From a7ed0531b30c0a1ed380598ca10ce9117666686a Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Mon, 29 May 2017 15:36:26 +0200
Subject: [PATCH] Implemented ENDPLUMED action
Fixes #236
---
src/core/PlumedMain.cpp | 5 ++-
src/core/PlumedMain.h | 11 +++++
src/generic/EndPlumed.cpp | 82 ++++++++++++++++++++++++++++++++++++++
user-doc/Miscelaneous.md | 2 +-
user-doc/plumed-syntax.awk | 6 +++
5 files changed, 103 insertions(+), 3 deletions(-)
create mode 100644 src/generic/EndPlumed.cpp
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index 0c5ee1415..c5066b457 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -73,6 +73,7 @@ PlumedMain::PlumedMain():
citations(*new Citations),
step(0),
active(false),
+ endPlumed(false),
atoms(*new Atoms(*this)),
actionSet(*new ActionSet(*this)),
bias(0.0),
@@ -512,7 +513,8 @@ void PlumedMain::readInputFile(std::string str) {
ifile.open(str);
ifile.allowNoEOL();
std::vector<std::string> words;
- while(Tools::getParsedLine(ifile,words) && words[0]!="ENDPLUMED") readInputWords(words);
+ while(Tools::getParsedLine(ifile,words) && !endPlumed) readInputWords(words);
+ endPlumed=false;
log.printf("END FILE: %s\n",str.c_str());
log.flush();
@@ -535,7 +537,6 @@ void PlumedMain::readInputLine(const std::string & str) {
void PlumedMain::readInputWords(const std::vector<std::string> & words) {
plumed_assert(initialized);
if(words.empty())return;
- else if(words[0]=="ENDPLUMED") return;
else if(words[0]=="_SET_SUFFIX") {
plumed_assert(words.size()==2);
setSuffix(words[1]);
diff --git a/src/core/PlumedMain.h b/src/core/PlumedMain.h
index ad2662844..64fda6f07 100644
--- a/src/core/PlumedMain.h
+++ b/src/core/PlumedMain.h
@@ -104,6 +104,10 @@ private:
/// Name of the input file
std::string plumedDat;
+/// End of input file.
+/// Set to true to terminate reading
+ bool endPlumed;
+
/// Object containing information about atoms (such as positions,...).
Atoms& atoms; // atomic coordinates
@@ -330,6 +334,8 @@ public:
void updateFlagsPop();
/// Get top of update flags
bool updateFlagsTop();
+/// Set end of input file
+ void setEndPlumed();
};
/////
@@ -395,6 +401,11 @@ bool PlumedMain::updateFlagsTop() {
return updateFlags.top();
}
+inline
+void PlumedMain::setEndPlumed() {
+ endPlumed=true;
+}
+
}
#endif
diff --git a/src/generic/EndPlumed.cpp b/src/generic/EndPlumed.cpp
new file mode 100644
index 000000000..fd8c57ff5
--- /dev/null
+++ b/src/generic/EndPlumed.cpp
@@ -0,0 +1,82 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2011-2017 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "core/ActionRegister.h"
+#include "core/ActionSet.h"
+#include "core/PlumedMain.h"
+
+using namespace std;
+
+namespace PLMD {
+namespace generic {
+
+//+PLUMEDOC GENERIC ENDPLUMED
+/*
+Terminate plumed input.
+
+Can be used to effectively comment out the rest of the input file.
+It can be useful to quickly ignore part of a long input file. However,
+one should keep in mind that when opening the file it might be difficult to
+find where the commented out part begins. Regular comments (with `#`) are
+usually easier to read. Notice that \ref VimSyntax "VIM syntax" should be able
+to detect this command and properly mark the rest of the file as a comment,
+although since vim doesn't parse the whole file it might fail in doing so for long
+input files.
+
+\par Examples
+
+\plumedfile
+d: DISTANCE ATOMS=1,10
+PRINT ARG=d FILE=COLVAR STRIDE=10
+ENDPLUMED
+commands here are ignored
+PRINT ARG=d FILE=COLVAR STRIDE=1
+\endplumedfile
+
+*/
+//+ENDPLUMEDOC
+class EndPlumed:
+ public Action
+{
+public:
+ explicit EndPlumed(const ActionOptions&ao);
+/// Register all the relevant keywords for the action
+ static void registerKeywords( Keywords& keys );
+ void calculate() {}
+ void apply() {}
+};
+
+PLUMED_REGISTER_ACTION(EndPlumed,"ENDPLUMED")
+
+void EndPlumed::registerKeywords( Keywords& keys ) {
+ Action::registerKeywords( keys );
+}
+
+EndPlumed::EndPlumed(const ActionOptions&ao):
+ Action(ao)
+{
+ checkRead();
+ plumed.setEndPlumed();
+}
+
+}
+}
+
diff --git a/user-doc/Miscelaneous.md b/user-doc/Miscelaneous.md
index dc706f0fa..dfc8e1bcb 100644
--- a/user-doc/Miscelaneous.md
+++ b/user-doc/Miscelaneous.md
@@ -25,7 +25,7 @@ UPPER_WALLS ARG=d1 AT=3.0 KAPPA=3.0 LABEL=Snout # In this same interlude it doth
\endplumedfile
(see \ref DISTANCE and \ref UPPER_WALLS)
-An alternative to including comments in this way is to use line starting ENDPLUMED. Everything in the PLUMED input after this
+An alternative to including comments in this way is to use the command \subpage ENDPLUMED. Everything in the PLUMED input after this
keyword will be ignored.
\page ContinuationLines Continuation lines
diff --git a/user-doc/plumed-syntax.awk b/user-doc/plumed-syntax.awk
index 7d261bca4..116b5e70d 100755
--- a/user-doc/plumed-syntax.awk
+++ b/user-doc/plumed-syntax.awk
@@ -1,6 +1,7 @@
{
if(match($0,"BEGIN_PLUMED_FILE")){
inside=1;
+ endplumed=0;
sub("BEGIN_PLUMED_FILE","");
print;
next;
@@ -18,6 +19,7 @@
# DRAFT LINK TO DOC:
copy=$0
sub("#.*","",copy);
+ if(endplumed) copy="";
nw=split(copy,words);
if(match(words[1],".*:$")){
action=words[2];
@@ -25,6 +27,9 @@
action=words[1];
}
if(action=="__FILL__") action=""
+ if(action=="ENDPLUMED"){
+ endplumed=1;
+ }
actionx="";
for(i=1;i<=length(action);i++){
letter=substr(action,i,1);
@@ -50,5 +55,6 @@
# sub("#","<span style=\"color:blue\">#");
# if(match($0,"span style=")) $0=$0 "</span>";
sub("#.*$","<span style=\"color:blue\">&</span>");
+ if(endplumed) sub("^.*$","<span style=\"color:blue\">&</span>");
print
}
--
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