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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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#include <iostream> |
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|
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#include "types/AtomType.hpp" |
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#include "utils/simError.h" |
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#define __C |
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#include "UseTheForce/DarkSide/atype_interface.h" |
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#include "UseTheForce/DarkSide/lj_interface.h" |
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#include "UseTheForce/DarkSide/eam_interface.h" |
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#include "UseTheForce/DarkSide/electrostatic_interface.h" |
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#include "UseTheForce/DarkSide/suttonchen_interface.h" |
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namespace oopse { |
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AtomType::AtomType(){ |
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|
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// initialize to an error: |
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atp.ident = -1; |
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|
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// and mass_less: |
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mass_ = 0.0; |
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|
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// atom type is a Tabula Rasa: |
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atp.is_Directional = 0; |
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atp.is_LennardJones = 0; |
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atp.is_Charge = 0; |
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atp.is_Dipole = 0; |
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atp.is_SplitDipole = 0; |
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atp.is_Quadrupole = 0; |
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atp.is_Sticky = 0; |
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atp.is_StickyPower = 0; |
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atp.is_GayBerne = 0; |
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atp.is_EAM = 0; |
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atp.is_Shape = 0; |
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atp.is_FLARB = 0; |
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atp.is_SC = 0; |
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atp.is_MEAM = 0; |
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} |
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|
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void AtomType::makeFortranAtomType() { |
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|
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int status; |
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|
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if (name_.empty()) { |
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sprintf( painCave.errMsg, |
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"Attempting to complete an AtomType without giving " |
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"it a name_!\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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if (atp.ident == -1) { |
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sprintf( painCave.errMsg, |
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"Attempting to complete AtomType %s without setting the" |
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" ident!/n", name_.c_str()); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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status = 0; |
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|
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makeAtype(&atp, &status); |
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|
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if (status != 0) { |
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sprintf( painCave.errMsg, |
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"Fortran rejected AtomType %s!\n", name_.c_str()); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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|
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void AtomType::complete() { |
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int isError; |
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GenericData* data; |
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|
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//notify a new LJtype atom type is created |
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if (isLennardJones()) { |
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data = getPropertyByName("LennardJones"); |
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if (data != NULL) { |
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LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
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|
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if (ljData != NULL) { |
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LJParam ljParam = ljData->getData(); |
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|
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newLJtype(&atp.ident, &ljParam.sigma, &ljParam.epsilon, &ljParam.soft_pot, |
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&isError); |
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|
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if (isError != 0) { |
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sprintf( painCave.errMsg, |
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"Fortran rejected newLJtype\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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} else { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to LJParam\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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if (isElectrostatic()) { |
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newElectrostaticType(&atp, &isError); |
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if (isError != 0) { |
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sprintf( painCave.errMsg, |
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"Fortran rejected newElectrostaticType\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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if (isCharge()) { |
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data = getPropertyByName("Charge"); |
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if (data != NULL) { |
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DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data); |
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|
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if (doubleData != NULL) { |
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double charge = doubleData->getData(); |
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setCharge(&atp.ident, &charge, &isError); |
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|
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if (isError != 0) { |
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sprintf( painCave.errMsg, |
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"Fortran rejected setCharge\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to DoubleGenericData\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, "Can not find Charge Parameters\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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if (isEAM()) { |
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data = getPropertyByName("EAM"); |
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if (data != NULL) { |
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EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data); |
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|
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if (eamData != NULL) { |
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|
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EAMParam eamParam = eamData->getData(); |
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|
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|
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newEAMtype(&eamParam.latticeConstant, &eamParam.nrho, &eamParam.drho, |
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&eamParam.nr, &eamParam.dr, &eamParam.rcut, &eamParam.rvals[0], |
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&eamParam.rhovals[0], &eamParam.Frhovals[0], &atp.ident, |
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&isError ); |
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|
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if (isError != 0) { |
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sprintf( painCave.errMsg, |
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"Fortran rejected newEAMtype\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to EAMParam\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, "Can not find EAM Parameters\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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|
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if (isSC()) { |
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data = getPropertyByName("SC"); |
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if (data != NULL) { |
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SCParamGenericData* SCData = dynamic_cast<SCParamGenericData*>(data); |
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|
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if (SCData != NULL) { |
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|
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SCParam scParam = SCData->getData(); |
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|
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|
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newSCtype(&atp.ident, &scParam.c, &scParam.m, |
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&scParam.n, &scParam.alpha, &scParam.epsilon, |
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&isError ); |
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|
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if (isError != 0) { |
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sprintf( painCave.errMsg, |
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"Fortran rejected newSCtype\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to SCParam\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, "Can not find SC Parameters\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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|
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|
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} |
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|
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void AtomType::addProperty(GenericData* genData) { |
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properties_.addProperty(genData); |
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} |
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|
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void AtomType::removeProperty(const std::string& propName) { |
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properties_.removeProperty(propName); |
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} |
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|
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void AtomType::clearProperties() { |
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properties_.clearProperties(); |
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} |
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|
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std::vector<std::string> AtomType::getPropertyNames() { |
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return properties_.getPropertyNames(); |
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} |
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|
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std::vector<GenericData*> AtomType::getProperties() { |
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return properties_.getProperties(); |
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} |
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|
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GenericData* AtomType::getPropertyByName(const std::string& propName) { |
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return properties_.getPropertyByName(propName); |
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} |
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} |
