AmoebaTorsionTorsionForceProxy.cpp

/* -------------------------------------------------------------------------- *
 *                                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) 2010 Stanford University and the Authors.           *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
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 * copy of this software and associated documentation files (the "Software"), *
 * to deal in the Software without restriction, including without limitation  *
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 * 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:       *
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 * 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,    *
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 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
 * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
 * -------------------------------------------------------------------------- */

#include "openmm/serialization/AmoebaTorsionTorsionForceProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h"
#include "openmm/AmoebaTorsionTorsionForce.h"
#include <sstream>

using namespace OpenMM;
using namespace std;

AmoebaTorsionTorsionForceProxy::AmoebaTorsionTorsionForceProxy() : SerializationProxy("AmoebaTorsionTorsionForce") {
}

static void loadGrid( const SerializationNode& grid, std::vector< std::vector< std::vector<double> > >& gridVector ){

    const std::vector<SerializationNode>& gridSerializationRows  = grid.getChildren();
    gridVector.resize( gridSerializationRows.size() );

    for( unsigned int ii = 0; ii < gridSerializationRows.size(); ii++) {
        const std::vector<SerializationNode>& gridSerializationColumns  = gridSerializationRows[ii].getChildren();
        gridVector[ii].resize( gridSerializationColumns.size() );
        for( unsigned int jj = 0; jj < gridSerializationColumns.size(); jj++) {
            const SerializationNode& gridSerializationColumnNode = gridSerializationColumns[jj];
            gridVector[ii][jj].resize( 6 );
            gridVector[ii][jj][0] = gridSerializationColumnNode.getDoubleProperty( "x" );
            gridVector[ii][jj][1] = gridSerializationColumnNode.getDoubleProperty( "y" );
            gridVector[ii][jj][2] = gridSerializationColumnNode.getDoubleProperty( "f" );
            gridVector[ii][jj][3] = gridSerializationColumnNode.getDoubleProperty( "fx" );
            gridVector[ii][jj][4] = gridSerializationColumnNode.getDoubleProperty( "fy" );
            gridVector[ii][jj][5] = gridSerializationColumnNode.getDoubleProperty( "fxy" );
        }
    }
}

void AmoebaTorsionTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
    node.setIntProperty("version", 1);
    const AmoebaTorsionTorsionForce& force = *reinterpret_cast<const AmoebaTorsionTorsionForce*>(object);

    // grid[xIdx][yIdx][6 values]

    // value0 = x-Grid value
    // value1 = y-Grid value
    // value2 = F          function value
    // value3 = F_x        partial f wrt x
    // value4 = F_y        partial f wrt y
    // value5 = F_xy       partial f wrt x,y

    SerializationNode& grids = node.createChildNode("TorsionTorsionGrids");
    grids.setIntProperty("size", static_cast<int>(force.getNumTorsionTorsionGrids()));
    for (unsigned int kk = 0; kk < static_cast<unsigned int>(force.getNumTorsionTorsionGrids()); kk++) {

        const std::vector< std::vector< std::vector<double> > > grid = force.getTorsionTorsionGrid( kk );

        unsigned int gridCount = 0;
        unsigned int gridYsize =  grid[0].size();
        for ( unsigned int ii = 0; ii < grid.size(); ii++) {
            gridCount += grid[ii].size();
        }

        SerializationNode& gridNode = grids.createChildNode("TorsionTorsionGrid").setIntProperty("size", static_cast<int>(gridCount) );
        for ( unsigned int ii = 0; ii < grid.size(); ii++) {
            SerializationNode& gridSerializationRow = gridNode.createChildNode("RowNode");
            gridSerializationRow.setIntProperty("dim", ii );
            gridSerializationRow.setIntProperty("size", static_cast<int>(grid[ii].size() ) );
            for ( unsigned int jj = 0; jj < grid[ii].size(); jj++) {
                SerializationNode& gridSerializationColumnNode = gridSerializationRow.createChildNode("ColumnNode");
                gridSerializationColumnNode.setIntProperty("dim", jj );
                unsigned int index = 0;
                gridSerializationColumnNode.setDoubleProperty("x",   grid[ii][jj][index++] );
                gridSerializationColumnNode.setDoubleProperty("y",   grid[ii][jj][index++] );
                gridSerializationColumnNode.setDoubleProperty("f",   grid[ii][jj][index++] );
                gridSerializationColumnNode.setDoubleProperty("fx",  grid[ii][jj][index++] );
                gridSerializationColumnNode.setDoubleProperty("fy",  grid[ii][jj][index++] );
                gridSerializationColumnNode.setDoubleProperty("fxy", grid[ii][jj][index++] );
            }
        }
    }

    SerializationNode& bonds = node.createChildNode("TorsionTorsion");
    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumTorsionTorsions()); ii++) {
        int particle1, particle2, particle3, particle4, particle5;
        int chiralCheckAtomIndex, gridIndex;
        force.getTorsionTorsionParameters(ii, particle1, particle2, particle3, particle4, particle5, chiralCheckAtomIndex, gridIndex );
        bonds.createChildNode("TorsionTorsion").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setIntProperty("p4", particle4).setIntProperty("p5", particle5).setIntProperty("chiralCheckAtomIndex", chiralCheckAtomIndex).setIntProperty("gridIndex", gridIndex );

    }
}

void* AmoebaTorsionTorsionForceProxy::deserialize(const SerializationNode& node) const {

    if (node.getIntProperty("version") != 1)
        throw OpenMMException("Unsupported version number");

    AmoebaTorsionTorsionForce* force = new AmoebaTorsionTorsionForce();
    try {

        const SerializationNode& grids                    = node.getChildNode("TorsionTorsionGrids");
        const std::vector<SerializationNode>& gridList    = grids.getChildren();
        for( unsigned int ii = 0; ii < gridList.size(); ii++) {
            std::vector< std::vector< std::vector<double> > > gridVector;
            loadGrid( gridList[ii], gridVector );
            force->setTorsionTorsionGrid( ii, gridVector );
        }

        const SerializationNode& bonds     = node.getChildNode("TorsionTorsion");
        vector<SerializationNode> children = bonds.getChildren();
        for (unsigned int i = 0; i < children.size(); i++) {
            SerializationNode& bond = children[i];
            force->addTorsionTorsion(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getIntProperty("p3"),  bond.getIntProperty("p4"), bond.getIntProperty("p5"), bond.getIntProperty("chiralCheckAtomIndex"), bond.getIntProperty("gridIndex"));
        }
    }
    catch (...) {
        delete force;
        throw;
    }
    return force;
}