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Macros | |
#define | p_j (p_1+j) |
#define | table_four_i (table_four + 16*table_i) |
#define | lj_pars (lj_row+lj_index) |
#define | f_j (f_1+j) |
#define | p_j (p_1+j) |
#define | table_four_i (table_four + 16*table_i) |
#define | lj_pars (lj_row+lj_index) |
#define | f_j (f_1+j) |
#define | p_j (p_1+j) |
#define | table_four_i (table_four + 16*table_i) |
#define | CODE_REDUNDANT 0 |
Functions | |
ALCHPAIR (myLambda=ALCH1(lambdaUp) ALCH2(lambdaDown) ALCH3(lambdaUp) ALCH4(lambdaDown);FEP(myLambda2=ALCH1(lambda2Up) ALCH2(lambda2Down) ALCH3(lambda2Up) ALCH4(lambda2Down);) myElecLambda=ALCH1(elecLambdaUp) ALCH2(elecLambdaDown) ALCH3(elecLambdaUp) ALCH4(elecLambdaDown);FEP(myElecLambda2=ALCH1(elecLambda2Up) ALCH2(elecLambda2Down) ALCH3(elecLambda2Up) ALCH4(elecLambda2Down);) myVdwLambda=ALCH1(vdwLambdaUp) ALCH2(vdwLambdaDown) ALCH3(vdwLambdaUp) ALCH4(vdwLambdaDown);FEP(myVdwLambda2=ALCH1(vdwLambda2Up) ALCH2(vdwLambda2Down) ALCH3(vdwLambda2Up) ALCH4(vdwLambda2Down);) ALCH1(myRepLambda=repLambdaUp) ALCH2(myRepLambda=repLambdaDown);FEP(ALCH1(myRepLambda2=repLambda2Up) ALCH2(myRepLambda2=repLambda2Down);) ALCH1(myVdwShift=vdwShiftUp) ALCH2(myVdwShift=vdwShiftDown);FEP(ALCH1(myVdwShift2=vdwShift2Up) ALCH2(myVdwShift2=vdwShift2Down);)) for(k=0 | |
ALCHPAIR (const BigReal r2=r2list[k]-r2_delta;FEP(ALCH1(fep_vdw_forceandenergies(A, B, r2, myVdwShift, myVdwShift2, switchdist2, cutoff2, switchfactor, vdwForceSwitching, myVdwLambda, myVdwLambda2, alchWCAOn, myRepLambda, myRepLambda2,&alch_vdw_energy,&alch_vdw_force,&alch_vdw_energy_2);) ALCH2(fep_vdw_forceandenergies(A, B, r2, myVdwShift, myVdwShift2, switchdist2, cutoff2, switchfactor, vdwForceSwitching, myVdwLambda, myVdwLambda2, alchWCAOn, myRepLambda, myRepLambda2,&alch_vdw_energy,&alch_vdw_force,&alch_vdw_energy_2);) ALCH3(ENERGY(alch_vdw_energy=-myVdwLambda *(((diffa *vdw_d *(1/6.)+vdw_c *(1/4.))*diffa+vdw_b *(1/2.))*diffa+vdw_a);) alch_vdw_energy_2=-myVdwLambda2 *(((diffa *vdw_d *(1/6.)+vdw_c *(1/4.))*diffa+vdw_b *(1/2.))*diffa+vdw_a);alch_vdw_force=myVdwLambda *((diffa *vdw_d+vdw_c)*diffa+vdw_b);) ALCH4(ENERGY(alch_vdw_energy=-myVdwLambda *(((diffa *vdw_d *(1/6.)+vdw_c *(1/4.))*diffa+vdw_b *(1/2.))*diffa+vdw_a);) alch_vdw_energy_2=-myVdwLambda2 *(((diffa *vdw_d *(1/6.)+vdw_c *(1/4.))*diffa+vdw_b *(1/2.))*diffa+vdw_a);alch_vdw_force=myVdwLambda *((diffa *vdw_d+vdw_c)*diffa+vdw_b);)) TI(ti_vdw_force_energy_dUdl(A, B, r2, myVdwShift, switchdist2, cutoff2, switchfactor, vdwForceSwitching, myVdwLambda, alchVdwShiftCoeff, alchWCAOn, myRepLambda,&alch_vdw_energy,&alch_vdw_force,&alch_vdw_dUdl);)) if(tabtype >=0) | |
if (ComputeNonbondedUtil::goMethod==2) | |
Variables | |
k< npairi;++k){TABENERGY(const int numtypes=simParams-> tableNumTypes;const float table_spacing=simParams-> tableSpacing;const int npertype=(int)(namdnearbyint(simParams-> tableMaxDist/simParams-> tableSpacing)+1);) int table_i=(r2iilist[2 *k] >> 14)+r2_delta_expc;const int j=pairlisti[k];#define p_j BigReal diffa=r2list[k]-r2_table[table_i];#define table_four_i TABENERGY(register const int tabtype=-1-(lj_pars-> A< 0?lj_pars->A:0);) BigReal kqq=kq_i *p_j-> | charge |
register const BigReal | p_ij_x = p_i_x - p_j->position.x |
register const BigReal | p_ij_y = p_i_y - p_j->position.y |
register const BigReal | p_ij_z = p_i_z - p_j->position.z |
const BigReal | A = scaling * lj_pars->A |
const BigReal | B = scaling * lj_pars->B |
BigReal | vdw_d = A * table_four_i[0] - B * table_four_i[4] |
BigReal | vdw_c = A * table_four_i[1] - B * table_four_i[5] |
BigReal | vdw_b = A * table_four_i[2] - B * table_four_i[6] |
BigReal | vdw_a = A * table_four_i[3] - B * table_four_i[7] |
else | |
BigReal | goNonnative = 0 |
BigReal | goForce = 0 |
register const CompAtomExt * | pExt_j = pExt_1 + j |
const BigReal | rgo = sqrt(r2go) |
fast_b = goForce | |
fast_c = vdw_c | |
fast_a = vdw_a | |
register BigReal | fast_dir |
BigReal | force_r = LAM(lambda_pair *) fast_dir |
#define CODE_REDUNDANT 0 |
#define f_j (f_1+j) |
Referenced by for().
#define f_j (f_1+j) |
#define lj_pars (lj_row+lj_index) |
Referenced by ExclElem::computeForce().
#define lj_pars (lj_row+lj_index) |
#define p_j (p_1+j) |
#define p_j (p_1+j) |
#define p_j (p_1+j) |
Referenced by ExclElem::computeForce().
#define table_four_i (table_four + 16*table_i) |
#define table_four_i (table_four + 16*table_i) |
Referenced by ExclElem::computeForce().
#define table_four_i (table_four + 16*table_i) |
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pure virtual |
Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.
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pure virtual |
Definition at line 226 of file ComputeNonbondedBase2.h.
else if | ( | ComputeNonbondedUtil::goMethod | = = 2 | ) |
Definition at line 434 of file ComputeNonbondedBase2.h.
References CompAtomExt::id.
Referenced by Controller::algorithm(), calcGBISPhase(), ExclElem::computeForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), PmeZPencil::fft_init(), PmeYPencil::fft_init(), PmeXPencil::fft_init(), gatherBondedForcesKernel(), ComputePmeMgr::initialize(), memusage_mallinfo(), modifiedExclusionForcesKernel(), Sequencer::reassignVelocities(), Controller::reassignVelocities(), ProxyMgr::recvProxies(), Sequencer::rescaleaccelMD(), Sequencer::runComputeObjects(), ComputePmeMgr::sendDataPart(), ComputePmeCUDAMgr::setupPencils(), spread_charge(), and void().
Definition at line 209 of file ComputeNonbondedBase2.h.
Referenced by CrosstermElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), ExclElem::computeForce(), crosstermForce(), fep_vdw_forceandenergies(), for(), Molecule::get_gro_force2(), get_lattice_from_ts(), Parameters::get_vdw_params(), ADistRestraint::GetGrad(), AnAngleRestraint::GetGrad(), ADiheRestraint::GetGrad(), GetRestraint(), proc_dihedralgrad(), proc_getdihedral(), Parameters::read_energy_type_cubspline(), ComputeNonbondedUtil::select(), Lattice::set(), and ti_vdw_force_energy_dUdl().
Definition at line 210 of file ComputeNonbondedBase2.h.
Referenced by CrosstermElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), ExclElem::computeForce(), crosstermForce(), for(), get_lattice_from_ts(), Parameters::get_vdw_params(), ADistRestraint::GetGrad(), AnAngleRestraint::GetGrad(), ADiheRestraint::GetGrad(), proc_dihedralgrad(), proc_getdihedral(), Parameters::read_energy_type_cubspline(), ComputeNonbondedUtil::select(), Lattice::set(), vdw_energy(), and vdw_forceandenergy().
k<npairi; ++k) { TABENERGY( const int numtypes = simParams->tableNumTypes; const float table_spacing = simParams->tableSpacing; const int npertype = (int) (namdnearbyint(simParams->tableMaxDist / simParams->tableSpacing) + 1); ) int table_i = (r2iilist[2*k] >> 14) + r2_delta_expc; const int j = pairlisti[k]; #define p_j BigReal diffa = r2list[k] - r2_table[table_i]; #define table_four_i TABENERGY( register const int tabtype = -1 - ( lj_pars->A < 0 ? lj_pars->A : 0 ); ) BigReal kqq = kq_i * p_j-> charge |
Definition at line 179 of file ComputeNonbondedBase2.h.
Referenced by Molecule::atomcharge(), buildAtomData(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), ComputeGridForce::do_calc(), ComputeQM::doWork(), GromacsTopFile::GromacsTopFile(), LSSSubsDat::LSSSubsDat(), outputCompressedFile(), PDB::PDB(), Molecule::prepare_qm(), ComputeQM::processFullQM(), ComputeExtMgr::recvCoord(), and Node::reloadCharges().
else |
Definition at line 299 of file ComputeNonbondedBase2.h.
fast_a = vdw_a |
Definition at line 484 of file ComputeNonbondedBase2.h.
Referenced by ExclElem::computeForce().
fast_b = goForce |
Definition at line 451 of file ComputeNonbondedBase2.h.
Referenced by ExclElem::computeForce(), and for().
fast_c = vdw_c |
Definition at line 482 of file ComputeNonbondedBase2.h.
Referenced by ExclElem::computeForce().
register BigReal fast_dir |
Definition at line 490 of file ComputeNonbondedBase2.h.
Referenced by ExclElem::computeForce(), and for().
Definition at line 493 of file ComputeNonbondedBase2.h.
Referenced by for().
BigReal goForce = 0 |
Definition at line 432 of file ComputeNonbondedBase2.h.
Referenced by Molecule::get_go_force(), and Molecule::get_go_force_new().
BigReal goNonnative = 0 |
Definition at line 431 of file ComputeNonbondedBase2.h.
register const BigReal p_ij_x = p_i_x - p_j->position.x |
Definition at line 196 of file ComputeNonbondedBase2.h.
Referenced by for().
register const BigReal p_ij_y = p_i_y - p_j->position.y |
Definition at line 197 of file ComputeNonbondedBase2.h.
Referenced by for().
register const BigReal p_ij_z = p_i_z - p_j->position.z |
Definition at line 198 of file ComputeNonbondedBase2.h.
Referenced by for().
register const CompAtomExt* pExt_j = pExt_1 + j |
Definition at line 433 of file ComputeNonbondedBase2.h.
const BigReal rgo = sqrt(r2go) |
Definition at line 439 of file ComputeNonbondedBase2.h.
BigReal vdw_a = A * table_four_i[3] - B * table_four_i[7] |
Definition at line 215 of file ComputeNonbondedBase2.h.
Referenced by ExclElem::computeForce().
BigReal vdw_b = A * table_four_i[2] - B * table_four_i[6] |
Definition at line 214 of file ComputeNonbondedBase2.h.
Referenced by ExclElem::computeForce(), and for().
BigReal vdw_c = A * table_four_i[1] - B * table_four_i[5] |
Definition at line 213 of file ComputeNonbondedBase2.h.
Referenced by ExclElem::computeForce().
BigReal vdw_d = A * table_four_i[0] - B * table_four_i[4] |
Definition at line 212 of file ComputeNonbondedBase2.h.
Referenced by ExclElem::computeForce().