lammps/lib/colvars/colvarcomp.cpp

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



colvar::cvc::cvc()
  : sup_coeff (1.0), sup_np (1),
    b_periodic (false),
    b_debug_gradients (false),
    b_inverse_gradients (false),
    b_Jacobian_derivative (false)
{}


colvar::cvc::cvc (std::string const &conf)
  : sup_coeff (1.0), sup_np (1),
    b_periodic (false),
    b_debug_gradients (false),
    b_inverse_gradients (false),
    b_Jacobian_derivative (false)
{
  if (cvm::debug())
    cvm::log ("Initializing cvc base object.\n");

  get_keyval (conf, "name", this->name, std::string (""), parse_silent);

  get_keyval (conf, "componentCoeff", sup_coeff, 1.0);
  get_keyval (conf, "componentExp", sup_np, 1);

  get_keyval (conf, "period", period, 0.0);
  get_keyval (conf, "wrapAround", wrap_center, 0.0);

  get_keyval (conf, "debugGradients", b_debug_gradients, false, parse_silent);

  if (cvm::debug())
    cvm::log ("Done initializing cvc base object.\n");
}


void colvar::cvc::parse_group (std::string const &conf, 
                               char const *group_key,
                               cvm::atom_group &group,
                               bool optional)
{
  if (key_lookup (conf, group_key)) {
    group.parse (conf, group_key);
  } else {
    if (! optional) {
      cvm::fatal_error ("Error: definition for atom group \""+
                      std::string (group_key)+"\" not found.\n");
    }
  }
}


colvar::cvc::~cvc()
{}


void colvar::cvc::calc_force_invgrads()
{
  cvm::fatal_error ("Error: calculation of inverse gradients is not implemented "
                    "for colvar components of type \""+function_type+"\".\n");
}


void colvar::cvc::calc_Jacobian_derivative()
{
  cvm::fatal_error ("Error: calculation of inverse gradients is not implemented "
                    "for colvar components of type \""+function_type+"\".\n");
}


void colvar::cvc::debug_gradients (cvm::atom_group &group)
{
  // this function should work for any scalar variable:
  // the only difference will be the name of the atom group (here, "group")

  // collect into a vector for convenience
  std::vector<cvm::rvector> gradients (group.size());
  for (size_t i = 0; i < group.size(); i++) {
    gradients[i] = group[i].grad;
  }

  cvm::rotation const rot_0 = group.rot;
  cvm::rotation const rot_inv = group.rot.inverse();

  cvm::real const x_0 = x.real_value;

  cvm::log ("gradients     = "+cvm::to_str (gradients)+"\n");

  // it only makes sense to debug the fit gradients
  // when the fitting group is the same as this group
  if (group.b_rotate || group.b_center)
    if (group.b_fit_gradients && (group.ref_pos_group == NULL)) {
      group.calc_fit_gradients();
      if (group.b_rotate) {
        // fit_gradients are in the original frame, we should print them in the rotated frame
        for (size_t j = 0; j < group.fit_gradients.size(); j++) {
          group.fit_gradients[j] = rot_0.rotate (group.fit_gradients[j]);
        }
      }
      cvm::log ("fit_gradients = "+cvm::to_str (group.fit_gradients)+"\n");
      if (group.b_rotate) {
        for (size_t j = 0; j < group.fit_gradients.size(); j++) {
          group.fit_gradients[j] = rot_inv.rotate (group.fit_gradients[j]);
        }
      }
    }

  for (size_t ia = 0; ia < group.size(); ia++) {

    // tests are best conducted in the unrotated (simulation) frame
    cvm::rvector const atom_grad = group.b_rotate ?
      rot_inv.rotate (group[ia].grad) :
      group[ia].grad;

    for (size_t id = 0; id < 3; id++) {
      // (re)read original positions
      group.read_positions();
      // change one coordinate 
      group[ia].pos[id] += cvm::debug_gradients_step_size;
      // (re)do the fit (if defined)
      if (group.b_center || group.b_rotate) {
        group.calc_apply_roto_translation();
      }
      calc_value();
      cvm::real const x_1 = x.real_value;
      cvm::log ("Atom "+cvm::to_str (ia)+", component "+cvm::to_str (id)+":\n");
      cvm::log ("dx(actual) = "+cvm::to_str (x_1 - x_0,
                             21, 14)+"\n");
      cvm::real const dx_pred = (group.fit_gradients.size() && (group.ref_pos_group == NULL)) ?
        (cvm::debug_gradients_step_size * (atom_grad[id] + group.fit_gradients[ia][id])) :
        (cvm::debug_gradients_step_size * atom_grad[id]);
      cvm::log ("dx(interp) = "+cvm::to_str (dx_pred,
                             21, 14)+"\n");
      cvm::log ("|dx(actual) - dx(interp)|/|dx(actual)| = "+
                cvm::to_str (std::fabs (x_1 - x_0 - dx_pred) /
                             std::fabs (x_1 - x_0),
                             12, 5)+
                ".\n");

    }
  }
}