// $Id$
//
//  Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include "Nonbonded.h"
#include "Params.h"
#include <cmath>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/utils.h>

namespace ForceFields {
namespace UFF {
namespace Utils {
double calcNonbondedMinimum(const AtomicParams *at1Params,
                            const AtomicParams *at2Params) {
  return sqrt(at1Params->x1 * at2Params->x1);
}
double calcNonbondedDepth(const AtomicParams *at1Params,
                          const AtomicParams *at2Params) {
  return sqrt(at1Params->D1 * at2Params->D1);
}

}  // namespace Utils

vdWContrib::vdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2,
                       const AtomicParams *at1Params,
                       const AtomicParams *at2Params, double threshMultiplier) {
  PRECONDITION(owner, "bad owner");
  PRECONDITION(at1Params, "bad params pointer");
  PRECONDITION(at2Params, "bad params pointer");
  URANGE_CHECK(idx1, owner->positions().size());
  URANGE_CHECK(idx2, owner->positions().size());

  dp_forceField = owner;
  d_at1Idx = idx1;
  d_at2Idx = idx2;

  // UFF uses the geometric mean of the vdW parameters:
  d_xij = Utils::calcNonbondedMinimum(at1Params, at2Params);
  d_wellDepth = Utils::calcNonbondedDepth(at1Params, at2Params);
  d_thresh = threshMultiplier * d_xij;

  // std::cerr << "  non-bonded: " << idx1 << "-" << idx2 << " " << d_xij << " "
  // << d_wellDepth << " " << d_thresh << std::endl;
}

double vdWContrib::getEnergy(double *pos) const {
  PRECONDITION(dp_forceField, "no owner");
  PRECONDITION(pos, "bad vector");

  double dist = dp_forceField->distance(d_at1Idx, d_at2Idx, pos);
  if (dist > d_thresh || dist <= 0.0) {
    return 0.0;
  }

  double r = d_xij / dist;
  double r6 = int_pow<6>(r);
  double r12 = r6 * r6;
  double res = d_wellDepth * (r12 - 2.0 * r6);
  // if(d_at1Idx==12 && d_at2Idx==21 ) std::cerr << "     >: " << d_at1Idx <<
  // "-" << d_at2Idx << " " << r << " = " << res << std::endl;
  return res;
}
void vdWContrib::getGrad(double *pos, double *grad) const {
  PRECONDITION(dp_forceField, "no owner");
  PRECONDITION(pos, "bad vector");
  PRECONDITION(grad, "bad vector");

  double dist = dp_forceField->distance(d_at1Idx, d_at2Idx, pos);
  if (dist > d_thresh) {
    return;
  }

  if (dist <= 0) {
    for (int i = 0; i < 3; i++) {
      // move in an arbitrary direction
      double dGrad = 100.0;
      grad[3 * d_at1Idx + i] += dGrad;
      grad[3 * d_at2Idx + i] -= dGrad;
    }
    return;
  }

  double r = d_xij / dist;
  double r7 = int_pow<7>(r);
  double r13 = int_pow<13>(r);
  double preFactor = 12. * d_wellDepth / d_xij * (r7 - r13);

  double *at1Coords = &(pos[3 * d_at1Idx]);
  double *at2Coords = &(pos[3 * d_at2Idx]);
  for (int i = 0; i < 3; i++) {
    double dGrad = preFactor * (at1Coords[i] - at2Coords[i]) / dist;
    grad[3 * d_at1Idx + i] += dGrad;
    grad[3 * d_at2Idx + i] -= dGrad;
  }
}
}  // namespace UFF
}  // namespace ForceFields