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gezelter |
1930 |
/* |
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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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gezelter |
1490 |
#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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tim |
1492 |
#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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gezelter |
1490 |
#ifdef IS_MPI |
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tim |
1492 |
#include "io/mpiBASS.h" |
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gezelter |
1490 |
#endif // is_mpi |
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|
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tim |
2187 |
MakeStamps::MakeStamps(){ |
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gezelter |
1490 |
} |
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tim |
2187 |
MakeStamps::~MakeStamps(){ |
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gezelter |
1490 |
|
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tim |
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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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gezelter |
1490 |
} |
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|
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tim |
2187 |
my_mols.clear(); |
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gezelter |
1490 |
|
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} |
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|
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tim |
2187 |
MoleculeStamp* MakeStamps::getMolStamp( std::string the_id ){ |
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gezelter |
1490 |
|
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tim |
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std::map<std::string, MoleculeStamp*>::iterator iter; |
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gezelter |
1490 |
|
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tim |
2187 |
iter = my_mols.find(the_id); |
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gezelter |
1490 |
|
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tim |
2187 |
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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gezelter |
1490 |
} |
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} |
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tim |
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void MakeStamps::addMolStamp( MoleculeStamp* the_stamp ){ |
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gezelter |
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|
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tim |
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std::map<std::string, MoleculeStamp*>::iterator iter; |
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gezelter |
1490 |
|
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tim |
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std::string molStampName(the_stamp->getID()); |
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gezelter |
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|
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tim |
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iter = my_mols.find(molStampName); |
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gezelter |
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|
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tim |
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if (iter != my_mols.end()) { |
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gezelter |
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sprintf( painCave.errMsg, |
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tim |
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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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gezelter |
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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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tim |
2187 |
|
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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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gezelter |
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} |
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} |
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int MakeStamps::newMolecule( event* the_event ){ |
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current_mol = new MoleculeStamp; |
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return 1; |
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} |
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int MakeStamps::moleculeAssign( event* the_event ){ |
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switch( the_event->evt.asmt.asmt_type ){ |
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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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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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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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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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int MakeStamps::moleculeEnd( event* the_event ){ |
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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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152 |
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addMolStamp( current_mol ); |
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return 1; |
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} |
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int MakeStamps::newRigidBody( event* the_event ){ |
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current_rigidbody = new RigidBodyStamp; |
159 |
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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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166 |
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int MakeStamps::rigidBodyAssign( event* the_event ){ |
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168 |
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switch( the_event->evt.asmt.asmt_type ){ |
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170 |
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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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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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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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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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int MakeStamps::rigidBodyMembers( event* the_event ){ |
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int i; |
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if( the_event->evt.mbrs.nMembers > 0 ){ |
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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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return 1; |
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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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220 |
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} |
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} |
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int MakeStamps::rigidBodyEnd( event* the_event ){ |
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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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return 1; |
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} |
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int MakeStamps::newCutoffGroup( event* the_event ){ |
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current_cutoffgroup = new CutoffGroupStamp; |
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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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int MakeStamps::cutoffGroupAssign( event* the_event ){ |
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switch( the_event->evt.asmt.asmt_type ){ |
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245 |
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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; |
250 |
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return 1; |
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break; |
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case DOUBLE: |
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the_event->err_msg = |
255 |
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current_cutoffgroup->assignDouble( the_event->evt.asmt.lhs, |
256 |
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the_event->evt.asmt.rhs.dval ); |
257 |
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if( the_event->err_msg != NULL ) return 0; |
258 |
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return 1; |
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break; |
260 |
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case INT: |
262 |
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the_event->err_msg = |
263 |
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current_cutoffgroup->assignInt( the_event->evt.asmt.lhs, |
264 |
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the_event->evt.asmt.rhs.ival ); |
265 |
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if( the_event->err_msg != NULL ) return 0; |
266 |
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return 1; |
267 |
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break; |
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269 |
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default: |
270 |
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the_event->err_msg = strdup( "MakeStamp error. Invalid CutoffGroup" |
271 |
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" assignment type" ); |
272 |
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return 0; |
273 |
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break; |
274 |
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} |
275 |
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return 0; |
276 |
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} |
277 |
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278 |
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int MakeStamps::cutoffGroupMembers( event* the_event ){ |
279 |
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280 |
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int i; |
281 |
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282 |
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if( the_event->evt.mbrs.nMembers > 0 ){ |
283 |
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284 |
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for (i = 0; i < the_event->evt.mbrs.nMembers; i++) { |
285 |
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current_cutoffgroup->addMember(the_event->evt.mbrs.memberList[i]); |
286 |
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} |
287 |
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288 |
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return 1; |
289 |
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290 |
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} else { |
291 |
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the_event->err_msg = strdup( "MakeStamp error. No members in memberList " |
292 |
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" for this CutoffGroup."); |
293 |
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return 0; |
294 |
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295 |
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} |
296 |
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} |
297 |
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298 |
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int MakeStamps::cutoffGroupEnd( event* the_event ){ |
299 |
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300 |
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the_event->err_msg = current_cutoffgroup->checkMe(); |
301 |
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if( the_event->err_msg != NULL ) return 0; |
302 |
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303 |
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return 1; |
304 |
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} |
305 |
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306 |
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int MakeStamps::newAtom( event* the_event ){ |
307 |
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|
308 |
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current_atom = new AtomStamp; |
309 |
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|
310 |
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the_event->err_msg = current_mol->addAtom( current_atom, |
311 |
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the_event->evt.blk_index ); |
312 |
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313 |
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if( the_event->err_msg != NULL ) return 0; |
314 |
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return 1; |
315 |
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} |
316 |
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|
317 |
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int MakeStamps::atomPosition( event* the_event ){ |
318 |
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|
319 |
|
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current_atom->setPosition( the_event->evt.pos.x, |
320 |
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the_event->evt.pos.y, |
321 |
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the_event->evt.pos.z ); |
322 |
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return 1; |
323 |
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} |
324 |
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325 |
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|
326 |
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int MakeStamps::atomOrientation( event* the_event ){ |
327 |
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|
328 |
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current_atom->setOrientation( the_event->evt.ornt.phi, |
329 |
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the_event->evt.ornt.theta, |
330 |
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the_event->evt.ornt.psi ); |
331 |
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return 1; |
332 |
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} |
333 |
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|
334 |
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int MakeStamps::atomAssign( event* the_event ){ |
335 |
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|
336 |
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switch( the_event->evt.asmt.asmt_type ){ |
337 |
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|
338 |
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case STRING: |
339 |
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the_event->err_msg = |
340 |
|
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current_atom->assignString( the_event->evt.asmt.lhs, |
341 |
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the_event->evt.asmt.rhs.sval ); |
342 |
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if( the_event->err_msg != NULL ) return 0; |
343 |
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return 1; |
344 |
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break; |
345 |
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|
346 |
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case DOUBLE: |
347 |
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the_event->err_msg = |
348 |
|
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current_atom->assignDouble( the_event->evt.asmt.lhs, |
349 |
|
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the_event->evt.asmt.rhs.dval ); |
350 |
|
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if( the_event->err_msg != NULL ) return 0; |
351 |
|
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return 1; |
352 |
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break; |
353 |
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|
354 |
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case INT: |
355 |
|
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the_event->err_msg = |
356 |
|
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current_atom->assignInt( the_event->evt.asmt.lhs, |
357 |
|
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the_event->evt.asmt.rhs.ival ); |
358 |
|
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if( the_event->err_msg != NULL ) return 0; |
359 |
|
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return 1; |
360 |
|
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break; |
361 |
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|
362 |
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default: |
363 |
|
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the_event->err_msg = strdup( "MakeStamp error. Invalid atom" |
364 |
|
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" assignment type" ); |
365 |
|
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return 0; |
366 |
|
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break; |
367 |
|
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} |
368 |
|
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return 0; |
369 |
|
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} |
370 |
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|
371 |
|
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int MakeStamps::atomEnd( event* the_event ){ |
372 |
|
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|
373 |
|
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the_event->err_msg = current_atom->checkMe(); |
374 |
|
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if( the_event->err_msg != NULL ) return 0; |
375 |
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|
376 |
|
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return 1; |
377 |
|
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} |
378 |
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|
379 |
|
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int MakeStamps::newBond( event* the_event ){ |
380 |
|
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|
381 |
|
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current_bond = new BondStamp; |
382 |
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|
383 |
|
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the_event->err_msg = current_mol->addBond( current_bond, |
384 |
|
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the_event->evt.blk_index ); |
385 |
|
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if( the_event->err_msg != NULL ) return 0; |
386 |
|
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|
387 |
|
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return 1; |
388 |
|
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} |
389 |
|
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|
390 |
|
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int MakeStamps::bondAssign( event* the_event ){ |
391 |
|
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|
392 |
|
|
switch( the_event->evt.asmt.asmt_type ){ |
393 |
|
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|
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 |
tim |
1957 |
|
578 |
|
|
switch( the_event->evt.mbrs.nMembers ) { |
579 |
|
|
case 4: |
580 |
gezelter |
1490 |
|
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 |
tim |
1957 |
break; |
587 |
|
|
case 3: |
588 |
|
|
|
589 |
gezelter |
1490 |
|
590 |
tim |
1957 |
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 |
gezelter |
1490 |
the_event->err_msg = strdup( "MakeStamp error. Wrong number of members " |
599 |
tim |
1957 |
"in torsion."); |
600 |
gezelter |
1490 |
return 0; |
601 |
tim |
1957 |
break; |
602 |
gezelter |
1490 |
} |
603 |
tim |
1957 |
return 0; |
604 |
|
|
|
605 |
gezelter |
1490 |
} |
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 |
|
|
} |