--- trunk/src/brains/Snapshot.cpp 2005/01/12 22:41:40 246 +++ trunk/src/brains/Snapshot.cpp 2009/11/25 20:02:06 1390 @@ -1,4 +1,4 @@ - /* +/* * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. * * The University of Notre Dame grants you ("Licensee") a @@ -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. @@ -37,124 +28,160 @@ * 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] Vardeman & Gezelter, in progress (2009). */ - /** - * @file Snapshot.cpp - * @author tlin - * @date 11/11/2004 - * @time 10:56am - * @version 1.0 - */ +/** + * @file Snapshot.cpp + * @author tlin + * @date 11/11/2004 + * @time 10:56am + * @version 1.0 + */ #include "brains/Snapshot.hpp" #include "utils/NumericConstant.hpp" #include "utils/simError.h" #include "utils/Utility.hpp" -namespace oopse { +namespace OpenMD { -void Snapshot::setHmat(const Mat3x3d& m) { - const double orthoTolerance = NumericConstant::epsilon; + void Snapshot::setHmat(const Mat3x3d& m) { hmat_ = m; invHmat_ = hmat_.inverse(); + //prepare fortran Hmat - double fortranHmat[9]; - double fortranInvHmat[9]; + RealType fortranHmat[9]; + RealType fortranInvHmat[9]; hmat_.getArray(fortranHmat); invHmat_.getArray(fortranInvHmat); //determine whether the box is orthoTolerance or not int oldOrthoRhombic = orthoRhombic_; - double smallDiag = fabs(hmat_(0, 0)); + RealType 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 tol = smallDiag * orthoTolerance_; orthoRhombic_ = 1; 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; - } - } - } + for (int j = 0 ; j < 3; j++) { + if (i != j) { + if (orthoRhombic_) { + if ( fabs(hmat_(i, j)) >= tol) + orthoRhombic_ = 0; + } + } + } } if( oldOrthoRhombic != orthoRhombic_ ){ - if( orthoRhombic_ ) { - sprintf( painCave.errMsg, - "OOPSE 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" - "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" - "\tvariable ( currently set to %G ) smaller.\n", - orthoTolerance); - painCave.severity = OOPSE_INFO; - simError(); - } - else { - sprintf( painCave.errMsg, - "OOPSE 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" - "\tthe Orthorhombic computations, make the orthoBoxTolerance\n" - "\tvariable ( currently set to %G ) larger.\n", - orthoTolerance); - painCave.severity = OOPSE_WARNING; - simError(); - } + if( orthoRhombic_ ) { + sprintf( painCave.errMsg, + "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 want the\n" + "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" + "\tvariable ( currently set to %G ) smaller.\n", + orthoTolerance_); + painCave.severity = OPENMD_INFO; + simError(); + } + else { + sprintf( painCave.errMsg, + "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 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 = OPENMD_WARNING; + simError(); + } } //notify fortran simulation box has changed setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_); -} + } -void Snapshot::wrapVector(Vector3d& pos) { + void Snapshot::wrapVector(Vector3d& pos) { int i; Vector3d scaled; if( !orthoRhombic_ ){ - // calc the scaled coordinates. - scaled = invHmat_* pos; + // calc the scaled coordinates. + scaled = invHmat_* pos; - // wrap the scaled coordinates - for (i = 0; i < 3; ++i) { - scaled[i] -= roundMe(scaled[i]); - } + // 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; + // calc the wrapped real coordinates from the wrapped scaled coordinates + pos = hmat_ * scaled; } else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element - // calc the scaled coordinates. - for (i=0; i<3; i++) { - scaled[i] = pos[i] * invHmat_(i, i); - } + // 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]); - } + // 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 - for (i=0; i<3; i++) { - pos[i] = scaled[i] * hmat_(i, i); - } + // calc the wrapped real coordinates from the wrapped scaled coordinates + for (i=0; i<3; i++) { + pos[i] = scaled[i] * hmat_(i, i); + } } -} + } + Vector3d Snapshot::getCOM() { + if( !hasCOM_ ) { + sprintf( painCave.errMsg, "COM was requested before COM was computed!\n"); + painCave.severity = OPENMD_ERROR; + simError(); + } + return COM_; + } + + Vector3d Snapshot::getCOMvel() { + if( !hasCOM_ ) { + sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n"); + painCave.severity = OPENMD_ERROR; + simError(); + } + return COMvel_; + } + + Vector3d Snapshot::getCOMw() { + if( !hasCOM_ ) { + sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n"); + painCave.severity = OPENMD_ERROR; + simError(); + } + return COMw_; + } + }