From 10e2afc64ab565e19b5f71eb0547c6b288e22ea7 Mon Sep 17 00:00:00 2001 From: Carlo Camilloni <carlo.camilloni@gmail.com> Date: Wed, 29 Nov 2023 16:19:57 +0100 Subject: [PATCH 1/4] closes #963 the solution is not optimal, but I think making something general is not trivial --- regtest/secondarystructure/rt32/plumed.dat | 4 ++-- src/secondarystructure/AntibetaRMSD.cpp | 6 +++--- src/secondarystructure/ParabetaRMSD.cpp | 8 ++++---- src/secondarystructure/SecondaryStructureRMSD.cpp | 3 ++- 4 files changed, 11 insertions(+), 10 deletions(-) diff --git a/regtest/secondarystructure/rt32/plumed.dat b/regtest/secondarystructure/rt32/plumed.dat index 180a6c5e80..aaf56d6e0b 100644 --- a/regtest/secondarystructure/rt32/plumed.dat +++ b/regtest/secondarystructure/rt32/plumed.dat @@ -1,12 +1,12 @@ MOLINFO STRUCTURE=helix.pdb -ALPHARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=a +ALPHARMSD RESIDUES=ALL TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=a ANTIBETARMSD RESIDUES=all TYPE=DRMSD STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=b PARABETARMSD RESIDUES=all TYPE=DRMSD STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=p PRINT ARG=a.*,b.*,p.* STRIDE=1 FILE=colvar FMT=%8.4f ALPHARMSD RESIDUES=2-7 TYPE=DRMSD R_0=0.08 NN=8 MM=12 LABEL=a2 ALPHARMSD RESIDUES=2-7 TYPE=DRMSD R_0=0.08 NN=8 MM=12 NUMERICAL_DERIVATIVES LABEL=a2num DUMPDERIVATIVES ARG=a2.*,a2num.* FILE=derivatives1 FMT=%8.4f STRIDE=1 -ANTIBETARMSD RESIDUES=3-5,8-10 STYLE=inter TYPE=OPTIMAL LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=b2 +ANTIBETARMSD RESIDUES=3-5,8-10 STYLE=INTER TYPE=OPTIMAL LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=b2 ANTIBETARMSD RESIDUES=3-5,8-10 STYLE=inter TYPE=OPTIMAL LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} NUMERICAL_DERIVATIVES LABEL=b2num DUMPDERIVATIVES ARG=b2.*,b2num.* FILE=derivatives2 FMT=%8.3f STRIDE=1 RESTRAINT ARG=b.lessthan,p.lessthan,a.lessthan,a2,b2.lessthan AT=0,1,2,3,4 KAPPA=1,2,3,4,5 SLOPE=5,4,3,2,1 diff --git a/src/secondarystructure/AntibetaRMSD.cpp b/src/secondarystructure/AntibetaRMSD.cpp index c06abc7e3c..bab794e256 100644 --- a/src/secondarystructure/AntibetaRMSD.cpp +++ b/src/secondarystructure/AntibetaRMSD.cpp @@ -112,11 +112,11 @@ AntibetaRMSD::AntibetaRMSD(const ActionOptions&ao): bool intra_chain(false), inter_chain(false); std::string style; parse("STYLE",style); - if( style=="all" ) { + if( Tools::caseInSensStringCompare(style, "all") ) { intra_chain=true; inter_chain=true; - } else if( style=="inter") { + } else if( Tools::caseInSensStringCompare(style, "inter") ) { intra_chain=false; inter_chain=true; - } else if( style=="intra") { + } else if( Tools::caseInSensStringCompare(style, "intra") ) { intra_chain=true; inter_chain=false; } else { error( style + " is not a valid directive for the STYLE keyword"); diff --git a/src/secondarystructure/ParabetaRMSD.cpp b/src/secondarystructure/ParabetaRMSD.cpp index 9e2e06ea52..1ef9fc9101 100644 --- a/src/secondarystructure/ParabetaRMSD.cpp +++ b/src/secondarystructure/ParabetaRMSD.cpp @@ -113,11 +113,11 @@ ParabetaRMSD::ParabetaRMSD(const ActionOptions&ao): bool intra_chain(false), inter_chain(false); std::string style; parse("STYLE",style); - if( style=="all" ) { + if( Tools::caseInSensStringCompare(style, "all") ) { intra_chain=true; inter_chain=true; - } else if( style=="inter") { + } else if( Tools::caseInSensStringCompare(style, "inter") ) { intra_chain=false; inter_chain=true; - } else if( style=="intra") { + } else if( Tools::caseInSensStringCompare(style, "intra") ) { intra_chain=true; inter_chain=false; } else { error( style + " is not a valid directive for the STYLE keyword"); @@ -148,7 +148,7 @@ ParabetaRMSD::ParabetaRMSD(const ActionOptions&ao): } // This constructs all conceivable sections of antibeta sheet that form between chains if( inter_chain ) { - if( chains.size()==1 && style!="all" ) error("there is only one chain defined so cannot use inter_chain option"); + if( chains.size()==1 && !Tools::caseInSensStringCompare(style, "all") ) error("there is only one chain defined so cannot use inter_chain option"); std::vector<unsigned> nlist(30); for(unsigned ichain=1; ichain<chains.size(); ++ichain) { unsigned iprev=0; for(unsigned i=0; i<ichain; ++i) iprev+=chains[i]; diff --git a/src/secondarystructure/SecondaryStructureRMSD.cpp b/src/secondarystructure/SecondaryStructureRMSD.cpp index 4b6febcefe..10b4c1db8a 100644 --- a/src/secondarystructure/SecondaryStructureRMSD.cpp +++ b/src/secondarystructure/SecondaryStructureRMSD.cpp @@ -115,7 +115,8 @@ void SecondaryStructureRMSD::readBackboneAtoms( const std::string& moltype, std: std::vector<std::string> resstrings; parseVector( "RESIDUES", resstrings ); if( !verbose_output ) { if(resstrings.size()==0) error("residues are not defined, check the keyword RESIDUES"); - else if(resstrings[0]=="all") { + else if( Tools::caseInSensStringCompare(resstrings[0], "all") ) { + resstrings[0]="all"; log.printf(" examining all possible secondary structure combinations\n"); } else { log.printf(" examining secondary structure in residue positions : %s \n",resstrings[0].c_str() ); From 25abfd876b6260465593b7c277d83e9e74cfc722 Mon Sep 17 00:00:00 2001 From: Carlo Camilloni <carlo.camilloni@gmail.com> Date: Wed, 29 Nov 2023 16:37:34 +0100 Subject: [PATCH 2/4] Update v2.9.md --- CHANGES/v2.9.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGES/v2.9.md b/CHANGES/v2.9.md index 04f779c25c..9ec0461967 100644 --- a/CHANGES/v2.9.md +++ b/CHANGES/v2.9.md @@ -55,5 +55,6 @@ Changes from version 2.8 which are relevant for users: - Step number is now stored as a `long long int`. Might facilitate Windows compatibility. ## Version 2.9.1 (to be released) +- Includes all fixes up to 2.8.4 - Plumed now fetches the massses correctly from QEspresso 7.0 From 9848506d2cd2add7cd65683b8afcc07adb395c03 Mon Sep 17 00:00:00 2001 From: Carlo Camilloni <carlo.camilloni@gmail.com> Date: Wed, 29 Nov 2023 16:37:34 +0100 Subject: [PATCH 3/4] Update v2.9.md --- CHANGES/v2.9.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGES/v2.9.md b/CHANGES/v2.9.md index 04f779c25c..9ec0461967 100644 --- a/CHANGES/v2.9.md +++ b/CHANGES/v2.9.md @@ -55,5 +55,6 @@ Changes from version 2.8 which are relevant for users: - Step number is now stored as a `long long int`. Might facilitate Windows compatibility. ## Version 2.9.1 (to be released) +- Includes all fixes up to 2.8.4 - Plumed now fetches the massses correctly from QEspresso 7.0 From 31b39e41e807dff6645aaf8772fcf29bb469d120 Mon Sep 17 00:00:00 2001 From: Michele Invernizzi <inve.michele@gmail.com> Date: Wed, 29 Nov 2023 17:53:04 +0100 Subject: [PATCH 4/4] OPES: Making parsing not reliant on NaN (#992) --- src/opes/ECVlinear.cpp | 22 +++++++++++++++++++--- src/opes/ECVmultiThermal.cpp | 24 ++++++++++++------------ src/opes/ECVmultiThermalBaric.cpp | 24 ++++++++++++++++++++---- 3 files changed, 51 insertions(+), 19 deletions(-) diff --git a/src/opes/ECVlinear.cpp b/src/opes/ECVlinear.cpp index 56e895e3c3..be573ed5e2 100644 --- a/src/opes/ECVlinear.cpp +++ b/src/opes/ECVlinear.cpp @@ -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(); @@ -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"); @@ -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); diff --git a/src/opes/ECVmultiThermal.cpp b/src/opes/ECVmultiThermal.cpp index df19c5ca0b..d714eba64e 100644 --- a/src/opes/ECVmultiThermal.cpp +++ b/src/opes/ECVmultiThermal.cpp @@ -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: @@ -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; @@ -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"); @@ -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) @@ -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(); @@ -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"); @@ -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 { @@ -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()); diff --git a/src/opes/ECVmultiThermalBaric.cpp b/src/opes/ECVmultiThermalBaric.cpp index 17b3d07e31..5ede40c3b0 100644 --- a/src/opes/ECVmultiThermalBaric.cpp +++ b/src/opes/ECVmultiThermalBaric.cpp @@ -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; @@ -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()); @@ -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"); @@ -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");