From 3c6645d72d0215bf70e77f495786de961971bc45 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Wed, 6 Sep 2017 12:58:46 +0200
Subject: [PATCH] Removed libmatheval
I removed matheval everywhere in the code. Now, MATHEVAL
(and CUSTOM) keywords are automatically using lepton (see #244).
Notice that env var PLUMED_USE_LEPTON is now ignored.
---
configure | 90 -------------------------
configure.ac | 4 --
src/core/CLToolMain.cpp | 3 -
src/function/Matheval.cpp | 114 +++++++-------------------------
src/tools/SwitchingFunction.cpp | 79 +---------------------
src/tools/SwitchingFunction.h | 10 ---
6 files changed, 25 insertions(+), 275 deletions(-)
diff --git a/configure b/configure
index d475becad..b47ddaa92 100755
--- a/configure
+++ b/configure
@@ -714,7 +714,6 @@ enable_external_lapack
enable_external_blas
enable_molfile_plugins
enable_external_molfile_plugins
-enable_matheval
enable_zlib
enable_readdir_r
enable_cregex
@@ -1383,7 +1382,6 @@ Optional Features:
--enable-external-molfile-plugins
enable search for external molfile_plugins, default:
yes
- --enable-matheval enable search for matheval, default: yes
--enable-zlib enable search for zlib, default: yes
--enable-readdir-r enable search for readdir_r (threadsafe), default:
yes
@@ -2764,24 +2762,6 @@ fi
-matheval=
-# Check whether --enable-matheval was given.
-if test "${enable_matheval+set}" = set; then :
- enableval=$enable_matheval; case "${enableval}" in
- (yes) matheval=true ;;
- (no) matheval=false ;;
- (*) as_fn_error $? "wrong argument to --enable-matheval" "$LINENO" 5 ;;
- esac
-else
- case "yes" in
- (yes) matheval=true ;;
- (no) matheval=false ;;
- esac
-
-fi
-
-
-
zlib=
# Check whether --enable-zlib was given.
if test "${enable_zlib+set}" = set; then :
@@ -6156,76 +6136,6 @@ $as_echo "$ac_cv_prog_cxx_openmp" >&6; }
-if test $matheval == true ; then
-
- found=ko
- ac_fn_cxx_check_header_mongrel "$LINENO" "matheval.h" "ac_cv_header_matheval_h" "$ac_includes_default"
-if test "x$ac_cv_header_matheval_h" = xyes; then :
-
- ac_fn_cxx_check_func "$LINENO" "evaluator_create" "ac_cv_func_evaluator_create"
-if test "x$ac_cv_func_evaluator_create" = xyes; then :
- found=ok
-else
-
- if test "${libsearch}" == true ; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for evaluator_create in -lmatheval" >&5
-$as_echo_n "checking for evaluator_create in -lmatheval... " >&6; }
-if ${ac_cv_lib_matheval_evaluator_create+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-lmatheval $LIBS"
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char evaluator_create ();
-int
-main ()
-{
-return evaluator_create ();
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_cxx_try_link "$LINENO"; then :
- ac_cv_lib_matheval_evaluator_create=yes
-else
- ac_cv_lib_matheval_evaluator_create=no
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_matheval_evaluator_create" >&5
-$as_echo "$ac_cv_lib_matheval_evaluator_create" >&6; }
-if test "x$ac_cv_lib_matheval_evaluator_create" = xyes; then :
- LIBS="-lmatheval $LIBS" && found=ok
-fi
-
- fi
-
-
-fi
-
-
-fi
-
-
- if test $found == ok ; then
- $as_echo "#define __PLUMED_HAS_MATHEVAL 1" >>confdefs.h
-
- else
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable __PLUMED_HAS_MATHEVAL" >&5
-$as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_MATHEVAL" >&2;}
- fi
-
-fi
if test $readdir_r == true ; then
found=ko
diff --git a/configure.ac b/configure.ac
index ee30c401e..5c8065f4b 100644
--- a/configure.ac
+++ b/configure.ac
@@ -191,7 +191,6 @@ PLUMED_CONFIG_ENABLE([external_lapack],[external-lapack],[search for external la
PLUMED_CONFIG_ENABLE([external_blas],[external-blas],[search for external blas],[yes])
PLUMED_CONFIG_ENABLE([molfile_plugins],[molfile-plugins],[use molfile_plugins],[yes])
PLUMED_CONFIG_ENABLE([external_molfile_plugins],[external-molfile-plugins],[search for external molfile_plugins],[yes])
-PLUMED_CONFIG_ENABLE([matheval],[matheval],[search for matheval],[yes])
PLUMED_CONFIG_ENABLE([zlib],[zlib],[search for zlib],[yes])
PLUMED_CONFIG_ENABLE([readdir_r],[readdir-r],[search for readdir_r (threadsafe)],[yes])
PLUMED_CONFIG_ENABLE([cregex],[cregex],[search for C regular expression],[yes])
@@ -549,9 +548,6 @@ fi
# when configuring with --disable-openmp
AC_OPENMP
-if test $matheval == true ; then
- PLUMED_CHECK_PACKAGE([matheval.h],[evaluator_create],[__PLUMED_HAS_MATHEVAL],[matheval])
-fi
if test $readdir_r == true ; then
PLUMED_CHECK_PACKAGE([dirent.h],[readdir_r],[__PLUMED_HAS_READDIR_R])
fi
diff --git a/src/core/CLToolMain.cpp b/src/core/CLToolMain.cpp
index cab6dc964..607a2d8fb 100644
--- a/src/core/CLToolMain.cpp
+++ b/src/core/CLToolMain.cpp
@@ -122,8 +122,6 @@ int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,Communicator& pc) {
} else if(a=="--has-mpi") {
if(Communicator::initialized()) return 0;
else return 1;
- } else if(a=="--has-matheval") {
- return (config::hasMatheval()?0:1);
} else if(a=="--has-cregex") {
return (config::hasCregex()?0:1);
} else if(a=="--has-dlopen") {
@@ -203,7 +201,6 @@ int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,Communicator& pc) {
" [help|-h|--help] : to print this help\n"
" [--is-installed] : fails if plumed is not installed\n"
" [--has-mpi] : fails if plumed is running without MPI\n"
- " [--has-matheval] : fails if plumed is compiled without matheval\n"
" [--has-dlopen] : fails if plumed is compiled without dlopen\n"
" [--load LIB] : loads a shared object (typically a plugin library)\n"
" [--standalone-executable] : tells plumed not to look for commands implemented as scripts\n"
diff --git a/src/function/Matheval.cpp b/src/function/Matheval.cpp
index a98b6bf48..64d112e14 100644
--- a/src/function/Matheval.cpp
+++ b/src/function/Matheval.cpp
@@ -22,10 +22,6 @@
#include "ActionRegister.h"
#include "Function.h"
-#ifdef __PLUMED_HAS_MATHEVAL
-#include <matheval.h>
-#endif
-
#include "lepton/Lepton.h"
using namespace std;
@@ -188,18 +184,14 @@ progression (S) and distance (Z) variables \cite perez2015atp.
class Matheval :
public Function
{
- const bool use_lepton;
lepton::CompiledExpression expression;
std::vector<lepton::CompiledExpression> expression_deriv;
- void* evaluator;
- vector<void*> evaluator_deriv;
vector<string> var;
string func;
vector<double> values;
vector<char*> names;
public:
explicit Matheval(const ActionOptions&);
- ~Matheval();
void calculate();
static void registerKeywords(Keywords& keys);
};
@@ -242,10 +234,7 @@ void Matheval::registerKeywords(Keywords& keys) {
Matheval::Matheval(const ActionOptions&ao):
Action(ao),
Function(ao),
- use_lepton(std::getenv("PLUMED_USE_LEPTON")),
expression_deriv(getNumberOfArguments()),
- evaluator(NULL),
- evaluator_deriv(getNumberOfArguments(),NULL),
values(getNumberOfArguments()),
names(getNumberOfArguments())
{
@@ -269,97 +258,42 @@ Matheval::Matheval(const ActionOptions&ao):
for(unsigned i=0; i<var.size(); i++) log.printf(" %s",var[i].c_str());
log.printf("\n");
- if(use_lepton) {
- log<<" WARNING: you are using lepton as a replacement for libmatheval\n";
- lepton::ParsedExpression pe=lepton::Parser::parse(func).optimize(leptonConstants);
- log<<" function as parsed by lepton: "<<pe<<"\n";
- expression=pe.createCompiledExpression();
- for(auto &p: expression.getVariables()) {
- if(std::find(var.begin(),var.end(),p)==var.end()) {
- error("variable " + p + " is not defined");
- }
- }
- log<<" derivatives as computed by lepton:\n";
- for(unsigned i=0; i<getNumberOfArguments(); i++) {
- lepton::ParsedExpression pe=lepton::Parser::parse(func).differentiate(var[i]).optimize(leptonConstants);
- log<<" "<<pe<<"\n";
- expression_deriv[i]=pe.createCompiledExpression();
+ lepton::ParsedExpression pe=lepton::Parser::parse(func).optimize(leptonConstants);
+ log<<" function as parsed by lepton: "<<pe<<"\n";
+ expression=pe.createCompiledExpression();
+ for(auto &p: expression.getVariables()) {
+ if(std::find(var.begin(),var.end(),p)==var.end()) {
+ error("variable " + p + " is not defined");
}
- } else {
-#ifdef __PLUMED_HAS_MATHEVAL
- evaluator=evaluator_create(const_cast<char*>(func.c_str()));
- if(!evaluator) error("There was some problem in parsing matheval formula "+func);
- char **check_names;
- int check_count;
- evaluator_get_variables(evaluator,&check_names,&check_count);
- if(check_count!=int(getNumberOfArguments())) {
- string sc;
- Tools::convert(check_count,sc);
- error("Your function string contains "+sc+" arguments. This should be equal to the number of ARGs");
- }
- for(unsigned i=0; i<getNumberOfArguments(); i++) {
- bool found=false;
- for(unsigned j=0; j<getNumberOfArguments(); j++) {
- if(var[i]==check_names[j])found=true;
- }
- if(!found)
- error("Variable "+var[i]+" cannot be found in your function string");
- }
- for(unsigned i=0; i<getNumberOfArguments(); i++)
- evaluator_deriv[i]=evaluator_derivative(evaluator,const_cast<char*>(var[i].c_str()));
- log.printf(" function as parsed by matheval: %s\n", evaluator_get_string(evaluator));
- log.printf(" derivatives as computed by matheval:\n");
- for(unsigned i=0; i<var.size(); i++) log.printf(" %s\n",evaluator_get_string(evaluator_deriv[i]));
-#else
- error("MATHEVAL not available, please export PLUMED_USE_LEPTON=yes");
-#endif
+ }
+ log<<" derivatives as computed by lepton:\n";
+ for(unsigned i=0; i<getNumberOfArguments(); i++) {
+ lepton::ParsedExpression pe=lepton::Parser::parse(func).differentiate(var[i]).optimize(leptonConstants);
+ log<<" "<<pe<<"\n";
+ expression_deriv[i]=pe.createCompiledExpression();
}
}
void Matheval::calculate() {
- if(use_lepton) {
- for(unsigned i=0; i<getNumberOfArguments(); i++) {
- try {
- expression.getVariableReference(var[i])=getArgument(i);
- } catch(PLMD::lepton::Exception& exc) {
+ for(unsigned i=0; i<getNumberOfArguments(); i++) {
+ try {
+ expression.getVariableReference(var[i])=getArgument(i);
+ } catch(PLMD::lepton::Exception& exc) {
// this is necessary since in some cases lepton things a variable is not present even though it is present
// e.g. func=0*x
- }
}
- setValue(expression.evaluate());
- for(unsigned i=0; i<getNumberOfArguments(); i++) {
- for(unsigned j=0; j<getNumberOfArguments(); j++) {
- try {
- expression_deriv[i].getVariableReference(var[j])=getArgument(j);
- } catch(PLMD::lepton::Exception& exc) {
+ }
+ setValue(expression.evaluate());
+ for(unsigned i=0; i<getNumberOfArguments(); i++) {
+ for(unsigned j=0; j<getNumberOfArguments(); j++) {
+ try {
+ expression_deriv[i].getVariableReference(var[j])=getArgument(j);
+ } catch(PLMD::lepton::Exception& exc) {
// this is necessary since in some cases lepton things a variable is not present even though it is present
// e.g. func=0*x
- }
}
- setDerivative(i,expression_deriv[i].evaluate());
}
- } else {
-#ifdef __PLUMED_HAS_MATHEVAL
- for(unsigned i=0; i<getNumberOfArguments(); i++) values[i]=getArgument(i);
- for(unsigned i=0; i<getNumberOfArguments(); i++) names[i]=const_cast<char*>(var[i].c_str());
- setValue(evaluator_evaluate(evaluator,names.size(),&names[0],&values[0]));
- for(unsigned i=0; i<getNumberOfArguments(); i++) {
- setDerivative(i,evaluator_evaluate(evaluator_deriv[i],names.size(),&names[0],&values[0]));
- }
-#else
- error("MATHEVAL not available, please export PLUMED_USE_LEPTON=yes");
-#endif
- }
-}
-
-Matheval::~Matheval() {
- if(evaluator) {
-#ifdef __PLUMED_HAS_MATHEVAL
- evaluator_destroy(evaluator);
- for(unsigned i=0; i<evaluator_deriv.size(); i++)evaluator_destroy(evaluator_deriv[i]);
-#else
- error("MATHEVAL not available, please export PLUMED_USE_LEPTON=yes");
-#endif
+ setDerivative(i,expression_deriv[i].evaluate());
}
}
diff --git a/src/tools/SwitchingFunction.cpp b/src/tools/SwitchingFunction.cpp
index a7df6332e..168d8452f 100644
--- a/src/tools/SwitchingFunction.cpp
+++ b/src/tools/SwitchingFunction.cpp
@@ -26,10 +26,6 @@
#include <vector>
#include <limits>
-#ifdef __PLUMED_HAS_MATHEVAL
-#include <matheval.h>
-#endif
-
using namespace std;
namespace PLMD {
@@ -253,7 +249,7 @@ void SwitchingFunction::set(const std::string & definition,std::string& errormsg
else if(name=="GAUSSIAN") type=gaussian;
else if(name=="CUBIC") type=cubic;
else if(name=="TANH") type=tanh;
- else if((name=="MATHEVAL" || name=="CUSTOM") && std::getenv("PLUMED_USE_LEPTON")) {
+ else if((name=="MATHEVAL" || name=="CUSTOM")) {
type=leptontype;
std::string func;
Tools::parse(data,"FUNC",func);
@@ -265,34 +261,6 @@ void SwitchingFunction::set(const std::string & definition,std::string& errormsg
expression_deriv.resize(OpenMP::getNumThreads());
for(auto & e : expression_deriv) e=ped.createCompiledExpression();
}
-#ifdef __PLUMED_HAS_MATHEVAL
- else if(name=="MATHEVAL" || name=="CUSTOM") {
- type=matheval;
- std::string func;
- Tools::parse(data,"FUNC",func);
- const unsigned nt=OpenMP::getNumThreads();
- plumed_assert(nt>0);
- evaluator.resize(nt);
- for(unsigned i=0; i<nt; i++) {
- evaluator[i]=evaluator_create(const_cast<char*>(func.c_str()));
- }
- char **check_names;
- int check_count;
- evaluator_get_variables(evaluator[0],&check_names,&check_count);
- if(check_count!=1) {
- errormsg="wrong number of arguments in MATHEVAL switching function";
- return;
- }
- if(std::string(check_names[0])!="x") {
- errormsg ="argument should be named 'x'";
- return;
- }
- evaluator_deriv.resize(nt);
- for(unsigned i=0; i<nt; i++) {
- evaluator_deriv[i]=evaluator_derivative(evaluator[i],const_cast<char*>("x"));
- }
- }
-#endif
else errormsg="cannot understand switching function type '"+name+"'";
if( !data.empty() ) {
errormsg="found the following rogue keywords in switching function input : ";
@@ -327,10 +295,6 @@ std::string SwitchingFunction::description() const {
ostr<<"tanh";
} else if(type==leptontype) {
ostr<<"lepton";
-#ifdef __PLUMED_HAS_MATHEVAL
- } else if(type==matheval) {
- ostr<<"matheval";
-#endif
} else {
plumed_merror("Unknown switching function type");
}
@@ -345,10 +309,6 @@ std::string SwitchingFunction::description() const {
ostr<<" dmax="<<dmax;
} else if(type==leptontype) {
ostr<<" func="<<lepton_func;
-#ifdef __PLUMED_HAS_MATHEVAL
- } else if(type==matheval) {
- ostr<<" func="<<evaluator_get_string(evaluator[0]);
-#endif
}
return ostr.str();
@@ -449,12 +409,6 @@ double SwitchingFunction::calculate(double distance,double&dfunc)const {
}
result=expression[t].evaluate();
dfunc=expression_deriv[t].evaluate();
-#ifdef __PLUMED_HAS_MATHEVAL
- } else if(type==matheval) {
- const unsigned it=OpenMP::getThreadNum();
- result=evaluator_evaluate_x(evaluator[it],rdist);
- dfunc=evaluator_evaluate_x(evaluator_deriv[it],rdist);
-#endif
} else plumed_merror("Unknown switching function type");
// this is for the chain rule:
dfunc*=invr0;
@@ -511,18 +465,6 @@ SwitchingFunction::SwitchingFunction(const SwitchingFunction&sf):
stretch(sf.stretch),
shift(sf.shift)
{
-#ifdef __PLUMED_HAS_MATHEVAL
- if(sf.evaluator.size()>0) {
- const unsigned nt=OpenMP::getNumThreads();
- plumed_assert(nt>0);
- evaluator.resize(nt);
- evaluator_deriv.resize(nt);
- for(unsigned i=0; i<nt; i++) {
- evaluator[i]=evaluator_create(evaluator_get_string(sf.evaluator[0]));
- evaluator_deriv[i]=evaluator_create(evaluator_get_string(sf.evaluator_deriv[0]));
- }
- }
-#endif
}
SwitchingFunction & SwitchingFunction::operator=(const SwitchingFunction& sf) {
@@ -545,18 +487,6 @@ SwitchingFunction & SwitchingFunction::operator=(const SwitchingFunction& sf) {
dmax_2=sf.dmax_2;
stretch=sf.stretch;
shift=sf.shift;
-#ifdef __PLUMED_HAS_MATHEVAL
- if(sf.evaluator.size()>0) {
- const unsigned nt=OpenMP::getNumThreads();
- plumed_assert(nt>0);
- evaluator.resize(nt);
- evaluator_deriv.resize(nt);
- for(unsigned i=0; i<nt; i++) {
- evaluator[i]=evaluator_create(evaluator_get_string(sf.evaluator[0]));
- evaluator_deriv[i]=evaluator_create(evaluator_get_string(sf.evaluator_deriv[0]));
- }
- }
-#endif
return *this;
}
@@ -596,13 +526,6 @@ double SwitchingFunction::get_dmax2() const {
return dmax_2;
}
-SwitchingFunction::~SwitchingFunction() {
-#ifdef __PLUMED_HAS_MATHEVAL
- for(unsigned i=0; i<evaluator.size(); i++) evaluator_destroy(evaluator[i]);
- for(unsigned i=0; i<evaluator_deriv.size(); i++) evaluator_destroy(evaluator_deriv[i]);
-#endif
-}
-
}
diff --git a/src/tools/SwitchingFunction.h b/src/tools/SwitchingFunction.h
index 65c90e711..1536b786e 100644
--- a/src/tools/SwitchingFunction.h
+++ b/src/tools/SwitchingFunction.h
@@ -75,20 +75,10 @@ class SwitchingFunction {
/// Lepton expression for derivative
/// \warning Since lepton::CompiledExpression is mutable, a vector is necessary for multithreading!
std::vector<lepton::CompiledExpression> expression_deriv;
-/// Evaluator for matheval:
-/// \warning Since evaluator is not thread safe, we should create one
-/// evaluator per thread.
- std::vector<void*> evaluator;
-/// Evaluator for matheval:
-/// \warning Since evaluator is not thread safe, we should create one
-/// evaluator per thread.
- std::vector<void*> evaluator_deriv;
public:
static void registerKeywords( Keywords& keys );
/// Constructor
SwitchingFunction();
-/// Destructor
- ~SwitchingFunction();
/// Copy constructor
SwitchingFunction(const SwitchingFunction&);
/// Assignment operator
--
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