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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* |
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* Contact: oopse@oopse.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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|
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/** |
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* @file Snapshot.cpp |
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* @author tlin |
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* @date 11/11/2004 |
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* @time 10:56am |
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* @version 1.0 |
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*/ |
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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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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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|
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int i; |
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Vector3d scaled; |
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|
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if( !orthoRhombic_ ){ |
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|
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// calc the scaled coordinates. |
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scaled = invHmat_* pos; |
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|
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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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|
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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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|
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} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element |
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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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} |
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|
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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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|
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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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} |
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|
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} |
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|
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} |
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