git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15073 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/Section_commands.html

@@ -618,13 +618,13 @@ This is indicated by additional letters in parenthesis: c = USER-CUDA,
 g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="12%" />
 <col width="15%" />
 <col width="13%" />
 <col width="11%" />
 <col width="12%" />
 <col width="11%" />
 <col width="16%" />
+<col width="11%" />
 <col width="12%" />
 </colgroup>
 <tbody valign="top">
@@ -639,129 +639,129 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
 </tr>
 <tr class="row-even"><td><a class="reference internal" href="fix_ave_histo.html"><span class="doc">ave/histo</span></a></td>
 <td><a class="reference internal" href="fix_ave_histo.html"><span class="doc">ave/histo/weight</span></a></td>
-<td><a class="reference internal" href="fix_ave_spatial.html"><span class="doc">ave/spatial</span></a></td>
 <td><a class="reference internal" href="fix_ave_time.html"><span class="doc">ave/time</span></a></td>
 <td><a class="reference internal" href="fix_balance.html"><span class="doc">balance</span></a></td>
 <td><a class="reference internal" href="fix_bond_break.html"><span class="doc">bond/break</span></a></td>
 <td><a class="reference internal" href="fix_bond_create.html"><span class="doc">bond/create</span></a></td>
 <td><a class="reference internal" href="fix_bond_swap.html"><span class="doc">bond/swap</span></a></td>
+<td><a class="reference internal" href="fix_box_relax.html"><span class="doc">box/relax</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_box_relax.html"><span class="doc">box/relax</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_deform.html"><span class="doc">deform (k)</span></a></td>
-<td><a class="reference internal" href="fix_deform.html"><span class="doc">deform (k)</span></a></td>
 <td><a class="reference internal" href="fix_deposit.html"><span class="doc">deposit</span></a></td>
 <td><a class="reference internal" href="fix_drag.html"><span class="doc">drag</span></a></td>
 <td><a class="reference internal" href="fix_dt_reset.html"><span class="doc">dt/reset</span></a></td>
 <td><a class="reference internal" href="fix_efield.html"><span class="doc">efield</span></a></td>
 <td><a class="reference internal" href="fix_ehex.html"><span class="doc">ehex</span></a></td>
 <td><a class="reference internal" href="fix_enforce2d.html"><span class="doc">enforce2d (c)</span></a></td>
+<td><a class="reference internal" href="fix_evaporate.html"><span class="doc">evaporate</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_evaporate.html"><span class="doc">evaporate</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_external.html"><span class="doc">external</span></a></td>
-<td><a class="reference internal" href="fix_external.html"><span class="doc">external</span></a></td>
 <td><a class="reference internal" href="fix_freeze.html"><span class="doc">freeze (c)</span></a></td>
 <td><a class="reference internal" href="fix_gcmc.html"><span class="doc">gcmc</span></a></td>
 <td><a class="reference internal" href="fix_gld.html"><span class="doc">gld</span></a></td>
 <td><a class="reference internal" href="fix_gravity.html"><span class="doc">gravity (co)</span></a></td>
 <td><a class="reference internal" href="fix_heat.html"><span class="doc">heat</span></a></td>
 <td><a class="reference internal" href="fix_indent.html"><span class="doc">indent</span></a></td>
+<td><a class="reference internal" href="fix_langevin.html"><span class="doc">langevin (k)</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_langevin.html"><span class="doc">langevin (k)</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_lineforce.html"><span class="doc">lineforce</span></a></td>
-<td><a class="reference internal" href="fix_lineforce.html"><span class="doc">lineforce</span></a></td>
 <td><a class="reference internal" href="fix_momentum.html"><span class="doc">momentum</span></a></td>
 <td><a class="reference internal" href="fix_move.html"><span class="doc">move</span></a></td>
 <td><a class="reference internal" href="fix_msst.html"><span class="doc">msst</span></a></td>
 <td><a class="reference internal" href="fix_neb.html"><span class="doc">neb</span></a></td>
 <td><a class="reference internal" href="fix_nh.html"><span class="doc">nph (ko)</span></a></td>
 <td><a class="reference internal" href="fix_nphug.html"><span class="doc">nphug (o)</span></a></td>
+<td><a class="reference internal" href="fix_nph_asphere.html"><span class="doc">nph/asphere (o)</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_nph_asphere.html"><span class="doc">nph/asphere (o)</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_nph_body.html"><span class="doc">nph/body</span></a></td>
-<td><a class="reference internal" href="fix_nph_body.html"><span class="doc">nph/body</span></a></td>
 <td><a class="reference internal" href="fix_nph_sphere.html"><span class="doc">nph/sphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_nh.html"><span class="doc">npt (ckio)</span></a></td>
 <td><a class="reference internal" href="fix_npt_asphere.html"><span class="doc">npt/asphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_npt_body.html"><span class="doc">npt/body</span></a></td>
 <td><a class="reference internal" href="fix_npt_sphere.html"><span class="doc">npt/sphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_nve.html"><span class="doc">nve (ckio)</span></a></td>
+<td><a class="reference internal" href="fix_nve_asphere.html"><span class="doc">nve/asphere (i)</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_nve_asphere.html"><span class="doc">nve/asphere (i)</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_nve_asphere_noforce.html"><span class="doc">nve/asphere/noforce</span></a></td>
-<td><a class="reference internal" href="fix_nve_asphere_noforce.html"><span class="doc">nve/asphere/noforce</span></a></td>
 <td><a class="reference internal" href="fix_nve_body.html"><span class="doc">nve/body</span></a></td>
 <td><a class="reference internal" href="fix_nve_limit.html"><span class="doc">nve/limit</span></a></td>
 <td><a class="reference internal" href="fix_nve_line.html"><span class="doc">nve/line</span></a></td>
 <td><a class="reference internal" href="fix_nve_noforce.html"><span class="doc">nve/noforce</span></a></td>
 <td><a class="reference internal" href="fix_nve_sphere.html"><span class="doc">nve/sphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_nve_tri.html"><span class="doc">nve/tri</span></a></td>
+<td><a class="reference internal" href="fix_nh.html"><span class="doc">nvt (ciko)</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_nh.html"><span class="doc">nvt (ciko)</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_nvt_asphere.html"><span class="doc">nvt/asphere (o)</span></a></td>
-<td><a class="reference internal" href="fix_nvt_asphere.html"><span class="doc">nvt/asphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_nvt_body.html"><span class="doc">nvt/body</span></a></td>
 <td><a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">nvt/sllod (io)</span></a></td>
 <td><a class="reference internal" href="fix_nvt_sphere.html"><span class="doc">nvt/sphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_oneway.html"><span class="doc">oneway</span></a></td>
 <td><a class="reference internal" href="fix_orient_fcc.html"><span class="doc">orient/fcc</span></a></td>
 <td><a class="reference internal" href="fix_planeforce.html"><span class="doc">planeforce</span></a></td>
+<td><a class="reference internal" href="fix_poems.html"><span class="doc">poems</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_poems.html"><span class="doc">poems</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_pour.html"><span class="doc">pour</span></a></td>
-<td><a class="reference internal" href="fix_pour.html"><span class="doc">pour</span></a></td>
 <td><a class="reference internal" href="fix_press_berendsen.html"><span class="doc">press/berendsen</span></a></td>
 <td><a class="reference internal" href="fix_print.html"><span class="doc">print</span></a></td>
 <td><a class="reference internal" href="fix_property_atom.html"><span class="doc">property/atom</span></a></td>
 <td><a class="reference internal" href="fix_qeq_comb.html"><span class="doc">qeq/comb (o)</span></a></td>
 <td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/dynamic</span></a></td>
 <td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/fire</span></a></td>
+<td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/point</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/point</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/shielded</span></a></td>
-<td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/shielded</span></a></td>
 <td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/slater</span></a></td>
 <td><a class="reference internal" href="fix_shake.html"><span class="doc">rattle</span></a></td>
 <td><a class="reference internal" href="fix_reax_bonds.html"><span class="doc">reax/bonds</span></a></td>
 <td><a class="reference internal" href="fix_recenter.html"><span class="doc">recenter</span></a></td>
 <td><a class="reference internal" href="fix_restrain.html"><span class="doc">restrain</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid (o)</span></a></td>
+<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/nph (o)</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/nph (o)</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/npt (o)</span></a></td>
-<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/npt (o)</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/nve (o)</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/nvt (o)</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small (o)</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nph</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/npt</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nve</span></a></td>
+<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nvt</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nvt</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_setforce.html"><span class="doc">setforce (ck)</span></a></td>
-<td><a class="reference internal" href="fix_setforce.html"><span class="doc">setforce (ck)</span></a></td>
 <td><a class="reference internal" href="fix_shake.html"><span class="doc">shake (c)</span></a></td>
 <td><a class="reference internal" href="fix_spring.html"><span class="doc">spring</span></a></td>
 <td><a class="reference internal" href="fix_spring_rg.html"><span class="doc">spring/rg</span></a></td>
 <td><a class="reference internal" href="fix_spring_self.html"><span class="doc">spring/self</span></a></td>
 <td><a class="reference internal" href="fix_srd.html"><span class="doc">srd</span></a></td>
 <td><a class="reference internal" href="fix_store_force.html"><span class="doc">store/force</span></a></td>
+<td><a class="reference internal" href="fix_store_state.html"><span class="doc">store/state</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_store_state.html"><span class="doc">store/state</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">temp/berendsen (c)</span></a></td>
-<td><a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">temp/berendsen (c)</span></a></td>
 <td><a class="reference internal" href="fix_temp_csvr.html"><span class="doc">temp/csld</span></a></td>
 <td><a class="reference internal" href="fix_temp_csvr.html"><span class="doc">temp/csvr</span></a></td>
 <td><a class="reference internal" href="fix_temp_rescale.html"><span class="doc">temp/rescale (c)</span></a></td>
 <td><a class="reference internal" href="fix_tfmc.html"><span class="doc">tfmc</span></a></td>
 <td><a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">thermal/conductivity</span></a></td>
 <td><a class="reference internal" href="fix_tmd.html"><span class="doc">tmd</span></a></td>
+<td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_tune_kspace.html"><span class="doc">tune/kspace</span></a></td>
-<td><a class="reference internal" href="fix_tune_kspace.html"><span class="doc">tune/kspace</span></a></td>
 <td><a class="reference internal" href="fix_vector.html"><span class="doc">vector</span></a></td>
 <td><a class="reference internal" href="fix_viscosity.html"><span class="doc">viscosity</span></a></td>
 <td><a class="reference internal" href="fix_viscous.html"><span class="doc">viscous (c)</span></a></td>
 <td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/colloid</span></a></td>
 <td><a class="reference internal" href="fix_wall_gran.html"><span class="doc">wall/gran</span></a></td>
 <td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/harmonic</span></a></td>
+<td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj1043</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj1043</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj126</span></a></td>
-<td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj126</span></a></td>
 <td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj93</span></a></td>
 <td><a class="reference internal" href="fix_wall_piston.html"><span class="doc">wall/piston</span></a></td>
 <td><a class="reference internal" href="fix_wall_reflect.html"><span class="doc">wall/reflect (k)</span></a></td>
 <td><a class="reference internal" href="fix_wall_region.html"><span class="doc">wall/region</span></a></td>
 <td><a class="reference internal" href="fix_wall_srd.html"><span class="doc">wall/srd</span></a></td>
 <td>&nbsp;</td>
+<td>&nbsp;</td>
 </tr>
 </tbody>
 </table>
@@ -771,74 +771,74 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
 <colgroup>
 <col width="15%" />
 <col width="15%" />
-<col width="15%" />
 <col width="20%" />
 <col width="14%" />
 <col width="22%" />
+<col width="15%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td><a class="reference internal" href="fix_adapt_fep.html"><span class="doc">adapt/fep</span></a></td>
 <td><a class="reference internal" href="fix_addtorque.html"><span class="doc">addtorque</span></a></td>
 <td><a class="reference internal" href="fix_atc.html"><span class="doc">atc</span></a></td>
 <td><a class="reference internal" href="fix_ave_correlate_long.html"><span class="doc">ave/correlate/long</span></a></td>
-<td><a class="reference internal" href="fix_ave_spatial_sphere.html"><span class="doc">ave/spatial/sphere</span></a></td>
 <td><a class="reference internal" href="fix_colvars.html"><span class="doc">colvars</span></a></td>
+<td><a class="reference internal" href="fix_drude.html"><span class="doc">drude</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_drude.html"><span class="doc">drude</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_drude_transform.html"><span class="doc">drude/transform/direct</span></a></td>
-<td><a class="reference internal" href="fix_drude_transform.html"><span class="doc">drude/transform/direct</span></a></td>
 <td><a class="reference internal" href="fix_drude_transform.html"><span class="doc">drude/transform/reverse</span></a></td>
 <td><a class="reference internal" href="fix_eos_cv.html"><span class="doc">eos/cv</span></a></td>
 <td><a class="reference internal" href="fix_eos_table.html"><span class="doc">eos/table</span></a></td>
 <td><a class="reference internal" href="fix_gle.html"><span class="doc">gle</span></a></td>
+<td><a class="reference internal" href="fix_imd.html"><span class="doc">imd</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_imd.html"><span class="doc">imd</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_ipi.html"><span class="doc">ipi</span></a></td>
-<td><a class="reference internal" href="fix_ipi.html"><span class="doc">ipi</span></a></td>
 <td><a class="reference internal" href="fix_langevin_drude.html"><span class="doc">langevin/drude</span></a></td>
 <td><a class="reference internal" href="fix_langevin_eff.html"><span class="doc">langevin/eff</span></a></td>
 <td><a class="reference internal" href="fix_lb_fluid.html"><span class="doc">lb/fluid</span></a></td>
 <td><a class="reference internal" href="fix_lb_momentum.html"><span class="doc">lb/momentum</span></a></td>
+<td><a class="reference internal" href="fix_lb_pc.html"><span class="doc">lb/pc</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_lb_pc.html"><span class="doc">lb/pc</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_lb_rigid_pc_sphere.html"><span class="doc">lb/rigid/pc/sphere</span></a></td>
-<td><a class="reference internal" href="fix_lb_rigid_pc_sphere.html"><span class="doc">lb/rigid/pc/sphere</span></a></td>
 <td><a class="reference internal" href="fix_lb_viscous.html"><span class="doc">lb/viscous</span></a></td>
 <td><a class="reference internal" href="fix_meso.html"><span class="doc">meso</span></a></td>
 <td><a class="reference internal" href="fix_manifoldforce.html"><span class="doc">manifoldforce</span></a></td>
 <td><a class="reference internal" href="fix_meso_stationary.html"><span class="doc">meso/stationary</span></a></td>
+<td><a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">nve/manifold/rattle</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">nve/manifold/rattle</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_nvt_manifold_rattle.html"><span class="doc">nvt/manifold/rattle</span></a></td>
-<td><a class="reference internal" href="fix_nvt_manifold_rattle.html"><span class="doc">nvt/manifold/rattle</span></a></td>
 <td><a class="reference internal" href="fix_nh_eff.html"><span class="doc">nph/eff</span></a></td>
 <td><a class="reference internal" href="fix_nh_eff.html"><span class="doc">npt/eff</span></a></td>
 <td><a class="reference internal" href="fix_nve_eff.html"><span class="doc">nve/eff</span></a></td>
 <td><a class="reference internal" href="fix_nh_eff.html"><span class="doc">nvt/eff</span></a></td>
+<td><a class="reference internal" href="fix_nvt_sllod_eff.html"><span class="doc">nvt/sllod/eff</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_nvt_sllod_eff.html"><span class="doc">nvt/sllod/eff</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_phonon.html"><span class="doc">phonon</span></a></td>
-<td><a class="reference internal" href="fix_phonon.html"><span class="doc">phonon</span></a></td>
 <td><a class="reference internal" href="fix_pimd.html"><span class="doc">pimd</span></a></td>
 <td><a class="reference internal" href="fix_qbmsst.html"><span class="doc">qbmsst</span></a></td>
 <td><a class="reference internal" href="fix_qeq_reax.html"><span class="doc">qeq/reax</span></a></td>
 <td><a class="reference internal" href="fix_qmmm.html"><span class="doc">qmmm</span></a></td>
+<td><a class="reference internal" href="fix_qtb.html"><span class="doc">qtb</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_qtb.html"><span class="doc">qtb</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_reax_bonds.html"><span class="doc">reax/c/bonds</span></a></td>
-<td><a class="reference internal" href="fix_reax_bonds.html"><span class="doc">reax/c/bonds</span></a></td>
 <td><a class="reference internal" href="fix_reaxc_species.html"><span class="doc">reax/c/species</span></a></td>
 <td><a class="reference internal" href="fix_saed_vtk.html"><span class="doc">saed/vtk</span></a></td>
 <td><a class="reference internal" href="fix_shardlow.html"><span class="doc">shardlow</span></a></td>
 <td><a class="reference internal" href="fix_smd.html"><span class="doc">smd</span></a></td>
+<td><a class="reference internal" href="fix_smd_adjust_dt.html"><span class="doc">smd/adjust/dt</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_smd_adjust_dt.html"><span class="doc">smd/adjust/dt</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_smd_integrate_tlsph.html"><span class="doc">smd/integrate/tlsph</span></a></td>
-<td><a class="reference internal" href="fix_smd_integrate_tlsph.html"><span class="doc">smd/integrate/tlsph</span></a></td>
 <td><a class="reference internal" href="fix_smd_integrate_ulsph.html"><span class="doc">smd/integrate/ulsph</span></a></td>
 <td><a class="reference internal" href="fix_smd_move_triangulated_surface.html"><span class="doc">smd/move/triangulated/surface</span></a></td>
 <td><a class="reference internal" href="fix_smd_setvel.html"><span class="doc">smd/setvel</span></a></td>
 <td><a class="reference internal" href="fix_smd_tlsph_reference_configuration.html"><span class="doc">smd/tlsph/reference/configuration</span></a></td>
+<td><a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">smd/wall/surface</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">smd/wall/surface</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_temp_rescale_eff.html"><span class="doc">temp/rescale/eff</span></a></td>
-<td><a class="reference internal" href="fix_temp_rescale_eff.html"><span class="doc">temp/rescale/eff</span></a></td>
 <td><a class="reference internal" href="fix_ti_rs.html"><span class="doc">ti/rs</span></a></td>
 <td><a class="reference internal" href="fix_ti_spring.html"><span class="doc">ti/spring</span></a></td>
 <td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm/mod</span></a></td>
 <td>&nbsp;</td>
+<td>&nbsp;</td>
 </tr>
 </tbody>
 </table>

doc/html/Section_howto.html

@@ -1086,7 +1086,7 @@ the sheared fluid and integrate the SLLOD equations of motion for the
 system.  Fix nvt/sllod uses <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a> to compute a thermal temperature
 by subtracting out the streaming velocity of the shearing atoms.  The
 velocity profile or other properties of the fluid can be monitored via
-the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> command.</p>
+the <span class="xref doc">fix ave/spatial</span> command.</p>
 <p>As discussed in the previous section on non-orthogonal simulation
 boxes, the amount of tilt or skew that can be applied is limited by
 LAMMPS for computational efficiency to be 1/2 of the parallel box
@@ -2011,13 +2011,13 @@ on each of two regions to add/subtract specified amounts of energy to
 both regions.  In both cases, the resulting temperatures of the two
 regions can be monitored with the &#8220;compute temp/region&#8221; command and
 the temperature profile of the intermediate region can be monitored
-with the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> and <a class="reference internal" href="compute_ke_atom.html"><span class="doc">compute ke/atom</span></a> commands.</p>
+with the <span class="xref doc">fix ave/spatial</span> and <a class="reference internal" href="compute_ke_atom.html"><span class="doc">compute ke/atom</span></a> commands.</p>
 <p>The third method is to perform a reverse non-equilibrium MD simulation
 using the <a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a>
 command which implements the rNEMD algorithm of Muller-Plathe.
 Kinetic energy is swapped between atoms in two different layers of the
 simulation box.  This induces a temperature gradient between the two
-layers which can be monitored with the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> and <a class="reference internal" href="compute_ke_atom.html"><span class="doc">compute ke/atom</span></a> commands.  The fix tallies the
+layers which can be monitored with the <span class="xref doc">fix ave/spatial</span> and <a class="reference internal" href="compute_ke_atom.html"><span class="doc">compute ke/atom</span></a> commands.  The fix tallies the
 cumulative energy transfer that it performs.  See the <a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a> command for
 details.</p>
 <p>The fourth method is based on the Green-Kubo (GK) formula which
@@ -2060,7 +2060,7 @@ used to shear the fluid in between them, again with some kind of
 thermostat that modifies only the thermal (non-shearing) components of
 velocity to prevent the fluid from heating up.</p>
 <p>In both cases, the velocity profile setup in the fluid by this
-procedure can be monitored by the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> command, which determines
+procedure can be monitored by the <span class="xref doc">fix ave/spatial</span> command, which determines
 grad(Vstream) in the equation above.  E.g. the derivative in the
 y-direction of the Vx component of fluid motion or grad(Vstream) =
 dVx/dy.  The Pxy off-diagonal component of the pressure or stress
@@ -2073,7 +2073,7 @@ using the <a class="reference internal" href="fix_viscosity.html"><span class="d
 the rNEMD algorithm of Muller-Plathe.  Momentum in one dimension is
 swapped between atoms in two different layers of the simulation box in
 a different dimension.  This induces a velocity gradient which can be
-monitored with the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> command.
+monitored with the <span class="xref doc">fix ave/spatial</span> command.
 The fix tallies the cummulative momentum transfer that it performs.
 See the <a class="reference internal" href="fix_viscosity.html"><span class="doc">fix viscosity</span></a> command for details.</p>
 <p>The fourth method is based on the Green-Kubo (GK) formula which

doc/html/_sources/Section_commands.txt

@@ -457,60 +457,60 @@ with the :doc:`appropriate accelerated package <Section_accelerate>`.
 This is indicated by additional letters in parenthesis: c = USER-CUDA,
 g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`adapt <fix_adapt>`                 | :doc:`addforce (c) <fix_addforce>`                   | :doc:`append/atoms <fix_append_atoms>`       | :doc:`atom/swap <fix_atom_swap>`      | :doc:`aveforce (c) <fix_aveforce>`         | :doc:`ave/atom <fix_ave_atom>`       | :doc:`ave/chunk <fix_ave_chunk>`                       | :doc:`ave/correlate <fix_ave_correlate>` |
+| :doc:`adapt <fix_adapt>`                             | :doc:`addforce (c) <fix_addforce>`           | :doc:`append/atoms <fix_append_atoms>` | :doc:`atom/swap <fix_atom_swap>`           | :doc:`aveforce (c) <fix_aveforce>`   | :doc:`ave/atom <fix_ave_atom>`                         | :doc:`ave/chunk <fix_ave_chunk>`     | :doc:`ave/correlate <fix_ave_correlate>` |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`ave/histo <fix_ave_histo>`         | :doc:`ave/histo/weight <fix_ave_histo>`              | :doc:`ave/spatial <fix_ave_spatial>`         | :doc:`ave/time <fix_ave_time>`        | :doc:`balance <fix_balance>`               | :doc:`bond/break <fix_bond_break>`   | :doc:`bond/create <fix_bond_create>`                   | :doc:`bond/swap <fix_bond_swap>`         |
+| :doc:`ave/histo <fix_ave_histo>`                     | :doc:`ave/histo/weight <fix_ave_histo>`      | :doc:`ave/time <fix_ave_time>`         | :doc:`balance <fix_balance>`               | :doc:`bond/break <fix_bond_break>`   | :doc:`bond/create <fix_bond_create>`                   | :doc:`bond/swap <fix_bond_swap>`     | :doc:`box/relax <fix_box_relax>`         |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`box/relax <fix_box_relax>`         | :doc:`deform (k) <fix_deform>`                       | :doc:`deposit <fix_deposit>`                 | :doc:`drag <fix_drag>`                | :doc:`dt/reset <fix_dt_reset>`             | :doc:`efield <fix_efield>`           | :doc:`ehex <fix_ehex>`                                 | :doc:`enforce2d (c) <fix_enforce2d>`     |
+| :doc:`deform (k) <fix_deform>`                       | :doc:`deposit <fix_deposit>`                 | :doc:`drag <fix_drag>`                 | :doc:`dt/reset <fix_dt_reset>`             | :doc:`efield <fix_efield>`           | :doc:`ehex <fix_ehex>`                                 | :doc:`enforce2d (c) <fix_enforce2d>` | :doc:`evaporate <fix_evaporate>`         |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`evaporate <fix_evaporate>`         | :doc:`external <fix_external>`                       | :doc:`freeze (c) <fix_freeze>`               | :doc:`gcmc <fix_gcmc>`                | :doc:`gld <fix_gld>`                       | :doc:`gravity (co) <fix_gravity>`    | :doc:`heat <fix_heat>`                                 | :doc:`indent <fix_indent>`               |
+| :doc:`external <fix_external>`                       | :doc:`freeze (c) <fix_freeze>`               | :doc:`gcmc <fix_gcmc>`                 | :doc:`gld <fix_gld>`                       | :doc:`gravity (co) <fix_gravity>`    | :doc:`heat <fix_heat>`                                 | :doc:`indent <fix_indent>`           | :doc:`langevin (k) <fix_langevin>`       |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`langevin (k) <fix_langevin>`       | :doc:`lineforce <fix_lineforce>`                     | :doc:`momentum <fix_momentum>`               | :doc:`move <fix_move>`                | :doc:`msst <fix_msst>`                     | :doc:`neb <fix_neb>`                 | :doc:`nph (ko) <fix_nh>`                               | :doc:`nphug (o) <fix_nphug>`             |
+| :doc:`lineforce <fix_lineforce>`                     | :doc:`momentum <fix_momentum>`               | :doc:`move <fix_move>`                 | :doc:`msst <fix_msst>`                     | :doc:`neb <fix_neb>`                 | :doc:`nph (ko) <fix_nh>`                               | :doc:`nphug (o) <fix_nphug>`         | :doc:`nph/asphere (o) <fix_nph_asphere>` |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`nph/asphere (o) <fix_nph_asphere>` | :doc:`nph/body <fix_nph_body>`                       | :doc:`nph/sphere (o) <fix_nph_sphere>`       | :doc:`npt (ckio) <fix_nh>`            | :doc:`npt/asphere (o) <fix_npt_asphere>`   | :doc:`npt/body <fix_npt_body>`       | :doc:`npt/sphere (o) <fix_npt_sphere>`                 | :doc:`nve (ckio) <fix_nve>`              |
+| :doc:`nph/body <fix_nph_body>`                       | :doc:`nph/sphere (o) <fix_nph_sphere>`       | :doc:`npt (ckio) <fix_nh>`             | :doc:`npt/asphere (o) <fix_npt_asphere>`   | :doc:`npt/body <fix_npt_body>`       | :doc:`npt/sphere (o) <fix_npt_sphere>`                 | :doc:`nve (ckio) <fix_nve>`          | :doc:`nve/asphere (i) <fix_nve_asphere>` |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`nve/asphere (i) <fix_nve_asphere>` | :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` | :doc:`nve/body <fix_nve_body>`               | :doc:`nve/limit <fix_nve_limit>`      | :doc:`nve/line <fix_nve_line>`             | :doc:`nve/noforce <fix_nve_noforce>` | :doc:`nve/sphere (o) <fix_nve_sphere>`                 | :doc:`nve/tri <fix_nve_tri>`             |
+| :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` | :doc:`nve/body <fix_nve_body>`               | :doc:`nve/limit <fix_nve_limit>`       | :doc:`nve/line <fix_nve_line>`             | :doc:`nve/noforce <fix_nve_noforce>` | :doc:`nve/sphere (o) <fix_nve_sphere>`                 | :doc:`nve/tri <fix_nve_tri>`         | :doc:`nvt (ciko) <fix_nh>`               |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`nvt (ciko) <fix_nh>`               | :doc:`nvt/asphere (o) <fix_nvt_asphere>`             | :doc:`nvt/body <fix_nvt_body>`               | :doc:`nvt/sllod (io) <fix_nvt_sllod>` | :doc:`nvt/sphere (o) <fix_nvt_sphere>`     | :doc:`oneway <fix_oneway>`           | :doc:`orient/fcc <fix_orient_fcc>`                     | :doc:`planeforce <fix_planeforce>`       |
+| :doc:`nvt/asphere (o) <fix_nvt_asphere>`             | :doc:`nvt/body <fix_nvt_body>`               | :doc:`nvt/sllod (io) <fix_nvt_sllod>`  | :doc:`nvt/sphere (o) <fix_nvt_sphere>`     | :doc:`oneway <fix_oneway>`           | :doc:`orient/fcc <fix_orient_fcc>`                     | :doc:`planeforce <fix_planeforce>`   | :doc:`poems <fix_poems>`                 |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`poems <fix_poems>`                 | :doc:`pour <fix_pour>`                               | :doc:`press/berendsen <fix_press_berendsen>` | :doc:`print <fix_print>`              | :doc:`property/atom <fix_property_atom>`   | :doc:`qeq/comb (o) <fix_qeq_comb>`   | :doc:`qeq/dynamic <fix_qeq>`                           | :doc:`qeq/fire <fix_qeq>`                |
+| :doc:`pour <fix_pour>`                               | :doc:`press/berendsen <fix_press_berendsen>` | :doc:`print <fix_print>`               | :doc:`property/atom <fix_property_atom>`   | :doc:`qeq/comb (o) <fix_qeq_comb>`   | :doc:`qeq/dynamic <fix_qeq>`                           | :doc:`qeq/fire <fix_qeq>`            | :doc:`qeq/point <fix_qeq>`               |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`qeq/point <fix_qeq>`               | :doc:`qeq/shielded <fix_qeq>`                        | :doc:`qeq/slater <fix_qeq>`                  | :doc:`rattle <fix_shake>`             | :doc:`reax/bonds <fix_reax_bonds>`         | :doc:`recenter <fix_recenter>`       | :doc:`restrain <fix_restrain>`                         | :doc:`rigid (o) <fix_rigid>`             |
+| :doc:`qeq/shielded <fix_qeq>`                        | :doc:`qeq/slater <fix_qeq>`                  | :doc:`rattle <fix_shake>`              | :doc:`reax/bonds <fix_reax_bonds>`         | :doc:`recenter <fix_recenter>`       | :doc:`restrain <fix_restrain>`                         | :doc:`rigid (o) <fix_rigid>`         | :doc:`rigid/nph (o) <fix_rigid>`         |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`rigid/nph (o) <fix_rigid>`         | :doc:`rigid/npt (o) <fix_rigid>`                     | :doc:`rigid/nve (o) <fix_rigid>`             | :doc:`rigid/nvt (o) <fix_rigid>`      | :doc:`rigid/small (o) <fix_rigid>`         | :doc:`rigid/small/nph <fix_rigid>`   | :doc:`rigid/small/npt <fix_rigid>`                     | :doc:`rigid/small/nve <fix_rigid>`       |
+| :doc:`rigid/npt (o) <fix_rigid>`                     | :doc:`rigid/nve (o) <fix_rigid>`             | :doc:`rigid/nvt (o) <fix_rigid>`       | :doc:`rigid/small (o) <fix_rigid>`         | :doc:`rigid/small/nph <fix_rigid>`   | :doc:`rigid/small/npt <fix_rigid>`                     | :doc:`rigid/small/nve <fix_rigid>`   | :doc:`rigid/small/nvt <fix_rigid>`       |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`rigid/small/nvt <fix_rigid>`       | :doc:`setforce (ck) <fix_setforce>`                  | :doc:`shake (c) <fix_shake>`                 | :doc:`spring <fix_spring>`            | :doc:`spring/rg <fix_spring_rg>`           | :doc:`spring/self <fix_spring_self>` | :doc:`srd <fix_srd>`                                   | :doc:`store/force <fix_store_force>`     |
+| :doc:`setforce (ck) <fix_setforce>`                  | :doc:`shake (c) <fix_shake>`                 | :doc:`spring <fix_spring>`             | :doc:`spring/rg <fix_spring_rg>`           | :doc:`spring/self <fix_spring_self>` | :doc:`srd <fix_srd>`                                   | :doc:`store/force <fix_store_force>` | :doc:`store/state <fix_store_state>`     |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`store/state <fix_store_state>`     | :doc:`temp/berendsen (c) <fix_temp_berendsen>`       | :doc:`temp/csld <fix_temp_csvr>`             | :doc:`temp/csvr <fix_temp_csvr>`      | :doc:`temp/rescale (c) <fix_temp_rescale>` | :doc:`tfmc <fix_tfmc>`               | :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`tmd <fix_tmd>`                     |
+| :doc:`temp/berendsen (c) <fix_temp_berendsen>`       | :doc:`temp/csld <fix_temp_csvr>`             | :doc:`temp/csvr <fix_temp_csvr>`       | :doc:`temp/rescale (c) <fix_temp_rescale>` | :doc:`tfmc <fix_tfmc>`               | :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`tmd <fix_tmd>`                 | :doc:`ttm <fix_ttm>`                     |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`ttm <fix_ttm>`                     | :doc:`tune/kspace <fix_tune_kspace>`                 | :doc:`vector <fix_vector>`                   | :doc:`viscosity <fix_viscosity>`      | :doc:`viscous (c) <fix_viscous>`           | :doc:`wall/colloid <fix_wall>`       | :doc:`wall/gran <fix_wall_gran>`                       | :doc:`wall/harmonic <fix_wall>`          |
+| :doc:`tune/kspace <fix_tune_kspace>`                 | :doc:`vector <fix_vector>`                   | :doc:`viscosity <fix_viscosity>`       | :doc:`viscous (c) <fix_viscous>`           | :doc:`wall/colloid <fix_wall>`       | :doc:`wall/gran <fix_wall_gran>`                       | :doc:`wall/harmonic <fix_wall>`      | :doc:`wall/lj1043 <fix_wall>`            |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
-| :doc:`wall/lj1043 <fix_wall>`            | :doc:`wall/lj126 <fix_wall>`                         | :doc:`wall/lj93 <fix_wall>`                  | :doc:`wall/piston <fix_wall_piston>`  | :doc:`wall/reflect (k) <fix_wall_reflect>` | :doc:`wall/region <fix_wall_region>` | :doc:`wall/srd <fix_wall_srd>`                         |                                          |
+| :doc:`wall/lj126 <fix_wall>`                         | :doc:`wall/lj93 <fix_wall>`                  | :doc:`wall/piston <fix_wall_piston>`   | :doc:`wall/reflect (k) <fix_wall_reflect>` | :doc:`wall/region <fix_wall_region>` | :doc:`wall/srd <fix_wall_srd>`                         |                                      |                                          |
-+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
 
 These are additional fix styles in USER packages, which can be used if
 :ref:`LAMMPS is built with the appropriate package <start_3>`.
 
-+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+
++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
-| :doc:`adapt/fep <fix_adapt_fep>`                     | :doc:`addtorque <fix_addtorque>`                     | :doc:`atc <fix_atc>`                                 | :doc:`ave/correlate/long <fix_ave_correlate_long>`                       | :doc:`ave/spatial/sphere <fix_ave_spatial_sphere>` | :doc:`colvars <fix_colvars>`                                                     |
+| :doc:`adapt/fep <fix_adapt_fep>`                     | :doc:`addtorque <fix_addtorque>`                     | :doc:`atc <fix_atc>`                                                     | :doc:`ave/correlate/long <fix_ave_correlate_long>` | :doc:`colvars <fix_colvars>`                                                     | :doc:`drude <fix_drude>`                             |
-+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+
++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
-| :doc:`drude <fix_drude>`                             | :doc:`drude/transform/direct <fix_drude_transform>`  | :doc:`drude/transform/reverse <fix_drude_transform>` | :doc:`eos/cv <fix_eos_cv>`                                               | :doc:`eos/table <fix_eos_table>`                   | :doc:`gle <fix_gle>`                                                             |
+| :doc:`drude/transform/direct <fix_drude_transform>`  | :doc:`drude/transform/reverse <fix_drude_transform>` | :doc:`eos/cv <fix_eos_cv>`                                               | :doc:`eos/table <fix_eos_table>`                   | :doc:`gle <fix_gle>`                                                             | :doc:`imd <fix_imd>`                                 |
-+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+
++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
-| :doc:`imd <fix_imd>`                                 | :doc:`ipi <fix_ipi>`                                 | :doc:`langevin/drude <fix_langevin_drude>`           | :doc:`langevin/eff <fix_langevin_eff>`                                   | :doc:`lb/fluid <fix_lb_fluid>`                     | :doc:`lb/momentum <fix_lb_momentum>`                                             |
+| :doc:`ipi <fix_ipi>`                                 | :doc:`langevin/drude <fix_langevin_drude>`           | :doc:`langevin/eff <fix_langevin_eff>`                                   | :doc:`lb/fluid <fix_lb_fluid>`                     | :doc:`lb/momentum <fix_lb_momentum>`                                             | :doc:`lb/pc <fix_lb_pc>`                             |
-+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+
++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
-| :doc:`lb/pc <fix_lb_pc>`                             | :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`   | :doc:`lb/viscous <fix_lb_viscous>`                   | :doc:`meso <fix_meso>`                                                   | :doc:`manifoldforce <fix_manifoldforce>`           | :doc:`meso/stationary <fix_meso_stationary>`                                     |
+| :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`   | :doc:`lb/viscous <fix_lb_viscous>`                   | :doc:`meso <fix_meso>`                                                   | :doc:`manifoldforce <fix_manifoldforce>`           | :doc:`meso/stationary <fix_meso_stationary>`                                     | :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>` |
-+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+
++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
-| :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>` | :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>` | :doc:`nph/eff <fix_nh_eff>`                          | :doc:`npt/eff <fix_nh_eff>`                                              | :doc:`nve/eff <fix_nve_eff>`                       | :doc:`nvt/eff <fix_nh_eff>`                                                      |
+| :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>` | :doc:`nph/eff <fix_nh_eff>`                          | :doc:`npt/eff <fix_nh_eff>`                                              | :doc:`nve/eff <fix_nve_eff>`                       | :doc:`nvt/eff <fix_nh_eff>`                                                      | :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`             |
-+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+
++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
-| :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`             | :doc:`phonon <fix_phonon>`                           | :doc:`pimd <fix_pimd>`                               | :doc:`qbmsst <fix_qbmsst>`                                               | :doc:`qeq/reax <fix_qeq_reax>`                     | :doc:`qmmm <fix_qmmm>`                                                           |
+| :doc:`phonon <fix_phonon>`                           | :doc:`pimd <fix_pimd>`                               | :doc:`qbmsst <fix_qbmsst>`                                               | :doc:`qeq/reax <fix_qeq_reax>`                     | :doc:`qmmm <fix_qmmm>`                                                           | :doc:`qtb <fix_qtb>`                                 |
-+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+
++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
-| :doc:`qtb <fix_qtb>`                                 | :doc:`reax/c/bonds <fix_reax_bonds>`                 | :doc:`reax/c/species <fix_reaxc_species>`            | :doc:`saed/vtk <fix_saed_vtk>`                                           | :doc:`shardlow <fix_shardlow>`                     | :doc:`smd <fix_smd>`                                                             |
+| :doc:`reax/c/bonds <fix_reax_bonds>`                 | :doc:`reax/c/species <fix_reaxc_species>`            | :doc:`saed/vtk <fix_saed_vtk>`                                           | :doc:`shardlow <fix_shardlow>`                     | :doc:`smd <fix_smd>`                                                             | :doc:`smd/adjust/dt <fix_smd_adjust_dt>`             |
-+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+
++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
-| :doc:`smd/adjust/dt <fix_smd_adjust_dt>`             | :doc:`smd/integrate/tlsph <fix_smd_integrate_tlsph>` | :doc:`smd/integrate/ulsph <fix_smd_integrate_ulsph>` | :doc:`smd/move/triangulated/surface <fix_smd_move_triangulated_surface>` | :doc:`smd/setvel <fix_smd_setvel>`                 | :doc:`smd/tlsph/reference/configuration <fix_smd_tlsph_reference_configuration>` |
+| :doc:`smd/integrate/tlsph <fix_smd_integrate_tlsph>` | :doc:`smd/integrate/ulsph <fix_smd_integrate_ulsph>` | :doc:`smd/move/triangulated/surface <fix_smd_move_triangulated_surface>` | :doc:`smd/setvel <fix_smd_setvel>`                 | :doc:`smd/tlsph/reference/configuration <fix_smd_tlsph_reference_configuration>` | :doc:`smd/wall/surface <fix_smd_wall_surface>`       |
-+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+
++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
-| :doc:`smd/wall/surface <fix_smd_wall_surface>`       | :doc:`temp/rescale/eff <fix_temp_rescale_eff>`       | :doc:`ti/rs <fix_ti_rs>`                             | :doc:`ti/spring <fix_ti_spring>`                                         | :doc:`ttm/mod <fix_ttm>`                           |                                                                                  |
+| :doc:`temp/rescale/eff <fix_temp_rescale_eff>`       | :doc:`ti/rs <fix_ti_rs>`                             | :doc:`ti/spring <fix_ti_spring>`                                         | :doc:`ttm/mod <fix_ttm>`                           |                                                                                  |                                                      |
-+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+
++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
 
 
 ----------

doc/html/_sources/change_box.txt

@@ -359,11 +359,12 @@ Restrictions
 
 If you use the *ortho* or *triclinic* keywords, then at the point in
 the input script when this command is issued, no :doc:`dumps <dump>` can
-be active, nor can a :doc:`fix ave/spatial <fix_ave_spatial>` or :doc:`fix deform <fix_deform>` be active.  This is because these commands
+be active, nor can a :doc:`fix deform <fix_deform>` be active.  This is
-test whether the simulation box is orthogonal when they are first
+because these commands test whether the simulation box is orthogonal
-issued.  Note that these commands can be used in your script before a
+when they are first issued.  Note that these commands can be used in
-change_box command is issued, so long as an :doc:`undump <undump>` or
+your script before a change_box command is issued, so long as an
-:doc:`unfix <unfix>` command is also used to turn them off.
+:doc:`undump <undump>` or :doc:`unfix <unfix>` command is also used to
+turn them off.
 
 Related commands
 """"""""""""""""

doc/html/_sources/compute.txt

@@ -106,11 +106,10 @@ ways:
 * Global values can be output via the :doc:`thermo_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
   Or the values can be referenced in a :doc:`variable equal <variable>` or
   :doc:`variable atom <variable>` command.
-* Per-atom values can be output via the :doc:`dump custom <dump>` command
+* Per-atom values can be output via the :doc:`dump custom <dump>` command.
-  or the :doc:`fix ave/spatial <fix_ave_spatial>` command.  Or they can be
+  Or they can be time-averaged via the :doc:`fix ave/atom <fix_ave_atom>`
-  time-averaged via the :doc:`fix ave/atom <fix_ave_atom>` command or
+  command or reduced by the :doc:`compute reduce <compute_reduce>`
-  reduced by the :doc:`compute reduce <compute_reduce>` command.  Or the
+  command.  Or the per-atom values can be referenced in an :doc:`atom-style variable <variable>`.
-  per-atom values can be referenced in an :doc:`atom-style variable <variable>`.
 * Local values can be reduced by the :doc:`compute reduce <compute_reduce>` command, or histogrammed by the :doc:`fix ave/histo <fix_ave_histo>` command, or output by the :doc:`dump local <dump>` command.
 The results of computes that calculate global quantities can be either
 "intensive" or "extensive" values.  Intensive means the value is
@@ -261,8 +260,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`uncompute <uncompute>`, :doc:`compute_modify <compute_modify>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/spatial <fix_ave_spatial>`,
+:doc:`uncompute <uncompute>`, :doc:`compute_modify <compute_modify>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/histo <fix_ave_histo>`
-:doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/histo <fix_ave_histo>`
 
 **Default:** none
 

doc/html/_sources/compute_property_atom.txt

@@ -107,7 +107,7 @@ in the group.  This is useful so that the values can be used by other
 :ref:`output commands <howto_15>` that take computes as
 inputs.  See for example, the :doc:`compute reduce <compute_reduce>`,
 :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/histo <fix_ave_histo>`,
-:doc:`fix ave/spatial <fix_ave_spatial>`, and :doc:`atom-style variable <variable>` commands.
+:doc:`fix ave/chunk <fix_ave_chunk>`, and :doc:`atom-style variable <variable>` commands.
 
 The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning, with some
 additional quantities that are only defined for certain :doc:`atom styles <atom_style>`.  Basically, this augmented list gives an
@@ -171,7 +171,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/spatial <fix_ave_spatial>`,
+:doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
 :doc:`fix property/atom <fix_property_atom>`
 
 **Default:** none

doc/html/_sources/compute_temp_deform.txt

@@ -90,7 +90,7 @@ fixes that work in this way include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/resc
    off an incorrect stream velocity, yielding a bogus thermal
    temperature.  You should NOT assume that your atoms are streaming at
    the same rate the box is deforming.  Rather, you should monitor their
-   velocity profile, e.g. via the :doc:`fix ave/spatial <fix_ave_spatial>`
+   velocity profile, e.g. via the :doc:`fix ave/chunk <fix_ave_chunk>`
    command.  And you can compare the results of this compute to :doc:`compute temp/profile <compute_temp_profile>`, which actually calculates the
    stream profile before subtracting it.  If the two computes do not give
    roughly the same temperature, then your atoms are not streaming

doc/html/_sources/fix.txt

@@ -131,11 +131,10 @@ In LAMMPS, the values generated by a fix can be used in several ways:
 * Global values can be output via the :doc:`thermo_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
   Or the values can be referenced in a :doc:`variable equal <variable>` or
   :doc:`variable atom <variable>` command.
-* Per-atom values can be output via the :doc:`dump custom <dump>` command
+* Per-atom values can be output via the :doc:`dump custom <dump>` command.
-  or the :doc:`fix ave/spatial <fix_ave_spatial>` command.  Or they can be
+  Or they can be time-averaged via the :doc:`fix ave/atom <fix_ave_atom>`
-  time-averaged via the :doc:`fix ave/atom <fix_ave_atom>` command or
+  command or reduced by the :doc:`compute reduce <compute_reduce>`
-  reduced by the :doc:`compute reduce <compute_reduce>` command.  Or the
+  command.  Or the per-atom values can be referenced in an :doc:`atom-style variable <variable>`.
-  per-atom values can be referenced in an :doc:`atom-style variable <variable>`.
 * Local values can be reduced by the :doc:`compute reduce <compute_reduce>` command, or histogrammed by the :doc:`fix ave/histo <fix_ave_histo>` command.
 See this :ref:`howto section <howto_15>` for a summary of
 various LAMMPS output options, many of which involve fixes.
@@ -176,7 +175,6 @@ of :ref:`this page <cmd_5>`.
 * :doc:`ave/chunk <fix_ave_chunk>` - compute per-chunk time-averaged quantities
 * :doc:`ave/correlate <fix_ave_correlate>` - compute/output time correlations
 * :doc:`ave/histo <fix_ave_histo>` - compute/output time-averaged histograms
-* :doc:`ave/spatial <fix_ave_spatial>` - compute/output time-averaged per-atom quantities by layer
 * :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
 * :doc:`balance <fix_balance>` - perform dynamic load-balancing
 * :doc:`bond/break <fix_bond_break>` - break bonds on the fly

doc/html/_sources/fix_ave_atom.txt

@@ -41,7 +41,7 @@ Description
 
 Use one or more per-atom vectors as inputs every few timesteps, and
 average them atom by atom over longer timescales.  The resulting
-per-atom averages can be used by other :ref:`output commands <howto_15>` such as the :doc:`fix ave/spatial <fix_ave_spatial>` or :doc:`dump custom <dump>` commands.
+per-atom averages can be used by other :ref:`output commands <howto_15>` such as the :doc:`fix ave/chunk <fix_ave_chunk>` or :doc:`dump custom <dump>` commands.
 
 The group specified with the command means only atoms within the group
 have their averages computed.  Results are set to 0.0 for atoms not in
@@ -152,7 +152,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute <compute>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/spatial <fix_ave_spatial>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`compute <compute>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
 :doc:`variable <variable>`,
 
 **Default:** none

doc/html/_sources/fix_ave_chunk.txt

@@ -73,8 +73,8 @@ Examples
 
 **NOTE:**
 
-If you are trying to replace an older fix ave/spatial command with the
+If you are trying to replace a deprectated fix ave/spatial command
-newer, more flexible fix ave/chunk and :doc:`compute chunk/atom <compute_chunk_atom>` commands, you simply need to split
+with the newer, more flexible fix ave/chunk and :doc:`compute chunk/atom <compute_chunk_atom>` commands, you simply need to split
 the fix ave/spatial arguments across the two new commands.  For
 example, this command:
 

doc/html/_sources/fix_ave_correlate.txt

@@ -87,10 +87,9 @@ Each listed value can be the result of a :doc:`compute <compute>` or
 :doc:`variable <variable>`.  In each case, the compute, fix, or variable
 must produce a global quantity, not a per-atom or local quantity.  If
 you wish to spatial- or time-average or histogram per-atom quantities
-from a compute, fix, or variable, then see the :doc:`fix ave/spatial <fix_ave_spatial>`, :doc:`fix ave/atom <fix_ave_atom>`,
+from a compute, fix, or variable, then see the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`, or
-or :doc:`fix ave/histo <fix_ave_histo>` commands.  If you wish to
+:doc:`fix ave/histo <fix_ave_histo>` commands.  If you wish to convert a
-convert a per-atom quantity into a single global value, see the
+per-atom quantity into a single global value, see the :doc:`compute reduce <compute_reduce>` command.
-:doc:`compute reduce <compute_reduce>` command.
 
 :doc:`Computes <compute>` that produce global quantities are those which
 do not have the word *atom* in their style name.  Only a few
@@ -340,7 +339,7 @@ Related commands
 """"""""""""""""
 
 :doc:`fix ave/correlate/long <fix_ave_correlate_long>`,
-:doc:`compute <compute>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/spatial <fix_ave_spatial>`,
+:doc:`compute <compute>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
 :doc:`fix ave/histo <fix_ave_histo>`, :doc:`variable <variable>`
 
 **Default:** none

doc/html/_sources/fix_ave_histo.txt

@@ -346,7 +346,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/spatial <fix_ave_spatial>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
 :doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`,
 
 **Default:** none

doc/html/_sources/fix_ave_time.txt

@@ -85,7 +85,7 @@ Each listed value can be the result of a :doc:`compute <compute>` or
 :doc:`variable <variable>`.  In each case, the compute, fix, or variable
 must produce a global quantity, not a per-atom or local quantity.  If
 you wish to spatial- or time-average or histogram per-atom quantities
-from a compute, fix, or variable, then see the :doc:`fix ave/spatial <fix_ave_spatial>`, :doc:`fix ave/atom <fix_ave_atom>`,
+from a compute, fix, or variable, then see the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`,
 or :doc:`fix ave/histo <fix_ave_histo>` commands.  If you wish to sum a
 per-atom quantity into a single global quantity, see the :doc:`compute reduce <compute_reduce>` command.
 
@@ -337,7 +337,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/spatial <fix_ave_spatial>`, :doc:`fix ave/histo <fix_ave_histo>`,
+:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
 :doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`,
 
 Default

doc/html/_sources/fix_deform.txt

@@ -524,7 +524,7 @@ box without explicit remapping of their coordinates.
    box.  E.g. for a shearing system the box deformation velocity may vary
    from 0 at the bottom to 10 at the top of the box.  But the stream
    velocity profile of the atoms may vary from -5 at the bottom to +5 at
-   the top.  You can monitor these effects using the :doc:`fix ave/spatial <fix_ave_spatial>`, :doc:`compute temp/deform <compute_temp_deform>`, and :doc:`compute temp/profile <compute_temp_profile>` commands.  One way to induce
+   the top.  You can monitor these effects using the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`compute temp/deform <compute_temp_deform>`, and :doc:`compute temp/profile <compute_temp_profile>` commands.  One way to induce
    atoms to stream consistent with the box deformation is to give them an
    initial velocity profile, via the :doc:`velocity ramp <velocity>`
    command, that matches the box deformation rate.  This also typically

doc/html/_sources/fix_thermal_conductivity.txt

@@ -68,8 +68,8 @@ temperature profile (assuming z = edim) to the file tmp.profile:
 
    compute   ke all ke/atom
    variable  temp atom c_ke/1.5
-   fix       3 all ave/spatial 10 100 1000 z lower 0.05 v_temp &
+   compute   layers all chunk/atom bin/1d z lower 0.05 units reduced
-               file tmp.profile units reduced
+   fix       3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile
 
 Note that by default, Nswap = 1, though this can be changed by the
 optional *swap* keyword.  Setting this parameter appropriately, in
@@ -154,8 +154,8 @@ bewteen solvent particles.
 Related commands
 """"""""""""""""
 
-:doc:`fix ehex <fix_ehex>`, :doc:`fix heat <fix_heat>`, 
+:doc:`fix ehex <fix_ehex>`, :doc:`fix heat <fix_heat>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix viscosity <fix_viscosity>`,
-:doc:`fix ave/spatial <fix_ave_spatial>`, :doc:`fix viscosity <fix_viscosity>`, :doc:`compute heat/flux <compute_heat_flux>`
+:doc:`compute heat/flux <compute_heat_flux>`
 
 Default
 """""""

doc/html/_sources/fix_viscosity.txt

@@ -65,8 +65,8 @@ which writes the profile to the file tmp.profile:
 
 .. parsed-literal::
 
-   fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
+   compute layers all chunk/atom z lower 0.05 units reduced
-       file tmp.profile units reduced
+   fix f1 all ave/chunk 100 10 1000 layers vx file tmp.profile
 
 Note that by default, Nswap = 1 and vtarget = INF, though this can be
 changed by the optional *swap* and *vtarget* keywords.  When vtarget =
@@ -158,7 +158,7 @@ solvent particles.
 Related commands
 """"""""""""""""
 
-:doc:`fix ave/spatial <fix_ave_spatial>`, :doc:`fix thermal/conductivity <fix_thermal_conductivity>`
+:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix thermal/conductivity <fix_thermal_conductivity>`
 
 Default
 """""""

doc/html/_sources/prd.txt

@@ -312,7 +312,8 @@ for dephasing.
 
 This command cannot be used when any fixes are defined that keep track
 of elapsed time to perform time-dependent operations.  Examples
-include the "ave" fixes such as :doc:`fix ave/spatial <fix_ave_spatial>`.  Also :doc:`fix dt/reset <fix_dt_reset>` and :doc:`fix deposit <fix_deposit>`.
+include the "ave" fixes such as :doc:`fix ave/chunk <fix_ave_chunk>`.
+Also :doc:`fix dt/reset <fix_dt_reset>` and :doc:`fix deposit <fix_deposit>`.
 
 Related commands
 """"""""""""""""

doc/html/_sources/tad.txt

@@ -293,7 +293,8 @@ restart, but :doc:`fix langevin <fix_langevin>` will not.
 
 This command cannot be used when any fixes are defined that keep track
 of elapsed time to perform time-dependent operations.  Examples
-include the "ave" fixes such as :doc:`fix ave/spatial <fix_ave_spatial>`.  Also :doc:`fix dt/reset <fix_dt_reset>` and :doc:`fix deposit <fix_deposit>`.
+include the "ave" fixes such as :doc:`fix ave/chunk <fix_ave_chunk>`.
+Also :doc:`fix dt/reset <fix_dt_reset>` and :doc:`fix deposit <fix_deposit>`.
 
 Related commands
 """"""""""""""""

doc/html/_sources/variable.txt

@@ -1189,7 +1189,7 @@ command evaluates the string between the parenthesis as an equal-style
 variable formula.
 
 Referencing a variable with a leading "v_" is an optional or required
-kind of argument for some commands (e.g. the :doc:`fix ave/spatial <fix_ave_spatial>` or :doc:`dump custom <dump>` or
+kind of argument for some commands (e.g. the :doc:`fix ave/chunk <fix_ave_chunk>` or :doc:`dump custom <dump>` or
 :doc:`thermo_style <thermo_style>` commands) if you wish it to evaluate
 a variable periodically during a run.  It can also be used in a
 variable formula if you wish to reference a second variable.  The

doc/html/_static/basic.css

@@ -85,10 +85,6 @@ div.sphinxsidebar #searchbox input[type="text"] {
     width: 170px;
 }
 
-div.sphinxsidebar #searchbox input[type="submit"] {
-    width: 30px;
-}
-
 img {
     border: 0;
     max-width: 100%;

doc/html/_static/doctools.js

@@ -124,6 +124,7 @@ var Documentation = {
     this.fixFirefoxAnchorBug();
     this.highlightSearchWords();
     this.initIndexTable();
+    
   },
 
   /**
@@ -252,6 +253,29 @@ var Documentation = {
     });
     var url = parts.join('/');
     return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+  },
+
+  initOnKeyListeners: function() {
+    $(document).keyup(function(event) {
+      var activeElementType = document.activeElement.tagName;
+      // don't navigate when in search box or textarea
+      if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') {
+        switch (event.keyCode) {
+          case 37: // left
+            var prevHref = $('link[rel="prev"]').prop('href');
+            if (prevHref) {
+              window.location.href = prevHref;
+              return false;
+            }
+          case 39: // right
+            var nextHref = $('link[rel="next"]').prop('href');
+            if (nextHref) {
+              window.location.href = nextHref;
+              return false;
+            }
+        }
+      }
+    });
   }
 };
 
@@ -260,4 +284,4 @@ _ = Documentation.gettext;
 
 $(document).ready(function() {
   Documentation.init();
-});
+});

doc/html/change_box.html

@@ -419,11 +419,12 @@ been previously used to define the lattice spacing.</p>
 <h2>Restrictions</h2>
 <p>If you use the <em>ortho</em> or <em>triclinic</em> keywords, then at the point in
 the input script when this command is issued, no <a class="reference internal" href="dump.html"><span class="doc">dumps</span></a> can
-be active, nor can a <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> or <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> be active.  This is because these commands
+be active, nor can a <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> be active.  This is
-test whether the simulation box is orthogonal when they are first
+because these commands test whether the simulation box is orthogonal
-issued.  Note that these commands can be used in your script before a
+when they are first issued.  Note that these commands can be used in
-change_box command is issued, so long as an <a class="reference internal" href="undump.html"><span class="doc">undump</span></a> or
+your script before a change_box command is issued, so long as an
-<a class="reference internal" href="unfix.html"><span class="doc">unfix</span></a> command is also used to turn them off.</p>
+<a class="reference internal" href="undump.html"><span class="doc">undump</span></a> or <a class="reference internal" href="unfix.html"><span class="doc">unfix</span></a> command is also used to
+turn them off.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>

doc/html/compute.html

@@ -222,11 +222,10 @@ or when atom velocities are created.</li>
 <li>Global values can be output via the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> or <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> command.
 Or the values can be referenced in a <a class="reference internal" href="variable.html"><span class="doc">variable equal</span></a> or
 <a class="reference internal" href="variable.html"><span class="doc">variable atom</span></a> command.</li>
-<li>Per-atom values can be output via the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command
+<li>Per-atom values can be output via the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command.
-or the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> command.  Or they can be
+Or they can be time-averaged via the <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>
-time-averaged via the <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a> command or
+command or reduced by the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a>
-reduced by the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a> command.  Or the
+command.  Or the per-atom values can be referenced in an <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>.</li>
-per-atom values can be referenced in an <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>.</li>
 <li>Local values can be reduced by the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a> command, or histogrammed by the <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a> command, or output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command.</li>
 </ul>
 <p>The results of computes that calculate global quantities can be either
@@ -361,8 +360,7 @@ section of <a class="reference internal" href="Section_commands.html#cmd-5"><spa
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="uncompute.html"><span class="doc">uncompute</span></a>, <a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>,
+<p><a class="reference internal" href="uncompute.html"><span class="doc">uncompute</span></a>, <a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>, <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a></p>
-<a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>, <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a></p>
 <p><strong>Default:</strong> none</p>
 </div>
 </div>

doc/html/compute_property_atom.html

@@ -221,7 +221,7 @@ in the group.  This is useful so that the values can be used by other
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a> that take computes as
 inputs.  See for example, the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a>,
 <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a>,
-<a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>, and <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a> commands.</p>
+<a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, and <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a> commands.</p>
 <p>The list of possible attributes is the same as that used by the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command, which describes their meaning, with some
 additional quantities that are only defined for certain <a class="reference internal" href="atom_style.html"><span class="doc">atom styles</span></a>.  Basically, this augmented list gives an
 input script access to any per-atom quantity stored by LAMMPS.</p>
@@ -273,7 +273,7 @@ units for q, etc.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a>, <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>,
+<p><a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a>, <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>,
 <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a></p>
 <p><strong>Default:</strong> none</p>
 </div>

doc/html/compute_temp_deform.html

@@ -205,7 +205,7 @@ matches the box deformation.  If not, then the compute will subtract
 off an incorrect stream velocity, yielding a bogus thermal
 temperature.  You should NOT assume that your atoms are streaming at
 the same rate the box is deforming.  Rather, you should monitor their
-velocity profile, e.g. via the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>
+velocity profile, e.g. via the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>
 command.  And you can compare the results of this compute to <a class="reference internal" href="compute_temp_profile.html"><span class="doc">compute temp/profile</span></a>, which actually calculates the
 stream profile before subtracting it.  If the two computes do not give
 roughly the same temperature, then your atoms are not streaming

doc/html/fix.html

@@ -242,11 +242,10 @@ various commands explain the details.</p>
 <li>Global values can be output via the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> or <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> command.
 Or the values can be referenced in a <a class="reference internal" href="variable.html"><span class="doc">variable equal</span></a> or
 <a class="reference internal" href="variable.html"><span class="doc">variable atom</span></a> command.</li>
-<li>Per-atom values can be output via the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command
+<li>Per-atom values can be output via the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command.
-or the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> command.  Or they can be
+Or they can be time-averaged via the <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>
-time-averaged via the <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a> command or
+command or reduced by the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a>
-reduced by the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a> command.  Or the
+command.  Or the per-atom values can be referenced in an <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>.</li>
-per-atom values can be referenced in an <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>.</li>
 <li>Local values can be reduced by the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a> command, or histogrammed by the <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a> command.</li>
 </ul>
 <p>See this <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">howto section</span></a> for a summary of
@@ -282,7 +281,6 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span class=
 <li><a class="reference internal" href="fix_ave_chunk.html"><span class="doc">ave/chunk</span></a> - compute per-chunk time-averaged quantities</li>
 <li><a class="reference internal" href="fix_ave_correlate.html"><span class="doc">ave/correlate</span></a> - compute/output time correlations</li>
 <li><a class="reference internal" href="fix_ave_histo.html"><span class="doc">ave/histo</span></a> - compute/output time-averaged histograms</li>
-<li><a class="reference internal" href="fix_ave_spatial.html"><span class="doc">ave/spatial</span></a> - compute/output time-averaged per-atom quantities by layer</li>
 <li><a class="reference internal" href="fix_ave_time.html"><span class="doc">ave/time</span></a> - compute/output global time-averaged quantities</li>
 <li><a class="reference internal" href="fix_balance.html"><span class="doc">balance</span></a> - perform dynamic load-balancing</li>
 <li><a class="reference internal" href="fix_bond_break.html"><span class="doc">bond/break</span></a> - break bonds on the fly</li>

doc/html/fix_ave_atom.html

@@ -160,7 +160,7 @@ one or more input values can be listed</li>
 <h2>Description</h2>
 <p>Use one or more per-atom vectors as inputs every few timesteps, and
 average them atom by atom over longer timescales.  The resulting
-per-atom averages can be used by other <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a> such as the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> or <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> commands.</p>
+per-atom averages can be used by other <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a> such as the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> or <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> commands.</p>
 <p>The group specified with the command means only atoms within the group
 have their averages computed.  Results are set to 0.0 for atoms not in
 the group.</p>
@@ -249,7 +249,7 @@ the <a class="reference internal" href="run.html"><span class="doc">run</span></
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a>, <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>, <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>,
+<p><a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a>, <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>,
 <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>,</p>
 <p><strong>Default:</strong> none</p>
 </div>

doc/html/fix_ave_chunk.html

@@ -192,8 +192,8 @@
 </pre></div>
 </div>
 <p><strong>NOTE:</strong></p>
-<p>If you are trying to replace an older fix ave/spatial command with the
+<p>If you are trying to replace a deprectated fix ave/spatial command
-newer, more flexible fix ave/chunk and <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> commands, you simply need to split
+with the newer, more flexible fix ave/chunk and <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> commands, you simply need to split
 the fix ave/spatial arguments across the two new commands.  For
 example, this command:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">spatial</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">y</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="n">vx</span> <span class="n">vz</span> <span class="n">norm</span> <span class="n">sample</span> <span class="n">file</span> <span class="n">vel</span><span class="o">.</span><span class="n">profile</span>

doc/html/fix_ave_correlate.html

@@ -205,10 +205,9 @@ fixes which store their own &#8220;group&#8221; definitions.</p>
 <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.  In each case, the compute, fix, or variable
 must produce a global quantity, not a per-atom or local quantity.  If
 you wish to spatial- or time-average or histogram per-atom quantities
-from a compute, fix, or variable, then see the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>,
+from a compute, fix, or variable, then see the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, or
-or <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a> commands.  If you wish to
+<a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a> commands.  If you wish to convert a
-convert a per-atom quantity into a single global value, see the
+per-atom quantity into a single global value, see the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a> command.</p>
-<a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a> command.</p>
 <p><a class="reference internal" href="compute.html"><span class="doc">Computes</span></a> that produce global quantities are those which
 do not have the word <em>atom</em> in their style name.  Only a few
 <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a> produce global quantities.  See the doc pages for
@@ -414,7 +413,7 @@ the <a class="reference internal" href="run.html"><span class="doc">run</span></
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
 <p><a class="reference internal" href="fix_ave_correlate_long.html"><span class="doc">fix ave/correlate/long</span></a>,
-<a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>,
+<a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>,
 <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a>, <a class="reference internal" href="variable.html"><span class="doc">variable</span></a></p>
 <p><strong>Default:</strong> none</p>
 <p>The option defaults are ave = one, type = auto, start = 0, no file

doc/html/fix_ave_histo.html

@@ -419,7 +419,7 @@ the <a class="reference internal" href="run.html"><span class="doc">run</span></
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>, <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>,
+<p><a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>,
 <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>, <a class="reference internal" href="fix_ave_correlate.html"><span class="doc">fix ave/correlate</span></a>,</p>
 <p><strong>Default:</strong> none</p>
 <p>The option defaults are mode = scalar, ave = one, start = 0, no file

doc/html/fix_ave_time.html

@@ -203,7 +203,7 @@ fixes which store their own &#8220;group&#8221; definitions.</p>
 <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.  In each case, the compute, fix, or variable
 must produce a global quantity, not a per-atom or local quantity.  If
 you wish to spatial- or time-average or histogram per-atom quantities
-from a compute, fix, or variable, then see the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>,
+from a compute, fix, or variable, then see the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>,
 or <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a> commands.  If you wish to sum a
 per-atom quantity into a single global quantity, see the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a> command.</p>
 <p><a class="reference internal" href="compute.html"><span class="doc">Computes</span></a> that produce global quantities are those which
@@ -408,7 +408,7 @@ the <a class="reference internal" href="run.html"><span class="doc">run</span></
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>, <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a>,
+<p><a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a>,
 <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>, <a class="reference internal" href="fix_ave_correlate.html"><span class="doc">fix ave/correlate</span></a>,</p>
 </div>
 <div class="section" id="default">

doc/html/fix_deform.html

@@ -577,7 +577,7 @@ pushing the atoms to flow in a manner consistent with the deforming
 box.  E.g. for a shearing system the box deformation velocity may vary
 from 0 at the bottom to 10 at the top of the box.  But the stream
 velocity profile of the atoms may vary from -5 at the bottom to +5 at
-the top.  You can monitor these effects using the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>, <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a>, and <a class="reference internal" href="compute_temp_profile.html"><span class="doc">compute temp/profile</span></a> commands.  One way to induce
+the top.  You can monitor these effects using the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a>, and <a class="reference internal" href="compute_temp_profile.html"><span class="doc">compute temp/profile</span></a> commands.  One way to induce
 atoms to stream consistent with the box deformation is to give them an
 initial velocity profile, via the <a class="reference internal" href="velocity.html"><span class="doc">velocity ramp</span></a>
 command, that matches the box deformation rate.  This also typically

doc/html/fix_thermal_conductivity.html

@@ -182,8 +182,8 @@ measured using commands such as the following, which writes the
 temperature profile (assuming z = edim) to the file tmp.profile:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>   <span class="n">ke</span> <span class="nb">all</span> <span class="n">ke</span><span class="o">/</span><span class="n">atom</span>
 <span class="n">variable</span>  <span class="n">temp</span> <span class="n">atom</span> <span class="n">c_ke</span><span class="o">/</span><span class="mf">1.5</span>
-<span class="n">fix</span>       <span class="mi">3</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">spatial</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">0.05</span> <span class="n">v_temp</span> <span class="o">&amp;</span>
+<span class="n">compute</span>   <span class="n">layers</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="nb">bin</span><span class="o">/</span><span class="mi">1</span><span class="n">d</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">0.05</span> <span class="n">units</span> <span class="n">reduced</span>
-            <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">profile</span> <span class="n">units</span> <span class="n">reduced</span>
+<span class="n">fix</span>       <span class="mi">3</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="n">layers</span> <span class="n">v_temp</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">profile</span>
 </pre></div>
 </div>
 <p>Note that by default, Nswap = 1, though this can be changed by the
@@ -258,8 +258,8 @@ bewteen solvent particles.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_ehex.html"><span class="doc">fix ehex</span></a>, <a class="reference internal" href="fix_heat.html"><span class="doc">fix heat</span></a>,
+<p><a class="reference internal" href="fix_ehex.html"><span class="doc">fix ehex</span></a>, <a class="reference internal" href="fix_heat.html"><span class="doc">fix heat</span></a>, <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, <a class="reference internal" href="fix_viscosity.html"><span class="doc">fix viscosity</span></a>,
-<a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>, <a class="reference internal" href="fix_viscosity.html"><span class="doc">fix viscosity</span></a>, <a class="reference internal" href="compute_heat_flux.html"><span class="doc">compute heat/flux</span></a></p>
+<a class="reference internal" href="compute_heat_flux.html"><span class="doc">compute heat/flux</span></a></p>
 </div>
 <div class="section" id="default">
 <h2>Default</h2>

doc/html/fix_viscosity.html

@@ -180,8 +180,8 @@ within each pair.  This resets their velocities, typically in opposite
 directions.  Over time, this induces a shear velocity profile in the
 system which can be measured using commands such as the following,
 which writes the profile to the file tmp.profile:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">f1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">spatial</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">0.05</span> <span class="n">vx</span> <span class="o">&amp;</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">layers</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">0.05</span> <span class="n">units</span> <span class="n">reduced</span>
-    <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">profile</span> <span class="n">units</span> <span class="n">reduced</span>
+<span class="n">fix</span> <span class="n">f1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">layers</span> <span class="n">vx</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">profile</span>
 </pre></div>
 </div>
 <p>Note that by default, Nswap = 1 and vtarget = INF, though this can be
@@ -262,7 +262,7 @@ solvent particles.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>, <a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a></p>
+<p><a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, <a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a></p>
 </div>
 <div class="section" id="default">
 <h2>Default</h2>

doc/html/genindex.html

@@ -994,14 +994,6 @@
   </dt>
 
       
-  <dt><a href="fix_ave_spatial.html#index-0">fix ave/spatial</a>
-  </dt>
-
-      
-  <dt><a href="fix_ave_spatial_sphere.html#index-0">fix ave/spatial/sphere</a>
-  </dt>
-
-      
   <dt><a href="fix_ave_time.html#index-0">fix ave/time</a>
   </dt>
 
@@ -1233,12 +1225,12 @@
   <dt><a href="fix_nve_eff.html#index-0">fix nve/eff</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="fix_nve_limit.html#index-0">fix nve/limit</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="fix_nve_line.html#index-0">fix nve/line</a>
   </dt>

doc/html/prd.html

@@ -379,7 +379,8 @@ produce identical results due to changes in the random numbers used
 for dephasing.</p>
 <p>This command cannot be used when any fixes are defined that keep track
 of elapsed time to perform time-dependent operations.  Examples
-include the &#8220;ave&#8221; fixes such as <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>.  Also <a class="reference internal" href="fix_dt_reset.html"><span class="doc">fix dt/reset</span></a> and <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a>.</p>
+include the &#8220;ave&#8221; fixes such as <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>.
+Also <a class="reference internal" href="fix_dt_reset.html"><span class="doc">fix dt/reset</span></a> and <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a>.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>

doc/html/tad.html

@@ -376,7 +376,8 @@ exact restarts. So <a class="reference internal" href="fix_nh.html"><span class=
 restart, but <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> will not.</p>
 <p>This command cannot be used when any fixes are defined that keep track
 of elapsed time to perform time-dependent operations.  Examples
-include the &#8220;ave&#8221; fixes such as <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>.  Also <a class="reference internal" href="fix_dt_reset.html"><span class="doc">fix dt/reset</span></a> and <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a>.</p>
+include the &#8220;ave&#8221; fixes such as <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>.
+Also <a class="reference internal" href="fix_dt_reset.html"><span class="doc">fix dt/reset</span></a> and <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a>.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>

doc/html/variable.html

@@ -1187,7 +1187,7 @@ string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script
 command evaluates the string between the parenthesis as an equal-style
 variable formula.</p>
 <p>Referencing a variable with a leading &#8220;<a href="#id7"><span class="problematic" id="id8">v_</span></a>&#8221; is an optional or required
-kind of argument for some commands (e.g. the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> or <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> or
+kind of argument for some commands (e.g. the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> or <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> or
 <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> commands) if you wish it to evaluate
 a variable periodically during a run.  It can also be used in a
 variable formula if you wish to reference a second variable.  The