restyled v2.10

plumed · Oct 4, 2024 · d80912c · d80912c
1 parent 473fe65
commit d80912c
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Showing 545 changed files with 34,537 additions and 16,698 deletions.
diff --git a/.astyle.options b/.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
diff --git a/src/adjmat/AdjacencyMatrixBase.cpp b/src/adjmat/AdjacencyMatrixBase.cpp
diff --git a/src/adjmat/AdjacencyMatrixBase.h b/src/adjmat/AdjacencyMatrixBase.h
@@ -50,7 +50,9 @@ class AdjacencyMatrixBase : public ActionWithMatrix {
 public:
   static void registerKeywords( Keywords& keys );
   explicit AdjacencyMatrixBase(const ActionOptions&);
-  bool isAdjacencyMatrix() const override { return true; }
+  bool isAdjacencyMatrix() const override {
+    return true;
+  }
   unsigned getNumberOfDerivatives() override ;
   unsigned getNumberOfColumns() const override;
   void prepare() override;
@@ -72,9 +74,14 @@ Vector AdjacencyMatrixBase::getPosition( const unsigned& indno, MultiValue& myva
 
 inline
 void AdjacencyMatrixBase::addAtomDerivatives( const unsigned& indno, const Vector& der, MultiValue& myvals ) const {
-  if( doNotCalculateDerivatives() ) return;
-  plumed_dbg_assert( indno<2 ); unsigned index = myvals.getTaskIndex();
-  if( indno==1 ) index = myvals.getSecondTaskIndex();
+  if( doNotCalculateDerivatives() ) {
+    return;
+  }
+  plumed_dbg_assert( indno<2 );
+  unsigned index = myvals.getTaskIndex();
+  if( indno==1 ) {
+    index = myvals.getSecondTaskIndex();
+  }
   unsigned w_index = getConstPntrToComponent(0)->getPositionInStream();
   myvals.addDerivative( w_index, 3*index+0, der[0] );
   myvals.addDerivative( w_index, 3*index+1, der[1] );
@@ -83,7 +90,9 @@ void AdjacencyMatrixBase::addAtomDerivatives( const unsigned& indno, const Vecto
 
 inline
 void AdjacencyMatrixBase::addThirdAtomDerivatives( const unsigned& indno, const Vector& der, MultiValue& myvals ) const {
-  if( doNotCalculateDerivatives() ) return;
+  if( doNotCalculateDerivatives() ) {
+    return;
+  }
   unsigned index = myvals.getIndices()[ indno + myvals.getSplitIndex() ];
   unsigned w_index = getConstPntrToComponent(0)->getPositionInStream();
   myvals.addDerivative( w_index, 3*index+0, der[0] );
@@ -93,7 +102,9 @@ void AdjacencyMatrixBase::addThirdAtomDerivatives( const unsigned& indno, const
 
 inline
 void AdjacencyMatrixBase::addBoxDerivatives( const Tensor& vir, MultiValue& myvals ) const {
-  if( doNotCalculateDerivatives() ) return;
+  if( doNotCalculateDerivatives() ) {
+    return;
+  }
   unsigned nbase = 3*getNumberOfAtoms();
   unsigned w_index = getConstPntrToComponent(0)->getPositionInStream();
   myvals.addDerivative( w_index, nbase+0, vir(0,0) );

diff --git a/src/adjmat/Bridge.cpp b/src/adjmat/Bridge.cpp
@@ -54,18 +54,30 @@ void Bridge::registerKeywords(Keywords& keys) {
            "group A");
   keys.add("optional","SWITCHB","The switchingfunction on the distance between the bridging atoms and the atoms in "
            "group B");
-  keys.needsAction("BRIDGE_MATRIX"); keys.needsAction("SUM");
+  keys.needsAction("BRIDGE_MATRIX");
+  keys.needsAction("SUM");
   keys.setValueDescription("the number of bridging atoms between the two groups");
 }
 
 Bridge::Bridge(const ActionOptions& ao):
   Action(ao),
-  ActionShortcut(ao)
-{
+  ActionShortcut(ao) {
   // Need to read in switch
-  std::string s_inp, sfinput; parse("SWITCH",sfinput); if( sfinput.length()>0 ) s_inp += "SWITCH={" + sfinput +"} ";
-  std::string sfinputa; parse("SWITCHA",sfinputa); if( sfinputa.length()>0 ) s_inp += "SWITCHA={" + sfinputa +"} ";
-  std::string sfinputb; parse("SWITCHB",sfinputb); if( sfinputb.length()>0 ) s_inp += "SWITCHB={" + sfinputb +"} ";
+  std::string s_inp, sfinput;
+  parse("SWITCH",sfinput);
+  if( sfinput.length()>0 ) {
+    s_inp += "SWITCH={" + sfinput +"} ";
+  }
+  std::string sfinputa;
+  parse("SWITCHA",sfinputa);
+  if( sfinputa.length()>0 ) {
+    s_inp += "SWITCHA={" + sfinputa +"} ";
+  }
+  std::string sfinputb;
+  parse("SWITCHB",sfinputb);
+  if( sfinputb.length()>0 ) {
+    s_inp += "SWITCHB={" + sfinputb +"} ";
+  }
   // Create the matrix object
   readInputLine( getShortcutLabel() + "_mat: BRIDGE_MATRIX " + s_inp + convertInputLineToString() );
   // Add all the elements of the matrix together

diff --git a/src/adjmat/BridgeMatrix.cpp b/src/adjmat/BridgeMatrix.cpp
@@ -83,23 +83,37 @@ void BridgeMatrix::registerKeywords( Keywords& keys ) {
 
 BridgeMatrix::BridgeMatrix(const ActionOptions&ao):
   Action(ao),
-  AdjacencyMatrixBase(ao)
-{
-  bool oneswitch; std::string sfinput,errors; parse("SWITCH",sfinput);
+  AdjacencyMatrixBase(ao) {
+  bool oneswitch;
+  std::string sfinput,errors;
+  parse("SWITCH",sfinput);
   if( sfinput.length()>0 ) {
-    sf1.set(sfinput,errors); oneswitch=true;
-    if( errors.length()!=0 ) error("problem reading SWITCH keyword : " + errors );
+    sf1.set(sfinput,errors);
+    oneswitch=true;
+    if( errors.length()!=0 ) {
+      error("problem reading SWITCH keyword : " + errors );
+    }
     sf2.set(sfinput,errors);
-    if( errors.length()!=0 ) error("problem reading SWITCH keyword : " + errors );
+    if( errors.length()!=0 ) {
+      error("problem reading SWITCH keyword : " + errors );
+    }
   } else {
     parse("SWITCHA",sfinput);
     if(sfinput.length()>0) {
-      sf1.set(sfinput,errors); oneswitch=false;
-      if( errors.length()!=0 ) error("problem reading SWITCHA keyword : " + errors );
-      sfinput.clear(); parse("SWITCHB",sfinput);
-      if(sfinput.length()==0) error("found SWITCHA keyword without SWITCHB");
+      sf1.set(sfinput,errors);
+      oneswitch=false;
+      if( errors.length()!=0 ) {
+        error("problem reading SWITCHA keyword : " + errors );
+      }
+      sfinput.clear();
+      parse("SWITCHB",sfinput);
+      if(sfinput.length()==0) {
+        error("found SWITCHA keyword without SWITCHB");
+      }
       sf2.set(sfinput,errors);
-      if( errors.length()!=0 ) error("problem reading SWITCHB keyword : " + errors );
+      if( errors.length()!=0 ) {
+        error("problem reading SWITCHB keyword : " + errors );
+      }
     } else {
       error("missing definition of switching functions");
     }
@@ -115,12 +129,25 @@ BridgeMatrix::BridgeMatrix(const ActionOptions&ao):
 }
 
 double BridgeMatrix::calculateWeight( const Vector& pos1, const Vector& pos2, const unsigned& natoms, MultiValue& myvals ) const {
-  double tot=0; if( pos2.modulo2()<epsilon ) return 0.0;
+  double tot=0;
+  if( pos2.modulo2()<epsilon ) {
+    return 0.0;
+  }
   for(unsigned i=0; i<natoms; ++i) {
-    Vector dij= getPosition(i,myvals); double dijm = dij.modulo2();
-    double dw1, w1=sf1.calculateSqr( dijm, dw1 ); if( dijm<epsilon ) { w1=0.0; dw1=0.0; }
-    Vector dik=pbcDistance( getPosition(i,myvals), pos2 ); double dikm=dik.modulo2();
-    double dw2, w2=sf2.calculateSqr( dikm, dw2 ); if( dikm<epsilon ) { w2=0.0; dw2=0.0; }
+    Vector dij= getPosition(i,myvals);
+    double dijm = dij.modulo2();
+    double dw1, w1=sf1.calculateSqr( dijm, dw1 );
+    if( dijm<epsilon ) {
+      w1=0.0;
+      dw1=0.0;
+    }
+    Vector dik=pbcDistance( getPosition(i,myvals), pos2 );
+    double dikm=dik.modulo2();
+    double dw2, w2=sf2.calculateSqr( dikm, dw2 );
+    if( dikm<epsilon ) {
+      w2=0.0;
+      dw2=0.0;
+    }
 
     tot += w1*w2;
     // And finish the calculation

diff --git a/src/adjmat/ContactMatrix.cpp b/src/adjmat/ContactMatrix.cpp
@@ -72,13 +72,16 @@ class ContactMatrix : public AdjacencyMatrixBase {
 /// This does nothing
   double calculateWeight( const Vector& pos1, const Vector& pos2, const unsigned& natoms, MultiValue& myvals ) const override;
 /// Override this so we write the graph properly
-  std::string writeInGraph() const override { return "CONTACT_MATRIX"; }
+  std::string writeInGraph() const override {
+    return "CONTACT_MATRIX";
+  }
 };
 
 PLUMED_REGISTER_ACTION(ContactMatrix,"CONTACT_MATRIX_PROPER")
 
 void ContactMatrix::registerKeywords( Keywords& keys ) {
-  AdjacencyMatrixBase::registerKeywords( keys ); keys.setDisplayName("CONTACT_MATRIX");
+  AdjacencyMatrixBase::registerKeywords( keys );
+  keys.setDisplayName("CONTACT_MATRIX");
   keys.add("compulsory","NN","6","The n parameter of the switching function ");
   keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN");
   keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
@@ -90,17 +93,24 @@ void ContactMatrix::registerKeywords( Keywords& keys ) {
 
 ContactMatrix::ContactMatrix( const ActionOptions& ao ):
   Action(ao),
-  AdjacencyMatrixBase(ao)
-{
-  std::string errors, input; parse("SWITCH",input);
+  AdjacencyMatrixBase(ao) {
+  std::string errors, input;
+  parse("SWITCH",input);
   if( input.length()>0 ) {
     switchingFunction.set( input, errors );
-    if( errors.length()!=0 ) error("problem reading switching function description " + errors);
+    if( errors.length()!=0 ) {
+      error("problem reading switching function description " + errors);
+    }
   } else {
-    double r_0=-1.0, d_0; int nn, mm;
-    parse("NN",nn); parse("MM",mm);
-    parse("R_0",r_0); parse("D_0",d_0);
-    if( r_0<0.0 ) error("you must set a value for R_0");
+    double r_0=-1.0, d_0;
+    int nn, mm;
+    parse("NN",nn);
+    parse("MM",mm);
+    parse("R_0",r_0);
+    parse("D_0",d_0);
+    if( r_0<0.0 ) {
+      error("you must set a value for R_0");
+    }
     switchingFunction.set(nn,mm,r_0,d_0);
   }
   // And set the link cell cutoff
@@ -109,11 +119,18 @@ ContactMatrix::ContactMatrix( const ActionOptions& ao ):
 }
 
 double ContactMatrix::calculateWeight( const Vector& pos1, const Vector& pos2, const unsigned& natoms, MultiValue& myvals ) const {
-  Vector distance = pos2; double mod2 = distance.modulo2();
-  if( mod2<epsilon ) return 0.0;  // Atoms can't be bonded to themselves
+  Vector distance = pos2;
+  double mod2 = distance.modulo2();
+  if( mod2<epsilon ) {
+    return 0.0;  // Atoms can't be bonded to themselves
+  }
   double dfunc, val = switchingFunction.calculateSqr( mod2, dfunc );
-  if( val<epsilon ) return 0.0;
-  if( doNotCalculateDerivatives() ) return val;
+  if( val<epsilon ) {
+    return 0.0;
+  }
+  if( doNotCalculateDerivatives() ) {
+    return val;
+  }
   addAtomDerivatives( 0, (-dfunc)*distance, myvals );
   addAtomDerivatives( 1, (+dfunc)*distance, myvals );
   addBoxDerivatives( (-dfunc)*Tensor(distance,distance), myvals );

diff --git a/src/adjmat/ContactMatrixShortcut.cpp b/src/adjmat/ContactMatrixShortcut.cpp
@@ -71,58 +71,87 @@ PLUMED_REGISTER_ACTION(ContactMatrixShortcut,"CONTACT_MATRIX")
 
 void ContactMatrixShortcut::registerKeywords(Keywords& keys) {
   AdjacencyMatrixBase::registerKeywords( keys );
-  keys.remove("GROUP"); keys.add("numbered","GROUP","specifies the list of atoms that should be assumed indistinguishable");
+  keys.remove("GROUP");
+  keys.add("numbered","GROUP","specifies the list of atoms that should be assumed indistinguishable");
   keys.add("compulsory","NN","6","The n parameter of the switching function ");
   keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN");
   keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
   keys.add("compulsory","R_0","The r_0 parameter of the switching function");
   keys.add("numbered","SWITCH","specify the switching function to use between two sets of indistinguishable atoms");
-  keys.addActionNameSuffix("_PROPER"); keys.needsAction("TRANSPOSE"); keys.needsAction("CONCATENATE");
+  keys.addActionNameSuffix("_PROPER");
+  keys.needsAction("TRANSPOSE");
+  keys.needsAction("CONCATENATE");
 }
 
 ContactMatrixShortcut::ContactMatrixShortcut(const ActionOptions& ao):
   Action(ao),
-  ActionShortcut(ao)
-{
-  std::vector<std::string> grp_str; std::string atomsstr="";
-  std::vector<std::string> atomsvec; parseVector("ATOMS",atomsvec);
+  ActionShortcut(ao) {
+  std::vector<std::string> grp_str;
+  std::string atomsstr="";
+  std::vector<std::string> atomsvec;
+  parseVector("ATOMS",atomsvec);
   if( atomsvec.size()>0 )  {
     for(unsigned i=0; i<atomsvec.size(); ++i) {
       Group* gg = plumed.getActionSet().selectWithLabel<Group*>( atomsvec[i] );
-      if( gg ) grp_str.push_back( atomsvec[i] );
+      if( gg ) {
+        grp_str.push_back( atomsvec[i] );
+      }
     }
     if( grp_str.size()!=atomsvec.size() ) {
       grp_str.resize(0);
-      atomsstr = " ATOMS=" + atomsvec[0]; for(unsigned i=1; i<atomsvec.size(); ++i) atomsstr += "," + atomsvec[i];
+      atomsstr = " ATOMS=" + atomsvec[0];
+      for(unsigned i=1; i<atomsvec.size(); ++i) {
+        atomsstr += "," + atomsvec[i];
+      }
     }
   } else {
     std::string grp_inpt;
     for(unsigned i=1;; ++i) {
-      if( !parseNumbered("GROUP",i,grp_inpt) ) break;
+      if( !parseNumbered("GROUP",i,grp_inpt) ) {
+        break;
+      }
       grp_str.push_back( grp_inpt );
     }
   }
-  if( grp_str.size()>9 ) error("cannot handle more than 9 groups");
-  if( grp_str.size()==0 )  { readInputLine( getShortcutLabel() + ": CONTACT_MATRIX_PROPER " + atomsstr + " " + convertInputLineToString() ); return; }
+  if( grp_str.size()>9 ) {
+    error("cannot handle more than 9 groups");
+  }
+  if( grp_str.size()==0 )  {
+    readInputLine( getShortcutLabel() + ": CONTACT_MATRIX_PROPER " + atomsstr + " " + convertInputLineToString() );
+    return;
+  }
 
   for(unsigned i=0; i<grp_str.size(); ++i) {
-    std::string sw_str, num; Tools::convert( i+1, num ); parseNumbered("SWITCH", (i+1)*10 + 1 + i,  sw_str );
-    if( sw_str.length()==0 ) error("missing SWITCH" + num + num + " keyword");
+    std::string sw_str, num;
+    Tools::convert( i+1, num );
+    parseNumbered("SWITCH", (i+1)*10 + 1 + i,  sw_str );
+    if( sw_str.length()==0 ) {
+      error("missing SWITCH" + num + num + " keyword");
+    }
     readInputLine( getShortcutLabel() + num +  num + ": CONTACT_MATRIX_PROPER GROUP=" + grp_str[i] + " SWITCH={" + sw_str + "}" );
     for(unsigned j=0; j<i; ++j) {
-      std::string sw_str2, jnum; Tools::convert( j+1, jnum ); parseNumbered("SWITCH", (j+1)*10 + 1 + i, sw_str2);
-      if( sw_str2.length()==0 ) error("missing SWITCH" + jnum + num + " keyword");
+      std::string sw_str2, jnum;
+      Tools::convert( j+1, jnum );
+      parseNumbered("SWITCH", (j+1)*10 + 1 + i, sw_str2);
+      if( sw_str2.length()==0 ) {
+        error("missing SWITCH" + jnum + num + " keyword");
+      }
       readInputLine( getShortcutLabel() + jnum + num + ": CONTACT_MATRIX_PROPER GROUPA=" + grp_str[j] + " GROUPB=" + grp_str[i] + " SWITCH={" + sw_str2 +"}");
       readInputLine( getShortcutLabel() + num +  jnum + ": TRANSPOSE ARG=" + getShortcutLabel() + jnum + num );
     }
   }
   std::string join_matrices = getShortcutLabel() + ": CONCATENATE";
   for(unsigned i=0; i<grp_str.size(); ++i) {
-    std::string inum; Tools::convert(i+1,inum);
+    std::string inum;
+    Tools::convert(i+1,inum);
     for(unsigned j=0; j<grp_str.size(); ++j) {
-      std::string jnum; Tools::convert(j+1,jnum);
-      if( i>j ) join_matrices += " MATRIX" + inum + jnum + "=" + getShortcutLabel() + inum +  jnum;
-      else join_matrices += " MATRIX" + inum + jnum + "=" + getShortcutLabel() + inum +  jnum;
+      std::string jnum;
+      Tools::convert(j+1,jnum);
+      if( i>j ) {
+        join_matrices += " MATRIX" + inum + jnum + "=" + getShortcutLabel() + inum +  jnum;
+      } else {
+        join_matrices += " MATRIX" + inum + jnum + "=" + getShortcutLabel() + inum +  jnum;
+      }
     }
   }
   readInputLine( join_matrices );

diff --git a/src/adjmat/DistanceMatrix.cpp b/src/adjmat/DistanceMatrix.cpp
@@ -58,8 +58,7 @@ void DistanceMatrix::registerKeywords( Keywords& keys ) {
 
 DistanceMatrix::DistanceMatrix( const ActionOptions& ao ):
   Action(ao),
-  AdjacencyMatrixBase(ao)
-{
+  AdjacencyMatrixBase(ao) {
   // And set the link cell cutoff
   log.printf("  weight is distance between atoms \n");
   parse("CUTOFF",cutoff);
@@ -72,7 +71,8 @@ DistanceMatrix::DistanceMatrix( const ActionOptions& ao ):
 }
 
 double DistanceMatrix::calculateWeight( const Vector& pos1, const Vector& pos2, const unsigned& natoms, MultiValue& myvals ) const {
-  Vector distance = pos2; double mod = distance.modulo();
+  Vector distance = pos2;
+  double mod = distance.modulo();
   if( cutoff<0 || mod<cutoff ) {
     double invd = 1.0/mod;
     addAtomDerivatives( 0, (-invd)*distance, myvals );