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Fixed some minor errors and omissions

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This commit is contained in:
Aidan P. Thompson
2019-11-25 14:32:37 -07:00
parent f98a0025d6
commit 2e4f514d40
6 changed files with 18 additions and 15 deletions
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14
doc/src/Commands_compute.rst
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@ -49,19 +49,19 @@ KOKKOS, o = USER-OMP, t = OPT.
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :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:`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:`snap <compute_sna_atom>` | :doc:`sna/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:`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:`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:`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/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/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/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/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/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:`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:`xrd <compute_xrd>` | | | | | |
| :doc:`voronoi/atom <compute_voronoi_atom>` | :doc:`xrd <compute_xrd>` | | | | |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+

7
doc/src/compute.rst
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@ -286,9 +286,10 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` -
* :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
* :doc:`smd/vol <compute_smd_vol>` - per-particle volumes and their sum in Smooth Mach Dynamics
* :doc:`sna/atom <compute_sna_atom>` - calculate bispectrum coefficients for each atom
* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum coefficients for each atom
* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum coefficients for each atom
* :doc:`snap <compute_sna_atom>` - bispectrum components and related quantities for a group of atoms
* :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum components for each atom
* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum components for each atom
* :doc:`spin <compute_spin>` - magnetic quantities for a system of atoms having spins
* :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
* :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes

2
doc/src/compute_sna_atom.rst
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@ -166,7 +166,7 @@ out by type. In between these are 3\*\ *N* rows containing the same values
computed by *snad/atom* (these are already summed over all atoms and
broken out by type). The element in the last column of each row contains
the potential energy, force, or stress, according to the row.
These quantities correspond to the user-specified refence potential
These quantities correspond to the user-specified reference potential
that must be subtracted from the target data when fitting SNAP.
The potential energy calculation uses the built in compute *thermo\_pe*.
The stress calculation uses a compute called *snap\_press* that is

1
doc/txt/Commands_compute.txt
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@ -130,6 +130,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
"smd/vol"_compute_smd_vol.html,
"snap"_compute_sna_atom.html,
"sna/atom"_compute_sna_atom.html,
"snad/atom"_compute_sna_atom.html,
"snav/atom"_compute_sna_atom.html,

7
doc/txt/compute.txt
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@ -277,9 +277,10 @@ compute"_Commands_compute.html doc page are followed by one or more of
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
"smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
"smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics
"sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
"snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
"snap"_compute_sna_atom.html - bispectrum components and related quantities for a group of atoms
"sna/atom"_compute_sna_atom.html - bispectrum components for each atom
"snad/atom"_compute_sna_atom.html - derivative of bispectrum components for each atom
"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum components for each atom
"spin"_compute_spin.html - magnetic quantities for a system of atoms having spins
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
"stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes

2
doc/txt/compute_sna_atom.txt
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@ -146,7 +146,7 @@ out by type. In between these are 3*{N} rows containing the same values
computed by {snad/atom} (these are already summed over all atoms and
broken out by type). The element in the last column of each row contains
the potential energy, force, or stress, according to the row.
These quantities correspond to the user-specified refence potential
These quantities correspond to the user-specified reference potential
that must be subtracted from the target data when fitting SNAP.
The potential energy calculation uses the built in compute {thermo_pe}.
The stress calculation uses a compute called {snap_press} that is