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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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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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* @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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#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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#include <cstdio> |
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void Snapshot::setHmat(const Mat3x3d& m) { |
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const double orthoTolerance = NumericConstant::epsilon; |
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namespace OpenMD { |
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|
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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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double fortranHmat[9]; |
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double fortranInvHmat[9]; |
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RealType fortranHmat[9]; |
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RealType fortranInvHmat[9]; |
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hmat_.getArray(fortranHmat); |
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invHmat_.getArray(fortranInvHmat); |
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//determine whether the box is orthoTolerance or not |
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int oldOrthoRhombic = orthoRhombic_; |
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double smallDiag = fabs(hmat_(0, 0)); |
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RealType 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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RealType tol = smallDiag * orthoTolerance_; |
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orthoRhombic_ = 1; |
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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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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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if( oldOrthoRhombic != orthoRhombic_ ){ |
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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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if( orthoRhombic_ ) { |
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sprintf( painCave.errMsg, |
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"OpenMD 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 want 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 = OPENMD_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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"OpenMD 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 want 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 = OPENMD_WARNING; |
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simError(); |
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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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void Snapshot::wrapVector(Vector3d& pos) { |
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void Snapshot::wrapVector(Vector3d& pos) { |
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int i; |
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Vector3d scaled; |
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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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// 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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// 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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// calc the wrapped real coordinates from the wrapped scaled coordinates |
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pos = hmat_ * scaled; |
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} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element |
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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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// 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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// 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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// 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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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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// 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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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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painCave.severity = OPENMD_ERROR; |
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simError(); |
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} |
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return COM_; |
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} |
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|
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Vector3d Snapshot::getCOMvel() { |
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if( !hasCOM_ ) { |
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sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n"); |
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painCave.severity = OPENMD_ERROR; |
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simError(); |
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} |
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return COMvel_; |
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} |
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|
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Vector3d Snapshot::getCOMw() { |
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if( !hasCOM_ ) { |
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sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n"); |
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painCave.severity = OPENMD_ERROR; |
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simError(); |
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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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