From: Mark Abraham Date: Fri, 10 Sep 2021 13:02:38 +0000 (+0200) Subject: Fix issues from downstream patches and suppressions X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=20b3039717a19c579f48489c7755852cc8d66946;p=alexxy%2Fgromacs.git Fix issues from downstream patches and suppressions --- diff --git a/docs/user-guide/mdrun-performance.rst b/docs/user-guide/mdrun-performance.rst index 1989c670c1..8fb1bdab82 100644 --- a/docs/user-guide/mdrun-performance.rst +++ b/docs/user-guide/mdrun-performance.rst @@ -922,7 +922,7 @@ The Wallcycle module is used for runtime performance measurement of :ref:`gmx md At the end of the log file of each run, the "Real cycle and time accounting" section provides a table with runtime statistics for different parts of the :ref:`gmx mdrun` code in rows of the table. -The table contains colums indicating the number of ranks and threads that +The table contains columns indicating the number of ranks and threads that executed the respective part of the run, wall-time and cycle count aggregates (across all threads and ranks) averaged over the entire run. The last column also shows what precentage of the total runtime each row represents. diff --git a/src/gromacs/analysisdata/modules/histogram.h b/src/gromacs/analysisdata/modules/histogram.h index c15844c6c3..0e653b6f79 100644 --- a/src/gromacs/analysisdata/modules/histogram.h +++ b/src/gromacs/analysisdata/modules/histogram.h @@ -2,7 +2,7 @@ * This file is part of the GROMACS molecular simulation package. * * Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team. - * Copyright (c) 2015,2018,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2015,2018,2019,2020,2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -438,7 +438,7 @@ private: * data. Each frame contains the histogram(s) for the points in that frame, * interpreted such that the first column passed to pointsAdded() determines * the bin and the rest give weights to be added to that bin (input data should - * have at least two colums, and at least two columns should be added at the + * have at least two columns, and at least two columns should be added at the * same time). * Each input data set is processed independently into the corresponding output * data set. @@ -502,7 +502,7 @@ private: * that bin. * The input data is interpreted such that the first column passed to * pointsAdded() determines the bin and the rest give values to be added to - * that bin (input data should have at least two colums, and at least two + * that bin (input data should have at least two columns, and at least two * columns should be added at the same time). * All input columns for a data set are averaged into the same histogram. * diff --git a/src/gromacs/gmxana/gmx_cluster.cpp b/src/gromacs/gmxana/gmx_cluster.cpp index 751c62f6d0..9fdaa533c9 100644 --- a/src/gromacs/gmxana/gmx_cluster.cpp +++ b/src/gromacs/gmxana/gmx_cluster.cpp @@ -4,7 +4,7 @@ * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team. - * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -353,7 +353,7 @@ static void gather(t_mat* m, real cutoff, t_clusters* clust) } if (k != nn) { - gmx_incons("gather algortihm"); + gmx_incons("gather algorithm"); } std::sort(d, d + nn, rms_dist_comp); diff --git a/src/gromacs/gmxana/gmx_dielectric.cpp b/src/gromacs/gmxana/gmx_dielectric.cpp index 3ab32fd482..eef8de7020 100644 --- a/src/gromacs/gmxana/gmx_dielectric.cpp +++ b/src/gromacs/gmxana/gmx_dielectric.cpp @@ -4,7 +4,7 @@ * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team. - * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -334,7 +334,7 @@ int gmx_dielectric(int argc, char* argv[]) dt = yd[0][1] - yd[0][0]; nxtail = std::min(static_cast(tail / dt), nx); - printf("Read data set containing %d colums and %d rows\n", ny, nx); + printf("Read data set containing %d columns and %d rows\n", ny, nx); printf("Assuming (from data) that timestep is %g, nxtail = %d\n", dt, nxtail); snew(y, 6); for (i = 0; (i < ny); i++) diff --git a/src/gromacs/gmxana/gmx_rmsf.cpp b/src/gromacs/gmxana/gmx_rmsf.cpp index c0c439afd6..ac302bbdde 100644 --- a/src/gromacs/gmxana/gmx_rmsf.cpp +++ b/src/gromacs/gmxana/gmx_rmsf.cpp @@ -4,7 +4,7 @@ * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team. - * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -212,7 +212,7 @@ int gmx_rmsf(int argc, char* argv[]) "respect to the reference structure is calculated.[PAR]", "With the option [TT]-aniso[tt], [THISMODULE] will compute anisotropic", "temperature factors and then it will also output average coordinates", - "and a [REF].pdb[ref] file with ANISOU records (corresonding to the [TT]-oq[tt]", + "and a [REF].pdb[ref] file with ANISOU records (corresponding to the [TT]-oq[tt]", "or [TT]-ox[tt] option). Please note that the U values", "are orientation-dependent, so before comparison with experimental data", "you should verify that you fit to the experimental coordinates.[PAR]", @@ -227,7 +227,7 @@ int gmx_rmsf(int argc, char* argv[]) static gmx_bool bRes = FALSE, bAniso = FALSE, bFit = TRUE; t_pargs pargs[] = { { "-res", FALSE, etBOOL, { &bRes }, "Calculate averages for each residue" }, - { "-aniso", FALSE, etBOOL, { &bAniso }, "Compute anisotropic termperature factors" }, + { "-aniso", FALSE, etBOOL, { &bAniso }, "Compute anisotropic temperature factors" }, { "-fit", FALSE, etBOOL, diff --git a/src/gromacs/gmxana/gmx_wham.cpp b/src/gromacs/gmxana/gmx_wham.cpp index 9162bbcd4e..921b166e21 100644 --- a/src/gromacs/gmxana/gmx_wham.cpp +++ b/src/gromacs/gmxana/gmx_wham.cpp @@ -4,7 +4,7 @@ * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team. - * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -135,7 +135,7 @@ enum bsMethod_trajGauss }; -//! Parameters of one pull coodinate +//! Parameters of one pull coordinate typedef struct { int pull_type; //!< such as constraint, umbrella, ... @@ -187,8 +187,8 @@ typedef struct double* k; //!< force constants for the nPull coords double* pos; //!< umbrella positions for the nPull coords double* z; //!< z=(-Fi/kT) for the nPull coords. These values are iteratively computed during wham - int* N; //!< nr of data points in nPull histograms. - int* Ntot; //!< also nr of data points. N and Ntot only differ if bHistEq==TRUE + int* N; //!< nr of data points in nPull histograms. + int* Ntot; //!< also nr of data points. N and Ntot only differ if bHistEq==TRUE /*! \brief g = 1 + 2*tau[int]/dt where tau is the integrated autocorrelation time. * @@ -244,10 +244,10 @@ typedef struct UmbrellaOptions // NOLINT(clang-analyzer-optin.performance.Paddin * \name Basic WHAM options */ /*!\{*/ - int bins; //!< nr of bins, min, max, and dz of profile - real min, max, dz; - real Temperature, Tolerance; //!< temperature, converged when probability changes less than Tolerance - gmx_bool bCycl; //!< generate cyclic (periodic) PMF + int bins; //!< nr of bins, min, max, and dz of profile + real min, max, dz; + real Temperature, Tolerance; //!< temperature, converged when probability changes less than Tolerance + gmx_bool bCycl; //!< generate cyclic (periodic) PMF /*!\}*/ /*! * \name Output control @@ -2123,7 +2123,7 @@ static void read_tpr_header(const char* fn, t_UmbrellaHeader* header, t_Umbrella gmx_fatal(FARGS, "%s: Pull coordinate %d is of type \"%s\", expected \"umbrella\". Only " "umbrella coodinates can enter WHAM.\n" - "If you have umrella and non-umbrella coordinates, you can select the " + "If you have umbrella and non-umbrella coordinates, you can select the " "umbrella coordinates with gmx wham -is\n", fn, i + 1, epull_names[header->pcrd[i].pull_type]); } diff --git a/src/gromacs/gmxpreprocess/gen_vsite.cpp b/src/gromacs/gmxpreprocess/gen_vsite.cpp index cb0735fce7..a30eb061f3 100644 --- a/src/gromacs/gmxpreprocess/gen_vsite.cpp +++ b/src/gromacs/gmxpreprocess/gen_vsite.cpp @@ -4,7 +4,7 @@ * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team. - * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -96,11 +96,7 @@ struct VirtualSiteConfiguration int nhyd, const std::string& nextheavy, const std::string& dummy) : - atomtype(type), - isplanar(planar), - nHydrogens(nhyd), - nextHeavyType(nextheavy), - dummyMass(dummy) + atomtype(type), isplanar(planar), nHydrogens(nhyd), nextHeavyType(nextheavy), dummyMass(dummy) { } //! Type for the XH3/XH2 atom. @@ -150,9 +146,7 @@ struct VirtualSiteTopology * \param[in] v Value for distance. */ VirtualSiteBond(const std::string& a1, const std::string& a2, real v) : - atom1(a1), - atom2(a2), - value(v) + atom1(a1), atom2(a2), value(v) { } //! Atom 1 in bond. @@ -176,10 +170,7 @@ struct VirtualSiteTopology * \param[in] v Value for angle. */ VirtualSiteAngle(const std::string& a1, const std::string& a2, const std::string& a3, real v) : - atom1(a1), - atom2(a2), - atom3(a3), - value(v) + atom1(a1), atom2(a2), atom3(a3), value(v) { } //! Atom 1 in angle. @@ -379,7 +370,7 @@ static void read_vsite_database(const char* ddbname, break; default: gmx_fatal(FARGS, - "Didnt find a case for directive %s in read_vsite_database\n", dirstr); + "Didn't find a case for directive %s in read_vsite_database\n", dirstr); } } } diff --git a/src/gromacs/linearalgebra/eigensolver.cpp b/src/gromacs/linearalgebra/eigensolver.cpp index f0643b413b..e5247e79ba 100644 --- a/src/gromacs/linearalgebra/eigensolver.cpp +++ b/src/gromacs/linearalgebra/eigensolver.cpp @@ -4,7 +4,7 @@ * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team. - * Copyright (c) 2017,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2017,2019,2020,2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -102,7 +102,7 @@ void eigensolver(real* a, int n, int index_lower, int index_upper, real* eigenva if (info != 0) { sfree(isuppz); - gmx_fatal(FARGS, "Internal errror in LAPACK diagonalization."); + gmx_fatal(FARGS, "Internal error in LAPACK diagonalization."); } lwork = static_cast(w0); diff --git a/src/gromacs/tools/eneconv.cpp b/src/gromacs/tools/eneconv.cpp index f918abed80..8fea09d047 100644 --- a/src/gromacs/tools/eneconv.cpp +++ b/src/gromacs/tools/eneconv.cpp @@ -4,7 +4,7 @@ * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team. - * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -442,7 +442,7 @@ int gmx_eneconv(int argc, char* argv[]) "Reads one energy file and writes another, applying the [TT]-dt[tt],", "[TT]-offset[tt], [TT]-t0[tt] and [TT]-settime[tt] options and", "converting to a different format if necessary (indicated by file", - "extentions).[PAR]", + "extensions).[PAR]", "[TT]-settime[tt] is applied first, then [TT]-dt[tt]/[TT]-offset[tt]", "followed by [TT]-b[tt] and [TT]-e[tt] to select which frames to write." }; diff --git a/src/gromacs/tools/trjconv.cpp b/src/gromacs/tools/trjconv.cpp index 43274a7522..8406a83ab5 100644 --- a/src/gromacs/tools/trjconv.cpp +++ b/src/gromacs/tools/trjconv.cpp @@ -4,7 +4,7 @@ * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team. - * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -467,7 +467,7 @@ int gmx_trjconv(int argc, char* argv[]) FALSE, etBOOL, { &bCONECT }, - "Add conect records when writing [REF].pdb[ref] files. Useful " + "Add CONECT PDB records when writing [REF].pdb[ref] files. Useful " "for visualization of non-standard molecules, e.g. " "coarse grained ones" } }; @@ -593,7 +593,7 @@ int gmx_trjconv(int argc, char* argv[]) fprintf(stderr, "WARNING: Option for unitcell representation (-ur %s)\n" " only has effect in combination with -pbc %s, %s or %s.\n" - " Ingoring unitcell representation.\n\n", + " Ignoring unitcell representation.\n\n", unitcell_opt[0], pbc_opt[2], pbc_opt[3], pbc_opt[4]); } } diff --git a/src/gromacs/utility/coolstuff.cpp b/src/gromacs/utility/coolstuff.cpp index 14c0f1561a..d04b713189 100644 --- a/src/gromacs/utility/coolstuff.cpp +++ b/src/gromacs/utility/coolstuff.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -295,7 +295,7 @@ std::string getCoolQuote() { "With a Lead Filled Snowshoe", "F. Zappa" }, { "Right Between the Eyes", "F. Zappa" }, { "BioBeat is Not Available In Regular Shops", "P.J. Meulenhoff" }, - { "Rub It Right Accross Your Eyes", "F. Zappa" }, + { "Rub It Right Across Your Eyes", "F. Zappa" }, { "Shake Yourself", "YES" }, { "I Am a Wonderful Thing", "Kid Creole" }, { "Way to Go Dude", "Beavis and Butthead" },