From 87b6d131976d37e648124ab1c730e54e4834bf94 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Tue, 15 Jan 2013 22:22:19 +0100
Subject: [PATCH] Improved error reporting and made expensive plumed_asserts
removable
If you want to but a plumed_assert in a loop you should now use
plumed_dbg_assert / plumed_dbg_massert. This will not be included
in the code if you compile with -DNDEBUG
---
src/analysis/Analysis.h | 4 +--
src/bias/External.cpp | 2 +-
src/bias/LWalls.cpp | 6 +----
src/bias/MetaD.cpp | 4 +--
src/bias/MovingRestraint.cpp | 4 ++-
src/bias/Ratchet.cpp | 4 +--
src/bias/Restraint.cpp | 3 ---
src/bias/UWalls.cpp | 6 +----
src/cltools/Driver.cpp | 30 ++++++++++++++--------
src/colvar/DHEnergy.cpp | 2 +-
src/core/Action.cpp | 7 +++--
src/core/Action.h | 2 +-
src/core/ActionAtomistic.h | 4 +--
src/core/ActionSetup.cpp | 3 +--
src/core/ActionWithValue.cpp | 2 +-
src/core/CLTool.cpp | 12 ++++++---
src/core/CLTool.h | 6 +++--
src/core/Value.h | 2 +-
src/generic/DumpAtoms.cpp | 2 +-
src/generic/DumpDerivatives.cpp | 2 +-
src/generic/DumpForces.cpp | 2 +-
src/generic/DumpProjections.cpp | 2 +-
src/generic/Include.cpp | 3 +--
src/imd/ActionIMD.cpp | 2 +-
src/multicolvar/AlphaRMSD.cpp | 3 ++-
src/multicolvar/AntibetaRMSD.cpp | 9 ++++---
src/multicolvar/Density.cpp | 2 +-
src/multicolvar/MultiColvar.cpp | 14 +++++-----
src/multicolvar/MultiColvar.h | 12 ++++-----
src/multicolvar/ParabetaRMSD.cpp | 9 ++++---
src/multicolvar/SecondaryStructureRMSD.cpp | 2 +-
src/multicolvar/VesselCVdens.cpp | 6 ++---
src/setup/Load.cpp | 3 +--
src/{core => tools}/CubicInterpolation.cpp | 10 ++++----
src/{core => tools}/CubicInterpolation.h | 8 +++---
src/tools/DynamicList.h | 12 ++++-----
src/tools/Exception.h | 12 +++++++++
src/tools/HistogramBead.cpp | 6 ++---
src/tools/HistogramBead.h | 2 +-
src/tools/KernelFunctions.cpp | 8 +++---
src/tools/Matrix.h | 6 ++---
src/tools/PDB.cpp | 4 +--
src/tools/SwitchingFunction.cpp | 3 +--
src/vatom/Center.cpp | 4 +--
src/vatom/Ghost.cpp | 4 +--
src/vesselbase/ActionWithVessel.cpp | 6 ++---
src/vesselbase/ActionWithVessel.h | 8 +++---
src/vesselbase/Vessel.h | 6 ++---
src/vesselbase/VesselAccumulator.h | 2 +-
src/vesselbase/VesselLessThan.cpp | 2 +-
src/vesselbase/VesselMean.cpp | 4 +--
src/vesselbase/VesselMoreThan.cpp | 2 +-
src/vesselbase/VesselSum.cpp | 2 +-
src/vesselbase/VesselValueAccess.h | 6 ++---
src/vesselbase/VesselWithin.cpp | 4 +--
src/vesselbase/WeightedSumVessel.h | 4 +--
56 files changed, 161 insertions(+), 140 deletions(-)
rename src/{core => tools}/CubicInterpolation.cpp (96%)
rename src/{core => tools}/CubicInterpolation.h (96%)
diff --git a/src/analysis/Analysis.h b/src/analysis/Analysis.h
index 092e18905..c4703184b 100644
--- a/src/analysis/Analysis.h
+++ b/src/analysis/Analysis.h
@@ -123,7 +123,7 @@ public:
inline
unsigned Analysis::getNumberOfDataPoints() const {
if( !reusing_data ){
- plumed_assert( data.size()==logweights.size() );
+ plumed_dbg_assert( data.size()==logweights.size() );
return data.size();
} else {
return mydatastash->getNumberOfDataPoints();
@@ -133,7 +133,7 @@ unsigned Analysis::getNumberOfDataPoints() const {
inline
void Analysis::getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const {
if( !reusing_data ){
- plumed_assert( idata<weights.size() && point.size()==getNumberOfArguments() );
+ plumed_dbg_assert( idata<weights.size() && point.size()==getNumberOfArguments() );
for(unsigned i=0;i<point.size();++i) point[i]=data[idata][i];
weight=weights[idata];
} else {
diff --git a/src/bias/External.cpp b/src/bias/External.cpp
index 3542e402e..fa818fb8f 100644
--- a/src/bias/External.cpp
+++ b/src/bias/External.cpp
@@ -125,7 +125,7 @@ BiasGrid_(NULL)
{
string filename;
parse("FILE",filename);
- plumed_assert(filename.length()>0);
+ if( filename.length()==0 ) error("No external potential file was specified");
bool sparsegrid=false;
parseFlag("SPARSE",sparsegrid);
bool nospline=false;
diff --git a/src/bias/LWalls.cpp b/src/bias/LWalls.cpp
index c6d570536..62c7d0e47 100644
--- a/src/bias/LWalls.cpp
+++ b/src/bias/LWalls.cpp
@@ -87,16 +87,12 @@ exp(getNumberOfArguments(),2.0),
eps(getNumberOfArguments(),1.0),
offset(getNumberOfArguments(),0.0)
{
+ // Note sizes of these vectors are automatically checked by parseVector :-)
parseVector("OFFSET",offset);
- plumed_assert(offset.size()==getNumberOfArguments());
parseVector("EPS",eps);
- plumed_assert(eps.size()==getNumberOfArguments());
parseVector("EXP",exp);
- plumed_assert(exp.size()==getNumberOfArguments());
parseVector("KAPPA",kappa);
- plumed_assert(kappa.size()==getNumberOfArguments());
parseVector("AT",at);
- plumed_assert(at.size()==getNumberOfArguments());
checkRead();
log.printf(" at");
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index fcf739096..a9d9652af 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -263,7 +263,7 @@ mw_n_(1), mw_dir_("./"), mw_id_(0), mw_rstride_(1)
vector<unsigned> gbin(getNumberOfArguments());
parseVector("GRID_BIN",gbin);
if(gbin.size()!=getNumberOfArguments() && gbin.size()!=0) error("not enough values for GRID_BIN");
- plumed_assert(gmin.size()==gmax.size() && gmin.size()==gbin.size());
+ if( gmin.size()!=gmax.size() || gmin.size()!=gbin.size() ) error("GRID MIN was specified without either GRID_MAX or GRID_BIN");
bool sparsegrid=false;
parseFlag("GRID_SPARSE",sparsegrid);
bool nospline=false;
@@ -283,7 +283,7 @@ mw_n_(1), mw_dir_("./"), mw_id_(0), mw_rstride_(1)
// Multiple walkers
parse("WALKERS_N",mw_n_);
parse("WALKERS_ID",mw_id_);
- if(mw_n_>1){plumed_assert(mw_n_>mw_id_);}
+ if(mw_n_>1) error("walker ID should be a numerical value less than the total number of walkers"); // plumed_assert(mw_n_>mw_id_);}
parse("WALKERS_DIR",mw_dir_);
parse("WALKERS_RSTRIDE",mw_rstride_);
diff --git a/src/bias/MovingRestraint.cpp b/src/bias/MovingRestraint.cpp
index 46267cd7d..ed668db49 100644
--- a/src/bias/MovingRestraint.cpp
+++ b/src/bias/MovingRestraint.cpp
@@ -131,7 +131,9 @@ verse(getNumberOfArguments())
for(int i=0;;i++){
// Read in step
if( !parseNumberedVector("STEP",i,ss) ) break;
- for(unsigned j=0;j<step.size();j++) plumed_massert(ss[0]>step[j],"in moving restraint step number must always increase");
+ for(unsigned j=0;j<step.size();j++){
+ if(ss[0]<step[j]) error("in moving restraint step number must always increase");
+ }
step.push_back(ss[0]);
// Try to read kappa
diff --git a/src/bias/Ratchet.cpp b/src/bias/Ratchet.cpp
index 2f4efa516..55d4f61e9 100644
--- a/src/bias/Ratchet.cpp
+++ b/src/bias/Ratchet.cpp
@@ -106,14 +106,12 @@ temp(getNumberOfArguments(),0.0),
seed(getNumberOfArguments(),time(0)),
random(getNumberOfArguments())
{
+ // Note : parseVector will check that number of arguments is correct
parseVector("KAPPA",kappa);
- plumed_assert(kappa.size()==getNumberOfArguments());
parseVector("MIN",min);
- if(min.size()==0) min.assign(getNumberOfArguments(),-1.0);
parseVector("NOISE",temp);
parseVector("SEED",seed);
parseVector("TO",to);
- plumed_assert(to.size()==getNumberOfArguments());
checkRead();
log.printf(" min");
diff --git a/src/bias/Restraint.cpp b/src/bias/Restraint.cpp
index 2a8dd1c5e..ce40dd80b 100644
--- a/src/bias/Restraint.cpp
+++ b/src/bias/Restraint.cpp
@@ -85,11 +85,8 @@ kappa(getNumberOfArguments(),0.0),
slope(getNumberOfArguments(),0.0)
{
parseVector("SLOPE",slope);
-// plumed_assert(slope.size()==getNumberOfArguments());
parseVector("KAPPA",kappa);
-// plumed_assert(kappa.size()==getNumberOfArguments());
parseVector("AT",at);
-// plumed_assert(at.size()==getNumberOfArguments());
checkRead();
log.printf(" at");
diff --git a/src/bias/UWalls.cpp b/src/bias/UWalls.cpp
index 84c541414..00c4f5154 100644
--- a/src/bias/UWalls.cpp
+++ b/src/bias/UWalls.cpp
@@ -87,16 +87,12 @@ exp(getNumberOfArguments(),2.0),
eps(getNumberOfArguments(),1.0),
offset(getNumberOfArguments(),0.0)
{
+ // Note : the sizes of these vectors are checked automatically by parseVector
parseVector("OFFSET",offset);
- plumed_assert(offset.size()==getNumberOfArguments());
parseVector("EPS",eps);
- plumed_assert(eps.size()==getNumberOfArguments());
parseVector("EXP",exp);
- plumed_assert(exp.size()==getNumberOfArguments());
parseVector("KAPPA",kappa);
- plumed_assert(kappa.size()==getNumberOfArguments());
parseVector("AT",at);
- plumed_assert(at.size()==getNumberOfArguments());
checkRead();
log.printf(" at");
diff --git a/src/cltools/Driver.cpp b/src/cltools/Driver.cpp
index ea62a50f7..4ed550a37 100644
--- a/src/cltools/Driver.cpp
+++ b/src/cltools/Driver.cpp
@@ -141,18 +141,21 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
bool debug_pd=parse("--debug-pd",fakein);
bool debug_dd=parse("--debug-dd",fakein);
- if( debug_pd || debug_dd ) plumed_massert(!noatoms,"cannot debug without atoms");
+ if( debug_pd || debug_dd ){
+ if(noatoms) error("cannot debug without atoms");
+ }
int multi=1;
FILE*multi_log=NULL;
bool debug_grex=parse("--debug-grex",fakein);
Communicator intracomm;
Communicator intercomm;
if(debug_grex){
- plumed_massert( !noatoms, "must have atoms to debug_grex");
+ if(noatoms) error("must have atoms to debug_grex");
Tools::convert(fakein,multi);
int ntot=pc.Get_size();
int nintra=ntot/multi;
- plumed_massert(multi*nintra==ntot,"xxx");
+ if(multi*nintra!=ntot) error("invalid number of processes for debug_grex");
+ //plumed_massert(multi*nintra==ntot,"xxx");
pc.Split(pc.Get_rank()/nintra,pc.Get_rank(),intracomm);
pc.Split(pc.Get_rank()%nintra,pc.Get_rank(),intercomm);
string n; Tools::convert(intercomm.Get_rank(),n);
@@ -194,7 +197,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
parse("--pdb",pdbfile);
if(pdbfile.length()>0){
bool check=pdb.read(pdbfile,false,1.0);
- plumed_massert(check,"error reading pdb file");
+ if(!check) error("error reading pdb file");
}
string pbc_cli_list; parse("--box",pbc_cli_list);
@@ -214,8 +217,10 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
}
}
- plumed_massert(!(debug_dd&debug_pd),"cannot use debug-dd and debug-pd at the same time");
- if(debug_pd || debug_dd) plumed_massert(Communicator::initialized(),"needs mpi for debug-pd");
+ if( debug_dd && debug_pd ) error("cannot use debug-dd and debug-pd at the same time");
+ if(debug_pd || debug_dd){
+ if( !Communicator::initialized() ) error("needs mpi for debug-pd");
+ }
Plumed p;
int rr=sizeof(real);
@@ -307,7 +312,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
for(unsigned i=0;i<pdb.size();++i){
AtomNumber an=pdb.getAtomNumbers()[i];
unsigned index=an.index();
- plumed_massert(index<unsigned(natoms),"atom index in pdb exceeds the number of atoms in trajectory");
+ if( index>=unsigned(natoms) ) error("atom index in pdb exceeds the number of atoms in trajectory");
masses[index]=pdb.getOccupancy()[i];
charges[index]=pdb.getBeta()[i];
}
@@ -320,7 +325,10 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
p.cmd("setNatoms",&natoms);
p.cmd("init");
}
- plumed_massert(checknatoms==natoms,"number of atom changed");
+ if(checknatoms!=natoms){
+ std::string stepstr; Tools::convert(step,stepstr);
+ error("number of atoms in frame " + stepstr + " does not match number of atoms in first frame");
+ }
coordinates.assign(3*natoms,real(0.0));
forces.assign(3*natoms,real(0.0));
@@ -383,7 +391,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
p.cmd("setStep",&step);
if(!noatoms){
bool ok=Tools::getline(fp,line);
- plumed_massert(ok,"premature end of file");
+ if(!ok) error("premature end of trajectory file");
std::vector<double> celld(9,0.0);
if(pbc_cli_given==false) {
@@ -396,7 +404,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
&celld[0], &celld[1], &celld[2],
&celld[3], &celld[4], &celld[5],
&celld[6], &celld[7], &celld[8]);
- } else plumed_merror("needed box in second line");
+ } else error("needed box in second line of xyz file");
} else { // from command line
celld=pbc_cli_box;
}
@@ -405,7 +413,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
// Read coordinates
for(int i=0;i<natoms;i++){
bool ok=Tools::getline(fp,line);
- plumed_massert(ok,"premature end of file");
+ if(!ok) error("premature end of trajectory file");
char dummy[1000];
double cc[3];
std::sscanf(line.c_str(),"%999s %100lf %100lf %100lf",dummy,&cc[0],&cc[1],&cc[2]);
diff --git a/src/colvar/DHEnergy.cpp b/src/colvar/DHEnergy.cpp
index 4344011f4..391c65888 100644
--- a/src/colvar/DHEnergy.cpp
+++ b/src/colvar/DHEnergy.cpp
@@ -105,7 +105,7 @@ constant(0.0)
parse("TEMP",T);
parse("EPSILON",epsilon);
checkRead();
- plumed_assert(!plumed.getAtoms().usingNaturalUnits());
+ if( plumed.getAtoms().usingNaturalUnits() ) error("DHENERGY cannot be used for calculations performed with natural units");
constant=138.935458111/atoms.getUnits().getEnergy()/atoms.getUnits().getLength();
k=sqrt(I/(epsilon*T))*502.903741125*atoms.getUnits().getLength();
checkRead();
diff --git a/src/core/Action.cpp b/src/core/Action.cpp
index 398f2af39..9b623eef9 100644
--- a/src/core/Action.cpp
+++ b/src/core/Action.cpp
@@ -69,8 +69,7 @@ Action::Action(const ActionOptions&ao):
std::string s; Tools::convert(plumed.getActionSet().size(),s);
label="@"+s;
}
- plumed_massert(!plumed.getActionSet().selectWithLabel<Action*>(label),
- "label " + label + " has been already used");
+ if( plumed.getActionSet().selectWithLabel<Action*>(label) ) error("label " + label + " has been already used");
log.printf(" with label %s\n",label.c_str());
}
@@ -115,7 +114,7 @@ void Action::parseFlag(const std::string&key,bool & t){
t=false;
} else if ( !keywords.getLogicalDefault(key,t) ){
log.printf("ERROR in action %s with label %s : flag %s has no default",name.c_str(),label.c_str(),key.c_str() );
- plumed_assert(0);
+ plumed_error();
}
}
}
@@ -192,7 +191,7 @@ void Action::prepare(){
return;
}
-void Action::error( const std::string & msg ){
+void Action::error( const std::string & msg ) const {
log.printf("ERROR in input to action %s with label %s : %s \n \n", name.c_str(), label.c_str(), msg.c_str() );
if( !line.empty() ) keywords.print( log );
plumed_merror("ERROR in input to action " + name + " with label " + label + " : " + msg );
diff --git a/src/core/Action.h b/src/core/Action.h
index 88a349b2c..c83bc7c40 100644
--- a/src/core/Action.h
+++ b/src/core/Action.h
@@ -127,7 +127,7 @@ public:
void parseFlag(const std::string&key,bool&t);
/// Crash calculation and print documentation
- void error( const std::string & msg );
+ void error( const std::string & msg ) const;
/// Issue a warning
void warning( const std::string & msg );
diff --git a/src/core/ActionAtomistic.h b/src/core/ActionAtomistic.h
index 6ed09140c..c06209bdf 100644
--- a/src/core/ActionAtomistic.h
+++ b/src/core/ActionAtomistic.h
@@ -132,8 +132,8 @@ double ActionAtomistic::getMass(int i)const{
}
inline
-double ActionAtomistic::getCharge(int i)const{
- plumed_assert( chargesWereSet );
+double ActionAtomistic::getCharge(int i) const {
+ if( !chargesWereSet ) error("charges were not passed to plumed");
return charges[i];
}
diff --git a/src/core/ActionSetup.cpp b/src/core/ActionSetup.cpp
index d11107c4c..12d72b05f 100644
--- a/src/core/ActionSetup.cpp
+++ b/src/core/ActionSetup.cpp
@@ -32,8 +32,7 @@ ActionSetup::ActionSetup(const ActionOptions&ao):
const ActionSet& actionset(plumed.getActionSet());
for(ActionSet::const_iterator p=actionset.begin();p!=actionset.end();++p){
// check that all the preceeding actions are ActionSetup
- plumed_massert(dynamic_cast<ActionSetup*>(*p),
- "Action " + getLabel() + " is a setup action, and should be only preceeded by other setup actions");
+ if( !dynamic_cast<ActionSetup*>(*p) ) error("Action " + getLabel() + " is a setup action, and should be only preceeded by other setup actions");
}
}
diff --git a/src/core/ActionWithValue.cpp b/src/core/ActionWithValue.cpp
index 66616a5bc..a93871b1b 100644
--- a/src/core/ActionWithValue.cpp
+++ b/src/core/ActionWithValue.cpp
@@ -137,7 +137,7 @@ int ActionWithValue::getComponent( const std::string& name ) const {
for(unsigned i=0;i<values.size();++i){
if (values[i]->name==thename) return i;
}
- plumed_massert(0,"there is no component with name" + name);
+ plumed_merror("there is no component with name" + name);
return -1;
}
diff --git a/src/core/CLTool.cpp b/src/core/CLTool.cpp
index a97dd192f..2f57506e0 100644
--- a/src/core/CLTool.cpp
+++ b/src/core/CLTool.cpp
@@ -54,7 +54,7 @@ void CLTool::parseFlag( const std::string&key, bool&t ){
plumed_assert(inputData.count(key)>0);
if( inputData[key]=="true") t=true;
else if( inputData[key]=="false") t=false;
- else plumed_assert(0);
+ else plumed_error();
}
bool CLTool::readInput( int argc, char**argv, FILE* in, FILE*out ){
@@ -105,7 +105,7 @@ bool CLTool::readCommandLineArgs( int argc, char**argv, FILE*out ){
}
}
if(!found){
- fprintf(out,"ERROR : unknown option %s\n\n", a.c_str() );
+ fprintf(stderr,"ERROR in input for command line tool %s : %s option is unknown \n\n", name.c_str(), a.c_str() );
printhelp=true;
}
}
@@ -176,7 +176,7 @@ bool CLTool::readInputFile( int argc, char**argv, FILE* in, FILE*out ){
}
}
if(!found){
- fprintf(stderr,"Unknown keyword found in input file :%s\n",keyword.c_str());
+ fprintf(stderr,"ERROR in input for command line tool %s : unknown keyword %s found in input file\n",name.c_str(),keyword.c_str());
if(mystdin) fclose(mystdin);
return false;
}
@@ -186,4 +186,10 @@ bool CLTool::readInputFile( int argc, char**argv, FILE* in, FILE*out ){
setRemainingToDefault(out);
return true;
}
+
+void CLTool::error( const std::string& msg ){
+ fprintf(stderr,"ERROR : in input for command line tool %s : %s\n",name.c_str(),msg.c_str());
+ plumed_error();
+}
+
}
diff --git a/src/core/CLTool.h b/src/core/CLTool.h
index 8afab7098..4362829e3 100644
--- a/src/core/CLTool.h
+++ b/src/core/CLTool.h
@@ -79,6 +79,8 @@ protected:
bool parse(const std::string&key,T&t);
/// Find out whether one of the command line flags is present or not
void parseFlag(const std::string&key,bool&t);
+/// Crash the command line tool with an error
+ void error(const std::string& msg);
public:
/// How is the input specified on the command line or in an input file
enum {unset,commandline,ifile} inputdata;
@@ -99,9 +101,9 @@ template<class T>
bool CLTool::parse(const std::string&key,T&t){
plumed_massert(keywords.exists(key),"keyword " + key + " has not been registered");
if(keywords.style(key,"compulsory") ){
- plumed_assert(inputData.count(key)>0);
+ if(inputData.count(key)==0) error("missing data for keyword " + key);
bool check=Tools::convert(inputData[key],t);
- plumed_assert(check);
+ if(!check) error("data input for keyword " + key + " has wrong type");
return true;
}
if( inputData.count(key)==0 ) return false;
diff --git a/src/core/Value.h b/src/core/Value.h
index cc35f5d31..701fa17b6 100644
--- a/src/core/Value.h
+++ b/src/core/Value.h
@@ -222,7 +222,7 @@ void Value::resizeDerivatives(int n){
inline
void Value::addDerivative(unsigned i,double d){
- plumed_massert(i<derivatives.size(),"derivative is out of bounds");
+ plumed_dbg_massert(i<derivatives.size(),"derivative is out of bounds");
derivatives[i]+=d;
}
diff --git a/src/generic/DumpAtoms.cpp b/src/generic/DumpAtoms.cpp
index 11eab78f4..44792d095 100644
--- a/src/generic/DumpAtoms.cpp
+++ b/src/generic/DumpAtoms.cpp
@@ -101,7 +101,7 @@ DumpAtoms::DumpAtoms(const ActionOptions&ao):
lenunit=plumed.getAtoms().getUnits().getLength()/myunit.getLength();
checkRead();
- plumed_assert(file.length()>0);
+ if(file.length()==0) error("name out output file was not specified");
of.link(*this);
of.open(file.c_str(),"w");
log.printf(" printing the following atoms in %s :", unitname.c_str() );
diff --git a/src/generic/DumpDerivatives.cpp b/src/generic/DumpDerivatives.cpp
index 7eb9942f8..a95575acc 100644
--- a/src/generic/DumpDerivatives.cpp
+++ b/src/generic/DumpDerivatives.cpp
@@ -87,7 +87,7 @@ ActionWithArguments(ao),
fmt("%15.10f")
{
parse("FILE",file);
- plumed_assert(file.length()>0);
+ if( file.length()==0 ) error("name of output file was not specified");
parse("FMT",fmt);
fmt=" "+fmt;
of.link(*this);
diff --git a/src/generic/DumpForces.cpp b/src/generic/DumpForces.cpp
index c010e6650..588873ce0 100644
--- a/src/generic/DumpForces.cpp
+++ b/src/generic/DumpForces.cpp
@@ -85,7 +85,7 @@ ActionPilot(ao),
ActionWithArguments(ao)
{
parse("FILE",file);
- plumed_assert(file.length()>0);
+ if( file.length()==0 ) error("name of file was not specified");
of.link(*this);
of.open(file,"wa");
log.printf(" on file %s\n",file.c_str());
diff --git a/src/generic/DumpProjections.cpp b/src/generic/DumpProjections.cpp
index f8a089c23..c29bfea4c 100644
--- a/src/generic/DumpProjections.cpp
+++ b/src/generic/DumpProjections.cpp
@@ -72,7 +72,7 @@ ActionWithArguments(ao),
fmt("%15.10f")
{
parse("FILE",file);
- plumed_assert(file.length()>0);
+ if( file.length()==0 ) error("filename not specified");
parse("FMT",fmt);
fmt=" "+fmt;
of.open(file.c_str(),"wa");
diff --git a/src/generic/Include.cpp b/src/generic/Include.cpp
index 0e61fa163..b848d3a2c 100644
--- a/src/generic/Include.cpp
+++ b/src/generic/Include.cpp
@@ -76,7 +76,7 @@ PLUMED_REGISTER_ACTION(Include,"INCLUDE")
void Include::registerKeywords( Keywords& keys ){
Action::registerKeywords(keys);
- keys.add("compulsory","FILE","-","file to be included");
+ keys.add("compulsory","FILE","file to be included");
}
Include::Include(const ActionOptions&ao):
@@ -85,7 +85,6 @@ Action(ao)
std::string f;
parse("FILE",f);
checkRead();
- plumed_assert(f!="-");
plumed.readInputFile(f);
}
diff --git a/src/imd/ActionIMD.cpp b/src/imd/ActionIMD.cpp
index 0b3979fcf..dd6696c67 100644
--- a/src/imd/ActionIMD.cpp
+++ b/src/imd/ActionIMD.cpp
@@ -242,7 +242,7 @@ void IMD::receive(){
}
else if(itype==2) comm.Bcast(&transferRate,1,0);
else if(itype==3) plumed.exit();
- else plumed_assert(0);
+ else plumed_error();
}
}
diff --git a/src/multicolvar/AlphaRMSD.cpp b/src/multicolvar/AlphaRMSD.cpp
index 49d453b5f..72ea6a048 100644
--- a/src/multicolvar/AlphaRMSD.cpp
+++ b/src/multicolvar/AlphaRMSD.cpp
@@ -102,7 +102,8 @@ SecondaryStructureRMSD(ao)
unsigned nres, nprevious=0; std::vector<unsigned> nlist(30);
for(unsigned i=0;i<chains.size();++i){
if( chains[i]<30 ) error("segment of backbone defined is not long enough to form an alpha helix. Each backbone fragment must contain a minimum of 6 residues");
- nres=chains[i]/5; plumed_assert( chains[i]%5==0 );
+ nres=chains[i]/5;
+ if( chains[i]%5!=0 ) error("backbone segment received does not contain a multiple of five residues");
for(unsigned ires=0;ires<nres-5;ires++){
unsigned accum=nprevious + 5*ires;
for(unsigned k=0;k<30;++k) nlist[k] = accum+k;
diff --git a/src/multicolvar/AntibetaRMSD.cpp b/src/multicolvar/AntibetaRMSD.cpp
index 32a38a9e7..ae868bc70 100644
--- a/src/multicolvar/AntibetaRMSD.cpp
+++ b/src/multicolvar/AntibetaRMSD.cpp
@@ -134,7 +134,8 @@ s_cutoff(0)
for(unsigned i=0;i<chains.size();++i){
if( chains[i]<40 ) error("segment of backbone is not long enough to form an antiparallel beta hairpin. Each backbone fragment must contain a minimum of 8 residues");
// Loop over all possible triples in each 8 residue segment of protein
- nres=chains[i]/5; plumed_assert( chains[i]%5==0 );
+ nres=chains[i]/5;
+ if( chains[i]%5!=0 ) error("backbone segment received does not contain a multiple of five residues");
for(unsigned ires=0;ires<nres-7;ires++){
for(unsigned jres=ires+7;jres<nres;jres++){
for(unsigned k=0;k<15;++k){
@@ -152,11 +153,13 @@ s_cutoff(0)
unsigned iprev,jprev,inres,jnres; std::vector<unsigned> nlist(30);
for(unsigned ichain=1;ichain<chains.size();++ichain){
iprev=0; for(unsigned i=0;i<ichain;++i) iprev+=chains[i];
- inres=chains[ichain]/5; plumed_assert( chains[ichain]%5==0 );
+ inres=chains[ichain]/5;
+ if( chains[ichain]%5!=0 ) error("backbone segment received does not contain a multiple of five residues");
for(unsigned ires=0;ires<inres-2;++ires){
for(unsigned jchain=0;jchain<ichain;++jchain){
jprev=0; for(unsigned i=0;i<jchain;++i) jprev+=chains[i];
- jnres=chains[jchain]/5; plumed_assert( chains[jchain]%5==0 );
+ jnres=chains[jchain]/5;
+ if( chains[jchain]%5!=0 ) error("backbone segment received does not contain a multiple of five residues");
for(unsigned jres=0;jres<jnres-2;++jres){
for(unsigned k=0;k<15;++k){
nlist[k]=iprev+ ires*5+k;
diff --git a/src/multicolvar/Density.cpp b/src/multicolvar/Density.cpp
index d6907ddc0..bd8418ac1 100644
--- a/src/multicolvar/Density.cpp
+++ b/src/multicolvar/Density.cpp
@@ -56,7 +56,7 @@ public:
virtual double compute( const unsigned& j );
Vector getCentralAtom();
/// Returns the number of coordinates of the field
- unsigned getNumberOfFieldDerivatives(){ plumed_assert(0); };
+ unsigned getNumberOfFieldDerivatives(){ plumed_merror("fields are not possible for density"); };
bool isPeriodic(){ return false; }
bool isDensity(){ return true; }
};
diff --git a/src/multicolvar/MultiColvar.cpp b/src/multicolvar/MultiColvar.cpp
index a7659f310..041647158 100644
--- a/src/multicolvar/MultiColvar.cpp
+++ b/src/multicolvar/MultiColvar.cpp
@@ -309,12 +309,12 @@ void MultiColvar::calculate(){
}
Vector MultiColvar::getCentralAtom(){
- plumed_massert(0,"gradient and related cv distribution functions are not available in this colvar");
+ plumed_merror("gradient and related cv distribution functions are not available in this colvar");
Vector dummy; return dummy;
}
void MultiColvar::setAlignedPositions( const std::vector<Vector>& apos ){
- plumed_assert( apos.size()==pos.size() );
+ plumed_dbg_assert( apos.size()==pos.size() );
for(unsigned i=0;i<pos.size();++i) pos[i]=apos[i];
}
@@ -353,13 +353,13 @@ Vector MultiColvar::retrieveCentralAtomPos(){
}
void MultiColvar::addCentralAtomDerivatives( const unsigned& iatom, const Tensor& der ){
- plumed_assert( iatom<colvar_atoms[current].getNumberActive() );
+ plumed_dbg_assert( iatom<colvar_atoms[current].getNumberActive() );
if( centralAtomDerivativesAreInFractional ) central_derivs[iatom] += matmul( ibox, der );
else central_derivs[iatom] += der;
}
double MultiColvar::getCentralAtomDerivative( const unsigned& iatom, const unsigned jcomp, const Vector& df ) const {
- plumed_assert( iatom<colvar_atoms[current].getNumberActive() && jcomp<3 );
+ plumed_dbg_assert( iatom<colvar_atoms[current].getNumberActive() && jcomp<3 );
return df[0]*central_derivs[iatom](0,jcomp) + df[1]*central_derivs[iatom](1,jcomp) + df[2]*central_derivs[iatom](2,jcomp);
}
@@ -368,7 +368,7 @@ void MultiColvar::chainRuleForElementDerivatives( const unsigned jcv, const unsi
int thisatom, thispos, in=0; unsigned innat=colvar_atoms[jcv].getNumberActive();
for(unsigned i=0;i<innat;++i){
thisatom=linkIndex( i, colvar_atoms[jcv], all_atoms );
- plumed_assert( thisatom>=0 ); thispos=vstart+3*thisatom;
+ plumed_dbg_assert( thisatom>=0 ); thispos=vstart+3*thisatom;
valout->addToBufferElement( thispos , df*getElementDerivative(in) ); in++;
valout->addToBufferElement( thispos+1, df*getElementDerivative(in) ); in++;
valout->addToBufferElement( thispos+2, df*getElementDerivative(in) ); in++;
@@ -388,12 +388,12 @@ void MultiColvar::chainRuleForElementDerivatives( const unsigned jcv, const unsi
}
void MultiColvar::transferDerivatives( const unsigned jcv, const Value& value_in, const double& df, Value* valout ){
- plumed_assert( value_in.getNumberOfDerivatives()==3*colvar_atoms[jcv].getNumberActive()+9);
+ plumed_dbg_assert( value_in.getNumberOfDerivatives()==3*colvar_atoms[jcv].getNumberActive()+9);
int thisatom; unsigned innat=colvar_atoms[jcv].getNumberActive();
for(unsigned i=0;i<innat;++i){
thisatom=linkIndex( i, colvar_atoms[jcv], all_atoms );
- plumed_assert( thisatom>=0 );
+ plumed_dbg_assert( thisatom>=0 );
valout->addDerivative( 3*thisatom+0, df*value_in.getDerivative(3*i+0) );
valout->addDerivative( 3*thisatom+1, df*value_in.getDerivative(3*i+1) );
valout->addDerivative( 3*thisatom+2, df*value_in.getDerivative(3*i+2) );
diff --git a/src/multicolvar/MultiColvar.h b/src/multicolvar/MultiColvar.h
index aa19b2b8b..5b1d03adb 100644
--- a/src/multicolvar/MultiColvar.h
+++ b/src/multicolvar/MultiColvar.h
@@ -128,7 +128,7 @@ public:
/// Calcualte the colvar
bool calculateThisFunction( const unsigned& j );
/// You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations
- virtual bool contributionIsSmall(){ plumed_assert( !isPossibleToSkip() ); return false; }
+ virtual bool contributionIsSmall(){ plumed_dbg_assert( !isPossibleToSkip() ); return false; }
/// And a virtual function which actually computes the colvar
virtual double compute( const unsigned& j )=0;
/// A virtual routine to get the position of the central atom - used for things like cv gradient
@@ -189,31 +189,31 @@ unsigned MultiColvar::getNAtoms() const {
inline
const Vector & MultiColvar::getPosition( unsigned iatom ) const {
- plumed_assert( iatom<colvar_atoms[current].getNumberActive() );
+ plumed_dbg_assert( iatom<colvar_atoms[current].getNumberActive() );
return ActionAtomistic::getPosition( colvar_atoms[current][iatom] );
}
inline
double MultiColvar::getMass(unsigned iatom ) const {
- plumed_assert( iatom<colvar_atoms[current].getNumberActive() );
+ plumed_dbg_assert( iatom<colvar_atoms[current].getNumberActive() );
return ActionAtomistic::getMass( colvar_atoms[current][iatom] );
}
inline
double MultiColvar::getCharge(unsigned iatom ) const {
- plumed_assert( iatom<colvar_atoms[current].getNumberActive() );
+ plumed_dbg_assert( iatom<colvar_atoms[current].getNumberActive() );
return ActionAtomistic::getCharge( colvar_atoms[current][iatom] );
}
inline
AtomNumber MultiColvar::getAbsoluteIndex(unsigned iatom) const {
- plumed_assert( iatom<colvar_atoms[current].getNumberActive() );
+ plumed_dbg_assert( iatom<colvar_atoms[current].getNumberActive() );
return ActionAtomistic::getAbsoluteIndex( colvar_atoms[current][iatom] );
}
inline
void MultiColvar::addAtomsDerivatives(const int& iatom, const Vector& der){
- plumed_assert( iatom<colvar_atoms[current].getNumberActive() );
+ plumed_dbg_assert( iatom<colvar_atoms[current].getNumberActive() );
addElementDerivative( 3*iatom+0, der[0] );
addElementDerivative( 3*iatom+1, der[1] );
addElementDerivative( 3*iatom+2, der[2] );
diff --git a/src/multicolvar/ParabetaRMSD.cpp b/src/multicolvar/ParabetaRMSD.cpp
index 7dbc68bd6..36728933f 100644
--- a/src/multicolvar/ParabetaRMSD.cpp
+++ b/src/multicolvar/ParabetaRMSD.cpp
@@ -134,7 +134,8 @@ s_cutoff(0)
for(unsigned i=0;i<chains.size();++i){
if( chains[i]<40 ) error("segment of backbone is not long enough to form an antiparallel beta hairpin. Each backbone fragment must contain a minimum of 8 residues");
// Loop over all possible triples in each 8 residue segment of protein
- nres=chains[i]/5; plumed_assert( chains[i]%5==0 );
+ nres=chains[i]/5;
+ if( chains[i]%5!=0 ) error("backbone segment received does not contain a multiple of five residues");
for(unsigned ires=0;ires<nres-8;ires++){
for(unsigned jres=ires+6;jres<nres-2;jres++){
for(unsigned k=0;k<15;++k){
@@ -153,11 +154,13 @@ s_cutoff(0)
unsigned iprev,jprev,inres,jnres; std::vector<unsigned> nlist(30);
for(unsigned ichain=1;ichain<chains.size();++ichain){
iprev=0; for(unsigned i=0;i<ichain;++i) iprev+=chains[i];
- inres=chains[ichain]/5; plumed_assert( chains[ichain]%5==0 );
+ inres=chains[ichain]/5;
+ if( chains[ichain]%5!=0 ) error("backbone segment received does not contain a multiple of five residues");
for(unsigned ires=0;ires<inres-2;++ires){
for(unsigned jchain=0;jchain<ichain;++jchain){
jprev=0; for(unsigned i=0;i<jchain;++i) jprev+=chains[i];
- jnres=chains[jchain]/5; plumed_assert( chains[jchain]%5==0 );
+ jnres=chains[jchain]/5;
+ if( chains[jchain]%5!=0 ) error("backbone segment received does not contain a multiple of five residues");
for(unsigned jres=0;jres<jnres-2;++jres){
for(unsigned k=0;k<15;++k){
nlist[k]=iprev + ires*5+k;
diff --git a/src/multicolvar/SecondaryStructureRMSD.cpp b/src/multicolvar/SecondaryStructureRMSD.cpp
index 1c07c8783..30cadfef9 100644
--- a/src/multicolvar/SecondaryStructureRMSD.cpp
+++ b/src/multicolvar/SecondaryStructureRMSD.cpp
@@ -137,7 +137,7 @@ double SecondaryStructureRMSD::compute( const unsigned& j ){
}
unsigned SecondaryStructureRMSD::getNumberOfFieldDerivatives(){
- plumed_massert(0,"Fields are not allowed for secondary structure variables");
+ plumed_merror("Fields are not allowed for secondary structure variables");
}
bool SecondaryStructureRMSD::usingRMSD() const {
diff --git a/src/multicolvar/VesselCVdens.cpp b/src/multicolvar/VesselCVdens.cpp
index 802b84b4d..cd7a7a5c8 100644
--- a/src/multicolvar/VesselCVdens.cpp
+++ b/src/multicolvar/VesselCVdens.cpp
@@ -160,7 +160,7 @@ void VesselCVDens::addDerivativesOfWeight( const unsigned& icv ){
int thisatom, thispos, in=0; unsigned innat=mycolv->colvar_atoms[icv].getNumberActive();
for(unsigned i=0;i<innat;++i){
thisatom=linkIndex( i, mycolv->colvar_atoms[icv], mycolv->all_atoms );
- plumed_assert( thisatom>=0 ); thispos=3*thisatom;
+ plumed_dbg_assert( thisatom>=0 ); thispos=3*thisatom;
addWeightDerivative( thispos , mycolv->getCentralAtomDerivative( i, 0, wdf ) ); in++;
addWeightDerivative( thispos+1,mycolv->getCentralAtomDerivative( i, 1, wdf ) ); in++;
addWeightDerivative( thispos+2,mycolv->getCentralAtomDerivative( i, 2, wdf ) ); in++;
@@ -168,7 +168,7 @@ void VesselCVDens::addDerivativesOfWeight( const unsigned& icv ){
}
double VesselCVDens::compute( const unsigned& icv, const unsigned& j, const double& val, double& df ){
- plumed_assert( j==0 );
+ plumed_dbg_assert( j==0 );
if(isDensity){
bool hasDerivatives; double ww;
ww=getWeight( icv, hasDerivatives );
@@ -180,7 +180,7 @@ double VesselCVDens::compute( const unsigned& icv, const unsigned& j, const doub
unsigned vstart=3*mycolv->getNumberOfAtoms() + 11; // two Values and the virial
for(unsigned i=0;i<innat;++i){
thisatom=linkIndex( i, mycolv->colvar_atoms[icv], mycolv->all_atoms );
- plumed_assert( thisatom>=0 ); thispos=vstart+3*thisatom;
+ plumed_dbg_assert( thisatom>=0 ); thispos=vstart+3*thisatom;
addToBufferElement( thispos , weight*mycolv->getElementDerivative(in) + val*mycolv->getCentralAtomDerivative( i, 0, wdf ) ); in++;
addToBufferElement( thispos+1,weight*mycolv->getElementDerivative(in) + val*mycolv->getCentralAtomDerivative( i, 1, wdf ) ); in++;
addToBufferElement( thispos+2,weight*mycolv->getElementDerivative(in) + val*mycolv->getCentralAtomDerivative( i, 2, wdf ) ); in++;
diff --git a/src/setup/Load.cpp b/src/setup/Load.cpp
index 1ef834d3b..2caba81b6 100644
--- a/src/setup/Load.cpp
+++ b/src/setup/Load.cpp
@@ -58,7 +58,7 @@ PLUMED_REGISTER_ACTION(Load,"LOAD")
void Load::registerKeywords( Keywords& keys ){
ActionSetup::registerKeywords(keys);
- keys.add("compulsory","FILE","-","file to be loaded");
+ keys.add("compulsory","FILE","file to be loaded");
}
Load::Load(const ActionOptions&ao):
@@ -68,7 +68,6 @@ ActionSetup(ao)
std::string f;
parse("FILE",f);
checkRead();
- plumed_assert(f!="-");
plumed.load(f);
}
diff --git a/src/core/CubicInterpolation.cpp b/src/tools/CubicInterpolation.cpp
similarity index 96%
rename from src/core/CubicInterpolation.cpp
rename to src/tools/CubicInterpolation.cpp
index 0f0f02655..ced2fe82d 100644
--- a/src/core/CubicInterpolation.cpp
+++ b/src/tools/CubicInterpolation.cpp
@@ -58,7 +58,7 @@ void CInterpolation::getNumbersOfPoints( std::vector<unsigned>& nspline ) const
}
unsigned CInterpolation::findBox( const std::vector<double>& pos ){
- plumed_massert( pos.size()==np.size(), "position size does not match the size of the grid");
+ plumed_dbg_massert( pos.size()==np.size(), "position size does not match the size of the grid");
unsigned jold, ccf_box, bnew=0;
for(unsigned i=0;i<np.size();++i){
@@ -67,7 +67,7 @@ unsigned CInterpolation::findBox( const std::vector<double>& pos ){
ccf_box=search1( i, pos[i], jold );
bnew+=ccf_box;
}
- plumed_assert( bold==0 ); bold=bnew;
+ plumed_dbg_assert( bold==0 ); bold=bnew;
for(unsigned i=0;i<np.size();++i){ lb[i]=splinepoints(bold,i); ub[i]=splinepoints(bold+stride[i],i); }
return bold;
}
@@ -98,7 +98,7 @@ unsigned CInterpolation::search1( const unsigned& kk, const double& x, const uns
jm = (ju+jl) / (2*inc) ;
if ( x>splinepoints(jm*inc,kk) ) jl=jm*inc; else ju=jm*inc;
}
- plumed_assert( jl%stride[kk]==0 && ju==jl+stride[kk] );
+ plumed_dbg_assert( jl%stride[kk]==0 && ju==jl+stride[kk] );
return jl;
}
@@ -125,7 +125,7 @@ void InterpolateCubic::set_table( const std::vector<Value>& ff ){
}
double InterpolateCubic::get_fdf( const std::vector<double>& pos ){
- plumed_assert( pos.size()==1 );
+ plumed_dbg_assert( pos.size()==1 );
unsigned mybox=findBox( pos );
double d1=ub[0] - lb[0];
@@ -210,7 +210,7 @@ void InterpolateBicubic::IBicCoeff( const std::vector<double>& y, const std::vec
double InterpolateBicubic::get_fdf( const std::vector<double>& pos ){
- plumed_assert( pos.size()==2 );
+ plumed_dbg_assert( pos.size()==2 );
unsigned mybox=findBox( pos );
double d1 = ub[0] - lb[0], d2 = ub[1] - lb[1];
double t = (pos[0] - lb[0]) / d1, u = (pos[1] - lb[1]) / d2;
diff --git a/src/core/CubicInterpolation.h b/src/tools/CubicInterpolation.h
similarity index 96%
rename from src/core/CubicInterpolation.h
rename to src/tools/CubicInterpolation.h
index d952ead36..1acd05499 100644
--- a/src/core/CubicInterpolation.h
+++ b/src/tools/CubicInterpolation.h
@@ -23,8 +23,8 @@
#define __PLUMED_core_CubicInterpolation_h
#include <vector>
-#include "tools/Matrix.h"
-#include "Value.h"
+#include "Matrix.h"
+#include "core/Value.h"
namespace PLMD {
@@ -58,7 +58,7 @@ unsigned CInterpolation::getNumberOfSplinePoints() const {
inline
void CInterpolation::getSplinePoint( const unsigned nn, std::vector<double>& pp ) const {
- plumed_assert( nn<splinepoints.nrows() && pp.size()==np.size() );
+ plumed_dbg_assert( nn<splinepoints.nrows() && pp.size()==np.size() );
for(unsigned i=0;i<np.size();++i) pp[i]=splinepoints(nn,i);
}
@@ -70,7 +70,7 @@ double CInterpolation::getPointSpacing( const unsigned dir, const unsigned k ) c
inline
double CInterpolation::getCrossTermDenominator( const unsigned i, const unsigned j ) const {
- plumed_assert( splinepoints.ncols()==2 );
+ plumed_dbg_assert( splinepoints.ncols()==2 );
unsigned iplus, iminus; iplus=(i+1)*stride[0]; iminus=(i-1)*stride[0];
return ( splinepoints(iplus,0) - splinepoints(iminus,0) ) * ( splinepoints(iplus+j+1,1) - splinepoints(iplus+j-1,1) );
}
diff --git a/src/tools/DynamicList.h b/src/tools/DynamicList.h
index f61eb5577..9d5fb9fbc 100644
--- a/src/tools/DynamicList.h
+++ b/src/tools/DynamicList.h
@@ -145,12 +145,12 @@ public:
DynamicList():inactive(true){}
/// An operator that returns the element from the current active list
inline T operator [] (const unsigned& i) const {
- plumed_assert(!inactive); plumed_assert( i<active.size() );
+ plumed_dbg_assert(!inactive); plumed_dbg_assert( i<active.size() );
return active[i];
}
/// An operator that returns the element from the full list (used in neighbour lists)
inline T operator () (const unsigned& i) const {
- plumed_assert( i<all.size() );
+ plumed_dbg_assert( i<all.size() );
return all[i];
}
inline bool get_inactive() const { return inactive; }
@@ -195,7 +195,7 @@ unsigned DynamicList<T>::fullSize() const {
template <typename T>
unsigned DynamicList<T>::getNumberActive() const {
- if( inactive && active.size()!=0 ) plumed_assert(0);
+ plumed_dbg_assert( !inactive || active.size()==0 );
return active.size();
}
@@ -252,10 +252,10 @@ void DynamicList<T>::updateActiveMembers(){
template <typename U>
unsigned linkIndex( const unsigned ii, const DynamicList<unsigned>& l1, const DynamicList<U>& l2 ){
- plumed_massert(ii<l1.active.size(),"ii is out of bounds");
+ plumed_dbg_massert(ii<l1.active.size(),"ii is out of bounds");
unsigned kk; kk=l1.active[ii];
- plumed_massert(kk<l2.all.size(),"the lists are mismatched");
- plumed_massert( l2.onoff[kk]==1, "This index is not currently in the second list" );
+ plumed_dbg_massert(kk<l2.all.size(),"the lists are mismatched");
+ plumed_dbg_massert( l2.onoff[kk]==1, "This index is not currently in the second list" );
unsigned nn; nn=l2.translator[kk];
return nn;
}
diff --git a/src/tools/Exception.h b/src/tools/Exception.h
index b1c815a3b..987140249 100644
--- a/src/tools/Exception.h
+++ b/src/tools/Exception.h
@@ -125,5 +125,17 @@ public:
/// Conditionally print file/line/function information plus msg and exit
#define plumed_massert(test,msg) if(!(test)) throw PLMD::Exception("assertion failed " #test ", " msg,__FILE__,__LINE__,__PRETTY_FUNCTION__)
+#ifdef NDEBUG
+#define plumed_dbg_assert(test)
+#define plumed_dbg_massert(test,msg)
+#else
+/// \relates PLMD::Exception
+/// Conditionally print file/line/function information and exit when NDEBUG flag is not present
+#define plumed_dbg_assert(test) if(!(test)) throw PLMD::Exception("assertion failed " #test,__FILE__,__LINE__,__PRETTY_FUNCTION__)
+/// \relates PLMD::Exception
+/// Conditionally print file/line/function information plus msg and exit when NDEBUG flast is not present
+#define plumed_dbg_massert(test,msg) if(!(test)) throw PLMD::Exception("assertion failed " #test ", " msg,__FILE__,__LINE__,__PRETTY_FUNCTION__)
+#endif
+
}
#endif
diff --git a/src/tools/HistogramBead.cpp b/src/tools/HistogramBead.cpp
index c8987c8b0..d5f328bee 100644
--- a/src/tools/HistogramBead.cpp
+++ b/src/tools/HistogramBead.cpp
@@ -105,7 +105,7 @@ std::string HistogramBead::description() const {
void HistogramBead::generateBins( const std::string& params, const std::string& dd, std::vector<std::string>& bins ){
if( dd.size()!=0 && params.find(dd)==std::string::npos) return;
std::vector<std::string> data=Tools::getWords(params);
- plumed_assert(data.size()>=1);
+ plumed_massert(data.size()>=1,"There is no input for this keyword");
std::string name=data[0];
@@ -135,7 +135,7 @@ void HistogramBead::generateBins( const std::string& params, const std::string&
void HistogramBead::set( const std::string& params, const std::string& dd, std::string& errormsg ){
if( dd.size()!=0 && params.find(dd)==std::string::npos) return;
std::vector<std::string> data=Tools::getWords(params);
- plumed_assert(data.size()>=1);
+ if(data.size()<1) errormsg="No input has been specified";
std::string name=data[0];
if(name=="GAUSSIAN") type=gaussian;
@@ -175,7 +175,7 @@ void HistogramBead::printKeywords( Log& log ) const {
double HistogramBead::calculate( double x, double& df ) const {
const double pi=3.141592653589793238462643383279502884197169399375105820974944592307;
- plumed_assert(init && periodicity!=unset );
+ plumed_dbg_assert(init && periodicity!=unset );
double lowB, upperB, f;
if( type==gaussian ){
lowB = difference( x, lowb ) / ( sqrt(2.0) * width );
diff --git a/src/tools/HistogramBead.h b/src/tools/HistogramBead.h
index 74759a8aa..478421975 100644
--- a/src/tools/HistogramBead.h
+++ b/src/tools/HistogramBead.h
@@ -97,7 +97,7 @@ double HistogramBead::difference( const double& d1, const double& d2 ) const {
newx=Tools::pbc(newx);
newx*=max_minus_min;
return d2-newx;
- } else plumed_assert(0);
+ } else plumed_merror("periodicty was not set");
return 0;
}
diff --git a/src/tools/KernelFunctions.cpp b/src/tools/KernelFunctions.cpp
index 4061b0157..c286d1cd7 100644
--- a/src/tools/KernelFunctions.cpp
+++ b/src/tools/KernelFunctions.cpp
@@ -89,7 +89,7 @@ width(sig)
unsigned ncv=center.size();
if( width.size()==ncv ) diagonal=true;
else if( width.size()==(ncv*(ncv+1))/2 ) diagonal=false;
- else plumed_massert(0,"specified sigma is neither diagonal or full covariance matrix");
+ else plumed_merror("specified sigma is neither diagonal or full covariance matrix");
// Setup the kernel type
if(type=="GAUSSIAN" || type=="gaussian"){
@@ -146,7 +146,7 @@ double KernelFunctions::getCutoff( const double& width ) const {
}
std::vector<unsigned> KernelFunctions::getSupport( const std::vector<double>& dx ) const {
- plumed_assert( ndim()==dx.size() );
+ plumed_dbg_assert( ndim()==dx.size() );
std::vector<unsigned> support( dx.size() );
if(diagonal){
for(unsigned i=0;i<dx.size();++i) support[i]=static_cast<unsigned>(ceil( getCutoff(width[i])/dx[i] ));
@@ -165,8 +165,10 @@ std::vector<unsigned> KernelFunctions::getSupport( const std::vector<double>& dx
}
double KernelFunctions::evaluate( const std::vector<Value*>& pos, std::vector<double>& derivatives, bool usederiv ) const {
- plumed_assert( pos.size()==ndim() && derivatives.size()==ndim() );
+ plumed_dbg_assert( pos.size()==ndim() && derivatives.size()==ndim() );
+#ifndef NDEBUG
if( usederiv ) plumed_massert( ktype!=uniform, "step function can not be differentiated" );
+#endif
double r2=0;
if(diagonal){
diff --git a/src/tools/Matrix.h b/src/tools/Matrix.h
index 2b7251e06..940fd9ac1 100644
--- a/src/tools/Matrix.h
+++ b/src/tools/Matrix.h
@@ -127,7 +127,7 @@ public:
}
/// Set the Matrix equal to the value of a standard vector - used for readin
Matrix<T>& operator=(const std::vector<T>& v){
- plumed_assert( v.size()==sz );
+ plumed_dbg_assert( v.size()==sz );
for(unsigned i=0;i<sz;++i){ data[i]=v[i]; }
return *this;
}
@@ -138,7 +138,7 @@ public:
}
/// Matrix addition
Matrix<T>& operator+=(const Matrix<T>& m){
- plumed_assert( m.rw==rw && m.cl==cl );
+ plumed_dbg_assert( m.rw==rw && m.cl==cl );
data+=m.data;
return *this;
}
@@ -149,7 +149,7 @@ public:
}
/// Matrix subtraction
Matrix<T>& operator-=(const Matrix<T>& m){
- plumed_assert( m.rw==rw && m.cl==cl );
+ plumed_dbg_assert( m.rw==rw && m.cl==cl );
data-=m.data;
return *this;
}
diff --git a/src/tools/PDB.cpp b/src/tools/PDB.cpp
index c7803bfea..4ecb6fbf4 100644
--- a/src/tools/PDB.cpp
+++ b/src/tools/PDB.cpp
@@ -158,7 +158,7 @@ void PDB::getAtomRange( const std::string& chainname, AtomNumber& a_start, AtomN
}
bool PDB::getBackbone( const unsigned& resnumber, const std::vector<std::string>& backnames, std::vector<AtomNumber>& backnumbers ) const {
- plumed_assert( backnames.size()==backnumbers.size() );
+ if( backnames.size()!=backnumbers.size() ) plumed_merror("mismatch between number of backbone names and number of backbone numbers");
bool foundresidue=false; std::vector<bool> found( backnames.size(), false );
for(unsigned i=0;i<size();++i){
if( residue[i]==resnumber ){
@@ -179,7 +179,7 @@ std::string PDB::getChainID(const unsigned& resnumber) const {
for(unsigned i=0;i<size();++i){
if(resnumber==residue[i]) return chain[i];
}
- plumed_massert(0,"Not enough residues in pdb input file");
+ plumed_merror("Not enough residues in pdb input file");
}
void PDB::renameAtoms( const std::string& old_name, const std::string& new_name ){
diff --git a/src/tools/SwitchingFunction.cpp b/src/tools/SwitchingFunction.cpp
index 61d35cefa..88d2ebd27 100644
--- a/src/tools/SwitchingFunction.cpp
+++ b/src/tools/SwitchingFunction.cpp
@@ -83,7 +83,7 @@ keyword D_MAX to assert that for \f$r>d_{\textrm{max}}\f$ the switching function
void SwitchingFunction::set(const std::string & definition,std::string& errormsg){
vector<string> data=Tools::getWords(definition);
- //plumed_assert(data.size()>=1);
+ if( data.size()<1 ) errormsg="missing all input for switching function";
string name=data[0];
data.erase(data.begin());
invr0=0.0;
@@ -94,7 +94,6 @@ void SwitchingFunction::set(const std::string & definition,std::string& errormsg
double r0;
bool found_r0=Tools::parse(data,"R_0",r0);
if(!found_r0) errormsg="R_0 is required";
-// plumed_massert(found_r0,"R_0 is needed");
invr0=1.0/r0;
Tools::parse(data,"D_0",d0);
Tools::parse(data,"D_MAX",dmax);
diff --git a/src/vatom/Center.cpp b/src/vatom/Center.cpp
index 301e8c6d4..010a5223e 100644
--- a/src/vatom/Center.cpp
+++ b/src/vatom/Center.cpp
@@ -90,10 +90,10 @@ Center::Center(const ActionOptions&ao):
for(unsigned i=0;i<atoms.size();++i) log.printf(" %d",atoms[i].serial());
if(weight_mass){
log<<" mass weighted\n";
- plumed_assert(weights.size()==0);
+ if(weights.size()!=0) error("WEIGHTS and MASS keywords should not be used simultaneously");
} else {
log<<" with weights";
- plumed_assert(weights.size()==atoms.size());
+ if( weights.size()!=atoms.size() ) error("number of elements in weight vector does not match the number of atoms");
for(unsigned i=0;i<weights.size();++i) log.printf(" %f",weights[i]);
log.printf("\n");
}
diff --git a/src/vatom/Ghost.cpp b/src/vatom/Ghost.cpp
index 1d8475b48..0bb8f16f4 100644
--- a/src/vatom/Ghost.cpp
+++ b/src/vatom/Ghost.cpp
@@ -74,10 +74,10 @@ Ghost::Ghost(const ActionOptions&ao):
{
vector<AtomNumber> atoms;
parseAtomList("ATOMS",atoms);
- plumed_massert(atoms.size()==3,"ATOMS should contain a list of three atoms");
+ if(atoms.size()!=3) error("ATOMS should contain a list of three atoms");
parseVector("COORDINATES",coord);
- plumed_massert(coord.size()==3,"COORDINATES should be a list of three real numbers");
+ if(coord.size()!=3) error("COORDINATES should be a list of three real numbers");
checkRead();
log.printf(" of atoms");
diff --git a/src/vesselbase/ActionWithVessel.cpp b/src/vesselbase/ActionWithVessel.cpp
index 96a78f206..82ba77b8f 100644
--- a/src/vesselbase/ActionWithVessel.cpp
+++ b/src/vesselbase/ActionWithVessel.cpp
@@ -153,11 +153,11 @@ void ActionWithVessel::calculateAllVessels( const int& stepn ){
// Check for conditions that allow us to just to skip the calculation
if( reduceAtNextStep && skipme ){
- plumed_massert( isPossibleToSkip(), "To make your action work you must write a routine to get weights");
+ plumed_dbg_massert( isPossibleToSkip(), "To make your action work you must write a routine to get weights");
deactivate(kk);
continue;
} else if( skipme ){
- plumed_massert( isPossibleToSkip(), "To make your action work you must write a routine to get weights");
+ plumed_dbg_massert( isPossibleToSkip(), "To make your action work you must write a routine to get weights");
continue;
}
@@ -207,7 +207,7 @@ void ActionWithVessel::calculateAllVessels( const int& stepn ){
}
void ActionWithVessel::retrieveDomain( std::string& min, std::string& max ){
- plumed_massert(0, "If your function is periodic you need to add a retrieveDomain function so that ActionWithVessel can retrieve the domain");
+ plumed_merror("If your function is periodic you need to add a retrieveDomain function so that ActionWithVessel can retrieve the domain");
}
}
diff --git a/src/vesselbase/ActionWithVessel.h b/src/vesselbase/ActionWithVessel.h
index 90653059b..605f6ac35 100644
--- a/src/vesselbase/ActionWithVessel.h
+++ b/src/vesselbase/ActionWithVessel.h
@@ -156,7 +156,7 @@ unsigned ActionWithVessel::getNumberOfActiveMembers() const {
inline
unsigned ActionWithVessel::getActiveMember(const unsigned& m ) const {
- plumed_assert( m<members.getNumberActive() );
+ plumed_dbg_assert( m<members.getNumberActive() );
return members[m];
}
@@ -178,7 +178,7 @@ unsigned ActionWithVessel::getNumberOfVessels() const {
inline
Vessel* ActionWithVessel::getPntrToVessel( const unsigned& i ){
- plumed_assert( i<functions.size() );
+ plumed_dbg_assert( i<functions.size() );
return functions[i];
}
@@ -194,13 +194,13 @@ void ActionWithVessel::setElementValue( const double& val ){
inline
double ActionWithVessel::getElementDerivative( const unsigned& ider ) const {
- plumed_assert( ider<derivatives.size() );
+ plumed_dbg_assert( ider<derivatives.size() );
return derivatives[ider];
}
inline
void ActionWithVessel::addElementDerivative( const unsigned& ider, const double& der ){
- plumed_assert( ider<derivatives.size() );
+ plumed_dbg_assert( ider<derivatives.size() );
derivatives[ider] += der;
}
diff --git a/src/vesselbase/Vessel.h b/src/vesselbase/Vessel.h
index 68c527dcf..2a4bc69c8 100644
--- a/src/vesselbase/Vessel.h
+++ b/src/vesselbase/Vessel.h
@@ -135,19 +135,19 @@ ActionWithVessel* Vessel::getAction(){
inline
void Vessel::setBufferElement( const unsigned& i, const double& val){
- plumed_assert( i<data_buffer.size() );
+ plumed_dbg_assert( i<data_buffer.size() );
data_buffer[i]=val;
}
inline
void Vessel::addToBufferElement( const unsigned& i, const double& val){
- plumed_assert( i<data_buffer.size() );
+ plumed_dbg_assert( i<data_buffer.size() );
data_buffer[i]+=val;
}
inline
double Vessel::getBufferElement( const unsigned& i ) const {
- plumed_assert( i<data_buffer.size() );
+ plumed_dbg_assert( i<data_buffer.size() );
return data_buffer[i];
}
diff --git a/src/vesselbase/VesselAccumulator.h b/src/vesselbase/VesselAccumulator.h
index d26ab98d1..494def9bb 100644
--- a/src/vesselbase/VesselAccumulator.h
+++ b/src/vesselbase/VesselAccumulator.h
@@ -55,7 +55,7 @@ public:
inline
Value* VesselAccumulator::getPntrToOutput( const unsigned& iout ){
- plumed_assert( iout<final_values.size() );
+ plumed_dbg_assert( iout<final_values.size() );
return final_values[iout];
}
diff --git a/src/vesselbase/VesselLessThan.cpp b/src/vesselbase/VesselLessThan.cpp
index ba7426cd2..11b1db0e8 100644
--- a/src/vesselbase/VesselLessThan.cpp
+++ b/src/vesselbase/VesselLessThan.cpp
@@ -64,7 +64,7 @@ void VesselLessThan::printKeywords(){
}
double VesselLessThan::compute( const unsigned& i, const double& val, double& df ){
- plumed_assert( i==0 );
+ plumed_dbg_assert( i==0 );
double f; f = sf.calculate(val, df); df*=val;
return f;
}
diff --git a/src/vesselbase/VesselMean.cpp b/src/vesselbase/VesselMean.cpp
index 90b758499..c2facc435 100644
--- a/src/vesselbase/VesselMean.cpp
+++ b/src/vesselbase/VesselMean.cpp
@@ -52,12 +52,12 @@ WeightedSumVessel(da)
}
double VesselMean::compute( const unsigned& i, const unsigned& j, const double& val, double& df ){
- plumed_assert( j==0 );
+ plumed_dbg_assert( j==0 );
df=1.0; return val;
}
double VesselMean::getWeight( const unsigned& i, bool& hasDerivatives ){
- plumed_assert( !getAction()->isPossibleToSkip() );
+ plumed_dbg_assert( !getAction()->isPossibleToSkip() );
hasDerivatives=false;
return 1.0;
}
diff --git a/src/vesselbase/VesselMoreThan.cpp b/src/vesselbase/VesselMoreThan.cpp
index 021101312..ce152ef49 100644
--- a/src/vesselbase/VesselMoreThan.cpp
+++ b/src/vesselbase/VesselMoreThan.cpp
@@ -65,7 +65,7 @@ void VesselMoreThan::printKeywords(){
}
double VesselMoreThan::compute( const unsigned& i, const double& val, double& df ){
- plumed_assert( i==0 );
+ plumed_dbg_assert( i==0 );
double f; f=1.0 - sf.calculate(val, df); df*=-val;
return f;
}
diff --git a/src/vesselbase/VesselSum.cpp b/src/vesselbase/VesselSum.cpp
index 1855f2de4..a6a2141bb 100644
--- a/src/vesselbase/VesselSum.cpp
+++ b/src/vesselbase/VesselSum.cpp
@@ -47,7 +47,7 @@ SumVessel(da)
}
double VesselSum::compute( const unsigned& i, const double& val, double& df ){
- plumed_assert( i==0 );
+ plumed_dbg_assert( i==0 );
df=1.0; return val;
}
diff --git a/src/vesselbase/VesselValueAccess.h b/src/vesselbase/VesselValueAccess.h
index 0c1e2f5e5..cdda43c07 100644
--- a/src/vesselbase/VesselValueAccess.h
+++ b/src/vesselbase/VesselValueAccess.h
@@ -55,13 +55,13 @@ public:
inline
unsigned VesselValueAccess::getNumberOfDerivatives( const unsigned& ival ) const {
- plumed_assert( ival<value_starts.size() );
+ plumed_dbg_assert( ival<value_starts.size() );
return value_starts[ival+1]-value_starts[ival]-1;
}
inline
void VesselValueAccess::getValue( const unsigned& icv, Value& val ) const {
- plumed_assert( icv<value_starts.size()-1 );
+ plumed_dbg_assert( icv<value_starts.size()-1 );
unsigned nder=(value_starts[icv+1]-value_starts[icv]-1);
if( val.getNumberOfDerivatives()!=nder ) val.resizeDerivatives( nder );
val.clearDerivatives();
@@ -71,7 +71,7 @@ void VesselValueAccess::getValue( const unsigned& icv, Value& val ) const {
inline
double VesselValueAccess::getValue( const unsigned& icv ) const {
- plumed_assert( icv<value_starts.size()-1 );
+ plumed_dbg_assert( icv<value_starts.size()-1 );
return getBufferElement( value_starts[icv] );
}
diff --git a/src/vesselbase/VesselWithin.cpp b/src/vesselbase/VesselWithin.cpp
index fec848c32..d2fc0867b 100644
--- a/src/vesselbase/VesselWithin.cpp
+++ b/src/vesselbase/VesselWithin.cpp
@@ -100,13 +100,13 @@ void VesselWithin::printKeywords(){
}
double VesselWithin::compute( const unsigned& icv, const unsigned& jfunc, const double& val, double& df ){
- plumed_assert( jfunc<hist.size() );
+ plumed_dbg_assert( jfunc<hist.size() );
double f; f=hist[jfunc].calculate( val , df );
return f;
}
double VesselWithin::getWeight( const unsigned& i, bool& hasDerivatives ){
- plumed_assert( !getAction()->isPossibleToSkip() );
+ plumed_dbg_assert( !getAction()->isPossibleToSkip() );
hasDerivatives=false;
return 1.0;
}
diff --git a/src/vesselbase/WeightedSumVessel.h b/src/vesselbase/WeightedSumVessel.h
index e9a3309e4..fb975551f 100644
--- a/src/vesselbase/WeightedSumVessel.h
+++ b/src/vesselbase/WeightedSumVessel.h
@@ -47,14 +47,14 @@ public:
/// This gets the weight
virtual double getWeight( const unsigned&, bool& )=0;
/// This adds the derivatives of the weight
- virtual void addDerivativesOfWeight( const unsigned& ){ plumed_assert(0); }
+ virtual void addDerivativesOfWeight( const unsigned& ){ plumed_merror("weights have no derivatives in this vessel"); }
/// This gets each value
virtual double compute( const unsigned& , const unsigned& , const double& val, double& df )=0;
};
inline
void WeightedSumVessel::addWeightDerivative( const unsigned& ider, const double& der ){
- plumed_assert( ider<getNumberOfDerivatives(0) );
+ plumed_dbg_assert( ider<getNumberOfDerivatives(0) );
addToBufferElement( ider+1, der );
}
--
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