| 1 |
#include <iostream> |
| 2 |
|
| 3 |
using namespace std; |
| 4 |
|
| 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, |
| 52 |
&quat); |
| 53 |
} |
| 54 |
else{ |
| 55 |
sprintf( painCave.errMsg, |
| 56 |
"Attempted to set Atom %d coordinates with an unallocated " |
| 57 |
"SimState object.\n", index ); |
| 58 |
painCave.isFatal = 1; |
| 59 |
simError(); |
| 60 |
} |
| 61 |
|
| 62 |
hasCoords = true; |
| 63 |
|
| 64 |
} |
| 65 |
|
| 66 |
void Atom::getPos( double theP[3] ){ |
| 67 |
|
| 68 |
if( hasCoords ){ |
| 69 |
theP[0] = pos[offsetX]; |
| 70 |
theP[1] = pos[offsetY]; |
| 71 |
theP[2] = pos[offsetZ]; |
| 72 |
} |
| 73 |
else{ |
| 74 |
|
| 75 |
sprintf( painCave.errMsg, |
| 76 |
"Attempt to get Pos for atom %d before coords set.\n", |
| 77 |
index ); |
| 78 |
painCave.isFatal = 1; |
| 79 |
simError(); |
| 80 |
} |
| 81 |
} |
| 82 |
|
| 83 |
void Atom::setPos( double theP[3] ){ |
| 84 |
|
| 85 |
if( hasCoords ){ |
| 86 |
pos[offsetX] = theP[0]; |
| 87 |
pos[offsetY] = theP[1]; |
| 88 |
pos[offsetZ] = theP[2]; |
| 89 |
} |
| 90 |
else{ |
| 91 |
|
| 92 |
sprintf( painCave.errMsg, |
| 93 |
"Attempt to set Pos for atom %d before coords set.\n", |
| 94 |
index ); |
| 95 |
painCave.isFatal = 1; |
| 96 |
simError(); |
| 97 |
} |
| 98 |
} |
| 99 |
|
| 100 |
void Atom::getVel( double theV[3] ){ |
| 101 |
|
| 102 |
if( hasCoords ){ |
| 103 |
theV[0] = vel[offsetX]; |
| 104 |
theV[1] = vel[offsetY]; |
| 105 |
theV[2] = vel[offsetZ]; |
| 106 |
} |
| 107 |
else{ |
| 108 |
|
| 109 |
sprintf( painCave.errMsg, |
| 110 |
"Attempt to get vel for atom %d before coords set.\n", |
| 111 |
index ); |
| 112 |
painCave.isFatal = 1; |
| 113 |
simError(); |
| 114 |
} |
| 115 |
|
| 116 |
} |
| 117 |
|
| 118 |
void Atom::setVel( double theV[3] ){ |
| 119 |
|
| 120 |
if( hasCoords ){ |
| 121 |
vel[offsetX] = theV[0]; |
| 122 |
vel[offsetY] = theV[1]; |
| 123 |
vel[offsetZ] = theV[2]; |
| 124 |
} |
| 125 |
else{ |
| 126 |
|
| 127 |
sprintf( painCave.errMsg, |
| 128 |
"Attempt to set vel for atom %d before coords set.\n", |
| 129 |
index ); |
| 130 |
painCave.isFatal = 1; |
| 131 |
simError(); |
| 132 |
} |
| 133 |
} |
| 134 |
|
| 135 |
void Atom::getFrc( double theF[3] ){ |
| 136 |
|
| 137 |
if( hasCoords ){ |
| 138 |
theF[0] = frc[offsetX]; |
| 139 |
theF[1] = frc[offsetY]; |
| 140 |
theF[2] = frc[offsetZ]; |
| 141 |
} |
| 142 |
else{ |
| 143 |
|
| 144 |
sprintf( painCave.errMsg, |
| 145 |
"Attempt to get frc for atom %d before coords set.\n", |
| 146 |
index ); |
| 147 |
painCave.isFatal = 1; |
| 148 |
simError(); |
| 149 |
} |
| 150 |
} |
| 151 |
|
| 152 |
void Atom::setFrc( double theF[3] ){ |
| 153 |
|
| 154 |
if( hasCoords ){ |
| 155 |
frc[offsetX] = theF[0]; |
| 156 |
frc[offsetY] = theF[1]; |
| 157 |
frc[offsetZ] = theF[2]; |
| 158 |
} |
| 159 |
else{ |
| 160 |
|
| 161 |
sprintf( painCave.errMsg, |
| 162 |
"Attempt to set frc for atom %d before coords set.\n", |
| 163 |
index ); |
| 164 |
painCave.isFatal = 1; |
| 165 |
simError(); |
| 166 |
} |
| 167 |
} |
| 168 |
|
| 169 |
void Atom::addFrc( double theF[3] ){ |
| 170 |
|
| 171 |
if( hasCoords ){ |
| 172 |
frc[offsetX] += theF[0]; |
| 173 |
frc[offsetY] += theF[1]; |
| 174 |
frc[offsetZ] += theF[2]; |
| 175 |
} |
| 176 |
else{ |
| 177 |
|
| 178 |
sprintf( painCave.errMsg, |
| 179 |
"Attempt to add frc for atom %d before coords set.\n", |
| 180 |
index ); |
| 181 |
painCave.isFatal = 1; |
| 182 |
simError(); |
| 183 |
} |
| 184 |
} |
| 185 |
|
| 186 |
|
| 187 |
void Atom::zeroForces( void ){ |
| 188 |
|
| 189 |
if( hasCoords ){ |
| 190 |
frc[offsetX] = 0.0; |
| 191 |
frc[offsetY] = 0.0; |
| 192 |
frc[offsetZ] = 0.0; |
| 193 |
} |
| 194 |
else{ |
| 195 |
|
| 196 |
sprintf( painCave.errMsg, |
| 197 |
"Attempt to zero frc for atom %d before coords set.\n", |
| 198 |
index ); |
| 199 |
painCave.isFatal = 1; |
| 200 |
simError(); |
| 201 |
} |
| 202 |
} |
| 203 |
|
