Unverified Commit 06dcc9e2 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'master' into improve-include-consistency 

# Conflicts:
#	src/USER-MESO/atom_vec_tdpd.cpp
parents 31e19e08 691fc357

doc/src/if.txt

+1 −2
Original line number Diff line number Diff line
@@ -57,8 +57,7 @@ Boolean expression is FALSE, then no commands are executed. 
The syntax for Boolean expressions is described below.



Each command (t1, f1, e1, etc) can be any valid LAMMPS input script

command, except an "include"_include.html command, which is not

allowed.  If the command is more than one word, it must enclosed in

command.  If the command is more than one word, it must enclosed in

quotes, so it will be treated as a single argument, as in the examples

above.

doc/src/pair_meamc.txt

+2 −1
Original line number Diff line number Diff line
@@ -147,7 +147,8 @@ asub = "A" parameter for MEAM (see e.g. "(Baskes)"_#Baskes) :pre 


The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the

standard MEAM parameters in the literature "(Baskes)"_#Baskes (the b

parameters are the standard beta parameters).  The rozero parameter is

parameters are the standard beta parameters). Note that only parameters

normalized to t0 = 1.0 are supported.  The rozero parameter is

an element-dependent density scaling that weights the reference

background density (see e.g. equation 4.5 in "(Gullet)"_#Gullet) and

is typically 1.0 for single-element systems.  The ibar parameter

doc/utils/sphinx-config/_themes/lammps_theme/static/css/theme.css

+13 −0
Original line number Diff line number Diff line
@@ -5092,4 +5092,17 @@ span[id*='MathJax-Span'] { 
  src: local("Roboto Slab Bold"), local("RobotoSlab-Bold"), url(../fonts/RobotoSlab-Bold.ttf) format("truetype");

}



.codeblock, pre.literal-block, .rst-content .literal-block, .rst-content pre.literal-block, div[class^='highlight'] {

  font-size: 12px;

  line-height: 1.5;

  display: block;

  overflow: auto;

  color: #404040;

  padding: 12px 12px;

}



.codeblock,div[class^='highlight'] {

  padding: 0;

}



/*# sourceMappingURL=theme.css.map */

lib/gpu/lal_lj96.cu

+1 −0
Original line number Diff line number Diff line
@@ -174,6 +174,7 @@ __kernel void k_lj96_fast(const __global numtyp4 *restrict x_, 
        numtyp r6inv = r2inv*r2inv*r2inv;

        numtyp r3inv = ucl_sqrt(r6inv);

        numtyp force = r2inv*r6inv*(lj1[mtype].x*r3inv-lj1[mtype].y);

        force*=factor_lj;



        f.x+=delx*force;

        f.y+=dely*force;

lib/gpu/lal_tersoff.cu

+7 −33
Original line number Diff line number Diff line
@@ -308,8 +308,6 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_, 
      delr1.z = jx.z-ix.z;

      numtyp rsq1 = delr1.x*delr1.x+delr1.y*delr1.y+delr1.z*delr1.z;



//      if (rsq1 > cutsq[ijparam]) continue;



      // compute zeta_ij

      z = (acctyp)0;
@@ -355,13 +353,9 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_, 
                  rsq1, rsq2, delr1, delr2);

      }



      //int jj = (nbor_j-offset_j-2*nbor_pitch)/n_stride;

      //int idx = jj*n_stride + i*t_per_atom + offset_j;

      // idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor

      int idx = nbor_j;

      if (dev_packed==dev_nbor) idx -= n_stride;

//      zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,

//               i, nbor_j, offset_j, idx);

      acc_zeta(z, tid, t_per_atom, offset_k);



      numtyp4 ts1_ijparam = ts1[ijparam]; //fetch4(ts1_ijparam,ijparam,ts1_tex);
@@ -585,14 +579,9 @@ __kernel void k_tersoff_three_center(const __global numtyp4 *restrict x_, 
      numtyp r1inv = ucl_rsqrt(rsq1);



      // look up for zeta_ij



      //int jj = (nbor_j-offset_j-2*nbor_pitch) / n_stride;

      //int idx = jj*n_stride + i*t_per_atom + offset_j;

      // idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor

      int idx = nbor_j;

      if (dev_packed==dev_nbor) idx -= n_stride;

//      zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,

//               i, nbor_j, offset_j, idx);

      acctyp4 zeta_ij = zetaij[idx]; // fetch(zeta_ij,idx,zeta_tex);

      numtyp force = zeta_ij.x*tpainv;

      numtyp prefactor = zeta_ij.y;
@@ -823,13 +812,9 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_, 
        offset_kf = red_acc[2*m+1];

      }



      //int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride;

      //int idx = iix*n_stride + j*t_per_atom + offset_kf;

      // idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor

      int idx = ijnum;

      if (dev_packed==dev_nbor) idx -= n_stride;

//      zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,

//               j, ijnum, offset_kf, idx);

      acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex);

      numtyp force = zeta_ji.x*tpainv;

      numtyp prefactor_ji = zeta_ji.y;
@@ -891,13 +876,10 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_, 
        f.y += fi[1];

        f.z += fi[2];



        //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;

        //int idx = kk*n_stride + j*t_per_atom + offset_k;

        // idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor

        int idx = nbor_k;

        if (dev_packed==dev_nbor) idx -= n_stride;

//        zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,

//                 j, nbor_k, offset_k, idx);



        acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);

        numtyp prefactor_jk = zeta_jk.y;

        int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype];
@@ -1068,13 +1050,9 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_, 
        offset_kf = red_acc[2*m+1];

      }



      //int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride;

      //int idx = iix*n_stride + j*t_per_atom + offset_kf;

      // idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor

      int idx = ijnum;

      if (dev_packed==dev_nbor) idx -= n_stride;

//      zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,

//               j, ijnum, offset_kf, idx);

      acctyp4 zeta_ji = zetaij[idx]; //  fetch(zeta_ji,idx,zeta_tex);

      numtyp force = zeta_ji.x*tpainv;

      numtyp prefactor_ji = zeta_ji.y;
@@ -1143,13 +1121,9 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_, 
        virial[4] += TWOTHIRD*(mdelr1[0]*fj[2] + delr2[0]*fk[2]);

        virial[5] += TWOTHIRD*(mdelr1[1]*fj[2] + delr2[1]*fk[2]);



        //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;

        //int idx = kk*n_stride + j*t_per_atom + offset_k;

        // idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor

        int idx = nbor_k;

        if (dev_packed==dev_nbor) idx -= n_stride;

//        zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,

//                 j, nbor_k, offset_k, idx);

        acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);

        numtyp prefactor_jk = zeta_jk.y;

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