Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2018 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #include "Colvar.h"
      23             : #include "tools/OpenMP.h"
      24             : #include <vector>
      25             : #include <string>
      26             : 
      27             : using namespace std;
      28             : namespace PLMD {
      29             : 
      30         722 : Colvar::Colvar(const ActionOptions&ao):
      31             :   Action(ao),
      32             :   ActionAtomistic(ao),
      33             :   ActionWithValue(ao),
      34         722 :   isEnergy(false)
      35             : {
      36         722 : }
      37             : 
      38         729 : void Colvar::registerKeywords( Keywords& keys ) {
      39         729 :   Action::registerKeywords( keys );
      40         729 :   ActionWithValue::registerKeywords( keys );
      41         729 :   ActionAtomistic::registerKeywords( keys );
      42         729 :   keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
      43         729 : }
      44             : 
      45         799 : void Colvar::requestAtoms(const vector<AtomNumber> & a) {
      46         799 :   plumed_massert(!isEnergy,"request atoms should not be called if this is energy");
      47             : // Tell actionAtomistic what atoms we are getting
      48         799 :   ActionAtomistic::requestAtoms(a);
      49             : // Resize the derivatives of all atoms
      50         799 :   for(int i=0; i<getNumberOfComponents(); ++i) getPntrToComponent(i)->resizeDerivatives(3*a.size()+9);
      51         799 : }
      52             : 
      53       43557 : void Colvar::apply() {
      54       43557 :   vector<Vector>&   f(modifyForces());
      55       43557 :   Tensor&           v(modifyVirial());
      56       43557 :   const unsigned    nat=getNumberOfAtoms();
      57       43557 :   const unsigned    ncp=getNumberOfComponents();
      58       43557 :   const unsigned    fsz=f.size();
      59             : 
      60       43557 :   unsigned stride=1;
      61       43557 :   unsigned rank=0;
      62       43557 :   if(ncp>4*comm.Get_size()) {
      63         838 :     stride=comm.Get_size();
      64         838 :     rank=comm.Get_rank();
      65             :   }
      66             : 
      67       43557 :   unsigned nt=OpenMP::getNumThreads();
      68       43557 :   if(nt>ncp/(2.*stride)) nt=1;
      69             : 
      70       43557 :   if(!isEnergy) {
      71       88304 :     #pragma omp parallel num_threads(nt)
      72             :     {
      73       44797 :       vector<Vector> omp_f(fsz);
      74       44807 :       Tensor         omp_v;
      75       89623 :       vector<double> forces(3*nat+9);
      76       44811 :       #pragma omp for
      77             :       for(unsigned i=rank; i<ncp; i+=stride) {
      78       84957 :         if(getPntrToComponent(i)->applyForce(forces)) {
      79     4756208 :           for(unsigned j=0; j<nat; ++j) {
      80     4729216 :             omp_f[j][0]+=forces[3*j+0];
      81     4729218 :             omp_f[j][1]+=forces[3*j+1];
      82     4729220 :             omp_f[j][2]+=forces[3*j+2];
      83             :           }
      84       26992 :           omp_v(0,0)+=forces[3*nat+0];
      85       26977 :           omp_v(0,1)+=forces[3*nat+1];
      86       26990 :           omp_v(0,2)+=forces[3*nat+2];
      87       26990 :           omp_v(1,0)+=forces[3*nat+3];
      88       26992 :           omp_v(1,1)+=forces[3*nat+4];
      89       26984 :           omp_v(1,2)+=forces[3*nat+5];
      90       26992 :           omp_v(2,0)+=forces[3*nat+6];
      91       26993 :           omp_v(2,1)+=forces[3*nat+7];
      92       26991 :           omp_v(2,2)+=forces[3*nat+8];
      93             :         }
      94             :       }
      95       89630 :       #pragma omp critical
      96             :       {
      97      555544 :         for(unsigned j=0; j<nat; ++j) f[j]+=omp_f[j];
      98       44815 :         v+=omp_v;
      99       44815 :       }
     100             :     }
     101             : 
     102       43507 :     if(ncp>4*comm.Get_size()) {
     103         838 :       if(fsz>0) comm.Sum(&f[0][0],3*fsz);
     104         838 :       comm.Sum(&v[0][0],9);
     105             :     }
     106             : 
     107          50 :   } else if( isEnergy ) {
     108          50 :     vector<double> forces(1);
     109          50 :     if(getPntrToComponent(0)->applyForce(forces)) modifyForceOnEnergy()+=forces[0];
     110             :   }
     111       43557 : }
     112             : 
     113      124186 : void Colvar::setBoxDerivativesNoPbc(Value* v) {
     114      124186 :   Tensor virial;
     115      124186 :   unsigned nat=getNumberOfAtoms();
     116    46880731 :   for(unsigned i=0; i<nat; i++) virial-=Tensor(getPosition(i),
     117             :                                           Vector(v->getDerivative(3*i+0),
     118    15585515 :                                               v->getDerivative(3*i+1),
     119    31171030 :                                               v->getDerivative(3*i+2)));
     120      124186 :   setBoxDerivatives(v,virial);
     121      124186 : }
     122        2523 : }