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Add rst versions of new documentation

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Richard Berger 2019-11-08 15:28:12 -05:00
parent 07a34382ae
commit b9648884bb
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96
doc/src/Commands_compute.rst
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@ -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

3
doc/src/compute.rst
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@ -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

20
doc/src/compute_gyration_shape.rst
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@ -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