--- trunk/src/brains/SimInfo.cpp 2009/10/23 18:41:09 1386 +++ branches/development/src/brains/SimInfo.cpp 2010/10/03 22:18:59 1505 @@ -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 +28,15 @@ * 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). */ /** @@ -55,12 +55,9 @@ #include "primitives/Molecule.hpp" #include "primitives/StuntDouble.hpp" #include "UseTheForce/fCutoffPolicy.h" -#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" -#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" #include "UseTheForce/DarkSide/fSwitchingFunctionType.h" #include "UseTheForce/doForces_interface.h" #include "UseTheForce/DarkSide/neighborLists_interface.h" -#include "UseTheForce/DarkSide/electrostatic_interface.h" #include "UseTheForce/DarkSide/switcheroo_interface.h" #include "utils/MemoryUtils.hpp" #include "utils/simError.h" @@ -74,7 +71,7 @@ #include "UseTheForce/DarkSide/simParallel_interface.h" #endif -namespace oopse { +namespace OpenMD { std::set getRigidSet(int index, std::map >& container) { std::map >::iterator i = container.find(index); std::set result; @@ -765,7 +762,6 @@ namespace oopse { useSP = 0; useBoxDipole = 0; - if (simParams_->haveElectrostaticSummationMethod()) { std::string myMethod = simParams_->getElectrostaticSummationMethod(); toUpper(myMethod); @@ -865,7 +861,6 @@ namespace oopse { MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); #endif - fInfo_.SIM_uses_PBC = usePBC; fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom; fInfo_.SIM_uses_LennardJones = useLennardJones; @@ -969,7 +964,7 @@ namespace oopse { sprintf( painCave.errMsg, "There was an error setting the simulation information in fortran.\n" ); painCave.isFatal = 1; - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; simError(); } @@ -1105,7 +1100,7 @@ namespace oopse { rsw_ = 0.85 * rcut_; sprintf(painCave.errMsg, "SimCreator Warning: No value was set for the switchingRadius.\n" - "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n" + "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" "\tswitchingRadius = %f. for this simulation\n", rsw_); painCave.isFatal = 0; simError(); @@ -1113,7 +1108,7 @@ namespace oopse { rsw_ = rcut_; sprintf(painCave.errMsg, "SimCreator Warning: No value was set for the switchingRadius.\n" - "\tOOPSE will use the same value as the cutoffRadius.\n" + "\tOpenMD will use the same value as the cutoffRadius.\n" "\tswitchingRadius = %f. for this simulation\n", rsw_); painCave.isFatal = 0; simError(); @@ -1139,7 +1134,7 @@ namespace oopse { if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { sprintf(painCave.errMsg, "SimCreator Warning: No value was set for the cutoffRadius.\n" - "\tOOPSE will use a default value of 15.0 angstroms" + "\tOpenMD will use a default value of 15.0 angstroms" "\tfor the cutoffRadius.\n"); painCave.isFatal = 0; simError(); @@ -1148,9 +1143,9 @@ namespace oopse { if (simParams_->haveElectrostaticSummationMethod()) { std::string myMethod = simParams_->getElectrostaticSummationMethod(); toUpper(myMethod); - - // For the time being, we're tethering the LJ shifted behavior to the - // electrostaticSummationMethod keyword options + + // For the time being, we're tethering the LJ shifted behavior to the + // electrostaticSummationMethod keyword options if (myMethod == "SHIFTED_POTENTIAL") { ljsp_ = 1; } else if (myMethod == "SHIFTED_FORCE") { @@ -1173,13 +1168,14 @@ namespace oopse { } else { sprintf(painCave.errMsg, "SimCreator Warning: No value was set for switchingRadius.\n" - "\tOOPSE will use a default value of\n" + "\tOpenMD will use a default value of\n" "\t0.85 * cutoffRadius for the switchingRadius\n"); painCave.isFatal = 0; simError(); rsw_ = 0.85 * rcut_; } + Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_); notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_); } else { @@ -1195,8 +1191,8 @@ namespace oopse { void SimInfo::setupElectrostaticSummationMethod( int isError ) { int errorOut; - int esm = NONE; - int sm = UNDAMPED; + ElectrostaticSummationMethod esm = NONE; + ElectrostaticScreeningMethod sm = UNDAMPED; RealType alphaVal; RealType dielectric; @@ -1283,12 +1279,11 @@ namespace oopse { } } - // let's pass some summation method variables to fortran - setElectrostaticSummationMethod( &esm ); - setFortranElectrostaticMethod( &esm ); - setScreeningMethod( &sm ); - setDampingAlpha( &alphaVal ); - setReactionFieldDielectric( &dielectric ); + + Electrostatic::setElectrostaticSummationMethod( esm ); + Electrostatic::setElectrostaticScreeningMethod( sm ); + Electrostatic::setDampingAlpha( alphaVal ); + Electrostatic::setReactionFieldDielectric( dielectric ); initFortranFF( &errorOut ); } @@ -1475,7 +1470,7 @@ namespace oopse { [ Ixx -Ixy -Ixz ] - J =| -Iyx Iyy -Iyz | + J =| -Iyx Iyy -Iyz | [ -Izx -Iyz Izz ] */ @@ -1634,5 +1629,5 @@ namespace oopse { return sdByGlobalIndex_.at(index); } */ -}//end namespace oopse +}//end namespace OpenMD