colvarcomp_rotations.C

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#include <cmath>

#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
#include "colvar.h"
#include "colvarcomp.h"



colvar::orientation::orientation (std::string const &conf)
  : cvc (conf)
{
  function_type = "orientation";
  parse_group (conf, "atoms", atoms);
  x.type (colvarvalue::type_quaternion);

  ref_pos.reserve (atoms.size());

  if (get_keyval (conf, "refPositions", ref_pos, ref_pos)) {
    cvm::log ("Using reference positions from input file.\n");
    if (ref_pos.size() != atoms.size()) {
      cvm::fatal_error ("Error: reference positions do not "
                        "match the number of atom indexes.\n");
    }
  }

  {
    std::string file_name;
    if (get_keyval (conf, "refPositionsFile", file_name)) {

      std::string file_col;
      get_keyval (conf, "refPositionsCol", file_col, std::string ("O"));

      double file_col_value;
      bool found = get_keyval (conf, "refPositionsColValue", file_col_value, 0.0);
      if (found && !file_col_value)
        cvm::fatal_error ("Error: refPositionsColValue, "
                          "if provided, must be non-zero.\n");

      ref_pos.resize (atoms.size());
      cvm::load_coords (file_name.c_str(), ref_pos, file_col, file_col_value);
    }
  }

  if (!ref_pos.size()) {
    cvm::fatal_error ("Error: must define a set of "
                      "reference coordinates.\n");
  }


  cvm::log ("Centering the reference coordinates: it is "
            "assumed that each atom is the closest "
            "periodic image to the center of geometry.\n");
  cvm::rvector cog (0.0, 0.0, 0.0);
  for (size_t i = 0; i < ref_pos.size(); i++) {
    cog += ref_pos[i];
  }
  cog /= cvm::real (ref_pos.size());
  for (size_t i = 0; i < ref_pos.size(); i++) {
    ref_pos[i] -= cog;
  }

  get_keyval (conf, "closestToQuaternion", ref_quat, cvm::quaternion (1.0, 0.0, 0.0, 0.0));

  // initialize rot member data
  if (!atoms.noforce) {
    rot.request_group2_gradients (atoms.size());
  }

  rot.b_debug_gradients = this->b_debug_gradients;
}

  
colvar::orientation::orientation()
  : cvc ()
{
  function_type = "orientation";
  x.type (colvarvalue::type_quaternion);
}


void colvar::orientation::calc_value()
{
  atoms.reset_atoms_data();
  atoms.read_positions();

  atoms_cog = atoms.center_of_geometry();

  rot.calc_optimal_rotation (ref_pos, atoms.positions_shifted (-1.0 * atoms_cog));

  if ((rot.q).inner (ref_quat) >= 0.0) {
    x.quaternion_value = rot.q;
  } else {
    x.quaternion_value = -1.0 * rot.q;
  }
}


void colvar::orientation::calc_gradients()
{
  // gradients have already been calculated and stored within the
  // member object "rot"; we're not using the "grad" member of each
  // atom object, because it only can represent the gradient of a
  // scalar colvar
}


void colvar::orientation::apply_force (colvarvalue const &force)
{
  cvm::quaternion const &FQ = force.quaternion_value;

  if (!atoms.noforce) {
    for (size_t ia = 0; ia < atoms.size(); ia++) {
      for (size_t i = 0; i < 4; i++) {
        atoms[ia].apply_force (FQ[i] * rot.dQ0_2[ia][i]);
      }
    }
  }
}



colvar::orientation_angle::orientation_angle (std::string const &conf)
  : orientation (conf)
{
  function_type = "orientation_angle";
  x.type (colvarvalue::type_scalar);
}


colvar::orientation_angle::orientation_angle()
  : orientation()
{
  function_type = "orientation_angle";
  x.type (colvarvalue::type_scalar);
}


void colvar::orientation_angle::calc_value()
{
  atoms.reset_atoms_data();
  atoms.read_positions();

  atoms_cog = atoms.center_of_geometry();

  rot.calc_optimal_rotation (ref_pos, atoms.positions_shifted (-1.0 * atoms_cog));

  if ((rot.q).q0 >= 0.0) {
    x.real_value = (180.0/PI) * 2.0 * ::acos ((rot.q).q0);
  } else {
    x.real_value = (180.0/PI) * 2.0 * ::acos (-1.0 * (rot.q).q0);
  }
}


void colvar::orientation_angle::calc_gradients()
{
  cvm::real const dxdq0 =
    ( ((rot.q).q0 * (rot.q).q0 < 1.0) ? 
      ((180.0 / PI) * (-2.0) / ::sqrt (1.0 - ((rot.q).q0 * (rot.q).q0))) :
      0.0 );

  for (size_t ia = 0; ia < atoms.size(); ia++) {
    atoms[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]);
  }
}


void colvar::orientation_angle::apply_force (colvarvalue const &force)
{
  cvm::real const &fw = force.real_value;

  if (!atoms.noforce) {
    atoms.apply_colvar_force (fw);
  }
}

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