Proposing: removing lines with more than one statements. (v2.10)

.astyle.options

@@ -1 +1,13 @@
--n --indent=spaces=2 --keep-one-line-statements --keep-one-line-blocks
+# long options can be written without the preceding '--'
+suffix=none #equivalent to "-n"
+style=attach
+add-braces
+indent=spaces=2
+break-one-line-headers
+
+# old options
+#suffix=none
+#indent=spaces=2
+#keep-one-line-statements
+#keep-one-line-blocks
+# end old options

.git-blame-ignore-revs

@@ -0,0 +1,6 @@
+# .git-blame-ignore-revs
+# https://docs.github.com/en/repositories/working-with-files/using-files/viewing-a-file#ignore-commits-in-the-blame-view
+# new astyle applied to v2.9.3
+2cd41d16623b7a062b2a716eaf5c91a741cc19ea
+# new astyle applied to v2.10
+df781b48652d8cdde2994dae1197cdb623f3f3fa

plugins/cudaCoord/Coordination.cu

@@ -259,14 +259,17 @@ void CudaCoordination<calculateFloat>::calculate() {
   }
 
   // in this way we do not resize with additional memory allocation
-  if (reductionMemoryCoord.size() > cudaCoordination.size())
+  if (reductionMemoryCoord.size() > cudaCoordination.size()) {
     reductionMemoryCoord.swap (cudaCoordination);
-  if (reductionMemoryVirial.size() > cudaVirial.size())
+  }
+  if (reductionMemoryVirial.size() > cudaVirial.size()) {
     reductionMemoryVirial.swap (cudaVirial);
+  }
   // this ensures that the memory is fully in the host ram
   cudaDeviceSynchronize();
-  for (unsigned i = 0; i < deriv.size(); ++i)
+  for (unsigned i = 0; i < deriv.size(); ++i) {
     setAtomsDerivatives (i, deriv[i]);
+  }
 
   setValue (coordination);
   setBoxDerivatives (virial);
@@ -349,8 +352,9 @@ getSelfCoord (const unsigned nat,
     // const unsigned j = threadIdx.y + blockIdx.y * blockDim.y;
 
     // Safeguard
-    if (idx == trueIndexes[j])
+    if (idx == trueIndexes[j]) {
       continue;
+    }
 
     d_0 = calculatePBC<usePBC> (coordinates[X (j)] - x, myPBC.X);
     d_1 = calculatePBC<usePBC> (coordinates[Y (j)] - y, myPBC.Y);
@@ -493,8 +497,9 @@ getCoordDual (const unsigned natActive,
     // const unsigned j = threadIdx.y + blockIdx.y * blockDim.y;
 
     // Safeguard
-    if (idx == trueIndexes[j])
+    if (idx == trueIndexes[j]) {
       continue;
+    }
 
     d_0 = calculatePBC<usePBC> (coordLoop[X (j)] - x, myPBC.X);
     d_1 = calculatePBC<usePBC> (coordLoop[Y (j)] - y, myPBC.Y);
@@ -597,8 +602,9 @@ getDerivDual (const unsigned natLoop,
     // const unsigned j = threadIdx.y + blockIdx.y * blockDim.y;
 
     // Safeguard
-    if (idx == trueIndexes[j])
+    if (idx == trueIndexes[j]) {
       continue;
+    }
 
     d_0 = calculatePBC<usePBC> (coordLoop[X (j)] - x, myPBC.X);
     d_1 = calculatePBC<usePBC> (coordLoop[Y (j)] - y, myPBC.Y);
@@ -880,7 +886,8 @@ CudaCoordination<calculateFloat>::CudaCoordination (const ActionOptions &ao)
   }
   std::string sw, errors;
 
-  { // loading data to the GPU
+  {
+    // loading data to the GPU
     int nn_ = 6;
     int mm_ = 0;
 
@@ -895,8 +902,9 @@ CudaCoordination<calculateFloat>::CudaCoordination (const ActionOptions &ao)
     if (mm_ == 0) {
       mm_ = 2 * nn_;
     }
-    if (mm_ % 2 != 0 || mm_ % 2 != 0)
+    if (mm_ % 2 != 0 || mm_ % 2 != 0) {
       error (" this implementation only works with both MM and NN even");
+    }
 
     switchingParameters.nn = nn_;
     switchingParameters.mm = mm_;

plugins/cudaCoord/Coordination.cuh

@@ -97,8 +97,9 @@ __device__ __forceinline__ calculateFloat pcuda_fastpow (calculateFloat base,
   }
   calculateFloat result = 1.0;
   while (expo) {
-    if (expo & 1)
+    if (expo & 1) {
       result *= base;
+    }
     expo >>= 1;
     base *= base;
   }
@@ -156,8 +157,9 @@ __global__ void getpcuda_Rational (const calculateFloat *rdists,
   if (rdists[i] <= 0.) {
     res[i] = 1.;
     dfunc[i] = 0.0;
-  } else
+  } else {
     res[i] = pcuda_Rational (rdists[i], NN, MM, dfunc[i]);
+  }
   // printf("stretch: %i: %f -> %f\n",i,rdists[i],res[i]);
 }
 

plugins/cudaCoord/cudaHelpers.cuh

@@ -40,7 +40,7 @@ struct DataInterface {
   double *ptr = nullptr;
   size_t size = 0;
   DataInterface() = delete;
-  
+
   // VectorGeneric is a "memory map" on an n linear array
   // &vg[0] gets the pointer to the first double in memory
   // C++ vectors align memory so we can safely use the vector variant of

plugins/pycv/PlumedPythonEmbeddedModule.cpp

@@ -110,7 +110,8 @@ PYBIND11_EMBEDDED_MODULE(plumedCommunications, m) {
     auto retAccessor = atomIndexes.mutable_unchecked<1>();
     for (decltype(nat) i=0; i < nat; ++i) {
       //at time of writing getAbsoluteIndexes returns const std::vector<AtomNumber> &
-      retAccessor(i)=self->getAbsoluteIndexes()[i].index();
+      retAccessor(i)
+      =self->getAbsoluteIndexes()[i].index();
     }
     return atomIndexes;
   },
@@ -129,7 +130,8 @@ PYBIND11_EMBEDDED_MODULE(plumedCommunications, m) {
     py::array_t<double> masses(shape);
     auto retAccessor = masses.mutable_unchecked<1>();
     for (decltype(nat) i=0; i < nat; ++i) {
-      retAccessor(i)=self->getMass(i);
+      retAccessor(i)
+      =self->getMass(i);
     }
     return masses;
   },
@@ -142,7 +144,8 @@ PYBIND11_EMBEDDED_MODULE(plumedCommunications, m) {
     py::array_t<double> charges(shape);
     auto retAccessor = charges.mutable_unchecked<1>();
     for (decltype(nat) i=0; i < nat; ++i) {
-      retAccessor(i)=self->getCharge(i);
+      retAccessor(i)
+      =self->getCharge(i);
     }
     return charges;
   },
@@ -196,7 +199,8 @@ return toRet;
     py::array_t<unsigned long> couples(shape);
     auto retAccessor = couples.mutable_unchecked<2>();
     for(size_t c=0; c< ncouples; ++c) {
-      retAccessor(c,0) = self->getClosePair(c).first;
+      retAccessor(c,0)
+      = self->getClosePair(c).first;
       retAccessor(c,1) = self->getClosePair(c).second;
     }
     return couples;

plugins/pycv/PythonCVInterface.cpp

@@ -523,17 +523,21 @@ PythonCVInterface::PythonCVInterface(const ActionOptions&ao) ://the catch only a
     std::vector<AtomNumber> groupB;
     pyParseAtomList("GROUPB",initDict,groupB);
 
-    if(atoms.size() !=0 && groupA.size()!=0)
+    if(atoms.size() !=0 && groupA.size()!=0) {
       error("you can choose only between using the neigbourlist OR the atoms");
+    }
 
-    if(atoms.size()==0&& groupA.size()==0 && groupB.size()==0)
+    if(atoms.size()==0&& groupA.size()==0 && groupB.size()==0) {
       error("At least one atom is required");
+    }
 
-    if (atoms.size() != 0 && groupA.size() != 0)
+    if (atoms.size() != 0 && groupA.size() != 0) {
       error("you can choose only between using the neigbourlist OR the atoms");
+    }
 
-    if (atoms.size() == 0 && groupA.size() == 0 && groupB.size() == 0)
+    if (atoms.size() == 0 && groupA.size() == 0 && groupB.size() == 0) {
       error("At least one atom is required");
+    }
 
     bool nopbc;
     pyParseFlag("NOPBC",initDict, nopbc);
@@ -551,11 +555,13 @@ PythonCVInterface::PythonCVInterface(const ActionOptions&ao) ://the catch only a
       int nl_st = 0;
       if (doneigh) {
         pyParse("NL_CUTOFF", initDict, nl_cut);
-        if (nl_cut <= 0.0)
+        if (nl_cut <= 0.0) {
           error("NL_CUTOFF should be explicitly specified and positive");
+        }
         pyParse("NL_STRIDE",initDict, nl_st);
-        if (nl_st <= 0)
+        if (nl_st <= 0) {
           error("NL_STRIDE should be explicitly specified and positive");
+        }
       }
       // endof WIP
       if (groupB.size() > 0) {
@@ -607,8 +613,9 @@ void PythonCVInterface::prepare() {
             error("Neighbor lists should be updated on exchange steps - choose a "
                   "NL_STRIDE which divides the exchange stride!");
         }
-        if (getExchangeStep())
+        if (getExchangeStep()) {
           firsttime = true;
+        }
       }
     }
     if (hasPrepare) {
@@ -680,8 +687,9 @@ void PythonCVInterface::readReturn(const py::object &r, Value* valPtr) {
     //shape returns long int
     auto natoms = static_cast<long int > (getPositions().size());
     if (rl.size() > 1) {
-      if(!valPtr->hasDerivatives())
+      if(!valPtr->hasDerivatives()) {
         error(valPtr->getName()+" was declared without derivatives, but python returned with derivatives");
+      }
       // 2nd return value: gradient: numpy array of (natoms, 3)
       py::array_t<pycvComm_t> grad(rl[1]);
       // Assert correct gradient shape
@@ -697,12 +705,14 @@ void PythonCVInterface::readReturn(const py::object &r, Value* valPtr) {
         Vector3d gi(grad.at(i, 0), grad.at(i, 1), grad.at(i, 2));
         setAtomsDerivatives(valPtr, i, gi);
       }
-    } else if (valPtr->hasDerivatives())
+    } else if (valPtr->hasDerivatives()) {
       error(valPtr->getName()+" was declared with derivatives, but python returned none");
+    }
 
     if (rl.size() > 2) {
-      if(!valPtr->hasDerivatives())
+      if(!valPtr->hasDerivatives()) {
         plumed_merror(valPtr->getName()+" was declared without derivatives, but python returned with box derivatives");
+      }
       py::array_t<pycvComm_t> pyBoxDev(rl[2]);
       // expecting the box derivatives
       Tensor boxDev;
@@ -724,18 +734,21 @@ void PythonCVInterface::readReturn(const py::object &r, Value* valPtr) {
         error("Python CV returned wrong box derivatives shape error");
       }
       setBoxDerivatives(valPtr, boxDev);
-    } else if (valPtr->hasDerivatives())
+    } else if (valPtr->hasDerivatives()) {
       warning(valPtr->getName()+" was declared with derivatives, but python returned no box derivatives");
+    }
   } else {
     // Only value returned. Might be an error as well.
-    if (valPtr->hasDerivatives())
+    if (valPtr->hasDerivatives()) {
       warning(BIASING_DISABLED);
+    }
     pycvComm_t value = r.cast<pycvComm_t>();
     valPtr->set(value);
   }
   //TODO: is this ok?
-  if (!pbc)
+  if (!pbc) {
     setBoxDerivativesNoPbc(valPtr);
+  }
 }
 
 
@@ -750,10 +763,11 @@ void PythonCVInterface::calculateMultiComponent(py::object &r) {
       std::string key=component->getName().substr(
                         2 + getLabel().size()
                         +PYCV_COMPONENTPREFIX.size());
-      if (dataDict.contains(key.c_str()))
+      if (dataDict.contains(key.c_str())) {
         readReturn(dataDict[key.c_str()], component);
-      else
+      } else {
         error( "python did not returned " + key );
+      }
     }
   } else {
     // In principle one could handle a "list" return case.
@@ -765,15 +779,18 @@ void PythonCVInterface::pyParseAtomList(const char* key, const ::pybind11::dict
   parseAtomList(key,myatoms);
 
   if(initDict.contains(key)) {
-    if (myatoms.size()>0)
+    if (myatoms.size()>0) {
       error(std::string("you specified the same keyword ").append(key)+ " both in python and in the settings file");
+    }
     auto atomlist=PLMD::Tools::getWords(
                     py::str(initDict[key]).cast<std::string>(),
                     "\t\n ,");
     interpretAtomList( atomlist, myatoms );
   }
 }
 
-NeighborList &PythonCVInterface::getNL() { return *nl; }
+NeighborList &PythonCVInterface::getNL() {
+  return *nl;
+}
 } // namespace pycvs
 } // namespace PLMD

plugins/pycv/PythonFunction.cpp

@@ -104,7 +104,8 @@ PLUMED_REGISTER_ACTION(PythonFunction,"PYFUNCTION")
 
 void PythonFunction::registerKeywords( Keywords& keys ) {
   Function::registerKeywords( keys );
-  keys.use("ARG"); keys.use("PERIODIC");
+  keys.use("ARG");
+  keys.use("PERIODIC");
   keys.add("compulsory","IMPORT","the python file to import, containing the function");
   keys.add("compulsory","CALCULATE",PYCV_DEFAULTCALCULATE,"the function to call");
   keys.add("compulsory","INIT",PYCV_DEFAULTINIT,"the function to call during the construction method of the function");
@@ -225,8 +226,9 @@ void PythonFunction::readReturn(const py::object &r, Value* valPtr) {
     valPtr->set(value);
     if (rl.size() > 1) {
       auto nargs = getNumberOfArguments();
-      if(!valPtr->hasDerivatives())
+      if(!valPtr->hasDerivatives()) {
         error(valPtr->getName()+" was declared without derivatives, but python returned with derivatives");
+      }
       // 2nd return value: gradient: numpy array
       py::array_t<pycvComm_t> grad(rl[1]);
       if(grad.ndim() != 1 || grad.shape(0) != nargs) {
@@ -240,8 +242,9 @@ void PythonFunction::readReturn(const py::object &r, Value* valPtr) {
       for(size_t i=0; i<nargs; i++) {
         valPtr->setDerivative(i,grad.at(i));
       }
-    } else if (valPtr->hasDerivatives())
+    } else if (valPtr->hasDerivatives()) {
       plumed_merror(valPtr->getName()+" was declared with derivatives, but python returned none");
+    }
 
   } else {
     // Only value returned. Might be an error as well.
@@ -262,10 +265,11 @@ void PythonFunction::calculateMultiComponent(py::object &r) {
       std::string key=component->getName().substr(
                         2 + getLabel().size()
                         +PYCV_COMPONENTPREFIX.size());
-      if (dataDict.contains(key.c_str()))
+      if (dataDict.contains(key.c_str())) {
         readReturn(dataDict[key.c_str()], component);
-      else
+      } else {
         error( "python did not returned " + key );
+      }
     }
   } else {
     // In principle one could handle a "list" return case.

python/plumed.pyx

@@ -551,7 +551,7 @@ def read_as_pandas(file_or_path,enable_constants=True,enable_conversion=True,ker
 
 # read the rest of the file
 # notice that if chunksize was provided the result will be an iterable object
-    df=pd.read_csv(file_or_path, delim_whitespace=True, comment="#", header=None,names=columns,
+    df=pd.read_csv(file_or_path, sep='\s+', comment="#", header=None,names=columns,
                     usecols=usecols,skiprows=skiprows,nrows=nrows,chunksize=chunksize,index_col=index_col)
 
     if chunksize is None: