Fix issues from downstream patches and suppressions

diff --git a/docs/user-guide/mdrun-performance.rst b/docs/user-guide/mdrun-performance.rst
index 1989c670c1061cbb9658335aa0dd849f343e5188..8fb1bdab826c0fb5a51860b8ed55730c3a4d2ffb 100644 (file)
--- 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 c15844c6c3438d9de25bb5ac68294770ee18b860..0e653b6f798ad0a6df77f87021d4806059ba7bf8 100644 (file)
--- 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 751c62f6d0f6515f428c441674a812634f64ffc0..9fdaa533c9b0653ccd605a1c3082fcb3862230a6 100644 (file)
--- 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 3ab32fd48236b93c0565fd1d5e3e8d45966bb212..eef8de70205d3543247043c52d45451af664c81b 100644 (file)
--- 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<int>(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 c0c439afd6af2c7174b364df59c64825402f4914..ac302bbddeb8927089cfe6d7de15635b1801207c 100644 (file)
--- 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 9162bbcd4e261732652a3293f19cd3f69ff4be6f..921b166e2175cd3eddaa58b448ada3dd9c0ad5c9 100644 (file)
--- 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 cb0735fce79848b34450c7adf4632a8c07bfc9f4..a30eb061f3c6e417350af5c357f0707f9263381f 100644 (file)
--- 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 f0643b413bba54f1ea79ce05226b44987aaee720..e5247e79bac037a961e483621adc6b2063b064ca 100644 (file)
--- 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<int>(w0);

diff --git a/src/gromacs/tools/eneconv.cpp b/src/gromacs/tools/eneconv.cpp
index f918abed80abcd6c62be83a94927b4afdb9d3c21..8fea09d047ea7649a23e53944d2f368f3bcf00cd 100644 (file)
--- 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 43274a7522d4cfdb496383daa71bb10959466e5e..8406a83ab592fa577e860794a03a404dd9fa52cc 100644 (file)
--- 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 14c0f1561a6bedffc198f96719528110ba584ea2..d04b7131896c3985853904545d572b014b74a9a1 100644 (file)
--- 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" },