1175 lines
47 KiB
Plaintext
1175 lines
47 KiB
Plaintext
// **************************************************************************
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// amoeba.cu
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// -------------------
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// Trung Dac Nguyen (Northwestern)
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//
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// Device code for acceleration of the amoeba pair style
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//
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// __________________________________________________________________________
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// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
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// __________________________________________________________________________
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//
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// begin :
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// email : trung.nguyen@northwestern.edu
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// ***************************************************************************
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#if defined(NV_KERNEL) || defined(USE_HIP)
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#include <stdio.h>
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#include "lal_aux_fun1.h"
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#ifdef LAMMPS_SMALLBIG
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#define tagint int
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#endif
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#ifdef LAMMPS_BIGBIG
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#include "inttypes.h"
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#define tagint int64_t
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#endif
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#ifdef LAMMPS_SMALLSMALL
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#define tagint int
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#endif
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#ifndef _DOUBLE_DOUBLE
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_texture( pos_tex,float4);
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_texture( q_tex,float);
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#else
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_texture_2d( pos_tex,int4);
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_texture( q_tex,int2);
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#endif
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#else
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#define pos_tex x_
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#define q_tex q_
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#endif
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#if (SHUFFLE_AVAIL == 0)
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#define local_allocate_store_ufld() \
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__local acctyp red_acc[6][BLOCK_PAIR];
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#define store_answers_tep(ufld, dufld, ii, inum,tid, t_per_atom, offset, \
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i, tep) \
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if (t_per_atom>1) { \
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red_acc[0][tid]=ufld[0]; \
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red_acc[1][tid]=ufld[1]; \
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red_acc[2][tid]=ufld[2]; \
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for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
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simdsync(); \
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if (offset < s) { \
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for (int r=0; r<3; r++) \
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red_acc[r][tid] += red_acc[r][tid+s]; \
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} \
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} \
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ufld[0]=red_acc[0][tid]; \
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ufld[1]=red_acc[1][tid]; \
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ufld[2]=red_acc[2][tid]; \
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red_acc[0][tid]=dufld[0]; \
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red_acc[1][tid]=dufld[1]; \
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red_acc[2][tid]=dufld[2]; \
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red_acc[3][tid]=dufld[3]; \
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red_acc[4][tid]=dufld[4]; \
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red_acc[5][tid]=dufld[5]; \
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for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
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simdsync(); \
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if (offset < s) { \
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for (int r=0; r<6; r++) \
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red_acc[r][tid] += red_acc[r][tid+s]; \
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} \
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} \
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dufld[0]=red_acc[0][tid]; \
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dufld[1]=red_acc[1][tid]; \
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dufld[2]=red_acc[2][tid]; \
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dufld[3]=red_acc[3][tid]; \
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dufld[4]=red_acc[4][tid]; \
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dufld[5]=red_acc[5][tid]; \
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} \
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if (offset==0 && ii<inum) { \
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numtyp4 t; \
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t.x = diz*ufld[1] - diy*ufld[2] + qixz*dufld[1] - qixy*dufld[3] + \
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(numtyp)2.0*qiyz*(dufld[2]-dufld[5]) + (qizz-qiyy)*dufld[4]; \
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t.y = dix*ufld[2] - diz*ufld[0] - qiyz*dufld[1] + qixy*dufld[4] + \
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(numtyp)2.0*qixz*(dufld[5]-dufld[0]) + (qixx-qizz)*dufld[3]; \
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t.z = diy*ufld[0] - dix*ufld[1] + qiyz*dufld[3] - qixz*dufld[4] + \
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(numtyp)2.0*qixy*(dufld[0]-dufld[2]) + (qiyy-qixx)*dufld[1]; \
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tep[i]=t; \
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}
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#define store_answers_fieldp(_fieldp, ii, inum,tid, t_per_atom, offset, i, \
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fieldp) \
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if (t_per_atom>1) { \
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red_acc[0][tid]=_fieldp[0]; \
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red_acc[1][tid]=_fieldp[1]; \
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red_acc[2][tid]=_fieldp[2]; \
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red_acc[3][tid]=_fieldp[3]; \
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red_acc[4][tid]=_fieldp[4]; \
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red_acc[5][tid]=_fieldp[5]; \
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for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
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simdsync(); \
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if (offset < s) { \
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for (int r=0; r<6; r++) \
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red_acc[r][tid] += red_acc[r][tid+s]; \
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} \
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} \
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_fieldp[0]=red_acc[0][tid]; \
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_fieldp[1]=red_acc[1][tid]; \
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_fieldp[2]=red_acc[2][tid]; \
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_fieldp[3]=red_acc[3][tid]; \
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_fieldp[4]=red_acc[4][tid]; \
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_fieldp[5]=red_acc[5][tid]; \
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} \
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if (offset==0 && ii<inum) { \
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numtyp4 f, fp; \
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f.x = _fieldp[0]; \
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f.y = _fieldp[1]; \
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f.z = _fieldp[2]; \
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fieldp[ii] = f; \
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fp.x = _fieldp[3]; \
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fp.y = _fieldp[4]; \
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fp.z = _fieldp[5]; \
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fieldp[ii+inum] = fp; \
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}
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#else
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#define local_allocate_store_ufld()
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#define store_answers_tep(ufld, dufld, ii, inum,tid, t_per_atom, offset, \
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i, tep) \
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if (t_per_atom>1) { \
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for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
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ufld[0] += shfl_down(ufld[0], s, t_per_atom); \
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ufld[1] += shfl_down(ufld[1], s, t_per_atom); \
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ufld[2] += shfl_down(ufld[2], s, t_per_atom); \
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dufld[0] += shfl_down(dufld[0], s, t_per_atom); \
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dufld[1] += shfl_down(dufld[1], s, t_per_atom); \
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dufld[2] += shfl_down(dufld[2], s, t_per_atom); \
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dufld[3] += shfl_down(dufld[3], s, t_per_atom); \
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dufld[4] += shfl_down(dufld[4], s, t_per_atom); \
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dufld[5] += shfl_down(dufld[5], s, t_per_atom); \
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} \
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} \
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if (offset==0 && ii<inum) { \
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numtyp4 t; \
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t.x = diz*ufld[1] - diy*ufld[2] + qixz*dufld[1] - qixy*dufld[3] + \
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(numtyp)2.0*qiyz*(dufld[2]-dufld[5]) + (qizz-qiyy)*dufld[4]; \
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t.y = dix*ufld[2] - diz*ufld[0] - qiyz*dufld[1] + qixy*dufld[4] + \
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(numtyp)2.0*qixz*(dufld[5]-dufld[0]) + (qixx-qizz)*dufld[3]; \
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t.z = diy*ufld[0] - dix*ufld[1] + qiyz*dufld[3] - qixz*dufld[4] + \
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(numtyp)2.0*qixy*(dufld[0]-dufld[2]) + (qiyy-qixx)*dufld[1]; \
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tep[i]=t; \
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}
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#define store_answers_fieldp(_fieldp, ii, inum, tid, t_per_atom, offset, i, \
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fieldp) \
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if (t_per_atom>1) { \
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for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \
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_fieldp[0] += shfl_down(_fieldp[0], s, t_per_atom); \
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_fieldp[1] += shfl_down(_fieldp[1], s, t_per_atom); \
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_fieldp[2] += shfl_down(_fieldp[2], s, t_per_atom); \
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_fieldp[3] += shfl_down(_fieldp[3], s, t_per_atom); \
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_fieldp[4] += shfl_down(_fieldp[4], s, t_per_atom); \
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_fieldp[5] += shfl_down(_fieldp[5], s, t_per_atom); \
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} \
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} \
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if (offset==0 && ii<inum) { \
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numtyp4 f, fp; \
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f.x = _fieldp[0]; \
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f.y = _fieldp[1]; \
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f.z = _fieldp[2]; \
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fieldp[ii] = f; \
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fp.x = _fieldp[3]; \
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fp.y = _fieldp[4]; \
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fp.z = _fieldp[5]; \
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fieldp[ii+inum] = fp; \
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}
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#endif
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#define MIN(A,B) ((A) < (B) ? (A) : (B))
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#define MY_PIS (acctyp)1.77245385090551602729
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/* ----------------------------------------------------------------------
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udirect2b = Ewald real direct field via list
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udirect2b computes the real space contribution of the permanent
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atomic multipole moments to the field via a neighbor list
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------------------------------------------------------------------------- */
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__kernel void k_amoeba_udirect2b(const __global numtyp4 *restrict x_,
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const __global numtyp *restrict extra,
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const __global numtyp4 *restrict damping,
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const __global numtyp4 *restrict sp_polar,
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const __global int *dev_nbor,
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const __global int *dev_packed,
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const __global int *dev_short_nbor,
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__global numtyp4 *restrict fieldp,
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const int inum, const int nall,
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const int nbor_pitch, const int t_per_atom,
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const numtyp aewald, const numtyp off2,
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const numtyp polar_dscale, const numtyp polar_uscale)
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{
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int tid, ii, offset, i;
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atom_info(t_per_atom,ii,tid,offset);
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int n_stride;
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local_allocate_store_charge();
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acctyp _fieldp[6];
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for (int l=0; l<6; l++) _fieldp[l]=(acctyp)0;
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numtyp dix,diy,diz,qixx,qixy,qixz,qiyy,qiyz,qizz;
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numtyp4* polar1 = (numtyp4*)(&extra[0]);
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numtyp4* polar2 = (numtyp4*)(&extra[4*nall]);
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numtyp4* polar3 = (numtyp4*)(&extra[8*nall]);
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//numtyp4 xi__;
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if (ii<inum) {
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int numj, nbor, nbor_end;
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const __global int* nbor_mem=dev_packed;
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nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
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n_stride,nbor_end,nbor);
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numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
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//numtyp qtmp; fetch(qtmp,i,q_tex);
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//int itype=ix.w;
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// recalculate numj and nbor_end for use of the short nbor list
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if (dev_packed==dev_nbor) {
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numj = dev_short_nbor[nbor];
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nbor += n_stride;
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nbor_end = nbor+fast_mul(numj,n_stride);
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nbor_mem = dev_short_nbor;
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}
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int itype,igroup;
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numtyp bn[4],bcn[3];
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numtyp fid[3],fip[3];
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dix = polar1[i].y; // rpole[i][1];
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diy = polar1[i].z; // rpole[i][2];
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diz = polar1[i].w; // rpole[i][3];
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qixx = polar2[i].x; // rpole[i][4];
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qixy = polar2[i].y; // rpole[i][5];
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qixz = polar2[i].z; // rpole[i][6];
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qiyy = polar2[i].w; // rpole[i][8];
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qiyz = polar3[i].x; // rpole[i][9];
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qizz = polar3[i].y; // rpole[i][12];
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itype = polar3[i].z; // amtype[i];
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igroup = polar3[i].w; // amgroup[i];
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// debug:
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// xi__ = ix; xi__.w = itype;
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numtyp pdi = damping[itype].x;
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numtyp pti = damping[itype].y;
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numtyp ddi = damping[itype].z;
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numtyp aesq2 = (numtyp)2.0 * aewald*aewald;
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numtyp aesq2n = (numtyp)0.0;
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if (aewald > (numtyp)0.0) aesq2n = (numtyp)1.0 / (MY_PIS*aewald);
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for ( ; nbor<nbor_end; nbor+=n_stride) {
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int jextra=nbor_mem[nbor];
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int j = jextra & NEIGHMASK15;
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numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
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//int jtype=jx.w;
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// Compute r12
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numtyp xr = jx.x - ix.x;
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numtyp yr = jx.y - ix.y;
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numtyp zr = jx.z - ix.z;
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numtyp r2 = xr*xr + yr*yr + zr*zr;
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//if (r2>off2) continue;
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numtyp r = ucl_sqrt(r2);
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numtyp rinv = ucl_recip(r);
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numtyp r2inv = rinv*rinv;
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numtyp rr1 = rinv;
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numtyp rr3 = rr1 * r2inv;
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numtyp rr5 = (numtyp)3.0 * rr3 * r2inv;
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numtyp rr7 = (numtyp)5.0 * rr5 * r2inv;
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numtyp ck = polar1[j].x; // rpole[j][0];
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numtyp dkx = polar1[j].y; // rpole[j][1];
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numtyp dky = polar1[j].z; // rpole[j][2];
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numtyp dkz = polar1[j].w; // rpole[j][3];
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numtyp qkxx = polar2[j].x; // rpole[j][4];
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numtyp qkxy = polar2[j].y; // rpole[j][5];
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numtyp qkxz = polar2[j].z; // rpole[j][6];
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numtyp qkyy = polar2[j].w; // rpole[j][8];
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numtyp qkyz = polar3[j].x; // rpole[j][9];
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numtyp qkzz = polar3[j].y; // rpole[j][12];
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int jtype = polar3[j].z; // amtype[j];
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int jgroup = polar3[j].w; // amgroup[j];
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numtyp factor_wscale, factor_dscale, factor_pscale, factor_uscale;
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const numtyp4 sp_pol = sp_polar[sbmask15(jextra)];
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factor_wscale = sp_pol.x; // sp_polar_wscale[sbmask15(jextra)];
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if (igroup == jgroup) {
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factor_pscale = sp_pol.y; // sp_polar_piscale[sbmask15(jextra)];
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factor_dscale = polar_dscale;
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factor_uscale = polar_uscale;
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} else {
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factor_pscale = sp_pol.z; // sp_polar_pscale[sbmask15(jextra)];
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factor_dscale = factor_uscale = (numtyp)1.0;
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}
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// intermediates involving moments and separation distance
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numtyp dir = dix*xr + diy*yr + diz*zr;
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numtyp qix = qixx*xr + qixy*yr + qixz*zr;
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numtyp qiy = qixy*xr + qiyy*yr + qiyz*zr;
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numtyp qiz = qixz*xr + qiyz*yr + qizz*zr;
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numtyp qir = qix*xr + qiy*yr + qiz*zr;
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numtyp dkr = dkx*xr + dky*yr + dkz*zr;
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numtyp qkx = qkxx*xr + qkxy*yr + qkxz*zr;
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numtyp qky = qkxy*xr + qkyy*yr + qkyz*zr;
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numtyp qkz = qkxz*xr + qkyz*yr + qkzz*zr;
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numtyp qkr = qkx*xr + qky*yr + qkz*zr;
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// calculate the real space Ewald error function terms
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numtyp ralpha = aewald * r;
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numtyp exp2a = ucl_exp(-ralpha*ralpha);
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numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*ralpha);
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numtyp _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * exp2a;
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//bn[0] = erfc(ralpha) / r;
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bn[0] = _erfc * rinv;
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numtyp aefac = aesq2n;
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for (int m = 1; m <= 3; m++) {
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numtyp bfac = (numtyp) (m+m-1);
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aefac = aesq2 * aefac;
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bn[m] = (bfac*bn[m-1]+aefac*exp2a) * r2inv;
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}
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// find the field components for Thole polarization damping
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numtyp scale3 = (numtyp)1.0;
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numtyp scale5 = (numtyp)1.0;
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numtyp scale7 = (numtyp)1.0;
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numtyp damp = pdi * damping[jtype].x; // pdamp[jtype]
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if (damp != (numtyp)0.0) {
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numtyp pgamma = MIN(ddi,damping[jtype].z); // dirdamp[jtype]
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if (pgamma != (numtyp)0.0) {
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damp = pgamma * ucl_powr(r/damp,(numtyp)1.5);
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if (damp < (numtyp)50.0) {
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numtyp expdamp = ucl_exp(-damp) ;
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scale3 = (numtyp)1.0 - expdamp ;
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scale5 = (numtyp)1.0 - expdamp*((numtyp)1.0+(numtyp)0.5*damp);
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scale7 = (numtyp)1.0 - expdamp*((numtyp)1.0+(numtyp)0.65*damp + (numtyp)0.15*damp*damp);
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}
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} else {
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pgamma = MIN(pti,damping[jtype].y); // thole[jtype]
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damp = pgamma * ucl_powr(r/damp,3.0);
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if (damp < (numtyp)50.0) {
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numtyp expdamp = ucl_exp(-damp);
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scale3 = (numtyp)1.0 - expdamp;
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scale5 = (numtyp)1.0 - expdamp*((numtyp)1.0+damp);
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scale7 = (numtyp)1.0 - expdamp*((numtyp)1.0+damp + (numtyp)0.6*damp*damp);
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}
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}
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} else { // damp == 0: ???
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}
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numtyp scalek = factor_dscale;
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bcn[0] = bn[1] - ((numtyp)1.0-scalek*scale3)*rr3;
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bcn[1] = bn[2] - ((numtyp)1.0-scalek*scale5)*rr5;
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bcn[2] = bn[3] - ((numtyp)1.0-scalek*scale7)*rr7;
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fid[0] = -xr*(bcn[0]*ck-bcn[1]*dkr+bcn[2]*qkr) - bcn[0]*dkx + (numtyp)2.0*bcn[1]*qkx;
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fid[1] = -yr*(bcn[0]*ck-bcn[1]*dkr+bcn[2]*qkr) - bcn[0]*dky + (numtyp)2.0*bcn[1]*qky;
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fid[2] = -zr*(bcn[0]*ck-bcn[1]*dkr+bcn[2]*qkr) - bcn[0]*dkz + (numtyp)2.0*bcn[1]*qkz;
|
|
|
|
scalek = factor_pscale;
|
|
bcn[0] = bn[1] - ((numtyp)1.0-scalek*scale3)*rr3;
|
|
bcn[1] = bn[2] - ((numtyp)1.0-scalek*scale5)*rr5;
|
|
bcn[2] = bn[3] - ((numtyp)1.0-scalek*scale7)*rr7;
|
|
fip[0] = -xr*(bcn[0]*ck-bcn[1]*dkr+bcn[2]*qkr) - bcn[0]*dkx + (numtyp)2.0*bcn[1]*qkx;
|
|
fip[1] = -yr*(bcn[0]*ck-bcn[1]*dkr+bcn[2]*qkr) - bcn[0]*dky + (numtyp)2.0*bcn[1]*qky;
|
|
fip[2] = -zr*(bcn[0]*ck-bcn[1]*dkr+bcn[2]*qkr) - bcn[0]*dkz + (numtyp)2.0*bcn[1]*qkz;
|
|
|
|
_fieldp[0] += fid[0];
|
|
_fieldp[1] += fid[1];
|
|
_fieldp[2] += fid[2];
|
|
_fieldp[3] += fip[0];
|
|
_fieldp[4] += fip[1];
|
|
_fieldp[5] += fip[2];
|
|
} // nbor
|
|
|
|
} // ii<inum
|
|
|
|
// accumulate field and fieldp
|
|
|
|
store_answers_fieldp(_fieldp,ii,inum,tid,t_per_atom,offset,i,fieldp);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
umutual2b = Ewald real mutual field via list
|
|
umutual2b computes the real space contribution of the induced
|
|
atomic dipole moments to the field via a neighbor list
|
|
------------------------------------------------------------------------- */
|
|
|
|
__kernel void k_amoeba_umutual2b(const __global numtyp4 *restrict x_,
|
|
const __global numtyp *restrict extra,
|
|
const __global numtyp4 *restrict damping,
|
|
const __global numtyp4 *restrict sp_polar,
|
|
const __global int *dev_nbor,
|
|
const __global int *dev_packed,
|
|
const __global int *dev_short_nbor,
|
|
__global numtyp4 *restrict fieldp,
|
|
const int inum, const int nall,
|
|
const int nbor_pitch, const int t_per_atom,
|
|
const numtyp aewald, const numtyp off2,
|
|
const numtyp polar_dscale, const numtyp polar_uscale)
|
|
{
|
|
int tid, ii, offset, i;
|
|
atom_info(t_per_atom,ii,tid,offset);
|
|
|
|
int n_stride;
|
|
local_allocate_store_charge();
|
|
|
|
acctyp _fieldp[6];
|
|
for (int l=0; l<6; l++) _fieldp[l]=(acctyp)0;
|
|
|
|
numtyp4* polar3 = (numtyp4*)(&extra[8*nall]);
|
|
numtyp4* polar4 = (numtyp4*)(&extra[12*nall]);
|
|
numtyp4* polar5 = (numtyp4*)(&extra[16*nall]);
|
|
|
|
//numtyp4 xi__;
|
|
|
|
if (ii<inum) {
|
|
int numj, nbor, nbor_end;
|
|
const __global int* nbor_mem=dev_packed;
|
|
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
|
|
n_stride,nbor_end,nbor);
|
|
|
|
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
|
|
//numtyp qtmp; fetch(qtmp,i,q_tex);
|
|
//int itype=ix.w;
|
|
|
|
// recalculate numj and nbor_end for use of the short nbor list
|
|
if (dev_packed==dev_nbor) {
|
|
numj = dev_short_nbor[nbor];
|
|
nbor += n_stride;
|
|
nbor_end = nbor+fast_mul(numj,n_stride);
|
|
nbor_mem = dev_short_nbor;
|
|
}
|
|
|
|
int itype,igroup;
|
|
numtyp bn[4],bcn[3];
|
|
numtyp fid[3],fip[3];
|
|
|
|
itype = polar3[i].z; // amtype[i];
|
|
igroup = polar3[i].w; // amgroup[i];
|
|
|
|
numtyp pdi = damping[itype].x;
|
|
numtyp ddi = damping[itype].z;
|
|
|
|
for ( ; nbor<nbor_end; nbor+=n_stride) {
|
|
|
|
int jextra=nbor_mem[nbor];
|
|
int j = jextra & NEIGHMASK15;
|
|
|
|
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
|
|
//int jtype=jx.w;
|
|
|
|
// Compute r12
|
|
numtyp xr = jx.x - ix.x;
|
|
numtyp yr = jx.y - ix.y;
|
|
numtyp zr = jx.z - ix.z;
|
|
numtyp r2 = xr*xr + yr*yr + zr*zr;
|
|
|
|
if (r2>off2) continue;
|
|
|
|
numtyp r = ucl_sqrt(r2);
|
|
numtyp rinv = ucl_recip(r);
|
|
numtyp r2inv = rinv*rinv;
|
|
numtyp rr1 = rinv;
|
|
numtyp rr3 = rr1 * r2inv;
|
|
numtyp rr5 = (numtyp)3.0 * rr3 * r2inv;
|
|
|
|
int jtype = polar3[j].z; // amtype[j];
|
|
int jgroup = polar3[j].w; // amgroup[j];
|
|
numtyp ukx = polar4[j].x; // uind[j][0];
|
|
numtyp uky = polar4[j].y; // uind[j][1];
|
|
numtyp ukz = polar4[j].z; // uind[j][2];
|
|
numtyp ukxp = polar5[j].x; // uinp[j][0];
|
|
numtyp ukyp = polar5[j].y; // uinp[j][1];
|
|
numtyp ukzp = polar5[j].z; // uinp[j][2];
|
|
|
|
numtyp factor_uscale;
|
|
|
|
// find terms needed later to compute mutual polarization
|
|
// if (poltyp != DIRECT)
|
|
numtyp scale3 = (numtyp)1.0;
|
|
numtyp scale5 = (numtyp)1.0;
|
|
numtyp damp = pdi * damping[jtype].x; // pdamp[jtype]
|
|
if (damp != (numtyp)0.0) {
|
|
numtyp pgamma = MIN(ddi,damping[jtype].z); // dirdamp[jtype]
|
|
if (pgamma != (numtyp)0.0) {
|
|
damp = pgamma * ucl_powr(r/damp,(numtyp)3.0);
|
|
if (damp < (numtyp)50.0) {
|
|
numtyp expdamp = ucl_exp(-damp);
|
|
scale3 = (numtyp)1.0 - expdamp;
|
|
scale5 = (numtyp)1.0 - expdamp*((numtyp)1.0+damp);
|
|
}
|
|
}
|
|
} else { // damp == 0: ???
|
|
}
|
|
|
|
numtyp scalek = factor_uscale;
|
|
bcn[0] = bn[1] - ((numtyp)1.0-scalek*scale3)*rr3;
|
|
bcn[1] = bn[2] - ((numtyp)1.0-scalek*scale5)*rr5;
|
|
numtyp tdipdip[6]; // the following tdipdip is incorrect!! needs work to store tdipdip
|
|
tdipdip[0] = -bcn[0] + bcn[1]*xr*xr;
|
|
tdipdip[1] = bcn[1]*xr*yr;
|
|
tdipdip[2] = bcn[1]*xr*zr;
|
|
tdipdip[3] = -bcn[0] + bcn[1]*yr*yr;
|
|
tdipdip[4] = bcn[1]*yr*zr;
|
|
tdipdip[5] = -bcn[0] + bcn[1]*zr*zr;
|
|
|
|
fid[0] = tdipdip[0]*ukx + tdipdip[1]*uky + tdipdip[2]*ukz;
|
|
fid[1] = tdipdip[1]*ukx + tdipdip[3]*uky + tdipdip[4]*ukz;
|
|
fid[2] = tdipdip[2]*ukx + tdipdip[4]*uky + tdipdip[5]*ukz;
|
|
|
|
fip[0] = tdipdip[0]*ukxp + tdipdip[1]*ukyp + tdipdip[2]*ukzp;
|
|
fip[1] = tdipdip[1]*ukxp + tdipdip[3]*ukyp + tdipdip[4]*ukzp;
|
|
fip[2] = tdipdip[2]*ukxp + tdipdip[4]*ukyp + tdipdip[5]*ukzp;
|
|
|
|
_fieldp[0] += fid[0];
|
|
_fieldp[1] += fid[1];
|
|
_fieldp[2] += fid[2];
|
|
_fieldp[3] += fip[0];
|
|
_fieldp[4] += fip[1];
|
|
_fieldp[5] += fip[2];
|
|
} // nbor
|
|
|
|
} // ii<inum
|
|
|
|
// accumulate field and fieldp
|
|
|
|
store_answers_fieldp(_fieldp,ii,inum,tid,t_per_atom,offset,i,fieldp);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
scan standard neighbor list and make it compatible with 1-5 neighbors
|
|
if IJ entry is a 1-2,1-3,1-4 neighbor then adjust offset to SBBITS15
|
|
else scan special15 to see if a 1-5 neighbor and adjust offset to SBBITS15
|
|
else do nothing to IJ entry
|
|
------------------------------------------------------------------------- */
|
|
|
|
__kernel void k_special15(__global int * dev_nbor,
|
|
const __global int * dev_packed,
|
|
const __global tagint *restrict tag,
|
|
const __global int *restrict nspecial15,
|
|
const __global tagint *restrict special15,
|
|
const int inum, const int nall, const int nbor_pitch,
|
|
const int t_per_atom) {
|
|
int tid, ii, offset, n_stride, i;
|
|
atom_info(t_per_atom,ii,tid,offset);
|
|
|
|
if (ii<inum) {
|
|
|
|
int numj, nbor, nbor_end;
|
|
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
|
|
n_stride,nbor_end,nbor);
|
|
|
|
int n15 = nspecial15[ii];
|
|
|
|
for ( ; nbor<nbor_end; nbor+=n_stride) {
|
|
|
|
int sj=dev_packed[nbor];
|
|
int which = sj >> SBBITS & 3;
|
|
int j = sj & NEIGHMASK;
|
|
tagint jtag = tag[j];
|
|
|
|
if (!which) {
|
|
int offset=ii;
|
|
for (int k=0; k<n15; k++) {
|
|
if (special15[offset] == jtag) {
|
|
which = 4;
|
|
break;
|
|
}
|
|
offset += nall;
|
|
}
|
|
}
|
|
|
|
if (which) dev_nbor[nbor] = j ^ (which << SBBITS15);
|
|
} // for nbor
|
|
|
|
} // if ii
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
polar_real = real-space portion of induced dipole polarization
|
|
adapted from Tinker epreal1d() routine
|
|
------------------------------------------------------------------------- */
|
|
|
|
__kernel void k_amoeba_polar(const __global numtyp4 *restrict x_,
|
|
const __global numtyp *restrict extra,
|
|
const __global numtyp4 *restrict damping,
|
|
const __global numtyp4 *restrict sp_polar,
|
|
const __global int *dev_nbor,
|
|
const __global int *dev_packed,
|
|
const __global int *dev_short_nbor,
|
|
__global acctyp4 *restrict ans,
|
|
__global acctyp *restrict engv,
|
|
__global numtyp4 *restrict tep,
|
|
const int eflag, const int vflag, const int inum,
|
|
const int nall, const int nbor_pitch, const int t_per_atom,
|
|
const numtyp aewald, const numtyp felec,
|
|
const numtyp off2, const numtyp polar_dscale,
|
|
const numtyp polar_uscale)
|
|
{
|
|
int tid, ii, offset, i;
|
|
atom_info(t_per_atom,ii,tid,offset);
|
|
|
|
int n_stride;
|
|
local_allocate_store_ufld();
|
|
local_allocate_store_charge();
|
|
|
|
acctyp4 f;
|
|
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
|
|
acctyp energy, e_coul, virial[6];
|
|
if (EVFLAG) {
|
|
energy=(acctyp)0;
|
|
e_coul=(acctyp)0;
|
|
for (int l=0; l<6; l++) virial[l]=(acctyp)0;
|
|
}
|
|
|
|
acctyp ufld[3];
|
|
ufld[0] = (acctyp)0; ufld[1]=(acctyp)0; ufld[2]=(acctyp)0;
|
|
acctyp dufld[6];
|
|
for (int l=0; l<6; l++) dufld[l]=(acctyp)0;
|
|
|
|
numtyp dix,diy,diz,qixx,qixy,qixz,qiyy,qiyz,qizz;
|
|
numtyp4* polar1 = (numtyp4*)(&extra[0]);
|
|
numtyp4* polar2 = (numtyp4*)(&extra[4*nall]);
|
|
numtyp4* polar3 = (numtyp4*)(&extra[8*nall]);
|
|
numtyp4* polar4 = (numtyp4*)(&extra[12*nall]);
|
|
numtyp4* polar5 = (numtyp4*)(&extra[16*nall]);
|
|
|
|
//numtyp4 xi__;
|
|
|
|
if (ii<inum) {
|
|
int k,m,itype,igroup;
|
|
numtyp bfac;
|
|
numtyp psc3,psc5,psc7;
|
|
numtyp dsc3,dsc5,dsc7;
|
|
numtyp usc3,usc5;
|
|
numtyp psr3,psr5,psr7;
|
|
numtyp dsr3,dsr5,dsr7;
|
|
numtyp usr5;
|
|
numtyp term1,term2,term3;
|
|
numtyp term4,term5;
|
|
numtyp term6,term7;
|
|
numtyp rc3[3],rc5[3],rc7[3];
|
|
numtyp prc3[3],prc5[3],prc7[3];
|
|
numtyp drc3[3],drc5[3],drc7[3];
|
|
numtyp urc3[3],urc5[3];
|
|
numtyp bn[5];
|
|
numtyp ci,uix,uiy,uiz,uixp,uiyp,uizp;
|
|
|
|
int numj, nbor, nbor_end;
|
|
const __global int* nbor_mem=dev_packed;
|
|
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
|
|
n_stride,nbor_end,nbor);
|
|
|
|
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
|
|
//numtyp qtmp; fetch(qtmp,i,q_tex);
|
|
//int itype=ix.w;
|
|
|
|
// recalculate numj and nbor_end for use of the short nbor list
|
|
if (dev_packed==dev_nbor) {
|
|
numj = dev_short_nbor[nbor];
|
|
nbor += n_stride;
|
|
nbor_end = nbor+fast_mul(numj,n_stride);
|
|
nbor_mem = dev_short_nbor;
|
|
}
|
|
|
|
ci = polar1[i].x; // rpole[i][0];
|
|
dix = polar1[i].y; // rpole[i][1];
|
|
diy = polar1[i].z; // rpole[i][2];
|
|
diz = polar1[i].w; // rpole[i][3];
|
|
qixx = polar2[i].x; // rpole[i][4];
|
|
qixy = polar2[i].y; // rpole[i][5];
|
|
qixz = polar2[i].z; // rpole[i][6];
|
|
qiyy = polar2[i].w; // rpole[i][8];
|
|
qiyz = polar3[i].x; // rpole[i][9];
|
|
qizz = polar3[i].y; // rpole[i][12];
|
|
itype = polar3[i].z; // amtype[i];
|
|
igroup = polar3[i].w; // amgroup[i];
|
|
uix = polar4[i].x; // uind[i][0];
|
|
uiy = polar4[i].y; // uind[i][1];
|
|
uiz = polar4[i].z; // uind[i][2];
|
|
uixp = polar5[i].x; // uinp[i][0];
|
|
uiyp = polar5[i].y; // uinp[i][1];
|
|
uizp = polar5[i].z; // uinp[i][2];
|
|
|
|
// debug:
|
|
// xi__ = ix; xi__.w = itype;
|
|
|
|
numtyp pdi = damping[itype].x;
|
|
numtyp pti = damping[itype].y;
|
|
|
|
for ( ; nbor<nbor_end; nbor+=n_stride) {
|
|
|
|
int jextra=nbor_mem[nbor];
|
|
int j = jextra & NEIGHMASK15;
|
|
|
|
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
|
|
//int jtype=jx.w;
|
|
|
|
// Compute r12
|
|
numtyp xr = jx.x - ix.x;
|
|
numtyp yr = jx.y - ix.y;
|
|
numtyp zr = jx.z - ix.z;
|
|
numtyp r2 = xr*xr + yr*yr + zr*zr;
|
|
|
|
//if (r2>off2) continue;
|
|
|
|
numtyp r = ucl_sqrt(r2);
|
|
|
|
numtyp ck = polar1[j].x; // rpole[j][0];
|
|
numtyp dkx = polar1[j].y; // rpole[j][1];
|
|
numtyp dky = polar1[j].z; // rpole[j][2];
|
|
numtyp dkz = polar1[j].w; // rpole[j][3];
|
|
numtyp qkxx = polar2[j].x; // rpole[j][4];
|
|
numtyp qkxy = polar2[j].y; // rpole[j][5];
|
|
numtyp qkxz = polar2[j].z; // rpole[j][6];
|
|
numtyp qkyy = polar2[j].w; // rpole[j][8];
|
|
numtyp qkyz = polar3[j].x; // rpole[j][9];
|
|
numtyp qkzz = polar3[j].y; // rpole[j][12];
|
|
int jtype = polar3[j].z; // amtype[j];
|
|
int jgroup = polar3[j].w; // amgroup[j];
|
|
numtyp ukx = polar4[j].x; // uind[j][0];
|
|
numtyp uky = polar4[j].y; // uind[j][1];
|
|
numtyp ukz = polar4[j].z; // uind[j][2];
|
|
numtyp ukxp = polar5[j].x; // uinp[j][0];
|
|
numtyp ukyp = polar5[j].y; // uinp[j][1];
|
|
numtyp ukzp = polar5[j].z; // uinp[j][2];
|
|
|
|
numtyp factor_wscale, factor_dscale, factor_pscale, factor_uscale;
|
|
const numtyp4 sp_pol = sp_polar[sbmask15(jextra)];
|
|
factor_wscale = sp_pol.x; // sp_polar_wscale[sbmask15(jextra)];
|
|
if (igroup == jgroup) {
|
|
factor_pscale = sp_pol.y; // sp_polar_piscale[sbmask15(jextra)];
|
|
factor_dscale = polar_dscale;
|
|
factor_uscale = polar_uscale;
|
|
} else {
|
|
factor_pscale = sp_pol.z; // sp_polar_pscale[sbmask15(jextra)];
|
|
factor_dscale = factor_uscale = (numtyp)1.0;
|
|
}
|
|
|
|
// intermediates involving moments and separation distance
|
|
|
|
numtyp dir = dix*xr + diy*yr + diz*zr;
|
|
numtyp qix = qixx*xr + qixy*yr + qixz*zr;
|
|
numtyp qiy = qixy*xr + qiyy*yr + qiyz*zr;
|
|
numtyp qiz = qixz*xr + qiyz*yr + qizz*zr;
|
|
numtyp qir = qix*xr + qiy*yr + qiz*zr;
|
|
numtyp dkr = dkx*xr + dky*yr + dkz*zr;
|
|
numtyp qkx = qkxx*xr + qkxy*yr + qkxz*zr;
|
|
numtyp qky = qkxy*xr + qkyy*yr + qkyz*zr;
|
|
numtyp qkz = qkxz*xr + qkyz*yr + qkzz*zr;
|
|
numtyp qkr = qkx*xr + qky*yr + qkz*zr;
|
|
numtyp uir = uix*xr + uiy*yr + uiz*zr;
|
|
numtyp uirp = uixp*xr + uiyp*yr + uizp*zr;
|
|
numtyp ukr = ukx*xr + uky*yr + ukz*zr;
|
|
numtyp ukrp = ukxp*xr + ukyp*yr + ukzp*zr;
|
|
|
|
// get reciprocal distance terms for this interaction
|
|
|
|
numtyp rinv = ucl_recip(r);
|
|
numtyp r2inv = rinv*rinv;
|
|
numtyp rr1 = felec * rinv;
|
|
numtyp rr3 = rr1 * r2inv;
|
|
numtyp rr5 = (numtyp)3.0 * rr3 * r2inv;
|
|
numtyp rr7 = (numtyp)5.0 * rr5 * r2inv;
|
|
numtyp rr9 = (numtyp)7.0 * rr7 * r2inv;
|
|
|
|
// calculate the real space Ewald error function terms
|
|
|
|
numtyp ralpha = aewald * r;
|
|
numtyp exp2a = ucl_exp(-ralpha*ralpha);
|
|
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*ralpha);
|
|
numtyp _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * exp2a;
|
|
//bn[0] = erfc(ralpha) / r;
|
|
bn[0] = _erfc * rinv;
|
|
numtyp alsq2 = (numtyp)2.0 * aewald*aewald;
|
|
numtyp alsq2n = (numtyp)0.0;
|
|
if (aewald > (numtyp)0.0) alsq2n = (numtyp)1.0 / (MY_PIS*aewald);
|
|
|
|
for (m = 1; m <= 4; m++) {
|
|
bfac = (numtyp) (m+m-1);
|
|
alsq2n = alsq2 * alsq2n;
|
|
bn[m] = (bfac*bn[m-1]+alsq2n*exp2a) / r2;
|
|
}
|
|
for (m = 0; m < 5; m++) bn[m] *= felec;
|
|
|
|
// apply Thole polarization damping to scale factors
|
|
|
|
numtyp sc3 = (numtyp)1.0;
|
|
numtyp sc5 = (numtyp)1.0;
|
|
numtyp sc7 = (numtyp)1.0;
|
|
for (k = 0; k < 3; k++) {
|
|
rc3[k] = (numtyp)0.0;
|
|
rc5[k] = (numtyp)0.0;
|
|
rc7[k] = (numtyp)0.0;
|
|
}
|
|
|
|
// apply Thole polarization damping to scale factors
|
|
|
|
numtyp damp = pdi * damping[jtype].x; // pdamp[jtype]
|
|
if (damp != (numtyp)0.0) {
|
|
numtyp pgamma = MIN(pti,damping[jtype].y); // thole[jtype]
|
|
damp = pgamma * ucl_powr(r/damp,(numtyp)3.0);
|
|
if (damp < (numtyp)50.0) {
|
|
numtyp expdamp = ucl_exp(-damp);
|
|
sc3 = (numtyp)1.0 - expdamp;
|
|
sc5 = (numtyp)1.0 - ((numtyp)1.0+damp)*expdamp;
|
|
sc7 = (numtyp)1.0 - ((numtyp)1.0+damp+(numtyp)0.6*damp*damp) * expdamp;
|
|
numtyp temp3 = (numtyp)3.0 * damp * expdamp * r2inv;
|
|
numtyp temp5 = damp;
|
|
numtyp temp7 = (numtyp)-0.2 + (numtyp)0.6*damp;
|
|
rc3[0] = xr * temp3;
|
|
rc3[1] = yr * temp3;
|
|
rc3[2] = zr * temp3;
|
|
rc5[0] = rc3[0] * temp5;
|
|
rc5[1] = rc3[1] * temp5;
|
|
rc5[2] = rc3[2] * temp5;
|
|
rc7[0] = rc5[0] * temp7;
|
|
rc7[1] = rc5[1] * temp7;
|
|
rc7[2] = rc5[2] * temp7;
|
|
}
|
|
|
|
psc3 = (numtyp)1.0 - sc3*factor_pscale;
|
|
psc5 = (numtyp)1.0 - sc5*factor_pscale;
|
|
psc7 = (numtyp)1.0 - sc7*factor_pscale;
|
|
dsc3 = (numtyp)1.0 - sc3*factor_dscale;
|
|
dsc5 = (numtyp)1.0 - sc5*factor_dscale;
|
|
dsc7 = (numtyp)1.0 - sc7*factor_dscale;
|
|
usc3 = (numtyp)1.0 - sc3*factor_uscale;
|
|
usc5 = (numtyp)1.0 - sc5*factor_uscale;
|
|
psr3 = bn[1] - psc3*rr3;
|
|
psr5 = bn[2] - psc5*rr5;
|
|
psr7 = bn[3] - psc7*rr7;
|
|
dsr3 = bn[1] - dsc3*rr3;
|
|
dsr5 = bn[2] - dsc5*rr5;
|
|
dsr7 = bn[3] - dsc7*rr7;
|
|
usr5 = bn[2] - usc5*rr5;
|
|
for (k = 0; k < 3; k++) {
|
|
prc3[k] = rc3[k] * factor_pscale;
|
|
prc5[k] = rc5[k] * factor_pscale;
|
|
prc7[k] = rc7[k] * factor_pscale;
|
|
drc3[k] = rc3[k] * factor_dscale;
|
|
drc5[k] = rc5[k] * factor_dscale;
|
|
drc7[k] = rc7[k] * factor_dscale;
|
|
urc3[k] = rc3[k] * factor_uscale;
|
|
urc5[k] = rc5[k] * factor_uscale;
|
|
}
|
|
} else { // damp == 0: ???
|
|
}
|
|
|
|
// get the induced dipole field used for dipole torques
|
|
|
|
numtyp tix3 = psr3*ukx + dsr3*ukxp;
|
|
numtyp tiy3 = psr3*uky + dsr3*ukyp;
|
|
numtyp tiz3 = psr3*ukz + dsr3*ukzp;
|
|
numtyp tuir = -psr5*ukr - dsr5*ukrp;
|
|
|
|
ufld[0] += tix3 + xr*tuir;
|
|
ufld[1] += tiy3 + yr*tuir;
|
|
ufld[2] += tiz3 + zr*tuir;
|
|
|
|
// get induced dipole field gradient used for quadrupole torques
|
|
|
|
numtyp tix5 = (numtyp)2.0 * (psr5*ukx+dsr5*ukxp);
|
|
numtyp tiy5 = (numtyp)2.0 * (psr5*uky+dsr5*ukyp);
|
|
numtyp tiz5 = (numtyp)2.0 * (psr5*ukz+dsr5*ukzp);
|
|
tuir = -psr7*ukr - dsr7*ukrp;
|
|
|
|
dufld[0] += xr*tix5 + xr*xr*tuir;
|
|
dufld[1] += xr*tiy5 + yr*tix5 + (numtyp)2.0*xr*yr*tuir;
|
|
dufld[2] += yr*tiy5 + yr*yr*tuir;
|
|
dufld[3] += xr*tiz5 + zr*tix5 + (numtyp)2.0*xr*zr*tuir;
|
|
dufld[4] += yr*tiz5 + zr*tiy5 + (numtyp)2.0*yr*zr*tuir;
|
|
dufld[5] += zr*tiz5 + zr*zr*tuir;
|
|
|
|
// get the dEd/dR terms used for direct polarization force
|
|
|
|
term1 = bn[2] - dsc3*rr5;
|
|
term2 = bn[3] - dsc5*rr7;
|
|
term3 = -dsr3 + term1*xr*xr - rr3*xr*drc3[0];
|
|
term4 = rr3*drc3[0] - term1*xr - dsr5*xr;
|
|
term5 = term2*xr*xr - dsr5 - rr5*xr*drc5[0];
|
|
term6 = (bn[4]-dsc7*rr9)*xr*xr - bn[3] - rr7*xr*drc7[0];
|
|
term7 = rr5*drc5[0] - (numtyp)2.0*bn[3]*xr + (dsc5+(numtyp)1.5*dsc7)*rr7*xr;
|
|
numtyp tixx = ci*term3 + dix*term4 + dir*term5 +
|
|
(numtyp)2.0*dsr5*qixx + (qiy*yr+qiz*zr)*dsc7*rr7 + (numtyp)2.0*qix*term7 + qir*term6;
|
|
numtyp tkxx = ck*term3 - dkx*term4 - dkr*term5 +
|
|
(numtyp)2.0*dsr5*qkxx + (qky*yr+qkz*zr)*dsc7*rr7 + (numtyp)2.0*qkx*term7 + qkr*term6;
|
|
|
|
term3 = -dsr3 + term1*yr*yr - rr3*yr*drc3[1];
|
|
term4 = rr3*drc3[1] - term1*yr - dsr5*yr;
|
|
term5 = term2*yr*yr - dsr5 - rr5*yr*drc5[1];
|
|
term6 = (bn[4]-dsc7*rr9)*yr*yr - bn[3] - rr7*yr*drc7[1];
|
|
term7 = rr5*drc5[1] - (numtyp)2.0*bn[3]*yr + (dsc5+(numtyp)1.5*dsc7)*rr7*yr;
|
|
numtyp tiyy = ci*term3 + diy*term4 + dir*term5 +
|
|
(numtyp)2.0*dsr5*qiyy + (qix*xr+qiz*zr)*dsc7*rr7 + (numtyp)2.0*qiy*term7 + qir*term6;
|
|
numtyp tkyy = ck*term3 - dky*term4 - dkr*term5 +
|
|
(numtyp)2.0*dsr5*qkyy + (qkx*xr+qkz*zr)*dsc7*rr7 + (numtyp)2.0*qky*term7 + qkr*term6;
|
|
|
|
term3 = -dsr3 + term1*zr*zr - rr3*zr*drc3[2];
|
|
term4 = rr3*drc3[2] - term1*zr - dsr5*zr;
|
|
term5 = term2*zr*zr - dsr5 - rr5*zr*drc5[2];
|
|
term6 = (bn[4]-dsc7*rr9)*zr*zr - bn[3] - rr7*zr*drc7[2];
|
|
term7 = rr5*drc5[2] - (numtyp)2.0*bn[3]*zr + (dsc5+(numtyp)1.5*dsc7)*rr7*zr;
|
|
numtyp tizz = ci*term3 + diz*term4 + dir*term5 +
|
|
(numtyp)2.0*dsr5*qizz + (qix*xr+qiy*yr)*dsc7*rr7 + (numtyp)2.0*qiz*term7 + qir*term6;
|
|
numtyp tkzz = ck*term3 - dkz*term4 - dkr*term5 +
|
|
(numtyp)2.0*dsr5*qkzz + (qkx*xr+qky*yr)*dsc7*rr7 + (numtyp)2.0*qkz*term7 + qkr*term6;
|
|
|
|
term3 = term1*xr*yr - rr3*yr*drc3[0];
|
|
term4 = rr3*drc3[0] - term1*xr;
|
|
term5 = term2*xr*yr - rr5*yr*drc5[0];
|
|
term6 = (bn[4]-dsc7*rr9)*xr*yr - rr7*yr*drc7[0];
|
|
term7 = rr5*drc5[0] - term2*xr;
|
|
numtyp tixy = ci*term3 - dsr5*dix*yr + diy*term4 + dir*term5 +
|
|
(numtyp)2.0*dsr5*qixy - (numtyp)2.0*dsr7*yr*qix + (numtyp)2.0*qiy*term7 + qir*term6;
|
|
numtyp tkxy = ck*term3 + dsr5*dkx*yr - dky*term4 - dkr*term5 +
|
|
(numtyp)2.0*dsr5*qkxy - (numtyp)2.0*dsr7*yr*qkx +(numtyp) 2.0*qky*term7 + qkr*term6;
|
|
|
|
term3 = term1*xr*zr - rr3*zr*drc3[0];
|
|
term5 = term2*xr*zr - rr5*zr*drc5[0];
|
|
term6 = (bn[4]-dsc7*rr9)*xr*zr - rr7*zr*drc7[0];
|
|
numtyp tixz = ci*term3 - dsr5*dix*zr + diz*term4 + dir*term5 +
|
|
(numtyp)2.0*dsr5*qixz - (numtyp)2.0*dsr7*zr*qix + (numtyp)2.0*qiz*term7 + qir*term6;
|
|
numtyp tkxz = ck*term3 + dsr5*dkx*zr - dkz*term4 - dkr*term5 +
|
|
(numtyp)2.0*dsr5*qkxz - (numtyp)2.0*dsr7*zr*qkx + (numtyp)2.0*qkz*term7 + qkr*term6;
|
|
|
|
term3 = term1*yr*zr - rr3*zr*drc3[1];
|
|
term4 = rr3*drc3[1] - term1*yr;
|
|
term5 = term2*yr*zr - rr5*zr*drc5[1];
|
|
term6 = (bn[4]-dsc7*rr9)*yr*zr - rr7*zr*drc7[1];
|
|
term7 = rr5*drc5[1] - term2*yr;
|
|
numtyp tiyz = ci*term3 - dsr5*diy*zr + diz*term4 + dir*term5 +
|
|
(numtyp)2.0*dsr5*qiyz - (numtyp)2.0*dsr7*zr*qiy + (numtyp)2.0*qiz*term7 + qir*term6;
|
|
numtyp tkyz = ck*term3 + dsr5*dky*zr - dkz*term4 - dkr*term5 +
|
|
(numtyp)2.0*dsr5*qkyz - (numtyp)2.0*dsr7*zr*qky + (numtyp)2.0*qkz*term7 + qkr*term6;
|
|
|
|
numtyp depx = tixx*ukxp + tixy*ukyp + tixz*ukzp - tkxx*uixp - tkxy*uiyp - tkxz*uizp;
|
|
numtyp depy = tixy*ukxp + tiyy*ukyp + tiyz*ukzp - tkxy*uixp - tkyy*uiyp - tkyz*uizp;
|
|
numtyp depz = tixz*ukxp + tiyz*ukyp + tizz*ukzp - tkxz*uixp - tkyz*uiyp - tkzz*uizp;
|
|
|
|
numtyp frcx = depx;
|
|
numtyp frcy = depy;
|
|
numtyp frcz = depz;
|
|
|
|
// get the dEp/dR terms used for direct polarization force
|
|
|
|
// tixx and tkxx
|
|
term1 = bn[2] - psc3*rr5;
|
|
term2 = bn[3] - psc5*rr7;
|
|
term3 = -psr3 + term1*xr*xr - rr3*xr*prc3[0];
|
|
term4 = rr3*prc3[0] - term1*xr - psr5*xr;
|
|
term5 = term2*xr*xr - psr5 - rr5*xr*prc5[0];
|
|
term6 = (bn[4]-psc7*rr9)*xr*xr - bn[3] - rr7*xr*prc7[0];
|
|
term7 = rr5*prc5[0] - (numtyp)2.0*bn[3]*xr + (psc5+(numtyp)1.5*psc7)*rr7*xr;
|
|
tixx = ci*term3 + dix*term4 + dir*term5 +
|
|
(numtyp)2.0*psr5*qixx + (qiy*yr+qiz*zr)*psc7*rr7 + (numtyp)2.0*qix*term7 + qir*term6;
|
|
tkxx = ck*term3 - dkx*term4 - dkr*term5 +
|
|
(numtyp)2.0*psr5*qkxx + (qky*yr+qkz*zr)*psc7*rr7 + (numtyp)2.0*qkx*term7 + qkr*term6;
|
|
|
|
// tiyy and tkyy
|
|
term3 = -psr3 + term1*yr*yr - rr3*yr*prc3[1];
|
|
term4 = rr3*prc3[1] - term1*yr - psr5*yr;
|
|
term5 = term2*yr*yr - psr5 - rr5*yr*prc5[1];
|
|
term6 = (bn[4]-psc7*rr9)*yr*yr - bn[3] - rr7*yr*prc7[1];
|
|
term7 = rr5*prc5[1] - (numtyp)2.0*bn[3]*yr + (psc5+(numtyp)1.5*psc7)*rr7*yr;
|
|
tiyy = ci*term3 + diy*term4 + dir*term5 +
|
|
(numtyp)2.0*psr5*qiyy + (qix*xr+qiz*zr)*psc7*rr7 + (numtyp)2.0*qiy*term7 + qir*term6;
|
|
tkyy = ck*term3 - dky*term4 - dkr*term5 +
|
|
(numtyp)2.0*psr5*qkyy + (qkx*xr+qkz*zr)*psc7*rr7 + (numtyp)2.0*qky*term7 + qkr*term6;
|
|
|
|
// tizz and tkzz
|
|
term3 = -psr3 + term1*zr*zr - rr3*zr*prc3[2];
|
|
term4 = rr3*prc3[2] - term1*zr - psr5*zr;
|
|
term5 = term2*zr*zr - psr5 - rr5*zr*prc5[2];
|
|
term6 = (bn[4]-psc7*rr9)*zr*zr - bn[3] - rr7*zr*prc7[2];
|
|
term7 = rr5*prc5[2] - (numtyp)2.0*bn[3]*zr + (psc5+(numtyp)1.5*psc7)*rr7*zr;
|
|
tizz = ci*term3 + diz*term4 + dir*term5 +
|
|
(numtyp)2.0*psr5*qizz + (qix*xr+qiy*yr)*psc7*rr7 + (numtyp)2.0*qiz*term7 + qir*term6;
|
|
tkzz = ck*term3 - dkz*term4 - dkr*term5 +
|
|
(numtyp)2.0*psr5*qkzz + (qkx*xr+qky*yr)*psc7*rr7 + (numtyp)2.0*qkz*term7 + qkr*term6;
|
|
|
|
// tixy and tkxy
|
|
term3 = term1*xr*yr - rr3*yr*prc3[0];
|
|
term4 = rr3*prc3[0] - term1*xr;
|
|
term5 = term2*xr*yr - rr5*yr*prc5[0];
|
|
term6 = (bn[4]-psc7*rr9)*xr*yr - rr7*yr*prc7[0];
|
|
term7 = rr5*prc5[0] - term2*xr;
|
|
tixy = ci*term3 - psr5*dix*yr + diy*term4 + dir*term5 +
|
|
(numtyp)2.0*psr5*qixy - (numtyp)2.0*psr7*yr*qix + (numtyp)2.0*qiy*term7 + qir*term6;
|
|
tkxy = ck*term3 + psr5*dkx*yr - dky*term4 - dkr*term5 +
|
|
(numtyp)2.0*psr5*qkxy - (numtyp)2.0*psr7*yr*qkx + (numtyp)2.0*qky*term7 + qkr*term6;
|
|
|
|
// tixz and tkxz
|
|
term3 = term1*xr*zr - rr3*zr*prc3[0];
|
|
term5 = term2*xr*zr - rr5*zr*prc5[0];
|
|
term6 = (bn[4]-psc7*rr9)*xr*zr - rr7*zr*prc7[0];
|
|
tixz = ci*term3 - psr5*dix*zr + diz*term4 + dir*term5 +
|
|
(numtyp)2.0*psr5*qixz - (numtyp)2.0*psr7*zr*qix + (numtyp)2.0*qiz*term7 + qir*term6;
|
|
tkxz = ck*term3 + psr5*dkx*zr - dkz*term4 - dkr*term5 +
|
|
(numtyp)2.0*psr5*qkxz - (numtyp)2.0*psr7*zr*qkx + (numtyp)2.0*qkz*term7 + qkr*term6;
|
|
|
|
// tiyz and tkyz
|
|
term3 = term1*yr*zr - rr3*zr*prc3[1];
|
|
term4 = rr3*prc3[1] - term1*yr;
|
|
term5 = term2*yr*zr - rr5*zr*prc5[1];
|
|
term6 = (bn[4]-psc7*rr9)*yr*zr - rr7*zr*prc7[1];
|
|
term7 = rr5*prc5[1] - term2*yr;
|
|
tiyz = ci*term3 - psr5*diy*zr + diz*term4 + dir*term5 +
|
|
(numtyp)2.0*psr5*qiyz - (numtyp)2.0*psr7*zr*qiy + (numtyp)2.0*qiz*term7 + qir*term6;
|
|
tkyz = ck*term3 + psr5*dky*zr - dkz*term4 - dkr*term5 +
|
|
(numtyp)2.0*psr5*qkyz - (numtyp)2.0*psr7*zr*qky + (numtyp)2.0*qkz*term7 + qkr*term6;
|
|
|
|
depx = tixx*ukx + tixy*uky + tixz*ukz - tkxx*uix - tkxy*uiy - tkxz*uiz;
|
|
depy = tixy*ukx + tiyy*uky + tiyz*ukz - tkxy*uix - tkyy*uiy - tkyz*uiz;
|
|
depz = tixz*ukx + tiyz*uky + tizz*ukz - tkxz*uix - tkyz*uiy - tkzz*uiz;
|
|
|
|
frcx = frcx + depx;
|
|
frcy = frcy + depy;
|
|
frcz = frcz + depz;
|
|
|
|
// get the dtau/dr terms used for mutual polarization force
|
|
// poltyp == MUTUAL && amoeba
|
|
|
|
term1 = bn[2] - usc3*rr5;
|
|
term2 = bn[3] - usc5*rr7;
|
|
term3 = usr5 + term1;
|
|
term4 = rr3 * factor_uscale;
|
|
term5 = -xr*term3 + rc3[0]*term4;
|
|
term6 = -usr5 + xr*xr*term2 - rr5*xr*urc5[0];
|
|
tixx = uix*term5 + uir*term6;
|
|
tkxx = ukx*term5 + ukr*term6;
|
|
|
|
term5 = -yr*term3 + rc3[1]*term4;
|
|
term6 = -usr5 + yr*yr*term2 - rr5*yr*urc5[1];
|
|
tiyy = uiy*term5 + uir*term6;
|
|
tkyy = uky*term5 + ukr*term6;
|
|
|
|
term5 = -zr*term3 + rc3[2]*term4;
|
|
term6 = -usr5 + zr*zr*term2 - rr5*zr*urc5[2];
|
|
tizz = uiz*term5 + uir*term6;
|
|
tkzz = ukz*term5 + ukr*term6;
|
|
|
|
term4 = -usr5 * yr;
|
|
term5 = -xr*term1 + rr3*urc3[0];
|
|
term6 = xr*yr*term2 - rr5*yr*urc5[0];
|
|
tixy = uix*term4 + uiy*term5 + uir*term6;
|
|
tkxy = ukx*term4 + uky*term5 + ukr*term6;
|
|
|
|
term4 = -usr5 * zr;
|
|
term6 = xr*zr*term2 - rr5*zr*urc5[0];
|
|
tixz = uix*term4 + uiz*term5 + uir*term6;
|
|
tkxz = ukx*term4 + ukz*term5 + ukr*term6;
|
|
|
|
term5 = -yr*term1 + rr3*urc3[1];
|
|
term6 = yr*zr*term2 - rr5*zr*urc5[1];
|
|
tiyz = uiy*term4 + uiz*term5 + uir*term6;
|
|
tkyz = uky*term4 + ukz*term5 + ukr*term6;
|
|
|
|
depx = tixx*ukxp + tixy*ukyp + tixz*ukzp
|
|
+ tkxx*uixp + tkxy*uiyp + tkxz*uizp;
|
|
depy = tixy*ukxp + tiyy*ukyp + tiyz*ukzp
|
|
+ tkxy*uixp + tkyy*uiyp + tkyz*uizp;
|
|
depz = tixz*ukxp + tiyz*ukyp + tizz*ukzp
|
|
+ tkxz*uixp + tkyz*uiyp + tkzz*uizp;
|
|
|
|
frcx = frcx + depx;
|
|
frcy = frcy + depy;
|
|
frcz = frcz + depz;
|
|
|
|
f.x -= frcx;
|
|
f.y -= frcy;
|
|
f.z -= frcz;
|
|
|
|
if (EVFLAG && vflag) {
|
|
numtyp vxx = xr * frcx;
|
|
numtyp vxy = (numtyp)0.5 * (yr*frcx+xr*frcy);
|
|
numtyp vxz = (numtyp)0.5 * (zr*frcx+xr*frcz);
|
|
numtyp vyy = yr * frcy;
|
|
numtyp vyz = (numtyp)0.5 * (zr*frcy+yr*frcz);
|
|
numtyp vzz = zr * frcz;
|
|
|
|
virial[0] += vxx;
|
|
virial[1] += vyy;
|
|
virial[2] += vzz;
|
|
virial[3] += vxy;
|
|
virial[4] += vxz;
|
|
virial[5] += vyz;
|
|
}
|
|
} // nbor
|
|
|
|
} // ii<inum
|
|
|
|
// accumulate ufld and dufld to compute tep
|
|
store_answers_tep(ufld,dufld,ii,inum,tid,t_per_atom,offset,i,tep);
|
|
|
|
// accumate force, energy and virial
|
|
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,
|
|
offset,eflag,vflag,ans,engv);
|
|
}
|
|
|
|
__kernel void k_amoeba_short_nbor(const __global numtyp4 *restrict x_,
|
|
const __global int * dev_nbor,
|
|
const __global int * dev_packed,
|
|
__global int * dev_short_nbor,
|
|
const numtyp off2,
|
|
const int inum, const int nbor_pitch,
|
|
const int t_per_atom) {
|
|
__local int n_stride;
|
|
int tid, ii, offset;
|
|
atom_info(t_per_atom,ii,tid,offset);
|
|
|
|
if (ii<inum) {
|
|
int nbor, nbor_end;
|
|
int i, numj;
|
|
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
|
|
n_stride,nbor_end,nbor);
|
|
|
|
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
|
|
|
|
int ncount = 0;
|
|
int m = nbor;
|
|
dev_short_nbor[m] = 0;
|
|
int nbor_short = nbor+n_stride;
|
|
|
|
for ( ; nbor<nbor_end; nbor+=n_stride) {
|
|
|
|
int j=dev_packed[nbor];
|
|
int nj = j;
|
|
j &= NEIGHMASK15;
|
|
|
|
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
|
|
|
|
// Compute r12
|
|
numtyp delx = ix.x-jx.x;
|
|
numtyp dely = ix.y-jx.y;
|
|
numtyp delz = ix.z-jx.z;
|
|
numtyp rsq = delx*delx+dely*dely+delz*delz;
|
|
|
|
if (rsq<off2) {
|
|
dev_short_nbor[nbor_short] = nj;
|
|
nbor_short += n_stride;
|
|
ncount++;
|
|
}
|
|
} // for nbor
|
|
|
|
// store the number of neighbors for each thread
|
|
dev_short_nbor[m] = ncount;
|
|
|
|
} // if ii
|
|
}
|