Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2023 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 DUMPPROJECTIONS
      32             : /*
      33             : Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).
      34             : 
      35             : Consider the following PLUMED input:
      36             : 
      37             : ```plumed
      38             : x1: CENTER ATOMS=1-10
      39             : x2: CENTER ATOMS=11-20
      40             : r: DISTANCE ATOMS=x1,x2
      41             : ```
      42             : 
      43             : The derivatives of the distance `r` with respect to the atomic positions, $X_i$, are given by:
      44             : 
      45             : $$
      46             : \frac{\partial r}{\partial X_i} = \frac{\partial r}{\partial x_1}\frac{\partial r}{\partial x_2}\frac{\partial x_1}{\partial X_i}\frac{\partial x_2}{\partial X_i}
      47             : $$
      48             : 
      49             : For the input above there are 69 of these derivatives in total. These include the derivatives of $r$ with respect to the $x$, $y$ and $z$ components of the 10 atomic
      50             : positions that are used to calculate $x_1$, the derivatives of $r$ with respect to the $x$, $y$ and $z$ components of the 10 atomic
      51             : positions that are used to calculate $x_2$ and the 9 derivatives of $r$ with respect to the cell vectors.
      52             : 
      53             : If we add a DUMPROJECTIONS command to the above input as shown below:
      54             : 
      55             : ```plumed
      56             : x1: CENTER ATOMS=1-10
      57             : x2: CENTER ATOMS=11-20
      58             : d: DISTANCE ATOMS=x1,x2
      59             : DUMPPROJECTIONS ARG=d FILE=proj STRIDE=20
      60             : ```
      61             : 
      62             : PLUMED will output these 69 derivatives to the proj file.
      63             : 
      64             : !!! caution "only works for scalars"
      65             : 
      66             :     This action cannot be used if non rank zero objects are passed between actions that are used to calculate the quantity (`d` in the above examples)
      67             :     whose projections are being output using the DUMPPROJECTIONS command
      68             : 
      69             : ## RESTART, UPDATE_FROM and UPDATE_UNTIL
      70             : 
      71             : Notice that the RESTART, UPDATE_FROM and UPDATE_UNTIL keywords keywords
      72             : can be used in this action in the same way as they are used for [PRINT](PRINT.md).
      73             : Consequently, if you would like to append derivatives to an existing file called `proj` instead of backing that
      74             : file up at the start of the calculation and outputting the data from the calculation on a new file called `proj`
      75             : you would use an input like the one shown below:
      76             : 
      77             : ```plumed
      78             : x1: CENTER ATOMS=1-10
      79             : x2: CENTER ATOMS=11-20
      80             : d: DISTANCE ATOMS=x1,x2
      81             : DUMPPROJECTIONS ARG=d STRIDE=1 FILE=proj FMT=%10.6f RESTART=YES
      82             : ```
      83             : 
      84             : Similarly, if you want to only output the derivatives during the 400 ps time interval after the first
      85             : 100 ps of the simulation you would use an input like the one shown below:
      86             : 
      87             : ```plumed
      88             : x1: CENTER ATOMS=1-10
      89             : x2: CENTER ATOMS=11-20
      90             : d: DISTANCE ATOMS=x1,x2
      91             : DUMPPROJECTIONS ARG=d STRIDE=1 FILE=d UPDATE_FROM=100 UPDATE_UNTIL=500
      92             : ```
      93             : 
      94             : 
      95             : */
      96             : //+ENDPLUMEDOC
      97             : 
      98             : class DumpProjections :
      99             :   public ActionPilot,
     100             :   public ActionWithArguments {
     101             :   std::string file;
     102             :   std::string fmt;
     103             :   OFile of;
     104             : public:
     105           3 :   void calculate() override {}
     106             :   explicit DumpProjections(const ActionOptions&);
     107             :   static void registerKeywords(Keywords& keys);
     108           3 :   void apply() override {}
     109             :   void update() override;
     110           3 :   bool checkNeedsGradients()const override {
     111           3 :     return true;
     112             :   }
     113             :   ~DumpProjections();
     114             : };
     115             : 
     116             : PLUMED_REGISTER_ACTION(DumpProjections,"DUMPPROJECTIONS")
     117             : 
     118           5 : void DumpProjections::registerKeywords(Keywords& keys) {
     119           5 :   Action::registerKeywords(keys);
     120           5 :   ActionPilot::registerKeywords(keys);
     121           5 :   ActionWithArguments::registerKeywords(keys);
     122          10 :   keys.addInputKeyword("compulsory","ARG","scalar","the labels of the values whose gradients should be outpu");
     123           5 :   keys.add("compulsory","STRIDE","1","the frequency with which the derivatives should be output");
     124           5 :   keys.add("compulsory","FILE","the name of the file on which to output the derivatives");
     125           5 :   keys.add("compulsory","FMT","%15.10f","the format with which the derivatives should be output");
     126           5 :   keys.use("RESTART");
     127           5 :   keys.use("UPDATE_FROM");
     128           5 :   keys.use("UPDATE_UNTIL");
     129           5 : }
     130             : 
     131           1 : DumpProjections::DumpProjections(const ActionOptions&ao):
     132             :   Action(ao),
     133             :   ActionPilot(ao),
     134             :   ActionWithArguments(ao),
     135           1 :   fmt("%15.10f") {
     136           2 :   parse("FILE",file);
     137           1 :   if( file.length()==0 ) {
     138           0 :     error("filename not specified");
     139             :   }
     140           1 :   parse("FMT",fmt);
     141           1 :   fmt=" "+fmt;
     142           1 :   of.link(*this);
     143           1 :   of.open(file);
     144           1 :   log.printf("  on file %s\n",file.c_str());
     145           1 :   log.printf("  with format %s\n",fmt.c_str());
     146           1 :   checkRead();
     147             : 
     148           3 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
     149           2 :     if( getPntrToArgument(i)->getRank()!=0 ) {
     150           0 :       error("cannot use DUMPPROJECTIONS with actions that are not scalars");
     151             :     }
     152           2 :     (getPntrToArgument(i)->getPntrToAction())->turnOnDerivatives();
     153             :   }
     154           1 : }
     155             : 
     156             : 
     157           3 : void DumpProjections::update() {
     158           6 :   of.fmtField(" %f").printField("time",getTime());
     159           9 :   for(unsigned i=0; i<getNumberOfArguments(); i++) {
     160          18 :     for(unsigned j=0; j<getNumberOfArguments(); j++) {
     161          12 :       of.fmtField(fmt);
     162          24 :       of.printField(getPntrToArgument(i)->getName()+"-"+getPntrToArgument(j)->getName(),getProjection(i,j));
     163             :     }
     164             :   }
     165           3 :   of.printField();
     166           3 : }
     167             : 
     168           2 : DumpProjections::~DumpProjections() {
     169           2 : }
     170             : 
     171             : }
     172             : 
     173             : 
     174             : }