--- trunk/src/brains/Snapshot.cpp 2005/04/15 22:04:00 507 +++ branches/development/src/brains/Snapshot.cpp 2012/05/22 21:55:31 1715 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,16 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ /** @@ -51,110 +52,122 @@ #include "utils/NumericConstant.hpp" #include "utils/simError.h" #include "utils/Utility.hpp" -namespace oopse { +#include +namespace OpenMD { + void Snapshot::setHmat(const Mat3x3d& m) { - const double orthoTolerance = NumericConstant::epsilon; - hmat_ = m; - invHmat_ = hmat_.inverse(); + frameData.hmat = m; + frameData.invHmat = frameData.hmat.inverse(); - //prepare fortran Hmat - double fortranHmat[9]; - double fortranInvHmat[9]; - hmat_.getArray(fortranHmat); - invHmat_.getArray(fortranInvHmat); - //determine whether the box is orthoTolerance or not - int oldOrthoRhombic = orthoRhombic_; + bool oldOrthoRhombic = frameData.orthoRhombic; - double smallDiag = fabs(hmat_(0, 0)); - if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1)); - if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2)); - double tol = smallDiag * orthoTolerance; + RealType smallDiag = fabs(frameData.hmat(0, 0)); + if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1)); + if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2)); + RealType tol = smallDiag * orthoTolerance_; - orthoRhombic_ = 1; + frameData.orthoRhombic = true; for (int i = 0; i < 3; i++ ) { for (int j = 0 ; j < 3; j++) { if (i != j) { - if (orthoRhombic_) { - if ( fabs(hmat_(i, j)) >= tol) - orthoRhombic_ = 0; + if (frameData.orthoRhombic) { + if ( fabs(frameData.hmat(i, j)) >= tol) + frameData.orthoRhombic = false; } } } } - if( oldOrthoRhombic != orthoRhombic_ ){ + if( oldOrthoRhombic != frameData.orthoRhombic){ - if( orthoRhombic_ ) { + if( frameData.orthoRhombic ) { sprintf( painCave.errMsg, - "OOPSE is switching from the default Non-Orthorhombic\n" + "OpenMD is switching from the default Non-Orthorhombic\n" "\tto the faster Orthorhombic periodic boundary computations.\n" - "\tThis is usually a good thing, but if you wan't the\n" + "\tThis is usually a good thing, but if you want the\n" "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" "\tvariable ( currently set to %G ) smaller.\n", - orthoTolerance); - painCave.severity = OOPSE_INFO; + orthoTolerance_); + painCave.severity = OPENMD_INFO; simError(); } else { sprintf( painCave.errMsg, - "OOPSE is switching from the faster Orthorhombic to the more\n" + "OpenMD is switching from the faster Orthorhombic to the more\n" "\tflexible Non-Orthorhombic periodic boundary computations.\n" "\tThis is usually because the box has deformed under\n" - "\tNPTf integration. If you wan't to live on the edge with\n" + "\tNPTf integration. If you want to live on the edge with\n" "\tthe Orthorhombic computations, make the orthoBoxTolerance\n" "\tvariable ( currently set to %G ) larger.\n", - orthoTolerance); - painCave.severity = OOPSE_WARNING; + orthoTolerance_); + painCave.severity = OPENMD_WARNING; simError(); } } - - //notify fortran simulation box has changed - setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_); } void Snapshot::wrapVector(Vector3d& pos) { + + Vector3d scaled = scaleVector(pos); + + for (int i = 0; i < 3; i++) + scaled[i] -= roundMe(scaled[i]); - int i; - Vector3d scaled; + if( !frameData.orthoRhombic ) + pos = frameData.hmat * scaled; + else { - if( !orthoRhombic_ ){ - - // calc the scaled coordinates. - scaled = invHmat_* pos; - - // wrap the scaled coordinates - for (i = 0; i < 3; ++i) { - scaled[i] -= roundMe(scaled[i]); - } - // calc the wrapped real coordinates from the wrapped scaled coordinates - pos = hmat_ * scaled; + for (int i=0; i<3; i++) { + pos[i] = scaled[i] * frameData.hmat(i, i); + } + } + } - } else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element + inline Vector3d Snapshot::scaleVector(Vector3d& pos) { - // calc the scaled coordinates. - for (i=0; i<3; i++) { - scaled[i] = pos[i] * invHmat_(i, i); - } - - // wrap the scaled coordinates - for (i = 0; i < 3; ++i) { - scaled[i] -= roundMe(scaled[i]); - } + Vector3d scaled; - // calc the wrapped real coordinates from the wrapped scaled coordinates - for (i=0; i<3; i++) { - pos[i] = scaled[i] * hmat_(i, i); - } - + if( !frameData.orthoRhombic ) + scaled = frameData.invHmat * pos; + else { + // calc the scaled coordinates. + for (int i=0; i<3; i++) + scaled[i] = pos[i] * frameData.invHmat(i, i); } + return scaled; } - + + Vector3d Snapshot::getCOM() { + if( !hasCOM_ ) { + sprintf( painCave.errMsg, "COM was requested before COM was computed!\n"); + painCave.severity = OPENMD_ERROR; + simError(); + } + return frameData.COM; + } + + Vector3d Snapshot::getCOMvel() { + if( !hasCOM_ ) { + sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n"); + painCave.severity = OPENMD_ERROR; + simError(); + } + return frameData.COMvel; + } + + Vector3d Snapshot::getCOMw() { + if( !hasCOM_ ) { + sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n"); + painCave.severity = OPENMD_ERROR; + simError(); + } + return frameData.COMw; + } }