From 97c17413b856835429eef67373548dabdb9da6ce Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Thu, 15 Oct 2015 15:28:27 +0200
Subject: [PATCH] UPDATE_IF
Add a UPDATE_IF keyword. This keyword start a block
that is conditionally updated depending on the value
of its ARGuments.
Closes #38
---
src/core/PlumedMain.cpp | 4 +-
src/generic/UpdateIf.cpp | 157 +++++++++++++++++++++++++++++++++++++++
2 files changed, 160 insertions(+), 1 deletion(-)
create mode 100644 src/generic/UpdateIf.cpp
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index 68fbdc159..a9ab9f5fc 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -79,7 +79,6 @@ PlumedMain::PlumedMain():
log.setLinePrefix("PLUMED: ");
stopwatch.start();
stopwatch.pause();
- updateFlags.push(true);
word_map["setBox"]=SETBOX;
word_map["setPositions"]=SETPOSITIONS;
word_map["setMasses"]=SETMASSES;
@@ -697,11 +696,14 @@ void PlumedMain::justApply(){
if(detailedTimers) stopwatch.start("5C Update");
// update step (for statistics, etc)
+ updateFlags.push(true);
for(ActionSet::iterator p=actionSet.begin();p!=actionSet.end();++p){
(*p)->beforeUpdate();
if((*p)->isActive() && (*p)->checkUpdate() && updateFlagsTop()) (*p)->update();
}
+ while(!updateFlags.empty()) updateFlags.pop();
if(detailedTimers) stopwatch.stop("5C Update");
+ if(!updateFlags.empty()) plumed_merror("non matching changes in the update flags");
// Check that no action has told the calculation to stop
if(stopNow){
if(stopFlag) (*stopFlag)=1;
diff --git a/src/generic/UpdateIf.cpp b/src/generic/UpdateIf.cpp
new file mode 100644
index 000000000..8938265e4
--- /dev/null
+++ b/src/generic/UpdateIf.cpp
@@ -0,0 +1,157 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2011-2015 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.
+
+ 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/ActionPilot.h"
+#include "core/ActionWithArguments.h"
+#include "core/ActionRegister.h"
+#include "core/PlumedMain.h"
+
+using namespace std;
+
+namespace PLMD{
+namespace generic{
+
+//+PLUMEDOC ANALYSIS UPDATE_IF
+/*
+Conditional update of other actions.
+
+
+This action can be used to enable and disable the update step for the following actions
+depending on the value of its arguments. This allows for example to extract snapshots
+with value of some CVs in a given range.
+
+When called with MORE_THAN and/or LESS_THAN keywords, this action starts an if block.
+The block is executed if all the arguments are less than all the respective values
+in the LESS_THAN keyword (if present) and all the arguments are more than all the
+respective values
+in the MORE_THAN keyword (if present).
+
+When called with the END flag, this action ends the corresponding IF block.
+Notice that in this case one should also provide the ARG keyword. It is recommended to
+use the same ARG keyword that was used to begin the block, so as to make the input more readable.
+
+Of course, blocks can be nested at will.
+
+There are many potential usages for this keyword. One might e.g. decide to analyze some variable
+only when another variable is within a given range.
+
+\warning
+Notice that not all the possible usage make
+particular sense. For example, conditionally updating a \ref METAD keyword
+(that is: adding hills only if a variable is within a given range)
+can lead to unexpected results.
+
+\par Examples
+The following input instructs plumed dump all the snapshots where an atom is in touch with
+the solute.
+\verbatim
+solute: GROUP ATOMS=1-124
+coord: COORDINATION GROUPA=solute GROUPB=500 R_0=0.5
+
+UPDATE_IF ARG=coord LESS_THAN=0.5
+DUMPATOMS ATOMS=solute,500 FILE=output.xyz
+UPDATE_IF ARG=coord END
+\endverbatim
+(See also \ref GROUP, \ref COORDINATION, and \ref DUMPATOMS)
+
+*/
+//+ENDPLUMEDOC
+
+class UpdateIf:
+public ActionPilot,
+public ActionWithArguments
+{
+ std::vector<double> lower;
+ std::vector<double> upper;
+ bool on;
+ bool end;
+public:
+ void prepare();
+ void calculate();
+ void beforeUpdate();
+ explicit UpdateIf(const ActionOptions&);
+ static void registerKeywords(Keywords& keys);
+ void apply(){}
+ ~UpdateIf();
+};
+
+PLUMED_REGISTER_ACTION(UpdateIf,"UPDATE_IF")
+
+void UpdateIf::registerKeywords(Keywords& keys){
+ Action::registerKeywords(keys);
+ ActionPilot::registerKeywords(keys);
+ ActionWithArguments::registerKeywords(keys);
+ keys.use("ARG");
+ keys.add("compulsory","STRIDE","1","the frequency with which the quantities of interest should be output");
+ keys.addFlag("END",false,"end");
+ keys.add("optional","LESS_THAN","upper bound");
+ keys.add("optional","MORE_THAN","lower bound");
+}
+
+UpdateIf::UpdateIf(const ActionOptions&ao):
+Action(ao),
+ActionPilot(ao),
+ActionWithArguments(ao),
+on(false),
+end(false)
+{
+ parseFlag("END",end);
+ parseVector("LESS_THAN",upper);
+ parseVector("MORE_THAN",lower);
+ if(end && upper.size()!=0) error("END and LESS_THAN are not compatible");
+ if(end && lower.size()!=0) error("END and MORE_THAN are not compatible");
+ if(upper.size()==0) upper.assign(getNumberOfArguments(),+std::numeric_limits<double>::max());
+ if(lower.size()==0) lower.assign(getNumberOfArguments(),-std::numeric_limits<double>::max());
+ if(upper.size()!=getNumberOfArguments()) error("LESS_THAN should have the same size as ARG");
+ if(lower.size()!=getNumberOfArguments()) error("MORE_THAN should have the same size as ARG");
+ for(unsigned i=0;i<getNumberOfArguments();++i){
+ log<<" boundaries for argument "<<i<<" "<<lower[i]<<" "<<upper[i]<<"\n";
+ }
+ checkRead();
+}
+
+void UpdateIf::prepare(){
+ on=false;
+}
+
+void UpdateIf::calculate(){
+ on=true;
+ for(unsigned i=0;i<getNumberOfArguments();++i){
+ if(getArgument(i)>=upper[i] || getArgument(i)<=lower[i]) on=false;
+ }
+}
+
+void UpdateIf::beforeUpdate(){
+ if(end) plumed.updateFlagsPop();
+ else {
+ if(on) plumed.updateFlagsPush(plumed.updateFlagsTop());
+ else plumed.updateFlagsPush(false);
+ }
+}
+
+
+UpdateIf::~UpdateIf(){
+}
+
+}
+
+
+}
--
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