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#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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/* |
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* 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 <iostream> |
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< |
|
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> |
#include <functional> |
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|
#include "types/MoleculeStamp.hpp" |
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+ |
#include "utils/Tuple.hpp" |
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|
|
47 |
< |
char MoleculeStamp::errMsg[500]; |
47 |
> |
namespace oopse { |
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MoleculeStamp::MoleculeStamp() { |
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DefineParameter(Name, "name"); |
50 |
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|
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> |
deprecatedKeywords_.insert("nAtoms"); |
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> |
deprecatedKeywords_.insert("nBonds"); |
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> |
deprecatedKeywords_.insert("nBends"); |
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> |
deprecatedKeywords_.insert("nTorsions"); |
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> |
deprecatedKeywords_.insert("nRigidBodies"); |
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> |
deprecatedKeywords_.insert("nCutoffGroups"); |
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|
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} |
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|
|
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< |
MoleculeStamp::MoleculeStamp(){ |
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|
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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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MoleculeStamp::~MoleculeStamp() { |
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|
|
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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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} |
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|
|
64 |
< |
have_name = 0; |
65 |
< |
have_atoms = 0; |
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< |
have_bonds = 0; |
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have_bends = 0; |
68 |
< |
have_torsions = 0; |
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< |
have_rigidbodies = 0; |
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have_cutoffgroups = 0; |
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bool MoleculeStamp::addAtomStamp( AtomStamp* atom) { |
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bool ret = addIndexSensitiveStamp(atomStamps_, atom); |
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if (!ret) { |
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std::cout << "multiple atoms have the same index: " << atom->getIndex() <<" in " << getName() << " Molecule\n"; |
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} |
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return ret; |
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|
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} |
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|
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bool MoleculeStamp::addBondStamp( BondStamp* bond) { |
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bondStamps_.push_back(bond); |
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return true; |
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} |
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|
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MoleculeStamp::~MoleculeStamp(){ |
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int i; |
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|
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if( unhandled != NULL) delete unhandled; |
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< |
|
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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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bool MoleculeStamp::addBendStamp( BendStamp* bend) { |
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bendStamps_.push_back(bend); |
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return true; |
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} |
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|
|
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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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} |
86 |
< |
delete[] cutoffGroups; |
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< |
|
53 |
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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; |
57 |
< |
|
58 |
< |
if( bonds != NULL ){ |
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< |
for( i=0; i<n_bonds; i++ ) delete bonds[i]; |
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< |
} |
61 |
< |
delete[] bonds; |
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|
63 |
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if( bends != NULL ){ |
64 |
< |
for( i=0; i<n_bends; i++ ) delete bends[i]; |
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< |
} |
66 |
< |
delete[] bends; |
67 |
< |
|
68 |
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if( torsions != NULL ){ |
69 |
< |
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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bool MoleculeStamp::addTorsionStamp( TorsionStamp* torsion) { |
84 |
> |
torsionStamps_.push_back(torsion); |
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return true; |
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} |
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|
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|
89 |
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|
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bool MoleculeStamp::addRigidBodyStamp( RigidBodyStamp* rigidbody) { |
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bool ret = addIndexSensitiveStamp(rigidBodyStamps_, rigidbody); |
90 |
> |
if (!ret) { |
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std::cout << "multiple rigidbodies have the same index: " << rigidbody->getIndex() <<" in " << getName() << " Molecule\n"; |
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} |
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return ret; |
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} |
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|
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char* MoleculeStamp::assignString( char* lhs, char* rhs ){ |
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|
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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 ); |
87 |
< |
have_extras = 1; |
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< |
} |
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return NULL; |
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> |
bool MoleculeStamp::addCutoffGroupStamp( CutoffGroupStamp* cutoffgroup) { |
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cutoffGroupStamps_.push_back(cutoffgroup); |
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return true; |
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|
} |
100 |
|
|
101 |
< |
char* MoleculeStamp::assignDouble( char* lhs, double rhs ){ |
102 |
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int i; |
103 |
< |
|
95 |
< |
if( !strcmp( lhs, "nAtoms" ) ){ |
96 |
< |
n_atoms = (int)rhs; |
101 |
> |
bool MoleculeStamp::addFragmentStamp( FragmentStamp* fragment) { |
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> |
return addIndexSensitiveStamp(fragmentStamps_, fragment); |
103 |
> |
} |
104 |
|
|
105 |
< |
if( have_atoms ){ |
106 |
< |
sprintf( errMsg, |
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< |
"MoleculeStamp error, n_atoms already declared" |
101 |
< |
" for molecule: %s\n", |
102 |
< |
name); |
103 |
< |
return strdup( errMsg ); |
104 |
< |
} |
105 |
< |
have_atoms = 1; |
106 |
< |
atoms = new AtomStamp*[n_atoms]; |
107 |
< |
for( i=0; i<n_atoms; i++ ) atoms[i] = NULL; |
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< |
} |
109 |
< |
|
110 |
< |
else if( !strcmp( lhs, "nBonds" ) ){ |
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n_bonds = (int)rhs; |
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> |
void MoleculeStamp::validate() { |
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DataHolder::validate(); |
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|
|
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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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atom2Rigidbody.resize(getNAtoms()); |
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// negative number means atom is a free atom, does not belong to rigidbody |
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//every element in atom2Rigidbody has unique negative number at the very beginning |
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for(int i = 0; i < atom2Rigidbody.size(); ++i) { |
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atom2Rigidbody[i] = -1 - i; |
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|
} |
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< |
have_bonds = 1; |
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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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} |
118 |
< |
|
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< |
else if( !strcmp( lhs, "nBends" ) ){ |
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< |
n_bends = (int)rhs; |
127 |
< |
|
128 |
< |
if( have_bends ){ |
129 |
< |
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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for (int i = 0; i < getNRigidBodies(); ++i) { |
115 |
> |
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
116 |
> |
std::vector<int> members = rbStamp->getMembers(); |
117 |
> |
for(std::vector<int>::iterator j = members.begin(); j != members.end(); ++j) { |
118 |
> |
atom2Rigidbody[*j] = i; |
119 |
> |
} |
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|
} |
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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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|
140 |
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else if( !strcmp( lhs, "nTorsions" ) ){ |
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n_torsions = (int)rhs; |
121 |
|
|
122 |
< |
if( have_torsions ){ |
123 |
< |
sprintf( errMsg, |
124 |
< |
"MoleculeStamp error, n_torsions already declared for" |
125 |
< |
" molecule: %s\n", |
126 |
< |
name ); |
127 |
< |
return strdup( errMsg ); |
122 |
> |
checkAtoms(); |
123 |
> |
checkBonds(); |
124 |
> |
fillBondInfo(); |
125 |
> |
checkBends(); |
126 |
> |
checkTorsions(); |
127 |
> |
checkRigidBodies(); |
128 |
> |
checkCutoffGroups(); |
129 |
> |
checkFragments(); |
130 |
> |
|
131 |
> |
int nrigidAtoms = 0; |
132 |
> |
for (int i = 0; i < getNRigidBodies(); ++i) { |
133 |
> |
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
134 |
> |
nrigidAtoms += rbStamp->getNMembers(); |
135 |
|
} |
136 |
< |
have_torsions = 1; |
151 |
< |
torsions = new TorsionStamp*[n_torsions]; |
152 |
< |
for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
153 |
< |
} |
136 |
> |
nintegrable_ = getNAtoms()+ getNRigidBodies() - nrigidAtoms; |
137 |
|
|
138 |
< |
else if( !strcmp( lhs, "nRigidBodies" ) ){ |
156 |
< |
n_rigidbodies = (int)rhs; |
138 |
> |
} |
139 |
|
|
140 |
< |
if( have_rigidbodies ){ |
141 |
< |
sprintf( errMsg, |
142 |
< |
"MoleculeStamp error, n_rigidbodies already declared for" |
143 |
< |
" molecule: %s\n", |
162 |
< |
name ); |
163 |
< |
return strdup( errMsg ); |
140 |
> |
void MoleculeStamp::checkAtoms() { |
141 |
> |
std::vector<AtomStamp*>::iterator ai = std::find(atomStamps_.begin(), atomStamps_.end(), static_cast<AtomStamp*>(NULL)); |
142 |
> |
if (ai != atomStamps_.end()) { |
143 |
> |
std::cout << "Error in Molecule " << getName() << ": atom[" << ai - atomStamps_.begin()<< "] is missing\n"; |
144 |
|
} |
165 |
– |
have_rigidbodies = 1; |
166 |
– |
rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
167 |
– |
for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
168 |
– |
} |
145 |
|
|
146 |
< |
else if( !strcmp( lhs, "nCutoffGroups" ) ){ |
147 |
< |
n_cutoffgroups = (int)rhs; |
148 |
< |
|
149 |
< |
if( have_cutoffgroups ){ |
150 |
< |
sprintf( errMsg, |
151 |
< |
"MoleculeStamp error, n_cutoffgroups already declared for" |
152 |
< |
" molecule: %s\n", |
177 |
< |
name ); |
178 |
< |
return strdup( errMsg ); |
146 |
> |
//make sure index is not out of range |
147 |
> |
int natoms = getNAtoms(); |
148 |
> |
for(int i = 0; i < getNBonds(); ++i) { |
149 |
> |
BondStamp* bondStamp = getBondStamp(i); |
150 |
> |
if (bondStamp->getA() >= natoms && bondStamp->getB() >= natoms) { |
151 |
> |
std::cout << "Error in Molecule " << getName() << ": bond between " << bondStamp->getA() << " and " << bondStamp->getB() << " is invalid\n"; |
152 |
> |
} |
153 |
|
} |
180 |
– |
have_cutoffgroups = 1; |
181 |
– |
cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups]; |
182 |
– |
for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL; |
183 |
– |
} |
184 |
– |
|
185 |
– |
else{ |
186 |
– |
if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
187 |
– |
else unhandled->add( lhs, rhs ); |
188 |
– |
have_extras = 1; |
189 |
– |
} |
190 |
– |
return NULL; |
154 |
|
} |
155 |
|
|
156 |
< |
char* MoleculeStamp::assignInt( char* lhs, int rhs ){ |
157 |
< |
int i; |
158 |
< |
|
159 |
< |
if( !strcmp( lhs, "nAtoms" ) ){ |
160 |
< |
n_atoms = rhs; |
156 |
> |
void MoleculeStamp::checkBonds() { |
157 |
> |
//make sure bonds are unique |
158 |
> |
std::set<std::pair<int, int> > allBonds; |
159 |
> |
for(int i = 0; i < getNBonds(); ++i) { |
160 |
> |
BondStamp* bondStamp= getBondStamp(i); |
161 |
> |
std::pair<int, int> bondPair(bondStamp->getA(), bondStamp->getB()); |
162 |
> |
//make sure bondTuple.first is always less than or equal to bondTuple.third |
163 |
> |
if (bondPair.first > bondPair.second) { |
164 |
> |
std::swap(bondPair.first, bondPair.second); |
165 |
> |
} |
166 |
> |
|
167 |
> |
std::set<std::pair<int, int> >::iterator iter = allBonds.find(bondPair); |
168 |
> |
if ( iter != allBonds.end()) { |
169 |
> |
std::cout << "Error in Molecule " << getName() << ": " << "Bond appears multiple times\n"; |
170 |
> |
} else { |
171 |
> |
allBonds.insert(bondPair); |
172 |
> |
} |
173 |
> |
} |
174 |
|
|
175 |
< |
if( have_atoms ){ |
176 |
< |
sprintf( errMsg, |
177 |
< |
"MoleculeStamp error, n_atoms already declared for" |
178 |
< |
" molecule: %s\n", |
179 |
< |
name); |
180 |
< |
return strdup( errMsg ); |
175 |
> |
//make sure atoms belong to same rigidbody do not bond to each other |
176 |
> |
for(int i = 0; i < getNBonds(); ++i) { |
177 |
> |
BondStamp* bondStamp = getBondStamp(i); |
178 |
> |
if (atom2Rigidbody[bondStamp->getA()] == atom2Rigidbody[bondStamp->getB()]) { |
179 |
> |
std::cout << "Error in Molecule " << getName() << ": "<<"bond between " << bondStamp->getA() << " and " << bondStamp->getB() << " belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n"; |
180 |
> |
} |
181 |
|
} |
182 |
< |
have_atoms = 1; |
183 |
< |
atoms = new AtomStamp*[n_atoms]; |
208 |
< |
for( i=0; i<n_atoms; i++ ) atoms[i] = NULL; |
209 |
< |
} |
210 |
< |
|
211 |
< |
else if( !strcmp( lhs, "nBonds" ) ){ |
212 |
< |
n_bonds = rhs; |
182 |
> |
|
183 |
> |
} |
184 |
|
|
185 |
< |
if( have_bonds ){ |
186 |
< |
sprintf( errMsg, |
187 |
< |
"MoleculeStamp error, n_bonds already declared for" |
188 |
< |
" molecule: %s\n", |
189 |
< |
name); |
219 |
< |
return strdup( errMsg ); |
185 |
> |
struct BendLessThan : public std::binary_function<IntTuple4, IntTuple4, bool> { |
186 |
> |
bool operator()(IntTuple3 b1, IntTuple3 b2) { |
187 |
> |
return b1.first < b2.first |
188 |
> |
|| (!(b2.first < b1.first) && b1.second < b2.second) |
189 |
> |
|| (!(b2.first < b1.first) && !(b2.second < b2.second) && b1.third < b2.third); |
190 |
|
} |
191 |
< |
have_bonds = 1; |
222 |
< |
bonds = new BondStamp*[n_bonds]; |
223 |
< |
for( i=0; i<n_bonds; i++ ) bonds[i] = NULL; |
224 |
< |
} |
225 |
< |
|
226 |
< |
else if( !strcmp( lhs, "nBends" ) ){ |
227 |
< |
n_bends = rhs; |
191 |
> |
}; |
192 |
|
|
193 |
< |
if( have_bends ){ |
194 |
< |
sprintf( errMsg, |
195 |
< |
"MoleculeStamp error, n_bends already declared for" |
196 |
< |
" molecule: %s\n", |
197 |
< |
name ); |
198 |
< |
return strdup( errMsg ); |
199 |
< |
} |
200 |
< |
have_bends = 1; |
237 |
< |
bends = new BendStamp*[n_bends]; |
238 |
< |
for( i=0; i<n_bends; i++ ) bends[i] = NULL; |
239 |
< |
} |
240 |
< |
|
241 |
< |
else if( !strcmp( lhs, "nTorsions" ) ){ |
242 |
< |
n_torsions = rhs; |
193 |
> |
void MoleculeStamp::checkBends() { |
194 |
> |
for(int i = 0; i < getNBends(); ++i) { |
195 |
> |
BendStamp* bendStamp = getBendStamp(i); |
196 |
> |
std::vector<int> bendAtoms = bendStamp->getMembers(); |
197 |
> |
std::vector<int>::iterator j =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
198 |
> |
if (j != bendAtoms.end()) { |
199 |
> |
std::cout << "Error in Molecule " << getName(); |
200 |
> |
} |
201 |
|
|
202 |
< |
if( have_torsions ){ |
203 |
< |
sprintf( errMsg, |
204 |
< |
"MoleculeStamp error, n_torsions already declared for" |
205 |
< |
" molecule: %s\n", |
206 |
< |
name); |
207 |
< |
return strdup( errMsg ); |
208 |
< |
} |
209 |
< |
have_torsions = 1; |
210 |
< |
torsions = new TorsionStamp*[n_torsions]; |
211 |
< |
for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
212 |
< |
} |
213 |
< |
|
214 |
< |
else if( !strcmp( lhs, "nRigidBodies" ) ){ |
215 |
< |
n_rigidbodies = rhs; |
216 |
< |
|
217 |
< |
if( have_rigidbodies ){ |
218 |
< |
sprintf( errMsg, |
219 |
< |
"MoleculeStamp error, n_rigidbodies already declared for" |
220 |
< |
" molecule: %s\n", |
263 |
< |
name); |
264 |
< |
return strdup( errMsg ); |
265 |
< |
} |
266 |
< |
have_rigidbodies = 1; |
267 |
< |
rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
268 |
< |
for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
269 |
< |
} |
270 |
< |
else if( !strcmp( lhs, "nCutoffGroups" ) ){ |
271 |
< |
n_cutoffgroups = rhs; |
272 |
< |
|
273 |
< |
if( have_cutoffgroups ){ |
274 |
< |
sprintf( errMsg, |
275 |
< |
"MoleculeStamp error, n_cutoffgroups already declared for" |
276 |
< |
" molecule: %s\n", |
277 |
< |
name); |
278 |
< |
return strdup( errMsg ); |
279 |
< |
} |
280 |
< |
have_cutoffgroups = 1; |
281 |
< |
cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups]; |
282 |
< |
for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL; |
283 |
< |
} |
284 |
< |
else{ |
285 |
< |
if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
286 |
< |
else unhandled->add( lhs, rhs ); |
287 |
< |
have_extras = 1; |
288 |
< |
} |
289 |
< |
return NULL; |
290 |
< |
} |
291 |
< |
|
292 |
< |
char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){ |
293 |
< |
|
294 |
< |
if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom; |
295 |
< |
else { |
296 |
< |
if( have_atoms ){ |
297 |
< |
sprintf( errMsg, "MoleculeStamp error, %d out of nAtoms range", |
298 |
< |
atomIndex ); |
299 |
< |
return strdup( errMsg ); |
300 |
< |
} |
301 |
< |
else return strdup("MoleculeStamp error, nAtoms not given before" |
302 |
< |
" first atom declaration." ); |
303 |
< |
} |
304 |
< |
|
305 |
< |
return NULL; |
306 |
< |
} |
307 |
< |
|
308 |
< |
char* MoleculeStamp::addRigidBody( RigidBodyStamp* the_rigidbody, |
309 |
< |
int rigidBodyIndex ){ |
310 |
< |
|
311 |
< |
if( have_rigidbodies && rigidBodyIndex < n_rigidbodies ) |
312 |
< |
rigidBodies[rigidBodyIndex] = the_rigidbody; |
313 |
< |
else { |
314 |
< |
if( have_rigidbodies ){ |
315 |
< |
sprintf( errMsg, "MoleculeStamp error, %d out of nRigidBodies range", |
316 |
< |
rigidBodyIndex ); |
317 |
< |
return strdup( errMsg ); |
202 |
> |
if (bendAtoms.size() == 2 ) { |
203 |
> |
if (!bendStamp->haveGhostVectorSource()) { |
204 |
> |
std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce is missing\n"; |
205 |
> |
}else{ |
206 |
> |
int ghostIndex = bendStamp->getGhostVectorSource(); |
207 |
> |
if (ghostIndex < getNAtoms()) { |
208 |
> |
if (std::find(bendAtoms.begin(), bendAtoms.end(), ghostIndex) == bendAtoms.end()) { |
209 |
> |
std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce "<< ghostIndex<<"is invalid\n"; |
210 |
> |
} |
211 |
> |
if (!getAtomStamp(ghostIndex)->haveOrientation()) { |
212 |
> |
std::cout << "Error in Molecule " << getName() << ": ghost atom must be a directioanl atom\n"; |
213 |
> |
} |
214 |
> |
}else { |
215 |
> |
std::cout << "Error in Molecule " << getName() << ": ghostVectorsource " << ghostIndex<< " is invalid\n"; |
216 |
> |
} |
217 |
> |
} |
218 |
> |
} else if (bendAtoms.size() == 3 && bendStamp->haveGhostVectorSource()) { |
219 |
> |
std::cout << "Error in Molecule " << getName() << ": normal bend should not have ghostVectorSouce\n"; |
220 |
> |
} |
221 |
|
} |
319 |
– |
else return strdup("MoleculeStamp error, nRigidBodies not given before" |
320 |
– |
" first rigidBody declaration." ); |
321 |
– |
} |
322 |
– |
|
323 |
– |
return NULL; |
324 |
– |
} |
222 |
|
|
223 |
< |
char* MoleculeStamp::addCutoffGroup( CutoffGroupStamp* the_cutoffgroup, |
224 |
< |
int cutoffGroupIndex ){ |
225 |
< |
|
226 |
< |
if( have_cutoffgroups && cutoffGroupIndex < n_cutoffgroups ) |
227 |
< |
cutoffGroups[cutoffGroupIndex] = the_cutoffgroup; |
228 |
< |
else { |
229 |
< |
if( have_cutoffgroups ){ |
230 |
< |
sprintf( errMsg, "MoleculeStamp error, %d out of nCutoffGroups range", |
231 |
< |
cutoffGroupIndex ); |
232 |
< |
return strdup( errMsg ); |
223 |
> |
for(int i = 0; i < getNBends(); ++i) { |
224 |
> |
BendStamp* bendStamp = getBendStamp(i); |
225 |
> |
std::vector<int> bendAtoms = bendStamp->getMembers(); |
226 |
> |
std::vector<int> rigidSet(getNRigidBodies(), 0); |
227 |
> |
std::vector<int>::iterator j; |
228 |
> |
for( j = bendAtoms.begin(); j != bendAtoms.end(); ++j) { |
229 |
> |
int rigidbodyIndex = atom2Rigidbody[*j]; |
230 |
> |
if (rigidbodyIndex >= 0) { |
231 |
> |
++rigidSet[rigidbodyIndex]; |
232 |
> |
if (rigidSet[rigidbodyIndex] > 1) { |
233 |
> |
std::cout << "Error in Molecule " << getName() << ": "; |
234 |
> |
//std::cout << "atoms of bend " << << "belong to same rigidbody " << rigidbodyIndex << "\n"; |
235 |
> |
} |
236 |
> |
} |
237 |
> |
} |
238 |
> |
} |
239 |
> |
|
240 |
> |
|
241 |
> |
std::set<IntTuple3, BendLessThan> allBends; |
242 |
> |
std::set<IntTuple3, BendLessThan>::iterator iter; |
243 |
> |
for(int i = 0; i < getNBends(); ++i) { |
244 |
> |
BendStamp* bendStamp= getBendStamp(i); |
245 |
> |
std::vector<int> bend = bendStamp->getMembers(); |
246 |
> |
if (bend.size() == 2) { |
247 |
> |
// in case we have two ghost bend. For example, |
248 |
> |
// bend { |
249 |
> |
// members (0, 1); |
250 |
> |
// ghostVectorSource = 0; |
251 |
> |
// } |
252 |
> |
// and |
253 |
> |
// bend { |
254 |
> |
// members (0, 1); |
255 |
> |
// ghostVectorSource = 0; |
256 |
> |
// } |
257 |
> |
// In order to distinguish them. we expand them to Tuple3. |
258 |
> |
// the first one is expanded to (0, 0, 1) while the second one is expaned to (0, 1, 1) |
259 |
> |
int ghostIndex = bendStamp->getGhostVectorSource(); |
260 |
> |
std::vector<int>::iterator j = std::find(bend.begin(), bend.end(), ghostIndex); |
261 |
> |
if (j != bend.end()) { |
262 |
> |
bend.insert(j, ghostIndex); |
263 |
> |
} |
264 |
> |
} |
265 |
> |
|
266 |
> |
IntTuple3 bendTuple(bend[0], bend[1], bend[2]); |
267 |
> |
//make sure bendTuple.first is always less than or equal to bendTuple.third |
268 |
> |
if (bendTuple.first > bendTuple.third) { |
269 |
> |
std::swap(bendTuple.first, bendTuple.third); |
270 |
> |
} |
271 |
> |
|
272 |
> |
iter = allBends.find(bendTuple); |
273 |
> |
if ( iter != allBends.end()) { |
274 |
> |
std::cout << "Error in Molecule " << getName() << ": " << "Bend appears multiple times\n"; |
275 |
> |
} else { |
276 |
> |
allBends.insert(bendTuple); |
277 |
> |
} |
278 |
|
} |
337 |
– |
else return strdup("MoleculeStamp error, nCutoffGroups not given before" |
338 |
– |
" first CutoffGroup declaration." ); |
339 |
– |
} |
340 |
– |
|
341 |
– |
return NULL; |
342 |
– |
} |
279 |
|
|
280 |
< |
char* MoleculeStamp::addBond( BondStamp* the_bond, int bondIndex ){ |
281 |
< |
|
282 |
< |
|
283 |
< |
if( have_bonds && bondIndex < n_bonds ) bonds[bondIndex] = the_bond; |
348 |
< |
else{ |
349 |
< |
if( have_bonds ){ |
350 |
< |
sprintf( errMsg, "MoleculeStamp error, %d out of nBonds range", |
351 |
< |
bondIndex ); |
352 |
< |
return strdup( errMsg ); |
353 |
< |
} |
354 |
< |
else return strdup("MoleculeStamp error, nBonds not given before" |
355 |
< |
"first bond declaration." ); |
356 |
< |
} |
280 |
> |
for (int i = 0; i < getNBonds(); ++i) { |
281 |
> |
BondStamp* bondStamp = getBondStamp(i); |
282 |
> |
int a = bondStamp->getA(); |
283 |
> |
int b = bondStamp->getB(); |
284 |
|
|
285 |
< |
return NULL; |
286 |
< |
} |
285 |
> |
AtomStamp* atomA = getAtomStamp(a); |
286 |
> |
AtomStamp* atomB = getAtomStamp(b); |
287 |
|
|
288 |
< |
char* MoleculeStamp::addBend( BendStamp* the_bend, int bendIndex ){ |
289 |
< |
|
290 |
< |
|
291 |
< |
if( have_bends && bendIndex < n_bends ) bends[bendIndex] = the_bend; |
292 |
< |
else{ |
293 |
< |
if( have_bends ){ |
294 |
< |
sprintf( errMsg, "MoleculeStamp error, %d out of nBends range", |
295 |
< |
bendIndex ); |
296 |
< |
return strdup( errMsg ); |
288 |
> |
//find bend c--a--b |
289 |
> |
AtomStamp::AtomIter ai; |
290 |
> |
for(int c= atomA->getFirstBonedAtom(ai);c != -1;c = atomA->getNextBonedAtom(ai)) |
291 |
> |
{ |
292 |
> |
if(b == c) |
293 |
> |
continue; |
294 |
> |
|
295 |
> |
IntTuple3 newBend(c, a, b); |
296 |
> |
if (newBend.first > newBend.third) { |
297 |
> |
std::swap(newBend.first, newBend.third); |
298 |
> |
} |
299 |
> |
|
300 |
> |
if (allBends.find(newBend) == allBends.end() ) { |
301 |
> |
allBends.insert(newBend); |
302 |
> |
BendStamp * newBendStamp = new BendStamp(); |
303 |
> |
newBendStamp->setMembers(newBend); |
304 |
> |
addBendStamp(newBendStamp); |
305 |
> |
} |
306 |
> |
} |
307 |
> |
|
308 |
> |
//find bend a--b--c |
309 |
> |
for(int c= atomB->getFirstBonedAtom(ai);c != -1;c = atomB->getNextBonedAtom(ai)) |
310 |
> |
{ |
311 |
> |
if(a == c) |
312 |
> |
continue; |
313 |
> |
|
314 |
> |
IntTuple3 newBend( a, b, c); |
315 |
> |
if (newBend.first > newBend.third) { |
316 |
> |
std::swap(newBend.first, newBend.third); |
317 |
> |
} |
318 |
> |
if (allBends.find(newBend) == allBends.end() ) { |
319 |
> |
allBends.insert(newBend); |
320 |
> |
BendStamp * newBendStamp = new BendStamp(); |
321 |
> |
newBendStamp->setMembers(newBend); |
322 |
> |
addBendStamp(newBendStamp); |
323 |
> |
} |
324 |
> |
} |
325 |
|
} |
371 |
– |
else return strdup("MoleculeStamp error, nBends not given before" |
372 |
– |
"first bend declaration." ); |
373 |
– |
} |
326 |
|
|
375 |
– |
return NULL; |
327 |
|
} |
328 |
|
|
329 |
< |
char* MoleculeStamp::addTorsion( TorsionStamp* the_torsion, int torsionIndex ){ |
330 |
< |
|
331 |
< |
|
332 |
< |
if( have_torsions && torsionIndex < n_torsions ) |
333 |
< |
torsions[torsionIndex] = the_torsion; |
334 |
< |
else{ |
335 |
< |
if( have_torsions ){ |
385 |
< |
sprintf( errMsg, "MoleculeStamp error, %d out of nTorsions range", |
386 |
< |
torsionIndex ); |
387 |
< |
return strdup( errMsg ); |
329 |
> |
struct TorsionLessThan : public std::binary_function<IntTuple4, IntTuple4, bool> { |
330 |
> |
bool operator()(IntTuple4 t1, IntTuple4 t2) { |
331 |
> |
|
332 |
> |
return t1.first < t2.first |
333 |
> |
|| (!(t2.first < t1.first) && t1.second < t2.second) |
334 |
> |
|| (!(t2.first < t1.first) && !(t2.second < t2.second) && t1.third < t2.third) |
335 |
> |
||(!(t2.first < t1.first) && !(t2.second < t2.second) && !(t2.third < t1.third) && t1.fourth < t2.fourth); |
336 |
|
} |
389 |
– |
else return strdup("MoleculeStamp error, nTorsions not given before" |
390 |
– |
"first torsion declaration." ); |
391 |
– |
} |
337 |
|
|
393 |
– |
return NULL; |
394 |
– |
} |
338 |
|
|
396 |
– |
char* MoleculeStamp::checkMe( void ){ |
397 |
– |
|
398 |
– |
int i; |
399 |
– |
short int no_atom, no_rigidbody, no_cutoffgroup; |
339 |
|
|
340 |
< |
if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name" |
402 |
< |
" was not given.\n" ); |
403 |
< |
|
404 |
< |
if( !have_atoms ){ |
405 |
< |
return strdup( "MoleculeStamp error. Molecule contains no atoms." ); |
406 |
< |
} |
407 |
< |
|
408 |
< |
no_rigidbody = 0; |
409 |
< |
for( i=0; i<n_rigidbodies; i++ ){ |
410 |
< |
if( rigidBodies[i] == NULL ) no_rigidbody = 1; |
411 |
< |
} |
340 |
> |
}; |
341 |
|
|
413 |
– |
if( no_rigidbody ){ |
414 |
– |
sprintf( errMsg, |
415 |
– |
"MoleculeStamp error. Not all of the RigidBodies were" |
416 |
– |
" declared in molecule \"%s\".\n", name ); |
417 |
– |
return strdup( errMsg ); |
418 |
– |
} |
342 |
|
|
343 |
< |
no_cutoffgroup = 0; |
344 |
< |
for( i=0; i<n_cutoffgroups; i++ ){ |
345 |
< |
if( cutoffGroups[i] == NULL ) no_cutoffgroup = 1; |
346 |
< |
} |
343 |
> |
void MoleculeStamp::checkTorsions() { |
344 |
> |
for(int i = 0; i < getNTorsions(); ++i) { |
345 |
> |
TorsionStamp* torsionStamp = getTorsionStamp(i); |
346 |
> |
std::vector<int> torsionAtoms = torsionStamp->getMembers(); |
347 |
> |
std::vector<int> rigidSet(getNRigidBodies(), 0); |
348 |
> |
std::vector<int>::iterator j; |
349 |
> |
for( j = torsionAtoms.begin(); j != torsionAtoms.end(); ++j) { |
350 |
> |
int rigidbodyIndex = atom2Rigidbody[*j]; |
351 |
> |
if (rigidbodyIndex >= 0) { |
352 |
> |
++rigidSet[rigidbodyIndex]; |
353 |
> |
if (rigidSet[rigidbodyIndex] > 1) { |
354 |
> |
std::cout << "Error in Molecule " << getName() << ": "; |
355 |
> |
//std::cout << "atoms of torsion " << << "belong to same rigidbody " << rigidbodyIndex << "\n"; |
356 |
> |
} |
357 |
> |
} |
358 |
> |
} |
359 |
> |
} |
360 |
|
|
361 |
< |
if( no_cutoffgroup ){ |
362 |
< |
sprintf( errMsg, |
363 |
< |
"MoleculeStamp error. Not all of the CutoffGroups were" |
364 |
< |
" declared in molecule \"%s\".\n", name ); |
365 |
< |
return strdup( errMsg ); |
366 |
< |
} |
367 |
< |
|
368 |
< |
no_atom = 0; |
369 |
< |
for( i=0; i<n_atoms; i++ ){ |
370 |
< |
if( atoms[i] == NULL ) no_atom = 1; |
371 |
< |
} |
361 |
> |
std::set<IntTuple4, TorsionLessThan> allTorsions; |
362 |
> |
std::set<IntTuple4, TorsionLessThan>::iterator iter; |
363 |
> |
for(int i = 0; i < getNTorsions(); ++i) { |
364 |
> |
TorsionStamp* torsionStamp= getTorsionStamp(i); |
365 |
> |
std::vector<int> torsion = torsionStamp->getMembers(); |
366 |
> |
if (torsion.size() == 3) { |
367 |
> |
int ghostIndex = torsionStamp->getGhostVectorSource(); |
368 |
> |
std::vector<int>::iterator j = std::find(torsion.begin(), torsion.end(), ghostIndex); |
369 |
> |
if (j != torsion.end()) { |
370 |
> |
torsion.insert(j, ghostIndex); |
371 |
> |
} |
372 |
> |
} |
373 |
|
|
374 |
< |
if( no_atom ){ |
375 |
< |
sprintf( errMsg, |
376 |
< |
"MoleculeStamp error. Not all of the atoms were" |
377 |
< |
" declared in molecule \"%s\".\n", name ); |
378 |
< |
return strdup( errMsg ); |
442 |
< |
} |
374 |
> |
IntTuple4 torsionTuple(torsion[0], torsion[1], torsion[2], torsion[3]); |
375 |
> |
if (torsionTuple.first > torsionTuple.fourth) { |
376 |
> |
std::swap(torsionTuple.first, torsionTuple.fourth); |
377 |
> |
std::swap(torsionTuple.second, torsionTuple.third); |
378 |
> |
} |
379 |
|
|
380 |
< |
n_integrable = n_atoms; |
381 |
< |
for (i = 0; i < n_rigidbodies; i++) |
382 |
< |
n_integrable = n_integrable - rigidBodies[i]->getNMembers() + 1; //rigidbody is an integrable object |
383 |
< |
|
384 |
< |
if (n_integrable <= 0 || n_integrable > n_atoms) { |
385 |
< |
sprintf( errMsg, |
386 |
< |
"MoleculeStamp error. n_integrable is either <= 0 or" |
451 |
< |
" greater than n_atoms in molecule \"%s\".\n", name ); |
452 |
< |
return strdup( errMsg ); |
453 |
< |
} |
380 |
> |
iter = allTorsions.find(torsionTuple); |
381 |
> |
if ( iter == allTorsions.end()) { |
382 |
> |
allTorsions.insert(torsionTuple); |
383 |
> |
} else { |
384 |
> |
std::cout << "Error in Molecule " << getName() << ": " << "Torsion appears multiple times\n"; |
385 |
> |
} |
386 |
> |
} |
387 |
|
|
388 |
< |
return NULL; |
389 |
< |
} |
388 |
> |
for (int i = 0; i < getNBonds(); ++i) { |
389 |
> |
BondStamp* bondStamp = getBondStamp(i); |
390 |
> |
int b = bondStamp->getA(); |
391 |
> |
int c = bondStamp->getB(); |
392 |
|
|
393 |
+ |
AtomStamp* atomB = getAtomStamp(b); |
394 |
+ |
AtomStamp* atomC = getAtomStamp(c); |
395 |
|
|
396 |
+ |
AtomStamp::AtomIter ai2; |
397 |
+ |
AtomStamp::AtomIter ai3; |
398 |
+ |
|
399 |
+ |
for(int a = atomB->getFirstBonedAtom(ai2);a != -1;a = atomB->getNextBonedAtom(ai2)) |
400 |
+ |
{ |
401 |
+ |
if(a == c) |
402 |
+ |
continue; |
403 |
+ |
|
404 |
+ |
for(int d = atomC->getFirstBonedAtom(ai3);d != -1;d = atomC->getNextBonedAtom(ai3)) |
405 |
+ |
{ |
406 |
+ |
if(d == b) |
407 |
+ |
continue; |
408 |
+ |
|
409 |
+ |
IntTuple4 newTorsion(a, b, c, d); |
410 |
+ |
//make sure the first element is always less than or equal to the fourth element in IntTuple4 |
411 |
+ |
if (newTorsion.first > newTorsion.fourth) { |
412 |
+ |
std::swap(newTorsion.first, newTorsion.fourth); |
413 |
+ |
std::swap(newTorsion.second, newTorsion.third); |
414 |
+ |
} |
415 |
+ |
if (allTorsions.find(newTorsion) == allTorsions.end() ) { |
416 |
+ |
allTorsions.insert(newTorsion); |
417 |
+ |
TorsionStamp * newTorsionStamp = new TorsionStamp(); |
418 |
+ |
newTorsionStamp->setMembers(newTorsion); |
419 |
+ |
addTorsionStamp(newTorsionStamp); |
420 |
+ |
} |
421 |
+ |
} |
422 |
+ |
} |
423 |
+ |
} |
424 |
+ |
|
425 |
+ |
} |
426 |
+ |
|
427 |
+ |
void MoleculeStamp::checkRigidBodies() { |
428 |
+ |
std::vector<RigidBodyStamp*>::iterator ri = std::find(rigidBodyStamps_.begin(), rigidBodyStamps_.end(), static_cast<RigidBodyStamp*>(NULL)); |
429 |
+ |
if (ri != rigidBodyStamps_.end()) { |
430 |
+ |
std::cout << "Error in Molecule " << getName() << ":rigidBody[" << ri - rigidBodyStamps_.begin()<< "] is missing\n"; |
431 |
+ |
} |
432 |
+ |
|
433 |
+ |
for (int i = 0; i < getNRigidBodies(); ++i) { |
434 |
+ |
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
435 |
+ |
std::vector<int> rigidAtoms = rbStamp ->getMembers(); |
436 |
+ |
std::vector<int>::iterator j =std::find_if(rigidAtoms.begin(), rigidAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
437 |
+ |
if (j != rigidAtoms.end()) { |
438 |
+ |
std::cout << "Error in Molecule " << getName(); |
439 |
+ |
} |
440 |
+ |
|
441 |
+ |
} |
442 |
+ |
} |
443 |
+ |
|
444 |
+ |
void MoleculeStamp::checkCutoffGroups() { |
445 |
+ |
|
446 |
+ |
for(int i = 0; i < getNCutoffGroups(); ++i) { |
447 |
+ |
CutoffGroupStamp* cutoffGroupStamp = getCutoffGroupStamp(i); |
448 |
+ |
std::vector<int> cutoffGroupAtoms = cutoffGroupStamp ->getMembers(); |
449 |
+ |
std::vector<int>::iterator j =std::find_if(cutoffGroupAtoms.begin(), cutoffGroupAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
450 |
+ |
if (j != cutoffGroupAtoms.end()) { |
451 |
+ |
std::cout << "Error in Molecule " << getName() << ": cutoffGroup" << " is out of range\n"; |
452 |
+ |
} |
453 |
+ |
} |
454 |
+ |
} |
455 |
+ |
|
456 |
+ |
void MoleculeStamp::checkFragments() { |
457 |
+ |
|
458 |
+ |
std::vector<FragmentStamp*>::iterator fi = std::find(fragmentStamps_.begin(), fragmentStamps_.end(), static_cast<FragmentStamp*>(NULL)); |
459 |
+ |
if (fi != fragmentStamps_.end()) { |
460 |
+ |
std::cout << "Error in Molecule " << getName() << ":fragment[" << fi - fragmentStamps_.begin()<< "] is missing\n"; |
461 |
+ |
} |
462 |
+ |
|
463 |
+ |
} |
464 |
+ |
|
465 |
+ |
void MoleculeStamp::fillBondInfo() { |
466 |
+ |
|
467 |
+ |
for (int i = 0; i < getNBonds(); ++i) { |
468 |
+ |
BondStamp* bondStamp = getBondStamp(i); |
469 |
+ |
int a = bondStamp->getA(); |
470 |
+ |
int b = bondStamp->getB(); |
471 |
+ |
AtomStamp* atomA = getAtomStamp(a); |
472 |
+ |
AtomStamp* atomB = getAtomStamp(b); |
473 |
+ |
atomA->addBond(i); |
474 |
+ |
atomA->addBondedAtom(b); |
475 |
+ |
atomB->addBond(i); |
476 |
+ |
atomB->addBondedAtom(a); |
477 |
+ |
|
478 |
+ |
} |
479 |
+ |
} |
480 |
+ |
|
481 |
+ |
|
482 |
+ |
|
483 |
|
//Function Name: isBondInSameRigidBody |
484 |
|
//Return true is both atoms of the bond belong to the same rigid body, otherwise return false |
485 |
|
bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){ |
527 |
|
numRb = this->getNRigidBodies(); |
528 |
|
|
529 |
|
for(int i = 0 ; i < numRb; i++){ |
530 |
< |
rbStamp = this->getRigidBody(i); |
530 |
> |
rbStamp = this->getRigidBodyStamp(i); |
531 |
|
numAtom = rbStamp->getNMembers(); |
532 |
|
for(int j = 0; j < numAtom; j++) |
533 |
< |
if (rbStamp->getMember(j) == atomIndex){ |
533 |
> |
if (rbStamp->getMemberAt(j) == atomIndex){ |
534 |
|
whichRigidBody = i; |
535 |
|
consAtomIndex = j; |
536 |
|
return true; |
544 |
|
//return the position of joint atom apears in rigidbody's definition |
545 |
|
//for the time being, we will use the most inefficient algorithm, the complexity is O(N2) |
546 |
|
//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first |
547 |
< |
vector<pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){ |
547 |
> |
std::vector<std::pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){ |
548 |
|
RigidBodyStamp* rbStamp1; |
549 |
|
RigidBodyStamp* rbStamp2; |
550 |
|
int natomInRb1; |
551 |
|
int natomInRb2; |
552 |
|
int atomIndex1; |
553 |
|
int atomIndex2; |
554 |
< |
vector<pair<int, int> > jointAtomIndexPair; |
554 |
> |
std::vector<std::pair<int, int> > jointAtomIndexPair; |
555 |
|
|
556 |
< |
rbStamp1 = this->getRigidBody(rb1); |
556 |
> |
rbStamp1 = this->getRigidBodyStamp(rb1); |
557 |
|
natomInRb1 =rbStamp1->getNMembers(); |
558 |
|
|
559 |
< |
rbStamp2 = this->getRigidBody(rb2); |
559 |
> |
rbStamp2 = this->getRigidBodyStamp(rb2); |
560 |
|
natomInRb2 =rbStamp2->getNMembers(); |
561 |
|
|
562 |
|
for(int i = 0; i < natomInRb1; i++){ |
563 |
< |
atomIndex1 = rbStamp1->getMember(i); |
563 |
> |
atomIndex1 = rbStamp1->getMemberAt(i); |
564 |
|
|
565 |
|
for(int j= 0; j < natomInRb1; j++){ |
566 |
< |
atomIndex2 = rbStamp2->getMember(j); |
566 |
> |
atomIndex2 = rbStamp2->getMemberAt(j); |
567 |
|
|
568 |
|
if(atomIndex1 == atomIndex2){ |
569 |
< |
jointAtomIndexPair.push_back(make_pair(i, j)); |
569 |
> |
jointAtomIndexPair.push_back(std::make_pair(i, j)); |
570 |
|
break; |
571 |
|
} |
572 |
|
|
573 |
< |
}//end for(j =0) |
573 |
> |
} |
574 |
|
|
575 |
< |
}//end for (i = 0) |
575 |
> |
} |
576 |
|
|
577 |
|
return jointAtomIndexPair; |
578 |
|
} |
579 |
+ |
|
580 |
+ |
} |