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/ActionWithArguments.h"
      24             : #include "core/ActionRegister.h"
      25             : 
      26             : namespace PLMD {
      27             : namespace generic {
      28             : 
      29             : //+PLUMEDOC PRINTANALYSIS PRINT
      30             : /*
      31             : Print quantities to a file.
      32             : 
      33             : This command can be used to output quantities to a file. The following demonstrates a very
      34             : simple example:
      35             : 
      36             : ```plumed
      37             : d: DISTANCE ATOMS=1,2
      38             : PRINT ARG=d FILE=colvar
      39             : ```
      40             : 
      41             : This command outputs the distance between atom 1 and 2 to a file called colvar every step of
      42             : trajectory. If you want to output the distance less frequently you can use the STRIDE keyword
      43             : as illustrated below:
      44             : 
      45             : ```plumed
      46             : d: DISTANCE ATOMS=1,2
      47             : PRINT ARG=d FILE=colvar STRIDE=10
      48             : ```
      49             : 
      50             : With the input above the distance is only output on every 10th step. Notice this distance will only
      51             : be calculated on every step as this quantity is not used on every other step.
      52             : 
      53             : You can also use the PRINT command to output objects that have a rank that is greater than zero.
      54             : For example, the following input calculates a vector of three distances. These three distances
      55             : are then output to the output colvar file every step.
      56             : 
      57             : ```plumed
      58             : d: DISTANCE ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6
      59             : PRINT ARG=d FILE=colvar
      60             : ```
      61             : 
      62             : Alterantively, we can output a matrix by using an input like the one shown below:
      63             : 
      64             : ```plumed
      65             : d: DISTANCE_MATRIX GROUP=1-4
      66             : PRINT ARG=d FILE=colvar
      67             : ```
      68             : 
      69             : The output `colvar` file here will contain the 16 elements of the matrix on each line output. You can
      70             : also use PRINT to output functions on grids. However, you are probably better using [DUMPGRID](DUMPGRID.md) or
      71             : [DUMPCUBE](DUMPCUBE.md) to output functions on grids.
      72             : 
      73             : The PRINT directive can be used multiple times in the input so you can print files with different strides or print different quantities
      74             : to different files as illustrated in the example input below:
      75             : 
      76             : ```plumed
      77             : # compute distance:
      78             : distance: DISTANCE ATOMS=2,5
      79             : # compute total energy (potential)
      80             : energy: ENERGY
      81             : # print distance on a file
      82             : PRINT ARG=distance          STRIDE=10   FILE=COLVAR
      83             : # print both variables on another file
      84             : PRINT ARG=distance,energy   STRIDE=1000 FILE=COLVAR_ALL
      85             : ```
      86             : 
      87             : The input above instructs plumed to print the distance between atoms 3 and 5 on a file
      88             : called COLVAR every 10 steps, and the distance and total energy on a file called COLVAR_ALL
      89             : every 1000 steps.
      90             : 
      91             : You can control the buffering of output using the [FLUSH](FLUSH.md) keyword. Furthermore, whether the output file is
      92             : appended or backed up depends on whetehr or not the [RESTART](RESTART.md) action is present on the file. If you add `RESTART=yes` on the
      93             : line containing the PRINT directive the file will be appended also.
      94             : 
      95             : Printing happens in the so-called "update" phase. This implies that printing
      96             : is affected by the presence of [UPDATE_IF](UPDATE_IF.md) actions. One can thus decide to start
      97             : and stop printing at preassigned values of time using the `UPDATE_FROM` and `UPDATE_UNTIL` keywords.
      98             : Keep into account that even on steps when the action is not updated (and thus the file is not printed)
      99             : the argument will be activated. In other words, if you use `UPDATE_FROM` to start printing at a given time,
     100             : the collective variables this PRINT statement depends on will be computed also before that time.
     101             : 
     102             : */
     103             : //+ENDPLUMEDOC
     104             : 
     105             : class Print :
     106             :   public ActionPilot,
     107             :   public ActionWithArguments {
     108             :   std::string file;
     109             :   OFile ofile;
     110             :   std::string fmt;
     111             : // small internal utility
     112             : /////////////////////////////////////////
     113             : // these are crazy things just for debug:
     114             : // they allow to change regularly the
     115             : // printed argument
     116             :   int rotate;
     117             :   int rotateCountdown;
     118             :   int rotateLast;
     119             :   std::vector<Value*> rotateArguments;
     120             : /////////////////////////////////////////
     121             : public:
     122      227868 :   void calculate() override {}
     123             :   void prepare() override;
     124             :   std::string writeInGraph() const override;
     125             :   explicit Print(const ActionOptions&);
     126             :   static void registerKeywords(Keywords& keys);
     127      227746 :   void apply() override {}
     128             :   void update() override;
     129             :   ~Print();
     130             : };
     131             : 
     132             : PLUMED_REGISTER_ACTION(Print,"PRINT")
     133             : 
     134        1156 : void Print::registerKeywords(Keywords& keys) {
     135        1156 :   Action::registerKeywords(keys);
     136        1156 :   ActionPilot::registerKeywords(keys);
     137        1156 :   ActionWithArguments::registerKeywords(keys);
     138        2312 :   keys.addInputKeyword("compulsory","ARG","scalar/vector/matrix","the labels of the values that you would like to print to the file");
     139        1156 :   keys.add("compulsory","STRIDE","1","the frequency with which the quantities of interest should be output");
     140        1156 :   keys.add("optional","FILE","the name of the file on which to output these quantities");
     141        1156 :   keys.add("optional","FMT","the format that should be used to output real numbers");
     142        1156 :   keys.add("hidden","_ROTATE","some funky thing implemented by GBussi");
     143        1156 :   keys.use("RESTART");
     144        1156 :   keys.use("UPDATE_FROM");
     145        1156 :   keys.use("UPDATE_UNTIL");
     146        1156 : }
     147             : 
     148        1154 : Print::Print(const ActionOptions&ao):
     149             :   Action(ao),
     150             :   ActionPilot(ao),
     151             :   ActionWithArguments(ao),
     152        1154 :   fmt("%f"),
     153        2308 :   rotate(0) {
     154        1154 :   ofile.link(*this);
     155        2308 :   parse("FILE",file);
     156        1154 :   if(file.length()>0) {
     157        1154 :     ofile.open(file);
     158        1154 :     log.printf("  on file %s\n",file.c_str());
     159             :   } else {
     160           0 :     log.printf("  on plumed log file\n");
     161           0 :     ofile.link(log);
     162             :   }
     163        1154 :   parse("FMT",fmt);
     164        1154 :   fmt=" "+fmt;
     165        1154 :   log.printf("  with format %s\n",fmt.c_str());
     166        7565 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
     167        6411 :     ofile.setupPrintValue( getPntrToArgument(i) );
     168        6411 :     getPntrToArgument(i)->buildDataStore(true);
     169             :   }
     170             : /////////////////////////////////////////
     171             : // these are crazy things just for debug:
     172             : // they allow to change regularly the
     173             : // printed argument
     174        1154 :   parse("_ROTATE",rotate);
     175        1154 :   if(rotate>0) {
     176           1 :     rotateCountdown=rotate;
     177           4 :     for(unsigned i=0; i<getNumberOfArguments(); ++i) {
     178           3 :       rotateArguments.push_back( getPntrToArgument(i) );
     179             :     }
     180           1 :     std::vector<Value*> a(1,rotateArguments[0]);
     181           1 :     requestArguments(std::vector<Value*>(1,rotateArguments[0]));
     182           1 :     rotateLast=0;
     183             :   }
     184             : /////////////////////////////////////////
     185        1154 :   checkRead();
     186        1154 : }
     187             : 
     188           8 : std::string Print::writeInGraph() const {
     189          16 :   return getName() + "\n" + "FILE=" + file;
     190             : }
     191             : 
     192      228012 : void Print::prepare() {
     193             : /////////////////////////////////////////
     194             : // these are crazy things just for debug:
     195             : // they allow to change regularly the
     196             : // printed argument
     197      228012 :   if(rotate>0) {
     198           5 :     rotateCountdown--;
     199           5 :     if(rotateCountdown==0) {
     200           2 :       rotateCountdown=rotate;
     201           2 :       rotateLast++;
     202           2 :       rotateLast%=rotateArguments.size();
     203           4 :       requestArguments(std::vector<Value*>(1,rotateArguments[rotateLast]));
     204             :     }
     205             :   }
     206             : /////////////////////////////////////////
     207      228012 : }
     208             : 
     209      220574 : void Print::update() {
     210      220574 :   ofile.fmtField(" %f");
     211      220574 :   ofile.printField("time",getTime());
     212      775474 :   for(unsigned i=0; i<getNumberOfArguments(); i++) {
     213      554900 :     ofile.fmtField(fmt);
     214      554900 :     getPntrToArgument(i)->print( ofile );
     215             :   }
     216      220574 :   ofile.printField();
     217      220574 : }
     218             : 
     219        2308 : Print::~Print() {
     220        2308 : }
     221             : 
     222             : }
     223             : 
     224             : 
     225             : }