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gezelter |
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/* |
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gezelter |
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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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#include <iostream> |
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47 |
tim |
1492 |
#include "types/MoleculeStamp.hpp" |
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gezelter |
1490 |
|
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char MoleculeStamp::errMsg[500]; |
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MoleculeStamp::MoleculeStamp(){ |
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53 |
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n_atoms = 0; |
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n_bonds = 0; |
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n_bends = 0; |
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n_torsions = 0; |
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n_rigidbodies = 0; |
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n_cutoffgroups = 0; |
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n_integrable = 0; |
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unhandled = NULL; |
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atoms = NULL; |
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bonds = NULL; |
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bends = NULL; |
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torsions = NULL; |
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rigidBodies = NULL; |
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cutoffGroups = NULL; |
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have_name = 0; |
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have_atoms = 0; |
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have_bonds = 0; |
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have_bends = 0; |
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have_torsions = 0; |
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have_rigidbodies = 0; |
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have_cutoffgroups = 0; |
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|
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} |
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MoleculeStamp::~MoleculeStamp(){ |
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int i; |
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if( unhandled != NULL) delete unhandled; |
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84 |
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if( rigidBodies != NULL ) { |
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for( i=0; i<n_rigidbodies; i++ ) delete rigidBodies[i]; |
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} |
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delete[] rigidBodies; |
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if( cutoffGroups != NULL ) { |
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for( i=0; i<n_cutoffgroups; i++ ) delete cutoffGroups[i]; |
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} |
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delete[] cutoffGroups; |
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if( atoms != NULL ){ |
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for( i=0; i<n_atoms; i++ ) delete atoms[i]; |
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} |
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delete[] atoms; |
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if( bonds != NULL ){ |
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for( i=0; i<n_bonds; i++ ) delete bonds[i]; |
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} |
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delete[] bonds; |
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if( bends != NULL ){ |
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for( i=0; i<n_bends; i++ ) delete bends[i]; |
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} |
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delete[] bends; |
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if( torsions != NULL ){ |
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for( i=0; i<n_torsions; i++ ) delete torsions[i]; |
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} |
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delete[] torsions; |
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} |
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char* MoleculeStamp::assignString( char* lhs, char* rhs ){ |
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if( !strcmp( lhs, "name" ) ){ |
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strcpy( name, rhs ); |
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have_name = 1; |
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} |
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else{ |
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if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
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else unhandled->add( lhs, rhs ); |
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have_extras = 1; |
129 |
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} |
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return NULL; |
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} |
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char* MoleculeStamp::assignDouble( char* lhs, double rhs ){ |
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int i; |
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if( !strcmp( lhs, "nAtoms" ) ){ |
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n_atoms = (int)rhs; |
138 |
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139 |
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if( have_atoms ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_atoms already declared" |
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" for molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
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have_atoms = 1; |
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atoms = new AtomStamp*[n_atoms]; |
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for( i=0; i<n_atoms; i++ ) atoms[i] = NULL; |
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} |
150 |
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else if( !strcmp( lhs, "nBonds" ) ){ |
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n_bonds = (int)rhs; |
153 |
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154 |
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if( have_bonds ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_bonds already declared for" |
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" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
161 |
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have_bonds = 1; |
162 |
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bonds = new BondStamp*[n_bonds]; |
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for( i=0; i<n_bonds; i++ ) bonds[i] = NULL; |
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} |
165 |
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166 |
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else if( !strcmp( lhs, "nBends" ) ){ |
167 |
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n_bends = (int)rhs; |
168 |
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169 |
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if( have_bends ){ |
170 |
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sprintf( errMsg, |
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"MoleculeStamp error, n_bends already declared for" |
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" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
176 |
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have_bends = 1; |
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bends = new BendStamp*[n_bends]; |
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for( i=0; i<n_bends; i++ ) bends[i] = NULL; |
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} |
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181 |
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else if( !strcmp( lhs, "nTorsions" ) ){ |
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n_torsions = (int)rhs; |
183 |
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184 |
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if( have_torsions ){ |
185 |
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sprintf( errMsg, |
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"MoleculeStamp error, n_torsions already declared for" |
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" molecule: %s\n", |
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name ); |
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return strdup( errMsg ); |
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} |
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have_torsions = 1; |
192 |
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torsions = new TorsionStamp*[n_torsions]; |
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for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
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} |
195 |
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196 |
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else if( !strcmp( lhs, "nRigidBodies" ) ){ |
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n_rigidbodies = (int)rhs; |
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199 |
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if( have_rigidbodies ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_rigidbodies already declared for" |
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" molecule: %s\n", |
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name ); |
204 |
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return strdup( errMsg ); |
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} |
206 |
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have_rigidbodies = 1; |
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rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
208 |
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for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
209 |
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} |
210 |
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211 |
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else if( !strcmp( lhs, "nCutoffGroups" ) ){ |
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n_cutoffgroups = (int)rhs; |
213 |
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214 |
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if( have_cutoffgroups ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_cutoffgroups already declared for" |
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" molecule: %s\n", |
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name ); |
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return strdup( errMsg ); |
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} |
221 |
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have_cutoffgroups = 1; |
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cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups]; |
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for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL; |
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} |
225 |
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226 |
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else{ |
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if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
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else unhandled->add( lhs, rhs ); |
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have_extras = 1; |
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} |
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return NULL; |
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} |
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char* MoleculeStamp::assignInt( char* lhs, int rhs ){ |
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int i; |
236 |
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237 |
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if( !strcmp( lhs, "nAtoms" ) ){ |
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n_atoms = rhs; |
239 |
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240 |
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if( have_atoms ){ |
241 |
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sprintf( errMsg, |
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"MoleculeStamp error, n_atoms already declared for" |
243 |
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" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
247 |
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have_atoms = 1; |
248 |
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atoms = new AtomStamp*[n_atoms]; |
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for( i=0; i<n_atoms; i++ ) atoms[i] = NULL; |
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} |
251 |
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252 |
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else if( !strcmp( lhs, "nBonds" ) ){ |
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n_bonds = rhs; |
254 |
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255 |
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if( have_bonds ){ |
256 |
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sprintf( errMsg, |
257 |
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"MoleculeStamp error, n_bonds already declared for" |
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" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
262 |
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have_bonds = 1; |
263 |
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bonds = new BondStamp*[n_bonds]; |
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for( i=0; i<n_bonds; i++ ) bonds[i] = NULL; |
265 |
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} |
266 |
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267 |
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else if( !strcmp( lhs, "nBends" ) ){ |
268 |
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n_bends = rhs; |
269 |
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270 |
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if( have_bends ){ |
271 |
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sprintf( errMsg, |
272 |
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"MoleculeStamp error, n_bends already declared for" |
273 |
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" molecule: %s\n", |
274 |
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name ); |
275 |
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return strdup( errMsg ); |
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} |
277 |
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have_bends = 1; |
278 |
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bends = new BendStamp*[n_bends]; |
279 |
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for( i=0; i<n_bends; i++ ) bends[i] = NULL; |
280 |
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} |
281 |
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282 |
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else if( !strcmp( lhs, "nTorsions" ) ){ |
283 |
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n_torsions = rhs; |
284 |
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285 |
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if( have_torsions ){ |
286 |
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sprintf( errMsg, |
287 |
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"MoleculeStamp error, n_torsions already declared for" |
288 |
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" molecule: %s\n", |
289 |
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name); |
290 |
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return strdup( errMsg ); |
291 |
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} |
292 |
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have_torsions = 1; |
293 |
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torsions = new TorsionStamp*[n_torsions]; |
294 |
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for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
295 |
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} |
296 |
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297 |
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else if( !strcmp( lhs, "nRigidBodies" ) ){ |
298 |
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n_rigidbodies = rhs; |
299 |
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300 |
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if( have_rigidbodies ){ |
301 |
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sprintf( errMsg, |
302 |
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"MoleculeStamp error, n_rigidbodies already declared for" |
303 |
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" molecule: %s\n", |
304 |
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name); |
305 |
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return strdup( errMsg ); |
306 |
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} |
307 |
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have_rigidbodies = 1; |
308 |
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rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
309 |
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for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
310 |
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} |
311 |
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else if( !strcmp( lhs, "nCutoffGroups" ) ){ |
312 |
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n_cutoffgroups = rhs; |
313 |
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|
314 |
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if( have_cutoffgroups ){ |
315 |
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sprintf( errMsg, |
316 |
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"MoleculeStamp error, n_cutoffgroups already declared for" |
317 |
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" molecule: %s\n", |
318 |
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name); |
319 |
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return strdup( errMsg ); |
320 |
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} |
321 |
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have_cutoffgroups = 1; |
322 |
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cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups]; |
323 |
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for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL; |
324 |
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} |
325 |
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else{ |
326 |
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if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
327 |
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else unhandled->add( lhs, rhs ); |
328 |
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have_extras = 1; |
329 |
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} |
330 |
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return NULL; |
331 |
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} |
332 |
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333 |
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char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){ |
334 |
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335 |
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if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom; |
336 |
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else { |
337 |
|
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if( have_atoms ){ |
338 |
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sprintf( errMsg, "MoleculeStamp error, %d out of nAtoms range", |
339 |
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atomIndex ); |
340 |
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return strdup( errMsg ); |
341 |
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} |
342 |
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else return strdup("MoleculeStamp error, nAtoms not given before" |
343 |
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" first atom declaration." ); |
344 |
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} |
345 |
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|
346 |
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return NULL; |
347 |
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} |
348 |
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|
349 |
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char* MoleculeStamp::addRigidBody( RigidBodyStamp* the_rigidbody, |
350 |
|
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int rigidBodyIndex ){ |
351 |
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|
352 |
|
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if( have_rigidbodies && rigidBodyIndex < n_rigidbodies ) |
353 |
|
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rigidBodies[rigidBodyIndex] = the_rigidbody; |
354 |
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else { |
355 |
|
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if( have_rigidbodies ){ |
356 |
|
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sprintf( errMsg, "MoleculeStamp error, %d out of nRigidBodies range", |
357 |
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rigidBodyIndex ); |
358 |
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return strdup( errMsg ); |
359 |
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} |
360 |
|
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else return strdup("MoleculeStamp error, nRigidBodies not given before" |
361 |
|
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" first rigidBody declaration." ); |
362 |
|
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} |
363 |
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364 |
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return NULL; |
365 |
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} |
366 |
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|
367 |
|
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char* MoleculeStamp::addCutoffGroup( CutoffGroupStamp* the_cutoffgroup, |
368 |
|
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int cutoffGroupIndex ){ |
369 |
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|
370 |
|
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if( have_cutoffgroups && cutoffGroupIndex < n_cutoffgroups ) |
371 |
|
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cutoffGroups[cutoffGroupIndex] = the_cutoffgroup; |
372 |
|
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else { |
373 |
|
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if( have_cutoffgroups ){ |
374 |
|
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sprintf( errMsg, "MoleculeStamp error, %d out of nCutoffGroups range", |
375 |
|
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cutoffGroupIndex ); |
376 |
|
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return strdup( errMsg ); |
377 |
|
|
} |
378 |
|
|
else return strdup("MoleculeStamp error, nCutoffGroups not given before" |
379 |
|
|
" first CutoffGroup declaration." ); |
380 |
|
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} |
381 |
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|
382 |
|
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return NULL; |
383 |
|
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} |
384 |
|
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|
385 |
|
|
char* MoleculeStamp::addBond( BondStamp* the_bond, int bondIndex ){ |
386 |
|
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|
387 |
|
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|
388 |
|
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if( have_bonds && bondIndex < n_bonds ) bonds[bondIndex] = the_bond; |
389 |
|
|
else{ |
390 |
|
|
if( have_bonds ){ |
391 |
|
|
sprintf( errMsg, "MoleculeStamp error, %d out of nBonds range", |
392 |
|
|
bondIndex ); |
393 |
|
|
return strdup( errMsg ); |
394 |
|
|
} |
395 |
|
|
else return strdup("MoleculeStamp error, nBonds not given before" |
396 |
|
|
"first bond declaration." ); |
397 |
|
|
} |
398 |
|
|
|
399 |
|
|
return NULL; |
400 |
|
|
} |
401 |
|
|
|
402 |
|
|
char* MoleculeStamp::addBend( BendStamp* the_bend, int bendIndex ){ |
403 |
|
|
|
404 |
|
|
|
405 |
|
|
if( have_bends && bendIndex < n_bends ) bends[bendIndex] = the_bend; |
406 |
|
|
else{ |
407 |
|
|
if( have_bends ){ |
408 |
|
|
sprintf( errMsg, "MoleculeStamp error, %d out of nBends range", |
409 |
|
|
bendIndex ); |
410 |
|
|
return strdup( errMsg ); |
411 |
|
|
} |
412 |
|
|
else return strdup("MoleculeStamp error, nBends not given before" |
413 |
|
|
"first bend declaration." ); |
414 |
|
|
} |
415 |
|
|
|
416 |
|
|
return NULL; |
417 |
|
|
} |
418 |
|
|
|
419 |
|
|
char* MoleculeStamp::addTorsion( TorsionStamp* the_torsion, int torsionIndex ){ |
420 |
|
|
|
421 |
|
|
|
422 |
|
|
if( have_torsions && torsionIndex < n_torsions ) |
423 |
|
|
torsions[torsionIndex] = the_torsion; |
424 |
|
|
else{ |
425 |
|
|
if( have_torsions ){ |
426 |
|
|
sprintf( errMsg, "MoleculeStamp error, %d out of nTorsions range", |
427 |
|
|
torsionIndex ); |
428 |
|
|
return strdup( errMsg ); |
429 |
|
|
} |
430 |
|
|
else return strdup("MoleculeStamp error, nTorsions not given before" |
431 |
|
|
"first torsion declaration." ); |
432 |
|
|
} |
433 |
|
|
|
434 |
|
|
return NULL; |
435 |
|
|
} |
436 |
|
|
|
437 |
|
|
char* MoleculeStamp::checkMe( void ){ |
438 |
|
|
|
439 |
|
|
int i; |
440 |
|
|
short int no_atom, no_rigidbody, no_cutoffgroup; |
441 |
|
|
|
442 |
|
|
if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name" |
443 |
|
|
" was not given.\n" ); |
444 |
|
|
|
445 |
|
|
if( !have_atoms ){ |
446 |
|
|
return strdup( "MoleculeStamp error. Molecule contains no atoms." ); |
447 |
|
|
} |
448 |
|
|
|
449 |
|
|
no_rigidbody = 0; |
450 |
|
|
for( i=0; i<n_rigidbodies; i++ ){ |
451 |
|
|
if( rigidBodies[i] == NULL ) no_rigidbody = 1; |
452 |
|
|
} |
453 |
|
|
|
454 |
|
|
if( no_rigidbody ){ |
455 |
|
|
sprintf( errMsg, |
456 |
|
|
"MoleculeStamp error. Not all of the RigidBodies were" |
457 |
|
|
" declared in molecule \"%s\".\n", name ); |
458 |
|
|
return strdup( errMsg ); |
459 |
|
|
} |
460 |
|
|
|
461 |
|
|
no_cutoffgroup = 0; |
462 |
|
|
for( i=0; i<n_cutoffgroups; i++ ){ |
463 |
|
|
if( cutoffGroups[i] == NULL ) no_cutoffgroup = 1; |
464 |
|
|
} |
465 |
|
|
|
466 |
|
|
if( no_cutoffgroup ){ |
467 |
|
|
sprintf( errMsg, |
468 |
|
|
"MoleculeStamp error. Not all of the CutoffGroups were" |
469 |
|
|
" declared in molecule \"%s\".\n", name ); |
470 |
|
|
return strdup( errMsg ); |
471 |
|
|
} |
472 |
|
|
|
473 |
|
|
no_atom = 0; |
474 |
|
|
for( i=0; i<n_atoms; i++ ){ |
475 |
|
|
if( atoms[i] == NULL ) no_atom = 1; |
476 |
|
|
} |
477 |
|
|
|
478 |
|
|
if( no_atom ){ |
479 |
|
|
sprintf( errMsg, |
480 |
|
|
"MoleculeStamp error. Not all of the atoms were" |
481 |
|
|
" declared in molecule \"%s\".\n", name ); |
482 |
|
|
return strdup( errMsg ); |
483 |
|
|
} |
484 |
|
|
|
485 |
|
|
n_integrable = n_atoms; |
486 |
|
|
for (i = 0; i < n_rigidbodies; i++) |
487 |
|
|
n_integrable = n_integrable - rigidBodies[i]->getNMembers() + 1; //rigidbody is an integrable object |
488 |
|
|
|
489 |
|
|
if (n_integrable <= 0 || n_integrable > n_atoms) { |
490 |
|
|
sprintf( errMsg, |
491 |
|
|
"MoleculeStamp error. n_integrable is either <= 0 or" |
492 |
|
|
" greater than n_atoms in molecule \"%s\".\n", name ); |
493 |
|
|
return strdup( errMsg ); |
494 |
|
|
} |
495 |
|
|
|
496 |
|
|
return NULL; |
497 |
|
|
} |
498 |
|
|
|
499 |
|
|
|
500 |
|
|
//Function Name: isBondInSameRigidBody |
501 |
|
|
//Return true is both atoms of the bond belong to the same rigid body, otherwise return false |
502 |
|
|
bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){ |
503 |
|
|
int rbA; |
504 |
|
|
int rbB; |
505 |
|
|
int consAtomA; |
506 |
|
|
int consAtomB; |
507 |
|
|
|
508 |
|
|
if (!isAtomInRigidBody(bond->getA(),rbA, consAtomA)) |
509 |
|
|
return false; |
510 |
|
|
|
511 |
|
|
if(!isAtomInRigidBody(bond->getB(),rbB, consAtomB) ) |
512 |
|
|
return false; |
513 |
|
|
|
514 |
|
|
if(rbB == rbA) |
515 |
|
|
return true; |
516 |
|
|
else |
517 |
|
|
return false; |
518 |
|
|
} |
519 |
|
|
|
520 |
|
|
// Function Name: isAtomInRigidBody |
521 |
|
|
//return false if atom does not belong to a rigid body, otherwise return true |
522 |
|
|
bool MoleculeStamp::isAtomInRigidBody(int atomIndex){ |
523 |
|
|
int whichRigidBody; |
524 |
|
|
int consAtomIndex; |
525 |
|
|
|
526 |
|
|
return isAtomInRigidBody(atomIndex, whichRigidBody, consAtomIndex); |
527 |
|
|
|
528 |
|
|
} |
529 |
|
|
|
530 |
|
|
// Function Name: isAtomInRigidBody |
531 |
|
|
//return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody |
532 |
|
|
//and consAtomIndex |
533 |
|
|
//atomIndex : the index of atom in component |
534 |
|
|
//whichRigidBody: the index of rigidbody in component |
535 |
|
|
//consAtomIndex: the position of joint atom apears in rigidbody's definition |
536 |
|
|
bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){ |
537 |
|
|
RigidBodyStamp* rbStamp; |
538 |
|
|
int numRb; |
539 |
|
|
int numAtom; |
540 |
|
|
|
541 |
|
|
whichRigidBody = -1; |
542 |
|
|
consAtomIndex = -1; |
543 |
|
|
|
544 |
|
|
numRb = this->getNRigidBodies(); |
545 |
|
|
|
546 |
|
|
for(int i = 0 ; i < numRb; i++){ |
547 |
|
|
rbStamp = this->getRigidBody(i); |
548 |
|
|
numAtom = rbStamp->getNMembers(); |
549 |
|
|
for(int j = 0; j < numAtom; j++) |
550 |
|
|
if (rbStamp->getMember(j) == atomIndex){ |
551 |
|
|
whichRigidBody = i; |
552 |
|
|
consAtomIndex = j; |
553 |
|
|
return true; |
554 |
|
|
} |
555 |
|
|
} |
556 |
|
|
|
557 |
|
|
return false; |
558 |
|
|
|
559 |
|
|
} |
560 |
|
|
|
561 |
|
|
//return the position of joint atom apears in rigidbody's definition |
562 |
|
|
//for the time being, we will use the most inefficient algorithm, the complexity is O(N2) |
563 |
|
|
//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first |
564 |
gezelter |
2204 |
std::vector<std::pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){ |
565 |
gezelter |
1490 |
RigidBodyStamp* rbStamp1; |
566 |
|
|
RigidBodyStamp* rbStamp2; |
567 |
|
|
int natomInRb1; |
568 |
|
|
int natomInRb2; |
569 |
|
|
int atomIndex1; |
570 |
|
|
int atomIndex2; |
571 |
gezelter |
2204 |
std::vector<std::pair<int, int> > jointAtomIndexPair; |
572 |
gezelter |
1490 |
|
573 |
|
|
rbStamp1 = this->getRigidBody(rb1); |
574 |
|
|
natomInRb1 =rbStamp1->getNMembers(); |
575 |
|
|
|
576 |
|
|
rbStamp2 = this->getRigidBody(rb2); |
577 |
|
|
natomInRb2 =rbStamp2->getNMembers(); |
578 |
|
|
|
579 |
|
|
for(int i = 0; i < natomInRb1; i++){ |
580 |
|
|
atomIndex1 = rbStamp1->getMember(i); |
581 |
|
|
|
582 |
|
|
for(int j= 0; j < natomInRb1; j++){ |
583 |
|
|
atomIndex2 = rbStamp2->getMember(j); |
584 |
|
|
|
585 |
|
|
if(atomIndex1 == atomIndex2){ |
586 |
gezelter |
1930 |
jointAtomIndexPair.push_back(std::make_pair(i, j)); |
587 |
gezelter |
1490 |
break; |
588 |
|
|
} |
589 |
|
|
|
590 |
|
|
}//end for(j =0) |
591 |
|
|
|
592 |
|
|
}//end for (i = 0) |
593 |
|
|
|
594 |
|
|
return jointAtomIndexPair; |
595 |
|
|
} |