From 5e6e6d6022c50624325b162bed67e4a59ff23d8a Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Wed, 12 Dec 2012 15:07:44 +0100
Subject: [PATCH] Moving setup actions in a separate dir
Since the SetupMolInfo action is used by other ones, I left it
in core/. It is however registered in setup/, so that it can be excluded
disabling that module. Moreover, I added a method so as to remove
a friend statement in PlumedMain
---
src/core/PlumedMain.h | 5 ++-
src/core/SetupMolInfo.cpp | 7 +++-
src/setup/.gitignore | 9 +++++
src/setup/ActionSetup.h | 25 +++++++++++++
src/{core/SetupLoad.cpp => setup/Load.cpp} | 18 +++++----
src/setup/Makefile | 5 +++
src/setup/MolInfo.cpp | 37 +++++++++++++++++++
.../SetupRestart.cpp => setup/Restart.cpp} | 22 ++++++-----
src/{core/SetupUnits.cpp => setup/Units.cpp} | 22 ++++++-----
src/setup/module.type | 1 +
10 files changed, 120 insertions(+), 31 deletions(-)
create mode 100644 src/setup/.gitignore
create mode 100644 src/setup/ActionSetup.h
rename src/{core/SetupLoad.cpp => setup/Load.cpp} (86%)
create mode 100644 src/setup/Makefile
create mode 100644 src/setup/MolInfo.cpp
rename src/{core/SetupRestart.cpp => setup/Restart.cpp} (84%)
rename src/{core/SetupUnits.cpp => setup/Units.cpp} (91%)
create mode 100644 src/setup/module.type
diff --git a/src/core/PlumedMain.h b/src/core/PlumedMain.h
index a99ccdd7f..540a6e098 100644
--- a/src/core/PlumedMain.h
+++ b/src/core/PlumedMain.h
@@ -71,8 +71,6 @@ It does not contain any static data.
class PlumedMain:
public WithCmd
{
-/// I restrict access to this class so that other classes cannot mistakely change the restart flag.
- friend class SetupRestart;
public:
/// Communicator for plumed.
/// Includes all the processors used by plumed.
@@ -137,6 +135,7 @@ public:
/// Flag to switch off virial calculation (for debug)
bool novirial;
+
/// Add a citation, returning a string containing the reference number, something like "[10]"
std::string cite(const std::string&);
@@ -246,6 +245,8 @@ public:
void fflush();
/// Check if restarting
bool getRestart()const;
+/// Set restart flag
+ void setRestart(bool f){restart=f;}
/// Stop the calculation cleanly (both the MD code and plumed)
void stop();
};
diff --git a/src/core/SetupMolInfo.cpp b/src/core/SetupMolInfo.cpp
index ee04b5cfd..9d4f4bc9d 100644
--- a/src/core/SetupMolInfo.cpp
+++ b/src/core/SetupMolInfo.cpp
@@ -61,7 +61,12 @@ ALPHARMSD BACKBONE=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL
//+ENDPLUMEDOC
-PLUMED_REGISTER_ACTION(SetupMolInfo,"MOLINFO")
+/*
+This action is defined in core/ as it is used by other actions.
+Anyway, it is registered in setup/, so that excluding that module from
+compilation will exclude it from plumed.
+*/
+
void SetupMolInfo::registerKeywords( Keywords& keys ){
ActionSetup::registerKeywords(keys);
diff --git a/src/setup/.gitignore b/src/setup/.gitignore
new file mode 100644
index 000000000..488855233
--- /dev/null
+++ b/src/setup/.gitignore
@@ -0,0 +1,9 @@
+/*
+# in this directory, only accept source, Makefile and README
+!/.gitignore
+!/*.c
+!/*.cpp
+!/*.h
+!/Makefile
+!/README
+!/module.type
diff --git a/src/setup/ActionSetup.h b/src/setup/ActionSetup.h
new file mode 100644
index 000000000..25d050ed6
--- /dev/null
+++ b/src/setup/ActionSetup.h
@@ -0,0 +1,25 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 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/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_setup_ActionSetup_h
+#define __PLUMED_setup_ActionSetup_h
+#include "core/ActionSetup.h"
+#endif
diff --git a/src/core/SetupLoad.cpp b/src/setup/Load.cpp
similarity index 86%
rename from src/core/SetupLoad.cpp
rename to src/setup/Load.cpp
index 28d160d7f..da4f2de98 100644
--- a/src/core/SetupLoad.cpp
+++ b/src/setup/Load.cpp
@@ -19,14 +19,15 @@
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 "core/ActionSetup.h"
+#include "core/ActionRegister.h"
+#include "core/PlumedMain.h"
#include "tools/PlumedException.h"
using namespace std;
namespace PLMD{
+namespace setup{
//+PLUMEDOC GENERIC LOAD
/*
@@ -45,22 +46,22 @@ LOAD FILE=extensions.so
*/
//+ENDPLUMEDOC
-class SetupLoad :
+class Load :
public virtual ActionSetup
{
public:
static void registerKeywords( Keywords& keys );
- SetupLoad(const ActionOptions&ao);
+ Load(const ActionOptions&ao);
};
-PLUMED_REGISTER_ACTION(SetupLoad,"LOAD")
+PLUMED_REGISTER_ACTION(Load,"LOAD")
-void SetupLoad::registerKeywords( Keywords& keys ){
+void Load::registerKeywords( Keywords& keys ){
ActionSetup::registerKeywords(keys);
keys.add("compulsory","FILE","-","file to be loaded");
}
-SetupLoad::SetupLoad(const ActionOptions&ao):
+Load::Load(const ActionOptions&ao):
Action(ao),
ActionSetup(ao)
{
@@ -72,4 +73,5 @@ ActionSetup(ao)
}
}
+}
diff --git a/src/setup/Makefile b/src/setup/Makefile
new file mode 100644
index 000000000..43a7e5620
--- /dev/null
+++ b/src/setup/Makefile
@@ -0,0 +1,5 @@
+USE=core tools
+BUILDAFTER=config
+
+#generic makefile
+include ../maketools/make.module
diff --git a/src/setup/MolInfo.cpp b/src/setup/MolInfo.cpp
new file mode 100644
index 000000000..57a7e6de7
--- /dev/null
+++ b/src/setup/MolInfo.cpp
@@ -0,0 +1,37 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 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 "core/ActionRegister.h"
+#include "core/SetupMolInfo.h"
+
+namespace PLMD{
+namespace setup{
+
+/*
+This action is defined in core/ as it is used by other actions.
+Anyway, it is registered here, so that excluding this module from
+compilation will exclude it from plumed.
+*/
+
+PLUMED_REGISTER_ACTION(SetupMolInfo,"MOLINFO")
+
+}
+}
diff --git a/src/core/SetupRestart.cpp b/src/setup/Restart.cpp
similarity index 84%
rename from src/core/SetupRestart.cpp
rename to src/setup/Restart.cpp
index 6e2d65cab..7b8f4e426 100644
--- a/src/core/SetupRestart.cpp
+++ b/src/setup/Restart.cpp
@@ -19,15 +19,16 @@
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 "Atoms.h"
+#include "core/ActionSetup.h"
+#include "core/ActionRegister.h"
+#include "core/PlumedMain.h"
+#include "core/Atoms.h"
#include "tools/PlumedException.h"
using namespace std;
namespace PLMD{
+namespace setup{
//+PLUMEDOC GENERIC RESTART
/*
@@ -59,26 +60,27 @@ This directive can have also other side effects, e.g. on \ref METAD
*/
//+ENDPLUMEDOC
-class SetupRestart :
+class Restart :
public virtual ActionSetup
{
public:
static void registerKeywords( Keywords& keys );
- SetupRestart(const ActionOptions&ao);
+ Restart(const ActionOptions&ao);
};
-PLUMED_REGISTER_ACTION(SetupRestart,"RESTART")
+PLUMED_REGISTER_ACTION(Restart,"RESTART")
-void SetupRestart::registerKeywords( Keywords& keys ){
+void Restart::registerKeywords( Keywords& keys ){
ActionSetup::registerKeywords(keys);
}
-SetupRestart::SetupRestart(const ActionOptions&ao):
+Restart::Restart(const ActionOptions&ao):
Action(ao),
ActionSetup(ao)
{
- plumed.restart=true;
+ plumed.setRestart(true);
log<<"Restarting simulation: files will be appended\n";
}
}
+}
diff --git a/src/core/SetupUnits.cpp b/src/setup/Units.cpp
similarity index 91%
rename from src/core/SetupUnits.cpp
rename to src/setup/Units.cpp
index b834063eb..35683e339 100644
--- a/src/core/SetupUnits.cpp
+++ b/src/setup/Units.cpp
@@ -19,15 +19,16 @@
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 "Atoms.h"
+#include "core/ActionSetup.h"
+#include "core/ActionRegister.h"
+#include "core/PlumedMain.h"
+#include "core/Atoms.h"
#include "tools/PlumedException.h"
using namespace std;
namespace PLMD{
+namespace setup{
//+PLUMEDOC GENERIC UNITS
/*
@@ -51,17 +52,17 @@ UNITS LENGTH=nm TIME=0.001
*/
//+ENDPLUMEDOC
-class SetupUnits :
+class Units :
public virtual ActionSetup
{
public:
static void registerKeywords( Keywords& keys );
- SetupUnits(const ActionOptions&ao);
+ Units(const ActionOptions&ao);
};
-PLUMED_REGISTER_ACTION(SetupUnits,"UNITS")
+PLUMED_REGISTER_ACTION(Units,"UNITS")
-void SetupUnits::registerKeywords( Keywords& keys ){
+void Units::registerKeywords( Keywords& keys ){
ActionSetup::registerKeywords(keys);
keys.add("optional","LENGTH","the units of lengths. Either specify a conversion factor from the default, nm, or A (for angstroms) or um");
keys.add("optional","ENERGY","the units of energy. Either specify a conversion factor from the default, kj/mol, or use j/mol or kcal/mol");
@@ -69,11 +70,11 @@ void SetupUnits::registerKeywords( Keywords& keys ){
keys.addFlag("NATURAL",false,"use natural units");
}
-SetupUnits::SetupUnits(const ActionOptions&ao):
+Units::Units(const ActionOptions&ao):
Action(ao),
ActionSetup(ao)
{
- Units u;
+ PLMD::Units u;
std::string s;
@@ -111,4 +112,5 @@ ActionSetup(ao)
}
}
+}
diff --git a/src/setup/module.type b/src/setup/module.type
new file mode 100644
index 000000000..fc25731b6
--- /dev/null
+++ b/src/setup/module.type
@@ -0,0 +1 @@
+default-on
--
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