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lammps/lib/colvars/colvar_rotation_derivative.h
Giacomo Fiorin cba479bf6e Update Colvars library to version 2025-04-18 
The following is a list of pull requests relevant to LAMMPS in the Colvars repository since 2024-08-06:

- 752 New tool poisson_integrator_conv
  https://github.com/Colvars/colvars/pull/752 (@jhenin)

- 733 Custom grids for all biases
  https://github.com/Colvars/colvars/pull/733 (@giacomofiorin, @jhenin)

- 776 Avoid error in acos and asin with fast-math
  https://github.com/Colvars/colvars/pull/776 (@jhenin)

- 773 fix: fix the clang build test failure of OPES
  https://github.com/Colvars/colvars/pull/773 (@HanatoK)

- 768 fix: clamp the input values of asin and acos in case of fast math on aarch64
  https://github.com/Colvars/colvars/pull/768 (@HanatoK)

- 761 Add debug code for the Jacobi failure
  https://github.com/Colvars/colvars/pull/761 (@HanatoK)

- 759 min_image fix; Saves long runs from crashes;
  https://github.com/Colvars/colvars/pull/759 (@PolyachenkoYA)

- 757 Fix MSVC OpenMP issue
  https://github.com/Colvars/colvars/pull/757 (@HanatoK)

- 755 Fix indentation of 'Init CVC' message in standard output
  https://github.com/Colvars/colvars/pull/755 (@jhenin)

- 750 Optimize and simplify the calculation of dihedral gradients
  https://github.com/Colvars/colvars/pull/750 (@HanatoK)

- 749 Add references to new Colvars paper
  https://github.com/Colvars/colvars/pull/749 (@jhenin, @giacomofiorin)

- 740 Report the specific C++ standard at init time, stop warning about C++97/03
  https://github.com/Colvars/colvars/pull/740 (@giacomofiorin)

- 731 Improve detection of hard/mathematical boundaries
  https://github.com/Colvars/colvars/pull/731 (@giacomofiorin)

- 729 Optimize the fit gradients
  https://github.com/Colvars/colvars/pull/729 (@HanatoK, @jhenin)

- 728 Fix undefined behavior when getting the current working directory from std::filesystem
  https://github.com/Colvars/colvars/pull/728 (@giacomofiorin)

- 727 Add patchversion scripting command
  https://github.com/Colvars/colvars/pull/727 (@giacomofiorin)

- 724 Fix gradients and metric functions of distanceDir
  https://github.com/Colvars/colvars/pull/724 (@giacomofiorin)

- 715 Add missing rotation in orientation component
  https://github.com/Colvars/colvars/pull/715 (@giacomofiorin)

- 713 fix: try to solve #87 for non-scala components
  https://github.com/Colvars/colvars/pull/713 (@HanatoK)

- 709 Implementation of OPES in Colvars
  https://github.com/Colvars/colvars/pull/709 (@HanatoK, @giacomofiorin, @jhenin)

- 706 BUGFIX for Segmentation fault in colvarbias_meta::calc_energy() with useGrids off
  https://github.com/Colvars/colvars/pull/706 (@alphataubio)

- 570 enable use of CVs defined by PyTorch neural network models
  https://github.com/Colvars/colvars/pull/570 (@zwpku, @giacomofiorin, @HanatoK, @jhenin)

Authors: @alphataubio, @EzryStIago, @giacomofiorin, @HanatoK, @jhenin, @PolyachenkoYA, @zwpku
2025-04-30 15:32:30 -04:00

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#ifndef COLVAR_ROTATION_DERIVATIVE
#define COLVAR_ROTATION_DERIVATIVE
#include "colvartypes.h"
#include <type_traits>
#include <cstring>
#ifndef _noalias
#if defined(__INTEL_COMPILER) || (defined(__PGI) && !defined(__NVCOMPILER))
#define _noalias restrict
#elif defined(__GNUC__) || defined(__INTEL_LLVM_COMPILER) || defined(__NVCOMPILER)
#define _noalias __restrict
#else
#define _noalias
#endif
#endif
/// \brief Helper function for loading the ia-th atom in the vector pos to x, y and z (C++11 SFINAE is used)
template <typename T, typename std::enable_if<std::is_same<T, cvm::atom_pos>::value, bool>::type = true>
inline void read_atom_coord(
size_t ia, const std::vector<T>& pos,
cvm::real* _noalias x, cvm::real* _noalias y, cvm::real* _noalias z) {
*x = pos[ia].x;
*y = pos[ia].y;
*z = pos[ia].z;
}
template <typename T, typename std::enable_if<std::is_same<T, cvm::atom>::value, bool>::type = true>
inline void read_atom_coord(
size_t ia, const std::vector<T>& pos,
cvm::real* _noalias x, cvm::real* _noalias y, cvm::real* _noalias z) {
*x = pos[ia].pos.x;
*y = pos[ia].pos.y;
*z = pos[ia].pos.z;
}
/// \brief Helper enum class for specifying options in rotation_derivative::prepare_derivative
enum class rotation_derivative_dldq {
/// Require the derivative of the leading eigenvalue with respect to the atom coordinates
use_dl = 1 << 0,
/// Require the derivative of the leading eigenvector with respect to the atom coordinates
use_dq = 1 << 1
};
inline constexpr rotation_derivative_dldq operator|(rotation_derivative_dldq Lhs, rotation_derivative_dldq Rhs) {
return static_cast<rotation_derivative_dldq>(
static_cast<std::underlying_type<rotation_derivative_dldq>::type>(Lhs) |
static_cast<std::underlying_type<rotation_derivative_dldq>::type>(Rhs));
}
inline constexpr bool operator&(rotation_derivative_dldq Lhs, rotation_derivative_dldq Rhs)
{
return (static_cast<std::underlying_type<rotation_derivative_dldq>::type>(Lhs) &
static_cast<std::underlying_type<rotation_derivative_dldq>::type>(Rhs));
}
/// \brief Helper class for calculating the derivative of rotation
template <typename T1, typename T2>
struct rotation_derivative {
static_assert(std::is_same<T1, cvm::atom_pos>::value || std::is_same<T1, cvm::atom>::value,
"class template rotation_derivative only supports cvm::atom_pos or cvm::atom types.");
static_assert(std::is_same<T2, cvm::atom_pos>::value || std::is_same<T2, cvm::atom>::value,
"class template rotation_derivative only supports cvm::atom_pos or cvm::atom types.");
/// \brief Reference to the rotation
const cvm::rotation &m_rot;
/// \brief Reference to the atom positions of group 1
const std::vector<T1> &m_pos1;
/// \brief Reference to the atom positions of group 2
const std::vector<T2> &m_pos2;
/// \brief Temporary variable that will be updated if prepare_derivative called
cvm::real tmp_Q0Q0[4][4];
cvm::real tmp_Q0Q0_L[4][4][4];
/*! @brief Constructor of the cvm::rotation::derivative class
* @param[in] rot The cvm::rotation object (must have called
* `calc_optimal_rotation` before calling
* `calc_derivative_wrt_group1` and
* `calc_derivative_wrt_group2`)
* @param[in] pos1 The atom positions of group 1
* @param[in] pos2 The atom positions of group 2
*/
rotation_derivative(
const cvm::rotation &rot,
const std::vector<T1> &pos1,
const std::vector<T2> &pos2):
m_rot(rot), m_pos1(pos1), m_pos2(pos2) {};
/*! @brief This function must be called before `calc_derivative_wrt_group1`
* and `calc_derivative_wrt_group2` in order to prepare the tmp_Q0Q0
* and tmp_Q0Q0_L.
* @param[in] require_dl_dq Require the calculation of the derivatives of L or/and Q
* with respect to atoms.
*/
void prepare_derivative(rotation_derivative_dldq require_dl_dq) {
if (require_dl_dq & rotation_derivative_dldq::use_dl) {
const auto &Q0 = m_rot.S_eigvec[0];
tmp_Q0Q0[0][0] = Q0[0] * Q0[0];
tmp_Q0Q0[0][1] = Q0[0] * Q0[1];
tmp_Q0Q0[0][2] = Q0[0] * Q0[2];
tmp_Q0Q0[0][3] = Q0[0] * Q0[3];
tmp_Q0Q0[1][0] = Q0[1] * Q0[0];
tmp_Q0Q0[1][1] = Q0[1] * Q0[1];
tmp_Q0Q0[1][2] = Q0[1] * Q0[2];
tmp_Q0Q0[1][3] = Q0[1] * Q0[3];
tmp_Q0Q0[2][0] = Q0[2] * Q0[0];
tmp_Q0Q0[2][1] = Q0[2] * Q0[1];
tmp_Q0Q0[2][2] = Q0[2] * Q0[2];
tmp_Q0Q0[2][3] = Q0[2] * Q0[3];
tmp_Q0Q0[3][0] = Q0[3] * Q0[0];
tmp_Q0Q0[3][1] = Q0[3] * Q0[1];
tmp_Q0Q0[3][2] = Q0[3] * Q0[2];
tmp_Q0Q0[3][3] = Q0[3] * Q0[3];
}
if (require_dl_dq & rotation_derivative_dldq::use_dq) {
const auto &Q0 = m_rot.S_eigvec[0];
const auto &Q1 = m_rot.S_eigvec[1];
const auto &Q2 = m_rot.S_eigvec[2];
const auto &Q3 = m_rot.S_eigvec[3];
cvm::real const L0 = m_rot.S_eigval[0];
cvm::real const L1 = m_rot.S_eigval[1];
cvm::real const L2 = m_rot.S_eigval[2];
cvm::real const L3 = m_rot.S_eigval[3];
tmp_Q0Q0_L[0][0][0] = (Q1[0] * Q0[0]) / (L0-L1) * Q1[0] +
(Q2[0] * Q0[0]) / (L0-L2) * Q2[0] +
(Q3[0] * Q0[0]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][0][0] = (Q1[0] * Q0[0]) / (L0-L1) * Q1[1] +
(Q2[0] * Q0[0]) / (L0-L2) * Q2[1] +
(Q3[0] * Q0[0]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][0][0] = (Q1[0] * Q0[0]) / (L0-L1) * Q1[2] +
(Q2[0] * Q0[0]) / (L0-L2) * Q2[2] +
(Q3[0] * Q0[0]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][0][0] = (Q1[0] * Q0[0]) / (L0-L1) * Q1[3] +
(Q2[0] * Q0[0]) / (L0-L2) * Q2[3] +
(Q3[0] * Q0[0]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][0][1] = (Q1[0] * Q0[1]) / (L0-L1) * Q1[0] +
(Q2[0] * Q0[1]) / (L0-L2) * Q2[0] +
(Q3[0] * Q0[1]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][0][1] = (Q1[0] * Q0[1]) / (L0-L1) * Q1[1] +
(Q2[0] * Q0[1]) / (L0-L2) * Q2[1] +
(Q3[0] * Q0[1]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][0][1] = (Q1[0] * Q0[1]) / (L0-L1) * Q1[2] +
(Q2[0] * Q0[1]) / (L0-L2) * Q2[2] +
(Q3[0] * Q0[1]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][0][1] = (Q1[0] * Q0[1]) / (L0-L1) * Q1[3] +
(Q2[0] * Q0[1]) / (L0-L2) * Q2[3] +
(Q3[0] * Q0[1]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][0][2] = (Q1[0] * Q0[2]) / (L0-L1) * Q1[0] +
(Q2[0] * Q0[2]) / (L0-L2) * Q2[0] +
(Q3[0] * Q0[2]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][0][2] = (Q1[0] * Q0[2]) / (L0-L1) * Q1[1] +
(Q2[0] * Q0[2]) / (L0-L2) * Q2[1] +
(Q3[0] * Q0[2]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][0][2] = (Q1[0] * Q0[2]) / (L0-L1) * Q1[2] +
(Q2[0] * Q0[2]) / (L0-L2) * Q2[2] +
(Q3[0] * Q0[2]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][0][2] = (Q1[0] * Q0[2]) / (L0-L1) * Q1[3] +
(Q2[0] * Q0[2]) / (L0-L2) * Q2[3] +
(Q3[0] * Q0[2]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][0][3] = (Q1[0] * Q0[3]) / (L0-L1) * Q1[0] +
(Q2[0] * Q0[3]) / (L0-L2) * Q2[0] +
(Q3[0] * Q0[3]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][0][3] = (Q1[0] * Q0[3]) / (L0-L1) * Q1[1] +
(Q2[0] * Q0[3]) / (L0-L2) * Q2[1] +
(Q3[0] * Q0[3]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][0][3] = (Q1[0] * Q0[3]) / (L0-L1) * Q1[2] +
(Q2[0] * Q0[3]) / (L0-L2) * Q2[2] +
(Q3[0] * Q0[3]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][0][3] = (Q1[0] * Q0[3]) / (L0-L1) * Q1[3] +
(Q2[0] * Q0[3]) / (L0-L2) * Q2[3] +
(Q3[0] * Q0[3]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][1][0] = (Q1[1] * Q0[0]) / (L0-L1) * Q1[0] +
(Q2[1] * Q0[0]) / (L0-L2) * Q2[0] +
(Q3[1] * Q0[0]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][1][0] = (Q1[1] * Q0[0]) / (L0-L1) * Q1[1] +
(Q2[1] * Q0[0]) / (L0-L2) * Q2[1] +
(Q3[1] * Q0[0]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][1][0] = (Q1[1] * Q0[0]) / (L0-L1) * Q1[2] +
(Q2[1] * Q0[0]) / (L0-L2) * Q2[2] +
(Q3[1] * Q0[0]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][1][0] = (Q1[1] * Q0[0]) / (L0-L1) * Q1[3] +
(Q2[1] * Q0[0]) / (L0-L2) * Q2[3] +
(Q3[1] * Q0[0]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][1][1] = (Q1[1] * Q0[1]) / (L0-L1) * Q1[0] +
(Q2[1] * Q0[1]) / (L0-L2) * Q2[0] +
(Q3[1] * Q0[1]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][1][1] = (Q1[1] * Q0[1]) / (L0-L1) * Q1[1] +
(Q2[1] * Q0[1]) / (L0-L2) * Q2[1] +
(Q3[1] * Q0[1]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][1][1] = (Q1[1] * Q0[1]) / (L0-L1) * Q1[2] +
(Q2[1] * Q0[1]) / (L0-L2) * Q2[2] +
(Q3[1] * Q0[1]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][1][1] = (Q1[1] * Q0[1]) / (L0-L1) * Q1[3] +
(Q2[1] * Q0[1]) / (L0-L2) * Q2[3] +
(Q3[1] * Q0[1]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][1][2] = (Q1[1] * Q0[2]) / (L0-L1) * Q1[0] +
(Q2[1] * Q0[2]) / (L0-L2) * Q2[0] +
(Q3[1] * Q0[2]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][1][2] = (Q1[1] * Q0[2]) / (L0-L1) * Q1[1] +
(Q2[1] * Q0[2]) / (L0-L2) * Q2[1] +
(Q3[1] * Q0[2]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][1][2] = (Q1[1] * Q0[2]) / (L0-L1) * Q1[2] +
(Q2[1] * Q0[2]) / (L0-L2) * Q2[2] +
(Q3[1] * Q0[2]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][1][2] = (Q1[1] * Q0[2]) / (L0-L1) * Q1[3] +
(Q2[1] * Q0[2]) / (L0-L2) * Q2[3] +
(Q3[1] * Q0[2]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][1][3] = (Q1[1] * Q0[3]) / (L0-L1) * Q1[0] +
(Q2[1] * Q0[3]) / (L0-L2) * Q2[0] +
(Q3[1] * Q0[3]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][1][3] = (Q1[1] * Q0[3]) / (L0-L1) * Q1[1] +
(Q2[1] * Q0[3]) / (L0-L2) * Q2[1] +
(Q3[1] * Q0[3]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][1][3] = (Q1[1] * Q0[3]) / (L0-L1) * Q1[2] +
(Q2[1] * Q0[3]) / (L0-L2) * Q2[2] +
(Q3[1] * Q0[3]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][1][3] = (Q1[1] * Q0[3]) / (L0-L1) * Q1[3] +
(Q2[1] * Q0[3]) / (L0-L2) * Q2[3] +
(Q3[1] * Q0[3]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][2][0] = (Q1[2] * Q0[0]) / (L0-L1) * Q1[0] +
(Q2[2] * Q0[0]) / (L0-L2) * Q2[0] +
(Q3[2] * Q0[0]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][2][0] = (Q1[2] * Q0[0]) / (L0-L1) * Q1[1] +
(Q2[2] * Q0[0]) / (L0-L2) * Q2[1] +
(Q3[2] * Q0[0]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][2][0] = (Q1[2] * Q0[0]) / (L0-L1) * Q1[2] +
(Q2[2] * Q0[0]) / (L0-L2) * Q2[2] +
(Q3[2] * Q0[0]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][2][0] = (Q1[2] * Q0[0]) / (L0-L1) * Q1[3] +
(Q2[2] * Q0[0]) / (L0-L2) * Q2[3] +
(Q3[2] * Q0[0]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][2][1] = (Q1[2] * Q0[1]) / (L0-L1) * Q1[0] +
(Q2[2] * Q0[1]) / (L0-L2) * Q2[0] +
(Q3[2] * Q0[1]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][2][1] = (Q1[2] * Q0[1]) / (L0-L1) * Q1[1] +
(Q2[2] * Q0[1]) / (L0-L2) * Q2[1] +
(Q3[2] * Q0[1]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][2][1] = (Q1[2] * Q0[1]) / (L0-L1) * Q1[2] +
(Q2[2] * Q0[1]) / (L0-L2) * Q2[2] +
(Q3[2] * Q0[1]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][2][1] = (Q1[2] * Q0[1]) / (L0-L1) * Q1[3] +
(Q2[2] * Q0[1]) / (L0-L2) * Q2[3] +
(Q3[2] * Q0[1]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][2][2] = (Q1[2] * Q0[2]) / (L0-L1) * Q1[0] +
(Q2[2] * Q0[2]) / (L0-L2) * Q2[0] +
(Q3[2] * Q0[2]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][2][2] = (Q1[2] * Q0[2]) / (L0-L1) * Q1[1] +
(Q2[2] * Q0[2]) / (L0-L2) * Q2[1] +
(Q3[2] * Q0[2]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][2][2] = (Q1[2] * Q0[2]) / (L0-L1) * Q1[2] +
(Q2[2] * Q0[2]) / (L0-L2) * Q2[2] +
(Q3[2] * Q0[2]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][2][2] = (Q1[2] * Q0[2]) / (L0-L1) * Q1[3] +
(Q2[2] * Q0[2]) / (L0-L2) * Q2[3] +
(Q3[2] * Q0[2]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][2][3] = (Q1[2] * Q0[3]) / (L0-L1) * Q1[0] +
(Q2[2] * Q0[3]) / (L0-L2) * Q2[0] +
(Q3[2] * Q0[3]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][2][3] = (Q1[2] * Q0[3]) / (L0-L1) * Q1[1] +
(Q2[2] * Q0[3]) / (L0-L2) * Q2[1] +
(Q3[2] * Q0[3]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][2][3] = (Q1[2] * Q0[3]) / (L0-L1) * Q1[2] +
(Q2[2] * Q0[3]) / (L0-L2) * Q2[2] +
(Q3[2] * Q0[3]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][2][3] = (Q1[2] * Q0[3]) / (L0-L1) * Q1[3] +
(Q2[2] * Q0[3]) / (L0-L2) * Q2[3] +
(Q3[2] * Q0[3]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][3][0] = (Q1[3] * Q0[0]) / (L0-L1) * Q1[0] +
(Q2[3] * Q0[0]) / (L0-L2) * Q2[0] +
(Q3[3] * Q0[0]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][3][0] = (Q1[3] * Q0[0]) / (L0-L1) * Q1[1] +
(Q2[3] * Q0[0]) / (L0-L2) * Q2[1] +
(Q3[3] * Q0[0]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][3][0] = (Q1[3] * Q0[0]) / (L0-L1) * Q1[2] +
(Q2[3] * Q0[0]) / (L0-L2) * Q2[2] +
(Q3[3] * Q0[0]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][3][0] = (Q1[3] * Q0[0]) / (L0-L1) * Q1[3] +
(Q2[3] * Q0[0]) / (L0-L2) * Q2[3] +
(Q3[3] * Q0[0]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][3][1] = (Q1[3] * Q0[1]) / (L0-L1) * Q1[0] +
(Q2[3] * Q0[1]) / (L0-L2) * Q2[0] +
(Q3[3] * Q0[1]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][3][1] = (Q1[3] * Q0[1]) / (L0-L1) * Q1[1] +
(Q2[3] * Q0[1]) / (L0-L2) * Q2[1] +
(Q3[3] * Q0[1]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][3][1] = (Q1[3] * Q0[1]) / (L0-L1) * Q1[2] +
(Q2[3] * Q0[1]) / (L0-L2) * Q2[2] +
(Q3[3] * Q0[1]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][3][1] = (Q1[3] * Q0[1]) / (L0-L1) * Q1[3] +
(Q2[3] * Q0[1]) / (L0-L2) * Q2[3] +
(Q3[3] * Q0[1]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][3][2] = (Q1[3] * Q0[2]) / (L0-L1) * Q1[0] +
(Q2[3] * Q0[2]) / (L0-L2) * Q2[0] +
(Q3[3] * Q0[2]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][3][2] = (Q1[3] * Q0[2]) / (L0-L1) * Q1[1] +
(Q2[3] * Q0[2]) / (L0-L2) * Q2[1] +
(Q3[3] * Q0[2]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][3][2] = (Q1[3] * Q0[2]) / (L0-L1) * Q1[2] +
(Q2[3] * Q0[2]) / (L0-L2) * Q2[2] +
(Q3[3] * Q0[2]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][3][2] = (Q1[3] * Q0[2]) / (L0-L1) * Q1[3] +
(Q2[3] * Q0[2]) / (L0-L2) * Q2[3] +
(Q3[3] * Q0[2]) / (L0-L3) * Q3[3];
tmp_Q0Q0_L[0][3][3] = (Q1[3] * Q0[3]) / (L0-L1) * Q1[0] +
(Q2[3] * Q0[3]) / (L0-L2) * Q2[0] +
(Q3[3] * Q0[3]) / (L0-L3) * Q3[0];
tmp_Q0Q0_L[1][3][3] = (Q1[3] * Q0[3]) / (L0-L1) * Q1[1] +
(Q2[3] * Q0[3]) / (L0-L2) * Q2[1] +
(Q3[3] * Q0[3]) / (L0-L3) * Q3[1];
tmp_Q0Q0_L[2][3][3] = (Q1[3] * Q0[3]) / (L0-L1) * Q1[2] +
(Q2[3] * Q0[3]) / (L0-L2) * Q2[2] +
(Q3[3] * Q0[3]) / (L0-L3) * Q3[2];
tmp_Q0Q0_L[3][3][3] = (Q1[3] * Q0[3]) / (L0-L1) * Q1[3] +
(Q2[3] * Q0[3]) / (L0-L2) * Q2[3] +
(Q3[3] * Q0[3]) / (L0-L3) * Q3[3];
}
}
/*! @brief Actual implementation of the derivative calculation
* @param[in] ds The derivative of matrix S with respect to an atom of
* either group 1 or group 2
* @param[out] dl0_out The output of derivative of L
* @param[out] dq0_out The output of derivative of Q
* @param[out] ds_out The output of derivative of overlap matrix S
*/
template <bool use_dl, bool use_dq, bool use_ds>
void calc_derivative_impl(
const cvm::rvector (&ds)[4][4],
cvm::rvector* _noalias const dl0_out,
cvm::vector1d<cvm::rvector>* _noalias const dq0_out,
cvm::matrix2d<cvm::rvector>* _noalias const ds_out) const {
if (use_ds) {
// this code path is for debug_gradients, so not necessary to unroll the loop
*ds_out = cvm::matrix2d<cvm::rvector>(4, 4);
for (int i = 0; i < 4; ++i) {
for (int j = 0; j < 4; ++j) {
(*ds_out)[i][j] = ds[i][j];
}
}
}
if (use_dl) {
/* manually loop unrolling of the following loop:
dl0_1.reset();
for (size_t i = 0; i < 4; i++) {
for (size_t j = 0; j < 4; j++) {
dl0_1 += Q0[i] * ds_1[i][j] * Q0[j];
}
}
*/
*dl0_out = tmp_Q0Q0[0][0] * ds[0][0] +
tmp_Q0Q0[0][1] * ds[0][1] +
tmp_Q0Q0[0][2] * ds[0][2] +
tmp_Q0Q0[0][3] * ds[0][3] +
tmp_Q0Q0[1][0] * ds[1][0] +
tmp_Q0Q0[1][1] * ds[1][1] +
tmp_Q0Q0[1][2] * ds[1][2] +
tmp_Q0Q0[1][3] * ds[1][3] +
tmp_Q0Q0[2][0] * ds[2][0] +
tmp_Q0Q0[2][1] * ds[2][1] +
tmp_Q0Q0[2][2] * ds[2][2] +
tmp_Q0Q0[2][3] * ds[2][3] +
tmp_Q0Q0[3][0] * ds[3][0] +
tmp_Q0Q0[3][1] * ds[3][1] +
tmp_Q0Q0[3][2] * ds[3][2] +
tmp_Q0Q0[3][3] * ds[3][3];
}
if (use_dq) {
// we can skip this check if a fixed-size array is used
if (dq0_out->size() != 4) dq0_out->resize(4);
/* manually loop unrolling of the following loop:
dq0_1.reset();
for (size_t p = 0; p < 4; p++) {
for (size_t i = 0; i < 4; i++) {
for (size_t j = 0; j < 4; j++) {
dq0_1[p] +=
(Q1[i] * ds_1[i][j] * Q0[j]) / (L0-L1) * Q1[p] +
(Q2[i] * ds_1[i][j] * Q0[j]) / (L0-L2) * Q2[p] +
(Q3[i] * ds_1[i][j] * Q0[j]) / (L0-L3) * Q3[p];
}
}
}
*/
(*dq0_out)[0] = tmp_Q0Q0_L[0][0][0] * ds[0][0] +
tmp_Q0Q0_L[0][0][1] * ds[0][1] +
tmp_Q0Q0_L[0][0][2] * ds[0][2] +
tmp_Q0Q0_L[0][0][3] * ds[0][3] +
tmp_Q0Q0_L[0][1][0] * ds[1][0] +
tmp_Q0Q0_L[0][1][1] * ds[1][1] +
tmp_Q0Q0_L[0][1][2] * ds[1][2] +
tmp_Q0Q0_L[0][1][3] * ds[1][3] +
tmp_Q0Q0_L[0][2][0] * ds[2][0] +
tmp_Q0Q0_L[0][2][1] * ds[2][1] +
tmp_Q0Q0_L[0][2][2] * ds[2][2] +
tmp_Q0Q0_L[0][2][3] * ds[2][3] +
tmp_Q0Q0_L[0][3][0] * ds[3][0] +
tmp_Q0Q0_L[0][3][1] * ds[3][1] +
tmp_Q0Q0_L[0][3][2] * ds[3][2] +
tmp_Q0Q0_L[0][3][3] * ds[3][3];
(*dq0_out)[1] = tmp_Q0Q0_L[1][0][0] * ds[0][0] +
tmp_Q0Q0_L[1][0][1] * ds[0][1] +
tmp_Q0Q0_L[1][0][2] * ds[0][2] +
tmp_Q0Q0_L[1][0][3] * ds[0][3] +
tmp_Q0Q0_L[1][1][0] * ds[1][0] +
tmp_Q0Q0_L[1][1][1] * ds[1][1] +
tmp_Q0Q0_L[1][1][2] * ds[1][2] +
tmp_Q0Q0_L[1][1][3] * ds[1][3] +
tmp_Q0Q0_L[1][2][0] * ds[2][0] +
tmp_Q0Q0_L[1][2][1] * ds[2][1] +
tmp_Q0Q0_L[1][2][2] * ds[2][2] +
tmp_Q0Q0_L[1][2][3] * ds[2][3] +
tmp_Q0Q0_L[1][3][0] * ds[3][0] +
tmp_Q0Q0_L[1][3][1] * ds[3][1] +
tmp_Q0Q0_L[1][3][2] * ds[3][2] +
tmp_Q0Q0_L[1][3][3] * ds[3][3];
(*dq0_out)[2] = tmp_Q0Q0_L[2][0][0] * ds[0][0] +
tmp_Q0Q0_L[2][0][1] * ds[0][1] +
tmp_Q0Q0_L[2][0][2] * ds[0][2] +
tmp_Q0Q0_L[2][0][3] * ds[0][3] +
tmp_Q0Q0_L[2][1][0] * ds[1][0] +
tmp_Q0Q0_L[2][1][1] * ds[1][1] +
tmp_Q0Q0_L[2][1][2] * ds[1][2] +
tmp_Q0Q0_L[2][1][3] * ds[1][3] +
tmp_Q0Q0_L[2][2][0] * ds[2][0] +
tmp_Q0Q0_L[2][2][1] * ds[2][1] +
tmp_Q0Q0_L[2][2][2] * ds[2][2] +
tmp_Q0Q0_L[2][2][3] * ds[2][3] +
tmp_Q0Q0_L[2][3][0] * ds[3][0] +
tmp_Q0Q0_L[2][3][1] * ds[3][1] +
tmp_Q0Q0_L[2][3][2] * ds[3][2] +
tmp_Q0Q0_L[2][3][3] * ds[3][3];
(*dq0_out)[3] = tmp_Q0Q0_L[3][0][0] * ds[0][0] +
tmp_Q0Q0_L[3][0][1] * ds[0][1] +
tmp_Q0Q0_L[3][0][2] * ds[0][2] +
tmp_Q0Q0_L[3][0][3] * ds[0][3] +
tmp_Q0Q0_L[3][1][0] * ds[1][0] +
tmp_Q0Q0_L[3][1][1] * ds[1][1] +
tmp_Q0Q0_L[3][1][2] * ds[1][2] +
tmp_Q0Q0_L[3][1][3] * ds[1][3] +
tmp_Q0Q0_L[3][2][0] * ds[2][0] +
tmp_Q0Q0_L[3][2][1] * ds[2][1] +
tmp_Q0Q0_L[3][2][2] * ds[2][2] +
tmp_Q0Q0_L[3][2][3] * ds[2][3] +
tmp_Q0Q0_L[3][3][0] * ds[3][0] +
tmp_Q0Q0_L[3][3][1] * ds[3][1] +
tmp_Q0Q0_L[3][3][2] * ds[3][2] +
tmp_Q0Q0_L[3][3][3] * ds[3][3];
}
}
/*! @brief Calculate the derivatives of S, the leading eigenvalue L and
* the leading eigenvector Q with respect to `m_pos1`
* @param[in] ia The index the of atom
* @param[out] dl0_1_out The output of derivative of L with respect to
* ia-th atom of group 1
* @param[out] dq0_1_out The output of derivative of Q with respect to
* ia-th atom of group 1
* @param[out] ds_1_out The output of derivative of overlap matrix S with
* respect to ia-th atom of group 1
*/
template <bool use_dl, bool use_dq, bool use_ds>
void calc_derivative_wrt_group1(
size_t ia, cvm::rvector* _noalias const dl0_1_out = nullptr,
cvm::vector1d<cvm::rvector>* _noalias const dq0_1_out = nullptr,
cvm::matrix2d<cvm::rvector>* _noalias const ds_1_out = nullptr) const {
// if (dl0_1_out == nullptr && dq0_1_out == nullptr) return;
cvm::real a2x, a2y, a2z;
// we can get rid of the helper function read_atom_coord if C++17 (constexpr) is available
read_atom_coord(ia, m_pos2, &a2x, &a2y, &a2z);
const cvm::rvector ds_1[4][4] = {
{{ a2x, a2y, a2z}, { 0.0, a2z, -a2y}, {-a2z, 0.0, a2x}, { a2y, -a2x, 0.0}},
{{ 0.0, a2z, -a2y}, { a2x, -a2y, -a2z}, { a2y, a2x, 0.0}, { a2z, 0.0, a2x}},
{{-a2z, 0.0, a2x}, { a2y, a2x, 0.0}, {-a2x, a2y, -a2z}, { 0.0, a2z, a2y}},
{{ a2y, -a2x, 0.0}, { a2z, 0.0, a2x}, { 0.0, a2z, a2y}, {-a2x, -a2y, a2z}}};
calc_derivative_impl<use_dl, use_dq, use_ds>(ds_1, dl0_1_out, dq0_1_out, ds_1_out);
}
/*! @brief Calculate the derivatives of S, the leading eigenvalue L and
* the leading eigenvector Q with respect to `m_pos2`
* @param[in] ia The index the of atom
* @param[out] dl0_2_out The output of derivative of L with respect to
* ia-th atom of group 2
* @param[out] dq0_2_out The output of derivative of Q with respect to
* ia-th atom of group 2
* @param[out] ds_2_out The output of derivative of overlap matrix S with
* respect to ia-th atom of group 2
*/
template <bool use_dl, bool use_dq, bool use_ds>
void calc_derivative_wrt_group2(
size_t ia, cvm::rvector* _noalias const dl0_2_out = nullptr,
cvm::vector1d<cvm::rvector>* _noalias const dq0_2_out = nullptr,
cvm::matrix2d<cvm::rvector>* _noalias const ds_2_out = nullptr) const {
// if (dl0_2_out == nullptr && dq0_2_out == nullptr) return;
cvm::real a1x, a1y, a1z;
// we can get rid of the helper function read_atom_coord if C++17 (constexpr) is available
read_atom_coord(ia, m_pos1, &a1x, &a1y, &a1z);
const cvm::rvector ds_2[4][4] = {
{{ a1x, a1y, a1z}, { 0.0, -a1z, a1y}, { a1z, 0.0, -a1x}, {-a1y, a1x, 0.0}},
{{ 0.0, -a1z, a1y}, { a1x, -a1y, -a1z}, { a1y, a1x, 0.0}, { a1z, 0.0, a1x}},
{{ a1z, 0.0, -a1x}, { a1y, a1x, 0.0}, {-a1x, a1y, -a1z}, { 0.0, a1z, a1y}},
{{-a1y, a1x, 0.0}, { a1z, 0.0, a1x}, { 0.0, a1z, a1y}, {-a1x, -a1y, a1z}}};
calc_derivative_impl<use_dl, use_dq, use_ds>(ds_2, dl0_2_out, dq0_2_out, ds_2_out);
}
};
/*! @brief Function for debugging gradients (allow using either
* std::vector<cvm::atom_pos> or std::vector<cvm::atom> for
* pos1 and pos2)
* @param[in] pos1 Atom positions of group 1
* @param[in] pos2 Atom positions of group 2
*/
template<typename T1, typename T2>
void debug_gradients(
cvm::rotation &rot,
const std::vector<T1> &pos1,
const std::vector<T2> &pos2) {
static_assert(std::is_same<T1, cvm::atom_pos>::value || std::is_same<T1, cvm::atom>::value, "");
static_assert(std::is_same<T2, cvm::atom_pos>::value || std::is_same<T2, cvm::atom>::value, "");
// eigenvalues and eigenvectors
cvm::real const L0 = rot.S_eigval[0];
cvm::real const L1 = rot.S_eigval[1];
cvm::real const L2 = rot.S_eigval[2];
cvm::real const L3 = rot.S_eigval[3];
cvm::quaternion const Q0(rot.S_eigvec[0]);
cvm::quaternion const Q1(rot.S_eigvec[1]);
cvm::quaternion const Q2(rot.S_eigvec[2]);
cvm::quaternion const Q3(rot.S_eigvec[3]);
cvm::log("L0 = "+cvm::to_str(L0, cvm::cv_width, cvm::cv_prec)+
", Q0 = "+cvm::to_str(Q0, cvm::cv_width, cvm::cv_prec)+
", Q0*Q0 = "+cvm::to_str(Q0.inner(Q0), cvm::cv_width, cvm::cv_prec)+
"\n");
cvm::log("L1 = "+cvm::to_str(L1, cvm::cv_width, cvm::cv_prec)+
", Q1 = "+cvm::to_str(Q1, cvm::cv_width, cvm::cv_prec)+
", Q0*Q1 = "+cvm::to_str(Q0.inner(Q1), cvm::cv_width, cvm::cv_prec)+
"\n");
cvm::log("L2 = "+cvm::to_str(L2, cvm::cv_width, cvm::cv_prec)+
", Q2 = "+cvm::to_str(Q2, cvm::cv_width, cvm::cv_prec)+
", Q0*Q2 = "+cvm::to_str(Q0.inner(Q2), cvm::cv_width, cvm::cv_prec)+
"\n");
cvm::log("L3 = "+cvm::to_str(L3, cvm::cv_width, cvm::cv_prec)+
", Q3 = "+cvm::to_str(Q3, cvm::cv_width, cvm::cv_prec)+
", Q0*Q3 = "+cvm::to_str(Q0.inner(Q3), cvm::cv_width, cvm::cv_prec)+
"\n");
rotation_derivative<T1, T2> deriv(rot, pos1, pos2);
cvm::rvector dl0_2;
cvm::vector1d<cvm::rvector> dq0_2(4);
cvm::matrix2d<cvm::rvector> ds_2;
#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]> *>(rot.jacobi);
#endif
deriv.prepare_derivative(rotation_derivative_dldq::use_dl | rotation_derivative_dldq::use_dq);
cvm::real S_new[4][4];
cvm::real S_new_eigval[4];
cvm::real S_new_eigvec[4][4];
for (size_t ia = 0; ia < pos2.size(); ++ia) {
deriv.template calc_derivative_wrt_group2<true, true, true>(ia, &dl0_2, &dq0_2, &ds_2);
// make an infitesimal move along each cartesian coordinate of
// this atom, and solve again the eigenvector problem
for (size_t comp = 0; comp < 3; comp++) {
std::memcpy(S_new, rot.S_backup, sizeof(cvm::real) * 4 * 4);
std::memset(S_new_eigval, 0, sizeof(cvm::real) * 4);
std::memset(S_new_eigvec, 0, sizeof(cvm::real) * 4 * 4);
for (size_t i = 0; i < 4; i++) {
for (size_t j = 0; j < 4; j++) {
S_new[i][j] +=
colvarmodule::debug_gradients_step_size * ds_2[i][j][comp];
}
}
#ifdef COLVARS_LAMMPS
ecalc->Diagonalize(S_new, S_new_eigval, S_new_eigvec);
#else
NR::diagonalize_matrix(S_new, S_new_eigval, S_new_eigvec);
#endif
cvm::real const &L0_new = S_new_eigval[0];
cvm::quaternion const Q0_new(S_new_eigvec[0]);
cvm::real const DL0 = (dl0_2[comp]) * colvarmodule::debug_gradients_step_size;
cvm::quaternion const DQ0(dq0_2[0][comp] * colvarmodule::debug_gradients_step_size,
dq0_2[1][comp] * colvarmodule::debug_gradients_step_size,
dq0_2[2][comp] * colvarmodule::debug_gradients_step_size,
dq0_2[3][comp] * colvarmodule::debug_gradients_step_size);
cvm::log( "|(l_0+dl_0) - l_0^new|/l_0 = "+
cvm::to_str(cvm::fabs(L0+DL0 - L0_new)/L0, cvm::cv_width, cvm::cv_prec)+
", |(q_0+dq_0) - q_0^new| = "+
cvm::to_str((Q0+DQ0 - Q0_new).norm(), cvm::cv_width, cvm::cv_prec)+
"\n");
}
}
}
#endif // COLVAR_ROTATION_DERIVATIVE
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