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

Macro Definition Documentation

#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)

Referenced by ExclElem::computeForce().

#define table_four_i (table_four + 16*table_i)

Referenced by ExclElem::computeForce().

#define table_four_i (table_four + 16*table_i)

Function Documentation

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);) )

pure virtual

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);) )

pure virtual

Definition at line 226 of file ComputeNonbondedBase2.h.

                           {
           register BigReal r1;
           r1 = sqrt(p_ij_x*p_ij_x + p_ij_y*p_ij_y + p_ij_z*p_ij_z);
 
           //CkPrintf("%i %i %f %f %i\n", npertype, tabtype, r1, table_spacing, (int) (namdnearbyint(r1 / table_spacing)));
           register int eneraddress;
           eneraddress = 2 * ((npertype * tabtype) + ((int) namdnearbyint(r1 / table_spacing)));
           //CkPrintf("Using distance bin %i for distance %f\n", eneraddress, r1);
 #ifndef A2_QPX
           vdw_d = 0.;
           vdw_c = 0.;
           vdw_b = table_ener[eneraddress + 1] / r1;
           vdw_a = (-1/2.) * diffa * vdw_b;
 #else
           vec_insert(0.,                               vdw_v, 0);
           vec_insert(0.,                               vdw_v, 1);
           vec_insert(table_ener[eneraddress + 1] / r1, vdw_v, 2);
           vec_insert((-1/2.) * diffa * vdw_b,          vdw_v, 3);
 #endif
           ENERGY(
             register BigReal vdw_val = table_ener[eneraddress];
             //CkPrintf("Found vdw energy of %f\n", vdw_val);
             vdwEnergy += LAM(lambda_pair *) vdw_val;
             FEP( vdwEnergy_s += d_lambda_pair * vdw_val; )
           )
         }  else {

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().

                                               {
          goForce = mol->get_go_force2(p_ij_x, p_ij_y, p_ij_z, pExt_i.id, pExt_j->id,&goNative,&goNonnative);
        } else {

Variable Documentation

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().