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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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|
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#include "types/MakeStamps.hpp" |
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#include "types/MoleculeStamp.hpp" |
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#include "types/RigidBodyStamp.hpp" |
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#include "types/CutoffGroupStamp.hpp" |
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#include "utils/simError.h" |
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#ifdef IS_MPI |
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#include "io/mpiBASS.h" |
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#endif // is_mpi |
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|
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MakeStamps::MakeStamps(){ |
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} |
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|
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MakeStamps::~MakeStamps(){ |
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|
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std::map<std::string, MoleculeStamp*>::iterator iter; |
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|
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for (iter=my_mols.begin(); iter!=my_mols.end(); ++iter) { |
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delete iter->second; |
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} |
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|
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my_mols.clear(); |
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|
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} |
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|
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MoleculeStamp* MakeStamps::getMolStamp( std::string the_id ){ |
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|
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std::map<std::string, MoleculeStamp*>::iterator iter; |
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|
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iter = my_mols.find(the_id); |
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|
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if (iter == my_mols.end()) { |
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return NULL; |
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} else { |
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return iter->second; |
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} |
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|
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} |
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|
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void MakeStamps::addMolStamp( MoleculeStamp* the_stamp ){ |
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|
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std::map<std::string, MoleculeStamp*>::iterator iter; |
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|
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std::string molStampName(the_stamp->getID()); |
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|
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iter = my_mols.find(molStampName); |
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|
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if (iter != my_mols.end()) { |
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sprintf( painCave.errMsg, |
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"Molecule Stamp Error. Two separate of declarations of " |
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"%s present.\n", |
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the_stamp->getID()); |
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painCave.isFatal = 1; |
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simError(); |
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#ifdef IS_MPI |
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if( painCave.isEventLoop ){ |
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if( worldRank == 0 ) mpiInterfaceExit(); |
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} |
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#endif //is_mpi |
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|
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} else { |
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my_mols.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, the_stamp)); |
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} |
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} |
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|
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|
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int MakeStamps::newMolecule( event* the_event ){ |
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|
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current_mol = new MoleculeStamp; |
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return 1; |
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} |
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|
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int MakeStamps::moleculeAssign( event* the_event ){ |
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|
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switch( the_event->evt.asmt.asmt_type ){ |
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|
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case STRING: |
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the_event->err_msg = current_mol->assignString( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.sval ); |
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break; |
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|
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case DOUBLE: |
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the_event->err_msg = current_mol->assignDouble( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.dval ); |
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break; |
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|
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case INT: |
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the_event->err_msg = current_mol->assignInt( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.ival ); |
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break; |
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|
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default: |
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the_event->err_msg = strdup( "MakeStamp error. Invalid molecule" |
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" assignment type" ); |
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return 0; |
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break; |
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} |
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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} |
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|
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int MakeStamps::moleculeEnd( event* the_event ){ |
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|
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the_event->err_msg = current_mol->checkMe(); |
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// if err_msg is set, then something is wrong |
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if( the_event->err_msg != NULL ) return 0; |
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|
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addMolStamp( current_mol ); |
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return 1; |
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} |
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|
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int MakeStamps::newRigidBody( event* the_event ){ |
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|
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current_rigidbody = new RigidBodyStamp; |
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|
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the_event->err_msg = current_mol->addRigidBody( current_rigidbody, |
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the_event->evt.blk_index ); |
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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} |
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|
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int MakeStamps::rigidBodyAssign( event* the_event ){ |
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|
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switch( the_event->evt.asmt.asmt_type ){ |
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|
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case STRING: |
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the_event->err_msg = |
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current_rigidbody->assignString( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.sval ); |
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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break; |
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|
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case DOUBLE: |
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the_event->err_msg = |
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current_rigidbody->assignDouble( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.dval ); |
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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break; |
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|
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case INT: |
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the_event->err_msg = |
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current_rigidbody->assignInt( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.ival ); |
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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break; |
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|
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default: |
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the_event->err_msg = strdup( "MakeStamp error. Invalid rigidBody" |
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" assignment type" ); |
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return 0; |
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break; |
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} |
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return 0; |
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} |
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|
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int MakeStamps::rigidBodyMembers( event* the_event ){ |
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|
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int i; |
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|
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if( the_event->evt.mbrs.nMembers > 0 ){ |
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|
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for (i = 0; i < the_event->evt.mbrs.nMembers; i++) { |
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current_rigidbody->addMember(the_event->evt.mbrs.memberList[i]); |
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} |
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|
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return 1; |
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|
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} else { |
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the_event->err_msg = strdup( "MakeStamp error. No members in memberList " |
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" for this rigidBody."); |
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return 0; |
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|
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} |
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} |
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|
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int MakeStamps::rigidBodyEnd( event* the_event ){ |
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|
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the_event->err_msg = current_rigidbody->checkMe(); |
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if( the_event->err_msg != NULL ) return 0; |
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|
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return 1; |
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} |
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|
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int MakeStamps::newCutoffGroup( event* the_event ){ |
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|
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current_cutoffgroup = new CutoffGroupStamp; |
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|
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the_event->err_msg = current_mol->addCutoffGroup( current_cutoffgroup, |
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the_event->evt.blk_index ); |
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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} |
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|
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int MakeStamps::cutoffGroupAssign( event* the_event ){ |
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|
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switch( the_event->evt.asmt.asmt_type ){ |
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|
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case STRING: |
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the_event->err_msg = |
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current_cutoffgroup->assignString( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.sval ); |
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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break; |
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|
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case DOUBLE: |
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the_event->err_msg = |
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current_cutoffgroup->assignDouble( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.dval ); |
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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break; |
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|
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case INT: |
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the_event->err_msg = |
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current_cutoffgroup->assignInt( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.ival ); |
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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break; |
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|
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default: |
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the_event->err_msg = strdup( "MakeStamp error. Invalid CutoffGroup" |
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" assignment type" ); |
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return 0; |
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break; |
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} |
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return 0; |
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} |
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|
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int MakeStamps::cutoffGroupMembers( event* the_event ){ |
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|
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int i; |
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|
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if( the_event->evt.mbrs.nMembers > 0 ){ |
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|
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for (i = 0; i < the_event->evt.mbrs.nMembers; i++) { |
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current_cutoffgroup->addMember(the_event->evt.mbrs.memberList[i]); |
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} |
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|
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return 1; |
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|
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} else { |
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the_event->err_msg = strdup( "MakeStamp error. No members in memberList " |
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" for this CutoffGroup."); |
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return 0; |
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|
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} |
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} |
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|
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int MakeStamps::cutoffGroupEnd( event* the_event ){ |
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|
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the_event->err_msg = current_cutoffgroup->checkMe(); |
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if( the_event->err_msg != NULL ) return 0; |
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|
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return 1; |
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} |
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|
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int MakeStamps::newAtom( event* the_event ){ |
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|
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current_atom = new AtomStamp; |
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|
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the_event->err_msg = current_mol->addAtom( current_atom, |
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the_event->evt.blk_index ); |
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|
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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} |
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|
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int MakeStamps::atomPosition( event* the_event ){ |
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|
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current_atom->setPosition( the_event->evt.pos.x, |
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the_event->evt.pos.y, |
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the_event->evt.pos.z ); |
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return 1; |
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} |
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|
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|
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int MakeStamps::atomOrientation( event* the_event ){ |
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|
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current_atom->setOrientation( the_event->evt.ornt.phi, |
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the_event->evt.ornt.theta, |
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the_event->evt.ornt.psi ); |
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return 1; |
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} |
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|
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int MakeStamps::atomAssign( event* the_event ){ |
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|
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switch( the_event->evt.asmt.asmt_type ){ |
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|
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case STRING: |
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the_event->err_msg = |
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current_atom->assignString( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.sval ); |
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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break; |
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|
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case DOUBLE: |
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the_event->err_msg = |
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current_atom->assignDouble( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.dval ); |
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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break; |
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|
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case INT: |
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the_event->err_msg = |
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current_atom->assignInt( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.ival ); |
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if( the_event->err_msg != NULL ) return 0; |
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return 1; |
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break; |
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|
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default: |
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the_event->err_msg = strdup( "MakeStamp error. Invalid atom" |
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" assignment type" ); |
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return 0; |
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break; |
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} |
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return 0; |
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} |
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|
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int MakeStamps::atomEnd( event* the_event ){ |
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|
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the_event->err_msg = current_atom->checkMe(); |
| 374 |
if( the_event->err_msg != NULL ) return 0; |
| 375 |
|
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return 1; |
| 377 |
} |
| 378 |
|
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int MakeStamps::newBond( event* the_event ){ |
| 380 |
|
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current_bond = new BondStamp; |
| 382 |
|
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the_event->err_msg = current_mol->addBond( current_bond, |
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the_event->evt.blk_index ); |
| 385 |
if( the_event->err_msg != NULL ) return 0; |
| 386 |
|
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return 1; |
| 388 |
} |
| 389 |
|
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int MakeStamps::bondAssign( event* the_event ){ |
| 391 |
|
| 392 |
switch( the_event->evt.asmt.asmt_type ){ |
| 393 |
|
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case STRING: |
| 395 |
current_bond->assignString( the_event->evt.asmt.lhs, |
| 396 |
the_event->evt.asmt.rhs.sval ); |
| 397 |
return 1; |
| 398 |
break; |
| 399 |
|
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case DOUBLE: |
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current_bond->assignDouble( the_event->evt.asmt.lhs, |
| 402 |
the_event->evt.asmt.rhs.dval ); |
| 403 |
return 1; |
| 404 |
break; |
| 405 |
|
| 406 |
case INT: |
| 407 |
current_bond->assignInt( the_event->evt.asmt.lhs, |
| 408 |
the_event->evt.asmt.rhs.ival ); |
| 409 |
return 1; |
| 410 |
break; |
| 411 |
|
| 412 |
default: |
| 413 |
the_event->err_msg = strdup( "MakeStamp error. Invalid bond" |
| 414 |
" assignment type" ); |
| 415 |
return 0; |
| 416 |
break; |
| 417 |
} |
| 418 |
return 0; |
| 419 |
} |
| 420 |
|
| 421 |
int MakeStamps::bondMembers( event* the_event ){ |
| 422 |
|
| 423 |
if( the_event->evt.mbrs.nMembers == 2 ){ |
| 424 |
|
| 425 |
current_bond->members( the_event->evt.mbrs.memberList[0], |
| 426 |
the_event->evt.mbrs.memberList[1] ); |
| 427 |
return 1; |
| 428 |
|
| 429 |
} else { |
| 430 |
the_event->err_msg = strdup( "MakeStamp error. Wrong number of members " |
| 431 |
" in bond"); |
| 432 |
return 0; |
| 433 |
|
| 434 |
} |
| 435 |
|
| 436 |
} |
| 437 |
|
| 438 |
int MakeStamps::bondConstraint( event* the_event ){ |
| 439 |
|
| 440 |
current_bond->constrain( the_event->evt.cnstr ); |
| 441 |
return 1; |
| 442 |
} |
| 443 |
|
| 444 |
int MakeStamps::bondEnd( event* the_event ){ |
| 445 |
|
| 446 |
the_event->err_msg = current_bond->checkMe(); |
| 447 |
if( the_event->err_msg != NULL ) return 0; |
| 448 |
|
| 449 |
return 1; |
| 450 |
} |
| 451 |
|
| 452 |
int MakeStamps::newBend( event* the_event ){ |
| 453 |
|
| 454 |
current_bend = new BendStamp; |
| 455 |
|
| 456 |
the_event->err_msg = current_mol->addBend( current_bend, |
| 457 |
the_event->evt.blk_index ); |
| 458 |
if( the_event->err_msg != NULL ) return 0; |
| 459 |
|
| 460 |
return 1; |
| 461 |
} |
| 462 |
|
| 463 |
int MakeStamps::bendAssign( event* the_event ){ |
| 464 |
|
| 465 |
switch( the_event->evt.asmt.asmt_type ){ |
| 466 |
|
| 467 |
case STRING: |
| 468 |
current_bend->assignString( the_event->evt.asmt.lhs, |
| 469 |
the_event->evt.asmt.rhs.sval ); |
| 470 |
return 1; |
| 471 |
break; |
| 472 |
|
| 473 |
case DOUBLE: |
| 474 |
current_bend->assignDouble( the_event->evt.asmt.lhs, |
| 475 |
the_event->evt.asmt.rhs.dval ); |
| 476 |
return 1; |
| 477 |
break; |
| 478 |
|
| 479 |
case INT: |
| 480 |
current_bend->assignInt( the_event->evt.asmt.lhs, |
| 481 |
the_event->evt.asmt.rhs.ival ); |
| 482 |
return 1; |
| 483 |
break; |
| 484 |
|
| 485 |
default: |
| 486 |
the_event->err_msg = strdup( "MakeStamp error. Invalid bend" |
| 487 |
" assignment type" ); |
| 488 |
return 0; |
| 489 |
break; |
| 490 |
} |
| 491 |
return 0; |
| 492 |
} |
| 493 |
|
| 494 |
int MakeStamps::bendMembers( event* the_event ){ |
| 495 |
|
| 496 |
|
| 497 |
switch( the_event->evt.mbrs.nMembers ) { |
| 498 |
case 3: |
| 499 |
current_bend->members( the_event->evt.mbrs.memberList[0], |
| 500 |
the_event->evt.mbrs.memberList[1], |
| 501 |
the_event->evt.mbrs.memberList[2]); |
| 502 |
return 1; |
| 503 |
break; |
| 504 |
case 2: |
| 505 |
current_bend->members( the_event->evt.mbrs.memberList[0], |
| 506 |
the_event->evt.mbrs.memberList[1], |
| 507 |
0 ); |
| 508 |
return 1; |
| 509 |
break; |
| 510 |
default: |
| 511 |
the_event->err_msg = strdup( "MakeStamp error. Wrong number of members " |
| 512 |
"in bend."); |
| 513 |
return 0; |
| 514 |
break; |
| 515 |
} |
| 516 |
return 0; |
| 517 |
} |
| 518 |
|
| 519 |
int MakeStamps::bendConstraint( event* the_event ){ |
| 520 |
|
| 521 |
current_bend->constrain( the_event->evt.cnstr ); |
| 522 |
return 1; |
| 523 |
} |
| 524 |
|
| 525 |
int MakeStamps::bendEnd( event* the_event ){ |
| 526 |
|
| 527 |
the_event->err_msg = current_bend->checkMe(); |
| 528 |
if( the_event->err_msg != NULL ) return 0; |
| 529 |
|
| 530 |
return 1; |
| 531 |
} |
| 532 |
|
| 533 |
int MakeStamps::newTorsion( event* the_event ){ |
| 534 |
|
| 535 |
current_torsion = new TorsionStamp; |
| 536 |
|
| 537 |
the_event->err_msg = current_mol->addTorsion( current_torsion, |
| 538 |
the_event->evt.blk_index ); |
| 539 |
if( the_event->err_msg != NULL ) return 0; |
| 540 |
|
| 541 |
return 1; |
| 542 |
} |
| 543 |
|
| 544 |
int MakeStamps::torsionAssign( event* the_event ){ |
| 545 |
|
| 546 |
switch( the_event->evt.asmt.asmt_type ){ |
| 547 |
|
| 548 |
case STRING: |
| 549 |
current_torsion->assignString( the_event->evt.asmt.lhs, |
| 550 |
the_event->evt.asmt.rhs.sval ); |
| 551 |
return 1; |
| 552 |
break; |
| 553 |
|
| 554 |
case DOUBLE: |
| 555 |
current_torsion->assignDouble( the_event->evt.asmt.lhs, |
| 556 |
the_event->evt.asmt.rhs.dval ); |
| 557 |
return 1; |
| 558 |
break; |
| 559 |
|
| 560 |
case INT: |
| 561 |
current_torsion->assignInt( the_event->evt.asmt.lhs, |
| 562 |
the_event->evt.asmt.rhs.ival ); |
| 563 |
return 1; |
| 564 |
break; |
| 565 |
|
| 566 |
default: |
| 567 |
the_event->err_msg = strdup( "MakeStamp error. Invalid torsion" |
| 568 |
" assignment type" ); |
| 569 |
return 0; |
| 570 |
break; |
| 571 |
} |
| 572 |
return 0; |
| 573 |
} |
| 574 |
|
| 575 |
int MakeStamps::torsionMembers( event* the_event ){ |
| 576 |
|
| 577 |
|
| 578 |
switch( the_event->evt.mbrs.nMembers ) { |
| 579 |
case 4: |
| 580 |
|
| 581 |
current_torsion->members( the_event->evt.mbrs.memberList[0], |
| 582 |
the_event->evt.mbrs.memberList[1], |
| 583 |
the_event->evt.mbrs.memberList[2], |
| 584 |
the_event->evt.mbrs.memberList[3]); |
| 585 |
return 1; |
| 586 |
break; |
| 587 |
case 3: |
| 588 |
|
| 589 |
|
| 590 |
current_torsion->members( the_event->evt.mbrs.memberList[0], |
| 591 |
the_event->evt.mbrs.memberList[1], |
| 592 |
the_event->evt.mbrs.memberList[2], |
| 593 |
-1); |
| 594 |
|
| 595 |
return 1; |
| 596 |
break; |
| 597 |
default: |
| 598 |
the_event->err_msg = strdup( "MakeStamp error. Wrong number of members " |
| 599 |
"in torsion."); |
| 600 |
return 0; |
| 601 |
break; |
| 602 |
} |
| 603 |
return 0; |
| 604 |
|
| 605 |
} |
| 606 |
|
| 607 |
int MakeStamps::torsionConstraint( event* the_event ){ |
| 608 |
|
| 609 |
current_torsion->constrain( the_event->evt.cnstr ); |
| 610 |
return 1; |
| 611 |
} |
| 612 |
|
| 613 |
int MakeStamps::torsionEnd( event* the_event ){ |
| 614 |
|
| 615 |
the_event->err_msg = current_torsion->checkMe(); |
| 616 |
if( the_event->err_msg != NULL ) return 0; |
| 617 |
|
| 618 |
return 1; |
| 619 |
} |
