diff --git a/.travis.yml b/.travis.yml
index 26f6e34bb9d744eb9112d97a783f6b090bf49c23..ef5f45aeb55846fbc2216283a425e1c6440fd70d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -143,7 +143,7 @@ install:
export COLUMNS=80 ;
wget https://raw.githubusercontent.com/GiovanniBussi/macports-ci/master/macports-ci ;
chmod +x ./macports-ci ;
- ./macports-ci install ;
+ ./macports-ci install --remove-brew ;
PATH="/opt/local/bin:$PATH" ;
make macports ;
./macports-ci localports macports ;
diff --git a/src/colvar/PathMSDBase.cpp b/src/colvar/PathMSDBase.cpp
index c244708d5daf79ba4de2f602fab816771d5bbb7b..b8746221ef613681b95da22048d4d5c750b24a97 100644
--- a/src/colvar/PathMSDBase.cpp
+++ b/src/colvar/PathMSDBase.cpp
@@ -139,7 +139,7 @@ void PathMSDBase::calculate() {
// resize the list to full
if(imgVec.empty()) { // this is the signal that means: recalculate all
imgVec.resize(nframes);
-#pragma simd
+ #pragma omp simd
for(unsigned i=0; i<nframes; i++) {
imgVec[i].property=indexvec[i];
imgVec[i].index=i;
@@ -170,7 +170,6 @@ void PathMSDBase::calculate() {
// and we need to accurately recalculate for all reference structures
computeRefClose = true;
imgVec.resize(nframes);
-#pragma simd
for(unsigned i=0; i<nframes; i++) {
imgVec[i].property=indexvec[i];
imgVec[i].index=i;
@@ -197,7 +196,7 @@ void PathMSDBase::calculate() {
for(unsigned i=rank; i<imgVec.size(); i+=stride) {
tmp_distances[i] = msdv[imgVec[i].index].calc_Rot(getPositions(), tmp_derivs, tmp_rotationRefClose[imgVec[i].index], true);
plumed_assert(tmp_derivs.size()==nat);
-#pragma simd
+ #pragma omp simd
for(unsigned j=0; j<nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
}
}
@@ -206,7 +205,7 @@ void PathMSDBase::calculate() {
for(unsigned i=rank; i<imgVec.size(); i+=stride) {
tmp_distances[i] = msdv[imgVec[i].index].calculateWithCloseStructure(getPositions(), tmp_derivs, rotationPosClose, rotationRefClose[imgVec[i].index], drotationPosCloseDrr01, true);
plumed_assert(tmp_derivs.size()==nat);
-#pragma simd
+ #pragma omp simd
for(unsigned j=0; j<nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
if (debugClose) {
double withclose = tmp_distances[i];
@@ -226,7 +225,7 @@ void PathMSDBase::calculate() {
for(unsigned i=rank; i<imgVec.size(); i+=stride) {
tmp_distances[i]=msdv[imgVec[i].index].calculate(getPositions(),tmp_derivs,true);
plumed_assert(tmp_derivs.size()==nat);
-#pragma simd
+ #pragma omp simd
for(unsigned j=0; j<nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
}
}
@@ -275,17 +274,18 @@ void PathMSDBase::calculate() {
val_z_path->set(-(1./lambda)*std::log(partition));
for(unsigned j=0; j<s_path.size(); j++) {
// clean up
-#pragma simd
+ #pragma omp simd
for(unsigned i=0; i< derivs_s.size(); i++) {derivs_s[i].zero();}
// do the derivative
-#pragma simd
for(const auto & it : imgVec) {
double expval=it.similarity;
tmp=lambda*expval*(s_path[j]-it.property[j])/partition;
-#pragma ivdep
+ #pragma omp simd
for(unsigned i=0; i< derivs_s.size(); i++) { derivs_s[i]+=tmp*it.distder[i] ;}
-#pragma ivdep
- if(j==0) {for(unsigned i=0; i< derivs_z.size(); i++) { derivs_z[i]+=it.distder[i]*expval/partition;}}
+ if(j==0) {
+ #pragma omp simd
+ for(unsigned i=0; i< derivs_z.size(); i++) { derivs_z[i]+=it.distder[i]*expval/partition;}
+ }
}
for(unsigned i=0; i< derivs_s.size(); i++) {
setAtomsDerivatives (val_s_path[j],i,derivs_s[i]);
diff --git a/src/tools/RMSD.cpp b/src/tools/RMSD.cpp
index ddbec1b2586dee7c0e31b3e1f412c71413072bb2..c719a9121b1ff35712261c9d16bb2854721d3f24 100644
--- a/src/tools/RMSD.cpp
+++ b/src/tools/RMSD.cpp
@@ -97,9 +97,9 @@ void RMSD::setReference(const vector<Vector> & reference) {
plumed_massert(displace.empty(),"you should first clear() an RMSD object, then set a new reference");
align.resize(n,1.0/n);
displace.resize(n,1.0/n);
-#pragma ivdep
+ #pragma omp simd
for(unsigned i=0; i<n; i++) reference_center+=this->reference[i]*align[i];
-#pragma ivdep
+ #pragma omp simd
for(unsigned i=0; i<n; i++) this->reference[i]-=reference_center;
reference_center_is_calculated=true;
reference_center_is_removed=true;
@@ -116,10 +116,10 @@ void RMSD::setAlign(const vector<double> & align, bool normalize_weights, bool r
this->align=align;
if(normalize_weights) {
double w=0.0;
-#pragma ivdep
+ #pragma omp simd
for(unsigned i=0; i<n; i++) w+=this->align[i];
double inv=1.0/w;
-#pragma ivdep
+ #pragma omp simd
for(unsigned i=0; i<n; i++) this->align[i]*=inv;
}
// recalculate the center anyway
@@ -149,11 +149,13 @@ void RMSD::setDisplace(const vector<double> & displace, bool normalize_weights)
plumed_massert(this->displace.size()==displace.size(),"mismatch in dimension of align/displace arrays");
this->displace=displace;
double w=0.0;
-#pragma ivdep
+ #pragma omp simd
for(unsigned i=0; i<n; i++) w+=this->displace[i];
double inv=1.0/w;
-#pragma ivdep
- if(normalize_weights) {for(unsigned i=0; i<n; i++) this->displace[i]*=inv;}
+ if(normalize_weights) {
+ #pragma omp simd
+ for(unsigned i=0; i<n; i++) this->displace[i]*=inv;
+ }
}
std::vector<double> RMSD::getDisplace() {
return displace;
@@ -971,7 +973,7 @@ void RMSDCoreData::doCoreCalc(bool safe,bool alEqDis, bool only_rotation) {
Vector cp; cp.zero(); if(!cpositions_is_removed)cp=cpositions;
Vector cr; cr.zero(); if(!creference_is_removed)cr=creference;
// second expensive loop: compute second moments wrt centers
-#pragma ivdep
+ #pragma omp simd
for(unsigned iat=0; iat<n; iat++) {
double w=align[iat];
rr00+=dotProduct(positions[iat]-cp,positions[iat]-cp)*w;
@@ -1082,15 +1084,16 @@ void RMSDCoreData::doCoreCalc(bool safe,bool alEqDis, bool only_rotation) {
// calculate rotation matrix derivatives and components distances needed for components only when align!=displacement
if(!alEqDis)ddist_drotation.zero();
-#pragma ivdep
+ #pragma omp simd
for(unsigned iat=0; iat<n; iat++) {
// components differences: this is useful externally
d[iat]=positions[iat]-cp - matmul(rotation,reference[iat]-cr);
//cerr<<"D "<<iat<<" "<<d[iat][0]<<" "<<d[iat][1]<<" "<<d[iat][2]<<"\n";
-
- // ddist_drotation if needed
- if(!alEqDis or !only_rotation) ddist_drotation+=-2*displace[iat]*extProduct(d[iat],reference[iat]-cr);
}
+ // ddist_drotation if needed
+ if(!alEqDis or !only_rotation)
+ for (unsigned iat=0; iat<n; iat++)
+ ddist_drotation+=-2*displace[iat]*extProduct(d[iat],reference[iat]-cr);
if(!alEqDis or !only_rotation) {
ddist_drr01.zero();
@@ -1112,7 +1115,7 @@ double RMSDCoreData::getDistance( bool squared) {
dist=eigenvals[0]+rr00+rr11;
const unsigned n=static_cast<unsigned int>(reference.size());
double localDist = 0;
-#pragma simd reduction(+:localDist)
+ #pragma omp simd reduction(+:localDist)
for(unsigned iat=0; iat<n; iat++) {
if(alEqDis) {
if(safe) localDist+=align[iat]*modulo2(d[iat]);
@@ -1145,7 +1148,7 @@ void RMSDCoreData::doCoreCalcWithCloseStructure(bool safe,bool alEqDis, Tensor &
Tensor rotation = matmul(rotationPosClose, rotationRefClose);
-#pragma simd
+ #pragma omp simd
for (unsigned iat=0; iat<natoms; iat++) {
d[iat] = positions[iat] - cp - matmul(rotation, reference[iat]-cr);
}
@@ -1178,7 +1181,7 @@ std::vector<Vector> RMSDCoreData::getDDistanceDPositions() {
if(!isInitialized)plumed_merror("getDPositionsDerivatives needs to initialize the coreData first!");
Vector csum;
Vector tmp1,tmp2;
-#pragma ivdep
+ #pragma omp simd
for(unsigned iat=0; iat<n; iat++) {
if(alEqDis) {
// there is no need for derivatives of rotation and shift here as it is by construction zero
@@ -1197,8 +1200,9 @@ std::vector<Vector> RMSDCoreData::getDDistanceDPositions() {
}
}
-#pragma ivdep
- if(!alEqDis) for(unsigned iat=0; iat<n; iat++) {derivatives[iat]= prefactor*(derivatives[iat]+(ddist_dcpositions-csum)*align[iat]); }
+ if(!alEqDis)
+ #pragma omp simd
+ for(unsigned iat=0; iat<n; iat++) {derivatives[iat]= prefactor*(derivatives[iat]+(ddist_dcpositions-csum)*align[iat]); }
return derivatives;
}
@@ -1220,7 +1224,7 @@ std::vector<Vector> RMSDCoreData::getDDistanceDReference() {
Tensor t_ddist_drr01=ddist_drr01.transpose();
// third expensive loop: derivatives
-#pragma simd
+ #pragma omp simd
for(unsigned iat=0; iat<n; iat++) {
if(alEqDis) {
// there is no need for derivatives of rotation and shift here as it is by construction zero
@@ -1240,8 +1244,9 @@ std::vector<Vector> RMSDCoreData::getDDistanceDReference() {
}
}
-#pragma ivdep
- if(!alEqDis) for(unsigned iat=0; iat<n; iat++) {derivatives[iat]= prefactor*(derivatives[iat]+(ddist_dcreference-csum)*align[iat]);}
+ if(!alEqDis)
+ #pragma omp simd
+ for(unsigned iat=0; iat<n; iat++) {derivatives[iat]= prefactor*(derivatives[iat]+(ddist_dcreference-csum)*align[iat]);}
return derivatives;
}
diff --git a/src/tools/Tools.cpp b/src/tools/Tools.cpp
index 6197ad775c206bae5a778db082f9b637e495df75..7e382d8765416ad6a28c31edd2a0a7f231619cef 100644
--- a/src/tools/Tools.cpp
+++ b/src/tools/Tools.cpp
@@ -189,7 +189,7 @@ bool Tools::getParsedLine(IFile& ifile,vector<string> & words) {
if(!w.empty()) {
if(inside && *(w.begin())=="...") {
inside=false;
- if(w.size()==2) plumed_massert(w[1]==words[0],"second word in terminating \"...\" lines, if present, should be equal to first word of directive");
+ if(w.size()==2) plumed_massert(w[1]==words[0],"second word in terminating \"...\" "+w[1]+" line, if present, should be equal to first word of directive: "+words[0]);
plumed_massert(w.size()<=2,"terminating \"...\" lines cannot consist of more than two words");
w.clear();
} else if(*(w.end()-1)=="...") {
diff --git a/user-doc/Installation.md b/user-doc/Installation.md
index cbca7ee845f598a87fadb24be95b6b99bb0aec98..a988bf8dc499169289dfb61f25b2b2ec0d318f78 100644
--- a/user-doc/Installation.md
+++ b/user-doc/Installation.md
@@ -273,14 +273,23 @@ you need to download the SOURCE of VMD, which contains
a plugins directory. Adapt build.sh and compile it. At
the end, you should get the molfile plugins compiled as a static
library `libmolfile_plugin.a`. Locate said file and `libmolfile_plugin.h`,
-and customize the configure command with something along
-the lines of:
+they should be in a directory called `/pathtovmdplugins/ARCH/molfile`
+(e.g. `/pathtovmdplugins/MACOSXX86_64/molfile`). Also locate file `molfile_plugin.h`,
+which should be in `/pathtovmdplugins/include`.
+Then customize the configure command with something along the lines of:
\verbatim
-./configure LDFLAGS="-ltcl8.5 -L/mypathtomolfilelibrary/ -L/mypathtotcl" CPPFLAGS="-I/mypathtolibmolfile_plugin.h/"
+./configure LDFLAGS="-L/pathtovmdplugins/ARCH/molfile" CPPFLAGS="-I/pathtovmdplugins/include -I/pathtovmdplugins/ARCH/molfile"
\endverbatim
-and rebuild.
+Notice that it might be necessary to add to `LDFLAGS` the path to your TCL interpreter, e.g.
+
+\verbatim
+./configure LDFLAGS="-ltcl8.5 -L/mypathtotcl -L/pathtovmdplugins/ARCH/molfile" \
+ CPPFLAGS="-I/pathtovmdplugins/include -I/pathtovmdplugins/ARCH/molfile"
+\endverbatim
+
+Then, rebuild plumed.
\section CompilingPlumed Compiling PLUMED