RigidBodyVisitor.cpp

/*
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 *    this software without specific prior written permission.
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 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#include "visitors/RigidBodyVisitor.hpp"
 
#include <memory>
 
#include "primitives/RigidBody.hpp"
 
namespace OpenMD {
 
  void LipidHeadVisitor::visit(RigidBody* rb) {
    int globalID;
    Vector3d pos;
    Vector3d u(0, 0, 1);
    Vector3d newVec;
    std::shared_ptr<GenericData> data;
    std::shared_ptr<AtomData> atomData;
    std::shared_ptr<AtomInfo> atomInfo;
    bool haveAtomData;
    RotMat3x3d rotMatrix;
 
    if (!canVisit(rb->getType())) return;
 
    globalID  = rb->getGlobalIndex();
    pos       = rb->getPos();
    rotMatrix = rb->getA();
    // matVecMul3(rotMatrix, u, newVec);
    newVec = rotMatrix * u;
 
    data = rb->getPropertyByName("ATOMDATA");
 
    if (data != nullptr) {
      atomData = std::dynamic_pointer_cast<AtomData>(data);
 
      if (atomData == nullptr) {
        std::cerr << "can not get Atom Data from " << rb->getType()
                  << std::endl;
 
        atomData     = std::make_shared<AtomData>();
        haveAtomData = false;
 
      } else
        haveAtomData = true;
 
    } else {
      atomData     = std::make_shared<AtomData>();
      haveAtomData = false;
    }
 
    atomInfo               = std::make_shared<AtomInfo>();
    atomInfo->atomTypeName = "X";
    atomInfo->globalID     = globalID;
    atomInfo->pos[0]       = pos[0];
    atomInfo->pos[1]       = pos[1];
    atomInfo->pos[2]       = pos[2];
    atomInfo->vec[0]       = newVec[0];
    atomInfo->vec[1]       = newVec[1];
    atomInfo->vec[2]       = newVec[2];
 
    atomData->addAtomInfo(atomInfo);
 
    if (!haveAtomData) {
      atomData->setID("ATOMDATA");
      rb->addProperty(atomData);
    }
  }
 
  void LipidHeadVisitor::addLipidHeadName(const std::string& name) {
    lipidHeadName.insert(name);
  }
 
  bool LipidHeadVisitor::canVisit(const std::string& name) {
    return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
  }
 
  const std::string LipidHeadVisitor::toString() {
    char buffer[65535];
    std::string result;
    std::set<std::string>::iterator i;
 
    snprintf(
        buffer, 65535,
        "------------------------------------------------------------------\n");
    result += buffer;
 
    snprintf(buffer, 65535, "Visitor name: %s\n", visitorName.c_str());
    result += buffer;
 
    // print the ignore type list
    snprintf(buffer, 65535, "lipidHeadName list contains below types:\n");
    result += buffer;
 
    for (i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i) {
      snprintf(buffer, 65535, "%s\t", i->c_str());
      result += buffer;
    }
 
    snprintf(buffer, 65535, "\n");
    result += buffer;
 
    snprintf(
        buffer, 65535,
        "------------------------------------------------------------------\n");
    result += buffer;
 
    return result;
  }
 
  void RBCOMVisitor::visit(RigidBody* rb) {
    std::shared_ptr<AtomData> atomData;
    std::shared_ptr<AtomInfo> atomInfo;
    Vector3d pos;
    pos = rb->getPos();
 
    atomInfo               = std::make_shared<AtomInfo>();
    atomInfo->atomTypeName = "X";
    atomInfo->pos[0]       = pos[0];
    atomInfo->pos[1]       = pos[1];
    atomInfo->pos[2]       = pos[2];
    atomInfo->vec[0]       = 0;
    atomInfo->vec[1]       = 0;
    atomInfo->vec[2]       = 0;
 
    atomData = std::make_shared<AtomData>();
    atomData->setID("ATOMDATA");
    atomData->addAtomInfo(atomInfo);
 
    rb->addProperty(atomData);
  }
 
  const std::string RBCOMVisitor::toString() {
    char buffer[65535];
    std::string result;
 
    snprintf(
        buffer, 65535,
        "------------------------------------------------------------------\n");
    result += buffer;
 
    snprintf(buffer, 65535, "Visitor name: %s\n", visitorName.c_str());
    result += buffer;
 
    // print the ignore type list
    snprintf(buffer, 65535,
             "Visitor Description: add a pseudo atom at the center of "
             "the mass of the "
             "rigidbody\n");
    result += buffer;
 
    snprintf(
        buffer, 65535,
        "------------------------------------------------------------------\n");
    result += buffer;
 
    return result;
  }
 
}  // namespace OpenMD