| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "visitors/RigidBodyVisitor.hpp" |
| 43 |
– |
|
| 44 |
|
#include "primitives/RigidBody.hpp" |
| 45 |
|
|
| 46 |
|
|
| 47 |
< |
namespace oopse { |
| 47 |
> |
namespace OpenMD { |
| 48 |
|
|
| 49 |
– |
|
| 50 |
– |
|
| 49 |
|
void LipidHeadVisitor::visit(RigidBody* rb){ |
| 52 |
– |
|
| 50 |
|
Vector3d pos; |
| 54 |
– |
|
| 51 |
|
Vector3d u(0, 0, 1); |
| 56 |
– |
|
| 52 |
|
Vector3d newVec; |
| 58 |
– |
|
| 53 |
|
GenericData* data; |
| 60 |
– |
|
| 54 |
|
AtomData* atomData; |
| 62 |
– |
|
| 55 |
|
AtomInfo* atomInfo; |
| 64 |
– |
|
| 56 |
|
bool haveAtomData; |
| 66 |
– |
|
| 57 |
|
RotMat3x3d rotMatrix; |
| 58 |
|
|
| 69 |
– |
|
| 70 |
– |
|
| 59 |
|
if(!canVisit(rb->getType())) |
| 72 |
– |
|
| 60 |
|
return; |
| 61 |
|
|
| 75 |
– |
|
| 76 |
– |
|
| 62 |
|
pos = rb->getPos(); |
| 78 |
– |
|
| 63 |
|
rotMatrix = rb->getA(); |
| 80 |
– |
|
| 64 |
|
//matVecMul3(rotMatrix, u, newVec); |
| 82 |
– |
|
| 65 |
|
newVec = rotMatrix * u; |
| 66 |
|
|
| 85 |
– |
|
| 86 |
– |
|
| 67 |
|
data = rb->getPropertyByName("ATOMDATA"); |
| 68 |
|
|
| 69 |
|
if(data != NULL){ |
| 90 |
– |
|
| 91 |
– |
|
| 92 |
– |
|
| 70 |
|
atomData = dynamic_cast<AtomData*>(data); |
| 71 |
< |
|
| 71 |
> |
|
| 72 |
|
if(atomData == NULL){ |
| 96 |
– |
|
| 73 |
|
std::cerr << "can not get Atom Data from " << rb->getType() << std::endl; |
| 74 |
< |
|
| 74 |
> |
|
| 75 |
|
atomData = new AtomData; |
| 100 |
– |
|
| 76 |
|
haveAtomData = false; |
| 77 |
< |
|
| 78 |
< |
} |
| 104 |
< |
|
| 105 |
< |
else |
| 106 |
< |
|
| 77 |
> |
|
| 78 |
> |
} else |
| 79 |
|
haveAtomData = true; |
| 80 |
< |
|
| 81 |
< |
} |
| 110 |
< |
|
| 111 |
< |
else{ |
| 112 |
< |
|
| 80 |
> |
|
| 81 |
> |
} else { |
| 82 |
|
atomData = new AtomData; |
| 114 |
– |
|
| 83 |
|
haveAtomData = false; |
| 84 |
< |
|
| 84 |
> |
|
| 85 |
|
} |
| 86 |
|
|
| 119 |
– |
|
| 120 |
– |
|
| 87 |
|
atomInfo = new AtomInfo; |
| 122 |
– |
|
| 88 |
|
atomInfo->atomTypeName = "X"; |
| 124 |
– |
|
| 89 |
|
atomInfo->pos[0] = pos[0]; |
| 126 |
– |
|
| 90 |
|
atomInfo->pos[1] = pos[1]; |
| 128 |
– |
|
| 91 |
|
atomInfo->pos[2] = pos[2]; |
| 92 |
+ |
atomInfo->vec[0] = newVec[0]; |
| 93 |
+ |
atomInfo->vec[1] = newVec[1]; |
| 94 |
+ |
atomInfo->vec[2] = newVec[2]; |
| 95 |
|
|
| 131 |
– |
atomInfo->dipole[0] = newVec[0]; |
| 132 |
– |
|
| 133 |
– |
atomInfo->dipole[1] = newVec[1]; |
| 134 |
– |
|
| 135 |
– |
atomInfo->dipole[2] = newVec[2]; |
| 136 |
– |
|
| 137 |
– |
|
| 138 |
– |
|
| 96 |
|
atomData->addAtomInfo(atomInfo); |
| 97 |
|
|
| 141 |
– |
|
| 142 |
– |
|
| 98 |
|
if(!haveAtomData){ |
| 144 |
– |
|
| 99 |
|
atomData->setID("ATOMDATA"); |
| 146 |
– |
|
| 100 |
|
rb->addProperty(atomData); |
| 148 |
– |
|
| 101 |
|
} |
| 102 |
|
|
| 151 |
– |
|
| 152 |
– |
|
| 103 |
|
} |
| 104 |
|
|
| 105 |
|
|
| 156 |
– |
|
| 106 |
|
void LipidHeadVisitor::addLipidHeadName(const std::string& name){ |
| 158 |
– |
|
| 107 |
|
lipidHeadName.insert(name); |
| 108 |
|
|
| 161 |
– |
|
| 162 |
– |
|
| 109 |
|
} |
| 110 |
|
|
| 165 |
– |
|
| 166 |
– |
|
| 111 |
|
bool LipidHeadVisitor::canVisit(const std::string& name){ |
| 168 |
– |
|
| 112 |
|
return lipidHeadName.find(name) != lipidHeadName.end() ? true : false; |
| 113 |
|
|
| 171 |
– |
|
| 172 |
– |
|
| 114 |
|
} |
| 115 |
|
|
| 116 |
|
|
| 176 |
– |
|
| 117 |
|
const std::string LipidHeadVisitor::toString(){ |
| 178 |
– |
|
| 118 |
|
char buffer[65535]; |
| 180 |
– |
|
| 119 |
|
std::string result; |
| 182 |
– |
|
| 120 |
|
std::set<std::string>::iterator i; |
| 121 |
|
|
| 185 |
– |
|
| 186 |
– |
|
| 122 |
|
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 188 |
– |
|
| 123 |
|
result += buffer; |
| 124 |
|
|
| 191 |
– |
|
| 192 |
– |
|
| 125 |
|
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 194 |
– |
|
| 126 |
|
result += buffer; |
| 127 |
|
|
| 197 |
– |
|
| 198 |
– |
|
| 128 |
|
//print the ignore type list |
| 200 |
– |
|
| 129 |
|
sprintf(buffer , "lipidHeadName list contains below types:\n"); |
| 202 |
– |
|
| 130 |
|
result += buffer; |
| 131 |
|
|
| 205 |
– |
|
| 206 |
– |
|
| 132 |
|
for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){ |
| 208 |
– |
|
| 133 |
|
sprintf(buffer ,"%s\t", i->c_str()); |
| 210 |
– |
|
| 134 |
|
result += buffer; |
| 212 |
– |
|
| 135 |
|
} |
| 136 |
|
|
| 215 |
– |
|
| 216 |
– |
|
| 137 |
|
sprintf(buffer ,"\n"); |
| 218 |
– |
|
| 138 |
|
result += buffer; |
| 139 |
|
|
| 221 |
– |
|
| 222 |
– |
|
| 140 |
|
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 224 |
– |
|
| 141 |
|
result += buffer; |
| 142 |
|
|
| 227 |
– |
|
| 228 |
– |
|
| 143 |
|
return result; |
| 144 |
|
|
| 231 |
– |
|
| 232 |
– |
|
| 145 |
|
} |
| 146 |
|
|
| 147 |
|
|
| 236 |
– |
|
| 148 |
|
void RBCOMVisitor::visit(RigidBody* rb){ |
| 238 |
– |
|
| 149 |
|
AtomData* atomData; |
| 240 |
– |
|
| 150 |
|
AtomInfo* atomInfo; |
| 242 |
– |
|
| 151 |
|
Vector3d pos; |
| 152 |
|
|
| 245 |
– |
|
| 246 |
– |
|
| 153 |
|
pos = rb->getPos(); |
| 248 |
– |
|
| 154 |
|
atomInfo = new AtomInfo; |
| 250 |
– |
|
| 155 |
|
atomInfo->atomTypeName = "X"; |
| 252 |
– |
|
| 156 |
|
atomInfo->pos[0] = pos[0]; |
| 254 |
– |
|
| 157 |
|
atomInfo->pos[1] = pos[1]; |
| 256 |
– |
|
| 158 |
|
atomInfo->pos[2] = pos[2]; |
| 159 |
+ |
atomInfo->vec[0] = 0; |
| 160 |
+ |
atomInfo->vec[1] = 0; |
| 161 |
+ |
atomInfo->vec[2] = 0; |
| 162 |
|
|
| 259 |
– |
atomInfo->dipole[0] = 0; |
| 260 |
– |
|
| 261 |
– |
atomInfo->dipole[1] = 0; |
| 262 |
– |
|
| 263 |
– |
atomInfo->dipole[2] = 0; |
| 264 |
– |
|
| 265 |
– |
|
| 266 |
– |
|
| 163 |
|
atomData = new AtomData; |
| 268 |
– |
|
| 164 |
|
atomData->setID("ATOMDATA"); |
| 270 |
– |
|
| 165 |
|
atomData->addAtomInfo(atomInfo); |
| 166 |
|
|
| 273 |
– |
|
| 274 |
– |
|
| 167 |
|
rb->addProperty(atomData); |
| 168 |
|
|
| 169 |
|
} |
| 170 |
|
|
| 171 |
|
|
| 280 |
– |
|
| 172 |
|
const std::string RBCOMVisitor::toString(){ |
| 282 |
– |
|
| 173 |
|
char buffer[65535]; |
| 284 |
– |
|
| 174 |
|
std::string result; |
| 175 |
|
|
| 287 |
– |
|
| 288 |
– |
|
| 176 |
|
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 290 |
– |
|
| 177 |
|
result += buffer; |
| 178 |
|
|
| 293 |
– |
|
| 294 |
– |
|
| 179 |
|
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 296 |
– |
|
| 180 |
|
result += buffer; |
| 181 |
|
|
| 299 |
– |
|
| 300 |
– |
|
| 182 |
|
//print the ignore type list |
| 302 |
– |
|
| 183 |
|
sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n"); |
| 304 |
– |
|
| 184 |
|
result += buffer; |
| 185 |
|
|
| 307 |
– |
|
| 308 |
– |
|
| 186 |
|
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 310 |
– |
|
| 187 |
|
result += buffer; |
| 188 |
|
|
| 313 |
– |
|
| 314 |
– |
|
| 189 |
|
return result; |
| 190 |
|
|
| 317 |
– |
|
| 318 |
– |
|
| 191 |
|
} |
| 192 |
|
|
| 193 |
+ |
}//namespace OpenMD |
| 194 |
|
|
| 322 |
– |
|
| 323 |
– |
|
| 324 |
– |
|
| 325 |
– |
}//namespace oopse |
| 326 |
– |
|
