From dcd82585c8c37562e6770bf9445063f82fcb1f59 Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Thu, 22 May 2014 15:56:18 +0200
Subject: [PATCH] CS2Backbone: small changes for better performacens (maybe)
---
src/colvar/CS2Backbone.cpp | 57 +++++++++++++++++++-------------------
1 file changed, 29 insertions(+), 28 deletions(-)
diff --git a/src/colvar/CS2Backbone.cpp b/src/colvar/CS2Backbone.cpp
index d21ad75f0..2d0084c78 100644
--- a/src/colvar/CS2Backbone.cpp
+++ b/src/colvar/CS2Backbone.cpp
@@ -141,15 +141,17 @@ PRINT ARG=cs
class CS2Backbone : public Colvar {
vector<CamShift2> cam_list;
Molecules molecules;
- int numResidues;
- int pperiod;
- int ens_dim;
+ unsigned numResidues;
+ unsigned pperiod;
+ unsigned ens_dim;
bool ensemble;
bool serial;
double **sh;
double ene_pl2alm;
double len_pl2alm;
double for_pl2alm;
+ Coor<double> coor;
+ Coor<double> csforces;
public:
CS2Backbone(const ActionOptions&);
~CS2Backbone();
@@ -200,7 +202,7 @@ PLUMED_COLVAR_INIT(ao)
int neigh_f=10;
parse("NEIGH_FREQ", neigh_f);
- int w_period=0;
+ unsigned w_period=0;
parse("WRITE_CS", w_period);
pperiod=w_period;
@@ -309,7 +311,7 @@ PLUMED_COLVAR_INIT(ao)
if(stride>1) log.printf(" Parallelized over %u processors\n", stride);
a.set_mpi(stride, rank);
- if(ensemble) { log.printf(" ENSEMBLE averaging over %i replicas\n", ens_dim); }
+ if(ensemble) { log.printf(" ENSEMBLE averaging over %u replicas\n", ens_dim); }
a.set_flat_bottom_const(grains);
a.set_box_nupdate(neigh_f);
@@ -318,7 +320,7 @@ PLUMED_COLVAR_INIT(ao)
sh = new double*[numResidues];
sh[0] = new double[numResidues*6];
- for (int i=1; i<numResidues; i++) sh[i]=sh[i-1]+6;
+ for(unsigned i=1;i<numResidues;i++) sh[i]=sh[i-1]+6;
/* Energy and Lenght conversion */
ene_pl2alm = 4.186/plumed.getAtoms().getUnits().getEnergy();
@@ -336,6 +338,10 @@ PLUMED_COLVAR_INIT(ao)
<<plumed.cite("Kohlhoff K, Robustelli P, Cavalli A, Salvatella A, Vendruscolo M, J. Am. Chem. Soc. 131, 13894 (2009)")
<<plumed.cite("Camilloni C, Robustelli P, De Simone A, Cavalli A, Vendruscolo M, J. Am. Chem. Soc. 134, 3968 (2012)") <<"\n";
+
+ coor.resize(atoms.size());
+ csforces.resize(atoms.size());
+
addValueWithDerivatives();
setNotPeriodic();
requestAtoms(atoms);
@@ -348,23 +354,18 @@ CS2Backbone::~CS2Backbone()
delete[] sh;
}
-
void CS2Backbone::calculate()
{
double energy=0.;
Tensor virial;
- virial.zero();
vector<Vector> deriv(getNumberOfAtoms());
- int N = getNumberOfAtoms();
- Coor<double> coor(N);
- Coor<double> forces(N);
+ unsigned N = getNumberOfAtoms();
- forces.clear();
- for(int i=0; i<numResidues; i++) for(unsigned j=0; j<6; j++) sh[i][j]=0.;
+ for(unsigned i=0;i<numResidues;i++) for(unsigned j=0;j<6;j++) sh[i][j]=0.;
if(getExchangeStep()) cam_list[0].set_box_count(0);
- for (int i = 0; i < N; i++) {
- int ipos = 4 * i;
+ for (unsigned i=0;i<N;i++) {
+ unsigned ipos = 4*i;
Vector Pos = getPosition(i);
coor.coor[ipos] = len_pl2alm*Pos[0];
coor.coor[ipos+1] = len_pl2alm*Pos[1];
@@ -394,28 +395,28 @@ void CS2Backbone::calculate()
if(comm.Get_rank()==0) { // I am the master of my replica
// among replicas
multi_sim_comm.Sum(&sh[0][0], numResidues*6);
- multi_sim_comm.Barrier();
- for(unsigned i=0;i<6;i++) for(int j=0;j<numResidues;j++) sh[j][i] *= fact;
- } else for(unsigned i=0;i<6;i++) for(int j=0;j<numResidues;j++) sh[j][i] = 0.;
+ for(unsigned i=0;i<6;i++) for(unsigned j=0;j<numResidues;j++) sh[j][i] *= fact;
+ } else for(unsigned i=0;i<6;i++) for(unsigned j=0;j<numResidues;j++) sh[j][i] = 0.;
// inside each replica
comm.Sum(&sh[0][0], numResidues*6);
}
- energy = cam_list[0].ens_energy_force(coor, forces, sh);
- if(!serial) comm.Sum(&forces[0][0], N*4);
+ csforces.clear();
+ energy = cam_list[0].ens_energy_force(coor, csforces, sh);
+ if(!serial) comm.Sum(&csforces[0][0], N*4);
- for (int i = 0; i < N; i++)
+ virial.zero();
+ for(unsigned i=0;i<N;i++)
{
- Vector For;
- int ipos = 4 * i;
- For[0] = forces.coor[ipos];
- For[1] = forces.coor[ipos+1];
- For[2] = forces.coor[ipos+2];
- deriv[i] = fact*for_pl2alm*For;
+ unsigned ipos=4*i;
+ double ff=fact*for_pl2alm;
+ deriv[i][0] = ff*csforces.coor[ipos];
+ deriv[i][1] = ff*csforces.coor[ipos+1];
+ deriv[i][2] = ff*csforces.coor[ipos+2];
+ setAtomsDerivatives(i,deriv[i]);
virial=virial+(-1.*Tensor(getPosition(i),deriv[i]));
}
- for(unsigned i=0;i<getNumberOfAtoms();++i) setAtomsDerivatives(i,deriv[i]);
setValue (ene_pl2alm*energy);
setBoxDerivatives (virial);
}
--
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