Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2019 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        1654 : Colvar::Colvar(const ActionOptions&ao):
      31             :   Action(ao),
      32             :   ActionAtomistic(ao),
      33             :   ActionWithValue(ao),
      34             :   isEnergy(false),
      35        1654 :   isExtraCV(false)
      36             : {
      37        1654 : }
      38             : 
      39        1627 : void Colvar::registerKeywords( Keywords& keys ) {
      40        1627 :   Action::registerKeywords( keys );
      41        1627 :   ActionWithValue::registerKeywords( keys );
      42        1627 :   ActionAtomistic::registerKeywords( keys );
      43        4881 :   keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
      44        1627 : }
      45             : 
      46        1981 : void Colvar::requestAtoms(const vector<AtomNumber> & a) {
      47        1981 :   plumed_massert(!isEnergy,"request atoms should not be called if this is energy");
      48             : // Tell actionAtomistic what atoms we are getting
      49        1981 :   ActionAtomistic::requestAtoms(a);
      50             : // Resize the derivatives of all atoms
      51       14133 :   for(int i=0; i<getNumberOfComponents(); ++i) getPntrToComponent(i)->resizeDerivatives(3*a.size()+9);
      52        1980 : }
      53             : 
      54      105225 : void Colvar::apply() {
      55      105225 :   vector<Vector>&   f(modifyForces());
      56      105225 :   Tensor&           v(modifyVirial());
      57             :   const unsigned    nat=getNumberOfAtoms();
      58      105225 :   const unsigned    ncp=getNumberOfComponents();
      59      105225 :   const unsigned    fsz=f.size();
      60             : 
      61             :   unsigned stride=1;
      62             :   unsigned rank=0;
      63      105225 :   if(ncp>4*comm.Get_size()) {
      64        1560 :     stride=comm.Get_size();
      65        1560 :     rank=comm.Get_rank();
      66             :   }
      67             : 
      68      105225 :   unsigned nt=OpenMP::getNumThreads();
      69      105225 :   if(nt>ncp/(4*stride)) nt=1;
      70             : 
      71      105225 :   if(!isEnergy && !isExtraCV) {
      72      204010 :     #pragma omp parallel num_threads(nt)
      73             :     {
      74      102612 :       vector<Vector> omp_f(fsz);
      75      102612 :       Tensor         omp_v;
      76      102614 :       vector<double> forces(3*nat+9);
      77      102616 :       #pragma omp for
      78             :       for(unsigned i=rank; i<ncp; i+=stride) {
      79      168569 :         if(getPntrToComponent(i)->applyForce(forces)) {
      80     1666529 :           for(unsigned j=0; j<nat; ++j) {
      81     2391417 :             omp_f[j][0]+=forces[3*j+0];
      82     2391417 :             omp_f[j][1]+=forces[3*j+1];
      83     2391417 :             omp_f[j][2]+=forces[3*j+2];
      84             :           }
      85      144502 :           omp_v(0,0)+=forces[3*nat+0];
      86      144502 :           omp_v(0,1)+=forces[3*nat+1];
      87      144502 :           omp_v(0,2)+=forces[3*nat+2];
      88      144502 :           omp_v(1,0)+=forces[3*nat+3];
      89      144502 :           omp_v(1,1)+=forces[3*nat+4];
      90      144502 :           omp_v(1,2)+=forces[3*nat+5];
      91      144502 :           omp_v(2,0)+=forces[3*nat+6];
      92      144502 :           omp_v(2,1)+=forces[3*nat+7];
      93      144502 :           omp_v(2,2)+=forces[3*nat+8];
      94             :         }
      95             :       }
      96      205232 :       #pragma omp critical
      97             :       {
      98     3415964 :         for(unsigned j=0; j<nat; ++j) f[j]+=omp_f[j];
      99      102616 :         v+=omp_v;
     100             :       }
     101             :     }
     102             : 
     103      101398 :     if(ncp>4*comm.Get_size()) {
     104        2970 :       if(fsz>0) comm.Sum(&f[0][0],3*fsz);
     105        1560 :       comm.Sum(&v[0][0],9);
     106             :     }
     107             : 
     108        3827 :   } else if( isEnergy ) {
     109        3787 :     vector<double> forces(1);
     110        3837 :     if(getPntrToComponent(0)->applyForce(forces)) modifyForceOnEnergy()+=forces[0];
     111          40 :   } else if( isExtraCV ) {
     112          40 :     vector<double> forces(1);
     113          80 :     if(getPntrToComponent(0)->applyForce(forces)) modifyForceOnExtraCV()+=forces[0];
     114             :   }
     115      105225 : }
     116             : 
     117      184510 : void Colvar::setBoxDerivativesNoPbc(Value* v) {
     118      184510 :   Tensor virial;
     119             :   unsigned nat=getNumberOfAtoms();
     120    78724310 :   for(unsigned i=0; i<nat; i++) virial-=Tensor(getPosition(i),
     121             :                                           Vector(v->getDerivative(3*i+0),
     122             :                                               v->getDerivative(3*i+1),
     123    31415920 :                                               v->getDerivative(3*i+2)));
     124      184510 :   setBoxDerivatives(v,virial);
     125      184510 : }
     126        5874 : }