--- trunk/src/brains/SimInfo.cpp 2005/11/21 22:59:13 763 +++ trunk/src/brains/SimInfo.cpp 2005/11/21 22:59:21 764 @@ -59,7 +59,6 @@ #include "UseTheForce/DarkSide/fSwitchingFunctionType.h" #include "UseTheForce/doForces_interface.h" #include "UseTheForce/DarkSide/electrostatic_interface.h" -#include "UseTheForce/notifyCutoffs_interface.h" #include "UseTheForce/DarkSide/switcheroo_interface.h" #include "utils/MemoryUtils.hpp" #include "utils/simError.h" @@ -922,84 +921,10 @@ namespace oopse { } #endif - - double SimInfo::calcMaxCutoffRadius() { - - - std::set atomTypes; - std::set::iterator i; - std::vector cutoffRadius; - - //get the unique atom types - atomTypes = getUniqueAtomTypes(); - //query the max cutoff radius among these atom types - for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { - cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); - } - - double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); -#ifdef IS_MPI - //pick the max cutoff radius among the processors -#endif - - return maxCutoffRadius; - } - - void SimInfo::getCutoff(double& rcut, double& rsw) { + void SimInfo::setupCutoff() { - if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { - - if (!simParams_->haveCutoffRadius()){ - sprintf(painCave.errMsg, - "SimCreator Warning: No value was set for the cutoffRadius.\n" - "\tOOPSE will use a default value of 15.0 angstroms" - "\tfor the cutoffRadius.\n"); - painCave.isFatal = 0; - simError(); - rcut = 15.0; - } else{ - rcut = simParams_->getCutoffRadius(); - } - - if (!simParams_->haveSwitchingRadius()){ - sprintf(painCave.errMsg, - "SimCreator Warning: No value was set for switchingRadius.\n" - "\tOOPSE will use a default value of\n" - "\t0.85 * cutoffRadius for the switchingRadius\n"); - painCave.isFatal = 0; - simError(); - rsw = 0.85 * rcut; - } else{ - rsw = simParams_->getSwitchingRadius(); - } - - } else { - // if charge, dipole or reaction field is not used and the cutofff radius is not specified in - //meta-data file, the maximum cutoff radius calculated from forcefiled will be used - - if (simParams_->haveCutoffRadius()) { - rcut = simParams_->getCutoffRadius(); - } else { - //set cutoff radius to the maximum cutoff radius based on atom types in the whole system - rcut = calcMaxCutoffRadius(); - } - - if (simParams_->haveSwitchingRadius()) { - rsw = simParams_->getSwitchingRadius(); - } else { - rsw = rcut; - } - - } - } - - void SimInfo::setupCutoff() { - getCutoff(rcut_, rsw_); - double rnblist = rcut_ + 1; // skin of neighbor list - - //Pass these cutoff radius etc. to fortran. This function should be called once and only once - + // Check the cutoff policy int cp = TRADITIONAL_CUTOFF_POLICY; if (simParams_->haveCutoffPolicy()) { std::string myPolicy = simParams_->getCutoffPolicy(); @@ -1021,16 +946,73 @@ namespace oopse { } } } - } + } + notifyFortranCutoffPolicy(&cp); - + // Check the Skin Thickness for neighborlists + double skin; if (simParams_->haveSkinThickness()) { - double skinThickness = simParams_->getSkinThickness(); - } + skin = simParams_->getSkinThickness(); + notifyFortranSkinThickness(&skin); + } + + // Check if the cutoff was set explicitly: + if (simParams_->haveCutoffRadius()) { + rcut_ = simParams_->getCutoffRadius(); + if (simParams_->haveSwitchingRadius()) { + rsw_ = simParams_->getSwitchingRadius(); + } else { + rsw_ = rcut_; + } + notifyFortranCutoffs(&rcut_, &rsw_); + + } else { + + // For electrostatic atoms, we'll assume a large safe value: + 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" + "\tfor the cutoffRadius.\n"); + painCave.isFatal = 0; + simError(); + rcut_ = 15.0; + + if (simParams_->haveElectrostaticSummationMethod()) { + std::string myMethod = simParams_->getElectrostaticSummationMethod(); + toUpper(myMethod); + if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { + if (simParams_->haveSwitchingRadius()){ + sprintf(painCave.errMsg, + "SimInfo Warning: A value was set for the switchingRadius\n" + "\teven though the electrostaticSummationMethod was\n" + "\tset to %s\n", myMethod.c_str()); + painCave.isFatal = 1; + simError(); + } + } + } + + if (simParams_->haveSwitchingRadius()){ + rsw_ = simParams_->getSwitchingRadius(); + } else { + sprintf(painCave.errMsg, + "SimCreator Warning: No value was set for switchingRadius.\n" + "\tOOPSE will use a default value of\n" + "\t0.85 * cutoffRadius for the switchingRadius\n"); + painCave.isFatal = 0; + simError(); + rsw_ = 0.85 * rcut_; + } + notifyFortranCutoffs(&rcut_, &rsw_); + } else { + // We didn't set rcut explicitly, and we don't have electrostatic atoms, so + // We'll punt and let fortran figure out the cutoffs later. + + notifyFortranYouAreOnYourOwn(); - notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); - // also send cutoff notification to electrostatics - setElectrostaticCutoffRadius(&rcut_, &rsw_); + } + } } void SimInfo::setupElectrostaticSummationMethod( int isError ) { @@ -1065,7 +1047,11 @@ namespace oopse { } else { // throw error sprintf( painCave.errMsg, - "SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() ); + "SimInfo error: Unknown electrostaticSummationMethod.\n" + "\t(Input file specified %s .)\n" + "\telectrostaticSummationMethod must be one of: \"none\",\n" + "\t\"shifted_potential\", \"shifted_force\", or \n" + "\t\"reaction_field\".\n", myMethod.c_str() ); painCave.isFatal = 1; simError(); } @@ -1086,14 +1072,18 @@ namespace oopse { if (!simParams_->haveDampingAlpha()) { //throw error sprintf( painCave.errMsg, - "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal); + "SimInfo warning: dampingAlpha was not specified in the input file.\n" + "\tA default value of %f (1/ang) will be used.\n", alphaVal); painCave.isFatal = 0; simError(); } } else { // throw error sprintf( painCave.errMsg, - "SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() ); + "SimInfo error: Unknown electrostaticScreeningMethod.\n" + "\t(Input file specified %s .)\n" + "\telectrostaticScreeningMethod must be one of: \"undamped\"\n" + "or \"damped\".\n", myScreen.c_str() ); painCave.isFatal = 1; simError(); } @@ -1102,10 +1092,11 @@ namespace oopse { // let's pass some summation method variables to fortran setElectrostaticSummationMethod( &esm ); + notifyFortranElectrostaticMethod( &esm ); setScreeningMethod( &sm ); setDampingAlpha( &alphaVal ); setReactionFieldDielectric( &dielectric ); - initFortranFF( &esm, &errorOut ); + initFortranFF( &errorOut ); } void SimInfo::setupSwitchingFunction() {