From fc11a5d30bb8b4577c0d3010a1dfd17e84a5d559 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Fri, 21 Sep 2012 17:48:31 +0200
Subject: [PATCH] Transformed LOAD & INCLUDE into actions
This allows proper documentation to be written.
I added a regtest for INCLUDE but not one for LOAD,
as dynamic loading could not be available
---
developer-doc/Doc.txt | 4 +-
regtest/rt3/dd | 4 ++
regtest/rt3/plumed.dat | 4 +-
src/GenericInclude.cpp | 92 ++++++++++++++++++++++++++++++++++++++++
src/PlumedMain.cpp | 13 ++----
src/PlumedMain.h | 2 +-
src/SetupLoad.cpp | 75 ++++++++++++++++++++++++++++++++
test/simplemd/plumed.dat | 3 +-
user-doc/Intro.txt | 14 +++---
9 files changed, 186 insertions(+), 25 deletions(-)
create mode 100644 regtest/rt3/dd
create mode 100644 src/GenericInclude.cpp
create mode 100644 src/SetupLoad.cpp
diff --git a/developer-doc/Doc.txt b/developer-doc/Doc.txt
index f4cf3d27a..a865a55cf 100644
--- a/developer-doc/Doc.txt
+++ b/developer-doc/Doc.txt
@@ -145,11 +145,11 @@ RESTRAINT ARG=dist AT=1.2 KAPPA=1.0 STRIDE=2
\endverbatim
- It is possible to include other files:
\verbatim
-INCLUDE anotherplumed.dat
+INCLUDE FILE=anotherplumed.dat
\endverbatim
- It is possible to load shared libraries implementing new CVs and methods:
\verbatim
-LOAD share-object.so
+LOAD FILE=share-object.so
\endverbatim
\section Install Install
diff --git a/regtest/rt3/dd b/regtest/rt3/dd
new file mode 100644
index 000000000..02f00c6a5
--- /dev/null
+++ b/regtest/rt3/dd
@@ -0,0 +1,4 @@
+d1: DISTANCE ATOMS={1 10}
+d2: DISTANCE ATOMS={c1 50}
+d3: DISTANCE ATOMS={50 c2}
+
diff --git a/regtest/rt3/plumed.dat b/regtest/rt3/plumed.dat
index fc31293ad..138f2abb5 100644
--- a/regtest/rt3/plumed.dat
+++ b/regtest/rt3/plumed.dat
@@ -7,9 +7,7 @@ g2: ...
c1: COM ATOMS={g1}
c2: COM ATOMS=g2
-d1: DISTANCE ATOMS={1 10}
-d2: DISTANCE ATOMS={c1 50}
-d3: DISTANCE ATOMS={50 c2}
+INCLUDE FILE=dd
RESTRAINT ARG=d2 AT=9 KAPPA=0.003
diff --git a/src/GenericInclude.cpp b/src/GenericInclude.cpp
new file mode 100644
index 000000000..4986a4758
--- /dev/null
+++ b/src/GenericInclude.cpp
@@ -0,0 +1,92 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ 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 "Action.h"
+#include "ActionRegister.h"
+#include "PlumedMain.h"
+#include "PlumedException.h"
+
+using namespace std;
+
+namespace PLMD{
+
+//+PLUMEDOC GENERIC INCLUDE
+/*
+Includes an external input file, similar to "#include" in C preprocessor.
+
+Useful to split very large plumed.dat files.
+
+\par Examples
+This input
+\verbatim
+c1: COM ATOMS=1-100
+c2: COM ATOMS=101-202
+d: DISTANCE ARG=c1,c2
+PRINT ARG=d
+\endverbatim
+
+can be replaced with
+\verbatim
+INCLUDE FILE=pippo.dat
+d: DISTANCE ARG=c1,c2
+PRINT ARG=d
+\endverbatim
+
+where the content of file pippo.dat is
+\verbatim
+c1: COM ATOMS=1-100
+c2: COM ATOMS=101-202
+\endverbatim
+
+(see also \ref COM, \ref DISTANCE, and \ref PRINT).
+
+*/
+//+ENDPLUMEDOC
+
+class GenericInclude :
+ public Action
+{
+public:
+ static void registerKeywords( Keywords& keys );
+ GenericInclude(const ActionOptions&ao);
+ void calculate(){};
+ void apply(){};
+};
+
+PLUMED_REGISTER_ACTION(GenericInclude,"INCLUDE")
+
+void GenericInclude::registerKeywords( Keywords& keys ){
+ Action::registerKeywords(keys);
+ keys.add("compulsory","FILE","-","file to be included");
+}
+
+GenericInclude::GenericInclude(const ActionOptions&ao):
+Action(ao)
+{
+ std::string f;
+ parse("FILE",f);
+ checkRead();
+ plumed_assert(f!="-");
+ plumed.readInputFile(f);
+}
+
+}
+
diff --git a/src/PlumedMain.cpp b/src/PlumedMain.cpp
index 9317d4909..cab8a3846 100644
--- a/src/PlumedMain.cpp
+++ b/src/PlumedMain.cpp
@@ -371,7 +371,6 @@ void PlumedMain::readInputFile(std::string str){
while(Tools::getParsedLine(ifile,words)){
if(words.empty())continue;
else if(words[0]=="ENDPLUMED") break;
- else if(words[0]=="LOAD") load(words);
else if(words[0]=="_SET_SUFFIX"){
plumed_assert(words.size()==2);
setSuffix(words[1]);
@@ -380,11 +379,6 @@ void PlumedMain::readInputFile(std::string str){
exchangePatterns.setFlag(exchangePatterns.RANDOM);
// I convert the seed to -seed because I think it is more general to use a positive seed in input
if(words.size()>2&&words[1]=="SEED") {int seed; Tools::convert(words[2],seed); exchangePatterns.setSeed(-seed); }
- }
- else if(words[0]=="INCLUDE"){
- plumed_assert(words.size()==2);
- readInputFile(words[1]);
- continue;
} else {
Tools::interpretLabel(words);
Action* action=actionRegister().create(ActionOptions(*this,words));
@@ -549,10 +543,9 @@ void PlumedMain::justApply(){
stopwatch.stop("5 Applying (backward loop)");
}
-void PlumedMain::load(std::vector<std::string> & words){
+void PlumedMain::load(const std::string& ss){
if(DLLoader::installed()){
- string s=words[1];
- plumed_assert(words.size()==2);
+ string s=ss;
size_t n=s.find_last_of(".");
string extension="";
string base=s;
@@ -571,7 +564,7 @@ void PlumedMain::load(std::vector<std::string> & words){
void *p=dlloader.load(s);
if(!p){
log<<"ERROR\n";
- log<<"I cannot load library "<<words[1].c_str()<<"\n";
+ log<<"I cannot load library "<<ss<<"\n";
log<<dlloader.error();
log<<"\n";
this->exit(1);
diff --git a/src/PlumedMain.h b/src/PlumedMain.h
index 48788c930..6494a4f64 100644
--- a/src/PlumedMain.h
+++ b/src/PlumedMain.h
@@ -220,7 +220,7 @@ public:
/// Stop the run
void exit(int c=0);
/// Load a shared library
- void load(std::vector<std::string> & words);
+ void load(const std::string&);
/// Get the suffix string
const std::string & getSuffix()const;
/// Set the suffix string
diff --git a/src/SetupLoad.cpp b/src/SetupLoad.cpp
new file mode 100644
index 000000000..0e4d27fb9
--- /dev/null
+++ b/src/SetupLoad.cpp
@@ -0,0 +1,75 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ 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 "ActionSetup.h"
+#include "ActionRegister.h"
+#include "PlumedMain.h"
+#include "PlumedException.h"
+
+using namespace std;
+
+namespace PLMD{
+
+//+PLUMEDOC GENERIC LOAD
+/*
+Loads a library, possibly defining new actions.
+
+It is available only
+on systems allowing for dynamic loading. It can also be fed with a cpp file,
+in which case the file is compiled first.
+
+\par Examples
+
+\verbatim
+LOAD FILE=extensions.so
+\endverbatim
+
+*/
+//+ENDPLUMEDOC
+
+class SetupLoad :
+ public virtual ActionSetup
+{
+public:
+ static void registerKeywords( Keywords& keys );
+ SetupLoad(const ActionOptions&ao);
+};
+
+PLUMED_REGISTER_ACTION(SetupLoad,"LOAD")
+
+void SetupLoad::registerKeywords( Keywords& keys ){
+ ActionSetup::registerKeywords(keys);
+ keys.add("compulsory","FILE","-","file to be loaded");
+}
+
+SetupLoad::SetupLoad(const ActionOptions&ao):
+Action(ao),
+ActionSetup(ao)
+{
+ std::string f;
+ parse("FILE",f);
+ checkRead();
+ plumed_assert(f!="-");
+ plumed.load(f);
+}
+
+}
+
diff --git a/test/simplemd/plumed.dat b/test/simplemd/plumed.dat
index 65730f06c..0df917abc 100644
--- a/test/simplemd/plumed.dat
+++ b/test/simplemd/plumed.dat
@@ -1,8 +1,7 @@
g1: GROUP ATOMS=1-10
c1: COM ATOMS=g1
-d1: DISTANCE ATOMS=1,10
-d2: DISTANCE ATOMS=c1,10
+INCLUDE FILE=aa
coord: COORDINATION GROUPA=g1 GROUPB=100-105 R_0=0.5
diff --git a/user-doc/Intro.txt b/user-doc/Intro.txt
index 3ddc696ce..58b187a2a 100644
--- a/user-doc/Intro.txt
+++ b/user-doc/Intro.txt
@@ -141,10 +141,10 @@ DISTANCE ...
\section includes Including other files in the plumed input
-If, for some reason, you want to spread your plumed input over a number of files you can use INCLUDE as shown below:
+If, for some reason, you want to spread your plumed input over a number of files you can use \ref INCLUDE as shown below:
\verbatim
-INCLUDE filename
+INCLUDE FILE=filename
\endverbatim
So, for example, a single "plumed.dat" file:
@@ -159,20 +159,20 @@ could be split up into two files as shown below:
\verbatim
DISTANCE ATOMS=0,1 LABEL=dist
-INCLUDE toBeIncluded.dat
+INCLUDE FILE=toBeIncluded.dat
\endverbatim
plus a "toBeIncluded.dat" file
\verbatim
RESTRAINT ARG=dist
\endverbatim
-However, when you do this it is important to recognise that INCLUDE is a real directive that is only resolved
+However, when you do this it is important to recognise that \ref INCLUDE is a real directive that is only resolved
after all the \ref comments have been stripped and the \ref ContinuationLines have been unrolled. This means it
is not possible to do things like:
\verbatim
# this is wrong:
-DISTANCE INCLUDE options.dat
+DISTANCE INCLUDE FILE=options.dat
RESTRAINT ARG=dist
\endverbatim
@@ -181,10 +181,10 @@ RESTRAINT ARG=dist
You can introduce new functionality into plumed by placing it directly into the src directory and recompiling the
plumed libraries. Alternatively, if you want to keep your code independent from the rest of plumed (perhaps
so you can release it independely - we won't be offended), then you can create your own dynamic library. To use this
-in conjuction with plumed you can then load it at runtime by using the LOAD keyword as shown below:
+in conjuction with plumed you can then load it at runtime by using the \ref LOAD keyword as shown below:
\verbatim
-LOAD library.so
+LOAD FILE=library.so
\endverbatim
N.B. If your system uses a different suffix for dynamic libraries (e.g. macs use .dylib) then PLUMED will try to
--
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