Merge pull request #99 from robertodr/format-code

Format sources using clang-format and YAPF

Author: bast

include/Config.hpp.in

@@ -40,15 +40,15 @@
 #endif
 
 #ifdef __GNUC__
-#  define UNUSED(x) UNUSED_ ## x __attribute__((__unused__))
+#define UNUSED(x) UNUSED_##x __attribute__((__unused__))
 #else
-#  define UNUSED(x) UNUSED_ ## x
+#define UNUSED(x) UNUSED_##x
 #endif
 
 #ifdef __GNUC__
-#  define UNUSED_FUNCTION(x) __attribute__((__unused__)) UNUSED_ ## x
+#define UNUSED_FUNCTION(x) __attribute__((__unused__)) UNUSED_##x
 #else
-#  define UNUSED_FUNCTION(x) UNUSED_ ## x
+#define UNUSED_FUNCTION(x) UNUSED_##x
 #endif
 
 // Inspired from Eigen EIGEN_DEFAULT_DENSE_INDEX_TYPE

src/bin/debug_wavcav.cpp

@@ -21,15 +21,15 @@
  * PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
  */
 
-#include <iostream>
 #include <fstream>
+#include <iostream>
 #include <string>
 
 #include <Eigen/Core>
 
 #include "PWCSolver.hpp"
-#include "Vacuum.hpp"
 #include "UniformDielectric.hpp"
+#include "Vacuum.hpp"
 #include "WaveletCavity.hpp"
 
 int main(int argc, char ** argv) {

src/bin/run_pcm.cpp

@@ -21,8 +21,8 @@
  * PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
  */
 
-#include <cstdlib>
 #include <cmath>
+#include <cstdlib>
 #include <cstring>
 #include <iostream>
 #include <map>
@@ -40,8 +40,8 @@
 
 #include "interface/Input.hpp"
 #include "interface/Meddle.hpp"
-#include "utils/Molecule.hpp"
 #include "utils/ChargeDistribution.hpp"
+#include "utils/Molecule.hpp"
 
 std::ofstream pcmsolver_out;
 

src/cavity/Element.cpp

@@ -106,8 +106,7 @@ void Element::spherical_polygon(Eigen::Vector3d & t_,
     }
     numb[i] = i;
     phinumb[i] = phi[i];
-  jump:
-    ; // Do nothing...
+  jump:; // Do nothing...
   }
   numb[nVertices_] = numb[0];
   phinumb[nVertices_] = 2 * M_PI;

src/green/SphericalDiffuse.cpp

@@ -39,9 +39,9 @@
 #include "GreenData.hpp"
 #include "GreensFunction.hpp"
 #include "cavity/Element.hpp"
-#include "utils/MathUtils.hpp"
 #include "dielectric_profile/ProfileTypes.hpp"
 #include "utils/ForId.hpp"
+#include "utils/MathUtils.hpp"
 
 namespace pcm {
 namespace green {

src/green/Vacuum.cpp

@@ -41,8 +41,7 @@ using cavity::Element;
 using dielectric_profile::Uniform;
 namespace green {
 template <typename DerivativeTraits>
-Vacuum<DerivativeTraits>::Vacuum()
-    : GreensFunction<DerivativeTraits, Uniform>() {
+Vacuum<DerivativeTraits>::Vacuum() : GreensFunction<DerivativeTraits, Uniform>() {
   this->profile_ = Uniform(1.0);
 }
 

src/interface/Input.cpp

@@ -25,21 +25,21 @@
 
 #include <iostream>
 #include <map>
-#include <vector>
 #include <string>
+#include <vector>
 
 #include "Config.hpp"
 
-#include <Eigen/Core>
 #include "utils/getkw/Getkw.h"
+#include <Eigen/Core>
 
 #include <boost/algorithm/string.hpp>
 
+#include "PCMInput.h"
 #include "bi_operators/BIOperatorData.hpp"
 #include "cavity/CavityData.hpp"
 #include "green/GreenData.hpp"
 #include "solver/SolverData.hpp"
-#include "PCMInput.h"
 #include "utils/Factory.hpp"
 #include "utils/Solvent.hpp"
 #include "utils/Sphere.hpp"
@@ -94,7 +94,8 @@ void Input::reader(const std::string & filename) {
       Eigen::Vector3d center;
       center = (Eigen::Vector3d() << spheresInput[j],
                 spheresInput[j + 1],
-                spheresInput[j + 2]).finished();
+                spheresInput[j + 2])
+                   .finished();
       Sphere sph(center, spheresInput[j + 3]);
       spheres_.push_back(sph);
       j += 4;

src/interface/Meddle.cpp

@@ -21,9 +21,9 @@
  * PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
  */
 
-#include "pcmsolver.h"
-#include "PCMInput.h"
 #include "Meddle.hpp"
+#include "PCMInput.h"
+#include "pcmsolver.h"
 
 #include <string>
 #include <vector>
@@ -36,19 +36,19 @@
 
 #include "bi_operators/BIOperatorData.hpp"
 #include "bi_operators/BoundaryIntegralOperator.hpp"
-#include "cavity/CavityData.hpp"
 #include "cavity/Cavity.hpp"
-#include "green/GreenData.hpp"
+#include "cavity/CavityData.hpp"
 #include "green/Green.hpp"
-#include "solver/SolverData.hpp"
+#include "green/GreenData.hpp"
 #include "solver/Solver.hpp"
+#include "solver/SolverData.hpp"
 
-#include "utils/Atom.hpp"
 #include "Citation.hpp"
-#include "utils/cnpy.hpp"
+#include "utils/Atom.hpp"
 #include "utils/Factory.hpp"
 #include "utils/Solvent.hpp"
 #include "utils/Sphere.hpp"
+#include "utils/cnpy.hpp"
 
 #ifndef AS_TYPE
 #define AS_TYPE(Type, Obj) reinterpret_cast<Type *>(Obj)

src/make_cmake_files.py

@@ -1,6 +1,5 @@
 #!/usr/bin/python
 
-
 #
 #  PCMSolver, an API for the Polarizable Continuum Model
 #  Copyright (C) 2017 Roberto Di Remigio, Luca Frediani and collaborators.
@@ -49,6 +48,7 @@
   -h --help                              Show this screen.
 """
 
+
 def glob_sources_cxx(dir_name):
     """Create a list of C++ headers and sources to be used in a CMakeLists.txt file."""
     headers = 'list(APPEND headers_list '
@@ -63,6 +63,7 @@ def glob_sources_cxx(dir_name):
             + '# List of sources\n' + sources
     return message
 
+
 def glob_sources_c(dir_name):
     """Create a list of C headers and sources to be used in a CMakeLists.txt file."""
     headers = 'list(APPEND headers_list '
@@ -77,6 +78,7 @@ def glob_sources_c(dir_name):
             + '# List of sources\n' + sources
     return message
 
+
 def glob_sources_fortran(dir_name):
     """Create a list of Fortran sources to be used in a CMakeLists.txt file."""
     types = ('*.f', '*.F', '*.f77', '*.F77', '*.f90', '*.F90')
@@ -90,6 +92,7 @@ def glob_sources_fortran(dir_name):
     message = '# List of sources\n' + sources
     return message
 
+
 try:
     arguments = docopt.docopt(options, argv=None)
 except docopt.DocoptExit:
@@ -99,7 +102,7 @@ def glob_sources_fortran(dir_name):
 
 # Grab command-line arguments
 libname = arguments['--libname']
-lang    = arguments['--lang']
+lang = arguments['--lang']
 
 root_directory = os.getcwd()
 dname = os.path.join(root_directory, libname)

src/solver/CPCMSolver.cpp

@@ -34,8 +34,8 @@
 
 #include "SolverData.hpp"
 #include "bi_operators/IBoundaryIntegralOperator.hpp"
-#include "cavity/ICavity.hpp"
 #include "cavity/Element.hpp"
+#include "cavity/ICavity.hpp"
 #include "green/IGreensFunction.hpp"
 #include "utils/MathUtils.hpp"