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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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#include "io/mpiBASS.h" |
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#endif // is_mpi |
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|
55 |
< |
LinkedMolStamp::~LinkedMolStamp(){ |
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if( mol_stamp != NULL ) delete mol_stamp; |
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if( next != NULL ) delete next; |
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> |
MakeStamps::MakeStamps(){ |
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} |
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|
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< |
void LinkedMolStamp::add( LinkedMolStamp* newbie ){ |
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> |
MakeStamps::~MakeStamps(){ |
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|
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< |
if( next != NULL ) next->add( newbie ); |
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else{ |
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next = newbie; |
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next->setPrev( this ); |
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} |
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} |
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> |
std::map<std::string, MoleculeStamp*>::iterator iter; |
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|
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< |
MoleculeStamp* LinkedMolStamp::match( char* id ){ |
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|
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if( mol_stamp != NULL ){ |
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if(!strcmp( mol_stamp->getID(), id )){ |
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|
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// make sure we aren't hiding somebody else with the same name |
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if(next != NULL ){ |
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< |
if( next->match( id ) != NULL){ |
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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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< |
id ); |
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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 return mol_stamp; |
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} |
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else return mol_stamp; |
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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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if( next != NULL ) return next->match( id ); |
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|
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return NULL; |
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} |
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|
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< |
LinkedMolStamp* LinkedMolStamp::extract( char* id ){ |
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> |
my_mols.clear(); |
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|
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if( mol_stamp != NULL ){ |
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if(!strcmp( mol_stamp->getID(), id )){ |
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|
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// make sure we aren't hiding somebody else with the same name |
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– |
if(next != NULL ){ |
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– |
if( next->match( id ) != NULL){ |
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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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id ); |
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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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} |
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|
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prev->setNext( next ); |
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if( next != NULL ) next->setPrev( prev ); |
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return this; |
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} |
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} |
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|
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if( next != NULL ) return next->extract( id ); |
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|
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return NULL; |
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} |
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|
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< |
MakeStamps::MakeStamps(){ |
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|
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int i; |
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MoleculeStamp* MakeStamps::getMolStamp( std::string the_id ){ |
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|
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hash_size = 47; |
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hash_shift = 4; |
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std::map<std::string, MoleculeStamp*>::iterator iter; |
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|
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my_mols = new LinkedMolStamp*[hash_size]; |
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for( i=0; i<hash_size; i++ ){ |
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my_mols[i] = new LinkedMolStamp(); |
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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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MakeStamps::~MakeStamps(){ |
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void MakeStamps::addMolStamp( MoleculeStamp* the_stamp ){ |
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|
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int i; |
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std::map<std::string, MoleculeStamp*>::iterator iter; |
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|
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for( i=0; i<hash_size; i++ ){ |
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if( my_mols[i] != NULL ) delete my_mols[i]; |
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} |
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delete[] my_mols; |
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} |
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std::string molStampName(the_stamp->getID()); |
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|
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int MakeStamps::hash( char* text ){ |
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iter = my_mols.find(molStampName); |
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|
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register unsigned short int i = 0; // loop counter |
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int key = 0; // the hash key |
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|
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while( text[i] != '\0' ){ |
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|
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key = ( ( key << hash_shift ) + text[i] ) % hash_size; |
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|
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i++; |
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} |
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|
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if( key < 0 ){ |
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|
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// if the key is less than zero, we've had an overflow error |
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|
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if (iter != my_mols.end()) { |
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sprintf( painCave.errMsg, |
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"There has been an overflow error in the MakeStamps hash key."); |
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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( 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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return key; |
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} |
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|
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LinkedMolStamp* MakeStamps::extractMolStamp( char* the_id ){ |
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int key; |
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|
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key = hash( the_id ); |
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if( my_mols[key] != NULL ){ |
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return my_mols[key]->extract( the_id ); |
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} |
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|
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return NULL; |
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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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int key; |
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LinkedMolStamp* linked_mol; |
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|
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key = hash( the_stamp->getID() ); |
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|
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linked_mol = new LinkedMolStamp; |
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linked_mol->setStamp( the_stamp ); |
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|
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my_mols[key]->add( linked_mol ); |
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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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|
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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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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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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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the_event->evt.asmt.rhs.ival ); |
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break; |
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|
|
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default: |
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|
|
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case STRING: |
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current_bond->assignString( the_event->evt.asmt.lhs, |
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< |
the_event->evt.asmt.rhs.sval ); |
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> |
the_event->evt.asmt.rhs.sval ); |
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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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current_bond->assignDouble( the_event->evt.asmt.lhs, |
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< |
the_event->evt.asmt.rhs.dval ); |
402 |
> |
the_event->evt.asmt.rhs.dval ); |
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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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current_bond->assignInt( the_event->evt.asmt.lhs, |
408 |
< |
the_event->evt.asmt.rhs.ival ); |
408 |
> |
the_event->evt.asmt.rhs.ival ); |
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|
return 1; |
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|
break; |
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|
|
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|
|
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|
case STRING: |
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|
current_bend->assignString( the_event->evt.asmt.lhs, |
469 |
< |
the_event->evt.asmt.rhs.sval ); |
469 |
> |
the_event->evt.asmt.rhs.sval ); |
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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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current_bend->assignDouble( the_event->evt.asmt.lhs, |
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the_event->evt.asmt.rhs.dval ); |
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> |
the_event->evt.asmt.rhs.dval ); |
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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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|
current_bend->assignInt( the_event->evt.asmt.lhs, |
481 |
< |
the_event->evt.asmt.rhs.ival ); |
481 |
> |
the_event->evt.asmt.rhs.ival ); |
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|
return 1; |
483 |
|
break; |
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|
|
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|
|
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|
case STRING: |
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|
current_torsion->assignString( the_event->evt.asmt.lhs, |
550 |
< |
the_event->evt.asmt.rhs.sval ); |
550 |
> |
the_event->evt.asmt.rhs.sval ); |
551 |
|
return 1; |
552 |
|
break; |
553 |
|
|
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|
case DOUBLE: |
555 |
|
current_torsion->assignDouble( the_event->evt.asmt.lhs, |
556 |
< |
the_event->evt.asmt.rhs.dval ); |
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 ); |
562 |
> |
the_event->evt.asmt.rhs.ival ); |
563 |
|
return 1; |
564 |
|
break; |
565 |
|
|
574 |
|
|
575 |
|
int MakeStamps::torsionMembers( event* the_event ){ |
576 |
|
|
577 |
< |
if( the_event->evt.mbrs.nMembers == 4 ){ |
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 |
< |
} else { |
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"); |
599 |
> |
"in torsion."); |
600 |
|
return 0; |
601 |
< |
|
601 |
> |
break; |
602 |
|
} |
603 |
+ |
return 0; |
604 |
+ |
|
605 |
|
} |
606 |
|
|
607 |
|
int MakeStamps::torsionConstraint( event* the_event ){ |