| 1 |
/* |
| 2 |
* The MIT License |
| 3 |
|
| 4 |
BLDConograph (Bravais lattice determination module in Conograph) |
| 5 |
|
| 6 |
Copyright (c) <2012> <Ryoko Oishi-Tomiyasu, KEK> |
| 7 |
|
| 8 |
Permission is hereby granted, free of charge, to any person obtaining a copy |
| 9 |
of this software and associated documentation files (the "Software"), to deal |
| 10 |
in the Software without restriction, including without limitation the rights |
| 11 |
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
| 12 |
copies of the Software, and to permit persons to whom the Software is |
| 13 |
furnished to do so, subject to the following conditions: |
| 14 |
|
| 15 |
The above copyright notice and this permission notice shall be included in |
| 16 |
all copies or substantial portions of the Software. |
| 17 |
|
| 18 |
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
| 19 |
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
| 20 |
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
| 21 |
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
| 22 |
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
| 23 |
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
| 24 |
THE SOFTWARE. |
| 25 |
* |
| 26 |
*/ |
| 27 |
#include "../utility_data_structure/FracMat.hh" |
| 28 |
#include "../utility_lattice_reduction/put_Selling_reduced_lattice.hh" |
| 29 |
#include "../utility_lattice_reduction/put_Buerger_reduced_lattice.hh" |
| 30 |
#include "ReducedLatticeToCheckBravais.hh" |
| 31 |
#include "LatticeFigureOfMerit.hh" |
| 32 |
|
| 33 |
const NRMat<Int4> LatticeFigureOfMerit::m_tmat_prim_to_face = put_transform_matrix_row3to4( transpose( BravaisType::putTransformMatrixFromPrimitiveToFace() ) ); |
| 34 |
const NRMat<Int4> LatticeFigureOfMerit::m_tmat_prim_to_body = put_transform_matrix_row3to4( BravaisType::putTransformMatrixFromBodyToPrimitive() ); |
| 35 |
const NRMat<Int4> LatticeFigureOfMerit::m_tmat_prim_to_rhomhex = put_transform_matrix_row3to4( transpose( BravaisType::putTransformMatrixFromPrimitiveToRhomHex() ) ); |
| 36 |
const NRMat<Int4> LatticeFigureOfMerit::m_tmat_prim_to_base[3] = |
| 37 |
{ |
| 38 |
put_transform_matrix_row3to4( transpose( BravaisType::putTransformMatrixFromPrimitiveToBase(BaseA_Axis) ) ), |
| 39 |
put_transform_matrix_row3to4( transpose( BravaisType::putTransformMatrixFromPrimitiveToBase(BaseB_Axis) ) ), |
| 40 |
put_transform_matrix_row3to4( transpose( BravaisType::putTransformMatrixFromPrimitiveToBase(BaseC_Axis) ) ) |
| 41 |
}; |
| 42 |
const NRMat<Int4> LatticeFigureOfMerit::m_tmat_prim_to_prim = put_transform_matrix_row3to4(); |
| 43 |
|
| 44 |
LatticeFigureOfMerit::LatticeFigureOfMerit() |
| 45 |
: m_S_red(3) |
| 46 |
{ |
| 47 |
} |
| 48 |
|
| 49 |
|
| 50 |
LatticeFigureOfMerit::LatticeFigureOfMerit(const BravaisType& brat, |
| 51 |
const SymMat43_Double& S) |
| 52 |
: m_S_red(3) |
| 53 |
{ |
| 54 |
this->setLatticeConstants43(brat, S); |
| 55 |
} |
| 56 |
|
| 57 |
#ifdef DEBUG |
| 58 |
static bool checkInitialLatticeParameters( |
| 59 |
const BravaisType& brat, |
| 60 |
const SymMat<Double>& S_red) |
| 61 |
{ |
| 62 |
const SymMat<Double> inv_S_red( Inverse3(S_red) ); |
| 63 |
|
| 64 |
if( brat.enumPointGroup() == C2h_Y && brat.enumCentringType() == Prim ) |
| 65 |
{ |
| 66 |
assert( inv_S_red(0,2) <= 0.0 && |
| 67 |
inv_S_red(0,0) * 0.9999 < inv_S_red(2,2) |
| 68 |
&& fabs( inv_S_red(0,2) ) * 1.9999 < inv_S_red(2,2) |
| 69 |
&& fabs( inv_S_red(0,2) ) * 1.9999 < inv_S_red(0,0) ); |
| 70 |
} |
| 71 |
else if( brat.enumPointGroup() == C2h_Z && brat.enumCentringType() == Prim ) |
| 72 |
{ |
| 73 |
assert( inv_S_red(0,1) <= 0.0 |
| 74 |
&& inv_S_red(0,0) * 0.9999 < inv_S_red(1,1) |
| 75 |
&& fabs( inv_S_red(0,1) ) * 1.9999 < inv_S_red(0,0) |
| 76 |
&& fabs( inv_S_red(0,1) ) * 1.9999 < inv_S_red(1,1) ); |
| 77 |
} |
| 78 |
else if( brat.enumPointGroup() == C2h_X && brat.enumCentringType() == Prim ) |
| 79 |
{ |
| 80 |
assert( inv_S_red(1,2) <= 0.0 |
| 81 |
&& inv_S_red(1,1) * 0.9999 < inv_S_red(2,2) |
| 82 |
&& fabs( inv_S_red(1,2) ) * 1.9999 < inv_S_red(1,1) |
| 83 |
&& fabs( inv_S_red(1,2) ) * 1.9999 < inv_S_red(2,2) ); |
| 84 |
} |
| 85 |
else if( brat.enumPointGroup() == C2h_Y && brat.enumCentringType() == BaseZ ) |
| 86 |
{ |
| 87 |
assert( inv_S_red(0,2) <= 0.0 |
| 88 |
&& fabs( inv_S_red(0,2) ) * 0.9999 < inv_S_red(2,2) |
| 89 |
&& fabs( inv_S_red(0,2) ) * 1.9999 < inv_S_red(0,0) ); |
| 90 |
} |
| 91 |
else if( brat.enumPointGroup() == C2h_Z && brat.enumCentringType() == BaseX ) |
| 92 |
{ |
| 93 |
assert( inv_S_red(0,1) <= 0.0 |
| 94 |
&& fabs( inv_S_red(0,1) ) * 0.9999 < inv_S_red(0,0) |
| 95 |
&& fabs( inv_S_red(0,1) ) * 1.9999 < inv_S_red(1,1) ); |
| 96 |
} |
| 97 |
else if( brat.enumPointGroup() == C2h_X && brat.enumCentringType() == BaseY ) |
| 98 |
{ |
| 99 |
assert( inv_S_red(1,2) <= 0.0 |
| 100 |
&& fabs( inv_S_red(1,2) ) * 0.9999 < inv_S_red(1,1) |
| 101 |
&& fabs( inv_S_red(1,2) ) * 1.9999 < inv_S_red(2,2) ); |
| 102 |
} |
| 103 |
else if( brat.enumBravaisType() == Orthorhombic_C ) |
| 104 |
{ |
| 105 |
assert( brat.enumCentringType() == BaseZ ); |
| 106 |
assert( inv_S_red(0,0) * 0.9999 < inv_S_red(1,1) ); |
| 107 |
} |
| 108 |
else if( brat.enumPointGroup() == D2h && brat.enumCentringType() == Prim ) |
| 109 |
{ |
| 110 |
assert( inv_S_red(0,0) * 0.9999 < inv_S_red(1,1) |
| 111 |
&& inv_S_red(1,1) * 0.9999 < inv_S_red(2,2) ); |
| 112 |
} |
| 113 |
return true; |
| 114 |
} |
| 115 |
#endif |
| 116 |
|
| 117 |
static void putTransformMatrixToBuergerReduced( |
| 118 |
const SymMat<Double>& S, NRMat<Int4>& trans_mat) |
| 119 |
{ |
| 120 |
assert( S.size() == 3 ); |
| 121 |
|
| 122 |
SymMat<Double> S_super_obtuse(4); |
| 123 |
put_Selling_reduced_dim_3(S, S_super_obtuse, trans_mat); |
| 124 |
moveSmallerDiagonalLeftUpper(S_super_obtuse, trans_mat); |
| 125 |
|
| 126 |
// S_red = trans_mat * S_super_obtuse * transpose(trans_mat). |
| 127 |
SymMat<Double> S_red(3); |
| 128 |
NRMat<Int4> trans_mat2; |
| 129 |
putBuergerReducedMatrix(S_super_obtuse, S_red, trans_mat2); |
| 130 |
trans_mat = mprod( trans_mat2, put_transform_matrix_row4to3(trans_mat) ); |
| 131 |
} |
| 132 |
|
| 133 |
|
| 134 |
void LatticeFigureOfMerit::setInverseOfBuergerReducedForm(NRMat<Int4>& trans_mat, const SymMat43_Double& S_optimized) |
| 135 |
{ |
| 136 |
if( m_brat.enumBravaisType() == Triclinic ) |
| 137 |
{ |
| 138 |
// trans_mat * Inverse(S_optimized.first) * transpose(trans_mat) is Buerger-reduced |
| 139 |
// <=> Inverse of transpose(Inverse(trans_mat)) * S_optimized.first * Inverse(trans_mat) is Buerger-reduced. |
| 140 |
putTransformMatrixToBuergerReduced(Inverse3(S_optimized.first), trans_mat); |
| 141 |
transpose_square_matrix(trans_mat); |
| 142 |
m_S_red = transform_sym_matrix(Inverse3(trans_mat), S_optimized.first); |
| 143 |
} |
| 144 |
else |
| 145 |
{ |
| 146 |
m_S_red = S_optimized.first; |
| 147 |
trans_mat = identity_matrix<Int4>(3); |
| 148 |
if( m_brat.enumBravaisType() == Monoclinic_P ) |
| 149 |
{ |
| 150 |
if( m_brat.enumPointGroup() == C2h_X ) |
| 151 |
{ |
| 152 |
putBuergerReducedMonoclinicP(1, 2, m_S_red, trans_mat); |
| 153 |
} |
| 154 |
else if( m_brat.enumPointGroup() == C2h_Y ) |
| 155 |
{ |
| 156 |
putBuergerReducedMonoclinicP(0, 2, m_S_red, trans_mat); |
| 157 |
} |
| 158 |
else //if( m_brat.enumPointGroup() == C2h_Z ) |
| 159 |
{ |
| 160 |
putBuergerReducedMonoclinicP(0, 1, m_S_red, trans_mat); |
| 161 |
} |
| 162 |
} |
| 163 |
else if( m_brat.enumBravaisType() == Monoclinic_B ) |
| 164 |
{ |
| 165 |
m_S_red = S_optimized.first; |
| 166 |
putBuergerReducedMonoclinicB(m_brat, m_S_red, trans_mat); |
| 167 |
} |
| 168 |
else if( m_brat.enumPointGroup() == D2h ) |
| 169 |
{ |
| 170 |
m_S_red = S_optimized.first; |
| 171 |
putBuergerReducedOrthorhombic(m_brat.enumCentringType(), m_S_red, trans_mat); |
| 172 |
} |
| 173 |
} |
| 174 |
|
| 175 |
assert( checkInitialLatticeParameters(m_brat, m_S_red) ); |
| 176 |
} |
| 177 |
|
| 178 |
|
| 179 |
void LatticeFigureOfMerit::setLatticeConstants43(const BravaisType& brat, const SymMat43_Double& S) |
| 180 |
{ |
| 181 |
m_brat = brat; |
| 182 |
|
| 183 |
NRMat<Int4> trans_mat; |
| 184 |
setInverseOfBuergerReducedForm(trans_mat, S); // Set m_S_red from S. |
| 185 |
} |
| 186 |
|
| 187 |
ZErrorMessage LatticeFigureOfMerit::setLatticeConstants(const BravaisType& brat, const SymMat<Double>& Sval) |
| 188 |
{ |
| 189 |
assert( Sval.size()==3 ); |
| 190 |
|
| 191 |
SymMat43_Double S_red_optimized = SymMat43_Double(Sval, NRMat<Int4>(4,3)); |
| 192 |
cal_average_crystal_system(brat.enumPointGroup(), S_red_optimized.first); |
| 193 |
if( brat.enumCentringType() == Face ) |
| 194 |
{ |
| 195 |
S_red_optimized.second = m_tmat_prim_to_face; |
| 196 |
} |
| 197 |
else if( brat.enumCentringType() == Inner ) |
| 198 |
{ |
| 199 |
S_red_optimized.second = m_tmat_prim_to_body; |
| 200 |
} |
| 201 |
else if( brat.enumCentringType() == BaseX |
| 202 |
|| brat.enumCentringType() == BaseY |
| 203 |
|| brat.enumCentringType() == BaseZ ) |
| 204 |
{ |
| 205 |
S_red_optimized.second = m_tmat_prim_to_base[ (size_t)brat.enumBASEaxis() ]; |
| 206 |
} |
| 207 |
else if( brat.enumCentringType() == Rhom_hex ) |
| 208 |
{ |
| 209 |
S_red_optimized.second = m_tmat_prim_to_rhomhex; |
| 210 |
} |
| 211 |
else // if( brat.enumCentringType() == Prim ) |
| 212 |
{ |
| 213 |
S_red_optimized.second = m_tmat_prim_to_prim; |
| 214 |
} |
| 215 |
|
| 216 |
// S_super_obtuse = trans_mat * S_red.first * Transpose(trans_mat). |
| 217 |
SymMat<Double> S_super_obtuse = transform_sym_matrix(S_red_optimized.second, S_red_optimized.first); |
| 218 |
if( !put_Selling_reduced_dim_3(S_super_obtuse, S_red_optimized.second) ) |
| 219 |
{ |
| 220 |
return ZErrorMessage(ZErrorArgument, "The argument matrix is not positive definite" __FILE__, __LINE__, __FUNCTION__); |
| 221 |
} |
| 222 |
moveSmallerDiagonalLeftUpper(S_super_obtuse, S_red_optimized.second); |
| 223 |
|
| 224 |
setLatticeConstants43(brat, S_red_optimized); |
| 225 |
|
| 226 |
return ZErrorMessage(); |
| 227 |
} |
| 228 |
|
| 229 |
|
| 230 |
inline bool checkIfFirstEntryIsPositive(const VecDat3<Int4>& rhs) |
| 231 |
{ |
| 232 |
for(Int4 i=0; i<3; i++) |
| 233 |
{ |
| 234 |
if( rhs[i] == 0 ) continue; |
| 235 |
if( rhs[i] > 0 ) return true; |
| 236 |
else return false; |
| 237 |
} |
| 238 |
return false; |
| 239 |
} |
| 240 |
|
| 241 |
|
| 242 |
|
| 243 |
void LatticeFigureOfMerit::printLatticeInformation( |
| 244 |
const eABCaxis& abc_axis, |
| 245 |
const eRHaxis& rh_axis, |
| 246 |
const Int4& label_start0, |
| 247 |
ostream* os) const |
| 248 |
{ |
| 249 |
Int4 label_start = label_start0; |
| 250 |
os->width(label_start); |
| 251 |
*os << "" << "<CrystalSystem>"; |
| 252 |
os->width(17); |
| 253 |
*os << put_bravais_type_name(this->enumBravaisType(), abc_axis); |
| 254 |
*os << " </CrystalSystem>\n\n"; |
| 255 |
|
| 256 |
os->width(label_start); *os << ""; |
| 257 |
*os << "<!-- a, b, c(angstrom), alpha, beta, gamma(deg.)-->\n"; |
| 258 |
|
| 259 |
VecDat3<Double> length_axis, angle_axis; |
| 260 |
if( this->enumBravaisType() == Rhombohedral ) |
| 261 |
{ |
| 262 |
this->putReducedLatticeConstantsDegree(abc_axis, Rho_Axis, length_axis, angle_axis); |
| 263 |
|
| 264 |
os->width(label_start); *os << ""; |
| 265 |
*os << "<UnitCellParameters axis=\"Rhombohedral\">"; |
| 266 |
os->width(14); |
| 267 |
*os << length_axis[0]; |
| 268 |
os->width(14); |
| 269 |
*os << length_axis[1]; |
| 270 |
os->width(14); |
| 271 |
*os << length_axis[2]; |
| 272 |
os->width(14); |
| 273 |
*os << angle_axis[0]; |
| 274 |
os->width(14); |
| 275 |
*os << angle_axis[1]; |
| 276 |
os->width(14); |
| 277 |
*os << angle_axis [2]; |
| 278 |
*os << " </UnitCellParameters>\n"; |
| 279 |
|
| 280 |
this->putReducedLatticeConstantsDegree(abc_axis, Hex_Axis, length_axis, angle_axis); |
| 281 |
|
| 282 |
os->width(label_start); *os << ""; |
| 283 |
*os << "<UnitCellParameters axis=\"Hexagonal\">"; |
| 284 |
os->width(14); |
| 285 |
*os << length_axis[0]; |
| 286 |
os->width(14); |
| 287 |
*os << length_axis[1]; |
| 288 |
os->width(14); |
| 289 |
*os << length_axis[2]; |
| 290 |
os->width(14); |
| 291 |
*os << angle_axis[0]; |
| 292 |
os->width(14); |
| 293 |
*os << angle_axis[1]; |
| 294 |
os->width(14); |
| 295 |
*os << angle_axis[2]; |
| 296 |
*os << " </UnitCellParameters>\n\n"; |
| 297 |
} |
| 298 |
else |
| 299 |
{ |
| 300 |
this->putReducedLatticeConstantsDegree(abc_axis, Rho_Axis, length_axis, angle_axis); |
| 301 |
|
| 302 |
os->width(label_start); *os << ""; |
| 303 |
*os << "<UnitCellParameters>"; |
| 304 |
os->width(14); |
| 305 |
*os << length_axis[0]; |
| 306 |
os->width(14); |
| 307 |
*os << length_axis[1]; |
| 308 |
os->width(14); |
| 309 |
*os << length_axis[2]; |
| 310 |
os->width(14); |
| 311 |
*os << angle_axis[0]; |
| 312 |
os->width(14); |
| 313 |
*os << angle_axis[1]; |
| 314 |
os->width(14); |
| 315 |
*os << angle_axis[2]; |
| 316 |
*os << " </UnitCellParameters>\n"; |
| 317 |
} |
| 318 |
} |
| 319 |
|
| 320 |
|
| 321 |
void LatticeFigureOfMerit::putLatticeConstantsDegree(const BravaisType& brat, const SymMat<Double>& S0, |
| 322 |
const eABCaxis& axis1, |
| 323 |
const eRHaxis& axis2, VecDat3<Double>& length_axis, VecDat3<Double>& angle_axis) |
| 324 |
{ |
| 325 |
SymMat<Double> S = S0; |
| 326 |
if( brat.enumBravaisType() == Rhombohedral && axis2 != brat.enumRHaxis() ) |
| 327 |
{ |
| 328 |
if( axis2 == Hex_Axis ) // Rho -> Hex. |
| 329 |
{ |
| 330 |
static const FracMat matrix_rho2hex = FInverse3( transpose(BravaisType::putTransformMatrixFromPrimitiveToRhomHex() ) ); |
| 331 |
S = transform_sym_matrix(matrix_rho2hex.mat, S)/(matrix_rho2hex.denom*matrix_rho2hex.denom); |
| 332 |
} |
| 333 |
else // if( axis2 == RhoAxis ) // Hex -> Rho. |
| 334 |
{ |
| 335 |
static const NRMat<Int4> matrix_hex2rho = transpose( BravaisType::putTransformMatrixFromPrimitiveToRhomHex() ); |
| 336 |
S = transform_sym_matrix(matrix_hex2rho, S); |
| 337 |
} |
| 338 |
} |
| 339 |
else if( brat.enumBravaisType() == Monoclinic_B ) |
| 340 |
{ |
| 341 |
const NRMat<Int4> this2output = put_transform_matrix_monoclinic_b(brat.enumABCaxis(), axis1); |
| 342 |
S = transform_sym_matrix(this2output, S); |
| 343 |
} |
| 344 |
|
| 345 |
calLatticeConstant( S, length_axis, angle_axis ); |
| 346 |
} |
Parent Directory
Revision Log