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#include "utils/NumericConstant.hpp" |
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#include "utils/simError.h" |
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#include "utils/Utility.hpp" |
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#include <cstdio> |
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|
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namespace OpenMD { |
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void Snapshot::setHmat(const Mat3x3d& m) { |
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hmat_ = m; |
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invHmat_ = hmat_.inverse(); |
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//prepare fortran Hmat |
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RealType fortranHmat[9]; |
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RealType fortranInvHmat[9]; |
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} |
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//notify fortran simulation box has changed |
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setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_); |
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// setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_); |
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} |
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void Snapshot::wrapVector(Vector3d& pos) { |
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Vector3d scaled = scaleVector(pos); |
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|
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for (int i = 0; i < 3; i++) |
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scaled[i] -= roundMe(scaled[i]); |
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|
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int i; |
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< |
Vector3d scaled; |
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> |
if( !orthoRhombic_ ) |
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> |
pos = hmat_ * scaled; |
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else { |
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|
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if( !orthoRhombic_ ){ |
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// calc the scaled coordinates. |
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scaled = invHmat_* pos; |
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// wrap the scaled coordinates |
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for (i = 0; i < 3; ++i) { |
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scaled[i] -= roundMe(scaled[i]); |
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} |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
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< |
pos = hmat_ * scaled; |
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> |
for (int i=0; i<3; i++) { |
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> |
pos[i] = scaled[i] * hmat_(i, i); |
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> |
} |
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> |
} |
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> |
} |
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|
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< |
} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element |
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> |
inline Vector3d Snapshot::scaleVector(Vector3d& pos) { |
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|
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< |
// calc the scaled coordinates. |
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< |
for (i=0; i<3; i++) { |
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< |
scaled[i] = pos[i] * invHmat_(i, i); |
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< |
} |
| 144 |
< |
|
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< |
// wrap the scaled coordinates |
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< |
for (i = 0; i < 3; ++i) { |
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< |
scaled[i] -= roundMe(scaled[i]); |
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< |
} |
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> |
Vector3d scaled; |
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|
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< |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
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< |
for (i=0; i<3; i++) { |
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< |
pos[i] = scaled[i] * hmat_(i, i); |
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< |
} |
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< |
|
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> |
if( !orthoRhombic_ ) |
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> |
scaled = invHmat_* pos; |
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> |
else { |
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> |
// calc the scaled coordinates. |
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> |
for (int i=0; i<3; i++) |
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> |
scaled[i] = pos[i] * invHmat_(i, i); |
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} |
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|
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+ |
return scaled; |
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} |
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< |
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> |
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Vector3d Snapshot::getCOM() { |
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if( !hasCOM_ ) { |
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sprintf( painCave.errMsg, "COM was requested before COM was computed!\n"); |
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} |
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return COMw_; |
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} |
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|
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} |
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