Merge branch 'v2.4'

[makedoc]

CHANGES/v2.4.md

@@ -93,3 +93,4 @@ Fixes after alpha release:
     Notice that this is an experimental feature and is not fully validated yet. See \issue{244}.
   - When parsing constants, PLUMED uses lepton library. This allows to pass
     arguments such as `HEIGHT=exp(0.5)`.
+  - \ref CUSTOM function has been added as an alias to \ref MAXENT.

regtest/basic/rt13-lepton/plumed.dat

@@ -9,7 +9,7 @@ cc1: MATHEVAL ARG=t1,t2,t3 FUNC=x^2+y+0*z+1 PERIODIC=NO
 cc2: MATHEVAL ARG=t1,t2,t3 FUNC=0*x^3+0*y^3+0*z^3 PERIODIC=NO
 cc3: MATHEVAL ARG=t1,t2 FUNC=x^2+y^2 PERIODIC=NO
 
-all: MATHEVAL ARG=t1,t2,t3,cc1,cc2,cc3 VAR=a1,a2,a3,a4,a5,a6 FUNC={ (a1+a2+a3+a4+a5+a6) / 6.0 } PERIODIC=NO
+all: CUSTOM ARG=t1,t2,t3,cc1,cc2,cc3 VAR=a1,a2,a3,a4,a5,a6 FUNC={ (a1+a2+a3+a4+a5+a6) / 6.0 } PERIODIC=NO
 
 RESTRAINT ARG=all AT=0 SLOPE=1.0
 

regtest/basic/rt20b-lepton/plumed.dat

 c:   COORDINATION GROUPA=1 GROUPB=2 SWITCH={MATHEVAL R_0=1.3 D_MAX=2.6 FUNC=1/(1+x^6) NOSTRETCH}
-cs:  COORDINATION GROUPA=1 GROUPB=2 SWITCH={MATHEVAL R_0=1.3 D_MAX=2.6 FUNC=1/(1+x^6)}
+cs:  COORDINATION GROUPA=1 GROUPB=2 SWITCH={CUSTOM R_0=1.3 D_MAX=2.6 FUNC=1/(1+x^6)}
 
 PRINT ...
   ARG=c,cs

src/bias/MaxEnt.cpp

@@ -78,6 +78,8 @@ The value of \f$ \xi(\lambda,t)\f$ is written in output as a component named: ar
 Setting \f$ \sigma =0\f$ is equivalent to enforce a pure Maximum Entropy restraint without any noise modelling.
 This method can be also used to enforce inequality restraint as shown in following examples.
 
+Notice that a similar method is available as \ref EDS, although with different features and using a different optimization algorithm.
+
 \par Examples
 
 The following input tells plumed to restrain the distance between atoms 7 and 15

src/eds/EDS.cpp

@@ -65,6 +65,8 @@ to zero with the default value of \f$s_i\f$ as this will cause a
 divide-by-zero error. Instead, set \f$s_i=1\f$ or modify the CV so the
 desired target value is no longer zero.
 
+Notice that a similar method is available as \ref MAXENT, although with different features and using a different optimization algorithm.
+
 \par Examples
 
 The following input for a harmonic oscillator of two beads will

src/function/Matheval.cpp

@@ -206,6 +206,32 @@ public:
 
 PLUMED_REGISTER_ACTION(Matheval,"MATHEVAL")
 
+//+PLUMEDOC FUNCTION CUSTOM
+/*
+An alias to the \ref MATHEVAL function.
+
+\par Examples
+
+Just replace \ref MATHEVAL with \ref CUSTOM.
+
+\plumedfile
+d: DISTANCE ATOMS=10,15
+m: CUSTOM ARG=d FUNC=0.5*step(0.5-x)+x*step(x-0.5) PERIODIC=NO
+# check the function you are applying:
+PRINT ARG=d,n FILE=checkme
+RESTRAINT ARG=d AT=0.5 KAPPA=10.0
+\endplumedfile
+(see also \ref DISTANCE, \ref PRINT, and \ref RESTRAINT)
+
+*/
+//+ENDPLUMEDOC
+
+class Custom :
+  public Matheval {
+};
+
+PLUMED_REGISTER_ACTION(Matheval,"CUSTOM")
+
 void Matheval::registerKeywords(Keywords& keys) {
   Function::registerKeywords(keys);
   keys.use("ARG"); keys.use("PERIODIC");

src/tools/SwitchingFunction.cpp

@@ -266,7 +266,7 @@ void SwitchingFunction::set(const std::string & definition,std::string& errormsg
     for(auto & e : expression_deriv) e=ped.createCompiledExpression();
   }
 #ifdef __PLUMED_HAS_MATHEVAL
-  else if(name=="MATHEVAL") {
+  else if(name=="MATHEVAL" || name=="CUSTOM") {
     type=matheval;
     std::string func;
     Tools::parse(data,"FUNC",func);