| 1 |
< |
#include <iostream> |
| 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 "primitives/Atom.hpp" |
| 43 |
> |
namespace oopse { |
| 44 |
|
|
| 45 |
< |
using namespace std; |
| 46 |
< |
|
| 5 |
< |
#include "simError.h" |
| 6 |
< |
#include "Atom.hpp" |
| 7 |
< |
|
| 8 |
< |
Atom::Atom(int theIndex, SimState* theConfig) { |
| 9 |
< |
|
| 10 |
< |
objType = OT_ATOM; |
| 11 |
< |
myConfig = theConfig; |
| 12 |
< |
hasCoords = false; |
| 13 |
< |
|
| 14 |
< |
has_dipole = 0; |
| 15 |
< |
has_charge = 0; |
| 16 |
< |
|
| 17 |
< |
index = theIndex; |
| 18 |
< |
offset = 0; |
| 19 |
< |
offsetX = offset; |
| 20 |
< |
offsetY = offset+1; |
| 21 |
< |
offsetZ = offset+2; |
| 22 |
< |
|
| 23 |
< |
Axx = 0; |
| 24 |
< |
Axy = Axx+1; |
| 25 |
< |
Axz = Axx+2; |
| 26 |
< |
|
| 27 |
< |
Ayx = Axx+3; |
| 28 |
< |
Ayy = Axx+4; |
| 29 |
< |
Ayz = Axx+5; |
| 30 |
< |
|
| 31 |
< |
Azx = Axx+6; |
| 32 |
< |
Azy = Axx+7; |
| 33 |
< |
Azz = Axx+8; |
| 34 |
< |
} |
| 35 |
< |
|
| 36 |
< |
void Atom::setIndex(int theIndex) { |
| 37 |
< |
index = theIndex; |
| 38 |
< |
} |
| 39 |
< |
|
| 40 |
< |
void Atom::setCoords(void){ |
| 41 |
< |
|
| 42 |
< |
if( myConfig->isAllocated() ){ |
| 43 |
< |
|
| 44 |
< |
myConfig->getAtomPointers( index, |
| 45 |
< |
&pos, |
| 46 |
< |
&vel, |
| 47 |
< |
&frc, |
| 48 |
< |
&trq, |
| 49 |
< |
&Amat, |
| 50 |
< |
&mu, |
| 51 |
< |
&ul); |
| 45 |
> |
Atom::Atom(AtomType* at) : StuntDouble(otAtom, &Snapshot::atomData) ,atomType_(at) { |
| 46 |
> |
mass_ = at->getMass(); |
| 47 |
|
} |
| 53 |
– |
else{ |
| 54 |
– |
sprintf( painCave.errMsg, |
| 55 |
– |
"Attempted to set Atom %d coordinates with an unallocated " |
| 56 |
– |
"SimState object.\n", index ); |
| 57 |
– |
painCave.isFatal = 1; |
| 58 |
– |
simError(); |
| 59 |
– |
} |
| 60 |
– |
|
| 61 |
– |
hasCoords = true; |
| 62 |
– |
|
| 63 |
– |
} |
| 48 |
|
|
| 49 |
< |
void Atom::getPos( double theP[3] ){ |
| 50 |
< |
|
| 51 |
< |
if( hasCoords ){ |
| 68 |
< |
theP[0] = pos[offsetX]; |
| 69 |
< |
theP[1] = pos[offsetY]; |
| 70 |
< |
theP[2] = pos[offsetZ]; |
| 71 |
< |
} |
| 72 |
< |
else{ |
| 49 |
> |
Mat3x3d Atom::getI() { |
| 50 |
> |
return Mat3x3d::identity(); |
| 51 |
> |
} |
| 52 |
|
|
| 53 |
< |
sprintf( painCave.errMsg, |
| 54 |
< |
"Attempt to get Pos for atom %d before coords set.\n", |
| 55 |
< |
index ); |
| 77 |
< |
painCave.isFatal = 1; |
| 78 |
< |
simError(); |
| 79 |
< |
} |
| 80 |
< |
} |
| 53 |
> |
std::vector<double> Atom::getGrad() { |
| 54 |
> |
std::vector<double> grad(3); |
| 55 |
> |
Vector3d force= getFrc(); |
| 56 |
|
|
| 57 |
< |
void Atom::setPos( double theP[3] ){ |
| 58 |
< |
|
| 59 |
< |
if( hasCoords ){ |
| 85 |
< |
pos[offsetX] = theP[0]; |
| 86 |
< |
pos[offsetY] = theP[1]; |
| 87 |
< |
pos[offsetZ] = theP[2]; |
| 88 |
< |
} |
| 89 |
< |
else{ |
| 90 |
< |
|
| 91 |
< |
sprintf( painCave.errMsg, |
| 92 |
< |
"Attempt to set Pos for atom %d before coords set.\n", |
| 93 |
< |
index ); |
| 94 |
< |
painCave.isFatal = 1; |
| 95 |
< |
simError(); |
| 96 |
< |
} |
| 97 |
< |
} |
| 98 |
< |
|
| 99 |
< |
void Atom::getVel( double theV[3] ){ |
| 100 |
< |
|
| 101 |
< |
if( hasCoords ){ |
| 102 |
< |
theV[0] = vel[offsetX]; |
| 103 |
< |
theV[1] = vel[offsetY]; |
| 104 |
< |
theV[2] = vel[offsetZ]; |
| 105 |
< |
} |
| 106 |
< |
else{ |
| 57 |
> |
grad[0] = -force[0]; |
| 58 |
> |
grad[1] = -force[1]; |
| 59 |
> |
grad[2] = -force[2]; |
| 60 |
|
|
| 61 |
< |
sprintf( painCave.errMsg, |
| 62 |
< |
"Attempt to get vel for atom %d before coords set.\n", |
| 110 |
< |
index ); |
| 111 |
< |
painCave.isFatal = 1; |
| 112 |
< |
simError(); |
| 113 |
< |
} |
| 61 |
> |
return grad; |
| 62 |
> |
} |
| 63 |
|
|
| 64 |
< |
} |
| 64 |
> |
void Atom::accept(BaseVisitor* v) { |
| 65 |
> |
v->visit(this); |
| 66 |
> |
} |
| 67 |
|
|
| 117 |
– |
void Atom::setVel( double theV[3] ){ |
| 118 |
– |
|
| 119 |
– |
if( hasCoords ){ |
| 120 |
– |
vel[offsetX] = theV[0]; |
| 121 |
– |
vel[offsetY] = theV[1]; |
| 122 |
– |
vel[offsetZ] = theV[2]; |
| 123 |
– |
} |
| 124 |
– |
else{ |
| 125 |
– |
|
| 126 |
– |
sprintf( painCave.errMsg, |
| 127 |
– |
"Attempt to set vel for atom %d before coords set.\n", |
| 128 |
– |
index ); |
| 129 |
– |
painCave.isFatal = 1; |
| 130 |
– |
simError(); |
| 131 |
– |
} |
| 68 |
|
} |
| 133 |
– |
|
| 134 |
– |
void Atom::getFrc( double theF[3] ){ |
| 135 |
– |
|
| 136 |
– |
if( hasCoords ){ |
| 137 |
– |
theF[0] = frc[offsetX]; |
| 138 |
– |
theF[1] = frc[offsetY]; |
| 139 |
– |
theF[2] = frc[offsetZ]; |
| 140 |
– |
} |
| 141 |
– |
else{ |
| 142 |
– |
|
| 143 |
– |
sprintf( painCave.errMsg, |
| 144 |
– |
"Attempt to get frc for atom %d before coords set.\n", |
| 145 |
– |
index ); |
| 146 |
– |
painCave.isFatal = 1; |
| 147 |
– |
simError(); |
| 148 |
– |
} |
| 149 |
– |
} |
| 150 |
– |
|
| 151 |
– |
void Atom::addFrc( double theF[3] ){ |
| 152 |
– |
|
| 153 |
– |
if( hasCoords ){ |
| 154 |
– |
frc[offsetX] += theF[0]; |
| 155 |
– |
frc[offsetY] += theF[1]; |
| 156 |
– |
frc[offsetZ] += theF[2]; |
| 157 |
– |
} |
| 158 |
– |
else{ |
| 159 |
– |
|
| 160 |
– |
sprintf( painCave.errMsg, |
| 161 |
– |
"Attempt to add frc for atom %d before coords set.\n", |
| 162 |
– |
index ); |
| 163 |
– |
painCave.isFatal = 1; |
| 164 |
– |
simError(); |
| 165 |
– |
} |
| 166 |
– |
} |
| 167 |
– |
|
| 168 |
– |
|
| 169 |
– |
void Atom::zeroForces( void ){ |
| 170 |
– |
|
| 171 |
– |
if( hasCoords ){ |
| 172 |
– |
frc[offsetX] = 0.0; |
| 173 |
– |
frc[offsetY] = 0.0; |
| 174 |
– |
frc[offsetZ] = 0.0; |
| 175 |
– |
} |
| 176 |
– |
else{ |
| 177 |
– |
|
| 178 |
– |
sprintf( painCave.errMsg, |
| 179 |
– |
"Attempt to zero frc for atom %d before coords set.\n", |
| 180 |
– |
index ); |
| 181 |
– |
painCave.isFatal = 1; |
| 182 |
– |
simError(); |
| 183 |
– |
} |
| 184 |
– |
} |
| 185 |
– |
|
