From 60e4ed7e229b54c47f5847128df2ede11d42a60d Mon Sep 17 00:00:00 2001 From: Alexey Shvetsov Date: Tue, 28 Jul 2015 19:37:24 +0300 Subject: [PATCH 1/1] Uncrustify files Change-Id: I07a194d10afdbcf27755bcde1e291d869360725d Signed-off-by: Alexey Shvetsov --- admin/copyright.py | 2 +- .../trajectoryanalysis/cmdlinerunner.cpp | 52 +++++++++++-------- .../trajectoryanalysis/cmdlinerunner.h | 3 +- src/python/include/numpy_conv.h | 17 +++--- 4 files changed, 43 insertions(+), 31 deletions(-) diff --git a/admin/copyright.py b/admin/copyright.py index 23c8a3b643..c5c60d37dc 100755 --- a/admin/copyright.py +++ b/admin/copyright.py @@ -303,7 +303,7 @@ def select_comment_handler(override, filename): dummy, ext2 = os.path.splitext(root) if ext2: ext = ext2 - if ext in ('.c', '.cu', '.cpp', '.h', '.cuh', '.y', '.l', '.pre', '.bm'): + if ext in ('.c', '.cu', '.cpp', '.h', '.cuh', '.y', '.l', '.pre', '.bm', '.sip'): filetype = 'c' elif ext in ('.tex',): filetype = 'tex' diff --git a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp index e70fafa138..0bc78ce8fa 100644 --- a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp +++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp @@ -81,7 +81,7 @@ class TrajectoryAnalysisCommandLineRunner::Impl void parseOptions(TrajectoryAnalysisSettings *settings, TrajectoryAnalysisRunnerCommon *common, SelectionCollection *selections, - int *argc, char *argv[], bool full=true); + int *argc, char *argv[], bool full = true); TrajectoryAnalysisModule *module_; bool bUseDefaultGroups_; @@ -111,14 +111,15 @@ TrajectoryAnalysisCommandLineRunner::Impl::parseOptions( FileNameOptionManager fileoptManager; SelectionOptionManager seloptManager(selections); Options options(NULL, NULL); - IOptionsContainer &commonOptions = options.addGroup(); - IOptionsContainer &moduleOptions = options.addGroup(); + IOptionsContainer &commonOptions = options.addGroup(); + IOptionsContainer &moduleOptions = options.addGroup(); options.addManager(&fileoptManager); options.addManager(&seloptManager); module_->initOptions(&moduleOptions, settings); - if (full) { + if (full) + { common->initOptions(&commonOptions); } selections->initOptions(&commonOptions); @@ -132,7 +133,8 @@ TrajectoryAnalysisCommandLineRunner::Impl::parseOptions( options.finish(); } - if (full) { + if (full) + { common->optionsFinished(); } module_->optionsFinished(settings); @@ -195,15 +197,16 @@ TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[]) const TopologyInformation &topology = common.topologyInformation(); module->initAnalysis(settings, topology); - TrajectoryAnalysisModule::Batch batch = module->getBatch(); + TrajectoryAnalysisModule::Batch batch = module->getBatch(); std::vector batchSelections; - std::vector impls; - for (size_t i = 0; i < batch.size(); i++) { + std::vector impls; + for (size_t i = 0; i < batch.size(); i++) + { TrajectoryAnalysisModule *bmodule = batch[i]; batchSelections.push_back(new SelectionCollection()); impls.push_back(new Impl(bmodule)); std::vector modArgv = module->getArgv(i); - int modArgc = modArgv.size(); + int modArgc = modArgv.size(); impls.back()->parseOptions(&settings, &common, batchSelections.back(), &modArgc, modArgv.data(), false); batch[i]->initAnalysis(settings, topology); @@ -221,14 +224,15 @@ TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[]) TrajectoryAnalysisModuleDataPointer pdata( module->startFrames(dataOptions, selections)); - std::vector batchOptions; + std::vector batchOptions; std::vector batchDataPointers; - for (size_t i = 0; i < batch.size(); i++) { + for (size_t i = 0; i < batch.size(); i++) + { batch[i]->initAfterFirstFrame(settings, common.frame()); batchOptions.push_back(AnalysisDataParallelOptions()); batchDataPointers.push_back(batch[i]->startFrames( - batchOptions.back(), *batchSelections[i])); + batchOptions.back(), *batchSelections[i])); } do @@ -240,7 +244,8 @@ TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[]) set_pbc(ppbc, topology.ePBC(), frame.box); } - for (size_t i = 0; i < batch.size(); i++) { + for (size_t i = 0; i < batch.size(); i++) + { batchSelections[i]->evaluate(&frame, ppbc); batch[i]->analyzeFrame(nframes, frame, ppbc, batchDataPointers[i].get()); batch[i]->finishFrameSerial(nframes); @@ -252,9 +257,11 @@ TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[]) ++nframes; } while (common.readNextFrame()); - for (size_t i = 0; i < batch.size(); i++) { + for (size_t i = 0; i < batch.size(); i++) + { batch[i]->finishFrames(batchDataPointers[i].get()); - if (batchDataPointers[i].get() != NULL) { + if (batchDataPointers[i].get() != NULL) + { batchDataPointers[i]->finish(); } batchDataPointers[i].reset(); @@ -278,7 +285,8 @@ TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[]) } // Restore the maximal groups for dynamic selections. - for (size_t i = 0; i < batch.size(); i++) { + for (size_t i = 0; i < batch.size(); i++) + { batchSelections[i]->evaluateFinal(nframes); batch[i]->finishAnalysis(nframes); batch[i]->writeOutput(); @@ -365,10 +373,10 @@ class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule virtual void writeHelp(const CommandLineHelpContext &context) const; private: - const char *name_; - const char *description_; - bool hasFunction_; - ModuleFactoryMethod factory_; + const char *name_; + const char *description_; + bool hasFunction_; + ModuleFactoryMethod factory_; ModuleFactoryFunctor *functor_; GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule); @@ -382,7 +390,7 @@ void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init( int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run( int argc, char *argv[]) { - TrajectoryAnalysisModulePointer module(hasFunction_? factory_() : (*functor_)()); + TrajectoryAnalysisModulePointer module(hasFunction_ ? factory_() : (*functor_)()); TrajectoryAnalysisCommandLineRunner runner(module.get()); return runner.run(argc, argv); } @@ -390,7 +398,7 @@ int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run( void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp( const CommandLineHelpContext &context) const { - TrajectoryAnalysisModulePointer module(hasFunction_? factory_() : (*functor_)()); + TrajectoryAnalysisModulePointer module(hasFunction_ ? factory_() : (*functor_)()); TrajectoryAnalysisCommandLineRunner runner(module.get()); runner.writeHelp(context); } diff --git a/src/gromacs/trajectoryanalysis/cmdlinerunner.h b/src/gromacs/trajectoryanalysis/cmdlinerunner.h index 9bcc013418..0b703ea268 100644 --- a/src/gromacs/trajectoryanalysis/cmdlinerunner.h +++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.h @@ -87,7 +87,8 @@ class TrajectoryAnalysisCommandLineRunner * This abstract class should be subclassed to be used. The main usage is for * python bindings. */ - class ModuleFactoryFunctor { + class ModuleFactoryFunctor + { public: /*! \brief * operator() that returns a pointer to valid TrajectoryAnalysisModule diff --git a/src/python/include/numpy_conv.h b/src/python/include/numpy_conv.h index b810832b05..67d04da321 100644 --- a/src/python/include/numpy_conv.h +++ b/src/python/include/numpy_conv.h @@ -39,25 +39,28 @@ #include #include -PyObject* array2dToNumpy(int dim1, int dim2, const void *data) { +PyObject* array2dToNumpy(int dim1, int dim2, const void *data) +{ npy_intp dims[] = {dim1, dim2}; #ifdef GMX_DOUBLE - return PyArray_SimpleNewFromData(2, dims, NPY_DOUBLE, (double*) data); + return PyArray_SimpleNewFromData(2, dims, NPY_DOUBLE, (double*) data); #else - return PyArray_SimpleNewFromData(2, dims, NPY_FLOAT, (float*) data); + return PyArray_SimpleNewFromData(2, dims, NPY_FLOAT, (float*) data); #endif } -PyObject* array1dToNumpy(int dim, const void *data) { +PyObject* array1dToNumpy(int dim, const void *data) +{ npy_intp n_dim = dim; #ifdef GMX_DOUBLE - return PyArray_SimpleNewFromData(1, &n_dim, NPY_DOUBLE, (double*) data); + return PyArray_SimpleNewFromData(1, &n_dim, NPY_DOUBLE, (double*) data); #else - return PyArray_SimpleNewFromData(1, &n_dim, NPY_FLOAT, (float*) data); + return PyArray_SimpleNewFromData(1, &n_dim, NPY_FLOAT, (float*) data); #endif } -PyObject* iarray1dToNumpy(int dim, const int *data) { +PyObject* iarray1dToNumpy(int dim, const int *data) +{ npy_intp n_dim = dim; return PyArray_SimpleNewFromData(1, &n_dim, NPY_INT, (int*) data); } -- 2.22.0