Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2020 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             : #ifndef __PLUMED_adjmat_ContactMatrixShortcut_h
      23             : #define __PLUMED_adjmat_ContactMatrixShortcut_h
      24             : #include "core/ActionShortcut.h"
      25             : #include "core/ActionRegister.h"
      26             : #include "core/PlumedMain.h"
      27             : #include "core/ActionSet.h"
      28             : #include "core/Group.h"
      29             : 
      30             : namespace PLMD {
      31             : namespace adjmat {
      32             : 
      33             : template <typename CM>
      34             : class ContactMatrixShortcut : public ActionShortcut {
      35             : public:
      36             :   static void registerKeywords(Keywords& keys);
      37             :   explicit ContactMatrixShortcut(const ActionOptions&);
      38             : };
      39             : 
      40             : 
      41             : template <typename CM>
      42         436 : void ContactMatrixShortcut<CM>::registerKeywords(Keywords& keys) {
      43         436 :   CM::registerKeywords( keys );
      44         436 :   keys.remove("GROUP");
      45         872 :   keys.remove("SWITCH");
      46         436 :   keys.add("numbered","GROUP","specifies the list of atoms that should be assumed indistinguishable");
      47         436 :   keys.add("numbered","SWITCH","the input for the switching function that acts upon the distance between each pair of atoms");
      48         872 :   keys.linkActionInDocs("SWITCH","LESS_THAN");
      49         436 :   keys.addActionNameSuffix("_PROPER");
      50         872 :   keys.addActionNameSuffix("_PROPERACC");
      51         436 :   if(!keys.exists("USEGPU")) {
      52           0 :     keys.addFlag("USEGPU",false,"run this calculation on the GPU");
      53           0 :     keys.addLinkInDocForFlag("USEGPU","plugin_openaccPTM.md");
      54             :   }
      55         436 :   keys.needsAction("TRANSPOSE");
      56         436 :   keys.needsAction("CONCATENATE");
      57         436 : }
      58             : 
      59             : template <typename CM>
      60         274 : ContactMatrixShortcut<CM>::ContactMatrixShortcut(const ActionOptions& ao):
      61             :   Action(ao),
      62         274 :   ActionShortcut(ao) {
      63         274 :   std::vector<std::string> grp_str;
      64         274 :   std::string atomsstr="";
      65         274 :   std::vector<std::string> atomsvec;
      66         274 :   parseVector("ATOMS",atomsvec);
      67         274 :   bool usegpuFLAG=false;
      68         274 :   parseFlag("USEGPU",usegpuFLAG);
      69         548 :   const std::string usegpu=(usegpuFLAG)?"ACC " : " ";
      70         274 :   if( atomsvec.size()>0 )  {
      71           0 :     for(unsigned i=0; i<atomsvec.size(); ++i) {
      72           0 :       Group* gg = plumed.getActionSet().template selectWithLabel<Group*>( atomsvec[i] );
      73           0 :       if( gg ) {
      74           0 :         grp_str.push_back( atomsvec[i] );
      75             :       }
      76             :     }
      77           0 :     if( grp_str.size()!=atomsvec.size() ) {
      78           0 :       grp_str.resize(0);
      79           0 :       atomsstr = " ATOMS=" + atomsvec[0];
      80           0 :       for(unsigned i=1; i<atomsvec.size(); ++i) {
      81           0 :         atomsstr += "," + atomsvec[i];
      82             :       }
      83             :     }
      84             :   } else {
      85             :     std::string grp_inpt;
      86           4 :     for(unsigned i=1;; ++i) {
      87         556 :       if( !parseNumbered("GROUP",i,grp_inpt) ) {
      88             :         break;
      89             :       }
      90           4 :       grp_str.push_back( grp_inpt );
      91             :     }
      92             :   }
      93         274 :   if( grp_str.size()>9 ) {
      94           0 :     error("cannot handle more than 9 groups");
      95             :   }
      96         274 :   if( grp_str.size()==0 )  {
      97         816 :     readInputLine( getShortcutLabel() + ": CONTACT_MATRIX_PROPER"+usegpu
      98             :                    + atomsstr + " " + convertInputLineToString() );
      99             :     return;
     100             :   }
     101             : 
     102           6 :   for(unsigned i=0; i<grp_str.size(); ++i) {
     103             :     std::string sw_str, num;
     104           4 :     Tools::convert( i+1, num );
     105           8 :     parseNumbered("SWITCH", (i+1)*10 + 1 + i,  sw_str );
     106           4 :     if( sw_str.length()==0 ) {
     107           0 :       error("missing SWITCH" + num + num + " keyword");
     108             :     }
     109          20 :     readInputLine( getShortcutLabel() + num +  num + ": CONTACT_MATRIX_PROPER"+usegpu
     110             :                    + "GROUP=" + grp_str[i]
     111             :                    +" SWITCH={" + sw_str + "}" );
     112           6 :     for(unsigned j=0; j<i; ++j) {
     113             :       std::string sw_str2, jnum;
     114           2 :       Tools::convert( j+1, jnum );
     115           4 :       parseNumbered("SWITCH", (j+1)*10 + 1 + i, sw_str2);
     116           2 :       if( sw_str2.length()==0 ) {
     117           0 :         error("missing SWITCH" + jnum + num + " keyword");
     118             :       }
     119          12 :       readInputLine( getShortcutLabel() + jnum + num + ": CONTACT_MATRIX_PROPER"+usegpu
     120           2 :                      + "GROUPA=" + grp_str[j]
     121             :                      +" GROUPB=" + grp_str[i]
     122             :                      +" SWITCH={" + sw_str2 +"}");
     123           6 :       readInputLine( getShortcutLabel() + num +  jnum + ": TRANSPOSE ARG=" + getShortcutLabel() + jnum + num );
     124             :     }
     125             :   }
     126           2 :   std::string join_matrices = getShortcutLabel() + ": CONCATENATE";
     127           6 :   for(unsigned i=0; i<grp_str.size(); ++i) {
     128             :     std::string inum;
     129           4 :     Tools::convert(i+1,inum);
     130          12 :     for(unsigned j=0; j<grp_str.size(); ++j) {
     131             :       std::string jnum;
     132           8 :       Tools::convert(j+1,jnum);
     133           8 :       if( i>j ) {
     134           6 :         join_matrices += " MATRIX" + inum + jnum + "=" + getShortcutLabel() + inum +  jnum;
     135             :       } else {
     136          18 :         join_matrices += " MATRIX" + inum + jnum + "=" + getShortcutLabel() + inum +  jnum;
     137             :       }
     138             :     }
     139             :   }
     140           2 :   readInputLine( join_matrices );
     141         548 : }
     142             : 
     143             : }
     144             : }
     145             : #endif // __PLUMED_adjmat_ContactMatrixShortcut_h