* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 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.
* calls the notification functions in \p module as if the module had
* been registered to the data object when the data was added.
*/
- void presentData(AbstractAnalysisData* data, IAnalysisDataModule* module);
+ void presentData(AbstractAnalysisData* data, IAnalysisDataModule* module) const;
//! List of modules added to the data.
ModuleList modules_;
}
}
-void AnalysisDataModuleManager::Impl::presentData(AbstractAnalysisData* data, IAnalysisDataModule* module)
+void AnalysisDataModuleManager::Impl::presentData(AbstractAnalysisData* data, IAnalysisDataModule* module) const
{
if (state_ == eNotStarted)
{
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, 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.
return;
}
- int step, i;
-
if (_impl->nstored == 2)
{
if (_impl->histm)
AnalysisDataFrameHeader header(_impl->nstored - 2, _impl->t, 0);
moduleManager().notifyFrameStart(header);
- for (i = _impl->ci - _impl->nmax, step = 1; step < _impl->nstored && i != _impl->ci;
+ for (int i = _impl->ci - _impl->nmax, step = 1; step < _impl->nstored && i != _impl->ci;
i -= _impl->nmax, ++step)
{
if (i < 0)
* 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.
AverageHistogramPointer AbstractAverageHistogram::resampleDoubleBinWidth(bool bIntegerBins) const
{
- int nbins;
- if (bIntegerBins)
- {
- nbins = (rowCount() + 1) / 2;
- }
- else
- {
- nbins = rowCount() / 2;
- }
+ const int nbins = bIntegerBins ? (rowCount() + 1) / 2 : rowCount() / 2;
AverageHistogramPointer dest(new StaticAverageHistogram(
histogramFromBins(settings().firstEdge(), nbins, 2 * xstep()).integerBins(bIntegerBins)));
dest->setColumnCount(columnCount());
dest->allocateValues();
- int i, j;
- for (i = j = 0; i < nbins; ++i)
+ for (int i = 0, j = 0; i < nbins; ++i)
{
const bool bFirstHalfBin = (bIntegerBins && i == 0);
for (int c = 0; c < columnCount(); ++c)
{
- real v1, v2;
- real e1, e2;
- if (bFirstHalfBin)
- {
- v1 = value(0, c).value();
- e1 = value(0, c).error();
- v2 = 0;
- e2 = 0;
- }
- else
- {
- v1 = value(j, c).value();
- e1 = value(j, c).error();
- v2 = value(j + 1, c).value();
- e2 = value(j + 1, c).error();
- }
+ const real v1 = bFirstHalfBin ? value(0, c).value() : value(j, c).value();
+ const real v2 = bFirstHalfBin ? 0 : value(j + 1, c).value();
+ const real e1 = bFirstHalfBin ? value(0, c).error() : value(j, c).error();
+ const real e2 = bFirstHalfBin ? 0 : value(j + 1, c).error();
dest->value(i, c).setValue(v1 + v2, std::sqrt(e1 * e1 + e2 * e2));
}
if (bFirstHalfBin)
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff