From c95b248eb6a82770589209a5f3e1eb70a3e13490 Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Wed, 10 Sep 2014 15:00:09 +0200
Subject: [PATCH] some cleaning in the code
---
src/colvar/CH3Shifts.cpp | 34 +++++++++-------------------------
src/colvar/CS2Backbone.cpp | 16 +++-------------
src/colvar/NOE.cpp | 15 +++------------
src/colvar/RDC.cpp | 7 +------
4 files changed, 16 insertions(+), 56 deletions(-)
diff --git a/src/colvar/CH3Shifts.cpp b/src/colvar/CH3Shifts.cpp
index e911980e8..4b2770025 100644
--- a/src/colvar/CH3Shifts.cpp
+++ b/src/colvar/CH3Shifts.cpp
@@ -183,7 +183,7 @@ PLUMED_COLVAR_INIT(ao)
if(ensemble&&comm.Get_rank()==0) {
if(multi_sim_comm.Get_size()<2) error("You CANNOT run Replica-Averaged simulations without running multiple replicas!\n");
else ens_dim=multi_sim_comm.Get_size();
- } else ens_dim=0;
+ } else ens_dim=1;
if(ensemble) comm.Sum(&ens_dim, 1);
stringadb = stringa_data + string("/CH3shifts.dat");
@@ -294,34 +294,19 @@ void CH3Shifts::calculate()
coor.coor[ipos+2] = len_pl2alm*Pos[2];
}
+ bool printout=false;
+ string csfile;
+ if(pperiod>0&&comm.Get_rank()==0) printout = (!(getStep()%pperiod));
+ if(printout) csfile = string("cs")+getLabel()+"-"+to_string(getStep())+string(".dat");
+
double fact=1.0;
if(!ensemble) {
energy = meth_list[0]->calc_cs_force(coor, forces);
- bool printout=false;
- if(pperiod>0&&comm.Get_rank()==0) printout = (!(getStep()%pperiod));
- if(printout) {
- string csfile;
- char tmps1[21];
- // add to the name the label of the cv in such a way to have different files
- // when there is more than one defined variable
- sprintf(tmps1, "%li", getStep());
- csfile = string("cs")+tmps1+string(".dat");
- meth_list[0]->write_cs(csfile.c_str());
- }
+ if(printout) meth_list[0]->write_cs(csfile.c_str());
} else {
meth_list[0]->calc_cs(coor);
- bool printout=false;
- if(pperiod>0&&comm.Get_rank()==0) printout = (!(getStep()%pperiod));
- if(printout) {
- string csfile;
- char tmps1[21], tmps2[21];
- // add to the name the label of the cv in such a way to have different files
- // when there is more than one defined variable
- sprintf(tmps1, "%li", getStep());
- sprintf(tmps2, "%i", multi_sim_comm.Get_rank());
- csfile = string("cs")+tmps2+"-"+tmps1+string(".dat");
- meth_list[0]->write_cs(csfile.c_str());
- }
+ if(printout) meth_list[0]->write_cs(csfile.c_str());
+
unsigned size = meth_list[0]->ala_calc_hb.size();
for(unsigned j=0;j<size;j++) sh[0][j] = meth_list[0]->ala_calc_hb[j];
size = meth_list[0]->ile_calc_hd.size();
@@ -342,7 +327,6 @@ void CH3Shifts::calculate()
if(comm.Get_rank()==0) { // I am the master of my replica
// among replicas
multi_sim_comm.Sum(&sh[0][0], numResidues*8);
- multi_sim_comm.Barrier();
for(unsigned i=0;i<8;i++) for(int j=0;j<numResidues;j++) sh[j][i] *= fact;
} else for(unsigned i=0;i<8;i++) for(int j=0;j<numResidues;j++) sh[j][i] = 0.;
// inside each replica
diff --git a/src/colvar/CS2Backbone.cpp b/src/colvar/CS2Backbone.cpp
index fa79121fd..0b5219b10 100644
--- a/src/colvar/CS2Backbone.cpp
+++ b/src/colvar/CS2Backbone.cpp
@@ -195,7 +195,7 @@ PLUMED_COLVAR_INIT(ao)
if(ensemble&&comm.Get_rank()==0) {
if(multi_sim_comm.Get_size()<2) error("You CANNOT run Replica-Averaged simulations without running multiple replicas!\n");
else ens_dim=multi_sim_comm.Get_size();
- } else ens_dim=0;
+ } else ens_dim=1;
if(ensemble) comm.Sum(&ens_dim, 1);
stringadb = stringa_data + string("/camshift.db");
@@ -320,7 +320,6 @@ 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());
@@ -355,15 +354,7 @@ void CS2Backbone::calculate()
bool printout=false;
if(pperiod>0&&comm.Get_rank()==0) printout = (!(getStep()%pperiod));
if(printout) {
- string csfile;
- char tmps1[21], tmps2[21];
- // add to the name the label of the cv in such a way to have different files
- // when there is more than one defined variable
- sprintf(tmps1, "%li", getStep());
- if(ensemble) {
- sprintf(tmps2, "%i", multi_sim_comm.Get_rank());
- csfile = string("cs-")+getLabel()+"-"+tmps2+"-"+tmps1+string(".dat");
- } else csfile = string("cs-")+getLabel()+"-"+tmps1+string(".dat");
+ string csfile = string("cs-")+getLabel()+"-"+to_string(getStep())+string(".dat");;
cam_list[0].printout_chemical_shifts(csfile.c_str());
}
@@ -380,8 +371,7 @@ void CS2Backbone::calculate()
}
csforces.clear();
- double energy;
- energy = cam_list[0].ens_energy_force(coor, csforces, sh);
+ double energy = cam_list[0].ens_energy_force(coor, csforces, sh);
if(!serial) comm.Sum(&csforces[0][0], N*4);
Tensor virial;
diff --git a/src/colvar/NOE.cpp b/src/colvar/NOE.cpp
index 6bddb2911..1f08891a4 100644
--- a/src/colvar/NOE.cpp
+++ b/src/colvar/NOE.cpp
@@ -162,13 +162,13 @@ serial(false)
if(ensemble&&comm.Get_rank()==0) {
if(multi_sim_comm.Get_size()<2) error("You CANNOT run Replica-Averaged simulations without running multiple replicas!\n");
else ens_dim=multi_sim_comm.Get_size();
- } else ens_dim=0;
+ } else ens_dim=1;
if(ensemble) comm.Sum(&ens_dim, 1);
// Ouput details of all contacts
unsigned index=0;
for(unsigned i=0;i<nga.size();++i){
- log.printf(" The %uth NOE is calculated using %i equivalent couples of atoms and compared with a %f reference distance\n", i, nga[i], noedist[i]);
+ log.printf(" The %uth NOE is calculated using %u equivalent couples of atoms and compared with a %f reference distance\n", i, nga[i], noedist[i]);
for(unsigned j=0;j<nga[i];j++) {
log.printf(" couple %u is %d %d.\n", j, ga_lista[index].serial(), gb_lista[index].serial() );
index++;
@@ -251,16 +251,7 @@ void NOE::calculate(){
bool printout=false;
if(pperiod>0&&comm.Get_rank()==0) printout = (!(getStep()%pperiod));
if(printout) {
- string csfile;
- char tmps1[21], tmps2[21];
- // add to the name the label of the cv in such a way to have different files
- // when there is more than one defined variable
- sprintf(tmps1, "%li", getStep());
- if(ensemble) {
- sprintf(tmps2, "%i", multi_sim_comm.Get_rank());
- csfile = string("noe")+tmps2+"-"+tmps1+string(".dat");
- } else csfile = string("noe")+tmps1+string(".dat");
- // now print it!!
+ string csfile = string("noe")+to_string(getStep())+string(".dat");
FILE *outfile = fopen(csfile.c_str(), "w");
fprintf(outfile, "#index calc exp\n");
for(unsigned i=0;i<nga.size();i++) {
diff --git a/src/colvar/RDC.cpp b/src/colvar/RDC.cpp
index a0a6f3940..ce0d3a841 100644
--- a/src/colvar/RDC.cpp
+++ b/src/colvar/RDC.cpp
@@ -442,12 +442,7 @@ void RDC::calculate()
bool printout=false;
if(pperiod>0&&comm.Get_rank()==0) printout = (!(getStep()%pperiod));
if(printout) {
- string dcfile;
- char tmps1[21];
- sprintf(tmps1, "%li", getStep());
- if(ensemble) {
- dcfile = string("rdc-")+getLabel()+"-"+tmps1+string(".dat");
- } else dcfile = string("rdc-")+getLabel()+"-"+tmps1+string(".dat");
+ string dcfile = string("rdc-")+getLabel()+"-"+to_string(getStep())+string(".dat");
FILE *outfile = fopen(dcfile.c_str(), "w");
fprintf(outfile, "#index calc exp\n");
double sum=0.;
--
GitLab