lammps/lib/colvars/colvartypes.cpp

// -*- c++ -*-

// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/Colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.

#include "colvarmodule.h"
#include "colvartypes.h"
#include "colvaratoms.h"
#include "colvar_rotation_derivative.h"

#ifdef COLVARS_LAMMPS
// Use open-source Jacobi implementation
#include "math_eigen_impl.h"
#else
// Fall back to NR routine
#include "nr_jacobi.h"
#endif


bool      colvarmodule::rotation::monitor_crossings = false;
cvm::real colvarmodule::rotation::crossing_threshold = 1.0E-02;


std::string cvm::rvector::to_simple_string() const
{
  std::ostringstream os;
  os.setf(std::ios::scientific, std::ios::floatfield);
  os.precision(cvm::cv_prec);
  os << x << " " << y << " " << z;
  return os.str();
}


int cvm::rvector::from_simple_string(std::string const &s)
{
  std::stringstream stream(s);
  if ( !(stream >> x) ||
       !(stream >> y) ||
       !(stream >> z) ) {
    return COLVARS_ERROR;
  }
  return COLVARS_OK;
}


std::ostream & operator << (std::ostream &os, colvarmodule::rvector const &v)
{
  std::streamsize const w = os.width();
  std::streamsize const p = os.precision();

  os.width(2);
  os << "( ";
  os.width(w); os.precision(p);
  os << v.x << " , ";
  os.width(w); os.precision(p);
  os << v.y << " , ";
  os.width(w); os.precision(p);
  os << v.z << " )";
  return os;
}


std::istream & operator >> (std::istream &is, colvarmodule::rvector &v)
{
  std::streampos const start_pos = is.tellg();
  char sep;
  if ( !(is >> sep) || !(sep == '(') ||
       !(is >> v.x) || !(is >> sep)  || !(sep == ',') ||
       !(is >> v.y) || !(is >> sep)  || !(sep == ',') ||
       !(is >> v.z) || !(is >> sep)  || !(sep == ')') ) {
    is.clear();
    is.seekg(start_pos, std::ios::beg);
    is.setstate(std::ios::failbit);
    return is;
  }
  return is;
}

std::string cvm::quaternion::to_simple_string() const
{
  std::ostringstream os;
  os.setf(std::ios::scientific, std::ios::floatfield);
  os.precision(cvm::cv_prec);
  os << q0 << " " << q1 << " " << q2 << " " << q3;
  return os.str();
}

int cvm::quaternion::from_simple_string(std::string const &s)
{
  std::stringstream stream(s);
  if ( !(stream >> q0) ||
       !(stream >> q1) ||
       !(stream >> q2) ||
       !(stream >> q3) ) {
    return COLVARS_ERROR;
  }
  return COLVARS_OK;
}

std::ostream & operator << (std::ostream &os, colvarmodule::quaternion const &q)
{
  std::streamsize const w = os.width();
  std::streamsize const p = os.precision();

  os.width(2);
  os << "( ";
  os.width(w); os.precision(p);
  os << q.q0 << " , ";
  os.width(w); os.precision(p);
  os << q.q1 << " , ";
  os.width(w); os.precision(p);
  os << q.q2 << " , ";
  os.width(w); os.precision(p);
  os << q.q3 << " )";
  return os;
}


std::istream & operator >> (std::istream &is, colvarmodule::quaternion &q)
{
  std::streampos const start_pos = is.tellg();
  char sep;
  if ( !(is >> sep)  || !(sep == '(') ||
       !(is >> q.q0) || !(is >> sep)  || !(sep == ',') ||
       !(is >> q.q1) || !(is >> sep)  || !(sep == ',') ||
       !(is >> q.q2) || !(is >> sep)  || !(sep == ',') ||
       !(is >> q.q3) || !(is >> sep)  || !(sep == ')') ) {
    is.clear();
    is.seekg(start_pos, std::ios::beg);
    is.setstate(std::ios::failbit);
  }
  return is;
}


#ifdef COLVARS_LAMMPS
namespace {
  inline void *new_Jacobi_solver(int size) {
    return reinterpret_cast<void *>(new MathEigen::Jacobi<cvm::real,
                                    cvm::vector1d<cvm::real> &,
                                    cvm::matrix2d<cvm::real> &>(4));
  }
}
#endif


int colvarmodule::rotation::init()
{
  b_debug_gradients = false;
  // lambda = 0.0;
  cvm::main()->cite_feature("Optimal rotation via flexible fitting");
  return COLVARS_OK;
}


colvarmodule::rotation::rotation()
{
  init();
#ifdef COLVARS_LAMMPS
  jacobi = new_Jacobi_solver(4);
#else
  jacobi = NULL;
#endif
}


colvarmodule::rotation::rotation(cvm::quaternion const &qi)
  : q(qi)
{
  init();
#ifdef COLVARS_LAMMPS
  jacobi = new_Jacobi_solver(4);
#else
  jacobi = NULL;
#endif
}


colvarmodule::rotation::rotation(cvm::real angle, cvm::rvector const &axis)
{
  init();
  cvm::rvector const axis_n = axis.unit();
  cvm::real const sina = cvm::sin(angle/2.0);
  q = cvm::quaternion(cvm::cos(angle/2.0),
                      sina * axis_n.x, sina * axis_n.y, sina * axis_n.z);
#ifdef COLVARS_LAMMPS
  jacobi = new_Jacobi_solver(4);
#else
  jacobi = NULL;
#endif
}


colvarmodule::rotation::~rotation()
{
#ifdef COLVARS_LAMMPS
  delete reinterpret_cast<
    MathEigen::Jacobi<cvm::real,
                      cvm::vector1d<cvm::real> &,
                      cvm::matrix2d<cvm::real> &> *>(jacobi);
#endif
}


void colvarmodule::rotation::build_correlation_matrix(
                                        std::vector<cvm::atom_pos> const &pos1,
                                        std::vector<cvm::atom_pos> const &pos2)
{
  // build the correlation matrix
  size_t i;
  for (i = 0; i < pos1.size(); i++) {
    C.xx += pos1[i].x * pos2[i].x;
    C.xy += pos1[i].x * pos2[i].y;
    C.xz += pos1[i].x * pos2[i].z;
    C.yx += pos1[i].y * pos2[i].x;
    C.yy += pos1[i].y * pos2[i].y;
    C.yz += pos1[i].y * pos2[i].z;
    C.zx += pos1[i].z * pos2[i].x;
    C.zy += pos1[i].z * pos2[i].y;
    C.zz += pos1[i].z * pos2[i].z;
  }
}

void colvarmodule::rotation::build_correlation_matrix(
                                        std::vector<cvm::atom> const &pos1,
                                        std::vector<cvm::atom_pos> const &pos2)
{
  // build the correlation matrix
  size_t i;
  for (i = 0; i < pos1.size(); i++) {
    C.xx += pos1[i].pos.x * pos2[i].x;
    C.xy += pos1[i].pos.x * pos2[i].y;
    C.xz += pos1[i].pos.x * pos2[i].z;
    C.yx += pos1[i].pos.y * pos2[i].x;
    C.yy += pos1[i].pos.y * pos2[i].y;
    C.yz += pos1[i].pos.y * pos2[i].z;
    C.zx += pos1[i].pos.z * pos2[i].x;
    C.zy += pos1[i].pos.z * pos2[i].y;
    C.zz += pos1[i].pos.z * pos2[i].z;
  }
}


void colvarmodule::rotation::compute_overlap_matrix()
{
  // build the "overlap" matrix, whose eigenvectors are stationary
  // points of the RMSD in the space of rotations
  S[0][0] =    C.xx + C.yy + C.zz;
  S[1][0] =    C.yz - C.zy;
  S[0][1] = S[1][0];
  S[2][0] =  - C.xz + C.zx ;
  S[0][2] = S[2][0];
  S[3][0] =    C.xy - C.yx;
  S[0][3] = S[3][0];
  S[1][1] =    C.xx - C.yy - C.zz;
  S[2][1] =    C.xy + C.yx;
  S[1][2] = S[2][1];
  S[3][1] =    C.xz + C.zx;
  S[1][3] = S[3][1];
  S[2][2] = - C.xx + C.yy - C.zz;
  S[3][2] =   C.yz + C.zy;
  S[2][3] = S[3][2];
  S[3][3] = - C.xx - C.yy + C.zz;
}


#ifndef COLVARS_LAMMPS
namespace NR {

int diagonalize_matrix(cvm::real m[4][4],
                        cvm::real eigval[4],
                        cvm::real eigvec[4][4])
{
  std::memset(eigval, 0, sizeof(cvm::real) * 4);
  std::memset(eigvec, 0, sizeof(cvm::real) * 4 * 4);

  // diagonalize
  int jac_nrot = 0;
  if (NR_Jacobi::jacobi(m, eigval, eigvec, &jac_nrot) !=
      COLVARS_OK) {
    return COLVARS_ERROR;
  }
  NR_Jacobi::eigsrt(eigval, eigvec);
  // jacobi saves eigenvectors by columns
  NR_Jacobi::transpose(eigvec);

  // normalize eigenvectors
  for (size_t ie = 0; ie < 4; ie++) {
    cvm::real norm2 = 0.0;
    size_t i;
    for (i = 0; i < 4; i++) {
      norm2 += eigvec[ie][i] * eigvec[ie][i];
    }
    cvm::real const norm = cvm::sqrt(norm2);
    for (i = 0; i < 4; i++) {
      eigvec[ie][i] /= norm;
    }
  }
  return COLVARS_OK;
}

}
#endif


// Calculate the rotation, plus its derivatives

void colvarmodule::rotation::calc_optimal_rotation(
                                        std::vector<cvm::atom_pos> const &pos1,
                                        std::vector<cvm::atom_pos> const &pos2)
{
  C.reset();
  build_correlation_matrix(pos1, pos2);

  calc_optimal_rotation_impl();

  if (b_debug_gradients) debug_gradients<cvm::atom_pos, cvm::atom_pos>(*this, pos1, pos2);
}

void colvarmodule::rotation::calc_optimal_rotation(
                                        std::vector<cvm::atom> const &pos1,
                                        std::vector<cvm::atom_pos> const &pos2)
{
  C.reset();
  build_correlation_matrix(pos1, pos2);

  calc_optimal_rotation_impl();

  if (b_debug_gradients) debug_gradients<cvm::atom, cvm::atom_pos>(*this, pos1, pos2);
}

// Calculate the optimal rotation between two groups, and implement it
// as a quaternion.  Uses the method documented in: Coutsias EA,
// Seok C, Dill KA.  Using quaternions to calculate RMSD.  J Comput
// Chem. 25(15):1849-57 (2004) DOI: 10.1002/jcc.20110 PubMed: 15376254
void colvarmodule::rotation::calc_optimal_rotation_impl() {
  compute_overlap_matrix();

  // S_backup = S;
  std::memcpy(&S_backup[0][0], &S, 4*4*sizeof(cvm::real));

  if (b_debug_gradients) {
    cvm::matrix2d<cvm::real> S_backup_out(4, 4);
    for (size_t i = 0; i < 4; ++i) {
      for (size_t j = 0; j < 4; ++j) {
        S_backup_out[i][j] = S_backup[i][j];
      }
    }
    cvm::log("S     = "+cvm::to_str(S_backup_out, cvm::cv_width, cvm::cv_prec)+"\n");
  }


#ifdef COLVARS_LAMMPS
  MathEigen::Jacobi<cvm::real,
                    cvm::real[4],
                    cvm::real[4][4]> *ecalc =
    reinterpret_cast<MathEigen::Jacobi<cvm::real,
                                       cvm::real[4],
                                       cvm::real[4][4]> *>(jacobi);

  int ierror = ecalc->Diagonalize(S, S_eigval, S_eigvec);
#else
  int ierror = NR::diagonalize_matrix(S, S_eigval, S_eigvec);
#endif
  if (ierror) {
    cvm::log("Failed to diagonalize the following overlapping matrix:\n");
    for (size_t i = 0; i < 4; ++i) {
      for (size_t j = 0; j < 4; ++j) {
        cvm::log(cvm::to_str(S[i][j]) + " ");
      }
      cvm::log("\n");
    }
    cvm::log("The corresponding correlation matrix is:\n");
    cvm::log(" " + cvm::to_str(C.xx) + " " + cvm::to_str(C.xy) + " " + cvm::to_str(C.xz));
    cvm::log(" " + cvm::to_str(C.yx) + " " + cvm::to_str(C.yy) + " " + cvm::to_str(C.yz));
    cvm::log(" " + cvm::to_str(C.zx) + " " + cvm::to_str(C.zy) + " " + cvm::to_str(C.zz) + "\n");
    cvm::error("Too many iterations in jacobi diagonalization.\n"
               "This is usually the result of an ill-defined set of atoms for "
               "rotational alignment (RMSD, rotateReference, etc).\n");
  }
  q = cvm::quaternion{S_eigvec[0][0], S_eigvec[0][1], S_eigvec[0][2], S_eigvec[0][3]};

  if (cvm::rotation::monitor_crossings) {
    if (q_old.norm2() > 0.0) {
      q.match(q_old);
      if (q_old.inner(q) < (1.0 - crossing_threshold)) {
        cvm::log("Warning: one molecular orientation has changed by more than "+
                 cvm::to_str(crossing_threshold)+": discontinuous rotation ?\n");
      }
    }
    q_old = q;
  }
}