NAMD
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#include <Molecule.h>
Friends | |
class | ExclElem |
class | BondElem |
class | AngleElem |
class | DihedralElem |
class | ImproperElem |
class | TholeElem |
class | AnisoElem |
class | CrosstermElem |
class | GromacsPairElem |
class | WorkDistrib |
Definition at line 151 of file Molecule.h.
Molecule::Molecule | ( | SimParameters * | simParams, |
Parameters * | param | ||
) |
Definition at line 429 of file Molecule.C.
Molecule::Molecule | ( | SimParameters * | simParams, |
Parameters * | param, | ||
char * | filename, | ||
ConfigList * | cfgList = NULL |
||
) |
Definition at line 442 of file Molecule.C.
References SimParameters::LCPOOn, and SimParameters::useCompressedPsf.
Molecule::Molecule | ( | SimParameters * | simParams, |
Parameters * | param, | ||
molfile_plugin_t * | pIOHdl, | ||
void * | pIOFileHdl, | ||
int | natoms | ||
) |
Definition at line 464 of file Molecule.C.
References SimParameters::LCPOOn, and NAMD_die().
Molecule::Molecule | ( | SimParameters * | , |
Parameters * | , | ||
Ambertoppar * | |||
) |
Molecule::Molecule | ( | SimParameters * | , |
Parameters * | , | ||
AmberParm7Reader::Ambertoppar * | |||
) |
Molecule::Molecule | ( | SimParameters * | , |
Parameters * | , | ||
const GromacsTopFile * | |||
) |
Molecule::~Molecule | ( | ) |
Definition at line 558 of file Molecule.C.
References atoms, atomSigPool, exclusions, and exclusionsByAtom.
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Definition at line 1052 of file Molecule.h.
Referenced by WorkDistrib::createAtomLists(), NamdState::loadStructure(), Sequencer::reloadCharges(), Sequencer::rescaleSoluteCharges(), colvarproxy_namd::update_atom_properties(), and colvarproxy_namd::update_group_properties().
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Definition at line 1042 of file Molecule.h.
References atoms.
Referenced by WorkDistrib::createAtomLists(), GlobalMasterEasy::getMass(), GlobalMasterFreeEnergy::getMass(), NamdState::loadStructure(), Tcl_centerOfMass(), Tcl_radiusOfGyration(), colvarproxy_namd::update_atom_properties(), and colvarproxy_namd::update_group_properties().
Bool Molecule::atoms_1to4 | ( | unsigned int | atom1, |
unsigned int | atom2 | ||
) |
Definition at line 1537 of file GoMolecule.C.
References bond::atom1, angle::atom1, dihedral::atom1, bond::atom2, angle::atom2, dihedral::atom2, angle::atom3, dihedral::atom3, dihedral::atom4, DebugM, FALSE, get_angle(), get_angles_for_atom(), get_bond(), get_bonds_for_atom(), get_dihedral(), get_dihedrals_for_atom(), and TRUE.
Referenced by build_go_arrays(), build_go_sigmas(), and build_go_sigmas2().
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Definition at line 1062 of file Molecule.h.
References atoms.
Referenced by WorkDistrib::createAtomLists(), and dumpbench().
void Molecule::build_alch_unpert_bond_lists | ( | char * | ) |
Referenced by NamdState::loadStructure().
void Molecule::build_constant_forces | ( | char * | ) |
Referenced by NamdState::loadStructure().
void Molecule::build_constorque_params | ( | StringList * | , |
StringList * | , | ||
StringList * | , | ||
StringList * | , | ||
StringList * | , | ||
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_constraint_params | ( | StringList * | , |
StringList * | , | ||
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_exPressure_atoms | ( | StringList * | , |
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_extra_bonds | ( | Parameters * | parameters, |
StringList * | file | ||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_fep_flags | ( | StringList * | , |
StringList * | , | ||
PDB * | , | ||
char * | , | ||
const char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_fixed_atoms | ( | StringList * | , |
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_go_arrays | ( | StringList * | goCoordFile, |
char * | cwd | ||
) |
goSigmas = new Real[numGoAtoms*numGoAtoms]; goWithinCutoff = new bool[numGoAtoms*numGoAtoms]; for (i=0; i<numGoAtoms; i++) { for (j=0; j<numGoAtoms; j++) { goSigmas[i*numGoAtoms + j] = 0.0; goWithinCutoff[i*numGoAtoms + j] = false; } }
Definition at line 950 of file GoMolecule.C.
References PDB::atom(), atomChainTypes, atoms_1to4(), StringList::data, DebugM, endi(), energyNative, energyNonnative, get_go_cutoff(), go_restricted(), goCoordinates, goPDB, goResids, goSigmaIndices, iINFO(), iout, NAMD_die(), NAMD_FILENAME_BUFFER_SIZE, StringList::next, PDB::num_atoms(), numAtoms, numGoAtoms, PDBAtom::residueseq(), PDBAtom::xcoor(), PDBAtom::ycoor(), and PDBAtom::zcoor().
Referenced by NamdState::loadStructure().
void Molecule::build_go_params | ( | StringList * | g | ) |
Definition at line 79 of file GoMolecule.C.
References StringList::data, endi(), iINFO(), iout, NAMD_die(), StringList::next, and read_go_file().
Referenced by NamdState::loadStructure().
void Molecule::build_go_sigmas | ( | StringList * | goCoordFile, |
char * | cwd | ||
) |
Definition at line 577 of file GoMolecule.C.
References PDB::atom(), atomChainTypes, atoms_1to4(), StringList::data, DebugM, endi(), get_go_cutoff(), get_go_exp_a(), get_go_exp_b(), go_restricted(), goPDB, goSigmaIndices, goSigmas, goWithinCutoff, iINFO(), iout, NAMD_die(), NAMD_FILENAME_BUFFER_SIZE, StringList::next, PDB::num_atoms(), numAtoms, and numGoAtoms.
Referenced by NamdState::loadStructure().
void Molecule::build_go_sigmas2 | ( | StringList * | goCoordFile, |
char * | cwd | ||
) |
Definition at line 747 of file GoMolecule.C.
References go_pair::A, ResizeArray< T >::add(), PDB::atom(), atomChainTypes, atoms_1to4(), go_pair::B, ResizeArray< T >::begin(), StringList::data, DebugM, ResizeArray< T >::end(), endi(), get_go_cutoff(), get_go_exp_a(), get_go_exp_b(), go_restricted(), go_pair::goIndxA, go_pair::goIndxB, goIndxLJA, goIndxLJB, goNumLJPair, goPDB, goResidIndices, goSigmaIndices, goSigmaPairA, goSigmaPairB, iINFO(), iout, NAMD_die(), NAMD_FILENAME_BUFFER_SIZE, StringList::next, PDB::num_atoms(), numAtoms, numGoAtoms, numLJPair, pointerToGoBeg, pointerToGoEnd, and sort.
Referenced by NamdState::loadStructure().
void Molecule::build_gridforce_params | ( | StringList * | gridfrcfile, |
StringList * | gridfrccol, | ||
StringList * | gridfrcchrgcol, | ||
StringList * | potfile, | ||
PDB * | initial_pdb, | ||
char * | cwd | ||
) |
Definition at line 6373 of file Molecule.C.
References PDB::atom(), DebugM, endi(), MGridforceParamsList::get_first(), MGridforceParams::gridforceCol, MGridforceParams::gridforceFile, MGridforceParams::gridforceQcol, MGridforceParams::gridforceVfile, iout, iWARN(), SimParameters::mgridforcelist, NAMD_die(), NAMD_FILENAME_BUFFER_SIZE, GridforceGrid::new_grid(), MGridforceParams::next, and PDB::num_atoms().
Referenced by NamdState::loadStructure().
void Molecule::build_gro_pair | ( | ) |
Referenced by NamdState::loadStructure().
void Molecule::build_langevin_params | ( | StringList * | , |
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
void Molecule::build_movdrag_params | ( | StringList * | , |
StringList * | , | ||
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_rotdrag_params | ( | StringList * | , |
StringList * | , | ||
StringList * | , | ||
StringList * | , | ||
StringList * | , | ||
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_ss_flags | ( | const StringList * | ssfile, |
const StringList * | sscol, | ||
PDB * | initial_pdb, | ||
const char * | cwd | ||
) |
Build the flags needed for solute scaling.
A PDB file is read, indicating which atoms are to be scaled, and an array is maintained marking which are to be included. Each marked atom then has its corresponding van der Waals type number reassigned to enable extending the LJTable with scaled interaction values.
ssfile | config "soluteScalingFile = my.pdb" for PDB filename |
sscol | config "soluteScalingCol = O" for column of PDB ATOM records |
initial_pdb | the initial PDB file |
cwd | current working directory |
Referenced by NamdState::loadStructure().
void Molecule::build_stirred_atoms | ( | StringList * | , |
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
int Molecule::checkexcl | ( | int | atom1, |
int | atom2 | ||
) | const |
void Molecule::compute_LJcorrection | ( | ) |
Referenced by NamdState::loadStructure().
Referenced by NamdState::loadStructure().
Definition at line 1547 of file MoleculeQM.C.
References bond::atom1, angle::atom1, dihedral::atom1, improper::atom1, crossterm::atom1, DebugM, endi(), SimParameters::extraBondsOn, iERROR(), iINFO(), iout, NAMD_die(), numAngles, numBonds, numCrossterms, numDihedrals, numImpropers, and numRealBonds.
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Definition at line 1038 of file Molecule.h.
Referenced by NamdState::loadStructure().
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Definition at line 1034 of file Molecule.h.
Referenced by NamdState::loadStructure().
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Definition at line 1109 of file Molecule.h.
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Definition at line 1072 of file Molecule.h.
Referenced by atoms_1to4(), and dumpbench().
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Definition at line 1151 of file Molecule.h.
Referenced by atoms_1to4(), and dumpbench().
int Molecule::get_atom_from_index_in_residue | ( | const char * | segid, |
int | resid, | ||
int | index | ||
) | const |
Definition at line 158 of file Molecule.C.
References NAMD_die().
Referenced by GlobalMasterEasy::getAtomID(), and GlobalMasterFreeEnergy::getAtomID().
int Molecule::get_atom_from_name | ( | const char * | segid, |
int | resid, | ||
const char * | aname | ||
) | const |
Definition at line 121 of file Molecule.C.
References atomNamePool, and NAMD_die().
Referenced by colvarproxy_namd::check_atom_id(), GlobalMasterEasy::getAtomID(), and GlobalMasterFreeEnergy::getAtomID().
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Definition at line 1069 of file Molecule.h.
Referenced by atoms_1to4(), and dumpbench().
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Definition at line 1149 of file Molecule.h.
Referenced by atoms_1to4(), and dumpbench().
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Definition at line 1027 of file Molecule.h.
Referenced by wrap_coor_int().
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Definition at line 1028 of file Molecule.h.
Referenced by wrap_coor_int().
Definition at line 1266 of file Molecule.h.
Referenced by ComputeRestraints::doForce().
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Definition at line 1340 of file Molecule.h.
References consTorqueIndexes, and consTorqueParams.
Referenced by ComputeConsTorque::doForce().
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Definition at line 1081 of file Molecule.h.
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Definition at line 1157 of file Molecule.h.
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Definition at line 875 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 871 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 870 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 873 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 869 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 872 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 874 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 1078 of file Molecule.h.
Referenced by atoms_1to4(), and dumpbench().
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Definition at line 1153 of file Molecule.h.
Referenced by atoms_1to4(), and dumpbench().
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Definition at line 1106 of file Molecule.h.
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Definition at line 1177 of file Molecule.h.
Referenced by dumpbench().
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Definition at line 1116 of file Molecule.h.
References exclusions.
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Definition at line 1159 of file Molecule.h.
References exclusionsByAtom.
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Definition at line 1389 of file Molecule.h.
References NAMD_die(), order, and simParams.
Referenced by AngleElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), AnisoElem::computeForce(), and BondElem::computeForce().
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Definition at line 1349 of file Molecule.h.
Referenced by CrosstermElem::computeForce(), TholeElem::computeForce(), WorkDistrib::createAtomLists(), and ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
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Definition at line 1161 of file Molecule.h.
Referenced by ComputeNonbondedCUDA::build_exclusions().
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Definition at line 1605 of file Molecule.h.
References go_val::cutoff, go_array, and MAX_GO_CHAINS.
Referenced by build_go_arrays(), build_go_sigmas(), build_go_sigmas2(), get_go_force(), get_go_force2(), and get_go_force_new().
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Definition at line 1614 of file Molecule.h.
References go_val::epsilon, go_array, and MAX_GO_CHAINS.
Referenced by get_go_force(), get_go_force2(), and get_go_force_new().
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Definition at line 1608 of file Molecule.h.
References go_val::epsilonRep, go_array, and MAX_GO_CHAINS.
Referenced by get_go_force(), get_go_force2(), and get_go_force_new().
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Definition at line 1617 of file Molecule.h.
References go_val::exp_a, go_array, and MAX_GO_CHAINS.
Referenced by build_go_sigmas(), build_go_sigmas2(), get_go_force(), get_go_force2(), and get_go_force_new().
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Definition at line 1620 of file Molecule.h.
References go_val::exp_b, go_array, and MAX_GO_CHAINS.
Referenced by build_go_sigmas(), build_go_sigmas2(), get_go_force(), get_go_force2(), and get_go_force_new().
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Definition at line 1623 of file Molecule.h.
References go_val::exp_rep, go_array, and MAX_GO_CHAINS.
Referenced by get_go_force(), get_go_force2(), and get_go_force_new().
BigReal Molecule::get_go_force | ( | BigReal | r, |
int | atom1, | ||
int | atom2, | ||
BigReal * | goNative, | ||
BigReal * | goNonnative | ||
) | const |
Definition at line 1260 of file GoMolecule.C.
References atomChainTypes, get_go_cutoff(), get_go_epsilon(), get_go_epsilonRep(), get_go_exp_a(), get_go_exp_b(), get_go_exp_rep(), get_go_sigmaRep(), goForce, goSigmaIndices, goSigmas, goWithinCutoff, and numGoAtoms.
BigReal Molecule::get_go_force2 | ( | BigReal | x, |
BigReal | y, | ||
BigReal | z, | ||
int | atom1, | ||
int | atom2, | ||
BigReal * | goNative, | ||
BigReal * | goNonnative | ||
) | const |
Definition at line 1456 of file GoMolecule.C.
References atomChainTypes, get_go_cutoff(), get_go_epsilon(), get_go_epsilonRep(), get_go_exp_a(), get_go_exp_b(), get_go_exp_rep(), get_go_sigmaRep(), go_restricted(), goIndxLJB, goResidIndices, goSigmaPairA, goSigmaPairB, pointerToGoBeg, pointerToGoEnd, and z.
BigReal Molecule::get_go_force_new | ( | BigReal | r, |
int | atom1, | ||
int | atom2, | ||
BigReal * | goNative, | ||
BigReal * | goNonnative | ||
) | const |
Definition at line 1334 of file GoMolecule.C.
References atomChainTypes, DebugM, get_go_cutoff(), get_go_epsilon(), get_go_epsilonRep(), get_go_exp_a(), get_go_exp_b(), get_go_exp_rep(), get_go_sigmaRep(), go_restricted(), goCoordinates, goForce, goResids, and goSigmaIndices.
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Definition at line 1611 of file Molecule.h.
References go_array, MAX_GO_CHAINS, and go_val::sigmaRep.
Referenced by get_go_force(), get_go_force2(), and get_go_force_new().
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Definition at line 1280 of file Molecule.h.
References numGridforceGrids.
Referenced by ComputeGridForce::doForce(), colvarproxy_namd::init_volmap(), Node::reloadGridforceGrid(), and Node::updateGridScale().
Definition at line 1274 of file Molecule.h.
Referenced by ComputeGridForce::do_calc().
BigReal Molecule::get_gro_force2 | ( | BigReal | x, |
BigReal | y, | ||
BigReal | z, | ||
int | atom1, | ||
int | atom2, | ||
BigReal * | pairLJEnergy, | ||
BigReal * | pairGaussEnergy | ||
) | const |
Definition at line 1173 of file GoMolecule.C.
References A, gA, giSigma1, giSigma2, gMu1, gMu2, gRepulsive, indxGaussB, indxLJB, pairC12, pairC6, pointerToGaussBeg, pointerToGaussEnd, pointerToLJBeg, pointerToLJEnd, and z.
int Molecule::get_groupSize | ( | int | ) |
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Definition at line 1075 of file Molecule.h.
Referenced by dumpbench().
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Definition at line 1155 of file Molecule.h.
Referenced by dumpbench().
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Definition at line 1085 of file Molecule.h.
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Definition at line 1163 of file Molecule.h.
int Molecule::get_mother_atom | ( | int | ) |
Definition at line 1325 of file Molecule.h.
Referenced by Sequencer::addMovDragToPosition().
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Definition at line 857 of file Molecule.h.
Referenced by ComputeQM::initialize().
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Definition at line 826 of file Molecule.h.
Referenced by ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), ComputePme::doQMWork(), ComputeQM::initialize(), ComputeQMMgr::procQMRes(), HomePatch::qmSwapAtoms(), ComputeQMMgr::recvPartQM(), and ComputeQM::saveResults().
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Definition at line 823 of file Molecule.h.
Referenced by ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), ComputePme::doQMWork(), ComputeQM::initialize(), HomePatch::qmSwapAtoms(), and ComputeQM::saveResults().
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Definition at line 824 of file Molecule.h.
Referenced by ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), ComputePme::doQMWork(), ComputeQM::initialize(), HomePatch::qmSwapAtoms(), and ComputeQM::saveResults().
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Definition at line 820 of file Molecule.h.
Referenced by ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), ComputePme::doQMWork(), ComputeQM::initialize(), HomePatch::qmSwapAtoms(), and ComputeQM::saveResults().
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Definition at line 821 of file Molecule.h.
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Definition at line 868 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 866 of file Molecule.h.
Referenced by ComputeQM::initialize().
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Definition at line 865 of file Molecule.h.
Referenced by ComputeQM::initialize().
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Definition at line 835 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
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Definition at line 840 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
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Definition at line 827 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
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Definition at line 838 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
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Definition at line 831 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 830 of file Molecule.h.
Referenced by ComputeQM::initialize(), and ComputeQMMgr::recvPartQM().
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Definition at line 832 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 836 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
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Definition at line 829 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
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Definition at line 848 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 846 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 847 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 850 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 852 of file Molecule.h.
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Definition at line 851 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 849 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 845 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 859 of file Molecule.h.
Referenced by ComputeQM::initialize().
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Definition at line 858 of file Molecule.h.
Referenced by ComputeQM::initialize(), and ComputeQMMgr::recvPartQM().
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Definition at line 860 of file Molecule.h.
Referenced by ComputeQM::initialize().
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Definition at line 837 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
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Definition at line 839 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
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Definition at line 842 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
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Definition at line 843 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
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Definition at line 853 of file Molecule.h.
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Definition at line 834 of file Molecule.h.
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Definition at line 828 of file Molecule.h.
Referenced by ComputeQM::initialize(), ComputeQMMgr::recvPartQM(), and ComputeQM::saveResults().
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Definition at line 862 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 855 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
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Definition at line 864 of file Molecule.h.
Referenced by ComputeQM::initialize().
int Molecule::get_residue_size | ( | const char * | segid, |
int | resid | ||
) | const |
Definition at line 144 of file Molecule.C.
References NAMD_die().
Referenced by GlobalMasterEasy::getNumAtoms(), GlobalMasterFreeEnergy::getNumAtoms(), and prepare_qm().
Definition at line 1331 of file Molecule.h.
Referenced by Sequencer::addRotDragToPosition().
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Definition at line 1355 of file Molecule.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), and Sequencer::rescaleSoluteCharges().
Definition at line 1306 of file Molecule.h.
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Definition at line 1318 of file Molecule.h.
Referenced by ComputeStir::doForce().
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Definition at line 1112 of file Molecule.h.
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Definition at line 1098 of file Molecule.h.
Referenced by buildCrosstermData().
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Definition at line 1097 of file Molecule.h.
Referenced by buildDihedralData().
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Definition at line 1111 of file Molecule.h.
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Definition at line 1096 of file Molecule.h.
Referenced by buildImproperData().
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Definition at line 1102 of file Molecule.h.
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Definition at line 491 of file Molecule.h.
References atoms.
Referenced by buildAtomData(), WorkDistrib::createAtomLists(), and outputCompressedFile().
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Definition at line 495 of file Molecule.h.
Referenced by buildAtomData().
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Definition at line 1036 of file Molecule.h.
Referenced by NamdState::loadStructure(), and outputCompressedFile().
Referenced by Controller::printEnergies().
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Definition at line 479 of file Molecule.h.
Referenced by HomePatch::setLcpoType().
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Definition at line 1032 of file Molecule.h.
Referenced by NamdState::loadStructure(), and outputCompressedFile().
Referenced by Controller::calcPressure().
Bool Molecule::go_restricted | ( | int | chain1, |
int | chain2, | ||
int | rDiff | ||
) |
Definition at line 525 of file GoMolecule.C.
References FALSE, go_array, MAX_GO_CHAINS, MAX_RESTRICTIONS, and TRUE.
Referenced by build_go_arrays(), build_go_sigmas(), build_go_sigmas2(), get_go_force2(), and get_go_force_new().
void Molecule::goInit | ( | ) |
Definition at line 54 of file GoMolecule.C.
References atomChainTypes, energyNative, energyNonnative, goCoordinates, goPDB, goResids, goSigmaIndices, goSigmas, goWithinCutoff, and numGoAtoms.
void Molecule::initialize | ( | ) |
|
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|
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Definition at line 1201 of file Molecule.h.
References FALSE, and numConstraints.
Referenced by ComputeRestraints::doForce().
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Definition at line 1451 of file Molecule.h.
References numExPressureAtoms.
Referenced by Sequencer::langevinPiston().
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Definition at line 1411 of file Molecule.h.
References numFixedAtoms.
Referenced by WorkDistrib::createAtomLists().
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Definition at line 1185 of file Molecule.h.
References FALSE, and numGridforceGrids.
Referenced by ComputeGridForce::do_calc().
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Definition at line 1218 of file Molecule.h.
References FALSE, and numMovDrag.
Referenced by Sequencer::addMovDragToPosition().
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Definition at line 1234 of file Molecule.h.
References FALSE, and numRotDrag.
Referenced by Sequencer::addRotDragToPosition().
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Definition at line 1432 of file Molecule.h.
References FALSE, and numStirredAtoms.
Referenced by ComputeStir::doForce().
Bool Molecule::is_drude | ( | int | ) |
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Bool Molecule::is_hydrogen | ( | int | ) |
Bool Molecule::is_hydrogenGroupParent | ( | int | ) |
Bool Molecule::is_lp | ( | int | ) |
Bool Molecule::is_oxygen | ( | int | ) |
Bool Molecule::is_water | ( | int | ) |
Referenced by outputCompressedFile(), and wrap_coor_int().
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Definition at line 1300 of file Molecule.h.
Referenced by WorkDistrib::createAtomLists().
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Definition at line 524 of file Molecule.h.
References num_fixed_atoms(), numAtoms, numConstraints, numFepInitial, numFixedRigidBonds, numLonepairs, numRigidBonds, simParams, and WAT_TIP4.
Referenced by Controller::Controller(), NamdState::loadStructure(), and Controller::receivePressure().
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Definition at line 498 of file Molecule.h.
References numFixedAtoms, and simParams.
Referenced by num_deg_freedom(), num_fixed_groups(), num_group_deg_freedom(), and Controller::receivePressure().
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Definition at line 504 of file Molecule.h.
References num_fixed_atoms(), and numFixedGroups.
Referenced by num_group_deg_freedom(), and Controller::receivePressure().
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Definition at line 511 of file Molecule.h.
References num_fixed_atoms(), num_fixed_groups(), numConstraints, numHydrogenGroups, and simParams.
Referenced by Controller::receivePressure().
void Molecule::prepare_qm | ( | const char * | pdbFileName, |
Parameters * | params, | ||
ConfigList * | cfgList | ||
) |
Prepares Live Solvent Selection
Data gathering from PDB to find QM atom and bond info
Multiplicity of each QM group
Charge of each QM group
Populate arrays that are used throughout the the calculations.
Overides Link Atom element with user selection.
Bond Schemes. Prepares for treatment of QM-MM bonds in ComputeQM.C
Live Solvent Selection
Custom Point Charge selection
Topology preparation
Definition at line 109 of file MoleculeQM.C.
References Parameters::assign_vdw_index(), qmSolvData::atmIDs, PDB::atom(), bond::atom1, bond::atom2, ResizeArray< T >::begin(), bond::bond_type, atom_constants::charge, charge, StringList::data, DebugM, PDBAtom::element(), ResizeArray< T >::end(), endi(), SimParameters::extraBondsOn, SortedArray< Type >::find(), ConfigList::find(), SimParameters::fixedAtomsOn, get_residue_size(), ObjectArena< Type >::getNewArray(), iERROR(), iINFO(), SortedArray< Type >::insert(), iout, iWARN(), ResidueLookupElem::lookup(), atom_constants::mass, NAMD_blank_string(), NAMD_die(), NAMD_read_line(), StringList::next, PDB::num_atoms(), numAtoms, numBonds, numRealBonds, PDBAtom::occupancy(), SimParameters::PMEOn, SimParameters::qmBondDist, SimParameters::qmBondOn, SimParameters::qmBondScheme, SimParameters::qmChrgFromPSF, SimParameters::qmColumn, SimParameters::qmCSMD, SimParameters::qmCustomPCSel, SimParameters::qmElecEmbed, SimParameters::qmFormat, QMFormatMOPAC, QMFormatORCA, SimParameters::qmLSSFreq, SimParameters::qmLSSMode, QMLSSMODECOM, QMLSSMODEDIST, SimParameters::qmLSSOn, SimParameters::qmLSSResname, SimParameters::qmMOPACAddConfigChrg, SimParameters::qmNoPC, SimParameters::qmPCSelFreq, QMSCHEMECS, QMSCHEMERCD, QMSCHEMEZ1, QMSCHEMEZ2, QMSCHEMEZ3, SimParameters::qmVDW, PDBAtom::residuename(), PDBAtom::residueseq(), PDBAtom::segmentname(), ResizeArray< T >::size(), split(), SimParameters::stepsPerCycle, and PDBAtom::temperaturefactor().
Referenced by NamdState::loadStructure().
void Molecule::print_atoms | ( | Parameters * | params | ) |
Definition at line 5337 of file Molecule.C.
References DebugM, endi(), and Parameters::get_vdw_params().
Referenced by NamdState::loadStructure().
void Molecule::print_bonds | ( | Parameters * | params | ) |
Definition at line 5380 of file Molecule.C.
References DebugM, endi(), and Parameters::get_bond_params().
Referenced by NamdState::loadStructure().
void Molecule::print_exclusions | ( | ) |
Definition at line 5417 of file Molecule.C.
References DebugM, and endi().
Referenced by NamdState::loadStructure().
void Molecule::print_go_params | ( | ) |
Definition at line 548 of file GoMolecule.C.
References DebugM, go_array, MAX_GO_CHAINS, and NumGoChains.
void Molecule::print_go_sigmas | ( | ) |
Definition at line 1134 of file GoMolecule.C.
References DebugM, goSigmaIndices, goSigmas, numAtoms, and numGoAtoms.
Definition at line 1312 of file Molecule.h.
void Molecule::read_alch_unpert_angles | ( | FILE * | fd | ) |
Definition at line 1783 of file Molecule.C.
References NAMD_die(), and NAMD_read_int().
void Molecule::read_alch_unpert_bonds | ( | FILE * | fd | ) |
Definition at line 1660 of file Molecule.C.
References bond::atom1, bond::atom2, NAMD_die(), and NAMD_read_int().
void Molecule::read_alch_unpert_dihedrals | ( | FILE * | fd | ) |
Definition at line 1931 of file Molecule.C.
References NAMD_die(), and NAMD_read_int().
void Molecule::read_go_file | ( | char * | fname | ) |
Definition at line 113 of file GoMolecule.C.
References go_val::cutoff, DebugM, endi(), go_val::epsilon, go_val::epsilonRep, go_val::exp_a, go_val::exp_b, go_val::exp_rep, FALSE, go_array, go_indices, iout, iWARN(), MAX_GO_CHAINS, MAX_RESTRICTIONS, NAMD_blank_string(), NAMD_die(), NAMD_find_first_word(), NAMD_read_line(), NumGoChains, go_val::restrictions, go_val::sigmaRep, and TRUE.
Referenced by build_go_params().
void Molecule::read_parm | ( | Ambertoppar * | ) |
void Molecule::read_parm | ( | AmberParm7Reader::Ambertoppar * | ) |
Definition at line 1744 of file GoMolecule.C.
References atomChainTypes, go_val::cutoff, go_val::epsilon, go_val::epsilonRep, go_val::exp_a, go_val::exp_b, go_val::exp_rep, MIStream::get(), go_array, go_indices, goCoordinates, SimParameters::goForcesOn, goIndxLJA, goIndxLJB, SimParameters::goMethod, goNumLJPair, goResidIndices, goResids, goSigmaIndices, goSigmaPairA, goSigmaPairB, goSigmas, goWithinCutoff, MAX_GO_CHAINS, MAX_RESTRICTIONS, NAMD_die(), numAtoms, numGoAtoms, NumGoChains, pointerToGoBeg, pointerToGoEnd, go_val::restrictions, and go_val::sigmaRep.
Definition at line 5806 of file Molecule.C.
References SimParameters::alchOn, gromacsPair::atom1, gromacsPair::atom2, atomNamePool, atoms, atomSigPool, SimParameters::consForceOn, SimParameters::consTorqueOn, SimParameters::constraintsOn, DebugM, SimParameters::excludeFromPressure, exclusions, SimParameters::fixedAtomsOn, MIStream::get(), Parameters::get_num_vdw_params(), SimParameters::goGroPair, gromacsPair::gromacsPair_type, SimParameters::langevinOn, SimParameters::LCPOOn, SimParameters::lesOn, SimParameters::mgridforceOn, SimParameters::movDragOn, numGaussPair, numLJPair, gromacsPair::pairC12, gromacsPair::pairC6, SimParameters::pairInteractionOn, SimParameters::qmForcesOn, SimParameters::rotDragOn, SimParameters::sdScaling, SimParameters::soluteScalingOn, SimParameters::stirOn, SimParameters::tCoupleOn, and GridforceGrid::unpack_grid().
Referenced by Node::resendMolecule().
void Molecule::reloadCharges | ( | float | charge[], |
int | n | ||
) |
Referenced by Node::reloadCharges().
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inline |
Definition at line 1457 of file Molecule.h.
Referenced by WorkDistrib::createAtomLists(), and outputCompressedFile().
Definition at line 1635 of file GoMolecule.C.
References atomChainTypes, go_val::cutoff, MOStream::end(), go_val::epsilon, go_val::epsilonRep, go_val::exp_a, go_val::exp_b, go_val::exp_rep, go_array, go_indices, goCoordinates, SimParameters::goForcesOn, goIndxLJA, goIndxLJB, SimParameters::goMethod, goNumLJPair, goResidIndices, goResids, goSigmaIndices, goSigmaPairA, goSigmaPairB, goSigmas, goWithinCutoff, MAX_GO_CHAINS, MAX_RESTRICTIONS, NAMD_die(), numAtoms, numGoAtoms, NumGoChains, pointerToGoBeg, pointerToGoEnd, MOStream::put(), go_val::restrictions, and go_val::sigmaRep.
Definition at line 5448 of file Molecule.C.
References SimParameters::alchOn, atomNamePool, atomSigPool, SimParameters::consForceOn, SimParameters::consTorqueOn, SimParameters::constraintsOn, DebugM, MOStream::end(), endi(), SimParameters::excludeFromPressure, SimParameters::fixedAtomsOn, Parameters::get_num_vdw_params(), SimParameters::goGroPair, SimParameters::langevinOn, SimParameters::LCPOOn, SimParameters::lesOn, SimParameters::mgridforceOn, SimParameters::movDragOn, numGaussPair, GridforceGrid::pack_grid(), SimParameters::pairInteractionOn, MOStream::put(), SimParameters::qmForcesOn, SimParameters::rotDragOn, SimParameters::sdScaling, SimParameters::soluteScalingOn, SimParameters::stirOn, and SimParameters::tCoupleOn.
Referenced by Node::resendMolecule().
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Definition at line 1289 of file Molecule.h.
References numGridforceGrids.
Referenced by Node::reloadGridforceGrid().
Definition at line 818 of file Molecule.h.
Referenced by NamdState::loadStructure().
void Molecule::setBFactorData | ( | molfile_atom_t * | atomarray | ) |
Definition at line 3243 of file Molecule.C.
void Molecule::setOccupancyData | ( | molfile_atom_t * | atomarray | ) |
Definition at line 3236 of file Molecule.C.
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Definition at line 216 of file Molecule.h.
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Definition at line 220 of file Molecule.h.
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Definition at line 215 of file Molecule.h.
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Definition at line 221 of file Molecule.h.
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Definition at line 217 of file Molecule.h.
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Definition at line 214 of file Molecule.h.
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Definition at line 223 of file Molecule.h.
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Definition at line 218 of file Molecule.h.
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Definition at line 219 of file Molecule.h.
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Definition at line 225 of file Molecule.h.
Angle* Molecule::alch_unpert_angles |
Definition at line 577 of file Molecule.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
Bond* Molecule::alch_unpert_bonds |
Definition at line 576 of file Molecule.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
Dihedral* Molecule::alch_unpert_dihedrals |
Definition at line 578 of file Molecule.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
int Molecule::alchDroppedAngles |
Definition at line 564 of file Molecule.h.
Referenced by NamdState::loadStructure().
int Molecule::alchDroppedDihedrals |
Definition at line 565 of file Molecule.h.
Referenced by NamdState::loadStructure().
int Molecule::alchDroppedImpropers |
Definition at line 566 of file Molecule.h.
Referenced by NamdState::loadStructure().
int32* Molecule::atomChainTypes |
Definition at line 644 of file Molecule.h.
Referenced by build_go_arrays(), build_go_sigmas(), build_go_sigmas2(), get_go_force(), get_go_force2(), get_go_force_new(), goInit(), receive_GoMolecule(), and send_GoMolecule().
Vector* Molecule::consForce |
Definition at line 614 of file Molecule.h.
Referenced by ComputeConsForce::doForce(), and ComputeMgr::recvComputeConsForceMsg().
int32* Molecule::consForceIndexes |
Definition at line 613 of file Molecule.h.
Referenced by ComputeConsForce::doForce(), and ComputeMgr::recvComputeConsForceMsg().
int32* Molecule::consTorqueIndexes |
Definition at line 616 of file Molecule.h.
Referenced by ComputeConsTorque::doForce(), get_constorque_params(), and is_atom_constorqued().
ConsTorqueParams* Molecule::consTorqueParams |
Definition at line 617 of file Molecule.h.
Referenced by get_constorque_params().
BigReal Molecule::energyNative |
Definition at line 685 of file Molecule.h.
Referenced by build_go_arrays(), and goInit().
BigReal Molecule::energyNonnative |
Definition at line 686 of file Molecule.h.
Referenced by build_go_arrays(), and goInit().
Real* Molecule::gA |
Definition at line 677 of file Molecule.h.
Referenced by get_gro_force2().
Real* Molecule::giSigma1 |
Definition at line 679 of file Molecule.h.
Referenced by get_gro_force2().
Real* Molecule::giSigma2 |
Definition at line 681 of file Molecule.h.
Referenced by get_gro_force2().
Real* Molecule::gMu1 |
Definition at line 678 of file Molecule.h.
Referenced by get_gro_force2().
Real* Molecule::gMu2 |
Definition at line 680 of file Molecule.h.
Referenced by get_gro_force2().
GoValue Molecule::go_array[MAX_GO_CHAINS *MAX_GO_CHAINS] |
Definition at line 1588 of file Molecule.h.
Referenced by get_go_cutoff(), get_go_epsilon(), get_go_epsilonRep(), get_go_exp_a(), get_go_exp_b(), get_go_exp_rep(), get_go_sigmaRep(), go_restricted(), print_go_params(), read_go_file(), receive_GoMolecule(), and send_GoMolecule().
int Molecule::go_indices[MAX_GO_CHAINS+1] |
Definition at line 1589 of file Molecule.h.
Referenced by read_go_file(), receive_GoMolecule(), and send_GoMolecule().
Real* Molecule::goCoordinates |
Definition at line 649 of file Molecule.h.
Referenced by build_go_arrays(), get_go_force_new(), goInit(), receive_GoMolecule(), and send_GoMolecule().
int* Molecule::goIndxLJA |
Definition at line 654 of file Molecule.h.
Referenced by build_go_sigmas2(), receive_GoMolecule(), and send_GoMolecule().
int* Molecule::goIndxLJB |
Definition at line 655 of file Molecule.h.
Referenced by build_go_sigmas2(), get_go_force2(), receive_GoMolecule(), and send_GoMolecule().
int Molecule::goNumLJPair |
Definition at line 653 of file Molecule.h.
Referenced by build_go_sigmas2(), receive_GoMolecule(), and send_GoMolecule().
PDB* Molecule::goPDB |
Definition at line 651 of file Molecule.h.
Referenced by build_go_arrays(), build_go_sigmas(), build_go_sigmas2(), and goInit().
int32* Molecule::goResidIndices |
Definition at line 646 of file Molecule.h.
Referenced by build_go_sigmas2(), get_go_force2(), receive_GoMolecule(), and send_GoMolecule().
int* Molecule::goResids |
Definition at line 650 of file Molecule.h.
Referenced by build_go_arrays(), get_go_force_new(), goInit(), receive_GoMolecule(), and send_GoMolecule().
int32* Molecule::goSigmaIndices |
Definition at line 645 of file Molecule.h.
Referenced by build_go_arrays(), build_go_sigmas(), build_go_sigmas2(), get_go_force(), get_go_force_new(), goInit(), print_go_sigmas(), receive_GoMolecule(), and send_GoMolecule().
double* Molecule::goSigmaPairA |
Definition at line 656 of file Molecule.h.
Referenced by build_go_sigmas2(), get_go_force2(), receive_GoMolecule(), and send_GoMolecule().
double* Molecule::goSigmaPairB |
Definition at line 657 of file Molecule.h.
Referenced by build_go_sigmas2(), get_go_force2(), receive_GoMolecule(), and send_GoMolecule().
Real* Molecule::goSigmas |
Definition at line 647 of file Molecule.h.
Referenced by build_go_sigmas(), get_go_force(), goInit(), print_go_sigmas(), receive_GoMolecule(), and send_GoMolecule().
bool* Molecule::goWithinCutoff |
Definition at line 648 of file Molecule.h.
Referenced by build_go_sigmas(), get_go_force(), goInit(), receive_GoMolecule(), and send_GoMolecule().
Real* Molecule::gRepulsive |
Definition at line 682 of file Molecule.h.
Referenced by get_gro_force2().
int* Molecule::gromacsPair_type |
Definition at line 670 of file Molecule.h.
HydrogenGroup Molecule::hydrogenGroup |
Definition at line 640 of file Molecule.h.
Referenced by WorkDistrib::createAtomLists(), and outputCompressedFile().
int* Molecule::indxGaussA |
Definition at line 675 of file Molecule.h.
int* Molecule::indxGaussB |
Definition at line 676 of file Molecule.h.
Referenced by get_gro_force2().
int* Molecule::indxLJA |
Definition at line 666 of file Molecule.h.
int* Molecule::indxLJB |
Definition at line 667 of file Molecule.h.
Referenced by get_gro_force2().
int Molecule::is_drude_psf |
Definition at line 462 of file Molecule.h.
int Molecule::is_lonepairs_psf |
Definition at line 463 of file Molecule.h.
int Molecule::isBFactorValid |
Definition at line 1469 of file Molecule.h.
int Molecule::isOccupancyValid |
Definition at line 1469 of file Molecule.h.
int Molecule::maxHydrogenGroupSize |
Definition at line 601 of file Molecule.h.
Referenced by NamdState::loadStructure(), and outputCompressedFile().
int Molecule::maxMigrationGroupSize |
Definition at line 603 of file Molecule.h.
Referenced by NamdState::loadStructure(), and outputCompressedFile().
int Molecule::num_alch_unpert_Angles |
Definition at line 574 of file Molecule.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
int Molecule::num_alch_unpert_Bonds |
Definition at line 573 of file Molecule.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
int Molecule::num_alch_unpert_Dihedrals |
Definition at line 575 of file Molecule.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
int Molecule::numAcceptors |
Definition at line 570 of file Molecule.h.
int Molecule::numAngles |
Definition at line 561 of file Molecule.h.
Referenced by buildAngleData(), delete_qm_bonded(), dumpbench(), AngleElem::getMoleculePointers(), and NamdState::loadStructure().
int Molecule::numAnisos |
Number of anisotropic terms.
Definition at line 584 of file Molecule.h.
Referenced by AnisoElem::getMoleculePointers().
int Molecule::numAtoms |
Definition at line 557 of file Molecule.h.
Referenced by GlobalMasterEasy::addForce(), GlobalMasterFreeEnergy::addForce(), WorkDistrib::assignNodeToPatch(), build12Excls(), build13Excls(), build14Excls(), ComputeNonbondedCUDA::build_exclusions(), build_go_arrays(), build_go_sigmas(), build_go_sigmas2(), buildAtomData(), buildBondData(), buildExclusions(), colvarproxy_namd::calculate(), colvarproxy_namd::check_atom_id(), Controller::compareChecksums(), ComputeMgr::createComputes(), dumpbench(), GlobalMasterEasy::getMass(), GlobalMasterFreeEnergy::getMass(), GlobalMasterSymmetry::GlobalMasterSymmetry(), GlobalMasterTMD::GlobalMasterTMD(), colvarproxy_namd::init_atom_group(), integrateAllAtomSigs(), loadMolInfo(), NamdState::loadStructure(), num_deg_freedom(), outputCompressedFile(), WorkDistrib::patchMapInit(), prepare_qm(), print_go_sigmas(), receive_GoMolecule(), Controller::receivePressure(), ComputeMgr::recvComputeConsForceMsg(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeGBISserMgr::recvCoord(), ComputeQMMgr::recvPartQM(), Node::reloadCharges(), GlobalMasterEasy::requestAtom(), GlobalMasterFreeEnergy::requestAtom(), Node::resendMolecule(), Node::resendMolecule2(), send_GoMolecule(), Node::startup(), Tcl_centerOfMass(), Tcl_centerOfNumber(), Tcl_loadCoords(), Tcl_radiusOfGyration(), and wrap_coor_int().
int Molecule::numBonds |
Definition at line 560 of file Molecule.h.
Referenced by buildBondData(), delete_qm_bonded(), dumpbench(), BondElem::getMoleculePointers(), NamdState::loadStructure(), and prepare_qm().
int Molecule::numCalcAngles |
Definition at line 623 of file Molecule.h.
Referenced by Controller::compareChecksums(), and dumpbench().
int Molecule::numCalcAnisos |
Definition at line 632 of file Molecule.h.
Referenced by Controller::compareChecksums().
int Molecule::numCalcBonds |
Definition at line 622 of file Molecule.h.
Referenced by Controller::compareChecksums(), and dumpbench().
int Molecule::numCalcCrossterms |
Definition at line 626 of file Molecule.h.
Referenced by Controller::compareChecksums().
int Molecule::numCalcDihedrals |
Definition at line 624 of file Molecule.h.
Referenced by Controller::compareChecksums(), and dumpbench().
int64 Molecule::numCalcExclusions |
Definition at line 627 of file Molecule.h.
Referenced by Controller::compareChecksums(), and dumpbench().
int64 Molecule::numCalcFullExclusions |
Definition at line 628 of file Molecule.h.
Referenced by Controller::compareChecksums().
int Molecule::numCalcImpropers |
Definition at line 625 of file Molecule.h.
Referenced by Controller::compareChecksums(), and dumpbench().
int Molecule::numCalcLJPair |
Definition at line 663 of file Molecule.h.
int Molecule::numCalcTholes |
Definition at line 631 of file Molecule.h.
Referenced by Controller::compareChecksums().
int Molecule::numConsForce |
Definition at line 612 of file Molecule.h.
Referenced by NamdState::loadStructure().
int Molecule::numConsTorque |
Definition at line 596 of file Molecule.h.
Referenced by is_atom_constorqued().
int Molecule::numConstraints |
Definition at line 589 of file Molecule.h.
Referenced by is_atom_constrained(), NamdState::loadStructure(), num_deg_freedom(), num_group_deg_freedom(), and Controller::receivePressure().
int Molecule::numCrossterms |
Definition at line 568 of file Molecule.h.
Referenced by buildCrosstermData(), delete_qm_bonded(), CrosstermElem::getMoleculePointers(), and NamdState::loadStructure().
int Molecule::numDihedrals |
Definition at line 562 of file Molecule.h.
Referenced by buildDihedralData(), delete_qm_bonded(), dumpbench(), DihedralElem::getMoleculePointers(), and NamdState::loadStructure().
int Molecule::numDonors |
Definition at line 569 of file Molecule.h.
int Molecule::numDrudeAtoms |
Number of Drude particles.
Definition at line 582 of file Molecule.h.
Referenced by NamdState::loadStructure(), and Controller::receivePressure().
int Molecule::numExclusions |
Definition at line 571 of file Molecule.h.
Referenced by ExclElem::getMoleculePointers(), and NamdState::loadStructure().
int Molecule::numExPressureAtoms |
Definition at line 599 of file Molecule.h.
Referenced by is_atom_exPressure().
int Molecule::numFepFinal |
Definition at line 609 of file Molecule.h.
Referenced by NamdState::loadStructure().
int Molecule::numFepInitial |
Definition at line 608 of file Molecule.h.
Referenced by NamdState::loadStructure(), num_deg_freedom(), and Controller::receivePressure().
int Molecule::numFixedAtoms |
Definition at line 597 of file Molecule.h.
Referenced by is_atom_fixed(), is_group_fixed(), NamdState::loadStructure(), num_fixed_atoms(), and Controller::receivePressure().
int Molecule::numFixedGroups |
Definition at line 604 of file Molecule.h.
Referenced by NamdState::loadStructure(), num_fixed_groups(), and Controller::receivePressure().
int Molecule::numFixedRigidBonds |
Definition at line 606 of file Molecule.h.
Referenced by NamdState::loadStructure(), num_deg_freedom(), and Controller::receivePressure().
int Molecule::numGaussPair |
Definition at line 674 of file Molecule.h.
int Molecule::numGoAtoms |
Definition at line 643 of file Molecule.h.
Referenced by build_go_arrays(), build_go_sigmas(), build_go_sigmas2(), get_go_force(), goInit(), print_go_sigmas(), receive_GoMolecule(), and send_GoMolecule().
int Molecule::NumGoChains |
Definition at line 1590 of file Molecule.h.
Referenced by print_go_params(), read_go_file(), receive_GoMolecule(), and send_GoMolecule().
int Molecule::numGridforceGrids |
Definition at line 591 of file Molecule.h.
Referenced by ComputeGridForce::doForce(), get_gridfrc_grid(), colvarproxy_namd::init_volmap(), is_atom_gridforced(), NamdState::loadStructure(), and set_gridfrc_grid().
int* Molecule::numGridforces |
Definition at line 592 of file Molecule.h.
int Molecule::numHydrogenGroups |
Definition at line 600 of file Molecule.h.
Referenced by NamdState::loadStructure(), num_group_deg_freedom(), outputCompressedFile(), and Controller::receivePressure().
int Molecule::numImpropers |
Definition at line 567 of file Molecule.h.
Referenced by buildImproperData(), delete_qm_bonded(), dumpbench(), ImproperElem::getMoleculePointers(), and NamdState::loadStructure().
int Molecule::numLJPair |
Definition at line 662 of file Molecule.h.
Referenced by build_go_sigmas2(), and GromacsPairElem::getMoleculePointers().
int Molecule::numLonepairs |
Number of lone pairs.
Definition at line 581 of file Molecule.h.
Referenced by NamdState::loadStructure(), num_deg_freedom(), and Controller::receivePressure().
int Molecule::numLphosts |
Number of lone pair host records in PSF.
Definition at line 585 of file Molecule.h.
int Molecule::numMigrationGroups |
Definition at line 602 of file Molecule.h.
Referenced by NamdState::loadStructure(), and outputCompressedFile().
int Molecule::numMovDrag |
Definition at line 594 of file Molecule.h.
Referenced by is_atom_movdragged().
int Molecule::numMultipleDihedrals |
Definition at line 636 of file Molecule.h.
Referenced by NamdState::loadStructure().
int Molecule::numMultipleImpropers |
Definition at line 638 of file Molecule.h.
Referenced by NamdState::loadStructure().
int Molecule::numPair |
Definition at line 661 of file Molecule.h.
int Molecule::numRealBonds |
Definition at line 559 of file Molecule.h.
Referenced by buildBondData(), delete_qm_bonded(), and prepare_qm().
int Molecule::numRigidBonds |
Definition at line 605 of file Molecule.h.
Referenced by NamdState::loadStructure(), num_deg_freedom(), and Controller::receivePressure().
int Molecule::numRotDrag |
Definition at line 595 of file Molecule.h.
Referenced by is_atom_rotdragged().
int Molecule::numStirredAtoms |
Definition at line 598 of file Molecule.h.
Referenced by is_atom_stirred(), and NamdState::loadStructure().
int Molecule::numTholes |
Number of Thole terms.
Definition at line 583 of file Molecule.h.
Referenced by TholeElem::getMoleculePointers().
int64 Molecule::numTotalExclusions |
Definition at line 572 of file Molecule.h.
int Molecule::numZeroMassAtoms |
Number of atoms with zero mass.
Definition at line 586 of file Molecule.h.
Real* Molecule::pairC12 |
Definition at line 669 of file Molecule.h.
Referenced by get_gro_force2().
Real* Molecule::pairC6 |
Definition at line 668 of file Molecule.h.
Referenced by get_gro_force2().
int* Molecule::pointerToGaussBeg |
Definition at line 672 of file Molecule.h.
Referenced by get_gro_force2().
int* Molecule::pointerToGaussEnd |
Definition at line 673 of file Molecule.h.
Referenced by get_gro_force2().
int* Molecule::pointerToGoBeg |
Definition at line 658 of file Molecule.h.
Referenced by build_go_sigmas2(), get_go_force2(), receive_GoMolecule(), and send_GoMolecule().
int* Molecule::pointerToGoEnd |
Definition at line 659 of file Molecule.h.
Referenced by build_go_sigmas2(), get_go_force2(), receive_GoMolecule(), and send_GoMolecule().
int* Molecule::pointerToLJBeg |
Definition at line 664 of file Molecule.h.
Referenced by get_gro_force2().
int* Molecule::pointerToLJEnd |
Definition at line 665 of file Molecule.h.
Referenced by get_gro_force2().
Real Molecule::r_ohc |
Definition at line 468 of file Molecule.h.
Real Molecule::r_om |
Definition at line 467 of file Molecule.h.
int* Molecule::ss_index |
Definition at line 459 of file Molecule.h.
int Molecule::ss_num_vdw_params |
Definition at line 457 of file Molecule.h.
Referenced by LJTable::LJTable().
int* Molecule::ss_vdw_type |
Definition at line 458 of file Molecule.h.
int Molecule::suspiciousAlchBonds |
Definition at line 563 of file Molecule.h.
Referenced by NamdState::loadStructure().
BigReal Molecule::tail_corr_dUdl_1 |
Definition at line 473 of file Molecule.h.
BigReal Molecule::tail_corr_dUdl_2 |
Definition at line 473 of file Molecule.h.
BigReal Molecule::tail_corr_ener |
Definition at line 471 of file Molecule.h.
Referenced by Controller::rescaleaccelMD().
BigReal Molecule::tail_corr_virial |
Definition at line 472 of file Molecule.h.
BigReal Molecule::tail_corr_virial_1 |
Definition at line 474 of file Molecule.h.
BigReal Molecule::tail_corr_virial_2 |
Definition at line 474 of file Molecule.h.