UFFAdapter.cpp

/*
 * Copyright (c) 2004-present, The University of Notre Dame. All rights
 * reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * 3. Neither the name of the copyright holder nor the names of its
 *    contributors may be used to endorse or promote products derived from
 *    this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * 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 appropriate papers when you publish your
 * work.  Good starting points are:
 *
 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
#include "types/UFFAdapter.hpp"
 
#include <cstdio>
#include <memory>
 
#include "utils/simError.h"
 
namespace OpenMD {
 
  bool UFFAdapter::isUFF() { return at_->hasProperty(UFFtypeID); }
 
  UFFAtypeParameters UFFAdapter::getUFFParam() {
    if (!isUFF()) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "UFFAdapter::getUFFParam was passed an atomType (%s)\n"
               "\tthat does not appear to be a UFF atom.\n",
               at_->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    std::shared_ptr<GenericData> data = at_->getPropertyByName(UFFtypeID);
    if (data == nullptr) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "UFFAdapter::getUFFParam could not find UFF\n"
               "\tparameters for atomType %s.\n",
               at_->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    std::shared_ptr<UFFAtypeData> uffData =
        std::dynamic_pointer_cast<UFFAtypeData>(data);
    if (uffData == NULL) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "UFFAdapter::getUFFParam could not convert\n"
               "\tGenericData to UFFAtypeData for atom type %s\n",
               at_->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    return uffData->getData();
  }
 
  RealType UFFAdapter::getR1() {
    UFFAtypeParameters uffParam = getUFFParam();
    return uffParam.r1;
  }
 
  RealType UFFAdapter::getTheta0() {
    UFFAtypeParameters uffParam = getUFFParam();
    return uffParam.theta0;
  }
 
  RealType UFFAdapter::getX1() {
    UFFAtypeParameters uffParam = getUFFParam();
    return uffParam.x1;
  }
 
  RealType UFFAdapter::getD1() {
    UFFAtypeParameters uffParam = getUFFParam();
    return uffParam.D1;
  }
 
  RealType UFFAdapter::getZeta() {
    UFFAtypeParameters uffParam = getUFFParam();
    return uffParam.zeta;
  }
 
  RealType UFFAdapter::getZ1() {
    UFFAtypeParameters uffParam = getUFFParam();
    return uffParam.Z1;
  }
 
  RealType UFFAdapter::getVi() {
    UFFAtypeParameters uffParam = getUFFParam();
    return uffParam.Vi;
  }
 
  RealType UFFAdapter::getUj() {
    UFFAtypeParameters uffParam = getUFFParam();
    return uffParam.Uj;
  }
 
  RealType UFFAdapter::getXi() {
    UFFAtypeParameters uffParam = getUFFParam();
    return uffParam.Xi;
  }
 
  RealType UFFAdapter::getHard() {
    UFFAtypeParameters uffParam = getUFFParam();
    return uffParam.Hard;
  }
 
  RealType UFFAdapter::getRadius() {
    UFFAtypeParameters uffParam = getUFFParam();
    return uffParam.Radius;
  }
 
  void UFFAdapter::makeUFF(RealType r1, RealType theta0, RealType x1,
                           RealType D1, RealType zeta, RealType Z1, RealType Vi,
                           RealType Uj, RealType Xi, RealType Hard,
                           RealType Radius) {
    if (isUFF()) { at_->removeProperty(UFFtypeID); }
 
    UFFAtypeParameters uffParam {};
 
    uffParam.r1     = r1;
    uffParam.theta0 = theta0;
    uffParam.x1     = x1;
    uffParam.D1     = D1;
    uffParam.zeta   = zeta;
    uffParam.Z1     = Z1;
    uffParam.Vi     = Vi;
    uffParam.Uj     = Uj;
    uffParam.Xi     = Xi;
    uffParam.Hard   = Hard;
    uffParam.Radius = Radius;
    at_->addProperty(std::make_shared<UFFAtypeData>(UFFtypeID, uffParam));
  }
}  // namespace OpenMD