/* -------------------------------------------------------------------------- * * OpenMMAmoeba * * -------------------------------------------------------------------------- * * This is part of the OpenMM molecular simulation toolkit originating from * * Simbios, the NIH National Center for Physics-Based Simulation of * * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * * Portions copyright (c) 2008-2014 Stanford University and the Authors. * * Authors: * * Contributors: * * * * Permission is hereby granted, free of charge, to any person obtaining a * * copy of this software and associated documentation files (the "Software"), * * to deal in the Software without restriction, including without limitation * * the rights to use, copy, modify, merge, publish, distribute, sublicense, * * and/or sell copies of the Software, and to permit persons to whom the * * Software is furnished to do so, subject to the following conditions: * * * * The above copyright notice and this permission notice shall be included in * * all copies or substantial portions of the Software. * * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL * * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, * * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR * * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE * * USE OR OTHER DEALINGS IN THE SOFTWARE. * * -------------------------------------------------------------------------- */ #include "openmm/Force.h" #include "openmm/OpenMMException.h" #include "openmm/AmoebaTorsionTorsionForce.h" #include "openmm/internal/AmoebaTorsionTorsionForceImpl.h" #include "openmm/internal/SplineFitter.h" using namespace OpenMM; using namespace std; AmoebaTorsionTorsionForce::AmoebaTorsionTorsionForce() { } int AmoebaTorsionTorsionForce::addTorsionTorsion(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) { torsionTorsions.push_back(TorsionTorsionInfo(particle1, particle2, particle3, particle4, particle5, chiralCheckAtomIndex, gridIndex)); return torsionTorsions.size()-1; } void AmoebaTorsionTorsionForce::getTorsionTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& chiralCheckAtomIndex, int& gridIndex) const { particle1 = torsionTorsions[index].particle1; particle2 = torsionTorsions[index].particle2; particle3 = torsionTorsions[index].particle3; particle4 = torsionTorsions[index].particle4; particle5 = torsionTorsions[index].particle5; chiralCheckAtomIndex = torsionTorsions[index].chiralCheckAtomIndex; gridIndex = torsionTorsions[index].gridIndex; } void AmoebaTorsionTorsionForce::setTorsionTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) { torsionTorsions[index].particle1 = particle1; torsionTorsions[index].particle2 = particle2; torsionTorsions[index].particle3 = particle3; torsionTorsions[index].particle4 = particle4; torsionTorsions[index].particle5 = particle5; torsionTorsions[index].chiralCheckAtomIndex = chiralCheckAtomIndex; torsionTorsions[index].gridIndex = gridIndex; } const TorsionTorsionGrid& AmoebaTorsionTorsionForce::getTorsionTorsionGrid(int index ) const { return torsionTorsionGrids[index].getTorsionTorsionGrid(); } void AmoebaTorsionTorsionForce::setTorsionTorsionGrid(int index, const TorsionTorsionGrid& grid ) { if( index >= static_cast(torsionTorsionGrids.size()) ){ torsionTorsionGrids.resize( index + 1); } torsionTorsionGrids[index] = grid; } ForceImpl* AmoebaTorsionTorsionForce::createImpl() const { return new AmoebaTorsionTorsionForceImpl(*this); } AmoebaTorsionTorsionForce::TorsionTorsionGridInfo::TorsionTorsionGridInfo(const TorsionTorsionGrid& grid) { if (grid[0][0][0] != grid[1][0][0]) _grid = grid; else { // We need to transpose the grid. int xsize = grid[0].size(); int ysize = grid.size(); _grid.resize(xsize); for (int i = 0; i < xsize; i++) { _grid[i].resize(ysize); for (int j = 0; j < ysize; j++) _grid[i][j] = grid[j][i]; } } _startValues[0] = _grid[0][0][0]; _startValues[1] = _grid[0][0][1]; _spacing[0] = static_cast(_grid.size()-1)/360.0; _spacing[1] = static_cast(_grid.size()-1)/360.0; _size[0] = static_cast(_grid.size()); _size[1] = static_cast(_grid[0].size()); if (_grid[0][0].size() == 3) { // We need to compute the derivatives ourselves. First determine if the grid is periodic. int xsize = _size[0]; int ysize = _size[1]; bool periodic = true; for (int i = 0; i < xsize; i++) if (_grid[i][0][2] != _grid[i][ysize-1][2]) periodic = false; for (int i = 0; i < ysize; i++) if (_grid[0][i][2] != _grid[xsize-1][i][2]) periodic = false; // Compute derivatives with respect to the first angle. vector x(xsize), y(ysize); for (int i = 0; i < xsize; i++) x[i] = _grid[i][0][0]; for (int i = 0; i < ysize; i++) y[i] = _grid[0][i][1]; vector d1(xsize*ysize), d2(xsize*ysize), d12(xsize*ysize); vector t(xsize), deriv(xsize); for (int i = 0; i < ysize; i++) { for (int j = 0; j < xsize; j++) t[j] = _grid[j][i][2]; if (periodic) SplineFitter::createPeriodicSpline(x, t, deriv); else SplineFitter::createNaturalSpline(x, t, deriv); for (int j = 0; j < xsize; j++) d1[j+xsize*i] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[j]); } // Compute derivatives with respect to the second angle. t.resize(ysize); deriv.resize(ysize); for (int i = 0; i < xsize; i++) { for (int j = 0; j < ysize; j++) t[j] = _grid[i][j][2]; if (periodic) SplineFitter::createPeriodicSpline(y, t, deriv); else SplineFitter::createNaturalSpline(y, t, deriv); for (int j = 0; j < ysize; j++) d2[i+xsize*j] = SplineFitter::evaluateSplineDerivative(y, t, deriv, y[j]); } // Compute cross derivatives. t.resize(xsize); deriv.resize(xsize); for (int i = 0; i < ysize; i++) { for (int j = 0; j < xsize; j++) t[j] = d2[j+xsize*i]; if (periodic) SplineFitter::createPeriodicSpline(x, t, deriv); else SplineFitter::createNaturalSpline(x, t, deriv); for (int j = 0; j < xsize; j++) d12[j+xsize*i] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[j]); } // Add the derivatives to the grid. for (int i = 0; i < xsize; i++) for (int j = 0; j < ysize; j++) { _grid[i][j].push_back(d1[i+xsize*j]); _grid[i][j].push_back(d2[i+xsize*j]); _grid[i][j].push_back(d12[i+xsize*j]); } } }