Loading doc/src/Commands_compute.rst +7 −7 Original line number Diff line number Diff line Loading @@ -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>` | | | | | +--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+ Loading doc/src/compute.rst +4 −3 Original line number Diff line number Diff line Loading @@ -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 Loading doc/src/compute_sna_atom.rst +1 −1 Original line number Diff line number Diff line Loading @@ -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 Loading doc/txt/Commands_compute.txt +1 −0 Original line number Diff line number Diff line Loading @@ -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, Loading doc/txt/compute.txt +4 −3 Original line number Diff line number Diff line Loading @@ -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 Loading Loading
doc/src/Commands_compute.rst +7 −7 Original line number Diff line number Diff line Loading @@ -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>` | | | | | +--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+ Loading
doc/src/compute.rst +4 −3 Original line number Diff line number Diff line Loading @@ -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 Loading
doc/src/compute_sna_atom.rst +1 −1 Original line number Diff line number Diff line Loading @@ -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 Loading
doc/txt/Commands_compute.txt +1 −0 Original line number Diff line number Diff line Loading @@ -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, Loading
doc/txt/compute.txt +4 −3 Original line number Diff line number Diff line Loading @@ -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 Loading
