From b9648884bbedacb43cd8ea738be84d64e1927be7 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Fri, 8 Nov 2019 15:28:12 -0500
Subject: [PATCH] Add rst versions of new documentation

---
 doc/src/Commands_compute.rst       | 96 +++++++++++++++---------------
 doc/src/compute.rst                |  3 +-
 doc/src/compute_gyration_shape.rst | 20 ++++---
 3 files changed, 62 insertions(+), 57 deletions(-)

diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst
index 63926b6d61..351eca3709 100644
--- a/doc/src/Commands_compute.rst
+++ b/doc/src/Commands_compute.rst
@@ -14,53 +14,55 @@ Some styles have accelerated versions.  This is indicated by
 additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
 KOKKOS, o = USER-OMP, t = OPT.
 
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`ackland/atom <compute_ackland_atom>`                       | :doc:`adf <compute_adf>`                                     | :doc:`aggregate/atom <compute_cluster_atom>`         | :doc:`angle <compute_angle>`                                 | :doc:`angle/local <compute_angle_local>`                   | :doc:`angmom/chunk <compute_angmom_chunk>`             |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`basal/atom <compute_basal_atom>`                           | :doc:`body/local <compute_body_local>`                       | :doc:`bond <compute_bond>`                           | :doc:`bond/local <compute_bond_local>`                       | :doc:`centro/atom <compute_centro_atom>`                   | :doc:`chunk/atom <compute_chunk_atom>`                 |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`chunk/spread/atom <compute_chunk_spread_atom>`             | :doc:`cluster/atom <compute_cluster_atom>`                   | :doc:`cna/atom <compute_cna_atom>`                   | :doc:`cnp/atom <compute_cnp_atom>`                           | :doc:`com <compute_com>`                                   | :doc:`com/chunk <compute_com_chunk>`                   |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`contact/atom <compute_contact_atom>`                       | :doc:`coord/atom <compute_coord_atom>`                       | :doc:`damage/atom <compute_damage_atom>`             | :doc:`dihedral <compute_dihedral>`                           | :doc:`dihedral/local <compute_dihedral_local>`             | :doc:`dilatation/atom <compute_dilatation_atom>`       |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`dipole/chunk <compute_dipole_chunk>`                       | :doc:`displace/atom <compute_displace_atom>`                 | :doc:`dpd <compute_dpd>`                             | :doc:`dpd/atom <compute_dpd_atom>`                           | :doc:`edpd/temp/atom <compute_edpd_temp_atom>`             | :doc:`entropy/atom <compute_entropy_atom>`             |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`erotate/asphere <compute_erotate_asphere>`                 | :doc:`erotate/rigid <compute_erotate_rigid>`                 | :doc:`erotate/sphere <compute_erotate_sphere>`       | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`     | :doc:`event/displace <compute_event_displace>`             | :doc:`fep <compute_fep>`                               |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`force/tally <compute_tally>`                               | :doc:`fragment/atom <compute_cluster_atom>`                  | :doc:`global/atom <compute_global_atom>`             | :doc:`group/group <compute_group_group>`                     | :doc:`gyration <compute_gyration>`                         | :doc:`gyration/chunk <compute_gyration_chunk>`         |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`gyration/shape <compute_gyration_shape>`                   | :doc:`heat/flux <compute_heat_flux>`                         | :doc:`heat/flux/tally <compute_tally>`               | :doc:`hexorder/atom <compute_hexorder_atom>`                 | :doc:`hma <compute_hma>`                                   | :doc:`improper <compute_improper>`                     |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`improper/local <compute_improper_local>`                   | :doc:`inertia/chunk <compute_inertia_chunk>`                 | :doc:`ke <compute_ke>`                               | :doc:`ke/atom <compute_ke_atom>`                             | :doc:`ke/atom/eff <compute_ke_atom_eff>`                   | :doc:`ke/eff <compute_ke_eff>`                         |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`ke/rigid <compute_ke_rigid>`                               | :doc:`meso/e/atom <compute_meso_e_atom>`                     | :doc:`meso/rho/atom <compute_meso_rho_atom>`         | :doc:`meso/t/atom <compute_meso_t_atom>`                     | :doc:`momentum <compute_momentum>`                         | :doc:`msd <compute_msd>`                               |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`msd/chunk <compute_msd_chunk>`                             | :doc:`msd/nongauss <compute_msd_nongauss>`                   | :doc:`omega/chunk <compute_omega_chunk>`             | :doc:`orientorder/atom <compute_orientorder_atom>`           | :doc:`pair <compute_pair>`                                 | :doc:`pair/local <compute_pair_local>`                 |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`pe <compute_pe>`                                           | :doc:`pe/atom <compute_pe_atom>`                             | :doc:`pe/mol/tally <compute_tally>`                  | :doc:`pe/tally <compute_tally>`                              | :doc:`plasticity/atom <compute_plasticity_atom>`           | :doc:`pressure <compute_pressure>`                     |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`pressure/cylinder <compute_pressure_cylinder>`             | :doc:`pressure/uef <compute_pressure_uef>`                   | :doc:`property/atom <compute_property_atom>`         | :doc:`property/chunk <compute_property_chunk>`               | :doc:`property/local <compute_property_local>`             | :doc:`ptm/atom <compute_ptm_atom>`                     |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`rdf <compute_rdf>`                                         | :doc:`reduce <compute_reduce>`                               | :doc:`reduce/chunk <compute_reduce_chunk>`           | :doc:`reduce/region <compute_reduce>`                        | :doc:`rigid/local <compute_rigid_local>`                   | :doc:`saed <compute_saed>`                             |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`slice <compute_slice>`                                     | :doc:`smd/contact/radius <compute_smd_contact_radius>`       | :doc:`smd/damage <compute_smd_damage>`               | :doc:`smd/hourglass/error <compute_smd_hourglass_error>`     | :doc:`smd/internal/energy <compute_smd_internal_energy>`   | :doc:`smd/plastic/strain <compute_smd_plastic_strain>` |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` | :doc:`smd/rho <compute_smd_rho>`                             | :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>` | :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`                   | :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` | :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`       |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`               | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`   | :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` | :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` | :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`     |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`     | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`           | :doc:`smd/vol <compute_smd_vol>`                     | :doc:`sna/atom <compute_sna_atom>`                           | :doc:`snad/atom <compute_sna_atom>`                        | :doc:`snav/atom <compute_sna_atom>`                    |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`spin <compute_spin>`                                       | :doc:`stress/atom <compute_stress_atom>`                     | :doc:`stress/mop <compute_stress_mop>`               | :doc:`stress/mop/profile <compute_stress_mop>`               | :doc:`stress/tally <compute_tally>`                        | :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`             |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`temp (k) <compute_temp>`                                   | :doc:`temp/asphere <compute_temp_asphere>`                   | :doc:`temp/body <compute_temp_body>`                 | :doc:`temp/chunk <compute_temp_chunk>`                       | :doc:`temp/com <compute_temp_com>`                         | :doc:`temp/cs <compute_temp_cs>`                       |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`temp/deform <compute_temp_deform>`                         | :doc:`temp/deform/eff <compute_temp_deform_eff>`             | :doc:`temp/drude <compute_temp_drude>`               | :doc:`temp/eff <compute_temp_eff>`                           | :doc:`temp/partial <compute_temp_partial>`                 | :doc:`temp/profile <compute_temp_profile>`             |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`temp/ramp <compute_temp_ramp>`                             | :doc:`temp/region <compute_temp_region>`                     | :doc:`temp/region/eff <compute_temp_region_eff>`     | :doc:`temp/rotate <compute_temp_rotate>`                     | :doc:`temp/sphere <compute_temp_sphere>`                   | :doc:`temp/uef <compute_temp_uef>`                     |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
-| :doc:`ti <compute_ti>`                                           | :doc:`torque/chunk <compute_torque_chunk>`                   | :doc:`vacf <compute_vacf>`                           | :doc:`vcm/chunk <compute_vcm_chunk>`                         | :doc:`voronoi/atom <compute_voronoi_atom>`                 | :doc:`xrd <compute_xrd>`                               |
-+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+--------------------------------------------------------+
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`ackland/atom <compute_ackland_atom>`             | :doc:`adf <compute_adf>`                                         | :doc:`aggregate/atom <compute_cluster_atom>`                 | :doc:`angle <compute_angle>`                             | :doc:`angle/local <compute_angle_local>`                     | :doc:`angmom/chunk <compute_angmom_chunk>`                 |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`basal/atom <compute_basal_atom>`                 | :doc:`body/local <compute_body_local>`                           | :doc:`bond <compute_bond>`                                   | :doc:`bond/local <compute_bond_local>`                   | :doc:`centro/atom <compute_centro_atom>`                     | :doc:`chunk/atom <compute_chunk_atom>`                     |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`chunk/spread/atom <compute_chunk_spread_atom>`   | :doc:`cluster/atom <compute_cluster_atom>`                       | :doc:`cna/atom <compute_cna_atom>`                           | :doc:`cnp/atom <compute_cnp_atom>`                       | :doc:`com <compute_com>`                                     | :doc:`com/chunk <compute_com_chunk>`                       |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`contact/atom <compute_contact_atom>`             | :doc:`coord/atom <compute_coord_atom>`                           | :doc:`damage/atom <compute_damage_atom>`                     | :doc:`dihedral <compute_dihedral>`                       | :doc:`dihedral/local <compute_dihedral_local>`               | :doc:`dilatation/atom <compute_dilatation_atom>`           |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`dipole/chunk <compute_dipole_chunk>`             | :doc:`displace/atom <compute_displace_atom>`                     | :doc:`dpd <compute_dpd>`                                     | :doc:`dpd/atom <compute_dpd_atom>`                       | :doc:`edpd/temp/atom <compute_edpd_temp_atom>`               | :doc:`entropy/atom <compute_entropy_atom>`                 |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`erotate/asphere <compute_erotate_asphere>`       | :doc:`erotate/rigid <compute_erotate_rigid>`                     | :doc:`erotate/sphere <compute_erotate_sphere>`               | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` | :doc:`event/displace <compute_event_displace>`               | :doc:`fep <compute_fep>`                                   |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`force/tally <compute_tally>`                     | :doc:`fragment/atom <compute_cluster_atom>`                      | :doc:`global/atom <compute_global_atom>`                     | :doc:`group/group <compute_group_group>`                 | :doc:`gyration <compute_gyration>`                           | :doc:`gyration/chunk <compute_gyration_chunk>`             |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`gyration/shape <compute_gyration_shape>`         | :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`       | :doc:`heat/flux <compute_heat_flux>`                         | :doc:`heat/flux/tally <compute_tally>`                   | :doc:`hexorder/atom <compute_hexorder_atom>`                 | :doc:`hma <compute_hma>`                                   |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`improper <compute_improper>`                     | :doc:`improper/local <compute_improper_local>`                   | :doc:`inertia/chunk <compute_inertia_chunk>`                 | :doc:`ke <compute_ke>`                                   | :doc:`ke/atom <compute_ke_atom>`                             | :doc:`ke/atom/eff <compute_ke_atom_eff>`                   |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`ke/eff <compute_ke_eff>`                         | :doc:`ke/rigid <compute_ke_rigid>`                               | :doc:`meso/e/atom <compute_meso_e_atom>`                     | :doc:`meso/rho/atom <compute_meso_rho_atom>`             | :doc:`meso/t/atom <compute_meso_t_atom>`                     | :doc:`momentum <compute_momentum>`                         |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`msd <compute_msd>`                               | :doc:`msd/chunk <compute_msd_chunk>`                             | :doc:`msd/nongauss <compute_msd_nongauss>`                   | :doc:`omega/chunk <compute_omega_chunk>`                 | :doc:`orientorder/atom <compute_orientorder_atom>`           | :doc:`pair <compute_pair>`                                 |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`pair/local <compute_pair_local>`                 | :doc:`pe <compute_pe>`                                           | :doc:`pe/atom <compute_pe_atom>`                             | :doc:`pe/mol/tally <compute_tally>`                      | :doc:`pe/tally <compute_tally>`                              | :doc:`plasticity/atom <compute_plasticity_atom>`           |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`pressure <compute_pressure>`                     | :doc:`pressure/cylinder <compute_pressure_cylinder>`             | :doc:`pressure/uef <compute_pressure_uef>`                   | :doc:`property/atom <compute_property_atom>`             | :doc:`property/chunk <compute_property_chunk>`               | :doc:`property/local <compute_property_local>`             |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`ptm/atom <compute_ptm_atom>`                     | :doc:`rdf <compute_rdf>`                                         | :doc:`reduce <compute_reduce>`                               | :doc:`reduce/chunk <compute_reduce_chunk>`               | :doc:`reduce/region <compute_reduce>`                        | :doc:`rigid/local <compute_rigid_local>`                   |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`saed <compute_saed>`                             | :doc:`slice <compute_slice>`                                     | :doc:`smd/contact/radius <compute_smd_contact_radius>`       | :doc:`smd/damage <compute_smd_damage>`                   | :doc:`smd/hourglass/error <compute_smd_hourglass_error>`     | :doc:`smd/internal/energy <compute_smd_internal_energy>`   |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`smd/plastic/strain <compute_smd_plastic_strain>` | :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` | :doc:`smd/rho <compute_smd_rho>`                             | :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>`     | :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`                   | :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`       | :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`               | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`       | :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` | :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`     | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`     | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`           | :doc:`smd/vol <compute_smd_vol>`                         | :doc:`sna/atom <compute_sna_atom>`                           | :doc:`snad/atom <compute_sna_atom>`                        |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`snav/atom <compute_sna_atom>`                    | :doc:`spin <compute_spin>`                                       | :doc:`stress/atom <compute_stress_atom>`                     | :doc:`stress/mop <compute_stress_mop>`                   | :doc:`stress/mop/profile <compute_stress_mop>`               | :doc:`stress/tally <compute_tally>`                        |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`             | :doc:`temp (k) <compute_temp>`                                   | :doc:`temp/asphere <compute_temp_asphere>`                   | :doc:`temp/body <compute_temp_body>`                     | :doc:`temp/chunk <compute_temp_chunk>`                       | :doc:`temp/com <compute_temp_com>`                         |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`temp/cs <compute_temp_cs>`                       | :doc:`temp/deform <compute_temp_deform>`                         | :doc:`temp/deform/eff <compute_temp_deform_eff>`             | :doc:`temp/drude <compute_temp_drude>`                   | :doc:`temp/eff <compute_temp_eff>`                           | :doc:`temp/partial <compute_temp_partial>`                 |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`temp/profile <compute_temp_profile>`             | :doc:`temp/ramp <compute_temp_ramp>`                             | :doc:`temp/region <compute_temp_region>`                     | :doc:`temp/region/eff <compute_temp_region_eff>`         | :doc:`temp/rotate <compute_temp_rotate>`                     | :doc:`temp/sphere <compute_temp_sphere>`                   |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`temp/uef <compute_temp_uef>`                     | :doc:`ti <compute_ti>`                                           | :doc:`torque/chunk <compute_torque_chunk>`                   | :doc:`vacf <compute_vacf>`                               | :doc:`vcm/chunk <compute_vcm_chunk>`                         | :doc:`voronoi/atom <compute_voronoi_atom>`                 |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+| :doc:`xrd <compute_xrd>`                               |                                                                  |                                                              |                                                          |                                                              |                                                            |
++--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
 
 
 .. _lws: http://lammps.sandia.gov
diff --git a/doc/src/compute.rst b/doc/src/compute.rst
index f95e8a3f32..419352a9ac 100644
--- a/doc/src/compute.rst
+++ b/doc/src/compute.rst
@@ -222,7 +222,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
 * :doc:`group/group <compute_group_group>` - energy/force between two groups of atoms
 * :doc:`gyration <compute_gyration>` - radius of gyration of group of atoms
 * :doc:`gyration/chunk <compute_gyration_chunk>` - radius of gyration for each chunk
-* :doc:`gyration/shape <compute_gyration_shape>` - compute shape parameters from radius of gyration tensor
+* :doc:`gyration/shape <compute_gyration_shape>` - shape parameters from gyration tensor
+* :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>` - shape parameters from gyration tensor for each chunk
 * :doc:`heat/flux <compute_heat_flux>` - heat flux through a group of atoms
 * :doc:`heat/flux/tally <compute_tally>` -
 * :doc:`hexorder/atom <compute_hexorder_atom>` - bond orientational order parameter q6
diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst
index 68c16f2511..5461825923 100644
--- a/doc/src/compute_gyration_shape.rst
+++ b/doc/src/compute_gyration_shape.rst
@@ -9,7 +9,7 @@ Syntax
 
 .. parsed-literal::
 
-   compute ID group-ID gyration compute-ID
+   compute ID group-ID gyration/shape compute-ID
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * gyration/shape = style name of this compute command
@@ -36,7 +36,9 @@ and the relative shape anisotropy, k:
 .. image:: Eqs/compute_shape_parameters.jpg
    :align: center
 
-where lx <= ly <= lz are the three eigenvalues of the gyration tensor.
+where lx <= ly <= lz are the three eigenvalues of the gyration tensor. A general description 
+of these parameters is provided in :ref:`(Mattice) <Mattice1>` while an application to polymer systems 
+can be found in :ref:`(Theodorou) <Theodorou1>`.
 The asphericity  is always non-negative and zero only when the three principal
 moments are equal. This zero condition is met when the distribution of particles
 is spherically symmetric (hence the name asphericity) but also whenever the particle
@@ -91,18 +93,18 @@ Related commands
 ----------
 
 
-.. _Theodorou:
-
-
-
-**(Theodorou)** Theodorou, Suter, Macromolecules, 18, 1206 (1985).
-
-.. _Mattice:
+.. _Mattice1:
 
 
 
 **(Mattice)** Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994.
 
+.. _Theodorou1:
+
+
+
+**(Theodorou)** Theodorou, Suter, Macromolecules, 18, 1206 (1985).
+
 
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html