CELL collective variables

src/colvar/Cell.cpp

+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2013 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed-code.org for more information.
+
+   This file is part of plumed, version 2.0.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "Colvar.h"
+#include "ActionRegister.h"
+
+#include <string>
+#include <cmath>
+
+using namespace std;
+
+namespace PLMD{
+namespace colvar{
+
+//+PLUMEDOC COLVAR CELL
+/*
+Calculate the components of the simulation cell
+
+\par Examples
+The following input tells plumed to print the squared modulo of each of the three lattice vectors
+\verbatim
+cell: CELL
+aaa:    COMBINE ARG=cell.ax,cell.ay,cell.az POWERS=2,2,2 PERIODIC=NO
+bbb:    COMBINE ARG=cell.bx,cell.by,cell.bz POWERS=2,2,2 PERIODIC=NO
+ccc:    COMBINE ARG=cell.cx,cell.cy,cell.cz POWERS=2,2,2 PERIODIC=NO
+PRINT ARG=aaa,bbb,ccc
+\endverbatim
+(See also \ref COMBINE and \ref PRINT).
+
+*/
+//+ENDPLUMEDOC
+
+
+class Cell : public Colvar {
+  Value* components[3][3];
+
+public:
+  Cell(const ActionOptions&);
+// active methods:
+  virtual void calculate();
+/// Register all the keywords for this action
+  static void registerKeywords( Keywords& keys );
+};
+
+PLUMED_REGISTER_ACTION(Cell,"CELL")
+
+Cell::Cell(const ActionOptions&ao):
+PLUMED_COLVAR_INIT(ao)
+{
+  std::vector<AtomNumber> atoms;
+  checkRead();
+
+  addComponentWithDerivatives("ax"); componentIsNotPeriodic("ax"); components[0][0]=getPntrToComponent("ax");
+  addComponentWithDerivatives("ay"); componentIsNotPeriodic("ay"); components[0][1]=getPntrToComponent("ay");
+  addComponentWithDerivatives("az"); componentIsNotPeriodic("az"); components[0][2]=getPntrToComponent("az");
+  addComponentWithDerivatives("bx"); componentIsNotPeriodic("bx"); components[1][0]=getPntrToComponent("bx");
+  addComponentWithDerivatives("by"); componentIsNotPeriodic("by"); components[1][1]=getPntrToComponent("by");
+  addComponentWithDerivatives("bz"); componentIsNotPeriodic("bz"); components[1][2]=getPntrToComponent("bz");
+  addComponentWithDerivatives("cx"); componentIsNotPeriodic("cx"); components[2][0]=getPntrToComponent("cx");
+  addComponentWithDerivatives("cy"); componentIsNotPeriodic("cy"); components[2][1]=getPntrToComponent("cy");
+  addComponentWithDerivatives("cz"); componentIsNotPeriodic("cz"); components[2][2]=getPntrToComponent("cz");
+  requestAtoms(atoms);
+}
+
+void Cell::registerKeywords( Keywords& keys ){
+  Action::registerKeywords( keys );
+  ActionWithValue::registerKeywords( keys );
+  ActionAtomistic::registerKeywords( keys );
+}
+
+
+// calculator
+void Cell::calculate(){
+
+  for(int i=0;i<3;i++) for(int j=0;j<3;j++) components[i][j]->set(getBox()[i][j]);
+  for(int l=0;l<3;l++) for(int m=0;m<3;m++){
+    Tensor der; for(int i=0;i<3;i++) der[i][m]=getBox()[l][i];
+    setBoxDerivatives(components[l][m],-der);
+  }
+}
+
+}
+}
+
+
+