Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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 "core/ActionPilot.h"
      23             : #include "core/ActionWithValue.h"
      24             : #include "core/ActionWithArguments.h"
      25             : #include "core/ActionRegister.h"
      26             : #include "tools/File.h"
      27             : 
      28             : namespace PLMD {
      29             : namespace generic {
      30             : 
      31             : //+PLUMEDOC PRINTANALYSIS DUMPDERIVATIVES
      32             : /*
      33             : Dump the derivatives with respect to the input parameters for scalar values (generally CVs, functions or biases).
      34             : 
      35             : You can use this command to output the derivatives of a scalar with respect to whatever input parameters are used to
      36             : calculate that scalar.  For example, the following input instructs plumed to write a file called deriv that contains both the
      37             : analytical and numerical derivatives of the distance between atoms 1 and 2.
      38             : 
      39             : ```plumed
      40             : distance: DISTANCE ATOMS=1,2
      41             : distanceN: DISTANCE ATOMS=1,2 NUMERICAL_DERIVATIVES
      42             : DUMPDERIVATIVES ARG=distance,distanceN STRIDE=1 FILE=deriv
      43             : ```
      44             : 
      45             : This input outputs the derivative of the distance with respect to the atom positions and the cell vectors (virial-like form).
      46             : It will thus output 15 deriatives for the two quantities output - the derivatives with respect to the x,y and z components of the input atoms
      47             : and the 9 components of the virial.
      48             : 
      49             : By contast the following input will only output 1 derivative; namely, the derivative of the switching function, `f`, with respect to the input distance, `d`.
      50             : 
      51             : ```plumed
      52             : d: DISTANCE ATOMS=1,2
      53             : f: LESS_THAN ARG=d SWITCH={RATIONAL R_0=0.2}
      54             : DUMPDERIVATIVES ARG=f STRIDE=1 FMT=%8.4f FILE=deriv
      55             : ```
      56             : 
      57             : !!! warning ""
      58             : 
      59             :     You can only use this command to output the derivatives of rank 0 (scalar) values.
      60             :     You cannot use it to output derivatives of vector, matrix of function values.
      61             : 
      62             : ## RESTART, UPDATE_FROM and UPDATE_UNTIL
      63             : 
      64             : Notice that the RESTART, UPDATE_FROM and UPDATE_UNTIL keywords keywords
      65             : can be used in this action in the same way as they are used for [PRINT](PRINT.md).
      66             : Consequently, if you would like to append derivatives to an existing file called `deriv` instead of backing that
      67             : file up at the start of the calculation and outputting the data from the calculation on a new file called `deriv`
      68             : you would use an input like the one shown below:
      69             : 
      70             : ```plumed
      71             : distance: DISTANCE ATOMS=1,2
      72             : DUMPDERIVATIVES ARG=distance STRIDE=1 FILE=deriv RESTART=YES
      73             : ```
      74             : 
      75             : Similarly, if you want to only output the derivatives during the 400 ps time interval after the first
      76             : 100 ps of the simulation you would use an input like the one shown below:
      77             : 
      78             : ```plumed
      79             : distance: DISTANCE ATOMS=1,2
      80             : DUMPDERIVATIVES ARG=distance STRIDE=1 FILE=deriv UPDATE_FROM=100 UPDATE_UNTIL=500
      81             : ```
      82             : 
      83             : */
      84             : //+ENDPLUMEDOC
      85             : 
      86             : class DumpDerivatives :
      87             :   public ActionPilot,
      88             :   public ActionWithArguments {
      89             :   std::string file;
      90             :   std::string fmt;
      91             :   OFile of;
      92             : public:
      93       13782 :   void calculate() override {}
      94             :   explicit DumpDerivatives(const ActionOptions&);
      95             :   static void registerKeywords(Keywords& keys);
      96       13740 :   void apply() override {}
      97             :   void update() override;
      98             :   ~DumpDerivatives();
      99             : };
     100             : 
     101             : PLUMED_REGISTER_ACTION(DumpDerivatives,"DUMPDERIVATIVES")
     102             : 
     103         232 : void DumpDerivatives::registerKeywords(Keywords& keys) {
     104         232 :   Action::registerKeywords(keys);
     105         232 :   ActionPilot::registerKeywords(keys);
     106         232 :   ActionWithArguments::registerKeywords(keys);
     107         464 :   keys.addInputKeyword("compulsory","ARG","scalar","the labels of the values whose derivatives should be output");
     108         232 :   keys.add("compulsory","STRIDE","1","the frequency with which the derivatives should be output");
     109         232 :   keys.add("compulsory","FILE","the name of the file on which to output the derivatives");
     110         232 :   keys.add("compulsory","FMT","%15.10f","the format with which the derivatives should be output");
     111         232 :   keys.use("RESTART");
     112         232 :   keys.use("UPDATE_FROM");
     113         232 :   keys.use("UPDATE_UNTIL");
     114         232 : }
     115             : 
     116         230 : DumpDerivatives::DumpDerivatives(const ActionOptions&ao):
     117             :   Action(ao),
     118             :   ActionPilot(ao),
     119             :   ActionWithArguments(ao),
     120         230 :   fmt("%15.10f") {
     121         460 :   parse("FILE",file);
     122         230 :   if( file.length()==0 ) {
     123           0 :     error("name of output file was not specified");
     124             :   }
     125         230 :   parse("FMT",fmt);
     126         230 :   fmt=" "+fmt;
     127         230 :   of.link(*this);
     128         230 :   of.open(file);
     129         230 :   log.printf("  on file %s\n",file.c_str());
     130         230 :   log.printf("  with format %s\n",fmt.c_str());
     131             :   unsigned nargs=getNumberOfArguments();
     132         230 :   if( nargs==0 ) {
     133           0 :     error("no arguments specified");
     134             :   }
     135         230 :   (getPntrToArgument(0)->getPntrToAction())->turnOnDerivatives();
     136         230 :   if( getPntrToArgument(0)->getRank()>0 ) {
     137           0 :     error("cannot dump derivatives of non-scalar objects");
     138             :   }
     139         230 :   unsigned npar=getPntrToArgument(0)->getNumberOfDerivatives();
     140         230 :   if( npar==0 ) {
     141           0 :     error("one or more arguments has no derivatives");
     142             :   }
     143         804 :   for(unsigned i=1; i<nargs; i++) {
     144         574 :     (getPntrToArgument(i)->getPntrToAction())->turnOnDerivatives();
     145         574 :     if( getPntrToArgument(i)->getRank()>0 ) {
     146           0 :       error("cannot dump derivatives of non-scalar objects");
     147             :     }
     148         574 :     if( npar!=getPntrToArgument(i)->getNumberOfDerivatives() ) {
     149           0 :       error("the number of derivatives must be the same in all values being dumped");
     150             :     }
     151             :   }
     152         230 :   checkRead();
     153         230 : }
     154             : 
     155             : 
     156        9055 : void DumpDerivatives::update() {
     157        9055 :   unsigned npar=getPntrToArgument(0)->getNumberOfDerivatives();
     158      672414 :   for(unsigned ipar=0; ipar<npar; ipar++) {
     159      663359 :     of.fmtField(" %f");
     160      663359 :     of.printField("time",getTime());
     161      663359 :     of.printField("parameter",(int)ipar);
     162     3315611 :     for(unsigned i=0; i<getNumberOfArguments(); i++) {
     163     2652252 :       of.fmtField(fmt);
     164     2652252 :       of.printField(getPntrToArgument(i)->getName(),getPntrToArgument(i)->getDerivative(ipar) );
     165             :     }
     166      663359 :     of.printField();
     167             :   }
     168        9055 : }
     169             : 
     170         460 : DumpDerivatives::~DumpDerivatives() {
     171         460 : }
     172             : 
     173             : }
     174             : 
     175             : 
     176             : }