Merge pull request #1229 from invemichele/fix_plumed_memory_leak

  p->cmd("getBias",&bias);

  // Pass virial to plumed

  // If energy is needed virial_plmd is equal to Lammps' virial

  // If energy is not needed virial_plmd is initialized to zero

  // If energy is needed plmd_virial is equal to Lammps' virial

  // If energy is not needed plmd_virial is initialized to zero

  // In the first case the virial will be rescaled and an extra term will be added

  // In the latter case only an extra term will be added

  p->cmd("setVirial",&plmd_virial[0][0]);

    plmd_virial[0][1]=-virial_lmp[3];

    plmd_virial[0][2]=-virial_lmp[4];

    plmd_virial[1][2]=-virial_lmp[5];

  } else {

    virial_lmp = new double[6];

    for (int i=0;i<6;i++) virial_lmp[i] = 0.;

  }

  // do the real calculation:

  p->cmd("performCalc");

  // retransform virial to lammps representation and assign it to this

  // fix's virial.  Plumed is giving back the full virial and therefore

  // we have to subtract the initial virial i.e. virial_lmp.

  // fix's virial. If the energy is biased, Plumed is giving back the full

  // virial and therefore we have to subtract the initial virial i.e. virial_lmp.

  // The vector virial contains only the contribution added by plumed.

  // The calculation of the pressure will be done by a compute pressure

  // and will include this contribution.

  if (plumedNeedsEnergy) {

    virial[0] = -plmd_virial[0][0]-virial_lmp[0];

    virial[1] = -plmd_virial[1][1]-virial_lmp[1];

    virial[2] = -plmd_virial[2][2]-virial_lmp[2];

    virial[3] = -plmd_virial[0][1]-virial_lmp[3];

    virial[4] = -plmd_virial[0][2]-virial_lmp[4];

    virial[5] = -plmd_virial[1][2]-virial_lmp[5];

  } else {

    virial[0] = -plmd_virial[0][0];

    virial[1] = -plmd_virial[1][1];

    virial[2] = -plmd_virial[2][2];

    virial[3] = -plmd_virial[0][1];

    virial[4] = -plmd_virial[0][2];

    virial[5] = -plmd_virial[1][2];

  }

  // Ask for the computes in the next time step

  // such that the virial and energy are tallied.