| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 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 |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
|
| 42 |
#include <stdlib.h> |
| 43 |
#include <stdio.h> |
| 44 |
#include <string.h> |
| 45 |
#include <iostream> |
| 46 |
|
| 47 |
#include "types/AtomType.hpp" |
| 48 |
#include "utils/simError.h" |
| 49 |
#define __C |
| 50 |
#include "UseTheForce/DarkSide/atype_interface.h" |
| 51 |
#include "UseTheForce/DarkSide/lj_interface.h" |
| 52 |
#include "UseTheForce/DarkSide/eam_interface.h" |
| 53 |
#include "UseTheForce/DarkSide/electrostatic_interface.h" |
| 54 |
namespace oopse { |
| 55 |
AtomType::AtomType(){ |
| 56 |
|
| 57 |
// initialize to an error: |
| 58 |
atp.ident = -1; |
| 59 |
|
| 60 |
// and mass_less: |
| 61 |
mass_ = 0.0; |
| 62 |
|
| 63 |
// atom type is a Tabula Rasa: |
| 64 |
atp.is_Directional = 0; |
| 65 |
atp.is_LennardJones = 0; |
| 66 |
atp.is_Charge = 0; |
| 67 |
atp.is_Dipole = 0; |
| 68 |
atp.is_SplitDipole = 0; |
| 69 |
atp.is_Quadrupole = 0; |
| 70 |
atp.is_Sticky = 0; |
| 71 |
atp.is_StickyPower = 0; |
| 72 |
atp.is_GayBerne = 0; |
| 73 |
atp.is_EAM = 0; |
| 74 |
atp.is_Shape = 0; |
| 75 |
atp.is_FLARB = 0; |
| 76 |
atp.is_SuttonChen = 0; |
| 77 |
atp.is_MEAM = 0; |
| 78 |
} |
| 79 |
|
| 80 |
void AtomType::makeFortranAtomType() { |
| 81 |
|
| 82 |
int status; |
| 83 |
|
| 84 |
if (name_.empty()) { |
| 85 |
sprintf( painCave.errMsg, |
| 86 |
"Attempting to complete an AtomType without giving " |
| 87 |
"it a name_!\n"); |
| 88 |
painCave.severity = OOPSE_ERROR; |
| 89 |
painCave.isFatal = 1; |
| 90 |
simError(); |
| 91 |
} |
| 92 |
|
| 93 |
if (atp.ident == -1) { |
| 94 |
sprintf( painCave.errMsg, |
| 95 |
"Attempting to complete AtomType %s without setting the" |
| 96 |
" ident!/n", name_.c_str()); |
| 97 |
painCave.severity = OOPSE_ERROR; |
| 98 |
painCave.isFatal = 1; |
| 99 |
simError(); |
| 100 |
} |
| 101 |
|
| 102 |
status = 0; |
| 103 |
|
| 104 |
makeAtype(&atp, &status); |
| 105 |
|
| 106 |
if (status != 0) { |
| 107 |
sprintf( painCave.errMsg, |
| 108 |
"Fortran rejected AtomType %s!\n", name_.c_str()); |
| 109 |
painCave.severity = OOPSE_ERROR; |
| 110 |
painCave.isFatal = 1; |
| 111 |
simError(); |
| 112 |
} |
| 113 |
} |
| 114 |
|
| 115 |
|
| 116 |
void AtomType::complete() { |
| 117 |
int isError; |
| 118 |
GenericData* data; |
| 119 |
|
| 120 |
//notify a new LJtype atom type is created |
| 121 |
if (isLennardJones()) { |
| 122 |
data = getPropertyByName("LennardJones"); |
| 123 |
if (data != NULL) { |
| 124 |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 125 |
|
| 126 |
if (ljData != NULL) { |
| 127 |
LJParam ljParam = ljData->getData(); |
| 128 |
|
| 129 |
newLJtype(&atp.ident, &ljParam.sigma, &ljParam.epsilon, &ljParam.soft_pot, |
| 130 |
&isError); |
| 131 |
|
| 132 |
if (isError != 0) { |
| 133 |
sprintf( painCave.errMsg, |
| 134 |
"Fortran rejected newLJtype\n"); |
| 135 |
painCave.severity = OOPSE_ERROR; |
| 136 |
painCave.isFatal = 1; |
| 137 |
simError(); |
| 138 |
} |
| 139 |
|
| 140 |
} else { |
| 141 |
sprintf( painCave.errMsg, |
| 142 |
"Can not cast GenericData to LJParam\n"); |
| 143 |
painCave.severity = OOPSE_ERROR; |
| 144 |
painCave.isFatal = 1; |
| 145 |
simError(); |
| 146 |
} |
| 147 |
} else { |
| 148 |
sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
| 149 |
painCave.severity = OOPSE_ERROR; |
| 150 |
painCave.isFatal = 1; |
| 151 |
simError(); |
| 152 |
} |
| 153 |
} |
| 154 |
|
| 155 |
if (isElectrostatic()) { |
| 156 |
newElectrostaticType(&atp, &isError); |
| 157 |
if (isError != 0) { |
| 158 |
sprintf( painCave.errMsg, |
| 159 |
"Fortran rejected newElectrostaticType\n"); |
| 160 |
painCave.severity = OOPSE_ERROR; |
| 161 |
painCave.isFatal = 1; |
| 162 |
simError(); |
| 163 |
} |
| 164 |
} |
| 165 |
|
| 166 |
if (isCharge()) { |
| 167 |
data = getPropertyByName("Charge"); |
| 168 |
if (data != NULL) { |
| 169 |
DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data); |
| 170 |
|
| 171 |
if (doubleData != NULL) { |
| 172 |
double charge = doubleData->getData(); |
| 173 |
setCharge(&atp.ident, &charge, &isError); |
| 174 |
|
| 175 |
if (isError != 0) { |
| 176 |
sprintf( painCave.errMsg, |
| 177 |
"Fortran rejected setCharge\n"); |
| 178 |
painCave.severity = OOPSE_ERROR; |
| 179 |
painCave.isFatal = 1; |
| 180 |
simError(); |
| 181 |
} |
| 182 |
} else { |
| 183 |
sprintf( painCave.errMsg, |
| 184 |
"Can not cast GenericData to DoubleGenericData\n"); |
| 185 |
painCave.severity = OOPSE_ERROR; |
| 186 |
painCave.isFatal = 1; |
| 187 |
simError(); |
| 188 |
} |
| 189 |
} else { |
| 190 |
sprintf( painCave.errMsg, "Can not find Charge Parameters\n"); |
| 191 |
painCave.severity = OOPSE_ERROR; |
| 192 |
painCave.isFatal = 1; |
| 193 |
simError(); |
| 194 |
} |
| 195 |
} |
| 196 |
|
| 197 |
if (isEAM()) { |
| 198 |
data = getPropertyByName("EAM"); |
| 199 |
if (data != NULL) { |
| 200 |
EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data); |
| 201 |
|
| 202 |
if (eamData != NULL) { |
| 203 |
|
| 204 |
EAMParam eamParam = eamData->getData(); |
| 205 |
|
| 206 |
|
| 207 |
newEAMtype(&eamParam.latticeConstant, &eamParam.nrho, &eamParam.drho, |
| 208 |
&eamParam.nr, &eamParam.dr, &eamParam.rcut, &eamParam.rvals[0], |
| 209 |
&eamParam.rhovals[0], &eamParam.Frhovals[0], &atp.ident, |
| 210 |
&isError ); |
| 211 |
|
| 212 |
if (isError != 0) { |
| 213 |
sprintf( painCave.errMsg, |
| 214 |
"Fortran rejected newEAMtype\n"); |
| 215 |
painCave.severity = OOPSE_ERROR; |
| 216 |
painCave.isFatal = 1; |
| 217 |
simError(); |
| 218 |
} |
| 219 |
} else { |
| 220 |
sprintf( painCave.errMsg, |
| 221 |
"Can not cast GenericData to EAMParam\n"); |
| 222 |
painCave.severity = OOPSE_ERROR; |
| 223 |
painCave.isFatal = 1; |
| 224 |
simError(); |
| 225 |
} |
| 226 |
} else { |
| 227 |
sprintf( painCave.errMsg, "Can not find EAM Parameters\n"); |
| 228 |
painCave.severity = OOPSE_ERROR; |
| 229 |
painCave.isFatal = 1; |
| 230 |
simError(); |
| 231 |
} |
| 232 |
} |
| 233 |
|
| 234 |
|
| 235 |
} |
| 236 |
|
| 237 |
void AtomType::addProperty(GenericData* genData) { |
| 238 |
properties_.addProperty(genData); |
| 239 |
} |
| 240 |
|
| 241 |
void AtomType::removeProperty(const std::string& propName) { |
| 242 |
properties_.removeProperty(propName); |
| 243 |
} |
| 244 |
|
| 245 |
void AtomType::clearProperties() { |
| 246 |
properties_.clearProperties(); |
| 247 |
} |
| 248 |
|
| 249 |
std::vector<std::string> AtomType::getPropertyNames() { |
| 250 |
return properties_.getPropertyNames(); |
| 251 |
} |
| 252 |
|
| 253 |
std::vector<GenericData*> AtomType::getProperties() { |
| 254 |
return properties_.getProperties(); |
| 255 |
} |
| 256 |
|
| 257 |
GenericData* AtomType::getPropertyByName(const std::string& propName) { |
| 258 |
return properties_.getPropertyByName(propName); |
| 259 |
} |
| 260 |
} |
