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*/ |
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#include "brains/Snapshot.hpp" |
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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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|
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namespace oopse { |
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|
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void Snapshot::setHmat(const Mat3x3d& m) { |
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const double orthoTolerance = NumericConstant::epsilon; |
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hmat_ = m; |
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invHmat_ = hmat_.inverse(); |
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|
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//prepare fortran Hmat |
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double fortranHmat[9]; |
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double fortranInvHmat[9]; |
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hmat_.getArray(fortranHmat); |
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invHmat_.getArray(fortranInvHmat); |
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|
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//determine whether the box is orthoTolerance or not |
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int oldOrthoRhombic = orthoRhombic_; |
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|
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double smallDiag = fabs(hmat_(0, 0)); |
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if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1)); |
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if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2)); |
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double tol = smallDiag * orthoTolerance; |
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|
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orthoRhombic_ = 1; |
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|
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for (int i = 0; i < 3; i++ ) { |
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for (int j = 0 ; j < 3; j++) { |
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if (i != j) { |
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if (orthoRhombic_) { |
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if ( fabs(hmat_(i, j)) >= tol) |
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orthoRhombic_ = 0; |
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} |
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} |
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} |
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} |
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|
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if( oldOrthoRhombic != orthoRhombic_ ){ |
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|
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if( orthoRhombic_ ) { |
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sprintf( painCave.errMsg, |
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"OOPSE is switching from the default Non-Orthorhombic\n" |
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"\tto the faster Orthorhombic periodic boundary computations.\n" |
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"\tThis is usually a good thing, but if you wan't the\n" |
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"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
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"\tvariable ( currently set to %G ) smaller.\n", |
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orthoTolerance); |
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painCave.severity = OOPSE_INFO; |
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simError(); |
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} |
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else { |
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sprintf( painCave.errMsg, |
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"OOPSE is switching from the faster Orthorhombic to the more\n" |
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"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
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"\tThis is usually because the box has deformed under\n" |
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"\tNPTf integration. If you wan't to live on the edge with\n" |
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"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
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"\tvariable ( currently set to %G ) larger.\n", |
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orthoTolerance); |
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painCave.severity = OOPSE_WARNING; |
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simError(); |
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} |
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} |
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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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} |
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|
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|
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void Snapshot::wrapVector(Vector3d& pos) { |
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int i; |
