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Commit 2dcdc107 authored by Davide Branduardi's avatar Davide Branduardi
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first try with regexp for arguments

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src/core/ActionSet.cpp
+ 10
− 0
View file @ 2dcdc107
......@@ -48,5 +48,15 @@ std::string ActionSet::getLabelList() const{
return outlist;
}
std::vector<std::string> ActionSet::getLabelVector() const{
std::vector<std::string> outlist;
for(const_iterator p=begin();p!=end();++p){
outlist.push_back(dynamic_cast<Action*>(*p)->getLabel());
};
return outlist;
}
}
src/core/ActionSet.h
+ 2
− 0
View file @ 2dcdc107
......@@ -62,6 +62,8 @@ public:
T selectWithLabel(const std::string&s)const;
/// get the labels in the list of actions in form of a string (useful to debug)
std::string getLabelList() const;
/// get the labels in the form of a vector of strings
std::vector<std::string> getLabelVector() const;
};
/////
......
src/core/ActionWithArguments.cpp
+ 146
− 68
View file @ 2dcdc107
......@@ -24,6 +24,12 @@
#include "tools/PDB.h"
#include "PlumedMain.h"
#include "ActionSet.h"
#include <iostream>
#define CREGEX
#ifdef CREGEX
#include <cstring>
#include "regex.h"
#endif
using namespace std;
namespace PLMD{
......@@ -37,75 +43,147 @@ void ActionWithArguments::parseArgumentList(const std::string&key,std::vector<Va
}
void ActionWithArguments::interpretArgumentList(const std::vector<std::string>& c, std::vector<Value*>&arg){
for(unsigned i=0;i<c.size();i++){
std::size_t dot=c[i].find_first_of('.');
string a=c[i].substr(0,dot);
string name=c[i].substr(dot+1);
if(c[i].find(".")!=string::npos){ // if it contains a dot:
if(a=="*" && name=="*"){
// Take all values from all actions
std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
if( all.empty() ) error("your input file is not telling plumed to calculate anything");
for(unsigned j=0;j<all.size();j++){
for(int k=0;k<all[j]->getNumberOfComponents();++k) arg.push_back(all[j]->copyOutput(k));
}
} else if ( name=="*"){
// Take all the values from an action with a specific name
ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(a);
if(!action){
std::string str=" (hint! the actions in this ActionSet are: ";
str+=plumed.getActionSet().getLabelList()+")";
error("cannot find action named " + a + str);
}
for(int k=0;k<action->getNumberOfComponents();++k) arg.push_back(action->copyOutput(k));
} else if ( a=="*" ){
// Take components from all actions with a specific name
std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
if( all.empty() ) error("your input file is not telling plumed to calculate anything");
unsigned nval=0;
for(unsigned j=0;j<all.size();j++){
std::string flab; flab=all[j]->getLabel() + "." + name;
if( all[j]->exists(flab) ){ arg.push_back(all[j]->copyOutput(flab)); nval++; }
}
if(nval==0) error("found no actions with a component called " + name );
} else {
// Take values with a specific name
ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(a);
if(!action){
std::string str=" (hint! the actions in this ActionSet are: ";
str+=plumed.getActionSet().getLabelList()+")";
error("cannot find action named " + a +str);
}
if( !(action->exists(c[i])) ){
std::string str=" (hint! the components in this actions are: ";
str+=action->getComponentsList()+")";
error("action " + a + " has no component named " + name + str);
} ;
arg.push_back(action->copyOutput(c[i]));
}
} else { // if it doesn't contain a dot
if(c[i]=="*"){
// Take all values from all actions
std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
if( all.empty() ) error("your input file is not telling plumed to calculate anything");
for(unsigned j=0;j<all.size();j++){
for(int k=0;k<all[j]->getNumberOfComponents();++k) arg.push_back(all[j]->copyOutput(k));
}
} else {
ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(c[i]);
if(!action){
std::string str=" (hint! the actions in this ActionSet are: ";
str+=plumed.getActionSet().getLabelList()+")";
error("cannot find action named " + c[i] + str );
}
if( !(action->exists(c[i])) ){
std::string str=" (hint! the components in this actions are: ";
str+=action->getComponentsList()+")";
error("action " + c[i] + " has no component named " + c[i] +str);
};
arg.push_back(action->copyOutput(c[i]));
}
}
// is a regex? then just interpret it. The signal is ()
std::size_t found1 = c[i].find("(");
std::size_t found2 ;
if(found1!=std::string::npos){
found2=c[i].find(")",found1+1,1); // find it again
if(found2!=std::string::npos){
// start regex parsing
#ifdef CREGEX
// take the string enclosed in quotes and put in round brackets
std::string myregex=c[i].substr(found1,found2-found1+1);
log.printf(" Evaluating regexp for this action: %s \n",myregex.c_str());
int errcode;
regex_t *preg = (regex_t*)malloc(sizeof(regex_t)); // pointer to the regular expression
regmatch_t *pmatch;
if ((errcode=regcomp(preg, myregex.c_str() ,REG_EXTENDED|REG_NEWLINE))) { // compile the regular expression
char* errbuf;
size_t errbuf_size;
// one can check the errors asking to regerror
errbuf_size = regerror(errcode, preg, NULL, 0);
if (!(errbuf=(char*)malloc(errbuf_size))) {
plumed_merror("cannot allocate the buffer for error detection in regexp!");
};
regerror(errcode, preg, errbuf, errbuf_size);
error(errbuf);
}
plumed_massert(preg->re_nsub==1,"I can parse with only one subexpression");
pmatch = (regmatch_t*)malloc(sizeof(regmatch_t)*preg->re_nsub);
// select all the actions that have a value
std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
if( all.empty() ) error("your input file is not telling plumed to calculate anything");
for(unsigned j=0;j<all.size();j++){
std::string thisargument=all[j]->getLabel();
std::vector<std::string> ss=all[j]->getComponentsVector();
for(unsigned k=0;k<ss.size();++k){
thisargument=ss[k];
unsigned ll=strlen(ss[k].c_str())+1;
char str[ll];strcpy(str,ss[k].c_str());
char *ppstr=str;
if(!regexec(preg, ppstr , preg->re_nsub, pmatch, 0)) {
log.printf(" Something matched with \"%s\" : ",ss[k].c_str());
do {
if (pmatch[0].rm_so != -1) { /* The regex is matching part of a string */
char *submatch;
size_t matchlen = pmatch[0].rm_eo - pmatch[0].rm_so;
submatch = (char*)malloc(matchlen+1);
strncpy(submatch, ppstr+pmatch[0].rm_so, matchlen+1);
submatch[matchlen]='\0';
log.printf(" subpattern %s\n", submatch);
// this is the match: try to see if it is a valid action
std::string putativeVal(submatch);
if( all[j]->exists(putativeVal) ){
arg.push_back(all[j]->copyOutput(putativeVal));
log.printf(" Action %s added! \n",putativeVal.c_str());
}
free(submatch);
};
ppstr += pmatch[0].rm_eo; /* Restart from last match */
} while(!regexec(preg,ppstr,preg->re_nsub,pmatch,0));
}
}
};
regfree(preg);
free(pmatch);
#else
plumed_merror("Regexp support not compiled!");
#endif
}else{
plumed_merror("did you want to use regexp to input arguments? enclose it between two round braces (...) with no spaces!");
}
}else{
std::size_t dot=c[i].find_first_of('.');
string a=c[i].substr(0,dot);
string name=c[i].substr(dot+1);
if(c[i].find(".")!=string::npos){ // if it contains a dot:
if(a=="*" && name=="*"){
// Take all values from all actions
std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
if( all.empty() ) error("your input file is not telling plumed to calculate anything");
for(unsigned j=0;j<all.size();j++){
for(int k=0;k<all[j]->getNumberOfComponents();++k) arg.push_back(all[j]->copyOutput(k));
}
} else if ( name=="*"){
// Take all the values from an action with a specific name
ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(a);
if(!action){
std::string str=" (hint! the actions in this ActionSet are: ";
str+=plumed.getActionSet().getLabelList()+")";
error("cannot find action named " + a + str);
}
for(int k=0;k<action->getNumberOfComponents();++k) arg.push_back(action->copyOutput(k));
} else if ( a=="*" ){
// Take components from all actions with a specific name
std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
if( all.empty() ) error("your input file is not telling plumed to calculate anything");
unsigned nval=0;
for(unsigned j=0;j<all.size();j++){
std::string flab; flab=all[j]->getLabel() + "." + name;
if( all[j]->exists(flab) ){ arg.push_back(all[j]->copyOutput(flab)); nval++; }
}
if(nval==0) error("found no actions with a component called " + name );
} else {
// Take values with a specific name
ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(a);
if(!action){
std::string str=" (hint! the actions in this ActionSet are: ";
str+=plumed.getActionSet().getLabelList()+")";
error("cannot find action named " + a +str);
}
if( !(action->exists(c[i])) ){
std::string str=" (hint! the components in this actions are: ";
str+=action->getComponentsList()+")";
error("action " + a + " has no component named " + name + str);
} ;
arg.push_back(action->copyOutput(c[i]));
}
} else { // if it doesn't contain a dot
if(c[i]=="*"){
// Take all values from all actions
std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
if( all.empty() ) error("your input file is not telling plumed to calculate anything");
for(unsigned j=0;j<all.size();j++){
for(int k=0;k<all[j]->getNumberOfComponents();++k) arg.push_back(all[j]->copyOutput(k));
}
} else {
ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(c[i]);
if(!action){
std::string str=" (hint! the actions in this ActionSet are: ";
str+=plumed.getActionSet().getLabelList()+")";
error("cannot find action named " + c[i] + str );
}
if( !(action->exists(c[i])) ){
std::string str=" (hint! the components in this actions are: ";
str+=action->getComponentsList()+")";
error("action " + c[i] + " has no component named " + c[i] +str);
};
arg.push_back(action->copyOutput(c[i]));
}
}
}
}
}
......
src/core/ActionWithValue.cpp
+ 10
− 1
View file @ 2dcdc107
......@@ -142,13 +142,22 @@ int ActionWithValue::getComponent( const std::string& name ) const {
std::string ActionWithValue::getComponentsList( ) const {
std::string complist;
plumed_massert( !exists( getLabel() ), "You should not be calling this routine if you are using a value");
//plumed_massert( !exists( getLabel() ), "You should not be calling this routine if you are using a value");
for(unsigned i=0;i<values.size();++i){
complist+=values[i]->name+" ";
}
return complist;
}
std::vector<std::string> ActionWithValue::getComponentsVector( ) const {
std::vector<std::string> complist;
//plumed_massert( !exists( getLabel() ), "You should not be calling this routine if you are using a value");
for(unsigned i=0;i<values.size();++i){
complist.push_back(values[i]->name);
}
return complist;
}
void ActionWithValue::componentIsNotPeriodic( const std::string& name ){
int kk=getComponent(name);
values[kk]->min=0; values[kk]->max=0;
......
src/core/ActionWithValue.h
+ 2
− 0
View file @ 2dcdc107
......@@ -134,6 +134,8 @@ public:
Value* copyOutput( const unsigned& n ) const;
/// get a string that contains all the available components
std::string getComponentsList( ) const ;
/// get a vector that contains the label for all the components
std::vector<std::string> getComponentsVector( ) const ;
// -- Routines for everything else -- //
......
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