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Merged
carlocamilloni merged 6 commits into from
Nov 29, 2023
Merged

OPES: Making parsing not reliant on NaN #992

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f7e4cd8
update OPES explore bibliography
invemichele Sep 28, 2023
336280b
Merge branch 'plumed:v2.8' into v2.8
invemichele Nov 29, 2023
9fc246e
test robust isnan
invemichele Nov 29, 2023
4cc2ce8
switch to robust isnan
invemichele Nov 29, 2023
89ae22a
fix warning message
invemichele Nov 29, 2023
fae2c45
astyle
invemichele Nov 29, 2023
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22 changes: 19 additions & 3 deletions src/opes/ECVlinear.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,22 @@ ECVlinear::ECVlinear(const ActionOptions&ao)
if(dimensionless)
beta0_=1;

//workaround needed for intel compiler
bool nan_support=true;
const double my_nan_value=-42;
if(!std::isnan(std::numeric_limits<double>::quiet_NaN()))
{
nan_support=false;
log.printf(" +++ WARNING +++ do not set LAMBDA_MIN/MAX=%g, see https://github.com/plumed/plumed2/pull/990\n", my_nan_value);
}
auto isNone=[nan_support,my_nan_value](const double value)
{
if(nan_support)
return std::isnan(value);
else
return value==my_nan_value;
};

//parse lambda info
parse("LAMBDA",lambda0_);
double lambda_min=std::numeric_limits<double>::quiet_NaN();
Expand All @@ -140,7 +156,7 @@ ECVlinear::ECVlinear(const ActionOptions&ao)
if(lambdas.size()>0)
{
plumed_massert(lambda_steps==0,"cannot set both LAMBDA_STEPS and LAMBDA_SET_ALL");
plumed_massert(std::isnan(lambda_min) && std::isnan(lambda_max),"cannot set both LAMBDA_SET_ALL and LAMBDA_MIN/MAX");
plumed_massert(isNone(lambda_min) && isNone(lambda_max),"cannot set both LAMBDA_SET_ALL and LAMBDA_MIN/MAX");
plumed_massert(lambdas.size()>=2,"set at least 2 lambdas with LAMBDA_SET_ALL");
for(unsigned k=0; k<lambdas.size()-1; k++)
plumed_massert(lambdas[k]<=lambdas[k+1],"LAMBDA_SET_ALL must be properly ordered");
Expand All @@ -152,12 +168,12 @@ ECVlinear::ECVlinear(const ActionOptions&ao)
}
else
{ //get LAMBDA_MIN and LAMBDA_MAX
if(std::isnan(lambda_min))
if(isNone(lambda_min))
{
lambda_min=0;
log.printf(" no LAMBDA_MIN provided, using LAMBDA_MIN = %g\n",lambda_min);
}
if(std::isnan(lambda_max))
if(isNone(lambda_max))
{
lambda_max=1;
log.printf(" no LAMBDA_MAX provided, using LAMBDA_MAX = %g\n",lambda_max);
Expand Down
24 changes: 12 additions & 12 deletions src/opes/ECVmultiThermal.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ Notice that \f$p=0.06022140857\f$ corresponds to 1 bar when using the default PL
*/
//+ENDPLUMEDOC

class ECVmultiCanonical :
class ECVmultiThermal :
public ExpansionCVs
{
private:
Expand All @@ -90,7 +90,7 @@ class ECVmultiCanonical :
void initECVs();

public:
explicit ECVmultiCanonical(const ActionOptions&);
explicit ECVmultiThermal(const ActionOptions&);
static void registerKeywords(Keywords& keys);
void calculateECVs(const double *) override;
const double * getPntrToECVs(unsigned) override;
Expand All @@ -100,9 +100,9 @@ class ECVmultiCanonical :
void initECVs_restart(const std::vector<std::string>&) override;
};

PLUMED_REGISTER_ACTION(ECVmultiCanonical,"ECV_MULTITHERMAL")
PLUMED_REGISTER_ACTION(ECVmultiThermal,"ECV_MULTITHERMAL")

void ECVmultiCanonical::registerKeywords(Keywords& keys)
void ECVmultiThermal::registerKeywords(Keywords& keys)
{
ExpansionCVs::registerKeywords(keys);
keys.remove("ARG");
Expand All @@ -114,7 +114,7 @@ void ECVmultiCanonical::registerKeywords(Keywords& keys)
keys.addFlag("NO_GEOM_SPACING",false,"do not use geometrical spacing in temperature, but instead linear spacing in inverse temperature");
}

ECVmultiCanonical::ECVmultiCanonical(const ActionOptions&ao)
ECVmultiThermal::ECVmultiThermal(const ActionOptions&ao)
: Action(ao)
, ExpansionCVs(ao)
, todoAutomatic_(false)
Expand Down Expand Up @@ -188,28 +188,28 @@ ECVmultiCanonical::ECVmultiCanonical(const ActionOptions&ao)
log.printf(" -- NO_GEOM_SPACING: inverse temperatures will be linearly spaced\n");
}

void ECVmultiCanonical::calculateECVs(const double * ene)
void ECVmultiThermal::calculateECVs(const double * ene)
{
for(unsigned k=0; k<derECVs_.size(); k++)
ECVs_[k]=derECVs_[k]*ene[0];
// derivatives never change: derECVs_k=(beta_k-beta0)
}

const double * ECVmultiCanonical::getPntrToECVs(unsigned j)
const double * ECVmultiThermal::getPntrToECVs(unsigned j)
{
plumed_massert(isReady_,"cannot access ECVs before initialization");
plumed_massert(j==0,getName()+" has only one CV, the ENERGY");
return &ECVs_[0];
}

const double * ECVmultiCanonical::getPntrToDerECVs(unsigned j)
const double * ECVmultiThermal::getPntrToDerECVs(unsigned j)
{
plumed_massert(isReady_,"cannot access ECVs before initialization");
plumed_massert(j==0,getName()+" has only one CV, the ENERGY");
return &derECVs_[0];
}

std::vector<std::string> ECVmultiCanonical::getLambdas() const
std::vector<std::string> ECVmultiThermal::getLambdas() const
{
plumed_massert(!todoAutomatic_,"cannot access lambdas before initializing them");
const double temp0=kbt_/plumed.getAtoms().getKBoltzmann();
Expand All @@ -223,7 +223,7 @@ std::vector<std::string> ECVmultiCanonical::getLambdas() const
return lambdas;
}

void ECVmultiCanonical::initECVs()
void ECVmultiThermal::initECVs()
{
plumed_massert(!isReady_,"initialization should not be called twice");
plumed_massert(!todoAutomatic_,"this should not happen");
Expand All @@ -233,7 +233,7 @@ void ECVmultiCanonical::initECVs()
log.printf(" *%4lu temperatures for %s\n",derECVs_.size(),getName().c_str());
}

void ECVmultiCanonical::initECVs_observ(const std::vector<double>& all_obs_cvs,const unsigned ncv,const unsigned index_j)
void ECVmultiThermal::initECVs_observ(const std::vector<double>& all_obs_cvs,const unsigned ncv,const unsigned index_j)
{
if(todoAutomatic_) //estimate the steps in beta from observations
{
Expand All @@ -250,7 +250,7 @@ void ECVmultiCanonical::initECVs_observ(const std::vector<double>& all_obs_cvs,c
calculateECVs(&all_obs_cvs[index_j]);
}

void ECVmultiCanonical::initECVs_restart(const std::vector<std::string>& lambdas)
void ECVmultiThermal::initECVs_restart(const std::vector<std::string>& lambdas)
{
std::size_t pos=lambdas[0].find("_");
plumed_massert(pos==std::string::npos,"this should not happen, only one CV is used in "+getName());
Expand Down
24 changes: 20 additions & 4 deletions src/opes/ECVmultiThermalBaric.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -146,6 +146,22 @@ ECVmultiThermalBaric::ECVmultiThermalBaric(const ActionOptions&ao)
const double kB=plumed.getAtoms().getKBoltzmann();
const double temp0=kbt_/kB;

//workaround needed for intel compiler
bool nan_support=true;
const double my_nan_value=-42;
if(!std::isnan(std::numeric_limits<double>::quiet_NaN()))
{
nan_support=false;
log.printf(" +++ WARNING +++ do not set PRESSURE_MIN/MAX=%g, see https://github.com/plumed/plumed2/pull/990\n", my_nan_value);
}
auto isNone=[nan_support,my_nan_value](const double value)
{
if(nan_support)
return std::isnan(value);
else
return value==my_nan_value;
};

//parse temp range
double temp_min=-1;
double temp_max=-1;
Expand Down Expand Up @@ -181,7 +197,7 @@ ECVmultiThermalBaric::ECVmultiThermalBaric(const ActionOptions&ao)
plumed_massert(temp_steps==0,"cannot set both SET_ALL_TEMP_PRESSURE and TEMP_STEPS");
plumed_massert(pres_steps==0,"cannot set both SET_ALL_TEMP_PRESSURE and PRESSURE_STEPS");
plumed_massert(temp_min==-1 && temp_max==-1,"cannot set both SET_ALL_TEMP_PRESSURE and TEMP_MIN/MAX");
plumed_massert(std::isnan(pres_min) && std::isnan(pres_max),"cannot set both SET_ALL_TEMP_PRESSURE and PRESSURE_MIN/MAX");
plumed_massert(isNone(pres_min) && isNone(pres_max),"cannot set both SET_ALL_TEMP_PRESSURE and PRESSURE_MIN/MAX");
plumed_massert(cut_corner.size()==0,"cannot set both SET_ALL_TEMP_PRESSURE and CUT_CORNER");
//setup the target temperature-pressure grid
derECVs_beta_.resize(custom_lambdas_.size());
Expand Down Expand Up @@ -257,7 +273,7 @@ ECVmultiThermalBaric::ECVmultiThermalBaric(const ActionOptions&ao)
if(pres_.size()>0)
{
plumed_massert(pres_steps==0,"cannot set both PRESSURE_STEPS and PRESSURE_SET_ALL");
plumed_massert(std::isnan(pres_min) && std::isnan(pres_max),"cannot set both PRESSURE_SET_ALL and PRESSURE_MIN/MAX");
plumed_massert(isNone(pres_min) && isNone(pres_max),"cannot set both PRESSURE_SET_ALL and PRESSURE_MIN/MAX");
plumed_massert(pres_.size()>=2,"set at least 2 pressures");
for(unsigned kk=0; kk<pres_.size()-1; kk++)
plumed_massert(pres_[kk]<=pres_[kk+1],"PRESSURE_SET_ALL must be properly ordered");
Expand All @@ -266,12 +282,12 @@ ECVmultiThermalBaric::ECVmultiThermalBaric(const ActionOptions&ao)
}
else
{ //get PRESSURE_MIN and PRESSURE_MAX
if(std::isnan(pres_min))
if(isNone(pres_min))
{
pres_min=pres0_;
log.printf(" no PRESSURE_MIN provided, using PRESSURE_MIN=PRESSURE\n");
}
if(std::isnan(pres_max))
if(isNone(pres_max))
{
pres_max=pres0_;
log.printf(" no PRESSURE_MAX provided, using PRESSURE_MAX=PRESSURE\n");
Expand Down