| 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" |
| 80 |
|
return result; |
| 81 |
|
} |
| 82 |
|
|
| 83 |
< |
SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
| 84 |
< |
ForceField* ff, Globals* simParams) : |
| 86 |
< |
stamps_(stamps), forceField_(ff), simParams_(simParams), |
| 83 |
> |
SimInfo::SimInfo(ForceField* ff, Globals* simParams) : |
| 84 |
> |
forceField_(ff), simParams_(simParams), |
| 85 |
|
ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
| 86 |
|
nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
| 87 |
|
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
| 89 |
|
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
| 90 |
|
sman_(NULL), fortranInitialized_(false) { |
| 91 |
|
|
| 94 |
– |
|
| 95 |
– |
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
| 92 |
|
MoleculeStamp* molStamp; |
| 93 |
|
int nMolWithSameStamp; |
| 94 |
|
int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
| 96 |
|
CutoffGroupStamp* cgStamp; |
| 97 |
|
RigidBodyStamp* rbStamp; |
| 98 |
|
int nRigidAtoms = 0; |
| 99 |
< |
|
| 100 |
< |
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
| 101 |
< |
molStamp = i->first; |
| 102 |
< |
nMolWithSameStamp = i->second; |
| 99 |
> |
std::vector<Component*> components = simParams->getComponents(); |
| 100 |
> |
|
| 101 |
> |
for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) { |
| 102 |
> |
molStamp = (*i)->getMoleculeStamp(); |
| 103 |
> |
nMolWithSameStamp = (*i)->getNMol(); |
| 104 |
|
|
| 105 |
|
addMoleculeStamp(molStamp, nMolWithSameStamp); |
| 106 |
|
|
| 107 |
|
//calculate atoms in molecules |
| 108 |
|
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
| 109 |
|
|
| 113 |
– |
|
| 110 |
|
//calculate atoms in cutoff groups |
| 111 |
|
int nAtomsInGroups = 0; |
| 112 |
|
int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
| 113 |
|
|
| 114 |
|
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
| 115 |
< |
cgStamp = molStamp->getCutoffGroup(j); |
| 115 |
> |
cgStamp = molStamp->getCutoffGroupStamp(j); |
| 116 |
|
nAtomsInGroups += cgStamp->getNMembers(); |
| 117 |
|
} |
| 118 |
|
|
| 125 |
|
int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
| 126 |
|
|
| 127 |
|
for (int j=0; j < nRigidBodiesInStamp; j++) { |
| 128 |
< |
rbStamp = molStamp->getRigidBody(j); |
| 128 |
> |
rbStamp = molStamp->getRigidBodyStamp(j); |
| 129 |
|
nAtomsInRigidBodies += rbStamp->getNMembers(); |
| 130 |
|
} |
| 131 |
|
|
| 164 |
|
} |
| 165 |
|
molecules_.clear(); |
| 166 |
|
|
| 171 |
– |
delete stamps_; |
| 167 |
|
delete sman_; |
| 168 |
|
delete simParams_; |
| 169 |
|
delete forceField_; |
| 270 |
|
} |
| 271 |
|
} |
| 272 |
|
|
| 273 |
< |
}//end for (integrableObject) |
| 274 |
< |
}// end for (mol) |
| 273 |
> |
} |
| 274 |
> |
} |
| 275 |
|
|
| 276 |
|
// n_constraints is local, so subtract them on each processor |
| 277 |
|
ndf_local -= nConstraints_; |
| 915 |
|
|
| 916 |
|
|
| 917 |
|
} |
| 923 |
– |
|
| 924 |
– |
#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(); |
| 918 |
|
|
| 936 |
– |
//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 |
| 919 |
|
#endif |
| 920 |
|
|
| 921 |
< |
return maxCutoffRadius; |
| 947 |
< |
} |
| 948 |
< |
|
| 949 |
< |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
| 921 |
> |
void SimInfo::setupCutoff() { |
| 922 |
|
|
| 923 |
< |
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 |
< |
|
| 923 |
> |
// Check the cutoff policy |
| 924 |
|
int cp = TRADITIONAL_CUTOFF_POLICY; |
| 925 |
|
if (simParams_->haveCutoffPolicy()) { |
| 926 |
|
std::string myPolicy = simParams_->getCutoffPolicy(); |
| 942 |
|
} |
| 943 |
|
} |
| 944 |
|
} |
| 945 |
< |
} |
| 945 |
> |
} |
| 946 |
> |
notifyFortranCutoffPolicy(&cp); |
| 947 |
|
|
| 948 |
< |
|
| 948 |
> |
// Check the Skin Thickness for neighborlists |
| 949 |
> |
double skin; |
| 950 |
|
if (simParams_->haveSkinThickness()) { |
| 951 |
< |
double skinThickness = simParams_->getSkinThickness(); |
| 952 |
< |
} |
| 951 |
> |
skin = simParams_->getSkinThickness(); |
| 952 |
> |
notifyFortranSkinThickness(&skin); |
| 953 |
> |
} |
| 954 |
> |
|
| 955 |
> |
// Check if the cutoff was set explicitly: |
| 956 |
> |
if (simParams_->haveCutoffRadius()) { |
| 957 |
> |
rcut_ = simParams_->getCutoffRadius(); |
| 958 |
> |
if (simParams_->haveSwitchingRadius()) { |
| 959 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
| 960 |
> |
} else { |
| 961 |
> |
rsw_ = rcut_; |
| 962 |
> |
} |
| 963 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
| 964 |
> |
|
| 965 |
> |
} else { |
| 966 |
> |
|
| 967 |
> |
// For electrostatic atoms, we'll assume a large safe value: |
| 968 |
> |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
| 969 |
> |
sprintf(painCave.errMsg, |
| 970 |
> |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
| 971 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
| 972 |
> |
"\tfor the cutoffRadius.\n"); |
| 973 |
> |
painCave.isFatal = 0; |
| 974 |
> |
simError(); |
| 975 |
> |
rcut_ = 15.0; |
| 976 |
> |
|
| 977 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
| 978 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 979 |
> |
toUpper(myMethod); |
| 980 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
| 981 |
> |
if (simParams_->haveSwitchingRadius()){ |
| 982 |
> |
sprintf(painCave.errMsg, |
| 983 |
> |
"SimInfo Warning: A value was set for the switchingRadius\n" |
| 984 |
> |
"\teven though the electrostaticSummationMethod was\n" |
| 985 |
> |
"\tset to %s\n", myMethod.c_str()); |
| 986 |
> |
painCave.isFatal = 1; |
| 987 |
> |
simError(); |
| 988 |
> |
} |
| 989 |
> |
} |
| 990 |
> |
} |
| 991 |
> |
|
| 992 |
> |
if (simParams_->haveSwitchingRadius()){ |
| 993 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
| 994 |
> |
} else { |
| 995 |
> |
sprintf(painCave.errMsg, |
| 996 |
> |
"SimCreator Warning: No value was set for switchingRadius.\n" |
| 997 |
> |
"\tOOPSE will use a default value of\n" |
| 998 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
| 999 |
> |
painCave.isFatal = 0; |
| 1000 |
> |
simError(); |
| 1001 |
> |
rsw_ = 0.85 * rcut_; |
| 1002 |
> |
} |
| 1003 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
| 1004 |
> |
} else { |
| 1005 |
> |
// We didn't set rcut explicitly, and we don't have electrostatic atoms, so |
| 1006 |
> |
// We'll punt and let fortran figure out the cutoffs later. |
| 1007 |
> |
|
| 1008 |
> |
notifyFortranYouAreOnYourOwn(); |
| 1009 |
|
|
| 1010 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
| 1011 |
< |
// also send cutoff notification to electrostatics |
| 1033 |
< |
setElectrostaticCutoffRadius(&rcut_, &rsw_); |
| 1010 |
> |
} |
| 1011 |
> |
} |
| 1012 |
|
} |
| 1013 |
|
|
| 1014 |
|
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
| 1043 |
|
} else { |
| 1044 |
|
// throw error |
| 1045 |
|
sprintf( painCave.errMsg, |
| 1046 |
< |
"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() ); |
| 1046 |
> |
"SimInfo error: Unknown electrostaticSummationMethod.\n" |
| 1047 |
> |
"\t(Input file specified %s .)\n" |
| 1048 |
> |
"\telectrostaticSummationMethod must be one of: \"none\",\n" |
| 1049 |
> |
"\t\"shifted_potential\", \"shifted_force\", or \n" |
| 1050 |
> |
"\t\"reaction_field\".\n", myMethod.c_str() ); |
| 1051 |
|
painCave.isFatal = 1; |
| 1052 |
|
simError(); |
| 1053 |
|
} |
| 1068 |
|
if (!simParams_->haveDampingAlpha()) { |
| 1069 |
|
//throw error |
| 1070 |
|
sprintf( painCave.errMsg, |
| 1071 |
< |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal); |
| 1071 |
> |
"SimInfo warning: dampingAlpha was not specified in the input file.\n" |
| 1072 |
> |
"\tA default value of %f (1/ang) will be used.\n", alphaVal); |
| 1073 |
|
painCave.isFatal = 0; |
| 1074 |
|
simError(); |
| 1075 |
|
} |
| 1076 |
|
} else { |
| 1077 |
|
// throw error |
| 1078 |
|
sprintf( painCave.errMsg, |
| 1079 |
< |
"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() ); |
| 1079 |
> |
"SimInfo error: Unknown electrostaticScreeningMethod.\n" |
| 1080 |
> |
"\t(Input file specified %s .)\n" |
| 1081 |
> |
"\telectrostaticScreeningMethod must be one of: \"undamped\"\n" |
| 1082 |
> |
"or \"damped\".\n", myScreen.c_str() ); |
| 1083 |
|
painCave.isFatal = 1; |
| 1084 |
|
simError(); |
| 1085 |
|
} |
| 1087 |
|
} |
| 1088 |
|
|
| 1089 |
|
// let's pass some summation method variables to fortran |
| 1090 |
< |
setElectrostaticSummationMethod( &esm ); |
| 1090 |
> |
setElectrostaticSumMethod( &esm ); |
| 1091 |
> |
setFortranElectrostaticMethod( &esm ); |
| 1092 |
|
setScreeningMethod( &sm ); |
| 1093 |
|
setDampingAlpha( &alphaVal ); |
| 1094 |
|
setReactionFieldDielectric( &dielectric ); |
| 1095 |
< |
initFortranFF( &esm, &errorOut ); |
| 1095 |
> |
initFortranFF( &errorOut ); |
| 1096 |
|
} |
| 1097 |
|
|
| 1098 |
|
void SimInfo::setupSwitchingFunction() { |
