1 |
gezelter |
828 |
#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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mmeineke |
377 |
#include <iostream> |
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#include "MoleculeStamp.hpp" |
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char MoleculeStamp::errMsg[500]; |
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MoleculeStamp::MoleculeStamp(){ |
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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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gezelter |
957 |
n_rigidbodies = 0; |
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gezelter |
1153 |
n_cutoffgroups = 0; |
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gezelter |
1103 |
n_integrable = 0; |
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mmeineke |
377 |
|
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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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gezelter |
957 |
rigidBodies = NULL; |
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gezelter |
1153 |
cutoffGroups = NULL; |
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mmeineke |
377 |
|
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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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gezelter |
957 |
have_rigidbodies = 0; |
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gezelter |
1153 |
have_cutoffgroups = 0; |
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mmeineke |
377 |
|
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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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gezelter |
957 |
|
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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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gezelter |
1153 |
|
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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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gezelter |
957 |
|
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mmeineke |
377 |
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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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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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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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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} |
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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; |
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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; |
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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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gezelter |
981 |
" for molecule: %s\n", |
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mmeineke |
377 |
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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} |
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else if( !strcmp( lhs, "nBonds" ) ){ |
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n_bonds = (int)rhs; |
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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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} |
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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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} |
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else if( !strcmp( lhs, "nBends" ) ){ |
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n_bends = (int)rhs; |
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if( have_bends ){ |
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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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} |
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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; |
129 |
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} |
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else if( !strcmp( lhs, "nTorsions" ) ){ |
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n_torsions = (int)rhs; |
133 |
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if( have_torsions ){ |
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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; |
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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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} |
145 |
gezelter |
957 |
|
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else if( !strcmp( lhs, "nRigidBodies" ) ){ |
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n_rigidbodies = (int)rhs; |
148 |
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149 |
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if( have_rigidbodies ){ |
150 |
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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 ); |
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return strdup( errMsg ); |
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} |
156 |
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have_rigidbodies = 1; |
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rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
158 |
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for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
159 |
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} |
160 |
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161 |
gezelter |
1153 |
else if( !strcmp( lhs, "nCutoffGroups" ) ){ |
162 |
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n_cutoffgroups = (int)rhs; |
163 |
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164 |
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if( have_cutoffgroups ){ |
165 |
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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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} |
171 |
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have_cutoffgroups = 1; |
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cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups]; |
173 |
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for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL; |
174 |
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} |
175 |
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176 |
mmeineke |
377 |
else{ |
177 |
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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; |
180 |
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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; |
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if( !strcmp( lhs, "nAtoms" ) ){ |
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n_atoms = rhs; |
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190 |
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if( have_atoms ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_atoms 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_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; |
200 |
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} |
201 |
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202 |
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else if( !strcmp( lhs, "nBonds" ) ){ |
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n_bonds = rhs; |
204 |
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205 |
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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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} |
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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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} |
216 |
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217 |
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else if( !strcmp( lhs, "nBends" ) ){ |
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n_bends = rhs; |
219 |
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220 |
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if( have_bends ){ |
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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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} |
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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; |
230 |
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} |
231 |
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232 |
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else if( !strcmp( lhs, "nTorsions" ) ){ |
233 |
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n_torsions = rhs; |
234 |
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235 |
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if( have_torsions ){ |
236 |
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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); |
240 |
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return strdup( errMsg ); |
241 |
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} |
242 |
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have_torsions = 1; |
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torsions = new TorsionStamp*[n_torsions]; |
244 |
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for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
245 |
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} |
246 |
gezelter |
957 |
|
247 |
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else if( !strcmp( lhs, "nRigidBodies" ) ){ |
248 |
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n_rigidbodies = rhs; |
249 |
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250 |
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if( have_rigidbodies ){ |
251 |
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sprintf( errMsg, |
252 |
gezelter |
1153 |
"MoleculeStamp error, n_rigidbodies already declared for" |
253 |
gezelter |
957 |
" molecule: %s\n", |
254 |
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name); |
255 |
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return strdup( errMsg ); |
256 |
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} |
257 |
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have_rigidbodies = 1; |
258 |
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rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
259 |
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for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
260 |
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} |
261 |
gezelter |
1153 |
else if( !strcmp( lhs, "nCutoffGroups" ) ){ |
262 |
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n_cutoffgroups = rhs; |
263 |
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264 |
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if( have_cutoffgroups ){ |
265 |
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sprintf( errMsg, |
266 |
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"MoleculeStamp error, n_cutoffgroups already declared for" |
267 |
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" molecule: %s\n", |
268 |
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name); |
269 |
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return strdup( errMsg ); |
270 |
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} |
271 |
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have_cutoffgroups = 1; |
272 |
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cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups]; |
273 |
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for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL; |
274 |
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} |
275 |
mmeineke |
377 |
else{ |
276 |
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if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
277 |
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else unhandled->add( lhs, rhs ); |
278 |
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have_extras = 1; |
279 |
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} |
280 |
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return NULL; |
281 |
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} |
282 |
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283 |
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char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){ |
284 |
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285 |
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if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom; |
286 |
gezelter |
1103 |
else { |
287 |
mmeineke |
377 |
if( have_atoms ){ |
288 |
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sprintf( errMsg, "MoleculeStamp error, %d out of nAtoms range", |
289 |
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atomIndex ); |
290 |
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return strdup( errMsg ); |
291 |
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} |
292 |
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else return strdup("MoleculeStamp error, nAtoms not given before" |
293 |
gezelter |
981 |
" first atom declaration." ); |
294 |
mmeineke |
377 |
} |
295 |
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296 |
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return NULL; |
297 |
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} |
298 |
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299 |
gezelter |
957 |
char* MoleculeStamp::addRigidBody( RigidBodyStamp* the_rigidbody, |
300 |
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int rigidBodyIndex ){ |
301 |
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302 |
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if( have_rigidbodies && rigidBodyIndex < n_rigidbodies ) |
303 |
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rigidBodies[rigidBodyIndex] = the_rigidbody; |
304 |
gezelter |
1103 |
else { |
305 |
gezelter |
957 |
if( have_rigidbodies ){ |
306 |
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sprintf( errMsg, "MoleculeStamp error, %d out of nRigidBodies range", |
307 |
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rigidBodyIndex ); |
308 |
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return strdup( errMsg ); |
309 |
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} |
310 |
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else return strdup("MoleculeStamp error, nRigidBodies not given before" |
311 |
gezelter |
981 |
" first rigidBody declaration." ); |
312 |
gezelter |
957 |
} |
313 |
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314 |
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return NULL; |
315 |
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} |
316 |
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|
317 |
gezelter |
1153 |
char* MoleculeStamp::addCutoffGroup( CutoffGroupStamp* the_cutoffgroup, |
318 |
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int cutoffGroupIndex ){ |
319 |
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320 |
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if( have_cutoffgroups && cutoffGroupIndex < n_cutoffgroups ) |
321 |
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cutoffGroups[cutoffGroupIndex] = the_cutoffgroup; |
322 |
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else { |
323 |
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if( have_cutoffgroups ){ |
324 |
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sprintf( errMsg, "MoleculeStamp error, %d out of nCutoffGroups range", |
325 |
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cutoffGroupIndex ); |
326 |
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return strdup( errMsg ); |
327 |
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} |
328 |
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else return strdup("MoleculeStamp error, nCutoffGroups not given before" |
329 |
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" first CutoffGroup declaration." ); |
330 |
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} |
331 |
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332 |
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return NULL; |
333 |
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} |
334 |
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|
335 |
mmeineke |
377 |
char* MoleculeStamp::addBond( BondStamp* the_bond, int bondIndex ){ |
336 |
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337 |
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338 |
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if( have_bonds && bondIndex < n_bonds ) bonds[bondIndex] = the_bond; |
339 |
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else{ |
340 |
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if( have_bonds ){ |
341 |
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sprintf( errMsg, "MoleculeStamp error, %d out of nBonds range", |
342 |
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bondIndex ); |
343 |
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return strdup( errMsg ); |
344 |
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} |
345 |
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else return strdup("MoleculeStamp error, nBonds not given before" |
346 |
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"first bond declaration." ); |
347 |
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} |
348 |
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349 |
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return NULL; |
350 |
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} |
351 |
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352 |
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char* MoleculeStamp::addBend( BendStamp* the_bend, int bendIndex ){ |
353 |
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354 |
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355 |
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if( have_bends && bendIndex < n_bends ) bends[bendIndex] = the_bend; |
356 |
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else{ |
357 |
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if( have_bends ){ |
358 |
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sprintf( errMsg, "MoleculeStamp error, %d out of nBends range", |
359 |
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bendIndex ); |
360 |
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return strdup( errMsg ); |
361 |
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} |
362 |
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else return strdup("MoleculeStamp error, nBends not given before" |
363 |
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"first bend declaration." ); |
364 |
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} |
365 |
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366 |
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return NULL; |
367 |
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} |
368 |
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369 |
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char* MoleculeStamp::addTorsion( TorsionStamp* the_torsion, int torsionIndex ){ |
370 |
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371 |
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372 |
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if( have_torsions && torsionIndex < n_torsions ) |
373 |
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torsions[torsionIndex] = the_torsion; |
374 |
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else{ |
375 |
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if( have_torsions ){ |
376 |
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sprintf( errMsg, "MoleculeStamp error, %d out of nTorsions range", |
377 |
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torsionIndex ); |
378 |
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return strdup( errMsg ); |
379 |
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} |
380 |
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else return strdup("MoleculeStamp error, nTorsions not given before" |
381 |
|
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"first torsion declaration." ); |
382 |
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} |
383 |
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384 |
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return NULL; |
385 |
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} |
386 |
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|
387 |
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|
char* MoleculeStamp::checkMe( void ){ |
388 |
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|
389 |
|
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int i; |
390 |
gezelter |
1153 |
short int no_atom, no_rigidbody, no_cutoffgroup; |
391 |
gezelter |
957 |
|
392 |
|
|
if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name" |
393 |
|
|
" was not given.\n" ); |
394 |
gezelter |
988 |
|
395 |
|
|
if( !have_atoms ){ |
396 |
|
|
return strdup( "MoleculeStamp error. Molecule contains no atoms." ); |
397 |
mmeineke |
377 |
} |
398 |
|
|
|
399 |
gezelter |
957 |
no_rigidbody = 0; |
400 |
|
|
for( i=0; i<n_rigidbodies; i++ ){ |
401 |
|
|
if( rigidBodies[i] == NULL ) no_rigidbody = 1; |
402 |
|
|
} |
403 |
|
|
|
404 |
|
|
if( no_rigidbody ){ |
405 |
|
|
sprintf( errMsg, |
406 |
|
|
"MoleculeStamp error. Not all of the RigidBodies were" |
407 |
|
|
" declared in molecule \"%s\".\n", name ); |
408 |
|
|
return strdup( errMsg ); |
409 |
|
|
} |
410 |
|
|
|
411 |
gezelter |
1153 |
no_cutoffgroup = 0; |
412 |
|
|
for( i=0; i<n_cutoffgroups; i++ ){ |
413 |
|
|
if( cutoffGroups[i] == NULL ) no_cutoffgroup = 1; |
414 |
|
|
} |
415 |
|
|
|
416 |
|
|
if( no_cutoffgroup ){ |
417 |
|
|
sprintf( errMsg, |
418 |
|
|
"MoleculeStamp error. Not all of the CutoffGroups were" |
419 |
|
|
" declared in molecule \"%s\".\n", name ); |
420 |
|
|
return strdup( errMsg ); |
421 |
|
|
} |
422 |
|
|
|
423 |
mmeineke |
377 |
no_atom = 0; |
424 |
|
|
for( i=0; i<n_atoms; i++ ){ |
425 |
|
|
if( atoms[i] == NULL ) no_atom = 1; |
426 |
|
|
} |
427 |
|
|
|
428 |
|
|
if( no_atom ){ |
429 |
|
|
sprintf( errMsg, |
430 |
|
|
"MoleculeStamp error. Not all of the atoms were" |
431 |
|
|
" declared in molecule \"%s\".\n", name ); |
432 |
|
|
return strdup( errMsg ); |
433 |
|
|
} |
434 |
|
|
|
435 |
gezelter |
1103 |
n_integrable = n_atoms; |
436 |
|
|
for (i = 0; i < n_rigidbodies; i++) |
437 |
tim |
1113 |
n_integrable = n_integrable - rigidBodies[i]->getNMembers() + 1; //rigidbody is an integrable object |
438 |
gezelter |
1103 |
|
439 |
|
|
if (n_integrable <= 0 || n_integrable > n_atoms) { |
440 |
|
|
sprintf( errMsg, |
441 |
|
|
"MoleculeStamp error. n_integrable is either <= 0 or" |
442 |
|
|
" greater than n_atoms in molecule \"%s\".\n", name ); |
443 |
|
|
return strdup( errMsg ); |
444 |
|
|
} |
445 |
|
|
|
446 |
mmeineke |
377 |
return NULL; |
447 |
gezelter |
988 |
} |