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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 ); |
257 |
if( the_event->err_msg != NULL ) return 0; |
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return 1; |
259 |
break; |
260 |
|
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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 ); |
265 |
if( the_event->err_msg != NULL ) return 0; |
266 |
return 1; |
267 |
break; |
268 |
|
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default: |
270 |
the_event->err_msg = strdup( "MakeStamp error. Invalid CutoffGroup" |
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" assignment type" ); |
272 |
return 0; |
273 |
break; |
274 |
} |
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return 0; |
276 |
} |
277 |
|
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int MakeStamps::cutoffGroupMembers( event* the_event ){ |
279 |
|
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int i; |
281 |
|
282 |
if( the_event->evt.mbrs.nMembers > 0 ){ |
283 |
|
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for (i = 0; i < the_event->evt.mbrs.nMembers; i++) { |
285 |
current_cutoffgroup->addMember(the_event->evt.mbrs.memberList[i]); |
286 |
} |
287 |
|
288 |
return 1; |
289 |
|
290 |
} else { |
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the_event->err_msg = strdup( "MakeStamp error. No members in memberList " |
292 |
" for this CutoffGroup."); |
293 |
return 0; |
294 |
|
295 |
} |
296 |
} |
297 |
|
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int MakeStamps::cutoffGroupEnd( event* the_event ){ |
299 |
|
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the_event->err_msg = current_cutoffgroup->checkMe(); |
301 |
if( the_event->err_msg != NULL ) return 0; |
302 |
|
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return 1; |
304 |
} |
305 |
|
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int MakeStamps::newAtom( event* the_event ){ |
307 |
|
308 |
current_atom = new AtomStamp; |
309 |
|
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the_event->err_msg = current_mol->addAtom( current_atom, |
311 |
the_event->evt.blk_index ); |
312 |
|
313 |
if( the_event->err_msg != NULL ) return 0; |
314 |
return 1; |
315 |
} |
316 |
|
317 |
int MakeStamps::atomPosition( event* the_event ){ |
318 |
|
319 |
current_atom->setPosition( the_event->evt.pos.x, |
320 |
the_event->evt.pos.y, |
321 |
the_event->evt.pos.z ); |
322 |
return 1; |
323 |
} |
324 |
|
325 |
|
326 |
int MakeStamps::atomOrientation( event* the_event ){ |
327 |
|
328 |
current_atom->setOrientation( the_event->evt.ornt.phi, |
329 |
the_event->evt.ornt.theta, |
330 |
the_event->evt.ornt.psi ); |
331 |
return 1; |
332 |
} |
333 |
|
334 |
int MakeStamps::atomAssign( event* the_event ){ |
335 |
|
336 |
switch( the_event->evt.asmt.asmt_type ){ |
337 |
|
338 |
case STRING: |
339 |
the_event->err_msg = |
340 |
current_atom->assignString( the_event->evt.asmt.lhs, |
341 |
the_event->evt.asmt.rhs.sval ); |
342 |
if( the_event->err_msg != NULL ) return 0; |
343 |
return 1; |
344 |
break; |
345 |
|
346 |
case DOUBLE: |
347 |
the_event->err_msg = |
348 |
current_atom->assignDouble( the_event->evt.asmt.lhs, |
349 |
the_event->evt.asmt.rhs.dval ); |
350 |
if( the_event->err_msg != NULL ) return 0; |
351 |
return 1; |
352 |
break; |
353 |
|
354 |
case INT: |
355 |
the_event->err_msg = |
356 |
current_atom->assignInt( the_event->evt.asmt.lhs, |
357 |
the_event->evt.asmt.rhs.ival ); |
358 |
if( the_event->err_msg != NULL ) return 0; |
359 |
return 1; |
360 |
break; |
361 |
|
362 |
default: |
363 |
the_event->err_msg = strdup( "MakeStamp error. Invalid atom" |
364 |
" assignment type" ); |
365 |
return 0; |
366 |
break; |
367 |
} |
368 |
return 0; |
369 |
} |
370 |
|
371 |
int MakeStamps::atomEnd( event* the_event ){ |
372 |
|
373 |
the_event->err_msg = current_atom->checkMe(); |
374 |
if( the_event->err_msg != NULL ) return 0; |
375 |
|
376 |
return 1; |
377 |
} |
378 |
|
379 |
int MakeStamps::newBond( event* the_event ){ |
380 |
|
381 |
current_bond = new BondStamp; |
382 |
|
383 |
the_event->err_msg = current_mol->addBond( current_bond, |
384 |
the_event->evt.blk_index ); |
385 |
if( the_event->err_msg != NULL ) return 0; |
386 |
|
387 |
return 1; |
388 |
} |
389 |
|
390 |
int MakeStamps::bondAssign( event* the_event ){ |
391 |
|
392 |
switch( the_event->evt.asmt.asmt_type ){ |
393 |
|
394 |
case STRING: |
395 |
current_bond->assignString( the_event->evt.asmt.lhs, |
396 |
the_event->evt.asmt.rhs.sval ); |
397 |
return 1; |
398 |
break; |
399 |
|
400 |
case DOUBLE: |
401 |
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 |
} |