| 36 |
|
entry_plug = &info; |
| 37 |
|
myFF = the_ff; |
| 38 |
|
|
| 39 |
< |
|
| 39 |
> |
|
| 40 |
|
c_natoms = info.n_atoms; |
| 41 |
|
c_atoms = info.atoms; |
| 42 |
< |
c_sr_interactions = info.sr_interactions; |
| 43 |
< |
c_n_SRI = info.n_SRI; |
| 42 |
> |
nMols = info.n_mol; |
| 43 |
> |
molecules = info.molecules; |
| 44 |
|
c_is_constrained = 0; |
| 45 |
|
c_box_x = info.box_x; |
| 46 |
|
c_box_y = info.box_y; |
| 67 |
|
|
| 68 |
|
Constraint *temp_con; |
| 69 |
|
Constraint *dummy_plug; |
| 70 |
< |
temp_con = new Constraint[c_n_SRI]; |
| 70 |
> |
temp_con = new Constraint[info.n_SRI]; |
| 71 |
|
|
| 72 |
|
c_n_constrained = 0; |
| 73 |
|
int constrained = 0; |
| 74 |
< |
|
| 75 |
< |
for(int i = 0; i < c_n_SRI; i++){ |
| 74 |
> |
SRI** theArray; |
| 75 |
> |
for(int i = 0; i < nMols; i++){ |
| 76 |
|
|
| 77 |
< |
constrained = c_sr_interactions[i]->is_constrained(); |
| 78 |
< |
|
| 79 |
< |
if(constrained){ |
| 77 |
> |
theArray = (SRI**) molecules[i].getMyBonds(); |
| 78 |
> |
for(int j=0; j<molecules[i].getNBonds(); j++){ |
| 79 |
|
|
| 80 |
< |
dummy_plug = c_sr_interactions[i]->get_constraint(); |
| 81 |
< |
temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
| 82 |
< |
temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
| 83 |
< |
temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
| 80 |
> |
constrained = theArray[j]->is_constrained(); |
| 81 |
> |
|
| 82 |
> |
if(constrained){ |
| 83 |
> |
|
| 84 |
> |
dummy_plug = theArray[j]->get_constraint(); |
| 85 |
> |
temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
| 86 |
> |
temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
| 87 |
> |
temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
| 88 |
> |
|
| 89 |
> |
c_n_constrained++; |
| 90 |
> |
constrained = 0; |
| 91 |
> |
} |
| 92 |
> |
} |
| 93 |
|
|
| 94 |
< |
c_n_constrained++; |
| 95 |
< |
constrained = 0; |
| 94 |
> |
theArray = (SRI**) molecules[i].getMyBends(); |
| 95 |
> |
for(int j=0; j<molecules[i].getNBends(); j++){ |
| 96 |
> |
|
| 97 |
> |
constrained = theArray[j]->is_constrained(); |
| 98 |
> |
|
| 99 |
> |
if(constrained){ |
| 100 |
> |
|
| 101 |
> |
dummy_plug = theArray[j]->get_constraint(); |
| 102 |
> |
temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
| 103 |
> |
temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
| 104 |
> |
temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
| 105 |
> |
|
| 106 |
> |
c_n_constrained++; |
| 107 |
> |
constrained = 0; |
| 108 |
> |
} |
| 109 |
> |
} |
| 110 |
> |
|
| 111 |
> |
theArray = (SRI**) molecules[i].getMyTorsions(); |
| 112 |
> |
for(int j=0; j<molecules[i].getNTorsions(); j++){ |
| 113 |
> |
|
| 114 |
> |
constrained = theArray[j]->is_constrained(); |
| 115 |
> |
|
| 116 |
> |
if(constrained){ |
| 117 |
> |
|
| 118 |
> |
dummy_plug = theArray[j]->get_constraint(); |
| 119 |
> |
temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
| 120 |
> |
temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
| 121 |
> |
temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
| 122 |
> |
|
| 123 |
> |
c_n_constrained++; |
| 124 |
> |
constrained = 0; |
| 125 |
> |
} |
| 126 |
|
} |
| 127 |
+ |
|
| 128 |
+ |
|
| 129 |
|
} |
| 130 |
|
|
| 131 |
|
if(c_n_constrained > 0){ |
| 134 |
|
c_constrained_i = new int[c_n_constrained]; |
| 135 |
|
c_constrained_j = new int[c_n_constrained]; |
| 136 |
|
c_constrained_dsqr = new double[c_n_constrained]; |
| 137 |
< |
|
| 137 |
> |
|
| 138 |
|
for( int i = 0; i < c_n_constrained; i++){ |
| 139 |
|
|
| 140 |
|
/* add 1 to the index for the fortran arrays. */ |
| 141 |
< |
|
| 141 |
> |
|
| 142 |
|
c_constrained_i[i] = temp_con[i].get_a() + 1; |
| 143 |
|
c_constrained_j[i] = temp_con[i].get_b() + 1; |
| 144 |
|
c_constrained_dsqr[i] = temp_con[i].get_dsqr(); |
