59 |
|
#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
60 |
|
#include "UseTheForce/doForces_interface.h" |
61 |
|
#include "UseTheForce/DarkSide/electrostatic_interface.h" |
62 |
– |
#include "UseTheForce/notifyCutoffs_interface.h" |
62 |
|
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
63 |
|
#include "utils/MemoryUtils.hpp" |
64 |
|
#include "utils/simError.h" |
921 |
|
} |
922 |
|
|
923 |
|
#endif |
925 |
– |
|
926 |
– |
double SimInfo::calcMaxCutoffRadius() { |
927 |
– |
|
928 |
– |
|
929 |
– |
std::set<AtomType*> atomTypes; |
930 |
– |
std::set<AtomType*>::iterator i; |
931 |
– |
std::vector<double> cutoffRadius; |
932 |
– |
|
933 |
– |
//get the unique atom types |
934 |
– |
atomTypes = getUniqueAtomTypes(); |
924 |
|
|
925 |
< |
//query the max cutoff radius among these atom types |
937 |
< |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
938 |
< |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
939 |
< |
} |
940 |
< |
|
941 |
< |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
942 |
< |
#ifdef IS_MPI |
943 |
< |
//pick the max cutoff radius among the processors |
944 |
< |
#endif |
945 |
< |
|
946 |
< |
return maxCutoffRadius; |
947 |
< |
} |
948 |
< |
|
949 |
< |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
925 |
> |
void SimInfo::setupCutoff() { |
926 |
|
|
927 |
< |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
952 |
< |
|
953 |
< |
if (!simParams_->haveCutoffRadius()){ |
954 |
< |
sprintf(painCave.errMsg, |
955 |
< |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
956 |
< |
"\tOOPSE will use a default value of 15.0 angstroms" |
957 |
< |
"\tfor the cutoffRadius.\n"); |
958 |
< |
painCave.isFatal = 0; |
959 |
< |
simError(); |
960 |
< |
rcut = 15.0; |
961 |
< |
} else{ |
962 |
< |
rcut = simParams_->getCutoffRadius(); |
963 |
< |
} |
964 |
< |
|
965 |
< |
if (!simParams_->haveSwitchingRadius()){ |
966 |
< |
sprintf(painCave.errMsg, |
967 |
< |
"SimCreator Warning: No value was set for switchingRadius.\n" |
968 |
< |
"\tOOPSE will use a default value of\n" |
969 |
< |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
970 |
< |
painCave.isFatal = 0; |
971 |
< |
simError(); |
972 |
< |
rsw = 0.85 * rcut; |
973 |
< |
} else{ |
974 |
< |
rsw = simParams_->getSwitchingRadius(); |
975 |
< |
} |
976 |
< |
|
977 |
< |
} else { |
978 |
< |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
979 |
< |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
980 |
< |
|
981 |
< |
if (simParams_->haveCutoffRadius()) { |
982 |
< |
rcut = simParams_->getCutoffRadius(); |
983 |
< |
} else { |
984 |
< |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
985 |
< |
rcut = calcMaxCutoffRadius(); |
986 |
< |
} |
987 |
< |
|
988 |
< |
if (simParams_->haveSwitchingRadius()) { |
989 |
< |
rsw = simParams_->getSwitchingRadius(); |
990 |
< |
} else { |
991 |
< |
rsw = rcut; |
992 |
< |
} |
993 |
< |
|
994 |
< |
} |
995 |
< |
} |
996 |
< |
|
997 |
< |
void SimInfo::setupCutoff() { |
998 |
< |
getCutoff(rcut_, rsw_); |
999 |
< |
double rnblist = rcut_ + 1; // skin of neighbor list |
1000 |
< |
|
1001 |
< |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
1002 |
< |
|
927 |
> |
// Check the cutoff policy |
928 |
|
int cp = TRADITIONAL_CUTOFF_POLICY; |
929 |
|
if (simParams_->haveCutoffPolicy()) { |
930 |
|
std::string myPolicy = simParams_->getCutoffPolicy(); |
946 |
|
} |
947 |
|
} |
948 |
|
} |
949 |
< |
} |
949 |
> |
} |
950 |
> |
notifyFortranCutoffPolicy(&cp); |
951 |
|
|
952 |
< |
|
952 |
> |
// Check the Skin Thickness for neighborlists |
953 |
> |
double skin; |
954 |
|
if (simParams_->haveSkinThickness()) { |
955 |
< |
double skinThickness = simParams_->getSkinThickness(); |
956 |
< |
} |
955 |
> |
skin = simParams_->getSkinThickness(); |
956 |
> |
notifyFortranSkinThickness(&skin); |
957 |
> |
} |
958 |
> |
|
959 |
> |
// Check if the cutoff was set explicitly: |
960 |
> |
if (simParams_->haveCutoffRadius()) { |
961 |
> |
rcut_ = simParams_->getCutoffRadius(); |
962 |
> |
if (simParams_->haveSwitchingRadius()) { |
963 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
964 |
> |
} else { |
965 |
> |
rsw_ = rcut_; |
966 |
> |
} |
967 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
968 |
> |
|
969 |
> |
} else { |
970 |
> |
|
971 |
> |
// For electrostatic atoms, we'll assume a large safe value: |
972 |
> |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
973 |
> |
sprintf(painCave.errMsg, |
974 |
> |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
975 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
976 |
> |
"\tfor the cutoffRadius.\n"); |
977 |
> |
painCave.isFatal = 0; |
978 |
> |
simError(); |
979 |
> |
rcut_ = 15.0; |
980 |
> |
|
981 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
982 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
983 |
> |
toUpper(myMethod); |
984 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
985 |
> |
if (simParams_->haveSwitchingRadius()){ |
986 |
> |
sprintf(painCave.errMsg, |
987 |
> |
"SimInfo Warning: A value was set for the switchingRadius\n" |
988 |
> |
"\teven though the electrostaticSummationMethod was\n" |
989 |
> |
"\tset to %s\n", myMethod.c_str()); |
990 |
> |
painCave.isFatal = 1; |
991 |
> |
simError(); |
992 |
> |
} |
993 |
> |
} |
994 |
> |
} |
995 |
> |
|
996 |
> |
if (simParams_->haveSwitchingRadius()){ |
997 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
998 |
> |
} else { |
999 |
> |
sprintf(painCave.errMsg, |
1000 |
> |
"SimCreator Warning: No value was set for switchingRadius.\n" |
1001 |
> |
"\tOOPSE will use a default value of\n" |
1002 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
1003 |
> |
painCave.isFatal = 0; |
1004 |
> |
simError(); |
1005 |
> |
rsw_ = 0.85 * rcut_; |
1006 |
> |
} |
1007 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
1008 |
> |
} else { |
1009 |
> |
// We didn't set rcut explicitly, and we don't have electrostatic atoms, so |
1010 |
> |
// We'll punt and let fortran figure out the cutoffs later. |
1011 |
> |
|
1012 |
> |
notifyFortranYouAreOnYourOwn(); |
1013 |
|
|
1014 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
1015 |
< |
// also send cutoff notification to electrostatics |
1033 |
< |
setElectrostaticCutoffRadius(&rcut_, &rsw_); |
1014 |
> |
} |
1015 |
> |
} |
1016 |
|
} |
1017 |
|
|
1018 |
|
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
1047 |
|
} else { |
1048 |
|
// throw error |
1049 |
|
sprintf( painCave.errMsg, |
1050 |
< |
"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() ); |
1050 |
> |
"SimInfo error: Unknown electrostaticSummationMethod.\n" |
1051 |
> |
"\t(Input file specified %s .)\n" |
1052 |
> |
"\telectrostaticSummationMethod must be one of: \"none\",\n" |
1053 |
> |
"\t\"shifted_potential\", \"shifted_force\", or \n" |
1054 |
> |
"\t\"reaction_field\".\n", myMethod.c_str() ); |
1055 |
|
painCave.isFatal = 1; |
1056 |
|
simError(); |
1057 |
|
} |
1072 |
|
if (!simParams_->haveDampingAlpha()) { |
1073 |
|
//throw error |
1074 |
|
sprintf( painCave.errMsg, |
1075 |
< |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal); |
1075 |
> |
"SimInfo warning: dampingAlpha was not specified in the input file.\n" |
1076 |
> |
"\tA default value of %f (1/ang) will be used.\n", alphaVal); |
1077 |
|
painCave.isFatal = 0; |
1078 |
|
simError(); |
1079 |
|
} |
1080 |
|
} else { |
1081 |
|
// throw error |
1082 |
|
sprintf( painCave.errMsg, |
1083 |
< |
"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() ); |
1083 |
> |
"SimInfo error: Unknown electrostaticScreeningMethod.\n" |
1084 |
> |
"\t(Input file specified %s .)\n" |
1085 |
> |
"\telectrostaticScreeningMethod must be one of: \"undamped\"\n" |
1086 |
> |
"or \"damped\".\n", myScreen.c_str() ); |
1087 |
|
painCave.isFatal = 1; |
1088 |
|
simError(); |
1089 |
|
} |
1092 |
|
|
1093 |
|
// let's pass some summation method variables to fortran |
1094 |
|
setElectrostaticSummationMethod( &esm ); |
1095 |
+ |
notifyFortranElectrostaticMethod( &esm ); |
1096 |
|
setScreeningMethod( &sm ); |
1097 |
|
setDampingAlpha( &alphaVal ); |
1098 |
|
setReactionFieldDielectric( &dielectric ); |
1099 |
< |
initFortranFF( &esm, &errorOut ); |
1099 |
> |
initFortranFF( &errorOut ); |
1100 |
|
} |
1101 |
|
|
1102 |
|
void SimInfo::setupSwitchingFunction() { |