From f272f0d14e85cc65f8771386e85e6ab20af7da73 Mon Sep 17 00:00:00 2001
From: davidebr <davide.branduardi@gmail.com>
Date: Thu, 23 Feb 2012 16:45:04 +0100
Subject: [PATCH] Projections and propagation of gradients
---
regtest/rt18/COLVAR.reference | 6 +
regtest/rt18/Makefile | 13 +
regtest/rt18/config | 3 +
regtest/rt18/forces.reference | 550 +++++++++++++++++++++++++++++
regtest/rt18/plumed.dat | 24 ++
regtest/rt18/projections.reference | 4 +
regtest/rt18/trajectory.xyz | 550 +++++++++++++++++++++++++++++
src/Action.cpp | 12 +
src/Action.h | 22 +-
src/ActionAtomistic.h | 2 +-
src/ActionWithArguments.cpp | 9 +
src/ActionWithArguments.h | 2 +
src/ActionWithValue.cpp | 5 +
src/ActionWithValue.h | 2 +
src/ActionWithVirtualAtom.cpp | 26 ++
src/ActionWithVirtualAtom.h | 9 +
src/GenericDumpProjections.cpp | 91 +++++
src/PlumedMain.cpp | 10 +-
src/Value.cpp | 49 +++
src/Value.h | 6 +
20 files changed, 1392 insertions(+), 3 deletions(-)
create mode 100644 regtest/rt18/COLVAR.reference
create mode 100644 regtest/rt18/Makefile
create mode 100644 regtest/rt18/config
create mode 100644 regtest/rt18/forces.reference
create mode 100644 regtest/rt18/plumed.dat
create mode 100644 regtest/rt18/projections.reference
create mode 100644 regtest/rt18/trajectory.xyz
create mode 100644 src/GenericDumpProjections.cpp
diff --git a/regtest/rt18/COLVAR.reference b/regtest/rt18/COLVAR.reference
new file mode 100644
index 000000000..d39bbbda2
--- /dev/null
+++ b/regtest/rt18/COLVAR.reference
@@ -0,0 +1,6 @@
+#! FIELDS time d1 d2 d3
+ 0.000000 1.163 2.690 1.304
+ 0.050000 1.131 2.726 1.218
+ 0.100000 1.098 2.779 1.170
+ 0.150000 1.080 2.800 1.191
+ 0.200000 1.087 2.788 1.221
diff --git a/regtest/rt18/Makefile b/regtest/rt18/Makefile
new file mode 100644
index 000000000..e243f28ec
--- /dev/null
+++ b/regtest/rt18/Makefile
@@ -0,0 +1,13 @@
+
+test:
+ ../scripts/run
+
+reset:
+ ../scripts/reset
+
+clean:
+ rm -fr tmp/ report.txt
+
+valgrind:
+ ../scripts/run --valgrind
+
diff --git a/regtest/rt18/config b/regtest/rt18/config
new file mode 100644
index 000000000..668c1ede7
--- /dev/null
+++ b/regtest/rt18/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
diff --git a/regtest/rt18/forces.reference b/regtest/rt18/forces.reference
new file mode 100644
index 000000000..0d521d984
--- /dev/null
+++ b/regtest/rt18/forces.reference
@@ -0,0 +1,550 @@
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+X 0.0000 0.0000 0.0000
+X 0.0000 0.0000 0.0000
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diff --git a/regtest/rt18/plumed.dat b/regtest/rt18/plumed.dat
new file mode 100644
index 000000000..8b422c9cf
--- /dev/null
+++ b/regtest/rt18/plumed.dat
@@ -0,0 +1,24 @@
+g1: GROUP ATOMS=1-10
+g2: GROUP ATOMS=30-40,5
+c2a: COM ATOMS=70
+c2b: COM ATOMS=71-79
+c1: COM ATOMS=g1
+c2: COM ATOMS=c2a,c2b
+
+d1: DISTANCE ATOMS=1,10
+d2: DISTANCE ATOMS=c1,50
+d3: DISTANCE ATOMS=50,c2
+
+RESTRAINT ARG=d2 AT=0.9 KAPPA=3.0
+DUMPPROJECTIONS ARG=d1,d3 FILE=projections STRIDE=20
+
+DEBUG logActivity
+
+PRINT ...
+ STRIDE=1
+ ARG=d1,d2,d3
+ FILE=COLVAR FMT=%6.3f
+... PRINT
+
+ENDPLUMED
+
diff --git a/regtest/rt18/projections.reference b/regtest/rt18/projections.reference
new file mode 100644
index 000000000..eb0a32970
--- /dev/null
+++ b/regtest/rt18/projections.reference
@@ -0,0 +1,4 @@
+#! FIELDS time d1-d1 d1-d3 d3-d1 d3-d3
+ 0.000000 2.0000000000 0.0000000000 0.0000000000 1.1000000000
+ 0.100000 2.0000000000 0.0000000000 0.0000000000 1.1000000000
+ 0.200000 2.0000000000 0.0000000000 0.0000000000 1.1000000000
diff --git a/regtest/rt18/trajectory.xyz b/regtest/rt18/trajectory.xyz
new file mode 100644
index 000000000..f3c9dd586
--- /dev/null
+++ b/regtest/rt18/trajectory.xyz
@@ -0,0 +1,550 @@
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+ Ar 3.39615360597383 1.06606421714045 4.15160907492794
+ Ar 3.39317315047633 1.74906165412885 3.829840222083043E-002
+ Ar 4.21494911633779 1.80203040880518 0.736983465230285
+ Ar 4.31016754071017 2.63869544682861 7.870451971871394E-002
+ Ar 3.39877116069656 2.49417514361512 0.895328581375493
+ Ar 3.43046483156166 1.72940805158736 1.84480612576827
+ Ar 4.18575172819875 1.73449608891478 2.70642857575136
+ Ar 4.17098587978233 2.44262911878011 1.68291782509776
+ Ar 3.38153229222238 2.47806724082894 2.59385052805114
+ Ar 3.27332287709101 1.90549856439275 3.44374420545942
+ Ar 4.21859711774123 1.76784920307225 4.42086154720453
+ Ar 4.20545854168167 2.46000291143715 3.48964674127964
+ Ar 3.28475820436697 2.57538134210400 4.36701459683137
+ Ar 3.39506433758779 3.26624750412182 4.107762344320081E-002
+ Ar 4.32622103735388 3.21482954005330 0.927977020564315
+ Ar 4.13412985645090 4.02325006679475 6.080895986874384E-002
+ Ar 3.29372086607892 4.23255420120987 1.04029427605013
+ Ar 3.49577371462389 3.35145578011939 1.55584747752986
+ Ar 4.19956823542160 3.37780135246845 2.41348593593863
+ Ar 4.12118864250303 4.21050970308083 1.68011405294024
+ Ar 3.29962417872968 4.38878323501144 2.36340382857920
+ Ar 3.28535095964371 3.21534338371035 3.39621591476258
+ Ar 4.30440692933406 3.24949161933914 4.22940851531796
+ Ar 4.14084086455829 3.87553484377385 3.29277241758537
+ Ar 3.41229836071068 4.09680820286438 4.19286599513161
diff --git a/src/Action.cpp b/src/Action.cpp
index ed4359683..f70314d98 100644
--- a/src/Action.cpp
+++ b/src/Action.cpp
@@ -112,6 +112,18 @@ void Action::activate(){
active=true;
}
+void Action::setOption(const std::string &s){
+// This overloads the action and activate some options
+ options.insert(s);
+ for(Dependencies::iterator p=after.begin();p!=after.end();p++) (*p)->setOption(s);
+};
+
+void Action::clearOptions(){
+// This overloads the action and activate some options
+ options.clear();
+};
+
+
void Action::clearDependencies(){
for(Dependencies::iterator p=after.begin();p!=after.end();p++){
(*p)->before.erase(this);
diff --git a/src/Action.h b/src/Action.h
index ecac916a8..9a5074033 100644
--- a/src/Action.h
+++ b/src/Action.h
@@ -60,7 +60,10 @@ private:
/// Switch to activate Action on this step.
bool active;
-protected:
+/// Option that you might have enabled
+ std::set<std::string> options;
+
+public:
/// Reference to main plumed object
PlumedMain& plumed;
@@ -165,18 +168,29 @@ public:
/// Set action to active
virtual void activate();
+///
+ virtual void setOption(const std::string &s);
+
+ virtual void clearOptions();
+
/// Set action to inactive
virtual void deactivate();
/// Check if action is active
bool isActive()const;
+/// Check if an option is on
+ bool isOptionOn(const std::string &s)const;
+
/// Return dependencies
const Dependencies & getDependencies()const{return after;}
/// Check if numerical derivatives should be performed
virtual bool checkNumericalDerivatives()const{return false;}
+/// Check if the action needs gradient
+ virtual bool checkNeedsGradients()const{return false;}
+
/// Perform calculation using numerical derivatives
virtual void calculateNumericalDerivatives();
@@ -282,6 +296,7 @@ bool Action::parseNumberedVector(const std::string&key, const int no, std::vecto
inline
void Action::deactivate(){
+ options.clear();
active=false;
}
@@ -290,6 +305,11 @@ bool Action::isActive()const{
return active;
}
+inline
+bool Action::isOptionOn(const std::string &s)const{
+ return options.count(s);
+}
+
}
#endif
diff --git a/src/ActionAtomistic.h b/src/ActionAtomistic.h
index 35af6dbde..e3803c8ff 100644
--- a/src/ActionAtomistic.h
+++ b/src/ActionAtomistic.h
@@ -34,7 +34,7 @@ class ActionAtomistic :
bool lockRequestAtoms; // forbid changes to request atoms
-protected:
+public:
/// Request an array of atoms.
/// This method is used to ask for a list of atoms. Atoms
/// should be asked for by number. If this routine is called
diff --git a/src/ActionWithArguments.cpp b/src/ActionWithArguments.cpp
index b501a1647..815a69688 100644
--- a/src/ActionWithArguments.cpp
+++ b/src/ActionWithArguments.cpp
@@ -102,6 +102,15 @@ void ActionWithArguments::calculateNumericalDerivatives(){
}
}
+double ActionWithArguments::getProjection(unsigned i,unsigned j)const{
+ plumed_massert(i<arguments.size()," making projections with an index which is too large");
+ plumed_massert(j<arguments.size()," making projections with an index which is too large");
+ const Value* v1=arguments[i];
+ const Value* v2=arguments[j];
+ return Value::projection(*v1,*v2);
+}
+
+
diff --git a/src/ActionWithArguments.h b/src/ActionWithArguments.h
index 23f9aa2a9..d97491daa 100644
--- a/src/ActionWithArguments.h
+++ b/src/ActionWithArguments.h
@@ -26,6 +26,8 @@ class ActionWithArguments:
protected:
ActionWithArguments(const ActionOptions&);
virtual ~ActionWithArguments(){};
+///
+ double getProjection(unsigned i,unsigned j)const;
public:
/// Registers the list of keywords
static void registerKeywords( Keywords& keys );
diff --git a/src/ActionWithValue.cpp b/src/ActionWithValue.cpp
index 6f7d2a950..4b22c1f1c 100644
--- a/src/ActionWithValue.cpp
+++ b/src/ActionWithValue.cpp
@@ -91,4 +91,9 @@ void ActionWithValue::clearDerivatives(){
for(unsigned i=0;i<values.size();i++) values[i]->clearDerivatives();
}
+void ActionWithValue::setGradientsIfNeeded(){
+ if(isOptionOn("GRADIENTS")) {
+ for(unsigned i=0;i<values.size();i++) values[i]->setGradients();
+ }
+}
diff --git a/src/ActionWithValue.h b/src/ActionWithValue.h
index 70a20185b..5c8f721ef 100644
--- a/src/ActionWithValue.h
+++ b/src/ActionWithValue.h
@@ -73,6 +73,8 @@ public:
void clearInputForces();
/// Clear the derivatives of values wrt parameters
void clearDerivatives();
+/// Calculate the gradients and store them for all the values (need for projections)
+ void setGradientsIfNeeded();
/// Set the value
void setValue(Value*,double);
/// Set the default value (the one without name)
diff --git a/src/ActionWithVirtualAtom.cpp b/src/ActionWithVirtualAtom.cpp
index 3b3a192ea..e7caf52c5 100644
--- a/src/ActionWithVirtualAtom.cpp
+++ b/src/ActionWithVirtualAtom.cpp
@@ -10,6 +10,7 @@ void ActionWithVirtualAtom::registerKeywords(Keywords& keys){
Action::registerKeywords(keys);
ActionAtomistic::registerKeywords(keys);
keys.add("atoms","ATOMS","the list of atoms which are involved the virtual atom's definition");
+ keys.addFlag("CALC_GRADIENTS", false, " calculate the vector of gradients");
}
ActionWithVirtualAtom::ActionWithVirtualAtom(const ActionOptions&ao):
@@ -35,4 +36,29 @@ void ActionWithVirtualAtom::requestAtoms(const std::vector<AtomNumber> & a){
derivatives.resize(a.size());
}
+void ActionWithVirtualAtom::setGradients(){
+ Atoms&atoms(plumed.getAtoms());
+ gradients.clear();
+ for(unsigned i=0;i<getNumberOfAtoms();i++){
+ AtomNumber an=getAbsoluteIndex(i);
+ // this case if the atom is a virtual one
+ if(atoms.isVirtualAtom(an.index())){
+ const ActionWithVirtualAtom* a=atoms.getVirtualAtomsAction(an.index());
+ for(std::map<AtomNumber,Tensor>::const_iterator p=a->gradients.begin();p!=a->gradients.end();++p){
+ gradients[(*p).first]+=matmul(derivatives[i],(*p).second);
+ }
+ // this case if the atom is a normal one
+ } else {
+ gradients[an]+=derivatives[i];
+ }
+ }
+}
+
+
+void ActionWithVirtualAtom::setGradientsIfNeeded(){
+ if(isOptionOn("GRADIENTS")) {
+ setGradients() ;
+ }
+}
+
}
diff --git a/src/ActionWithVirtualAtom.h b/src/ActionWithVirtualAtom.h
index 8d69c1a99..ee03aa593 100644
--- a/src/ActionWithVirtualAtom.h
+++ b/src/ActionWithVirtualAtom.h
@@ -23,6 +23,7 @@ class ActionWithVirtualAtom:
{
unsigned index;
std::vector<Tensor> derivatives;
+ std::map<AtomNumber,Tensor> gradients;
void apply();
protected:
/// Set position of the virtual atom
@@ -36,11 +37,14 @@ protected:
/// Set the derivatives of virtual atom coordinate wrt atoms on which it dependes
void setAtomsDerivatives(const std::vector<Tensor> &d);
public:
+ void setGradients();
+ const std::map<AtomNumber,Tensor> & getGradients()const;
/// Return the atom id of the corresponding virtual atom
AtomNumber getIndex()const;
ActionWithVirtualAtom(const ActionOptions&ao);
~ActionWithVirtualAtom();
static void registerKeywords(Keywords& keys);
+ void setGradientsIfNeeded();
};
inline
@@ -68,6 +72,11 @@ void ActionWithVirtualAtom::setAtomsDerivatives(const std::vector<Tensor> &d){
derivatives=d;
}
+inline
+const std::map<AtomNumber,Tensor> & ActionWithVirtualAtom::getGradients()const{
+ return gradients;
+}
+
}
#endif
diff --git a/src/GenericDumpProjections.cpp b/src/GenericDumpProjections.cpp
new file mode 100644
index 000000000..7abecfbe9
--- /dev/null
+++ b/src/GenericDumpProjections.cpp
@@ -0,0 +1,91 @@
+#include "ActionPilot.h"
+#include "ActionWithArguments.h"
+#include "ActionRegister.h"
+#include "PlumedCommunicator.h"
+#include <cassert>
+
+using namespace std;
+
+namespace PLMD{
+
+//+PLUMEDOC ANALYSIS DUMPPROJECTIONS
+/**
+Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).
+
+*/
+//+ENDPLUMEDOC
+
+class GenericDumpProjections :
+public ActionPilot,
+public ActionWithArguments
+{
+ string file;
+ string fmt;
+ FILE* fp;
+public:
+ void calculate(){};
+ GenericDumpProjections(const ActionOptions&);
+ static void registerKeywords(Keywords& keys);
+ void apply(){};
+ void update();
+ bool checkNeedsGradients()const{return true;}
+ ~GenericDumpProjections();
+};
+
+PLUMED_REGISTER_ACTION(GenericDumpProjections,"DUMPPROJECTIONS")
+
+void GenericDumpProjections::registerKeywords(Keywords& keys){
+ Action::registerKeywords(keys);
+ ActionPilot::registerKeywords(keys);
+ ActionWithArguments::registerKeywords(keys);
+ keys.add("compulsory","STRIDE","1","the frequency with which the derivatives should be output");
+ keys.add("compulsory","FILE","the name of the file on which to output the derivatives");
+ keys.add("compulsory","FMT","%15.10f","the format with which the derivatives should be output");
+}
+
+GenericDumpProjections::GenericDumpProjections(const ActionOptions&ao):
+Action(ao),
+ActionPilot(ao),
+ActionWithArguments(ao),
+fmt("%15.10f"),
+fp(NULL)
+{
+ parse("FILE",file);
+ assert(file.length()>0);
+ parse("FMT",fmt);
+ fmt=" "+fmt;
+ if(comm.Get_rank()==0){
+ fp=fopen(file.c_str(),"wa");
+ log.printf(" on file %s\n",file.c_str());
+ log.printf(" with format %s\n",fmt.c_str());
+ fprintf(fp,"%s","#! FIELDS time ");
+ const std::vector<Value*>& arguments(getArguments());
+ for(unsigned i=0;i<getNumberOfArguments();i++){
+ for(unsigned j=0;j<getNumberOfArguments();j++){
+ fprintf(fp," %s-%s",arguments[i]->getFullName().c_str(),arguments[j]->getFullName().c_str());
+ }
+ };
+ fprintf(fp,"%s","\n");
+ }
+ checkRead();
+}
+
+
+void GenericDumpProjections::update(){
+ if(comm.Get_rank()!=0)return;
+ fprintf(fp," %f",getTime());
+ for(unsigned i=0;i<getNumberOfArguments();i++){
+ for(unsigned j=0;j<getNumberOfArguments();j++){
+ fprintf(fp,fmt.c_str(),getProjection(i,j));
+ }
+ };
+ fprintf(fp,"\n");
+}
+
+GenericDumpProjections::~GenericDumpProjections(){
+ if(fp) fclose(fp);
+}
+
+}
+
+
diff --git a/src/PlumedMain.cpp b/src/PlumedMain.cpp
index 916c1410f..afda4e337 100644
--- a/src/PlumedMain.cpp
+++ b/src/PlumedMain.cpp
@@ -4,6 +4,7 @@
#include "ActionPilot.h"
#include "ActionWithValue.h"
#include "ActionAtomistic.h"
+#include "ActionWithVirtualAtom.h"
#include "Atoms.h"
#include <set>
#include "PlumedConfig.h"
@@ -381,7 +382,10 @@ void PlumedMain::prepareDependencies(){
//
// First switch off all actions
- for(ActionSet::iterator p=actionSet.begin();p!=actionSet.end();p++) (*p)->deactivate();
+ for(ActionSet::iterator p=actionSet.begin();p!=actionSet.end();p++){
+ (*p)->deactivate();
+ (*p)->clearOptions();
+ }
// for optimization, an "active" flag remains false if no action at all is active
active=false;
@@ -399,6 +403,7 @@ void PlumedMain::prepareDependencies(){
if(Colvar *c=dynamic_cast<Colvar*>(*p)) {
if(c->checkIsEnergy()) collectEnergy=true;
}
+ if((*p)->checkNeedsGradients()) (*p)->setOption("GRADIENTS");
}
}
atoms.setCollectEnergy(collectEnergy);
@@ -452,6 +457,9 @@ void PlumedMain::justCalculate(){
if(av)for(int i=0;i<av->getNumberOfValues();++i){
if(av->getValue(i)->getName()=="bias") bias+=av->getValue(i)->get();
}
+ if(av)av->setGradientsIfNeeded();
+ ActionWithVirtualAtom*avv=dynamic_cast<ActionWithVirtualAtom*>(*p);
+ if(avv)avv->setGradientsIfNeeded();
}
}
stopwatch.stop("4 Calculating (forward loop)");
diff --git a/src/Value.cpp b/src/Value.cpp
index ac93c6b2b..f3ea75151 100644
--- a/src/Value.cpp
+++ b/src/Value.cpp
@@ -1,6 +1,11 @@
#include "Value.h"
#include "ActionWithValue.h"
+#include "ActionAtomistic.h"
+#include "ActionWithArguments.h"
+#include "ActionWithVirtualAtom.h"
#include "PlumedException.h"
+#include "Atoms.h"
+#include "PlumedMain.h"
using namespace PLMD;
@@ -49,5 +54,49 @@ void Value::enableDerivatives()
deriv=true;derivatives.resize(action.getNumberOfParameters());
}
+void Value::setGradients(){
+ gradients.clear();
+ ActionAtomistic*aa=dynamic_cast<ActionAtomistic*>(&action);
+ ActionWithArguments*aw=dynamic_cast<ActionWithArguments*>(&action);
+ if(aa){
+ Atoms&atoms((aa->plumed).getAtoms());
+ for(unsigned j=0;j<aa->getNumberOfAtoms();++j){
+ AtomNumber an=aa->getAbsoluteIndex(j);
+ if(atoms.isVirtualAtom(an.index())){
+ const ActionWithVirtualAtom* a=atoms.getVirtualAtomsAction(an.index());
+ for(std::map<AtomNumber,Tensor>::const_iterator p=a->getGradients().begin();p!=a->getGradients().end();++p){
+// controllare l'ordine del matmul:
+ gradients[(*p).first]+=matmul(Vector(derivatives[3*j],derivatives[3*j+1],derivatives[3*j+2]),(*p).second);
+ }
+ } else {
+ for(unsigned i=0;i<3;i++) gradients[an][i]+=derivatives[3*j+i];
+ }
+ }
+ } else if(aw){
+ std::vector<Value*> values=aw->getArguments();
+ for(unsigned j=0;j<derivatives.size();j++){
+ for(std::map<AtomNumber,Vector>::const_iterator p=values[j]->gradients.begin();p!=values[j]->gradients.end();++p){
+ AtomNumber iatom=(*p).first;
+ gradients[iatom]+=(*p).second*derivatives[j];
+ }
+ }
+ } else plumed_error();
+}
+
+double Value::projection(const Value& v1,const Value&v2){
+ double proj=0.0;
+ const std::map<AtomNumber,Vector> & grad1(v1.gradients);
+ const std::map<AtomNumber,Vector> & grad2(v2.gradients);
+ for(std::map<AtomNumber,Vector>::const_iterator p1=grad1.begin();p1!=grad1.end();++p1){
+ AtomNumber a=(*p1).first;
+ std::map<AtomNumber,Vector>::const_iterator p2=grad2.find(a);
+ if(p2!=grad2.end()){
+ proj+=dotProduct((*p1).second,(*p2).second);
+ }
+ }
+ return proj;
+}
+
+
diff --git a/src/Value.h b/src/Value.h
index ca777c452..5963b6f3b 100644
--- a/src/Value.h
+++ b/src/Value.h
@@ -3,8 +3,11 @@
#include <vector>
#include <string>
+#include <map>
#include "PlumedException.h"
#include "Tools.h"
+#include "AtomNumber.h"
+#include "Vector.h"
namespace PLMD{
@@ -21,6 +24,7 @@ class Value{
double inputForce;
bool forced;
std::vector<double> derivatives;
+ std::map<AtomNumber,Vector> gradients;
std::string name;
bool deriv;
enum {unset,periodic,notperiodic} periodicity;
@@ -28,6 +32,7 @@ class Value{
double max_minus_min;
double inv_max_minus_min;
public:
+ void setGradients();
Value(ActionWithValue&action,const std::string& name);
void set(double);
double get()const;
@@ -53,6 +58,7 @@ public:
/// check if a force has been added at this step
bool checkForced()const;
+ static double projection(const Value&,const Value&);
};
--
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