CVS diff ComputeNonbondedBase.h

Difference for src/ComputeNonbondedBase.h from version 1.1189 to 1.1190

version 1.1189

version 1.1190

Line 289

SHORT

(

ENERGY( BigReal electEnergy = 0; )

Vector f_net = 0.;

)

FEP

Line 302

Line 303

)

#ifndef A2_QPX

FAST

(

SHORT

(

BigReal virial_xx = 0;

BigReal virial_xy = 0;

BigReal virial_xz = 0;

BigReal virial_yy = 0;

BigReal virial_yz = 0;

BigReal virial_zz = 0;

)

FULL

(

ENERGY( BigReal fullElectEnergy = 0; )

Vector fullf_net = 0.;

FEP

(

ENERGY( BigReal fullElectEnergy_s = 0; )

)

BigReal fullElectVirial_xx = 0;

BigReal fullElectVirial_xy = 0;

BigReal fullElectVirial_xz = 0;

BigReal fullElectVirial_yy = 0;

BigReal fullElectVirial_yz = 0;

BigReal fullElectVirial_zz = 0;

)

#else

vector4double virial_v0 = (vector4double)(0.0);

Vector fullf_net = 0.;

vector4double virial_v1 = (vector4double)(0.0);

vector4double virial_v2 = (vector4double)(0.0);

vector4double fullvirial_v0 = (vector4double) (0.0);

vector4double fullvirial_v1 = (vector4double) (0.0);

vector4double fullvirial_v2 = (vector4double) (0.0);

BigReal fullElectEnergy = 0;

BigReal fullElectEnergy_s = 0;

#endif

Line 809

Line 788

#if ( SHORT( FAST( 1+ ) ) 0 )

#if ( PAIR( 1+ ) 0 )

Force *f_0 = params->ff[0];

#if ( PAIR( 1+ ) 0 )

Force *f_1 = params->ff[1];

#else

#define f_1 f_0

NBWORKARRAY(Force,f_0,i_upper)

memset( (void*) f_0, 0, i_upper * sizeof(Force) );

#endif

#if ( FULL( 1+ ) 0 )

#if ( PAIR( 1+ ) 0 )

Force *fullf_0 = params->fullf[0];

#if ( PAIR( 1+ ) 0 )

Force *fullf_1 = params->fullf[1];

#else

#define fullf_1 fullf_0

NBWORKARRAY(Force,fullf_0,i_upper);

memset( (void*) fullf_0, 0, i_upper * sizeof(Force) );

#endif

Line 1816

Line 1791

Vector fda = -dfda * rda;

Vector fdd = -dfdd * rdd;

SHORT(f_net) NOSHORT(fullf_net) += (faa + fad) + (fda + fdd);

params->ff[0][i] += faa + fad;

params->ff[0][i+1] += fda + fdd;

params->ff[1][j] -= faa + fda;

params->ff[1][j+1] -= fad + fdd;

reduction[virialIndex_XX] += faa.x * raa.x + fad.x * rad.x

+ fda.x * rda.x + fdd.x * rdd.x;

reduction[virialIndex_XY] += faa.x * raa.y + fad.x * rad.y

+ fda.x * rda.y + fdd.x * rdd.y;

reduction[virialIndex_XZ] += faa.x * raa.z + fad.x * rad.z

+ fda.x * rda.z + fdd.x * rdd.z;

reduction[virialIndex_YX] += faa.y * raa.x + fad.y * rad.x

+ fda.y * rda.x + fdd.y * rdd.x;

reduction[virialIndex_YY] += faa.y * raa.y + fad.y * rad.y

+ fda.y * rda.y + fdd.y * rdd.y;

reduction[virialIndex_YZ] += faa.y * raa.z + fad.y * rad.z

+ fda.y * rda.z + fdd.y * rdd.z;

reduction[virialIndex_ZX] += faa.z * raa.x + fad.z * rad.x

+ fda.z * rda.x + fdd.z * rdd.x;

reduction[virialIndex_ZY] += faa.z * raa.y + fad.z * rad.y

+ fda.z * rda.y + fdd.z * rdd.y;

reduction[virialIndex_ZZ] += faa.z * raa.z + fad.z * rad.z

+ fda.z * rda.z + fdd.z * rdd.z;

reduction[electEnergyIndex] += ethole;

}

Line 1937

Line 1895

params->ff[0][i] += force;

params->ff[1][j] -= force;

}

SHORT(f_net) NOSHORT(fullf_net) += force;

reduction[virialIndex_XX] += force.x * sep.x;

reduction[virialIndex_XY] += force.x * sep.y;

reduction[virialIndex_XZ] += force.x * sep.z;

reduction[virialIndex_YX] += force.y * sep.x;

reduction[virialIndex_YY] += force.y * sep.y;

reduction[virialIndex_YZ] += force.y * sep.z;

reduction[virialIndex_ZX] += force.z * sep.x;

reduction[virialIndex_ZY] += force.z * sep.y;

reduction[virialIndex_ZZ] += force.z * sep.z;

}

#endif

Line 2161

Line 2110

#endif

#ifndef NAMD_CUDA

SHORT( FAST( f_net.x += f_i_x; ) )

SHORT( FAST( f_net.y += f_i_y; ) )

SHORT( FAST( f_net.z += f_i_z; ) )

FULL( fullf_net.x += fullf_i_x; )

FULL( fullf_net.y += fullf_i_y; )

FULL( fullf_net.z += fullf_i_z; )

SHORT( FAST( f_0[i].x += f_i_x; ) )

SHORT( FAST( f_0[i].y += f_i_y; ) )

SHORT( FAST( f_0[i].z += f_i_z; ) )

Line 2182

Line 2137

// PAIR(iout << "++++++++\n" << endi;)

PAIR( if ( savePairlists ) { pairlists.setIndexValue(i); } )

#ifdef A2_QPX

BigReal virial_xx = vec_extract (virial_v0, 0);

BigReal virial_xy = vec_extract (virial_v0, 1);

BigReal virial_xz = vec_extract (virial_v0, 2);

BigReal virial_yy = vec_extract (virial_v1, 1);

BigReal virial_yz = vec_extract (virial_v1, 2);

BigReal virial_zz = vec_extract (virial_v2, 2);

#endif

#ifdef f_1

#undef f_1

#endif

#if ( SHORT( FAST( 1+ ) ) 0 )

#if ( SELF( 1+ ) 0 )

#if ( PAIR( 1+ ) 0 )

{

Force *patch_f_0 = params->ff[0];

#ifndef NAMD_CUDA

#ifndef ARCH_POWERPC

BigReal virial_xx = f_net.x * params->offset_f.x;

#pragma ivdep

BigReal virial_xy = f_net.x * params->offset_f.y;

#endif

BigReal virial_xz = f_net.x * params->offset_f.z;

for ( int i = 0; i < i_upper; ++i ) {

BigReal virial_yy = f_net.y * params->offset_f.y;

patch_f_0[i].x += f_0[i].x;

BigReal virial_yz = f_net.y * params->offset_f.z;

patch_f_0[i].y += f_0[i].y;

BigReal virial_zz = f_net.z * params->offset_f.z;

patch_f_0[i].z += f_0[i].z;

virial_xx += f_0[i].x * p_0[i].position.x;

reduction[virialIndex_XX] += virial_xx;

virial_xy += f_0[i].x * p_0[i].position.y;

reduction[virialIndex_XY] += virial_xy;

virial_xz += f_0[i].x * p_0[i].position.z;

reduction[virialIndex_XZ] += virial_xz;

virial_yy += f_0[i].y * p_0[i].position.y;

reduction[virialIndex_YX] += virial_xy;

virial_yz += f_0[i].y * p_0[i].position.z;

reduction[virialIndex_YY] += virial_yy;

virial_zz += f_0[i].z * p_0[i].position.z;

reduction[virialIndex_YZ] += virial_yz;

}

reduction[virialIndex_ZX] += virial_xz;

reduction[virialIndex_ZY] += virial_yz;

reduction[virialIndex_ZZ] += virial_zz;

#endif

}

#endif

#ifdef A2_QPX

BigReal fullElectVirial_xx = vec_extract(fullvirial_v0, 0);

BigReal fullElectVirial_xy = vec_extract(fullvirial_v0, 1);

BigReal fullElectVirial_xz = vec_extract(fullvirial_v0, 2);

BigReal fullElectVirial_yy = vec_extract(fullvirial_v1, 1);

BigReal fullElectVirial_yz = vec_extract(fullvirial_v1, 2);

BigReal fullElectVirial_zz = vec_extract(fullvirial_v2, 2);

#endif

#ifdef fullf_1

#undef fullf_1

#endif

#if ( FULL( 1+ ) 0 )

#if ( SELF( 1+ ) 0 )

#if ( PAIR( 1+ ) 0 )

{

Force *patch_fullf_0 = params->fullf[0];

#ifndef NAMD_CUDA

#ifndef ARCH_POWERPC

BigReal fullElectVirial_xx = fullf_net.x * params->offset_f.x;

#pragma ivdep

BigReal fullElectVirial_xy = fullf_net.x * params->offset_f.y;

#endif

BigReal fullElectVirial_xz = fullf_net.x * params->offset_f.z;

for ( int i = 0; i < i_upper; ++i ) {

BigReal fullElectVirial_yy = fullf_net.y * params->offset_f.y;

patch_fullf_0[i].x += fullf_0[i].x;

BigReal fullElectVirial_yz = fullf_net.y * params->offset_f.z;

patch_fullf_0[i].y += fullf_0[i].y;

BigReal fullElectVirial_zz = fullf_net.z * params->offset_f.z;

patch_fullf_0[i].z += fullf_0[i].z;

fullElectVirial_xx += fullf_0[i].x * p_0[i].position.x;

reduction[fullElectVirialIndex_XX] += fullElectVirial_xx;

fullElectVirial_xy += fullf_0[i].x * p_0[i].position.y;

reduction[fullElectVirialIndex_XY] += fullElectVirial_xy;

fullElectVirial_xz += fullf_0[i].x * p_0[i].position.z;

reduction[fullElectVirialIndex_XZ] += fullElectVirial_xz;

fullElectVirial_yy += fullf_0[i].y * p_0[i].position.y;

reduction[fullElectVirialIndex_YX] += fullElectVirial_xy;

fullElectVirial_yz += fullf_0[i].y * p_0[i].position.z;

reduction[fullElectVirialIndex_YY] += fullElectVirial_yy;

fullElectVirial_zz += fullf_0[i].z * p_0[i].position.z;

reduction[fullElectVirialIndex_YZ] += fullElectVirial_yz;

}

reduction[fullElectVirialIndex_ZX] += fullElectVirial_xz;

reduction[fullElectVirialIndex_ZY] += fullElectVirial_yz;

reduction[fullElectVirialIndex_ZZ] += fullElectVirial_zz;

#endif

}

#endif

Line 2280

Line 2221

TI(reduction[electEnergyIndex_ti_2] += electEnergy_ti_2;)

)

SHORT

(

reduction[virialIndex_XX] += virial_xx;

reduction[virialIndex_XY] += virial_xy;

reduction[virialIndex_XZ] += virial_xz;

reduction[virialIndex_YX] += virial_xy;

reduction[virialIndex_YY] += virial_yy;

reduction[virialIndex_YZ] += virial_yz;

reduction[virialIndex_ZX] += virial_xz;

reduction[virialIndex_ZY] += virial_yz;

reduction[virialIndex_ZZ] += virial_zz;

)

FULL

(

Line 2302

Line 2231

TI(reduction[fullElectEnergyIndex_ti_1] += fullElectEnergy_ti_1;)

TI(reduction[fullElectEnergyIndex_ti_2] += fullElectEnergy_ti_2;)

)

reduction[fullElectVirialIndex_XX] += fullElectVirial_xx;

reduction[fullElectVirialIndex_XY] += fullElectVirial_xy;

reduction[fullElectVirialIndex_XZ] += fullElectVirial_xz;

reduction[fullElectVirialIndex_YX] += fullElectVirial_xy;

reduction[fullElectVirialIndex_YY] += fullElectVirial_yy;

reduction[fullElectVirialIndex_YZ] += fullElectVirial_yz;

reduction[fullElectVirialIndex_ZX] += fullElectVirial_xz;

reduction[fullElectVirialIndex_ZY] += fullElectVirial_yz;

reduction[fullElectVirialIndex_ZZ] += fullElectVirial_zz;

)

delete [] excl_flags_buff;

Legend:

Removed in v.1.1189
changed lines
	Added in v.1.1190

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