Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2019 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 "Function.h"
      23             : #include "ActionRegister.h"
      24             : #include "tools/OpenMP.h"
      25             : 
      26             : using namespace std;
      27             : 
      28             : namespace PLMD {
      29             : namespace function {
      30             : 
      31             : //+PLUMEDOC FUNCTION LOCALENSEMBLE
      32             : /*
      33             : Calculates the average over multiple arguments.
      34             : 
      35             : If more than one collective variable is given for each argument then they
      36             : are averaged separately. The average is stored in a component labelled <em>label</em>.cvlabel.
      37             : 
      38             : \par Examples
      39             : 
      40             : The following input tells plumed to calculate the chemical shifts for four
      41             : different proteins in the same simulation box then average them, calculated
      42             : the sum of the squared deviation with respect to the experimental values and
      43             : applies a linear restraint.
      44             : \plumedfile
      45             : MOLINFO STRUCTURE=data/template.pdb
      46             : 
      47             : chaina: GROUP ATOMS=1-1640
      48             : chainb: GROUP ATOMS=1641-3280
      49             : chainc: GROUP ATOMS=3281-4920
      50             : chaind: GROUP ATOMS=4921-6560
      51             : 
      52             : WHOLEMOLECULES ENTITY0=chaina ENTITY1=chainb ENTITY2=chainc ENTITY3=chaind
      53             : 
      54             : csa: CS2BACKBONE ATOMS=chaina NRES=100 DATA=data/ TEMPLATE=chaina.pdb NOPBC
      55             : csb: CS2BACKBONE ATOMS=chainb NRES=100 DATA=data/ TEMPLATE=chainb.pdb NOPBC
      56             : csc: CS2BACKBONE ATOMS=chainc NRES=100 DATA=data/ TEMPLATE=chainc.pdb NOPBC
      57             : csd: CS2BACKBONE ATOMS=chaind NRES=100 DATA=data/ TEMPLATE=chaind.pdb NOPBC
      58             : 
      59             : ensca: LOCALENSEMBLE NUM=4 ARG1=(csa\.ca_.*) ARG2=(csb\.ca_.*) ARG3=(csc\.ca_.*) ARG4=(csd\.ca_.*)
      60             : enscb: LOCALENSEMBLE NUM=4 ARG1=(csa\.cb_.*) ARG2=(csb\.cb_.*) ARG3=(csc\.cb_.*) ARG4=(csd\.cb_.*)
      61             : ensco: LOCALENSEMBLE NUM=4 ARG1=(csa\.co_.*) ARG2=(csb\.co_.*) ARG3=(csc\.co_.*) ARG4=(csd\.co_.*)
      62             : enshn: LOCALENSEMBLE NUM=4 ARG1=(csa\.hn_.*) ARG2=(csb\.hn_.*) ARG3=(csc\.hn_.*) ARG4=(csd\.hn_.*)
      63             : ensnh: LOCALENSEMBLE NUM=4 ARG1=(csa\.nh_.*) ARG2=(csb\.nh_.*) ARG3=(csc\.nh_.*) ARG4=(csd\.nh_.*)
      64             : 
      65             : stca: STATS ARG=(ensca\.csa\.ca_.*) PARARG=(csa\.expca_.*) SQDEVSUM
      66             : stcb: STATS ARG=(enscb\.csa\.cb_.*) PARARG=(csa\.expcb_.*) SQDEVSUM
      67             : stco: STATS ARG=(ensco\.csa\.co_.*) PARARG=(csa\.expco_.*) SQDEVSUM
      68             : sthn: STATS ARG=(enshn\.csa\.hn_.*) PARARG=(csa\.exphn_.*) SQDEVSUM
      69             : stnh: STATS ARG=(ensnh\.csa\.nh_.*) PARARG=(csa\.expnh_.*) SQDEVSUM
      70             : 
      71             : res: RESTRAINT ARG=stca.*,stcb.*,stco.*,sthn.*,stnh.* AT=0.,0.,0.,0.,0. KAPPA=0.,0.,0.,0.,0 SLOPE=16.,16.,12.,24.,0.5
      72             : \endplumedfile
      73             : 
      74             : */
      75             : //+ENDPLUMEDOC
      76             : 
      77             : 
      78           4 : class LocalEnsemble :
      79             :   public Function
      80             : {
      81             :   unsigned ens_dim;
      82             :   unsigned narg;
      83             : public:
      84             :   explicit LocalEnsemble(const ActionOptions&);
      85             :   void     calculate() override;
      86             :   static void registerKeywords(Keywords& keys);
      87             : };
      88             : 
      89             : 
      90        7836 : PLUMED_REGISTER_ACTION(LocalEnsemble,"LOCALENSEMBLE")
      91             : 
      92           3 : void LocalEnsemble::registerKeywords(Keywords& keys) {
      93           3 :   Function::registerKeywords(keys);
      94           6 :   keys.use("ARG");
      95          12 :   keys.add("compulsory","NUM","the number of local replicas");
      96           3 :   useCustomisableComponents(keys);
      97           3 : }
      98             : 
      99           2 : LocalEnsemble::LocalEnsemble(const ActionOptions&ao):
     100             :   Action(ao),
     101             :   Function(ao),
     102           2 :   ens_dim(0)
     103             : {
     104           4 :   parse("NUM",ens_dim);
     105           2 :   if(ens_dim==0) error("NUM should be greater or equal to 1");
     106             : 
     107             :   vector<Value*> arg;
     108             :   int oldsize=-1;
     109          16 :   for(unsigned i=1; i<=ens_dim; ++i ) {
     110             :     vector<Value*> larg;
     111          12 :     if(!parseArgumentList("ARG",i,larg)) break;
     112          30 :     for(unsigned j=0; j<larg.size(); j++) arg.push_back(larg[j]);
     113           6 :     if(oldsize!=-1&&oldsize!=static_cast<int>(larg.size())) error("In LOCALENSEMBLE you should have the same number of arguments for each ARG keyword");
     114           6 :     oldsize = larg.size();
     115           6 :     if(!larg.empty()) {
     116           6 :       log.printf("  with arguments %u: ", i);
     117          42 :       for(unsigned j=0; j<larg.size(); j++) log.printf(" %s",larg[j]->getName().c_str());
     118           6 :       log.printf("\n");
     119             :     }
     120             :   }
     121           2 :   requestArguments(arg);
     122           2 :   narg = arg.size()/ens_dim;
     123             : 
     124             :   // these are the averages
     125           6 :   for(unsigned i=0; i<narg; i++) {
     126           4 :     std::string s=getPntrToArgument(i)->getName();
     127           4 :     addComponentWithDerivatives(s);
     128           4 :     getPntrToComponent(i)->setNotPeriodic();
     129             :   }
     130             : 
     131           2 :   log.printf("  averaging over %u replicas.\n", ens_dim);
     132           2 : }
     133             : 
     134          40 : void LocalEnsemble::calculate()
     135             : {
     136          40 :   const double fact = 1.0/static_cast<double>(ens_dim);
     137         119 :   #pragma omp parallel for num_threads(OpenMP::getNumThreads())
     138          79 :   for(unsigned i=0; i<narg; ++i) {
     139             :     double mean = 0.;
     140          80 :     Value* v=getPntrToComponent(i);
     141         319 :     for(unsigned j=0; j<ens_dim; ++j) {
     142         239 :       const unsigned index = j*narg+i;
     143             :       setDerivative(v, index, fact);
     144         239 :       mean += fact*getArgument(index);
     145             :     }
     146             :     v->set(mean);
     147             :   }
     148          40 : }
     149             : 
     150             : }
     151        5874 : }
     152             : 
     153             :