : andershaf@gmail.com + ***************************************************************************/ + +#if defined(USE_OPENCL) +#include "vashishta_cl.h" +#elif defined(USE_CUDART) +const char *vashishta=0; +#else +#include "vashishta_cubin.h" +#endif + +#include "lal_vashishta.h" +#include +using namespace LAMMPS_AL; +#define VashishtaT Vashishta + +extern Device device; + +template +VashishtaT::Vashishta() : BaseThree(), _allocated(false) { +} + +template +VashishtaT::~Vashishta() { + clear(); +} + +template +int VashishtaT::bytes_per_atom(const int max_nbors) const { + return this->bytes_per_atom_atomic(max_nbors); +} + +template +int VashishtaT::init(const int ntypes, const int nlocal, const int nall, const int max_nbors, + const double cell_size, const double gpu_split, FILE *_screen, + int* host_map, const int nelements, int*** host_elem2param, const int nparams, + const double* cutsq, const double* r0, + const double* gamma, const double* eta, + const double* lam1inv, const double* lam4inv, + const double* zizj, const double* mbigd, + const double* dvrc, const double* big6w, + const double* heta, const double* bigh, + const double* bigw, const double* c0, + const double* costheta, const double* bigb, + const double* big2b, const double* bigc) +{ + int success; + success=this->init_three(nlocal,nall,max_nbors,0,cell_size,gpu_split, + _screen,vashishta,"k_vashishta","k_vashishta_three_center", + "k_vashishta_three_end"); + if (success!=0) + return success; + + // If atom type constants fit in shared memory use fast kernel + int lj_types=ntypes; + shared_types=false; + int max_shared_types=this->device->max_shared_types(); + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + shared_types=true; + } + _lj_types=lj_types; + + _nparams = nparams; + _nelements = nelements; + + UCL_H_Vec dview(nparams,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; iucl_device),UCL_READ_ONLY); + + for (int i=0; i(eta[i]); + dview[i].y=static_cast(lam1inv[i]); + dview[i].z=static_cast(lam4inv[i]); + dview[i].w=static_cast(zizj[i]); + } + + ucl_copy(param1,dview,false); + param1_tex.get_texture(*(this->pair_program),"param1_tex"); + param1_tex.bind_float(param1,4); + + param2.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY); + + for (int i=0; i(mbigd[i]); + dview[i].y=static_cast(dvrc[i]); + dview[i].z=static_cast(big6w[i]); + dview[i].w=static_cast(heta[i]); + } + + ucl_copy(param2,dview,false); + param2_tex.get_texture(*(this->pair_program),"param2_tex"); + param2_tex.bind_float(param2,4); + + param3.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY); + + for (int i=0; i(bigh[i]); + dview[i].y=static_cast(bigw[i]); + dview[i].z=static_cast(dvrc[i]); + dview[i].w=static_cast(c0[i]); + } + + ucl_copy(param3,dview,false); + param3_tex.get_texture(*(this->pair_program),"param3_tex"); + param3_tex.bind_float(param3,4); + + param4.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY); + + for (int i=0; i(r0sq); + dview[i].y=static_cast(gamma[i]); + dview[i].z=static_cast(cutsq[i]); + dview[i].w=static_cast(r0[i]); + } + + ucl_copy(param4,dview,false); + param4_tex.get_texture(*(this->pair_program),"param4_tex"); + param4_tex.bind_float(param4,4); + + param5.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY); + + for (int i=0; i(bigc[i]); + dview[i].y=static_cast(costheta[i]); + dview[i].z=static_cast(bigb[i]); + dview[i].w=static_cast(big2b[i]); + } + + ucl_copy(param5,dview,false); + param5_tex.get_texture(*(this->pair_program),"param5_tex"); + param5_tex.bind_float(param5,4); + + UCL_H_Vec dview_elem2param(nelements*nelements*nelements, + *(this->ucl_device), UCL_WRITE_ONLY); + + elem2param.alloc(nelements*nelements*nelements,*(this->ucl_device), + UCL_READ_ONLY); + + for (int i = 0; i < nelements; i++) + for (int j = 0; j < nelements; j++) + for (int k = 0; k < nelements; k++) { + int idx = i*nelements*nelements+j*nelements+k; + dview_elem2param[idx] = host_elem2param[i][j][k]; + } + + ucl_copy(elem2param,dview_elem2param,false); + + UCL_H_Vec dview_map(lj_types, *(this->ucl_device), UCL_WRITE_ONLY); + for (int i = 0; i < ntypes; i++) + dview_map[i] = host_map[i]; + + map.alloc(lj_types,*(this->ucl_device), UCL_READ_ONLY); + ucl_copy(map,dview_map,false); + + _allocated=true; + this->_max_bytes=param1.row_bytes()+param2.row_bytes()+param3.row_bytes()+param4.row_bytes()+param5.row_bytes()+ + map.row_bytes()+elem2param.row_bytes(); + return 0; +} + +template +void VashishtaT::clear() { + if (!_allocated) + return; + _allocated=false; + + param1.clear(); + param2.clear(); + param3.clear(); + param4.clear(); + param5.clear(); + map.clear(); + elem2param.clear(); + this->clear_atomic(); +} + +template +double VashishtaT::host_memory_usage() const { + return this->host_memory_usage_atomic()+sizeof(Vashishta); +} + +#define KTHREADS this->_threads_per_atom +#define JTHREADS this->_threads_per_atom +// --------------------------------------------------------------------------- +// Calculate energies, forces, and torques +// --------------------------------------------------------------------------- +template +void VashishtaT::loop(const bool _eflag, const bool _vflag, const int evatom) { + // Compute the block size and grid size to keep all cores busy + int BX=this->block_pair(); + int eflag, vflag; + if (_eflag) + eflag=1; + else + eflag=0; + + if (_vflag) + vflag=1; + else + vflag=0; + + int GX=static_cast(ceil(static_cast(this->ans->inum())/ + (BX/this->_threads_per_atom))); + + // this->_nbor_data == nbor->dev_packed for gpu_nbor == 0 and tpa > 1 + // this->_nbor_data == nbor->dev_nbor for gpu_nbor == 1 or tpa == 1 + int ainum=this->ans->inum(); + int nbor_pitch=this->nbor->nbor_pitch(); + this->time_pair.start(); + + this->k_pair.set_size(GX,BX); + this->k_pair.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, + &map, &elem2param, &_nelements, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->ans->force, &this->ans->engv, + &eflag, &vflag, &ainum, &nbor_pitch, + &this->_threads_per_atom); + + BX=this->block_size(); + GX=static_cast(ceil(static_cast(this->ans->inum())/ + (BX/(KTHREADS*JTHREADS)))); + + this->k_three_center.set_size(GX,BX); + this->k_three_center.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, + &map, &elem2param, &_nelements, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum, + &nbor_pitch, &this->_threads_per_atom, &evatom); + Answer *end_ans; + #ifdef THREE_CONCURRENT + end_ans=this->ans2; + #else + end_ans=this->ans; + #endif + if (evatom!=0) { + + this->k_three_end_vatom.set_size(GX,BX); + this->k_three_end_vatom.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, + &map, &elem2param, &_nelements, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->nbor->dev_acc, + &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, + &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); + } else { + + this->k_three_end.set_size(GX,BX); + this->k_three_end.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, + &map, &elem2param, &_nelements, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->nbor->dev_acc, + &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, + &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); + } + + this->time_pair.stop(); +} + +template class Vashishta; + diff --git a/lib/gpu/lal_vashishta.cu b/lib/gpu/lal_vashishta.cu new file mode 100644 index 0000000000..caa3c03613 --- /dev/null +++ b/lib/gpu/lal_vashishta.cu @@ -0,0 +1,744 @@ +// ************************************************************************** +// vashishta.cu +// ------------------- +// Anders Hafreager (UiO) +// +// Device code for acceleration of the vashishta pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : Mon June 12, 2017 +// email : andershaf@gmail.com +// ***************************************************************************/ + +#ifdef NV_KERNEL +#include "lal_aux_fun1.h" + +#ifndef _DOUBLE_DOUBLE +texture pos_tex; +texture param1_tex; +texture param2_tex; +texture param3_tex; +texture param4_tex; +texture param5_tex; +#else +texture pos_tex; +texture param1_tex; +texture param2_tex; +texture param3_tex; +texture param4_tex; +texture param5_tex; +#endif + +#else +#define pos_tex x_ +#define param1_tex param1 +#define param2_tex param2 +#define param3_tex param3 +#define param4_tex param4 +#define param5_tex param5 +#endif + +#define THIRD (numtyp)0.66666666666666666667 + +//#define THREE_CONCURRENT + +#if (ARCH < 300) + +#define store_answers_p(f, energy, virial, ii, inum, tid, t_per_atom, offset, \ + eflag, vflag, ans, engv) \ + if (t_per_atom>1) { \ + __local acctyp red_acc[6][BLOCK_ELLIPSE]; \ + red_acc[0][tid]=f.x; \ + red_acc[1][tid]=f.y; \ + red_acc[2][tid]=f.z; \ + red_acc[3][tid]=energy; \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + if (offset < s) { \ + for (int r=0; r<4; r++) \ + red_acc[r][tid] += red_acc[r][tid+s]; \ + } \ + } \ + f.x=red_acc[0][tid]; \ + f.y=red_acc[1][tid]; \ + f.z=red_acc[2][tid]; \ + energy=red_acc[3][tid]; \ + if (vflag>0) { \ + for (int r=0; r<6; r++) \ + red_acc[r][tid]=virial[r]; \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + if (offset < s) { \ + for (int r=0; r<6; r++) \ + red_acc[r][tid] += red_acc[r][tid+s]; \ + } \ + } \ + for (int r=0; r<6; r++) \ + virial[r]=red_acc[r][tid]; \ + } \ + } \ + if (offset==0) { \ + int ei=ii; \ + if (eflag>0) { \ + engv[ei]+=energy*(acctyp)0.5; \ + ei+=inum; \ + } \ + if (vflag>0) { \ + for (int i=0; i<6; i++) { \ + engv[ei]+=virial[i]*(acctyp)0.5; \ + ei+=inum; \ + } \ + } \ + acctyp4 old=ans[ii]; \ + old.x+=f.x; \ + old.y+=f.y; \ + old.z+=f.z; \ + ans[ii]=old; \ + } + +#else + +#define store_answers_p(f, energy, virial, ii, inum, tid, t_per_atom, offset, \ + eflag, vflag, ans, engv) \ + if (t_per_atom>1) { \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + f.x += shfl_xor(f.x, s, t_per_atom); \ + f.y += shfl_xor(f.y, s, t_per_atom); \ + f.z += shfl_xor(f.z, s, t_per_atom); \ + energy += shfl_xor(energy, s, t_per_atom); \ + } \ + if (vflag>0) { \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + for (int r=0; r<6; r++) \ + virial[r] += shfl_xor(virial[r], s, t_per_atom); \ + } \ + } \ + } \ + if (offset==0) { \ + int ei=ii; \ + if (eflag>0) { \ + engv[ei]+=energy*(acctyp)0.5; \ + ei+=inum; \ + } \ + if (vflag>0) { \ + for (int i=0; i<6; i++) { \ + engv[ei]+=virial[i]*(acctyp)0.5; \ + ei+=inum; \ + } \ + } \ + acctyp4 old=ans[ii]; \ + old.x+=f.x; \ + old.y+=f.y; \ + old.z+=f.z; \ + ans[ii]=old; \ + } + +#endif + + +__kernel void k_vashishta(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict param1, + const __global numtyp4 *restrict param2, + const __global numtyp4 *restrict param3, + const __global numtyp4 *restrict param4, + const __global numtyp4 *restrict param5, + const __global int *restrict map, + const __global int *restrict elem2param, + const int nelements, + const __global int * dev_nbor, + const __global int * dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, const int t_per_atom) { + __local int n_stride; + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + acctyp energy=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + __syncthreads(); + + if (ii0) + energy += (param3_bigh*reta+vc2-vc3-param3_bigw*r6inv-r*param3_dvrc+param3_c0); + + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + } // for nbor + + store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, + ans,engv); + } // if ii + +} + +#define threebody(delr1x, delr1y, delr1z, eflag, energy) \ +{ \ + numtyp r1 = ucl_sqrt(rsq1); \ + numtyp rinvsq1 = ucl_recip(rsq1); \ + numtyp rainv1 = ucl_recip(r1 - param_r0_ij); \ + numtyp gsrainv1 = param_gamma_ij * rainv1; \ + numtyp gsrainvsq1 = gsrainv1*rainv1/r1; \ + numtyp expgsrainv1 = ucl_exp(gsrainv1); \ + \ + numtyp r2 = ucl_sqrt(rsq2); \ + numtyp rinvsq2 = ucl_recip(rsq2); \ + numtyp rainv2 = ucl_recip(r2 - param_r0_ik); \ + numtyp gsrainv2 = param_gamma_ik * rainv2; \ + numtyp gsrainvsq2 = gsrainv2*rainv2/r2; \ + numtyp expgsrainv2 = ucl_exp(gsrainv2); \ + \ + numtyp rinv12 = ucl_recip(r1*r2); \ + numtyp cs = (delr1x*delr2x + delr1y*delr2y + delr1z*delr2z) * rinv12; \ + numtyp delcs = cs - param_costheta_ijk; \ + numtyp delcssq = delcs*delcs; \ + numtyp pcsinv = param_bigc_ijk*delcssq+1.0; \ + numtyp pcsinvsq = pcsinv*pcsinv; \ + numtyp pcs = delcssq/pcsinv; \ + \ + numtyp facexp = expgsrainv1*expgsrainv2; \ + \ + numtyp facrad = param_bigb_ijk * facexp*pcs; \ + numtyp frad1 = facrad*gsrainvsq1; \ + numtyp frad2 = facrad*gsrainvsq2; \ + numtyp facang = param_big2b_ijk * facexp*delcs/pcsinvsq; \ + numtyp facang12 = rinv12*facang; \ + numtyp csfacang = cs*facang; \ + numtyp csfac1 = rinvsq1*csfacang; \ + \ + fjx = delr1x*(frad1+csfac1)-delr2x*facang12; \ + fjy = delr1y*(frad1+csfac1)-delr2y*facang12; \ + fjz = delr1z*(frad1+csfac1)-delr2z*facang12; \ + \ + numtyp csfac2 = rinvsq2*csfacang; \ + \ + fkx = delr2x*(frad2+csfac2)-delr1x*facang12; \ + fky = delr2y*(frad2+csfac2)-delr1y*facang12; \ + fkz = delr2z*(frad2+csfac2)-delr1z*facang12; \ + \ + if (eflag>0) \ + energy+=facrad; \ + if (vflag>0) { \ + virial[0] += delr1x*fjx + delr2x*fkx; \ + virial[1] += delr1y*fjy + delr2y*fky; \ + virial[2] += delr1z*fjz + delr2z*fkz; \ + virial[3] += delr1x*fjy + delr2x*fky; \ + virial[4] += delr1x*fjz + delr2x*fkz; \ + virial[5] += delr1y*fjz + delr2y*fkz; \ + } \ +} + +#define threebody_half(delr1x, delr1y, delr1z) \ +{ \ + numtyp r1 = ucl_sqrt(rsq1); \ + numtyp rinvsq1 = ucl_recip(rsq1); \ + numtyp rainv1 = ucl_recip(r1 - param_r0_ij); \ + numtyp gsrainv1 = param_gamma_ij * rainv1; \ + numtyp gsrainvsq1 = gsrainv1*rainv1/r1; \ + numtyp expgsrainv1 = ucl_exp(gsrainv1); \ + \ + numtyp r2 = ucl_sqrt(rsq2); \ + numtyp rainv2 = ucl_recip(r2 - param_r0_ik); \ + numtyp gsrainv2 = param_gamma_ik * rainv2; \ + numtyp expgsrainv2 = ucl_exp(gsrainv2); \ + \ + numtyp rinv12 = ucl_recip(r1*r2); \ + numtyp cs = (delr1x*delr2x + delr1y*delr2y + delr1z*delr2z) * rinv12; \ + numtyp delcs = cs - param_costheta_ijk; \ + numtyp delcssq = delcs*delcs; \ + numtyp pcsinv = param_bigc_ijk*delcssq+1.0; \ + numtyp pcsinvsq = pcsinv*pcsinv; \ + numtyp pcs = delcssq/pcsinv; \ + \ + numtyp facexp = expgsrainv1*expgsrainv2; \ + \ + numtyp facrad = param_bigb_ijk * facexp*pcs; \ + numtyp frad1 = facrad*gsrainvsq1; \ + numtyp facang = param_big2b_ijk * facexp*delcs/pcsinvsq; \ + numtyp facang12 = rinv12*facang; \ + numtyp csfacang = cs*facang; \ + numtyp csfac1 = rinvsq1*csfacang; \ + \ + fjx = delr1x*(frad1+csfac1)-delr2x*facang12; \ + fjy = delr1y*(frad1+csfac1)-delr2y*facang12; \ + fjz = delr1z*(frad1+csfac1)-delr2z*facang12; \ +} + +__kernel void k_vashishta_three_center(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict param1, + const __global numtyp4 *restrict param2, + const __global numtyp4 *restrict param3, + const __global numtyp4 *restrict param4, + const __global numtyp4 *restrict param5, + const __global int *restrict map, + const __global int *restrict elem2param, + const int nelements, + const __global int * dev_nbor, + const __global int * dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, + const int inum, const int nbor_pitch, + const int t_per_atom, const int evatom) { + __local int tpa_sq, n_stride; + tpa_sq=fast_mul(t_per_atom,t_per_atom); + numtyp param_gamma_ij, param_r0sq_ij, param_r0_ij, param_gamma_ik, param_r0sq_ik, param_r0_ik; + numtyp param_costheta_ijk, param_bigc_ijk, param_bigb_ijk, param_big2b_ijk; + + int tid, ii, offset; + atom_info(tpa_sq,ii,tid,offset); + + acctyp energy=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + __syncthreads(); + + if (ii param_r0sq_ij) continue; + param_gamma_ij=param4_ijparam.y; + param_r0_ij=param4_ijparam.w; + + int nbor_k=nbor_j-offset_j+offset_k; + if (nbor_k<=nbor_j) + nbor_k+=n_stride; + + for ( ; nbor_k param_r0sq_ij) continue; + + param_gamma_ij=param4_ijparam.y; + param_r0_ij = param4_ijparam.w; + + int nbor_k,numk; + if (dev_nbor==dev_packed) { + if (gpu_nbor) nbor_k=j+nbor_pitch; + else nbor_k=dev_acc[j]+nbor_pitch; + numk=dev_nbor[nbor_k]; + nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); + k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); + nbor_k+=offset_k; + } else { + nbor_k=dev_acc[j]+nbor_pitch; + numk=dev_nbor[nbor_k]; + nbor_k+=nbor_pitch; + nbor_k=dev_nbor[nbor_k]; + k_end=nbor_k+numk; + nbor_k+=offset_k; + } + + for ( ; nbor_k param_r0sq_ij) continue; + + param_gamma_ij=param4_ijparam.y; + param_r0_ij=param4_ijparam.w; + + int nbor_k,numk; + if (dev_nbor==dev_packed) { + if (gpu_nbor) nbor_k=j+nbor_pitch; + else nbor_k=dev_acc[j]+nbor_pitch; + numk=dev_nbor[nbor_k]; + nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); + k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); + nbor_k+=offset_k; + } else { + nbor_k=dev_acc[j]+nbor_pitch; + numk=dev_nbor[nbor_k]; + nbor_k+=nbor_pitch; + nbor_k=dev_nbor[nbor_k]; + k_end=nbor_k+numk; + nbor_k+=offset_k; + } + + for ( ; nbor_k +class Vashishta : public BaseThree { + public: + Vashishta(); + ~Vashishta(); + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successfull + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, const int nlocal, const int nall, const int max_nbors, + const double cell_size, const double gpu_split, FILE *screen, + int* host_map, const int nelements, int*** host_elem2param, const int nparams, + const double* cutsq, const double* r0, + const double* gamma, const double* eta, + const double* lam1inv, const double* lam4inv, + const double* zizj, const double* mbigd, + const double* dvrc, const double* big6w, + const double* heta, const double* bigh, + const double* bigw, const double* c0, + const double* costheta, const double* bigb, + const double* big2b, const double* bigc); + + /// Clear all host and device data + /** \note This is called at the beginning of the init() routine **/ + void clear(); + + /// Returns memory usage on device per atom + int bytes_per_atom(const int max_nbors) const; + + /// Total host memory used by library for pair style + double host_memory_usage() const; + + // --------------------------- TYPE DATA -------------------------- + + /// If atom type constants fit in shared memory, use fast kernels + bool shared_types; + + /// Number of atom types + int _lj_types; + + /// param1.x = eta, param1.y = lam1inv, param1.z = lam4inv, param1.w = zizj + UCL_D_Vec param1; + /// param2.x = mbigd, param2.y = dvrc, param2.z = big6w, param2.w = heta + UCL_D_Vec param2; + /// param3.x = bigh, param3.y = bigw, param3.z = dvrc, param3.w = c0 + UCL_D_Vec param3; + /// param4.x = r0sq, param4.y = gamma, param4.z = cutsq, param4.w = r0 + UCL_D_Vec param4; + /// param5.x = bigc, param5.y = costheta, param5.z = bigb, param5.w = big2b + UCL_D_Vec param5; + + UCL_D_Vec elem2param; + UCL_D_Vec map; + int _nparams,_nelements; + + UCL_Texture param1_tex, param2_tex, param3_tex, param4_tex, param5_tex; + + private: + bool _allocated; + void loop(const bool _eflag, const bool _vflag, const int evatom); + +}; + +} + +#endif + diff --git a/lib/gpu/lal_vashishta_ext.cpp b/lib/gpu/lal_vashishta_ext.cpp new file mode 100644 index 0000000000..22f530a7ed --- /dev/null +++ b/lib/gpu/lal_vashishta_ext.cpp @@ -0,0 +1,134 @@ +/*************************************************************************** + vashishta_ext.cpp + ------------------- + Anders Hafreager (UiO) + + Class for acceleration of the vashishta pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : Mon June 12, 2017 + email : andershaf@gmail.com + ***************************************************************************/ + +#include +#include +#include + +#include "lal_vashishta.h" +using namespace LAMMPS_AL; + +static Vashishta VashishtaMF; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int vashishta_gpu_init(const int ntypes, const int inum, const int nall, const int max_nbors, + const double cell_size, int &gpu_mode, FILE *screen, + int* host_map, const int nelements, int*** host_elem2param, const int nparams, + const double* cutsq, const double* r0, + const double* gamma, const double* eta, + const double* lam1inv, const double* lam4inv, + const double* zizj, const double* mbigd, + const double* dvrc, const double* big6w, + const double* heta, const double* bigh, + const double* bigw, const double* c0, + const double* costheta, const double* bigb, + const double* big2b, const double* bigc) { + VashishtaMF.clear(); + gpu_mode=VashishtaMF.device->gpu_mode(); + double gpu_split=VashishtaMF.device->particle_split(); + int first_gpu=VashishtaMF.device->first_device(); + int last_gpu=VashishtaMF.device->last_device(); + int world_me=VashishtaMF.device->world_me(); + int gpu_rank=VashishtaMF.device->gpu_rank(); + int procs_per_gpu=VashishtaMF.device->procs_per_gpu(); + + // disable host/device split for now + if (gpu_split != 1.0) + return -8; + + VashishtaMF.device->init_message(screen,"vashishta/gpu",first_gpu,last_gpu); + + bool message=false; + if (VashishtaMF.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=VashishtaMF.init(ntypes, inum, nall, 500, cell_size, gpu_split, screen, + host_map, nelements, host_elem2param, nparams, + cutsq, r0, gamma, eta, lam1inv, + lam4inv, zizj, mbigd, dvrc, big6w, heta, bigh, bigw, + c0, costheta, bigb, big2b, bigc); + + VashishtaMF.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; igpu_barrier(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + VashishtaMF.estimate_gpu_overhead(); + + return init_ok; +} + +void vashishta_gpu_clear() { + VashishtaMF.clear(); +} + +int ** vashishta_gpu_compute_n(const int ago, const int inum_full, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success) { + return VashishtaMF.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success); +} + +void vashishta_gpu_compute(const int ago, const int nlocal, const int nall, + const int nlist, double **host_x, int *host_type, + int *ilist, int *numj, int **firstneigh, const bool eflag, + const bool vflag, const bool eatom, const bool vatom, + int &host_start, const double cpu_time, bool &success) { + VashishtaMF.compute(ago,nlocal,nall,nlist,host_x,host_type,ilist,numj, + firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success); +} + +double vashishta_gpu_bytes() { + return VashishtaMF.host_memory_usage(); +} + + diff --git a/lib/kokkos/CHANGELOG.md b/lib/kokkos/CHANGELOG.md index c6fe991b97..acb54ff22f 100644 --- a/lib/kokkos/CHANGELOG.md +++ b/lib/kokkos/CHANGELOG.md @@ -1,5 +1,53 @@ # Change Log + +## [2.03.05](https://github.com/kokkos/kokkos/tree/2.03.05) (2017-05-27) +[Full Changelog](https://github.com/kokkos/kokkos/compare/2.03.00...2.03.05) + +**Implemented enhancements:** + +- Harmonize Custom Reductions over nesting levels [\#802](https://github.com/kokkos/kokkos/issues/802) +- Prevent users directly including KokkosCore\_config.h [\#815](https://github.com/kokkos/kokkos/issues/815) +- DualView aborts on concurrent host/device modify \(in debug mode\) [\#814](https://github.com/kokkos/kokkos/issues/814) +- Abort when running on a NVIDIA CC5.0 or higher architecture with code compiled for CC \< 5.0 [\#813](https://github.com/kokkos/kokkos/issues/813) +- Add "name" function to ExecSpaces [\#806](https://github.com/kokkos/kokkos/issues/806) +- Allow null Future in task spawn dependences [\#795](https://github.com/kokkos/kokkos/issues/795) +- Add Unit Tests for Kokkos::complex [\#785](https://github.com/kokkos/kokkos/issues/785) +- Add pow function for Kokkos::complex [\#784](https://github.com/kokkos/kokkos/issues/784) +- Square root of a complex [\#729](https://github.com/kokkos/kokkos/issues/729) +- Command line processing of --threads argument prevents users from having any commandline arguments starting with --threads [\#760](https://github.com/kokkos/kokkos/issues/760) +- Protected deprecated API with appropriate macro [\#756](https://github.com/kokkos/kokkos/issues/756) +- Allow task scheduler memory pool to be used by tasks [\#747](https://github.com/kokkos/kokkos/issues/747) +- View bounds checking on host-side performance: constructing a std::string [\#723](https://github.com/kokkos/kokkos/issues/723) +- Add check for AppleClang as compiler distinct from check for Clang. [\#705](https://github.com/kokkos/kokkos/issues/705) +- Uninclude source files for specific configurations to prevent link warning. [\#701](https://github.com/kokkos/kokkos/issues/701) +- Add --small option to snapshot script [\#697](https://github.com/kokkos/kokkos/issues/697) +- CMake Standalone Support [\#674](https://github.com/kokkos/kokkos/issues/674) +- CMake build unit test and install [\#808](https://github.com/kokkos/kokkos/issues/808) +- CMake: Fix having kokkos as a subdirectory in a pure cmake project [\#629](https://github.com/kokkos/kokkos/issues/629) +- Tribits macro assumes build directory is in top level source directory [\#654](https://github.com/kokkos/kokkos/issues/654) +- Use bin/nvcc\_wrapper, not config/nvcc\_wrapper [\#562](https://github.com/kokkos/kokkos/issues/562) +- Allow MemoryPool::allocate\(\) to be called from multiple threads per warp. [\#487](https://github.com/kokkos/kokkos/issues/487) +- Allow MemoryPool::allocate\\(\\) to be called from multiple threads per warp. [\#487](https://github.com/kokkos/kokkos/issues/487) +- Move OpenMP 4.5 OpenMPTarget backend into Develop [\#456](https://github.com/kokkos/kokkos/issues/456) +- Testing on ARM testbed [\#288](https://github.com/kokkos/kokkos/issues/288) + +**Fixed bugs:** + +- Fix label in OpenMP parallel\_reduce verify\_initialized [\#834](https://github.com/kokkos/kokkos/issues/834) +- TeamScratch Level 1 on Cuda hangs [\#820](https://github.com/kokkos/kokkos/issues/820) +- \[bug\] memory pool. [\#786](https://github.com/kokkos/kokkos/issues/786) +- Some Reduction Tests fail on Intel 18 with aggressive vectorization on [\#774](https://github.com/kokkos/kokkos/issues/774) +- Error copying dynamic view on copy of memory pool [\#773](https://github.com/kokkos/kokkos/issues/773) +- CUDA stack overflow with TaskDAG test [\#758](https://github.com/kokkos/kokkos/issues/758) +- ThreadVectorRange Customized Reduction Bug [\#739](https://github.com/kokkos/kokkos/issues/739) +- set\_scratch\_size overflows [\#726](https://github.com/kokkos/kokkos/issues/726) +- Get wrong results for compiler checks in Makefile on OS X. [\#706](https://github.com/kokkos/kokkos/issues/706) +- Fix check if multiple host architectures enabled. [\#702](https://github.com/kokkos/kokkos/issues/702) +- Threads Backend Does not Pass on Cray Compilers [\#609](https://github.com/kokkos/kokkos/issues/609) +- Rare bug in memory pool where allocation can finish on superblock in empty state [\#452](https://github.com/kokkos/kokkos/issues/452) +- LDFLAGS in core/unit\_test/Makefile: potential "undefined reference" to pthread lib [\#148](https://github.com/kokkos/kokkos/issues/148) + ## [2.03.00](https://github.com/kokkos/kokkos/tree/2.03.00) (2017-04-25) [Full Changelog](https://github.com/kokkos/kokkos/compare/2.02.15...2.03.00) diff --git a/lib/kokkos/CMakeLists.txt b/lib/kokkos/CMakeLists.txt index 1c820660ae..b2771ed527 100644 --- a/lib/kokkos/CMakeLists.txt +++ b/lib/kokkos/CMakeLists.txt @@ -5,11 +5,12 @@ ELSE() ENDIF() IF(NOT KOKKOS_HAS_TRILINOS) - CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11 FATAL_ERROR) - INCLUDE(cmake/tribits.cmake) - SET(CMAKE_CXX_STANDARD 11) -ENDIF() + cmake_minimum_required(VERSION 3.1 FATAL_ERROR) + project(Kokkos CXX) + INCLUDE(cmake/kokkos.cmake) +ELSE() +#------------------------------------------------------------------------------ # # A) Forward delcare the package so that certain options are also defined for # subpackages @@ -17,14 +18,13 @@ ENDIF() TRIBITS_PACKAGE_DECL(Kokkos) # ENABLE_SHADOWING_WARNINGS) + #------------------------------------------------------------------------------ # # B) Define the common options for Kokkos first so they can be used by # subpackages as well. # - - # mfh 01 Aug 2016: See Issue #61: # # https://github.com/kokkos/kokkos/issues/61 @@ -83,10 +83,10 @@ TRIBITS_ADD_OPTION_AND_DEFINE( ) ASSERT_DEFINED(TPL_ENABLE_Pthread) -IF (Kokkos_ENABLE_Pthread AND NOT TPL_ENABLE_Pthread) +IF(Kokkos_ENABLE_Pthread AND NOT TPL_ENABLE_Pthread) MESSAGE(FATAL_ERROR "You set Kokkos_ENABLE_Pthread=ON, but Trilinos' support for Pthread(s) is not enabled (TPL_ENABLE_Pthread=OFF). This is not allowed. Please enable Pthreads in Trilinos before attempting to enable Kokkos' support for Pthreads.") -ENDIF () -IF (NOT TPL_ENABLE_Pthread) +ENDIF() +IF(NOT TPL_ENABLE_Pthread) ADD_DEFINITIONS(-DGTEST_HAS_PTHREAD=0) ENDIF() @@ -98,12 +98,13 @@ TRIBITS_ADD_OPTION_AND_DEFINE( ) TRIBITS_ADD_OPTION_AND_DEFINE( - Kokkos_ENABLE_Qthreads + Kokkos_ENABLE_QTHREAD KOKKOS_HAVE_QTHREADS "Enable Qthreads support in Kokkos." - "${TPL_ENABLE_QTHREADS}" + "${TPL_ENABLE_QTHREAD}" ) +# TODO: No longer an option in Kokkos. Needs to be removed. TRIBITS_ADD_OPTION_AND_DEFINE( Kokkos_ENABLE_CXX11 KOKKOS_HAVE_CXX11 @@ -118,6 +119,7 @@ TRIBITS_ADD_OPTION_AND_DEFINE( "${TPL_ENABLE_HWLOC}" ) +# TODO: This is currently not used in Kokkos. Should it be removed? TRIBITS_ADD_OPTION_AND_DEFINE( Kokkos_ENABLE_MPI KOKKOS_HAVE_MPI @@ -154,13 +156,27 @@ TRIBITS_ADD_OPTION_AND_DEFINE( "${Kokkos_ENABLE_Debug_Bounds_Check_DEFAULT}" ) +TRIBITS_ADD_OPTION_AND_DEFINE( + Kokkos_ENABLE_Debug_DualView_Modify_Check + KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK + "Enable abort when Kokkos::DualView modified on host and device without sync." + "${Kokkos_ENABLE_DEBUG}" + ) + TRIBITS_ADD_OPTION_AND_DEFINE( Kokkos_ENABLE_Profiling - KOKKOS_ENABLE_PROFILING_INTERNAL + KOKKOS_ENABLE_PROFILING "Enable KokkosP profiling support for kernel data collections." "${TPL_ENABLE_DLlib}" ) +TRIBITS_ADD_OPTION_AND_DEFINE( + Kokkos_ENABLE_Profiling_Load_Print + KOKKOS_ENABLE_PROFILING_LOAD_PRINT + "Print to standard output which profiling library was loaded." + OFF + ) + # placeholder for future device... TRIBITS_ADD_OPTION_AND_DEFINE( Kokkos_ENABLE_Winthread @@ -169,6 +185,7 @@ TRIBITS_ADD_OPTION_AND_DEFINE( "${TPL_ENABLE_Winthread}" ) +# TODO: No longer an option in Kokkos. Needs to be removed. # use new/old View TRIBITS_ADD_OPTION_AND_DEFINE( Kokkos_USING_DEPRECATED_VIEW @@ -177,12 +194,12 @@ TRIBITS_ADD_OPTION_AND_DEFINE( OFF ) + #------------------------------------------------------------------------------ # # C) Install Kokkos' executable scripts # - # nvcc_wrapper is Kokkos' wrapper for NVIDIA's NVCC CUDA compiler. # Kokkos needs nvcc_wrapper in order to build. Other libraries and # executables also need nvcc_wrapper. Thus, we need to install it. @@ -199,6 +216,8 @@ INSTALL(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/bin/nvcc_wrapper DESTINATION bin) TRIBITS_PROCESS_SUBPACKAGES() + +#------------------------------------------------------------------------------ # # E) If Kokkos itself is enabled, process the Kokkos package # @@ -213,3 +232,4 @@ TRIBITS_EXCLUDE_FILES( ) TRIBITS_PACKAGE_POSTPROCESS() +ENDIF() diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos index 5b094dba8c..24cd772e00 100644 --- a/lib/kokkos/Makefile.kokkos +++ b/lib/kokkos/Makefile.kokkos @@ -35,23 +35,26 @@ KOKKOS_INTERNAL_USE_MEMKIND := $(strip $(shell echo $(KOKKOS_USE_TPLS) | grep "e # Check for advanced settings. KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "aggressive_vectorization" | wc -l)) KOKKOS_INTERNAL_DISABLE_PROFILING := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "disable_profiling" | wc -l)) +KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "disable_dualview_modify_check" | wc -l)) +KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "enable_profile_load_print" | wc -l)) KOKKOS_INTERNAL_CUDA_USE_LDG := $(strip $(shell echo $(KOKKOS_CUDA_OPTIONS) | grep "use_ldg" | wc -l)) KOKKOS_INTERNAL_CUDA_USE_UVM := $(strip $(shell echo $(KOKKOS_CUDA_OPTIONS) | grep "force_uvm" | wc -l)) KOKKOS_INTERNAL_CUDA_USE_RELOC := $(strip $(shell echo $(KOKKOS_CUDA_OPTIONS) | grep "rdc" | wc -l)) KOKKOS_INTERNAL_CUDA_USE_LAMBDA := $(strip $(shell echo $(KOKKOS_CUDA_OPTIONS) | grep "enable_lambda" | wc -l)) # Check for Kokkos Host Execution Spaces one of which must be on. -KOKKOS_INTERNAL_USE_OPENMP := $(strip $(shell echo $(KOKKOS_DEVICES) | grep OpenMP | wc -l)) +KOKKOS_INTERNAL_USE_OPENMPTARGET := $(strip $(shell echo $(KOKKOS_DEVICES) | grep OpenMPTarget | wc -l)) +KOKKOS_INTERNAL_USE_OPENMP := $(strip $(shell echo $(subst OpenMPTarget,,$(KOKKOS_DEVICES)) | grep OpenMP | wc -l)) KOKKOS_INTERNAL_USE_PTHREADS := $(strip $(shell echo $(KOKKOS_DEVICES) | grep Pthread | wc -l)) KOKKOS_INTERNAL_USE_QTHREADS := $(strip $(shell echo $(KOKKOS_DEVICES) | grep Qthreads | wc -l)) KOKKOS_INTERNAL_USE_SERIAL := $(strip $(shell echo $(KOKKOS_DEVICES) | grep Serial | wc -l)) ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 0) -ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 0) -ifeq ($(KOKKOS_INTERNAL_USE_QTHREADS), 0) - KOKKOS_INTERNAL_USE_SERIAL := 1 -endif -endif + ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 0) + ifeq ($(KOKKOS_INTERNAL_USE_QTHREADS), 0) + KOKKOS_INTERNAL_USE_SERIAL := 1 + endif + endif endif # Check for other Execution Spaces. @@ -64,24 +67,25 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) endif # Check OS. -KOKKOS_OS := $(shell uname -s) -KOKKOS_INTERNAL_OS_CYGWIN := $(shell uname -s | grep CYGWIN | wc -l) -KOKKOS_INTERNAL_OS_LINUX := $(shell uname -s | grep Linux | wc -l) -KOKKOS_INTERNAL_OS_DARWIN := $(shell uname -s | grep Darwin | wc -l) +KOKKOS_OS := $(strip $(shell uname -s)) +KOKKOS_INTERNAL_OS_CYGWIN := $(strip $(shell uname -s | grep CYGWIN | wc -l)) +KOKKOS_INTERNAL_OS_LINUX := $(strip $(shell uname -s | grep Linux | wc -l)) +KOKKOS_INTERNAL_OS_DARWIN := $(strip $(shell uname -s | grep Darwin | wc -l)) # Check compiler. -KOKKOS_INTERNAL_COMPILER_INTEL := $(shell $(CXX) --version 2>&1 | grep "Intel Corporation" | wc -l) -KOKKOS_INTERNAL_COMPILER_PGI := $(shell $(CXX) --version 2>&1 | grep PGI | wc -l) -KOKKOS_INTERNAL_COMPILER_XL := $(shell $(CXX) -qversion 2>&1 | grep XL | wc -l) -KOKKOS_INTERNAL_COMPILER_CRAY := $(shell $(CXX) -craype-verbose 2>&1 | grep "CC-" | wc -l) -KOKKOS_INTERNAL_COMPILER_NVCC := $(shell $(CXX) --version 2>&1 | grep "nvcc" | wc -l) +KOKKOS_INTERNAL_COMPILER_INTEL := $(strip $(shell $(CXX) --version 2>&1 | grep "Intel Corporation" | wc -l)) +KOKKOS_INTERNAL_COMPILER_PGI := $(strip $(shell $(CXX) --version 2>&1 | grep PGI | wc -l)) +KOKKOS_INTERNAL_COMPILER_XL := $(strip $(shell $(CXX) -qversion 2>&1 | grep XL | wc -l)) +KOKKOS_INTERNAL_COMPILER_CRAY := $(strip $(shell $(CXX) -craype-verbose 2>&1 | grep "CC-" | wc -l)) +KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell $(CXX) --version 2>&1 | grep nvcc | wc -l)) +KOKKOS_INTERNAL_COMPILER_CLANG := $(strip $(shell $(CXX) --version 2>&1 | grep clang | wc -l)) +KOKKOS_INTERNAL_COMPILER_APPLE_CLANG := $(strip $(shell $(CXX) --version 2>&1 | grep "apple-darwin" | wc -l)) ifneq ($(OMPI_CXX),) - KOKKOS_INTERNAL_COMPILER_NVCC := $(shell $(OMPI_CXX) --version 2>&1 | grep "nvcc" | wc -l) + KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell $(OMPI_CXX) --version 2>&1 | grep "nvcc" | wc -l)) endif ifneq ($(MPICH_CXX),) - KOKKOS_INTERNAL_COMPILER_NVCC := $(shell $(MPICH_CXX) --version 2>&1 | grep "nvcc" | wc -l) + KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell $(MPICH_CXX) --version 2>&1 | grep "nvcc" | wc -l)) endif -KOKKOS_INTERNAL_COMPILER_CLANG := $(shell $(CXX) --version 2>&1 | grep "clang" | wc -l) ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 2) KOKKOS_INTERNAL_COMPILER_CLANG = 1 @@ -90,6 +94,11 @@ ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 2) KOKKOS_INTERNAL_COMPILER_XL = 1 endif +# Apple Clang passes both clang and apple clang tests, so turn off clang. +ifeq ($(KOKKOS_INTERNAL_COMPILER_APPLE_CLANG), 1) + KOKKOS_INTERNAL_COMPILER_CLANG = 0 +endif + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) KOKKOS_INTERNAL_COMPILER_CLANG_VERSION := $(shell clang --version | grep version | cut -d ' ' -f3 | tr -d '.') @@ -97,29 +106,43 @@ ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_CLANG_VERSION) -lt 400; echo $$?),0) $(error Compiling Cuda code directly with Clang requires version 4.0.0 or higher) endif + KOKKOS_INTERNAL_CUDA_USE_LAMBDA := 1 endif endif +# Set OpenMP flags. ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) KOKKOS_INTERNAL_OPENMP_FLAG := -mp else ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp=libomp else - ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 1) - KOKKOS_INTERNAL_OPENMP_FLAG := -qsmp=omp + ifeq ($(KOKKOS_INTERNAL_COMPILER_APPLE_CLANG), 1) + KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp=libomp else - ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1) - # OpenMP is turned on by default in Cray compiler environment. - KOKKOS_INTERNAL_OPENMP_FLAG := + ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 1) + KOKKOS_INTERNAL_OPENMP_FLAG := -qsmp=omp else - KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp + ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1) + # OpenMP is turned on by default in Cray compiler environment. + KOKKOS_INTERNAL_OPENMP_FLAG := + else + KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp + endif endif endif endif endif +ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 1) + KOKKOS_INTERNAL_OPENMPTARGET_FLAG := -DKOKKOS_IBM_XL_OMP45_WORKAROUND -qsmp=omp -qoffload -qnoeh +else + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + KOKKOS_INTERNAL_OPENMPTARGET_FLAG := -DKOKKOS_BUG_WORKAROUND_IBM_CLANG_OMP45_VIEW_INIT -fopenmp-implicit-declare-target -fopenmp-targets=nvptx64-nvidia-cuda -fopenmp -fopenmp=libomp + endif +endif +# Set C++11 flags. ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) KOKKOS_INTERNAL_CXX11_FLAG := --c++11 else @@ -146,7 +169,7 @@ KOKKOS_INTERNAL_USE_ARCH_SKX := $(strip $(shell echo $(KOKKOS_ARCH) | grep SKX | KOKKOS_INTERNAL_USE_ARCH_KNL := $(strip $(shell echo $(KOKKOS_ARCH) | grep KNL | wc -l)) # NVIDIA based. -NVCC_WRAPPER := $(KOKKOS_PATH)/config/nvcc_wrapper +NVCC_WRAPPER := $(KOKKOS_PATH)/bin/nvcc_wrapper KOKKOS_INTERNAL_USE_ARCH_KEPLER30 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Kepler30 | wc -l)) KOKKOS_INTERNAL_USE_ARCH_KEPLER32 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Kepler32 | wc -l)) KOKKOS_INTERNAL_USE_ARCH_KEPLER35 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Kepler35 | wc -l)) @@ -180,10 +203,20 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0) + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53) | bc)) endif +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 1) + ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + KOKKOS_INTERNAL_NVCC_PATH := $(shell which nvcc) + CUDA_PATH ?= $(KOKKOS_INTERNAL_NVCC_PATH:/bin/nvcc=) + KOKKOS_INTERNAL_OPENMPTARGET_FLAG := $(KOKKOS_INTERNAL_OPENMPTARGET_FLAG) --cuda-path=$(CUDA_PATH) + endif + endif +endif # ARM based. KOKKOS_INTERNAL_USE_ARCH_ARMV80 := $(strip $(shell echo $(KOKKOS_ARCH) | grep ARMv80 | wc -l)) KOKKOS_INTERNAL_USE_ARCH_ARMV81 := $(strip $(shell echo $(KOKKOS_ARCH) | grep ARMv81 | wc -l)) KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX := $(strip $(shell echo $(KOKKOS_ARCH) | grep ARMv8-ThunderX | wc -l)) +KOKKOS_INTERNAL_USE_ARCH_ARM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX) | bc)) # IBM based. KOKKOS_INTERNAL_USE_ARCH_BGQ := $(strip $(shell echo $(KOKKOS_ARCH) | grep BGQ | wc -l)) @@ -206,8 +239,11 @@ KOKKOS_INTERNAL_USE_ISA_X86_64 := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ KOKKOS_INTERNAL_USE_ISA_KNC := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_KNC) | bc )) KOKKOS_INTERNAL_USE_ISA_POWERPCLE := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_POWER8)+$(KOKKOS_INTERNAL_USE_ARCH_POWER9) | bc )) +# Decide whether we can support transactional memory +KOKKOS_INTERNAL_USE_TM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_BDW)+$(KOKKOS_INTERNAL_USE_ARCH_SKX) | bc )) + # Incompatible flags? -KOKKOS_INTERNAL_USE_ARCH_MULTIHOST := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_AVX)+$(KOKKOS_INTERNAL_USE_ARCH_AVX2)+$(KOKKOS_INTERNAL_USE_ARCH_KNC)+$(KOKKOS_INTERNAL_USE_ARCH_IBM)+$(KOKKOS_INTERNAL_USE_ARCH_AMDAVX)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX)>1" | bc )) +KOKKOS_INTERNAL_USE_ARCH_MULTIHOST := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_AVX)+$(KOKKOS_INTERNAL_USE_ARCH_AVX2)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON)+$(KOKKOS_INTERNAL_USE_ARCH_KNC)+$(KOKKOS_INTERNAL_USE_ARCH_IBM)+$(KOKKOS_INTERNAL_USE_ARCH_ARM)>1" | bc )) KOKKOS_INTERNAL_USE_ARCH_MULTIGPU := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_NVIDIA)>1" | bc)) ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MULTIHOST), 1) @@ -240,12 +276,22 @@ tmp := $(shell echo "Makefile constructed configuration:" >> KokkosCore_config.t tmp := $(shell date >> KokkosCore_config.tmp) tmp := $(shell echo "----------------------------------------------*/" >> KokkosCore_config.tmp) +tmp := $(shell echo '\#if !defined(KOKKOS_MACROS_HPP) || defined(KOKKOS_CORE_CONFIG_H)' >> KokkosCore_config.tmp) +tmp := $(shell echo '\#error "Do not include KokkosCore_config.h directly; include Kokkos_Macros.hpp instead."' >> KokkosCore_config.tmp) +tmp := $(shell echo '\#else' >> KokkosCore_config.tmp) +tmp := $(shell echo '\#define KOKKOS_CORE_CONFIG_H' >> KokkosCore_config.tmp) +tmp := $(shell echo '\#endif' >> KokkosCore_config.tmp) + tmp := $(shell echo "/* Execution Spaces */" >> KokkosCore_config.tmp) ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) tmp := $(shell echo "\#define KOKKOS_HAVE_CUDA 1" >> KokkosCore_config.tmp ) endif +ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) + tmp := $(shell echo '\#define KOKKOS_ENABLE_OPENMPTARGET 1' >> KokkosCore_config.tmp) +endif + ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) tmp := $(shell echo '\#define KOKKOS_HAVE_OPENMP 1' >> KokkosCore_config.tmp) endif @@ -262,6 +308,12 @@ ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) tmp := $(shell echo "\#define KOKKOS_HAVE_SERIAL 1" >> KokkosCore_config.tmp ) endif +ifeq ($(KOKKOS_INTERNAL_USE_TM), 1) + tmp := $(shell echo "\#ifndef __CUDA_ARCH__" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ENABLE_TM" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#endif" >> KokkosCore_config.tmp ) +endif + ifeq ($(KOKKOS_INTERNAL_USE_ISA_X86_64), 1) tmp := $(shell echo "\#ifndef __CUDA_ARCH__" >> KokkosCore_config.tmp ) tmp := $(shell echo "\#define KOKKOS_USE_ISA_X86_64" >> KokkosCore_config.tmp ) @@ -293,13 +345,21 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX1Z), 1) endif ifeq ($(KOKKOS_INTERNAL_ENABLE_DEBUG), 1) -ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) - KOKKOS_CXXFLAGS += -lineinfo -endif + ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) + KOKKOS_CXXFLAGS += -lineinfo + endif + KOKKOS_CXXFLAGS += -g KOKKOS_LDFLAGS += -g -ldl tmp := $(shell echo "\#define KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK 1" >> KokkosCore_config.tmp ) tmp := $(shell echo "\#define KOKKOS_HAVE_DEBUG 1" >> KokkosCore_config.tmp ) + ifeq ($(KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK), 0) + tmp := $(shell echo "\#define KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK 1" >> KokkosCore_config.tmp ) + endif +endif + +ifeq ($(KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT), 1) + tmp := $(shell echo "\#define KOKKOS_ENABLE_PROFILING_LOAD_PRINT 1" >> KokkosCore_config.tmp ) endif ifeq ($(KOKKOS_INTERNAL_USE_HWLOC), 1) @@ -311,8 +371,6 @@ endif ifeq ($(KOKKOS_INTERNAL_USE_LIBRT), 1) tmp := $(shell echo "\#define KOKKOS_USE_LIBRT 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define PREC_TIMER 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOSP_ENABLE_RTLIB 1" >> KokkosCore_config.tmp ) KOKKOS_LIBS += -lrt endif @@ -323,8 +381,8 @@ ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) tmp := $(shell echo "\#define KOKKOS_HAVE_HBWSPACE 1" >> KokkosCore_config.tmp ) endif -ifeq ($(KOKKOS_INTERNAL_DISABLE_PROFILING), 1) - tmp := $(shell echo "\#define KOKKOS_ENABLE_PROFILING 0" >> KokkosCore_config.tmp ) +ifeq ($(KOKKOS_INTERNAL_DISABLE_PROFILING), 0) + tmp := $(shell echo "\#define KOKKOS_ENABLE_PROFILING" >> KokkosCore_config.tmp ) endif tmp := $(shell echo "/* Optimization Settings */" >> KokkosCore_config.tmp) @@ -336,39 +394,44 @@ endif tmp := $(shell echo "/* Cuda Settings */" >> KokkosCore_config.tmp) ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) + ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LDG), 1) + tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LDG_INTRINSIC 1" >> KokkosCore_config.tmp ) + else + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LDG_INTRINSIC 1" >> KokkosCore_config.tmp ) + endif + endif -ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LDG), 1) - tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LDG_INTRINSIC 1" >> KokkosCore_config.tmp ) -endif + ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1) + tmp := $(shell echo "\#define KOKKOS_CUDA_USE_UVM 1" >> KokkosCore_config.tmp ) + endif -ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1) - tmp := $(shell echo "\#define KOKKOS_CUDA_USE_UVM 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_USE_CUDA_UVM 1" >> KokkosCore_config.tmp ) -endif + ifeq ($(KOKKOS_INTERNAL_CUDA_USE_RELOC), 1) + tmp := $(shell echo "\#define KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE 1" >> KokkosCore_config.tmp ) + KOKKOS_CXXFLAGS += --relocatable-device-code=true + KOKKOS_LDFLAGS += --relocatable-device-code=true + endif -ifeq ($(KOKKOS_INTERNAL_CUDA_USE_RELOC), 1) - tmp := $(shell echo "\#define KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += --relocatable-device-code=true - KOKKOS_LDFLAGS += --relocatable-device-code=true -endif + ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LAMBDA), 1) + ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) + ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION) -gt 70; echo $$?),0) + tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LAMBDA 1" >> KokkosCore_config.tmp ) + KOKKOS_CXXFLAGS += -expt-extended-lambda + else + $(warning Warning: Cuda Lambda support was requested but NVCC version is too low. This requires NVCC for Cuda version 7.5 or higher. Disabling Lambda support now.) + endif + endif -ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LAMBDA), 1) - ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) - ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION) -gt 70; echo $$?),0) + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LAMBDA 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += -expt-extended-lambda - else - $(warning Warning: Cuda Lambda support was requested but NVCC version is too low. This requires NVCC for Cuda version 7.5 or higher. Disabling Lambda support now.) endif endif ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) - tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LAMBDA 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_CUDA_CLANG_WORKAROUND" >> KokkosCore_config.tmp ) endif endif -endif - # Add Architecture flags. ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV80), 1) @@ -469,7 +532,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER9), 1) endif endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX2), 1) +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_HSW), 1) tmp := $(shell echo "\#define KOKKOS_ARCH_AVX2 1" >> KokkosCore_config.tmp ) ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1) @@ -491,6 +554,28 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX2), 1) endif endif +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_BDW), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_AVX2 1" >> KokkosCore_config.tmp ) + + ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1) + KOKKOS_CXXFLAGS += -xCORE-AVX2 + KOKKOS_LDFLAGS += -xCORE-AVX2 + else + ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1) + + else + ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) + KOKKOS_CXXFLAGS += -tp=haswell + KOKKOS_LDFLAGS += -tp=haswell + else + # Assume that this is a really a GNU compiler. + KOKKOS_CXXFLAGS += -march=core-avx2 -mtune=core-avx2 -mrtm + KOKKOS_LDFLAGS += -march=core-avx2 -mtune=core-avx2 -mrtm + endif + endif + endif +endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC), 1) tmp := $(shell echo "\#define KOKKOS_ARCH_AVX512MIC 1" >> KokkosCore_config.tmp ) @@ -501,12 +586,12 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC), 1) ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1) else - ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) + ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) else # Asssume that this is really a GNU compiler. - KOKKOS_CXXFLAGS += -march=knl - KOKKOS_LDFLAGS += -march=knl + KOKKOS_CXXFLAGS += -march=knl -mtune=knl + KOKKOS_LDFLAGS += -march=knl -mtune=knl endif endif endif @@ -526,8 +611,8 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON), 1) else # Nothing here yet. - KOKKOS_CXXFLAGS += -march=skylake-avx512 - KOKKOS_LDFLAGS += -march=skylake-avx512 + KOKKOS_CXXFLAGS += -march=skylake-avx512 -mtune=skylake-avx512 -mrtm + KOKKOS_LDFLAGS += -march=skylake-avx512 -mtune=skylake-avx512 -mrtm endif endif endif @@ -541,70 +626,67 @@ endif # Figure out the architecture flag for Cuda. ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) + ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG=-arch + endif + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG=--cuda-gpu-arch + KOKKOS_CXXFLAGS += -x cuda + endif -ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) - KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG=-arch -endif -ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) - KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG=--cuda-gpu-arch - KOKKOS_CXXFLAGS += -x cuda -endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER30), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER30 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_30 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER32), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER32 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_32 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER35), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER35 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_35 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER37), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER37 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_37 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL50 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_50 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL52 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_52 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL53 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_53 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL60), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL60 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_60 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL61), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL61 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_61 + endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER30), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER30 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_30 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_30 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER32), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER32 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_32 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_32 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER35), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER35 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_35 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_35 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER37), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER37 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_37 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_37 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL50 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_50 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_50 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL52 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_52 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_52 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL53 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_53 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_53 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL61), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL61 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_61 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_61 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL60), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL60 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_60 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_60 -endif + ifneq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0) + KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG) + ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) + KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG) + endif + endif endif KOKKOS_INTERNAL_LS_CONFIG := $(shell ls KokkosCore_config.h) @@ -630,9 +712,24 @@ KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/containers/src/impl/*.cpp) ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.cpp) KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.hpp) - KOKKOS_CXXFLAGS += -I$(CUDA_PATH)/include + KOKKOS_CPPFLAGS += -I$(CUDA_PATH)/include KOKKOS_LDFLAGS += -L$(CUDA_PATH)/lib64 KOKKOS_LIBS += -lcudart -lcuda + + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + KOKKOS_CXXFLAGS += --cuda-path=$(CUDA_PATH) + endif +endif + +ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) + KOKKOS_SRC += $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Exec.cpp $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp + KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/OpenMPTarget/*.hpp) + ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) + KOKKOS_CXXFLAGS += -Xcompiler $(KOKKOS_INTERNAL_OPENMPTARGET_FLAG) + else + KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_OPENMPTARGET_FLAG) + endif + KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_OPENMPTARGET_FLAG) endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) @@ -666,10 +763,27 @@ endif ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) KOKKOS_INTERNAL_GCC_PATH = $(shell which g++) KOKKOS_INTERNAL_GCC_TOOLCHAIN = $(KOKKOS_INTERNAL_GCC_PATH:/bin/g++=) - KOKKOS_CXXFLAGS += --gcc-toolchain=$(KOKKOS_INTERNAL_GCC_TOOLCHAIN) -DKOKKOS_CUDA_CLANG_WORKAROUND -DKOKKOS_CUDA_USE_LDG_INTRINSIC + KOKKOS_CXXFLAGS += --gcc-toolchain=$(KOKKOS_INTERNAL_GCC_TOOLCHAIN) KOKKOS_LDFLAGS += --gcc-toolchain=$(KOKKOS_INTERNAL_GCC_TOOLCHAIN) endif +# Don't include Kokkos_HBWSpace.cpp if not using MEMKIND to avoid a link warning. +ifneq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) + KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp,$(KOKKOS_SRC)) +endif + +# Don't include Kokkos_Profiling_Interface.cpp if not using profiling to avoid a link warning. +ifeq ($(KOKKOS_INTERNAL_DISABLE_PROFILING), 1) + KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_Profiling_Interface.cpp,$(KOKKOS_SRC)) +endif + +# Don't include Kokkos_Serial.cpp or Kokkos_Serial_Task.cpp if not using Serial +# device to avoid a link warning. +ifneq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) + KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial.cpp,$(KOKKOS_SRC)) + KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial_Task.cpp,$(KOKKOS_SRC)) +endif + # With Cygwin functions such as fdopen and fileno are not defined # when strict ansi is enabled. strict ansi gets enabled with --std=c++11 # though. So we hard undefine it here. Not sure if that has any bad side effects diff --git a/lib/kokkos/Makefile.targets b/lib/kokkos/Makefile.targets index 54cacb741b..3cb52a04cd 100644 --- a/lib/kokkos/Makefile.targets +++ b/lib/kokkos/Makefile.targets @@ -53,11 +53,20 @@ Kokkos_Qthreads_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Qthreads/K endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) -Kokkos_OpenMPexec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMPexec.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMPexec.cpp +Kokkos_OpenMP_Exec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Exec.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Exec.cpp Kokkos_OpenMP_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp endif +ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) +Kokkos_OpenMPTarget_Exec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Exec.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Exec.cpp +Kokkos_OpenMPTargetSpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp +#Kokkos_OpenMPTarget_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Task.cpp +# $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Task.cpp +endif + Kokkos_HBWSpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp diff --git a/lib/kokkos/algorithms/src/KokkosAlgorithms_dummy.cpp b/lib/kokkos/algorithms/src/KokkosAlgorithms_dummy.cpp index e69de29bb2..9c08a088b0 100644 --- a/lib/kokkos/algorithms/src/KokkosAlgorithms_dummy.cpp +++ b/lib/kokkos/algorithms/src/KokkosAlgorithms_dummy.cpp @@ -0,0 +1 @@ +void KOKKOS_ALGORITHMS_SRC_DUMMY_PREVENT_LINK_ERROR() {} diff --git a/lib/kokkos/algorithms/src/Kokkos_Random.hpp b/lib/kokkos/algorithms/src/Kokkos_Random.hpp index 4b58d9d7c3..9082e47052 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Random.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Random.hpp @@ -674,7 +674,7 @@ namespace Kokkos { const double V = 2.0*drand() - 1.0; S = U*U+V*V; } - return U*sqrt(-2.0*log(S)/S); + return U*std::sqrt(-2.0*log(S)/S); } KOKKOS_INLINE_FUNCTION @@ -923,7 +923,7 @@ namespace Kokkos { const double V = 2.0*drand() - 1.0; S = U*U+V*V; } - return U*sqrt(-2.0*log(S)/S); + return U*std::sqrt(-2.0*log(S)/S); } KOKKOS_INLINE_FUNCTION @@ -1183,7 +1183,7 @@ namespace Kokkos { const double V = 2.0*drand() - 1.0; S = U*U+V*V; } - return U*sqrt(-2.0*log(S)/S); + return U*std::sqrt(-2.0*log(S)/S); } KOKKOS_INLINE_FUNCTION diff --git a/lib/kokkos/algorithms/unit_tests/Makefile b/lib/kokkos/algorithms/unit_tests/Makefile index 3027c6a94b..b74192ef18 100644 --- a/lib/kokkos/algorithms/unit_tests/Makefile +++ b/lib/kokkos/algorithms/unit_tests/Makefile @@ -8,7 +8,7 @@ default: build_all echo "End Build" ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES))) - CXX = $(KOKKOS_PATH)/config/nvcc_wrapper + CXX = $(KOKKOS_PATH)/bin/nvcc_wrapper else CXX = g++ endif @@ -21,8 +21,8 @@ include $(KOKKOS_PATH)/Makefile.kokkos KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/algorithms/unit_tests -TEST_TARGETS = -TARGETS = +TEST_TARGETS = +TARGETS = ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) OBJ_CUDA = TestCuda.o UnitTestMain.o gtest-all.o @@ -49,16 +49,16 @@ ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) endif KokkosAlgorithms_UnitTest_Cuda: $(OBJ_CUDA) $(KOKKOS_LINK_DEPENDS) - $(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_CUDA) $(KOKKOS_LIBS) $(LIB) -o KokkosAlgorithms_UnitTest_Cuda + $(LINK) $(EXTRA_PATH) $(OBJ_CUDA) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_Cuda KokkosAlgorithms_UnitTest_Threads: $(OBJ_THREADS) $(KOKKOS_LINK_DEPENDS) - $(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_THREADS) $(KOKKOS_LIBS) $(LIB) -o KokkosAlgorithms_UnitTest_Threads + $(LINK) $(EXTRA_PATH) $(OBJ_THREADS) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_Threads KokkosAlgorithms_UnitTest_OpenMP: $(OBJ_OPENMP) $(KOKKOS_LINK_DEPENDS) - $(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_OPENMP) $(KOKKOS_LIBS) $(LIB) -o KokkosAlgorithms_UnitTest_OpenMP + $(LINK) $(EXTRA_PATH) $(OBJ_OPENMP) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_OpenMP KokkosAlgorithms_UnitTest_Serial: $(OBJ_SERIAL) $(KOKKOS_LINK_DEPENDS) - $(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_SERIAL) $(KOKKOS_LIBS) $(LIB) -o KokkosAlgorithms_UnitTest_Serial + $(LINK) $(EXTRA_PATH) $(OBJ_SERIAL) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_Serial test-cuda: KokkosAlgorithms_UnitTest_Cuda ./KokkosAlgorithms_UnitTest_Cuda @@ -76,7 +76,7 @@ build_all: $(TARGETS) test: $(TEST_TARGETS) -clean: kokkos-clean +clean: kokkos-clean rm -f *.o $(TARGETS) # Compilation rules @@ -84,6 +84,5 @@ clean: kokkos-clean %.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -gtest-all.o:$(GTEST_PATH)/gtest/gtest-all.cc +gtest-all.o:$(GTEST_PATH)/gtest/gtest-all.cc $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $(GTEST_PATH)/gtest/gtest-all.cc - diff --git a/lib/kokkos/algorithms/unit_tests/TestCuda.cpp b/lib/kokkos/algorithms/unit_tests/TestCuda.cpp index ba3938f497..710eeb8ada 100644 --- a/lib/kokkos/algorithms/unit_tests/TestCuda.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestCuda.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,12 +36,15 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ -#include +#include +#ifdef KOKKOS_ENABLE_CUDA + +#include #include #include @@ -49,8 +52,6 @@ #include -#ifdef KOKKOS_ENABLE_CUDA - #include #include @@ -105,6 +106,7 @@ CUDA_SORT_UNSIGNED(171) #undef CUDA_RANDOM_XORSHIFT1024 #undef CUDA_SORT_UNSIGNED } - +#else +void KOKKOS_ALGORITHMS_UNITTESTS_TESTCUDA_PREVENT_LINK_ERROR() {} #endif /* #ifdef KOKKOS_ENABLE_CUDA */ diff --git a/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp b/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp index f4d582d0bb..1e7ee68549 100644 --- a/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,13 +36,16 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ -#include +#include +#ifdef KOKKOS_ENABLE_OPENMP + +#include #include //---------------------------------------------------------------------------- @@ -52,7 +55,6 @@ namespace Test { -#ifdef KOKKOS_ENABLE_OPENMP class openmp : public ::testing::Test { protected: static void SetUpTestCase() @@ -97,6 +99,8 @@ OPENMP_SORT_UNSIGNED(171) #undef OPENMP_RANDOM_XORSHIFT64 #undef OPENMP_RANDOM_XORSHIFT1024 #undef OPENMP_SORT_UNSIGNED -#endif } // namespace test +#else +void KOKKOS_ALGORITHMS_UNITTESTS_TESTOPENMP_PREVENT_LINK_ERROR() {} +#endif diff --git a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp index c906b9f2cd..9cf02f74b4 100644 --- a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp @@ -295,7 +295,7 @@ struct test_random_scalar { parallel_reduce (num_draws/1024, functor_type (pool, density_1d, density_3d), result); //printf("Result: %lf %lf %lf\n",result.mean/num_draws/3,result.variance/num_draws/3,result.covariance/num_draws/2); - double tolerance = 1.6*sqrt(1.0/num_draws); + double tolerance = 1.6*std::sqrt(1.0/num_draws); double mean_expect = 0.5*Kokkos::rand::max(); double variance_expect = 1.0/3.0*mean_expect*mean_expect; double mean_eps = mean_expect/(result.mean/num_draws/3)-1.0; @@ -321,7 +321,7 @@ struct test_random_scalar { typedef test_histogram1d_functor functor_type; parallel_reduce (HIST_DIM1D, functor_type (density_1d, num_draws), result); - double tolerance = 6*sqrt(1.0/HIST_DIM1D); + double tolerance = 6*std::sqrt(1.0/HIST_DIM1D); double mean_expect = 1.0*num_draws*3/HIST_DIM1D; double variance_expect = 1.0*num_draws*3/HIST_DIM1D*(1.0-1.0/HIST_DIM1D); double covariance_expect = -1.0*num_draws*3/HIST_DIM1D/HIST_DIM1D; @@ -354,7 +354,7 @@ struct test_random_scalar { typedef test_histogram3d_functor functor_type; parallel_reduce (HIST_DIM1D, functor_type (density_3d, num_draws), result); - double tolerance = 6*sqrt(1.0/HIST_DIM1D); + double tolerance = 6*std::sqrt(1.0/HIST_DIM1D); double mean_expect = 1.0*num_draws/HIST_DIM1D; double variance_expect = 1.0*num_draws/HIST_DIM1D*(1.0-1.0/HIST_DIM1D); double covariance_expect = -1.0*num_draws/HIST_DIM1D/HIST_DIM1D; diff --git a/lib/kokkos/algorithms/unit_tests/TestSerial.cpp b/lib/kokkos/algorithms/unit_tests/TestSerial.cpp index 6ac80cf73a..a1df93e07b 100644 --- a/lib/kokkos/algorithms/unit_tests/TestSerial.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestSerial.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,11 +36,14 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ +#include +#ifdef KOKKOS_ENABLE_SERIAL + #include #include @@ -55,7 +58,6 @@ namespace Test { -#ifdef KOKKOS_ENABLE_SERIAL class serial : public ::testing::Test { protected: static void SetUpTestCase() @@ -93,7 +95,9 @@ SERIAL_SORT_UNSIGNED(171) #undef SERIAL_RANDOM_XORSHIFT1024 #undef SERIAL_SORT_UNSIGNED -#endif // KOKKOS_ENABLE_SERIAL } // namespace Test +#else +void KOKKOS_ALGORITHMS_UNITTESTS_TESTSERIAL_PREVENT_LINK_ERROR() {} +#endif // KOKKOS_ENABLE_SERIAL diff --git a/lib/kokkos/algorithms/unit_tests/TestSort.hpp b/lib/kokkos/algorithms/unit_tests/TestSort.hpp index 61ffa6f43a..04be98f1cc 100644 --- a/lib/kokkos/algorithms/unit_tests/TestSort.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestSort.hpp @@ -1,12 +1,12 @@ //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -35,12 +35,12 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER -#ifndef TESTSORT_HPP_ -#define TESTSORT_HPP_ +#ifndef KOKKOS_ALGORITHMS_UNITTESTS_TESTSORT_HPP +#define KOKKOS_ALGORITHMS_UNITTESTS_TESTSORT_HPP #include #include @@ -212,7 +212,12 @@ void test_dynamic_view_sort(unsigned int n ) const size_t upper_bound = 2 * n ; typename KeyDynamicViewType::memory_pool - pool( memory_space() , 2 * n * sizeof(KeyType) ); + pool( memory_space() + , n * sizeof(KeyType) * 1.2 + , 500 /* min block size in bytes */ + , 30000 /* max block size in bytes */ + , 1000000 /* min superblock size in bytes */ + ); KeyDynamicViewType keys("Keys",pool,upper_bound); @@ -272,4 +277,4 @@ void test_sort(unsigned int N) } } -#endif /* TESTSORT_HPP_ */ +#endif /* KOKKOS_ALGORITHMS_UNITTESTS_TESTSORT_HPP */ diff --git a/lib/kokkos/algorithms/unit_tests/TestThreads.cpp b/lib/kokkos/algorithms/unit_tests/TestThreads.cpp index 36d438b643..08749779ff 100644 --- a/lib/kokkos/algorithms/unit_tests/TestThreads.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestThreads.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,11 +36,14 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ +#include +#ifdef KOKKOS_ENABLE_THREADS + #include #include @@ -55,7 +58,6 @@ namespace Test { -#ifdef KOKKOS_ENABLE_PTHREAD class threads : public ::testing::Test { protected: static void SetUpTestCase() @@ -107,7 +109,9 @@ THREADS_SORT_UNSIGNED(171) #undef THREADS_RANDOM_XORSHIFT1024 #undef THREADS_SORT_UNSIGNED -#endif } // namespace Test +#else +void KOKKOS_ALGORITHMS_UNITTESTS_TESTTHREADS_PREVENT_LINK_ERROR() {} +#endif diff --git a/lib/kokkos/benchmarks/bytes_and_flops/Makefile b/lib/kokkos/benchmarks/bytes_and_flops/Makefile index 6a1917a523..5ddf78f28e 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/Makefile +++ b/lib/kokkos/benchmarks/bytes_and_flops/Makefile @@ -7,7 +7,7 @@ default: build echo "Start Build" ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES))) -CXX = ${KOKKOS_PATH}/config/nvcc_wrapper +CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper EXE = bytes_and_flops.cuda KOKKOS_DEVICES = "Cuda,OpenMP" KOKKOS_ARCH = "SNB,Kepler35" @@ -22,7 +22,7 @@ CXXFLAGS = -O3 -g DEPFLAGS = -M LINK = ${CXX} -LINKFLAGS = +LINKFLAGS = OBJ = $(SRC:.cpp=.o) LIB = @@ -34,7 +34,7 @@ build: $(EXE) $(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS) $(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE) -clean: kokkos-clean +clean: kokkos-clean rm -f *.o *.cuda *.host # Compilation rules diff --git a/lib/kokkos/benchmarks/gather/Makefile b/lib/kokkos/benchmarks/gather/Makefile index fd1feab6fa..0ea9fb1dd2 100644 --- a/lib/kokkos/benchmarks/gather/Makefile +++ b/lib/kokkos/benchmarks/gather/Makefile @@ -7,7 +7,7 @@ default: build echo "Start Build" ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES))) -CXX = ${KOKKOS_PATH}/config/nvcc_wrapper +CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper EXE = gather.cuda KOKKOS_DEVICES = "Cuda,OpenMP" KOKKOS_ARCH = "SNB,Kepler35" @@ -22,7 +22,7 @@ CXXFLAGS = -O3 -g DEPFLAGS = -M LINK = ${CXX} -LINKFLAGS = +LINKFLAGS = OBJ = $(SRC:.cpp=.o) LIB = @@ -35,10 +35,10 @@ build: $(EXE) $(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS) $(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE) -clean: kokkos-clean +clean: kokkos-clean rm -f *.o *.cuda *.host # Compilation rules -%.o:%.cpp $(KOKKOS_CPP_DEPENDS) gather_unroll.hpp gather.hpp +%.o:%.cpp $(KOKKOS_CPP_DEPENDS) gather_unroll.hpp gather.hpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< diff --git a/lib/kokkos/cmake/KokkosConfig.cmake.in b/lib/kokkos/cmake/KokkosConfig.cmake.in new file mode 100644 index 0000000000..fc099a494c --- /dev/null +++ b/lib/kokkos/cmake/KokkosConfig.cmake.in @@ -0,0 +1,18 @@ +# - Config file for the Kokkos package +# It defines the following variables +# Kokkos_INCLUDE_DIRS - include directories for Kokkos +# Kokkos_LIBRARIES - libraries to link against + +# Compute paths +GET_FILENAME_COMPONENT(Kokkos_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) +SET(Kokkos_INCLUDE_DIRS "@CONF_INCLUDE_DIRS@") + +# Our library dependencies (contains definitions for IMPORTED targets) +IF(NOT TARGET kokkos AND NOT Kokkos_BINARY_DIR) + INCLUDE("${Kokkos_CMAKE_DIR}/KokkosTargets.cmake") +ENDIF() + +# These are IMPORTED targets created by KokkosTargets.cmake +SET(Kokkos_LIBRARY_DIRS @INSTALL_LIB_DIR@) +SET(Kokkos_LIBRARIES @Kokkos_LIBRARIES_NAMES@) +SET(Kokkos_TPL_LIBRARIES @KOKKOS_LIBS@) diff --git a/lib/kokkos/cmake/Modules/FindHWLOC.cmake b/lib/kokkos/cmake/Modules/FindHWLOC.cmake new file mode 100644 index 0000000000..273dcb5c8a --- /dev/null +++ b/lib/kokkos/cmake/Modules/FindHWLOC.cmake @@ -0,0 +1,20 @@ +#.rst: +# FindHWLOC +# ---------- +# +# Try to find HWLOC. +# +# The following variables are defined: +# +# HWLOC_FOUND - System has HWLOC +# HWLOC_INCLUDE_DIR - HWLOC include directory +# HWLOC_LIBRARIES - Libraries needed to use HWLOC + +find_path(HWLOC_INCLUDE_DIR hwloc.h) +find_library(HWLOC_LIBRARIES hwloc) + +include(FindPackageHandleStandardArgs) +find_package_handle_standard_args(HWLOC DEFAULT_MSG + HWLOC_INCLUDE_DIR HWLOC_LIBRARIES) + +mark_as_advanced(HWLOC_INCLUDE_DIR HWLOC_LIBRARIES) diff --git a/lib/kokkos/cmake/Modules/FindMemkind.cmake b/lib/kokkos/cmake/Modules/FindMemkind.cmake new file mode 100644 index 0000000000..245fb44c19 --- /dev/null +++ b/lib/kokkos/cmake/Modules/FindMemkind.cmake @@ -0,0 +1,20 @@ +#.rst: +# FindMemkind +# ---------- +# +# Try to find Memkind. +# +# The following variables are defined: +# +# MEMKIND_FOUND - System has Memkind +# MEMKIND_INCLUDE_DIR - Memkind include directory +# MEMKIND_LIBRARIES - Libraries needed to use Memkind + +find_path(MEMKIND_INCLUDE_DIR memkind.h) +find_library(MEMKIND_LIBRARIES memkind) + +include(FindPackageHandleStandardArgs) +find_package_handle_standard_args(Memkind DEFAULT_MSG + MEMKIND_INCLUDE_DIR MEMKIND_LIBRARIES) + +mark_as_advanced(MEMKIND_INCLUDE_DIR MEMKIND_LIBRARIES) diff --git a/lib/kokkos/cmake/Modules/FindQthreads.cmake b/lib/kokkos/cmake/Modules/FindQthreads.cmake new file mode 100644 index 0000000000..a254b0e996 --- /dev/null +++ b/lib/kokkos/cmake/Modules/FindQthreads.cmake @@ -0,0 +1,20 @@ +#.rst: +# FindQthreads +# ---------- +# +# Try to find Qthreads. +# +# The following variables are defined: +# +# QTHREADS_FOUND - System has Qthreads +# QTHREADS_INCLUDE_DIR - Qthreads include directory +# QTHREADS_LIBRARIES - Libraries needed to use Qthreads + +find_path(QTHREADS_INCLUDE_DIR qthread.h) +find_library(QTHREADS_LIBRARIES qthread) + +include(FindPackageHandleStandardArgs) +find_package_handle_standard_args(Qthreads DEFAULT_MSG + QTHREADS_INCLUDE_DIR QTHREADS_LIBRARIES) + +mark_as_advanced(QTHREADS_INCLUDE_DIR QTHREADS_LIBRARIES) diff --git a/lib/kokkos/cmake/kokkos.cmake b/lib/kokkos/cmake/kokkos.cmake new file mode 100644 index 0000000000..235b7eaba4 --- /dev/null +++ b/lib/kokkos/cmake/kokkos.cmake @@ -0,0 +1,1198 @@ + + +# Set which Kokkos backend to use. +set(KOKKOS_ENABLE_CUDA OFF CACHE BOOL "Use Kokkos CUDA backend") +set(KOKKOS_ENABLE_OPENMP ON CACHE BOOL "Use Kokkos OpenMP backend") +set(KOKKOS_ENABLE_PTHREAD OFF CACHE BOOL "Use Kokkos Pthreads backend") +set(KOKKOS_ENABLE_QTHREADS OFF CACHE BOOL "Use Kokkos Qthreads backend") +set(KOKKOS_ENABLE_SERIAL ON CACHE BOOL "Use Kokkos Serial backend") + +# List of possible host architectures. +list(APPEND KOKKOS_HOST_ARCH_LIST + None # No architecture optimization + AMDAVX # AMD chip + ARMv80 # ARMv8.0 Compatible CPU + ARMv81 # ARMv8.1 Compatible CPU + ARMv8-ThunderX # ARMv8 Cavium ThunderX CPU + SNB # Intel Sandy/Ivy Bridge CPUs + HSW # Intel Haswell CPUs + BDW # Intel Broadwell Xeon E-class CPUs + SKX # Intel Sky Lake Xeon E-class HPC CPUs (AVX512) + KNC # Intel Knights Corner Xeon Phi + KNL # Intel Knights Landing Xeon Phi + BGQ # IBM Blue Gene Q + Power7 # IBM POWER7 CPUs + Power8 # IBM POWER8 CPUs + Power9 # IBM POWER9 CPUs + ) + +# Setting this variable to a value other than "None" can improve host +# performance by turning on architecture specific code. +set(KOKKOS_HOST_ARCH "None" CACHE STRING "Optimize for specific host architecture.") +set_property(CACHE KOKKOS_HOST_ARCH PROPERTY STRINGS ${KOKKOS_HOST_ARCH_LIST}) + +# List of possible GPU architectures. +list(APPEND KOKKOS_GPU_ARCH_LIST + None # No architecture optimization + Kepler # NVIDIA Kepler default (generation CC 3.5) + Kepler30 # NVIDIA Kepler generation CC 3.0 + Kepler32 # NVIDIA Kepler generation CC 3.2 + Kepler35 # NVIDIA Kepler generation CC 3.5 + Kepler37 # NVIDIA Kepler generation CC 3.7 + Maxwell # NVIDIA Maxwell default (generation CC 5.0) + Maxwell50 # NVIDIA Maxwell generation CC 5.0 + Maxwell52 # NVIDIA Maxwell generation CC 5.2 + Maxwell53 # NVIDIA Maxwell generation CC 5.3 + Pascal60 # NVIDIA Pascal generation CC 6.0 + Pascal61 # NVIDIA Pascal generation CC 6.1 + ) + +# Setting this variable to a value other than "None" can improve GPU +# performance by turning on architecture specific code. +set(KOKKOS_GPU_ARCH "None" CACHE STRING "Optimize for specific GPU architecture.") +set_property(CACHE KOKKOS_GPU_ARCH PROPERTY STRINGS ${KOKKOS_GPU_ARCH_LIST}) + +set(KOKKOS_SEPARATE_LIBS OFF CACHE BOOL "OFF = kokkos. ON = kokkoscore, kokkoscontainers, and kokkosalgorithms.") + +# Enable hwloc library. +set(KOKKOS_ENABLE_HWLOC OFF CACHE BOOL "Enable hwloc for better process placement.") +set(KOKKOS_HWLOC_DIR "" CACHE PATH "Location of hwloc library.") + +# Enable memkind library. +set(KOKKOS_ENABLE_MEMKIND OFF CACHE BOOL "Enable memkind.") +set(KOKKOS_MEMKIND_DIR "" CACHE PATH "Location of memkind library.") + +set(KOKKOS_ENABLE_LIBRT OFF CACHE BOOL "Enable librt for more precise timer.") + +# Enable debugging. +set(KOKKOS_DEBUG OFF CACHE BOOL "Enable debugging in Kokkos.") + +# Enable profiling. +set(KOKKOS_ENABLE_PROFILING ON CACHE BOOL "Enable profiling.") + +# Enable aggressive vectorization. +set(KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION OFF CACHE BOOL "Enable aggressive vectorization.") + +# Qthreads options. +set(KOKKOS_QTHREADS_DIR "" CACHE PATH "Location of Qthreads library.") + +# CUDA options. +set(KOKKOS_CUDA_DIR "" CACHE PATH "Location of CUDA library. Defaults to where nvcc installed.") +set(KOKKOS_ENABLE_CUDA_LDG_INTRINSIC OFF CACHE BOOL "Enable CUDA LDG.") +set(KOKKOS_ENABLE_CUDA_UVM OFF CACHE BOOL "Enable CUDA unified virtual memory.") +set(KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE OFF CACHE BOOL "Enable relocatable device code for CUDA.") +set(KOKKOS_ENABLE_CUDA_LAMBDA ON CACHE BOOL "Enable lambdas for CUDA.") + +################################### FUNCTIONS ################################## + +# Sets the following compiler variables that are analogous to the CMAKE_* +# versions. We add the ability to detect NVCC (really nvcc_wrapper). +# KOKKOS_CXX_COMPILER +# KOKKOS_CXX_COMPILER_ID +# KOKKOS_CXX_COMPILER_VERSION +# +# Also verifies the compiler version meets the minimum required by Kokkos. +function(set_kokkos_cxx_compiler) + # Since CMake doesn't recognize the nvcc compiler until 3.8, we use our own + # version of the CMake variables and detect nvcc ourselves. Initially set to + # the CMake variable values. + set(INTERNAL_CXX_COMPILER ${CMAKE_CXX_COMPILER}) + set(INTERNAL_CXX_COMPILER_ID ${CMAKE_CXX_COMPILER_ID}) + set(INTERNAL_CXX_COMPILER_VERSION ${CMAKE_CXX_COMPILER_VERSION}) + + # Check if the compiler is nvcc (which really means nvcc_wrapper). + execute_process(COMMAND ${INTERNAL_CXX_COMPILER} --version + COMMAND grep nvcc + COMMAND wc -l + OUTPUT_VARIABLE INTERNAL_HAVE_COMPILER_NVCC + OUTPUT_STRIP_TRAILING_WHITESPACE) + + string(REGEX REPLACE "^ +" "" + INTERNAL_HAVE_COMPILER_NVCC ${INTERNAL_HAVE_COMPILER_NVCC}) + + if(INTERNAL_HAVE_COMPILER_NVCC) + # Set the compiler id to nvcc. We use the value used by CMake 3.8. + set(INTERNAL_CXX_COMPILER_ID NVIDIA) + + # Set nvcc's compiler version. + execute_process(COMMAND ${INTERNAL_CXX_COMPILER} --version + COMMAND grep release + OUTPUT_VARIABLE INTERNAL_CXX_COMPILER_VERSION + OUTPUT_STRIP_TRAILING_WHITESPACE) + + string(REGEX MATCH "[0-9]+\.[0-9]+\.[0-9]+$" + INTERNAL_CXX_COMPILER_VERSION ${INTERNAL_CXX_COMPILER_VERSION}) + endif() + + # Enforce the minimum compilers supported by Kokkos. + set(KOKKOS_MESSAGE_TEXT "Compiler not supported by Kokkos. Required compiler versions:") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Clang 3.5.2 or higher") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n GCC 4.7.2 or higher") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Intel 14.0.4 or higher") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n NVCC 7.0.28 or higher") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n PGI 17.1 or higher\n") + + if(INTERNAL_CXX_COMPILER_ID STREQUAL Clang) + if(INTERNAL_CXX_COMPILER_VERSION VERSION_LESS 3.5.2) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") + endif() + elseif(INTERNAL_CXX_COMPILER_ID STREQUAL GNU) + if(INTERNAL_CXX_COMPILER_VERSION VERSION_LESS 4.7.2) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") + endif() + elseif(INTERNAL_CXX_COMPILER_ID STREQUAL Intel) + if(INTERNAL_CXX_COMPILER_VERSION VERSION_LESS 14.0.4) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") + endif() + elseif(INTERNAL_CXX_COMPILER_ID STREQUAL NVIDIA) + if(INTERNAL_CXX_COMPILER_VERSION VERSION_LESS 7.0.28) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") + endif() + elseif(INTERNAL_CXX_COMPILER_ID STREQUAL PGI) + if(INTERNAL_CXX_COMPILER_VERSION VERSION_LESS 17.1) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") + endif() + endif() + + # Enforce that extensions are turned off for nvcc_wrapper. + if(INTERNAL_CXX_COMPILER_ID STREQUAL NVIDIA) + if(NOT DEFINED CMAKE_CXX_EXTENSIONS OR CMAKE_CXX_EXTENSIONS STREQUAL ON) + message(FATAL_ERROR "NVCC doesn't support C++ extensions. Set CMAKE_CXX_EXTENSIONS to OFF in your CMakeLists.txt.") + endif() + endif() + + if(KOKKOS_ENABLE_CUDA) + # Enforce that the compiler can compile CUDA code. + if(INTERNAL_CXX_COMPILER_ID STREQUAL Clang) + if(INTERNAL_CXX_COMPILER_VERSION VERSION_LESS 4.0.0) + message(FATAL_ERROR "Compiling CUDA code directly with Clang requires version 4.0.0 or higher.") + endif() + elseif(NOT INTERNAL_CXX_COMPILER_ID STREQUAL NVIDIA) + message(FATAL_ERROR "Invalid compiler for CUDA. The compiler must be nvcc_wrapper or Clang.") + endif() + endif() + + set(KOKKOS_CXX_COMPILER ${INTERNAL_CXX_COMPILER} PARENT_SCOPE) + set(KOKKOS_CXX_COMPILER_ID ${INTERNAL_CXX_COMPILER_ID} PARENT_SCOPE) + set(KOKKOS_CXX_COMPILER_VERSION ${INTERNAL_CXX_COMPILER_VERSION} PARENT_SCOPE) +endfunction() + +# Transitively enforces that the appropriate CXX standard compile flags (C++11 +# or above) are added to targets that use the Kokkos library. Compile features +# are used if possible. Otherwise, the appropriate flags are added to +# KOKKOS_CXX_FLAGS. Values set by the user to CMAKE_CXX_STANDARD and +# CMAKE_CXX_EXTENSIONS are honored. +function(set_kokkos_compiler_standard) + # The following table lists the versions of CMake that supports CXX_STANDARD + # and the CXX compile features for different compilers. The versions are + # based on CMake documentation, looking at CMake code, and verifying by + # testing with specific CMake versions. + # + # COMPILER CXX_STANDARD Compile Features + # --------------------------------------------------------------- + # Clang 3.1 3.1 + # GNU 3.1 3.2 + # AppleClang 3.2 3.2 + # Intel 3.6 3.6 + # Cray No No + # PGI No No + # XL No No + # + # For compiling CUDA code using nvcc_wrapper, we will use the host compiler's + # flags for turning on C++11. Since for compiler ID and versioning purposes + # CMake recognizes the host compiler when calling nvcc_wrapper, this just + # works. Both NVCC and nvcc_wrapper only recognize '-std=c++11' which means + # that we can only use host compilers for CUDA builds that use those flags. + # It also means that extensions (gnu++11) can't be turned on for CUDA builds. + + # Check if we can use compile features. + if(NOT KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) + if(CMAKE_CXX_COMPILER_ID STREQUAL Clang) + if(NOT CMAKE_VERSION VERSION_LESS 3.1) + set(INTERNAL_USE_COMPILE_FEATURES ON) + endif() + elseif(CMAKE_CXX_COMPILER_ID STREQUAL AppleClang OR CMAKE_CXX_COMPILER_ID STREQUAL GNU) + if(NOT CMAKE_VERSION VERSION_LESS 3.2) + set(INTERNAL_USE_COMPILE_FEATURES ON) + endif() + elseif(CMAKE_CXX_COMPILER_ID STREQUAL Intel) + if(NOT CMAKE_VERSION VERSION_LESS 3.6) + set(INTERNAL_USE_COMPILE_FEATURES ON) + endif() + endif() + endif() + + if(INTERNAL_USE_COMPILE_FEATURES) + # Use the compile features aspect of CMake to transitively cause C++ flags + # to populate to user code. + + # I'm using a hack by requiring features that I know force the lowest version + # of the compilers we want to support. Clang 3.3 and later support all of + # the C++11 standard. With CMake 3.8 and higher, we could switch to using + # cxx_std_11. + set(KOKKOS_CXX11_FEATURES + cxx_nonstatic_member_init # Forces GCC 4.7 or later and Intel 14.0 or later. + PARENT_SCOPE + ) + else() + # CXX compile features are not yet implemented for this combination of + # compiler and version of CMake. + + if(CMAKE_CXX_COMPILER_ID STREQUAL AppleClang) + # Versions of CMAKE before 3.2 don't support CXX_STANDARD or C++ compile + # features for the AppleClang compiler. Set compiler flags transitively + # here such that they trickle down to a call to target_compile_options(). + + # The following two blocks of code were copied from + # /Modules/Compiler/AppleClang-CXX.cmake from CMake 3.7.2 and then + # modified. + if(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.0) + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION "-std=c++11") + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION "-std=gnu++11") + endif() + + if(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 6.1) + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "-std=c++14") + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "-std=gnu++14") + elseif(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.1) + # AppleClang 5.0 knows this flag, but does not set a __cplusplus macro + # greater than 201103L. + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "-std=c++1y") + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "-std=gnu++1y") + endif() + elseif(CMAKE_CXX_COMPILER_ID STREQUAL Intel) + # Versions of CMAKE before 3.6 don't support CXX_STANDARD or C++ compile + # features for the Intel compiler. Set compiler flags transitively here + # such that they trickle down to a call to target_compile_options(). + + # The following three blocks of code were copied from + # /Modules/Compiler/Intel-CXX.cmake from CMake 3.7.2 and then modified. + if("x${CMAKE_CXX_SIMULATE_ID}" STREQUAL "xMSVC") + set(_std -Qstd) + set(_ext c++) + else() + set(_std -std) + set(_ext gnu++) + endif() + + if(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 15.0.2) + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "${_std}=c++14") + # TODO: There is no gnu++14 value supported; figure out what to do. + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "${_std}=c++14") + elseif(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 15.0.0) + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "${_std}=c++1y") + # TODO: There is no gnu++14 value supported; figure out what to do. + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "${_std}=c++1y") + endif() + + if(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 13.0) + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION "${_std}=c++11") + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION "${_std}=${_ext}11") + elseif(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 12.1) + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION "${_std}=c++0x") + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION "${_std}=${_ext}0x") + endif() + elseif(CMAKE_CXX_COMPILER_ID STREQUAL Cray) + # CMAKE doesn't support CXX_STANDARD or C++ compile features for the Cray + # compiler. Set compiler options transitively here such that they trickle + # down to a call to target_compile_options(). + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION "-hstd=c++11") + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION "-hstd=c++11") + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "-hstd=c++11") + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "-hstd=c++11") + elseif(CMAKE_CXX_COMPILER_ID STREQUAL PGI) + # CMAKE doesn't support CXX_STANDARD or C++ compile features for the PGI + # compiler. Set compiler options transitively here such that they trickle + # down to a call to target_compile_options(). + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION "--c++11") + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION "--c++11") + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "--c++11") + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "--c++11") + elseif(CMAKE_CXX_COMPILER_ID STREQUAL XL) + # CMAKE doesn't support CXX_STANDARD or C++ compile features for the XL + # compiler. Set compiler options transitively here such that they trickle + # down to a call to target_compile_options(). + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION "-std=c++11") + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION "-std=c++11") + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "-std=c++11") + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "-std=c++11") + else() + # Assume GNU. CMAKE_CXX_STANDARD is handled correctly by CMake 3.1 and + # above for this compiler. If the user explicitly requests a C++ + # standard, CMake takes care of it. If not, transitively require C++11. + if(NOT CMAKE_CXX_STANDARD) + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION ${CMAKE_CXX11_STANDARD_COMPILE_OPTION}) + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION ${CMAKE_CXX11_EXTENSION_COMPILE_OPTION}) + endif() + endif() + + # Set the C++ standard info for Kokkos respecting user set values for + # CMAKE_CXX_STANDARD and CMAKE_CXX_EXTENSIONS. + if(CMAKE_CXX_STANDARD EQUAL 14) + if(DEFINED CMAKE_CXX_EXTENSIONS AND CMAKE_CXX_EXTENSIONS STREQUAL OFF) + set(INTERNAL_CXX_FLAGS ${INTERNAL_CXX14_STANDARD_COMPILE_OPTION}) + else() + set(INTERNAL_CXX_FLAGS ${INTERNAL_CXX14_EXTENSION_COMPILE_OPTION}) + endif() + elseif(CMAKE_CXX_STANDARD EQUAL 11) + if(DEFINED CMAKE_CXX_EXTENSIONS AND CMAKE_CXX_EXTENSIONS STREQUAL OFF) + set(INTERNAL_CXX_FLAGS ${INTERNAL_CXX11_STANDARD_COMPILE_OPTION}) + else() + set(INTERNAL_CXX_FLAGS ${INTERNAL_CXX11_EXTENSION_COMPILE_OPTION}) + endif() + else() + # The user didn't explicitly request a standard, transitively require + # C++11 respecting CMAKE_CXX_EXTENSIONS. + if(DEFINED CMAKE_CXX_EXTENSIONS AND CMAKE_CXX_EXTENSIONS STREQUAL OFF) + set(INTERNAL_CXX_FLAGS ${INTERNAL_CXX11_STANDARD_COMPILE_OPTION}) + else() + set(INTERNAL_CXX_FLAGS ${INTERNAL_CXX11_EXTENSION_COMPILE_OPTION}) + endif() + endif() + + set(KOKKOS_CXX_FLAGS ${INTERNAL_CXX_FLAGS} PARENT_SCOPE) + endif() +endfunction() + +########################## COMPILER AND FEATURE CHECKS ######################### + +# TODO: We are assuming that nvcc_wrapper is using g++ as the host compiler. +# Should we allow the user the option to change this? The host compiler +# for nvcc_wrapper can be set via the NVCC_WRAPPER_DEFAULT_COMPILER +# environment variable or by passing a different host compiler with the +# -ccbin flag. + +# TODO: Fully add CUDA support for Clang. +set_kokkos_cxx_compiler() + +set_kokkos_compiler_standard() + +######################### INITIALIZE INTERNAL VARIABLES ######################## + +# Add Kokkos' modules to CMake's module path. +set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${Kokkos_SOURCE_DIR}/cmake/Modules/") + +# Start with all global variables set to false. This guarantees correct +# results with changes and multiple configures. +set(KOKKOS_HAVE_CUDA OFF CACHE INTERNAL "") +set(KOKKOS_USE_CUDA_UVM OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_CUDA_RDC OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_CUDA_LAMBDA OFF CACHE INTERNAL "") +set(KOKKOS_CUDA_CLANG_WORKAROUND OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_OPENMP OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_PTHREAD OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_QTHREADS OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_SERIAL OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_HWLOC OFF CACHE INTERNAL "") +set(KOKKOS_ENABLE_HBWSPACE OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_DEBUG OFF CACHE INTERNAL "") +set(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK OFF CACHE INTERNAL "") +set(KOKKOS_ENABLE_ISA_X86_64 OFF CACHE INTERNAL "") +set(KOKKOS_ENABLE_ISA_KNC OFF CACHE INTERNAL "") +set(KOKKOS_ENABLE_ISA_POWERPCLE OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_ARMV80 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_ARMV81 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_ARMV8_THUNDERX OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_AVX OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_AVX2 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_AVX512MIC OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_AVX512XEON OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_KNC OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_POWER8 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_POWER9 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_KEPLER OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_KEPLER30 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_KEPLER32 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_KEPLER35 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_KEPLER37 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_MAXWELL OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_MAXWELL50 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_MAXWELL52 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_MAXWELL53 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_PASCAL OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_PASCAL60 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_PASCAL61 OFF CACHE INTERNAL "") + +############################## SET BACKEND OPTIONS ############################# + +# Make sure at least one backend is selected. +if(NOT KOKKOS_ENABLE_CUDA AND NOT KOKKOS_ENABLE_OPENMP AND NOT KOKKOS_ENABLE_PTHREAD AND NOT KOKKOS_ENABLE_QTHREADS AND NOT KOKKOS_ENABLE_SERIAL) + message(FATAL_ERROR "Must set one of KOKKOS_ENABLE_CUDA, KOKKOS_ENABLE_OPENMP, KOKKOS_ENABLE_PTHREAD, KOKKOS_ENABLE_QTHREADS, or KOKKOS_ENABLE_SERIAL") +endif() + +# Only one of OpenMP, Pthreads, and Qthreads can be set. +set(KOKKOS_MESSAGE_TEXT "Only one of KOKKOS_ENABLE_OPENMP, KOKKOS_ENABLE_PTHREAD, and KOKKOS_ENABLE_QTHREADS can be selected") +if(KOKKOS_ENABLE_OPENMP AND KOKKOS_ENABLE_PTHREAD) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") +elseif(KOKKOS_ENABLE_OPENMP AND KOKKOS_ENABLE_QTHREADS) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") +elseif(KOKKOS_ENABLE_PTHREAD AND KOKKOS_ENABLE_QTHREADS) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") +endif() + +# Get source files. +file(GLOB KOKKOS_CORE_SRCS core/src/impl/*.cpp) +file(GLOB KOKKOS_CONTAINERS_SRCS containers/src/impl/*.cpp) + +# Set options if using CUDA backend. +if(KOKKOS_ENABLE_CUDA) + if(KOKKOS_CUDA_DIR) + set(CUDA_TOOLKIT_ROOT_DIR ${KOKKOS_CUDA_DIR}) + endif() + + find_package(CUDA) + + if(NOT CUDA_FOUND) + if(KOKKOS_CUDA_DIR) + message(FATAL_ERROR "Couldn't find CUDA in default locations, and KOKKOS_CUDA_DIR points to an invalid installation.") + else() + message(FATAL_ERROR "Couldn't find CUDA in default locations. Set KOKKOS_CUDA_DIR.") + endif() + endif() + + list(APPEND KOKKOS_INCLUDE_DIRS ${CUDA_INCLUDE_DIRS}) + list(APPEND KOKKOS_LD_FLAGS -L${CUDA_TOOLKIT_ROOT_DIR}/lib64) + list(APPEND KOKKOS_LIBS cudart cuda) + + set(KOKKOS_HAVE_CUDA ON CACHE INTERNAL "") + file(GLOB KOKKOS_CUDA_SRCS core/src/Cuda/*.cpp) + list(APPEND KOKKOS_CORE_SRCS ${KOKKOS_CUDA_SRCS}) + + # Set CUDA UVM if requested. + if(KOKKOS_ENABLE_CUDA_UVM) + set(KOKKOS_USE_CUDA_UVM ON CACHE INTERNAL "") + endif() + + # Set CUDA relocatable device code if requested. + if(KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE) + set(KOKKOS_HAVE_CUDA_RDC ON CACHE INTERNAL "") + list(APPEND KOKKOS_CXX_FLAGS --relocatable-device-code=true) + list(APPEND KOKKOS_LD_FLAGS --relocatable-device-code=true) + endif() + + # Set CUDA lambda if requested. + if(KOKKOS_ENABLE_CUDA_LAMBDA) + set(KOKKOS_HAVE_CUDA_LAMBDA ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) + if(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 7.5) + message(FATAL_ERROR "CUDA lambda support requires CUDA 7.5 or higher. Disable it or use a 7.5 or later compiler.") + else() + list(APPEND KOKKOS_CXX_FLAGS -expt-extended-lambda) + endif() + endif() + endif() + + # Set Clang specific options. + if(KOKKOS_CXX_COMPILER_ID STREQUAL Clang) + list(APPEND KOKKOS_CXX_FLAGS --cuda-path=${CUDA_TOOLKIT_ROOT_DIR}) + + set(KOKKOS_CUDA_CLANG_WORKAROUND ON CACHE INTERNAL "") + + # Force CUDA_LDG_INTRINSIC on when using Clang. + set(KOKKOS_ENABLE_CUDA_LDG_INTRINSIC ON CACHE BOOL "Enable CUDA LDG." FORCE) + endif() +endif() + +# Set options if using OpenMP backend. +if(KOKKOS_ENABLE_OPENMP) + find_package(OpenMP REQUIRED) + + if(OPENMP_FOUND) + if(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) + list(APPEND KOKKOS_CXX_FLAGS -Xcompiler) + endif() + + list(APPEND KOKKOS_CXX_FLAGS ${OpenMP_CXX_FLAGS}) + list(APPEND KOKKOS_LD_FLAGS ${OpenMP_CXX_FLAGS}) + endif() + + set(KOKKOS_HAVE_OPENMP ON CACHE INTERNAL "") + file(GLOB KOKKOS_OPENMP_SRCS core/src/OpenMP/*.cpp) + list(APPEND KOKKOS_CORE_SRCS ${KOKKOS_OPENMP_SRCS}) +endif() + +# Set options if using Pthreads backend. +if(KOKKOS_ENABLE_PTHREAD) + find_package(Threads REQUIRED) + + list(APPEND KOKKOS_LIBS Threads::Threads) + + set(KOKKOS_HAVE_PTHREAD ON CACHE INTERNAL "") + file(GLOB KOKKOS_PTHREAD_SRCS core/src/Threads/*.cpp) + list(APPEND KOKKOS_CORE_SRCS ${KOKKOS_PTHREAD_SRCS}) +endif() + +# Set options if using Qthreads backend. +if(KOKKOS_ENABLE_QTHREADS) + if(KOKKOS_QTHREADS_DIR) + list(APPEND CMAKE_PREFIX_PATH ${KOKKOS_QTHREADS_DIR}) + endif() + + find_package(Qthreads) + + if(NOT QTHREADS_FOUND) + if(KOKKOS_QTHREADS_DIR) + message(FATAL_ERROR "Couldn't find Qthreads in default locations, and KOKKOS_QTHREADS_DIR points to an invalid installation.") + else() + message(FATAL_ERROR "Couldn't find Qthreads in default locations. Set KOKKOS_QTHREADS_DIR.") + endif() + endif() + + list(APPEND KOKKOS_INCLUDE_DIRS ${QTHREADS_INCLUDE_DIR}) + list(APPEND KOKKOS_LIBS ${QTHREADS_LIBRARIES}) + + set(KOKKOS_HAVE_QTHREADS ON CACHE INTERNAL "") + file(GLOB KOKKOS_QTHREADS_SRCS core/src/Threads/*.cpp) + list(APPEND KOKKOS_CORE_SRCS ${KOKKOS_QTHREADS_SRCS}) + + if(KOKKOS_QTHREADS_DIR) + list(REMOVE_AT CMAKE_PREFIX_PATH -1) + endif() +endif() + +# Set options if using Serial backend. +if(KOKKOS_ENABLE_SERIAL) + set(KOKKOS_HAVE_SERIAL ON CACHE INTERNAL "") +else() + # Remove serial source files. + list(REMOVE_ITEM KOKKOS_CORE_SRCS + "${Kokkos_SOURCE_DIR}/core/src/impl/Kokkos_Serial.cpp" + "${Kokkos_SOURCE_DIR}/core/src/impl/Kokkos_Serial_Task.cpp") +endif() + +########################### SET ARCHITECTURE OPTIONS ########################### + +# Make sure the host architecture option is valid. Need to verify in case user +# passes the option via the command line. +list(FIND KOKKOS_HOST_ARCH_LIST "${KOKKOS_HOST_ARCH}" KOKKOS_VALID_HOST_ARCH) +if(KOKKOS_VALID_HOST_ARCH EQUAL -1) + set(KOKKOS_ARCH_TEXT "\n ${KOKKOS_HOST_ARCH_LIST}") + string(REPLACE ";" "\n " KOKKOS_ARCH_TEXT "${KOKKOS_ARCH_TEXT}") + set(KOKKOS_MESSAGE_TEXT "Invalid architecture for KOKKOS_HOST_ARCH: '${KOKKOS_HOST_ARCH}'") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Choices:${KOKKOS_ARCH_TEXT}\n") + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") +endif() + +# Make sure the GPU architecture option is valid. Need to verify in case user +# passes the option via the command line. +list(FIND KOKKOS_GPU_ARCH_LIST "${KOKKOS_GPU_ARCH}" KOKKOS_VALID_GPU_ARCH) +if(KOKKOS_VALID_GPU_ARCH EQUAL -1) + set(KOKKOS_ARCH_TEXT "\n ${KOKKOS_GPU_ARCH_LIST}") + string(REPLACE ";" "\n " KOKKOS_ARCH_TEXT "${KOKKOS_ARCH_TEXT}") + set(KOKKOS_MESSAGE_TEXT "Invalid architecture for KOKKOS_GPU_ARCH: '${KOKKOS_GPU_ARCH}'") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Choices:${KOKKOS_ARCH_TEXT}\n") + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") +endif() + +# Decide what ISA level we are able to support. +if(KOKKOS_HOST_ARCH STREQUAL SNB OR KOKKOS_HOST_ARCH STREQUAL HSW OR KOKKOS_HOST_ARCH STREQUAL BDW OR + KOKKOS_HOST_ARCH STREQUAL SKX OR KOKKOS_HOST_ARCH STREQUAL KNL) + set(KOKKOS_ENABLE_ISA_X86_64 ON CACHE INTERNAL "") +endif() + +if(KOKKOS_HOST_ARCH STREQUAL KNC) + set(KOKKOS_ENABLE_ISA_KNC ON CACHE INTERNAL "") +endif() + +if(KOKKOS_HOST_ARCH STREQUAL Power8 OR KOKKOS_HOST_ARCH STREQUAL Power9) + set(KOKKOS_ENABLE_ISA_POWERPCLE ON CACHE INTERNAL "") +endif() + +# Add host architecture options. +if(KOKKOS_HOST_ARCH STREQUAL ARMv80) + set(KOKKOS_ARCH_ARMV80 ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -march=armv8-a) + list(APPEND KOKKOS_LD_FLAGS -march=armv8-a) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL ARMv81) + set(KOKKOS_ARCH_ARMV81 ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -march=armv8.1-a) + list(APPEND KOKKOS_LD_FLAGS -march=armv8.1-a) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL ARMv8-ThunderX) + set(KOKKOS_ARCH_ARMV80 ON CACHE INTERNAL "") + set(KOKKOS_ARCH_ARMV8_THUNDERX ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -march=armv8-a -mtune=thunderx) + list(APPEND KOKKOS_LD_FLAGS -march=armv8-a -mtune=thunderx) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL SNB OR KOKKOS_HOST_ARCH STREQUAL AMDAVX) + set(KOKKOS_ARCH_AVX ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Intel) + list(APPEND KOKKOS_CXX_FLAGS -mavx) + list(APPEND KOKKOS_LD_FLAGS -mavx) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + list(APPEND KOKKOS_CXX_FLAGS -tp=sandybridge) + list(APPEND KOKKOS_LD_FLAGS -tp=sandybridge) + else() + list(APPEND KOKKOS_CXX_FLAGS -mavx) + list(APPEND KOKKOS_LD_FLAGS -mavx) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL HSW OR KOKKOS_HOST_ARCH STREQUAL BDW) + set(KOKKOS_ARCH_AVX2 ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Intel) + list(APPEND KOKKOS_CXX_FLAGS -xCORE-AVX2) + list(APPEND KOKKOS_LD_FLAGS -xCORE-AVX2) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + list(APPEND KOKKOS_CXX_FLAGS -tp=haswell) + list(APPEND KOKKOS_LD_FLAGS -tp=haswell) + else() + list(APPEND KOKKOS_CXX_FLAGS -march=core-avx2 -mtune=core-avx2) + list(APPEND KOKKOS_LD_FLAGS -march=core-avx2 -mtune=core-avx2) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL KNL) + set(KOKKOS_ARCH_AVX512MIC ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Intel) + list(APPEND KOKKOS_CXX_FLAGS -xMIC-AVX512) + list(APPEND KOKKOS_LD_FLAGS -xMIC-AVX512) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -march=knl) + list(APPEND KOKKOS_LD_FLAGS -march=knl) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL SKX) + set(KOKKOS_ARCH_AVX512XEON ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Intel) + list(APPEND KOKKOS_CXX_FLAGS -xCORE-AVX512) + list(APPEND KOKKOS_LD_FLAGS -xCORE-AVX512) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -march=skylake-avx512) + list(APPEND KOKKOS_LD_FLAGS -march=skylake-avx512) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL KNC) + set(KOKKOS_ARCH_KNC ON CACHE INTERNAL "") + list(APPEND KOKKOS_CXX_FLAGS -mmic) + list(APPEND KOKKOS_LD_FLAGS -mmic) +elseif(KOKKOS_HOST_ARCH STREQUAL Power8) + set(KOKKOS_ARCH_POWER8 ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -mcpu=power8 -mtune=power8) + list(APPEND KOKKOS_LD_FLAGS -mcpu=power8 -mtune=power8) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL Power9) + set(KOKKOS_ARCH_POWER9 ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -mcpu=power9 -mtune=power9) + list(APPEND KOKKOS_LD_FLAGS -mcpu=power9 -mtune=power9) + endif() +endif() + +# Add GPU architecture options. +if(KOKKOS_ENABLE_CUDA) + if(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) + set(KOKKOS_GPU_ARCH_FLAG -arch) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL Clang) + list(APPEND KOKKOS_CXX_FLAGS -x cuda) + set(KOKKOS_GPU_ARCH_FLAG --cuda-gpu-arch) + endif() + + if(KOKKOS_GPU_ARCH STREQUAL Kepler30) + set(KOKKOS_ARCH_KEPLER ON CACHE INTERNAL "") + set(KOKKOS_ARCH_KEPLER30 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_30) + elseif(KOKKOS_GPU_ARCH STREQUAL Kepler32) + set(KOKKOS_ARCH_KEPLER ON CACHE INTERNAL "") + set(KOKKOS_ARCH_KEPLER32 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_32) + elseif(KOKKOS_GPU_ARCH STREQUAL Kepler35 OR KOKKOS_GPU_ARCH STREQUAL Kepler) + set(KOKKOS_ARCH_KEPLER ON CACHE INTERNAL "") + set(KOKKOS_ARCH_KEPLER35 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_35) + elseif(KOKKOS_GPU_ARCH STREQUAL Kepler37) + set(KOKKOS_ARCH_KEPLER ON CACHE INTERNAL "") + set(KOKKOS_ARCH_KEPLER37 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_37) + elseif(KOKKOS_GPU_ARCH STREQUAL Maxwell50 OR KOKKOS_GPU_ARCH STREQUAL Maxwell) + set(KOKKOS_ARCH_MAXWELL ON CACHE INTERNAL "") + set(KOKKOS_ARCH_MAXWELL50 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_50) + elseif(KOKKOS_GPU_ARCH STREQUAL Maxwell52) + set(KOKKOS_ARCH_MAXWELL ON CACHE INTERNAL "") + set(KOKKOS_ARCH_MAXWELL52 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_52) + elseif(KOKKOS_GPU_ARCH STREQUAL Maxwell53) + set(KOKKOS_ARCH_MAXWELL ON CACHE INTERNAL "") + set(KOKKOS_ARCH_MAXWELL53 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_53) + elseif(KOKKOS_GPU_ARCH STREQUAL Pascal60) + set(KOKKOS_ARCH_PASCAL ON CACHE INTERNAL "") + set(KOKKOS_ARCH_PASCAL60 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_60) + elseif(KOKKOS_GPU_ARCH STREQUAL Pascal61) + set(KOKKOS_ARCH_PASCAL ON CACHE INTERNAL "") + set(KOKKOS_ARCH_PASCAL61 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_61) + endif() + + if(NOT KOKKOS_GPU_ARCH STREQUAL None) + list(APPEND KOKKOS_CXX_FLAGS ${KOKKOS_GPU_ARCH_FLAG}) + + if(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) + list(APPEND KOKKOS_LD_FLAGS ${KOKKOS_GPU_ARCH_FLAG}) + endif() + endif() +endif() + +############################### SET OTHER OPTIONS ############################## + +# Set options if using hwloc. +if(KOKKOS_ENABLE_HWLOC) + if(KOKKOS_HWLOC_DIR) + list(APPEND CMAKE_PREFIX_PATH ${KOKKOS_HWLOC_DIR}) + endif() + + find_package(HWLOC) + + if(NOT HWLOC_FOUND) + if(KOKKOS_HWLOC_DIR) + message(FATAL_ERROR "Couldn't find HWLOC in default locations, and KOKKOS_HWLOC_DIR points to an invalid installation.") + else() + message(FATAL_ERROR "Couldn't find HWLOC in default locations. Set KOKKOS_HWLOC_DIR.") + endif() + endif() + + list(APPEND KOKKOS_INCLUDE_DIRS ${HWLOC_INCLUDE_DIR}) + list(APPEND KOKKOS_LIBS ${HWLOC_LIBRARIES}) + + set(KOKKOS_HAVE_HWLOC ON CACHE INTERNAL "") + + if(KOKKOS_HWLOC_DIR) + list(REMOVE_AT CMAKE_PREFIX_PATH -1) + endif() +endif() + +# Set options if using memkind. +if(KOKKOS_ENABLE_MEMKIND) + if(KOKKOS_MEMKIND_DIR) + list(APPEND CMAKE_PREFIX_PATH ${KOKKOS_MEMKIND_DIR}) + endif() + + find_package(Memkind) + + if(NOT MEMKIND_FOUND) + if(KOKKOS_MEMKIND_DIR) + message(FATAL_ERROR "Couldn't find Memkind in default locations, and KOKKOS_MEMKIND_DIR points to an invalid installation.") + else() + message(FATAL_ERROR "Couldn't find Memkind in default locations. Set KOKKOS_MEMKIND_DIR.") + endif() + endif() + + set(KOKKOS_ENABLE_HBWSPACE ON CACHE INTERNAL "") + list(APPEND KOKKOS_INCLUDE_DIRS ${MEMKIND_INCLUDE_DIR}) + list(APPEND KOKKOS_LIBS ${MEMKIND_LIBRARIES}) + + if(KOKKOS_MEMKIND_DIR) + list(REMOVE_AT CMAKE_PREFIX_PATH -1) + endif() +else() + # Remove HBW source file. + list(REMOVE_ITEM KOKKOS_CORE_SRCS + "${Kokkos_SOURCE_DIR}/core/src/impl/Kokkos_HBWSpace.cpp") +endif() + +# Set options if using librt. +if(KOKKOS_ENABLE_LIBRT) + list(APPEND KOKKOS_LIBS rt) +endif() + +# Set debugging if requested. +if(KOKKOS_DEBUG) + set(KOKKOS_HAVE_DEBUG ON CACHE INTERNAL "") + set(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COVIDIA) + list(APPEND KOKKOS_CXX_FLAGS -lineinfo) + endif() + + list(APPEND KOKKOS_CXX_FLAGS -g) + list(APPEND KOKKOS_LD_FLAGS -g) +endif() + +# Set profiling if requested. +if(KOKKOS_ENABLE_PROFILING) + list(APPEND KOKKOS_LIBS dl) +else() + # Remove profiling source file. + list(REMOVE_ITEM KOKKOS_CORE_SRCS + "${Kokkos_SOURCE_DIR}/core/src/impl/Kokkos_Profiling_Interface.cpp") +endif() + +# Use GCC toolchain with Clang. +if(KOKKOS_CXX_COMPILER_ID STREQUAL Clang AND NOT APPLE) + find_program(KOKKOS_GCC_PATH g++) + if(NOT KOKKOS_GCC_PATH) + message(FATAL_ERROR "Can't find GCC path to get toolchain for Clang.") + endif() + string(REPLACE "/bin/g++" "" KOKKOS_GCC_PATH ${KOKKOS_GCC_PATH}) + + list(APPEND KOKKOS_CXX_FLAGS --gcc-toolchain=${KOKKOS_GCC_PATH}) + list(APPEND KOKKOS_LD_FLAGS --gcc-toolchain=${KOKKOS_GCC_PATH}) +endif() + +############################ Detect if submodule ############################### +# +# With thanks to StackOverflow: +# http://stackoverflow.com/questions/25199677/how-to-detect-if-current-scope-has-a-parent-in-cmake +# +get_directory_property(HAS_PARENT PARENT_DIRECTORY) +if(HAS_PARENT) + message(STATUS "Submodule build") + SET(KOKKOS_HEADER_DIR "include/kokkos") +else() + message(STATUS "Standalone build") + SET(KOKKOS_HEADER_DIR "include") +endif() + +############################ PRINT CONFIGURE STATUS ############################ + +message(STATUS "") +message(STATUS "****************** Kokkos Settings ******************") +message(STATUS "Execution Spaces") + +if(KOKKOS_ENABLE_CUDA) + message(STATUS " Device Parallel: Cuda") +else() + message(STATUS " Device Parallel: None") +endif() + +if(KOKKOS_ENABLE_OPENMP) + message(STATUS " Host Parallel: OpenMP") +elseif(KOKKOS_ENABLE_PTHREAD) + message(STATUS " Host Parallel: Pthread") +elseif(KOKKOS_ENABLE_QTHREADS) + message(STATUS " Host Parallel: Qthreads") +else() + message(STATUS " Host Parallel: None") +endif() + +if(KOKKOS_ENABLE_SERIAL) + message(STATUS " Host Serial: Serial") +else() + message(STATUS " Host Serial: None") +endif() + +message(STATUS "") +message(STATUS "Architectures") +message(STATUS " Host Architecture: ${KOKKOS_HOST_ARCH}") +message(STATUS " Device Architecture: ${KOKKOS_GPU_ARCH}") + +message(STATUS "") +message(STATUS "Enabled options") + +if(KOKKOS_SEPARATE_LIBS) + message(STATUS " KOKKOS_SEPARATE_LIBS") +endif() + +if(KOKKOS_ENABLE_HWLOC) + message(STATUS " KOKKOS_ENABLE_HWLOC") +endif() + +if(KOKKOS_ENABLE_MEMKIND) + message(STATUS " KOKKOS_ENABLE_MEMKIND") +endif() + +if(KOKKOS_DEBUG) + message(STATUS " KOKKOS_DEBUG") +endif() + +if(KOKKOS_ENABLE_PROFILING) + message(STATUS " KOKKOS_ENABLE_PROFILING") +endif() + +if(KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION) + message(STATUS " KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION") +endif() + +if(KOKKOS_ENABLE_CUDA) + if(KOKKOS_ENABLE_CUDA_LDG_INTRINSIC) + message(STATUS " KOKKOS_ENABLE_CUDA_LDG_INTRINSIC") + endif() + + if(KOKKOS_ENABLE_CUDA_UVM) + message(STATUS " KOKKOS_ENABLE_CUDA_UVM") + endif() + + if(KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE) + message(STATUS " KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE") + endif() + + if(KOKKOS_ENABLE_CUDA_LAMBDA) + message(STATUS " KOKKOS_ENABLE_CUDA_LAMBDA") + endif() + + if(KOKKOS_CUDA_DIR) + message(STATUS " KOKKOS_CUDA_DIR: ${KOKKOS_CUDA_DIR}") + endif() +endif() + +if(KOKKOS_QTHREADS_DIR) + message(STATUS " KOKKOS_QTHREADS_DIR: ${KOKKOS_QTHREADS_DIR}") +endif() + +if(KOKKOS_HWLOC_DIR) + message(STATUS " KOKKOS_HWLOC_DIR: ${KOKKOS_HWLOC_DIR}") +endif() + +if(KOKKOS_MEMKIND_DIR) + message(STATUS " KOKKOS_MEMKIND_DIR: ${KOKKOS_MEMKIND_DIR}") +endif() + +message(STATUS "*****************************************************") +message(STATUS "") + +################################ SET UP PROJECT ################################ + +configure_file( + ${Kokkos_SOURCE_DIR}/core/cmake/KokkosCore_config.h.in + ${Kokkos_BINARY_DIR}/KokkosCore_config.h +) + +SET(INSTALL_LIB_DIR lib CACHE PATH "Installation directory for libraries") +SET(INSTALL_BIN_DIR bin CACHE PATH "Installation directory for executables") +SET(INSTALL_INCLUDE_DIR ${KOKKOS_HEADER_DIR} CACHE PATH + "Installation directory for header files") +IF(WIN32 AND NOT CYGWIN) + SET(DEF_INSTALL_CMAKE_DIR CMake) +ELSE() + SET(DEF_INSTALL_CMAKE_DIR lib/CMake/Kokkos) +ENDIF() + +SET(INSTALL_CMAKE_DIR ${DEF_INSTALL_CMAKE_DIR} CACHE PATH + "Installation directory for CMake files") + +# Make relative paths absolute (needed later on) +FOREACH(p LIB BIN INCLUDE CMAKE) + SET(var INSTALL_${p}_DIR) + IF(NOT IS_ABSOLUTE "${${var}}") + SET(${var} "${CMAKE_INSTALL_PREFIX}/${${var}}") + ENDIF() +ENDFOREACH() + +# set up include-directories +SET (Kokkos_INCLUDE_DIRS + ${Kokkos_SOURCE_DIR}/core/src + ${Kokkos_SOURCE_DIR}/containers/src + ${Kokkos_SOURCE_DIR}/algorithms/src + ${Kokkos_BINARY_DIR} # to find KokkosCore_config.h +) + +INCLUDE_DIRECTORIES(${Kokkos_INCLUDE_DIRS}) + +IF(KOKKOS_SEPARATE_LIBS) + # kokkoscore + ADD_LIBRARY( + kokkoscore + ${KOKKOS_CORE_SRCS} + ) + + target_compile_options( + kokkoscore + PUBLIC ${KOKKOS_CXX_FLAGS} + ) + + target_compile_features( + kokkoscore + PUBLIC ${KOKKOS_CXX11_FEATURES} + ) + + # Install the kokkoscore library + INSTALL (TARGETS kokkoscore + ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin + ) + + # Install the kokkoscore headers + INSTALL (DIRECTORY + ${Kokkos_SOURCE_DIR}/core/src/ + DESTINATION ${KOKKOS_HEADER_DIR} + FILES_MATCHING PATTERN "*.hpp" + ) + + # Install KokkosCore_config.h header + INSTALL (FILES + ${Kokkos_BINARY_DIR}/KokkosCore_config.h + DESTINATION ${KOKKOS_HEADER_DIR} + ) + + TARGET_LINK_LIBRARIES( + kokkoscore + ${KOKKOS_LD_FLAGS} + ${KOKKOS_LIBS} + ) + + # kokkoscontainers + ADD_LIBRARY( + kokkoscontainers + ${KOKKOS_CONTAINERS_SRCS} + ) + + TARGET_LINK_LIBRARIES( + kokkoscontainers + kokkoscore + ) + + # Install the kokkocontainers library + INSTALL (TARGETS kokkoscontainers + ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin) + + # Install the kokkoscontainers headers + INSTALL (DIRECTORY + ${Kokkos_SOURCE_DIR}/containers/src/ + DESTINATION ${KOKKOS_HEADER_DIR} + FILES_MATCHING PATTERN "*.hpp" + ) + + # kokkosalgorithms - Build as interface library since no source files. + ADD_LIBRARY( + kokkosalgorithms + INTERFACE + ) + + target_include_directories( + kokkosalgorithms + INTERFACE ${Kokkos_SOURCE_DIR}/algorithms/src + ) + + TARGET_LINK_LIBRARIES( + kokkosalgorithms + INTERFACE kokkoscore + ) + + # Install the kokkoalgorithms library + INSTALL (TARGETS kokkosalgorithms + ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin) + + # Install the kokkosalgorithms headers + INSTALL (DIRECTORY + ${Kokkos_SOURCE_DIR}/algorithms/src/ + DESTINATION ${KOKKOS_INSTALL_INDLUDE_DIR} + FILES_MATCHING PATTERN "*.hpp" + ) + + SET (Kokkos_LIBRARIES_NAMES kokkoscore kokkoscontainers kokkosalgorithms) + +ELSE() + # kokkos + ADD_LIBRARY( + kokkos + ${KOKKOS_CORE_SRCS} + ${KOKKOS_CONTAINERS_SRCS} + ) + + target_compile_options( + kokkos + PUBLIC ${KOKKOS_CXX_FLAGS} + ) + + target_compile_features( + kokkos + PUBLIC ${KOKKOS_CXX11_FEATURES} + ) + + TARGET_LINK_LIBRARIES( + kokkos + ${KOKKOS_LD_FLAGS} + ${KOKKOS_LIBS} + ) + + # Install the kokkos library + INSTALL (TARGETS kokkos + EXPORT KokkosTargets + ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin) + + + # Install the kokkos headers + INSTALL (DIRECTORY + EXPORT KokkosTargets + ${Kokkos_SOURCE_DIR}/core/src/ + DESTINATION ${KOKKOS_HEADER_DIR} + FILES_MATCHING PATTERN "*.hpp" + ) + INSTALL (DIRECTORY + EXPORT KokkosTargets + ${Kokkos_SOURCE_DIR}/containers/src/ + DESTINATION ${KOKKOS_HEADER_DIR} + FILES_MATCHING PATTERN "*.hpp" + ) + INSTALL (DIRECTORY + EXPORT KokkosTargets + ${Kokkos_SOURCE_DIR}/algorithms/src/ + DESTINATION ${KOKKOS_HEADER_DIR} + FILES_MATCHING PATTERN "*.hpp" + ) + + INSTALL (FILES + ${Kokkos_BINARY_DIR}/KokkosCore_config.h + DESTINATION ${KOKKOS_HEADER_DIR} + ) + + include_directories(${Kokkos_BINARY_DIR}) + include_directories(${Kokkos_SOURCE_DIR}/core/src) + include_directories(${Kokkos_SOURCE_DIR}/containers/src) + include_directories(${Kokkos_SOURCE_DIR}/algorithms/src) + + + SET (Kokkos_LIBRARIES_NAMES kokkos) + +endif() + +# Add all targets to the build-tree export set +export(TARGETS ${Kokkos_LIBRARIES_NAMES} + FILE "${Kokkos_BINARY_DIR}/KokkosTargets.cmake") + +# Export the package for use from the build-tree +# (this registers the build-tree with a global CMake-registry) +export(PACKAGE Kokkos) + +# Create the KokkosConfig.cmake and KokkosConfigVersion files +file(RELATIVE_PATH REL_INCLUDE_DIR "${INSTALL_CMAKE_DIR}" + "${INSTALL_INCLUDE_DIR}") +# ... for the build tree +set(CONF_INCLUDE_DIRS "${Kokkos_SOURCE_DIR}" "${Kokkos_BINARY_DIR}") +configure_file(${Kokkos_SOURCE_DIR}/cmake/KokkosConfig.cmake.in + "${Kokkos_BINARY_DIR}/KokkosConfig.cmake" @ONLY) +# ... for the install tree +set(CONF_INCLUDE_DIRS "\${Kokkos_CMAKE_DIR}/${REL_INCLUDE_DIR}") +configure_file(${Kokkos_SOURCE_DIR}/cmake/KokkosConfig.cmake.in + "${Kokkos_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/KokkosConfig.cmake" @ONLY) + +# Install the KokkosConfig.cmake and KokkosConfigVersion.cmake +install(FILES + "${Kokkos_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/KokkosConfig.cmake" + DESTINATION "${INSTALL_CMAKE_DIR}") + +# Install the export set for use with the install-tree +INSTALL(EXPORT KokkosTargets DESTINATION + "${INSTALL_CMAKE_DIR}") diff --git a/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt b/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt index 961e4186ec..0f24487814 100644 --- a/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt +++ b/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt @@ -60,34 +60,12 @@ Step 2: // -------------------------------------------------------------------------------- // Step 3: - 3.1. Build and test Trilinos with 3 different configurations; a configure-all script is provided in Trilinos and should be modified to test each of the following 3 configurations with appropriate environment variable(s): + 3.1. Build and test Trilinos with 4 different configurations; Run scripts for white and shepard are provided in kokkos/config/trilinos-integration - - GCC/4.7.2-OpenMP/Complex - Run tests with the following environment variable: + Usually its a good idea to run those script via nohup. + You can run all four at the same time, use separate directories for each. - export OMP_NUM_THREADS=2 - - - - Intel/15.0.2-Serial/NoComplex - - - - GCC/4.8.4/CUDA/7.5.18-Cuda/Serial/NoComplex - Run tests with the following environment variables: - - export CUDA_LAUNCH_BLOCKING=1 - export CUDA_MANAGED_FORCE_DEVICE_ALLOC=1 - - - mkdir Build - cd Build - cp TRILINOS_PATH/sampleScripts/Sandia-SEMS/configure-all ./ - ** Set the path to Trilinos appropriately within the configure-all script ** - source $SEMS_MODULE_ROOT/utils/sems-modules-init.sh kokkos - source configure-all - make -k (-k means "keep going" to get past build errors; -j12 can also be specified to build with 12 threads, for example) - ctest - - 3.2. Compare the failed test output to the test output on the dashboard ( testing.sandia.gov/cdash select Trilinos ); investigate and fix problems if new tests fail after the Kokkos snapshot + 3.2. Compare the failed test output between the pristine and the updated runs; investigate and fix problems if new tests fail after the Kokkos snapshot // -------------------------------------------------------------------------------- // @@ -134,7 +112,7 @@ Step 4: Once all Trilinos tests pass promote Kokkos develop branch to master on master: sha1 develop: sha1 - git push --follow-tags origin master + 4.4. Do NOT push yet // -------------------------------------------------------------------------------- // @@ -156,9 +134,15 @@ Step 5: python KOKKOS_PATH/config/snapshot.py KOKKOS_PATH TRILINOS_PATH/packages - 5.3. Push the updated develop branch of Trilinos to Github - congratulations!!! + 5.3. Run checkin-test to push to trilinos using the CI build modules (gcc/4.9.3) - (From Trilinos directory): - git push + The modules are listed in kokkos/config/trilinos-integration/checkin-test + Run checkin-test, forward dependencies and optional dependencies must be enabled + If push failed because someone else clearly broke something, push manually. + If push failed for unclear reasons, investigate, fix, and potentially start over from step 2 after reseting your local kokkos/master branch + +Step 6: Push Kokkos to master + + git push --follow-tags origin master // -------------------------------------------------------------------------------- // diff --git a/lib/kokkos/config/kokkos_dev/config-core-all.sh b/lib/kokkos/config/kokkos_dev/config-core-all.sh index d4fb25a8e1..1867de7204 100755 --- a/lib/kokkos/config/kokkos_dev/config-core-all.sh +++ b/lib/kokkos/config/kokkos_dev/config-core-all.sh @@ -13,7 +13,7 @@ # module load cmake/2.8.11.2 gcc/4.8.3 cuda/6.5.14 nvcc-wrapper/gnu # # The 'nvcc-wrapper' module should load a script that matches -# kokkos/config/nvcc_wrapper +# kokkos/bin/nvcc_wrapper # #----------------------------------------------------------------------------- # Source and installation directories: diff --git a/lib/kokkos/config/kokkos_dev/config-core-cuda-omp-hwloc.sh b/lib/kokkos/config/kokkos_dev/config-core-cuda-omp-hwloc.sh index c2e17bb944..5a6cc1493e 100755 --- a/lib/kokkos/config/kokkos_dev/config-core-cuda-omp-hwloc.sh +++ b/lib/kokkos/config/kokkos_dev/config-core-cuda-omp-hwloc.sh @@ -13,7 +13,7 @@ # module load cmake/2.8.11.2 gcc/4.8.3 cuda/6.5.14 nvcc-wrapper/gnu # # The 'nvcc-wrapper' module should load a script that matches -# kokkos/config/nvcc_wrapper +# kokkos/bin/nvcc_wrapper # #----------------------------------------------------------------------------- # Source and installation directories: diff --git a/lib/kokkos/config/kokkos_dev/config-core-cuda.sh b/lib/kokkos/config/kokkos_dev/config-core-cuda.sh index 39b72d5ce1..606755da81 100755 --- a/lib/kokkos/config/kokkos_dev/config-core-cuda.sh +++ b/lib/kokkos/config/kokkos_dev/config-core-cuda.sh @@ -13,7 +13,7 @@ # module load cmake/2.8.11.2 gcc/4.8.3 cuda/6.5.14 nvcc-wrapper/gnu # # The 'nvcc-wrapper' module should load a script that matches -# kokkos/config/nvcc_wrapper +# kokkos/bin/nvcc_wrapper # #----------------------------------------------------------------------------- # Source and installation directories: diff --git a/lib/kokkos/config/master_history.txt b/lib/kokkos/config/master_history.txt index 9eaecb5031..cc6f4c97d7 100644 --- a/lib/kokkos/config/master_history.txt +++ b/lib/kokkos/config/master_history.txt @@ -5,4 +5,5 @@ tag: 2.02.00 date: 10:30:2016 master: 6c90a581 develop: ca3dd56e tag: 2.02.01 date: 11:01:2016 master: 9c698c86 develop: b0072304 tag: 2.02.07 date: 12:16:2016 master: 4b4cc4ba develop: 382c0966 tag: 2.02.15 date: 02:10:2017 master: 8c64cd93 develop: 28dea8b6 -tag: 2.03.00 date: 04:25:2017 master: 120d9ce7 develop: 015ba641 +tag: 2.03.00 date: 04:25:2017 master: 120d9ce7 develop: 015ba641 +tag: 2.03.05 date: 05:27:2017 master: 36b92f43 develop: 79073186 diff --git a/lib/kokkos/config/snapshot.py b/lib/kokkos/config/snapshot.py index d816cd0c9c..bfa97bf48a 100755 --- a/lib/kokkos/config/snapshot.py +++ b/lib/kokkos/config/snapshot.py @@ -27,7 +27,7 @@ import subprocess, argparse, re, doctest, os, datetime, traceback def parse_cmdline(description): parser = argparse.ArgumentParser(usage="snapshot.py [options] source destination", description=description) - parser.add_argument("-n", "--no-comit", action="store_false", dest="create_commit", default=True, + parser.add_argument("-n", "--no-commit", action="store_false", dest="create_commit", default=True, help="Do not perform a commit or create a commit message.") parser.add_argument("-v", "--verbose", action="store_true", dest="verbose_mode", default=False, help="Enable verbose mode.") @@ -39,6 +39,8 @@ def parse_cmdline(description): help="Type of repository of the source, use none to skip all repository operations.") parser.add_argument("--dest-repo", choices=["git","none"], default="", help="Type of repository of the destination, use none to skip all repository operations.") + parser.add_argument("--small", action="store_true", dest="small_mode", + help="Don't include tests and other extra files when copying.") parser.add_argument("source", help="Source project to snapshot from.") parser.add_argument("destination", help="Destination to snapshot too.") @@ -58,9 +60,9 @@ def validate_options(options): options.source = os.path.abspath(options.source) options.destination = os.path.abspath(options.destination) - + if os.path.exists(options.source): - apparent_source_repo_type, source_root = deterimine_repo_type(options.source) + apparent_source_repo_type, source_root = determine_repo_type(options.source) else: raise RuntimeError("Could not find source directory of %s." % options.source) options.source_root = source_root @@ -69,7 +71,7 @@ def validate_options(options): print "Could not find destination directory of %s so it will be created." % options.destination os.makedirs(options.destination) - apparent_dest_repo_type, dest_root = deterimine_repo_type(options.destination) + apparent_dest_repo_type, dest_root = determine_repo_type(options.destination) options.dest_root = dest_root #error on svn repo types for now @@ -111,7 +113,7 @@ def run_cmd(cmd, options, working_dir="."): print "==== %s stderr ====" % cmd_str print proc_stderr print "==== %s stderr ====" % cmd_str - + if ret_val != 0: raise RuntimeError("Command '%s' failed with error code %d. Error message:%s%s%sstdout:%s" % \ (cmd_str, ret_val, os.linesep, proc_stderr, os.linesep, proc_stdout)) @@ -119,7 +121,7 @@ def run_cmd(cmd, options, working_dir="."): return proc_stdout, proc_stderr #end run_cmd -def deterimine_repo_type(location): +def determine_repo_type(location): apparent_repo_type = "none" while location != "": @@ -133,16 +135,32 @@ def deterimine_repo_type(location): location = location[:location.rfind(os.sep)] return apparent_repo_type, location - -#end deterimine_repo_type +#end determine_repo_type def rsync(source, dest, options): rsync_cmd = ["rsync", "-ar", "--delete"] if options.debug_mode: rsync_cmd.append("-v") + if options.small_mode or options.source_repo == "git": + rsync_cmd.append("--delete-excluded") + + if options.small_mode: + rsync_cmd.append("--include=config/master_history.txt") + rsync_cmd.append("--include=cmake/tpls") + rsync_cmd.append("--exclude=benchmarks/") + rsync_cmd.append("--exclude=config/*") + rsync_cmd.append("--exclude=doc/") + rsync_cmd.append("--exclude=example/") + rsync_cmd.append("--exclude=tpls/") + rsync_cmd.append("--exclude=HOW_TO_SNAPSHOT") + rsync_cmd.append("--exclude=unit_test") + rsync_cmd.append("--exclude=unit_tests") + rsync_cmd.append("--exclude=perf_test") + rsync_cmd.append("--exclude=performance_tests") + if options.source_repo == "git": - rsync_cmd.append("--exclude=.git") + rsync_cmd.append("--exclude=.git*") rsync_cmd.append(options.source) rsync_cmd.append(options.destination) @@ -171,28 +189,27 @@ def find_git_commit_information(options): ('sems', 'software.sandia.gov:/git/sems') """ git_log_cmd = ["git", "log", "-1"] - + output, error = run_cmd(git_log_cmd, options, options.source) - + commit_match = re.match("commit ([0-9a-fA-F]+)", output) commit_id = commit_match.group(1) commit_log = output - + git_remote_cmd = ["git", "remote", "-v"] output, error = run_cmd(git_remote_cmd, options, options.source) - + remote_match = re.search("origin\s([^ ]*/([^ ]+))", output, re.MULTILINE) if not remote_match: raise RuntimeError("Could not find origin of repo at %s. Consider using none for source repo type." % (options.source)) source_location = remote_match.group(1) source_name = remote_match.group(2).strip() - + if source_name[-1] == "/": source_name = source_name[:-1] return commit_id, commit_log, source_name, source_location - #end find_git_commit_information def do_git_commit(message, options): @@ -201,10 +218,10 @@ def do_git_commit(message, options): git_add_cmd = ["git", "add", "-A"] run_cmd(git_add_cmd, options, options.destination) - + git_commit_cmd = ["git", "commit", "-m%s" % message] run_cmd(git_commit_cmd, options, options.destination) - + git_log_cmd = ["git", "log", "--format=%h", "-1"] commit_sha1, error = run_cmd(git_log_cmd, options, options.destination) @@ -214,7 +231,7 @@ def do_git_commit(message, options): def verify_git_repo_clean(location, options): git_status_cmd = ["git", "status", "--porcelain"] output, error = run_cmd(git_status_cmd, options, location) - + if output != "": if options.no_validate_repo == False: raise RuntimeError("%s is not clean.%sPlease commit or stash all changes before running snapshot." @@ -223,7 +240,6 @@ def verify_git_repo_clean(location, options): print "WARNING: %s is not clean. Proceeding anyway." % location print "WARNING: This could lead to differences in the source and destination." print "WARNING: It could also lead to extra files being included in the snapshot commit." - #end verify_git_repo_clean def main(options): @@ -238,14 +254,14 @@ def main(options): commit_log = "Unknown commit from %s snapshotted at: %s" % (options.source, datetime.datetime.now()) repo_name = options.source repo_location = options.source - + commit_message = create_commit_message(commit_id, commit_log, repo_name, repo_location) + os.linesep*2 - + if options.dest_repo == "git": verify_git_repo_clean(options.destination, options) rsync(options.source, options.destination, options) - + if options.dest_repo == "git": do_git_commit(commit_message, options) elif options.dest_repo == "none": @@ -256,10 +272,6 @@ def main(options): cwd = os.getcwd() print "No commit done by request. Please use file at:" print "%s%sif you wish to commit this to a repo later." % (cwd+"/"+file_name, os.linesep) - - - - #end main if (__name__ == "__main__"): @@ -267,7 +279,7 @@ if (__name__ == "__main__"): doctest.testmod() sys.exit(0) - try: + try: options = parse_cmdline(__doc__) main(options) except RuntimeError, e: @@ -275,5 +287,5 @@ if (__name__ == "__main__"): if "--debug" in sys.argv: traceback.print_exc() sys.exit(1) - else: + else: sys.exit(0) diff --git a/lib/kokkos/config/test_all_sandia b/lib/kokkos/config/test_all_sandia index 6909606643..8e1246bf8b 100755 --- a/lib/kokkos/config/test_all_sandia +++ b/lib/kokkos/config/test_all_sandia @@ -24,6 +24,8 @@ elif [[ "$HOSTNAME" =~ node.* ]]; then # Warning: very generic name fi elif [[ "$HOSTNAME" =~ apollo ]]; then MACHINE=apollo +elif [[ "$HOSTNAME" =~ sullivan ]]; then + MACHINE=sullivan elif [ ! -z "$SEMS_MODULEFILES_ROOT" ]; then MACHINE=sems else @@ -152,7 +154,7 @@ if [ "$MACHINE" = "sems" ]; then "gcc/5.1.0 $BASE_MODULE_LIST "Serial" g++ $GCC_WARNING_FLAGS" "intel/16.0.1 $BASE_MODULE_LIST "OpenMP" icpc $INTEL_WARNING_FLAGS" "clang/3.9.0 $BASE_MODULE_LIST "Pthread_Serial" clang++ $CLANG_WARNING_FLAGS" - "cuda/8.0.44 $CUDA8_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/8.0.44 $CUDA8_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) else # Format: (compiler module-list build-list exe-name warning-flag) @@ -164,6 +166,7 @@ if [ "$MACHINE" = "sems" ]; then "clang/3.6.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" "clang/3.7.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" "clang/3.8.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" + "clang/3.9.0 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" "cuda/7.0.28 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" "cuda/8.0.44 $CUDA8_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" @@ -184,7 +187,7 @@ elif [ "$MACHINE" = "white" ]; then # Format: (compiler module-list build-list exe-name warning-flag) COMPILERS=("gcc/5.4.0 $BASE_MODULE_LIST $IBM_BUILD_LIST g++ $GCC_WARNING_FLAGS" "ibm/13.1.3 $IBM_MODULE_LIST $IBM_BUILD_LIST xlC $IBM_WARNING_FLAGS" - "cuda/8.0.44 $CUDA_MODULE_LIST $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/config/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/8.0.44 $CUDA_MODULE_LIST $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) if [ -z "$ARCH_FLAG" ]; then @@ -221,7 +224,7 @@ elif [ "$MACHINE" = "sullivan" ]; then BASE_MODULE_LIST="/" # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("gcc/5.3.0 $BASE_MODULE_LIST $ARM_GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS") + COMPILERS=("gcc/6.1.0 $BASE_MODULE_LIST $ARM_GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS") if [ -z "$ARCH_FLAG" ]; then ARCH_FLAG="--arch=ARMv8-ThunderX" @@ -278,11 +281,11 @@ elif [ "$MACHINE" = "apollo" ]; then "intel/16.0.1 $BASE_MODULE_LIST "OpenMP" icpc $INTEL_WARNING_FLAGS" "clang/3.9.0 $BASE_MODULE_LIST "Pthread_Serial" clang++ $CLANG_WARNING_FLAGS" "clang/head $CLANG_MODULE_LIST "Cuda_Pthread" clang++ $CUDA_WARNING_FLAGS" - "cuda/8.0.44 $CUDA_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/8.0.44 $CUDA_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) else # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("cuda/8.0.44 $CUDA8_MODULE_LIST $BUILD_LIST_CUDA_NVCC $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" + COMPILERS=("cuda/8.0.44 $CUDA8_MODULE_LIST $BUILD_LIST_CUDA_NVCC $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" "clang/head $CLANG_MODULE_LIST $BUILD_LIST_CUDA_CLANG clang++ $CUDA_WARNING_FLAGS" "clang/3.9.0 $CLANG_MODULE_LIST $BUILD_LIST_CLANG clang++ $CLANG_WARNING_FLAGS" "gcc/4.7.2 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" @@ -295,8 +298,8 @@ elif [ "$MACHINE" = "apollo" ]; then "intel/16.0.1 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" "clang/3.5.2 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" "clang/3.6.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" - "cuda/7.0.28 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" - "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/7.0.28 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) fi diff --git a/lib/kokkos/config/testing_scripts/jenkins_test_driver b/lib/kokkos/config/testing_scripts/jenkins_test_driver index 9cba7fa518..f393940304 100755 --- a/lib/kokkos/config/testing_scripts/jenkins_test_driver +++ b/lib/kokkos/config/testing_scripts/jenkins_test_driver @@ -48,7 +48,7 @@ esac #nvcc wrapper and make the wrapper the compiler. if [ $cuda_compiler != "" ]; then export NVCC_WRAPPER_DEFAULT_COMPILER=$compiler - compiler=$kokkos_path/config/nvcc_wrapper + compiler=$kokkos_path/bin/nvcc_wrapper fi if [ $host_compiler_brand == "intel" -a $cuda_compiler != "" ]; then diff --git a/lib/kokkos/config/trilinos-integration/checkin-test b/lib/kokkos/config/trilinos-integration/checkin-test new file mode 100644 index 0000000000..92a1b1c068 --- /dev/null +++ b/lib/kokkos/config/trilinos-integration/checkin-test @@ -0,0 +1,4 @@ +module purge +module load sems-env sems-gcc/4.9.3 sems-openmpi/1.10.1 sems-hdf5/1.8.12/parallel sems-netcdf/4.3.2/parallel sems-python/2.7.9 sems-zlib/1.2.8/base sems-cmake/3.5.2 sems-parmetis/4.0.3/64bit_parallel sems-scotch/6.0.3/nopthread_64bit_parallel sems-boost/1.59.0/base + +#Run Trilinos CheckinTest diff --git a/lib/kokkos/config/trilinos-integration/prepare_trilinos_repos.sh b/lib/kokkos/config/trilinos-integration/prepare_trilinos_repos.sh index 2692f76038..b81a3b1566 100755 --- a/lib/kokkos/config/trilinos-integration/prepare_trilinos_repos.sh +++ b/lib/kokkos/config/trilinos-integration/prepare_trilinos_repos.sh @@ -1,5 +1,18 @@ #!/bin/bash -le +TRILINOS_UPDATE_BRANCH=$1 +TRILINOS_PRISTINE_BRANCH=$2 + +if [ -z $TRILINOS_UPDATE_BRANCH ] +then + TRILINOS_UPDATE_BRANCH=develop +fi + +if [ -z $TRILINOS_PRISTINE_BRANCH ] +then + TRILINOS_PRISTINE_BRANCH=develop +fi + export TRILINOS_UPDATED_PATH=${PWD}/trilinos-update export TRILINOS_PRISTINE_PATH=${PWD}/trilinos-pristine @@ -16,8 +29,8 @@ if [ ! -d "${TRILINOS_PRISTINE_PATH}" ]; then fi cd ${TRILINOS_UPDATED_PATH} -git checkout develop -git reset --hard origin/develop +git checkout $TRILINOS_UPDATE_BRANCH +git reset --hard origin/$TRILINOS_UPDATE_BRANCH git pull cd .. @@ -28,18 +41,14 @@ echo "" echo "" echo "Trilinos State:" git log --pretty=oneline --since=7.days -SHA=`git log --pretty=oneline --since=7.days | head -n 2 | tail -n 1 | awk '{print $1}'` cd .. cd ${TRILINOS_PRISTINE_PATH} git status -git log --pretty=oneline --since=7.days -echo "Checkout develop" -git checkout develop +echo "Checkout $TRILINOS_PRISTINE_BRANCH" +git checkout $TRILINOS_PRISTINE_BRANCH echo "Pull" git pull -echo "Checkout SHA" -git checkout ${SHA} cd .. cd ${TRILINOS_PRISTINE_PATH} diff --git a/lib/kokkos/config/trilinos-integration/shepard_jenkins_run_script_pthread_intel b/lib/kokkos/config/trilinos-integration/shepard_jenkins_run_script_pthread_intel new file mode 100755 index 0000000000..23968e8c0f --- /dev/null +++ b/lib/kokkos/config/trilinos-integration/shepard_jenkins_run_script_pthread_intel @@ -0,0 +1,60 @@ +#!/bin/bash -el +ulimit -c 0 +module load devpack/openmpi/1.10.0/intel/16.1.056/cuda/none + +KOKKOS_BRANCH=$1 +TRILINOS_UPDATE_BRANCH=$2 +TRILINOS_PRISTINE_BRANCH=$3 + +if [ -z $KOKKOS_BRANCH ] +then + KOKKOS_BRANCH=develop +fi + +if [ -z $TRILINOS_UPDATE_BRANCH ] +then + TRILINOS_UPDATE_BRANCH=develop +fi + +if [ -z $TRILINOS_PRISTINE_BRANCH ] +then + TRILINOS_PRISTINE_BRANCH=develop +fi + +export OMP_NUM_THREADS=8 +export JENKINS_DO_CUDA=OFF +export JENKINS_DO_OPENMP=OFF +export JENKINS_DO_PTHREAD=ON +export JENKINS_DO_SERIAL=OFF +export JENKINS_DO_COMPLEX=OFF + +export ARCH_CXX_FLAG="-xCORE-AVX2 -mkl" +export ARCH_C_FLAG="-xCORE-AVX2 -mkl" +export BLAS_LIBRARIES="-mkl;${MKLROOT}/lib/intel64/libmkl_intel_lp64.a;${MKLROOT}/lib/intel64/libmkl_intel_thread.a;${MKLROOT}/lib/intel64/libmkl_core.a" +export LAPACK_LIBRARIES=${BLAS_LIBRARIES} + +export JENKINS_DO_TESTS=ON +export JENKINS_DO_EXAMPLES=ON +export JENKINS_DO_SHARED=OFF + +export QUEUE=haswell + + +module load python + + +export KOKKOS_PATH=${PWD}/kokkos + +#Already done: +if [ ! -d "${KOKKOS_PATH}" ]; then + git clone https://github.com/kokkos/kokkos ${KOKKOS_PATH} +fi + +cd ${KOKKOS_PATH} +git checkout $KOKKOS_BRANCH +git pull +cd .. + +source ${KOKKOS_PATH}/config/trilinos-integration/prepare_trilinos_repos.sh $TRILINOS_UPDATE_BRANCH $TRILINOS_PRISTINE_BRANCH + +${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/run_repo_comparison_slurm ${TRILINOS_UPDATED_PATH} ${TRILINOS_PRISTINE_PATH} ${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/configure-testbeds-jenkins-all TestCompare ${QUEUE} diff --git a/lib/kokkos/config/trilinos-integration/shepard_jenkins_run_script_serial_intel b/lib/kokkos/config/trilinos-integration/shepard_jenkins_run_script_serial_intel new file mode 100755 index 0000000000..964de3a002 --- /dev/null +++ b/lib/kokkos/config/trilinos-integration/shepard_jenkins_run_script_serial_intel @@ -0,0 +1,60 @@ +#!/bin/bash -el +ulimit -c 0 +module load devpack/openmpi/1.10.0/intel/16.1.056/cuda/none + +KOKKOS_BRANCH=$1 +TRILINOS_UPDATE_BRANCH=$2 +TRILINOS_PRISTINE_BRANCH=$3 + +if [ -z $KOKKOS_BRANCH ] +then + KOKKOS_BRANCH=develop +fi + +if [ -z $TRILINOS_UPDATE_BRANCH ] +then + TRILINOS_UPDATE_BRANCH=develop +fi + +if [ -z $TRILINOS_PRISTINE_BRANCH ] +then + TRILINOS_PRISTINE_BRANCH=develop +fi + +export OMP_NUM_THREADS=8 +export JENKINS_DO_CUDA=OFF +export JENKINS_DO_OPENMP=OFF +export JENKINS_DO_PTHREAD=OFF +export JENKINS_DO_SERIAL=ON +export JENKINS_DO_COMPLEX=ON + +export ARCH_CXX_FLAG="-xCORE-AVX2 -mkl" +export ARCH_C_FLAG="-xCORE-AVX2 -mkl" +export BLAS_LIBRARIES="-mkl;${MKLROOT}/lib/intel64/libmkl_intel_lp64.a;${MKLROOT}/lib/intel64/libmkl_intel_thread.a;${MKLROOT}/lib/intel64/libmkl_core.a" +export LAPACK_LIBRARIES=${BLAS_LIBRARIES} + +export JENKINS_DO_TESTS=ON +export JENKINS_DO_EXAMPLES=ON +export JENKINS_DO_SHARED=OFF + +export QUEUE=haswell + + +module load python + + +export KOKKOS_PATH=${PWD}/kokkos + +#Already done: +if [ ! -d "${KOKKOS_PATH}" ]; then + git clone https://github.com/kokkos/kokkos ${KOKKOS_PATH} +fi + +cd ${KOKKOS_PATH} +git checkout $KOKKOS_BRANCH +git pull +cd .. + +source ${KOKKOS_PATH}/config/trilinos-integration/prepare_trilinos_repos.sh $TRILINOS_UPDATE_BRANCH $TRILINOS_PRISTINE_BRANCH + +${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/run_repo_comparison_slurm ${TRILINOS_UPDATED_PATH} ${TRILINOS_PRISTINE_PATH} ${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/configure-testbeds-jenkins-all TestCompare ${QUEUE} diff --git a/lib/kokkos/config/trilinos-integration/white_run_jenkins_script_cuda b/lib/kokkos/config/trilinos-integration/white_run_jenkins_script_cuda new file mode 100755 index 0000000000..52af024858 --- /dev/null +++ b/lib/kokkos/config/trilinos-integration/white_run_jenkins_script_cuda @@ -0,0 +1,63 @@ +#!/bin/bash -el +ulimit -c 0 + +KOKKOS_BRANCH=$1 +TRILINOS_UPDATE_BRANCH=$2 +TRILINOS_PRISTINE_BRANCH=$3 + +if [ -z $KOKKOS_BRANCH ] +then + KOKKOS_BRANCH=develop +fi + +if [ -z $TRILINOS_UPDATE_BRANCH ] +then + TRILINOS_UPDATE_BRANCH=develop +fi + +if [ -z $TRILINOS_PRISTINE_BRANCH ] +then + TRILINOS_PRISTINE_BRANCH=develop +fi + +module load devpack/openmpi/1.10.4/gcc/5.4.0/cuda/8.0.44 +export OMP_NUM_THREADS=8 +export JENKINS_DO_CUDA=ON +export JENKINS_DO_OPENMP=OFF +export JENKINS_DO_PTHREAD=OFF +export JENKINS_DO_SERIAL=ON +export JENKINS_DO_COMPLEX=OFF + +export JENKINS_ARCH_CXX_FLAG="-mcpu=power8 -arch=sm_37" +export JENKINS_ARCH_C_FLAG="-mcpu=power8" +export BLAS_LIBRARIES="${BLAS_ROOT}/lib/libblas.a;gfortran;gomp" +export LAPACK_LIBRARIES="${LAPACK_ROOT}/lib/liblapack.a;gfortran;gomp" + +export JENKINS_DO_TESTS=ON +export JENKINS_DO_EXAMPLES=ON + +export QUEUE=rhel7F + +module load python + +export KOKKOS_PATH=${PWD}/kokkos + +#Already done: +if [ ! -d "${KOKKOS_PATH}" ]; then + git clone https://github.com/kokkos/kokkos ${KOKKOS_PATH} +fi + +export OMPI_CXX=${KOKKOS_PATH}/bin/nvcc_wrapper + +cd ${KOKKOS_PATH} +git checkout $KOKKOS_BRANCH +git pull +cd .. + +export CUDA_LAUNCH_BLOCKING=1 +export CUDA_MANAGED_FORCE_DEVICE_ALLOC=1 + +source ${KOKKOS_PATH}/config/trilinos-integration/prepare_trilinos_repos.sh $TRILINOS_UPDATE_BRANCH $TRILINOS_PRISTINE_BRANCH + +${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/run_repo_comparison_lsf ${TRILINOS_UPDATED_PATH} ${TRILINOS_PRISTINE_PATH} ${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/configure-testbeds-jenkins-all TestCompare ${QUEUE} + diff --git a/lib/kokkos/config/trilinos-integration/white_run_jenkins_script_omp b/lib/kokkos/config/trilinos-integration/white_run_jenkins_script_omp new file mode 100755 index 0000000000..452165eef2 --- /dev/null +++ b/lib/kokkos/config/trilinos-integration/white_run_jenkins_script_omp @@ -0,0 +1,58 @@ +#!/bin/bash -el +ulimit -c 0 + +KOKKOS_BRANCH=$1 +TRILINOS_UPDATE_BRANCH=$2 +TRILINOS_PRISTINE_BRANCH=$3 + +if [ -z $KOKKOS_BRANCH ] +then + KOKKOS_BRANCH=develop +fi + +if [ -z $TRILINOS_UPDATE_BRANCH ] +then + TRILINOS_UPDATE_BRANCH=develop +fi + +if [ -z $TRILINOS_PRISTINE_BRANCH ] +then + TRILINOS_PRISTINE_BRANCH=develop +fi + +module load devpack/openmpi/1.10.4/gcc/5.4.0/cuda/8.0.44 +export OMP_NUM_THREADS=8 +export JENKINS_DO_CUDA=OFF +export JENKINS_DO_OPENMP=ON +export JENKINS_DO_PTHREAD=OFF +export JENKINS_DO_SERIAL=OFF +export JENKINS_DO_COMPLEX=OFF + +export JENKINS_ARCH_CXX_FLAG="-mcpu=power8" +export JENKINS_ARCH_C_FLAG="-mcpu=power8" +export BLAS_LIBRARIES="${BLAS_ROOT}/lib/libblas.a;gfortran;gomp" +export LAPACK_LIBRARIES="${LAPACK_ROOT}/lib/liblapack.a;gfortran;gomp" + +export JENKINS_DO_TESTS=ON +export JENKINS_DO_EXAMPLES=ON + +export QUEUE=rhel7F + +module load python + +export KOKKOS_PATH=${PWD}/kokkos + +#Already done: +if [ ! -d "${KOKKOS_PATH}" ]; then + git clone https://github.com/kokkos/kokkos ${KOKKOS_PATH} +fi + +cd ${KOKKOS_PATH} +git checkout $KOKKOS_BRANCH +git pull +cd .. + +source ${KOKKOS_PATH}/config/trilinos-integration/prepare_trilinos_repos.sh $TRILINOS_UPDATE_BRANCH $TRILINOS_PRISTINE_BRANCH + +${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/run_repo_comparison_lsf ${TRILINOS_UPDATED_PATH} ${TRILINOS_PRISTINE_PATH} ${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/configure-testbeds-jenkins-all TestCompare ${QUEUE} + diff --git a/lib/kokkos/containers/performance_tests/Makefile b/lib/kokkos/containers/performance_tests/Makefile index fa3bc77701..edaaf1ee51 100644 --- a/lib/kokkos/containers/performance_tests/Makefile +++ b/lib/kokkos/containers/performance_tests/Makefile @@ -8,7 +8,7 @@ default: build_all echo "End Build" ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES))) - CXX = $(KOKKOS_PATH)/config/nvcc_wrapper + CXX = $(KOKKOS_PATH)/bin/nvcc_wrapper else CXX = g++ endif @@ -21,8 +21,8 @@ include $(KOKKOS_PATH)/Makefile.kokkos KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/containers/performance_tests -TEST_TARGETS = -TARGETS = +TEST_TARGETS = +TARGETS = ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) OBJ_CUDA = TestCuda.o TestMain.o gtest-all.o @@ -65,7 +65,7 @@ build_all: $(TARGETS) test: $(TEST_TARGETS) -clean: kokkos-clean +clean: kokkos-clean rm -f *.o $(TARGETS) # Compilation rules @@ -73,6 +73,5 @@ clean: kokkos-clean %.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -gtest-all.o:$(GTEST_PATH)/gtest/gtest-all.cc +gtest-all.o:$(GTEST_PATH)/gtest/gtest-all.cc $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $(GTEST_PATH)/gtest/gtest-all.cc - diff --git a/lib/kokkos/containers/performance_tests/TestCuda.cpp b/lib/kokkos/containers/performance_tests/TestCuda.cpp index d5cad06a47..208387425f 100644 --- a/lib/kokkos/containers/performance_tests/TestCuda.cpp +++ b/lib/kokkos/containers/performance_tests/TestCuda.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,12 +36,15 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ -#include +#include +#if defined( KOKKOS_ENABLE_CUDA ) + +#include #include #include #include @@ -52,8 +55,6 @@ #include -#if defined( KOKKOS_ENABLE_CUDA ) - #include #include @@ -79,7 +80,7 @@ protected: } }; -TEST_F( cuda, dynrankview_perf ) +TEST_F( cuda, dynrankview_perf ) { std::cout << "Cuda" << std::endl; std::cout << " DynRankView vs View: Initialization Only " << std::endl; @@ -105,5 +106,6 @@ TEST_F( cuda, unordered_map_performance_far) } } - +#else +void KOKKOS_CONTAINERS_PERFORMANCE_TESTS_TESTCUDA_PREVENT_EMPTY_LINK_ERROR() {} #endif /* #if defined( KOKKOS_ENABLE_CUDA ) */ diff --git a/lib/kokkos/containers/performance_tests/TestDynRankView.hpp b/lib/kokkos/containers/performance_tests/TestDynRankView.hpp index d96a3f7432..4c0ccb6b88 100644 --- a/lib/kokkos/containers/performance_tests/TestDynRankView.hpp +++ b/lib/kokkos/containers/performance_tests/TestDynRankView.hpp @@ -1,13 +1,13 @@ //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,7 +36,7 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER @@ -263,3 +263,4 @@ void test_dynrankview_op_perf( const int par_size ) } //end Performance #endif + diff --git a/lib/kokkos/containers/performance_tests/TestOpenMP.cpp b/lib/kokkos/containers/performance_tests/TestOpenMP.cpp index da74d32ac1..b674ec4a74 100644 --- a/lib/kokkos/containers/performance_tests/TestOpenMP.cpp +++ b/lib/kokkos/containers/performance_tests/TestOpenMP.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,11 +36,14 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ +#include +#if defined( KOKKOS_ENABLE_OPENMP ) + #include #include @@ -93,7 +96,7 @@ protected: } }; -TEST_F( openmp, dynrankview_perf ) +TEST_F( openmp, dynrankview_perf ) { std::cout << "OpenMP" << std::endl; std::cout << " DynRankView vs View: Initialization Only " << std::endl; @@ -137,4 +140,7 @@ TEST_F( openmp, unordered_map_performance_far) } } // namespace test +#else +void KOKKOS_CONTAINERS_PERFORMANCE_TESTS_TESTOPENMP_PREVENT_EMPTY_LINK_ERROR() {} +#endif diff --git a/lib/kokkos/containers/performance_tests/TestThreads.cpp b/lib/kokkos/containers/performance_tests/TestThreads.cpp index 4179b7de4c..a8910a3c72 100644 --- a/lib/kokkos/containers/performance_tests/TestThreads.cpp +++ b/lib/kokkos/containers/performance_tests/TestThreads.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,11 +36,14 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ +#include +#if defined( KOKKOS_ENABLE_THREADS ) + #include #include @@ -87,7 +90,7 @@ protected: } }; -TEST_F( threads, dynrankview_perf ) +TEST_F( threads, dynrankview_perf ) { std::cout << "Threads" << std::endl; std::cout << " DynRankView vs View: Initialization Only " << std::endl; @@ -132,4 +135,7 @@ TEST_F( threads, unordered_map_performance_far) } // namespace Performance +#else +void KOKKOS_CONTAINERS_PERFORMANCE_TESTS_TESTTHREADS_PREVENT_EMPTY_LINK_ERROR() {} +#endif diff --git a/lib/kokkos/containers/src/Kokkos_Bitset.hpp b/lib/kokkos/containers/src/Kokkos_Bitset.hpp index 74da5f61b5..7714506e92 100644 --- a/lib/kokkos/containers/src/Kokkos_Bitset.hpp +++ b/lib/kokkos/containers/src/Kokkos_Bitset.hpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,7 +36,7 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ @@ -435,3 +435,4 @@ void deep_copy( ConstBitset & dst, ConstBitset const& src) } // namespace Kokkos #endif //KOKKOS_BITSET_HPP + diff --git a/lib/kokkos/containers/src/Kokkos_DualView.hpp b/lib/kokkos/containers/src/Kokkos_DualView.hpp index 3a0196ee4c..937eab0d88 100644 --- a/lib/kokkos/containers/src/Kokkos_DualView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DualView.hpp @@ -442,6 +442,17 @@ public: modified_host () = (modified_device () > modified_host () ? modified_device () : modified_host ()) + 1; } + +#ifdef KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK + if (modified_host() && modified_device()) { + std::string msg = "Kokkos::DualView::modify ERROR: "; + msg += "Concurrent modification of host and device views "; + msg += "in DualView \""; + msg += d_view.label(); + msg += "\"\n"; + Kokkos::abort(msg.c_str()); + } +#endif } //@} @@ -624,3 +635,4 @@ deep_copy (const ExecutionSpace& exec , } // namespace Kokkos #endif + diff --git a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp index acb37f7f75..8e464506f9 100644 --- a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,7 +36,7 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ @@ -140,21 +140,21 @@ struct DynRankDimTraits { static typename std::enable_if< (std::is_same::value) , Layout>::type createLayout( const Layout& layout ) { return Layout( layout.dimension[0] != unspecified ? layout.dimension[0] : 1 - , layout.stride[0] + , layout.stride[0] , layout.dimension[1] != unspecified ? layout.dimension[1] : 1 - , layout.stride[1] + , layout.stride[1] , layout.dimension[2] != unspecified ? layout.dimension[2] : 1 - , layout.stride[2] + , layout.stride[2] , layout.dimension[3] != unspecified ? layout.dimension[3] : 1 - , layout.stride[3] + , layout.stride[3] , layout.dimension[4] != unspecified ? layout.dimension[4] : 1 - , layout.stride[4] + , layout.stride[4] , layout.dimension[5] != unspecified ? layout.dimension[5] : 1 - , layout.stride[5] + , layout.stride[5] , layout.dimension[6] != unspecified ? layout.dimension[6] : 1 - , layout.stride[6] + , layout.stride[6] , layout.dimension[7] != unspecified ? layout.dimension[7] : 1 - , layout.stride[7] + , layout.stride[7] ); } @@ -188,7 +188,7 @@ struct DynRankDimTraits { KOKKOS_INLINE_FUNCTION static typename std::enable_if< (std::is_same::value || std::is_same::value) && std::is_integral::value , Layout >::type reconstructLayout( const Layout& layout , iType dynrank ) { - return Layout( dynrank > 0 ? layout.dimension[0] : ~size_t(0) + return Layout( dynrank > 0 ? layout.dimension[0] : ~size_t(0) , dynrank > 1 ? layout.dimension[1] : ~size_t(0) , dynrank > 2 ? layout.dimension[2] : ~size_t(0) , dynrank > 3 ? layout.dimension[3] : ~size_t(0) @@ -205,27 +205,27 @@ struct DynRankDimTraits { static typename std::enable_if< (std::is_same::value) && std::is_integral::value , Layout >::type reconstructLayout( const Layout& layout , iType dynrank ) { return Layout( dynrank > 0 ? layout.dimension[0] : ~size_t(0) - , dynrank > 0 ? layout.stride[0] : (0) + , dynrank > 0 ? layout.stride[0] : (0) , dynrank > 1 ? layout.dimension[1] : ~size_t(0) - , dynrank > 1 ? layout.stride[1] : (0) + , dynrank > 1 ? layout.stride[1] : (0) , dynrank > 2 ? layout.dimension[2] : ~size_t(0) - , dynrank > 2 ? layout.stride[2] : (0) + , dynrank > 2 ? layout.stride[2] : (0) , dynrank > 3 ? layout.dimension[3] : ~size_t(0) - , dynrank > 3 ? layout.stride[3] : (0) + , dynrank > 3 ? layout.stride[3] : (0) , dynrank > 4 ? layout.dimension[4] : ~size_t(0) - , dynrank > 4 ? layout.stride[4] : (0) + , dynrank > 4 ? layout.stride[4] : (0) , dynrank > 5 ? layout.dimension[5] : ~size_t(0) - , dynrank > 5 ? layout.stride[5] : (0) + , dynrank > 5 ? layout.stride[5] : (0) , dynrank > 6 ? layout.dimension[6] : ~size_t(0) - , dynrank > 6 ? layout.stride[6] : (0) + , dynrank > 6 ? layout.stride[6] : (0) , dynrank > 7 ? layout.dimension[7] : ~size_t(0) - , dynrank > 7 ? layout.stride[7] : (0) + , dynrank > 7 ? layout.stride[7] : (0) ); } /** \brief Debug bounds-checking routines */ -// Enhanced debug checking - most infrastructure matches that of functions in +// Enhanced debug checking - most infrastructure matches that of functions in // Kokkos_ViewMapping; additional checks for extra arguments beyond rank are 0 template< unsigned , typename iType0 , class MapType > KOKKOS_INLINE_FUNCTION @@ -235,20 +235,20 @@ bool dyn_rank_view_verify_operator_bounds( const iType0 & , const MapType & ) template< unsigned R , typename iType0 , class MapType , typename iType1 , class ... Args > KOKKOS_INLINE_FUNCTION bool dyn_rank_view_verify_operator_bounds - ( const iType0 & rank + ( const iType0 & rank , const MapType & map , const iType1 & i , Args ... args ) { - if ( static_cast(R) < rank ) { + if ( static_cast(R) < rank ) { return ( size_t(i) < map.extent(R) ) && dyn_rank_view_verify_operator_bounds( rank , map , args ... ); } else if ( i != 0 ) { printf("DynRankView Debug Bounds Checking Error: at rank %u\n Extra arguments beyond the rank must be zero \n",R); return ( false ) - && dyn_rank_view_verify_operator_bounds( rank , map , args ... ); + && dyn_rank_view_verify_operator_bounds( rank , map , args ... ); } else { return ( true ) @@ -281,20 +281,24 @@ void dyn_rank_view_error_operator_bounds } // op_rank = rank of the operator version that was called -template< typename iType0 , typename iType1 , class MapType , class ... Args > +template< typename MemorySpace + , typename iType0 , typename iType1 , class MapType , class ... Args > KOKKOS_INLINE_FUNCTION void dyn_rank_view_verify_operator_bounds - ( const iType0 & op_rank , const iType1 & rank , const char* label , const MapType & map , Args ... args ) + ( const iType0 & op_rank , const iType1 & rank + , const Kokkos::Impl::SharedAllocationTracker & tracker + , const MapType & map , Args ... args ) { if ( static_cast(rank) > op_rank ) { - Kokkos::abort( "DynRankView Bounds Checking Error: Need at least rank arguments to the operator()" ); + Kokkos::abort( "DynRankView Bounds Checking Error: Need at least rank arguments to the operator()" ); } if ( ! dyn_rank_view_verify_operator_bounds<0>( rank , map , args ... ) ) { #if defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST ) enum { LEN = 1024 }; char buffer[ LEN ]; - int n = snprintf(buffer,LEN,"DynRankView bounds error of view %s (", label); + const std::string label = tracker.template get_label(); + int n = snprintf(buffer,LEN,"DynRankView bounds error of view %s (", label.c_str()); dyn_rank_view_error_operator_bounds<0>( buffer + n , LEN - n , map , args ... ); Kokkos::Impl::throw_runtime_exception(std::string(buffer)); #else @@ -347,7 +351,7 @@ private: std::is_same< typename DstTraits::array_layout , typename SrcTraits::array_layout >::value || std::is_same< typename DstTraits::array_layout - , Kokkos::LayoutStride >::value + , Kokkos::LayoutStride >::value }; public: @@ -381,9 +385,9 @@ public: } //end Impl /* \class DynRankView - * \brief Container that creates a Kokkos view with rank determined at runtime. + * \brief Container that creates a Kokkos view with rank determined at runtime. * Essentially this is a rank 7 view that wraps the access operators - * to yield the functionality of a view + * to yield the functionality of a view * * Changes from View * 1. The rank of the DynRankView is returned by the method rank() @@ -410,14 +414,14 @@ class DynRankView : public ViewTraits< DataType , Properties ... > { static_assert( !std::is_array::value && !std::is_pointer::value , "Cannot template DynRankView with array or pointer datatype - must be pod" ); -private: +private: template < class , class ... > friend class DynRankView ; template < class , class ... > friend class Impl::ViewMapping ; -public: +public: typedef ViewTraits< DataType , Properties ... > drvtraits ; - typedef View< DataType******* , Properties...> view_type ; + typedef View< DataType******* , Properties...> view_type ; typedef ViewTraits< DataType******* , Properties ... > traits ; @@ -430,7 +434,7 @@ private: map_type m_map ; unsigned m_rank; -public: +public: KOKKOS_INLINE_FUNCTION view_type & DownCast() const { return ( view_type & ) (*this); } KOKKOS_INLINE_FUNCTION @@ -588,7 +592,7 @@ private: // rank of the calling operator - included as first argument in ARG #define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( ARG ) \ DynRankView::template verify_space< Kokkos::Impl::ActiveExecutionMemorySpace >::check(); \ - Kokkos::Experimental::Impl::dyn_rank_view_verify_operator_bounds ARG ; + Kokkos::Experimental::Impl::dyn_rank_view_verify_operator_bounds< typename traits::memory_space > ARG ; #else @@ -607,14 +611,10 @@ public: // Rank 0 KOKKOS_INLINE_FUNCTION reference_type operator()() const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (0 , this->rank() , NULL , m_map) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (0 , this->rank() , m_track.template get_label().c_str(),m_map) ) - #endif + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (0 , this->rank(), m_track, m_map) ) return implementation_map().reference(); - //return m_map.reference(0,0,0,0,0,0,0); + //return m_map.reference(0,0,0,0,0,0,0); } // Rank 1 @@ -624,6 +624,8 @@ public: typename std::enable_if< std::is_same::value && std::is_integral::value, reference_type>::type operator[](const iType & i0) const { + //Phalanx is violating this, since they use the operator to access ALL elements in the allocation + //KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank(), m_track, m_map) ) return data()[i0]; } @@ -647,14 +649,10 @@ public: template< typename iType > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_same::value && std::is_integral::value), reference_type>::type - operator()(const iType & i0 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank() , NULL , m_map , i0) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank() , m_track.template get_label().c_str(),m_map,i0) ) - #endif - return m_map.reference(i0); + operator()(const iType & i0 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank(), m_track, m_map, i0) ) + return m_map.reference(i0); } template< typename iType > @@ -662,11 +660,7 @@ public: typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type operator()(const iType & i0 ) const { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank() , NULL , m_map , i0) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank() , m_track.template get_label().c_str(),m_map,i0) ) - #endif + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank(), m_track, m_map, i0) ) return m_map.reference(i0,0,0,0,0,0,0); } @@ -674,155 +668,111 @@ public: template< typename iType0 , typename iType1 > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank() , NULL , m_map , i0 , i1) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1) ) - #endif - return m_map.reference(i0,i1); + operator()(const iType0 & i0 , const iType1 & i1 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank(), m_track, m_map, i0, i1) ) + return m_map.reference(i0,i1); } template< typename iType0 , typename iType1 > KOKKOS_INLINE_FUNCTION typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank() , NULL , m_map , i0 , i1) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1) ) - #endif - return m_map.reference(i0,i1,0,0,0,0,0); + operator()(const iType0 & i0 , const iType1 & i1 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank(), m_track, m_map, i0, i1) ) + return m_map.reference(i0,i1,0,0,0,0,0); } // Rank 3 template< typename iType0 , typename iType1 , typename iType2 > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank() , NULL , m_map , i0 , i1 , i2) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2) ) - #endif - return m_map.reference(i0,i1,i2); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank(), m_track, m_map, i0, i1, i2) ) + return m_map.reference(i0,i1,i2); } template< typename iType0 , typename iType1 , typename iType2 > KOKKOS_INLINE_FUNCTION typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank() , NULL , m_map , i0 , i1 , i2) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2) ) - #endif - return m_map.reference(i0,i1,i2,0,0,0,0); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank(), m_track, m_map, i0, i1, i2) ) + return m_map.reference(i0,i1,i2,0,0,0,0); } // Rank 4 template< typename iType0 , typename iType1 , typename iType2 , typename iType3 > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3) ) - #endif - return m_map.reference(i0,i1,i2,i3); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank(), m_track, m_map, i0, i1, i2, i3) ) + return m_map.reference(i0,i1,i2,i3); } template< typename iType0 , typename iType1 , typename iType2 , typename iType3 > KOKKOS_INLINE_FUNCTION typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3) ) - #endif - return m_map.reference(i0,i1,i2,i3,0,0,0); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank(), m_track, m_map, i0, i1, i2, i3) ) + return m_map.reference(i0,i1,i2,i3,0,0,0); } // Rank 5 template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3,i4) ) - #endif - return m_map.reference(i0,i1,i2,i3,i4); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4) ) + return m_map.reference(i0,i1,i2,i3,i4); } template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 > KOKKOS_INLINE_FUNCTION typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3,i4) ) - #endif - return m_map.reference(i0,i1,i2,i3,i4,0,0); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4) ) + return m_map.reference(i0,i1,i2,i3,i4,0,0); } // Rank 6 template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 , typename iType5 > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4 , i5) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3,i4,i5) ) - #endif - return m_map.reference(i0,i1,i2,i3,i4,i5); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4, i5) ) + return m_map.reference(i0,i1,i2,i3,i4,i5); } template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 , typename iType5 > KOKKOS_INLINE_FUNCTION typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4 , i5) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3,i4,i5) ) - #endif - return m_map.reference(i0,i1,i2,i3,i4,i5,0); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4, i5) ) + return m_map.reference(i0,i1,i2,i3,i4,i5,0); } // Rank 7 template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 , typename iType5 , typename iType6 > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 , const iType6 & i6 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (7 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4 , i5 , i6) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (7 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3,i4,i5,i6) ) - #endif - return m_map.reference(i0,i1,i2,i3,i4,i5,i6); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 , const iType6 & i6 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (7 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4, i5, i6) ) + return m_map.reference(i0,i1,i2,i3,i4,i5,i6); } #undef KOKKOS_IMPL_VIEW_OPERATOR_VERIFY //---------------------------------------- - // Standard constructor, destructor, and assignment operators... + // Standard constructor, destructor, and assignment operators... KOKKOS_INLINE_FUNCTION ~DynRankView() {} @@ -840,7 +790,7 @@ public: DynRankView & operator = ( const DynRankView & rhs ) { m_track = rhs.m_track; m_map = rhs.m_map; m_rank = rhs.m_rank; return *this; } KOKKOS_INLINE_FUNCTION - DynRankView & operator = ( DynRankView && rhs ) { m_track = rhs.m_track; m_map = rhs.m_map; m_rank = rhs.m_rank; return *this; } + DynRankView & operator = ( DynRankView && rhs ) { m_track = rhs.m_track; m_map = rhs.m_map; m_rank = rhs.m_rank; return *this; } //---------------------------------------- // Compatible view copy constructor and assignment @@ -1068,7 +1018,7 @@ public: DynRankView( const Label & arg_label , typename std::enable_if< Kokkos::Experimental::Impl::is_view_label